@article {19693, title = {Tree-based Label Dependency Topic Models}, journal = {cs.umd.edu}, year = {Submitted}, abstract = {Abstract Multi-labeled corpora, where each document is tagged with a set of labels, are ubiquitous. When the number of unique labels in the dataset is large, there are naturally some dependencies among the labels. In this paper, we propose TREELAD{\textemdash}a ...}, url = {http://www.cs.umd.edu/~vietan/2013_l2h.pdf}, author = {Nguyen, V A and Jordan Boyd-Graber and Chang, J and Resnik, P} } @article {20548, title = {Rapid, quantitative therapeutic screening for Alzheimer{\textquoteright}s enzymes enabled by optimal signal transduction with transistors}, journal = {The Analyst}, volume = {145}, year = {2020}, month = {Feb-04-2021}, pages = {2925 - 2936}, issn = {0003-2654}, doi = {10.1039/C9AN01804B}, url = {http://xlink.rsc.org/?DOI=C9AN01804Bhttp://pubs.rsc.org/en/content/articlepdf/2020/AN/C9AN01804Bhttp://pubs.rsc.org/en/content/articlepdf/2020/AN/C9AN01804B}, author = {Le, Son T. and Morris, Michelle A. and Cardone, Antonio and Guros, Nicholas B. and Klauda, Jeffery B. and Sperling, Brent A. and Richter, Curt A. and Pant, Harish C. and Balijepalli, Arvind} } @article {20391, title = {Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children}, journal = {Journal of Oral Microbiology}, year = {2019}, month = {12/2018}, pages = {1557986}, abstract = {Studies of the microbiome associated with dental caries have largely relied on 16S rRNA sequence analysis, which is associated with PCR biases, low taxonomic resolution, and inability to accurately study functions. Here, we employed whole metagenome shotgun sequencing, coupled with high-resolution analysis algorithm, to analyze supragingival microbiomes from 30 children with or without dental caries. A total of 726 bacterial strains belonging to 406 species, in addition to 34 bacteriophages were identified. A core bacteriome was identified at the species and strain levels. Species of Prevotella, Veillonella, as yet unnamed Actinomyces, and Atopobium showed strongest association with caries; Streptococcus sp. AS14 and Leptotrichia sp. Oral taxon 225, among others, were overabundant in caries-free. For several species, the association was strain-specific. Furthermore, for some species, e.g. Streptococcus mitis and Streptococcus sanguinis, sister strains showed differential associations. Noteworthy, associations were also identified for phages: Streptococcus phage M102 with caries and Haemophilus phage HP1 with caries-free. Functionally, potentially relevant features were identified including urate, vitamin K2, and polyamine biosynthesis in association with caries; and three deiminases and lactate dehydrogenase with health. The results demonstrate new associations between the microbiome and dental caries at the strain and functional levels that need further investigation.}, doi = {10.1080/20002297.2018.1557986}, url = {https://www.tandfonline.com/doi/full/10.1080/20002297.2018.1557986}, author = {Al-Hebshi, Nezar Noor and Baraniya, Divyashri and Chen, Tsute and Hill, Jennifer and Puri, Sumant and Tellez, Marisol and Hassan, Nur A. and Rita R Colwell and Ismail, Amid} } @article {20449, title = {Quantum Capacitance-Limited MoS2 Biosensors Enable Remote Label-Free Enzyme Measurements}, journal = {Nanoscale}, year = {2019}, month = {Jan-01-2019}, issn = {2040-3364}, doi = {10.1039/C9NR03171E}, url = {http://pubs.rsc.org/en/Content/ArticleLanding/2019/NR/C9NR03171Ehttp://pubs.rsc.org/en/content/articlepdf/2019/NR/C9NR03171E}, author = {Le, Son T and Guros, Nicholas B and Bruce, Robert C and Cardone, Antonio and Amin, Niranjana D and Zhang, Siyuan and Klauda, Jeffery and Pant, Harish C and Richter, Curt A and Balijepalli, Arvind} } @article {20295, title = {Biofilms Comprise a Component of the Annual Cycle of Vibrio cholerae in the Bay of Bengal Estuary}, journal = {mBio}, year = {2018}, month = {Feb-05-2018}, pages = {e00483-18}, abstract = {Vibrio cholerae, an estuarine bacterium, is the causative agent of cholera, a severe diarrheal disease that demonstrates seasonal incidence in Bangladesh. In an extensive study of V. cholerae occurrence in a natural aquatic environment, water and plankton samples were collected biweekly between December 2005 and November 2006 from Mathbaria, an estuarine village of Bangladesh near the mangrove forests of the Sundarbans. Toxigenic V. cholerae exhibited two seasonal growth peaks, one in spring (March to May) and another in autumn (September to November), corresponding to the two annual seasonal outbreaks of cholera in this region. The total numbers of bacteria determined by heterotrophic plate count (HPC), representing culturable bacteria, accounted for 1\% to 2.7\% of the total numbers obtained using acridine orange direct counting (AODC). The highest bacterial culture counts, including toxigenic V. cholerae, were recorded in the spring. The direct fluorescent antibody (DFA) assay was used to detect V. cholerae O1 cells throughout the year, as free-living cells, within clusters, or in association with plankton. V. cholerae O1 varied significantly in morphology, appearing as distinctly rod-shaped cells in the spring months, while small coccoid cells within thick clusters of biofilm were observed during interepidemic periods of the year, notably during the winter months. Toxigenic V. cholerae O1 was culturable in natural water during the spring when the temperature rose sharply. The results of this study confirmed biofilms to be a means of persistence for bacteria and an integral component of the annual life cycle of toxigenic V. cholerae in the estuarine environment of Bangladesh.}, doi = {10.1128/mBio.00483-18}, url = {https://mbio.asm.org/content/9/2/e00483-18}, author = {Sultana, Marzia and Nusrin, Suraia and Hasan, Nur A. and Sadique, Abdus and Ahmed, Kabir U. and Islam, Atiqul and Hossain, Anwar and Longini, Ira and Nizam, Azhar and Huq, Anwar and Siddique, Abul K. and Sack, David A. and Sack, Richard B. and Rita R Colwell and Alam, Munirul}, editor = {Vidaver, Anne K.} } @article {20288, title = {Characterization of the Microbiome at the World{\textquoteright}s Largest Potable Water Reuse Facility}, journal = {Frontiers in Microbiology}, year = {2018}, month = {Feb-10-2020}, abstract = {Conventional water resources are not sufficient in many regions to meet the needs of growing populations. Due to cyclical weather cycles, drought, and climate change, water stress has increased worldwide including in Southern California, which serves as a model for regions that integrate reuse of wastewater for both potable and non-potable use. The Orange County Water District (OCWD) Advanced Water Purification Facility (AWPF) is a highly engineered system designed to treat and produce up to 100 million gallons per day (MGD) of purified water from a municipal wastewater source for potable reuse. Routine facility microbial water quality analysis is limited to standard indicators at this and similar facilities. Given recent advances in high throughput DNA sequencing techniques, complete microbial profiling of communities in water samples is now possible. By using 16S/18S rRNA gene sequencing, metagenomic and metatranscriptomic sequencing coupled to a highly accurate identification method along with 16S rRNA gene qPCR, we describe a detailed view of the total microbial community throughout the facility. The total bacterial load of the water at stages of the treatment train ranged from 3.02 {\texttimes} 106 copies in source, unchlorinated wastewater feed to 5.49 {\texttimes} 101 copies of 16S rRNA gene/mL after treatment (consisting of microfiltration, reverse osmosis, and ultraviolet/advanced oxidation). Microbial diversity and load decreased by several orders of magnitude after microfiltration and reverse osmosis treatment, falling to almost non-detectable levels that more closely resembled controls of molecular grade laboratory water than the biomass detected in the source water. The presence of antibiotic resistance genes and viruses was also greatly reduced. Overall, system design performance was achieved, and comprehensive microbial community analysis was found to enable a more complete characterization of the water/wastewater microbial signature. Keywords: water reuse, pathogens, water purification, metatranscriptomics, metagenomics}, doi = {10.3389/fmicb.2018.02435}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2018.02435/full}, author = {Stamps, Blake W. and Leddy, Menu B. and Plumlee, Megan H. and Hasan, Nur A. and Rita R Colwell and Spear, John R.} } @article {20293, title = {Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome Between Neonatal Intensive Care Unit (NICU) Environments}, journal = {Frontiers in Microbiology}, year = {2018}, month = {Jan-06-2020}, doi = {10.3389/fmicb.2018.01361}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.01361/full}, author = {Hourigan, Suchitra K. and Subramanian, Poorani and Hasan, Nur A. and Ta, Allison and Klein, Elisabeth and Chettout, Nassim and Huddleston, Kathi and Deopujari, Varsha and Levy, Shira and Baveja, R and Clemency, Nicole C. and Baker, Robin L. and Niederhuber, John E. and Rita R Colwell} } @article {20252, title = {Deep-learning-assisted Volume Visualization}, journal = {IEEE Transactions on Visualization and Computer Graphics}, year = {2018}, month = {Jan-01-2018}, pages = {1 - 1}, issn = {1077-2626}, doi = {10.1109/TVCG.2018.2796085}, url = {http://ieeexplore.ieee.org/document/8265023/http://xplorestaging.ieee.org/ielx7/2945/4359476/08265023.pdf?arnumber=8265023}, author = {Cheng, Hsueh-Chien and Cardone, Antonio and Jain, Somay and Krokos, Eric and Narayan, Kedar and Subramaniam, Sriram and Varshney, Amitabh} } @article {20297, title = {Distinct consequences of amoxicillin and ertapenem exposure in the porcine gut microbiome}, journal = {Anaerobe}, volume = {53}, year = {2018}, month = {Jan-10-2018}, pages = {82 - 93}, issn = {10759964}, doi = {10.1016/j.anaerobe.2018.04.012}, url = {https://www.sciencedirect.com/science/article/pii/S1075996418300696?via\%3Dihub}, author = {Connelly, Sheila and Subramanian, Poorani and Hasan, Nur A. and Rita R Colwell and Kaleko, Michael} } @article {20289, title = {Environmental and hydroclimatic factors influencing Vibrio populations in the estuarine zone of the Bengal delta}, journal = {Environmental Monitoring and Assessment}, year = {2018}, month = {Jan-10-2018}, abstract = {The objective of this study was to determine environmental parameters driving Vibrio populations in the estuarine zone of the Bengal delta. Spatio-temporal data were collected at river estuary, mangrove, beach, pond, and canal sites. Effects of salinity, tidal amplitude, and a cyclone and tsunami were included in the study. Vibrio population shifts were found to be correlated with tide-driven salinity and suspended particulate matter (SPM). Increased abundance of Vibrio spp. in surface water was observed after a cyclone, attributed to re-suspension of benthic particulate organic carbon (POC), and increased availability of chitin and dissolved organic carbon (DOC). Approximately a two log10 increase in the (p < 0.05) number of Vibrio spp. was observed in < 20 μm particulates, compared with microphytoplankton (20{\textendash}60 μm) and zooplankton > 60 μm fractions. Benthic and suspended sediment comprised a major reservoir of Vibrio spp. Results of microcosm experiments showed enhanced growth of vibrios was related to concentration of organic matter in SPM. It is concluded that SPM, POC, chitin, and salinity significantly influence abundance and distribution of vibrios in the Bengal delta estuarine zone. Keywords Vibrio Salinity Cyclone Tide Chitin Sediment dynamics }, issn = {0167-6369}, doi = {10.1007/s10661-018-6925-7}, url = {https://link.springer.com/article/10.1007\%2Fs10661-018-6925-7}, author = {Neogi, Sucharit and Rubin, Lara and Alam, Munirul and Harder, Jens and Yamasaki, Shinji and Rita R Colwell} } @article {20300, title = {High-Throughput DNA Sequencing To Profile Microbial Water Quality Of Potable Reuse}, year = {2018}, url = {https://www.wateronline.com/doc/high-throughput-dna-sequencing-to-profile-microbial-water-quality-of-potable-reuse-0001}, author = {Menu B. Leddy and Megan H. Plumlee and Rose S. Kantor and Kara L. Nelson and Scott E. Miller and Lauren C. Kennedy and Blake W. Stamps and John R. Spear and Nur A. Hasan and Rita R Colwell} } @conference {20251, title = {Interpolation-Based Gray-Level Co-Occurrence Matrix Computation for Texture Directionality Estimation}, booktitle = {IEEE 22nd Signal Processing Algorithms, Architectures, Arrangements, and Applications Conference}, year = {2018}, month = {12/06/2018}, publisher = {IEEE}, organization = {IEEE}, address = {Poznan, Poland}, abstract = {A novel interpolation-based model for the computation of the Gray Level Co-occurrence Matrix (GLCM) is presented. The model enables GLCM computation for any real valued angles and offsets, as opposed to the traditional, lattice-based model. A texture directionality estimation algorithm is defined using the GLCM-derived correlation feature. The robustness of the algorithm with respect to image blur and additive Gaussian noise is evaluated. It is concluded that directionality estimation is robust to image blur and low noise levels. For high noise levels, the mean error increases but remains bounded. The performance of the directionality estimation algorithm is illustrated on fluorescence microscopy images of fibroblast cells. The algorithm was implemented in C++ and the source code is available in an openly accessible repository.}, isbn = { 978-8-3620-6533-2}, doi = {10.23919/SPA.2018.8563413 }, url = {https://ieeexplore.ieee.org/document/8563413}, author = {Marcin Kociolek and Mary Brady and Peter Bajcsy and Cardone, Antonio} } @article {20283, title = {A Metagenomic Approach to Evaluating Surface Water Quality in Haiti}, journal = {International Journal of Environmental Research and Public Health}, volume = {1542}, year = {2018}, month = {Jan-10-2018}, pages = {2211}, abstract = {The cholera epidemic that occurred in Haiti post-earthquake in 2010 has resulted in over 9000 deaths during the past eight years. Currently, morbidity and mortality rates for cholera have declined, but cholera cases still occur on a daily basis. One continuing issue is an inability to accurately predict and identify when cholera outbreaks might occur. To explore this surveillance gap, a metagenomic approach employing environmental samples was taken. In this study, surface water samples were collected at two time points from several sites near the original epicenter of the cholera outbreak in the Central Plateau of Haiti. These samples underwent whole genome sequencing and subsequent metagenomic analysis to characterize the microbial community of bacteria, fungi, protists, and viruses, and to identify antibiotic resistance and virulence associated genes. Replicates from sites were analyzed by principle components analysis, and distinct genomic profiles were obtained for each site. Cholera toxin converting phage was detected at one site, and Shiga toxin converting phages at several sites. Members of the Acinetobacter family were frequently detected in samples, including members implicated in waterborne diseases. These results indicate a metagenomic approach to evaluating water samples can be useful for source tracking and the surveillance of pathogens such as Vibrio cholerae over time, as well as for monitoring virulence factors such as cholera toxin.}, url = {https://www.ncbi.nlm.nih.gov/pubmed/30309013}, author = {Roy, Monika and Arnaud, Jean and Jasmin, Paul and Hamner, Steve and Hasan, Nur and Rita R Colwell and Ford, Timothy} } @article {20299, title = {Occurrence of Vibrio cholerae in water reservoirs of Burkina Faso}, journal = {Research in Microbiology}, volume = {169}, year = {2018}, month = {Jan-01-2018}, pages = {1 - 10}, abstract = {Africa is currently an important region in which cholera epidemics occur. Little is known about the presence of Vibrio cholerae in freshwater bodies in Africa. There are ca. 1700 lakes and reservoirs in Burkina Faso, most of which have been built within recent decades to secure water resources. The purpose of this study was to investigate the presence of V. cholerae in the water of reservoirs, using the most-probable-number polymerase chain reaction. Results showed that V. cholerae could be detected in water samples collected from 14 of 39 sampled reservoirs. The concentrations varied from 0 MPN/l to more than 1100 MPN/l. Fifty strains of V. cholerae isolated on CHROMagar{\texttrademark} vibrio were identified as V. cholerae non-O1/non-O139, none of which carried the ctxA gene. A significant positive correlation was found between the presence of V. cholerae in the reservoirs and both alkaline pH and phytoplankton biomass. V. cholerae was present in significantly higher numbers in reservoirs of urban areas than in rural areas. Since V. cholerae non-O1/non-O139 has been shown to be a causative agent of endemic diarrheal outbreaks, their presence in Burkina Faso reservoirs suggests they may play a role in gastroenteritis in that country.}, issn = {09232508}, doi = {10.1016/j.resmic.2017.08.004}, url = {https://www.sciencedirect.com/science/article/pii/S092325081730147X?via\%3Dihub}, author = {Kabor{\'e}, Saidou and Cecchi, Philippe and Mosser, Thomas and Toubiana, Myl{\`e}ne and Traor{\'e}, Oumar and Ouattara, Aboubakar S. and Traor{\'e}, Alfred S. and Barro, Nicolas and Rita R Colwell and Monfort, Patrick} } @article {20296, title = {Satellites and Cell Phones Form a Cholera Early-Warning System}, journal = {Eos}, volume = {99}, year = {2018}, month = {Mar-03-2020}, doi = {10.1029/2018EO094839}, url = {https://eos.org/project-updates/satellites-and-cell-phones-form-a-cholera-early-warning-system}, author = {Akanda, Ali and Aziz, Sonia and Jutla, Antarpreet and Huq, Anwar and Alam, Munirul and Ahsan, Gias and Rita R Colwell} } @article {20290, title = {Spores and soil from six sides: interdisciplinarity and the environmental biology of anthrax (Bacillus anthracis)}, journal = {Biological Reviews}, year = {2018}, month = {Jan-11-2018}, pages = {1813 - 1831}, abstract = {Environmentally transmitted diseases are comparatively poorly understood and managed, and their ecology is particularly understudied. Here we identify challenges of studying environmental transmission and persistence with a six-sided interdisciplinary review of the biology of anthrax (Bacillus anthracis). Anthrax is a zoonotic disease capable of maintaining infectious spore banks in soil for decades (or even potentially centuries), and the mechanisms of its environmental persistence have been the topic of significant research and controversy. Where anthrax is endemic, it plays an important ecological role, shaping the dynamics of entire herbivore communities. The complex eco-epidemiology of anthrax, and the mysterious biology of Bacillus anthracis during its environmental stage, have necessitated an interdisciplinary approach to pathogen research. Here, we illustrate different disciplinary perspectives through key advances made by researchers working in Etosha National Park, a long-term ecological research site in Namibia that has exemplified the complexities of the enzootic process of anthrax over decades of surveillance. In Etosha, the role of scavengers and alternative routes (waterborne transmission and flies) has proved unimportant relative to the long-term persistence of anthrax spores in soil and their infection of herbivore hosts. Carcass deposition facilitates green-ups of vegetation to attract herbivores, potentially facilitated by the role of anthrax spores in the rhizosphere. The underlying seasonal pattern of vegetation, and herbivores{\textquoteright} immune and behavioural responses to anthrax risk, interact to produce regular {\textquoteleft}anthrax seasons{\textquoteright} that appear to be a stable feature of the Etosha ecosystem. Through the lens of microbiologists, geneticists, immunologists, ecologists, epidemiologists, and clinicians, we discuss how anthrax dynamics are shaped at the smallest scale by population genetics and interactions within the bacterial communities up to the broadest scales of ecosystem structure. We illustrate the benefits and challenges of this interdisciplinary approach to disease ecology, and suggest ways anthrax might offer insights into the biology of other important pathogens. Bacillus anthracis, and the more recently emerged Bacillus cereus biovar anthracis, share key features with other environmentally transmitted pathogens, including several zoonoses and panzootics of special interest for global health and conservation efforts. Understanding the dynamics of anthrax, and developing interdisciplinary research programs that explore environmental persistence, is a critical step forward for understanding these emerging threats. }, doi = {10.1111/brv.12420}, url = {https://onlinelibrary.wiley.com/doi/full/10.1111/brv.12420}, author = {Carlson, Colin J. and Getz, Wayne M. and Kausrud, Kyrre L. and Cizauskas, Carrie A. and Blackburn, Jason K. and Bustos Carrillo, Fausto A. and Rita R Colwell and Easterday, W. Ryan and Ganz, Holly H. and Kamath, Pauline L. and {\O}kstad, Ole A. and Turner, Wendy C. and Kolsto, Anne-Brit and Stenseth, Nils C.} } @article {20298, title = {Virulence-Related Genes Identified from the Genome Sequence of the Non-O1/Non-O139 Vibrio cholerae Strain VcN1, Isolated from Dhaka, Bangladesh}, journal = {Genome Announcements}, year = {2018}, month = {Aug-03-2018}, abstract = {We report here the first draft genome sequence of the non-O1/non-O139 Vibrio cholerae strain VcN1, isolated from Dhaka, Bangladesh. The data submitted to GenBank for this strain will contribute to advancing our understanding of this environmentally disseminated bacterium, including its virulence and its evolution as an important pathogen.}, doi = {10.1128/genomeA.01513-17}, url = {https://mra.asm.org/content/6/10/e01513-17}, author = {Hossain, Maqsud and Alam, Munirul and Khaleque, Abdul and Islam, Sohidul and Sadique, Abdus and Khan, Nayeim and Halim, Zahra and Sarker, Mrinmoy and El-Sayed, Najib M. and Huq, Anwar and Ahsan, Gias Uddin and Rita R Colwell} } @article {20320, title = {Application of a paper based device containing a new culture medium to detect Vibrio cholerae in water samples collected in Haiti}, journal = {Journal of Microbiological Methods}, volume = {133}, year = {2017}, month = {Jan-02-2017}, pages = {23 - 31}, issn = {01677012}, doi = {10.1016/j.mimet.2016.12.014}, url = {https://www.sciencedirect.com/science/article/pii/S0167701216303578?via\%3Dihub}, author = {Briquaire, Romain and Rita R Colwell and Boncy, Jacques and Rossignol, Emmanuel and Dardy, Aline and Pandini, Isabelle and Villeval, Fran{\c c}ois and Machuron, Jean-Louis and Huq, Anwar and Rashed, Shah and Vandevelde, Thierry and Rozand, Christine} } @article {20315, title = {Assessment of Risk of Cholera in Haiti following Hurricane Matthew}, journal = {The American Journal of Tropical Medicine and Hygiene}, volume = {97}, year = {2017}, month = {Jul-09-2017}, pages = {896 - 903}, abstract = {Damage to the inferior and fragile water and sanitation infrastructure of Haiti after Hurricane Matthew has created an urgent public health emergency in terms of likelihood of cholera occurring in the human population. Using satellite-derived data on precipitation, gridded air temperature, and hurricane path and with information on water and sanitation (WASH) infrastructure, we tracked changing environmental conditions conducive for growth of pathogenic vibrios. Based on these data, we predicted and validated the likelihood of cholera cases occurring past hurricane. The risk of cholera in the southwestern part of Haiti remained relatively high since November 2016 to the present. Findings of this study provide a contemporary process for monitoring ground conditions that can guide public health intervention to control cholera in human population by providing access to vaccines, safe WASH facilities. Assuming current social and behavioral patterns remain constant, it is recommended that WASH infrastructure should be improved and considered a priority especially before 2017 rainy season.}, issn = {0002-9637}, doi = {10.4269/ajtmh.17-0048}, url = {http://www.ajtmh.org/content/journals/10.4269/ajtmh.17-0048}, author = {Huq, Anwar and Anwar, Rifat and Rita R Colwell and McDonald, Michael D. and Khan, Rakib and Jutla, Antarpreet and Akanda, Shafqat} } @article {20314, title = {Beyond cost-effectiveness: Using systems analysis for infectious disease preparedness}, journal = {Vaccine}, volume = {35}, year = {2017}, month = {Jan-01-2017}, pages = {A46 - A49}, abstract = {Until the recent outbreaks, Ebola vaccines ranked low in decision makers{\textquoteright} priority lists based on cost-effectiveness analysis and (or) corporate profitability. Despite a relatively small number of Ebola-related cases and deaths (compared to other causes), Ebola vaccines suddenly leapt to highest priority among international health agencies and vaccine developers. Clearly, earlier cost-effectiveness analyses badly missed some factors affecting real world decisions. Multi-criteria systems analysis can improve evaluation and prioritization of vaccine development and also of many other health policy and investment decisions. Neither cost-effectiveness nor cost-benefit analysis can capture important aspects of problems such as Ebola or the emerging threat of Zika, especially issues of inequality and disparity{\textemdash}issues that dominate the planning of many global health and economic organizations. Cost-benefit analysis requires assumptions about the specific value of life{\textemdash}an idea objectionable to many analysts and policy makers. Additionally, standard cost-effectiveness calculations cannot generally capture effects on people uninfected with Ebola for example, but nevertheless affected through such factors as contagion, herd immunity, and fear of dread disease, reduction of travel and commerce, and even the hope of disease eradication. Using SMART Vaccines, we demonstrate how systems analysis can visibly include important {\textquotedblleft}other factors{\textquotedblright} and more usefully guide decision making and beneficially alter priority setting processes.}, issn = {0264410X}, doi = {10.1016/j.vaccine.2016.08.090}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0264410X16309501}, author = {Phelps, Charles and Madhavan, Guruprasad and Rappuoli, Rino and Rita R Colwell and Fineberg, Harvey} } @article {20448, title = {A Bioinformatics 3D Cellular Morphotyping Strategy for Assessing Biomaterial Scaffold Niches}, journal = {ACS Biomaterials Science \& Engineering}, volume = {3}, year = {2017}, month = {Sep-10-2017}, pages = {2302 - 2313}, issn = {2373-9878}, doi = {10.1021/acsbiomaterials.7b00473}, url = {http://pubs.acs.org/doi/10.1021/acsbiomaterials.7b00473http://pubs.acs.org/doi/pdf/10.1021/acsbiomaterials.7b00473}, author = {Florczyk, Stephen J. and Simon, Mylene and Juba, Derek and Pine, P. Scott and Sarkar, Sumona and Chen, Desu and Baker, Paula J. and Bodhak, Subhadip and Cardone, Antonio and Brady, Mary C. and Bajcsy, Peter and Simon, Carl G.} } @article {20307, title = {Characterization of Microbial Signatures From Advanced Treated Wastewater Biofilms}, journal = {Journal - American Water Works Association}, volume = {109}, year = {2017}, month = {Jan-11-2017}, pages = {E503 - E512}, abstract = {Next-generation sequencing (NGS) and metagenomics were used to identify microbial communities in biofilms of microfiltration (MF) and reverse osmosis (RO) membranes in an advanced water purification facility (AWPF) that treats municipal wastewater to produce potable quality water. Secondary treated wastewater effluent is the source of influent to the AWPF treatment train and was also characterized by NGS. Results show low bacterial diversity in biofilms obtained from the feed-side surfaces of MF and RO membranes. Microbial communities and antibiotic resistance genes (ARGs) in the RO biofilm were compared with those of the MF and influent, revealing lower abundance of bacterial species and ARGs in the RO biofilm than in the other samples. Opportunistic pathogens were detected in all samples; however, indicator bacteria, viruses, and bacteriophages were not detected in the RO biofilm. It is concluded that NGS has great potential for improved detection and characterization of microbial communities in biofilms that form on AWPF MF and RO membranes.}, doi = {10.5942/jawwa.2017.109.0116}, url = {http://doi.wiley.com/10.5942/jawwa.2017.109.0116}, author = {Leddy, Menu B. and Hasan, Nur A. and Subramanian, Poorani and Heberling, Colin and Cotruvo, Joseph and Rita R Colwell} } @article {20306, title = {Characterization of Pathogenic Vibrio parahaemolyticus from the Chesapeake Bay, Maryland}, journal = {Frontiers in Microbiology}, year = {2017}, month = {Mar-12-2018}, doi = {10.3389/fmicb.2017.02460}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.02460}, author = {Chen, Arlene J. and Hasan, Nur A. and Haley, Bradd J. and Taviani, Elisa and Tarnowski, Mitch and Brohawn, Kathy and Johnson, Crystal N. and Rita R Colwell and Huq, Anwar} } @article {20305, title = {Characterization of Two Cryptic Plasmids Isolated in Haiti from Clinical Vibrio cholerae Non-O1/Non-O139}, journal = {Frontiers in Microbiology}, year = {2017}, month = {Nov-11-2018}, doi = {10.3389/fmicb.2017.02283}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.02283}, author = {Ceccarelli, Daniela and Garriss, Genevieve and Choi, Seon Y. and Hasan, Nur A. and Stepanauskas, Ramunas and Pop, Mihai and Huq, Anwar and Rita R Colwell} } @article {20310, title = {Comparative genomic analysis and characterization of incompatibility group FIB plasmid encoded virulence factors of Salmonella enterica isolated from food sources}, journal = {BMC Genomics}, year = {2017}, month = {Jan-12-2017}, abstract = {BACKGROUND: The degree to which the chromosomal mediated iron acquisition system contributes to virulence of many bacterial pathogens is well defined. However, the functional roles of plasmid encoded iron acquisition systems, specifically Sit and aerobactin, have yet to be determined for Salmonella spp. In a recent study, Salmonella enterica strains isolated from different food sources were sequenced on the Illumina MiSeq platform and found to harbor the incompatibility group (Inc) FIB plasmid. In this study, we examined sequence diversity and the contribution of factors encoded on the IncFIB plasmid to the virulence of S. enterica. RESULTS: Whole genome sequences of seven S. enterica isolates were compared to genomes of serovars of S. enterica isolated from food, animal, and human sources. SeqSero analysis predicted that six strains were serovar Typhimurium and one was Heidelberg. Among the S. Typhimurium strains, single nucleotide polymorphism (SNP)-based phylogenetic analyses revealed that five of the isolates clustered as a single monophyletic S. Typhimurium subclade, while one of the other strains branched with S. Typhimurium from a bovine source. DNA sequence based phylogenetic diversity analyses showed that the IncFIB plasmid-encoded Sit and aerobactin iron acquisition systems are conserved among bacterial species including S. enterica. The IncFIB plasmid was transferred to an IncFIB plasmid deficient strain of S. enterica by conjugation. The transconjugant SE819::IncFIB persisted in human intestinal epithelial (Caco-2) cells at a higher rate than the recipient SE819. Genes of the Sit and aerobactin operons in the IncFIB plasmid were differentially expressed in iron-rich and iron-depleted growth media. CONCLUSIONS: Minimal sequence diversity was detected in the Sit and aerobactin operons in the IncFIB plasmids present among different bacterial species, including foodborne Salmonella strains. IncFIB plasmid encoded factors play a role during infection under low-iron conditions in host cells.}, doi = {10.1186/s12864-017-3954-5}, url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3954-5}, author = {Khajanchi, Bijay K. and Hasan, Nur A. and Choi, Seon Young and Han, Jing and Zhao, Shaohua and Rita R Colwell and Cerniglia, Carl E. and Foley, Steven L.} } @article {20311, title = {Comparative Genomics of Escherichia coli Isolated from Skin and Soft Tissue and Other Extraintestinal Infections}, journal = {mBio}, year = {2017}, month = {Jun-09-2017}, abstract = {Escherichia coli, an intestinal Gram-negative bacterium, has been shown to be associated with a variety of diseases in addition to intestinal infections, such as urinary tract infections (UTIs), meningitis in neonates, septicemia, skin and soft tissue infections (SSTIs), and colisepticemia. Thus, for nonintestinal infections, it is categorized as extraintestinal pathogenic E. coli (ExPEC). It is also an opportunistic pathogen, causing cross infections, notably as an agent of zoonotic diseases. However, comparative genomic data providing functional and genetic coordinates for ExPEC strains associated with these different types of infections have not proven conclusive. In the study reported here, ExPEC E. coli isolated from SSTIs was characterized, including virulence and drug resistance profiles, and compared with isolates from patients suffering either pyelonephritis or septicemia. Results revealed that the majority of the isolates belonged to two pathogenic phylogroups, B2 and D. Approximately 67\% of the isolates were multidrug resistant (MDR), with 85\% producing extended-spectrum beta-lactamase (ESBL) and 6\% producing metallo-beta-lactamase (MBL). The blaCTX-M-15 genotype was observed in at least 70\% of the E. coli isolates in each category, conferring resistance to an extended range of beta-lactam antibiotics. Whole-genome sequencing and comparative genomics of the ExPEC isolates revealed that two of the four isolates from SSTIs, NA633 and NA643, belong to pandemic sequence type ST131, whereas functional characteristics of three of the ExPEC pathotypes revealed that they had equal capabilities to form biofilm and were resistant to human serum. Overall, the isolates from a variety of ExPEC infections demonstrated similar resistomes and virulomes and did not display any disease-specific functional or genetic coordinates. IMPORTANCE Infections caused by extraintestinal pathogenic E. coli (ExPEC) are of global concern as they result in significant costs to health care facilities management. The recent emergence of a multidrug-resistant pandemic clone, Escherichia coli ST131, is of primary concern as a global threat. In developing countries, such as India, skin and soft tissue infections (SSTIs) associated with E. coli are marginally addressed. In this study, we employed both genomic analysis and phenotypic assays to determine relationships, if any, among the ExPEC pathotypes. Similarity between antibiotic resistance and virulence profiles was observed, ST131 isolates from SSTIs were reported, and genomic similarities among strains isolated from different disease conditions were detected. This study provides functional molecular infection epidemiology insight into SSTI-associated E. coli compared with ExPEC pathotypes.}, doi = {10.1128/mBio.01070-17}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.01070-17}, author = {Ranjan, Amit and Shaik, Sabiha and Nandanwar, Nishant and Hussain, Arif and Tiwari, Sumeet K. and Semmler, Torsten and Jadhav, Savita and Wieler, Lothar H. and Alam, Munirul and Rita R Colwell and Ahmed, Niyaz}, editor = {Cossart, Pascale F.} } @article {20308, title = {Comprehensive benchmarking and ensemble approaches for metagenomic classifiers}, journal = {Genome Biology}, year = {2017}, month = {Jan-12-2017}, doi = {10.1186/s13059-017-1299-7}, url = {http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1299-7}, author = {McIntyre, Alexa B. R. and Ounit, Rachid and Afshinnekoo, Ebrahim and Prill, Robert J. and H{\'e}naff, Elizabeth and Alexander, Noah and Minot, Samuel S. and Danko, David and Foox, Jonathan and Ahsanuddin, Sofia and Tighe, Scott and Hasan, Nur A. and Subramanian, Poorani and Moffat, Kelly and Levy, Shawn and Lonardi, Stefano and Greenfield, Nick and Rita R Colwell and Rosen, Gail L. and Mason, Christopher E.} } @article {20318, title = {CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules}, journal = {Journal of Bacteriology}, year = {2017}, month = {Mar-05-2018}, abstract = {Pathogenicity islands (PAIs) are mobile integrated genetic elements that contain a diverse range of virulence factors. PAIs integrate into the host chromosome at a tRNA locus that contains their specific bacterial attachment site, attB, via integrase-mediated site-specific recombination generating attL and attR sites. We identified conserved recombination modules (integrases and att sites) previously described in choleragenic Vibrio cholerae PAIs but with novel cargo genes. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins) and a type VI secretion system (T6SS) gene cluster were identified at the Vibrio pathogenicity island 1 (VPI-1) insertion site in 19 V. cholerae strains and contained the same recombination module. Two divergent type I-F CRISPR-Cas systems were identified, which differed in Cas protein homology and content. The CRISPR repeat sequence was identical among all V. cholerae strains, but the CRISPR spacer sequences and the number of spacers varied. In silico analysis suggests that the CRISPR-Cas systems were active against phages and plasmids. A type III secretion system (T3SS) was present in 12 V. cholerae strains on a 68-kb island inserted at the same tRNA-serine insertion site as VPI-2 and contained the same recombination module. Bioinformatics analysis showed that two divergent T3SSs exist among the strains examined. Both the CRISPR and T3SS islands excised site specifically from the bacterial chromosome as complete units, and the cognate integrases were essential for this excision. These data demonstrated that identical recombination modules that catalyze integration and excision from the chromosome can acquire diverse cargo genes, signifying a novel method of acquisition for both CRISPR-Cas systems and T3SSs.}, issn = {0021-9193}, doi = {10.1128/JB.00842-16}, url = {http://jb.asm.org/lookup/doi/10.1128/JB.00842-16}, author = {Carpenter, Megan R. and Kalburge, Sai S. and Borowski, Joseph D. and Peters, Molly C. and Rita R Colwell and Boyd, E. Fidelma}, editor = {DiRita, Victor J.} } @proceedings {20156, title = {Deep-learning-assisted visualization for live-cell images}, year = {2017}, month = {09/2017}, publisher = {IEEE}, address = {Beijing, China}, abstract = {Analyzing live-cell images is particularly challenging because cells move at the same time they undergo systematic changes. Visually inspecting live-cell images therefore involves simultaneously tracking individual cells and detecting relevant spatio-temporal changes. The high cognitive burden of such a complex task makes this kind of analysis inefficient and error-prone. In this paper we describe a deep-learning-assisted visualization based on automatically derived high-level features to identify target cell changes in live-cell images. Applying a novel user-mediated color assignment scheme that maps abstract features into corresponding colors, we create color-based visual annotations that facilitate visual reasoning and analysis of complex time varying live-cell imagery datasets. The visual representations can be used to study temporal changes in cells, such as the morphological changes in cell at various stages of life cycle.}, keywords = {deep learning, live-cell images, Visualization}, author = {Hsueh-Chien Cheng and Cardone, Antonio and Krokos, Eric and Stoica, Bogdan and Faden, Alan and Varshney, Amitabh} } @article {20313, title = {Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP)}, journal = {Journal of Biomolecular Techniques : JBT}, volume = {28}, year = {2017}, month = {Jan-04-2017}, pages = {31 - 39}, abstract = {The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the {\textquotedblleft}Door to Hell{\textquotedblright} crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.}, issn = {1524-0215}, doi = {10.7171/jbt.17-2801-004}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345951/}, author = {Tighe, Scott and Afshinnekoo, Ebrahim and Rock, Tara M. and McGrath, Ken and Alexander, Noah and McIntyre, Alexa and Ahsanuddin, Sofia and Bezdan, Daniela and Green, Stefan J. and Joye, Samantha and Stewart Johnson, Sarah and Baldwin, Don A. and Bivens, Nathan and Ajami, Nadim and Carmical, Joseph R. and Herriott, Ian Charold and Rita R Colwell and Donia, Mohamed and Foox, Jonathan and Greenfield, Nick and Hunter, Tim and Hoffman, Jessica and Hyman, Joshua and Jorgensen, Ellen and Krawczyk, Diana and Lee, Jodie and Levy, Shawn and Garcia-Reyero, {\`a}lia and Settles, Matthew and Thomas, Kelley and {\'o}mez, Felipe and Schriml, Lynn and Kyrpides, Nikos and Zaikova, Elena and Penterman, Jon and Mason, Christopher E.} } @article {20322, title = {Hydroclimatic sustainability assessment of changing climate on cholera in the Ganges-Brahmaputra basin}, journal = {Advances in Water Resources}, volume = {108}, year = {2017}, month = {Jan-10-2017}, pages = {332 - 344}, abstract = {The association of cholera and climate has been extensively documented. However, determining the effects of changing climate on the occurrence of disease remains a challenge. Bimodal peaks of cholera in Bengal Delta are hypothesized to be linked to asymmetric flow of the Ganges and Brahmaputra rivers. Spring cholera is related to intrusion of bacteria-laden coastal seawater during low flow seasons, while autumn cholera results from cross-contamination of water resources when high flows in the rivers cause massive inundation. Coarse resolution of General Circulation Model (GCM) output (usually at 100 {\textendash} 300 km)cannot be used to evaluate variability at the local scale(10{\textendash}20 km),hence the goal of this study was to develop a framework that could be used to understand impacts of climate change on occurrence of cholera. Instead of a traditional approach of downscaling precipitation, streamflow of the two rivers was directly linked to GCM outputs, achieving reasonable accuracy (R2 = 0.89 for the Ganges and R2 = 0.91 for the Brahmaputra)using machine learning algorithms (Support Vector Regression-Particle Swarm Optimization). Copula methods were used to determine probabilistic risks of cholera under several discharge conditions. Key results, using model outputs from ECHAM5, GFDL, andHadCM3for A1B and A2 scenarios, suggest that the combined low flow of the two rivers may increase in the future, with high flows increasing for first half of this century, decreasing thereafter. Spring and autumn cholera, assuming societal conditions remain constant e.g., at the current rate, may decrease. However significant shifts were noted in the magnitude of river discharge suggesting that cholera dynamics of the delta may well demonstrate an uncertain predictable pattern of occurrence over the next century.}, issn = {03091708}, doi = {10.1016/j.advwatres.2016.11.018}, url = {https://linkinghub.elsevier.com/retrieve/pii/S030917081630728X}, author = {Nasr-Azadani, Fariborz and Khan, Rakibul and Rahimikollu, Javad and Unnikrishnan, Avinash and Akanda, Ali and Alam, Munirul and Huq, Anwar and Jutla, Antarpreet and Rita R Colwell} } @conference {20155, title = {Interactive exploration of microstructural features in gigapixel microscopy images}, booktitle = {IEEE International Conference on Image Processing}, year = {2017}, month = {09/2017}, publisher = {IEEE}, organization = {IEEE}, address = {Beijing, China}, abstract = {Modern imaging technologies enable the study of microstructural features, which require capturing the finest details in high-resolution gigapixel images. Nevertheless, the resolution disparity between gigapixel images and megapixel displays presents a challenge to effective visual analysis because subtle texture differences are hardly perceivable at coarser resolutions. In this paper we present a hierarchical segmentation technique based on joint distribution of intensity and noise-resistant local binary patterns to differentiate subtle microstructural textures across various scales. The coarse-to-fine segmentation procedure subdivides each parent segment into texturally-distinct child segments at progressively higher resolutions. The hierarchical structure of segments allows creating intermediate segmentation results interactively. Based on the intermediate results, we highlight regions with texture differences using distinct colors, which provide salient visual hints to users despite of the current viewing resolution. Our new technique has been validated on large microscopy images and shows promising results.}, keywords = {gigapixel images, Image segmentation}, author = {Hsueh-Chien Cheng and Cardone, Antonio and Varshney, Amitabh} } @article {20317, title = {Vibrio cholerae O1 with Reduced Susceptibility to Ciprofloxacin and Azithromycin Isolated from a Rural Coastal Area of Bangladesh}, journal = {Frontiers in Microbiology}, year = {2017}, month = {Sep-02-2018}, abstract = {Cholera outbreaks occur each year in the remote coastal areas of Bangladesh and epidemiological surveillance and routine monitoring of cholera in these areas is challenging. In this study, a total of 97 Vibrio cholerae O1 isolates from Mathbaria, Bangladesh, collected during 2010 and 2014 were analyzed for phenotypic and genotypic traits, including antimicrobial susceptibility. Of the 97 isolates, 95 possessed CTX-phage mediated genes, ctxA, ace, and zot, and two lacked the cholera toxin gene, ctxA. Also both CTX+ and CTX- V. cholerae O1 isolated in this study carried rtxC, tcpAET, and hlyA. The classical cholera toxin gene, ctxB1, was detected in 87 isolates, while eight had ctxB7. Of 95 CTX+ V. cholerae O1, 90 contained rstRET and 5 had rstRCL. All isolates, except two, contained SXT related integrase intSXT. Resistance to penicillin, streptomycin, nalidixic acid, sulfamethoxazole-trimethoprim, erythromycin, and tetracycline varied between the years of study period. Most importantly, 93\% of the V. cholerae O1 were multidrug resistant. Six different resistance profiles were observed, with resistance to streptomycin, nalidixic acid, tetracycline, and sulfamethoxazole-trimethoprim predominant every year. Ciprofloxacin and azithromycin MIC were 0.003{\textendash}0.75 and 0.19{\textendash}2.00 μg/ml, respectively, indicating reduced susceptibility to these antibiotics. Sixteen of the V. cholerae O1 isolates showed higher MIC for azithromycin (>=0.5 μg/ml) and were further examined for 10 macrolide resistance genes, erm(A), erm(B), erm(C), ere(A), ere(B), mph(A), mph(B), mph(D), mef(A), and msr(A) with none testing positive for the macrolide resistance genes.}, doi = {10.3389/fmicb.2017.00252}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.00252}, author = {Rashed, Shah M. and Hasan, Nur A. and Alam, Munirul and Sadique, Abdus and Sultana, Marzia and Hoq, Md. Mozammel and Sack, R. Bradley and Rita R Colwell and Huq, Anwar} } @article {20312, title = {Membrane Bioreactor-Based Wastewater Treatment Plant in Saudi Arabia: Reduction of Viral Diversity, Load, and Infectious Capacity}, journal = {Water}, volume = {96046Volume 70}, year = {2017}, month = {Jan-07-2017}, pages = {534}, doi = {10.3390/w9070534}, url = {http://www.mdpi.com/2073-4441/9/7/534}, author = {Jumat, Muhammad and Hasan, Nur and Subramanian, Poorani and Heberling, Colin and Rita R Colwell and Hong, Pei-Ying} } @article {20309, title = {The microbiomes of blowflies and houseflies as bacterial transmission reservoirs}, journal = {Scientific Reports}, year = {2017}, month = {Jan-12-2017}, abstract = {Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome. Legs and wings displayed the largest microbial diversity and were shown to be an important route for microbial dispersion. The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.}, doi = {10.1038/s41598-017-16353-x}, url = {http://www.nature.com/articles/s41598-017-16353-x}, author = {Junqueira, AC and Ratan, Aakrosh and Acerbi, Enzo and Drautz-Moses, Daniela I. and Premkrishnan, BNV and Costea, PI and Linz, Bodo and Purbojati, Rikky W. and Paulo, Daniel F. and Gaultier, Nicolas E. and Subramanian, Poorani and Hasan, Nur A. and Rita R Colwell and Bork, Peer and Azeredo-Espin, Ana Maria L. and Bryant, Donald A. and Schuster, Stephan C.} } @article {20323, title = {Natural Disasters and Cholera Outbreaks: Current Understanding and Future Outlook}, journal = {Current Environmental Health Reports}, year = {2017}, month = {Jan-03-2017}, pages = {99 - 107}, abstract = {Purpose of Review Diarrheal diseases remain a serious global public health threat, especially for those populations lacking access to safe water and sanitation infrastructure. Although association of several diarrheal diseases, e.g., cholera, shigellosis, etc., with climatic processes has been documented, the global human population remains at heightened risk of outbreak of diseases after natural disasters, such as earthquakes, floods, or droughts. In this review, cholera was selected as a signature diarrheal disease and the role of natural disasters in triggering and transmitting cholera was analyzed. Recent Findings Key observations include identification of an inherent feedback loop that includes societal structure, prevailing climatic processes, and spatio-temporal seasonal variability of natural disasters. Data obtained from satellite-based remote sensing are concluded to have application, although limited, in predicting risks of a cholera outbreak(s). Summary We argue that with the advent of new high spectral and spatial resolution data, earth observation systems should be seamlessly integrated in a decision support mechanism to be mobilize resources when a region suffers a natural disaster. A framework is proposed that can be used to assess the impact of natural disasters with response to outbreak of cholera, providing assessment of short- and long-term influence of climatic processes on disease outbreaks.}, doi = {10.1007/s40572-017-0132-5}, url = {http://link.springer.com/10.1007/s40572-017-0132-5}, author = {Jutla, Antarpreet and Khan, Rakibul and Rita R Colwell} } @article {20316, title = {SYN-004 (ribaxamase), an oral beta-lactamase, mitigates antibiotic-mediated dysbiosis in a porcine gut microbiome model}, journal = {Journal of Applied Microbiology}, year = {2017}, month = {Jan-07-2017}, pages = {66 - 79}, abstract = { Aim To evaluate an antibiotic inactivation strategy to protect the gut microbiome from antibiotic-mediated damage. Methods and Results SYN-004 (ribaxamase) is an orally delivered beta-lactamase intended to degrade penicillins and cephalosporins within the gastrointestinal tract to protect the microbiome. Pigs (20 kg, n = 10) were treated with ceftriaxone (CRO) (IV, 50 mg kg-1, SID) for 7 days and a cohort (n = 5) received ribaxamase (PO, 75 mg, QID) for 9 days beginning the day before antibiotic administration. Ceftriaxone serum levels were not statistically different in the antibiotic-alone and antibiotic + ribaxamase groups, indicating ribaxamase did not alter systemic antibiotic levels. Whole-genome metagenomic analyses of pig faecal DNA revealed that CRO caused significant changes to the gut microbiome and an increased frequency of antibiotic resistance genes. With ribaxamase, the gut microbiomes were not significantly different from pretreatment and antibiotic resistance gene frequency was not increased. Conclusion Ribaxamase mitigated CRO-mediated gut microbiome dysbiosis and attenuated propagation of the antibiotic resistance genes in pigs. Significance and Impact of the Study Damage of the microbiome can lead to overgrowth of pathogenic organisms and antibiotic exposure can promote selection for antibiotic-resistant micro-organisms. Ribaxamase has the potential to become the first therapy designed to protect the gut microbiome from antibiotic-mediated dysbiosis and reduce emergence of antibiotic resistance. }, doi = {10.1111/jam.13432}, url = {https://onlinelibrary.wiley.com/doi/10.1111/jam.13432}, author = {Connelly, S. and Bristol, J.A. and Hubert, S. and Subramanian, P. and Hasan, N.A. and Rita R Colwell and Kaleko, M.} } @conference {20065, title = {3D Cellular Morphotyping of Scaffold Niches}, booktitle = {2016 32nd Southern Biomedical Engineering Conference (SBEC)}, year = {2016}, publisher = {IEEE}, organization = {IEEE}, author = {Florczyk, Stephen J and Simon, Mylene and Juba, Derek and Pine, P Scott and Sarkar, Sumona and Chen, Desu and Baker, Paula J and Bodhak, Subhadip and Cardone, Antonio and Brady, Mary and others} } @article {20328, title = {Are natural reservoirs important for cholera surveillance? The case of an outbreak in a Brazilian estuary}, journal = {Letters in Applied Microbiology}, year = {2016}, month = {Jan-09-2016}, pages = {183 - 188}, abstract = {Paranagu{\'a} Bay is one of the largest estuarine systems on the Southern Brazilian coast. The only recorded cholera outbreak in this region since the early 20th century occurred in 1999 and resulted in 467 cases and at least three reported deaths in a population of approx. 150 000 people. This short communication reports historical, unpublished data related to that outbreak. Water, zooplankton and bivalve samples were collected and evaluated using direct fluorescence assay to determine whether Vibrio cholerae serogroups O1 and O139 were present in the estuarine system at that time. Most of the water (83\%) and zooplankton samples (75\%) were positive for V. cholerae O1, while V. cholerae O139 was not detected. Shellfish (Mytella sp.) were also positive for V. cholerae O1. These results indicate that the estuary, including biological vectors such as copepods and bivalves, comprise an important reservoir of V. cholerae O1 and a probable waterborne pathway for the disease, in addition to contamination with untreated sewage. }, doi = {10.1111/lam.12614}, url = {https://onlinelibrary.wiley.com/doi/10.1111/lam.12614}, author = {Martinelli Filho, J.E. and Lopes, R.M. and Rivera, I.N.G. and Rita R Colwell} } @article {20324, title = {Chitin promotes Mycobacterium ulcerans growth}, journal = {FEMS Microbiology Ecology}, volume = {928565871}, year = {2016}, month = {Jun-06-2017}, pages = {fiw067}, abstract = {Mycobacterium ulcerans (MU) is the causative agent of Buruli ulcer, an emerging human infectious disease. However, both the ecology and life cycle of MU are poorly understood. The occurrence of MU has been linked to the aquatic environment, notably water bodies affected by human activities. It has been hypothesized that one or a combination of environmental factor(s) connected to human activities could favour growth of MU in aquatic systems. Here, we tested in vitro the growth effect of two ubiquitous polysaccharides and five chemical components on MU at concentration ranges shown to occur in endemic regions. Real-time PCR showed that chitin increased MU growth significantly providing a nutrient source or environmental support for the bacillus, thereby, providing a focus on the association between MU and aquatic arthropods. Aquatic environments with elevated population of arthropods provide increased chitin availability and, thereby, enhanced multiplication of MU. If calcium very slightly enhanced MU growth, iron, zinc, sulphate and phosphate did not stimulate MU growth, and at the concentration ranges of this study would limit MU population in natural ecosystems.}, doi = {10.1093/femsec/fiw067}, url = {https://academic.oup.com/femsec/article-lookup/doi/10.1093/femsec/fiw067}, author = {Sanhueza, Daniel and Chevillon, Christine and Rita R Colwell and Babonneau, J{\'e}r{\'e}mie and Marion, Estelle and Marsollier, Laurent and {\'e}gan, {\c c}ois}, editor = {Sobecky, Patricia} } @article {20329, title = {Climate influence on Vibrio and associated human diseases during the past half-century in the coastal North Atlantic}, journal = {Proceedings of the National Academy of Sciences}, year = {2016}, month = {Nov-08-2017}, pages = {E5062 - E5071}, abstract = {Climate change is having a dramatic impact on marine animal and plant communities but little is known of its influence on marine prokaryotes, which represent the largest living biomass in the world oceans and play a fundamental role in maintaining life on our planet. In this study, for the first time to our knowledge, experimental evidence is provided on the link between multidecadal climatic variability in the temperate North Atlantic and the presence and spread of an important group of marine prokaryotes, the vibrios, which are responsible for several infections in both humans and animals. Using archived formalin-preserved plankton samples collected by the Continuous Plankton Recorder survey over the past half-century (1958{\textendash}2011), we assessed retrospectively the relative abundance of vibrios, including human pathogens, in nine areas of the North Atlantic and North Sea and showed correlation with climate and plankton changes. Generalized additive models revealed that long-term increase in Vibrio abundance is promoted by increasing sea surface temperatures (up to \~{}1.5 {\textdegree}C over the past 54 y) and is positively correlated with the Northern Hemisphere Temperature (NHT) and Atlantic Multidecadal Oscillation (AMO) climatic indices (P < 0.001). Such increases are associated with an unprecedented occurrence of environmentally acquired Vibrio infections in the human population of Northern Europe and the Atlantic coast of the United States in recent years.}, issn = {0027-8424}, doi = {10.1073/pnas.1609157113}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1609157113}, author = {Vezzulli, Luigi and Grande, Chiara and Reid, Philip C. and {\'e}laou{\"e}t, Pierre and Edwards, Martin and {\"o}fle, Manfred G. and Brettar, Ingrid and Rita R Colwell and Pruzzo, Carla} } @article {20332, title = {Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1}, journal = {FEMS Microbiology Letters}, volume = {36389}, year = {2016}, month = {Nov-06-2017}, pages = {fnw116}, abstract = {Vibrio cholerae causes cholera, a severe diarrheal disease. Understanding the local genetic diversity and transmission of V. cholerae will improve our ability to control cholera. Vibrio cholerae isolates clustered in genetically related groups (clonal complexes, CC) by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (WGS). Isolates in CC1 had been isolated from two geographical locations. Isolates in a second genetically distinct group, CC2, were isolated only at one location. Using WGS, CC1 isolates from both locations revealed, on average, 43.8 nucleotide differences, while those strains comprising CC2 averaged 19.7 differences. Strains from both MLVA-CCs had an average difference of 106.6. Thus, isolates comprising CC1 were more closely related (P < 10-6) to each other than to isolates in CC2. Within a MLVA-CC, after removing all paralogs, alternative alleles were found in all possible combinations on separate chromosomes indicative of recombination within the core genome. Including recombination did not affect the distinctiveness of the MLVA-CCs when measured by WGS. We found that WGS generally reflected the same genetic relatedness of isolates as MLVA, indicating that isolates from the same MLVA-CC shared a more recent common ancestor than isolates from the same location that clustered in a distinct MLVA-CC.}, doi = {10.1093/femsle/fnw116}, url = {https://academic.oup.com/femsle/article-lookup/doi/10.1093/femsle/fnw116}, author = {Rashid, Mahamud-ur and Almeida, Mathieu and Azman, Andrew S. and Lindsay, Brianna R. and Sack, David A. and Rita R Colwell and Huq, Anwar and Morris, J. Glenn and Alam, Munirul and Stine, O. Colin}, editor = {Winstanley, Craig} } @article {20060, title = {Computational study of the inhibitory mechanism of~the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore}, journal = {Journal of Computer-Aided Molecular Design}, volume = {30}, year = {2016}, month = {Jan-06-2016}, pages = {513 - 521}, issn = {0920-654X}, doi = {10.1007/s10822-016-9922-3}, url = {http://link.springer.com/10.1007/s10822-016-9922-3http://link.springer.com/content/pdf/10.1007/s10822-016-9922-3http://link.springer.com/content/pdf/10.1007/s10822-016-9922-3.pdfhttp://link.springer.com/article/10.1007/s10822-016-9922-3/fulltext.html}, author = {Cardone, Antonio and Brady, M. and Sriram, R. and Pant, H. C. and Hassan, S. A.} } @article {20336, title = {Cross-talk among flesh-eating Aeromonas hydrophila strains in mixed infection leading to necrotizing fasciitis}, journal = {Proceedings of the National Academy of Sciences}, volume = {11312161268}, year = {2016}, month = {Jul-01-2017}, pages = {722 - 727}, abstract = {Necrotizing fasciitis (NF) caused by flesh-eating bacteria is associated with high case fatality. In an earlier study, we reported infection of an immunocompetent individual with multiple strains of Aeromonas hydrophila (NF1{\textendash}NF4), the latter three constituted a clonal group whereas NF1 was phylogenetically distinct. To understand the complex interactions of these strains in NF pathophysiology, a mouse model was used, whereby either single or mixed A. hydrophila strains were injected intramuscularly. NF2, which harbors exotoxin A (exoA) gene, was highly virulent when injected alone, but its virulence was attenuated in the presence of NF1 (exoA-minus). NF1 alone, although not lethal to animals, became highly virulent when combined with NF2, its virulence augmented by cis-exoA expression when injected alone in mice. Based on metagenomics and microbiological analyses, it was found that, in mixed infection, NF1 selectively disseminated to mouse peripheral organs, whereas the other strains (NF2, NF3, and NF4) were confined to the injection site and eventually cleared. In vitro studies showed NF2 to be more effectively phagocytized and killed by macrophages than NF1. NF1 inhibited growth of NF2 on solid media, but ExoA of NF2 augmented virulence of NF1 and the presence of NF1 facilitated clearance of NF2 from animals either by enhanced priming of host immune system or direct killing via a contact-dependent mechanism.}, issn = {0027-8424}, doi = {10.1073/pnas.1523817113}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1523817113}, author = {Ponnusamy, Duraisamy and Kozlova, Elena V. and Sha, Jian and Erova, Tatiana E. and Azar, Sasha R. and Fitts, Eric C. and Kirtley, Michelle L. and Tiner, Bethany L. and Andersson, Jourdan A. and Grim, Christopher J. and Isom, Richard P. and Hasan, Nur A. and Rita R Colwell and Chopra, Ashok K.} } @article {20325, title = {Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak}, journal = {BMC Microbiology}, year = {2016}, month = {Jan-12-2016}, doi = {10.1186/s12866-016-0894-1}, url = {http://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-016-0894-1}, author = {Ottesen, Andrea and Ramachandran, Padmini and Reed, Elizabeth and White, James R. and Hasan, Nur and Subramanian, Poorani and Ryan, Gina and Jarvis, Karen and Grim, Christopher and Daquiqan, Ninalynn and Hanes, Darcy and Allard, Marc and Rita R Colwell and Brown, Eric and Chen, Yi} } @article {20331, title = {In Plain View: A Transparent Systems Approach for Enhancing Health Policy Decisions}, year = {2016}, month = {07/2016}, url = {https://www.nae.edu/19582/Bridge/155266/155393.aspx}, author = {Guru Madhavan and Charles E. Phelps and Rita R Colwell and Rino Rappuoli and Harvey V. Fineberg} } @article {20330, title = {IncA/C Conjugative Plasmids Mobilize a New Family of Multidrug Resistance Islands in Clinical Vibrio cholerae Non-O1/Non-O139 Isolates from Haiti}, journal = {mBio}, year = {2016}, month = {Jul-09-2016}, abstract = {Mobile genetic elements play a pivotal role in the adaptation of bacterial populations, allowing them to rapidly cope with hostile conditions, including the presence of antimicrobial compounds. IncA/C conjugative plasmids (ACPs) are efficient vehicles for dissemination of multidrug resistance genes in a broad range of pathogenic species of Enterobacteriaceae. ACPs have sporadically been reported in Vibrio cholerae, the infectious agent of the diarrheal disease cholera. The regulatory network that controls ACP mobility ultimately depends on the transcriptional activation of multiple ACP-borne operons by the master activator AcaCD. Beyond ACP conjugation, AcaCD has also recently been shown to activate the expression of genes located in the Salmonella genomic island 1 (SGI1). Here, we describe MGIVchHai6, a novel and unrelated mobilizable genomic island (MGI) integrated into the 3' end of trmE in chromosome I of V. cholerae HC-36A1, a non-O1/non-O139 multidrug-resistant clinical isolate recovered from Haiti in 2010. MGIVchHai6 contains a mercury resistance transposon and an integron In104-like multidrug resistance element similar to the one of SGI1. We show that MGIVchHai6 excises from the chromosome in an AcaCD-dependent manner and is mobilized by ACPs. Acquisition of MGIVchHai6 confers resistance to β-lactams, sulfamethoxazole, tetracycline, chloramphenicol, trimethoprim, and streptomycin/spectinomycin. In silico analyses revealed that MGIVchHai6-like elements are carried by several environmental and clinical V. cholerae strains recovered from the Indian subcontinent, as well as from North and South America, including all non-O1/non-O139 clinical isolates from Haiti.}, doi = {10.1128/mBio.00509-16}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.00509-16}, author = {Carraro, Nicolas and Rivard, Nicolas and Ceccarelli, Daniela and Rita R Colwell and Burrus, Vincent} } @article {20321, title = {Modeling Sustainability: Population, Inequality, Consumption, and Bidirectional Coupling of the Earth and Human Systems}, journal = {National Science Review}, year = {2016}, month = {Nov-12-2016}, pages = {nww081}, abstract = {Over the last two centuries, the impact of the Human System has grown dramatically, becoming strongly dominant within the Earth System in many different ways. Consumption, inequality, and population have increased extremely fast, especially since about 1950, threatening to overwhelm the many critical functions and ecosystems of the Earth System. Changes in the Earth System, in turn, have important feedback effects on the Human System, with costly and potentially serious consequences. However, current models do not incorporate these critical feedbacks. We argue that in order to understand the dynamics of either system, Earth System Models must be coupled with Human System Models through bidirectional couplings representing the positive, negative, and delayed feedbacks that exist in the real systems. In particular, key Human System variables, such as demographics, inequality, economic growth, and migration, are not coupled with the Earth System but are instead driven by exogenous estimates, such as United Nations population projections. This makes current models likely to miss important feedbacks in the real Earth{\textendash}Human system, especially those that may result in unexpected or counterintuitive outcomes, and thus requiring different policy interventions from current models. The importance and imminence of sustainability challenges, the dominant role of the Human System in the Earth System, and the essential roles the Earth System plays for the Human System, all call for collaboration of natural scientists, social scientists, and engineers in multidisciplinary research and modeling to develop coupled Earth{\textendash}Human system models for devising effective science-based policies and measures to benefit current and future generations.}, issn = {2095-5138}, doi = {10.1093/nsr/nww081}, url = {https://academic.oup.com/nsr/article-lookup/doi/10.1093/nsr/nww081}, author = {Motesharrei, Safa and Rivas, Jorge and Kalnay, Eugenia and Asrar, Ghassem R. and Busalacchi, Antonio J. and Cahalan, Robert F. and Cane, Mark A. and Rita R Colwell and Feng, Kuishuang and Franklin, Rachel S. and Hubacek, Klaus and Miralles-Wilhelm, Fernando and Miyoshi, Takemasa and Ruth, Matthias and Sagdeev, Roald and Shirmohammadi, Adel and Shukla, Jagadish and Srebric, Jelena and Yakovenko, Victor M. and Zeng, Ning} } @article {20335, title = {Phylogenetic Diversity of Vibrio cholerae Associated with Endemic Cholera in Mexico from 1991 to 2008}, journal = {mBio}, volume = {7}, year = {2016}, month = {Apr-05-2016}, abstract = {An outbreak of cholera occurred in 1991 in Mexico, where it had not been reported for more than a century and is now endemic. Vibrio cholerae O1 prototype El Tor and classical strains coexist with altered El Tor strains (1991 to 1997). Nontoxigenic (CTX-) V. cholerae El Tor dominated toxigenic (CTX+) strains (2001 to 2003), but V. cholerae CTX+ variant El Tor was isolated during 2004 to 2008, outcompeting CTX- V. cholerae. Genomes of six Mexican V. cholerae O1 strains isolated during 1991 to 2008 were sequenced and compared with both contemporary and archived strains of V. cholerae. Three were CTX+ El Tor, two were CTX- El Tor, and the remaining strain was a CTX+ classical isolate. Whole-genome sequence analysis showed the six isolates belonged to five distinct phylogenetic clades. One CTX- isolate is ancestral to the 6th and 7th pandemic CTX+ V. cholerae isolates. The other CTX- isolate joined with CTX- non-O1/O139 isolates from Haiti and seroconverted O1 isolates from Brazil and Amazonia. One CTX+ isolate was phylogenetically placed with the sixth pandemic classical clade and the V. cholerae O395 classical reference strain. Two CTX+ El Tor isolates possessing intact Vibrio seventh pandemic island II (VSP-II) are related to hybrid El Tor isolates from Mozambique and Bangladesh. The third CTX+ El Tor isolate contained West African-South American (WASA) recombination in VSP-II and showed relatedness to isolates from Peru and Brazil. Except for one isolate, all Mexican isolates lack SXT/R391 integrative conjugative elements (ICEs) and sensitivity to selected antibiotics, with one isolate resistant to streptomycin. No isolates were related to contemporary isolates from Asia, Africa, or Haiti, indicating phylogenetic diversity.}, doi = {10.1128/mBio.02160-15}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.02160-15}, author = {Choi, Seon Y and Rashed, Shah M. and Hasan, Nur A. and Alam, Munirul and Islam, Tarequl and Sadique, Abdus and Johura, Fatema-Tuz and Eppinger, Mark and Ravel, Jacques and Huq, Anwar and Cravioto, Alejandro and Rita R Colwell} } @article {20327, title = {Recognition of achievement {\textendash} priorities and process}, journal = {Materials Today}, volume = {19}, year = {2016}, month = {Jan-12-2016}, pages = {547 - 549}, issn = {13697021}, doi = {10.1016/j.mattod.2016.08.001}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1369702116301055}, author = {Madsen, Lynnette D. and Rita R Colwell} } @article {20326, title = {Reduced Susceptibility to Extended-Spectrum β-Lactams in Vibrio cholerae Isolated in Bangladesh}, journal = {Frontiers in Public Health}, year = {2016}, month = {Jun-10-2017}, doi = {10.3389/fpubh.2016.00231}, url = {http://journal.frontiersin.org/article/10.3389/fpubh.2016.00231/full}, author = {Ceccarelli, Daniela and Alam, Munirul and Huq, Anwar and Rita R Colwell} } @article {20333, title = {Strategic Planning in Population Health and Public Health Practice: A Call to Action for Higher Education}, journal = {The Milbank Quarterly}, volume = {94906033}, year = {2016}, month = {Jan-03-2016}, pages = {109 - 125}, abstract = {POLICY POINTS: Scarce resources, especially in population health and public health practice, underlie the importance of strategic planning. Public health agencies{\textquoteright} current planning and priority setting efforts are often narrow, at times opaque, and focused on single metrics such as cost-effectiveness. As demonstrated by SMART Vaccines, a decision support software system developed by the Institute of Medicine and the National Academy of Engineering, new approaches to strategic planning allow the formal incorporation of multiple stakeholder views and multicriteria decision making that surpass even those sophisticated cost-effectiveness analyses widely recommended and used for public health planning. Institutions of higher education can and should respond by building on modern strategic planning tools as they teach their students how to improve population health and public health practice. CONTEXT: Strategic planning in population health and public health practice often uses single indicators of success or, when using multiple indicators, provides no mechanism for coherently combining the assessments. Cost-effectiveness analysis, the most complex strategic planning tool commonly applied in public health, uses only a single metric to evaluate programmatic choices, even though other factors often influence actual decisions. METHODS: Our work employed a multicriteria systems analysis approach--specifically, multiattribute utility theory--to assist in strategic planning and priority setting in a particular area of health care (vaccines), thereby moving beyond the traditional cost-effectiveness analysis approach. FINDINGS: (1) Multicriteria systems analysis provides more flexibility, transparency, and clarity in decision support for public health issues compared with cost-effectiveness analysis. (2) More sophisticated systems-level analyses will become increasingly important to public health as disease burdens increase and the resources to deal with them become scarcer. CONCLUSIONS: The teaching of strategic planning in public health must be expanded in order to fill a void in the profession{\textquoteright}s planning capabilities. Public health training should actively incorporate model building, promote the interactive use of software tools, and explore planning approaches that transcend restrictive assumptions of cost-effectiveness analysis. The Strategic Multi-Attribute Ranking Tool for Vaccines (SMART Vaccines), which was recently developed by the Institute of Medicine and the National Academy of Engineering to help prioritize new vaccine development, is a working example of systems analysis as a basis for decision support.}, doi = {10.1111/1468-0009.12182}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941964/}, author = {Phelps, Charles and Madhavan, Guruprasad and Rappuoli, Rino and LEVIN, SCOTT and Shortlife, Edward and Rita R Colwell} } @article {20341, title = {Building Infectious Disease Research Programs to Promote Security and Enhance Collaborations with Countries of the Former Soviet Union}, journal = {Frontiers in Public Health}, volume = {35361632}, year = {2015}, month = {Feb-11-2017}, doi = {10.3389/fpubh.2015.00271}, url = {http://journal.frontiersin.org/Article/10.3389/fpubh.2015.00271/abstract}, author = {Bartholomew, James C. and Pearson, Andrew D. and Stenseth, Nils C. and LeDuc, James W. and Hirschberg, David L. and Rita R Colwell} } @article {20349, title = {Concordance and discordance of sequence survey methods for molecular epidemiology}, journal = {PeerJ}, year = {2015}, month = {Jan-01-2015}, pages = {e761}, abstract = {The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes), and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST) impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly associated with geography, irrespective of the molecular survey approach used, while Brucella spp. phylogeny appears to be strongly associated with geography and host origin. We contrast inferences made among monomorphic (clonal) and non-monomorphic bacteria, and between intra- and inter-specific datasets. We also discuss our results in light of underlying assumptions of different approaches.}, doi = {10.7717/peerj.761}, url = {https://peerj.com/articles/761}, author = {Castro-Nallar, Eduardo and Hasan, Nur A. and Cebula, Thomas A. and Rita R Colwell and Robison, Richard A. and Johnson, W. Evan and Crandall, Keith A.} } @article {20348, title = {Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species}, journal = {Proceedings of the National Academy of Sciences}, year = {2015}, month = {Feb-05-2017}, pages = {E2813 - E2819}, abstract = {Vibrio species are both ubiquitous and abundant in marine coastal waters, estuaries, ocean sediment, and aquaculture settings worldwide. We report here the isolation, characterization, and genome sequence of a novel Vibrio species, Vibrio antiquarius, isolated from a mesophilic bacterial community associated with hydrothermal vents located along the East Pacific Rise, near the southwest coast of Mexico. Genomic and phenotypic analysis revealed V. antiquarius is closely related to pathogenic Vibrio species, namely Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio harveyi, and Vibrio vulnificus, but sufficiently divergent to warrant a separate species status. The V. antiquarius genome encodes genes and operons with ecological functions relevant to the environment conditions of the deep sea and also harbors factors known to be involved in human disease caused by freshwater, coastal, and brackish water vibrios. The presence of virulence factors in this deep-sea Vibrio species suggests a far more fundamental role of these factors for their bacterial host. Comparative genomics revealed a variety of genomic events that may have provided an important driving force in V. antiquarius evolution, facilitating response to environmental conditions of the deep sea.}, issn = {0027-8424}, doi = {10.1073/pnas.1503928112}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1503928112}, author = {Hasan, Nur A. and Grim, Christopher J. and Lipp, Erin K. and Rivera, Irma N. G. and Chun, Jongsik and Haley, Bradd J. and Taviani, Elisa and Choi, Seon Young and Hoq, Mozammel and Munk, A. Christine and Brettin, Thomas S. and Bruce, David and Challacombe, Jean F. and Detter, J. Chris and Han, Cliff S. and Eisen, Jonathan A. and Huq, Anwar and Rita R Colwell} } @article {19903, title = {Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation.}, journal = {J Comput Chem}, year = {2015}, month = {2015 Mar 18}, abstract = {

A method is proposed to study protein-ligand binding in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the proteins configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific, sparsely populated binding modes with multiple interfaces. The method is based on the notion that a discrete set of preferential first-encounter modes are metastable states from which stable (prerelaxation) complexes at equilibrium evolve. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks. The method is applied to a peptide-protein complex. The peptide adopts several low-population conformers and binds in a variety of modes with a broad range of affinities. The system is thus well suited to analyze general features of binding, including conformational selection, multiplicity of binding modes, and nonspecific interactions, and to illustrate how the method can be applied to study these problems systematically. The equilibrium distributions can be used to generate biasing functions for simulations of multiprotein systems from which bulk thermodynamic quantities can be calculated. {\textcopyright} 2015 Wiley Periodicals, Inc.

}, issn = {1096-987X}, doi = {10.1002/jcc.23883}, author = {Cardone, Antonio and Bornstein, Aaron and Pant, Harish C and Brady, Mary and Sriram, Ram and Hassan, Sergio A} } @article {20350, title = {Diagnostic Approach for Monitoring Hydroclimatic Conditions Related to Emergence of West Nile Virus in West Virginia}, journal = {Frontiers in Public Health}, year = {2015}, month = {Dec-02-2015}, abstract = {West Nile virus (WNV), mosquito-borne and water-based disease, is increasingly a global threat to public health. Since its appearance in the northeastern United States in 1999, WNV has since been reported in several states in the continental United States. The objective of this study is to highlight role of hydroclimatic processes estimated through satellite sensors in capturing conditions for emergence of the vectors in historically disease free regions. We tested the hypothesis that an increase in surface temperature, in combination with intensification of vegetation, and enhanced precipitation, lead to conditions favorable for vector (mosquito) growth. Analysis of land surface temperature (LST) pattern shows that temperature values >16{\textdegree}C, with heavy precipitation, may lead to abundance of the mosquito population. This hypothesis was tested in West Virginia where a sudden epidemic of WNV infection was reported in 2012. Our results emphasize the value of hydroclimatic processes estimated by satellite remote sensing, as well as continued environmental surveillance of mosquitoes, because when a vector-borne infection like WNV is discovered in contiguous regions, the risk of spread of WNV mosquitoes increase at points where appropriate hydroclimatic processes intersect with the vector niche.}, doi = {10.3389/fpubh.2015.00010}, url = {http://journal.frontiersin.org/Article/10.3389/fpubh.2015.00010/abstract}, author = {Jutla, Antarpreet and Huq, Anwar and Rita R Colwell} } @article {20343, title = {Downscaling river discharge to assess the effects of climate change on cholera outbreaks in the Bengal Delta}, journal = {Climate Research}, volume = {64}, year = {2015}, month = {Jul-08-2017}, pages = {257 - 274}, abstract = {Endemic cholera in the Bengal Delta region of South Asia has been associated with asymmetric and episodic variability of river discharge. Spring cholera was found to be related to intrusion of bacteria-laden coastal seawater during low flow seasons. Autumn cholera was hypothesized to result from cross-contamination of water resources when high river discharge causes massive inland inundation. The effect of climate change on diarrheal diseases has not been explored, because of the difficulties in establishing linkages between coarse-resolution global climate model outputs with localized disease outbreaks. Since rivers act as corridors for transport of cholera bacteria, the first step is to understand the discharge variability that may occur with climate change and whether it is linked to cholera. Here, we present a framework for downscaling precipitation from global climate models for river discharge in the Ganges-Brahmaputra-Meghna basin. Using a data-mining method that includes particle swarm optimization-based support vector regression, precipitation was downscaled for a statistical multiple regressive model to estimate river discharge in the basin. Key results from an ensemble of HadCM3, GFDL, and ECHAM5 models indicated 8 and 7.5\% increase in flows for the IPCC A1B and A2 scenarios, respectively. The majority of the changes are attributable to increases in flows from February through August for both scenarios, with little to no change in seasonality of high and low flows during the next century. The probability of spring and autumn cholera is likely to increase steadily in the endemic region of the Bengal Delta. }, issn = {0936-577X}, doi = {10.3354/cr01310}, url = {http://www.int-res.com/abstracts/cr/v64/n3/p257-274/}, author = {Nasr-Azadani, F and Unnikrishnan, A and Akanda, A and Islam, S and Alam, M and Huq, A and Jutla, A and Rita R Colwell} } @article {20337, title = {Environmental Surveillance for Toxigenic Vibrio cholerae in Surface Waters of Haiti}, journal = {The American Journal of Tropical Medicine and Hygiene}, volume = {92}, year = {2015}, month = {Jul-01-2015}, pages = {118 - 125}, abstract = {Epidemic cholera was reported in Haiti in 2010, with no information available on the occurrence or geographic distribution of toxigenic Vibrio cholerae in Haitian waters. In a series of field visits conducted in Haiti between 2011 and 2013, water and plankton samples were collected at 19 sites. Vibrio cholerae was detected using culture, polymerase chain reaction, and direct viable count methods (DFA-DVC). Cholera toxin genes were detected by polymerase chain reaction in broth enrichments of samples collected in all visits except March 2012. Toxigenic V. cholerae was isolated from river water in 2011 and 2013. Whole genome sequencing revealed that these isolates were a match to the outbreak strain. The DFA-DVC tests were positive for V. cholerae O1 in plankton samples collected from multiple sites. Results of this survey show that toxigenic V. cholerae could be recovered from surface waters in Haiti more than 2 years after the onset of the epidemic.}, issn = {0002-9637}, doi = {10.4269/ajtmh.13-0601}, url = {http://www.ajtmh.org/content/journals/10.4269/ajtmh.13-0601}, author = {Hill, Vincent R. and Humphrys, Michael S. and Kahler, Amy M. and Boncy, Jacques and Tarr, Cheryl L. and Huq, Anwar and Chen, Arlene and Katz, Lee S. and Mull, Bonnie J. and Derado, Gordana and Haley, Bradd J. and Freeman, Nicole and Rita R Colwell and Turnsek, Maryann} } @conference {20066, title = {Estimating Actin Fiber Orientation using Interpolation-Based Grey-Level Co-Occurrence Matrix Computation}, booktitle = {BioImage Informatics Conference }, year = {2015}, month = {10/2015}, author = {Cardone, Antonio and Brady, Mary and Kociolek, Marcin and Bajcsy, Peter} } @article {20347, title = {Hybrid Vibrio~cholerae El Tor Lacking SXT Identified as the Cause of a Cholera Outbreak in the Philippines}, journal = {mBio}, year = {2015}, month = {Jan-05-2015}, abstract = {Cholera continues to be a global threat, with high rates of morbidity and mortality. In 2011, a cholera outbreak occurred in Palawan, Philippines, affecting more than 500 people, and 20 individuals died. Vibrio cholerae O1 was confirmed as the etiological agent. Source attribution is critical in cholera outbreaks for proper management of the disease, as well as to control spread. In this study, three V. cholerae O1 isolates from a Philippines cholera outbreak were sequenced and their genomes analyzed to determine phylogenetic relatedness to V. cholerae O1 isolates from recent outbreaks of cholera elsewhere. The Philippines V. cholerae O1 isolates were determined to be V. cholerae O1 hybrid El Tor belonging to the seventh-pandemic clade. They clustered tightly, forming a monophyletic clade closely related to V. cholerae O1 hybrid El Tor from Asia and Africa. The isolates possess a unique multilocus variable-number tandem repeat analysis (MLVA) genotype (12-7-9-18-25 and 12-7-10-14-21) and lack SXT. In addition, they possess a novel 15-kb genomic island (GI-119) containing a predicted type I restriction-modification system. The CTXΦ-RS1 array of the Philippines isolates was similar to that of V. cholerae O1 MG116926, a hybrid El Tor strain isolated in Bangladesh in 1991. Overall, the data indicate that the Philippines V. cholerae O1 isolates are unique, differing from recent V. cholerae O1 isolates from Asia, Africa, and Haiti. Furthermore, the results of this study support the hypothesis that the Philippines isolates of V. cholerae O1 are indigenous and exist locally in the aquatic ecosystem of the Philippines.}, doi = {10.1128/mBio.00047-15}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.00047-15}, author = {Klinzing, David C. and Choi, Seon Young and Hasan, Nur A. and Matias, Ronald R. and Tayag, Enrique and Geronimo, Josefina and Skowronski, Evan and Rashed, Shah M. and Kawashima, Kent and Rosenzweig, C. Nicole and Gibbons, Henry S. and Torres, Brian C. and Liles, Veni and Alfon, Alicia C. and Juan, Maria Luisa and Natividad, Filipinas F. and Cebula, Thomas A. and Rita R Colwell} } @article {20345, title = {Molecular tools in understanding the evolution of Vibrio cholerae}, journal = {Frontiers in Microbiology}, year = {2015}, month = {Jun-10-2015}, abstract = {Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies.}, doi = {10.3389/fmicb.2015.01040}, url = {http://journal.frontiersin.org/Article/10.3389/fmicb.2015.01040/abstract}, author = {Rahaman, Md. Habibur and Islam, Tarequl and Rita R Colwell and Alam, Munirul} } @article {20351, title = {Non-O1/Non-O139 Vibrio cholerae Carrying Multiple Virulence Factors and V. cholerae O1 in the Chesapeake Bay, Maryland}, journal = {Applied and Environmental Microbiology}, year = {2015}, month = {Mar-03-2016}, pages = {1909 - 1918}, abstract = {Non-O1/non-O139 Vibrio cholerae inhabits estuarine and coastal waters globally, but its clinical significance has not been sufficiently investigated, despite the fact that it has been associated with septicemia and gastroenteritis. The emergence of virulent non-O1/non-O139 V. cholerae is consistent with the recognition of new pathogenic variants worldwide. Oyster, sediment, and water samples were collected during a vibrio surveillance program carried out from 2009 to 2012 in the Chesapeake Bay, Maryland. V. cholerae O1 was detected by a direct fluorescent-antibody (DFA) assay but was not successfully cultured, whereas 395 isolates of non-O1/non-O139 V. cholerae were confirmed by multiplex PCR and serology. Only a few of the non-O1/non-O139 V. cholerae isolates were resistant to ampicillin and/or penicillin. Most of the isolates were sensitive to all antibiotics tested, and 77 to 90\% carried the El Tor variant hemolysin gene hlyA ET, the actin cross-linking repeats in toxin gene rtxA, the hemagglutinin protease gene hap, and the type 6 secretion system. About 19 to 21\% of the isolates carried the neuraminidase-encoding gene nanH and/or the heat-stable toxin (NAG-ST), and only 5\% contained a type 3 secretion system. None of the non-O1/non-O139 V. cholerae isolates contained Vibrio pathogenicity island-associated genes. However, ctxA, ace, or zot was present in nine isolates. Fifty-five different genotypes showed up to 12 virulence factors, independent of the source of isolation, and represent the first report of both antibiotic susceptibility and virulence associated with non-O1/non-O139 V. cholerae from the Chesapeake Bay. Since these results confirm the presence of potentially pathogenic non-O1/non-O139 V. cholerae, monitoring for total V. cholerae, regardless of serotype, should be done within the context of public health.}, issn = {0099-2240}, doi = {10.1128/AEM.03540-14}, url = {http://aem.asm.org/lookup/doi/10.1128/AEM.03540-14}, author = {Ceccarelli, Daniela and Chen, Arlene and Hasan, Nur A. and Rashed, Shah M. and Huq, Anwar and Rita R Colwell}, editor = {Elkins, C. A.} } @article {20338, title = {Nontoxigenic Vibrio cholerae Non-O1/O139 Isolate from a Case of Human Gastroenteritis in the U.S. Gulf Coast}, journal = {Journal of Clinical Microbiology}, year = {2015}, month = {Jun-01-2016}, pages = {9 - 14}, abstract = {An occurrence of Vibrio cholerae non-O1/O139 gastroenteritis in the U.S. Gulf Coast is reported here. Genomic analysis revealed that the isolate lacked known virulence factors associated with the clinical outcome of a V. cholerae infection but did contain putative genomic islands and other accessory virulence factors. Many of these factors are widespread among environmental strains of V. cholerae, suggesting that there might be additional virulence factors in non-O1/O139 V. cholerae yet to be determined. Phylogenetic analysis revealed that the isolate belonged to a phyletic lineage of environmental V. cholerae isolates associated with sporadic cases of gastroenteritis in the Western Hemisphere, suggesting a need to monitor non-O1/O139 V. cholerae in the interest of public health.}, issn = {0095-1137}, doi = {10.1128/JCM.02187-14}, url = {http://jcm.asm.org/lookup/doi/10.1128/JCM.02187-14}, author = {Hasan, Nur A. and Rezayat, Talayeh and Blatz, Peter J. and Choi, Seon Young and Griffitt, Kimberly J. and Rashed, Shah M. and Huq, Anwar and Conger, Nicholas G. and Rita R Colwell and Grimes, D. Jay}, editor = {Munson, E.} } @article {20319, title = {Occurrence and Diversity of Clinically Important Vibrio Species in the Aquatic Environment of Georgia}, journal = {Frontiers in Public Health}, year = {2015}, month = {10/2015}, doi = {10.3389/fpubh.2015.00232}, url = {http://journal.frontiersin.org/Article/10.3389/fpubh.2015.00232/}, author = {Kokashvili, Tamar and Whitehouse, Chris A. and Tskhvediani, Ana and Grim, Christopher J. and Elbakidze, Tinatin and Mitaishvili, Nino and Janelidze, Nino and Jaiani, Ekaterine and Haley, Bradd J. and Lashkhi, Nino and Huq, Anwar and Rita R Colwell and Tediashvili, Marina} } @article {20339, title = {Predictive Time Series Analysis Linking Bengal Cholera with Terrestrial Water Storage Measured from Gravity Recovery and Climate Experiment Sensors}, journal = {The American Journal of Tropical Medicine and Hygiene}, volume = {93}, year = {2015}, month = {Sep-12-2015}, pages = {1179 - 1186}, abstract = {Outbreaks of diarrheal diseases, including cholera, are related to floods and droughts in regions where water and sanitation infrastructure are inadequate or insufficient. However, availability of data on water scarcity and abundance in transnational basins, are a prerequisite for developing cholera forecasting systems. With more than a decade of terrestrial water storage (TWS) data from the Gravity Recovery and Climate Experiment, conditions favorable for predicting cholera occurrence may now be determined. We explored lead{\textendash}lag relationships between TWS in the Ganges{\textendash}Brahmaputra{\textendash}Meghna basin and endemic cholera in Bangladesh. Since bimodal seasonal peaks in cholera in Bangladesh occur during spring and autumn seasons, two separate logistical models between TWS and disease time series (2002{\textendash}2010) were developed. TWS representing water availability showed an asymmetrical, strong association with cholera prevalence in the spring (τ = -0.53; P < 0.001) and autumn (τ = 0.45; P < 0.001) up to 6 months in advance. One unit (centimeter of water) decrease in water availability in the basin increased odds of above normal cholera by 24\% (confidence interval [CI] = 20{\textendash}31\%; P < 0.05) in the spring, while an increase in regional water by 1 unit, through floods, increased odds of above average cholera in the autumn by 29\% (CI = 22{\textendash}33\%; P < 0.05).}, issn = {0002-9637}, doi = {10.4269/ajtmh.14-0648}, url = {http://www.ajtmh.org/content/journals/10.4269/ajtmh.14-0648}, author = {Rita R Colwell and Unnikrishnan, Avinash and Jutla, Antarpreet and Huq, Anwar and Akanda, Ali} } @article {20344, title = {Rapid Proliferation of Vibrio parahaemolyticus, Vibrio vulnificus, and Vibrio cholerae during Freshwater Flash Floods in French Mediterranean Coastal Lagoons}, journal = {Applied and Environmental Microbiology}, year = {2015}, month = {Jan-11-2015}, pages = {7600 - 7609}, abstract = {Vibrio parahaemolyticus, Vibrio vulnificus, and Vibrio cholerae of the non-O1/non-O139 serotype are present in coastal lagoons of southern France. In these Mediterranean regions, the rivers have long low-flow periods followed by short-duration or flash floods during and after heavy intense rainstorms, particularly at the end of the summer and in autumn. These floods bring large volumes of freshwater into the lagoons, reducing their salinity. Water temperatures recorded during sampling (15 to 24{\textdegree}C) were favorable for the presence and multiplication of vibrios. In autumn 2011, before heavy rainfalls and flash floods, salinities ranged from 31.4 to 36.1{\textperthousand} and concentrations of V. parahaemolyticus, V. vulnificus, and V. cholerae varied from 0 to 1.5 {\texttimes} 103 most probable number (MPN)/liter, 0.7 to 2.1 {\texttimes} 103 MPN/liter, and 0 to 93 MPN/liter, respectively. Following heavy rainstorms that generated severe flash flooding and heavy discharge of freshwater, salinity decreased, reaching 2.2 to 16.4{\textperthousand} within 15 days, depending on the site, with a concomitant increase in Vibrio concentration to ca. 104 MPN/liter. The highest concentrations were reached with salinities between 10 and 20{\textperthousand} for V. parahaemolyticus, 10 and 15{\textperthousand} for V. vulnificus, and 5 and 12{\textperthousand} for V. cholerae. Thus, an abrupt decrease in salinity caused by heavy rainfall and major flooding favored growth of human-pathogenic Vibrio spp. and their proliferation in the Languedocian lagoons. Based on these results, it is recommended that temperature and salinity monitoring be done to predict the presence of these Vibrio spp. in shellfish-harvesting areas of the lagoons.}, issn = {0099-2240}, doi = {10.1128/AEM.01848-15}, url = {http://aem.asm.org/lookup/doi/10.1128/AEM.01848-15}, author = {Esteves, Kevin and Hervio-Heath, Dominique and Mosser, Thomas and Rodier, Claire and Tournoud, Marie-George and Jumas-Bilak, Estelle and Rita R Colwell and Monfort, Patrick}, editor = {Wommack, K. E.} } @article {20342, title = {Satellite Based Assessment of Hydroclimatic Conditions Related to Cholera in Zimbabwe}, journal = {PLOS ONE}, year = {2015}, month = {May-09-2017}, pages = {e0137828}, abstract = {Introduction Cholera, an infectious diarrheal disease, has been shown to be associated with large scale hydroclimatic processes. The sudden and sporadic occurrence of epidemic cholera is linked with high mortality rates, in part, due to uncertainty in timing and location of outbreaks. Improved understanding of the relationship between pathogenic abundance and climatic processes allows prediction of disease outbreak to be an achievable goal. In this study, we show association of large scale hydroclimatic processes with the cholera epidemic in Zimbabwe reported to have begun in Chitungwiza, a city in Mashonaland East province, in August, 2008. Principal Findings Climatic factors in the region were found to be associated with triggering cholera outbreak and are shown to be related to anomalies of temperature and precipitation, validating the hypothesis that poor conditions of sanitation, coupled with elevated temperatures, and followed by heavy rainfall can initiate outbreaks of cholera. Spatial estimation by satellite of precipitation and global gridded air temperature captured sensitivities in hydroclimatic conditions that permitted identification of the location in the region where the disease outbreak began. Discussion Satellite derived hydroclimatic processes can be used to capture environmental conditions related to epidemic cholera, as occurred in Zimbabwe, thereby providing an early warning system. Since cholera cannot be eradicated because the causative agent, Vibrio cholerae, is autochthonous to the aquatic environment, prediction of conditions favorable for its growth and estimation of risks of triggering the disease in a given population can be used to alert responders, potentially decreasing infection and saving lives. }, doi = {10.1371/journal.pone.0137828}, url = {https://dx.plos.org/10.1371/journal.pone.0137828}, author = {Jutla, Antarpreet and Aldaach, Haidar and Billian, Hannah and Akanda, Ali and Huq, Anwar and Rita R Colwell}, editor = {Schumann, Guy J-P.} } @conference {20067, title = {Segmentation and sub-cellular feature-based analysis of microscopy images}, booktitle = {BioImage Informatics Conference }, year = {2015}, month = {10/2015}, author = {Cardone, Antonio and Chalfoun, Joe and Peskin, Adele and Bajcsy, Peter and Kociolek, Marcin and Bhadriraju, Kiran and Brady, Mary} } @article {20062, title = {Survey statistics of automated segmentations applied to optical imaging of mammalian cells}, journal = {BMC bioinformatics}, volume = {16}, year = {2015}, pages = {1}, author = {Bajcsy, Peter and Cardone, Antonio and Chalfoun, Joe and Halter, Michael and Juba, Derek and Kociolek, Marcin and Majurski, Michael and Peskin, Adele and Simon, Carl and Simon, Mylene and others} } @article {20340, title = {A unified initiative to harness Earth{\textquoteright}s microbiomes}, journal = {Science}, year = {2015}, month = {Jun-10-2017}, pages = {507 - 508}, issn = {0036-8075}, doi = {10.1126/science.aac8480}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.aac8480}, author = {Alivisatos, A. P. and Blaser, M. J. and Brodie, E. L. and Chun, M. and Dangl, J. L. and Donohue, T. J. and Dorrestein, P. C. and Gilbert, J. A. and Green, J. L. and Jansson, J. K. and Knight, R. and Maxon, M. E. and McFall-Ngai, M. J. and Miller, J. F. and Pollard, K. S. and Ruby, E. G. and Taha, S. A. and Rita R Colwell} } @article {20346, title = {Use of Environmental Parameters to Model Pathogenic Vibrios in Chesapeake Bay}, journal = {Journal of Environmental Informatics}, year = {2015}, month = {Jan-01-2015}, abstract = {Although the transportation sector is a major contributor to urban air pollution and global climate change due to its substantial energy consumptions, previous studies for evacuation practices in this sector seldom took environmental consequences into account. As an attempt in event-related evacuation planning under uncertainty, this study proposed an emission-mitigation-oriented fuzzy evacuation management (emoFEM) model. Comprehensive considerations over system efficiency, environmental protection, economic cost and resource availability were incorporated within a general modeling formulation to facilitate evacuation management in a systematic and compromise manner. Vague and ambiguous information embedded within evacuation problems could be quantified and directly communicated into the optimization process, greatly improving conventional tools for evacuation management under uncertainty. The proposed emoFEM model was then applied to a hypothetic but representative case. Useful solutions were generated, which could help identify timely, safe and cost-effective evacuation schemes without significant disturbances over normal municipal traffic and environmental quality. The advantages of emoFEM were further revealed through comparing its solutions with those from its deterministic counterpart. }, issn = {17262135}, doi = {10.3808/jei.201500307}, url = {http://www.iseis.org/jei/abstract.asp?no=201500307}, author = {Zaitchik, B. F. and Guikema, S. D. and Haley, B. J. and Taviani, E. and Chen, A. and Brown, M.E. and Huq, A. and Rita R Colwell} } @article {20365, title = {Global diarrhoea action plan needs integrated climate-based surveillance}, journal = {The Lancet Global Health}, volume = {2}, year = {2014}, month = {Jan-02-2014}, pages = {e69 - e70}, issn = {2214109X}, doi = {10.1016/S2214-109X(13)70155-4}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2214109X13701554}, author = {Akanda, Ali S and Jutla, Antarpreet S and Rita R Colwell} } @article {20359, title = {Vibrio metoecus sp. nov., a close relative of Vibrio cholerae isolated from coastal brackish ponds and clinical specimens}, journal = {INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY}, year = {2014}, month = {Jan-09-2014}, pages = {3208 - 3214}, issn = {1466-5026}, doi = {10.1099/ijs.0.060145-0}, url = {http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.060145-0}, author = {Kirchberger, P. C. and Turnsek, M. and Hunt, D. E. and Haley, B. J. and Rita R Colwell and Polz, M. F. and Tarr, C. L. and Boucher, Y.} } @article {20358, title = {Vibrio ecology, pathogenesis, and evolution}, journal = {Frontiers in Microbiology}, year = {2014}, month = {Apr-05-2016}, doi = {10.3389/fmicb.2014.00256}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2014.00256}, author = {Ceccarelli, Daniela and Rita R Colwell} } @article {20361, title = {Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing}, journal = {PLoS ONE}, year = {2014}, month = {Aug-05-2015}, pages = {e97699}, abstract = {Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90\% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.}, doi = {10.1371/journal.pone.0097699}, url = {https://dx.plos.org/10.1371/journal.pone.0097699}, author = {Hasan, Nur A. and Young, Brian A. and Minard-Smith, Angela T. and Saeed, Kelly and Li, Huai and Heizer, Esley M. and McMillan, Nancy J. and Isom, Richard and Abdullah, Abdul Shakur and Bornman, Daniel M. and Faith, Seth A. and Choi, Seon Young and Dickens, Michael L. and Cebula, Thomas A. and Rita R Colwell}, editor = {Ahmed, Niyaz} } @article {20362, title = {Molecular diversity and predictability of Vibrio parahaemolyticus along the Georgian coastal zone of the Black Sea}, journal = {Frontiers in Microbiology}, volume = {5}, year = {2014}, month = {Jan-01-2014}, abstract = {Vibrio parahaemolyticus is a leading cause of seafood-related gastroenteritis and is also an autochthonous member of marine and estuarine environments worldwide. One-hundred seventy strains of V. parahaemolyticus were isolated from water and plankton samples collected along the Georgian coast of the Black Sea during 28 months of sample collection. All isolated strains were tested for presence of tlh, trh, and tdh. A subset of strains were serotyped and tested for additional factors and markers of pandemicity. Twenty-six serotypes, five of which are clinically relevant, were identified. Although all 170 isolates were negative for tdh, trh, and the Kanagawa Phenomenon, 7 possessed the GS-PCR sequence and 27 the 850 bp sequence of V. parahaemolyticus pandemic strains. The V. parahaemolyticus population in the Black Sea was estimated to be genomically heterogeneous by rep-PCR and the serodiversity observed did not correlate with rep-PCR genomic diversity. Statistical modeling was used to predict presence of V. parahaemolyticus as a function of water temperature, with strongest concordance observed for Green Cape site samples (Percent of total variance = 70, P < 0.001). Results demonstrate a diverse population of V. parahaemolyticus in the Black Sea, some of which carry pandemic markers, with increased water temperature correlated to an increase in abundance of V. parahaemolyticus.}, doi = {10.3389/fmicb.2014.00045}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2014.00045}, author = {Haley, Bradd J. and Kokashvili, Tamar and Tskshvediani, Ana and Janelidze, Nino and Mitaishvili, Nino and Grim, Christopher J. and Constantin_de_Magny, Guillaume and Chen, Arlene J. and Taviani, Elisa and Eliashvili, Tamar and Tediashvili, Marina and Whitehouse, Chris A. and Rita R Colwell and Huq, Anwar} } @article {20334, title = {Occurrence in Mexico, 1998{\textendash}2008, of Vibrio cholerae CTX + El Tor carrying an additional truncated CTX prophage}, journal = {Proceedings of the National Academy of Sciences}, volume = {111}, year = {2014}, month = {Aug-07-2014}, pages = {9917 - 9922}, issn = {0027-8424}, doi = {10.1073/pnas.1323408111}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1323408111}, author = {Alam, Munirul and Rashed, Shah M and Mannan, Shahnewaj Bin and Islam, Tarequl and Lizarraga-Partida, Marcial L. and Delgado, Gabriela and Morales-Espinosa, Rosario and Mendez, Jose Luis and Navarro, Armando and Watanabe, Haruo and Ohnishi, Makoto and Hasan, Nur A. and Huq, Anwar and Sack, R. Bradley and Rita R Colwell and Cravioto, Alejandro} } @article {20357, title = {Phylodynamic Analysis of Clinical and Environmental Vibrio cholerae Isolates from Haiti Reveals Diversification Driven by Positive Selection}, journal = {mBio}, year = {2014}, month = {Jul-12-2016}, abstract = {Phylodynamic analysis of genome-wide single-nucleotide polymorphism (SNP) data is a powerful tool to investigate underlying evolutionary processes of bacterial epidemics. The method was applied to investigate a collection of 65 clinical and environmental isolates of Vibrio cholerae from Haiti collected between 2010 and 2012. Characterization of isolates recovered from environmental samples identified a total of four toxigenic V. cholerae O1 isolates, four non-O1/O139 isolates, and a novel nontoxigenic V. cholerae O1 isolate with the classical tcpA gene. Phylogenies of strains were inferred from genome-wide SNPs using coalescent-based demographic models within a Bayesian framework. A close phylogenetic relationship between clinical and environmental toxigenic V. cholerae O1 strains was observed. As cholera spread throughout Haiti between October 2010 and August 2012, the population size initially increased and then fluctuated over time. Selection analysis along internal branches of the phylogeny showed a steady accumulation of synonymous substitutions and a progressive increase of nonsynonymous substitutions over time, suggesting diversification likely was driven by positive selection. Short-term accumulation of nonsynonymous substitutions driven by selection may have significant implications for virulence, transmission dynamics, and even vaccine efficacy.}, doi = {10.1128/mBio.01824-14}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.01824-14}, author = {Azarian, Taj and Ali, Afsar and Johnson, Judith A. and Mohr, David and Prosperi, Mattia and Veras, Nazle M. and Jubair, Mohammed and Strickland, Samantha L. and Rashid, Mohammad H. and Alam, Meer T. and Weppelmann, Thomas A. and Katz, Lee S. and Tarr, Cheryl L. and Rita R Colwell and Morris, J. Glenn and Salemi, Marco} } @article {20360, title = {Validation of high throughput sequencing and microbial forensics applications}, journal = {Investigative Genetics}, volume = {5}, year = {2014}, month = {Jan-01-2014}, pages = {9}, abstract = {High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security.}, issn = {2041-2223}, doi = {10.1186/2041-2223-5-9}, url = {http://investigativegenetics.biomedcentral.com/articles/10.1186/2041-2223-5-9}, author = {Budowle, Bruce and Connell, Nancy D and Bielecka-Oder, Anna and Rita R Colwell and Corbett, Cindi R and Fletcher, Jacqueline and Forsman, Mats and Kadavy, Dana R and Markotic, Alemka and Morse, Stephen A and Murch, Randall S and Sajantila, Antti and Schmedes, Sarah E and Ternus, Krista L and Turner, Stephen D and Minot, Samuel} } @article {20366, title = {Viewing Marine Bacteria, Their Activity and Response to Environmental Drivers from Orbit}, journal = {Microbial Ecology}, year = {2014}, month = {Jan-04-2014}, pages = {489 - 500}, abstract = {Satellite-based remote sensing of marine microorganisms has become a useful tool in predicting human health risks associated with these microscopic targets. Early applications were focused on harmful algal blooms, but more recently methods have been developed to interrogate the ocean for bacteria. As satellite-based sensors have become more sophisticated and our ability to interpret information derived from these sensors has advanced, we have progressed from merely making fascinating pictures from space to developing process models with predictive capability. Our understanding of the role of marine microorganisms in primary production and global elemental cycles has been vastly improved as has our ability to use the combination of remote sensing data and models to provide early warning systems for disease outbreaks. This manuscript will discuss current approaches to monitoring cyanobacteria and vibrios, their activity and response to environmental drivers, and will also suggest future directions.}, issn = {0095-3628}, doi = {10.1007/s00248-013-0363-4}, url = {http://link.springer.com/10.1007/s00248-013-0363-4}, author = {Grimes, D. Jay and Ford, Tim E. and Rita R Colwell and Baker-Austin, Craig and Martinez-Urtaza, Jaime and Subramaniam, Ajit and Capone, Douglas G.} } @book {20379, title = {Current Topics in Microbiology and Immunology One Health: The Human-Animal-Environment Interfaces in Emerging Infectious Diseases The Human Environment Interface: Applying Ecosystem Concepts to Health}, volume = {365}, year = {2013}, pages = {83 - 100}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, address = {Berlin, Heidelberg}, isbn = {978-3-642-36888-2}, issn = {0070-217X}, doi = {10.1007/978-3-642-36889-9}, url = {http://link.springer.com/10.1007/978-3-642-36889-9}, author = {Preston, Nicholas D. and Daszak, Peter and Rita R Colwell}, editor = {Mackenzie, John S. and Jeggo, Martyn and Daszak, Peter and Richt, Juergen A.} } @article {20378, title = {Detection of Vibrio cholerae in environmental waters including drinking water reservoirs of Azerbaijan}, journal = {Environmental Microbiology Reports}, year = {2013}, month = {Jan-02-2013}, pages = {30 - 38}, doi = {10.1111/j.1758-2229.2012.00369.x }, url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2012.00369.x}, author = {Rashid, Ahmadov and Haley, Bradd J. and Rajabov, Mukhtar and Ahmadova, Sevinj and Gurbanov, Shair and Rita R Colwell and Huq, Anwar} } @article {20370, title = {Distribution of Virulence Genes in Clinical and Environmental Vibrio cholerae Strains in Bangladesh}, journal = {Applied and Environmental Microbiology}, year = {2013}, month = {Mar-09-2014}, pages = {5782 - 5785}, abstract = {Vibrio cholerae, an environmental organism, is a facultative human pathogen. Here, we report the virulence profiles, comprising 18 genetic markers, of 102 clinical and 692 environmental V. cholerae strains isolated in Bangladesh between March 2004 and January 2006, showing the variability of virulence determinants within the context of public health. }, issn = {0099-2240}, doi = {10.1128/AEM.01113-13}, url = {http://aem.asm.org/lookup/doi/10.1128/AEM.01113-13}, author = {Hasan, Nur A. and Ceccarelli, Daniela and Grim, Christopher J. and Taviani, Elisa and Choi, Jinna and Sadique, Abdus and Alam, Munirul and Siddique, Abul K. and Sack, R. Bradley and Huq, Anwar and Rita R Colwell} } @article {20367, title = {Drug response and genetic properties of Vibrio cholerae associated with endemic cholera in north-eastern Thailand, 2003-2011}, journal = {Journal of Medical Microbiology}, year = {2013}, month = {Jan-04-2013}, pages = {599 - 609}, abstract = {Cholera, caused by Vibrio cholerae, results in significant morbidity and mortality worldwide, including Thailand. Representative V. cholerae strains associated with endemic cholera (n = 32), including strains (n = 3) from surface water sources, in Khon Kaen, Thailand (2003{\textendash}2011), were subjected to microbiological, molecular and phylogenetic analyses. According to phenotypic and related genetic data, all tested V. cholerae strains belonged to serogroup O1, biotype El Tor (ET), Inaba (IN) or Ogawa (OG). All of the strains were sensitive to gentamicin and ciprofloxacin, while multidrug-resistant (MDR) strains showing resistance to erythromycin, tetracycline, trimethoprim/sulfamethoxazole and ampicillin were predominant in 2007. V. cholerae strains isolated before and after 2007 were non-MDR. All except six diarrhoeal strains possessed ctxA and ctxB genes and were toxigenic altered ET, confirmed by MAMA-PCR and DNA sequencing. Year-wise data revealed that V. cholerae INET strains isolated between 2003 and 2004, plus one strain isolated in 2007, lacked the RS1 sequence (rstC) and toxin-linked cryptic plasmid (TLC)-specific genetic marker, but possessed CTXCL prophage genes ctxB CL and rstR CL. A sharp genetic transition was noted, namely the majority of V. cholerae strains in 2007 and all in 2010 and 2011 were not repressor genotype rstR CL but instead were rstR ET, and all ctx + strains possessed RS1 and TLC-specific genetic markers. DNA sequencing data revealed that strains isolated since 2007 had a mutation in the tcpA gene at amino acid position 64 (N{\textrightarrow}S). Four clonal types, mostly of environmental origin, including subtypes, reflected genetic diversity, while distinct signatures were observed for clonally related, altered ET from Thailand, Vietnam and Bangladesh, confirmed by distinct subclustering patterns observed in the PFGE (NotI)-based dendrogram, suggesting that endemic cholera is caused by V. cholerae indigenous to Khon Kaen.}, issn = {0022-2615}, doi = {10.1099/jmm.0.053801-0}, url = {http://jmm.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.053801-0}, author = {Chomvarin, C. and Johura, F.-T. and Mannan, S. B. and Jumroenjit, W. and Kanoktippornchai, B. and Tangkanakul, W. and Tantisuwichwong, N. and Huttayananont, S. and Watanabe, H. and Hasan, N. A. and Huq, A. and Cravioto, A. and Rita R Colwell and Alam, M.} } @article {20363, title = {Engaging Actively with Issues in the Responsible Conduct of Science: Lessons from International Efforts Are Relevant for Undergraduate Education in the United States}, journal = {CBE{\textemdash}Life Sciences Education}, year = {2013}, month = {Jan-12-2013}, pages = {596 - 603}, abstract = {Numerous studies are demonstrating that engaging undergraduate students in original research can improve their achievement in the science, technology, engineering, and mathematics (STEM) fields and increase the likelihood that some of them will decide to pursue careers in these disciplines. Associated with this increased prominence of research in the undergraduate curriculum are greater expectations from funders, colleges, and universities that faculty mentors will help those students, along with their graduate students and postdoctoral fellows, develop an understanding and sense of personal and collective obligation for responsible conduct of science (RCS). This Feature describes an ongoing National Research Council (NRC) project and a recent report about educating faculty members in culturally diverse settings (Middle East/North Africa and Asia) to employ active-learning strategies to engage their students and colleagues deeply in issues related to RCS. The NRC report describes the first phase of this project, which took place in Aqaba and Amman, Jordan, in September 2012 and April 2013, respectively. Here we highlight the findings from that report and our subsequent experience with a similar interactive institute in Kuala Lumpur, Malaysia. Our work provides insights and perspectives for faculty members in the United States as they engage undergraduate and graduate students, as well as postdoctoral fellows, to help them better understand the intricacies of and connections among various components of RCS. Further, our experiences can provide insights for those who may wish to establish {\textquotedblleft}train-the-trainer{\textquotedblright} programs at their home institutions.}, doi = {10.1187/cbe.13-09-0184}, url = {https://www.lifescied.org/doi/10.1187/cbe.13-09-0184}, author = {Clements, John D. and Connell, Nancy D. and Dirks, Clarissa and El-Faham, Mohamed and Hay, Alastair and Heitman, Elizabeth and Stith, James H. and Bond, Enriqueta C. and Rita R Colwell and Anestidou, Lida and Husbands, Jo L. and Labov, Jay B.} } @article {20372, title = {Environmental Factors Influencing Epidemic Cholera}, journal = {The American Journal of Tropical Medicine and Hygiene}, volume = {89}, year = {2013}, month = {Apr-09-2013}, pages = {597 - 607}, abstract = {Cholera outbreak following the earthquake of 2010 in Haiti has reaffirmed that the disease is a major public health threat. Vibrio cholerae is autochthonous to aquatic environment, hence, it cannot be eradicated but hydroclimatology-based prediction and prevention is an achievable goal. Using data from the 1800s, we describe uniqueness in seasonality and mechanism of occurrence of cholera in the epidemic regions of Asia and Latin America. Epidemic regions are located near regional rivers and are characterized by sporadic outbreaks, which are likely to be initiated during episodes of prevailing warm air temperature with low river flows, creating favorable environmental conditions for growth of cholera bacteria. Heavy rainfall, through inundation or breakdown of sanitary infrastructure, accelerates interaction between contaminated water and human activities, resulting in an epidemic. This causal mechanism is markedly different from endemic cholera where tidal intrusion of seawater carrying bacteria from estuary to inland regions, results in outbreaks.}, issn = {0002-9637}, doi = {10.4269/ajtmh.12-0721}, url = {http://www.ajtmh.org/content/journals/10.4269/ajtmh.12-0721}, author = {Huq, Anwar and Hasan, Nur and Akanda, Ali and Whitcombe, Elizabeth and Rita R Colwell and Haley, Bradd and Alam, Munir and Jutla, Antarpreet and Sack, R. Bradley} } @article {20380, title = {Fostering advances in interdisciplinary climate science}, journal = {Proceedings of the National Academy of Sciences}, year = {2013}, month = {Feb-02-2015}, pages = {3653 - 3656}, issn = {0027-8424}, doi = {10.1073/pnas.1301104110}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1301104110}, author = {Shaman, J. and Solomon, S. and Rita R Colwell and Field, C. B.} } @conference {19454, title = {"I Want to Imagine How That Place Looks": Designing Technologies to Support Connectivity Between Africans Living Abroad and Home}, booktitle = {SIGCHI {\textquoteright}13}, series = {CHI {\textquoteright}13}, year = {2013}, month = {2013///}, pages = {2755 - 2764}, publisher = {ACM}, organization = {ACM}, abstract = {Uneven access to Information and Communication Technologies (ICTs) in parts of the African continent make it challenging for some Africans who migrate to the U.S. to communicate with family members in their countries of origin. However, Internet access is becoming more widespread throughout the continent and this development presents an opportunity to explore how future interactive systems can support exchanges between families with members living in developed and less developed countries. To investigate these design possibilities we interviewed 27 African-born students, currently living in Virginia, U.S., and asked them how they used ICTs to connect with family members in their home countries. Our findings informed the development of a low-fidelity prototype that eight students lived with for four to five months. Findings from this deployment study motivate a discussion regarding features to include in interfaces designed to support transnational family communication. Features include personally meaningful imagery, country specific content, and the ability to monitor the weather and changing currency rates in migrants{\textquoteright} countries of origin.}, keywords = {diaspora communities, family communication, hci4d/ictd, Interaction design, research through design, transnational}, isbn = {978-1-4503-1899-0}, url = {http://doi.acm.org/10.1145/2470654.2481381}, author = {Wyche, Susan P. and Marshini Chetty} } @article {20364, title = {Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments}, journal = {Aquatic Biosystems}, volume = {9}, year = {2013}, month = {Jan-01-2013}, pages = {17}, abstract = {Background The Cariaco Basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. Marine water samples were collected in May, 2005 and 2006, at the sampling stations A (10{\textdegree}30' N, 64{\textdegree}40' W), B (10{\textdegree}40' N, 64{\textdegree}45' W) and D (10{\textdegree}43{\textquoteright}N, 64{\textdegree}32{\textquoteright}W) from different depths, including surface, redox interface, and anoxic zones. In order to enrich for sulfate reducing bacteria (SRB), water samples were inoculated into anaerobic media amended with lactate or acetate as carbon source. To analyze the composition of enrichment cultures, we performed DNA extraction, PCR-DGGE, and sequencing of selected bands. Results DGGE results indicate that many bacterial genera were present that are associated with the sulfur cycle, including Desulfovibrio spp., as well as heterotrophs belonging to Vibrio, Enterobacter, Shewanella, Fusobacterium, Marinifilum, Mariniliabilia, and Spirochaeta. These bacterial populations are related to sulfur coupling and carbon cycles in an environment of variable redox conditions and oxygen availability. Conclusions In our studies, we found an association of SRB-like Desulfovibrio with Vibrio species and other genera that have a previously defined relevant role in sulfur transformation and coupling of carbon and sulfur cycles in an environment where there are variable redox conditions and oxygen availability. This study provides new information about microbial species that were culturable on media for SRB at anaerobic conditions at several locations and water depths in the Cariaco Basin.}, issn = {2046-9063}, doi = {10.1186/2046-9063-9-17}, url = {http://aquaticbiosystems.biomedcentral.com/articles/10.1186/2046-9063-9-17}, author = {Bozo-Hurtado, Lorelei and Garc{\'\i}a-Amado, M and Chistoserdov, Andrei and Varela, Ramon and Narvaez, J and Rita R Colwell and Su{\'a}rez, Paula} } @article {19700, title = {Improving public transit accessibility for blind riders by crowdsourcing bus stop landmark locations with Google street view}, journal = {The 15th International ACM SIGACCESS Conference}, year = {2013}, month = {2013/00/21}, pages = {16 - 8}, publisher = {SIGACCESS, ACM Special Interest Group on Accessible ComputingACM}, address = {New York, New York, USA}, abstract = {Abstract Low-vision and blind bus riders often rely on known physical landmarks to help locate and verify bus stop locations (eg., by searching for a shelter, bench, newspaper bin). However, there are currently few, if any, methods to determine this information a priori via ...}, isbn = {9781450324052}, doi = {10.1145/2513383.2513448}, url = {http://dl.acm.org/citation.cfm?doid=2513383.2513448}, author = {Hara, Kotaro and Azenkot, Shiri and Campbell, Megan and Bennett, Cynthia L and Le, Vicki and Pannella, Sean and Moore, Robert and Minckler, Kelly and Ng, Rochelle H and Jon Froehlich} } @article {19703, title = {An Initial Study of Automatic Curb Ramp Detection with Crowdsourced Verification Using Google Street View Images}, journal = {First AAAI Conference on Human Computation and Crowdsourcing}, year = {2013}, month = {2013/00/11}, abstract = {In our previous research, we examined whether minimally trained crowd workers could find, categorize, and assess sidewalk accessibility problems using Google Street View (GSV) images. This poster paper presents a first step towards combining automated methods ( e.g., machine vision-based curb ramp detectors) in concert with human computation to improve the overall scalability of our approach.}, url = {http://www.aaai.org/ocs/index.php/HCOMP/HCOMP13/paper/view/7507}, author = {Hara, Kotaro and Sun, Jin and Chazan, Jonah and Jacobs, David and Jon Froehlich} } @article {19686, title = {Modeling topic control to detect influence in conversations using nonparametric topic models}, journal = {Machine Learning}, year = {2013}, month = {2013/00/01}, pages = {1 - 41}, publisher = {Springer US}, abstract = {Abstract Identifying influential speakers in multi-party conversations has been the focus of research in communication, sociology, and psychology for decades. It has been long acknowledged qualitatively that controlling the topic of a conversation is a sign of ...}, doi = {10.1007/s10994-013-5417-9/fulltext.html}, url = {http://link.springer.com/article/10.1007/s10994-013-5417-9/fulltext.html}, author = {Nguyen, Viet-An and Jordan Boyd-Graber and Resnik, Philip and Cai, Deborah A and Midberry, Jennifer E and Wang, Yuanxin} } @article {20371, title = {A new integrative conjugative element detected in Haitian isolates of Vibrio cholerae non-O1/non-O139}, journal = {Research in Microbiology}, volume = {164}, year = {2013}, month = {Jan-11-2013}, pages = {891 - 893}, abstract = {The presence of SXT/R391-related integrating conjugative elements (ICEs) in Vibrio cholerae O1 and non-O1/non-O139 isolated from clinical and environmental samples in Haiti in 2010 was studied. The main finding of this work was the identification of the novel ICEVchHai2 among closely related V. cholerae non-O1/non-O139 clinical strains. The mosaic structure of this element confirms the role of ICEs as efficient recombination systems whereby new genetic material can be acquired and exchanged, according V. cholerae strains new accessory functions. }, issn = {09232508}, doi = {10.1016/j.resmic.2013.08.004}, url = {https://linkinghub.elsevier.com/retrieve/pii/S092325081300154X}, author = {Ceccarelli, Daniela and Spagnoletti, Matteo and Hasan, Nur A. and Lansing, Stephanie and Huq, Anwar and Rita R Colwell} } @article {20368, title = {Ocean Warming and Spread of Pathogenic Vibrios in the Aquatic Environment}, journal = {Microbial Ecology}, year = {2013}, month = {Jan-05-2013}, pages = {817 - 825}, abstract = {Vibrios are among the most common bacteria that inhabit surface waters throughout the world and are responsible for a number of severe infections both in humans and animals. Several reports recently showed that human Vibrio illnesses are increasing worldwide including fatal acute diarrheal diseases, such as cholera, gastroenteritis, wound infections, and septicemia. Many scientists believe this increase may be associated with global warming and rise in sea surface temperature (SST), although not enough evidence is available to support a causal link between emergence of Vibrio infections and climate warming. The effect of increased SST in promoting spread of vibrios in coastal and brackish waters is considered a causal factor explaining this trend. Field and laboratory studies carried out over the past 40 years supported this hypothesis, clearly showing temperature promotes Vibrio growth and persistence in the aquatic environment. Most recently, a long-term retrospective microbiological study carried out in the coastal waters of the southern North Sea provided the first experimental evidence for a positive and significant relationship between SST and Vibrio occurrence over a multidecadal time scale. As a future challenge, macroecological studies of the effects of ocean warming on Vibrio persistence and spread in the aquatic environment over large spatial and temporal scales would conclusively support evidence acquired to date combined with studies of the impact of global warming on epidemiologically relevant variables, such as host susceptibility and exposure. Assessing a causal link between ongoing climate change and enhanced growth and spread of vibrios and related illness is expected to improve forecast and mitigate future outbreaks associated with these pathogens.}, issn = {0095-3628}, doi = {10.1007/s00248-012-0163-2}, url = {http://link.springer.com/10.1007/s00248-012-0163-2}, author = {Vezzulli, Luigi and Rita R Colwell and Pruzzo, Carla} } @article {19372, title = {Parallel geometric classification of stem cells by their three-dimensional morphology}, journal = {Computational Science \& Discovery}, volume = {6}, year = {2013}, month = {01/2013}, pages = {015007}, doi = {10.1088/1749-4699/6/1/015007}, author = {Juba,Derek and Cardone, Antonio and Ip, Cheuk Yiu and Simon Jr, Carl G and K Tison, Christopher and Kumar, Girish and Brady,Mary and Varshney, Amitabh} } @article {19666, title = {Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures}, journal = {Science}, volume = {342}, year = {2013}, month = {2013/11/29/}, pages = {1100 - 1104}, abstract = {Changes in gene regulation have likely played an important role in the evolution of primates. Differences in messenger RNA (mRNA) expression levels across primates have often been documented; however, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are probably more important in determining phenotypic differences. We used high-resolution, quantitative mass spectrometry to collect protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines and compared them to transcript expression data from the same samples. We found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest that protein expression levels evolve under stronger evolutionary constraint than mRNA levels.Don{\textquoteright}t Ape Protein Variation Changes in DNA and messenger RNA (mRNA) expression levels have been used to estimate evolutionary changes between species. However protein expression levels may better reflect selection on divergent and constrained phenotypes. Khan et al. (p. 1100, published online 17 October; see the Perspective by Vogel) measured the differences among and within species between mRNA expression and protein levels in humans, chimpanzees, and rhesus macaques, identifying protein transcripts that seem to be under lineage-specific constraint between humans and chimpanzees. }, isbn = {0036-8075, 1095-9203}, url = {http://www.sciencemag.org/content/342/6162/1100}, author = {Zia Khan and Ford, Michael J. and Cusanovich, Darren A. and Mitrano, Amy and Pritchard, Jonathan K. and Gilad, Yoav} } @article {20369, title = {Quantification of Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae in French Mediterranean coastal lagoons}, journal = {Research in Microbiology}, volume = {164}, year = {2013}, month = {Jan-10-2013}, pages = {867 - 874}, abstract = {Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae are human pathogens. Little is known about these Vibrio spp. in the coastal lagoons of France. The purpose of this study was to investigate their incidence in water, shellfish and sediment of three French Mediterranean coastal lagoons using the most probable number-polymerase chain reaction (MPN-PCR). In summer, the total number of V. parahaemolyticus in water, sediment, mussels and clams collected from the three lagoons varied from 1 to >1.1 {\texttimes} 103 MPN/l, 0.09 to 1.1 {\texttimes} 103 MPN/ml, 9 to 210 MPN/g and 1.5 to 2.1 MPN/g, respectively. In winter, all samples except mussels contained V. parahaemolyticus, but at very low concentrations. Pathogenic (tdh- or trh2-positive) V. parahaemolyticus were present in water, sediment and shellfish samples collected from these lagoons. The number of V. vulnificus in water, sediment and shellfish samples ranged from 1 to 1.1 {\texttimes} 103 MPN/l, 0.07 to 110 MPN/ml and 0.04 to 15 MPN/g, respectively, during summer. V. vulnificus was not detected during winter. V. cholerae was rarely detected in water and sediment during summer. In summary, results of this study highlight the finding that the three human pathogenic Vibrio spp. are present in the lagoons and constitute a potential public health hazard.}, issn = {09232508}, doi = {10.1016/j.resmic.2013.06.005}, url = {https://linkinghub.elsevier.com/retrieve/pii/S092325081300106X}, author = {Cantet, Franck and Hervio-Heath, Dominique and Caro, Audrey and Le Mennec, C{\'e}cile and Monteil, Caroline and Qu{\'e}m{\'e}r{\'e}, Catherine and Jolivet-Gougeon, Anne and Rita R Colwell and Monfort, Patrick} } @article {19371, title = {Segmenting time-lapse phase contrast images of adjacent NIH 3T3 cells.}, journal = {Journal of microscopy}, volume = {249}, year = {2013}, month = {2013 Jan}, pages = {41-52}, abstract = {We present a new method for segmenting phase contrast images of NIH 3T3 fibroblast cells that is accurate even when cells are physically in contact with each other. The problem of segmentation, when cells are in contact, poses a challenge to the accurate automation of cell counting, tracking and lineage modelling in cell biology. The segmentation method presented in this paper consists of (1) background reconstruction to obtain noise-free foreground pixels and (2) incorporation of biological insight about dividing and nondividing cells into the segmentation process to achieve reliable separation of foreground pixels defined as pixels associated with individual cells. The segmentation results for a time-lapse image stack were compared against 238 manually segmented images (8219 cells) provided by experts, which we consider as reference data. We chose two metrics to measure the accuracy of segmentation: the {\textquoteright}Adjusted Rand Index{\textquoteright} which compares similarities at a pixel level between masks resulting from manual and automated segmentation, and the {\textquoteright}Number of Cells per Field{\textquoteright} (NCF) which compares the number of cells identified in the field by manual versus automated analysis. Our results show that the automated segmentation compared to manual segmentation has an average adjusted rand index of 0.96 (1 being a perfect match), with a standard deviation of 0.03, and an average difference of the two numbers of cells per field equal to 5.39\% with a standard deviation of 4.6\%.}, keywords = {Animals, Cell Adhesion, Cell Count, Cell Division, Cell Shape, Computational Biology, Fibroblasts, Image Processing, Computer-Assisted, Mice, Microscopy, Phase-Contrast, NIH 3T3 Cells, Reproducibility of results, Sensitivity and Specificity, Time-Lapse Imaging}, issn = {1365-2818}, doi = {10.1111/j.1365-2818.2012.03678.x}, author = {Chalfoun, J and Kociolek, M and Dima, A and Halter, M and Cardone, Antonio and Peskin, A and Bajcsy, P and Brady, M.} } @article {20373, title = {Species composition of limnetic zooplankton from the southern coastal areas (Mathbaria and Bakerganj) in Bangladesh}, journal = {Journal of the Asiatic Society of Bangladesh, Science}, volume = {38}, year = {2013}, month = {Apr-06-2014}, abstract = {We studied the coastal zooplankton community structure of six waterbodies of Mathbaria and Bakerganj from January 2008 to June 2009. In total 35 zooplankton species were identified under 26 genera under 20 families under 8 orders from Mathbaria. Among them 6 were protozoans, 24 were rotifers, 3 were copepods, 1 was cladocerans and 1 was ostracods. From Bakergonj a total of 42 zooplankton species were identified under 23 genera under 17 Families under 7 orders. Among them 3 were protozoans, 25 were rotifers, 7 were copepods, 6 were cladocerans and 1 was ostracods. Results showed that abundance of rotifera group from both area was higher in Mathbaria (64.86\%) and Bakerganj (60.98\%) than other groups while abundance of ostracoda of Bakerganj area was lowest.}, issn = {1016-6947}, doi = {10.3329/jasbs.v38i1.15326}, url = {http://banglajol.info/index.php/JASBS/article/view/15326}, author = {Mozumder, Pronob K and Nahar, Samsun and Naser, M Niamul and Alam, Munirul and Huq, Anwar and Sack, R Bradley and Rita R Colwell} } @article {19413, title = {Specific and Non-Specific Protein Association in Solution: Computation of Solvent Effects and Prediction of First-Encounter Modes for Efficient Configurational Bias Monte Carlo Simulations}, journal = {The Journal of Physical Chemistry B}, volume = {117}, year = {2013}, month = {May-10-2014}, pages = {12360 - 12374}, issn = {1520-6106}, doi = {10.1021/jp4050594}, url = {http://pubs.acs.org/doi/abs/10.1021/jp4050594}, author = {Cardone, Antonio and Pant, Harish and Hassan, Sergio A.} } @article {20064, title = {Understanding the impact of image quality on segmentation accuracy}, journal = {SPIE Newsroom}, year = {2013}, month = {2013}, author = {Li-Baboud, Ya-Shian and Cardone, Antonio and Chalfoun, Joe and Bajcsy, Peter and Elliott, John} } @article {20377, title = {A water marker monitored by satellites to predict seasonal endemic cholera}, journal = {Remote Sensing Letters}, volume = {4472741982394456}, year = {2013}, month = {Jan-08-2013}, pages = {822 - 831}, abstract = {The ability to predict an occurrence of cholera, a water-related disease, offers a significant public health advantage. Satellite-based estimates of chlorophyll, a surrogate for plankton abundance, have been linked to cholera incidence. However, cholera bacteria can survive under a variety of coastal ecological conditions, thus constraining the predictive ability of the chlorophyll, since it provides only an estimate of greenness of seawater. Here, a new remote-sensing-based index is proposed: Satellite Water Marker (SWM), which estimates the condition of coastal water, based on observed variability in the difference between blue (412 nm) and green (555 nm) wavelengths that can be related to seasonal cholera incidence. The index is bounded between physically separable wavelengths for relatively clear (blue) and turbid (green) water. Using SWM, prediction of cholera with reasonable accuracy, at least two months in advance, can potentially be achieved in the endemic coastal regions. }, issn = {2150-704X}, doi = {10.1080/2150704X.2013.802097}, url = {http://www.tandfonline.com/doi/abs/10.1080/2150704X.2013.802097}, author = {Jutla, Antarpreet and Akanda, Ali Shafqat and Huq, Anwar and Faruque, Abu Syed Golam and Rita R Colwell and Islam, Shafiqul} } @article {20375, title = {An additional step in the transmission of Yersinia pestis?}, journal = {The ISME Journal}, year = {2012}, month = {Jan-02-2012}, pages = {231 - 236}, abstract = {Plague, caused by the bacterium Yersinia pestis, is a mammalian vector-borne disease, transmitted by fleas that serve as the vector between rodent hosts. For many pathogens, including Y. pestis, there are strong evolutionary pressures that lead to a reduction in {\textquoteleft}useless genes{\textquoteright}, with only those retained that reflect function in the specific environment inhabited by the pathogen. Genetic traits critical for survival and transmission between two environments, the rodent and the flea, are conserved in epizootic/epidemic plague strains. However, there are genes that remain conserved for which no function in the flea{\textendash}rodent cycle has yet been observed, indicating an additional environment may exist in the transmission cycle of plague. Here, we present evidence for highly conserved genes that suggests a role in the persistence of Y. pestis after death of its host. Furthermore, maintenance of these genes points to Y. pestis traversing a post-mortem path between, and possibly within, epizootic periods and offering insight into mechanisms that may allow Y. pestis an alternative route of transmission in the natural environment.}, issn = {1751-7362}, doi = {10.1038/ismej.2011.105}, url = {http://www.nature.com/articles/ismej2011105}, author = {Easterday, W Ryan and Kausrud, Kyrre L and Star, Bastiaan and Heier, Lise and Haley, Bradd J and Ageyev, Vladimir and Rita R Colwell and Stenseth, Nils Chr} } @article {12980, title = {BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics}, journal = {Systematic BiologySyst Biol}, volume = {61}, year = {2012}, month = {2012/01/01/}, pages = {170 - 173}, abstract = {Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.}, keywords = {Bayesian phylogenetics, gpu, maximum likelihood, parallel computing}, isbn = {1063-5157, 1076-836X}, doi = {10.1093/sysbio/syr100}, url = {http://sysbio.oxfordjournals.org/content/61/1/170}, author = {Ayres,Daniel L and Darling,Aaron and Zwickl,Derrick J and Beerli,Peter and Holder,Mark T and Lewis,Paul O and Huelsenbeck,John P and Ronquist,Fredrik and Swofford,David L and Cummings, Michael P. and Rambaut,Andrew and Suchard,Marc A} } @article {20063, title = {Biases from model assumptions in texture sub-cellular image segmentation}, journal = {SPIE Newsroom}, volume = {13}, year = {2012}, author = {Cardone, Antonio and Amelot, Julien and Li-Baboud, Ya-Shian and Brady, Mary and Bajcsy, Peter} } @article {12433, title = {A Blur-robust Descriptor with Applications to Face Recognition}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {PP}, year = {2012}, month = {2012/01/10/}, pages = {1 - 1}, abstract = {Understanding the effect of blur is an important problem in unconstrained visual analysis. We address this problem in the context of image-based recognition, by a fusion of image-formation models, and differential geometric tools. First, we discuss the space spanned by blurred versions of an image and then under certain assumptions, provide a differential geometric analysis of that space. More specifically, we create a subspace resulting from convolution of an image with a complete set of orthonormal basis functions of a pre-specified maximum size (that can represent an arbitrary blur kernel within that size), and show that the corresponding subspaces created from a clean image and its blurred versions are equal under the ideal case of zero noise, and some assumptions on the properties of blur kernels. We then study the practical utility of this subspace representation for the problem of direct recognition of blurred faces, by viewing the subspaces as points on the Grassmann manifold and present methods to perform recognition for cases where the blur is both homogenous and spatially varying. We empirically analyze the effect of noise, as well as the presence of other facial variations between the gallery and probe images, and provide comparisons with existing approaches on standard datasets.}, keywords = {Blur, convolution, Face, face recognition, Grassmann manifold, Kernel, Manifolds, NOISE, PROBES}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2012.15}, author = {Gopalan,R. and Taheri, S. and Turaga,P. and Chellapa, Rama} } @inbook {19641, title = {On the Centrality of Off-Line E-Cash to Concrete Partial Information Games}, booktitle = {Security and Cryptography for Networks}, series = {Lecture Notes in Computer Science}, year = {2012}, month = {2012/01/01/}, pages = {264 - 280}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Cryptography has developed numerous protocols for solving {\textquotedblleft}partial information games{\textquotedblright} that are seemingly paradoxical. Some protocols are generic (e.g., secure multi-party computation) and others, due to the importance of the scenario they represent, are designed to solve a concrete problem directly. Designing efficient and secure protocols for (off-line) e-cash, e-voting, and e-auction are some of the most heavily researched concrete problems, representing various settings where privacy and correctness of the procedure is highly important. In this work, we initiate the exploration of the relationships among e-cash, e-voting and e-auction in the universal composability (UC) framework, by considering general variants of the three problems. In particular, we first define ideal functionalities for e-cash, e-voting, and e-auction, and then give a construction of a protocol that UC-realizes the e-voting (resp., e-auction) functionality in the e-cash hybrid model. This (black-box) reducibility demonstrates the centrality of off-line e-cash and implies that designing a solution to e-cash may bear fruits in other areas. Constructing a solution to one protocol problem based on a second protocol problem has been traditional in cryptography, but typically has concentrated on building complex protocols on simple primitives (e.g., secure multi-party computation from Oblivious Transfer, signature from one-way functions, etc.). The novelty here is reducibility among mature protocols and using the ideal functionality as a design tool in realizing other ideal functionalities. We suggest this new approach, and we only consider the very basic general properties from the various primitives to demonstrate its viability. Namely, we only consider the basic coin e-cash model, the e-voting that is correct and private and relies on trusted registration, and e-auction relying on a trusted auctioneer. Naturally, relationships among protocols with further properties (i.e., extended functionalities), using the approach advocated herein, are left as open questions.}, keywords = {Computer Appl. in Administrative Data Processing, Computer Communication Networks, Data Encryption, Management of Computing and Information Systems, Systems and Data Security}, isbn = {978-3-642-32927-2, 978-3-642-32928-9}, url = {http://link.springer.com/chapter/10.1007/978-3-642-32928-9_15}, author = {Choi, Seung Geol and Dana Dachman-Soled and Yung, Moti}, editor = {Visconti, Ivan and Prisco, Roberto De} } @inbook {19632, title = {Computational Extractors and Pseudorandomness}, booktitle = {Theory of Cryptography}, series = {Lecture Notes in Computer Science}, year = {2012}, month = {2012/01/01/}, pages = {383 - 403}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Computational extractors are efficient procedures that map a source of sufficiently high min-entropy to an output that is computationally indistinguishable from uniform. By relaxing the statistical closeness property of traditional randomness extractors one hopes to improve the efficiency and entropy parameters of these extractors, while keeping their utility for cryptographic applications. In this work we investigate computational extractors and consider questions of existence and inherent complexity from the theoretical and practical angles, with particular focus on the relationship to pseudorandomness. An obvious way to build a computational extractor is via the {\textquotedblleft}extract-then-prg{\textquotedblright} method: apply a statistical extractor and use its output to seed a PRG. This approach carries with it the entropy cost inherent to implementing statistical extractors, namely, the source entropy needs to be substantially higher than the PRG{\textquoteright}s seed length. It also requires a PRG and thus relies on one-way functions. We study the necessity of one-way functions in the construction of computational extractors and determine matching lower and upper bounds on the {\textquotedblleft}black-box efficiency{\textquotedblright} of generic constructions of computational extractors that use a one-way permutation as an oracle. Under this efficiency measure we prove a direct correspondence between the complexity of computational extractors and that of pseudorandom generators, showing the optimality of the extract-then-prg approach for generic constructions of computational extractors and confirming the intuition that to build a computational extractor via a PRG one needs to make up for the entropy gap intrinsic to statistical extractors. On the other hand, we show that with stronger cryptographic primitives one can have more entropy- and computationally-efficient constructions. In particular, we show a construction of a very practical computational extractor from any weak PRF without resorting to statistical extractors.}, keywords = {Algorithm Analysis and Problem Complexity, Coding and Information Theory, Computer Communication Networks, Data Encryption, Math Applications in Computer Science, Systems and Data Security}, isbn = {978-3-642-28913-2, 978-3-642-28914-9}, url = {http://link.springer.com/chapter/10.1007/978-3-642-28914-9_22}, author = {Dana Dachman-Soled and Gennaro, Rosario and Krawczyk, Hugo and Malkin, Tal}, editor = {Cramer, Ronald} } @article {12853, title = {Conversion of viable but nonculturable enteric bacteria to culturable by co-culture with eukaryotic cells}, journal = {Microbiology and Immunology}, volume = {56}, year = {2012}, month = {2012/04/27/}, pages = {342 - 345}, abstract = {Viable but nonculturable (VBNC) Vibrio cholerae non-O1/non-O139, V. parahaemolyticus, enterohemorrhagic Escherichia coli, enterotoxigenic E. coli, enteropathogenic E. coli, Shigella flexneri, and Salmonella enterica were converted to the culturable state by co-culture with selected eukaryotic cells, e.g., HT-29, Caco-2, T84, HeLa, Intestine 407, and CHO cells.}, keywords = {conversion to culturability, enteric bacteria, viable but nonculturable}, isbn = {1348-0421}, doi = {10.1111/j.1348-0421.2012.00440.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1348-0421.2012.00440.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Senoh,Mitsutoshi and Ghosh-Banerjee,Jayeeta and Ramamurthy,Thandavarayan and Rita R Colwell and Miyoshi,Shin-ichi and Nair,G. Balakrish and Takeda,Yoshifumi} } @article {19128, title = {Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease}, journal = {PloS one}, volume = {7}, year = {2012}, month = {2012}, abstract = {The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (~2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ~90\%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.}, author = {Liu,B. and Faller, L.L. and Klitgord, N. and Mazumdar, V. and Ghodsi,M. and Sommer, D.D. and Gibbons, T.R. and Treangen, T.J. and Chang, Y.C. and Li,S.} } @article {20376, title = {Detection, Isolation, and Identification of Vibrio cholerae from the Environment}, journal = {Current Protocols in Microbiology}, volume = {26}, year = {2012}, month = {08/2012}, publisher = {John Wiley \& Sons, Inc.}, chapter = {Unit 6A.5}, address = {Hoboken, NJ, USA}, abstract = {Recent molecular advances in microbiology have greatly improved the detection of bacterial pathogens in the environment. These improvements and a downward trend in the cost of molecular detection methods have contributed to increased frequency of detection of pathogenic microorganisms where traditional culture-based detection methods have failed. Culture methods also have been greatly improved, and the confluence of the two suites of methods provides a powerful tool for detection, isolation, and characterization of pathogens. While molecular detection provides data on the presence and type of pathogens, culturing methods allow a researcher to preserve the organism of interest for {\textquotedblleft}-omics{\textquotedblright} studies, such as genomic, metabolomic, secretomic, and transcriptomic analysis, which are rapidly becoming more affordable. This has yielded a clearer understanding of the ecology and epidemiology of microorganisms that cause disease. In this unit, we present commonly accepted methods for isolation, detection, and characterization of V. cholerae, providing more extensive knowledge of the ecology and epidemiology of this organism. This unit has been fully revised and updated from the earlier version with the latest knowledge and additional information not previously included. Curr. Protoc. Microbiol. 26:6A.5.1-6A.5.51. {\textcopyright} 2012 by John Wiley \& Sons, Inc. }, doi = {10.1002/9780471729259.mc06a05s26}, url = {http://doi.wiley.com/10.1002/9780471729259.mc06a05s26}, author = {Huq, Anwar and Haley, Bradd J. and Taviani, Elisa and Chen, Arlene and Hasan, Nur A. and Rita R Colwell}, editor = {Coico, Richard and Kowalik, Tim and Quarles, John and Stevenson, Brian and Taylor, Ron} } @article {12432, title = {Dictionary-based Face Recognition Under Variable Lighting and Pose}, journal = {IEEE Transactions on Information Forensics and Security}, volume = {PP}, year = {2012}, month = {2012/02/27/}, pages = {1 - 1}, abstract = {We present a face recognition algorithm based on simultaneous sparse approximations under varying illumination and pose. A dictionary is learned for each class based on given training examples which minimizes the representation error with a sparseness constraint. A novel test image is projected onto the span of the atoms in each learned dictionary. The resulting residual vectors are then used for classification. To handle variations in lighting conditions and pose, an image relighting technique based on pose-robust albedo estimation is used to generate multiple frontal images of the same person with variable lighting. As a result, the proposed algorithm has the ability to recognize human faces with high accuracy even when only a single or a very few images per person are provided for training. The efficiency of the proposed method is demonstrated using publicly available databases and it is shown that this method is efficient and can perform significantly better than many competitive face recognition algorithms.}, keywords = {Biometrics, dictionary learning, face recognition, illumination variation,, outlier rejection}, isbn = {1556-6013}, doi = {10.1109/TIFS.2012.2189205}, author = {Patel, Vishal M. and Wu,T. and Biswas,S. and Phillips,P. and Chellapa, Rama} } @article {13288, title = {Dimension-independent multi-resolution morse complexes}, journal = {Computers \& Graphics}, year = {2012}, month = {2012///}, author = {De Floriani, Leila and {\v C}omi{\'c},L.} } @article {14328, title = {Disaggregated water sensing from a single, pressure-based sensor: An extended analysis of HydroSense using staged experiments}, journal = {Pervasive and Mobile Computing}, volume = {8}, year = {2012}, month = {2012/02//}, pages = {82 - 102}, abstract = {We present an extended analysis of our previous work on the HydroSense technology, which is a low-cost and easily installed single-point sensor of pressure for automatically disaggregating water usage activities in the home (Froehlich et~al., 2009~[53]). We expand upon this work by providing a survey of existing and emerging water disaggregation techniques, a more comprehensive description of the theory of operation behind our approach, and an expanded analysis section that includes hot versus cold water valve usage classification and a comparison between two classification approaches: the template-based matching scheme used in Froehlich et~al. (2009)~[53] and a new stochastic approach using a Hidden Markov Model. We show that both are successful in identifying valve- and fixture-level water events with greater than 90\% accuracies. We conclude with a discussion of the limitations in our experimental methodology and open problems going forward.}, keywords = {Activity sensing, H1.2, H5.2, Infrastructure-mediated sensing, Sensors, Water usage}, isbn = {1574-1192}, doi = {10.1016/j.pmcj.2010.08.008}, url = {http://www.sciencedirect.com/science/article/pii/S1574119210000842}, author = {Larson,Eric and Jon Froehlich and Campbell,Tim and Haggerty,Conor and Atlas,Les and Fogarty,James and Patel,Shwetak N.} } @article {20387, title = {Ecology of Vibrio parahaemolyticus and Vibrio vulnificus in the Coastal and Estuarine Waters of Louisiana, Maryland, Mississippi, and Washington (United States)}, journal = {Applied and Environmental Microbiology}, year = {2012}, month = {Mar-10-2013}, pages = {7249 - 7257}, abstract = {Vibrio parahaemolyticus and Vibrio vulnificus, which are native to estuaries globally, are agents of seafood-borne or wound infections, both potentially fatal. Like all vibrios autochthonous to coastal regions, their abundance varies with changes in environmental parameters. Sea surface temperature (SST), sea surface height (SSH), and chlorophyll have been shown to be predictors of zooplankton and thus factors linked to vibrio populations. The contribution of salinity, conductivity, turbidity, and dissolved organic carbon to the incidence and distribution of Vibrio spp. has also been reported. Here, a multicoastal, 21-month study was conducted to determine relationships between environmental parameters and V. parahaemolyticus and V. vulnificus populations in water, oysters, and sediment in three coastal areas of the United States. Because ecologically unique sites were included in the study, it was possible to analyze individual parameters over wide ranges. Molecular methods were used to detect genes for thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) as indicators of V. parahaemolyticus and the hemolysin gene vvhA for V. vulnificus. SST and suspended particulate matter were found to be strong predictors of total and potentially pathogenic V. parahaemolyticus and V. vulnificus. Other predictors included chlorophyll a, salinity, and dissolved organic carbon. For the ecologically unique sites included in the study, SST was confirmed as an effective predictor of annual variation in vibrio abundance, with other parameters explaining a portion of the variation not attributable to SST.}, issn = {0099-2240}, doi = {10.1128/AEM.01296-12}, url = {http://aem.asm.org/lookup/doi/10.1128/AEM.01296-12}, author = {Johnson, Crystal N. and Bowers, John C. and Griffitt, Kimberly J. and Molina, Vanessa and Clostio, Rachel W. and Pei, Shaofeng and Laws, Edward and Paranjpye, Rohinee N. and Strom, Mark S. and Chen, Arlene and Hasan, Nur A. and Huq, Anwar and Noriea, Nicholas F. and Grimes, D. Jay and Rita R Colwell} } @inbook {19634, title = {Efficient Password Authenticated Key Exchange via Oblivious Transfer}, booktitle = {Public Key Cryptography {\textendash} PKC 2012}, series = {Lecture Notes in Computer Science}, year = {2012}, month = {2012/01/01/}, pages = {449 - 466}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We present a new framework for constructing efficient password authenticated key exchange (PAKE) protocols based on oblivious transfer (OT). Using this framework, we obtain: an efficient and simple UC-secure PAKE protocol that is secure against adaptive corruptions without erasures. efficient and simple PAKE protocols under the Computational Diffie-Hellman (CDH) assumption and the hardness of factoring. (Previous efficient constructions rely on hash proof systems, which appears to be inherently limited to decisional assumptions.) All of our constructions assume a common reference string (CRS) but do not rely on random oracles.}, keywords = {adaptive security, Algorithm Analysis and Problem Complexity, Computer Communication Networks, Data Encryption, Discrete Mathematics in Computer Science, Management of Computing and Information Systems, oblivious transfer, Password Authenticated Key Exchange, search assumptions, Systems and Data Security, UC security}, isbn = {978-3-642-30056-1, 978-3-642-30057-8}, url = {http://link.springer.com/chapter/10.1007/978-3-642-30057-8_27}, author = {Canetti, Ran and Dana Dachman-Soled and Vaikuntanathan, Vinod and Wee, Hoeteck}, editor = {Fischlin, Marc and Buchmann, Johannes and Manulis, Mark} } @article {19126, title = {Exploiting sparseness in de novo genome assembly}, journal = {BMC bioinformatics}, volume = {13}, year = {2012}, month = {2012}, abstract = {The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments.In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k-mers as nodes and the links between these nodes allows the de novo assembly of even moderately-sized genomes (~500 M) on a typical laptop computer. We implement this sparse graph concept in a proof-of-principle software package, SparseAssembler, utilizing a new sparse k-mer graph structure evolved from the de Bruijn graph. We test our SparseAssembler with both simulated and real data, achieving ~90\% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers. }, author = {Ye, C. and Ma, Z.S. and Cannon, C.H. and Pop, Mihai and Yu, D.W.} } @article {13066, title = {Face Identification Using Large Feature Sets}, journal = {Image Processing, IEEE Transactions on}, volume = {21}, year = {2012}, month = {2012/04//}, pages = {2245 - 2255}, abstract = {With the goal of matching unknown faces against a gallery of known people, the face identification task has been studied for several decades. There are very accurate techniques to perform face identification in controlled environments, particularly when large numbers of samples are available for each face. However, face identification under uncontrolled environments or with a lack of training data is still an unsolved problem. We employ a large and rich set of feature descriptors (with more than 70 000 descriptors) for face identification using partial least squares to perform multichannel feature weighting. Then, we extend the method to a tree-based discriminative structure to reduce the time required to evaluate probe samples. The method is evaluated on Facial Recognition Technology (FERET) and Face Recognition Grand Challenge (FRGC) data sets. Experiments show that our identification method outperforms current state-of-the-art results, particularly for identifying faces acquired across varying conditions.}, keywords = {(mathematics);, approximations;trees, challenge, data, data;tree-based, discriminative, environments;face, feature, FERET;FRGC, grand, identification, least, recognition, recognition;least, sets;face, sets;facial, squares, squares;training, structure;uncontrolled, task;face, technology;multichannel, weighting;partial}, isbn = {1057-7149}, doi = {10.1109/TIP.2011.2176951}, author = {Schwartz, W.R. and Guo,Huimin and Choi,Jonghyun and Davis, Larry S.} } @article {14330, title = {Fast track article: Disaggregated water sensing from a single, pressure-based sensor: An extended analysis of HydroSense using staged experiments}, journal = {Pervasive Mob. Comput.}, volume = {8}, year = {2012}, month = {2012/02//}, pages = {82 - 102}, abstract = {We present an extended analysis of our previous work on the HydroSense technology, which is a low-cost and easily installed single-point sensor of pressure for automatically disaggregating water usage activities in the home (Froehlich et al., 2009 [53]). We expand upon this work by providing a survey of existing and emerging water disaggregation techniques, a more comprehensive description of the theory of operation behind our approach, and an expanded analysis section that includes hot versus cold water valve usage classification and a comparison between two classification approaches: the template-based matching scheme used in Froehlich et al. (2009) [53] and a new stochastic approach using a Hidden Markov Model. We show that both are successful in identifying valve- and fixture-level water events with greater than 90\% accuracies. We conclude with a discussion of the limitations in our experimental methodology and open problems going forward.}, keywords = {Activity sensing, H1.2, H5.2, Infrastructure-mediated sensing, Sensors, Water usage}, isbn = {1574-1192}, doi = {10.1016/j.pmcj.2010.08.008}, url = {http://dx.doi.org/10.1016/j.pmcj.2010.08.008}, author = {Larson,Eric and Jon Froehlich and Campbell,Tim and Haggerty,Conor and Atlas,Les and Fogarty,James and Patel,Shwetak N.} } @article {19131, title = {A framework for human microbiome research}, journal = {Nature}, volume = {486}, year = {2012}, month = {2012}, pages = {215 - 221}, abstract = {A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.}, author = {Meth{\'e}, B.A. and Nelson,K. E and Pop, Mihai and Creasy, H.H. and Giglio, M.G. and Huttenhower, C. and Gevers, D. and Petrosino, J.F. and Abubucker, S. and Badger, J.H.} } @article {20374, title = {Genetic characteristics of drug-resistant Vibrio cholerae O1 causing endemic cholera in Dhaka, 2006-2011}, journal = {Journal of Medical Microbiology}, year = {2012}, month = {Jan-12-2012}, pages = {1736 - 1745}, abstract = {Vibrio cholerae O1 biotype El Tor (ET), causing the seventh cholera pandemic, was recently replaced in Bangladesh by an altered ET possessing ctxB of the Classical (CL) biotype, which caused the first six cholera pandemics. In the present study, V. cholerae O1 strains associated with endemic cholera in Dhaka between 2006 and 2011 were analysed for major phenotypic and genetic characteristics. Of 54 representative V. cholerae isolates tested, all were phenotypically ET and showed uniform resistance to trimethoprim/sulfamethoxazole (SXT) and furazolidone (FR). Resistance to tetracycline (TE) and erythromycin (E) showed temporal fluctuation, varying from year to year, while all isolates were susceptible to gentamicin (CN) and ciprofloxacin (CIP). Year-wise data revealed erythromycin resistance to be 33.3 \% in 2006 and 11 \% in 2011, while tetracycline resistance accounted for 33, 78, 0, 100 and 27 \% in 2006, 2007, 2008, 2009 and 2010, respectively; interestingly, all isolates tested were sensitive to TE in 2011, as observed in 2008. All V. cholerae isolates tested possessed genetic elements such as SXT, ctxAB, tcpA ET, rstR ET and rtxC; none had IntlI (Integron I). Double mismatch amplification mutation assay (DMAMA)-PCR followed by DNA sequencing and analysis of the ctxB gene revealed a point mutation at position 58 (C{\textrightarrow}A), which has resulted in an amino acid substitution from histidine (H) to asparagine (N) at position 20 (genotype 7) since 2008. Although the multi-resistant strains having tetracycline resistance showed minor genetic divergence, V. choleraestrains were clonal, as determined by a PFGE (NotI)-based dendrogram. This study shows 2008{\textendash}2010 to be the time of transition from ctxB genotype 1 to genotype 7 in V. cholerae ET causing endemic cholera in Dhaka, Bangladesh.}, issn = {0022-2615}, doi = {10.1099/jmm.0.049635-0}, url = {http://jmm.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.049635-0}, author = {Rashed, S. M. and Mannan, S. B. and Johura, F.-T. and Islam, M. T. and Sadique, A. and Watanabe, H. and Sack, R. B. and Huq, A. and Rita R Colwell and Cravioto, A. and Alam, M.} } @article {20384, title = {Genomic analysis of ICE Vch Ban8: An atypical genetic element in Vibrio cholerae}, journal = {FEBS Letters}, year = {2012}, month = {Apr-06-2012}, pages = {1617 - 1621}, abstract = {Genomic islands (GIs) and integrative conjugative elements (ICEs) are major players in bacterial evolution since they encode genes involved in adaptive functions of medical or environmental importance. Here we performed the genomic analysis of ICEVchBan8, an unusual ICE found in the genome of a clinical non-toxigenic Vibrio cholerae O37 isolate. ICEVchBan8 shares most of its genetic structure with SXT/R391 ICEs. However, this ICE codes for a different integration/excision module is located at a different insertion site, and part of its genetic cargo shows homology to other pathogenicity islands of V. cholerae.}, doi = {10.1016/j.febslet.2012.03.064}, url = {http://doi.wiley.com/10.1016/j.febslet.2012.03.064}, author = {Taviani, Elisa and Spagnoletti, Matteo and Ceccarelli, Daniela and Haley, Bradd J. and Hasan, Nur A. and Chen, Arlene and Colombo, Mauro M. and Huq, Anwar and Rita R Colwell} } @article {20386, title = {Genomic diversity of 2010 Haitian cholera outbreak strains}, journal = {Proceedings of the National Academy of Sciences}, year = {2012}, month = {05/2012}, pages = {E2010 - E2017}, issn = {0027-8424}, doi = {10.1073/pnas.1207359109}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1207359109}, author = {Hasan, N. A. and Choi, S. Y. and Eppinger, M. and Clark, P. W. and Chen, A. and Alam, M. and Haley, B. J. and Taviani, E. and Hine, E. and Su, Q. and Tallon, L. J. and Prosper, J. B. and Furth, K. and Hoq, M. M. and Li, H. and Fraser-Liggett, C. M. and Cravioto, A. and Huq, A. and Ravel, J. and Cebula, T. A. and Rita R Colwell} } @article {15917, title = {Gradient-based Image Recovery Methods from Incomplete Fourier Measurements}, journal = {IEEE Transactions on Image Processing}, volume = {PP}, year = {2012}, month = {2012///}, pages = {1 - 1}, abstract = {A major problem in imaging applications such as Magnetic Resonance Imaging (MRI) and Synthetic Aperture Radar (SAR) is the task of trying to reconstruct an image with the smallest possible set of Fourier samples, every single one of which has a potential time and/or power cost. The theory of Compressive Sensing (CS) points to ways of exploiting inherent sparsity in such images in order to achieve accurate recovery using sub- Nyquist sampling schemes. Traditional CS approaches to this problem consist of solving total-variation minimization programs with Fourier measurement constraints or other variations thereof. This paper takes a different approach: Since the horizontal and vertical differences of a medical image are each more sparse or compressible than the corresponding total-variational image, CS methods will be more successful in recovering these differences individually. We develop an algorithm called GradientRec that uses a CS algorithm to recover the horizontal and vertical gradients and then estimates the original image from these gradients. We present two methods of solving the latter inverse problem: one based on least squares optimization and the other based on a generalized Poisson solver. After a thorough derivation of our complete algorithm, we present the results of various experiments that compare the effectiveness of the proposed method against other leading methods.}, keywords = {Compressed sensing, Fourier transforms, Image coding, Image edge detection, Image reconstruction, L1{\textendash}minimization, minimization, Noise measurement, OPTIMIZATION, Poisson solver, Sparse recovery, Total variation, TV}, isbn = {1057-7149}, doi = {10.1109/TIP.2011.2159803}, author = {Patel, Vishal M. and Maleh,R. and Gilbert,A. C and Chellapa, Rama} } @conference {18848, title = {Gripper synthesis for indirect manipulation of cells using Holographic Optical Tweezers}, year = {2012}, month = {2012/05//}, pages = {2749 - 2754}, abstract = {Optical Tweezers (OT) are used for highly accurate manipulations of biological cells. However, the direct exposure of cells to focused laser beam may negatively influence their biological functions. In order to overcome this problem, we generate multiple optical traps to grab and move a 3D ensemble of inert particles such as silica microspheres to act as a reconfigurable gripper for a manipulated cell. The relative positions of the microspheres are important in order for the gripper to be robust against external environmental forces and the exposure of high intensity laser on the cell to be minimized. In this paper, we present results of different gripper configurations, experimentally tested using our OT setup, that provide robust gripping as well as minimize laser intensity experienced by the cell. We developed a computational approach that allowed us to perform preliminary modeling and synthesis of the gripper configurations. The gripper synthesis is cast as a multi-objective optimization problem.}, doi = {10.1109/ICRA.2012.6225153}, author = {Chowdhury,Sagar and Svec,Petr and Wang,Chenlu and Losert,Wolfgang and Gupta, Satyandra K.} } @article {19216, title = {Individuals among commuters: Building personalised transport information services from fare collection systems}, journal = {Pervasive and Mobile Computing}, year = {2012}, month = {2012}, author = {Lathia,N. and Smith,C. and Jon Froehlich and Capra,L.} } @article {19721, title = {InterPro in 2011: new developments in the family and domain prediction database.}, journal = {Nucleic Acids Res}, volume = {40}, year = {2012}, month = {2012 Jan}, pages = {D306-12}, abstract = {

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces.

}, keywords = {Databases, Protein, Protein Structure, Tertiary, Proteins, Sequence Analysis, Protein, software, Terminology as Topic, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkr948}, author = {Hunter, Sarah and Jones, Philip and Mitchell, Alex and Apweiler, Rolf and Attwood, Teresa K and Bateman, Alex and Bernard, Thomas and Binns, David and Bork, Peer and Burge, Sarah and de Castro, Edouard and Coggill, Penny and Corbett, Matthew and Das, Ujjwal and Daugherty, Louise and Duquenne, Lauranne and Finn, Robert D and Fraser, Matthew and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Kahn, Daniel and Kelly, Elizabeth and Letunic, Ivica and Lonsdale, David and Lopez, Rodrigo and Madera, Martin and Maslen, John and McAnulla, Craig and McDowall, Jennifer and McMenamin, Conor and Mi, Huaiyu and Mutowo-Muellenet, Prudence and Mulder, Nicola and Natale, Darren and Orengo, Christine and Pesseat, Sebastien and Punta, Marco and Quinn, Antony F and Rivoire, Catherine and Sangrador-Vegas, Amaia and Jeremy D Selengut and Sigrist, Christian J A and Scheremetjew, Maxim and Tate, John and Thimmajanarthanan, Manjulapramila and Thomas, Paul D and Wu, Cathy H and Yeats, Corin and Yong, Siew-Yit} } @article {12854, title = {Vibrio Cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico}, journal = {Journal of Clinical Microbiology}, year = {2012}, month = {04/2012}, abstract = {Vibrio cholerae O1 Classical (CL) biotype caused the 5th and 6th, and probably the earlier cholera pandemics, before the El Tor (ET) biotype initiated the 7th pandemic in Asia in the 1970{\textquoteright}s by completely displacing the CL biotype. Although the CL biotype was thought to be extinct in Asia, and it had never been reported from Latin America, V. cholerae CL and ET biotypes, including hybrid ET were found associated with endemic cholera in Mexico between 1991 and 1997. In this study, CL biotype strains isolated from endemic cholera in Mexico, between 1983 and 1997 were characterized in terms of major phenotypic and genetic traits, and compared with CL biotype strains isolated in Bangladesh between 1962 and 1989. According to sero- and bio-typing data, all V. cholerae strains tested had the major phenotypic and genotypic characteristics specific for the CL biotype. Antibiograms revealed the majority of the Bangladeshi strains to be resistant to trimethoprim/sulfamethoxazole, furazolidone, ampicillin, and gentamycin, while the Mexican strains were sensitive to all of these drugs, as well as to ciprofloxacin, erythromycin, and tetracycline. Pulsed-field gel electrophoresis (PFGE) of NotI-digested genomic DNA revealed characteristic banding patterns for all the CL biotype strains, although the Mexican strains differed with the Bangladeshi strains in 1-2 DNA bands. The difference may be subtle, but consistent, as confirmed by the sub-clustering patterns in the PFGE-based dendrogram, and can serve as regional signature, suggesting pre-1991 existence and evolution of the CL biotype strains in the Americas, independent from that of Asia.}, isbn = {0095-1137, 1098-660X}, doi = {10.1128/JCM.00189-12}, url = {http://jcm.asm.org/content/early/2012/04/12/JCM.00189-12}, author = {Alam,Munirul and Islam,M. Tarequl and Rashed,Shah Manzur and Johura,Fatema-Tuz and Bhuiyan,Nurul A. and Delgado,Gabriela and Morales,Rosario and Mendez,Jose Luis and Navarro,Armando and Watanabe,Haruo and Hasan,Nur-A. and Rita R Colwell and Cravioto,Alejandro} } @article {20382, title = {Vibrio cholerae in a historically cholera-free country}, journal = {Environmental Microbiology Reports}, year = {2012}, month = {Jan-08-2012}, pages = {381 - 389}, abstract = {We report the autochthonous existence of Vibrio cholerae in coastal waters of Iceland, a geothermally active country where cholera is absent and has never been reported. Seawater, mussel and macroalgae samples were collected close to, and distant from, sites where geothermal activity causes a significant increase in water temperature during low tides. Vibrio cholerae was detected only at geothermal-influenced sites during low-tides. None of the V. cholerae isolates encoded cholera toxin (ctxAB) and all were non-O1/non-O139 serogroups. However, all isolates encoded other virulence factors that are associated with cholera as well as extra-intestinal V. cholerae infections. The virulence factors were functional at temperatures of coastal waters of Iceland, suggesting an ecological role. It is noteworthy that V. cholerae was isolated from samples collected at sites distant from anthropogenic influence, supporting the conclusion that V. cholerae is autochthonous to the aquatic environment of Iceland.}, doi = {10.1111/j.1758-2229.2012.00332.x}, url = {http://doi.wiley.com/10.1111/j.1758-2229.2012.00332.x}, author = {Haley, Bradd J. and Chen, Arlene and Grim, Christopher J. and Clark, Philip and Diaz, Celia M and Taviani, Elisa and Hasan, Nur A. and Sancomb, Elizabeth and Elnemr, Wessam M and Islam, Muhammad A. and Huq, Anwar and Rita R Colwell and Benediktsd{\'o}ttir, Eva} } @article {18540, title = {Lithium: Event-Driven Network Control}, volume = {GT-CS-12-03}, year = {2012}, month = {2012///}, institution = {Georgia Institute of Technology}, abstract = {This paper introduces event-driven network control, a network control framework that makes networks easier to manage by automating many tasks that must currently be performed by manually modifying low-level, distributed, and complex device configuration. We identify four policy domains that inherently capture many events: time, user, history, and traffic flow. We then present Lithium, an event-driven network control framework that can implement policies expressed using these domains. Lithium can support policies that automatically react to a wide range of events, from fluctuations in traffic volumes to changes in the time of day. Lithium allows network operators to specify networkwide policies in terms of a high-level, event-driven policy model, as opposed to configuring individual network devices with low-level commands. To show that Lithium is practical, general, and applicable in different types of network scenarios, we have deployed Lithium in both a campus network and a home network and used it to implement more flexible and dynamic network policies. We also perform evaluations to show that Lithium introduces negligible overhead beyond a conventional OpenFlow-based control framework.}, url = {http://hdl.handle.net/1853/43377}, author = {Kim,H. and Voellmy,A. and Burnett,S. and Feamster, Nick and Clark,R.} } @conference {13585, title = {Local Segmentation of Touching Characters using Contour based Shape Decomposition}, booktitle = {Document Analysis Systems}, year = {2012}, month = {2012///}, abstract = {We propose a contour based shape decomposition approach that provides local segmentation of touching characters. The shape contour is linearized into edgelets and edgelets are merged into boundary fragments. Connection cost between boundary fragments is obtained by considering local smoothness, connection length and a stroke-level property Similar Stroke Rate. Samples of connections among boundary fragments are randomly generated and the one with the minimum global cost is selected to produce optimal segmentation of the shape. To obtain a binary segmentation using this approach, we make an iterative search for the parameters that yields two components on a shape. Experimental results on a number of synthetic shape images and the LTP dataset showed that this contour based shape decomposition technique is promising and it is effective on providing local segmentation of touching characters.}, author = {Kang,Le and David Doermann and Cao,Huiagu and Prasad,Rohit and Natarajan,Prem} } @article {20381, title = {Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios}, journal = {The ISME Journal}, volume = {6111114882511}, year = {2012}, month = {Jan-01-2012}, pages = {21 - 30}, abstract = {The long-term effects of ocean warming on prokaryotic communities are unknown because of lack of historical data. We overcame this gap by applying a retrospective molecular analysis to the bacterial community on formalin-fixed samples from the historical Continuous Plankton Recorder archive, which is one of the longest and most geographically extensive collections of marine biological samples in the world. We showed that during the last half century, ubiquitous marine bacteria of the Vibrio genus, including Vibrio cholerae, increased in dominance within the plankton-associated bacterial community of the North Sea, where an unprecedented increase in bathing infections related to these bacteria was recently reported. Among environmental variables, increased sea surface temperature explained 45\% of the variance in Vibrio data, supporting the view that ocean warming is favouring the spread of vibrios and may be the cause of the globally increasing trend in their associated diseases.}, issn = {1751-7362}, doi = {10.1038/ismej.2011.89}, url = {http://www.nature.com/articles/ismej201189}, author = {Vezzulli, Luigi and Brettar, Ingrid and Pezzati, Elisabetta and Reid, Philip C and Rita R Colwell and H{\"o}fle, Manfred G and Pruzzo, Carla} } @article {13829, title = {Modality and Negation in SIMT Use of Modality and Negation in Semantically-Informed Syntactic MT}, journal = {Computational Linguistics}, year = {2012}, month = {2012///}, pages = {1 - 48}, abstract = {This paper describes the resource- and system-building efforts of an eight-week Johns Hopkins University Human Language Technology Center of Excellence Summer Camp for Applied Language Exploration (SCALE-2009) on Semantically-Informed Machine Translation (SIMT). We describe a new modality/negation (MN) annotation scheme, the creation of a (publicly available) MN lexicon, and two automated MN taggers that we built using the annotation scheme and lexicon. Our annotation scheme isolates three components of modality and negation: a trigger (a word that conveys modality or negation), a target (an action associated with modality or negation) and a holder (an experiencer of modality). We describe how our MN lexicon was semi-automatically produced and we demonstrate that a structure-based MN tagger results in precision around 86\% (depending on genre) for tagging of a standard LDC data set.}, isbn = {0891-2017}, doi = {10.1162/COLI_a_00099}, url = {http://dx.doi.org/10.1162/COLI_a_00099}, author = {Baker,Kathryn and Bloodgood,Michael and Dorr, Bonnie J and Callison-Burch,Chris and Filardo,Nathaniel W. and Piatko,Christine and Levin,Lori and Miller,Scott} } @article {12857, title = {Occurrence of protozoans \& their limnological relationships in some ponds of Mathbaria, Bangladesh}, journal = {University Journal of Zoology, Rajshahi University}, volume = {29}, year = {2012}, month = {2012///}, pages = {69 - 71}, isbn = {1023-6104}, url = {http://journals.sfu.ca/bd/index.php/UJZRU}, author = {Mozumder,P. K. and Banu,M. A. and Naser,M. N. and Ali,M. S. and Alam,M. and Sack,R. B. and Rita R Colwell and Huq,A.} } @conference {17641, title = {Optimizing epidemic protection for socially essential workers}, booktitle = {Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium}, series = {IHI {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {31 - 40}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Public-health policy makers have many tools to mitigate an epidemic{\textquoteright}s effects. Most related research focuses on the direct effects on those infected (in terms of health, life, or productivity). Interventions including treatment, prophylaxis, quarantine, and social distancing are well studied in this context. These interventions do not address indirect effects due to the loss of critical services and infrastructures when too many of those responsible for their day-to-day operations fall ill. We examine, both analytically and through simulation, the protection of such essential subpopulations by sequestering them, effectively isolating them into groups during an epidemic. We develop a framework for studying the benefits of sequestering and heuristics for when to sequester. We also prove a key property of sequestering placement which helps partition the subpopulations optimally. Thus we provide a first step toward determining how to allocate resources between the direct protection of a population, and protection of those responsible for critical services.}, keywords = {epidemiology, OPTIMIZATION, public health informatics}, isbn = {978-1-4503-0781-9}, doi = {10.1145/2110363.2110371}, url = {http://doi.acm.org/10.1145/2110363.2110371}, author = {Barrett,Chris and Beckman,Richard and Bisset,Keith and Chen,Jiangzhuo and DuBois,Thomas and Eubank,Stephen and Kumar,V. S. Anil and Lewis,Bryan and Marathe,Madhav V. and Srinivasan, Aravind and Stretz,Paula E.} } @article {19255, title = {Preparation and probing of coherent vibrational wave packets in the ground electronic state of HD^{+}}, journal = {Physical Review A}, volume = {85}, year = {2012}, month = {2012}, abstract = {We have investigated the formation of coherent vibrational wave packets in the ground electronic state of HD+ on exposure to intense ultrashort laser pulses of wavelength 1060 nm. The effects of the duration and field strength of the pulse on the final composition of the residual bound nuclear wave packet generated by such impulsive excitations have been studied. The resulting wave packet is allowed to evolve freely on the potential surface for some time, after which a weak pulse of sufficiently large duration is used for probing its composition. This pulse can cause only single-photon dissociation. The simulations have been performed with different probe wavelengths for accessing information about different portions of the wave packet in the vibrational quantum number space. Our aim was to investigate the extent to which information obtained from the kinetic-energy spectra of the photofragments induced by the probe pulse can be correlated to the structure of the wave packet. Simple time-dependent perturbation calculations have also been performed for obtaining the relative strengths of photofragment signals arising from different vibrational levels due to wave-packet dissociation. A comparison with our numerical results indicates that though the general features of the photofragment kinetic-energy spectra from a wave packet are consistent with the perturbation theory results in the intensity regime studied, dynamical evolution during a long pulse can modify the relative heights of the kinetic-energy peaks through nonperturbative interactions in some cases.}, url = {http://link.aps.org/doi/10.1103/PhysRevA.85.033424}, author = {Bhattacharya, Rangana and Chatterjee, Souvik and Bhattacharyya, Shuvra S.} } @article {19668, title = {Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS}, journal = {Molecular Systems Biology}, volume = {8}, year = {2012}, month = {2012/01/01/}, abstract = {Understanding the genetic basis of gene regulatory variation is a key goal of evolutionary and medical genetics. Regulatory variation can act in an allele-specific manner (cis-acting) or it can affect both alleles of a gene (trans-acting). Differential allele-specific expression (ASE), in which the expression of one allele differs from another in a diploid, implies the presence of cis-acting regulatory variation. While microarrays and high-throughput sequencing have enabled genome-wide measurements of transcriptional ASE, methods for measurement of protein ASE (pASE) have lagged far behind. We describe a flexible, accurate, and scalable strategy for measurement of pASE by liquid chromatography-coupled mass spectrometry (LC-MS). We apply this approach to a hybrid between the yeast species Saccharomyces cerevisiae and Saccharomyces bayanus. Our results provide the first analysis of the relative contribution of cis-acting and trans-acting regulatory differences to protein expression divergence between yeast species.Synopsis A novel strategy for the quantitative measurement of allele-specific protein expression is used to infer the contributions of cis- and trans-acting factors influencing the divergence of protein levels between yeast species. Rigorous experimental controls and analyses confirm the accuracy of the new strategy for the quantitative measurement of allele-specific protein expression by high-throughput mass spectrometry.Analysis of allele-specific protein expression in an interspecies yeast hybrid and protein expression differences between species reveals that both cis-effects and trans-effects contribute to protein expression divergence between two yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus. }, keywords = {allele specific, divergence, mass spectrometry, protein expression, proteomics}, url = {http://msb.embopress.org/content/8/1/602}, author = {Zia Khan and Bloom, Joshua S. and Amini, Sasan and Singh, Mona and Perlman, David H. and Caudy, Amy A. and Kruglyak, Leonid} } @article {19458, title = {Refactoring Network Infrastructure to Improve Manageability: A Case Study of Home Networking}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {42}, year = {2012}, month = {2012/06//}, pages = {54 - 61}, abstract = {Managing a home network is challenging because the underlying infrastructure is so complex. Existing interfaces either hide or expose the network{\textquoteright}s underlying complexity, but in both cases, the information that is shown does not necessarily allow a user to complete desired tasks. Recent advances in software defined networking, however, permit a redesign of the underlying network and protocols, potentially allowing designers to move complexity further from the user and, in some cases, eliminating it entirely. In this paper, we explore whether the choices of what to make visible to the user in the design of today{\textquoteright}s home network infrastructure, performance, and policies make sense. We also examine whether new capabilities for refactoring the network infrastructure - changing the underlying system without compromising existing functionality - should cause us to revisit some of these choices. Our work represents a case study of how co-designing an interface and its underlying infrastructure could ultimately improve interfaces for that infrastructure.}, keywords = {home networking, management, Monitoring, software defined networking}, isbn = {0146-4833}, url = {http://doi.acm.org/10.1145/2317307.2317318}, author = {Marshini Chetty and Feamster, Nick} } @article {20385, title = {Role of GbpA protein, an important virulence-related colonization factor, for Vibrio cholerae{\textquoteright}s survival in the aquatic environment}, journal = {Environmental Microbiology Reports}, year = {2012}, month = {Jan-08-2012}, pages = {439 - 445}, abstract = {Vibrio cholerae N-acetyl glucosamine-binding protein A (GbpA) is a chitin binding protein and a virulence factor involved in the colonization of human intestine. We investigated the distribution and genetic variations of gbpA in 488 V. cholerae strains of environmental and clinical origin, belonging to different serogroups and biotypes. We found that the gene is consistently present and highly conserved including an environmental V. cholerae-related strain of ancestral origin. The gene was also consistently expressed in a number of representative V. cholerae strains cultured in laboratory aquatic microcosms under conditions simulating those found in temperate marine environments. Functional analysis carried out on V. cholerae O1 El Tor N16961 showed that GbpA is not involved in adhesion to inorganic surfaces but promotes interaction with environmental biotic substrates (plankton and bivalve hepatopancreas cells) representing known marine reservoir or host for the bacterium. It is suggested that the ability of GbpA to colonize human intestinal cells most probably originated from its primary function in the aquatic environment.}, doi = {10.1111/j.1758-2229.2012.00356.x}, url = {http://doi.wiley.com/10.1111/j.1758-2229.2012.00356.x}, author = {Stauder, Monica and Huq, Anwar and Pezzati, Elisabetta and Grim, Christopher J. and Ramoino, Paola and Pane, Luigi and Rita R Colwell and Pruzzo, Carla and Vezzulli, Luigi} } @article {12855, title = {Role of Shrimp Chitin in the Ecology of Toxigenic Vibrio cholerae and Cholera Transmission}, journal = {Frontiers in Microbiology}, volume = {2:260}, year = {2012}, month = {01/2012}, abstract = {Seasonal plankton blooms correlate with occurrence of cholera in Bangladesh, although the mechanism of how dormant Vibrio cholerae, enduring interepidemic period in biofilms and plankton, initiates seasonal cholera is not fully understood. In this study, laboratory microcosms prepared with estuarine Mathbaria water (MW) samples supported active growth of toxigenic V. cholerae O1 up to 7 weeks as opposed to 6 months when microcosms were supplemented with dehydrated shrimp chitin chips (CC) as the single source of nutrient. Bacterial counting and detection of wbe and ctxA genes were done employing culture, direct fluorescent antibody (DFA) assay, and multiplex-polymerase chain reaction methods. In MW microcosm, the aqueous phase became clear as the non-culturable cells settled, whereas the aqueous phase of the MW{\textendash}CC microcosm became turbid from bacterial growth stimulated by chitin. Bacterial chitin degradation and biofilm formation proceeded from an initial steady state to a gradually declining bacterial culturable count. V. cholerae within the microenvironments of chitin and chitin-associated biofilms remained metabolically active even in a high acidic environment without losing either viability or virulence. It is concluded that the abundance of chitin that occurs during blooms plays an important role in the aquatic life cycle of V. cholerae and, ultimately, in the seasonal transmission of cholera.}, isbn = {1664-302X}, doi = {10.3389/fmicb.2011.00260}, author = {Nahar,Shamsun and Sultana,Marzia and Naser,M. Niamul and Nair,Gopinath B. and Watanabe,Haruo and Ohnishi,Makoto and Yamamoto,Shouji and Endtz,Hubert and Cravioto,Alejandro and Sack,R. Bradley and Hasan,Nur A. and Sadique,Abdus and Huq,Anwar and Rita R Colwell and Alam,Munirul} } @article {15182, title = {Secure multi-party computation of boolean circuits with applications to privacy in on-line marketplaces}, journal = {Topics in Cryptology{\textendash}CT-RSA 2012}, year = {2012}, month = {2012///}, pages = {416 - 432}, abstract = {Protocols for generic secure multi-party computation (MPC) generally come in two forms: they either represent the function being computed as a boolean circuit, or as an arithmetic circuit over a large field. Either type of protocol can be used for any function, but the choice of which protocol to use can have a significant impact on efficiency. The magnitude of the effect, however, has never been quantified.With this in mind, we implement the MPC protocol of Goldreich, Micali, and Wigderson [13], which uses a boolean representation and is secure against a semi-honest adversary corrupting any number of parties. We then consider applications of secure MPC in on-line marketplaces, where customers select resources advertised by providers and it is desired to ensure privacy to the extent possible. Problems here are more naturally formulated in terms of boolean circuits, and we study the performance of our MPC implementation relative to existing ones that use an arithmetic-circuit representation. Our protocol easily handles tens of customers/providers and thousands of resources, and outperforms existing implementations including FairplayMP [3], VIFF [11], and SEPIA [7]. }, doi = {10.1007/978-3-642-27954-6_26}, author = {Choi,S. and Hwang,K.W. and Katz, Jonathan and Malkin,T. and Rubenstein,D.} } @inbook {19644, title = {Securing Circuits against Constant-Rate Tampering}, booktitle = {Advances in Cryptology {\textendash} CRYPTO 2012}, series = {Lecture Notes in Computer Science}, year = {2012}, month = {2012/01/01/}, pages = {533 - 551}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We present a compiler that converts any circuit into one that remains secure even if a constant fraction of its wires are tampered with. Following the seminal work of Ishai et. al. (Eurocrypt 2006), we consider adversaries who may choose an arbitrary set of wires to corrupt, and may set each such wire to 0 or to 1, or may toggle with the wire. We prove that such adversaries, who continuously tamper with the circuit, can learn at most logarithmically many bits of secret information (in addition to black-box access to the circuit). Our results are information theoretic.}, keywords = {circuit compiler, Computer Communication Networks, computers and society, Data Encryption, Discrete Mathematics in Computer Science, Management of Computing and Information Systems, PCP of proximity, side-channel attacks, Systems and Data Security, tampering}, isbn = {978-3-642-32008-8, 978-3-642-32009-5}, url = {http://link.springer.com/chapter/10.1007/978-3-642-32009-5_31}, author = {Dana Dachman-Soled and Kalai, Yael Tauman}, editor = {Safavi-Naini, Reihaneh and Canetti, Ran} } @conference {19314, title = {Sharpness Estimation for Document and Scene Images}, booktitle = {International Conference on Pattern Recognition (ICPR 2012)}, year = {2012}, pages = {3292-3295}, abstract = {Images of document pages have different characteristics than images of natural scenes, and so the sharpness measures developed for natural scene images do not necessarily extend to document images primarily composed of text. We present an efficient and simple method for effectively estimating the sharpness/ blurriness of document images that also performs well on natural scenes. Our method can be used to predict the sharpness in scenarios where images are blurred due to camera-motion (or hand-shake), defocus, or inherent properties of the imaging system. The proposed method outperforms the perceptually-based, no-reference sharpness work of [1] and [4], which was shown to perform better than 14 other no-reference sharpness measures on the LIVE dataset.}, author = {Kumar,Jayant and Chen, Francine and David Doermann} } @article {19132, title = {Structure, function and diversity of the healthy human microbiome}, journal = {Nature}, volume = {486}, year = {2012}, month = {2012}, pages = {207 - 214}, abstract = {Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat{\textquoteright}s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81{\textendash}99\% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.}, author = {Huttenhower, C. and Gevers, D. and Knight,R. and Abubucker, S. and Badger, J.H. and Chinwalla, A.T. and Creasy, H.H. and Earl, A.M. and Fitzgerald, M.G. and Fulton, R.S. and others} } @conference {19374, title = {Sub-cellular feature detection and automated extraction of collocalized actin and myosin regions}, booktitle = {the 2nd ACM SIGHIT symposiumProceedings of the 2nd ACM SIGHIT symposium on International health informatics - IHI {\textquoteright}12}, year = {2012}, pages = {399}, publisher = {ACM Press}, organization = {ACM Press}, address = {Miami, Florida, USANew York, New York, USA}, isbn = {9781450307819}, doi = {10.1145/211036310.1145/2110363.2110409}, author = {Martineau, Justin and Mokashi,Ronil and Chapman, David and Grasso, Michael and Brady,Mary and Yesha,Yelena and Yesha,Yaacov and Cardone, Antonio and Dima, Alden} } @article {19220, title = {Systems and Methods for Energy Harvesting in a Contained Fluid Circuit}, year = {2012}, month = {2012}, publisher = {UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION, CAMPBELL, Tim, LARSON, Eric, COHN, Gabriel, ALCAIDE, Ramses, FROEHLICH, Jon, PATEL, Shwetak}, abstract = {Systems and methods for harvesting energy from a closed fluid circuit, such as a water pipe system in a building. An energy harvester can be installed at a point in a water circuit and can generate energy from pressure differentials caused when a valve is opened or closed at any other point in the water circuit that is in fluid communication with the energy harvester. The energy can be used to power, for example, a sensor and/or a transmitter., L{\textquoteright}invention concerne des syst{\`e}mes et des proc{\'e}d{\'e}s de collecte de l{\textquoteright}{\'e}nergie qui provient d{\textquoteright}un circuit de fluide ferm{\'e}, comme un syst{\`e}me de conduites d{\textquoteright}eau dans un immeuble. Un collecteur d{\textquoteright}{\'e}nergie peut {\^e}tre install{\'e} {\`a} un certain point au sein d{\textquoteright}un circuit d{\textquoteright}eau et peut g{\'e}n{\'e}rer de l{\textquoteright}{\'e}nergie {\`a} partir des diff{\'e}rentiels de pression provoqu{\'e}s lorsqu{\textquoteright}une soupape est ouverte ou ferm{\'e}e {\`a} n{\textquoteright}importe quel autre point au sein du circuit d{\textquoteright}eau qui est en communication fluidique avec le collecteur d{\textquoteright}{\'e}nergie. L{\textquoteright}{\'e}nergie peut {\^e}tre utilis{\'e}e pour alimenter, par exemple, un capteur et/ou un {\'e}metteur.}, keywords = {Systems and Methods for Energy Harvesting in a Contained Fluid Circuit}, isbn = {WO/2012/021551}, url = {http://patentscope.wipo.int/search/en/WO2012021551}, author = {Campbell,Tim and Larson,Eric and Cohn, Gabriel and Alcaide,Ramses and Jon Froehlich and Patel,Shwetak} } @article {12858, title = {Temporal and Spatial Variability in the Distribution of Vibrio vulnificus in the Chesapeake Bay: A Hindcast Study}, journal = {EcoHealth}, year = {2012}, month = {2012///}, pages = {1 - 12}, abstract = {Vibrio vulnificus, an estuarine bacterium, is the causative agent of seafood-related gastroenteritis, primary septicemia, and wound infections worldwide. It occurs as part of the normal microflora of coastal marine environments and can be isolated from water, sediment, and oysters. Hindcast prediction was undertaken to determine spatial and temporal variability in the likelihood of occurrence of V. vulnificus in surface waters of the Chesapeake Bay. Hindcast predictions were achieved by forcing a multivariate habitat suitability model with simulated sea surface temperature and salinity in the Bay for the period between 1991 and 2005 and the potential hotspots of occurrence of V. vulnificus in the Chesapeake Bay were identified. The likelihood of occurrence of V. vulnificus during high and low rainfall years was analyzed. From results of the study, it is concluded that hindcast prediction yields an improved understanding of environmental conditions associated with occurrence of V. vulnificus in the Chesapeake Bay.}, doi = {10.1007/s10393-011-0736-4}, author = {Banakar,V. and Constantin de Magny,G. and Jacobs,J. and Murtugudde,R. and Huq,A. and J. Wood,R. and Rita R Colwell} } @conference {16031, title = {Towards event sequence representation, reasoning and visualization for EHR data}, booktitle = {Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium}, series = {IHI {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {801 - 806}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Efficient analysis of event sequences and the ability to answer time-related, clinically important questions can accelerate clinical research in several areas such as causality assessments, decision support systems, and retrospective studies. The Clinical Narrative Temporal Reasoning Ontology (CNTRO)-based system is designed for semantically representing, annotating, and inferring temporal relations and constraints for clinical events in Electronic Health Records (EHR) represented in both structured and unstructured ways. The LifeFlow system is designed to support an interactive exploration of event sequences using visualization techniques. The combination of the two systems will provide a comprehensive environment for users to visualize inferred temporal relationships from EHR data. This paper discusses our preliminary efforts on connecting the two systems and the benefits we envision from such an environment.}, keywords = {ehr, semantic web, temporal relation reasoning, time trend visualization}, isbn = {978-1-4503-0781-9}, doi = {10.1145/2110363.2110461}, url = {http://doi.acm.org/10.1145/2110363.2110461}, author = {Tao,Cui and Wongsuphasawat,Krist and Clark,Kimberly and Plaisant, Catherine and Shneiderman, Ben and Chute,Christopher G.} } @conference {19465, title = {You{\textquoteright}Re Capped: Understanding the Effects of Bandwidth Caps on Broadband Use in the Home}, booktitle = {SIGCHI {\textquoteright}12}, series = {CHI {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {3021 - 3030}, publisher = {ACM}, organization = {ACM}, abstract = {Bandwidth caps, a limit on the amount of data users can upload and download in a month, are common globally for both home and mobile Internet access. With caps, each bit of data consumed comes at a cost against a monthly quota or a running tab. Yet, relatively little work has considered the implications of this usage-based pricing model on the user experience. In this paper, we present results from a qualitative study of households living with bandwidth caps. Our findings suggest home users grapple with three uncertainties regarding their bandwidth usage: invisible balances, mysterious processes, and multiple users. We discuss how these uncertainties impact their usage and describe the potential for better tools to help monitor and manage data caps. We conclude that as a community we need to cater for users under Internet cost constraints.}, keywords = {Bandwidth, bandwidth cap, data cap, Internet, metered use, pricing, usage-based billing, usage-based pricing}, isbn = {978-1-4503-1015-4}, url = {http://doi.acm.org/10.1145/2207676.2208714}, author = {Marshini Chetty and Banks, Richard and Brush, A.J. and Donner, Jonathan and Grinter, Rebecca} } @article {19650, title = {Accurate proteome-wide protein quantification from high-resolution 15N mass spectra}, journal = {Genome Biology}, volume = {12}, year = {2011}, month = {2011/12/19/}, abstract = {In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of 15N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach. We have addressed this challenge by introducing a new computational methodology for analyzing 15N spectra in which quantification is integrated with identification. Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods.PMID: 22182234 }, isbn = {1465-6906}, url = {http://genomebiology.com/2011/12/12/R122/abstract}, author = {Zia Khan and Amini, Sasan and Bloom, Joshua S. and Ruse, Cristian and Caudy, Amy A. and Kruglyak, Leonid and Singh, Mona and Perlman, David H. and Tavazoie, Saeed} } @conference {14431, title = {Active inference for retrieval in camera networks}, booktitle = {Person-Oriented Vision (POV), 2011 IEEE Workshop on}, year = {2011}, month = {2011/01//}, pages = {13 - 20}, abstract = {We address the problem of searching camera network videos to retrieve frames containing specified individuals. We show the benefit of utilizing a learned probabilistic model that captures dependencies among the cameras. In addition, we develop an active inference framework that can request human input at inference time, directing human attention to the portions of the videos whose correct annotation would provide the biggest performance improvements. Our primary contribution is to show that by mapping video frames in a camera network onto a graphical model, we can apply collective classification and active inference algorithms to significantly increase the performance of the retrieval system, while minimizing the number of human annotations required.}, keywords = {active, annotation;probabilistic, frame;cameras;inference, inference;camera, mechanisms;probability;search, model;human, model;retrieval, network;graphical, problem;video, problems;video, processing;, retrieval;video, signal, system;searching}, doi = {10.1109/POV.2011.5712363}, author = {Daozheng Chen and Bilgic,M. and Getoor, Lise and Jacobs, David W. and Mihalkova,L. and Tom Yeh} } @conference {18330, title = {Active inference for retrieval in camera networks}, booktitle = {Person-Oriented Vision (POV), 2011 IEEE Workshop on}, year = {2011}, month = {2011/01//}, pages = {13 - 20}, publisher = {IEEE}, organization = {IEEE}, abstract = {We address the problem of searching camera network videos to retrieve frames containing specified individuals. We show the benefit of utilizing a learned probabilistic model that captures dependencies among the cameras. In addition, we develop an active inference framework that can request human input at inference time, directing human attention to the portions of the videos whose correct annotation would provide the biggest performance improvements. Our primary contribution is to show that by mapping video frames in a camera network onto a graphical model, we can apply collective classification and active inference algorithms to significantly increase the performance of the retrieval system, while minimizing the number of human annotations required.}, isbn = {978-1-61284-036-9}, doi = {10.1109/POV.2011.5712363}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5712363\&tag=1}, author = {Daozheng Chen and Bilgic,Mustafa and Getoor, Lise and Jacobs, David W. and Mihalkova,Lilyana and Tom Yeh} } @article {12461, title = {Advances in Video-Based Biometrics}, journal = {Advances in Imaging and Electron Physics}, volume = {83}, year = {2011}, month = {2011///}, pages = {183 - 203}, author = {Chellapa, Rama and Turaga,P.} } @conference {19269, title = {Applying graphics processor acceleration in a software defined radio prototyping environment}, booktitle = {2011 22nd IEEE International Symposium on Rapid System Prototyping (RSP)}, year = {2011}, month = {2011}, pages = {67 - 73}, abstract = {With higher bandwidth requirements and more complex protocols, software defined radio (SDR) has ever growing computational demands. SDR applications have different levels of parallelism that can be exploited on multicore platforms, but design and programming difficulties have inhibited the adoption of specialized multicore platforms like graphics processors (GPUs). In this work we propose a new design flow that augments a popular existing SDR development environment (GNU Radio), with a dataflow foundation and a stand-alone GPU accelerated library. The approach gives an SDR developer the ability to prototype a GPU accelerated application and explore its design space fast and effectively. We demonstrate this design flow on a standard SDR benchmark and show that deciding how to utilize a GPU can be non-trivial for even relatively simple applications.}, keywords = {Acceleration, coprocessors, dataflow foundation, GNU radio, Graphics processing unit, graphics processor acceleration, Kernel, Libraries, multicore platforms, Multicore processing, PARALLEL PROCESSING, Pipelines, Protocols, software defined radio prototyping environment, software radio, stand-alone GPU accelerated library}, author = {Plishker,W. and Zaki, G.F. and Bhattacharyya, Shuvra S. and Clancy, C. and Kuykendall, J.} } @article {12868, title = {Aquatic Realm and Cholera}, journal = {Epidemiological and Molecular Aspects on Cholera}, year = {2011}, month = {2011///}, pages = {311 - 339}, abstract = {Cholera is an ancient disease that can be severe and life threatening. It occurs predominantly in areas of the world where populations lack safe drinking water. Epidemics of cholera are linked with malnutrition, poor sanitation, and conditions resulting from natural disasters such as severe flooding. According to a report published by WHO in 2000 [1], cholera remains a major public health problem and is becoming increasingly important since the number of countries in which cholera is endemic continues to increase. Unfortunately, outbreaks of the disease continue into the twenty-first century with ominous portent in the wake of global climate change [1]. Yet cholera is a preventable disease if people have access to safe drinking water and are properly educated how to protect themselves from the risk of infection with vibrios. Cholera also is an easily treatable disease. Oral rehydration therapy, a solution containing glucose and appropriate salts, has proven to be effective for treatment of most cholera victims [2]. Nevertheless, each year, tens of thousands of people are victims of the disease, bringing this {\textquotedblleft}curse of humankind{\textquotedblright} to modern civilization. Present understanding of cholera is based on studies conducted over the past three decades and significant new information has been gained concerning environmental factors associated with this disease, especially how to detect the bacterium and where it lives in the natural environment, outside the human gut, and what triggers the annual outbreaks that occur with remarkable regularity. Environmental research on Vibrio cholerae and cholera has provided insights for prediction and prevention of the disease it causes, while the race for effective vaccines against cholera continues.}, doi = {10.1007/978-1-60327-265-0_18}, author = {Huq,A. and Grim,C. J. and Rita R Colwell} } @article {12114, title = {An assessment of systems and software engineering scholars and institutions (2003{\textendash}2007 and 2004{\textendash}2008)}, journal = {Journal of Systems and Software}, volume = {84}, year = {2011}, month = {2011/01//}, pages = {162 - 168}, abstract = {An ongoing, annual survey of publications in systems and software engineering identifies the top 15 scholars and institutions in the field over a 5-year period. Each ranking is based on the weighted scores of the number of papers published in TSE, TOSEM, JSS, SPE, EMSE, IST, and Software of the corresponding period. This report summarizes the results for 2003{\textendash}2007 and 2004{\textendash}2008. The top-ranked institution is Korea Advanced Institute of Science and Technology, Korea for 2003{\textendash}2007, and Simula Research Laboratory, Norway for 2004{\textendash}2008, while Magne J{\o}rgensen is the top-ranked scholar for both periods.}, keywords = {Research publications, Systems and software engineering, Top institutions, Top scholars}, isbn = {0164-1212}, doi = {10.1016/j.jss.2010.09.036}, url = {http://www.sciencedirect.com/science/article/pii/S0164121210002682}, author = {Wong,W. Eric and Tse,T.H. and Glass,Robert L. and Basili, Victor R. and Chen,T.Y.} } @conference {18333, title = {Associating the visual representation of user interfaces with their internal structures and metadata}, booktitle = {Proceedings of the 24th annual ACM symposium on User interface software and technology}, series = {UIST {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {245 - 256}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Pixel-based methods are emerging as a new and promising way to develop new interaction techniques on top of existing user interfaces. However, in order to maintain platform independence, other available low-level information about GUI widgets, such as accessibility metadata, was neglected intentionally. In this paper, we present a hybrid framework, PAX, which associates the visual representation of user interfaces (i.e. the pixels) and their internal hierarchical metadata (i.e. the content, role, and value). We identify challenges to building such a framework. We also develop and evaluate two new algorithms for detecting text at arbitrary places on the screen, and for segmenting a text image into individual word blobs. Finally, we validate our framework in implementations of three applications. We enhance an existing pixel-based system, Sikuli Script, and preserve the readability of its script code at the same time. Further, we create two novel applications, Screen Search and Screen Copy, to demonstrate how PAX can be applied to development of desktop-level interactive systems.}, keywords = {accessibility api, Graphical user interfaces, Pixel, text detection, text segmentation}, isbn = {978-1-4503-0716-1}, doi = {10.1145/2047196.2047228}, url = {http://doi.acm.org/10.1145/2047196.2047228}, author = {Chang,Tsung-Hsiang and Tom Yeh and Miller,Rob} } @conference {13069, title = {AVSS 2011 demo session: A large-scale benchmark dataset for event recognition in surveillance video}, booktitle = {Advanced Video and Signal-Based Surveillance (AVSS), 2011 8th IEEE International Conference on}, year = {2011}, month = {2011/09/30/2}, pages = {527 - 528}, abstract = {We introduce to the surveillance community the VIRAT Video Dataset[1], which is a new large-scale surveillance video dataset designed to assess the performance of event recognition algorithms in realistic scenes1.}, doi = {10.1109/AVSS.2011.6027400}, author = {Oh,Sangmin and Hoogs,Anthony and Perera,Amitha and Cuntoor,Naresh and Chen,Chia-Chih and Lee,Jong Taek and Mukherjee,Saurajit and Aggarwal, JK and Lee,Hyungtae and Davis, Larry S. and Swears,Eran and Wang,Xiaoyang and Ji,Qiang and Reddy,Kishore and Shah,Mubarak and Vondrick,Carl and Pirsiavash,Hamed and Ramanan,Deva and Yuen,Jenny and Torralba,Antonio and Song,Bi and Fong,Anesco and Roy-Chowdhury,Amit and Desai,Mita} } @conference {12435, title = {Blurring-invariant Riemannian metrics for comparing signals and images}, booktitle = {2011 IEEE International Conference on Computer Vision (ICCV)}, year = {2011}, month = {2011/11/06/13}, pages = {1770 - 1775}, publisher = {IEEE}, organization = {IEEE}, abstract = {We propose a novel Riemannian framework for comparing signals and images in a manner that is invariant to their levels of blur. This framework uses a log-Fourier representation of signals/images in which the set of all possible Gaussian blurs of a signal, i.e. its orbits under semigroup action of Gaussian blur functions, is a straight line. Using a set of Riemannian metrics under which the group actions are by isometries, the orbits are compared via distances between orbits. We demonstrate this framework using a number of experimental results involving 1D signals and 2D images.}, keywords = {blurring-invariant Riemannian metrics, Estimation, Fourier transforms, Gaussian blur function, Gaussian processes, image representation, log-Fourier representation, measurement, Orbits, Polynomials, signal representation, Space vehicles, vectors}, isbn = {978-1-4577-1101-5}, doi = {10.1109/ICCV.2011.6126442}, author = {Zhengwu Zhang and Klassen, E. and Srivastava, A. and Turaga,P. and Chellapa, Rama} } @conference {17982, title = {Brief announcement: better speedups for parallel max-flow}, booktitle = {Proceedings of the 23rd ACM symposium on Parallelism in algorithms and architectures}, year = {2011}, month = {2011///}, pages = {131 - 134}, abstract = {We present a parallel solution to the Maximum-Flow (Max-Flow) problem, suitable for a modern many-core architec- ture. We show that by starting from a PRAM algorithm, following an established {\textquotedblleft}programmer{\textquoteright}s workflow{\textquotedblright} and tar- geting XMT, a PRAM-inspired many-core architecture, we achieve significantly higher speed-ups than previous approaches. Comparison with the fastest known serial max-flow imple- mentation on a modern CPU demonstrates for the first time potential for orders-of-magnitude performance improvement for Max-Flow. Using XMT, the PRAM Max-Flow algorithm is also much easier to program than for other parallel plat- forms, contributing a powerful example toward dual valida- tion of both PRAM algorithmics and XMT. }, author = {Caragea,G.C. and Vishkin, Uzi} } @article {18510, title = {Broadband internet performance: A view from the gateway}, journal = {SIGCOMM-Computer Communication Review}, volume = {41}, year = {2011}, month = {2011///}, pages = {134 - 134}, abstract = {We present the first study of network access link performance mea-sured directly from home gateway devices. Policymakers, ISPs, and users are increasingly interested in studying the performance of Internet access links. Because of many confounding factors in a home network or on end hosts, however, thoroughly understanding access network performance requires deploying measurement in- frastructure in users{\textquoteright} homes as gateway devices. In conjunction with the Federal Communication Commission{\textquoteright}s study of broad- band Internet access in the United States, we study the throughput and latency of network access links using longitudinal measure- ments from nearly 4,000 gateway devices across 8 ISPs from a de- ployment of over 4,200 devices. We study the performance users achieve and how various factors ranging from the user{\textquoteright}s choice of modem to the ISP{\textquoteright}s traffic shaping policies can affect performance. Our study yields many important findings about the characteristics of existing access networks. Our findings also provide insights into the ways that access network performance should be measured and presented to users, which can help inform ongoing broader efforts to benchmark the performance of access networks. }, author = {Sundaresan,S. and de Donato,W. and Feamster, Nick and Teixeira,R. and Crawford,S. and Pescap{\`e},A.} } @article {12984, title = {Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?}, journal = {Systematic BiologySyst Biol}, volume = {60}, year = {2011}, month = {2011/12/01/}, pages = {782 - 796}, abstract = {This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia ( > 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45\% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78{\textendash}85\% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A {\textquotedblleft}more-genes-only{\textquotedblright} data set (41 taxa{\texttimes}26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.}, keywords = {Ditrysia, gene sampling, Hexapoda, Lepidoptera, missing data, molecular phylogenetics, nuclear genes, taxon sampling}, isbn = {1063-5157, 1076-836X}, doi = {10.1093/sysbio/syr079}, url = {http://sysbio.oxfordjournals.org/content/60/6/782}, author = {Cho,Soowon and Zwick,Andreas and Regier,Jerome C and Mitter,Charles and Cummings, Michael P. and Yao,Jianxiu and Du,Zaile and Zhao,Hong and Kawahara,Akito Y and Weller,Susan and Davis,Donald R and Baixeras,Joaquin and Brown,John W and Parr,Cynthia} } @article {17571, title = {Capacity of wireless networks under SINR interference constraints}, journal = {Wireless Networks}, volume = {17}, year = {2011}, month = {2011///}, pages = {1605 - 1624}, abstract = {A fundamental problem in wireless networks is to estimate their throughput capacity{\textemdash}given a set of wireless nodes and a set of connections, what is the maximum rate at which data can be sent on these connections. Most of the research in this direction has focused either on random distributions of points, or has assumed simple graph-based models for wireless interference. In this paper, we study the capacity estimation problem using a realistic Signal to Interference Plus Noise Ratio (SINR) model for interference, on arbitrary wireless networks without any assumptions on node distributions. The problem becomes much more challenging for this setting, because of the non-locality of the SINR model. Recent work by Moscibroda et al. (IEEE INFOCOM 2006, ACM MobiHoc 2006) has shown that the throughput achieved by using SINR models can differ significantly from that obtained by using graph-based models. In this work, we develop polynomial time algorithms to provably approximate the throughput capacity of wireless network under the SINR model.}, isbn = {1022-0038}, url = {http://dx.doi.org/10.1007/s11276-011-0367-2}, author = {Chafekar,Deepti and Anil Kumar,V. and Marathe,Madhav and Parthasarathy,Srinivasan and Srinivasan, Aravind} } @article {19369, title = {Cell cycle dependent TN-C promoter activity determined by live cell imaging.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {79}, year = {2011}, month = {2011 Mar}, pages = {192-202}, abstract = {The extracellular matrix protein tenascin-C plays a critical role in development, wound healing, and cancer progression, but how it is controlled and how it exerts its physiological responses remain unclear. By quantifying the behavior of live cells with phase contrast and fluorescence microscopy, the dynamic regulation of TN-C promoter activity is examined. We employ an NIH 3T3 cell line stably transfected with the TN-C promoter ligated to the gene sequence for destabilized green fluorescent protein (GFP). Fully automated image analysis routines, validated by comparison with data derived from manual segmentation and tracking of single cells, are used to quantify changes in the cellular GFP in hundreds of individual cells throughout their cell cycle during live cell imaging experiments lasting 62 h. We find that individual cells vary substantially in their expression patterns over the cell cycle, but that on average TN-C promoter activity increases during the last 40\% of the cell cycle. We also find that the increase in promoter activity is proportional to the activity earlier in the cell cycle. This work illustrates the application of live cell microscopy and automated image analysis of a promoter-driven GFP reporter cell line to identify subtle gene regulatory mechanisms that are difficult to uncover using population averaged measurements.}, keywords = {Animals, cell cycle, Gene Expression Regulation, Green Fluorescent Proteins, Image Processing, Computer-Assisted, Mice, Microscopy, Fluorescence, Microscopy, Phase-Contrast, NIH 3T3 Cells, Promoter Regions, Genetic, Tenascin}, issn = {1552-4930}, doi = {10.1002/cyto.a.21028}, author = {Halter, Michael and Sisan, Daniel R and Chalfoun, Joe and Stottrup, Benjamin L and Cardone, Antonio and Dima,Alden A. and Tona, Alessandro and Plant,Anne L. and Elliott, John T} } @conference {18667, title = {Characterizing Attackers and Attacks: An Empirical Study}, year = {2011}, month = {2011/12//}, pages = {174 - 183}, abstract = {This paper describes an empirical research study to characterize attackers and attacks against targets of opportunity. A honey net infrastructure was built and deployed over 167 days that leveraged three different honey pot configurations and a SSH-based authentication proxy to attract and follow attackers over several weeks. A total of 211 attack sessions were recorded and evidence was collected at each stage of the attack sequence: from discovery to intrusion and exploitation of rogue software. This study makes two important contributions: 1) we introduce a new approach to measure attacker skills, and 2) we leverage keystroke profile analysis to differentiate attackers beyond their IP address of origin.}, keywords = {attack sessions, attacker characterization, attacker skill measurement, honey net infrastructure, honey pot configurations, IP address, keystroke profile analysis, opportunity target, rogue software exploitation, security of data, SSH-based authentication proxy}, doi = {10.1109/PRDC.2011.29}, author = {Salles-Loustau,G. and Berthier,R. and Collange,E. and Sobesto,B. and Michel Cukier} } @article {12869, title = {Clonal transmission, dual peak, and off-season cholera in Bangladesh}, journal = {Infection Ecology \& Epidemiology}, volume = {1}, year = {2011}, month = {08/2011}, abstract = {Vibrio cholerae is an estuarine bacterium associated with a single peak of cholera (March{\textendash}May) in coastal villages of Bangladesh. For an unknown reason, however, cholera occurs in a unique dual peak (March{\textendash}May and September{\textendash}November) pattern in the city of Dhaka that is bordered by a heavily polluted freshwater river system and flood embankment. In August 2007, extreme flooding was accompanied by an unusually severe diarrhea outbreak in Dhaka that resulted in a record high illness. This study was aimed to understand the unusual outbreak and if it was related to the circulation of a new V. cholerae clone. Nineteen V. cholerae isolated during the peak of the 2007 outbreak were subjected to extensive phenotypic and molecular analyses, including multi-locus genetic screening by polymerase chain reaction (PCR), sequence-typing of the ctxB gene, and pulsed-field gel electrophoresis (PFGE). Factors associated with the unusual incidence of cholera were determined and analysis of the disease severity was done. Overall, microbiological and molecular data confirmed that the hypervirulent V. cholerae was O1 biotype El Tor (ET) that possessed cholera toxin (CT) of the classical biotype. The PFGE (NotI) and dendrogram clustering confirmed that the strains were clonal and related to the pre-2007 variant ET from Dhaka and Matlab and resembled one of two distinct clones of the variant ET confirmed to be present in the estuarine ecosystem of Bangladesh. Results of the analyses of both diarrheal case data for three consecutive years (2006{\textendash}2008) and regional hydroclimatology over three decades (1980{\textendash}2009) clearly indicate that the pattern of cholera occurring in Dhaka, and not seen at other endemic sites, was associated with flood waters transmitting the infectious clone circulating via the fecal-oral route during and between the dual seasonal cholera peaks in Dhaka. Circular river systems and flood embankment likely facilitate transmission of infectious V. cholerae throughout the year that leads to both sudden and off-season outbreaks in the densely populated urban ecosystem of Dhaka. Clonal recycling of hybrid El Tor with increasing virulence in a changing climate and in a region with a growing urban population represents a serious public health concern for Bangladesh.}, doi = {10.3402/iee.v1i0.7273}, author = {Alam,M. and Islam,A. and Bhuiyan,N. A. and Rahim,N. and Hossain,A. and Khan,G. Y. and Ahmed,D. and Watanabe,H. and Izumiya,H. and Faruque,A. S. G. and Rita R Colwell} } @article {19442, title = {Communicating with Caps: Managing Usage Caps in Home Networks}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {41}, year = {2011}, month = {2011/08//}, pages = {470 - 471}, abstract = {As Internet service providers increasingly implement and impose "usage caps", consumers need better ways to help them understand and control how devices in the home use up the available network resources or available capacity. Towards this goal, we will demonstrate a system that allows users to monitor and manage their usage caps. The system uses the BISMark firmware running on network gateways to collect usage statistics and report them to a logically centralized controller, which displays usage information. The controller allows users to specify policies about how different people, devices, and applications should consume the usage cap; it implements and enforces these policies via a secure OpenFlow control channel to each gateway device. The demonstration will show various use cases, such as limiting the usage of a particular application, visualizing usage statistics, and allowing users within a single household to "trade" caps with one another.}, keywords = {home network, openflow, usage cap}, isbn = {0146-4833}, url = {http://doi.acm.org/10.1145/2043164.2018526}, author = {Kim, Hyojoon and Sundaresan, Srikanth and Marshini Chetty and Feamster, Nick and Edwards, W. Keith} } @article {18557, title = {Communicating with caps: managing usage caps in home networks}, journal = {ACM SIGCOMM Computer Communication Review}, volume = {41}, year = {2011}, month = {2011/08//}, pages = {470 - 471}, abstract = {As Internet service providers increasingly implement and impose "usage caps", consumers need better ways to help them understand and control how devices in the home use up the available network resources or available capacity. Towards this goal, we will demonstrate a system that allows users to monitor and manage their usage caps. The system uses the BISMark firmware running on network gateways to collect usage statistics and report them to a logically centralized controller, which displays usage information. The controller allows users to specify policies about how different people, devices, and applications should consume the usage cap; it implements and enforces these policies via a secure OpenFlow control channel to each gateway device. The demonstration will show various use cases, such as limiting the usage of a particular application, visualizing usage statistics, and allowing users within a single household to "trade" caps with one another.}, keywords = {home network, openflow, usage cap}, isbn = {0146-4833}, doi = {10.1145/2043164.2018526}, url = {http://doi.acm.org/10.1145/2043164.2018526}, author = {Kim,Hyojoon and Sundaresan,Srikanth and Marshini Chetty and Feamster, Nick and Edwards,W. Keith} } @conference {12447, title = {Component-based restoration of speckled images}, booktitle = {2011 18th IEEE International Conference on Image Processing (ICIP)}, year = {2011}, month = {2011/09/11/14}, pages = {2797 - 2800}, publisher = {IEEE}, organization = {IEEE}, abstract = {Many coherent imaging modalities are often characterized by a multiplicative noise, known as speckle which often makes the interpretation of data difficult. In this paper, we present a speckle reduction algorithm based on separating the structure and texture components of SAR images. An iterative algorithm based on surrogate functionals is presented that solves the component optimization formulation. Experiments indicate this proposed method performs favorably compared to state-of-the-art speckle reduction methods.}, keywords = {coherent imaging modalities, component optimization formulation, component-based restoration, Dictionaries, image restoration, iterative algorithm, iterative methods, multiplicative noise, NOISE, optimisation, radar imaging, SAR images, Speckle, speckle reduction algorithm, speckled images, structure components, surrogate functionals, synthetic aperture radar, texture components, transforms, TV}, isbn = {978-1-4577-1304-0}, doi = {10.1109/ICIP.2011.6116252}, author = {Patel, Vishal M. and Easley,G. R and Chellapa, Rama} } @article {19647, title = {A computational statistics approach for estimating the spatial range of morphogen gradients}, journal = {Development}, volume = {138}, year = {2011}, month = {2011/11/15/}, pages = {4867 - 4874}, abstract = {A crucial issue in studies of morphogen gradients relates to their range: the distance over which they can act as direct regulators of cell signaling, gene expression and cell differentiation. To address this, we present a straightforward statistical framework that can be used in multiple developmental systems. We illustrate the developed approach by providing a point estimate and confidence interval for the spatial range of the graded distribution of nuclear Dorsal, a transcription factor that controls the dorsoventral pattern of the Drosophila embryo.}, keywords = {Computational Biology, Confidence interval, Dorsal gradient, Drosophila embryo, Morphogen gradient, Statistics}, isbn = {0950-1991, 1477-9129}, url = {http://dev.biologists.org/content/138/22/4867}, author = {Kanodia, Jitendra S. and Kim, Yoosik and Tomer, Raju and Zia Khan and Chung, Kwanghun and Storey, John D. and Lu, Hang and Keller, Philipp J. and Shvartsman, Stanislav Y.} } @conference {12986, title = {Computing the Tree of Life: Leveraging the Power of Desktop and Service Grids}, booktitle = {Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on}, year = {2011}, month = {2011/05//}, pages = {1896 - 1902}, abstract = {The trend in life sciences research, particularly in molecular evolutionary systematics, is toward larger data sets and ever-more detailed evolutionary models, which can generate substantial computational loads. Over the past several years we have developed a grid computing system aimed at providing researchers the computational power needed to complete such analyses in a timely manner. Our grid system, known as The Lattice Project, was the first to combine two models of grid computing - the service model, which mainly federates large institutional HPC resources, and the desktop model, which harnesses the power of PCs volunteered by the general public. Recently we have developed a "science portal" style web interface that makes it easier than ever for phylogenetic analyses to be completed using GARLI, a popular program that uses a maximum likelihood method to infer the evolutionary history of organisms on the basis of genetic sequence data. This paper describes our approach to scheduling thousands of GARLI jobs with diverse requirements to heterogeneous grid resources, which include volunteer computers running BOINC software. A key component of this system provides a priori GARLI runtime estimates using machine learning with random forests.}, keywords = {(artificial, (mathematics);user, analysis;science, BOINC, computation;grid, computational, computing, computing;information, computing;machine, data;grid, estimation;portals;trees, evolutionary, Grid, grids;service, handling;evolutionary, history;evolutionary, intelligence);maximum, interface;computational, interfaces;, jobs;HPC, learning;maximum, likelihood, load;Internet;data, method;molecular, model;genetic, model;substantial, portal;service, power;data, project;life, resource;lattice, resource;Web, sequence, services;learning, sets;evolutionary, software;GARLI, system;heterogeneous, systematics;phylogenetic, tree}, doi = {10.1109/IPDPS.2011.344}, author = {Bazinet,A. L and Cummings, Michael P.} } @conference {13081, title = {Creating contextual help for GUIs using screenshots}, booktitle = {Proceedings of the 24th annual ACM symposium on User interface software and technology}, series = {UIST {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {145 - 154}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Contextual help is effective for learning how to use GUIs by showing instructions and highlights on the actual interface rather than in a separate viewer. However, end-users and third-party tech support typically cannot create contextual help to assist other users because it requires programming skill and source code access. We present a creation tool for contextual help that allows users to apply common computer skills-taking screenshots and writing simple scripts. We perform pixel analysis on screenshots to make this tool applicable to a wide range of applications and platforms without source code access. We evaluated the tool{\textquoteright}s usability with three groups of participants: developers, in-structors, and tech support. We further validated the applicability of our tool with 60 real tasks supported by the tech support of a university campus.}, keywords = {contextual help, help, pixel analysis}, isbn = {978-1-4503-0716-1}, doi = {10.1145/2047196.2047214}, url = {http://doi.acm.org/10.1145/2047196.2047214}, author = {Tom Yeh and Chang,Tsung-Hsiang and Xie,Bo and Walsh,Greg and Watkins,Ivan and Wongsuphasawat,Krist and Huang,Man and Davis, Larry S. and Bederson, Benjamin B.} } @conference {13257, title = {A Decomposition-based Approach to Modeling and Understanding Arbitrary Shapes}, booktitle = {Eurographics Italian Chapter Conference 2011}, year = {2011}, month = {2011///}, pages = {53 - 60}, author = {Canino,D. and De Floriani, Leila} } @conference {19260, title = {Design methods for Wireless Sensor Network Building Energy Monitoring Systems}, booktitle = {2011 IEEE 36th Conference on Local Computer Networks (LCN)}, year = {2011}, month = {2011}, pages = {974 - 981}, abstract = {In this paper, we present a new energy analysis method for evaluating energy consumption of embedded sensor nodes at the application level and the network level. Then we apply the proposed energy analysis method to develop new energy management schemes in order to maximize lifetime for Wireless Sensor Network Building Energy Monitoring Systems (WSNBEMS). At the application level, we develop a new design approach that uses dataflow techniques to model the application-level interfacing behavior between the processor and sensors on an embedded sensor node. At the network level, we analyze the energy consumption of the IEEE 802.15.4 MAC functionality. Based on our techniques for modeling and energy analysis, we have implemented an optimized WSNBEMS for a real building, and validated our energy analysis techniques through measurements on this implementation. The performance of our implementation is also evaluated in terms of monitoring accuracy and energy consumption savings. We have demonstrated that by applying the proposed scheme, system lifetime can be improved significantly without affecting monitoring accuracy.}, keywords = {Analytical models, application-level interfacing behavior, building energy monitoring system, Buildings, dataflow technique, embedded sensor node, energy analysis method, Energy consumption, energy management systems, Energy resolution, IEEE 802.15.4 MAC functionality, Monitoring, OPTIMIZATION, wireless sensor network, Wireless sensor networks, WSNBEMS, Zigbee}, author = {Cho, Inkeun and Chung-Ching Shen and Potbhare, S. and Bhattacharyya, Shuvra S. and Goldsman,N.} } @article {15741, title = {Designing Optimal Spectral Filters for Inverse Problems}, journal = {SIAM Journal on Scientific Computing}, volume = {33}, year = {2011}, month = {2011///}, doi = {DOI: 10.1137/100809787}, author = {Chung,Julianne M. and Chung,Matthias and O{\textquoteright}Leary, Dianne P.} } @article {13289, title = {Dimension-independent simplification and refinement of Morse complexes}, journal = {Graphical Models}, volume = {73}, year = {2011}, month = {2011/09//}, pages = {261 - 285}, abstract = {Ascending and descending Morse complexes, determined by a scalar field f defined over a manifold M, induce a subdivision of M into regions associated with critical points of f, and compactly represent the topology of M. We define two simplification operators on Morse complexes, which work in arbitrary dimensions, and we define their inverse refinement operators. We describe how simplification and refinement operators affect Morse complexes on M, and we show that these operators form a complete set of atomic operators to create and update Morse complexes on M. Thus, any operator that modifies Morse complexes on M can be expressed as a suitable sequence of the atomic simplification and refinement operators we have defined. The simplification and refinement operators also provide a suitable basis for the construction of a multi-resolution representation of Morse complexes.}, keywords = {Morse complexes, Morse theory, Refinement, shape modeling, simplification, Topological representations}, isbn = {1524-0703}, doi = {10.1016/j.gmod.2011.05.001}, url = {http://www.sciencedirect.com/science/article/pii/S1524070311000154}, author = {{\v C}omi{\'c},Lidija and De Floriani, Leila} } @article {19656, title = {Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization}, journal = {Nature Medicine}, volume = {17}, year = {2011}, month = {2011/09//}, pages = {1101 - 1108}, abstract = {Although the role of miR-200s in regulating E-cadherin expression and epithelial-to-mesenchymal transition is well established, their influence on metastatic colonization remains controversial. Here we have used clinical and experimental models of breast cancer metastasis to discover a pro-metastatic role of miR-200s that goes beyond their regulation of E-cadherin and epithelial phenotype. Overexpression of miR-200s is associated with increased risk of metastasis in breast cancer and promotes metastatic colonization in mouse models, phenotypes that cannot be recapitulated by E-cadherin expression alone. Genomic and proteomic analyses revealed global shifts in gene expression upon miR-200 overexpression toward that of highly metastatic cells. miR-200s promote metastatic colonization partly through direct targeting of Sec23a, which mediates secretion of metastasis-suppressive proteins, including Igfbp4 and Tinagl1, as validated by functional and clinical correlation studies. Overall, these findings suggest a pleiotropic role of miR-200s in promoting metastatic colonization by influencing E-cadherin{\textendash}dependent epithelial traits and Sec23a-mediated tumor cell secretome.View full text }, isbn = {1078-8956}, url = {http://www.nature.com/nm/journal/v17/n9/abs/nm.2401.html}, author = {Korpal, Manav and Ell, Brian J. and Buffa, Francesca M. and Ibrahim, Toni and Blanco, Mario A. and Celi{\`a}-Terrassa, Toni and Mercatali, Laura and Zia Khan and Goodarzi, Hani and Hua, Yuling and Wei, Yong and Hu, Guohong and Garcia, Benjamin A. and Ragoussis, Jiannis and Amadori, Dino and Harris, Adrian L. and Kang, Yibin} } @article {14317, title = {Disaggregated End-Use Energy Sensing for the Smart Grid}, journal = {IEEE Pervasive Computing}, volume = {10}, year = {2011}, month = {2011/03//Jan}, pages = {28 - 39}, abstract = {This article surveys existing and emerging disaggregation techniques for energy-consumption data and highlights signal features that might be used to sense disaggregated data in an easily installed and cost-effective manner.}, keywords = {Calibration, disaggregated end-use energy sensing, Disaggregated energy sensing, disaggregation data techniques, Electricity, Energy consumption, Energy efficiency, energy-consumption data, Gas, Home appliances, Sensors, Smart grid, Smart grids, smart power grids, Sustainability, Water}, isbn = {1536-1268}, doi = {10.1109/MPRV.2010.74}, author = {Jon Froehlich and Larson,E. and Gupta,S. and Cohn,G. and Reynolds,M. and Patel,S.} } @inbook {12455, title = {Distributed Sensing and Processing for Multi-Camera Networks}, booktitle = {Distributed Video Sensor NetworksDistributed Video Sensor Networks}, year = {2011}, month = {2011///}, pages = {85 - 101}, publisher = {Springer London}, organization = {Springer London}, abstract = {Sensor networks with large numbers of cameras are becoming increasingly prevalent in a wide range of applications, including video conferencing, motion capture, surveillance, and clinical diagnostics. In this chapter, we identify some of the fundamental challenges in designing such systems: robust statistical inference, computationally efficiency, and opportunistic and parsimonious sensing. We show that the geometric constraints induced by the imaging process are extremely useful for identifying and designing optimal estimators for object detection and tracking tasks. We also derive pipelined and parallelized implementations of popular tools used for statistical inference in non-linear systems, of which multi-camera systems are examples. Finally, we highlight the use of the emerging theory of compressive sensing in reducing the amount of data sensed and communicated by a camera network.}, isbn = {978-0-85729-127-1}, url = {http://dx.doi.org/10.1007/978-0-85729-127-1_6}, author = {Sankaranarayanan,Aswin C. and Chellapa, Rama and Baraniuk,Richard G.}, editor = {Bhanu,Bir and Ravishankar,Chinya V. and Roy-Chowdhury,Amit K. and Aghajan,Hamid and Terzopoulos,Demetri} } @conference {19441, title = {A Dive into Online Community Properties}, booktitle = {CSCW {\textquoteright}11}, series = {CSCW {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {725 - 728}, publisher = {ACM}, organization = {ACM}, abstract = {As digital communities grow in size their feature sets also grow with them. Different users have different experiences with the same tools and communities. Enterprises and other organizations seeking to leverage these communities need a straightforward way to analyze and compare a variety of salient attributes of these communities. We describe a taxonomy and tool for crowd-sourcing user based evaluations of enterprise relevant attributes of digital communities and present the results of a small scale study on its usefulness and stability across multiple raters.}, keywords = {enterprise, Online communities, Taxonomy, Visualization}, isbn = {978-1-4503-0556-3}, url = {http://doi.acm.org/10.1145/1958824.1958955}, author = {Wagstrom, Patrick and Martino, Jacquelyn and von Kaenel, Juerg and Marshini Chetty and Thomas, John and Jones, Lauretta} } @conference {12437, title = {Domain adaptation for object recognition: An unsupervised approach}, booktitle = {2011 IEEE International Conference on Computer Vision (ICCV)}, year = {2011}, month = {2011/11/06/13}, pages = {999 - 1006}, publisher = {IEEE}, organization = {IEEE}, abstract = {Adapting the classifier trained on a source domain to recognize instances from a new target domain is an important problem that is receiving recent attention. In this paper, we present one of the first studies on unsupervised domain adaptation in the context of object recognition, where we have labeled data only from the source domain (and therefore do not have correspondences between object categories across domains). Motivated by incremental learning, we create intermediate representations of data between the two domains by viewing the generative subspaces (of same dimension) created from these domains as points on the Grassmann manifold, and sampling points along the geodesic between them to obtain subspaces that provide a meaningful description of the underlying domain shift. We then obtain the projections of labeled source domain data onto these subspaces, from which a discriminative classifier is learnt to classify projected data from the target domain. We discuss extensions of our approach for semi-supervised adaptation, and for cases with multiple source and target domains, and report competitive results on standard datasets.}, keywords = {Data models, data representations, discriminative classifier, Feature extraction, Grassmann manifold, image sampling, incremental learning, labeled source domain, Manifolds, measurement, object category, Object recognition, Principal component analysis, sampling points, semisupervised adaptation, target domain, underlying domain shift, unsupervised approach, unsupervised domain adaptation, Unsupervised learning, vectors}, isbn = {978-1-4577-1101-5}, doi = {10.1109/ICCV.2011.6126344}, author = {Gopalan,R. and Ruonan Li and Chellapa, Rama} } @article {19257, title = {The DSPCAD Lightweight Dataflow Environment: Introduction to LIDE Version 0.1}, year = {2011}, month = {2011}, abstract = {LIDE (the DSPCAD Lightweight Dataflow Environment) is a flexible,lightweight design environment that allows designers to experiment with dataflow-based approaches for design and implementation of digital signal processing (DSP) systems. LIDE contains libraries of dataflow graph elements (primitive actors, hierarchical actors, and edges) and utilities that assist designers in modeling, simulating, and implementing DSP systems using formal dataflow techniques. The libraries of dataflow graph elements (mainly actors) contained in LIDE provide useful building blocks that can be used to construct signal processing applications, and that can be used as examples that designers can adapt to create their own, customized LIDE actors. Furthermore, by using LIDE along with the DSPCAD Integrative Command Line Environment (DICE), designers can efficiently create and execute unit tests for user-designed actors. This report provides an introduction to LIDE. The report includes details on the process for setting up the LIDE environment, and covers methods for using pre-designed libraries of graph elements, as well as creating user-designed libraries and associated utilities using the C language. The report also gives an introduction to the C language plug-in for dicelang. This plug-in, called dicelang-C, provides features for efficient C-based project development and maintenance that are useful to apply when working with LIDE. }, keywords = {Technical Report}, isbn = {UMIACS-TR-2011-17}, doi = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/12147}, author = {Chung-Ching Shen and Wang, Lai-Huei and Cho, Inkeun and Kim, Scott and Won, Stephen and Plishker,William and Bhattacharyya, Shuvra S.} } @conference {14315, title = {Dynamic inference of static types for ruby}, booktitle = {Proceedings of the 38th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages}, series = {POPL {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {459 - 472}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {There have been several efforts to bring static type inference to object-oriented dynamic languages such as Ruby, Python, and Perl. In our experience, however, such type inference systems are extremely difficult to develop, because dynamic languages are typically complex, poorly specified, and include features, such as eval and reflection, that are hard to analyze. In this paper, we introduce constraint-based dynamic type inference, a technique that infers static types based on dynamic program executions. In our approach, we wrap each run-time value to associate it with a type variable, and the wrapper generates constraints on this type variable when the wrapped value is used. This technique avoids many of the often overly conservative approximations of static tools, as constraints are generated based on how values are used during actual program runs. Using wrappers is also easy to implement, since we need only write a constraint resolution algorithm and a transformation to introduce the wrappers. The best part is that we can eat our cake, too: our algorithm will infer sound types as long as it observes every path through each method body---note that the number of such paths may be dramatically smaller than the number of paths through the program as a whole. We have developed Rubydust, an implementation of our algorithm for Ruby. Rubydust takes advantage of Ruby{\textquoteright}s dynamic features to implement wrappers as a language library. We applied Rubydust to a number of small programs and found it to be both easy to use and useful: Rubydust discovered 1 real type error, and all other inferred types were correct and readable.}, keywords = {dynamic languages, dynamic type inference, ruby, static types}, isbn = {978-1-4503-0490-0}, doi = {10.1145/1926385.1926437}, url = {http://doi.acm.org/10.1145/1926385.1926437}, author = {An,Jong-hoon (David) and Chaudhuri,Avik and Foster, Jeffrey S. and Hicks, Michael W.} } @article {14430, title = {Dynamic Processing Allocation in Video}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {33}, year = {2011}, month = {2011/11//}, pages = {2174 - 2187}, abstract = {Large stores of digital video pose severe computational challenges to existing video analysis algorithms. In applying these algorithms, users must often trade off processing speed for accuracy, as many sophisticated and effective algorithms require large computational resources that make it impractical to apply them throughout long videos. One can save considerable effort by applying these expensive algorithms sparingly, directing their application using the results of more limited processing. We show how to do this for retrospective video analysis by modeling a video using a chain graphical model and performing inference both to analyze the video and to direct processing. We apply our method to problems in background subtraction and face detection, and show in experiments that this leads to significant improvements over baseline algorithms.}, keywords = {algorithms;digital, allocation;video, analysis;computer, background, detection;graphical, detection;resource, graphics;face, model;resource, processing;, processing;face, recognition;object, signal, subtraction;baseline, video}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2011.55}, author = {Daozheng Chen and Bilgic,M. and Getoor, Lise and Jacobs, David W.} } @article {16040, title = {Empirical Studies in Information Visualization: Seven Scenarios}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {PP}, year = {2011}, month = {2011///}, pages = {1 - 1}, abstract = {We take a new, scenario based look at evaluation in information visualization. Our seven scenarios, evaluating visual data analysis and reasoning, evaluating user performance, evaluating user experience, evaluating environments and work practices, evaluating communication through visualization, evaluating visualization algorithms, and evaluating collaborative data analysis were derived through an extensive literature review of over 800 visualization publications. These scenarios distinguish different study goals and types of research questions and are illustrated through example studies. Through this broad survey and the distillation of these scenarios we make two contributions. One, we encapsulate the current practices in the information visualization research community and, two, we provide a different approach to reaching decisions about what might be the most effective evaluation of a given information visualization. Scenarios can be used to choose appropriate research questions and goals and the provided examples can be consulted for guidance on how to design one{\textquoteright}s own study.}, isbn = {1077-2626}, doi = {10.1109/TVCG.2011.279}, author = {Lam,H. and Bertini,E. and Isenberg,P. and Plaisant, Catherine and Carpendale,S.} } @conference {12450, title = {Entropy rate superpixel segmentation}, booktitle = {2011 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)}, year = {2011}, month = {2011/06/20/25}, pages = {2097 - 2104}, publisher = {IEEE}, organization = {IEEE}, abstract = {We propose a new objective function for superpixel segmentation. This objective function consists of two components: entropy rate of a random walk on a graph and a balancing term. The entropy rate favors formation of compact and homogeneous clusters, while the balancing function encourages clusters with similar sizes. We present a novel graph construction for images and show that this construction induces a matroid - a combinatorial structure that generalizes the concept of linear independence in vector spaces. The segmentation is then given by the graph topology that maximizes the objective function under the matroid constraint. By exploiting submodular and mono-tonic properties of the objective function, we develop an efficient greedy algorithm. Furthermore, we prove an approximation bound of {\textonehalf} for the optimality of the solution. Extensive experiments on the Berkeley segmentation benchmark show that the proposed algorithm outperforms the state of the art in all the standard evaluation metrics.}, keywords = {balancing function, Berkeley segmentation benchmark, Complexity theory, Entropy, entropy rate, graph construction, graph theory, graph topology, greedy algorithm, Greedy algorithms, homogeneous clusters, Image edge detection, Image segmentation, matrix algebra, matroid constraint, measurement, pattern clustering, Random variables, standard evaluation metrics, superpixel segmentation, vector spaces}, isbn = {978-1-4577-0394-2}, doi = {10.1109/CVPR.2011.5995323}, author = {Ming-Yu Liu and Tuzel, O. and Ramalingam, S. and Chellapa, Rama} } @article {12448, title = {ON THE ESTIMATION OF 3D HUMAN BODY MODELS AND POSE FROM MULTIPLE CAMERAS}, journal = {EMERGING TOPICS IN COMPUTER VISION AND ITS APPLICATIONS}, year = {2011}, month = {2011/09//undefin}, pages = {3 - 25}, abstract = {We present a completely automatic algorithm for initializing and tracking the articulated motion of humans using image sequences obtained from multiple cameras. We discuss the challenges in solving this problem and compare our work to some of the state of the art techniques today. We use a detailed articulated human body model composed of sixteen rigid segments that allows both translation and rotation at joints. Voxel data of the subject obtained from the images is segmented into the different articulated chains using Laplacian Eigenmaps. The segmented chains are registered in a subset of the frames using a single-frame registration technique and subsequently used to initialize the pose in the sequence. A temporal registration method is then used to identify the partially segmented or unregistered articulated chains in the remaining frames in the sequence. The tracker uses motion cues such as pixel displacement as well as 2D and 3D shape cues such as silhouettes, motion residues and skeleton curves. The use of complementary cues in the tracking algorithm alleviates the twin problems of drift and convergence to incorrect solutions. The use of multiple cameras also allows us to deal with the problems due to self-occlusion and kinematic singularity. We present tracking results on sequences with different kinds of motion to illustrate the effectiveness of our approach.}, author = {Sundaresan, A. and Chellapa, Rama} } @conference {12438, title = {The evolution of stochastic grammars for representation and recognition of activities in videos}, booktitle = {2011 IEEE International Conference on Computer Vision Workshops (ICCV Workshops)}, year = {2011}, month = {2011/11/06/13}, pages = {688 - 688}, publisher = {IEEE}, organization = {IEEE}, abstract = {The speaker is one of the privileged many to have been taught syntactic pattern recognition methods by the Late Prof. K.S. Fu. In this talk, I will discuss the evolution of stochastic image grammars from the early seventies to now with a focus on image and video understanding applications.}, keywords = {activity recognition, activity representation, Conferences, Educational institutions, Grammar, Image analysis, image recognition, image representation, image understanding, pattern recognition, stochastic image grammars, syntactic pattern recognition methods, video signal processing, video understanding, Videos}, isbn = {978-1-4673-0062-9}, doi = {10.1109/ICCVW.2011.6130309}, author = {Chellapa, Rama} } @article {12440, title = {Example-Driven Manifold Priors for Image Deconvolution}, journal = {Image Processing, IEEE Transactions on}, volume = {20}, year = {2011}, month = {2011/11//}, pages = {3086 - 3096}, abstract = {Image restoration methods that exploit prior information about images to be estimated have been extensively studied, typically using the Bayesian framework. In this paper, we consider the role of prior knowledge of the object class in the form of a patch manifold to address the deconvolution problem. Specifically, we incorporate unlabeled image data of the object class, say natural images, in the form of a patch-manifold prior for the object class. The manifold prior is implicitly estimated from the given unlabeled data. We show how the patch-manifold prior effectively exploits the available sample class data for regularizing the deblurring problem. Furthermore, we derive a generalized cross-validation (GCV) function to automatically determine the regularization parameter at each iteration without explicitly knowing the noise variance. Extensive experiments show that this method performs better than many competitive image deconvolution methods.}, keywords = {Bayesian, cross-validation, data;Bayes, deconvolution;image, determination;deblurring, estimation;, framework;GCV, function;automatic, function;image, image, image;patch-manifold, manifold, method;iteration, method;natural, methods;deconvolution;image, methods;natural, parameter, prior;generalized, prior;unlabeled, problem, regularization, regularization;example-driven, restoration, restoration;iterative, scenes;parameter}, isbn = {1057-7149}, doi = {10.1109/TIP.2011.2145386}, author = {Ni,Jie and Turaga,P. and Patel, Vishal M. and Chellapa, Rama} } @conference {18210, title = {Exploring compression effects for improved source camera identification using strongly compressed video}, booktitle = {Image Processing (ICIP), 2011 18th IEEE International Conference on}, year = {2011}, month = {2011/09//}, pages = {1953 - 1956}, abstract = {This paper presents a study of the video compression effect on source camera identification based on the Photo-Response Non-Uniformity (PRNU). Specifically, the reliability of different types of frames in a compressed video is first investigated, which shows quantitatively that I-frames are more reliable than P-frames for PRNU estimation. Motivated by this observation, a new mechanism for estimating the reference PRNU and two mechanisms for estimating the test-video PRNU are proposed to achieve higher accuracy with fewer frames used. Experiments are performed to validate the effectiveness of the proposed mechanisms.}, keywords = {camera, cameras;video, coding;, compression;computer, compression;video, estimation;photoresponse, forensics;data, identification;video, non-uniformity;reliability;source, PRNU}, doi = {10.1109/ICIP.2011.6115855}, author = {Chuang,Wei-Hong and Su,Hui and M. Wu} } @inbook {12459, title = {Face Detection}, booktitle = {Visual Analysis of HumansVisual Analysis of Humans}, year = {2011}, month = {2011///}, pages = {71 - 90}, publisher = {Springer London}, organization = {Springer London}, abstract = {Face detection in still images and videos has been extensively studied over the last two decades. Attributed to the recent proliferation of cameras in consumer applications, research in face detection has gradually transformed into more unconstrained settings, with the goal of achieving performance close to humans. This presents two main challenges: (i) in addition to modeling the facial characteristics, understanding the information portrayed by the surrounding scene is important in resolving visual ambiguities, and (ii) the computational time needed for decision making should be compatible for real-time applications, since detection is primarily a front-end process on which additional knowledge extraction is built upon. This chapter begins with a review of recent work in modeling face-specific information, including appearance-based methods used by sliding window classifiers, concepts from learning and local interest-point descriptors, and then focuses on representing the contextual information shared by faces with the surrounding scene. To provide better understanding of working concepts, we discuss a method for learning the semantic context shared by the face with other human body parts that facilitates reasoning under occlusion, and then present an image representation which efficiently encodes contour information to enable fast detection of faces. We conclude the chapter by discussing some existing challenges.}, isbn = {978-0-85729-997-0}, url = {http://dx.doi.org/10.1007/978-0-85729-997-0_5}, author = {Gopalan,Raghuraman and Schwartz,William R. and Chellapa, Rama and Srivastava,Ankur}, editor = {Moeslund,Thomas B. and Hilton,Adrian and Kr{\"u}ger,Volker and Sigal,Leonid} } @inbook {12460, title = {Face Tracking and Recognition in Video}, booktitle = {Handbook of Face RecognitionHandbook of Face Recognition}, year = {2011}, month = {2011///}, pages = {323 - 351}, publisher = {Springer London}, organization = {Springer London}, abstract = {In this chapter, we describe the utility of videos in enhancing performance of image-based recognition tasks. We discuss a joint tracking-recognition framework that allows for using the motion information in a video to better localize and identify the person in the video using still galleries. We discuss how to jointly capture facial appearance and dynamics to obtain a parametric representation for video-to-video recognition. We discuss recognition in multi-camera networks where the probe and gallery both consist of multi-camera videos. Concluding remarks and directions for future research are provided.}, isbn = {978-0-85729-932-1}, url = {http://dx.doi.org/10.1007/978-0-85729-932-1_13}, author = {Chellapa, Rama and Du,Ming and Turaga,Pavan and Zhou,Shaohua Kevin}, editor = {Li,Stan Z. and Jain,Anil K.} } @conference {12444, title = {Face tracking in low resolution videos under illumination variations}, booktitle = {2011 18th IEEE International Conference on Image Processing (ICIP)}, year = {2011}, month = {2011/09/11/14}, pages = {781 - 784}, publisher = {IEEE}, organization = {IEEE}, abstract = {In practical face tracking applications, the face region is often small and affected by illumination variations. We address this problem by using a new feature, namely the Gradient-Logarithmic Field (GLF) feature, in the particle filter framework. The GLF feature is robust under illumination variations and the GLF-based tracker does not assume any model for the face being tracked and is effective in low-resolution video. Experimental results show that the proposed GFL-based tracker works well under significant illumination changes and outperforms some of the state-of-the-art algorithms.}, keywords = {Adaptation models, Computational modeling, Face, face recognition, face tracking, GLF-based tracker, gradient methods, gradient-logarithmic field feature, illumination variations, lighting, low resolution videos, low-resolution, particle filter, particle filter framework, particle filtering (numerical methods), Robustness, tracking, video signal processing, Videos, Visual face tracking}, isbn = {978-1-4577-1304-0}, doi = {10.1109/ICIP.2011.6116672}, author = {Zou, W.W.W. and Chellapa, Rama and Yuen, P.C.} } @article {12454, title = {A Fast Bilinear Structure from Motion Algorithm Using a Video Sequence and Inertial Sensors}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {33}, year = {2011}, month = {2011/01//}, pages = {186 - 193}, abstract = {In this paper, we study the benefits of the availability of a specific form of additional information-the vertical direction (gravity) and the height of the camera, both of which can be conveniently measured using inertial sensors and a monocular video sequence for 3D urban modeling. We show that in the presence of this information, the SfM equations can be rewritten in a bilinear form. This allows us to derive a fast, robust, and scalable SfM algorithm for large scale applications. The SfM algorithm developed in this paper is experimentally demonstrated to have favorable properties compared to the sparse bundle adjustment algorithm. We provide experimental evidence indicating that the proposed algorithm converges in many cases to solutions with lower error than state-of-art implementations of bundle adjustment. We also demonstrate that for the case of large reconstruction problems, the proposed algorithm takes lesser time to reach its solution compared to bundle adjustment. We also present SfM results using our algorithm on the Google StreetView research data set.}, keywords = {3D urban modeling, algorithms, Artificial intelligence, CAMERAS, computer vision., Convergence, fast bilinear structure, Google StreetView research data set, Image Interpretation, Computer-Assisted, Image reconstruction, Image sensors, Image sequences, Imaging, Three-Dimensional, inertial sensors, Information Storage and Retrieval, Linear systems, minimization, MOTION, motion algorithm, Motion estimation, multiple view geometry, Pattern Recognition, Automated, Sensors, SfM equations, sparse bundle adjustment algorithm, structure from motion, Three dimensional displays, vertical direction, Video Recording, video sequence, video signal processing}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2010.163}, author = {Ramachandran, M. and Veeraraghavan,A. and Chellapa, Rama} } @conference {17175, title = {From slacktivism to activism: participatory culture in the age of social media}, booktitle = {Proceedings of the 2011 annual conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {819 - 822}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Social networking sites (e.g. Facebook), microblogging services (e.g. Twitter), and content-sharing sites (e.g. YouTube and Flickr) have introduced the opportunity for wide-scale, online social participation. Visibility of national and international priorities such as public health, political unrest, disaster relief, and climate change has increased, yet we know little about the benefits - and possible costs - of engaging in social activism via social media. These powerful social issues introduce a need for scientific research into technology mediated social participation. What are the actual, tangible benefits of "greening" Twitter profile pictures in support of the Iranian elections? Does cartooning a Facebook profile picture really raise awareness of child abuse? Are there unintended negative effects through low-risk, low-cost technology-mediated participation? And, is there a difference - in both outcome and engagement level - between different types of online social activism? This SIG will investigate technology mediated social participation through a critical lens, discussing both the potential positive and negative outcomes of such participation. Approaches to designing for increased participation, evaluating effects of participation, and next steps in scientific research directions will be discussed.}, keywords = {activism, change, design, participation, slacktivism, social media}, isbn = {978-1-4503-0268-5}, doi = {10.1145/1979742.1979543}, url = {http://doi.acm.org/10.1145/1979742.1979543}, author = {Rotman,Dana and Vieweg,Sarah and Yardi,Sarita and Chi,Ed and Preece,Jenny and Shneiderman, Ben and Pirolli,Peter and Glaisyer,Tom} } @article {14613, title = {Gene Coexpression Network Topology of Cardiac Development, Hypertrophy, and FailureClinical Perspective}, journal = {Circulation: Cardiovascular GeneticsCirc Cardiovasc Genet}, volume = {4}, year = {2011}, month = {2011/02/01/}, pages = {26 - 35}, abstract = {Background{\textemdash} Network analysis techniques allow a more accurate reflection of underlying systems biology to be realized than traditional unidimensional molecular biology approaches. Using gene coexpression network analysis, we define the gene expression network topology of cardiac hypertrophy and failure and the extent of recapitulation of fetal gene expression programs in failing and hypertrophied adult myocardium.Methods and Results{\textemdash} We assembled all myocardial transcript data in the Gene Expression Omnibus (n=1617). Because hierarchical analysis revealed species had primacy over disease clustering, we focused this analysis on the most complete (murine) dataset (n=478). Using gene coexpression network analysis, we derived functional modules, regulatory mediators, and higher-order topological relationships between genes and identified 50 gene coexpression modules in developing myocardium that were not present in normal adult tissue. We found that known gene expression markers of myocardial adaptation were members of upregulated modules but not hub genes. We identified ZIC2 as a novel transcription factor associated with coexpression modules common to developing and failing myocardium. Of 50 fetal gene coexpression modules, 3 (6\%) were reproduced in hypertrophied myocardium and 7 (14\%) were reproduced in failing myocardium. One fetal module was common to both failing and hypertrophied myocardium. Conclusions{\textemdash} Network modeling allows systems analysis of cardiovascular development and disease. Although we did not find evidence for a global coordinated program of fetal gene expression in adult myocardial adaptation, our analysis revealed specific gene expression modules active during both development and disease and specific candidates for their regulation. }, keywords = {fetal, Gene expression, heart failure, hypertrophy, myocardium}, isbn = {1942-325X, 1942-3268}, doi = {10.1161/CIRCGENETICS.110.941757}, url = {http://circgenetics.ahajournals.org/content/4/1/26}, author = {Dewey,Frederick E and Perez,Marco V and Wheeler,Matthew T and Watt,Clifton and Spin,Joshua and Langfelder,Peter and Horvath,Steve and Hannenhalli, Sridhar and Cappola,Thomas P. and Ashley,Euan A} } @article {17180, title = {Graph Analytics-Lessons Learned and Challenges Ahead}, volume = {31}, year = {2011}, month = {2011///}, pages = {18 - 29}, abstract = {Graph analytics is one of the most influential and important R\&D topics in the visual analytics community. Researchers with diverse backgrounds from information visualization, human-computer interaction, computer graphics, graph drawing, and data mining have pursued graph analytics from scientific, technical, and social approaches. These studies have addressed both distinct and common challenges. Past successes and mistakes can provide valuable lessons for revising the research agenda. In this article, six researchers from four academic and research institutes identify graph analytics{\textquoteright} fundamental challenges and present both insightful lessons learned from their experience and good practices in graph analytics research. The goal is to critically assess those lessons and shed light on how they can stimulate research and draw attention to grand challenges for graph analytics. The article also establishes principles that could lead to measurable standards and criteria for research.}, keywords = {citation analysis, citespace, Computer Graphics, document analysis, graphics and multimedia, greengrid, jigsaw system, modeling, power grid analysis, semantic substrates, simulation, social networks, text analysis, Visualization}, isbn = {0272-1716}, author = {Wong,Pak Chung and Chen,Chaomei and Gorg,Carsten and Shneiderman, Ben and Stasko,John and Thomas,Jim} } @article {15477, title = {GUI Interaction Testing: Incorporating Event Context}, journal = {Software Engineering, IEEE Transactions on}, volume = {37}, year = {2011}, month = {2011/08//july}, pages = {559 - 574}, abstract = {Graphical user interfaces (GUIs), due to their event-driven nature, present an enormous and potentially unbounded way for users to interact with software. During testing, it is important to $\#$x201C;adequately cover $\#$x201D; this interaction space. In this paper, we develop a new family of coverage criteria for GUI testing grounded in combinatorial interaction testing. The key motivation of using combinatorial techniques is that they enable us to incorporate $\#$x201C;context $\#$x201D; into the criteria in terms of event combinations, sequence length, and by including all possible positions for each event. Our new criteria range in both efficiency (measured by the size of the test suite) and effectiveness (the ability of the test suites to detect faults). In a case study on eight applications, we automatically generate test cases and systematically explore the impact of context, as captured by our new criteria. Our study shows that by increasing the event combinations tested and by controlling the relative positions of events defined by the new criteria, we can detect a large number of faults that were undetectable by earlier techniques.}, keywords = {automatic test case generation, automatic test pattern generation, combinatorial interaction testing, event driven nature, graphical user interface, Graphical user interfaces, GUI interaction testing, program testing}, isbn = {0098-5589}, doi = {10.1109/TSE.2010.50}, author = {Xun Yuan and Cohen,M. B and Memon, Atif M.} } @conference {19452, title = {Helping Users Shop for ISPs with Internet Nutrition Labels}, booktitle = {ACM SIGCOMM Workshop on Home Networks {\textquoteright}11}, series = {HomeNets {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {13 - 18}, publisher = {ACM}, organization = {ACM}, abstract = {When purchasing home broadband access from Internet service providers (ISPs), users must decide which service plans are most appropriate for their needs. Today, ISPs advertise their available service plans using only generic upload and download speeds. Unfortunately, these metrics do not always accurately reflect the varying performance that home users will experience for a wide range of applications. In this paper, we propose that each ISP service plan carry a "nutrition label" that conveys more comprehensive information about network metrics along many dimensions, including various aspects of throughput, latency, loss rate, and jitter. We first justify why these metrics should form the basis of a network nutrition label. Then, we demonstrate that current plans that are superficially similar with respect to advertised download rates may have different performance according to the label metrics. We close with a discussion of the challenges involved in presenting a nutrition label to users in a way that is both accurate and easy to understand.}, keywords = {access networks, benchmarking, bismark, broadband networks, gateway measurements}, isbn = {978-1-4503-0798-7}, url = {http://doi.acm.org/10.1145/2018567.2018571}, author = {Sundaresan, Srikanth and Feamster, Nick and Teixeira, Renata and Tang, Anthony and Edwards, W. Keith and Grinter, Rebecca E. and Marshini Chetty and de Donato, Walter} } @conference {18677, title = {How secure are networked office devices?}, year = {2011}, month = {2011/06//}, pages = {465 - 472}, abstract = {Many office devices have a history of being networked (such as printers) and others without the same past are increasingly becoming networked (such as photocopiers). The modern networked versions of previously non-networked devices have much in common with traditional networked servers in terms of features and functions. While an organization may have policies and procedures for securing traditional network servers, securing networked office devices providing similar services can easily be overlooked. In this paper we present an evaluation of privacy and security risks found when examining over 1,800 networked office devices connected to a large university network. We use the STRIDE threat model to categorize threats and vulnerabilities and then we group the devices according to assessed risk from the perspective of the university. We found that while steps had been taken to secure some devices, many were using default or unsecured configurations.}, keywords = {computer network security, data privacy, networked office device security, privacy risk assessment, Risk management, security risk assessment, STRIDE threat model, university network}, doi = {10.1109/DSN.2011.5958259}, author = {Condon,E. and Cummins,E. and Afoulki,Z. and Michel Cukier} } @article {13296, title = {IA*: An adjacency-based representation for non-manifold simplicial shapes in arbitrary dimensions}, journal = {Computers \& Graphics}, volume = {35}, year = {2011}, month = {2011/06//}, pages = {747 - 753}, abstract = {We propose a compact, dimension-independent data structure for manifold, non-manifold and non-regular simplicial complexes, that we call the Generalized Indexed Data Structure with Adjacencies (IA⁎ data structure). It encodes only top simplices, i.e. the ones that are not on the boundary of any other simplex, plus a suitable subset of the adjacency relations. We describe the IA⁎ data structure in arbitrary dimensions, and compare the storage requirements of its 2D and 3D instances with both dimension-specific and dimension-independent representations. We show that the IA⁎ data structure is more cost effective than other dimension-independent representations and is even slightly more compact than the existing dimension-specific ones. We present efficient algorithms for navigating a simplicial complex described as an IA⁎ data structure. This shows that the IA⁎ data structure allows retrieving all topological relations of a given simplex by considering only its local neighborhood and thus it is a more efficient alternative to incidence-based representations when information does not need to be encoded for boundary simplices.}, keywords = {Non-manifold data structures, simplicial complexes, Topological data structures}, isbn = {0097-8493}, doi = {10.1016/j.cag.2011.03.009}, url = {http://www.sciencedirect.com/science/article/pii/S0097849311000483}, author = {Canino,David and De Floriani, Leila and Weiss,Kenneth} } @conference {12446, title = {Illumination robust dictionary-based face recognition}, booktitle = {2011 18th IEEE International Conference on Image Processing (ICIP)}, year = {2011}, month = {2011/09/11/14}, pages = {777 - 780}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we present a face recognition method based on simultaneous sparse approximations under varying illumination. Our method consists of two main stages. In the first stage, a dictionary is learned for each face class based on given training examples which minimizes the representation error with a sparseness constraint. In the second stage, a test image is projected onto the span of the atoms in each learned dictionary. The resulting residual vectors are then used for classification. Furthermore, to handle changes in lighting conditions, we use a relighting approach based on a non-stationary stochastic filter to generate multiple images of the same person with different lighting. As a result, our algorithm has the ability to recognize human faces with good accuracy even when only a single or a very few images are provided for training. The effectiveness of the proposed method is demonstrated on publicly available databases and it is shown that this method is efficient and can perform significantly better than many competitive face recognition algorithms.}, keywords = {albedo, approximation theory, classification, competitive face recognition algorithms, Databases, Dictionaries, Face, face recognition, face recognition method, filtering theory, human face recognition, illumination robust dictionary-based face recognition, illumination variation, image representation, learned dictionary, learning (artificial intelligence), lighting, lighting conditions, multiple images, nonstationary stochastic filter, publicly available databases, relighting, relighting approach, representation error, residual vectors, Robustness, simultaneous sparse approximations, simultaneous sparse signal representation, sparseness constraint, Training, varying illumination, vectors}, isbn = {978-1-4577-1304-0}, doi = {10.1109/ICIP.2011.6116670}, author = {Patel, Vishal M. and Tao Wu and Biswas,S. and Phillips,P.J. and Chellapa, Rama} } @inbook {12456, title = {Image and Video-Based Biometrics}, booktitle = {Visual Analysis of HumansVisual Analysis of Humans}, year = {2011}, month = {2011///}, pages = {437 - 454}, publisher = {Springer London}, organization = {Springer London}, abstract = {Biometrics deals with the problem of identifying individuals based on physiological or behavioral characteristics. Since many physical characteristics, such as face, iris, etc., and behavioral characteristics, such as voice, expression, etc., are unique to an individual, biometric analysis offers a reliable and natural solution to the problem of identity verification. In this chapter, we discuss image and video-based biometrics involving face, iris and gait. In particular, we discuss several recent approaches to physiological biometrics based on Sparse Representations and Compressed Sensing. Some of the most compelling challenges and issues that confront research in biometrics are also addressed.}, isbn = {978-0-85729-997-0}, url = {http://dx.doi.org/10.1007/978-0-85729-997-0_22}, author = {Patel, Vishal M. and Pillai,Jaishanker K. and Chellapa, Rama}, editor = {Moeslund,Thomas B. and Hilton,Adrian and Kr{\"u}ger,Volker and Sigal,Leonid} } @inbook {19034, title = {Implicit Authentication through Learning User Behavior}, booktitle = {Information Security}, series = {Lecture Notes in Computer Science}, volume = {6531}, year = {2011}, month = {2011}, pages = {99 - 113}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Users are increasingly dependent on mobile devices. However, current authentication methods like password entry are significantly more frustrating and difficult to perform on these devices, leading users to create and reuse shorter passwords and pins, or no authentication at all. We present implicit authentication - authenticating users based on behavior patterns. We describe our model for performing implicit authentication and assess our techniques using more than two weeks of collected data from over 50 subjects.}, keywords = {Computer science}, isbn = {978-3-642-18177-1}, url = {http://www.springerlink.com/content/m57u551u3133475m/abstract/}, author = {Elaine Shi and Niu, Yuan and Jakobsson, Markus and Chow, Richard}, editor = {Burmester, Mike and Tsudik, Gene and Magliveras, Spyros and Ilic, Ivana} } @article {12866, title = {The Importance of Chitin in the Marine Environment}, journal = {Marine Biotechnology}, year = {2011}, month = {2011///}, pages = {1 - 8}, abstract = {Chitin is the most abundant renewable polymer in the oceans and is an important source of carbon and nitrogen for marine organisms. The process of chitin degradation is a key step in the cycling of nutrients in the oceans and chitinolytic bacteria play a significant role in this process. These bacteria are autochthonous to both marine and freshwater ecosystems and produce chitinases that degrade chitin, an insoluble polysaccharide, to a biologically useful form. In this brief review, a description of the structure of chitin and diversity of chitinolytic bacteria in the oceans is provided, in the context of the significance of chitin degradation for marine life.}, doi = {10.1007/s10126-011-9388-1}, author = {Souza,C. P. and Almeida,B. C. and Rita R Colwell and Rivera,I. N. G.} } @article {16043, title = {Improved Identification and Visualization of Emergency Department Patient Visits}, journal = {Annals of Emergency Medicine}, volume = {58}, year = {2011}, month = {2011///}, pages = {S309 - S309}, author = {Hettinger,AZ and Rackoff,A. and Wongsuphasawat,K. and Cheng,H. and Fairbanks,RJ and Plaisant, Catherine and Smith,M. S} } @article {13003, title = {Increased gene sampling provides stronger support for higher-level groups within gracillariid leaf mining moths and relatives (Lepidoptera: Gracillariidae)}, journal = {BMC Evol Biol}, volume = {11:182}, year = {2011}, month = {2011///}, author = {Kawahara,A. Y and Ohshima,I and Kawakita,A and Regier,J. C and Mitter,C and Cummings, Michael P. and Davis,DR and Wagner,DL and De Prinis,J and Lopez-Vaamonde,C} } @article {13004, title = {Increased gene sampling yields robust support for higher-level clades within Bombycoidea (Lepidoptera)}, journal = {Systematic Entomology}, volume = {36}, year = {2011}, month = {2011/01/01/}, pages = {31 - 43}, abstract = {This study has as its primary aim the robust resolution of higher-level relationships within the lepidopteran superfamily Bombycoidea. Our study builds on an earlier analysis of five genes (\~{}6.6 kbp) sequenced for 50 taxa from Bombycoidea and its sister group Lasiocampidae, plus representatives of other macrolepidoteran superfamilies. The earlier study failed to yield strong support for the monophyly of and basal splits within Bombycoidea, among others. Therefore, in an effort to increase support specifically for higher-level nodes, we generated 11.7 kbp of additional data from 20 genes for 24 of 50 bombycoid and lasiocampid taxa. The data from the genes are all derived from protein-coding nuclear genes previously used to resolve other lepidopteran relationships. With these additional data, all but a few higher-level nodes are strongly supported. Given our decision to minimize project costs by augmenting genes for only 24 of the 50 taxa, we explored whether the resulting pattern of missing data in the combined-gene matrix introduced a nonphylogenetic bias, a possibility reported by others. This was achieved by comparing node support values (i.e. nonparametric bootstrap values) based on likelihood and parsimony analyses of three datasets that differ in their number of taxa and level of missing data: 50 taxa/5 genes (dataset A), 50 taxa/25 genes (dataset B) and 24 taxa/25 genes (dataset C). Whereas datasets B and C provided similar results for common nodes, both frequently yielded higher node support relative to dataset A, arguing that: (i) more data yield increased node support and (ii) partial gene augmentation does not introduce an obvious nonphylogenetic bias. A comparison of single-gene bootstrap analyses identified four nodes for which one or two of the 25 genes provided modest to strong support for a grouping not recovered by the combined-gene result. As a summary proposal, two of these four groupings (one each within Bombycoidea and Lasiocampidae) were deemed sufficiently problematic to regard them as unresolved trichotomies. Since the alternative groupings were always highly localized on the tree, we did not judge a combined-gene analysis to present a problem outside those regions. Based on our robustly resolved results, we have revised the classification of Bombycoidea: the family Bombycidae is restricted to its nominate subfamily, and its tribe Epiini is elevated to subfamily rank (Epiinae stat.rev.), whereas the bombycid subfamily Phiditiinae is reinstated as a separate family (Phiditiidae stat.rev.). The bombycid subfamilies Oberthueriinae Kuznetzov \& Stekolnikov, 1985, syn.nov. and Prismostictinae Forbes, 1955, syn.nov., and the family Mirinidae Kozlov, 1985, syn.nov. are established as subjective junior synonyms of Endromidae Boisduval, 1828. The family Anthelidae (Lasiocampoidea) is reincluded in the superfamily Bombycoidea.}, isbn = {1365-3113}, doi = {10.1111/j.1365-3113.2010.00543.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3113.2010.00543.x/abstract;jsessionid=B5B1F8BF73034A4C41427FB1FBD7383F.d02t04}, author = {Zwick,Andreas and Regier,Jerome C and Mitter,Charles and Cummings, Michael P.} } @article {18579, title = {Instrumenting home networks}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {41}, year = {2011}, month = {2011///}, pages = {84 - 89}, abstract = {In managing and troubleshooting home networks, one of the challenges is in knowing what is actually happening. Availability of a record of events that occurred on the home network before trouble appeared would go a long way toward addressing that challenge. In this position/work-in-progress paper, we consider requirements for a general-purpose logging facility for home networks. Such a facility, if properly designed, would potentially have other uses. We describe several such uses and discuss requirements to be considered in the design of a logging platform that would be widely supported and accepted. We also report on our initial deployment of such a facility.}, keywords = {home network management, home network troubleshooting}, isbn = {0146-4833}, doi = {10.1145/1925861.1925875}, url = {http://doi.acm.org/10.1145/1925861.1925875}, author = {Calvert,Kenneth L. and Edwards,W. Keith and Feamster, Nick and Grinter,Rebecca E. and Deng,Ye and Zhou,Xuzi} } @article {12867, title = {Interaction of Vibrio cholerae non-O1/non-O139 with Copepods, Cladocerans and Competing Bacteria in the Large Alkaline Lake Neusiedler See, Austria}, journal = {Microbial ecology}, volume = {61}, year = {2011}, month = {2011///}, pages = {496 - 506}, abstract = {Vibrio cholerae is a human pathogen and natural inhabitant of aquatic environments. Serogroups O1/O139 have been associated with epidemic cholera, while non-O1/non-O139 serogroups usually cause human disease other than classical cholera. V. cholerae non-O1/non-O139 from the Neusiedler See, a large Central European lake, have caused ear and wound infections, including one case of fatal septicaemia. Recent investigations demonstrated rapid planktonic growth of V. cholerae non-O1/non-O139 and correlation with zooplankton biomass. The aim of this study was to elucidate the interaction of autochthonous V. cholerae with two dominant crustacean zooplankton species in the lake and investigate the influence of the natural bacterial community on this interaction. An existing data set was evaluated for statistical relationships between zooplankton species and V. cholerae and co-culture experiments were performed in the laboratory. A new fluorescence in situ hybridisation protocol was applied for quantification of V. cholerae non-O1/non-O139 cells, which significantly reduced analysis time. The experiments clearly demonstrated a significant relationship of autochthonous V. cholerae non-O1/non-O139 with cladocerans by promoting growth of V. cholerae non-O1/non-O139 in the water and on the surfaces of the cladocerans. In contrast, copepods had a negative effect on the growth of V. cholerae non-O1/non-O139 via competing bacteria from their surfaces. Thus, beside other known factors, biofilm formation by V. cholerae on crustacean zooplankton appears to be zooplankton taxon specific and may be controlled by the natural bacterial community.}, doi = {10.1007/s00248-010-9764-9}, author = {Kirschner,A. K. T. and Schauer,S. and Steinberger,B. and Wilhartitz,I. and Grim,C. J. and Huq,A. and Rita R Colwell and Herzig,A. and Sommer,R.} } @article {13274, title = {An iterative algorithm for homology computation on simplicial shapes}, journal = {Computer-Aided Design}, volume = {43}, year = {2011}, month = {2011/11//}, pages = {1457 - 1467}, abstract = {We propose a new iterative algorithm for computing the homology of arbitrary shapes discretized through simplicial complexes. We demonstrate how the simplicial homology of a shape can be effectively expressed in terms of the homology of its sub-components. The proposed algorithm retrieves the complete homological information of an input shape including the Betti numbers, the torsion coefficients and the representative homology generators.To the best of our knowledge, this is the first algorithm based on the constructive Mayer{\textendash}Vietoris sequence, which relates the homology of a topological space to the homologies of its sub-spaces, i.e. the sub-components of the input shape and their intersections. We demonstrate the validity of our approach through a specific shape decomposition, based only on topological properties, which minimizes the size of the intersections between the sub-components and increases the efficiency of the algorithm. }, keywords = {Computational topology, Generators, Mayer{\textendash}Vietoris sequence, shape decomposition, simplicial complexes, Z -homology}, isbn = {0010-4485}, doi = {10.1016/j.cad.2011.08.015}, url = {http://www.sciencedirect.com/science/article/pii/S0010448511002144}, author = {Boltcheva,Dobrina and Canino,David and Merino Aceituno,Sara and L{\'e}on,Jean-Claude and De Floriani, Leila and H{\'e}troy,Franck} } @article {12865, title = {Vibrio Cholerae O1 Detection in Estuarine and Coastal Zooplankton}, journal = {Journal of Plankton Research}, volume = {33}, year = {2011}, month = {01/2011}, pages = {51 - 62}, abstract = {Vibrio cholerae is an autochthonous marine bacterium, and its association with diverse planktonic crustaceans has been extensively investigated; however, the presence of V. cholerae on individuals of most phyla of planktonic animals is still incompletely understood. The objective of this study was to analyze the distribution of V. cholerae serogroup O1 associated with specific zooplankton taxa in an estuary and the adjacent continental shelf of the southeastern Brazilian coast. The occurrence of the bacterium was assessed in zooplankton samples, specifically on the most abundant taxa, using direct fluorescence assay (DFA) and direct viable count{\textendash}direct fluorescence assay (DVC{\textendash}DFA) methods. Vibrio cholerae O1 was detected in 88\% of samples collected from the Santos-Bertioga estuary and in 67\% of samples from the shelf. The salinity of the estuarine water ranged from 21.8 to 34.6, significantly lower than the shelf water which was 32.1{\textendash}36.1. Salinity was the only environmental variable measured that displayed a significant correlation with the presence of V. cholerae (P< 0.05). Vibrio cholerae O1 was detected in chaetognaths, pluteus larvae of echinoderms and planktonic fish eggs (Engraulidae), all new sites for this bacterium.}, keywords = {DFA, estuary, plankton, Southwest Atlantic}, isbn = {0142-7873, 1464-3774}, doi = {10.1093/plankt/fbq093}, url = {http://plankt.oxfordjournals.org/content/33/1/51}, author = {Martinelli Filho,Jos{\'e} E. and Lopes,Rubens M. and Rivera,Irma N. G. and Rita R Colwell} } @conference {14226, title = {Language Models for Semantic Extraction and Filtering in Video Action Recognition}, booktitle = {Workshops at the Twenty-Fifth AAAI Conference on Artificial Intelligence}, year = {2011}, month = {2011/08/24/}, abstract = {The paper addresses the following issues: (a) how to represent semantic information from natural language so that a vision model can utilize it? (b) how to extract the salient textual information relevant to vision? For a given domain, we present a new model of semantic extraction that takes into account word relatedness as well as word disambiguation in order to apply to a vision model. We automatically process the text transcripts and perform syntactic analysis to extract dependency relations. We then perform semantic extraction on the output to filter semantic entities related to actions. The resulting data are used to populate a matrix of co-occurrences utilized by the vision processing modules. Results show that explicitly modeling the co-occurrence of actions and tools significantly improved performance.}, url = {https://www.aaai.org/ocs/index.php/WS/AAAIW11/paper/viewPaper/3919}, author = {Tzoukermann,Evelyne and Neumann, Jan and Kosecka,Jana and Ferm{\"u}ller, Cornelia and Perera,Ian and Ferraro,Frank and Sapp,Ben and Chaudhry,Rizwan and Singh,Gautam} } @conference {13074, title = {A large-scale benchmark dataset for event recognition in surveillance video}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on}, year = {2011}, month = {2011/06//}, pages = {3153 - 3160}, abstract = {We introduce a new large-scale video dataset designed to assess the performance of diverse visual event recognition algorithms with a focus on continuous visual event recognition (CVER) in outdoor areas with wide coverage. Previous datasets for action recognition are unrealistic for real-world surveillance because they consist of short clips showing one action by one individual [15, 8]. Datasets have been developed for movies [11] and sports [12], but, these actions and scene conditions do not apply effectively to surveillance videos. Our dataset consists of many outdoor scenes with actions occurring naturally by non-actors in continuously captured videos of the real world. The dataset includes large numbers of instances for 23 event types distributed throughout 29 hours of video. This data is accompanied by detailed annotations which include both moving object tracks and event examples, which will provide solid basis for large-scale evaluation. Additionally, we propose different types of evaluation modes for visual recognition tasks and evaluation metrics along with our preliminary experimental results. We believe that this dataset will stimulate diverse aspects of computer vision research and help us to advance the CVER tasks in the years ahead.}, keywords = {algorithm;evaluation, CVER, databases;, databases;video, dataset;moving, event, metrics;large-scale, object, recognition, recognition;diverse, recognition;video, scenes;surveillance, surveillance;visual, tasks;computer, tracks;outdoor, video, video;computer, vision;continuous, vision;image, visual}, doi = {10.1109/CVPR.2011.5995586}, author = {Oh,Sangmin and Hoogs, A. and Perera,A. and Cuntoor, N. and Chen,Chia-Chih and Lee,Jong Taek and Mukherjee,S. and Aggarwal, JK and Lee,Hyungtae and Davis, Larry S. and Swears,E. and Wang,Xioyang and Ji,Qiang and Reddy,K. and Shah,M. and Vondrick,C. and Pirsiavash,H. and Ramanan,D. and Yuen,J. and Torralba,A. and Song,Bi and Fong,A. and Roy-Chowdhury, A. and Desai,M.} } @conference {18922, title = {The Life Game: Cognitive Strategies for Repeated Stochastic Games}, year = {2011}, month = {2011/10//}, pages = {95 - 102}, abstract = {Standard models in bio-evolutionary game theory involve repetitions of a single stage game (e.g., the Prisoner{\textquoteright}s Dilemma or the Stag Hunt); but it is clear that repeatedly playing the same stage game is not an accurate model of most individuals{\textquoteright} lives. Rather, individuals{\textquoteright} interactions with others correspond to many different kinds of stage games. In this work, we concentrate on discovering behavioral strategies that are successful for the life game, in which the stage game is chosen stochastically at each iteration. We present a cognitive agent model based on Social Value Orientation (SVO) theory. We provide extensive evaluations of our model{\textquoteright}s performance, both against standard agents from the game theory literature and against a large set of life-game agents written by students in two different countries. Our empirical results suggest that for life-game strategies to be successful in environments with such agents, it is important (i) to be unforgiving with respect to trust behavior and (ii) to use adaptive, fine-grained opponent models of the other agents.}, keywords = {adaptive model, behavioral strategy, bioevolutionary game theory, cognitive agent model, fine-grained opponent model, game theory, iteration, iterative methods, life game, prisoner{\textquoteright}s dilemma, repeated stochastic games, social value orientation theory, stag hunt, stage game, Stochastic processes, trust behavior}, doi = {10.1109/PASSAT/SocialCom.2011.62}, author = {Cheng,Kan-Leung and Zuckerman,I. and Nau, Dana S. and Golbeck,J.} } @inbook {14324, title = {A Longitudinal Study of Pressure Sensing to Infer Real-World Water Usage Events in the Home}, booktitle = {Pervasive ComputingPervasive Computing}, series = {Lecture Notes in Computer Science}, volume = {6696}, year = {2011}, month = {2011///}, pages = {50 - 69}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present the first longitudinal study of pressure sensing to infer real-world water usage events in the home (e.g., dishwasher, upstairs bathroom sink, downstairs toilet). In order to study the pressure-based approach out in the wild , we deployed a ground truth sensor network for five weeks in three homes and two apartments that directly monitored valve-level water usage by fixtures and appliances . We use this data to, first, demonstrate the practical challenges in constructing water usage activity inference algorithms and, second, to inform the design of a new probabilistic-based classification approach. Inspired by algorithms in speech recognition, our novel Bayesian approach incorporates template matching, a language model, grammar, and prior probabilities. We show that with a single pressure sensor, our probabilistic algorithm can classify real-world water usage at the fixture level with 90\% accuracy and at the fixturecategory level with 96\% accuracy. With two pressure sensors, these accuracies increase to 94\% and 98\%. Finally, we show how our new approach can be trained with fewer examples than a strict template-matching approach alone.}, isbn = {978-3-642-21725-8}, url = {http://dx.doi.org/10.1007/978-3-642-21726-5_4}, author = {Jon Froehlich and Larson,Eric and Saba,Elliot and Campbell,Tim and Atlas,Les and Fogarty,James and Patel,Shwetak}, editor = {Lyons,Kent and Hightower,Jeffrey and Huang,Elaine} } @inbook {19186, title = {A Longitudinal Study of Pressure Sensing to Infer Real-World Water Usage Events in the Home}, booktitle = {Pervasive Computing}, series = {Lecture Notes in Computer Science}, volume = {6696}, year = {2011}, month = {2011}, pages = {50 - 69}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present the first longitudinal study of pressure sensing to infer real-world water usage events in the home (e.g., dishwasher, upstairs bathroom sink, downstairs toilet). In order to study the pressure-based approach out in the wild , we deployed a ground truth sensor network for five weeks in three homes and two apartments that directly monitored valve-level water usage by fixtures and appliances . We use this data to, first, demonstrate the practical challenges in constructing water usage activity inference algorithms and, second, to inform the design of a new probabilistic-based classification approach. Inspired by algorithms in speech recognition, our novel Bayesian approach incorporates template matching, a language model, grammar, and prior probabilities. We show that with a single pressure sensor, our probabilistic algorithm can classify real-world water usage at the fixture level with 90\% accuracy and at the fixturecategory level with 96\% accuracy. With two pressure sensors, these accuracies increase to 94\% and 98\%. Finally, we show how our new approach can be trained with fewer examples than a strict template-matching approach alone.}, isbn = {978-3-642-21725-8}, url = {http://dx.doi.org/10.1007/978-3-642-21726-5_4}, author = {Jon Froehlich and Larson,Eric and Saba,Elliot and Campbell,Tim and Atlas,Les and Fogarty,James and Patel,Shwetak}, editor = {Lyons,Kent and Hightower,Jeffrey and Huang,Elaine} } @article {12864, title = {Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios}, journal = {The ISME Journal}, volume = {6}, year = {2011}, month = {2011/07/14/}, pages = {21 - 30}, abstract = {The long-term effects of ocean warming on prokaryotic communities are unknown because of lack of historical data. We overcame this gap by applying a retrospective molecular analysis to the bacterial community on formalin-fixed samples from the historical Continuous Plankton Recorder archive, which is one of the longest and most geographically extensive collections of marine biological samples in the world. We showed that during the last half century, ubiquitous marine bacteria of the Vibrio genus, including Vibrio cholerae, increased in dominance within the plankton-associated bacterial community of the North Sea, where an unprecedented increase in bathing infections related to these bacteria was recently reported. Among environmental variables, increased sea surface temperature explained 45\% of the variance in Vibrio data, supporting the view that ocean warming is favouring the spread of vibrios and may be the cause of the globally increasing trend in their associated diseases.}, keywords = {ecophysiology, ecosystems, environmental biotechnology, geomicrobiology, ISME J, microbe interactions, microbial communities, microbial ecology, microbial engineering, microbial epidemiology, microbial genomics, microorganisms}, isbn = {1751-7362}, doi = {10.1038/ismej.2011.89}, url = {http://www.nature.com/ismej/journal/v6/n1/full/ismej201189a.html?WT.ec_id=ISMEJ-201201}, author = {Vezzulli,Luigi and Brettar,Ingrid and Pezzati,Elisabetta and Reid,Philip C. and Rita R Colwell and H{\"o}fle,Manfred G. and Pruzzo,Carla} } @article {17980, title = {A Low-Overhead Asynchronous Interconnection Network for GALS Chip Multiprocessors}, journal = {Computer-Aided Design of Integrated Circuits and Systems, IEEE Transactions on}, volume = {30}, year = {2011}, month = {2011/04//}, pages = {494 - 507}, abstract = {A new asynchronous interconnection network is introduced for globally-asynchronous locally-synchronous (GALS) chip multiprocessors. The network eliminates the need for global clock distribution, and can interface multiple synchronous timing domains operating at unrelated clock rates. In particular, two new highly-concurrent asynchronous components are introduced which provide simple routing and arbitration/merge functions. Post-layout simulations in identical commercial 90 nm technology indicate that comparable recent synchronous router nodes have 5.6-10.7 more energy per packet and 2.8-6.4 greater area than the new asynchronous nodes. Under random traffic, the network provides significantly lower latency and identical throughput over the entire operating range of the 800 MHz network and through mid-range traffic rates for the 1.36 GHz network, but with degradation at higher traffic rates. Preliminary evaluations are also presented for a mixed-timing (GALS) network in a shared-memory parallel architecture, running both random traffic and parallel benchmark kernels, as well as directions for further improvement.}, keywords = {1.36, 800, 90, architecture;size, architectures;shared, asynchronous, benchmark, chip, chips;multiprocessor, distribution, distribution;frequency, GALS, GHz;frequency, interconnection, kernel;post-layout, layout;clock, locally-synchronous, memory, MHz;globally-asynchronous, multiple, multiprocessor;clock, multiprocessor;interface, network;mixed-timing, network;network, networks;microprocessor, networks;network, nm;circuit, Parallel, routing;network-on-chip;parallel, routing;parallel, simulation;random, synchronous, systems;, timing;low-overhead, traffic;shared-memory}, isbn = {0278-0070}, doi = {10.1109/TCAD.2011.2114970}, author = {Horak,M.N. and Nowick,S.M. and Carlberg,M. and Vishkin, Uzi} } @inbook {13822, title = {Machine Translation Evaluation and Optimization}, booktitle = {Handbook of Natural Language Processing and Machine TranslationHandbook of Natural Language Processing and Machine Translation}, year = {2011}, month = {2011///}, pages = {745 - 843}, publisher = {Springer New York}, organization = {Springer New York}, abstract = {The evaluation of machine translation (MT) systems is a vital field of research, both for determining the effectiveness of existing MT systems and for optimizing the performance of MT systems. This part describes a range of different evaluation approaches used in the GALE community and introduces evaluation protocols and methodologies used in the program. We discuss the development and use of automatic, human, task-based and semi-automatic (human-in-the-loop) methods of evaluating machine translation, focusing on the use of a human-mediated translation error rate HTER as the evaluation standard used in GALE. We discuss the workflow associated with the use of this measure, including post editing, quality control, and scoring. We document the evaluation tasks, data, protocols, and results of recent GALE MT Evaluations. In addition, we present a range of different approaches for optimizing MT systems on the basis of different measures. We outline the requirements and specific problems when using different optimization approaches and describe how the characteristics of different MT metrics affect the optimization. Finally, we describe novel recent and ongoing work on the development of fully automatic MT evaluation metrics that have the potential to substantially improve the effectiveness of evaluation and optimization of MT systems.}, isbn = {978-1-4419-7713-7}, url = {http://dx.doi.org/10.1007/978-1-4419-7713-7_5}, author = {Dorr, Bonnie J and Olive,Joseph and McCary,John and Christianson,Caitlin}, editor = {Olive,Joseph and Christianson,Caitlin and McCary,John} } @booklet {19456, title = {Making infrastructure visible: a case study of home networking}, year = {2011}, month = {2011/06/24/}, abstract = {In this dissertation, I examine how making infrastructure visible affects users{\textquoteright} engagement with that infrastructure, through the case study of home networking. I present empirical evidence of the visibility issues that home networks present to users and how these results informed the design of a prototype called Kermit to visualize aspects of the home network. Through my implementation and evaluation of Kermit, I derive implications for making infrastructure visible in ways that enable end-users to manage and understand the systems they use everyday. I conclude with suggestions for future work for making home networks, and infrastructure more generally, more visible.}, keywords = {Home computer networks, home networking, Human computer interaction, Human-computer interaction, infrastructure, Inspectability, Local area networks (Computer networks), visibility}, doi = {Dissertation}, url = {https://smartech.gatech.edu/handle/1853/41152}, author = {Marshini Chetty} } @conference {17904, title = {MDMap: A system for data-driven layout and exploration of molecular dynamics simulations}, booktitle = {Biological Data Visualization (BioVis), 2011 IEEE Symposium on}, year = {2011}, month = {2011/10//}, pages = {111 - 118}, abstract = {Contemporary molecular dynamics simulations result in a glut of simulation data, making analysis and discovery a difficult and burdensome task. We present MDMap, a system designed to summarize long-running molecular dynamics (MD) simulations. We represent a molecular dynamics simulation as a state transition graph over a set of intermediate (stable and semi-stable) states. The transitions amongst the states together with their frequencies represent the flow of a biomolecule through the trajectory space. MDMap automatically determines potential intermediate conformations and the transitions amongst them by analyzing the conformational space explored by the MD simulation. MDMap is an automated system to visualize MD simulations as state-transition diagrams, and can replace the current tedious manual layouts of biomolecular folding landscapes with an automated tool. The layout of the representative states and the corresponding transitions among them is presented to the user as a visual synopsis of the long-running MD simulation. We compare and contrast multiple presentations of the state transition diagrams, such as conformational embedding, and spectral, hierarchical, and force-directed graph layouts. We believe this system could provide a road-map for the visualization of other stochastic time-varying simulations in a variety of different domains.}, keywords = {computing;digital, driven, DYNAMICS, exploration;data, folding, graph;stochastic, landscapes;data, layout;molecular, MDMap;biomolecular, method;stochastic, processes;, simulation;graph, simulations;state, simulations;trajectory, space;biology, theory;molecular, time-varying, transition}, doi = {10.1109/BioVis.2011.6094055}, author = {Patro,R. and Ip, Cheuk Yiu and Bista,S. and Cho,S.S. and Thirumalai,D. and Varshney, Amitabh} } @article {12859, title = {Metagenomic 16S rDNA Targeted PCR-DGGE in Determining Bacterial Diversity in Aquatic Ecosystem}, journal = {Bangladesh Journal of Microbiology}, volume = {27}, year = {2011}, month = {2011/12/13/}, abstract = {Bacterial numbers in surface water samples, collected randomly from six different water bodies, were estimated by acridine orange direct counting (AODC) and conventional culture-based heterotrophic plate counting (HPC). Bacterial genomic DNA was prepared from water samples by employing methods used for stool samples, including the population dynamics, were determined by primer extension of the 16S rDNA (V6/V8 region) using polymerase chain reaction (PCR), followed by denaturing gradient gel electrophoresis (DGGE), a metagenomic tool that is capable of separating unrelated DNAs based on the differences in their sequences and GC contents. The bacterial numbers in water samples ranged from 103 {\textendash} 106 CFU/ mL for HPC and 104 {\textendash} 107 cells/ mL for AODC, showing that a great majority of bacteria prevail as uncultivable which do not respond to culture methods that are used widely for tracking bacterial pathogens. The acridine orange-stained bacteria varied in sizes and shapes, and appeared either as planktonic (solitary) cells or as clusters of biofilms, showing the presence of diverse community under the epifluorescence microscope. The DGGE of the ca. 457 bp amplicons, as confirmed by agarose gel electrophoresis, produced bands that ranged in intensities and numbers from 18 to 31, with each band possibly indicating the presence of one or more closely related bacterial species. The enrichment of pathogenic bacteria in the aquatic ecosystem is known to precede the seasonal diarrhoeal outbreaks; therefore, bacterial community dynamics determined by Metagenomic 16S PCR-DGGE during pre-epidemic enrichment appears promising in predicting the upcoming diarrheal outbreaks.}, isbn = {1011-9981}, doi = {10.3329/bjm.v27i2.9171}, url = {http://www.banglajol.info/bd/index.php/BJM/article/view/9171}, author = {Hasan,Nur A. and Chowdhury,W Bari and Rahim,Niaz and Sultana,Marzia and Shabnam,S Antara and Mai,Volker and Ali,Afsar and Morris,Glen J and Sack,R. Bradley and Huq,Anwar and Rita R Colwell and Endtz,Hubert Ph and Cravioto,Alejandro and Alam,Munirul} } @article {12443, title = {Method and system for markerless motion capture using multiple cameras}, volume = {11/937,834}, year = {2011}, month = {2011/09/20/}, abstract = {Completely automated end-to-end method and system for markerless motion capture performs segmentation of articulating objects in Laplacian Eigenspace and is applicable to handling of the poses of some complexity. 3D voxel representation of acquired images are mapped to a higher dimensional space (k), where k depends on the number of articulated chains of the subject body, so as to extract the 1-D representations of the articulating chains. A bottom-up approach is suggested in order to build a parametric (spline-based) representation of a general articulated body in the high dimensional space followed by a top-down probabilistic approach that registers the segments to an average human body model. The parameters of the model are further optimized using the segmented and registered voxels.}, url = {http://www.google.com/patents?id=-THwAQAAEBAJ}, author = {Sundaresan,Aravind and Chellapa, Rama}, editor = {University of Maryland} } @article {16489, title = {New models and algorithms for throughput maximization in broadcast scheduling}, journal = {Approximation and Online Algorithms}, year = {2011}, month = {2011///}, pages = {71 - 82}, author = {Chekuri,C. and Gal,A. and Im,S. and Khuller, Samir and Li,J. and McCutchen,R. and Moseley,B. and Raschid, Louiqa} } @article {15774, title = {Nouveau-ROUGE: A Novelty Metric for Update Summarization}, journal = {Computational Linguistics}, volume = {37}, year = {2011}, month = {2011///}, pages = {1 - 8}, abstract = {An update summary should provide a fluent summarization of new information on a time-evolving topic, assuming that the reader has already reviewed older documents or summaries. In 2007 and 2008, an annual summarization evaluation included an update summarization task. Several participating systems produced update summaries indistinguishable from human-generated summaries when measured using ROUGE. However, no machine system performed near human-level performance in manual evaluations such as pyramid and overall responsiveness scoring.}, isbn = {0891-2017}, doi = {10.1162/coli_a_00033}, url = {http://dx.doi.org/10.1162/coli_a_00033}, author = {Conroy,John M. and Schlesinger,Judith D. and O{\textquoteright}Leary, Dianne P.} } @conference {14994, title = {NSF/IEEE-TCPP curriculum initiative on parallel and distributed computing: core topics for undergraduates}, booktitle = {Proceedings of the 42nd ACM technical symposium on Computer science education}, year = {2011}, month = {2011///}, pages = {617 - 618}, author = {Prasad,S. K. and Chtchelkanova,A. and Das,S. and Dehne,F. and Gouda,M. and Gupta,A. and JaJa, Joseph F. and Kant,K. and La Salle,A. and LeBlanc,R. and others} } @inbook {19037, title = {Oblivious RAM with O((logN)^3) Worst-Case Cost}, booktitle = {Advances in Cryptology {\textendash} ASIACRYPT 2011}, series = {Lecture Notes in Computer Science}, volume = {7073}, year = {2011}, month = {2011}, pages = {197 - 214}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Oblivious RAM is a useful primitive that allows a client to hide its data access patterns from an untrusted server in storage outsourcing applications. Until recently, most prior works on Oblivious RAM aim to optimize its amortized cost, while suffering from linear or even higher worst-case cost. Such poor worst-case behavior renders these schemes impractical in realistic settings, since a data access request can occasionally be blocked waiting for an unreasonably large number of operations to complete. This paper proposes novel Oblivious RAM constructions that achieves poly-logarithmic worst-case cost, while consuming constant client-side storage. To achieve the desired worst-case asymptotic performance, we propose a novel technique in which we organize the O-RAM storage into a binary tree over data buckets, while moving data blocks obliviously along tree edges.}, keywords = {Computer science}, isbn = {978-3-642-25384-3}, url = {http://www.springerlink.com/content/2214q8013376rj37/abstract/}, author = {Elaine Shi and Chan, T. and Stefanov, Emil and Li, Mingfei}, editor = {Lee, Dong and Wang, Xiaoyun} } @article {20383, title = {Occurrence of Vibrio cholerae in Municipal and Natural Waters and Incidence of Cholera in Azerbaijan}, journal = {EcoHealth}, year = {2011}, month = {Jan-12-2011}, pages = {468 - 477}, abstract = {Cholera, a waterborne disease caused by Vibrio cholerae, is an autochthonous member of the aquatic environment and predominantly reported from developing countries. Technical reports and proceedings were reviewed to determine the relationship between occurrence of V. cholerae in natural waters, including sources of municipal water, and cases of cholera in Azerbaijan. Water samples collected from different environmental sources from 1970 to 1998 were tested for V. cholerae and 0.73\% (864/117,893) were positive. The results showed that in April of each year, when the air temperature rose by approximately 5{\textdegree}C, V. cholerae could be isolated. With each increase in air temperature, 6{\textendash}8 weeks after, impact on cases of cholera was recorded. The incidence of cholera peaked when the air temperature reached >25{\textdegree}C during the month of September. It is concluded that a distinct seasonality in cholera incidence exists in Azerbaijan, with increased occurrence during warmer months.}, issn = {1612-9202}, doi = {10.1007/s10393-012-0756-8}, url = {http://link.springer.com/10.1007/s10393-012-0756-8}, author = {Gurbanov, Shair and Akhmadov, Rashid and Shamkhalova, Gulnara and Akhmadova, Sevinj and Haley, Bradd J. and Rita R Colwell and Huq, Anwar} } @conference {12449, title = {P2C2: Programmable pixel compressive camera for high speed imaging}, booktitle = {2011 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)}, year = {2011}, month = {2011/06/20/25}, pages = {329 - 336}, publisher = {IEEE}, organization = {IEEE}, abstract = {We describe an imaging architecture for compressive video sensing termed programmable pixel compressive camera (P2C2). P2C2 allows us to capture fast phenomena at frame rates higher than the camera sensor. In P2C2, each pixel has an independent shutter that is modulated at a rate higher than the camera frame-rate. The observed intensity at a pixel is an integration of the incoming light modulated by its specific shutter. We propose a reconstruction algorithm that uses the data from P2C2 along with additional priors about videos to perform temporal super-resolution. We model the spatial redundancy of videos using sparse representations and the temporal redundancy using brightness constancy constraints inferred via optical flow. We show that by modeling such spatio-temporal redundancies in a video volume, one can faithfully recover the underlying high-speed video frames from the observed low speed coded video. The imaging architecture and the reconstruction algorithm allows us to achieve temporal super-resolution without loss in spatial resolution. We implement a prototype of P2C2 using an LCOS modulator and recover several videos at 200 fps using a 25 fps camera.}, keywords = {Brightness, brightness constancy constraint, camera sensor, CAMERAS, compressive video sensing, high speed imaging, high-speed video frames, Image sequences, imaging, imaging architecture, independent shutter, Liquid crystal on silicon, low speed coded video, Modulation, optical flow, P2C2, programmable pixel compressive camera, reconstruction algorithm, sparse representation, Spatial resolution, spatio-temporal redundancies, temporal redundancy, temporal super-resolution, video coding}, isbn = {978-1-4577-0394-2}, doi = {10.1109/CVPR.2011.5995542}, author = {Reddy, D. and Veeraraghavan,A. and Chellapa, Rama} } @conference {13079, title = {Piecing together the segmentation jigsaw using context}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on}, year = {2011}, month = {2011/06//}, pages = {2001 - 2008}, abstract = {We present an approach to jointly solve the segmentation and recognition problem using a multiple segmentation framework. We formulate the problem as segment selection from a pool of segments, assigning each selected segment a class label. Previous multiple segmentation approaches used local appearance matching to select segments in a greedy manner. In contrast, our approach formulates a cost function based on contextual information in conjunction with appearance matching. This relaxed cost function formulation is minimized using an efficient quadratic programming solver and an approximate solution is obtained by discretizing the relaxed solution. Our approach improves labeling performance compared to other segmentation based recognition approaches.}, keywords = {algorithms;image, approximation, formulation;greedy, function, information;cost, manner;image, programming;approximation, recognition;image, segmentation;, segmentation;jigsaw, segmentation;quadratic, solution;contextual, theory;greedy}, doi = {10.1109/CVPR.2011.5995367}, author = {Chen,Xi and Jain, A. and Gupta,A. and Davis, Larry S.} } @conference {13461, title = {Playing to Program: Towards an Intelligent Programming Tutor for RUR-PLE}, booktitle = {Second AAAI Symposium on Educational Advances in Artificial Intelligence}, year = {2011}, month = {2011/04/08/}, abstract = {Intelligent tutoring systems (ITSs) provide students with a one-on-one tutor, allowing them to work at their own pace, and helping them to focus on their weaker areas. The RUR1{\textendash}Python Learning Environment (RUR-PLE), a game-like virtual environment to help students learn to program, provides an interface for students to write their own Python code and visualize the code execution (Roberge 2005). RUR-PLE provides a fixed sequence of learning lessons for students to explore. We are extending RUR-PLE to develop the Playing to Program (PtP) ITS, which consists of three components: (1) a Bayesian student model that tracks student competence, (2) a diagnosis module that provides tailored feedback to students, and (3) a problem selection module that guides the student{\textquoteright}s learning process. In this paper, we summarize RUR-PLE and the PtP design, and describe an ongoing user study to evaluate the predictive accuracy of our student modeling approach.}, url = {http://www.aaai.org/ocs/index.php/EAAI/EAAI11/paper/viewPaper/3497}, author = {desJardins, Marie and Ciavolino,Amy and Deloatch,Robert and Feasley,Eliana} } @conference {19042, title = {Privacy settings from contextual attributes: A case study using Google Buzz}, year = {2011}, month = {2011}, pages = {257 - 262}, abstract = {Social networks provide users with privacy settings to control what information is shared with connections and other users. In this paper, we analyze factors influencing changes in privacy-related settings in the Google Buzz social network. Specifically, we show statistics on contextual data related to privacy settings that are derived from crawled datasets and analyze the characteristics of users who changed their privacy settings. We also investigate potential neighboring effects among such users.}, keywords = {contextual attributes, data privacy, Google Buzz, privacy settings, social networking (online), social networks, Statistics}, author = {Mashima, D. and Elaine Shi and Chow, R. and Sarkar, P. and Li,C. and Song,D.} } @conference {19019, title = {Privacy-preserving aggregation of time-series data}, volume = {17}, year = {2011}, month = {2011}, abstract = {We consider how an untrusted data aggregator canlearn desired statistics over multiple participants{\textquoteright} data, without compromising each individual{\textquoteright}s privacy. We propose a construction that allows a group of partici- pants to periodically upload encrypted values to a data aggregator, such that the aggregator is able to compute the sum of all participants{\textquoteright} values in every time period, but is unable to learn anything else. We achieve strong privacy guarantees using two main techniques. First, we show how to utilize applied cryptographic techniques to allow the aggregator to decrypt the sum from multiple ciphertexts encrypted under different user keys. Second, we describe a distributed data randomization procedure that guarantees the differential privacy of the outcome statistic, even when a subset of participants might be compromised. }, url = {http://www.eecs.berkeley.edu/~elaines/docs/ndss2011.pdf}, author = {Elaine Shi and Chan, T. and Rieffel, E. and Chow, R. and Song,D.} } @article {19043, title = {Private and Continual Release of Statistics}, journal = {ACM Transactions on Information and System Security (TISSEC)}, volume = {14}, year = {2011}, month = {2011}, pages = {26:1 - 26:24}, abstract = {We ask the question: how can Web sites and data aggregators continually release updated statistics, and meanwhile preserve each individual user{\textquoteright}s privacy? Suppose we are given a stream of 0{\textquoteright}s and 1{\textquoteright}s. We propose a differentially private continual counter that outputs at every time step the approximate number of 1{\textquoteright}s seen thus far. Our counter construction has error that is only poly-log in the number of time steps. We can extend the basic counter construction to allow Web sites to continually give top-k and hot items suggestions while preserving users{\textquoteright} privacy.}, keywords = {continual mechanism, Differential privacy, streaming algorithm}, isbn = {1094-9224}, url = {http://doi.acm.org/10.1145/2043621.2043626}, author = {Chan, T.-H. Hubert and Elaine Shi and Song, Dawn} } @article {18793, title = {Recent advances and future challenges in automated manufacturing planning}, journal = {Journal of Computing and Information Science in Engineering}, volume = {11}, year = {2011}, month = {2011///}, pages = {021006 - 021006}, author = {Bourne,D. and Corney,J. and Gupta,S.K.} } @conference {12453, title = {Recent advances in age and height estimation from still images and video}, booktitle = {2011 IEEE International Conference on Automatic Face \& Gesture Recognition and Workshops (FG 2011)}, year = {2011}, month = {2011/03/21/25}, pages = {91 - 96}, publisher = {IEEE}, organization = {IEEE}, abstract = {Soft-biometrics such as gender, age, race, etc have been found to be useful characterizations that enable fast pre-filtering and organization of data for biometric applications. In this paper, we focus on two useful soft-biometrics - age and height. We discuss their utility and the factors involved in their estimation from images and videos. In this context, we highlight the role that geometric constraints such as multiview-geometry, and shape-space geometry play. Then, we present methods based on these geometric constraints for age and height-estimation. These methods provide a principled means by fusing image-formation models, multi-view geometric constraints, and robust statistical methods for inference.}, keywords = {age estimation, biometrics (access control), Calibration, Estimation, Geometry, height estimation, HUMANS, image fusion, image-formation model fusion, Legged locomotion, multiview-geometry, Robustness, SHAPE, shape-space geometry, soft-biometrics, statistical analysis, statistical methods, video signal processing}, isbn = {978-1-4244-9140-7}, doi = {10.1109/FG.2011.5771367}, author = {Chellapa, Rama and Turaga,P.} } @article {12434, title = {Remote identification of faces: Problems, prospects, and progress}, journal = {Pattern Recognition Letters}, year = {2011}, month = {2011/12//}, abstract = {Face recognition in unconstrained acquisition conditions is one of the most challenging problems that has been actively researched in recent years. It is well known that many state-of-the-art still face recognition algorithms perform well, when constrained (frontal, well illuminated, high-resolution, sharp, and full) face images are acquired. However, their performance degrades significantly when the test images contain variations that are not present in the training images. In this paper, we highlight some of the key issues in remote face recognition. We define the remote face recognition as one where faces are several tens of meters (10{\textendash}250\&$\#$xa0;m) from the cameras. We then describe a remote face database which has been acquired in an unconstrained outdoor maritime environment. Recognition performance of a subset of existing still image-based face recognition algorithms is evaluated on the remote face data set. Further, we define the remote re-identification problem as matching a subject at one location with candidate sets acquired at a different location and over time in remote conditions. We provide preliminary experimental results on remote re-identification. It is demonstrated that in addition to applying a good classification algorithm, finding features that are robust to variations mentioned above and developing statistical models which can account for these variations are very important for remote face recognition.}, keywords = {Blur, illumination, low-resolution, pose variation, Re-identification, Remote face recognition}, isbn = {0167-8655}, doi = {10.1016/j.patrec.2011.11.020}, url = {http://www.sciencedirect.com/science/article/pii/S0167865511004107}, author = {Chellapa, Rama and Ni,Jie and Patel, Vishal M.} } @article {12861, title = {Role of Zooplankton Diversity in Vibrio Cholerae Population Dynamics and in the Incidence of Cholera in the Bangladesh Sundarbans}, journal = {Applied and Environmental Microbiology}, volume = {77}, year = {2011}, month = {09/2011}, pages = {6125 - 6132}, abstract = {Vibrio cholerae, a bacterium autochthonous to the aquatic environment, is the causative agent of cholera, a severe watery, life-threatening diarrheal disease occurring predominantly in developing countries. V. cholerae, including both serogroups O1 and O139, is found in association with crustacean zooplankton, mainly copepods, and notably in ponds, rivers, and estuarine systems globally. The incidence of cholera and occurrence of pathogenic V. cholerae strains with zooplankton were studied in two areas of Bangladesh: Bakerganj and Mathbaria. Chitinous zooplankton communities of several bodies of water were analyzed in order to understand the interaction of the zooplankton population composition with the population dynamics of pathogenic V. cholerae and incidence of cholera. Two dominant zooplankton groups were found to be consistently associated with detection of V. cholerae and/or occurrence of cholera cases, namely, rotifers and cladocerans, in addition to copepods. Local differences indicate there are subtle ecological factors that can influence interactions between V. cholerae, its plankton hosts, and the incidence of cholera.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.01472-10}, url = {http://aem.asm.org/content/77/17/6125}, author = {De Magny,Guillaume Constantin and Mozumder,Pronob K. and Grim,Christopher J. and Hasan,Nur A. and Naser,M. Niamul and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @article {16041, title = {Seven guiding scenarios for information visualization evaluation}, volume = {2011-992-04}, year = {2011}, month = {2011///}, institution = {Department of Computer Science, University of Calgary}, abstract = {We take a new, scenario based look at evaluation in information visualization. Our seven scenarios, evaluatingvisual data analysis and reasoning, evaluating user performance, evaluating user experience, evaluating environments and work practices, evaluating communication through visualization, automated evaluation of visualizations, and evaluating collaborative data analysis were derived through an extensive literature review of over 800 visualization publications. These scenarios are described through their goals, the types of questions they embody and illustrated through example studies. Through this broad survey and the distillation of these scenarios we make two contributions. One, we encapsulate the current practices in the information visualization research community and, two, we provide a different approach to reaching decisions about what might be the most effective evaluation of a given information visualization. For example, if the research goals or evaluative questions are known they can be used to map to specific scenarios, where practical existing examples can be considered for effective evaluation approaches. }, author = {Lam,H. and Bertini,E. and Isenberg,P. and Plaisant, Catherine and Carpendale,S.} } @conference {13643, title = {Shape Codebook based Handwritten and Machine Printed Text Zone Extraction}, booktitle = {Document Recognition and Retrieval}, year = {2011}, month = {2011/01//}, pages = {7874:1-8 - 7874:1-8}, address = {San Francisco}, abstract = {We present a novel method for extracting handwritten and printed text zones from noisy document images with mixed content. We use Triple-Adjacent-Segment (TAS) based features which encode local shape characteristics of text in a consistent manner. We first construct two different codebooks of the shape features extracted from a set of handwritten and printed text documents. In the next step, we compute the normalized histogram of codewords for each segmented zone and use it to train Support Vector Machine (SVM) classifier. Due to a codebook based approach, our method is robust to the background noise present in the image. The TAS features used are invariant to translation, scale and rotation of text. In our experimental results, we show that a pixel-weighted zone classification accuracy of 98\% can be achieved for noisy Arabic documents. Further, we demonstrate the effectiveness of our method for document page classification and show that a high precision can be achieved for machine printed documents. The proposed method is robust to the size of zones, which may contain text content at word, line or paragraph level.}, author = {Kumar,Jayant and Prasad,Rohit and Cao,Huiagu and Abd-Almageed, Wael and David Doermann and Natarajan,Prem} } @article {11906, title = {Silhouette-based gesture and action recognition via modeling trajectories on Riemannian shape manifolds}, journal = {Computer Vision and Image Understanding}, volume = {115}, year = {2011}, month = {2011/03//}, pages = {439 - 455}, abstract = {This paper addresses the problem of recognizing human gestures from videos using models that are built from the Riemannian geometry of shape spaces. We represent a human gesture as a temporal sequence of human poses, each characterized by a contour of the associated human silhouette. The shape of a contour is viewed as a point on the shape space of closed curves and, hence, each gesture is characterized and modeled as a trajectory on this shape space. We propose two approaches for modeling these trajectories. In the first template-based approach, we use dynamic time warping (DTW) to align the different trajectories using elastic geodesic distances on the shape space. The gesture templates are then calculated by averaging the aligned trajectories. In the second approach, we use a graphical model approach similar to an exemplar-based hidden Markov model, where we cluster the gesture shapes on the shape space, and build non-parametric statistical models to capture the variations within each cluster. We model each gesture as a Markov model of transitions between these clusters. To evaluate the proposed approaches, an extensive set of experiments was performed using two different data sets representing gesture and action recognition applications. The proposed approaches not only are successfully able to represent the shape and dynamics of the different classes for recognition, but are also robust against some errors resulting from segmentation and background subtraction.}, keywords = {Action recognition, Gesture recognition, Riemannian manifolds, Shape space, Silhouette-based approaches}, isbn = {1077-3142}, doi = {16/j.cviu.2010.10.006}, url = {http://www.sciencedirect.com/science/article/pii/S1077314210002377}, author = {Abdelkader,Mohamed F. and Abd-Almageed, Wael and Srivastava,Anuj and Chellapa, Rama} } @conference {13329, title = {Simplifying morphological representations of 2D and 3D scalar fields}, booktitle = {Proceedings of the 19th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems}, series = {GIS {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {437 - 440}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We describe a dual graph-based representation for the ascending and descending Morse complexes of a scalar field, and a compact and dimension-independent data structure based on it, which assumes a discrete representation of the field as a simplicial mesh. We present atomic dimension-independent simplification operators on the graph-based representation. Based on such operators, we have developed a simplification algorithm, which allows generalization of the ascending and descending Morse complexes at different levels of resolution. We show here the results of our implementation, discussing the computation times and the size of the resulting simplified graphs, also in comparison with the size of the original full-resolution graph.}, keywords = {morphological representations, Morse complexes, multi-dimensional data sets, simplification}, isbn = {978-1-4503-1031-4}, doi = {10.1145/2093973.2094042}, url = {http://doi.acm.org/10.1145/2093973.2094042}, author = {{\v C}omi{\'c},Lidija and De Floriani, Leila and Iuricich,Federico} } @conference {13330, title = {Smale-like decomposition and forman theory for discrete scalar fields}, booktitle = {Discrete Geometry for Computer Imagery}, year = {2011}, month = {2011///}, pages = {477 - 488}, abstract = {Forman theory, which is a discrete alternative for cell complexes to the well-known Morse theory, is currently finding several applications in areas where the data to be handled are discrete, such as image processing and computer graphics. Here, we show that a discrete scalar field f, defined on the vertices of a triangulated multidimensional domain Σ, and its gradient vector field Grad f through the Smale-like decomposition of f [6], are both the restriction of a Forman function F and its gradient field Grad F that extends f over all the simplexes of Σ. We present an algorithm that gives an explicit construction of such an extension. Hence, the scalar field f inherits the properties of Forman gradient vector fields and functions from field Grad F and function F.}, doi = {10.1007/978-3-642-19867-0_40}, author = {{\v C}omi{\'c},L. and Mesmoudi,M. and De Floriani, Leila} } @article {13072, title = {Smart task-driven video collection}, volume = {11/649,393}, year = {2011}, month = {2011/06/14/}, abstract = {A multi-camera system that collects images and videos of moving objects in dynamic and crowded scenes, subject to task constraints is disclosed. The system constructs {\textquotedblleft}task visibility intervals{\textquotedblright} comprising information about what can be sensed in future time intervals. Methods for constructing these intervals applying prediction of future object motion and including consideration of factors such as object occlusion and camera control parameters are also disclosed. Using a plane-sweep algorithm, these atomic intervals can be combined in a method to form multi-task intervals, during which a single camera can collect videos suitable for multiple tasks simultaneously. Methods for fast camera scheduling that yield solutions within a small constant factor of an optimal solution are also disclosed.}, url = {http://www.google.com/patents?id=pgPnAQAAEBAJ}, author = {Lim,Ser-Nam and Mittal,Anurag and Davis, Larry S.}, editor = {Siemens Corporation} } @conference {12436, title = {Sparse dictionary-based representation and recognition of action attributes}, booktitle = {2011 IEEE International Conference on Computer Vision (ICCV)}, year = {2011}, month = {2011/11/06/13}, pages = {707 - 714}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present an approach for dictionary learning of action attributes via information maximization. We unify the class distribution and appearance information into an objective function for learning a sparse dictionary of action attributes. The objective function maximizes the mutual information between what has been learned and what remains to be learned in terms of appearance information and class distribution for each dictionary item. We propose a Gaussian Process (GP) model for sparse representation to optimize the dictionary objective function. The sparse coding property allows a kernel with a compact support in GP to realize a very efficient dictionary learning process. Hence we can describe an action video by a set of compact and discriminative action attributes. More importantly, we can recognize modeled action categories in a sparse feature space, which can be generalized to unseen and unmodeled action categories. Experimental results demonstrate the effectiveness of our approach in action recognition applications.}, keywords = {action attributes, appearance information, class distribution, Dictionaries, dictionary learning process, Encoding, Entropy, Gaussian process model, Gaussian processes, Histograms, HUMANS, Image coding, image representation, information maximization, learning (artificial intelligence), modeled action categories, Mutual information, Object recognition, probabilistic logic, sparse coding property, sparse dictionary-based recognition, sparse dictionary-based representation, sparse feature space, unmodeled action categories}, isbn = {978-1-4577-1101-5}, doi = {10.1109/ICCV.2011.6126307}, author = {Qiang Qiu and Zhuolin Jiang and Chellapa, Rama} } @article {15907, title = {Sparsity-motivated automatic target recognition}, journal = {Applied OpticsAppl. Opt.}, volume = {50}, year = {2011}, month = {2011/04/01/}, pages = {1425 - 1433}, abstract = {We present an automatic target recognition algorithm using the recently developed theory of sparse representations and compressive sensing. We show how sparsity can be helpful for efficient utilization of data for target recognition. We verify the efficacy of the proposed algorithm in terms of the recognition rate and confusion matrices on the well known Comanche (Boeing{\textendash}Sikorsky, USA) forward-looking IR data set consisting of ten different military targets at different orientations.}, keywords = {IMAGE PROCESSING, Image recognition, algorithms and filters, pattern recognition, Vision - patterns and recognition}, doi = {10.1364/AO.50.001425}, url = {http://ao.osa.org/abstract.cfm?URI=ao-50-10-1425}, author = {Patel, Vishal M. and Nasrabadi,Nasser M. and Chellapa, Rama} } @article {12442, title = {Special Issue on Video Analysis on Resource-Limited Systems}, journal = {IEEE Transactions on Circuits and Systems for Video Technology}, volume = {21}, year = {2011}, month = {2011/10//}, pages = {1349 - 1352}, abstract = {The 17 papers in this special issue focus on resource-limited systems.}, keywords = {computational complexity, Image Enhancement, Special issues and sections, Video compression}, isbn = {1051-8215}, doi = {10.1109/TCSVT.2011.2165795}, author = {Chellapa, Rama and Cavallaro, A. and Wu,Y. and Shan, C. and Fu, Y. and Pulli, K.} } @inbook {17378, title = {Speeding Up Network Layout and Centrality Measures for Social Computing Goals}, booktitle = {Social Computing, Behavioral-Cultural Modeling and PredictionSocial Computing, Behavioral-Cultural Modeling and Prediction}, series = {Lecture Notes in Computer Science}, volume = {6589}, year = {2011}, month = {2011///}, pages = {244 - 251}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper presents strategies for speeding up calculation of graph metrics and layout by exploiting the parallel architecture of modern day Graphics Processing Units (GPU), specifically Compute Unified Device Architecture ( CUDA ) by Nvidia . Graph centrality metrics like Eigenvector , Betweenness , Page Rank and layout algorithms like Fruchterman - Rheingold are essential components of Social Network Analysis ( SNA ). With the growth in adoption of SNA in different domains and increasing availability of huge networked datasets for analysis, social network analysts require faster tools that are also scalable. Our results, using NodeXL, show up to 802 times speedup for a Fruchterman-Rheingold graph layout and up to 17,972 times speedup for Eigenvector centrality metric calculations on a 240 core CUDA-capable GPU.}, isbn = {978-3-642-19655-3}, url = {http://dx.doi.org/10.1007/978-3-642-19656-0_35}, author = {Sharma,Puneet and Khurana,Udayan and Shneiderman, Ben and Scharrenbroich,Max and Locke,John}, editor = {Salerno,John and Yang,Shanchieh and Nau, Dana S. and Chai,Sun-Ki} } @article {12439, title = {Statistical Computations on Grassmann and Stiefel Manifolds for Image and Video-Based Recognition}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {33}, year = {2011}, month = {2011/11//}, pages = {2273 - 2286}, abstract = {In this paper, we examine image and video-based recognition applications where the underlying models have a special structure-the linear subspace structure. We discuss how commonly used parametric models for videos and image sets can be described using the unified framework of Grassmann and Stiefel manifolds. We first show that the parameters of linear dynamic models are finite-dimensional linear subspaces of appropriate dimensions. Unordered image sets as samples from a finite-dimensional linear subspace naturally fall under this framework. We show that an inference over subspaces can be naturally cast as an inference problem on the Grassmann manifold. To perform recognition using subspace-based models, we need tools from the Riemannian geometry of the Grassmann manifold. This involves a study of the geometric properties of the space, appropriate definitions of Riemannian metrics, and definition of geodesics. Further, we derive statistical modeling of inter and intraclass variations that respect the geometry of the space. We apply techniques such as intrinsic and extrinsic statistics to enable maximum-likelihood classification. We also provide algorithms for unsupervised clustering derived from the geometry of the manifold. Finally, we demonstrate the improved performance of these methods in a wide variety of vision applications such as activity recognition, video-based face recognition, object recognition from image sets, and activity-based video clustering.}, keywords = {activity based video clustering, activity recognition, computational geometry, Computational modeling, Data models, face recognition, feature representation, finite dimensional linear subspaces, geometric properties, Geometry, Grassmann Manifolds, Grassmann., HUMANS, Image and video models, image recognition, linear dynamic models, linear subspace structure, Manifolds, maximum likelihood classification, maximum likelihood estimation, Object recognition, Riemannian geometry, Riemannian metrics, SHAPE, statistical computations, statistical models, Stiefel, Stiefel Manifolds, unsupervised clustering, video based face recognition, video based recognition, video signal processing}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2011.52}, author = {Turaga,P. and Veeraraghavan,A. and Srivastava, A. and Chellapa, Rama} } @conference {12441, title = {Synthesis-based recognition of low resolution faces}, booktitle = {2011 International Joint Conference on Biometrics (IJCB)}, year = {2011}, month = {2011/10/11/13}, pages = {1 - 6}, publisher = {IEEE}, organization = {IEEE}, abstract = {Recognition of low resolution face images is a challenging problem in many practical face recognition systems. Methods have been proposed in the face recognition literature for the problem when the probe is of low resolution, and a high resolution gallery is available for recognition. These methods modify the probe image such that the resultant image provides better discrimination. We formulate the problem differently by leveraging the information available in the high resolution gallery image and propose a generative approach for classifying the probe image. An important feature of our algorithm is that it can handle resolution changes along with illumination variations. The effective- ness of the proposed method is demonstrated using standard datasets and a challenging outdoor face dataset. It is shown that our method is efficient and can perform significantly better than many competitive low resolution face recognition algorithms.}, keywords = {Dictionaries, Face, face images, face recognition, face recognition literature, face recognition systems, illumination variations, image resolution, low resolution faces, Organizations, PROBES, support vector machines, synthesis based recognition}, isbn = {978-1-4577-1358-3}, doi = {10.1109/IJCB.2011.6117545}, author = {Shekhar, S. and Patel, Vishal M. and Chellapa, Rama} } @article {12860, title = {Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus}, journal = {The ISME Journal}, volume = {6}, year = {2011}, month = {2011/12/08/}, pages = {835 - 846}, abstract = {Sea surface temperatures (SST) are rising because of global climate change. As a result, pathogenic Vibrio species that infect humans and marine organisms during warmer summer months are of growing concern. Coral reefs, in particular, are already experiencing unprecedented degradation worldwide due in part to infectious disease outbreaks and bleaching episodes that are exacerbated by increasing SST. For example, Vibrio coralliilyticus, a globally distributed bacterium associated with multiple coral diseases, infects corals at temperatures above 27 {\textdegree}C. The mechanisms underlying this temperature-dependent pathogenicity, however, are unknown. In this study, we identify potential virulence mechanisms using whole genome sequencing of V. coralliilyticus ATCC (American Type Culture Collection) BAA-450. Furthermore, we demonstrate direct temperature regulation of numerous virulence factors using proteomic analysis and bioassays. Virulence factors involved in motility, host degradation, secretion, antimicrobial resistance and transcriptional regulation are upregulated at the higher virulent temperature of 27 {\textdegree}C, concurrent with phenotypic changes in motility, antibiotic resistance, hemolysis, cytotoxicity and bioluminescence. These results provide evidence that temperature regulates multiple virulence mechanisms in V. coralliilyticus, independent of abundance. The ecological and biological significance of this temperature-dependent virulence response is reinforced by climate change models that predict tropical SST to consistently exceed 27 {\textdegree}C during the spring, summer and fall seasons. We propose V. coralliilyticus as a model Gram-negative bacterium to study temperature-dependent pathogenicity in Vibrio-related diseases.}, keywords = {ecophysiology, ecosystems, environmental biotechnology, geomicrobiology, ISME J, microbe interactions, microbial communities, microbial ecology, microbial engineering, microbial epidemiology, microbial genomics, microorganisms}, isbn = {1751-7362}, doi = {10.1038/ismej.2011.154}, url = {http://www.nature.com/ismej/journal/v6/n4/full/ismej2011154a.html}, author = {Kimes,Nikole E. and Grim,Christopher J. and Johnson,Wesley R. and Hasan,Nur A. and Tall,Ben D. and Kothary,Mahendra H. and Kiss,Hajnalka and Munk,A. Christine and Tapia,Roxanne and Green,Lance and Detter,Chris and Bruce,David C. and Brettin,Thomas S. and Rita R Colwell and Morris,Pamela J.} } @inbook {16046, title = {Temporal Visualization of Social Network Dynamics: Prototypes for Nation of Neighbors}, booktitle = {Social Computing, Behavioral-Cultural Modeling and PredictionSocial Computing, Behavioral-Cultural Modeling and Prediction}, series = {Lecture Notes in Computer Science}, volume = {6589}, year = {2011}, month = {2011///}, pages = {309 - 316}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Information visualization is a powerful tool for analyzing the dynamic nature of social communities. Using Nation of Neighbors community network as a testbed, we propose five principles of implementing temporal visualizations for social networks and present two research prototypes: NodeXL and TempoVis. Three different states are defined in order to visualize the temporal changes of social networks. We designed the prototypes to show the benefits of the proposed ideas by letting users interactively explore temporal changes of social networks.}, isbn = {978-3-642-19655-3}, url = {http://dx.doi.org/10.1007/978-3-642-19656-0_43}, author = {Ahn,Jae-wook and Taieb-Maimon,Meirav and Sopan,Awalin and Plaisant, Catherine and Shneiderman, Ben}, editor = {Salerno,John and Yang,Shanchieh and Nau, Dana S. and Chai,Sun-Ki} } @conference {17979, title = {Toolchain for Programming, Simulating and Studying the XMT Many-Core Architecture}, booktitle = {Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on}, year = {2011}, month = {2011/05//}, pages = {1282 - 1291}, abstract = {The Explicit Multi-Threading (XMT) is a general-purpose many-core computing platform, with the vision of a 1000-core chip that is easy to program but does not compromise on performance. This paper presents a publicly available tool chain for XMT, complete with a highly configurable cycle-accurate simulator and an optimizing compiler. The XMT tool chain has matured and has been validated to a point where its description merits publication. In particular, research and experimentation enabled by the tool chain played a central role in supporting the ease-of-programming and performance aspects of the XMT architecture. The compiler and the simulator are also important milestones for an efficient programmer{\textquoteright}s workflow from PRAM algorithms to programs that run on the shared memory XMT hardware. This workflow is a key component in accomplishing the dual goal of ease-of-programming and performance. The applicability of our tool chain extends beyond specific XMT choices. It can be used to explore the much greater design space of shared memory many-cores by system researchers or by programmers. As the tool chain can practically run on any computer, it provides a supportive environment for teaching parallel algorithmic thinking with a programming component. Unobstructed by techniques such as decomposition-first and programming for locality, this environment may be useful in deferring the teaching of these techniques, when desired, to more advanced or platform-specific courses.}, keywords = {algorithm;XMT, architecture;XMT, architectures;shared, chain;cycle-accurate, compiler;programmer, compilers;parallel, component;shared, computing;optimizing, hardware;shared, many-core, many-core;concurrency, memory, multithreading;general-purpose, PRAM, simulator;ease-of-programming;explicit, systems;, theory;multi-threading;optimising, tool, workflow;programming, XMT}, doi = {10.1109/IPDPS.2011.270}, author = {Keceli,F. and Tzannes,A. and Caragea,G.C. and Barua,R. and Vishkin, Uzi} } @conference {12452, title = {Towards view-invariant expression analysis using analytic shape manifolds}, booktitle = {2011 IEEE International Conference on Automatic Face \& Gesture Recognition and Workshops (FG 2011)}, year = {2011}, month = {2011/03/21/25}, pages = {306 - 313}, publisher = {IEEE}, organization = {IEEE}, abstract = {Facial expression analysis is one of the important components for effective human-computer interaction. However, to develop robust and generalizable models for expression analysis one needs to break the dependence of the models on the choice of the coordinate frame of the camera i.e. expression models should generalize across facial poses. To perform this systematically, one needs to understand the space of observed images subject to projective transformations. However, since the projective shape-space is cumbersome to work with, we address this problem by deriving models for expressions on the affine shape-space as an approximation to the projective shape-space by using a Riemannian interpretation of deformations that facial expressions cause on different parts of the face. We use landmark configurations to represent facial deformations and exploit the fact that the affine shape-space can be studied using the Grassmann manifold. This representation enables us to perform various expression analysis and recognition algorithms without the need for the normalization as a preprocessing step. We extend some of the available approaches for expression analysis to the Grassmann manifold and experimentally show promising results, paving the way for a more general theory of view-invariant expression analysis.}, keywords = {Databases, Deformable models, Face, face recognition, facial expression analysis, Geometry, Gold, Human-computer interaction, Manifolds, projective transformation, Riemannian interpretation, SHAPE, view invariant expression analysis}, isbn = {978-1-4244-9140-7}, doi = {10.1109/FG.2011.5771415}, author = {Taheri, S. and Turaga,P. and Chellapa, Rama} } @inbook {12458, title = {Tracking and Identification via Object Reflectance Using a Hyperspectral Video Camera}, booktitle = {Machine Vision Beyond Visible SpectrumMachine Vision Beyond Visible Spectrum}, series = {Augmented Vision and Reality}, volume = {1}, year = {2011}, month = {2011///}, pages = {201 - 219}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Recent advances in electronics and sensor design have enabled the development of a hyperspectral video camera that can capture hyperspectral datacubes at near video rates. The sensor offers the potential for novel and robust methods for surveillance by combining methods from computer vision and hyperspectral image analysis. Here, we focus on the problem of tracking objects through challenging conditions, such as rapid illumination and pose changes, occlusions, and in the presence of confusers. A new framework that incorporates radiative transfer theory to estimate object reflectance and particle filters to simultaneously track and identify an object based on its reflectance spectra is proposed. By exploiting high-resolution spectral features in the visible and near-infrared regimes, the framework is able to track objects that appear featureless to the human eye. For example, we demonstrate that near-IR spectra of human skin can also be used to distinguish different people in a video sequence. These capabilities are illustrated using experiments conducted on real hyperspectral video data.}, isbn = {978-3-642-11568-4}, url = {http://dx.doi.org/10.1007/978-3-642-11568-4_9}, author = {Nguyen,Hien Van and Banerjee,Amit and Burlina,Philippe and Broadwater,Joshua and Chellapa, Rama}, editor = {Hammoud,Riad and Fan,Guoliang and McMillan,Robert W. W. and Ikeuchi,Katsushi and Hammoud,Riad I. and Wolff,Lawrence B.} } @conference {14850, title = {Trainable 3D recognition using stereo matching}, booktitle = {Computer Vision Workshops (ICCV Workshops), 2011 IEEE International Conference on}, year = {2011}, month = {2011///}, pages = {625 - 631}, abstract = {Stereo matching has been used for face recognition in the presence of pose variation. In this approach, stereo matching is used to compare two 2-D images based on correspondences that reflect the effects of viewpoint variation and allow for occlusion. We show how to use stereo matching to derive image descriptors that can be used to train a classifier. This improves face recognition performance, producing the best published results on the CMU PIE dataset. We also demonstrate that classification based on stereo matching can be used for general object classification in the presence of pose variation. In preliminary experiments we show promising results on the 3D object class dataset, a standard, challenging 3D classification data set.}, keywords = {2D, 3D, class, classification, classification;image, data, dataset;CMU, dataset;face, descriptor;occlusion;pose, estimation;solid, image, image;3D, matching;pose, matching;trainable, modelling;stereo, object, PIE, processing;, recognition;face, recognition;image, set;3D, variation;stereo}, doi = {10.1109/ICCVW.2011.6130301}, author = {Castillo,C. D and Jacobs, David W.} } @article {17445, title = {Tutorial-Graph Analytics {\textemdash} Lessons Learned and Challenges Ahead}, journal = {IEEE Computer Graphics and Applications}, volume = {31}, year = {2011}, month = {2011///}, pages = {18 - 18}, author = {Wong,P.C. and Chen,C. and G{\"o}rg,C. and Shneiderman, Ben and Stasko,J. and Thomas,J.} } @conference {12445, title = {Variable remapping of images from very different sources}, booktitle = {2011 18th IEEE International Conference on Image Processing (ICIP)}, year = {2011}, month = {2011/09/11/14}, pages = {1501 - 1504}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present a system which registers image sequences acquired by very different sources, so that multiple views could be transformed to the same coordinates system. This enables the functionality of automatic object identification and confirmation across views and platforms. The capability of the system comes from three ingredients: 1) image context enlargement through temporal integration; 2) robust motion estimation using the G-RANSAC framework with a relaxed correspondence criteria; 3) constrained motion estimation within the G-RANSAC framework. The proposed system has worked successfully on thousands of frames from multiple collections with significant variations in scale and resolution.}, keywords = {automatic object identification, Buildings, CAMERAS, Conferences, constrained motion estimation, coordinates system, Estimation, G-RANSAC framework, image context enlargement, Image Enhancement, image registration, image sequence registration, Image sequences, Motion estimation, Robustness, temporal integration, variable image remapping}, isbn = {978-1-4577-1304-0}, doi = {10.1109/ICIP.2011.6115729}, author = {Wei Zhang and Yanlin Guo and Meth, R. and Sokoloff, H. and Pope, A. and Strat, T. and Chellapa, Rama} } @conference {19259, title = {Vectorization and mapping of software defined radio applications on heterogeneous multi-processor platforms}, booktitle = {2011 IEEE Workshop on Signal Processing Systems (SiPS)}, year = {2011}, month = {2011}, pages = {31 - 36}, abstract = {A variety of multiprocessor architectures have proliferated even for off-the-shelf computing platforms. To improve performance and productivity for common heterogeneous systems, we have developed a workflow to generate efficient solutions. By starting with a formal description of an application and the mapping problem we are able to generate a range of designs that efficiently trade-of latency and throughput. In this approach, efficient utilization of SIMD cores is achieved by applying extensive block processing in conjunction with efficient mapping and scheduling. We demonstrate our approach through an integration into the GNU Radio environment for software defined radio system design.}, keywords = {Benchmark testing, block processing, Design methodology, formal description, GNU radio environment, Graphic Processor Unit, Graphics processing unit, heterogeneous multiprocessor platform, mapping problem, Multicore processing, Multiprocessing systems, multiprocessor architecture, multiprocessor scheduling, operating systems (computers), PARALLEL PROCESSING, Processor scheduling, Schedules, SIMD core, Software Defined Radio, software defined radio system design, software radio, telecommunication computing, Throughput, vectorization, workflow}, author = {Zaki, G.F. and Plishker,W. and Bhattacharyya, Shuvra S. and Clancy, C. and Kuykendall, J.} } @conference {17484, title = {Visual Analysis of Temporal Trends in Social Networks Using Edge Color Coding and Metric Timelines}, booktitle = {Privacy, Security, Risk and Trust (PASSAT), 2011 IEEE Third International Conference on and 2011 IEEE Third International Confernece on Social Computing (SocialCom)}, year = {2011}, month = {2011/10/09/11}, pages = {549 - 554}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present Net EvViz, a visualization tool for analysis and exploration of a dynamic social network. There are plenty of visual social network analysis tools but few provide features for visualization of dynamically changing networks featuring the addition or deletion of nodes or edges. Our tool extends the code base of the Node XL template for Microsoft Excel, a popular network visualization tool. The key features of this work are (1) The ability of the user to specify and edit temporal annotations to the network components in an Excel sheet, (2) See the dynamics of the network with multiple graph metrics plotted over the time span of the graph, called the Timeline, and (3) Temporal exploration of the network layout using an edge coloring scheme and a dynamic Time slider. The objectives of the new features presented in this paper are to let the data analysts, computer scientists and others to observe the dynamics or evolution in a network interactively. We presented Net EvViz to five users of Node XL and received positive responses.}, keywords = {Color, computer scientists, data analysts, data visualisation, Data visualization, dynamic social network, dynamic timeslider, edge color coding, excel sheet, Image coding, image colour analysis, Layout, measurement, metric timelines, Microsoft excel, multiple graph metrics, Net EvViz, network components, network layout, network visualization tool, NodeXL template, social networking (online), temporal trends, Twitter, Visualization}, isbn = {978-1-4577-1931-8}, doi = {10.1109/PASSAT/SocialCom.2011.212}, author = {Khurana,U. and Nguyen,Viet-An and Hsueh-Chien Cheng and Ahn,Jae-wook and Chen,Xi and Shneiderman, Ben} } @article {12862, title = {Warming Oceans, Phytoplankton, and River Discharge: Implications for Cholera Outbreaks}, journal = {The American Journal of Tropical Medicine and Hygiene}, volume = {85}, year = {2011}, month = {08/2011}, pages = {303 - 308}, abstract = {Phytoplankton abundance is inversely related to sea surface temperature (SST). However, a positive relationship is observed between SST and phytoplankton abundance in coastal waters of Bay of Bengal. This has led to an assertion that in a warming climate, rise in SST may increase phytoplankton blooms and, therefore, cholera outbreaks. Here, we explain why a positive SST-phytoplankton relationship exists in the Bay of Bengal and the implications of such a relationship on cholera dynamics. We found clear evidence of two independent physical drivers for phytoplankton abundance. The first one is the widely accepted phytoplankton blooming produced by the upwelling of cold, nutrient-rich deep ocean waters. The second, which explains the Bay of Bengal findings, is coastal phytoplankton blooming during high river discharges with terrestrial nutrients. Causal mechanisms should be understood when associating SST with phytoplankton and subsequent cholera outbreaks in regions where freshwater discharge are a predominant mechanism for phytoplankton production.}, isbn = {0002-9637,}, doi = {10.4269/ajtmh.2011.11-0181}, url = {http://www.ajtmh.org/content/85/2/303}, author = {Jutla,Antarpreet S. and Akanda,Ali S. and Griffiths,Jeffrey K. and Rita R Colwell and Islam,Shafiqul} } @conference {19464, title = {Why is My Internet Slow?: Making Network Speeds Visible}, booktitle = {SIGCHI {\textquoteright}11}, series = {CHI {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {1889 - 1898}, publisher = {ACM}, organization = {ACM}, abstract = {With widespread broadband adoption, more households report experiencing sub-optimal speeds. Not only are slow speeds frustrating, they may indicate consumers are not receiving the services they are paying for from their internet service providers. Yet, determining the speed and source of slow-downs is difficult because few tools exist for broadband management. We report on results of a field trial with 10 households using a visual network probe designed to address these problems. We describe the results of the study and provide design implications for future tools. More importantly, we argue that tools like this can educate and empower consumers by making broadband speeds and sources of slow-downs more visible.}, keywords = {broadband speed, broadband tools, home networks}, isbn = {978-1-4503-0228-9}, url = {http://doi.acm.org/10.1145/1978942.1979217}, author = {Marshini Chetty and Haslem, David and Baird, Andrew and Ofoha, Ugochi and Sumner, Bethany and Grinter, Rebecca} } @conference {14831, title = {Wide-baseline stereo for face recognition with large pose variation}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on}, year = {2011}, month = {2011/06//}, pages = {537 - 544}, abstract = {2-D face recognition in the presence of large pose variations presents a significant challenge. When comparing a frontal image of a face to a near profile image, one must cope with large occlusions, non-linear correspondences, and significant changes in appearance due to viewpoint. Stereo matching has been used to handle these problems, but performance of this approach degrades with large pose changes. We show that some of this difficulty is due to the effect that foreshortening of slanted surfaces has on window-based matching methods, which are needed to provide robustness to lighting change. We address this problem by designing a new, dynamic programming stereo algorithm that accounts for surface slant. We show that on the CMU PIE dataset this method results in significant improvements in recognition performance.}, keywords = {2D, algorithm;frontal, dataset;dynamic, estimation;stereo, Face, image, image;near, image;pose, MATCHING, matching;pose, matching;surface, method;dynamic, performance;stereo, PIE, processing;, profile, Programming, programming;face, recognition;CMU, recognition;image, slant;wide-baseline, stereo, stereo;window-based, variation;recognition}, doi = {10.1109/CVPR.2011.5995559}, author = {Castillo,C. D and Jacobs, David W.} } @article {15832, title = {Windowed Spectral Regularization of Inverse Problems}, journal = {SIAM Journal on Scientific Computing}, volume = {33}, year = {2011}, month = {2011///}, doi = {DOI: 10.1137/100809787}, author = {Chung,Julianne M. and Easley,Glenn R and O{\textquoteright}Leary, Dianne P.} } @article {12495, title = {Adaptive Threshold Estimation via Extreme Value Theory}, journal = {Signal Processing, IEEE Transactions on}, volume = {58}, year = {2010}, month = {2010/02//}, pages = {490 - 500}, abstract = {Determining a detection threshold to automatically maintain a low false alarm rate is a challenging problem. In a number of different applications, the underlying parametric assumptions of most automatic target detection algorithms are invalid. Therefore, thresholds derived using these incorrect distribution assumptions do not produce desirable results when applied to real sensor data. Monte Carlo methods for threshold determination work well but tend to perform poorly when targets are present. In order to mitigate these effects, we propose an algorithm using extreme value theory through the use of the generalized Pareto distribution (GPD) and a Kolmogorov-Smirnov statistical test. Unlike previous work based on GPD estimates, this algorithm incorporates a way to adaptively maintain low false alarm rates in the presence of targets. Both synthetic and real-world detection results demonstrate the usefulness of this algorithm.}, keywords = {detection;, detection;Pareto, distribution;adaptive, distribution;signal, estimation;extreme, estimation;signal, Kolmogorov-Smirnov, Pareto, statistical, test;adaptive, theory;generalized, threshold, value}, isbn = {1053-587X}, doi = {10.1109/TSP.2009.2031285}, author = {Broadwater, J.B. and Chellapa, Rama} } @inbook {12498, title = {Advances in Video-Based Human Activity Analysis: Challenges and Approaches}, booktitle = {Advances in ComputersAdvances in Computers}, volume = {Volume 80}, year = {2010}, month = {2010///}, pages = {237 - 290}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {Videos play an ever increasing role in our everyday lives with applications ranging from news, entertainment, scientific research, security, and surveillance. Coupled with the fact that cameras and storage media are becoming less expensive, it has resulted in people producing more video content than ever before. Analysis of human activities in video is important for several important applications. Interpretation and identification of human activities requires approaches that address the following questions (a) what are the appropriate atomic primitives for human activities, (b) how to combine primitives to produce complex activities, (c) what are the required invariances for inference algorithms, and (d) how to build computational models for each of these. In this chapter, we provide a broad overview and discussion of these issues. We shall review state-of-the-art computer vision algorithms that address these issues and then provide a unified perspective from which specific algorithms can be derived. We will then present supporting experimental results.}, isbn = {0065-2458}, url = {http://www.sciencedirect.com/science/article/pii/S0065245810800075}, author = {Turaga,Pavan and Chellapa, Rama and Veeraraghavan,Ashok}, editor = {Zelkowitz, Marvin V} } @inbook {12503, title = {Aligning Spatio-Temporal Signals on a Special Manifold}, booktitle = {Computer Vision {\textendash} ECCV 2010Computer Vision {\textendash} ECCV 2010}, series = {Lecture Notes in Computer Science}, volume = {6315}, year = {2010}, month = {2010///}, pages = {547 - 560}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We investigate the spatio-temporal alignment of videos or features/signals extracted from them. Specifically, we formally define an alignment manifold and formulate the alignment problem as an optimization procedure on this non-linear space by exploiting its intrinsic geometry. We focus our attention on semantically meaningful videos or signals, e.g., those describing or capturing human motion or activities, and propose a new formalism for temporal alignment accounting for executing rate variations among realizations of the same video event. By construction, we address this static and deterministic alignment task in a dynamic and stochastic manner: we regard the search for optimal alignment parameters as a recursive state estimation problem for a particular dynamic system evolving on the alignment manifold. Consequently, a Sequential Importance Sampling iteration on the alignment manifold is designed for effective and efficient alignment. We demonstrate the performance on several types of input data that arise in vision problems.}, isbn = {978-3-642-15554-3}, url = {http://dx.doi.org/10.1007/978-3-642-15555-0_40}, author = {Ruonan Li and Chellapa, Rama}, editor = {Daniilidis,Kostas and Maragos,Petros and Paragios,Nikos} } @article {12474, title = {Applications of a Simple Characterization of Human Gait in Surveillance}, journal = {Systems, Man, and Cybernetics, Part B: Cybernetics, IEEE Transactions on}, volume = {40}, year = {2010}, month = {2010/08//}, pages = {1009 - 1020}, abstract = {Applications of a simple spatiotemporal characterization of human gait in the surveillance domain are presented. The approach is based on decomposing a video sequence into x-t slices, which generate periodic patterns referred to as double helical signatures (DHSs). The features of DHS are given as follows: 1) they naturally encode the appearance and kinematics of human motion and reveal geometric symmetries and 2) they are effective and efficient for recovering gait parameters and detecting simple events. We present an iterative local curve embedding algorithm to extract the DHS from video sequences. Two applications are then considered. First, the DHS is used for simultaneous segmentation and labeling of body parts in cluttered scenes. Experimental results showed that the algorithm is robust to size, viewing angles, camera motion, and severe occlusion. Then, the DHS is used to classify load-carrying conditions. By examining various symmetries in DHS, activities such as carrying, holding, and walking with objects that are attached to legs are detected. Our approach possesses several advantages: a compact representation that can be computed in real time is used; furthermore, it does not depend on silhouettes or landmark tracking, which are sensitive to errors in background subtraction stage.}, keywords = {algorithms, Artificial intelligence, Automated;Photography;Reproducibility of Results;Sensitivity and Specificity;Video Recording;, Biometry, Computer-Assisted;Pattern Recognition, double helical signatures, Gait, gait analysis, human gait, human motion kinematics, HUMANS, Image Enhancement, Image Interpretation, Image motion analysis, iterative local curve embedding algorithm, Object detection, simple spatiotemporal characterization, video sequence, Video surveillance}, isbn = {1083-4419}, doi = {10.1109/TSMCB.2010.2044173}, author = {Yang Ran and Qinfen Zheng and Chellapa, Rama and Strat, T.M.} } @article {14548, title = {Approximation Algorithms for Non-Uniform Buy-at-Bulk Network Design}, journal = {SIAM Journal on Computing}, volume = {39}, year = {2010}, month = {2010///}, pages = {1772 - 1798}, author = {Chekuri,C. and Hajiaghayi, Mohammad T. and Kortsarz,G. and Salavatipour,M. R} } @inbook {12504, title = {Articulation-Invariant Representation of Non-planar Shapes}, booktitle = {Computer Vision {\textendash} ECCV 2010Computer Vision {\textendash} ECCV 2010}, series = {Lecture Notes in Computer Science}, volume = {6313}, year = {2010}, month = {2010///}, pages = {286 - 299}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Given a set of points corresponding to a 2D projection of a non-planar shape, we would like to obtain a representation invariant to articulations (under no self-occlusions). It is a challenging problem since we need to account for the changes in 2D shape due to 3D articulations, viewpoint variations, as well as the varying effects of imaging process on different regions of the shape due to its non-planarity. By modeling an articulating shape as a combination of approximate convex parts connected by non-convex junctions, we propose to preserve distances between a pair of points by (i) estimating the parts of the shape through approximate convex decomposition, by introducing a robust measure of convexity and (ii) performing part-wise affine normalization by assuming a weak perspective camera model, and then relating the points using the inner distance which is insensitive to planar articulations. We demonstrate the effectiveness of our representation on a dataset with non-planar articulations, and on standard shape retrieval datasets like MPEG-7.}, isbn = {978-3-642-15557-4}, url = {http://dx.doi.org/10.1007/978-3-642-15558-1_21}, author = {Gopalan,Raghuraman and Turaga,Pavan and Chellapa, Rama}, editor = {Daniilidis,Kostas and Maragos,Petros and Paragios,Nikos} } @conference {19026, title = {Authentication in the clouds: a framework and its application to mobile users}, series = {CCSW {\textquoteright}10}, year = {2010}, month = {2010}, pages = {1 - 6}, publisher = {ACM}, organization = {ACM}, abstract = {Cloud computing is a natural fit for mobile security. Typical handsets have input constraints and practical computational and power limitations, which must be respected by mobile security technologies in order to be effective. We describe how cloud computing can address these issues. Our approach is based on a flexible framework for supporting authentication decisions we call TrustCube (to manage the authentication infrastructure) and on a behavioral authentication approach referred to as implicit authentication (to translate user behavior into authentication scores). The combination results in a new authentication paradigm for users of mobile technologies, one where an appropriate balance between usability and trust can be managed through flexible policies and dynamic tuning.}, keywords = {Authentication, Cloud computing, Mobile computing}, isbn = {978-1-4503-0089-6}, url = {http://doi.acm.org/10.1145/1866835.1866837}, author = {Chow, Richard and Jakobsson, Markus and Masuoka, Ryusuke and Molina,Jesus and Niu, Yuan and Elaine Shi and Song,Zhexuan} } @conference {12471, title = {Automatic target recognition based on simultaneous sparse representation}, booktitle = {Image Processing (ICIP), 2010 17th IEEE International Conference on}, year = {2010}, month = {2010/09//}, pages = {1377 - 1380}, abstract = {In this paper, an automatic target recognition algorithm is presented based on a framework for learning dictionaries for simultaneous sparse signal representation and feature extraction. The dictionary learning algorithm is based on class supervised simultaneous orthogonal matching pursuit while a matching pursuit-based similarity measure is used for classification. We show how the proposed framework can be helpful for efficient utilization of data, with the possibility of developing real-time, robust target classification. We verify the efficacy of the proposed algorithm using confusion matrices on the well known Comanche forward-looking infrared data set consisting of ten different military targets at different orientations.}, keywords = {(artificial, algorithm;feature, based, classification;iterative, classification;learning, Comanche, data, dictionary;matching, extraction;image, forward-looking, infrared, intelligence);military, learning, MATCHING, matrix;dictionary, measure;military, methods;learning, orthogonal, pursuit, pursuit;confusion, recognition;class, recognition;target, representation;feature, representation;sparse, set;automatic, signal, similarity, simultaneous, sparse, supervised, systems;object, target, target;simultaneous, tracking;}, doi = {10.1109/ICIP.2010.5652306}, author = {Patel, Vishal M. and Nasrabadi,N.M. and Chellapa, Rama} } @article {12983, title = {Broader incorporation of bioinformatics in education: opportunities and challenges}, journal = {Brief Bioinform}, volume = {11}, year = {2010}, month = {2010///}, abstract = {The major opportunities for broader incorporation of bioinformatics in education can be placed into three general categories: general applicability of bioinformatics in life science and related curricula; inherent fit of bioinformatics for promoting student learning in most biology programs; and the general experience and associated comfort students have with computers and technology. Conversely, the major challenges for broader incorporation of bioinformatics in education can be placed into three general categories: required infrastructure and logistics; instructor knowledge of bioinformatics and continuing education; and the breadth of bioinformatics, and the diversity of students and educational objectives. Broader incorporation of bioinformatics at all education levels requires overcoming the challenges to using transformative computer- requiring learning activities, assisting faculty in collecting assessment data on mastery of student learning outcomes, as well as creating more faculty development opportunities that span diverse skill levels, with an emphasis placed on providing resource materials that are kept up-to-date as the field and tools change.}, author = {Cummings, Michael P. and Temple,GG} } @article {12506, title = {Comment-Gait-Based Human Recognition by Classification of Cyclostationary Processes on Nonlinear Shape Manifolds}, journal = {Journal of the American Statistical Association}, volume = {102}, year = {2010}, month = {2010///}, pages = {1126 - 1126}, author = {Chellapa, Rama and Veeraraghavan,A.} } @article {12881, title = {Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae}, journal = {BMC Microbiology}, volume = {10}, year = {2010}, month = {2010///}, abstract = {In recent years genome sequencing has been used to characterize new bacterial species, a method of analysis available as a result of improved methodology and reduced cost. Included in a constantly expanding list of Vibrio species are several that have been reclassified as novel members of the Vibrionaceae. The description of two putative new Vibrio species, Vibrio sp. RC341 and Vibrio sp. RC586 for which we propose the names V. metecus and V. parilis, respectively, previously characterized as non-toxigenic environmental variants of V. cholerae is presented in this study. Results Based on results of whole-genome average nucleotide identity (ANI), average amino acid identity (AAI), rpoB similarity, MLSA, and phylogenetic analysis, the new species are concluded to be phylogenetically closely related to V. cholerae and V. mimicus. Vibrio sp. RC341 and Vibrio sp. RC586 demonstrate features characteristic of V. cholerae and V. mimicus, respectively, on differential and selective media, but their genomes show a 12 to 15\% divergence (88 to 85\% ANI and 92 to 91\% AAI) compared to the sequences of V. cholerae and V. mimicus genomes (ANI <95\% and AAI <96\% indicative of separate species). Vibrio sp. RC341 and Vibrio sp. RC586 share 2104 ORFs (59\%) and 2058 ORFs (56\%) with the published core genome of V. cholerae and 2956 (82\%) and 3048 ORFs (84\%) with V. mimicus MB-451, respectively. The novel species share 2926 ORFs with each other (81\% Vibrio sp. RC341 and 81\% Vibrio sp. RC586). Virulence-associated factors and genomic islands of V. cholerae and V. mimicus, including VSP-I and II, were found in these environmental Vibrio spp. Conclusions Results of this analysis demonstrate these two environmental vibrios, previously characterized as variant V. cholerae strains, are new species which have evolved from ancestral lineages of the V. cholerae and V. mimicus clade. The presence of conserved integration loci for genomic islands as well as evidence of horizontal gene transfer between these two new species, V. cholerae, and V. mimicus suggests genomic islands and virulence factors are transferred between these species.}, author = {Bradd,H. and Christopher,G. and Nur,H. and Seon-Young,C. and Jongsik,C. and Thomas,B. and David,B. and Jean,C. and Chris,D. J. and Cliff,H. and Rita R Colwell} } @article {12870, title = {Comparative Genomics of Clinical and Environmental Vibrio Mimicus}, journal = {Proceedings of the National Academy of SciencesPNAS}, volume = {107}, year = {2010}, month = {2010/12/07/}, pages = {21134 - 21139}, abstract = {Whether Vibrio mimicus is a variant of Vibrio cholerae or a separate species has been the subject of taxonomic controversy. A genomic analysis was undertaken to resolve the issue. The genomes of V. mimicus MB451, a clinical isolate, and VM223, an environmental isolate, comprise ca. 4,347,971 and 4,313,453 bp and encode 3,802 and 3,290 ORFs, respectively. As in other vibrios, chromosome I (C-I) predominantly contains genes necessary for growth and viability, whereas chromosome II (C-II) bears genes for adaptation to environmental change. C-I harbors many virulence genes, including some not previously reported in V. mimicus, such as mannose-sensitive hemagglutinin (MSHA), and enterotoxigenic hemolysin (HlyA); C-II encodes a variant of Vibrio pathogenicity island 2 (VPI-2), and Vibrio seventh pandemic island II (VSP-II) cluster of genes. Extensive genomic rearrangement in C-II indicates it is a hot spot for evolution and genesis of speciation for the genus Vibrio. The number of virulence regions discovered in this study (VSP-II, MSHA, HlyA, type IV pilin, PilE, and integron integrase, IntI4) with no notable difference in potential virulence genes between clinical and environmental strains suggests these genes also may play a role in the environment and that pathogenic strains may arise in the environment. Significant genome synteny with prototypic pre-seventh pandemic strains of V. cholerae was observed, and the results of phylogenetic analysis support the hypothesis that, in the course of evolution, V. mimicus and V. cholerae diverged from a common ancestor with a prototypic sixth pandemic genomic backbone.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.1013825107}, url = {http://www.pnas.org/content/107/49/21134}, author = {Hasan,Nur A. and Grim,Christopher J. and Haley,Bradd J. and Jongsik Chun and Alam,Munirul and Taviani,Elisa and Mozammel Hoq and Munk,A. Christine and Rita R Colwell} } @article {15912, title = {Compressed Synthetic Aperture Radar}, journal = {IEEE Journal of Selected Topics in Signal Processing}, volume = {4}, year = {2010}, month = {2010/04//}, pages = {244 - 254}, abstract = {In this paper, we introduce a new synthetic aperture radar (SAR) imaging modality which can provide a high-resolution map of the spatial distribution of targets and terrain using a significantly reduced number of needed transmitted and/or received electromagnetic waveforms. This new imaging scheme, requires no new hardware components and allows the aperture to be compressed. It also presents many new applications and advantages which include strong resistance to countermesasures and interception, imaging much wider swaths and reduced on-board storage requirements.}, keywords = {Compressed sensing, compressed sensing (CS), compressive sensing, electromagnetic waveforms, image resolution, radar imaging, SAR imaging modality, synthetic aperture radar, Synthetic aperture radar (SAR), targets spatial distribution}, isbn = {1932-4553}, doi = {10.1109/JSTSP.2009.2039181}, author = {Patel, Vishal M. and Easley,G. R and Healy,D. M and Chellapa, Rama} } @inbook {12500, title = {Compressive Acquisition of Dynamic Scenes}, booktitle = {Computer Vision {\textendash} ECCV 2010Computer Vision {\textendash} ECCV 2010}, series = {Lecture Notes in Computer Science}, volume = {6311}, year = {2010}, month = {2010///}, pages = {129 - 142}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Compressive sensing (CS) is a new approach for the acquisition and recovery of sparse signals and images that enables sampling rates significantly below the classical Nyquist rate. Despite significant progress in the theory and methods of CS, little headway has been made in compressive video acquisition and recovery. Video CS is complicated by the ephemeral nature of dynamic events, which makes direct extensions of standard CS imaging architectures and signal models infeasible. In this paper, we develop a new framework for video CS for dynamic textured scenes that models the evolution of the scene as a linear dynamical system (LDS). This reduces the video recovery problem to first estimating the model parameters of the LDS from compressive measurements, from which the image frames are then reconstructed. We exploit the low-dimensional dynamic parameters (the state sequence) and high-dimensional static parameters (the observation matrix) of the LDS to devise a novel compressive measurement strategy that measures only the dynamic part of the scene at each instant and accumulates measurements over time to estimate the static parameters. This enables us to considerably lower the compressive measurement rate considerably. We validate our approach with a range of experiments including classification experiments that highlight the effectiveness of the proposed approach.}, isbn = {978-3-642-15548-2}, url = {http://dx.doi.org/10.1007/978-3-642-15549-9_10}, author = {Sankaranarayanan,Aswin and Turaga,Pavan and Baraniuk,Richard and Chellapa, Rama}, editor = {Daniilidis,Kostas and Maragos,Petros and Paragios,Nikos} } @article {12467, title = {COMPRESSIVE SENSING SYSTEM AND METHOD FOR BEARING ESTIMATION OF SPARSE SOURCES IN THE ANGLE DOMAIN}, volume = {12/740,947}, year = {2010}, month = {2010/10/21/}, abstract = {Compressive Sensing (CS) is an emerging area which uses a relatively small number of non-traditional samples in the form of randomized projections to reconstruct sparse or com-pressible signals. Direction-of-arrival (DOA) estimation is performed with an array of sensors using CS. Using random projections of the sensor data, along with a full waveform recording on one reference sensor, a sparse angle space scenario can be reconstructed, giving the number of sources and their DOA{\textquoteright}s. Signal processing algorithms are also developed and described herein for randomly deployable wireless sensor arrays that are severely constrained in communication bandwidth. There is a focus on the acoustic bearing estimation problem and it is shown that when the target bearings are modeled as a sparse vector in the angle space, functions of the low dimensional random projections of the microphone signals can be used to determine multiple source bearings as a solution of an 1]-norm minimization problem.}, url = {http://www.google.com/patents?id=xDLYAAAAEBAJ}, author = {Cevher,Volkan and Gurbuz,Ali Cafer and McClellan,James H. and Chellapa, Rama} } @article {12463, title = {Compressive Video Acquisition, Fusion and Processing}, year = {2010}, month = {2010/12/14/}, abstract = {Modern developments in sensor technology, signal processing, and wireless communications have enabled the conception and deployment of large-scale networked sensing systems spanning numerous collection platforms and varied modalities. These systems have the potential to make intelligent decisions by integrating information from massive amounts of sensor data. Before such benefits can be achieved, significant advances must be made in methods for communicating, fusing, and processing this evergrowing volume of diverse data. In this one-year research project, we aimed to expose the fundamental issues and pave the way for further careful study of compressive approaches to video acquisition, fusion, and processing. In doing so, we developed a theoretical definition of video temporal bandwidth and applied the theory to compressive sampling and reconstruction. We created a new framework for compressive video sensing based on linear dynamical systems, lowering the compressive measurement rate. Finally, we applied our own joint manifold model to a variety of relevant image processing problems, demonstrating the model{\textquoteright}s effectiveness and ability to overcome noise and occlusion obstacles. We also showed how joint manifold models can discover an object{\textquoteright}s trajectory, an important step towards video fusion.}, keywords = {*DATA FUSION, *DETECTORS, *SIGNAL PROCESSING, *VIDEO SIGNALS, ACQUISITION, COLLECTION, COMMUNICATION AND RADIO SYSTEMS, COMPRESSIVE PROPERTIES, COMPRESSIVE SAMPLING, compressive sensing, COMPRESSIVE VIDEO, decision making, DEPLOYMENT, DETECTION, DYNAMICS, IMAGE PROCESSING, Linear systems, Linearity, MANIFOLDS(ENGINES), measurement, MISCELLANEOUS DETECTION AND DETECTORS, MODELS, sampling, THEORY, TRAJECTORIES}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA533703}, author = {Baraniuk,Richard G. and Chellapa, Rama and Wakin,Michael} } @article {16254, title = {Computational Approaches for Genome Assembly Validation}, journal = {Biological Data Mining}, year = {2010}, month = {2010///}, pages = {163 - 163}, author = {Choi,J.H. and Tang,H. and Kim,S. and Pop, Mihai} } @article {14509, title = {Context-Aware Query Recommendations}, volume = {12/408,726}, year = {2010}, month = {2010/09/23/}, abstract = {Described is a search-related technology in which context information regarding a user{\textquoteright}s prior search actions is used in making query recommendations for a current user action, such as a query or click. To determine whether each set or subset of context information is relevant to the user action, data obtained from a query log is evaluated. More particularly, a query transition (query-query) graph and a query click (query-URL) graph are extracted from the query log; vectors are computed for the current action and each context/sub-context and evaluated against vectors in the graphs to determine current action-to-context similarity. Also described is using similar context to provide the query recommendations, using parameters to control the similarity strictness, and/or whether more recent context information is more relevant than less recent context information, and using context information to distinguish between user sessions.}, url = {http://www.google.com/patents?id=nubWAAAAEBAJ}, author = {Ntoulas,Alexandros and Hwang,Heasoo and Getoor, Lise and Paparizos,Stelios and Lauw,Hady Wirawan}, editor = {Microsoft Corporation} } @article {12873, title = {Conversion of viable but nonculturable Vibrio cholerae to the culturable state by co-culture with eukaryotic cells}, journal = {Microbiology and Immunology}, volume = {54}, year = {2010}, month = {2010/06/14/}, pages = {502 - 507}, abstract = {VBNC Vibrio cholerae O139 VC-280 obtained by incubation in 1\% solution of artificial sea water IO at 4{\textdegree}C for 74 days converted to the culturable state when co-cultured with CHO cells. Other eukaryotic cell lines, including HT-29, Caco-2, T84, HeLa, and Intestine 407, also supported conversion of VBNC cells to the culturable state. Conversion of VBNC V. cholerae O1 N16961 and V. cholerae O139 VC-280/pG13 to the culturable state, under the same conditions, was also confirmed. When VBNC V. cholerae O139 VC-280 was incubated in 1\% IO at 4{\textdegree}C for up to 91 days, the number of cells converted by co-culture with CHO cells declined with each additional day of incubation and after 91 days conversion was not observed.}, keywords = {conversion to culturability, co-culture, eukaryotic cell, viable but nonculturable (VBNC) Vibrio cholerae}, isbn = {1348-0421}, doi = {10.1111/j.1348-0421.2010.00245.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1348-0421.2010.00245.x/full}, author = {Senoh,Mitsutoshi and Ghosh-Banerjee,Jayeeta and Ramamurthy,Thandavarayan and Hamabata,Takashi and Kurakawa,Takashi and Takeda,Makoto and Rita R Colwell and Nair,G. Balakrish and Takeda,Yoshifumi} } @conference {18559, title = {Decoupling policy from configuration in campus and enterprise networks}, booktitle = {Local and Metropolitan Area Networks (LANMAN), 2010 17th IEEE Workshop on}, year = {2010}, month = {2010/05//}, pages = {1 - 6}, abstract = {This paper surveys our ongoing work on the use of software-defined networking to simplify two acute policy problems in campus and enterprise network operations: access control and information flow control. We describe how the current coupling of high-level policy with low-level configuration makes these problems challenging today. We describe the specific policy problems faced by campus and enterprise network operators; illustrate our approach, which leverages recent trends in separating the network{\textquoteright}s $\#$x201C;control plane $\#$x201D; from the data plane; and show how this approach can be applied to simplify these two enterprise network management tasks. We also describe our ongoing deployment efforts to build a campus network testbed where trial designs can be deployed and evaluated. We close with a summary of current and future research challenges for solving challenges within enterprise networks within the context of this new paradigm.}, keywords = {Access control, Business communication, campus network, decoupling policy, enterprise network management tasks, enterprise network operator, information flow control, software defined network, software radio, telecommunication network management, telecommunication security}, doi = {10.1109/LANMAN.2010.5507162}, author = {Feamster, Nick and Nayak,A. and Kim,Hyojoon and Clark,R. and Mundada,Y. and Ramachandran,A. and bin Tariq,M.} } @conference {19445, title = {Deliberate Interactions: Characterizing Technology Use in Nairobi, Kenya}, booktitle = {SIGCHI {\textquoteright}10}, series = {CHI {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {2593 - 2602}, publisher = {ACM}, organization = {ACM}, abstract = {We present results from a qualitative study examining how professionals living and working in Nairobi, Kenya regularly use ICT in their everyday lives. There are two contributions of this work for the HCI community. First, we provide empirical evidence demonstrating constraints our participants encountered when using technology in an infrastructure-poor setting. These constraints are limited bandwidth, high costs, differing perceptions of responsiveness, and threats to physical and virtual security. Second, we use our findings to critically evaluate the "access, anytime and anywhere" construct shaping the design of future technologies. We present an alternative vision called deliberate interactions--a planned and purposeful interaction style that involves offline preparation and discuss ways ICT can support this online usage behavior.}, keywords = {everyday technology, hci4d, Kenya, urban computing}, isbn = {978-1-60558-929-9}, url = {http://doi.acm.org/10.1145/1753326.1753719}, author = {Wyche, Susan P. and Smyth, Thomas N. and Marshini Chetty and Aoki, Paul M. and Grinter, Rebecca E.} } @conference {19281, title = {Design and implementation of real-time signal processing applications on heterogeneous multiprocessor arrays}, booktitle = {2010 Conference Record of the Forty Fourth Asilomar Conference on Signals, Systems and Computers (ASILOMAR)}, year = {2010}, month = {2010}, pages = {2121 - 2125}, abstract = {Processing structures based on arrays of computational elements form an important class of architectures, which includes field programmable gate arrays (FPGAs), systolic arrays, and various forms of multicore processors. A wide variety of design methods and tools have been targeted to regular processing arrays involving homogeneous processing elements. In this paper, we introduce the concept of field programmable X arrays (FPXAs) as an abstract model for design and implementation of heterogeneous multiprocessor arrays for signal processing systems. FPXAs are abstract structures that can be targeted for implementation on application-specific integrated circuits, FPGAs, or other kinds of reconfigurable processors. FPXAs can also be mapped onto multicore processors for flexible emulation. We discuss the use of dataflow models as an integrated application representation and intermediate representation for efficient specification and mapping of signal processing systems on FPXAs. We demonstrate our proposed models and techniques with a case study involving the embedding of an application-specific FPXA system on an off-the-shelf FPGA device.}, keywords = {application specific integrated circuits, application-specific integrated circuits, computational elements, Computer architecture, decoding, Field programmable gate arrays, field programmable X arrays, FPGA, FPXA, Integrated circuit modeling, Logic Design, microprocessor chips, multicore processors, multiprocessor arrays, real-time signal processing, reconfigurable architectures, reconfigurable processors, Routing, Signal processing, Signal processing systems, systolic arrays, Viterbi algorithm}, author = {Wu, Hsiang-Huang and Chung-Ching Shen and Bhattacharyya, Shuvra S. and Compton, K. and Schulte, M. and Wolf, M. and Zhang, Tong} } @article {12874, title = {Discovery of novel Vibrio cholerae VSP-II genomic islands using comparative genomic analysis}, journal = {FEMS Microbiology Letters}, volume = {308}, year = {2010}, month = {2010/05/06/}, pages = {130 - 137}, abstract = {This report describes Vibrio seventh pandemic island II (VSP-II) and three novel variants revealed by comparative genomics of 23 Vibrio cholerae strains and their presence among a large and diverse collection of V. cholerae isolates. Three VSP-II variants were reported previously and our results demonstrate the presence of three novel VSP-II in clinical and environmental V. cholerae marked by major deletions and genetic rearrangements. A new VSP-II cluster was found in the seventh pandemic V. cholerae O1 El Tor strain CIRS101, which is dominant (95\%) among the recent (2004{\textendash}2007) seven pandemic V. cholerae O1 El Tor isolates from two endemic sites, but was not found in older strains from the same region. Two other variants were found in V. cholerae TMA21 and RC385, two environmental strains from coastal Brazil and the Chesapeake Bay, respectively, the latter being prevalent among environmental V. cholerae non-O1/non-O139 and Vibrio mimicus. The results of this study indicate that the VSP-II island has undergone significant rearrangement through a complex evolutionary pathway in V. cholerae. Interestingly, one of the new VSP-II revealed the presence of {\textquoteleft}old{\textquoteright} and {\textquoteleft}new{\textquoteright}V. cholerae O1 El Tor pandemic clones circulating in some of the areas where cholera is endemic.}, keywords = {Vibrio cholerae, Vibrio mimicus, VPS-II}, isbn = {1574-6968}, doi = {10.1111/j.1574-6968.2010.02008.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2010.02008.x/full}, author = {Taviani,Elisa and Grim,Christopher J. and Choi,Jinna and Jongsik Chun and Haley,Bradd and Hasan,Nur A. and Huq,Anwar and Rita R Colwell} } @article {12876, title = {Diversity and distribution of cholix toxin, a novel ADP-ribosylating factor from Vibrio cholerae}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2010}, month = {2010/02/08/}, pages = {198 - 207}, abstract = {Non-toxigenic non-O1, non-O139 Vibrio cholerae strains isolated from both environmental and clinical settings carry a suite of virulence factors aside from cholera toxin. Among V. cholerae strains isolated from coastal waters of southern California, this includes cholix toxin, an ADP-ribosylating factor that is capable of halting protein synthesis in eukaryotic cells. The prevalence of the gene encoding cholix toxin, chxA, was assessed among a collection of 155 diverse V. cholerae strains originating from both clinical and environmental settings in Bangladesh and Mexico and other countries around the globe. The chxA gene was present in 47\% of 83 non-O1, non-O139 strains and 16\% of 72 O1/O139 strains screened as part of this study. A total of 86 chxA gene sequences were obtained, and phylogenetic analysis revealed that they fall into two distinct clades. These two clades were also observed in the phylogenies of several housekeeping genes, suggesting that the divergence observed in chxA extends to other regions of the V. cholerae genome, and most likely has arisen from vertical descent rather than horizontal transfer. Our results clearly indicate that ChxA is a major toxin of V. cholerae with a worldwide distribution that is preferentially associated with non-pandemic strains.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2010.00139.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2010.00139.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Purdy,Alexandra E. and Balch,Deborah and Liz{\'a}rraga-Partida,Marcial Leonardo and Islam,Mohammad Sirajul and Martinez-Urtaza,Jaime and Huq,Anwar and Rita R Colwell and Bartlett,Douglas H.} } @conference {14688, title = {Dynamically checking ownership policies in concurrent c/c++ programs}, booktitle = {Proceedings of the 37th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages}, series = {POPL {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {457 - 470}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Concurrent programming errors arise when threads share data incorrectly. Programmers often avoid these errors by using synchronization to enforce a simple ownership policy: data is either owned exclusively by a thread that can read or write the data, or it is read owned by a set of threads that can read but not write the data. Unfortunately, incorrect synchronization often fails to enforce these policies and memory errors in languages like C and C++ can violate these policies even when synchronization is correct. In this paper, we present a dynamic analysis for checking ownership policies in concurrent C and C++ programs despite memory errors. The analysis can be used to find errors in commodity multi-threaded programs and to prevent attacks that exploit these errors. We require programmers to write ownership assertions that describe the sharing policies used by different parts of the program. These policies may change over time, as may the policies{\textquoteright} means of enforcement, whether it be locks, barriers, thread joins, etc. Our compiler inserts checks in the program that signal an error if these policies are violated at runtime. We evaluated our tool on several benchmark programs. The run-time overhead was reasonable: between 0 and 49\% with an average of 26\%. We also found the tool easy to use: the total number of ownership assertions is small, and the asserted specification and implementation can be debugged together by running the instrumented program and addressing the errors that arise. Our approach enjoys a pleasing modular soundness property: if a thread executes a sequence of statements on variables it owns, the statements are serializable within a valid execution, and thus their effects can be reasoned about in isolation from other threads in the program.}, keywords = {concurrency, Debugging, Dynamic analysis, Security, Testing, tools}, isbn = {978-1-60558-479-9}, doi = {10.1145/1706299.1706351}, url = {http://doi.acm.org/10.1145/1706299.1706351}, author = {Martin,Jean-Phillipe and Hicks, Michael W. and Costa,Manuel and Akritidis,Periklis and Castro,Miguel} } @article {12872, title = {Effect on Human Cells of Environmental Vibrio Parahaemolyticus Strains Carrying Type III Secretion System 2}, journal = {Infection and ImmunityInfect. Immun.}, volume = {78}, year = {2010}, month = {2010/07/01/}, pages = {3280 - 3287}, abstract = {Vibrio parahaemolyticus is an inhabitant of estuarine and marine environments that causes seafood-borne gastroenteritis worldwide. Recently, a type 3 secretion system (T3SS2) able to secrete and translocate virulence factors into the eukaryotic cell has been identified in a pathogenicity island (VP-PAI) located on the smaller chromosome. These virulence-related genes have previously been detected only in clinical strains. Classical virulence genes for this species (tdh, trh) are rarely detected in environmental strains, which are usually considered to lack virulence potential. However, during screening of a collection of environmental V. parahaemolyticus isolates obtained in the North Adriatic Sea in Italy, a number of marine strains carrying virulence-related genes, including genes involved in the T3SS2, were detected. In this study, we investigated the pathogenic potential of these marine V. parahaemolyticus strains by studying their adherence ability, their cytotoxicity, their effect on zonula occludin protein 1 (ZO-1) of the tight junctions, and their effect on transepithelial resistance (TER) in infected Caco-2 cells. By performing a reverse transcription-PCR, we also tested the expression of the T3SS2 genes vopT and vopB2, encoding an effector and a translocon protein, respectively. Our results indicate that, similarly to clinical strains, marine V. parahaemolyticus strains carrying vopT and vopB2 and that other genes included in the VP-PAI are capable of adhering to human cells and of causing cytoskeletal disruption and loss of membrane integrity in infected cells. On the basis of data presented here, environmental V. parahaemolyticus strains should be included in coastal water surveillance plans, as they may represent a risk for human health.}, isbn = {0019-9567, 1098-5522}, doi = {10.1128/IAI.00050-10}, url = {http://iai.asm.org/content/78/7/3280}, author = {Caburlotto,Greta and Lle{\`o},Maria M. and Hilton,Tamara and Huq,Anwar and Rita R Colwell and Kaper,James B.} } @article {12477, title = {An Efficient and Robust Algorithm for Shape Indexing and Retrieval}, journal = {Multimedia, IEEE Transactions on}, volume = {12}, year = {2010}, month = {2010/08//}, pages = {372 - 385}, abstract = {Many shape matching methods are either fast but too simplistic to give the desired performance or promising as far as performance is concerned but computationally demanding. In this paper, we present a very simple and efficient approach that not only performs almost as good as many state-of-the-art techniques but also scales up to large databases. In the proposed approach, each shape is indexed based on a variety of simple and easily computable features which are invariant to articulations, rigid transformations, etc. The features characterize pairwise geometric relationships between interest points on the shape. The fact that each shape is represented using a number of distributed features instead of a single global feature that captures the shape in its entirety provides robustness to the approach. Shapes in the database are ordered according to their similarity with the query shape and similar shapes are retrieved using an efficient scheme which does not involve costly operations like shape-wise alignment or establishing correspondences. Depending on the application, the approach can be used directly for matching or as a first step for obtaining a short list of candidate shapes for more rigorous matching. We show that the features proposed to perform shape indexing can be used to perform the rigorous matching as well, to further improve the retrieval performance.}, keywords = {activity, algorithm;shape, classification;human, databases;robust, estimation;large, indexing;shape, MATCHING, matching;image, methods;shape, pose, recognition;, retrieval;image, retrieval;indexing;shape}, isbn = {1520-9210}, doi = {10.1109/TMM.2010.2050735}, author = {Biswas,S. and Aggarwal,G. and Chellapa, Rama} } @conference {18902, title = {Emergence of cooperative societies in evolutionary games}, series = {GECCO {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {1793 - 1800}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We utilize evolutionary game theory to study the evolution of cooperative societies and the behaviors of individual agents (i.e., players) in it. We present a novel player model based upon empirical evidence from the social and behavioral sciences, stating that: (1) an individual{\textquoteright}s behavior may often be motivated not only by self-interest but also by the consequences for the others, and (2) individuals vary in their interpersonal social tendencies, which reflect stable personal orientations that influence their choices. Alongside the formal player model we provide an analysis that considers possible interactions between different types of individuals. We present series of evolutionary simulations that ratify previous findings on evolution of cooperation, and provide new insights on the evolutionary process of cooperative behavior in a society as well as on the emergence of cooperative societies. Our main experimental result demonstrate that in contrast to previous common knowledge, increasing the value of mutual Reward or increasing mutual Punishment in the Prisoner{\textquoteright}s dilemma game do not result in the same type of cooperative society: while increasing R does result in a more cooperative society, increasing P does not.}, keywords = {evolutionary game theory, social orientations}, isbn = {978-1-4503-0073-5}, doi = {10.1145/1830761.1830805}, url = {http://doi.acm.org/10.1145/1830761.1830805}, author = {Cheng,Kan-Leung and Zuckerman,Inon and Kuter,Ugur and Nau, Dana S.} } @article {12880, title = {Environmental reservoirs of Vibrio cholerae and their role in cholera}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2010}, month = {2010/01/15/}, pages = {27 - 33}, abstract = {In the aquatic environment, Vibrio cholerae has been reported to be associated with a variety of living organisms, including animals with an exoskeleton of chitin, aquatic plants, protozoa, bivalves, waterbirds, as well as abiotic substrates (e.g. sediments). Most of these are well-known or putative environmental reservoirs for the bacterium, defined as places where the pathogen lives over time, with the potential to be released and to cause human infection. Environmental reservoirs also serve as V. cholerae disseminators and vectors. They can be responsible for the start of an epidemic, may be critical to cholera endemicity, and affect the evolution of pathogen virulence. To date, in addition to the generally recognized role of zooplankton as the largest environmental reservoir for V. cholerae, other environmental reservoirs play some role in cholera epidemiology by favouring persistence of the pathogen during inter-epidemic periods. Little is known about the ecological factors affecting V. cholerae survival in association with aquatic substrates. Studies aimed at these aspects, i.e. understanding how environmental reservoirs interact, are affected by climate, and contribute to disease epidemiology, will be useful for understanding global implications of V. cholerae and the disease cholera.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2009.00128.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2009.00128.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Vezzulli,Luigi and Pruzzo,Carla and Huq,Anwar and Rita R Colwell} } @article {19585, title = {Evaluating Call-By-Need on the Control Stack}, journal = {arXiv:1009.3174 [cs]}, year = {2010}, note = {Comment: Symposium on Trends in Functional Programming (TFP 2010), Norman, Oklahoma, May 2010}, month = {2010/09/16/}, abstract = {Ariola and Felleisen{\textquoteright}s call-by-need {\lambda}-calculus replaces a variable occurrence with its value at the last possible moment. To support this gradual notion of substitution, function applications-once established-are never discharged. In this paper we show how to translate this notion of reduction into an abstract machine that resolves variable references via the control stack. In particular, the machine uses the static address of a variable occurrence to extract its current value from the dynamic control stack.}, keywords = {Computer Science - Programming Languages, D.3.1}, url = {http://arxiv.org/abs/1009.3174}, author = {Chang, Stephen and David Van Horn and Felleisen, Matthias} } @conference {12472, title = {Evaluation of state-of-the-art algorithms for remote face recognition}, booktitle = {Image Processing (ICIP), 2010 17th IEEE International Conference on}, year = {2010}, month = {2010/09//}, pages = {1581 - 1584}, abstract = {In this paper, we describe a remote face database which has been acquired in an unconstrained outdoor environment. The face images in this database suffer from variations due to blur, poor illumination, pose, and occlusion. It is well known that many state-of-the-art still image-based face recognition algorithms work well, when constrained (frontal, well illuminated, high-resolution, sharp, and complete) face images are presented. In this paper, we evaluate the effectiveness of a subset of existing still image-based face recognition algorithms for the remote face data set. We demonstrate that in addition to applying a good classification algorithm, consistent detection of faces with fewer false alarms and finding features that are robust to variations mentioned above are very important for remote face recognition. Also setting up a comprehensive metric to evaluate the quality of face images is necessary in order to reject images that are of low quality.}, keywords = {alarm;feature, algorithm;still, classification;image, classification;visual, database;remote, databases;, extraction;hidden, extraction;image, Face, feature, image-based, image;false, quality;occlusion;remote, recognition;face, recognition;feature, recognition;state-of-the-art, removal;image}, doi = {10.1109/ICIP.2010.5652608}, author = {Ni,Jie and Chellapa, Rama} } @article {12426, title = {Evaluation of the Interaction of Cyclin-Dependent Kinase 5 with Activator p25 and with p25-Derived Inhibitor CIP}, journal = {Journal of Computational Biology}, volume = {17}, year = {2010}, month = {2010///}, pages = {707 - 721}, author = {Cardone, Antonio and Albers,R.W. and Sriram,R.D. and Pant,H.C.} } @article {18903, title = {Evolution of state-dependent risk preferences}, journal = {ACM Transactions on Intelligent Systems and Technology (TIST)}, volume = {1}, year = {2010}, month = {2010/10//}, pages = {6:1{\textendash}6:21 - 6:1{\textendash}6:21}, abstract = {Researchers have invested much effort in constructing models of the state-dependent (sometimes risk-averse and sometimes risk-prone) nature of human decision making. An important open question is how state-dependent risk behavior can arise and remain prominent in populations. We believe that one part of the answer is the interplay between risk-taking and sequentiality of choices in populations subject to evolutionary population dynamics. To support this hypothesis, we provide simulation and analytical results for evolutionary lottery games, including results on evolutionary stability. We consider a parameterized class of imitation dynamics in which the parameter 0 <= α <= 1 yields the replicator dynamic with α = 1 and the imitate-the-better dynamic with α = 0. Our results demonstrate that for every population dynamic in this class except for the replicator dynamic, the interplay between risk-taking and sequentiality of choices allows state-dependent risk behavior to have an evolutionary advantage over expected-value maximization.}, keywords = {decision theory, Evolutionary games, Population Dynamics, risk}, isbn = {2157-6904}, doi = {10.1145/1858948.1858954}, url = {http://doi.acm.org/10.1145/1858948.1858954}, author = {Roos,Patrick and Carr,J. Ryan and Nau, Dana S.} } @inbook {12995, title = {Evolutionary framework for Lepidoptera model systems}, booktitle = {Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera}, year = {2010}, month = {2010///}, pages = {1 - 24}, publisher = {Taylor \& Francis}, organization = {Taylor \& Francis}, address = {Boca Raton}, abstract = {{\textquotedblleft}Model systems{\textquotedblright} are specific organisms upon which detailed studies have been conducted examining a fundamental biological question. If the studies are robust, their results can be extrapolated among an array of organisms that possess features in common with the subject organism. The true power of model systems lies in the ability to extrapolate these details across larger groups of organisms. In order to generalize these results, comparative studies are essential and require that model systems be placed into their evolutionary or phylogenetic context. This chapter examines model systems in the insect order Lepidoptera from the perspective of several different superfamilies. Historically, many species of Lepidoptera have been essential in the development of invaluable model systems in the fields of development biology, genetics, molecular biology, physiology, co-evolution, population dynamics, and ecology.}, author = {Roe,A. and Weller,S. and Baixeras,J. and Brown,J. W and Cummings, Michael P. and Davis,DR and Horak,M and Kawahara,A. Y and Mitter,C and Parr,C.S. and Regier,J. C and Rubinoff,D and Simonsen,TJ and Wahlberg,N and Zwick,A.}, editor = {Goldsmith,M and Marec,F} } @article {12494, title = {Face Recognition by Computers and Humans}, journal = {Computer}, volume = {43}, year = {2010}, month = {2010/02//}, pages = {46 - 55}, abstract = {This article talks about how the study of how humans perceive faces can be used to help design practical systems for face recognition. Besides applications related to identification and verification-such as access control, law enforcement, ID and licensing, and surveillance-face recognition has also proven useful in applications such as human-computer interaction, virtual reality, database retrieval, multimedia, and computer entertainment. Continuing research into face recognition will provide scientists and engineers with many vital projects, in areas such as homeland security, human-computer interaction, and numerous consumer applications. The areas we are considering pursuing are recognition from unconstrained video sequences, incorporating familiarity into algorithms, modeling effects of aging, and developing biologically plausible models for human face recognition ability.}, keywords = {access, Computer, control;aging;computer, control;face, entertainment;database, interaction;national, interaction;unconstrained, reality;access, recognition;homeland, recognition;human, retrieval;face, security;, security;human, sequences;virtual, video}, isbn = {0018-9162}, doi = {10.1109/MC.2010.37}, author = {Chellapa, Rama and Sinha, P. and Phillips,P.J.} } @conference {12483, title = {Fast directional chamfer matching}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2010 IEEE Conference on}, year = {2010}, month = {2010/06//}, pages = {1696 - 1703}, abstract = {We study the object localization problem in images given a single hand-drawn example or a gallery of shapes as the object model. Although many shape matching algorithms have been proposed for the problem over the decades, chamfer matching remains to be the preferred method when speed and robustness are considered. In this paper, we significantly improve the accuracy of chamfer matching while reducing the computational time from linear to sublinear (shown empirically). Specifically, we incorporate edge orientation information in the matching algorithm such that the resulting cost function is piecewise smooth and the cost variation is tightly bounded. Moreover, we present a sublinear time algorithm for exact computation of the directional chamfer matching score using techniques from 3D distance transforms and directional integral images. In addition, the smooth cost function allows to bound the cost distribution of large neighborhoods and skip the bad hypotheses within. Experiments show that the proposed approach improves the speed of the original chamfer matching upto an order of 45 $\#$x00D7;, and it is much faster than many state of art techniques while the accuracy is comparable.}, keywords = {3D, algorithm;edge, algorithms;single, chamfer, cost, detection;image, directional, distance, distribution;cost, example;smooth, function;sublinear, hand-drawn, images;edge, information;fast, integral, localization, MATCHING, matching;gallery, matching;transforms;, model;piecewise, of, orientation, problem;object, score;directional, shapes;object, smooth;shape, TIME, time;cost, transforms;computational, variation;directional}, doi = {10.1109/CVPR.2010.5539837}, author = {Ming-Yu Liu and Tuzel, O. and Veeraraghavan,A. and Chellapa, Rama} } @article {16265, title = {Finishing genomes with limited resources: lessons from an ensemble of microbial genomes}, journal = {BMC Genomics}, volume = {11}, year = {2010}, month = {2010/04/16/}, pages = {242 - 242}, abstract = {While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-11-242}, url = {http://www.biomedcentral.com/1471-2164/11/242}, author = {Nagarajan,Niranjan and Cook,Christopher and Di Bonaventura,Maria Pia and Ge,Hong and Richards,Allen and Bishop-Lilly,Kimberly A and DeSalle,Robert and Read,Timothy D. and Pop, Mihai} } @article {18152, title = {A framework for theoretical analysis of content fingerprinting}, journal = {Proc. of SPIE Media Forensics and Security}, year = {2010}, month = {2010///}, abstract = {The popularity of video sharing platforms such as Youtube has prompted the need for the development of efficienttechniques for multimedia identification. Content fingerprinting is a promising solution for this problem, whereby a short {\textquotedblleft}fingerprint{\textquotedblright} that captures robust and unique characteristics of a signal is computed from each multimedia document. This fingerprint is then compared with a database to identify the multimedia. Several fingerprinting techniques have been proposed in the literature and have been evaluated using experiments. To complement these experimental evaluations and gain a deeper understanding, this paper proposes a framework for theoretical modeling and analysis of content fingerprinting schemes. Analysis of some key modules for fingerprint encoding and matching are also presented under this framework. }, author = {Varna,A.L. and Chuang,W.H. and Wu,M.} } @inbook {19194, title = {GasSense: Appliance-Level, Single-Point Sensing of Gas Activity in the Home}, booktitle = {Pervasive Computing}, series = {Lecture Notes in Computer Science}, volume = {6030}, year = {2010}, month = {2010}, pages = {265 - 282}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper presents GasSense, a low-cost, single-point sensing solution for automatically identifying gas use down to its source (e.g., water heater, furnace, fireplace). This work adds a complementary sensing solution to the growing body of work in infrastructure-mediated sensing. GasSense analyzes the acoustic response of a home{\textquoteright}s government mandated gas regulator, which provides the unique capability of sensing both the individual appliance at which gas is currently being consumed as well as an estimate of the amount of gas flow. Our approach provides a number of appealing features including the ability to be easily and safely installed without the need of a professional. We deployed our solution in nine different homes and initial results show that GasSense has an average accuracy of 95.2\% in identifying individual appliance usage.}, isbn = {978-3-642-12653-6}, url = {http://dx.doi.org/10.1007/978-3-642-12654-3_16}, author = {Cohn,Gabe and Gupta,Sidhant and Jon Froehlich and Larson,Eric and Patel,Shwetak}, editor = {Flor{\'e}en,Patrik and Kr{\"u}ger,Antonio and Spasojevic,Mirjana} } @conference {17988, title = {General-purpose vs. gpu: Comparison of many-cores on irregular workloads}, booktitle = {Proceedings of the Second Usenix Workshop on Hot Topics in Parallelism}, year = {2010}, month = {2010///}, pages = {14 - 15}, abstract = {XMT1 is a general-purpose many-core parallel architec-ture. The foremost design objective for XMT was to meet the highest standards for ease of parallel programming. GPUs, on the other hand, have acquired a strong reputa- tion on performance, sometimes at the expense of ease- of-programming. The current paper presents a perfor- mance comparison on diverse workloads between XMT and an NVIDIA CUDA-enabled GPU. Configured with roughly the same amount of chip resources as the GPU, XMT achieves an average speedup of 6.05x on irregu- lar applications, while incurring an average slowdown of 2.07x on regular ones. Namely, XMT comes ahead for significant applications without having to pay a (possibly worthwhile) price for easier programming. This surpris- ing result suggests a yet untapped opportunity: A high- performance easy-to-program general-purpose 1000-core computer. }, author = {Caragea,G.C. and Keceli,F. and Tzannes,A. and Vishkin, Uzi} } @article {12871, title = {Genome Sequence of Hybrid Vibrio Cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. Cholerae}, journal = {Journal of BacteriologyJ. Bacteriol.}, volume = {192}, year = {2010}, month = {2010/07/01/}, pages = {3524 - 3533}, abstract = {The genomes of Vibrio cholerae O1 Matlab variant MJ-1236, Mozambique O1 El Tor variant B33, and altered O1 El Tor CIRS101 were sequenced. All three strains were found to belong to the phylocore group 1 clade of V. cholerae, which includes the 7th-pandemic O1 El Tor and serogroup O139 isolates, despite displaying certain characteristics of the classical biotype. All three strains were found to harbor a hybrid variant of CTXΦ and an integrative conjugative element (ICE), leading to their establishment as successful clinical clones and the displacement of prototypical O1 El Tor. The absence of strain- and group-specific genomic islands, some of which appear to be prophages and phage-like elements, seems to be the most likely factor in the recent establishment of dominance of V. cholerae CIRS101 over the other two hybrid strains.}, isbn = {0021-9193, 1098-5530}, doi = {10.1128/JB.00040-10}, url = {http://jb.asm.org/content/192/13/3524}, author = {Grim,Christopher J. and Hasan,Nur A. and Taviani,Elisa and Haley,Bradd and Jongsik Chun and Brettin,Thomas S. and Bruce,David C. and Detter,J. Chris and Han,Cliff S. and Chertkov,Olga and Challacombe,Jean and Huq,Anwar and Nair,G. Balakrish and Rita R Colwell} } @article {19094, title = {Genomic characterization of the Yersinia genus}, journal = {Genome biology}, volume = {11}, year = {2010}, month = {2010}, author = {Chen, P.E. and Cook, C. and Stewart, A.C. and Nagarajan,N. and Sommer, D.D. and Pop, Mihai and Thomason, B. and Thomason, M.P.K. and Lentz, S. and Nolan, N. and others} } @conference {12484, title = {Group motion segmentation using a Spatio-Temporal Driving Force Model}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2010 IEEE Conference on}, year = {2010}, month = {2010/06//}, pages = {2038 - 2045}, abstract = {We consider the {\textquoteleft}group motion segmentation{\textquoteright} problem and provide a solution for it. The group motion segmentation problem aims at analyzing motion trajectories of multiple objects in video and finding among them the ones involved in a {\textquoteleft}group motion pattern{\textquoteright}. This problem is motivated by and serves as the basis for the {\textquoteleft}multi-object activity recognition{\textquoteright} problem, which is currently an active research topic in event analysis and activity recognition. Specifically, we learn a Spatio-Temporal Driving Force Model to characterize a group motion pattern and design an approach for segmenting the group motion. We illustrate the approach using videos of American football plays, where we identify the offensive players, who follow an offensive motion pattern, from motions of all players in the field. Experiments using GaTech Football Play Dataset validate the effectiveness of the segmentation algorithm.}, keywords = {activity, American, analysis;image, dataset;group, driving, football, force, model;image, MOTION, pattern;group, play, plays;GaTech, problem;spatiotemporal, recognition, recognition;image, segmentation;, segmentation;motion, trajectories;multiobject}, doi = {10.1109/CVPR.2010.5539880}, author = {Ruonan Li and Chellapa, Rama} } @conference {18341, title = {GUI testing using computer vision}, booktitle = {Proceedings of the 28th international conference on Human factors in computing systems}, series = {CHI {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {1535 - 1544}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Testing a GUI{\textquoteright}s visual behavior typically requires human testers to interact with the GUI and to observe whether the expected results of interaction are presented. This paper presents a new approach to GUI testing using computer vision for testers to automate their tasks. Testers can write a visual test script that uses images to specify which GUI components to interact with and what visual feedback to be observed. Testers can also generate visual test scripts by demonstration. By recording both input events and screen images, it is possible to extract the images of components interacted with and the visual feedback seen by the demonstrator, and generate a visual test script automatically. We show that a variety of GUI behavior can be tested using this approach. Also, we show how this approach can facilitate good testing practices such as unit testing, regression testing, and test-driven development.}, keywords = {gui automation, GUI testing, test by demonstration}, isbn = {978-1-60558-929-9}, doi = {10.1145/1753326.1753555}, url = {http://doi.acm.org/10.1145/1753326.1753555}, author = {Chang,Tsung-Hsiang and Tom Yeh and Miller,Robert C.} } @article {12875, title = {Identification of Pathogenic Vibrio Species by Multilocus PCR-Electrospray Ionization Mass Spectrometry and Its Application to Aquatic Environments of the Former Soviet Republic of Georgia}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {76}, year = {2010}, month = {2010/03/15/}, pages = {1996 - 2001}, abstract = {The Ibis T5000 is a novel diagnostic platform that couples PCR and mass spectrometry. In this study, we developed an assay that can identify all known pathogenic Vibrio species and field-tested it using natural water samples from both freshwater lakes and the Georgian coastal zone of the Black Sea. Of the 278 total water samples screened, 9 different Vibrio species were detected, 114 (41\%) samples were positive for V. cholerae, and 5 (0.8\%) samples were positive for the cholera toxin A gene (ctxA). All ctxA-positive samples were from two freshwater lakes, and no ctxA-positive samples from any of the Black Sea sites were detected.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.01919-09}, url = {http://aem.asm.org/content/76/6/1996}, author = {Whitehouse,Chris A. and Baldwin,Carson and Sampath,Rangarajan and Blyn,Lawrence B. and Melton,Rachael and Li,Feng and Hall,Thomas A. and Harpin,Vanessa and Matthews,Heather and Tediashvili,Marina and Jaiani,Ekaterina and Kokashvili,Tamar and Janelidze,Nino and Grim,Christopher and Rita R Colwell and Huq,Anwar} } @article {14510, title = {Identifying Modifiers in Web Queries Over Structured Data}, volume = {12/473,286}, year = {2010}, month = {2010/12/02/}, abstract = {Described is using modifiers in online search queries for queries that map to a database table. A modifier (e.g., an adjective or a preposition) specifies the intended meaning of a target, in which the target maps to a column in that table. The modifier thus corresponds to one or more functions that determine which rows of data in the column match the query, e.g., {\textquotedblleft}cameras under $400{\textquotedblright} maps to a camera (or product) table, and {\textquotedblleft}under{\textquotedblright} is the modifier that represents a function (less than) that is used to evaluate a {\textquotedblleft}price{\textquotedblright} target/data column. Also described are different classes of modifiers, and generating the dictionaries for a domain (corresponding to a table) via query log mining.}, url = {http://www.google.com/patents?id=gQTkAAAAEBAJ}, author = {Paparizos,Stelios and Joshi,Amrula Sadanand and Getoor, Lise and Ntoulas,Alexandros}, editor = {Microsoft Corporation} } @conference {12429, title = {Image classification of vascular smooth muscle cells}, booktitle = {Proceedings of the 1st ACM International Health Informatics Symposium}, series = {IHI {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {484 - 486}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {cell biology, digital image processing, machine learning}, isbn = {978-1-4503-0030-8}, doi = {10.1145/1882992.1883068}, url = {http://doi.acm.org/10.1145/1882992.1883068}, author = {Grasso,Michael A. and Mokashi,Ronil and Dalvi,Darshana and Cardone, Antonio and Dima,Alden A. and Bhadriraju,Kiran and Plant,Anne L. and Brady,Mary and Yesha,Yaacov and Yesha,Yelena} } @article {12967, title = {Intensity normalization improves color calling in SOLiD sequencing}, journal = {Nat MethNat Meth}, volume = {7}, year = {2010}, month = {2010/05//}, pages = {336 - 337}, isbn = {1548-7091}, doi = {10.1038/nmeth0510-336}, url = {http://dx.doi.org/10.1038/nmeth0510-336}, author = {Wu,Hao and Irizarry,Rafael A and Corrada Bravo, Hector} } @article {15883, title = {Investigating multi-label classification for human values}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {47}, year = {2010}, month = {2010///}, pages = {1 - 4}, author = {Ishita,E. and Oard, Douglas and Fleischmann,K.R. and Cheng,A.S. and Templeton,T.C.} } @article {12502, title = {Large-scale matrix factorization with missing data under additional constraints}, journal = {Advances in Neural Information Processing Systems}, volume = {23}, year = {2010}, month = {2010///}, pages = {1642 - 1650}, abstract = {Matrix factorization in the presence of missing data is at the core of many com-puter vision problems such as structure from motion (SfM), non-rigid SfM and photometric stereo. We formulate the problem of matrix factorization with miss- ing data as a low-rank semidefinite program (LRSDP) with the advantage that: 1) an efficient quasi-Newton implementation of the LRSDP enables us to solve large-scale factorization problems, and 2) additional constraints such as ortho- normality, required in orthographic SfM, can be directly incorporated in the new formulation. Our empirical evaluations suggest that, under the conditions of ma- trix completion theory, the proposed algorithm finds the optimal solution, and also requires fewer observations compared to the current state-of-the-art algorithms. We further demonstrate the effectiveness of the proposed algorithm in solving the affine SfM problem, non-rigid SfM and photometric stereo problems. }, author = {Mitra, K. and Sheorey,S. and Chellapa, Rama} } @conference {17986, title = {Lazy binary-splitting: a run-time adaptive work-stealing scheduler}, booktitle = {Proceedings of the 15th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming}, series = {PPoPP {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {179 - 190}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present Lazy Binary Splitting (LBS), a user-level scheduler of nested parallelism for shared-memory multiprocessors that builds on existing Eager Binary Splitting work-stealing (EBS) implemented in Intel{\textquoteright}s Threading Building Blocks (TBB), but improves performance and ease-of-programming. In its simplest form (SP), EBS requires manual tuning by repeatedly running the application under carefully controlled conditions to determine a stop-splitting-threshold (sst)for every do-all loop in the code. This threshold limits the parallelism and prevents excessive overheads for fine-grain parallelism. Besides being tedious, this tuning also over-fits the code to some particular dataset, platform and calling context of the do-all loop, resulting in poor performance portability for the code. LBS overcomes both the performance portability and ease-of-programming pitfalls of a manually fixed threshold by adapting dynamically to run-time conditions without requiring tuning. We compare LBS to Auto-Partitioner (AP), the latest default scheduler of TBB, which does not require manual tuning either but lacks context portability, and outperform it by 38.9\% using TBB{\textquoteright}s default AP configuration, and by 16.2\% after we tuned AP to our experimental platform. We also compare LBS to SP by manually finding SP{\textquoteright}s sst using a training dataset and then running both on a different execution dataset. LBS outperforms SP by 19.5\% on average. while allowing for improved performance portability without requiring tedious manual tuning. LBS also outperforms SP with sst=1, its default value when undefined, by 56.7\%, and serializing work-stealing (SWS), another work-stealer by 54.7\%. Finally, compared to serializing inner parallelism (SI) which has been used by OpenMP, LBS is 54.2\% faster.}, keywords = {Dynamic scheduling, load balancing, nested parallelism, thread scheduling, work stealing}, isbn = {978-1-60558-877-3}, doi = {10.1145/1693453.1693479}, url = {http://doi.acm.org/10.1145/1693453.1693479}, author = {Tzannes,Alexandros and Caragea,George C. and Barua,Rajeev and Vishkin, Uzi} } @article {12493, title = {A Learning Approach Towards Detection and Tracking of Lane Markings}, journal = {IEEE Transactions on Intelligent Transportation Systems}, volume = {PP}, year = {2010}, month = {2010/02/17/}, pages = {1 - 12}, abstract = {Road scene analysis is a challenging problem that has applications in autonomous navigation of vehicles. An integral component of this system is the robust detection and tracking of lane markings. It is a hard problem primarily due to large appearance variations in lane markings caused by factors such as occlusion (traffic on the road), shadows (from objects like trees), and changing lighting conditions of the scene (transition from day to night). In this paper, we address these issues through a learning-based approach using visual inputs from a camera mounted in front of a vehicle. We propose the following: 1) a pixel-hierarchy feature descriptor to model the contextual information shared by lane markings with the surrounding road region; 2) a robust boosting algorithm to select relevant contextual features for detecting lane markings; and 3) particle filters to track the lane markings, without knowledge of vehicle speed, by assuming the lane markings to be static through the video sequence and then learning the possible road scene variations from the statistics of tracked model parameters. We investigate the effectiveness of our algorithm on challenging daylight and night-time road video sequences.}, keywords = {Boosting, Context, Context modeling, Feature extraction, lane marking detection, outlier robustness, Roads, tracking and learning, Training, Vehicles}, isbn = {1524-9050}, doi = {10.1109/TITS.2012.2184756}, author = {Gopalan,R. and Hong, T. and Shneier, M. and Chellapa, Rama} } @conference {14316, title = {Mining Public Transport Usage for Personalised Intelligent Transport Systems}, booktitle = {2010 IEEE 10th International Conference on Data Mining (ICDM)}, year = {2010}, month = {2010}, pages = {887 - 892}, publisher = {IEEE}, organization = {IEEE}, abstract = {Traveller information, route planning, and service updates have become essential components of public transport systems: they help people navigate built environments by providing access to information regarding delays and service disruptions. However, one aspect that these systems lack is a way of tailoring the information they offer in order to provide personalised trip time estimates and relevant notifications to each traveller. Mining each user{\textquoteright}s travel history, collected by automated ticketing systems, has the potential to address this gap. In this work, we analyse one such dataset of travel history on the London underground. We then propose and evaluate methods to (a) predict personalised trip times for the system users and (b) rank stations based on future mobility patterns, in order to identify the subset of stations that are of greatest interest to the user and thus provide useful travel updates.}, keywords = {automated ticketing systems, data mining, Intelligent Transport Systems, London underground, mobility patterns, personalised intelligent transport systems, personalised trip times, Personalization, public administration, public information systems, public transport systems, rapid transit systems, route planning, service disruptions, service updates, traffic information systems, travel history, traveller information}, isbn = {978-1-4244-9131-5}, doi = {10.1109/ICDM.2010.46}, author = {Lathia,N. and Jon Froehlich and Capra,L.} } @conference {14279, title = {Mixing type checking and symbolic execution}, booktitle = {ACM SIGPLAN Notices}, volume = {45}, year = {2010}, month = {2010///}, pages = {436 - 447}, author = {Khoo,Y.P. and Chang,B.Y.E. and Foster, Jeffrey S.} } @conference {12479, title = {Moving vistas: Exploiting motion for describing scenes}, booktitle = {2010 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)}, year = {2010}, month = {2010/06/13/18}, pages = {1911 - 1918}, publisher = {IEEE}, organization = {IEEE}, abstract = {Scene recognition in an unconstrained setting is an open and challenging problem with wide applications. In this paper, we study the role of scene dynamics for improved representation of scenes. We subsequently propose dynamic attributes which can be augmented with spatial attributes of a scene for semantically meaningful categorization of dynamic scenes. We further explore accurate and generalizable computational models for characterizing the dynamics of unconstrained scenes. The large intra-class variation due to unconstrained settings and the complex underlying physics present challenging problems in modeling scene dynamics. Motivated by these factors, we propose using the theory of chaotic systems to capture dynamics. Due to the lack of a suitable dataset, we compiled a dataset of {\textquoteleft}in-the-wild{\textquoteright} dynamic scenes. Experimental results show that the proposed framework leads to the best classification rate among other well-known dynamic modeling techniques. We also show how these dynamic features provide a means to describe dynamic scenes with motion-attributes, which then leads to meaningful organization of the video data.}, keywords = {Application software, Automation, Chaos, chaotic system, Computational modeling, Computer vision, dynamic scene categorization, Educational institutions, HUMANS, image recognition, in the wild dynamic scene, Layout, motion attribute, natural scenes, Physics, probability, scene recognition, Snow, video data}, isbn = {978-1-4244-6984-0}, doi = {10.1109/CVPR.2010.5539864}, author = {Shroff, N. and Turaga,P. and Chellapa, Rama} } @article {12488, title = {Multiscale directional filtering of noisy InSAR phase images}, journal = {Proceedings of SPIE}, volume = {7703}, year = {2010}, month = {2010/04/05/}, pages = {770308-770308-9 - 770308-770308-9}, abstract = {In this work, we present a new approach for the problem of interferometric phase noise reduction in synthetic aperture radar interferometry based on the shearlet representation. Shearlets provide a multidirectional and multiscale decomposition that have advantages when dealing with noisy phase fringes over standard filtering methods. Using a shearlet decomposition of a noisy phase image, we can adaptively estimate a phase representation in a multiscale and anisotropic fashion. Such denoised phase interferograms can be used to provide much better digital elevation maps (DEM). Experiments show that this method performs significantly better than many competitive methods.}, isbn = {0277786X}, doi = {doi:10.1117/12.849576}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/7703/1/770308_1?isAuthorized=no}, author = {Patel, Vishal M. and Easley,Glenn R and Chellapa, Rama} } @conference {12499, title = {Nearest-neighbor search algorithms on non-Euclidean manifolds for computer vision applications}, booktitle = {Proceedings of the Seventh Indian Conference on Computer Vision, Graphics and Image Processing}, series = {ICVGIP {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {282 - 289}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Nearest-neighbor searching is a crucial component in many computer vision applications such as face recognition, object recognition, texture classification, and activity recognition. When large databases are involved in these applications, it is also important to perform these searches in a fast manner. Depending on the problem at hand, nearest neighbor strategies need to be devised over feature and model spaces which in many cases are not Euclidean in nature. Thus, metrics that are tuned to the geometry of this space are required which are also known as geodesics. In this paper, we address the problem of fast nearest neighbor searching in non-Euclidean spaces, where in addition to dealing with the large size of the dataset, the significant computational load involves geodesic computations. We study the applicability of the various classes of nearest neighbor algorithms toward this end. Exact nearest neighbor methods that rely solely on the existence of a metric can be extended, albeit with a huge computational cost. We derive an approximate method of searching via approximate embeddings using the logarithmic map. We study the error incurred in such an embedding and show that it performs well in real experiments.}, keywords = {Grassmann manifold, hashing, manifold, nearest-neighbor, region covariance, shapes}, isbn = {978-1-4503-0060-5}, doi = {10.1145/1924559.1924597}, url = {http://doi.acm.org/10.1145/1924559.1924597}, author = {Turaga,Pavan and Chellapa, Rama} } @conference {18641, title = {Nfsight: netflow-based network awareness tool}, year = {2010}, month = {2010///}, abstract = {Network awareness is highly critical for network and se-curity administrators. It enables informed planning and management of network resources, as well as detection and a comprehensive understanding of malicious activ- ity. It requires a set of tools to efficiently collect, process, and represent network data. While many such tools al- ready exist, there is no flexible and practical solution for visualizing network activity at various granularities, and quickly gaining insights about the status of network as- sets. To address this issue, we developed Nfsight, a Net- Flow processing and visualization application designed to offer a comprehensive network awareness solution. Nfsight constructs bidirectional flows out of the unidi- rectional NetFlow flows and leverages these bidirectional flows to provide client/server identification and intrusion detection capabilities. We present in this paper the in- ternal architecture of Nfsight, the evaluation of the ser- vice, and intrusion detection algorithms. We illustrate the contributions of Nfsight through several case studies conducted by security administrators on a large univer- sity network. }, url = {http://www.usenix.org/event/lisa10/tech/full_papers/Berthier.pdf}, author = {Berthier,R. and Michel Cukier and Hiltunen,M. and Kormann,D. and Vesonder,G. and Sheleheda,D.} } @article {14513, title = {Object Classification Using Taxonomies}, volume = {12/414,065}, year = {2010}, month = {2010/07/22/}, abstract = {As provided herein objects from a source catalog, such as a provider{\textquoteright}s catalog, can be added to a target catalog, such as an enterprise master catalog, in a scalable manner utilizing catalog taxonomies. A baseline classifier determines probabilities for source objects to target catalog classes. Source objects can be assigned to those classes with probabilities that meet a desired threshold and meet a desired rate. A classification cost for target classes can be determined for respective unassigned source objects, which can comprise determining an assignment cost and separation cost for the source objects for respective desired target classes. The separation and assignment costs can be combined to determine the classification cost, and the unassigned source objects can be assigned to those classes having a desired classification cost.}, url = {http://www.google.com/patents?id=oXDSAAAAEBAJ}, author = {Tsaparas,Panayiotis and Papadimitriou,Panagiotis and Fuxman,Ariel D. and Getoor, Lise and Agrawal,Rakesh}, editor = {Microsoft Corporation} } @conference {12481, title = {Object Dependent Manifold Priors for Image Deconvolution}, booktitle = {Digital Image Processing and Analysis}, series = {OSA Technical Digest (CD)}, year = {2010}, month = {2010/06/07/}, pages = {DMC2 - DMC2}, publisher = {Optical Society of America}, organization = {Optical Society of America}, abstract = {In this paper we propose a manifold based deconvolution algorithm by estimating a manifold from a set of natural images that exploits the availability of the sample class data for regularizing the deblurring problem.}, keywords = {Deconvolution, IMAGE PROCESSING, Inverse problems}, url = {http://www.opticsinfobase.org/abstract.cfm?URI=DIPA-2010-DMC2}, author = {Ni,Jie and Turaga,Pavan and M.Patel,Vishal and Chellapa, Rama} } @article {12879, title = {Occurrence of the Vibrio cholerae seventh pandemic VSP-I island and a new variant}, journal = {OMICS: A Journal of Integrative Biology}, volume = {14}, year = {2010}, month = {2010/02//}, pages = {1 - 7}, isbn = {1536-2310, 1557-8100}, doi = {10.1089/omi.2009.0087}, url = {http://online.liebertpub.com/doi/abs/10.1089/omi.2009.0087}, author = {Grim,Christopher J. and Choi,Jinna and Jongsik Chun and Jeon,Yoon-Seong and Taviani,Elisa and Hasan,Nur A. and Haley,Bradd and Huq,Anwar and Rita R Colwell} } @conference {19023, title = {One experience collecting sensitive mobile data}, year = {2010}, month = {2010}, abstract = {We report on our efforts to collect behavioral data basedon activities recorded by phones. We recruited Android de- vice owners and offered entry into a raffle for participants. Our application was distributed from the Android Market, and its placement there unexpectedly helped us find par- ticipants from casual users browsing for free applications. We collected data from 267 total participants who gave us varying amounts of data. }, url = {http://www2.parc.com/csl/members/eshi/docs/users.pdf}, author = {Niu, Y. and Elaine Shi and Chow, R. and Golle, P. and Jakobsson, M.} } @article {12476, title = {Online Empirical Evaluation of Tracking Algorithms}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {32}, year = {2010}, month = {2010/08//}, pages = {1443 - 1458}, abstract = {Evaluation of tracking algorithms in the absence of ground truth is a challenging problem. There exist a variety of approaches for this problem, ranging from formal model validation techniques to heuristics that look for mismatches between track properties and the observed data. However, few of these methods scale up to the task of visual tracking, where the models are usually nonlinear and complex and typically lie in a high-dimensional space. Further, scenarios that cause track failures and/or poor tracking performance are also quite diverse for the visual tracking problem. In this paper, we propose an online performance evaluation strategy for tracking systems based on particle filters using a time-reversed Markov chain. The key intuition of our proposed methodology relies on the time-reversible nature of physical motion exhibited by most objects, which in turn should be possessed by a good tracker. In the presence of tracking failures due to occlusion, low SNR, or modeling errors, this reversible nature of the tracker is violated. We use this property for detection of track failures. To evaluate the performance of the tracker at time instant t, we use the posterior of the tracking algorithm to initialize a time-reversed Markov chain. We compute the posterior density of track parameters at the starting time t = 0 by filtering back in time to the initial time instant. The distance between the posterior density of the time-reversed chain (at t = 0) and the prior density used to initialize the tracking algorithm forms the decision statistic for evaluation. It is observed that when the data are generated by the underlying models, the decision statistic takes a low value. We provide a thorough experimental analysis of the evaluation methodology. Specifically, we demonstrate the effectiveness of our approach for tackling common challenges such as occlusion, pose, and illumination changes and provide the Receiver Operating Characteristic (ROC) curves. Finally, we also s how the applicability of the core ideas of the paper to other tracking algorithms such as the Kanade-Lucas-Tomasi (KLT) feature tracker and the mean-shift tracker.}, keywords = {Back, Biomedical imaging, Computer vision, Filtering, formal model validation techniques, formal verification, ground truth, Kanade Lucas Tomasi feature tracker, Karhunen-Loeve transforms, lighting, Markov processes, mean shift tracker, model validation., online empirical evaluation, particle filtering (numerical methods), Particle filters, Particle tracking, performance evaluation, receiver operating characteristic curves, Robustness, SNR, Statistics, Surveillance, time reversed Markov chain, tracking, tracking algorithms, visual tracking}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2009.135}, author = {Wu,Hao and Sankaranarayanan,A. C and Chellapa, Rama} } @article {19373, title = {Overlap-based cell tracker}, journal = {The Journal of Research of the National Institute of Standards and Technology}, volume = {115}, year = {2010}, month = {11/2010}, chapter = {477}, abstract = { order to facilitate the extraction of quantitative data from live cell image sets, automated image analysis methods are needed. This paper presents an introduction to the general principle of an overlap cell tracking software developed by the National Institute of Standards and Technology (NIST). This cell tracker has the ability to track cells across a set of time lapse images acquired at high rates based on the amount of overlap between cellular regions in consecutive frames. It is designed to be highly flexible, requires little user parameterization, and has a fast execution time. }, author = {Chalfoun, J and Cardone, Antonio and Dima, A.A. and Allen, D.P. and Halter, M.W.} } @article {12466, title = {PADS: A Probabilistic Activity Detection Framework for Video Data}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {32}, year = {2010}, month = {2010/12//}, pages = {2246 - 2261}, abstract = {There is now a growing need to identify various kinds of activities that occur in videos. In this paper, we first present a logical language called Probabilistic Activity Description Language (PADL) in which users can specify activities of interest. We then develop a probabilistic framework which assigns to any subvideo of a given video sequence a probability that the subvideo contains the given activity, and we finally develop two fast algorithms to detect activities within this framework. OffPad finds all minimal segments of a video that contain a given activity with a probability exceeding a given threshold. In contrast, the OnPad algorithm examines a video during playout (rather than afterwards as OffPad does) and computes the probability that a given activity is occurring (even if the activity is only partially complete). Our prototype Probabilistic Activity Detection System (PADS) implements the framework and the two algorithms, building on top of existing image processing algorithms. We have conducted detailed experiments and compared our approach to four different approaches presented in the literature. We show that-for complex activity definitions-our approach outperforms all the other approaches.}, keywords = {Automated;Programming Languages;Video Recording;, Computer-Assisted;Models, PADL;PADS;image processing algorithms;offPad algorithm;onPad algorithm;probabilistic activity description language;probabilistic activity detection framework;video data;video sequence;image sequences;object detection;probability;video surveillance;Algorit, Statistical;Movement;Pattern Recognition}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2010.33}, author = {Albanese, M. and Chellapa, Rama and Cuntoor, N. and Moscato, V. and Picariello, A. and V.S. Subrahmanian and Udrea,O.} } @article {18260, title = {Performance impact of ordinal ranking on content fingerprinting}, journal = {IEEE Int. Conf. on Image Processing}, year = {2010}, month = {2010///}, abstract = {Content fingerprinting provides a compact representation ofmultimedia objects for copy identification. This paper ana- lyzes the impact of the ordinal-ranking based feature encod- ing on the performance of content fingerprinting. Expressions are derived for the identification performance of a fingerprint- ing system with and without ordinal ranking. The analysis in- dicates that when the number of features is moderately large, ordinal ranking can improve the robustness of the fingerprint- ing system to large distortions of the features and significantly increase the probability of detection. These results enhance understandings of ordinal ranking and provide design guide- lines for choosing different system parameters to achieve a desired identification accuracy. }, author = {Chuang,W.H. and Varna,A.L. and Wu,M.} } @article {18708, title = {Perturbing the Ubiquitin Pathway Reveals How Mitosis Is Hijacked to Denucleate and Regulate Cell Proliferation and Differentiation In Vivo}, journal = {PLoS ONEPLoS ONE}, volume = {5}, year = {2010}, month = {2010/10/20/}, pages = {e13331 - e13331}, abstract = {BackgroundThe eye lens presents a unique opportunity to explore roles for specific molecules in cell proliferation, differentiation and development because cells remain in place throughout life and, like red blood cells and keratinocytes, they go through the most extreme differentiation, including removal of nuclei and cessation of protein synthesis. Ubiquitination controls many critical cellular processes, most of which require specific lysines on ubiquitin (Ub). Of the 7 lysines (K) least is known about effects of modification of K6. Methodology and Principal Findings We replaced K6 with tryptophan (W) because K6 is the most readily modified K and W is the most structurally similar residue to biotin. The backbone of K6W-Ub is indistinguishable from that of Wt-Ub. K6W-Ub is effectively conjugated and deconjugated but the conjugates are not degraded via the ubiquitin proteasome pathways (UPP). Expression of K6W-ubiquitin in the lens and lens cells results in accumulation of intracellular aggregates and also slows cell proliferation and the differentiation program, including expression of lens specific proteins, differentiation of epithelial cells into fibers, achieving proper fiber cell morphology, and removal of nuclei. The latter is critical for transparency, but the mechanism by which cell nuclei are removed has remained an age old enigma. This was also solved by expressing K6W-Ub. p27kip, a UPP substrate accumulates in lenses which express K6W-Ub. This precludes phosphorylation of nuclear lamin by the mitotic kinase, a prerequisite for disassembly of the nuclear membrane. Thus the nucleus remains intact and DNAseIIβ neither gains entry to the nucleus nor degrades the DNA. These results could not be obtained using chemical proteasome inhibitors that cannot be directed to specific tissues. Conclusions and Significance K6W-Ub provides a novel, genetic means to study functions of the UPP because it can be targeted to specific cells and tissues. A fully functional UPP is required to execute most stages of lens differentiation, specifically removal of cell nuclei. In the absence of a functional UPP, small aggregate prone, cataractous lenses are formed. }, doi = {10.1371/journal.pone.0013331}, url = {http://dx.doi.org/10.1371/journal.pone.0013331}, author = {Caceres,Andrea and Shang,Fu and Wawrousek,Eric and Liu,Qing and Avidan,Orna and Cvekl,Ales and Yang,Ying and Haririnia,Aydin and Storaska,Andrew and Fushman, David and Kuszak,Jer and Dudek,Edward and Smith,Donald and Taylor,Allen} } @conference {12486, title = {Pose estimation in heavy clutter using a multi-flash camera}, booktitle = {Robotics and Automation (ICRA), 2010 IEEE International Conference on}, year = {2010}, month = {2010/05//}, pages = {2028 - 2035}, abstract = {We propose a novel solution to object detection, localization and pose estimation with applications in robot vision. The proposed method is especially applicable when the objects of interest may not be richly textured and are immersed in heavy clutter. We show that a multi-flash camera (MFC) provides accurate separation of depth edges and texture edges in such scenes. Then, we reformulate the problem, as one of finding matches between the depth edges obtained in one or more MFC images to the rendered depth edges that are computed offline using 3D CAD model of the objects. In order to facilitate accurate matching of these binary depth edge maps, we introduce a novel cost function that respects both the position and the local orientation of each edge pixel. This cost function is significantly superior to traditional Chamfer cost and leads to accurate matching even in heavily cluttered scenes where traditional methods are unreliable. We present a sub-linear time algorithm to compute the cost function using techniques from 3D distance transforms and integral images. Finally, we also propose a multi-view based pose-refinement algorithm to improve the estimated pose. We implemented the algorithm on an industrial robot arm and obtained location and angular estimation accuracy of the order of 1 mm and 2 $\#$x00B0; respectively for a variety of parts with minimal texture.}, keywords = {3D, algorithm;object, based, camera;multiview, depth, detection;object, detection;pose, distance, edge, edges;cameras;image, edges;integral, estimation;binary, estimation;multiflash, estimation;robot, function;depth, images;location, localization;pose, maps, matching;cost, matching;image, pose-refinement, texture;object, transforms;angular, vision;texture, vision;transforms;}, doi = {10.1109/ROBOT.2010.5509897}, author = {Ming-Yu Liu and Tuzel, O. and Veeraraghavan,A. and Chellapa, Rama and Agrawal,A. and Okuda, H.} } @conference {12485, title = {Pose-robust albedo estimation from a single image}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2010 IEEE Conference on}, year = {2010}, month = {2010/06//}, pages = {2683 - 2690}, abstract = {We present a stochastic filtering approach to perform albedo estimation from a single non-frontal face image. Albedo estimation has far reaching applications in various computer vision tasks like illumination-insensitive matching, shape recovery, etc. We extend the formulation proposed in that assumes face in known pose and present an algorithm that can perform albedo estimation from a single image even when pose information is inaccurate. 3D pose of the input face image is obtained as a byproduct of the algorithm. The proposed approach utilizes class-specific statistics of faces to iteratively improve albedo and pose estimates. Illustrations and experimental results are provided to show the effectiveness of the approach. We highlight the usefulness of the method for the task of matching faces across variations in pose and illumination. The facial pose estimates obtained are also compared against ground truth.}, keywords = {3D, albedo, estimation;, estimation;shape, Face, filtering;face, image;single, image;stochastic, information;pose-robust, matching;pose, nonfrontal, pose;class-specific, recognition;filtering, recovery;single, statistics;computer, theory;pose, vision;illumination-insensitive}, doi = {10.1109/CVPR.2010.5539987}, author = {Biswas,S. and Chellapa, Rama} } @article {12877, title = {The pre-seventh pandemic Vibrio cholerae BX 330286 El Tor genome: evidence for the environment as a genome reservoir}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2010}, month = {2010/02/01/}, pages = {208 - 216}, abstract = {Vibrio cholerae O1 El Tor BX 330286 was isolated from a water sample in Australia in 1986, 9 years after an indigenous outbreak of cholera occurred in that region. This environmental strain encodes virulence factors highly similar to those of clinical strains, suggesting an ability to cause disease in humans. We demonstrate its high similarity in gene content and genome-wide nucleotide sequence to clinical V. cholerae strains, notably to pre-seventh pandemic O1 El Tor strains isolated in 1910 (V. cholerae NCTC 8457) and 1937 (V. cholerae MAK 757), as well as seventh pandemic strains isolated after 1960 globally. Here we demonstrate that this strain represents a transitory clone with shared characteristics between pre-seventh and seventh pandemic strains of V. cholerae. Interestingly, this strain was isolated 25 years after the beginning of the seventh pandemic, suggesting the environment as a genome reservoir in areas where cholera does not occur in sporadic, endemic or epidemic form.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2010.00141.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2010.00141.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Haley,Bradd J. and Grim,Christopher J. and Hasan,Nur A. and Taviani,Elisa and Jongsik Chun and Brettin,Thomas S. and Bruce,David C. and Challacombe,Jean F. and Detter,J. Chris and Han,Cliff S. and Huq,Anwar and Nair,G. Balakrish and Rita R Colwell} } @conference {12473, title = {Recognizing offensive strategies from football videos}, booktitle = {Image Processing (ICIP), 2010 17th IEEE International Conference on}, year = {2010}, month = {2010/09//}, pages = {4585 - 4588}, abstract = {We address the problem of recognizing offensive play strategies from American football play videos. Specifically, we propose a probabilistic model which describes the generative process of an observed football play and takes into account practical issues in real football videos, such as difficulty in identifying offensive players, view changes, and tracking errors. In particular, we exploit the geometric properties of nonlinear spaces of involved variables and design statistical models on these manifolds. Then recognition is performed via {\textquoteright}analysis-by-synthesis{\textquoteright} technique. Experiments on a newly established dataset of American football videos demonstrate the effectiveness of the approach.}, keywords = {American, analysis;video, changes;image, errors;variables, football, identification;tracking, models;geometric, models;view, play, players, processing;, properties;nonlinear, recognition;offensive, recognition;statistical, signal, spaces;offensive, statistical, strategies, technique;design, videos;analysis-by-synthesis}, doi = {10.1109/ICIP.2010.5652192}, author = {Ruonan Li and Chellapa, Rama} } @conference {15493, title = {Repairing GUI Test Suites Using a Genetic Algorithm}, booktitle = {Software Testing, Verification and Validation (ICST), 2010 Third International Conference on}, year = {2010}, month = {2010/04//}, pages = {245 - 254}, abstract = {Recent advances in automated functional testing of Graphical User Interfaces (GUIs) rely on deriving graph models that approximate all possible sequences of events that may be executed on the GUI, and then use the graphs to generate test cases (event sequences) that achieve a specified coverage goal. However, because these models are only approximations of the actual event flows, the generated test cases may suffer from problems of infeasibility, i.e., some events may not be available for execution causing the test case to terminate prematurely. In this paper we develop a method to automatically repair GUI test suites, generating new test cases that are feasible. We use a genetic algorithm to evolve new test cases that increase our test suite{\textquoteright}s coverage while avoiding infeasible sequences. We experiment with this algorithm on a set of synthetic programs containing different types of constraints and for test sequences of varying lengths. Our results suggest that we can generate new test cases to cover most of the feasible coverage and that the genetic algorithm outperforms a random algorithm trying to achieve the same goal in almost all cases.}, keywords = {automated functional testing, genetic algorithm, Genetic algorithms, graph model, graphical user interface, Graphical user interfaces, GUI test suite, program testing, random algorithm, synthetic program, test case}, doi = {10.1109/ICST.2010.39}, author = {Huang,Si and Cohen,M. B and Memon, Atif M.} } @conference {17984, title = {Resource-Aware Compiler Prefetching for Many-Cores}, booktitle = {Parallel and Distributed Computing (ISPDC), 2010 Ninth International Symposium on}, year = {2010}, month = {2010/07//}, pages = {133 - 140}, abstract = {Super-scalar, out-of-order processors that can have tens of read and write requests in the execution window place significant demands on Memory Level Parallelism (MLP). Multi-and many-cores with shared parallel caches further increase MLP demand. Current cache hierarchies however have been unable to keep up with this trend, with modern designs allowing only 4-16 concurrent cache misses. This disconnect is exacerbated by recent highly parallel architectures (e.g. GPUs) where power and area per-core budget favor lighter cores with less resources. Support for hardware and software prefetch increase MLP pressure since these techniques overlap multiple memory requests with existing computation. In this paper, we propose and evaluate a novel Resource-Aware Prefetching (RAP) compiler algorithm that is aware of the number of simultaneous prefetches supported, and optimized for the same. We show that in situations where not enough resources are available to issue prefetch instructions for all references in a loop, it is more beneficial to decrease the prefetch distance and prefetch for as many references as possible, rather than use a fixed prefetched distance and skip prefetching for some references, as in current approaches. We implemented our algorithm in a GCC-derived compiler and evaluated its performance using an emerging fine-grained many-core architecture. Our results show that the RAP algorithm outperforms a well-known loop prefetching algorithm by up to 40.15\% and the state-of-the art GCC implementation by up to 34.79\%. Moreover, we compare the RAP algorithm with a simple hardware prefetching mechanism, and show improvements of up to 24.61\%.}, keywords = {algorithm;memory, architecture;hardware-software, architectures;parallel, architectures;resource, aware, caches;super-scalar, compiler, compiler;Multicore, compilers;parallel, GCC-derived, level, management;, many-core, memories;storage, out-of-order, Parallel, parallelism;parallel, prefetch;loop, prefetching, prefetching;shared, processor;fine-grained, processors;multiprocessing, systems;optimising}, doi = {10.1109/ISPDC.2010.16}, author = {Caragea,G.C. and Tzannes,A. and Keceli,F. and Barua,R. and Vishkin, Uzi} } @article {12475, title = {Robust Height Estimation of Moving Objects From Uncalibrated Videos}, journal = {IEEE Transactions on Image Processing}, volume = {19}, year = {2010}, month = {2010/08//}, pages = {2221 - 2232}, abstract = {This paper presents an approach for video metrology. From videos acquired by an uncalibrated stationary camera, we first recover the vanishing line and the vertical point of the scene based upon tracking moving objects that primarily lie on a ground plane. Using geometric properties of moving objects, a probabilistic model is constructed for simultaneously grouping trajectories and estimating vanishing points. Then we apply a single view mensuration algorithm to each of the frames to obtain height measurements. We finally fuse the multiframe measurements using the least median of squares (LMedS) as a robust cost function and the Robbins-Monro stochastic approximation (RMSA) technique. This method enables less human supervision, more flexibility and improved robustness. From the uncertainty analysis, we conclude that the method with auto-calibration is robust in practice. Results are shown based upon realistic tracking data from a variety of scenes.}, keywords = {algorithms, Biometry, Calibration, EM algorithm, geometric properties, Geometry, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, least median of squares, least squares approximations, MOTION, motion information, multiframe measurements, Pattern Recognition, Automated, Reproducibility of results, Robbins-Monro stochastic approximation, robust height estimation, Sensitivity and Specificity, Signal Processing, Computer-Assisted, stochastic approximation, Subtraction Technique, tracking data, uncalibrated stationary camera, uncalibrated videos, uncertainty analysis, vanishing point, video metrology, Video Recording, video signal processing}, isbn = {1057-7149}, doi = {10.1109/TIP.2010.2046368}, author = {Jie Shao and Zhou,S. K and Chellapa, Rama} } @conference {12492, title = {Robust regression using sparse learning for high dimensional parameter estimation problems}, booktitle = {Acoustics Speech and Signal Processing (ICASSP), 2010 IEEE International Conference on}, year = {2010}, month = {2010/03//}, pages = {3846 - 3849}, abstract = {Algorithms such as Least Median of Squares (LMedS) and Random Sample Consensus (RANSAC) have been very successful for low-dimensional robust regression problems. However, the combinatorial nature of these algorithms makes them practically unusable for high-dimensional applications. In this paper, we introduce algorithms that have cubic time complexity in the dimension of the problem, which make them computationally efficient for high-dimensional problems. We formulate the robust regression problem by projecting the dependent variable onto the null space of the independent variables which receives significant contributions only from the outliers. We then identify the outliers using sparse representation/learning based algorithms. Under certain conditions, that follow from the theory of sparse representation, these polynomial algorithms can accurately solve the robust regression problem which is, in general, a combinatorial problem. We present experimental results that demonstrate the efficacy of the proposed algorithms. We also analyze the intrinsic parameter space of robust regression and identify an efficient and accurate class of algorithms for different operating conditions. An application to facial age estimation is presented.}, keywords = {algorithm;random, analysis;, combinatorial, complexity;least, complexity;parameter, consensus;robust, Estimation, estimation;polynomials;regression, learning;sparse, median, of, problem;cubic, problem;polynomial, problem;sparse, regression, representation;computational, sample, squares;parameter, TIME}, doi = {10.1109/ICASSP.2010.5495830}, author = {Mitra, K. and Veeraraghavan,A. and Chellapa, Rama} } @conference {12482, title = {Robust RVM regression using sparse outlier model}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2010 IEEE Conference on}, year = {2010}, month = {2010/06//}, pages = {1887 - 1894}, abstract = {Kernel regression techniques such as Relevance Vector Machine (RVM) regression, Support Vector Regression and Gaussian processes are widely used for solving many computer vision problems such as age, head pose, 3D human pose and lighting estimation. However, the presence of outliers in the training dataset makes the estimates from these regression techniques unreliable. In this paper, we propose robust versions of the RVM regression that can handle outliers in the training dataset. We decompose the noise term in the RVM formulation into a (sparse) outlier noise term and a Gaussian noise term. We then estimate the outlier noise along with the model parameters. We present two approaches for solving this estimation problem: (1) a Bayesian approach, which essentially follows the RVM framework and (2) an optimization approach based on Basis Pursuit Denoising. In the Bayesian approach, the robust RVM problem essentially becomes a bigger RVM problem with the advantage that it can be solved efficiently by a fast algorithm. Empirical evaluations, and real experiments on image de-noising and age estimation demonstrate the better performance of the robust RVM algorithms over that of the RVM reg ression.}, keywords = {3D, analysis;, approach;Gaussian, denoising;computer, denoising;lighting, denoising;regression, estimation;relevance, human, machine;robust, model;Gaussian, noise;basis, noise;computer, outlier, pose;Bayesian, pursuit, regression;sparse, RVM, vector, vision;image}, doi = {10.1109/CVPR.2010.5539861}, author = {Mitra, K. and Veeraraghavan,A. and Chellapa, Rama} } @conference {12490, title = {The role of geometry in age estimation}, booktitle = {2010 IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP)}, year = {2010}, month = {2010/03/14/19}, pages = {946 - 949}, publisher = {IEEE}, organization = {IEEE}, abstract = {Understanding and modeling of aging in human faces is an important problem in many real-world applications such as biometrics, authentication, and synthesis. In this paper, we consider the role of geometric attributes of faces, as described by a set of landmark points on the face, in age perception. Towards this end, we show that the space of landmarks can be interpreted as a Grassmann manifold. Then the problem of age estimation is posed as a problem of function estimation on the manifold. The warping of an average face to a given face is quantified as a velocity vector that transforms the average to a given face along a smooth geodesic in unit-time. This deformation is then shown to contain important information about the age of the face. We show in experiments that exploiting geometric cues in a principled manner provides comparable performance to several systems that utilize both geometric and textural cues. We show results on age estimation using the standard FG-Net dataset and a passport dataset which illustrate the effectiveness of the approach.}, keywords = {age estimation, Aging, Biometrics, computational geometry, Face, Face Geometry, Facial animation, Feature extraction, function estimation problem, geometric face attributes, Geometry, Grassmann manifold, human face modeling, human face understanding, HUMANS, Mouth, regression, Regression analysis, SHAPE, Solid modeling, solid modelling, velocity vector}, isbn = {978-1-4244-4295-9}, doi = {10.1109/ICASSP.2010.5495292}, author = {Turaga,P. and Biswas,S. and Chellapa, Rama} } @conference {15918, title = {Sectored Random Projections for Cancelable Iris Biometrics}, booktitle = {2010 IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP)}, year = {2010}, month = {2010/03//}, pages = {1838 - 1841}, publisher = {IEEE}, organization = {IEEE}, abstract = {Privacy and security are essential requirements in practical biometric systems. In order to prevent the theft of biometric patterns, it is desired to modify them through revocable and non invertible transformations called Cancelable Biometrics. In this paper, we propose an efficient algorithm for generating a Cancelable Iris Biometric based on Sectored Random Projections. Our algorithm can generate a new pattern if the existing one is stolen, retain the original recognition performance and prevent extraction of useful information from the transformed patterns. Our method also addresses some of the drawbacks of existing techniques and is robust to degradations due to eyelids and eyelashes.}, keywords = {biometric pattern, Biometrics, Cancelable Biometrics, cancelable iris biometrics, data mining, data privacy, Degradation, Eyelashes, Eyelids, Iris, iris recognition, pattern recognition, privacy, random processes, Random Projections, Robustness, sectored random projection, Secure Biometrics, Security, security of data}, isbn = {978-1-4244-4295-9}, doi = {10.1109/ICASSP.2010.5495383}, author = {Pillai,J.K. and Patel, Vishal M. and Chellapa, Rama and Ratha,N. K} } @article {12501, title = {Secure and robust iris recognition using random projections and sparse representations}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, year = {2010}, month = {2010///}, pages = {1 - 1}, author = {Pillai, J. and Patel, Vishal M. and Chellapa, Rama and Ratha, N.} } @article {19283, title = {Selective excitation of LI2 by chirped laser pulses with all possible interstate radiative couplings}, journal = {The Journal of Chemical Physics}, volume = {133}, year = {2010}, month = {2010}, pages = {164313 - 164313-9}, abstract = {We have numerically explored the feasibility and the mechanism of population transfer to the excited E 1Σg electronic state of Li2 from the v = 0 level of the ground electronic state X 1Σg using the A 1Σu state as an intermediate. In this system, the use of transform limited pulses with a frequency difference greater than the maximum Rabi frequency does not produce population transfer when all possible radiative couplings are taken into account. We have employed two synchronous pulses far detuned from the allowed transition frequencies, mainly with the lower frequency pulse positively chirped, and both pulses coupling the successive pair of states, X-A and A-E. The adiabaticity of the process has been investigated by a generalized Floquet calculation in the basis of 12 field dressed molecular states, and the results have been compared with those obtained from the full solution of time dependent Schr{\"o}dinger equation. The conventional representation of the process in terms of three (or four) adiabatic potentials is not valid. It has been found that for cases of almost complete population transfer in full calculations with the conservation of the vibrational quantum number, adiabatic passage is attained with the 12 state Floquet model but not with the six state model. The agreement between the full calculations and the 12 state Floquet calculations is generally good when the transfer is adiabatic. Another characteristic feature of this work is the gaining of control over the vibrational state preparation in the final electronic state by careful tuning of the laser parameters as well as the chirp rate sign. This causes time dependent changes in the adiabatic potentials and nonadiabatic transfers can be made to occur between them.}, isbn = {00219606}, url = {http://jcp.aip.org/resource/1/jcpsa6/v133/i16/p164313_s1}, author = {Chatterjee, Souvik and Bhattacharyya, Shuvra S.} } @inbook {12507, title = {Semantic Video Content Analysis}, booktitle = {Video Search and MiningVideo Search and Mining}, series = {Studies in Computational Intelligence}, volume = {287}, year = {2010}, month = {2010///}, pages = {147 - 176}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In recent years, there has been significant interest in the area of automatically recognizing activities occurring in a camera{\textquoteright}s field of view and detecting abnormalities. The practical applications of such a system could include airport tarmac monitoring, or monitoring of activities in secure installations, to name a few. The difficulty of the problem is compounded by several factors: detection of primitive actions in spite of changes in illumination, occlusions and noise; complexmultiagent interaction;mapping of higher-level activities to lower-level primitive actions; variations in which the same semantic activity can be performed. In this chapter, we develop a theory of semantic activity analysis that addresses each of these issues in an integrated manner. Specifically, we discuss ontological representations of knowledge of a domain, integration of domain knowledge and statistical models for achieving semantic mappings, definition of logical languages to describe activities, and design of frameworks which integrate all the above aspects in a coherent way, thus laying the foundations of effective Semantic Video Content Analysis systems.}, isbn = {978-3-642-12899-8}, url = {http://dx.doi.org/10.1007/978-3-642-12900-1_6}, author = {Albanese,Massimiliano and Turaga,Pavan and Chellapa, Rama and Pugliese,Andrea and Subrahmanian,V.}, editor = {Schonfeld,Dan and Shan,Caifeng and Tao,Dacheng and Wang,Liang} } @conference {18282, title = {Semi non-intrusive training for cell-phone camera model linkage}, booktitle = {Information Forensics and Security (WIFS), 2010 IEEE International Workshop on}, year = {2010}, month = {2010/12//}, pages = {1 - 6}, abstract = {This paper presents a study of cell-phone camera model linkage that matches digital images against potential makes / models of cell-phone camera sources using camera color interpolation features. The matching performance is examined and the dependency on the content of training image collection is evaluated via variance analysis. Training content dependency can be dealt with under the framework of component forensics, where cell-phone camera model linkage is seen as a combination of semi non-intrusive training and completely non-intrusive testing. Such a viewpoint suggests explicitly the goodness criterion of testing accuracy for training data selection. It also motivates other possible alternative training procedures based on different criteria, such as the training complexity, for which preliminary but promising experiment designs and results have been obtained.}, keywords = {accuracy;training, analysis;cameras;cellular, analysis;image, camera, Color, colour, complexity;training, content, dependency;variance, feature;cell, forensics;digital, forensics;image, image, Interpolation, linkage;component, matching;interpolation;, matching;semi, model, nonintrusive, phone, radio;computer, training;testing}, doi = {10.1109/WIFS.2010.5711468}, author = {Chuang,Wei-Hong and M. Wu} } @article {12878, title = {Serodiversity and ecological distribution of Vibrio parahaemolyticus in the Venetian Lagoon, Northeast Italy}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2010}, month = {2010/02/01/}, pages = {151 - 157}, abstract = {Vibrio parahaemolyticus is a natural inhabitant of estuarine and marine environments constituting part of the autochthonous microflora. This species is associated with human gastroenteritis caused by ingestion of contaminated water and undercooked seafood. During the past several years, the number of V. parahaemolyticus gastroenteritis cases have increased worldwide, causing over half of all food-poisoning outbreaks of bacterial origin. Vibrio populations in water are known to be influenced by environmental factors. Notably, it has been shown that in different parts of the world the distribution of V. parahaemolyticus in the marine environment is related to the water temperature. In this study, we identified environmental determinants affecting distribution of V. parahaemolyticus in the Venetian Lagoon, in the Italian North Adriatic Sea. Data obtained revealed that sea surface temperature constitutes the key factor influencing occurrence of V. parahaemolyticus, but salinity and chlorophyll concentration are also important. Serotyping of a collection of V. parahaemolyticus environmental isolates revealed high serodiversity, with serotypes O3:KUT and O1:KUT, belonging to the {\textquoteleft}pandemic group{\textquoteright}, occurring with higher frequency. From our results, we conclude that there is no correlation between serotype and specific geographic site or season of the year. However, certain serotypes were isolated in the Lagoon during the entire 18 months of the study, strongly suggesting persistence in this environment.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2009.00123.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2009.00123.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Caburlotto,Greta and Haley,Bradd J. and Lle{\`o},Maria M. and Huq,Anwar and Rita R Colwell} } @article {19298, title = {Signal Processing on Platforms with Multiple Cores: Part 2-Applications and Design [From the Guest Editors]}, journal = {IEEE Signal Processing Magazine}, volume = {27}, year = {2010}, month = {2010}, pages = {20 - 21}, abstract = {Platforms with multiple cores are now prevalent everywhere from desktops and graphics processors to laptops and embedded systems. By adding more parallel computational resources while managing power consumption, multicore platforms offer better programmability, performance, and power efficiency. Signal processing systems of tomorrow will be and must be implemented on platforms with multiple cores. Writing efficient parallel applications that utilize the computing capability of many processing cores require some effort. Signal processing algorithm designers must understand the nuances of a multicore computing engine; only then can the tremendous computing power that such platforms provide be harnessed efficiently. To give a thorough perspective of the area, we have organized two special issues on this topic.}, keywords = {Concurrent computing, Embedded system, Energy management, Graphics, Multicore processing, Portable computers, Resource management, Signal design, Signal processing, Signal processing algorithms}, isbn = {1053-5888}, author = {Chen,Y. and Chakrabarti,C. and Bhattacharyya, Shuvra S. and Bougard, B.} } @conference {15921, title = {Sparse representations and Random Projections for robust and cancelable biometrics}, booktitle = {Control Automation Robotics Vision (ICARCV), 2010 11th International Conference on}, year = {2010}, month = {2010/12//}, pages = {1 - 6}, abstract = {In recent years, the theories of Sparse Representation (SR) and Compressed Sensing (CS) have emerged as powerful tools for efficiently processing data in non-traditional ways. An area of promise for these theories is biome $\#$x0301;trie identification. In this paper, we review the role of sparse representation and CS for efficient biome $\#$x0301;trie identification. Algorithms to perform identification from face and iris data are reviewed. By applying Random Projections it is possible to purposively hide the biome $\#$x0301;trie data within a template. This procedure can be effectively employed for securing and protecting personal biome $\#$x0301;trie data against theft. Some of the most compelling challenges and issues that confront research in biometrics using sparse representations and CS are also addressed.}, keywords = {Biometric identification, Cancelable Biometrics, Compressed sensing, face data, face recognition, iris data, iris recognition, personal biometric data, Random Projections, robust biometrics, sparse representations}, doi = {10.1109/ICARCV.2010.5707955}, author = {Patel, Vishal M. and Chellapa, Rama and Tistarelli,M.} } @article {12487, title = {Sparsity inspired automatic target recognition}, journal = {Proceedings of SPIE}, volume = {7696}, year = {2010}, month = {2010/04/23/}, pages = {76960Q-76960Q-8 - 76960Q-76960Q-8}, abstract = {In this paper, we develop a framework for using only the needed data for automatic target recognition (ATR) algorithms using the recently developed theory of sparse representations and compressive sensing (CS). We show how sparsity can be helpful for efficient utilization of data, with the possibility of developing real-time, robust target classification. We verify the efficacy of the proposed algorithm in terms of the recognition rate on the well known Comanche forward-looking infrared (FLIR) data set consisting of ten different military targets at different orientations.}, isbn = {0277786X}, doi = {doi:10.1117/12.850533}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/7696/1/76960Q_1?isAuthorized=no}, author = {Patel, Vishal M. and Nasrabadi,Nasser M. and Chellapa, Rama} } @article {12469, title = {Sparsity Motivated Automated Target Recognition}, year = {2010}, month = {2010/09/29/}, abstract = {Sparsity-based methods have recently been suggested for tasks such as face and iris recognition. In this project, we evaluated the effectiveness of such methods for automatic target recognition in infrared images. We show how sparsity can be helpful for efficient utilization of data for target recognition. We evaluated the effectiveness of the proposed algorithm in terms of recognition rate and confusion matrices on the well known Comanche forward-looking infrared (FLIR) data set consisting of ten different military targets at different orientations. This work was done in collaboration with Dr. Nasser Nasrabadi, Chief Scientist, SEDD, Army research laboratory. This work will be presented at the International Conference on Image Processing being held in Hong Kong in September 2010. A journal paper reporting our work is under preparation.}, keywords = {*ALGORITHMS, *INFRARED IMAGES, *TARGET RECOGNITION, ARMY RESEARCH, efficiency, FORWARD LOOKING INFRARED SYSTEMS, IMAGE PROCESSING, NUMERICAL MATHEMATICS, OPTICS, PE611102, TARGET DETECTION, TARGET DIRECTION, RANGE AND POSITION FINDING}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA535014}, author = {Chellapa, Rama} } @article {12470, title = {Sparsity-Inspired Recognition of Targets in Infrared Images}, year = {2010}, month = {2010/09/29/}, abstract = {Sparsity-based methods have recently been suggested for tasks such as face and iris recognition. In this project, we evaluated the effectiveness of such methods for automatic target recognition in infrared images. We show how sparsity can be helpful for efficient utilization of data for target recognition. We evaluated the effectiveness of the proposed algorithm in terms of recognition rate and confusion matrices on the well known Comanche forward-looking infrared (FLIR) data set consisting of ten different military targets at different orientations. This work was done in collaboration with Dr. Nasser Nasrabadi, Chief Scientist, SEDD, Army research laboratory. This work will be presented at the International Conference on Image Processing being held in Hong Kong in September 2010. A journal paper reporting our work is under preparation.}, keywords = {*FORWARD LOOKING INFRARED SYSTEMS, *IMAGE PROCESSING, *TARGET RECOGNITION, algorithms, ARMY RESEARCH, ATR(AUTOMATIC TARGET RECOGNITION), AUTOMATIC, CNN(CONVENTIONAL NEURAL NETWORKS), CS(COMPRESSIVE SENSING), DISCRIMINANT ANALYSIS, FLIR(FORWARD LOOKING INFRARED), INFRARED DETECTION AND DETECTORS, INFRARED IMAGES, LDA(LINEAR DISCRIMINANT ANALYSIS), MILITARY OPERATIONS, MNN(MODULAR NEURAL NETWORKS), neural nets, PCA(PRINCIPAL COMPONENT ANALYSIS), PE611102, SPARSITY, TARGET DIRECTION, RANGE AND POSITION FINDING}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA535424}, author = {Chellapa, Rama} } @article {12468, title = {Special Section on Distributed Camera Networks: Sensing, Processing, Communication, and Implementation}, journal = {Image Processing, IEEE Transactions on}, volume = {19}, year = {2010}, month = {2010/10//}, pages = {2513 - 2515}, abstract = {The eight papers in this special section span across theoretical and practical considerations of various aspects of distributed camera networks, including adaptive sensing, distributed processing, efficient communications, and versatile implementations.}, isbn = {1057-7149}, doi = {10.1109/TIP.2010.2063650}, author = {Chellapa, Rama and Heinzelman, W. and Konrad, J. and Schonfeld, D. and Wolf, M.} } @conference {17423, title = {The state of visual analytics: Views on what visual analytics is and where it is going}, booktitle = {2010 IEEE Symposium on Visual Analytics Science and Technology (VAST)}, year = {2010}, month = {2010/10/25/26}, pages = {257 - 259}, publisher = {IEEE}, organization = {IEEE}, abstract = {In the 2005 publication "Illuminating the Path" visual analytics was defined as "the science of analytical reasoning facilitated by interactive visual interfaces." A lot of work has been done in visual analytics over the intervening five years. While visual analytics started in the United States with a focus on security, it is now a worldwide research agenda with a broad range of application domains. This is evidenced by efforts like the European VisMaster program and the upcoming Visual Analytics and Knowledge Discovery (VAKD) workshop, just to name two.There are still questions concerning where and how visual analytics fits in the large body of research and applications represented by the VisWeek community. This panel will present distinct viewpoints on what visual analytics is and its role in understanding complex information in a complex world. The goal of this panel is to engender discussion from the audience on the emergence and continued advancement of visual analytics and its role relative to fields of related research. Four distinguished panelists will provide their perspective on visual analytics focusing on what it is, what it should be, and thoughts about a development path between these two states. The purpose of the presentations is not to give a critical review of the literature but rather to give a review on the field and to provide a contextual perspective based on the panelists{\textquoteright} years of experience and accumulated knowledge.}, keywords = {analytical reasoning, Data analysis, data mining, data visualisation, European VisMaster program, interactive visual interfaces, knowledge discovery, United States, visual analytics, VisWeek community}, isbn = {978-1-4244-9488-0}, doi = {10.1109/VAST.2010.5649078}, author = {May,R. and Hanrahan,P. and Keim,D. A and Shneiderman, Ben and Card,S.} } @inbook {12497, title = {Statistical Analysis on Manifolds and Its Applications to Video Analysis}, booktitle = {Video Search and MiningVideo Search and Mining}, series = {Studies in Computational Intelligence}, volume = {287}, year = {2010}, month = {2010///}, pages = {115 - 144}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The analysis and interpretation of video data is an important component of modern vision applications such as biometrics, surveillance, motionsynthesis and web-based user interfaces. A common requirement among these very different applications is the ability to learn statistical models of appearance and motion from a collection of videos, and then use them for recognizing actions or persons in a new video. These applications in video analysis require statistical inference methods to be devised on non-Euclidean spaces or more formally on manifolds. This chapter outlines a broad survey of applications in video analysis that involve manifolds. We develop the required mathematical tools needed to perform statistical inference on manifolds and show their effectiveness in real video-understanding applications.}, isbn = {978-3-642-12899-8}, url = {http://dx.doi.org/10.1007/978-3-642-12900-1_5}, author = {Turaga,Pavan and Veeraraghavan,Ashok and Srivastava,Anuj and Chellapa, Rama}, editor = {Schonfeld,Dan and Shan,Caifeng and Tao,Dacheng and Wang,Liang} } @book {12505, title = {Statistical Methods and Models for Video-Based Tracking, Modeling, and Recognition}, year = {2010}, month = {2010///}, publisher = {Now Publishers Inc}, organization = {Now Publishers Inc}, abstract = {Computer vision systems attempt to understand a scene and its components from mostly visual information. The geometry exhibited by the real world, the influence of material properties on scattering of incident light, and the process of imaging introduce constraints and properties that are key to solving some of these tasks. In the presence of noisy observations and other uncertainties, the algorithms make use of statistical methods for robust inference. Statistical Methods and Models for Video-based Tracking, Modeling, and Recognition highlights the role of geometric constraints in statistical estimation methods, and how the interplay of geometry and statistics leads to the choice and design of algorithms. In particular, it illustrates the role of imaging, illumination, and motion constraints in classical vision problems such as tracking, structure from motion, metrology, activity analysis and recognition, and appropriate statistical methods used in each of these problems.}, keywords = {Computers / Computer Vision \& Pattern Recognition, Computers / Image Processing, Technology \& Engineering / Electronics / General, Technology \& Engineering / General}, isbn = {9781601983145}, author = {Chellapa, Rama and Sankaranarayanan,Aswin C. and Veeraraghavan,Ashok} } @article {19368, title = {Structural and dynamic determinants of ligand binding and regulation of cyclin-dependent kinase 5 by pathological activator p25 and inhibitory peptide CIP.}, journal = {Journal of molecular biology}, volume = {401}, year = {2010}, month = {2010 Aug 20}, pages = {478-92}, abstract = {The crystal structure of the cdk5/p25 complex has provided information on possible molecular mechanisms of the ligand binding, specificity, and regulation of the kinase. Comparative molecular dynamics simulations are reported here for physiological conditions. This study provides new insight on the mechanisms that modulate such processes, which may be exploited to control pathological activation by p25. The structural changes observed in the kinase are stabilized by a network of interactions involving highly conserved residues within the cyclin-dependent kinase (cdk) family. Collective motions of the proteins (cdk5, p25, and CIP) and their complexes are identified by principal component analysis, revealing two conformational states of the activation loop upon p25 complexation, which are absent in the uncomplexed kinase and not apparent from the crystal. Simulations of the uncomplexed inhibitor CIP show structural rearrangements and increased flexibility of the interfacial loop containing the critical residue E240, which becomes fully hydrated and available for interactions with one of several positively charged residues in the kinase. These changes provide a rationale for the observed high affinity and enhanced inhibitory action of CIP when compared to either p25 or the physiological activators of cdk5.}, keywords = {Crystallography, X-Ray, Cyclin-Dependent Kinase 5, Cyclin-Dependent Kinase Inhibitor Proteins, HUMANS, Ligands, molecular dynamics simulation, Nerve Tissue Proteins, Principal component analysis, Protein Binding, Protein Conformation}, issn = {1089-8638}, doi = {10.1016/j.jmb.2010.06.040}, author = {Cardone, Antonio and Hassan, S A and Albers,R.W. and Sriram,R.D. and Pant,H.C.} } @conference {14292, title = {Symbolic security analysis of ruby-on-rails web applications}, booktitle = {Proceedings of the 17th ACM conference on Computer and communications security}, year = {2010}, month = {2010///}, pages = {585 - 594}, author = {Chaudhuri,A. and Foster, Jeffrey S.} } @article {13869, title = {System and method for analysis of an opinion expressed in documents with regard to a particular topic}, volume = {11/808,278}, year = {2010}, month = {2010//01/28}, abstract = {System and method for analysis of an opinion expressed in documents on a particular topic computes opinion strength on a continuous numeric scale, or qualitatively. A variety of opinion scoring techniques are plugged in to score opinion expressing words and sentences in documents. These scores are aggregated to measure the opinion intensity of documents. Multilingual opinion analysis is supported by capability to concurrently identify and visualize the opinion intensity expressed in documents in multiple languages. A multi-dimensional representation of the measured opinion intensity is generated which is agreeable with multi-lingual domain.}, url = {http://www.google.com/patents?id=j9fLAAAAEBAJ}, author = {V.S. Subrahmanian and Picariello,Antonio and Dorr, Bonnie J and Reforgiato,Diego Recupero and Cesarano,Carmine and Sagoff,Amelia} } @conference {12480, title = {Tracking via object reflectance using a hyperspectral video camera}, booktitle = {2010 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)}, year = {2010}, month = {2010/06/13/18}, pages = {44 - 51}, publisher = {IEEE}, organization = {IEEE}, abstract = {Recent advances in electronics and sensor design have enabled the development of a hyperspectral video camera that can capture hyperspectral datacubes at near video rates. The sensor offers the potential for novel and robust methods for surveillance by combining methods from computer vision and hyperspectral image analysis. Here, we focus on the problem of tracking objects through challenging conditions, such as rapid illumination and pose changes, occlusions, and in the presence of confusers. A new framework that incorporates radiative transfer theory to estimate object reflectance and the mean shift algorithm to simultaneously track the object based on its reflectance spectra is proposed. The combination of spectral detection and motion prediction enables the tracker to be robust against abrupt motions, and facilitate fast convergence of the mean shift tracker. In addition, the system achieves good computational efficiency by using random projection to reduce spectral dimension. The tracker has been evaluated on real hyperspectral video data.}, keywords = {Computer vision, electronic design, hyperspectral datacubes, hyperspectral image analysis, Hyperspectral imaging, Hyperspectral sensors, hyperspectral video camera, Image motion analysis, Image sensors, lighting, Motion estimation, motion prediction, Object detection, object reflectance tracking, random projection, Reflectivity, robust methods, Robustness, sensor design, spectral detection, Surveillance, tracking, Video surveillance}, isbn = {978-1-4244-7029-7}, doi = {10.1109/CVPRW.2010.5543780}, author = {Nguyen,Hien Van and Banerjee, A. and Chellapa, Rama} } @conference {18890, title = {Using a Social Orientation Model for the Evolution of Cooperative Societies}, year = {2010}, month = {2010///}, pages = {431 - 438}, abstract = {We utilize evolutionary game theory to studythe evolution of cooperative societies and the behaviors of individual agents (i.e., players) in such societies. We present a novel player model based upon empirical evidence from the social and behavioral sciences stating that: (1) an individual{\textquoteright}s behavior may often be motivated not only by self-interest but also by the consequences for others, and (2) individuals vary in their interpersonal social tendencies, which reflect stable personal orientations that influence their choices. Alongside the formal player model we provide an analysis that considers possible interactions between different types of individuals and identifies five general steady-state behavioral patterns. We present evolutionary simulations that ratify previous findings on evolution of cooperation, and provide new insights on the evolutionary process of cooperative behavior in a society as well as on the emergence of cooperative societies. Our main experimental result demonstrates that in contrast to previous common knowledge, increasing mutual reward or mutual punishment in the Prisoner{\textquoteright}s dilemma game does not result in the same type of cooperative society: while increasing reward does increase the society{\textquoteright}s cooperativeness level, increasing mutual punishment does not. }, url = {http://www.ariel.ac.il/sites/inon/papers/iat10Kan.pdf}, author = {Cheng,K. L. and Zuckerman,I. and Kuter,U. and Nau, Dana S.} } @article {13030, title = {Validating the systematic position of {\i}t Plationus Segers, Murugan \& Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase}, journal = {Hydrobiologia}, volume = {644}, year = {2010}, month = {2010/05//}, pages = {361 - 370}, abstract = {Members of the family Brachionidae are free-living organisms that range in size from 170 to 250 microns. They comprise part of the zooplankton in freshwater and marine systems worldwide. Morphologically, members of the family are characterized by a single piece loricated body without furrows, grooves, sulci or dorsal head shields, and a malleate trophi. Differences in these structures have been traditionally used to recognize 217 species that are classified into seven genera. However, the validity of the species, Plationus patulus, P. patulus macracanthus P. polyacanthus, and P. felicitas have been confused because they were alternatively assigned in Brachionus or Platyias, when considering only morphological and ecological characters. Based on scanning electron microscope (SEM) images of the trophi, these taxa were assigned in a new genus, Plationus. In this study, we examined the systematic position of P. patulus and P. patulus macracanthus using DNA sequences of two genes: the cytochrome oxidase subunit 1 (cox1) and domains D2 and D3 of the large subunit of the nuclear ribosomal RNA (LSU). In addition, the cox1 and LSU sequences representing five genera of Brachionidae (Anuraeopsis, Brachionus, Keratella, Plationus, and Platyias) plus four species of three families from the order Ploima were used as the outgroup. The maximum likelihood (ML) analyses were conducted for each individual gene as well as for the combined (cox1 + LSU) data set. The ML tree from the combined data set yielded the family Brachionidae as a monophyletic group with weak bootstrap support (< 50\%). Five main clades in this tree had high (> 85\%) bootstrap support. The first clade was composed of three populations of P. patulus + P. patulus macracanthus. The second clade was composed of a single species of Platyias. The third clade was composed of six species of Brachionus. The fourth clade included a single species of the genus Anuraeopsis, and the fifth clade was composed of three species of the genus Keratella. The genetic divergence between Plationus and Platyias ranged from 18.4 to 19.2\% for cox1, and from 4.5 to 4.9\% for LSU, and between Brachionus and Plationus, it ranged from 16.9 to 23.1\% (cox1), and from 7.3 to 9.1\% (LSU). Morphological evidence, the amount of genetic divergence, the systematic position of Plationus within the family Brachionidae, and the position of Plationus as a sister group of Brachionus and Platyias support the validity of Plationus patulus and P. patulus macracanthus into the genus Plationus.}, keywords = {Cox1;, likelihood;, LSU;, maximum, Phylogeny, Plationus;}, doi = {DOI 10.1007/s10750-010-0203-1}, author = {Reyna-Fabian,ME and Laclette,J. P and Cummings, Michael P. and Garc{\'\i}a-Varela,M} } @conference {15862, title = {Values of Stakeholders in the Net Neutrality Debate: Applying Content Analysis to Telecommunications Policy}, booktitle = {Hawaii International Conference on System Sciences}, year = {2010}, month = {2010///}, pages = {1 - 10}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Net neutrality is an important telecommunications policy debate. This debate is closely tied to technological innovation, economic development, and information access. Values help shape stakeholders{\textquoteright} positions on this debate. This paper examines the role of values in shaping the Net neutrality debate through a content analysis of public hearings on Net neutrality. The paper presents a quantitative analysis that reveals the top values implicated in the Net neutrality debate and statistically significant differences among individuals on opposite sides of the Net neutrality debate. A qualitative analysis reveals insights into the connection between specific values and positions on the Net neutrality debate. The paper concludes that values, technology, and policy are interconnected, and that it is useful to understand the values of the various stakeholders within policy debates.}, isbn = {978-0-7695-3869-3}, doi = {http://doi.ieeecomputersociety.org/10.1109/HICSS.2010.434}, author = {Cheng,An-Shou and Fleischmann,Kenneth R. and Wang,Ping and Ishita,Emi and Oard, Douglas} } @article {12478, title = {Video Metrology Using a Single Camera}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {32}, year = {2010}, month = {2010/07//}, pages = {1329 - 1335}, abstract = {This paper presents a video metrology approach using an uncalibrated single camera that is either stationary or in planar motion. Although theoretically simple, measuring the length of even a line segment in a given video is often a difficult problem. Most existing techniques for this task are extensions of single image-based techniques and do not achieve the desired accuracy especially in noisy environments. In contrast, the proposed algorithm moves line segments on the reference plane to share a common endpoint using the vanishing line information followed by fitting multiple concentric circles on the image plane. A fully automated real-time system based on this algorithm has been developed to measure vehicle wheelbases using an uncalibrated stationary camera. The system estimates the vanishing line using invariant lengths on the reference plane from multiple frames rather than the given parallel lines, which may not exist in videos. It is further extended to a camera undergoing a planar motion by automatically selecting frames with similar vanishing lines from the video. Experimental results show that the measurement results are accurate enough to classify moving vehicles based on their size.}, keywords = {camera;vanishing, circles;uncalibrated, concentric, image-based, information;vehicle, line, measurement;video, metrology;cameras;image, processing;, segment;multiple, segmentation;video, signal, single, techniques;line, wheelbase}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2010.26}, author = {Guo,Feng and Chellapa, Rama} } @article {12464, title = {Video Pr{\'e}cis: Highlighting Diverse Aspects of Videos}, journal = {IEEE Transactions on Multimedia}, volume = {12}, year = {2010}, month = {2010/12//}, pages = {853 - 868}, abstract = {Summarizing long unconstrained videos is gaining importance in surveillance, web-based video browsing, and video-archival applications. Summarizing a video requires one to identify key aspects that contain the essence of the video. In this paper, we propose an approach that optimizes two criteria that a video summary should embody. The first criterion, {\textquotedblleft}coverage,{\textquotedblright} requires that the summary be able to represent the original video well. The second criterion, {\textquotedblleft}diversity,{\textquotedblright} requires that the elements of the summary be as distinct from each other as possible. Given a user-specified summary length, we propose a cost function to measure the quality of a summary. The problem of generating a précis is then reduced to a combinatorial optimization problem of minimizing the proposed cost function. We propose an efficient method to solve the optimization problem. We demonstrate through experiments (on KTH data, unconstrained skating video, a surveillance video, and a YouTube home video) that optimizing the proposed criterion results in meaningful video summaries over a wide range of scenarios. Summaries thus generated are then evaluated using both quantitative measures and user studies.}, keywords = {$K$-means, CAMERAS, combinatorial mathematics, combinatorial optimization, Cost function, data compression, Exemplar selection, Image segmentation, Internet, Iron, Length measurement, multimedia systems, Ncut, optimisation, Optimization methods, original video, Permission, shot segmentation, Surveillance, user specified summary length, video précis, Video sharing, video signal processing, Video summarization}, isbn = {1520-9210}, doi = {10.1109/TMM.2010.2058795}, author = {Shroff, N. and Turaga,P. and Chellapa, Rama} } @conference {14351, title = {WATTR: a method for self-powered wireless sensing of water activity in the home}, booktitle = {Proceedings of the 12th ACM international conference on Ubiquitous computing}, series = {Ubicomp {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {169 - 172}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {power harvesting, sensing, water conservation}, isbn = {978-1-60558-843-8}, doi = {10.1145/1864349.1864378}, url = {http://doi.acm.org/10.1145/1864349.1864378}, author = {Campbell,Tim and Larson,Eric and Cohn,Gabe and Jon Froehlich and Alcaide,Ramses and Patel,Shwetak N.} } @conference {19463, title = {Who{\textquoteright}s Hogging the Bandwidth: The Consequences of Revealing the Invisible in the Home}, booktitle = {SIGCHI {\textquoteright}10}, series = {CHI {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {659 - 668}, publisher = {ACM}, organization = {ACM}, abstract = {As more technologies enter the home, householders are burdened with the task of digital housekeeping-managing and sharing digital resources like bandwidth. In response to this, we created and evaluated a domestic tool for bandwidth management called Home Watcher. Our field trial showed that when resource contention amongst different household members is made visible, people{\textquoteright}s understanding of bandwidth changes and household politics are revealed. In this paper, we describe the consequences of showing real time resource usage in a home, and how this varies depending on the social make up of the household.}, keywords = {bandwidth monitoring, home broadband, home networks}, isbn = {978-1-60558-929-9}, url = {http://doi.acm.org/10.1145/1753326.1753423}, author = {Marshini Chetty and Banks, Richard and Harper, Richard and Regan, Tim and Sellen, Abigail and Gkantsidis, Christos and Karagiannis, Thomas and Key, Peter} } @article {12527, title = {3D Face Recognition: Technology and Applications}, journal = {Handbook of Remote Biometrics}, year = {2009}, month = {2009///}, pages = {217 - 246}, author = {Tistarelli,M. and Li, S.Z. and Chellapa, Rama and Akarun, L.} } @article {12528, title = {Advanced Technologies for Touchless Fingerprint Recognition}, journal = {Handbook of Remote Biometrics}, year = {2009}, month = {2009///}, pages = {83 - 109}, author = {Tistarelli,M. and Li, S.Z. and Chellapa, Rama} } @article {16059, title = {Advancing User-Centered Evaluation of Visual Analytic Environments Through Contests}, journal = {Information VisualizationInformation Visualization}, volume = {8}, year = {2009}, month = {2009/09/21/}, pages = {230 - 238}, abstract = {In this paper, the authors describe the Visual Analytics Science and Technology (VAST) Symposium contests run in 2006 and 2007 and the VAST 2008 and 2009 challenges. These contests were designed to provide researchers with a better understanding of the tasks and data that face potential end users. Access to these end users is limited because of time constraints and the classified nature of the tasks and data. In that respect, the contests serve as an intermediary, with the metrics and feedback serving as measures of utility to the end users. The authors summarize the lessons learned and the future directions for VAST Challenges.}, keywords = {metrics, synthetic data, user-centered evaluation, visual analytics}, isbn = {1473-8716, 1473-8724}, doi = {10.1057/ivs.2009.16}, url = {http://ivi.sagepub.com/content/8/3/230}, author = {Costello,Loura and Grinstein,Georges and Plaisant, Catherine and Scholtz,Jean} } @article {12533, title = {Age progression in human faces: A survey}, journal = {Journal of Visual Languages and Computing}, volume = {15}, year = {2009}, month = {2009///}, pages = {3349 - 3361}, abstract = {Facial aging, a new dimension that has recently beenadded to the problem of face recognition, poses interesting theo- retical and practical challenges to the research community. The problem which originally generated interest in the psychophysics and human perception community, has recently found enhanced interest in the computer vision community. How do humans perceive age ? What constitutes an age-invariant signature that can be derived from faces ? How compactly can the facial growth event be described ? How does facial aging impact recognition performance ? In this paper, we give a thorough analysis on the problem of facial aging and further provide a complete account of the many interesting studies that have been performed on this topic from different fields. We offer a comparative analysis of various approaches that have been proposed for problems such as age estimation, appearance prediction, face verification etc. and offer insights into future research on this topic. }, author = {Ramanathan,N. and Chellapa, Rama and Biswas,S.} } @article {13355, title = {Algorithms for distributional and adversarial pipelined filter ordering problems}, journal = {ACM Trans. Algorithms}, volume = {5}, year = {2009}, month = {2009/03//}, pages = {24:1{\textendash}24:34 - 24:1{\textendash}24:34}, abstract = {Pipelined filter ordering is a central problem in database query optimization. The problem is to determine the optimal order in which to apply a given set of commutative filters (predicates) to a set of elements (the tuples of a relation), so as to find, as efficiently as possible, the tuples that satisfy all of the filters. Optimization of pipelined filter ordering has recently received renewed attention in the context of environments such as the Web, continuous high-speed data streams, and sensor networks. Pipelined filter ordering problems are also studied in areas such as fault detection and machine learning under names such as learning with attribute costs, minimum-sum set cover, and satisficing search. We present algorithms for two natural extensions of the classical pipelined filter ordering problem: (1) a distributional-type problem where the filters run in parallel and the goal is to maximize throughput, and (2) an adversarial-type problem where the goal is to minimize the expected value of multiplicative regret. We present two related algorithms for solving (1), both running in time O(n2), which improve on the O(n3 log n) algorithm of Kodialam. We use techniques from our algorithms for (1) to obtain an algorithm for (2).}, keywords = {flow algorithms, Pipelined filter ordering, Query optimization, selection ordering}, isbn = {1549-6325}, doi = {10.1145/1497290.1497300}, url = {http://doi.acm.org/10.1145/1497290.1497300}, author = {Condon,Anne and Deshpande, Amol and Hellerstein,Lisa and Wu,Ning} } @article {12886, title = {Analysis of clonally related environmental Vibrio cholerae O1 El Tor isolated before 1992 from Varanasi, India reveals origin of SXT-ICEs belonging to O139 and O1 serogroups}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2009}, month = {2009/07/21/}, pages = {50 - 57}, abstract = {In this study, we report the presence of SXT in environmental Vibrio cholerae O1 El Tor strains isolated before 1992 from Varanasi, India. All isolates, except one, were resistant to Tm, and/or Sul, Sm, Fr, Na and Am. None contained plasmids. PCR and DNA sequencing revealed the presence of SXT containing dfrA1 and/or sulII, strAB in six isolates and dfr18, sulII and strAB in five isolates. Three clinical V. cholerae O1 isolated during 1992 contained the antibiotic resistance gene cassette aadA1 in the class 1 integron. Conjugation experiments, followed by PCR analysis of transconjugants, provided evidence of the transferable nature of SXT and associated antibiotic resistance genes, and its integration into the prfC site. Results of phylogenetic analysis of the intSXT gene of clonally similar V. cholerae showed a clear difference between dfr18+ and dfrA1+V. cholerae O1 isolates. This is the first report of the occurrence of SXT harbouring sulII, strAB, dfr18 and/or dfrA1 genes in environmental V. cholerae O1 isolated prior to 1992 from Varanasi, India, and suggests emergence of SXT+ antibiotic-resistant V. cholerae O139 and O1 from an environmental V. cholerae progenitor by acquisition of SXT and antibiotic-resistant gene clusters.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2009.00051.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2009.00051.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Mohapatra,Saswat S. and Mantri,Chinmay K. and Mohapatra,Harapriya and Rita R Colwell and Singh,Durg V.} } @conference {16974, title = {Analyzing (social media) networks with NodeXL}, booktitle = {Proceedings of the fourth international conference on Communities and technologies}, series = {C\&$\#$38;T {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {255 - 264}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present NodeXL, an extendible toolkit for network overview, discovery and exploration implemented as an add-in to the Microsoft Excel 2007 spreadsheet software. We demonstrate NodeXL data analysis and visualization features with a social media data sample drawn from an enterprise intranet social network. A sequence of NodeXL operations from data import to computation of network statistics and refinement of network visualization through sorting, filtering, and clustering functions is described. These operations reveal sociologically relevant differences in the patterns of interconnection among employee participants in the social media space. The tool and method can be broadly applied.}, keywords = {excel, network analysis, social media, social network, spreadsheet, Visualization}, isbn = {978-1-60558-713-4}, doi = {10.1145/1556460.1556497}, url = {http://doi.acm.org/10.1145/1556460.1556497}, author = {Smith,Marc A. and Shneiderman, Ben and Milic-Frayling,Natasa and Mendes Rodrigues,Eduarda and Barash,Vladimir and Dunne,Cody and Capone,Tony and Perer,Adam and Gleave,Eric} } @conference {18659, title = {Analyzing the process of installing rogue software}, year = {2009}, month = {2009/07/29/2}, pages = {560 - 565}, abstract = {This practical experience report presents the results of an experiment aimed at understanding the sequence of malicious actions following a remote compromise. The type of rogue software installed during attacks was used to classify and understand sequences of malicious actions. For this experiment, we used four Linux target computers running SSH with simple passwords. During the eight-month data collection period, we recorded a total of 1,171 attack sessions. In these sessions, attackers typed a total of 20,335 commands that we categorized into 24 specific actions. These actions were analyzed based on the type of rogue software installed by attackers.}, keywords = {Linux, Linux target computers, malicious actions, rogue software installation, security of data}, doi = {10.1109/DSN.2009.5270293}, author = {Berthier,R. and Arjona,J. and Michel Cukier} } @article {12522, title = {Appearance Modeling Using a Geometric Transform}, journal = {Image Processing, IEEE Transactions on}, volume = {18}, year = {2009}, month = {2009/04//}, pages = {889 - 902}, abstract = {A general transform, called the geometric transform (GeT), that models the appearance inside a closed contour is proposed. The proposed GeT is a functional of an image intensity function and a region indicator function derived from a closed contour. It can be designed to combine the shape and appearance information at different resolutions and to generate models invariant to deformation, articulation, or occlusion. By choosing appropriate functionals and region indicator functions, the GeT unifies Radon transform, trace transform, and a class of image warpings. By varying the region indicator and the types of features used for appearance modeling, five novel types of GeTs are introduced and applied to fingerprinting the appearance inside a contour. They include the GeTs based on a level set, shape matching, feature curves, and the GeT invariant to occlusion, and a multiresolution GeT (MRGeT). Applications of GeT to pedestrian identity recognition, human body part segmentation, and image synthesis are illustrated. The proposed approach produces promising results when applied to fingerprinting the appearance of a human and body parts despite the presence of nonrigid deformations and articulated motion.}, keywords = {body, contour;feature, curve;fingerprinting;geometric, function;image, function;shape, geometry;image, identity, indicator, INTENSITY, matching;trace, method;pedestrian, modeling;closed, part, Radon, recognition;region, resolution;image, segmentation;, segmentation;image, set, synthesis;image, transform;appearance, transform;human, transform;Radon, transforms;computational, warping;level}, isbn = {1057-7149}, doi = {10.1109/TIP.2008.2011381}, author = {Li,Jian and Zhou,S. K and Chellapa, Rama} } @article {12531, title = {An architectural level design methodology for smart camera applications}, journal = {International Journal of Embedded Systems}, volume = {4}, year = {2009}, month = {2009///}, pages = {83 - 97}, abstract = {Today{\textquoteright}s embedded computing applications are characterised by increased functionality, and hence increased design complexity and processing requirements. The resulting design spaces are vast and designers are typically able to evaluate only small subsets of solutions due to lack of efficient design tools. In this paper, we propose an architectural level design methodology that provides a means for a comprehensive design space exploration for smart camera applications and enable designers to select higher quality solutions and provides substantial savings on the overall cost of the system. We present efficient, accurate and intuitive models for performance estimation and validate them with experiments.}, author = {Saha,S. and Kianzad,V. and Schlessman,J. and Aggarwal,G. and Bhattacharyya, Shuvra S. and Chellapa, Rama and Wolf,W.} } @article {12113, title = {An assessment of systems and software engineering scholars and institutions (2002{\textendash}2006)}, journal = {Journal of Systems and Software}, volume = {82}, year = {2009}, month = {2009/08//}, pages = {1370 - 1373}, abstract = {This paper summarizes a survey of publications in the field of systems and software engineering from 2002 to 2006. The survey is an ongoing, annual event that identifies the top 15 scholars and institutions over a 5-year period. The rankings are calculated based on the number of papers published in TSE, TOSEM, JSS, SPE, EMSE, IST, and Software. The top-ranked institution is Korea Advanced Institute of Science and Technology, Korea, and the top-ranked scholar is Magne J{\o}rgensen of Simula Research Laboratory, Norway.}, keywords = {Research publications, Systems and software engineering, Top institutions, Top scholars}, isbn = {0164-1212}, doi = {10.1016/j.jss.2009.06.018}, url = {http://www.sciencedirect.com/science/article/pii/S0164121209001265}, author = {Wong,W. Eric and Tse,T.H. and Glass,Robert L. and Basili, Victor R. and Chen,T.Y.} } @article {15876, title = {Automatic classification of human values: Applying computational thinking to information ethics}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {46}, year = {2009}, month = {2009///}, pages = {1 - 4}, author = {Fleischmann,K.R. and Oard, Douglas and Cheng,A.S. and Wang,P. and Ishita,E.} } @article {18695, title = {Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains}, journal = {Nature Structural \& Molecular Biology}, volume = {16}, year = {2009}, month = {2009///}, pages = {883 - 889}, abstract = {Ubiquitin (denoted Ub) receptor proteins as a group must contain a diverse set of binding specificities to distinguish the many forms of polyubiquitin (polyUb) signals. Previous studies suggested that the large class of ubiquitin-associated (UBA) domains contains members with intrinsic specificity for Lys63-linked polyUb or Lys48-linked polyUb, thus explaining how UBA-containing proteins can mediate diverse signaling events. Here we show that previously observed Lys63-polyUb selectivity in UBA domains is the result of an artifact in which the dimeric fusion partner, glutathione S-transferase (GST), positions two UBAs for higher affinity, avid interactions with Lys63-polyUb, but not with Lys48-polyUb. Freed from GST, these UBAs are either nonselective or prefer Lys48-polyUb. Accordingly, NMR experiments reveal no Lys63-polyUb{\textendash}specific binding epitopes for these UBAs. We reexamine previous conclusions based on GST-UBAs and present an alternative model for how UBAs achieve a diverse range of linkage specificities.}, keywords = {apoptosis, basic cellular processes, Biochemistry, biophysics, cell biology, cell cycle, cell surface proteins, cell-cell interactions, checkpoints, chromatin, chromatin remodeling, chromatin structure, content, DNA recombination, DNA repair, DNA replication, Gene expression, Genetics, intracellular signaling, journal, macromolecules, mechanism, membrane processes, molecular, molecular basis of disease, molecular biology, molecular interactions, multi-component complexes, nature publishing group, nature structural molecular biology, nucleic acids, protein degradation, protein folding, protein processing, Proteins, regulation of transcription, regulation of translation, RNA, RNA processing, RNAi, signal transduction, single molecule studies, structure and function of proteins, transcription, translation}, isbn = {1545-9993}, doi = {10.1038/nsmb.1637}, url = {http://www.nature.com/nsmb/journal/v16/n8/abs/nsmb.1637.html}, author = {Sims,Joshua J. and Haririnia,Aydin and Dickinson,Bryan C. and Fushman, David and Cohen,Robert E.} } @conference {12399, title = {Better vocabularies for assistive communication aids: connecting terms using semantic networks and untrained annotators}, booktitle = {Proceedings of the 11th international ACM SIGACCESS conference on Computers and accessibility}, series = {Assets {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {171 - 178}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The difficulties of navigating vocabulary in an assistive communication device are exacerbated for individuals with lexical access disorders like those due to aphasia. We present the design and implementation of a vocabulary network based on WordNet, a resource that attempts to model human semantic memory, that enables users to find words easily. To correct for the sparsity of links among words, we augment WordNet with additional connections derived from human judgments of semantic similarity collected in an online experiment. We evaluate the resulting system, the visual vocabulary for aphasia (ViVA), and describe its potential to adapt to a user{\textquoteright}s profile and enable faster search and improved navigation.}, keywords = {adaptive tools, aphasia, assistive communication, semantic networks, visual vocabularies}, isbn = {978-1-60558-558-1}, doi = {10.1145/1639642.1639673}, url = {http://doi.acm.org/10.1145/1639642.1639673}, author = {Nikolova,Sonya and Jordan Boyd-Graber and Fellbaum,Christiane and Cook,Perry} } @article {12889, title = {Biological agent detection technologies}, journal = {Molecular Ecology Resources}, volume = {9}, year = {2009}, month = {2009/04/21/}, pages = {51 - 57}, abstract = {The challenge for first responders, physicians in the emergency room, public health personnel, as well as for food manufacturers, distributors and retailers is accurate and reliable identification of pathogenic agents and their corresponding diseases. This is the weakest point in biological agent detection capability today.There is intense research for new molecular detection technologies that could be used for very accurate detection of pathogens that would be a concern to first responders. These include the need for sensors for multiple applications as varied as understanding the ecology of pathogenic micro-organisms, forensics, environmental sampling for detect-to-treat applications, biological sensors for {\textquoteleft}detect to warn{\textquoteright} in infrastructure protection, responses to reports of {\textquoteleft}suspicious powders{\textquoteright}, and customs and borders enforcement, to cite a few examples. The benefits of accurate detection include saving millions of dollars annually by reducing disruption of the workforce and the national economy and improving delivery of correct countermeasures to those who are most in need of the information to provide protective and/or response measures. }, keywords = {barcoding, biological agent, DETECTION, identification, sequencing}, isbn = {1755-0998}, doi = {10.1111/j.1755-0998.2009.02632.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2009.02632.x/full}, author = {Jakupciak,John P. and Rita R Colwell} } @conference {17994, title = {Brief announcement: performance potential of an easy-to-program PRAM-on-chip prototype versus state-of-the-art processor}, booktitle = {Proceedings of the twenty-first annual symposium on Parallelism in algorithms and architectures}, year = {2009}, month = {2009///}, pages = {163 - 165}, author = {Caragea,G.C. and Saybasili,A. B and Wen,X. and Vishkin, Uzi} } @article {14950, title = {Call for Papers: Special Issue of the Journal of Parallel and Distributed Computing: Cloud Computing}, journal = {J. Parallel Distrib. Comput.}, volume = {69}, year = {2009}, month = {2009/09//}, pages = {813{\textendash} - 813{\textendash}}, isbn = {0743-7315}, doi = {10.1016/j.jpdc.2009.07.002}, url = {http://dx.doi.org/10.1016/j.jpdc.2009.07.002}, author = {Chockler,Gregory and Dekel,Eliezer and JaJa, Joseph F. and Jimmy Lin} } @inbook {15726, title = {CLASSY 2009: Summarization and Metrics}, booktitle = {TAC 2009 Workshop ProceedingsTAC 2009 Workshop Proceedings}, year = {2009}, month = {2009/11/16/17}, publisher = {NIST}, organization = {NIST}, url = {http://www.nist.gov/tac/publications/2009/participant.papers/CLASSY.proceedings.pdfhttp://www.nist.gov/tac/publications/2009/participant.papers/CLASSY.proceedings.pdf}, author = {Conroy,John M. and Schlesinger,Judith D. and O{\textquoteright}Leary, Dianne P.} } @article {14482, title = {Common effect of antipsychotics on the biosynthesis and regulation of fatty acids and cholesterol supports a key role of lipid homeostasis in schizophrenia}, journal = {Schizophrenia Research}, volume = {108}, year = {2009}, month = {2009/03//}, pages = {134 - 142}, abstract = {For decades, the dopamine hypothesis has gained the most attention in an attempt to explain the origin and the symptoms of schizophrenia. While this hypothesis offers an explanation for the relationship between psychotic symptoms and dopamine kinetics, it does not provide a direct explanation of the etiology of schizophrenia which remains poorly understood. Consequently, current antipsychotics that target neurotransmitter receptors, have limited and inconsistent efficacy. To gain insights into the mechanism of action of these drugs, we studied the expression profile of 12,490 human genes in a cell line treated with 18 antipsychotics, and compared it to that of a library of 448 other compounds used in a variety of disorders. Analysis reveals a common effect of antipsychotics on the biosynthesis and regulation of fatty acids and cholesterol, which is discussed in the context of a lipid hypothesis where alterations in lipid homeostasis might underlie the pathogenesis of schizophrenia. This finding may help research aimed at the development of novel treatments for this devastating disease.}, keywords = {Antipsychotic action, Gene expression, Lipid homeostasis, Pathogenesis}, isbn = {0920-9964}, doi = {10.1016/j.schres.2008.11.025}, url = {http://www.sciencedirect.com/science/article/pii/S0920996408005306}, author = {Polymeropoulos,Mihael H. and Licamele,Louis and Volpi,Simona and Mack,Kendra and Mitkus,Shruti N. and Carstea,Eugene D. and Getoor, Lise and Thompson,Andrew and Lavedan,Christian} } @article {12895, title = {Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae}, journal = {Proceedings of the National Academy of Sciences}, volume = {106}, year = {2009}, month = {2009///}, pages = {15442 - 15447}, abstract = {Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a {\textquotedblleft}shift{\textquotedblright} between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a {\textquotedblleft}drift{\textquotedblright} between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0907787106}, url = {http://www.pnas.org/content/106/36/15442}, author = {Chun,J. and Grim,C. J. and Hasan,N. A. and Lee,J. H. and Choi,S. Y. and Haley,B. J. and Taviani,E. and Jeon,Y. S. and Kim,D.W. and Lee,J. H. and Rita R Colwell} } @conference {15908, title = {Compressed sensing for Synthetic Aperture Radar imaging}, booktitle = {2009 16th IEEE International Conference on Image Processing (ICIP)}, year = {2009}, month = {2009/11//}, pages = {2141 - 2144}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we introduce a new Synthetic Aperture Radar (SAR) imaging modality that provides a high resolution map of the spatial distribution of targets and terrain based on a significant reduction in the number of transmitted and/or received electromagnetic waveforms. This new imaging scheme, which requires no new hardware components, allows the aperture to be compressed and presents many important applications and advantages among which include resolving ambiguities, strong resistance to countermeasures and interception, and reduced on-board storage constraints.}, keywords = {Compressed sensing, High-resolution imaging, Image coding, image resolution, Optical imaging, Radar antennas, radar imaging, Radar polarimetry, Reflectivity, SAR, spatial distribution, synthetic aperture radar, synthetic aperture radar imaging}, isbn = {978-1-4244-5653-6}, doi = {10.1109/ICIP.2009.5414307}, author = {Patel, Vishal M. and Easley,G. R and Healy,D. M and Chellapa, Rama} } @article {12518, title = {Computational methods for modeling facial aging: A survey}, journal = {Journal of Visual Languages \& Computing}, volume = {20}, year = {2009}, month = {2009/06//}, pages = {131 - 144}, abstract = {Facial aging, a new dimension that has recently been added to the problem of face recognition, poses interesting theoretical and practical challenges to the research community. The problem which originally generated interest in the psychophysics and human perception community has recently found enhanced interest in the computer vision community. How do humans perceive age? What constitutes an age-invariant signature that can be derived from faces? How compactly can the facial growth event be described? How does facial aging impact recognition performance? In this paper, we give a thorough analysis on the problem of facial aging and further provide a complete account of the many interesting studies that have been performed on this topic from different fields. We offer a comparative analysis of various approaches that have been proposed for problems such as age estimation, appearance prediction, face verification, etc. and offer insights into future research on this topic.}, keywords = {age estimation, Age progression, Craniofacial growth, face recognition}, isbn = {1045-926X}, doi = {10.1016/j.jvlc.2009.01.011}, url = {http://www.sciencedirect.com/science/article/pii/S1045926X09000032}, author = {Ramanathan,Narayanan and Chellapa, Rama and Biswas,Soma} } @conference {19443, title = {Computer Help at Home: Methods and Motivations for Informal Technical Support}, booktitle = {SIGCHI {\textquoteright}09}, series = {CHI {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {739 - 748}, publisher = {ACM}, organization = {ACM}, abstract = {Prior research suggests that people may ask their family and friends for computer help. But what influences whether and how a "helper" will provide help? To answer this question, we conducted a qualitative investigation of people who participated in computer support activities with family and friends in the past year. We describe how factors including maintenance of one{\textquoteright}s personal identity as a computer expert and accountability to one{\textquoteright}s social network determine who receives help and the quality of help provided. We also discuss the complex, fractured relationship between the numerous stakeholders involved in the upkeep of home computing infrastructures. Based on our findings, we provide implications for the design of systems to support informal help-giving in residential settings.}, keywords = {help-giving, help-seeking, Home computing, identity management, social networks}, isbn = {978-1-60558-246-7}, url = {http://doi.acm.org/10.1145/1518701.1518816}, author = {Poole, Erika Shehan and Marshini Chetty and Morgan, Tom and Grinter, Rebecca E. and Edwards, W. Keith} } @conference {12402, title = {Connections between the lines: augmenting social networks with text}, booktitle = {Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining}, series = {KDD {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {169 - 178}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Network data is ubiquitous, encoding collections of relationships between entities such as people, places, genes, or corporations. While many resources for networks of interesting entities are emerging, most of these can only annotate connections in a limited fashion. Although relationships between entities are rich, it is impractical to manually devise complete characterizations of these relationships for every pair of entities on large, real-world corpora. In this paper we present a novel probabilistic topic model to analyze text corpora and infer descriptions of its entities and of relationships between those entities. We develop variational methods for performing approximate inference on our model and demonstrate that our model can be practically deployed on large corpora such as Wikipedia. We show qualitatively and quantitatively that our model can construct and annotate graphs of relationships and make useful predictions.}, keywords = {Graphical models, social network learning, statistical topic models}, isbn = {978-1-60558-495-9}, doi = {10.1145/1557019.1557044}, url = {http://doi.acm.org/10.1145/1557019.1557044}, author = {Chang,Jonathan and Jordan Boyd-Graber and Blei,David M.} } @conference {19444, title = {Contemporary domestic infrastructures and technology design}, booktitle = {SIGCHI EA {\textquoteright}09}, series = {CHI EA {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {3109 - 3112}, publisher = {ACM}, organization = {ACM}, abstract = {In this proposal, I describe my examination of two contemporary domestic infrastructures. Specifically, I am investigating whether we need to surface more information about these systems to make them intelligible to end-users. I describe my empirical research to date and the design of two technology probes which I will use to learn more how home infrastructure affects domestic technology design.}, keywords = {Home, home networks, infrastructure, resource delivery systems}, isbn = {978-1-60558-247-4}, url = {http://doi.acm.org/10.1145/1520340.1520439}, author = {Marshini Chetty} } @conference {19029, title = {Controlling data in the cloud: outsourcing computation without outsourcing control}, series = {CCSW {\textquoteright}09}, year = {2009}, month = {2009}, pages = {85 - 90}, publisher = {ACM}, organization = {ACM}, abstract = {Cloud computing is clearly one of today{\textquoteright}s most enticing technology areas due, at least in part, to its cost-efficiency and flexibility. However, despite the surge in activity and interest, there are significant, persistent concerns about cloud computing that are impeding momentum and will eventually compromise the vision of cloud computing as a new IT procurement model. In this paper, we characterize the problems and their impact on adoption. In addition, and equally importantly, we describe how the combination of existing research thrusts has the potential to alleviate many of the concerns impeding adoption. In particular, we argue that with continued research advances in trusted computing and computation-supporting encryption, life in the cloud can be advantageous from a business intelligence standpoint over the isolated alternative that is more common today.}, keywords = {Cloud computing, privacy, Security}, isbn = {978-1-60558-784-4}, url = {http://doi.acm.org/10.1145/1655008.1655020}, author = {Chow, Richard and Golle, Philippe and Jakobsson, Markus and Elaine Shi and Staddon, Jessica and Masuoka, Ryusuke and Molina,Jesus} } @conference {14670, title = {Cross-tier, label-based security enforcement for web applications}, booktitle = {Proceedings of the 35th SIGMOD international conference on Management of data}, series = {SIGMOD {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {269 - 282}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper presents SELinks, a programming language focused on building secure multi-tier web applications. SELinks provides a uniform programming model, in the style of LINQ and Ruby on Rails, with language syntax for accessing objects residing either in the database or at the server. Object-level security policies are expressed as fully-customizable, first-class labels which may themselves be subject to security policies. Access to labeled data is mediated via trusted, user-provided policy enforcement functions. SELinks has two novel features that ensure security policies are enforced correctly and efficiently. First, SELinks implements a type system called Fable that allows a protected object{\textquoteright}s type to refer to its protecting label. The type system can check that labeled data is never accessed directly by the program without first consulting the appropriate policy enforcement function. Second, SELinks compiles policy enforcement code to database-resident user-defined functions that can be called directly during query processing. Database-side checking avoids transferring data to the server needlessly, while still allowing policies to be expressed in a customizable and portable manner. Our experience with two sizable web applications, a modelhealth-care database and a secure wiki with fine-grained security policies, indicates that cross-tier policy enforcement in SELinks is flexible, relatively easy to use, and, when compared to a single-tier approach, improves throughput by nearly an order of magnitude. SELinks is freely available.}, keywords = {compilers, database programming, security enforcement, type systems, web applications}, isbn = {978-1-60558-551-2}, doi = {10.1145/1559845.1559875}, url = {http://doi.acm.org/10.1145/1559845.1559875}, author = {Corcoran,Brian J. and Swamy,Nikhil and Hicks, Michael W.} } @conference {12416, title = {The design of ViVA: a mixed-initiative visual vocabulary for aphasia}, booktitle = {Proceedings of the 27th international conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {4015 - 4020}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this paper, we present the design of ViVA, a visual vocabulary for aphasia. Aphasia is an acquired language disorder that causes variability of impairments affecting individual{\textquoteright}s ability to speak, comprehend, read and write. Existing communication aids lack flexibility and adequate customization functionality failing to address this variability and to satisfy individual user needs. We tackle these shortcomings by incorporating adaptive and adaptable capabilities in ViVA which is designed to assist communication for users suffering from aphasia. The visual vocabulary for aphasia implements a novel approach that organizes the words in the vocabulary according to user preferences, word usage and certain semantic measures, thus continuously tailoring the tool to the user{\textquoteright}s profile.}, keywords = {adaptive and adaptable interfaces, assistive communication tools, multi-modal interfaces}, isbn = {978-1-60558-247-4}, doi = {10.1145/1520340.1520610}, url = {http://doi.acm.org/10.1145/1520340.1520610}, author = {Nikolova,Sonya and Jordan Boyd-Graber and Cook,Perry R.} } @article {12532, title = {Detecting humans carrying objects}, journal = {SPIE Newsroom}, year = {2009}, month = {2009///}, abstract = {Decomposing an image sequence into slices that generate twisted patterns sufficiently characterizes human gait and a particular class of activities.}, isbn = {18182259}, doi = {10.1117/2.1200902.1511}, url = {https://spie.org/x33692.xml?ArticleID=x33692}, author = {Yang Ran and Qinfen Zheng and Chellapa, Rama} } @article {12883, title = {Detection of toxigenic Vibrio cholerae O1 in freshwater lakes of the former Soviet Republic of Georgia}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2009}, month = {2009/09/03/}, pages = {2 - 6}, abstract = {Three freshwater lakes, Lisi Lake, Kumisi Lake and Tbilisi Sea, near Tbilisi, Georgia, were studied from January 2006 to December 2007 to determine the presence of Vibrio cholerae employing both bacteriological culture method and direct detection methods, namely PCR and direct fluorescent antibody (DFA). For PCR, DNA extracted from water samples was tested for presence of V. cholerae and genes coding for selected virulence factors. Vibrio cholerae non-O1/non-O139 was routinely isolated by culture from all three lakes; whereas V. cholerae O1 and O139 were not. Water samples collected during the summer months from Lisi Lake and Kumisi Lake were positive for both V. cholerae and V. cholerae ctxA, tcpA, zot, ompU and toxR by PCR. Water samples collected during the same period from both Lisi and Kumisi Lake were also positive for V. cholerae serogroup O1 by DFA. All of the samples were negative for V. cholerae serotype O139. The results of this study provide evidence for an environmental presence of toxigenic V. cholerae O1, which may represent a potential source of illness as these lakes serve as recreational water in Tbilisi, Georgia.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2009.00073.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2009.00073.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Grim,Christopher J. and Jaiani,Ekaterina and Whitehouse,Chris A. and Janelidze,Nino and Kokashvili,Tamuna and Tediashvili,Marina and Rita R Colwell and Huq,Anwar} } @article {12891, title = {Determination of relationships among non-toxigenic Vibrio cholerae O1 biotype El Tor strains from housekeeping gene sequences and ribotype patterns}, journal = {Research in Microbiology}, volume = {160}, year = {2009}, month = {2009/01//}, pages = {57 - 62}, abstract = {Sequencing of three housekeeping genes, mdh, dnaE and recA, and ribotyping for seven non-toxigenic Vibrio cholerae O1 strains isolated from different geographic sources indicate a phylogenetic relationship among the strains. Results of MLST and ribotyping indicate a clear difference between three toxigenic strains (N16961, O395, and 569B) and three non-toxigenic strains from India (GS1, GS2, and GW87) and one Guam strain (X392), the latter of which were similar in both MLST and ribotyping, while two other non-toxigenic strains from the USA and India (2740-80 and OR69) appeared to be more closely related to toxigenic strains than to non-toxigenic strains, although this was not supported by ribotyping. These results provide clues to the emergence of toxigenic strains from a non-toxigenic progenitor by acquisition of virulence gene clusters. Results of split decomposition analysis suggest that widespread recombination occurs among the three housekeeping genes and that recombination plays an important role in the emergence of toxigenic strains of V. cholerae O1.}, keywords = {Housekeeping genes, Ribotyping, sequencing, Vibrio cholerae}, isbn = {0923-2508}, doi = {10.1016/j.resmic.2008.10.008}, url = {http://www.sciencedirect.com/science/article/pii/S0923250808001794}, author = {Mohapatra,Saswat S. and Ramachandran,Dhanya and Mantri,Chinmay K. and Rita R Colwell and Singh,Durg V.} } @article {12890, title = {Diversity and Seasonality of Bioluminescent Vibrio Cholerae Populations in Chesapeake Bay}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, month = {2009/01/01/}, pages = {135 - 146}, abstract = {Association of luminescence with phenotypic and genotypic traits and with environmental parameters was determined for 278 strains of Vibrio cholerae isolated from the Chesapeake Bay during 1998 to 2000. Three clusters of luminescent strains (A, B, and C) and two nonluminescent clusters (X and Y) were identified among 180 clonal types. V. cholerae O1 strains isolated during pandemics and endemic cholera in the Ganges Delta were related to cluster Y. Heat-stable enterotoxin (encoded by stn) and the membrane protein associated with bile resistance (encoded by ompU) were found to be linked to luminescence in strains of cluster A. Succession from nonluminescent to luminescent populations of V. cholerae occurred during spring to midsummer. Occurrence of cluster A strains in water with neutral pH was contrasted with that of cluster Y strains in water with a pH of >8. Cluster A was found to be associated with a specific calanoid population cooccurring with cyclopoids. Cluster B was related to cluster Y, with its maximal prevalence at pH 8. Occurrence of cluster B strains was more frequent with warmer water temperatures and negatively correlated with maturity of the copepod community. It is concluded that each cluster of luminescent V. cholerae strains occupies a distinct ecological niche. Since the dynamics of these niche-specific subpopulations are associated with zooplankton community composition, the ecology of luminescent V. cholerae is concluded to be related to its interaction with copepods and related crustacean species.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.02894-07}, url = {http://aem.asm.org/content/75/1/135}, author = {Zo,Young-Gun and Chokesajjawatee,Nipa and Grim,Christopher and Arakawa,Eiji and Watanabe,Haruo and Rita R Colwell} } @conference {18941, title = {Energy loss in MEMS resonators and the impact on inertial and RF devices}, year = {2009}, month = {2009/06//}, pages = {688 - 695}, abstract = {In this paper, we review the current understanding of energy loss mechanisms in micromachined (MEMS and NEMS) devices. We describe the importance of high quality factor (Q) to the performance of MEMS gyros and MEMS resonators used in radio-frequency applications.}, keywords = {energy loss, gyroscopes, inertial devices, MEMS gyros, MEMS resonators, micromachined devices, micromechanical resonators, NEMS devices, Q-factor, quality factor, radiofrequency applications, RF devices}, doi = {10.1109/SENSOR.2009.5285418}, author = {Weinberg,M. and Candler,R. and Chandorkar,S. and Varsanik,J. and Kenny,T. and Duwel,A.} } @conference {12517, title = {Enforcing integrability by error correction using l1-minimization}, booktitle = {Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on}, year = {2009}, month = {2009/06//}, pages = {2350 - 2357}, abstract = {Surface reconstruction from gradient fields is an important final step in several applications involving gradient manipulations and estimation. Typically, the resulting gradient field is non-integrable due to linear/non-linear gradient manipulations, or due to presence of noise/outliers in gradient estimation. In this paper, we analyze integrability as error correction, inspired from recent work in compressed sensing, particulary lscr0 - lscr1 equivalence. We propose to obtain the surface by finding the gradient field which best fits the corrupted gradient field in lscr1 sense. We present an exhaustive analysis of the properties of lscr1 solution for gradient field integration using linear algebra and graph analogy. We consider three cases: (a) noise, but no outliers (b) no-noise but outliers and (c) presence of both noise and outliers in the given gradient field. We show that lscr1 solution performs as well as least squares in the absence of outliers. While previous lscr0 - lscr1 equivalence work has focused on the number of errors (outliers), we show that the location of errors is equally important for gradient field integration. We characterize the lscr1 solution both in terms of location and number of outliers, and outline scenarios where lscr1 solution is equivalent to lscr0 solution. We also show that when lscr1 solution is not able to remove outliers, the property of local error confinement holds: i.e., the errors do not propagate to the entire surface as in least squares. We compare with previous techniques and show that lscr1 solution performs well across all scenarios without the need for any tunable parameter adjustments.}, keywords = {-, algebra;lscr0, algebra;minimisation;, analogy;integrability;least, compressed, correction;gradient, equivalence;lscr1-minimization;noise-outlier;surface, estimation;gradient, field, integration;gradient, lscr1, manipulation;graph, methods;graph, reconstruction;error, reconstruction;linear, sensing;error, squares;linear, theory;image}, doi = {10.1109/CVPR.2009.5206603}, author = {Reddy, D. and Agrawal,A. and Chellapa, Rama} } @conference {12511, title = {Enhancing sparsity using gradients for compressive sensing}, booktitle = {Image Processing (ICIP), 2009 16th IEEE International Conference on}, year = {2009}, month = {2009/11//}, pages = {3033 - 3036}, abstract = {In this paper, we propose a reconstruction method that recovers images assumed to have a sparse representation in a gradient domain by using partial measurement samples that are collected in the Fourier domain. A key improvement of this technique is that it makes use of a robust generalized Poisson solver that greatly aids in achieving a significantly improved performance over similar proposed methods. Experiments provided also demonstrate that this new technique is more flexible to work with either random or restricted sampling scenarios better than its competitors.}, keywords = {analysis;gradient, domain;compressive, domain;image, Fourier, generalized, measurement, methods;, methods;image, Poisson, reconstruction;image, reconstruction;partial, representation;Fourier, representation;sampling, samples;robust, scenarios;sparse, sensing;enhancing, solver;sampling, sparsity;gradient}, doi = {10.1109/ICIP.2009.5414411}, author = {Patel, Vishal M. and Easley,G. R and Chellapa, Rama and Healy,D. M} } @article {18637, title = {Evaluating Attack Resiliency for Host Intrusion Detection Systems}, journal = {Journal of Information Assurance and Security}, volume = {4}, year = {2009}, month = {2009///}, pages = {001 - 009}, abstract = {Host intrusion detection systems (HIDSs) areimportant tools used to provide security to computer systems. Many HIDSs exist and security practitioners need a way to determine the optimal security solution for their environment. Current evaluations of HIDSs focus on detection accuracy and typically do not account for the possibility that an adversary may subvert the HIDS and modify the outcome. As some elements from the HIDS need to reside within the system under supervi- sion, evaluating the strength against HIDS subversion is critical. This paper defines HIDS subversion and presents HIDS resiliency as a metric of HIDS strength in the event of an attack against the system being supervised. To estimate HIDS resiliency, we evaluated the inde- pendency between the system being supervised and the HIDS. Then we integrated resiliency into current frame- works to evaluate detection accuracy. }, url = {http://www.softcomputing.net/jias/molina.pdf}, author = {Molina,J. and Michel Cukier} } @conference {18669, title = {Evaluating Files to Audit for Detecting Intrusions in FileSystem Data}, year = {2009}, month = {2009/07//}, pages = {163 - 170}, abstract = {Monitoring filesystem data is a common method used to detect intrusions. Once a computer is compromised, an attacker may alter files, add new files or delete existing files. The changes that attackers make may target any part of the filesystem, including metadata along with files (e.g., permissions, ownerships and inodes). The accuracy of detecting an intrusion depends on the data audited: if an intrusion does not manifest in the data, the intrusion will not be detected. Moreover, not all files, which contain filesystem activity, are suitable to detect intrusions, as some may fail to provide useful information. In this paper, we describe an empirical study that focused on filesystem attack activity after a SSH compromise. Three types of attacker action are considered: reconnaissance, password modification, and malware download. For each type of action, we evaluated the files to audit using metrics derived from the field of information theory and estimated with the empirical SSH compromise data.}, keywords = {authorisation, Bayes methods, Bayesian metric, data auditing, empirical SSH compromise data, Entropy, entropy-based metric, file evaluation, file organisation, filesystem attack activity, filesystem data monitoring, honeypot, information theory, intrusion detection system, invasive software, malware download, meta data, optimisation, optimization problem, password modification, probability, reconnaissance action, unauthorized user}, doi = {10.1109/NCA.2009.38}, author = {Molina,J. and Michel Cukier} } @article {18655, title = {An evaluation of connection characteristics for separating network attacks}, journal = {International Journal of Security and Networks}, volume = {4}, year = {2009}, month = {2009/01/01/}, pages = {110 - 124}, abstract = {The goal of this paper is to evaluate the efficiency of connection characteristics to separate different attack families that target a single TCP port. Identifying the most relevant characteristics might allow statistically separating attack families without systematically using forensics. This study is based on a dataset collected over 117 days using a test-bed of two high interaction honeypots. The results indicated that to separate unsuccessful from successful attacks in malicious traffic: the number of bytes is a relevant characteristic; time-based characteristics are poor characteristics; using combinations of characteristics does not improve the efficiency of separating attacks.}, doi = {10.1504/IJSN.2009.02343}, url = {http://dx.doi.org/10.1504/IJSN.2009.02343}, author = {Berthier,Robin and Michel Cukier} } @article {18701, title = {Evidence for Bidentate Substrate Binding as the Basis for the K48 Linkage Specificity of Otubain 1}, journal = {Journal of Molecular Biology}, volume = {386}, year = {2009}, month = {2009/03/06/}, pages = {1011 - 1023}, abstract = {Otubain 1 belongs to the ovarian tumor (OTU) domain class of cysteine protease deubiquitinating enzymes. We show here that human otubain 1 (hOtu1) is highly linkage-specific, cleaving Lys48 (K48)-linked polyubiquitin but not K63-, K29-, K6-, or K11-linked polyubiquitin, or linear α-linked polyubiquitin. Cleavage is not limited to either end of a polyubiquitin chain, and both free and substrate-linked polyubiquitin are disassembled. Intriguingly, cleavage of K48-diubiquitin by hOtu1 can be inhibited by diubiquitins of various linkage types, as well as by monoubiquitin. NMR studies and activity assays suggest that both the proximal and distal units of K48-diubiquitin bind to hOtu1. Reaction of Cys23 with ubiquitin-vinylsulfone identified a ubiquitin binding site that is distinct from the active site, which includes Cys91. Occupancy of the active site is needed to enable tight binding to the second site. We propose that distinct binding sites for the ubiquitins on either side of the scissile bond allow hOtu1 to discriminate among different isopeptide linkages in polyubiquitin substrates. Bidentate binding may be a general strategy used to achieve linkage-specific deubiquitination.}, keywords = {deubiquitination, isopeptide, linkage specificity, otubain, polyubiquitin}, isbn = {0022-2836}, doi = {10.1016/j.jmb.2008.12.085}, url = {http://www.sciencedirect.com/science/article/pii/S0022283608016124}, author = {Wang,Tao and Yin,Luming and Cooper,Eric M. and Lai,Ming-Yih and Dickey,Seth and Pickart,Cecile M. and Fushman, David and Wilkinson,Keith D. and Cohen,Robert E. and Wolberger,Cynthia} } @article {14573, title = {Evidence for Coregulation of Myocardial Gene Expression by MEF2 and NFAT in Human Heart Failure / CLINICAL PERSPECTIVE}, journal = {Circulation: Cardiovascular Genetics}, volume = {2}, year = {2009}, month = {2009/06/01/}, pages = {212 - 219}, abstract = {Background{\textemdash} Pathological stresses induce heart failure in animal models through activation of multiple cardiac transcription factors (TFs) working cooperatively. However, interactions among TFs in human heart failure are less understood. Here, we use genomic data to examine the evidence that 5 candidate TF families coregulate gene expression in human heart failure.Methods and Results{\textemdash} RNA isolates from failing (n=86) and nonfailing (n=16) human hearts were hybridized with Affymetrix HU133A arrays. For each gene on the array, we determined conserved MEF2, NFAT, NKX , GATA , and FOX binding motifs within the -1-kb promoter region using human-murine sequence alignments and the TRANSFAC database. Across 9076 genes expressed in the heart, TF-binding motifs tended to cluster together in nonrandom patterns within promoters of specific genes (P values ranging from 10-2 to 10-21), suggesting coregulation. We then modeled differential expression as a function of TF combinations present in promoter regions. Several combinations predicted increased odds of differential expression in the failing heart, with the highest odds ratios noted for genes containing both MEF2 and NFAT binding motifs together in the same promoter region (peak odds ratio, 3.47; P=0.005).Conclusions{\textemdash} These findings provide genomic evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failure. In doing so, they extend the paradigm of combinatorial regulation of gene expression to the human heart and identify new target genes for mechanistic study. More broadly, we demonstrate how integrating diverse sources of genomic data yields novel insight into human cardiovascular disorders.}, doi = {10.1161/CIRCGENETICS.108.816686}, url = {http://circgenetics.ahajournals.org/content/2/3/212.abstract}, author = {Putt,Mary E. and Hannenhalli, Sridhar and Lu,Yun and Haines,Philip and Chandrupatla,Hareesh R. and Morrisey,Edward E. and Margulies,Kenneth B. and Cappola,Thomas P.} } @article {12997, title = {Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development}, journal = {Sci Transl Med}, volume = {1}, year = {2009}, month = {2009/10//}, pages = {2ra5 - 2ra5}, abstract = {Vaccines directed against the blood stages of Plasmodium falciparum malaria are intended to prevent the parasite from invading and replicating within host cells. No blood-stage malaria vaccine has shown clinical efficacy in humans. Most malaria vaccine antigens are parasite surface proteins that have evolved extensive genetic diversity, and this diversity could allow malaria parasites to escape vaccine-induced immunity. We examined the extent and within-host dynamics of genetic diversity in the blood-stage malaria vaccine antigen apical membrane antigen-1 in a longitudinal study in Mali. Two hundred and fourteen unique apical membrane antigen-1 haplotypes were identified among 506 human infections, and amino acid changes near a putative invasion machinery binding site were strongly associated with the development of clinical symptoms, suggesting that these residues may be important to consider in designing polyvalent apical membrane antigen-1 vaccines and in assessing vaccine efficacy in field trials. This extreme diversity may pose a serious obstacle to an effective polyvalent recombinant subunit apical membrane antigen-1 vaccine.}, doi = {10.1126/scitranslmed.3000257}, author = {Takala,S. L and Coulibaly,D. and Thera,M. A and Batchelor,A. H and Cummings, Michael P. and Escalante,A. A and Ouattara,A. and Traor{\'e},K. and Niangaly,A. and Djimd{\'e},A. A and Doumbo,OK and Plowe,CV} } @inbook {12526, title = {Face Recognition from Video}, booktitle = {The Essential Guide to Video Processing (Second Edition)The Essential Guide to Video Processing (Second Edition)}, year = {2009}, month = {2009///}, pages = {653 - 688}, publisher = {Academic Press}, organization = {Academic Press}, address = {Boston}, isbn = {978-0-12-374456-2}, url = {http://www.sciencedirect.com/science/article/pii/B9780123744562000232}, author = {Zhou,Shaohua Kevin and Chellapa, Rama and Aggarwal,Gaurav}, editor = {Al Bovik} } @conference {17168, title = {First Steps to Netviz Nirvana: Evaluating Social Network Analysis with NodeXL}, booktitle = {International Conference on Computational Science and Engineering, 2009. CSE {\textquoteright}09}, volume = {4}, year = {2009}, month = {2009/08/29/31}, pages = {332 - 339}, publisher = {IEEE}, organization = {IEEE}, abstract = {Social Network Analysis (SNA) has evolved as a popular, standard method for modeling meaningful, often hidden structural relationships in communities. Existing SNA tools often involve extensive pre-processing or intensive programming skills that can challenge practitioners and students alike. NodeXL, an open-source template for Microsoft Excel, integrates a library of common network metrics and graph layout algorithms within the familiar spreadsheet format, offering a potentially low-barrier-to-entry framework for teaching and learning SNA. We present the preliminary findings of 2 user studies of 21 graduate students who engaged in SNA using NodeXL. The majority of students, while information professionals, had little technical background or experience with SNA techniques. Six of the participants had more technical backgrounds and were chosen specifically for their experience with graph drawing and information visualization. Our primary objectives were (1) to evaluate NodeXL as an SNA tool for a broad base of users and (2) to explore methods for teaching SNA. Our complementary dual case-study format demonstrates the usability of NodeXL for a diverse set of users, and significantly, the power of a tightly integrated metrics/visualization tool to spark insight and facilitate sense-making for students of SNA.}, keywords = {Computer science, computer science education, data visualisation, Data visualization, Educational institutions, graph drawing, graph layout algorithm, Information services, Information Visualization, Internet, Libraries, Microsoft Excel open-source template, MILC, multi-dimensional in-depth long-term case studies, Netviz Nirvana, NodeXL, Open source software, Programming profession, SNA, social network analysis, Social network services, social networking (online), spreadsheet programs, structural relationship, teaching, visual analytics, visualization tool, Web sites}, isbn = {978-1-4244-5334-4}, doi = {10.1109/CSE.2009.120}, author = {Bonsignore,E. M and Dunne,C. and Rotman,D. and Smith,M. and Capone,T. and Hansen,D. L and Shneiderman, Ben} } @article {14614, title = {Gene Profiling of Human Adipose Tissue During Evoked Inflammation In Vivo}, journal = {DiabetesDiabetes}, volume = {58}, year = {2009}, month = {2009/10/01/}, pages = {2211 - 2219}, abstract = {OBJECTIVE Adipose inflammation plays a central role in obesity-related metabolic and cardiovascular complications. However, few human adipose-secreted proteins are known to mediate these processes. We hypothesized that microarray mRNA profiling of human adipose during evoked inflammation could identify novel adipocytokines.RESEARCH DESIGN AND METHODS Healthy human volunteers (n = 14) were treated with intravenous endotoxin (3 ng/kg lipopolysaccharide [LPS]) and underwent subcutaneous adipose biopsies before and after LPS. On Affymetrix U133Plus 2.0 arrays, adipose mRNAs modulated >1.5-fold (with P < 0.00001) were selected. SignalP 3.0 and SecretomeP 2.0 identified genes predicted to encode secreted proteins. Of these, 86 candidates were chosen for validation in adipose from an independent human endotoxemia protocol (N = 7, with 0.6 ng/kg LPS) and for exploration of cellular origin in primary human adipocytes and macrophages in vitro. RESULTS Microarray identified 776 adipose genes modulated by LPS; 298 were predicted to be secreted. Of detectable prioritized genes, 82 of 85 (96\% [95\% CI 90{\textendash}99]) were upregulated (fold changes >1.0) during the lower-dose (LPS 0.6 ng/kg) validation study and 51 of 85 (59\% [49{\textendash}70]) were induced greater than 1.5-fold. Treatment of primary adipocytes with LPS and macrophage polarization to M1 proinflammatory phenotype increased expression by 1.5-fold for 58 and 73\% of detectable genes, respectively. CONCLUSIONS We demonstrate that evoked inflammation of human adipose in vivo modulated expression of multiple genes likely secreted by adipocytes and monocytes. These included established adipocytokines and chemokines implicated in recruitment and activation of lymphocytes, adhesion molecules, antioxidants, and several novel genes with unknown function. Such candidates may represent biomarkers and therapeutic targets for obesity-related complications. }, isbn = {0012-1797, 1939-327X}, doi = {10.2337/db09-0256}, url = {http://diabetes.diabetesjournals.org/content/58/10/2211}, author = {Shah,Rachana and Lu,Yun and Hinkle,Christine C and McGillicuddy,Fiona C and Kim,Roy and Hannenhalli, Sridhar and Cappola,Thomas P. and Heffron,Sean and Wang,XingMei and Mehta,Nehal N and Putt,Mary and Reilly,Muredach P} } @article {12896, title = {Genome assortment, not serogroup, defines Vibrio cholerae pandemic strains}, journal = {Nature}, year = {2009}, month = {2009///}, abstract = {Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the 6th and the current 7th pandemics, respectively. Cholera researchers continually face newly emerging and re-emerging pathogenic clones carrying combinations of new serogroups as well as of phenotypic and genotypic properties. These genotype and phenotype changes have hampered control of the disease. Here we compare the complete genome sequences of 23 strains of V. cholerae isolated from a variety of sources and geographical locations over the past 98 years in an effort to elucidate the evolutionary mechanisms governing genetic diversity and genesis of new pathogenic clones. The genome-based phylogeny revealed 12 distinct V. cholerae phyletic lineages, of which one, designated the V. cholerae core genome (CG), comprises both O1 classical and EI Tor biotypes. All 7th pandemic clones share nearly identical gene content, i.e., the same genome backbone. The transition from 6th to 7th pandemic strains is defined here as a {\textquoteright}shift{\textquoteright} between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages within the CG clade. In contrast, transition among clones during the present 7th pandemic period can be characterized as a {\textquoteright}drift{\textquoteright} between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V.cholerae serogroup O139 and V.cholerae O1 El Tor hybrid clones that produce cholera toxin of classical biotype. Based on the comprehensive comparative genomics presented in this study it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.}, keywords = {59; CHOLERA; GENES; GENETICS; GENOTYPE; ISLANDS; ORIGIN; PHENOTYPE; PUBLIC HEALTH; RECOMBINATION; STRAINS; TOXINS}, url = {http://www.osti.gov/energycitations/servlets/purl/962365-icnke9/}, author = {Brettin,Thomas S[Los Alamos National Laboratory and Bruce,David C[Los Alamos National Laboratory and Challacombe,Jean F[Los Alamos National Laboratory and Detter,John C[Los Alamos National Laboratory and Han,Cliff S[Los Alamos National Laboratory and Munik,A. C[Los Alamos National Laboratory and Chertkov,Olga[Los Alamos National Laboratory and Meincke,Linda[Los Alamos National Laboratory and Saunders,Elizabeth[Los Alamos National Laboratory and Choi,Seon Y[SEOUL NATL UNIV and Haley,Bradd J[U MARYLAND and Taviani,Elisa[U MARYLAND and Jeon,Yoon-Seong[INTL VACCINE INST SEOUL and Kim,Dong Wook[INTL VACCINE INST SEOUL and Lee,Jae-Hak[SEOUL NATL UNIV and Walters,Ronald A[PNNL and Hug,Anwar[NATL INST CHOLERIC ENTERIC DIS and Rita R Colwell} } @inbook {12893, title = {The Genus Vibrio and Related Genera}, booktitle = {Practical handbook of microbiologyPractical handbook of microbiology}, year = {2009}, month = {2009///}, pages = {267 - 267}, publisher = {CRC Press}, organization = {CRC Press}, isbn = {9780849393655}, author = {Rita R Colwell and Chun,J.}, editor = {Goldman,Emanuel and Green,Lorrence H.} } @conference {12509, title = {How would you look as you age ?}, booktitle = {Image Processing (ICIP), 2009 16th IEEE International Conference on}, year = {2009}, month = {2009/11//}, pages = {53 - 56}, abstract = {Facial appearances change with increase in age. While generic growth patterns that are characteristic of different age groups can be identified, facial growth is also observed to be influenced by individual-specific attributes such as one{\textquoteright}s gender, ethnicity, life-style etc. In this paper, we propose a facial growth model that comprises of transformation models for facial shape and texture. We collected empirical data pertaining to facial growth from a database of age-separated face images of adults and used the same in developing the aforementioned transformation models. The proposed model finds applications in predicting one{\textquoteright}s appearance across ages and in performing face verification across ages.}, keywords = {age-separated, appearances;facial, database;face, Face, growth, image, model;face, model;facial, models;facial, recognition;image, SHAPE, TEXTURE, texture;, transformation, verification;facial}, doi = {10.1109/ICIP.2009.5413998}, author = {Ramanathan,N. and Chellapa, Rama} } @conference {14321, title = {HydroSense: infrastructure-mediated single-point sensing of whole-home water activity}, booktitle = {Proceedings of the 11th international conference on Ubiquitous computing, September}, year = {2009}, month = {2009///}, author = {Jon Froehlich and Larson,E. and Campbell,T. and Haggerty,C. and Fogarty,J. and Patel,S.N.} } @conference {19033, title = {Implicit authentication for mobile devices}, series = {HotSec{\textquoteright}09}, year = {2009}, month = {2009}, pages = {9 - 9}, publisher = {USENIX Association}, organization = {USENIX Association}, abstract = {We introduce the notion of implicit authentication - the ability to authenticate mobile users based on actions they would carry out anyway. We develop a model for how to perform implicit authentication, and describe experiments aimed at assessing the benefits of our techniques. Our preliminary findings support that this is a meaningful approach, whether used to increase usability or increase security.}, url = {http://dl.acm.org/citation.cfm?id=1855628.1855637}, author = {Jakobsson, Markus and Elaine Shi and Golle, Philippe and Chow, Richard} } @inbook {19638, title = {Improved Non-committing Encryption with Applications to Adaptively Secure Protocols}, booktitle = {Advances in Cryptology {\textendash} ASIACRYPT 2009}, series = {Lecture Notes in Computer Science}, year = {2009}, month = {2009/01/01/}, pages = {287 - 302}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We present a new construction of non-committing encryption schemes. Unlike the previous constructions of Canetti et al. (STOC {\textquoteright}96) and of Damg{\r a}rd and Nielsen (Crypto {\textquoteright}00), our construction achieves all of the following properties: Optimal round complexity. Our encryption scheme is a 2-round protocol, matching the round complexity of Canetti et al. and improving upon that in Damg{\r a}rd and Nielsen. Weaker assumptions. Our construction is based on trapdoor simulatable cryptosystems, a new primitive that we introduce as a relaxation of those used in previous works. We also show how to realize this primitive based on hardness of factoring. Improved efficiency. The amortized complexity of encrypting a single bit is O(1) public key operations on a constant-sized plaintext in the underlying cryptosystem. As a result, we obtain the first non-committing public-key encryption schemes under hardness of factoring and worst-case lattice assumptions; previously, such schemes were only known under the CDH and RSA assumptions. Combined with existing work on secure multi-party computation, we obtain protocols for multi-party computation secure against a malicious adversary that may adaptively corrupt an arbitrary number of parties under weaker assumptions than were previously known. Specifically, we obtain the first adaptively secure multi-party protocols based on hardness of factoring in both the stand-alone setting and the UC setting with a common reference string.}, keywords = {adaptive corruption, Algorithm Analysis and Problem Complexity, Applications of Mathematics, Data Encryption, Data Structures, Cryptology and Information Theory, Discrete Mathematics in Computer Science, non-committing encryption, public-key encryption, secure multi-party computation, Systems and Data Security}, isbn = {978-3-642-10365-0, 978-3-642-10366-7}, url = {http://link.springer.com/chapter/10.1007/978-3-642-10366-7_17}, author = {Choi, Seung Geol and Dana Dachman-Soled and Malkin, Tal and Wee, Hoeteck}, editor = {Matsui, Mitsuru} } @conference {16679, title = {Improved statistical machine translation using monolingually-derived paraphrases}, booktitle = {Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 1-Volume 1}, year = {2009}, month = {2009///}, pages = {381 - 390}, author = {Marton,Y. and Callison-Burch,C. and Resnik, Philip} } @conference {16317, title = {Incremental covering array failure characterization in large configuration spaces}, booktitle = {Proceedings of the eighteenth international symposium on Software testing and analysis}, year = {2009}, month = {2009///}, pages = {177 - 188}, author = {Fouch{\'e},S. and Cohen,M. B and Porter, Adam} } @inbook {17233, title = {Information Visualization}, booktitle = {Human-Computer InteractionHuman-Computer Interaction}, volume = {20093960}, year = {2009}, month = {2009/03/02/}, pages = {181 - 215}, publisher = {CRC Press}, organization = {CRC Press}, isbn = {978-1-4200-8885-4, 978-1-4200-8886-1}, url = {http://www.crcnetbase.com/doi/abs/10.1201/9781420088861.ch10}, author = {Card,Stuart}, editor = {Sears,Andrew and Jacko,Julie} } @article {19460, title = {The Ins and Outs of Home Networking: The Case for Useful and Usable Domestic Networking}, journal = {ACM Trans. Comput.-Hum. Interact.}, volume = {16}, year = {2009}, month = {2009/06//}, pages = {8:1 - 8:28}, abstract = {Householders are increasingly adopting home networking as a solution to the demands created by the presence of multiple computers, devices, and the desire to access the Internet. However, current network solutions are derived from the world of work (and initially the military) and provide poor support for the needs of the home. We present the key findings to emerge from empirical studies of home networks in the UK and US. The studies reveal two key kinds of work that effective home networking relies upon: one, the technical work of setting up and maintaining the home network, and the other, the collaborative and socially organized work of the home which the network is embedded in and supports. The two are thoroughly intertwined and rely upon one another for their realization, yet neither is adequately supported by current networking technologies and applications. Explication of the {\textquotedblleft}work to make the home network work{\textquotedblright} opens up the design space for the continued integration of the home network in domestic life and elaboration of future support. Key issues for development include the development of networking facilities that do not require advanced networking knowledge, that are flexible and support the local social order of the home and the evolution of its routines, and which ultimately make the home network visible and accountable to household members.}, keywords = {home networking, Human computer interaction}, isbn = {1073-0516}, url = {http://doi.acm.org/10.1145/1534903.1534905}, author = {Grinter, Rebecca E. and Edwards, W. Keith and Marshini Chetty and Poole, Erika S. and Sung, Ja-Young and Yang, Jeonghwa and Crabtree, Andy and Tolmie, Peter and Rodden, Tom and Greenhalgh, Chris and Benford, Steve} } @conference {17242, title = {Interacting with eHealth: towards grand challenges for HCI}, booktitle = {Proceedings of the 27th international conference extended abstracts on Human factors in computing systems}, year = {2009}, month = {2009///}, pages = {3309 - 3312}, abstract = {While health records are increasingly stored electronically, we, as citizens, have little access to this data about ourselves. We are not used to thinking of these official records either as ours or as useful to us. We increasingly turn to the Web, however, to query any ache, pain or health goal we may have before consulting with health care professionals. Likewise, for proactive health care such as nutrition or fitness, or to find fellow-sufferers for post diagnosis support, we turn to online resources. There is a potential disconnect between points at which professional and lay eHealth data and resources intersect for preventative or proactive health care. Such gaps in information sharing may have direct impact on practices we decide to take up, the care we seek, or the support professionals offer. In this panel, we consider several places within proactive, preventative health care in particular HCI has a role towards enhancing health knowledge discovery and health support interaction. Our goal is to demonstrate how now is the time for eHealth to come to the forefront of the HCI research agenda.}, author = {Andr{\'e},P. and White,R. and Tan,D. and Berners-Lee,T. and Consolvo,S. and Jacobs,R. and Kohane,I. and Le Dantec,C.A. and Mamykina,L. and Marsden,G.} } @conference {19455, title = {It{\textquoteright}s Not Easy Being Green: Understanding Home Computer Power Management}, booktitle = {SIGCHI {\textquoteright}09}, series = {CHI {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {1033 - 1042}, publisher = {ACM}, organization = {ACM}, abstract = {Although domestic computer use is increasing, most efforts to reduce energy use through improved power management have focused on computers in the workplace. We studied 20 households to understand how people use power management strategies on their home computers. We saw computers in the home, particularly desktop computers, are left on much more than they are actively used suggesting opportunities for economic and energy savings. However, for most of our participants, the economic incentives were too minor to motivate them to turn off devices when not in use, especially given other frustrations such as long boot up times. We suggest research directions for home computer power management that could help users be more green without having to dramatically change their home computing habits.}, keywords = {home computer use, power management, Sustainability}, isbn = {978-1-60558-246-7}, url = {http://doi.acm.org/10.1145/1518701.1518860}, author = {Marshini Chetty and Brush, A.J. Bernheim and Meyers, Brian R. and Johns, Paul} } @inbook {12536, title = {Knowledge Extraction from Surveillance Sensors}, booktitle = {Wiley Handbook of Science and Technology for Homeland SecurityWiley Handbook of Science and Technology for Homeland Security}, year = {2009}, month = {2009///}, publisher = {John Wiley \& Sons, Inc.}, organization = {John Wiley \& Sons, Inc.}, keywords = {multi-camera tracking, multi-modal fusion, recognition, sensor networks, Surveillance}, isbn = {9780470087923}, url = {http://onlinelibrary.wiley.com/doi/10.1002/9780470087923.hhs510/abstract;jsessionid=D0D752EF5D04327BE003BDFBD2F96134.d01t03}, author = {Chellapa, Rama and Veeraraghavan,Ashok and Sankaranarayanan,Aswin C.} } @article {12534, title = {Learning Facial Aging Models: A Face Recognition Perspective}, journal = {Biometrics: theory, methods, and applications}, volume = {9}, year = {2009}, month = {2009///}, pages = {271 - 271}, author = {Ramanathan,N. and Chellapa, Rama} } @conference {12519, title = {Learning multi-modal densities on Discriminative Temporal Interaction Manifold for group activity recognition}, booktitle = {Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on}, year = {2009}, month = {2009/06//}, pages = {2450 - 2457}, abstract = {While video-based activity analysis and recognition has received much attention, existing body of work mostly deals with single object/person case. Coordinated multi-object activities, or group activities, present in a variety of applications such as surveillance, sports, and biological monitoring records, etc., are the main focus of this paper. Unlike earlier attempts which model the complex spatial temporal constraints among multiple objects with a parametric Bayesian network, we propose a Discriminative Temporal Interaction Manifold (DTIM) framework as a data-driven strategy to characterize the group motion pattern without employing specific domain knowledge. In particular, we establish probability densities on the DTIM, whose element, the discriminative temporal interaction matrix, compactly describes the coordination and interaction among multiple objects in a group activity. For each class of group activity we learn a multi-modal density function on the DTIM. A Maximum a Posteriori (MAP) classifier on the manifold is then designed for recognizing new activities. Experiments on football play recognition demonstrate the effectiveness of the approach.}, keywords = {a, activities;parametric, activity, analysis;belief, analysis;pattern, Bayesian, classification;image, classifier;multimodal, complex, constraints;data-driven, density, equipment;video, function;multiobject, interaction, manifold;discriminative, matrix;football, MOTION, network;video-based, networks;image, play, posteriori, processing;, recognition, recognition;group, recognition;maximum, signal, spatial, strategy;discriminative, temporal}, doi = {10.1109/CVPR.2009.5206676}, author = {Ruonan Li and Chellapa, Rama and Zhou,S. K} } @conference {12516, title = {Locally time-invariant models of human activities using trajectories on the grassmannian}, booktitle = {Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on}, year = {2009}, month = {2009/06//}, pages = {2435 - 2441}, abstract = {Human activity analysis is an important problem in computer vision with applications in surveillance and summarization and indexing of consumer content. Complex human activities are characterized by non-linear dynamics that make learning, inference and recognition hard. In this paper, we consider the problem of modeling and recognizing complex activities which exhibit time-varying dynamics. To this end, we describe activities as outputs of linear dynamic systems (LDS) whose parameters vary with time, or a time-varying linear dynamic system (TV-LDS). We discuss parameter estimation methods for this class of models by assuming that the parameters are locally time-invariant. Then, we represent the space of LDS models as a Grassmann manifold. Then, the TV-LDS model is defined as a trajectory on the Grassmann manifold. We show how trajectories on the Grassmannian can be characterized using appropriate distance metrics and statistical methods that reflect the underlying geometry of the manifold. This results in more expressive and powerful models for complex human activities. We demonstrate the strength of the framework for activity-based summarization of long videos and recognition of complex human actions on two datasets.}, keywords = {action, activity, analysis;local, analysis;video, content, dynamic, Estimation, estimation;statistical, Grassmann, indexing;distance, linear, manifold;activity-based, method;statistical, method;surveillance;time-varying, metrics;human, model;parameter, recognition;human, recognition;indexing;parameter, summarization;computer, surveillance;, system;computer, time-invariant, vision;consumer, vision;image}, doi = {10.1109/CVPR.2009.5206710}, author = {Turaga,P. and Chellapa, Rama} } @article {15552, title = {Maintaining nets and net trees under incremental motion}, journal = {Algorithms and Computation}, year = {2009}, month = {2009///}, pages = {1134 - 1143}, abstract = {The problem of maintaining geometric structures for points in motion has been well studied over the years. Much theoretical work to date has been based on the assumption that point motion is continuous and predictable, but in practice, motion is typically presented incrementally in discrete time steps and may not be predictable. We consider the problem of maintaining a data structure for a set of points undergoing such incremental motion. We present a simple online model in which two agents cooperate to maintain the structure. One defines the data structure and provides a collection of certificates, which guarantee the structure{\textquoteright}s correctness. The other checks that the motion over time satisfies these certificates and notifies the first agent of any violations.We present efficient online algorithms for maintaining both nets and net trees for a point set undergoing incremental motion in a space of constant dimension. We analyze our algorithms{\textquoteright} efficiencies by bounding their competitive ratios relative to an optimal algorithm. We prove a constant factor competitive ratio for maintaining a slack form of nets, and our competitive ratio for net trees is proportional to the square of the tree{\textquoteright}s height. }, doi = {10.1007/978-3-642-10631-6_114}, author = {Cho,M. and Mount, Dave and Park,E.} } @conference {18581, title = {Measurement methods for fast and accurate blackhole identification with binary tomography}, booktitle = {Proceedings of the 9th ACM SIGCOMM conference on Internet measurement conference}, series = {IMC {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {254 - 266}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Binary tomography - the process of identifying faulty network links through coordinated end-to-end probes - is a promising method for detecting failures that the network does not automatically mask (e.g., network "blackholes"). Because tomography is sensitive to the quality of the input, however, na{\"\i}ve end-to-end measurements can introduce inaccuracies. This paper develops two methods for generating inputs to binary tomography algorithms that improve their inference speed and accuracy. Failure confirmation is a per-path probing technique to distinguish packet losses caused by congestion from persistent link or node failures. Aggregation strategies combine path measurements from unsynchronized monitors into a set of consistent observations. When used in conjunction with existing binary tomography algorithms, our methods identify all failures that are longer than two measurement cycles, while inducing relatively few false alarms. In two wide-area networks, our techniques decrease the number of alarms by as much as two orders of magnitude. Compared to the state of the art in binary tomography, our techniques increase the identification rate and avoid hundreds of false alarms.}, keywords = {diagnosis, network tomography, troubleshooting}, isbn = {978-1-60558-771-4}, doi = {10.1145/1644893.1644924}, url = {http://doi.acm.org/10.1145/1644893.1644924}, author = {Cunha,{\'I}talo and Teixeira,Renata and Feamster, Nick and Diot,Christophe} } @article {19664, title = {Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays}, journal = {BMC Genomics}, volume = {10}, year = {2009}, month = {2009/12/01/}, pages = {1 - 10}, abstract = {Background High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression. Results Consequently, we compared full length cDNA sequencing to 2-channel gene expression microarrays in the context of measuring differential gene expression. Because of its comparable cost to a gene expression microarray, our study focused on the data obtainable from a single lane of an Illumina 1 G sequencer. We compared sequencing data to a highly replicated microarray experiment profiling two divergent strains of S. cerevisiae. Conclusion Using a large number of quantitative PCR (qPCR) assays, more than previous studies, we found that neither technology is decisively better at measuring differential gene expression. Further, we report sequencing results from a diploid hybrid of two strains of S. cerevisiae that indicate full length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.}, keywords = {Animal Genetics and Genomics, Life Sciences, general, Microarrays, Microbial Genetics and Genomics, Plant Genetics \& Genomics, proteomics}, isbn = {1471-2164}, url = {http://link.springer.com/article/10.1186/1471-2164-10-221}, author = {Bloom, Joshua S. and Zia Khan and Kruglyak, Leonid and Singh, Mona and Caudy, Amy A.} } @article {12888, title = {Microbial oceanography in a sea of opportunity}, journal = {Nature}, volume = {459}, year = {2009}, month = {2009/05/13/}, pages = {180 - 184}, abstract = {Plankton use solar energy to drive the nutrient cycles that make the planet habitable for larger organisms. We can now explore the diversity and functions of plankton using genomics, revealing the gene repertoires associated with survival in the oceans. Such studies will help us to appreciate the sensitivity of ocean systems and of the ocean{\textquoteright}s response to climate change, improving the predictive power of climate models.}, keywords = {Astronomy, astrophysics, Biochemistry, Bioinformatics, Biology, biotechnology, cancer, cell cycle, cell signalling, climate change, Computational Biology, development, developmental biology, DNA, drug discovery, earth science, ecology, environmental science, Evolution, evolutionary biology, functional genomics, Genetics, Genomics, geophysics, immunology, interdisciplinary science, life, marine biology, materials science, medical research, medicine, metabolomics, molecular biology, molecular interactions, nanotechnology, Nature, neurobiology, neuroscience, palaeobiology, pharmacology, Physics, proteomics, quantum physics, RNA, Science, science news, science policy, signal transduction, structural biology, systems biology, transcriptomics}, isbn = {0028-0836}, doi = {10.1038/nature08056}, url = {http://www.nature.com/nature/journal/v459/n7244/abs/nature08056.html}, author = {Bowler,Chris and Karl,David M. and Rita R Colwell} } @article {12968, title = {Model-based quality assessment and base-calling for second-generation sequencing data}, journal = {Johns Hopkins University, Dept. of Biostatistics Working Papers}, year = {2009}, month = {2009///}, pages = {184 - 184}, author = {Irizarry,R. A and Corrada Bravo, Hector} } @conference {18243, title = {Modeling and analysis of ordinal ranking in content fingerprinting}, booktitle = {Information Forensics and Security, 2009. WIFS 2009. First IEEE International Workshop on}, year = {2009}, month = {2009/12//}, pages = {116 - 120}, abstract = {Content fingerprinting provides a compact representation of multimedia objects for copy detection. This paper analyzes the robustness of the ordinal ranking module frequently used in content fingerprinting by examining the changes in ranks as local variations are introduced in feature values. Closed-form expressions to measure such sensitivity are derived when feature values are jointly Gaussian-distributed. The results show that sensitivity depends on the strength of local variation, the total number of blocks, and the correlations among block-based feature values. Experiments with both synthesized data and image data validate the analysis and provide interesting insights, inspiring an approach to reduce the sensitivity.}, keywords = {detection;, detection;multimedia, fingerprinting;copy, Gaussian-distributed;content, identification;multimedia, objects;ordinal, processes;fingerprint, ranking;Gaussian, systems;object}, doi = {10.1109/WIFS.2009.5386472}, author = {Chuang,Wei-Hong and Varna,A.L. and M. Wu} } @article {17917, title = {Modeling and visualization of human activities for multicamera networks}, journal = {EURASIP Journal on Image and Video Processing}, volume = {2009}, year = {2009}, month = {2009///}, author = {Sankaranarayanan,A. C and Patro,R. and Turaga,P. and Varshney, Amitabh and Chellapa, Rama} } @article {12524, title = {Moving Object Verification in Airborne Video Sequences}, journal = {Circuits and Systems for Video Technology, IEEE Transactions on}, volume = {19}, year = {2009}, month = {2009/01//}, pages = {77 - 89}, abstract = {This paper presents an end-to-end system for moving object verification in airborne video sequences. Using a sample selection module, the system first selects frames from a short sequence and stores them in an exemplar database. To handle appearance change due to potentially large aspect angle variations, a homography-based view synthesis method is then used to generate a novel view of each image in the exemplar database at the same pose as the testing object in each frame of a testing video segment. A rotationally invariant color matcher and a spatial-feature matcher based on distance transforms are combined using a weighted average rule to compare the novel view and the testing object. After looping over all testing frames, the set of match scores is passed to a temporal analysis module to examine the behavior of the testing object, and calculate a final likelihood. Very good verification performance is achieved over thousands of trials for both color and infrared video sequences using the proposed system.}, keywords = {airborne, database;homography-based, databases;, matcher;color, matcher;image, matching;image, method;infrared, object, sequences;color, sequences;distance, sequences;moving, sequences;video, synthesis, system;exemplar, transforms;end-to-end, verification;spatial-feature, video, view}, isbn = {1051-8215}, doi = {10.1109/TCSVT.2008.2009243}, author = {Yue,Zhanfeng and Guarino, D. and Chellapa, Rama} } @article {12513, title = {Multicamera Tracking of Articulated Human Motion Using Shape and Motion Cues}, journal = {Image Processing, IEEE Transactions on}, volume = {18}, year = {2009}, month = {2009/09//}, pages = {2114 - 2126}, abstract = {We present a completely automatic algorithm for initializing and tracking the articulated motion of humans using image sequences obtained from multiple cameras. A detailed articulated human body model composed of sixteen rigid segments that allows both translation and rotation at joints is used. Voxel data of the subject obtained from the images is segmented into the different articulated chains using Laplacian eigenmaps. The segmented chains are registered in a subset of the frames using a single-frame registration technique and subsequently used to initialize the pose in the sequence. A temporal registration method is proposed to identify the partially segmented or unregistered articulated chains in the remaining frames in the sequence. The proposed tracker uses motion cues such as pixel displacement as well as 2-D and 3-D shape cues such as silhouettes, motion residue, and skeleton curves. The tracking algorithm consists of a predictor that uses motion cues and a corrector that uses shape cues. The use of complementary cues in the tracking alleviates the twin problems of drift and convergence to local minima. The use of multiple cameras also allows us to deal with the problems due to self-occlusion and kinematic singularity. We present tracking results on sequences with different kinds of motion to illustrate the effectiveness of our approach. The pose of the subject is correctly tracked for the duration of the sequence as can be verified by inspection.}, keywords = {2D shape cues, 3D shape cues, algorithms, Anatomic;Models, articulated human motion, automatic algorithm, Biological;Movement;Posture;Skeleton;Video Recording;, Computer-Assisted;Models, Eigenvalues and eigenfunctions, human pose estimation, HUMANS, Image motion analysis, IMAGE PROCESSING, image registration, Image segmentation, Image sequences, kinematic singularity, Laplacian eigenmaps, multicamera tracking algorithm, pixel displacement, pose estimation, single-frame registration technique, temporal registration method, tracking}, isbn = {1057-7149}, doi = {10.1109/TIP.2009.2022290}, author = {Sundaresan, A. and Chellapa, Rama} } @article {12887, title = {New records of phytoplankton for Bangladesh. 9. Some rare and a new species}, journal = {Bangladesh Journal of Plant Taxonomy}, volume = {16}, year = {2009}, month = {2009/06/25/}, abstract = {Ten taxa belonging to Chlorophyceae, Cyanophyceae, Bacillariophyceae and Euglenophyceae, and one with an uncertain taxonomic position have been described in this paper. Of these, 10 taxa have been found to be globally rare and new records for Bangladesh, whereas Strombomonas islamii Khondker sp. nov. has been described as new to science.}, isbn = {1028-2092}, doi = {10.3329/bjpt.v16i1.2734}, url = {http://www.banglajol.info/bd/index.php/BJPT/article/viewArticle/2734}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasmin,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @article {12972, title = {A phylogenetic mixture model for the evolution of gene expression}, journal = {Molecular biology and evolution}, volume = {26}, year = {2009}, month = {2009///}, pages = {2363 - 2363}, author = {Eng,K. H and Corrada Bravo, Hector and Kele{\c s},S.} } @article {12892, title = {Predicting the distribution of Vibrio spp. in the Chesapeake Bay: a Vibrio cholerae case study}, journal = {EcoHealth}, volume = {6}, year = {2009}, month = {2009///}, pages = {378 - 389}, abstract = {Vibrio cholerae, the causative agent of cholera, is a naturally occurring inhabitant of the Chesapeake Bay and serves as a predictor for other clinically important vibrios, including Vibrio parahaemolyticus and Vibrio vulnificus. A system was constructed to predict the likelihood of the presence of V. cholerae in surface waters of the Chesapeake Bay, with the goal to provide forecasts of the occurrence of this and related pathogenic Vibrio spp. Prediction was achieved by driving an available multivariate empirical habitat model estimating the probability of V. cholerae within a range of temperatures and salinities in the Bay, with hydrodynamically generated predictions of ambient temperature and salinity. The experimental predictions provided both an improved understanding of the in situ variability of V. cholerae, including identification of potential hotspots of occurrence, and usefulness as an early warning system. With further development of the system, prediction of the probability of the occurrence of related pathogenic vibrios in the Chesapeake Bay, notably V. parahaemolyticus and V. vulnificus, will be possible, as well as its transport to any geographical location where sufficient relevant data are available.}, doi = {10.1007/s10393-009-0273-6}, author = {Constantin de Magny,G. and Long,W. and Brown,C. W. and Hood,R. R. and Huq,A. and Murtugudde,R. and Rita R Colwell} } @article {18686, title = {Prioritizing Vulnerability Remediation by Determining Attacker-Targeted Vulnerabilities}, journal = {Security Privacy, IEEE}, volume = {7}, year = {2009}, month = {2009/02//jan}, pages = {42 - 48}, abstract = {This article attempts to empirically analyze which vulnerabilities attackers tend to target in order to prioritize vulnerability remediation. This analysis focuses on the link between malicious connections and vulnerabilities, where each connection is considered malicious. Attacks requiring multiple connections are counted as multiple attacks. As the number of connections increases, so does the cost of recovering from the intrusion. The authors deployed four honey pots for four months, each running a different Windows service pack with its associated set of vulnerabilities. They then performed three empirical analyses to determine the relationship between the number of malicious connections and the total number of vulnerabilities, the number of malicious connections and the number of the vulnerabilities for different services, and the number of known successful attacks and the number of vulnerabilities for different services.}, keywords = {attacker-targeted vulnerabilities, intrusion detection, malicious connections, security of data, vulnerability remediation, Windows service pack}, isbn = {1540-7993}, doi = {10.1109/MSP.2009.13}, author = {Michel Cukier and Panjwani,S.} } @conference {17329, title = {Promoting social creativity: a component of a national initiative for social participation}, booktitle = {Proceedings of the seventh ACM conference on Creativity and cognition}, series = {C\&$\#$38;C {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {7 - 8}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This panel will discuss group processes that promote social creativity in science, engineering, arts, and humanities. We will offer positive and negative examples of social creativity projects, while suggesting research directions for dramatically increased social participation. The goal is to develop strategies that would expand resources and opportunities for research and education in social creativity. This requires our community to develop a unified position, then reach out to national science funding agencies, while building the case for the importance of this topic beyond our own community. How can social creativity, collaborative discovery, distributed innovation, and collective intelligence be framed as an international priority to cope with the problems of the 21st century and how can we identify a clear set of research challenges? The theme of technology-mediated social participation is outlined in the white paper for a National Initiative for Social Participation (http://iparticipate.wikispaces.com). The white paper suggests that successful research challenges should have three key elements: (1) compelling national need (healthcare, national security, community safety, education, innovation, cultural heritage, energy sustainability, environmental protection, etc.), (2) scientific foundation based on established theories and well-defined research questions (privacy, reciprocity, trust, motivation, recognition, etc.), and (3) computer science research challenges (security, privacy protection, scalability, visualization, end-user development, distributed data handling for massive user-generated content, network analysis of community evolution, cross network comparison, etc.). We seek recommendations for ways to increase the resources and attention for this field. We hope to inspire: universities to change course content, add courses, and offer new degree programs industry to help researchers on social creativity government to support these ideas and try them out in government applications scientists and artists to open themselves to more social/collaborative approaches}, keywords = {research agenda, social creativity, social participation}, isbn = {978-1-60558-865-0}, doi = {10.1145/1640233.1640237}, url = {http://doi.acm.org/10.1145/1640233.1640237}, author = {Shneiderman, Ben and Churchill,Elizabeth and Fischer,Gerhard and Goldberg,Ken} } @article {18527, title = {Pushing Enterprise Security Down the Network Stack}, volume = {GT-CS-09-03}, year = {2009}, month = {2009///}, institution = {Georgia Institute of Technology}, abstract = {Network security is typically reactive: Networks provide connectivity and subsequently alter this connectivity according to various security policies, as implemented in middleboxes, or at higher layers. This approach gives rise to complicated interactions between protocols and systems that can cause incorrect behavior and slow response to attacks. In this paper, we propose a proactive approach to securing networks, whereby security-related actions (e.g., dropping or redirecting traffic) are embedded into the network fabric itself, leaving only a fixed set of actions to higher layers. We explore this approach in the context of network access control. Our design uses programmable switches to manipulate traffic at lower layers; these switches interact with policy and monitoring at higher layers. We apply our approach to Georgia Tech{\textquoteright}s network access control system, show how the new design can both overcome the current shortcomings and provide new security functions, describe our proposed deployment, and discuss open research questions.}, url = {http://hdl.handle.net/1853/30782}, author = {Clark,R. and Feamster, Nick and Nayak,A. and Reimers,A.} } @article {12515, title = {Rate-Invariant Recognition of Humans and Their Activities}, journal = {Image Processing, IEEE Transactions on}, volume = {18}, year = {2009}, month = {2009/06//}, pages = {1326 - 1339}, abstract = {Pattern recognition in video is a challenging task because of the multitude of spatio-temporal variations that occur in different videos capturing the exact same event. While traditional pattern-theoretic approaches account for the spatial changes that occur due to lighting and pose, very little has been done to address the effect of temporal rate changes in the executions of an event. In this paper, we provide a systematic model-based approach to learn the nature of such temporal variations (time warps) while simultaneously allowing for the spatial variations in the descriptors. We illustrate our approach for the problem of action recognition and provide experimental justification for the importance of accounting for rate variations in action recognition. The model is composed of a nominal activity trajectory and a function space capturing the probability distribution of activity-specific time warping transformations. We use the square-root parameterization of time warps to derive geodesics, distance measures, and probability distributions on the space of time warping functions. We then design a Bayesian algorithm which treats the execution rate function as a nuisance variable and integrates it out using Monte Carlo sampling, to generate estimates of class posteriors. This approach allows us to learn the space of time warps for each activity while simultaneously capturing other intra- and interclass variations. Next, we discuss a special case of this approach which assumes a uniform distribution on the space of time warping functions and show how computationally efficient inference algorithms may be derived for this special case. We discuss the relative advantages and disadvantages of both approaches and show their efficacy using experiments on gait-based person identification and activity recognition.}, keywords = {Automated;Video Recording;, Bayesian algorithm;Monte Carlo sampling;action recognition;activity-specific time warping transformations;computationally efficient inference algorithms;distance measures;execution rate function;function space;gait-based person identification;geodesics;no, Statistical;Monte Carlo Method;Movement;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2009.2017143}, author = {Veeraraghavan,A. and Srivastava, A. and Roy-Chowdhury, A.K. and Chellapa, Rama} } @conference {12412, title = {Reading tea leaves: How humans interpret topic models}, booktitle = {Proceedings of the 23rd Annual Conference on Neural Information Processing Systems}, volume = {31}, year = {2009}, month = {2009///}, abstract = {Probabilistic topic models are a popular tool for the unsupervised analysis of text, providing both a predictive model of future text and a latent topic representation of the corpus. Practitioners typically assume that the latent space is semantically meaningful. It is used to check models, summarize the corpus, and guide explo- ration of its contents. However, whether the latent space is interpretable is in need of quantitative evaluation. In this paper, we present new quantitative methods for measuring semantic meaning in inferred topics. We back these measures with large-scale user studies, showing that they capture aspects of the model that are undetected by previous measures of model quality based on held-out likelihood. Surprisingly, topic models which perform better on held-out likelihood may infer less semantically meaningful topics.}, author = {Chang,J. and Jordan Boyd-Graber and Gerrish,S. and Wang,C. and Blei,D.M.} } @conference {12512, title = {Recognition of quantized still face images}, booktitle = {Biometrics: Theory, Applications, and Systems, 2009. BTAS {\textquoteright}09. IEEE 3rd International Conference on}, year = {2009}, month = {2009/09//}, pages = {1 - 6}, abstract = {In applications such as document understanding, only binary face images may be available as inputs to a face recognition (FR) algorithm. In this paper, we investigate the effects of the number of grey levels on PCA, multiple exemplar discriminant analysis (MEDA) and the elastic bunch graph matching (EBGM) FR algorithms. The inputs to these FR algorithms are quantized images (binary images or images with small number of grey levels) modified by distance and Box-Cox transforms. The performances of PCA and MEDA algorithms are at 87.66\% for images in FRGC version 1 experiment 1 after they are thresholded and transformed while the EBGM algorithm achieves only 37.5\%. In many document understanding applications, it is also required to verify a degraded low-quality image against a high-quality image, both of which are from the same source. For this problem, the performances of PCA and MEDA are stable when the images were degraded by noise, downsampling or different thresholding parameters.}, keywords = {(signal);, algorithm;grey, algorithms;face, analysis;quantisation, analysis;quantized, Box-Cox, bunch, component, discriminant, exemplar, Face, FR, graph, images;distance, images;face, levels;multiple, MATCHING, recognition, recognition;principal, transforms;document, transforms;PCA;binary, understanding;elastic}, doi = {10.1109/BTAS.2009.5339030}, author = {Tao Wu and Chellapa, Rama} } @conference {12521, title = {Recognizing coordinated multi-object activities using a dynamic event ensemble model}, booktitle = {Acoustics, Speech and Signal Processing, 2009. ICASSP 2009. IEEE International Conference on}, year = {2009}, month = {2009/04//}, pages = {3541 - 3544}, abstract = {While video-based activity analysis and recognition has received broad attention, existing body of work mostly deals with single object/person case. Modeling involving multiple objects and recognition of coordinated group activities, present in a variety of applications such as surveillance, sports, biological records, and so on, is the main focus of this paper. Unlike earlier attempts which model the complex spatial temporal constraints among different activities of multiple objects with a parametric Bayesian network, we propose a dynamic dasiaevent ensemblepsila framework as a data-driven strategy to characterize the group motion pattern without employing any specific domain knowledge. In particular, we exploit the Riemannian geometric property of the set of ensemble description functions and develop a compact representation for group activities on the ensemble manifold. An appropriate classifier on the manifold is then designed for recognizing new activities. Experiments on football play recognition demonstrate the effectiveness of the framework.}, keywords = {activities, activity, analysis;Bayes, Bayesian, classification;video, description, ensemble, event, framework;dynamic, functions;ensemble, geometric, manifold;football, methods;geometry;image, model;ensemble, multiobject, network;video-based, play, processing;, property;classifier;coordinated, recognition;data-driven, recognition;parametric, Riemannian, signal, strategy;dynamic}, doi = {10.1109/ICASSP.2009.4960390}, author = {Ruonan Li and Chellapa, Rama} } @conference {12773, title = {Recovering Views of Inter-System Interaction Behaviors}, booktitle = {Reverse Engineering, Working Conference on}, year = {2009}, month = {2009///}, pages = {53 - 61}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper presents an approach for recovering application-level views of the interaction behaviors between systems that communicate via networks. Rather than illustrating a single behavior, a sequence diagram is constructed that describes the characteristics of multiple combined behaviors. The approach has several properties that make it particularly suitable for analyzing heterogeneous systems. First, since the interactions are retrieved from observing the network communication, our technique can be applied to systems that are implemented in different languages and run on different platforms. Second, it does not require the availability or modification of source code. After the behaviors are extracted, we employ methods to merge multiple observed behaviors to a single sequence diagram that illustrates the overall behavior.The contributions of this paper are a technique for observing and processing the network communication to derive a model of the behavior. Furthermore, it describes a series of model transformations to construct a sequence diagram view of all observed behaviors.}, keywords = {distributed systems, program understanding, reliability}, doi = {http://doi.ieeecomputersociety.org/10.1109/WCRE.2009.34}, author = {Ackermann,Christopher and Lindvall,Mikael and Cleaveland, Rance} } @article {14640, title = {Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians}, journal = {Clinical Endocrinology}, volume = {70}, year = {2009}, month = {2009/05/01/}, pages = {698 - 705}, abstract = {Objective Resistin causes insulin resistance and diabetes in mice whereas in humans it is linked to inflammation and atherosclerosis. Few human genetic studies of resistin in inflammation and atherosclerosis have been performed. We hypothesized that the {\textendash}420C>G putative gain-of-function resistin variant would be associated with inflammatory markers and atherosclerosis but not with metabolic syndrome or adipokines in humans.Design and methods We examined the association of three resistin polymorphisms, {\textendash}852A>G, {\textendash}420C>G and +157C>T, and related haplotypes with plasma resistin, cytokines, C-reactive protein (CRP), adipokines, plasma lipoproteins, metabolic syndrome and coronary artery calcification (CAC) in nondiabetic Caucasians (n~=~851). Results Resistin levels were higher, dose-dependently, with the {\textendash}420G allele (CC 5{\textperiodcentered}9~{\textpm}~2{\textperiodcentered}7~ng/ml, GC 6{\textperiodcentered}5~{\textpm}~4{\textperiodcentered}0~ng/ml and GG 7{\textperiodcentered}2~{\textpm}~4{\textperiodcentered}8~ng/ml, trend P~=~0{\textperiodcentered}04) after age and gender adjustment [fold higher for GC~+~GG vs. CC; 1{\textperiodcentered}07~(1{\textperiodcentered}00{\textendash}1{\textperiodcentered}15), P~<~0{\textperiodcentered}05)]. The {\textendash}852A>G single nucleotide polymorphism (SNP) was associated with higher soluble tumour necrosis factor-receptor~2 (sol-TNFR2) levels in fully adjusted models [1{\textperiodcentered}06~(95\%~CI 1{\textperiodcentered}01{\textendash}1{\textperiodcentered}11), P~=~0{\textperiodcentered}01)]. The estimated resistin haplotype (GGT) was associated with sol-TNFR2 (P~=~0{\textperiodcentered}04) and the AGT haplotype was related to CRP (P~=~0{\textperiodcentered}04) in the fully adjusted models. Resistin SNPs and haplotypes were not associated with body mass index (BMI), fasting glucose, insulin resistance, metabolic syndrome, adipokines or CAC scores. Conclusions Despite modest associations with plasma resistin and inflammatory biomarkers, resistin 5' variants were not associated with metabolic parameters or coronary calcification. This suggests that resistin is an inflammatory cytokine in humans but has little influence on adiposity, metabolic syndrome or atherosclerosis. }, isbn = {1365-2265}, doi = {10.1111/j.1365-2265.2008.03375.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2265.2008.03375.x/abstract;jsessionid=3EAA174C4993EDEE1267334CDA36E086.d01t01}, author = {Qasim,Atif N and Metkus,Thomas S and Tadesse,Mahlet and Lehrke,Michael and Restine,Stephanie and Wolfe,Megan L and Hannenhalli, Sridhar and Cappola,Thomas and Rader,Daniel J and Reilly,Muredach P} } @conference {18598, title = {Resonance: dynamic access control for enterprise networks}, booktitle = {Proceedings of the 1st ACM workshop on Research on enterprise networking}, series = {WREN {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {11 - 18}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Enterprise network security is typically reactive, and it relies heavily on host security and middleboxes. This approach creates complicated interactions between protocols and systems that can cause incorrect behavior and slow response to attacks. We argue that imbuing the network layer with mechanisms for dynamic access control can remedy these ills. We propose Resonance, a system for securing enterprise networks, where the network elements themselves enforce dynamic access control policies based on both flow-level information and real-time alerts. Resonance uses programmable switches to manipulate traffic at lower layers; these switches take actions (e.g., dropping or redirecting traffic) to enforce high-level security policies based on input from both higherlevel security policies and distributed monitoring and inference systems. We describe the design of Resonance, apply it to Georgia Tech{\textquoteright}s network access control system, show how it can both overcome the current shortcomings and provide new security functions, describe our proposed deployment, and discuss open research questions.}, keywords = {Access control, enterprise networks, programmable networks}, isbn = {978-1-60558-443-0}, doi = {10.1145/1592681.1592684}, url = {http://doi.acm.org/10.1145/1592681.1592684}, author = {Nayak,Ankur Kumar and Reimers,Alex and Feamster, Nick and Clark,Russ} } @article {12884, title = {RNA Colony Blot Hybridization Method for Enumeration of Culturable Vibrio Cholerae and Vibrio Mimicus Bacteria}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, month = {2009/09/01/}, pages = {5439 - 5444}, abstract = {A species-specific RNA colony blot hybridization protocol was developed for enumeration of culturable Vibrio cholerae and Vibrio mimicus bacteria in environmental water samples. Bacterial colonies on selective or nonselective plates were lysed by sodium dodecyl sulfate, and the lysates were immobilized on nylon membranes. A fluorescently labeled oligonucleotide probe targeting a phylogenetic signature sequence of 16S rRNA of V. cholerae and V. mimicus was hybridized to rRNA molecules immobilized on the nylon colony lift blots. The protocol produced strong positive signals for all colonies of the 15 diverse V. cholerae-V. mimicus strains tested, indicating 100\% sensitivity of the probe for the targeted species. For visible colonies of 10 nontarget species, the specificity of the probe was calculated to be 90\% because of a weak positive signal produced by Grimontia (Vibrio) hollisae, a marine bacterium. When both the sensitivity and specificity of the assay were evaluated using lake water samples amended with a bioluminescent V. cholerae strain, no false-negative or false-positive results were found, indicating 100\% sensitivity and specificity for culturable bacterial populations in freshwater samples when G. hollisae was not present. When the protocol was applied to laboratory microcosms containing V. cholerae attached to live copepods, copepods were found to carry approximately 10,000 to 50,000 CFU of V. cholerae per copepod. The protocol was also used to analyze pond water samples collected in an area of cholera endemicity in Bangladesh over a 9-month period. Water samples collected from six ponds demonstrated a peak in abundance of total culturable V. cholerae bacteria 1 to 2 months prior to observed increases in pathogenic V. cholerae and in clinical cases recorded by the area health clinic. The method provides a highly specific and sensitive tool for monitoring the dynamics of V. cholerae in the environment. The RNA blot hybridization protocol can also be applied to detection of other gram-negative bacteria for taxon-specific enumeration.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.02007-08}, url = {http://aem.asm.org/content/75/17/5439}, author = {Grim,Christopher J. and Zo,Young-Gun and Hasan,Nur A. and Ali,Afsar and Chowdhury,Wasimul B. and Islam,Atiqul and Rashid,Mohammed H. and Alam,Munirul and Morris,J. Glenn and Huq,Anwar and Rita R Colwell} } @article {12520, title = {Robust Estimation of Albedo for Illumination-Invariant Matching and Shape Recovery}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {31}, year = {2009}, month = {2009/05//}, pages = {884 - 899}, abstract = {We present a nonstationary stochastic filtering framework for the task of albedo estimation from a single image. There are several approaches in the literature for albedo estimation, but few include the errors in estimates of surface normals and light source direction to improve the albedo estimate. The proposed approach effectively utilizes the error statistics of surface normals and illumination direction for robust estimation of albedo, for images illuminated by single and multiple light sources. The albedo estimate obtained is subsequently used to generate albedo-free normalized images for recovering the shape of an object. Traditional shape-from-shading (SFS) approaches often assume constant/piecewise constant albedo and known light source direction to recover the underlying shape. Using the estimated albedo, the general problem of estimating the shape of an object with varying albedo map and unknown illumination source is reduced to one that can be handled by traditional SFS approaches. Experimental results are provided to show the effectiveness of the approach and its application to illumination-invariant matching and shape recovery. The estimated albedo maps are compared with the ground truth. The maps are used as illumination-invariant signatures for the task of face recognition across illumination variations. The recognition results obtained compare well with the current state-of-the-art approaches. Impressive shape recovery results are obtained using images downloaded from the Web with little control over imaging conditions. The recovered shapes are also used to synthesize novel views under novel illumination conditions.}, keywords = {albedo estimation;error statistics;face recognition;illumination-invariant matching;nonstationary stochastic filtering;robust estimation;shape recovery;shape-from-shading approach;error statistics;face recognition;filtering theory;image matching;Algorithm, Automated;Photometry;Reproducibility of Results;Sensitivity and Specificity;, Computer-Assisted;Imaging, Three-Dimensional;Lighting;Pattern Recognition}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2008.135}, author = {Biswas,S. and Aggarwal,G. and Chellapa, Rama} } @article {12529, title = {Robust human detection under occlusion by integrating face and person detectors}, journal = {Proceedings of the Third International Conference on Advances in Biometrics}, year = {2009}, month = {2009///}, pages = {970 - 979}, abstract = {Human detection under occlusion is a challenging problemin computer vision. We address this problem through a framework which integrates face detection and person detection. We first investigate how the response of a face detector is correlated with the response of a person detector. From these observations, we formulate hypotheses that capture the intuitive feedback between the responses of face and person detectors and use it to verify if the individual detectors{\textquoteright} outputs are true or false. We illustrate the performance of our integration framework on challeng- ing images that have considerable amount of occlusion, and demonstrate its advantages over individual face and person detectors. }, author = {Schwartz, W.R. and Gopalan,R. and Chellapa, Rama and Davis, Larry S.} } @conference {17911, title = {Salient Clustering for View-dependent Multiresolution Rendering}, booktitle = {Computer Graphics and Image Processing (SIBGRAPI), 2009 XXII Brazilian Symposium on}, year = {2009}, month = {2009/10//}, pages = {56 - 63}, abstract = {Perceptual information is quickly gaining importance in mesh representation, analysis and rendering. User studies, eye tracking and other techniques are able to provide ever more useful insights for many user-centric systems, which form the bulk of computer graphics applications. In this work we build upon the concept of Mesh Saliency - an automatic measure of visual importance for triangle meshes based on models of low-level human visual attention - applying it to the problem of mesh segmentation and view-dependent rendering. We introduce a technique for segmentation that partitions an object into a set of face clusters, each encompassing a group of locally interesting features; Mesh Saliency is incorporated in a propagative mesh clustering framework, guiding cluster seed selection and triangle propagation costs and leading to a convergence of face clusters around perceptually important features. We compare our technique with different fully automatic segmentation algorithms, showing that it provides similar or better segmentation without the need for user input. We illustrate application of our clustering results through a saliency-guided view-dependent rendering system, achieving significant frame rate increases with little loss of visual detail.}, keywords = {(computer, algorithms;cluster, analysis;mesh, attention;mesh, AUTOMATIC, centred, clustering, clustering;rendering, clustering;user-centric, clusters;low-level, dependent, design;, framework;salient, graphics);user, graphics;face, human, information;propagative, mesh, multiresolution, rendering;image, representation;mesh, resolution;image, saliency;mesh, seed, segmentation, segmentation;pattern, segmentation;perceptual, selection;computer, system;view, visual}, doi = {10.1109/SIBGRAPI.2009.34}, author = {Barni,R. and Comba,J. and Varshney, Amitabh} } @conference {12154, title = {Scope error detection and handling concerning software estimation models}, booktitle = {Proceedings of the 2009 3rd International Symposium on Empirical Software Engineering and Measurement}, series = {ESEM {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {123 - 132}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {Over the last 25+ years, the software community has been searching for the best models for estimating variables of interest (e.g., cost, defects, and fault proneness). However, little research has been done to improve the reliability of the estimates. Over the last decades, scope error and error analysis have been substantially ignored by the community. This work attempts to fill this gap in the research and enhance a common understanding within the community. Results provided in this study can eventually be used to support human judgment-based techniques and be an addition to the portfolio. The novelty of this work is that, we provide a way of detecting and handling the scope error arising from estimation models. The answer whether or not scope error will occur is a pre-condition to safe use of an estimation model. We also provide a handy procedure for dealing with outliers as to whether or not to include them in the training set for building a new version of the estimation model. The majority of the work is empirically based, applying computational intelligence techniques to some COCOMO model variations with respect to a publicly available cost estimation data set in the PROMISE repository.}, isbn = {978-1-4244-4842-5}, doi = {10.1109/ESEM.2009.5316020}, url = {http://dx.doi.org/10.1109/ESEM.2009.5316020}, author = {Sarcia,Salvatore Alessandro and Basili, Victor R. and Cantone,Giovanni} } @article {13856, title = {Semantically informed machine translation (SIMT)}, journal = {SCALE summer workshop final report, Human Language Technology Center Of Excellence}, year = {2009}, month = {2009///}, author = {Baker,K. and Bethard,S. and Bloodgood,M. and Brown,R. and Callison-Burch,C. and Coppersmith,G. and Dorr, Bonnie J and Filardo,W. and Giles,K. and Irvine,A. and others} } @article {12882, title = {Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, month = {2009/10/01/}, pages = {6268 - 6274}, abstract = {Forty-two strains of Vibrio parahaemolyticus were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes toxR and tlh were confirmed by PCR in all but two strains, which also lacked toxR. A total of 18 (41\%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (trh) gene, but not tdh. Ten (23\%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed tdh. Of the 18 tdh-positive strains, 17 (94\%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single trh-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., {\textquotedblleft}clonal cluster,{\textquotedblright} as did pandemic strains of diverse origin. The demonstrated prevalence of tdh-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.00266-09}, url = {http://aem.asm.org/content/75/19/6268}, author = {Alam,Munirul and Chowdhury,Wasimul B. and Bhuiyan,N. A. and Islam,Atiqul and Hasan,Nur A. and Nair,G. Balakrish and Watanabe,H. and Siddique,A. K. and Huq,Anwar and Sack,R. Bradley and Akhter,M. Z. and Grim,Christopher J. and Kam,K.-M. and Luey,C. K. Y. and Endtz,Hubert P. and Cravioto,Alejandro and Rita R Colwell} } @conference {18354, title = {Sikuli: using GUI screenshots for search and automation}, booktitle = {Proceedings of the 22nd annual ACM symposium on User interface software and technology}, series = {UIST {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {183 - 192}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present Sikuli, a visual approach to search and automation of graphical user interfaces using screenshots. Sikuli allows users to take a screenshot of a GUI element (such as a toolbar button, icon, or dialog box) and query a help system using the screenshot instead of the element{\textquoteright}s name. Sikuli also provides a visual scripting API for automating GUI interactions, using screenshot patterns to direct mouse and keyboard events. We report a web-based user study showing that searching by screenshot is easy to learn and faster to specify than keywords. We also demonstrate several automation tasks suitable for visual scripting, such as map navigation and bus tracking, and show how visual scripting can improve interactive help systems previously proposed in the literature.}, keywords = {Automation, image search, online help}, isbn = {978-1-60558-745-5}, doi = {10.1145/1622176.1622213}, url = {http://doi.acm.org/10.1145/1622176.1622213}, author = {Tom Yeh and Chang,Tsung-Hsiang and Miller,Robert C.} } @inbook {19645, title = {Simple, Black-Box Constructions of Adaptively Secure Protocols}, booktitle = {Theory of Cryptography}, series = {Lecture Notes in Computer Science}, year = {2009}, month = {2009/01/01/}, pages = {387 - 402}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We present a compiler for transforming an oblivious transfer (OT) protocol secure against an adaptive semi-honest adversary into one that is secure against an adaptive malicious adversary. Our compiler achieves security in the universal composability framework, assuming access to an ideal commitment functionality, and improves over previous work achieving the same security guarantee in two ways: it uses black-box access to the underlying protocol and achieves a constant multiplicative overhead in the round complexity. As a corollary, we obtain the first constructions of adaptively secure protocols in the stand-alone model using black-box access to a low-level primitive.}, keywords = {Algorithm Analysis and Problem Complexity, computers and society, Data Encryption, Discrete Mathematics in Computer Science, Management of Computing and Information Systems, Systems and Data Security}, isbn = {978-3-642-00456-8, 978-3-642-00457-5}, url = {http://link.springer.com/chapter/10.1007/978-3-642-00457-5_23}, author = {Choi, Seung Geol and Dana Dachman-Soled and Malkin, Tal and Wee, Hoeteck}, editor = {Reingold, Omer} } @conference {15922, title = {Sparsity inspired selection and recognition of iris images}, booktitle = {Biometrics: Theory, Applications, and Systems, 2009. BTAS {\textquoteright}09. IEEE 3rd International Conference on}, year = {2009}, month = {2009/09//}, pages = {1 - 6}, abstract = {Iris images acquired from a partially cooperating subject often suffer from blur, occlusion due to eyelids, and specular reflections. The performance of existing iris recognition systems degrade significantly on these images. Hence it is essential to select good images from the incoming iris video stream, before they are input to the recognition algorithm. In this paper, we propose a sparsity based algorithm for selection of good iris images and their subsequent recognition. Unlike most existing algorithms for iris image selection, our method can handle segmentation errors and a wider range of acquisition artifacts common in iris image capture. We perform selection and recognition in a single step which is more efficient than devising separate specialized algorithms for the two. Recognition from partially cooperating users is a significant step towards deploying iris systems in a wide variety of applications.}, keywords = {biometrics (access control), image recognition, Image segmentation, iris image recognition, iris image selection, iris video stream, sparsity inspired selection, video signal processing, video streaming}, doi = {10.1109/BTAS.2009.5339067}, author = {Pillai,J.K. and Patel, Vishal M. and Chellapa, Rama} } @conference {12414, title = {Speaking through pictures: images vs. icons}, booktitle = {Proceedings of the 11th international ACM SIGACCESS conference on Computers and accessibility}, series = {Assets {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {163 - 170}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {People with aphasia, a condition that impairs the ability to understand or generate written or spoken language, are aided by assistive technology that helps them communicate through a vocabulary of icons. These systems are akin to language translation systems, translating icon arrangements into spoken or written language and vice versa. However, these icon-based systems have little vocabulary breadth or depth, making it difficult for people with aphasia to apply their usage to multiple real world situations. Pictures from the web are numerous, varied, and easily accessible and thus, could potentially address the small size issues of icon-based systems. We present results from two studies that investigate this potential and demonstrate that images can be as effective as icons when used as a replacement for English language communication. The first study uses elderly subjects to investigate the efficacy of images vs. icons in conveying word meaning; the second study examines the retention of word-level meaning by both images and icons with a population of aphasics. We conclude that images collected from the web are as functional as icons in conveying information and thus, are feasible to use in assistive technology that supports people with aphasia.}, keywords = {aphasia, computerized visual communication (C-VIC), visual communication (VIC)}, isbn = {978-1-60558-558-1}, doi = {10.1145/1639642.1639672}, url = {http://doi.acm.org/10.1145/1639642.1639672}, author = {Ma,Xiaojuan and Jordan Boyd-Graber and Nikolova,Sonya and Cook,Perry R.} } @article {16062, title = {The Story of One: Humanity scholarship with visualization and text analysis}, journal = {Relation}, volume = {10}, year = {2009}, month = {2009///}, pages = {8485 - 8485}, author = {Clement,T. and Plaisant, Catherine and Vuillemot,R.} } @article {18721, title = {Structure of the S5a:K48-Linked Diubiquitin Complex and Its Interactions with Rpn13}, journal = {Molecular Cell}, volume = {35}, year = {2009}, month = {2009/08/14/}, pages = {280 - 290}, abstract = {SummaryDegradation by the proteasome typically requires substrate ubiquitination. Two ubiquitin receptors exist in the proteasome, S5a/Rpn10 and Rpn13. Whereas Rpn13 has only one ubiquitin-binding surface, S5a binds ubiquitin with two independent ubiquitin-interacting motifs (UIMs). Here, we use nuclear magnetic resonance (NMR) and analytical ultracentrifugation to define at atomic level resolution how S5a binds K48-linked diubiquitin, in which K48 of~one ubiquitin subunit (the {\textquotedblleft}proximal{\textquotedblright} one) is covalently bonded to G76 of the other (the {\textquotedblleft}distal{\textquotedblright} subunit). We demonstrate that S5a{\textquoteright}s UIMs bind the two subunits simultaneously with a preference for UIM2 binding to the proximal subunit while UIM1 binds to the distal one. In addition, NMR experiments reveal that Rpn13 and S5a bind K48-linked diubiquitin simultaneously with subunit specificity, and a model structure of S5a and Rpn13 bound to K48-linked polyubiquitin is provided. Altogether, our data demonstrate that S5a is highly adaptive and cooperative toward binding ubiquitin chains. }, keywords = {Proteins}, isbn = {1097-2765}, doi = {10.1016/j.molcel.2009.06.010}, url = {http://www.sciencedirect.com/science/article/pii/S1097276509004018}, author = {Zhang,Naixia and Wang,Qinghua and Ehlinger,Aaron and Randles,Leah and Lary,Jeffrey W. and Kang,Yang and Haririnia,Aydin and Storaska,Andrew J. and Cole,James L. and Fushman, David and Walters,Kylie J.} } @article {12539, title = {Surface reconstruction from gradient fields via gradient transformations}, journal = {International Journal of Computer Vision}, year = {2009}, month = {2009///}, author = {Agrawal,A. and Raskar, R. and Chellapa, Rama} } @conference {18285, title = {Tampering identification using Empirical Frequency Response}, booktitle = {Acoustics, Speech and Signal Processing, 2009. ICASSP 2009. IEEE International Conference on}, year = {2009}, month = {2009/04//}, pages = {1517 - 1520}, abstract = {With the widespread popularity of digital images and the presence of easy-to-use image editing software, content integrity can no longer be taken for granted, and there is a strong need for techniques that not only detect the presence of tampering but also identify its type. This paper focusses on tampering-type identification and introduces a new approach based on the empirical frequency response (EFR) to address this problem. We show that several types of tampering operations, both linear shift invariant (LSI) and non-LSI, can be characterized consistently and distinctly by their EFRs. We then extend the approach to estimate the EFR for scenarios where only the final image is available. Theoretical reasoning supported by experimental results verify the effectiveness of this method for identifying the type of a tampering operation.}, keywords = {aproach;JPEG, coding;multimedia, compression;frequency, compression;LSI, computing;security, data;, editing, EFR, forensics;tampering-type, Frequency, identification;data, image, invariant;multimedia, of, response;image, response;linear, shift, software;empirical, system;digital}, doi = {10.1109/ICASSP.2009.4959884}, author = {Chuang,Wei-Hong and Swaminathan,A. and M. Wu} } @article {19726, title = {Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.}, journal = {Appl Environ Microbiol}, volume = {75}, year = {2009}, month = {2009 Apr}, pages = {2046-56}, abstract = {

The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N(2) fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.

}, keywords = {Anti-Bacterial Agents, bacteria, Biological Transport, Carbohydrate Metabolism, Cyanobacteria, DNA, Bacterial, Fungi, Genome, Bacterial, Macrolides, Molecular Sequence Data, Nitrogen, Phylogeny, Proteobacteria, Sequence Analysis, DNA, sequence homology, Soil Microbiology}, issn = {1098-5336}, doi = {10.1128/AEM.02294-08}, author = {Ward, Naomi L and Challacombe, Jean F and Janssen, Peter H and Henrissat, Bernard and Coutinho, Pedro M and Wu, Martin and Xie, Gary and Haft, Daniel H and Sait, Michelle and Badger, Jonathan and Barabote, Ravi D and Bradley, Brent and Brettin, Thomas S and Brinkac, Lauren M and Bruce, David and Creasy, Todd and Daugherty, Sean C and Davidsen, Tanja M and DeBoy, Robert T and Detter, J Chris and Dodson, Robert J and Durkin, A Scott and Ganapathy, Anuradha and Gwinn-Giglio, Michelle and Han, Cliff S and Khouri, Hoda and Kiss, Hajnalka and Kothari, Sagar P and Madupu, Ramana and Nelson, Karen E and Nelson, William C and Paulsen, Ian and Penn, Kevin and Ren, Qinghu and Rosovitz, M J and Jeremy D Selengut and Shrivastava, Susmita and Sullivan, Steven A and Tapia, Roxanne and Thompson, L Sue and Watkins, Kisha L and Yang, Qi and Yu, Chunhui and Zafar, Nikhat and Zhou, Liwei and Kuske, Cheryl R} } @article {18724, title = {Together, Rpn10 and Dsk2 Can Serve as a Polyubiquitin Chain-Length Sensor}, journal = {Molecular Cell}, volume = {36}, year = {2009}, month = {2009/12/24/}, pages = {1018 - 1033}, abstract = {SummaryAs a signal for substrate targeting, polyubiquitin meets various layers of receptors upstream to the 26S proteasome. We obtained structural information on two receptors, Rpn10 and Dsk2, alone and in complex with (poly)ubiquitin or with each other. A~hierarchy of affinities emerges with Dsk2 binding monoubiquitin tighter than Rpn10 does, whereas Rpn10 prefers the ubiquitin-like domain of Dsk2 to monoubiquitin, with increasing affinities for longer polyubiquitin chains. We demonstrated the formation of ternary complexes of both receptors simultaneously with (poly)ubiquitin and found that, depending on the ubiquitin chain length, the orientation of the resulting complex is entirely different, providing for alternate signals. Dynamic rearrangement provides a chain-length sensor, possibly explaining how accessibility of Dsk2 to the proteasome is limited unless it carries a properly tagged cargo. We propose a mechanism for a malleable ubiquitin signal that depends both on chain length and combination of receptors to produce tetraubiquitin as an efficient signal threshold. }, keywords = {Proteins, signaling}, isbn = {1097-2765}, doi = {10.1016/j.molcel.2009.11.012}, url = {http://www.sciencedirect.com/science/article/pii/S1097276509008260}, author = {Zhang,Daoning and Chen,Tony and Ziv,Inbal and Rosenzweig,Rina and Matiuhin,Yulia and Bronner,Vered and Glickman,Michael H. and Fushman, David} } @article {13026, title = {Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study}, journal = {BMC Evol Biol}, volume = {9}, year = {2009}, month = {2009///}, pages = {280 - 280}, abstract = {BACKGROUND: In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98\% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis. RESULTS: Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (P < 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (P < or = 0.005), and nearly so for the superfamily Drepanoidea as currently defined (P < 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data. CONCLUSION: Our results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.}, doi = {10.1186/1471-2148-9-280}, author = {Regier,J. C and Zwick,A. and Cummings, Michael P. and Kawahara,A. Y and Cho,S. and Weller,S. and Roe,A. and Baixeras,J. and Brown,J. W and Parr,C. and Davis,DR and Epstein,M and Hallwachs,W and Hausmann,A and Janzen,DH and Kitching,IJ and Solis,MA and Yen,S-H and Bazinet,A. L and Mitter,C} } @conference {15495, title = {Towards Dynamic Adaptive Automated Test Generation for Graphical User Interfaces}, booktitle = {Software Testing, Verification and Validation Workshops, 2009. ICSTW {\textquoteright}09. International Conference on}, year = {2009}, month = {2009/04//}, pages = {263 - 266}, abstract = {Graphical user interfaces (GUIs) present an enormous number of potential event sequences to users. During testing it is necessary to cover this space, however the complexity of modern GUIs has made this an increasingly difficult task. Our past work has demonstrated that it is important to incorporate "context{\textquotedblright} into GUI test cases, in terms of event combinations, event sequence length, and by considering all possible starting and ending positions for each event. Despite the use of our most refined modeling techniques, many of the generated test cases remain unexecutable. In this paper, we posit that due to the dynamic state-based nature of GUIs, it is important to incorporate feedback from the execution of tests into test case generation algorithms. We propose the use of an evolutionary algorithm to generate test suites with fewer unexecutable test cases and higher event interaction coverage.}, keywords = {adaptive automated test generation, computational complexity, event sequence length, evolutionary algorithm, evolutionary computation, graphical user interface, Graphical user interfaces, GUI test case, program testing}, doi = {10.1109/ICSTW.2009.26}, author = {Xun Yuan and Cohen,M. B and Memon, Atif M.} } @article {13341, title = {Tree-Based Encoding for Cancellations on Morse Complexes}, journal = {Combinatorial Image Analysis}, year = {2009}, month = {2009///}, pages = {330 - 343}, abstract = {A scalar function f, defined on a manifold M, can be simplified by applying a sequence of removal and contraction operators, which eliminate its critical points in pairs, and simplify the topological representation of M, provided by Morse complexes of f. The inverse refinement operators, together with a dependency relation between them, enable a construction of a multi-resolution representation of such complexes. Here, we encode a sequence of simplification operators in a data structure called an augmented cancellation forest, which will enable procedural encoding of the inverse refinement operators, and reduce the dependency relation between modifications of the Morse complexes. In this way, this representation will induce a high flexibility of the hierarchical representation of the Morse complexes, producing a large number of Morse complexes at different resolutions that can be obtained from the hierarchy.}, doi = {10.1007/978-3-642-10210-3_26}, author = {{\v C}omi{\'c},L. and De Floriani, Leila} } @conference {14346, title = {UbiGreen: investigating a mobile tool for tracking and supporting green transportation habits}, booktitle = {Proceedings of the 27th international conference on Human factors in computing systems}, series = {CHI {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {1043 - 1052}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {ambient displays, mobile phones, sensing, Sustainability, transportation, ubicomp}, isbn = {978-1-60558-246-7}, doi = {10.1145/1518701.1518861}, url = {http://doi.acm.org/10.1145/1518701.1518861}, author = {Jon Froehlich and Dillahunt,Tawanna and Klasnja,Predrag and Mankoff,Jennifer and Consolvo,Sunny and Harrison,Beverly and Landay,James A.} } @article {12523, title = {Unsupervised view and rate invariant clustering of video sequences}, journal = {Computer Vision and Image Understanding}, volume = {113}, year = {2009}, month = {2009/03//}, pages = {353 - 371}, abstract = {Videos play an ever increasing role in our everyday lives with applications ranging from news, entertainment, scientific research, security and surveillance. Coupled with the fact that cameras and storage media are becoming less expensive, it has resulted in people producing more video content than ever before. This necessitates the development of efficient indexing and retrieval algorithms for video data. Most state-of-the-art techniques index videos according to the global content in the scene such as color, texture, brightness, etc. In this paper, we discuss the problem of activity-based indexing of videos. To address the problem, first we describe activities as a cascade of dynamical systems which significantly enhances the expressive power of the model while retaining many of the computational advantages of using dynamical models. Second, we also derive methods to incorporate view and rate-invariance into these models so that similar actions are clustered together irrespective of the viewpoint or the rate of execution of the activity. We also derive algorithms to learn the model parameters from a video stream and demonstrate how a single video sequence may be clustered into different clusters where each cluster represents an activity. Experimental results for five different databases show that the clusters found by the algorithm correspond to semantically meaningful activities.}, keywords = {Affine invariance, Cascade of linear dynamical systems, Rate invariance, Summarization, Surveillance, Video clustering, View invariance}, isbn = {1077-3142}, doi = {10.1016/j.cviu.2008.08.009}, url = {http://www.sciencedirect.com/science/article/pii/S1077314208001367}, author = {Turaga,Pavan and Veeraraghavan,Ashok and Chellapa, Rama} } @article {12846, title = {Using formal specifications to support testing}, journal = {ACM Computing Surveys}, volume = {41}, year = {2009}, month = {2009/02/01/}, pages = {1 - 76}, isbn = {03600300}, doi = {10.1145/1459352.1459354}, url = {http://dl.acm.org/citation.cfm?id=1459352.1459354}, author = {Hierons,Robert M. and Krause,Paul and L{\"u}ttgen,Gerald and Simons,Anthony J. H. and Vilkomir,Sergiy and Woodward,Martin R. and Zedan,Hussein and Bogdanov,Kirill and Bowen,Jonathan P. and Cleaveland, Rance and Derrick,John and Dick,Jeremy and Gheorghe,Marian and Harman,Mark and Kapoor,Kalpesh} } @article {12885, title = {Using Satellite Images of Environmental Changes to Predict Infectious Disease Outbreaks}, journal = {Emerging Infectious DiseasesEmerg Infect Dis}, volume = {15}, year = {2009}, month = {2009/09//}, pages = {1341 - 1346}, abstract = {A strong global satellite imaging system is essential for predicting outbreaks., Recent events clearly illustrate a continued vulnerability of large populations to infectious diseases, which is related to our changing human-constructed and natural environments. A single person with multidrug-resistant tuberculosis in 2007 provided a wake-up call to the United States and global public health infrastructure, as the health professionals and the public realized that today{\textquoteright}s ease of airline travel can potentially expose hundreds of persons to an untreatable disease associated with an infectious agent. Ease of travel, population increase, population displacement, pollution, agricultural activity, changing socioeconomic structures, and international conflicts worldwide have each contributed to infectious disease events. Today, however, nothing is larger in scale, has more potential for long-term effects, and is more uncertain than the effects of climate change on infectious disease outbreaks, epidemics, and pandemics. We discuss advances in our ability to predict these events and, in particular, the critical role that satellite imaging could play in mounting an effective response.}, isbn = {1080-6040}, doi = {10.3201/eid/1509.081334}, author = {Ford,Timothy E. and Rita R Colwell and Rose,Joan B. and Morse,Stephen S. and Rogers,David J. and Yates,Terry L.} } @article {14887, title = {Using Stereo Matching with General Epipolar Geometry for 2D Face Recognition across Pose}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {31}, year = {2009}, month = {2009/12//}, pages = {2298 - 2304}, abstract = {Face recognition across pose is a problem of fundamental importance in computer vision. We propose to address this problem by using stereo matching to judge the similarity of two, 2D images of faces seen from different poses. Stereo matching allows for arbitrary, physically valid, continuous correspondences. We show that the stereo matching cost provides a very robust measure of similarity of faces that is insensitive to pose variations. To enable this, we show that, for conditions common in face recognition, the epipolar geometry of face images can be computed using either four or three feature points. We also provide a straightforward adaptation of a stereo matching algorithm to compute the similarity between faces. The proposed approach has been tested on the CMU PIE data set and demonstrates superior performance compared to existing methods in the presence of pose variation. It also shows robustness to lighting variation.}, keywords = {2D face recognition;CMU PIE data set;computer vision;continuous correspondences;general epipolar geometry;lighting variation;pose variation;stereo matching;computer vision;face recognition;geometry;image matching;pose estimation;stereo image processing;Al, Automated;, Computer-Assisted;Pattern Recognition}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2009.123}, author = {Castillo,C. D and Jacobs, David W.} } @conference {12167, title = {Using uncertainty as a model selection and comparison criterion}, booktitle = {Proceedings of the 5th International Conference on Predictor Models in Software Engineering}, series = {PROMISE {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {18:1{\textendash}18:9 - 18:1{\textendash}18:9}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Over the last 25+ years, software estimation research has been searching for the best model for estimating variables of interest (e.g., cost, defects, and fault proneness). This research effort has not lead to a common agreement. One problem is that, they have been using accuracy as the basis for selection and comparison. But accuracy is not invariant; it depends on the test sample, the error measure, and the chosen error statistics (e.g., MMRE, PRED, Mean and Standard Deviation of error samples). Ideally, we would like an invariant criterion. In this paper, we show that uncertainty can be used as an invariant criterion to figure out which estimation model should be preferred over others. The majority of this work is empirically based, applying Bayesian prediction intervals to some COCOMO model variations with respect to a publicly available cost estimation data set coming from the PROMISE repository.}, keywords = {accuracy, Bayesian prediction intervals, Calibration, cost estimation, cost model, model evaluation, model selection, prediction interval, Uncertainty}, isbn = {978-1-60558-634-2}, doi = {10.1145/1540438.1540464}, url = {http://doi.acm.org/10.1145/1540438.1540464}, author = {Sarcia{\textquoteright},Salvatore Alessandro and Basili, Victor R. and Cantone,Giovanni} } @conference {12806, title = {Validating Automotive Control Software Using Instrumentation-Based Verification}, booktitle = {Automated Software Engineering, International Conference on}, year = {2009}, month = {2009///}, pages = {15 - 25}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper discusses the results of an application of a formally based verification technique, called Instrumentation-Based Verification (IBV), to a production automotive lighting controller. The goal of the study is to assess, from both a tools as well as a methodological perspective, the performance of IBV in an industrial setting. The insights obtained as a result of the project include a refinement of a previously developed architecture for requirements specifications; observations about changes to model-based design workflows; insights into the role of requirements during development; and the capability of automated verification to detect inconsistencies among requirements as well as between requirements and design models.}, doi = {http://doi.ieeecomputersociety.org/10.1109/ASE.2009.98}, author = {Ray,Arnab and Morschhaeuser,Iris and Ackermann,Chris and Cleaveland, Rance and Shelton,Charles and Martin,Chris} } @article {12525, title = {Vehicle Speed Estimation Using Acoustic Wave Patterns}, journal = {Signal Processing, IEEE Transactions on}, volume = {57}, year = {2009}, month = {2009/01//}, pages = {30 - 47}, abstract = {We estimate a vehicle{\textquoteright}s speed, its wheelbase length, and tire track length by jointly estimating its acoustic wave pattern with a single passive acoustic sensor that records the vehicle{\textquoteright}s drive-by noise. The acoustic wave pattern is determined using the vehicle{\textquoteright}s speed, the Doppler shift factor, the sensor{\textquoteright}s distance to the vehicle{\textquoteright}s closest-point-of-approach, and three envelope shape (ES) components, which approximate the shape variations of the received signal{\textquoteright}s power envelope. We incorporate the parameters of the ES components along with estimates of the vehicle engine RPM, the number of cylinders, and the vehicle{\textquoteright}s initial bearing, loudness and speed to form a vehicle profile vector. This vector provides a fingerprint that can be used for vehicle identification and classification. We also provide possible reasons why some of the existing methods are unable to provide unbiased vehicle speed estimates using the same framework. The approach is illustrated using vehicle speed estimation and classification results obtained with field data.}, keywords = {acoustic, Doppler, estimation;passive, estimation;road, estimation;wheelbase, factor;acoustic, identification;vehicle, length;Doppler, length;vehicle, likelihood, patterns;envelope, processing;maximum, profile, sensor;tire, shape;maximum, shift, shift;acoustic, signal, speed, track, vector;vehicle, vehicles;, wave}, isbn = {1053-587X}, doi = {10.1109/TSP.2008.2005750}, author = {Cevher, V. and Chellapa, Rama and McClellan, J.H.} } @article {12894, title = {Viable but not cultivable bacteria}, journal = {Uncultivated Microorganisms}, year = {2009}, month = {2009///}, pages = {121 - 129}, abstract = {A well-studied, long-term survival mechanism employed by Gram-positive bacteria is formation of endospores. For Gram-negative bacteria, the assumption has been that a survival state does not exist. However, a dormancy state has been described for Gram-negative bacteria and designated as the viable but nonculturable (VBNC) strategy of nonspore-forming cells. A variety of environmental factors are involved in induction of the viable but nonculturable state and Vibrio cholerae provides a useful paradigm for the VBNC phenomenon. It is now accepted that plate counts cannot be relied upon to enumerate or detect VBNC cells. Therefore, direct methods employing fluorescent staining, molecular genetic probes, and other molecular methods have proven both useful and reliable in detecting and enumerating both culturable and nonculturable cells. A predictive model for cholera has been developed, based on ground truth data gathered using these molecular methods and combining them with data obtained by remote sensing, employing satellites. It is clear that microbiology in the twenty-first century has been enhanced by these new tools and paradigms.}, doi = {10.1007/978-3-540-85465-4_1}, author = {Rita R Colwell} } @article {12538, title = {Video-Based Face Recognition Algorithms}, journal = {Handbook of Remote Biometrics}, year = {2009}, month = {2009///}, pages = {193 - 216}, abstract = {Traditional face recognition systems have relied on a gallery of still images for learning and a probe of still images for recognition. While the advantage of using motion information in face videos has been widely recognized, computational models for video-based face recognition have only recently gained attention. This chapter reviews some recent advances in this novel framework. In particular, the utility of videos in enhancing performance of image-based tasks (such as recognition or localization) will be summarized. Subsequently, spatiotemporal video-based face recognition systems based on particle filters, hidden Markov models , and system theoretic approaches will be presented. Further, some useful face databases employable by researchers interested in this field will be described. Finally, some open research issues will be proposed and discussed.}, author = {Chellapa, Rama and Bicego, M. and Turaga,P.} } @book {12535, title = {Video-based Lane Detection using Boosting Principles}, year = {2009}, month = {2009///}, publisher = {Snowbird}, organization = {Snowbird}, abstract = {Autonomous navigation of road vehicles is a challenging problem that has widespread applications in intelligent systems, and robotics. An integral componentof such a system is to understand how the road is structured. Detection of road lane markings assumes importance in this regard, and this problem has been approached with different visual input- based inference algorithms ([1], [2]), besides other sensing modalities such as the GPS sensor and the internal vehicle- state sensors. But the challenge still remains when there is considerable amount of shadows on the road, variations in outdoor lighting conditions of the scene (transition from day to night), among others. To address such issues, we propose a machine learning approach based on Real Adaboost [3], and train linear classifiers for both the appearance and edge cues of the training examplars. Additionally, we incorporate prior knowledge about the relative importance of the training samples by computing their weights using kernel discriminant analysis [4], before learning the classification function through boosting. The regions identified as lane markings are then analyzed for gradient direction consistency before making the final detection decision. We illustrate the effectiveness of our algorithm on challenging daylight and night- time road scenarios. }, author = {Gopalan,R. and Hong, T. and Shneier, M. and Chellapa, Rama} } @article {13107, title = {Visual Tracking by Continuous Density Propagation in Sequential Bayesian Filtering Framework}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {31}, year = {2009}, month = {2009/05//}, pages = {919 - 930}, abstract = {Particle filtering is frequently used for visual tracking problems since it provides a general framework for estimating and propagating probability density functions for nonlinear and non-Gaussian dynamic systems. However, this algorithm is based on a Monte Carlo approach and the cost of sampling and measurement is a problematic issue, especially for high-dimensional problems. We describe an alternative to the classical particle filter in which the underlying density function has an analytic representation for better approximation and effective propagation. The techniques of density interpolation and density approximation are introduced to represent the likelihood and the posterior densities with Gaussian mixtures, where all relevant parameters are automatically determined. The proposed analytic approach is shown to perform more efficiently in sampling in high-dimensional space. We apply the algorithm to real-time tracking problems and demonstrate its performance on real video sequences as well as synthetic examples.}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Computer-Assisted;Pattern Recognition, Computer-Assisted;Subtraction Technique;, Monte Carlo approach;continuous density propagation;density approximation;density interpolation;nonGaussian dynamic systems;nonlinear dynamic systems;particle filtering;probability density functions;sequential Bayesian filtering framework;video sequences;}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2008.134}, author = {Han,Bohyung and Zhu,Ying and Comaniciu, D. and Davis, Larry S.} } @conference {16057, title = {What{\textquoteright}s being said near "Martha"? Exploring name entities in literary text collections}, booktitle = {Visual Analytics Science and Technology, 2009. VAST 2009. IEEE Symposium on}, year = {2009}, month = {2009/10//}, pages = {107 - 114}, abstract = {A common task in literary analysis is to study characters in a novel or collection. Automatic entity extraction, text analysis and effective user interfaces facilitate character analysis. Using our interface, called POSvis, the scholar uses word clouds and self-organizing graphs to review vocabulary, to filter by part of speech, and to explore the network of characters located near characters under review. Further, visualizations show word usages within an analysis window (i.e. a book chapter), which can be compared with a reference window (i.e. the whole book). We describe the interface and report on an early case study with a humanities scholar.}, keywords = {analysis;humanities, analysis;literary, analysis;user, clouds;word, collection;name, entity, entity;part-of-speech, extraction;character, filtering;linguistics;text, filtering;self-organizing, graph;text, interface;vocabulary;word, interfaces;vocabulary;, POSvis;automatic, scholar;literary, text, usage;data, visualisation;information}, doi = {10.1109/VAST.2009.5333248}, author = {Vuillemot,R. and Clement,T. and Plaisant, Catherine and Kumar,A.} } @conference {18926, title = {Within epsilon of optimal play in the cultaptation social learning game}, series = {AAMAS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {1327 - 1328}, publisher = {International Foundation for Autonomous Agents and Multiagent Systems}, organization = {International Foundation for Autonomous Agents and Multiagent Systems}, address = {Richland, SC}, abstract = {Social learning, in which members of a society learn by observing the behavior of others, is an important foundation for human culture, and is observed in many other species as well. It seems natural to assume that social learning evolved due to the inherent superiority of copying others{\textquoteright} success rather than learning on one{\textquoteright}s own via trial-and-error innovation. However, there has also been substantial work questioning this intuition [3, 5, 1, 6, 4]. For example, blindly copying information from others is not useful if the information is wrong---or if it once was right but has since become outdated. Under what conditions does social learning outperform trial-and-error learning, and what kinds of social-learning strategies are likely to perform well?}, isbn = {978-0-9817381-7-8}, url = {http://dl.acm.org/citation.cfm?id=1558109.1558276}, author = {Carr,Ryan and Raboin,Eric and Parker,Austin and Nau, Dana S.} } @article {12561, title = {3D shape-encoded particle filter for object tracking and its application to human body tracking}, journal = {J. Image Video Process.}, volume = {2008}, year = {2008}, month = {2008/01//}, pages = {12:1{\textendash}12:16 - 12:1{\textendash}12:16}, abstract = {We present a nonlinear state estimation approach using particle filters, for tracking objects whose approximate 3D shapes are known. The unnormalized conditional density for the solution to the nonlinear filtering problem leads to the Zakai equation, and is realized by the weights of the particles. The weight of a particle represents its geometric and temporal fit, which is computed bottom-up from the raw image using a shape-encoded filter. The main contribution of the paper is the design of smoothing filters for feature extraction combined with the adoption of unnormalized conditional density weights. The "shape filter" has the overall form of the predicted 2D projection of the 3D model, while the cross-section of the filter is designed to collect the gradient responses along the shape. The 3D-model-based representation is designed to emphasize the changes in 2D object shape due to motion, while de-emphasizing the variations due to lighting and other imaging conditions. We have found that the set of sparse measurements using a relatively small number of particles is able to approximate the high-dimensional state distribution very effectively. As a measure to stabilize the tracking, the amount of random diffusion is effectively adjusted using a Kalman updating of the covariance matrix. For a complex problem of human body tracking, we have successfully employed constraints derived from joint angles and walking motion.}, isbn = {1687-5176}, doi = {10.1155/2008/596989}, url = {http://dx.doi.org/10.1155/2008/596989}, author = {Moon, H. and Chellapa, Rama} } @article {12558, title = {Activity Modeling Using Event Probability Sequences}, journal = {Image Processing, IEEE Transactions on}, volume = {17}, year = {2008}, month = {2008/04//}, pages = {594 - 607}, abstract = {Changes in motion properties of trajectories provide useful cues for modeling and recognizing human activities. We associate an event with significant changes that are localized in time and space, and represent activities as a sequence of such events. The localized nature of events allows for detection of subtle changes or anomalies in activities. In this paper, we present a probabilistic approach for representing events using the hidden Markov model (HMM) framework. Using trained HMMs for activities, an event probability sequence is computed for every motion trajectory in the training set. It reflects the probability of an event occurring at every time instant. Though the parameters of the trained HMMs depend on viewing direction, the event probability sequences are robust to changes in viewing direction. We describe sufficient conditions for the existence of view invariance. The usefulness of the proposed event representation is illustrated using activity recognition and anomaly detection. Experiments using the indoor University of Central Florida human action dataset, the Carnegie Mellon University Credo Intelligence, Inc., Motion Capture dataset, and the outdoor Transportation Security Administration airport tarmac surveillance dataset show encouraging results.}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;Video Recording;, Biological;Models, Carnegie Mellon University;Credo Intelligence, Computer-Assisted;Models, Inc.;Motion Capture dataset;Transportation Security Administration;University Central Florida;airport tarmac surveillance dataset;anomaly detection;event probability sequence;event representation;hidden Markov model;human action dataset;human activity rec, Statistical;Motor Activity;Movement;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2008.916991}, author = {Cuntoor, N.P. and Yegnanarayana,B. and Chellapa, Rama} } @article {12562, title = {Activity representation using 3D shape models}, journal = {J. Image Video Process.}, volume = {2008}, year = {2008}, month = {2008/01//}, pages = {5:1{\textendash}5:16 - 5:1{\textendash}5:16}, abstract = {We present a method for characterizing human activities using 3D deformable shape models. The motion trajectories of points extracted from objects involved in the activity are used to build models for each activity, and these models are used for classification and detection of unusual activities. The deformable models are learnt using the factorization theorem for nonrigid 3D models. We present a theory for characterizing the degree of deformation in the 3D models from a sequence of tracked observations. This degree, termed as deformation index (DI), is used as an input to the 3D model estimation process. We study the special case of ground plane activities in detail because of its importance in video surveillance applications. We present results of our activity modeling approach using videos of both high-resolution single individual activities and ground plane surveillance activities.}, isbn = {1687-5176}, doi = {10.1155/2008/347050}, url = {http://dx.doi.org/10.1155/2008/347050}, author = {Abdelkader,Mohamed F. and Roy-Chowdhury,Amit K. and Chellapa, Rama and Akdemir,Umut} } @conference {14323, title = {Activity sensing in the wild: a field trial of ubifit garden}, booktitle = {Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems}, year = {2008}, month = {2008///}, pages = {1797 - 1806}, author = {Consolvo,S. and McDonald,D.W. and Toscos,T. and Chen,M.Y. and Jon Froehlich and Harrison,B. and Klasnja,P. and LaMarca,A. and LeGrand,L. and Libby,R. and others} } @conference {12111, title = {Adopting Curvilinear Component Analysis to Improve Software Cost Estimation Accuracy. Model, Application Strategy, and an Experimental Verification}, booktitle = {In G. Visaggio (Ed.), 12 th International Conference on Evaluation and Assessment in Software Engineering. BCS eWIC}, year = {2008}, month = {2008///}, abstract = {Cost estimation is a critical issue for software organizations. Good estimates can help us make more informed decisions (controlling and planning software risks), if they are reliable (correct) and valid (stable). In this study, we apply a variable reduction technique (based on auto-associative feed--forward neural networks {\textendash} called Curvilinear component analysis) to log-linear regression functions calibrated with ordinary least squares. Based on a COCOMO 81 data set, we show that Curvilinear component analysis can improve the estimation model accuracy by turning the initial input variables into an equivalent and more compact representation. We show that, the models obtained by applying Curvilinear component analysis are more parsimonious, correct, and reliable.}, author = {Sarcia,Salvatore A. and Cantone,Giovanni and Basili, Victor R.} } @article {15857, title = {Advancing social science research by applying computational linguistics}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {45}, year = {2008}, month = {2008///}, pages = {1 - 12}, author = {Cheng,A.S. and Fleischmann,K.R. and Wang,P. and Oard, Douglas} } @article {12552, title = {Algorithmic and Architectural Optimizations for Computationally Efficient Particle Filtering}, journal = {Image Processing, IEEE Transactions on}, volume = {17}, year = {2008}, month = {2008/05//}, pages = {737 - 748}, abstract = {In this paper, we analyze the computational challenges in implementing particle filtering, especially to video sequences. Particle filtering is a technique used for filtering nonlinear dynamical systems driven by non-Gaussian noise processes. It has found widespread applications in detection, navigation, and tracking problems. Although, in general, particle filtering methods yield improved results, it is difficult to achieve real time performance. In this paper, we analyze the computational drawbacks of traditional particle filtering algorithms, and present a method for implementing the particle filter using the Independent Metropolis Hastings sampler, that is highly amenable to pipelined implementations and parallelization. We analyze the implementations of the proposed algorithm, and, in particular, concentrate on implementations that have minimum processing times. It is shown that the design parameters for the fastest implementation can be chosen by solving a set of convex programs. The proposed computational methodology was verified using a cluster of PCs for the application of visual tracking. We demonstrate a linear speedup of the algorithm using the methodology proposed in the paper.}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Computer-Assisted;Models, Computer-Assisted;Video Recording;, convex program;independent Metropolis Hastings sampler;nonGaussian noise process;nonlinear dynamical system filtering;particle filtering algorithm;pipelined architectural optimization;video sequences;visual tracking;convex programming;image sequences;opti, Statistical;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2008.920760}, author = {Sankaranarayanan,A. C and Srivastava, A. and Chellapa, Rama} } @conference {18658, title = {Analysis of Computer Security Incident Data Using Time Series Models}, year = {2008}, month = {2008/11//}, pages = {77 - 86}, abstract = {Organizations face increasing challenges in addressing and preventing computer and network security incidents. There are financial consequences from security incidents. These include lost time and resources used during recovery, possible theft of personal and/or proprietary information, and reputational damage that may negatively impact stock prices or reduce consumer confidence in a company. Being able to understand and predict trends in computer and network security incidents can aid an organization with resource allocation for prevention of such incidents, as well as evaluation of mitigation strategies. We look at using time series models with a large set of security incident data. We examine appropriateness of the data for modeling and consider needed transformations. Parameter search and model selection criteria are discussed. Then, forecasts from time series models are compared to forecasts from Non-Homogeneous Poisson Process (NHPP) software reliability growth (SRG) models.}, keywords = {Computer networks, computer security incident data, NETWORK SECURITY, resource allocation, security of data, telecommunication security, time series, time series model}, doi = {10.1109/ISSRE.2008.39}, author = {Condon,E. and He,A. and Michel Cukier} } @conference {17559, title = {Approximation Algorithms for Computing Capacity of Wireless Networks with SINR Constraints}, booktitle = {IEEE INFOCOM 2008. The 27th Conference on Computer Communications}, year = {2008}, month = {2008/04/13/18}, pages = {1166 - 1174}, publisher = {IEEE}, organization = {IEEE}, abstract = {A fundamental problem in wireless networks is to estimate its throughput capacity - given a set of wireless nodes, and a set of connections, what is the maximum rate at which data can be sent on these connections. Most of the research in this direction has focused on either random distributions of points, or has assumed simple graph-based models for wireless interference. In this paper, we study capacity estimation problem using the more general Signal to Interference Plus Noise Ratio (SINR) model for interference, on arbitrary wireless networks. The problem becomes much harder in this setting, because of the non-locality of the SINR model. Recent work by Moscibroda et al. (2006) has shown that the throughput in this model can differ from graph based models significantly. We develop polynomial time algorithms to provably approximate the total throughput in this setting.}, keywords = {Algorithm design and analysis, approximation algorithm, Approximation algorithms, approximation theory, Computer networks, Computer science, graph theory, graph-based model, Interference constraints, polynomial time algorithm, Propagation losses, Protocols, radio networks, radiofrequency interference, signal to interference plus noise ratio, Signal to noise ratio, Throughput, wireless interference, wireless network, Wireless networks}, isbn = {978-1-4244-2025-4}, doi = {10.1109/INFOCOM.2008.172}, author = {Chafekar,D. and Kumart,V. S.A and Marathe,M. V and Parthasarathy,S. and Srinivasan, Aravind} } @inbook {15716, title = {Arabic/English Multi-document Summarization with CLASSYThe Past and the Future}, booktitle = {Computational Linguistics and Intelligent Text Processing, Lecture Notes in Computer Science Volume 4919Computational Linguistics and Intelligent Text Processing, Lecture Notes in Computer Science Volume 4919}, year = {2008}, month = {2008///}, pages = {568 - 581}, publisher = {Springer Berlin}, organization = {Springer Berlin}, url = {http://dx.doi.org/10.1007/978-3-540-78135-6_49http://dx.doi.org/10.1007/978-3-540-78135-6_49}, author = {Schlesinger,Judith D. and O{\textquoteright}Leary, Dianne P. and Conroy,John M.} } @article {12112, title = {An assessment of systems and software engineering scholars and institutions (2001{\textendash}2005)}, journal = {Journal of Systems and Software}, volume = {81}, year = {2008}, month = {2008/06//}, pages = {1059 - 1062}, abstract = {This paper presents the findings of a five-year study of the top scholars and institutions in the systems and software engineering field, as measured by the quantity of papers published in the journals of the field in 2001{\textendash}2005. The top scholar is Magne J{\o}rgensen of Simula Research Laboratory, Norway, and the top institution is Korea Advanced Institute of Science and Technology, Korea.This paper is part of an ongoing study, conducted annually, that identifies the top 15 scholars and institutions in the most recent five-year period. }, keywords = {Research publications, Systems and software engineering, Top institutions, Top scholars}, isbn = {0164-1212}, doi = {10.1016/j.jss.2007.09.018}, url = {http://www.sciencedirect.com/science/article/pii/S0164121207002300}, author = {Wong,W. Eric and Tse,T.H. and Glass,Robert L. and Basili, Victor R. and Chen,T.Y.} } @article {12905, title = {Biofilms in water, its role and impact in human disease transmission}, journal = {Current Opinion in Biotechnology}, volume = {19}, year = {2008}, month = {2008/06//}, pages = {244 - 247}, abstract = {Understanding the mechanism of biofilm formation is the first step in determining its function and, thereby, its impact and role in the environment. Extensive studies accomplished during the past few years have elucidated the genetics and biochemistry of biofilm formation. Cell-to-cell communication, that is, quorum sensing, is a key factor in the initiation of biofilm. Occurrence of viable but nonculturable bacteria, including Vibrio cholerae in biofilms has been reported and most likely such cells were overlooked previously because appropriate methods of detection were not employed. For this reason discovery and investigation of this important bacterial ecological niche in the environment were impeded.}, isbn = {0958-1669}, doi = {10.1016/j.copbio.2008.04.005}, url = {http://www.sciencedirect.com/science/article/pii/S0958166908000505}, author = {Huq,Anwar and Whitehouse,Chris A. and Grim,Christopher J. and Alam,Munirul and Rita R Colwell} } @inbook {19630, title = {Black-Box Construction of a Non-malleable Encryption Scheme from Any Semantically Secure One}, booktitle = {Theory of Cryptography}, series = {Lecture Notes in Computer Science}, year = {2008}, month = {2008/01/01/}, pages = {427 - 444}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We show how to transform any semantically secure encryption scheme into a non-malleable one, with a black-box construction that achieves a quasi-linear blow-up in the size of the ciphertext. This improves upon the previous non-black-box construction of Pass, Shelat and Vaikuntanathan (Crypto {\textquoteright}06). Our construction also extends readily to guarantee non-malleability under a bounded-CCA2 attack, thereby simultaneously improving on both results in the work of Cramer et al. (Asiacrypt {\textquoteright}07). Our construction departs from the oft-used paradigm of re-encrypting the same message with different keys and then proving consistency of encryptions; instead, we encrypt an encoding of the message with certain locally testable and self-correcting properties. We exploit the fact that low-degree polynomials are simultaneously good error-correcting codes and a secret-sharing scheme.}, keywords = {Algorithm Analysis and Problem Complexity, black-box constructions, computers and society, Data Encryption, Discrete Mathematics in Computer Science, Management of Computing and Information Systems, non-malleability, public-key encryption, semantic security, Systems and Data Security}, isbn = {978-3-540-78523-1, 978-3-540-78524-8}, url = {http://link.springer.com/chapter/10.1007/978-3-540-78524-8_24}, author = {Choi, Seung Geol and Dana Dachman-Soled and Malkin, Tal and Wee, Hoeteck}, editor = {Canetti, Ran} } @conference {13275, title = {Cancellation of critical points in 2D and 3D Morse and Morse-Smale complexes}, booktitle = {Discrete Geometry for Computer Imagery}, year = {2008}, month = {2008///}, pages = {117 - 128}, abstract = {Morse theory studies the relationship between the topology of a manifold M and the critical points of a scalar function f defined on M. The Morse-Smale complex associated with f induces a subdivision of M into regions of uniform gradient flow, and represents the topology of M in a compact way. Function f can be simplified by cancelling its critical points in pairs, thus simplifying the topological representation of M, provided by the Morse-Smale complex. Here, we investigate the effect of the cancellation of critical points of f in Morse-Smale complexes in two and three dimensions by showing how the change of connectivity of a Morse-Smale complex induced by a cancellation can be interpreted and understood in a more intuitive and straightforward way as a change of connectivity in the corresponding ascending and descending Morse complexes. We consider a discrete counterpart of the Morse-Smale complex, called a quasi-Morse complex, and we present a compact graph-based representation of such complex and of its associated discrete Morse complexes, showing also how such representation is affected by a cancellation.}, doi = {10.1007/978-3-540-79126-3_12}, author = {{\v C}omi{\'c},L. and De Floriani, Leila} } @conference {17570, title = {Capacity of Asynchronous Random-Access Scheduling in Wireless Networks}, booktitle = {IEEE INFOCOM 2008. The 27th Conference on Computer Communications}, year = {2008}, month = {2008/04/13/18}, pages = {1148 - 1156}, publisher = {IEEE}, organization = {IEEE}, abstract = {We study the throughput capacity of wireless networks which employ (asynchronous) random-access scheduling as opposed to deterministic scheduling. The central question we answer is: how should we set the channel-access probability for each link in the network so that the network operates close to its optimal throughput capacity? We design simple and distributed channel-access strategies for random-access networks which are provably competitive with respect to the optimal scheduling strategy, which is deterministic, centralized, and computationally infeasible. We show that the competitiveness of our strategies are nearly the best achievable via random-access scheduling, thus establishing fundamental limits on the performance of random- access. A notable outcome of our work is that random access compares well with deterministic scheduling when link transmission durations differ by small factors, and much worse otherwise. The distinguishing aspects of our work include modeling and rigorous analysis of asynchronous communication, asymmetry in link transmission durations, and hidden terminals under arbitrary link-conflict based wireless interference models.}, keywords = {asynchronous random-access scheduling, channel access probability, Computer networks, Computer science, Educational institutions, Interference, Optimal scheduling, Peer to peer computing, probability, Processor scheduling, radio link, radio links, radio networks, Routing, scheduling, Throughput, throughput capacity, wireless channels, Wireless networks}, isbn = {978-1-4244-2025-4}, doi = {10.1109/INFOCOM.2008.170}, author = {Chafekar,D. and Levin,D. and Kumar,V. S.A and Marathe,M. V and Parthasarathy,S. and Srinivasan, Aravind} } @conference {18681, title = {On the Comparison of Network Attack Datasets: An Empirical Analysis}, year = {2008}, month = {2008/12//}, pages = {39 - 48}, abstract = {Network malicious activity can be collected and reported by various sources using different attack detection solutions. The granularity of these solutions provides either very detailed information (intrusion detection systems, honeypots) or high-level trends (CAIDA, SANS). The problem for network security operators is often to select the sources of information to better protect their network. How much information from these sources is redundant and how much is unique? The goal of this paper is to show empirically that while some global attack events can be correlated across various sensors, the majority of incoming malicious activity has local specificities. This study presents a comparative analysis of four different attack datasets offering three different levels of granularity: 1) two high interaction honeynets deployed at two different locations (i.e., a corporate and an academic environment); 2) ATLAS which is a distributed network telescope from Arbor; and 3) Internet Protecttrade which is a global alerting service from AT amp;T.}, keywords = {ATLAS, distributed network telescope, Internet, intrusion detection systems, network attack datasets, network malicious activity, network security operators, security of data}, doi = {10.1109/HASE.2008.50}, author = {Berthier,R. and Korman,D. and Michel Cukier and Hiltunen,M. and Vesonder,G. and Sheleheda,D.} } @article {12898, title = {The Complete Genome Sequence of Thermococcus Onnurineus NA1 Reveals a Mixed Heterotrophic and Carboxydotrophic Metabolism}, journal = {Journal of BacteriologyJ. Bacteriol.}, volume = {190}, year = {2008}, month = {2008/11/15/}, pages = {7491 - 7499}, abstract = {Members of the genus Thermococcus, sulfur-reducing hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent systems and are considered to play a significant role in the microbial consortia. We present the complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of genomic analysis, T. onnurineus NA1 possesses the metabolic pathways for organotrophic growth on peptides, amino acids, or sugars. More interesting was the discovery that the genome encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation of CO to CO2, thereby providing a mechanistic basis for growth with CO as a substrate. This lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy supply for T. onnurineus NA1 potentially allowing it to cope with nutrient stress in the surrounding of hydrothermal vents, providing the first genomic evidence for the carboxydotrophy in Thermococcus.}, isbn = {0021-9193, 1098-5530}, doi = {10.1128/JB.00746-08}, url = {http://jb.asm.org/content/190/22/7491}, author = {Lee,Hyun Sook and Kang,Sung Gyun and Bae,Seung Seob and Lim,Jae Kyu and Cho,Yona and Kim,Yun Jae and Jeon,Jeong Ho and Cha,Sun-Shin and Kwon,Kae Kyoung and Kim,Hyung-Tae and Park,Cheol-Joo and Lee,Hee-Wook and Kim,Seung Il and Jongsik Chun and Rita R Colwell and Kim,Sang-Jin and Lee,Jung-Hyun} } @conference {12547, title = {Compressed sensing for multi-view tracking and 3-D voxel reconstruction}, booktitle = {Image Processing, 2008. ICIP 2008. 15th IEEE International Conference on}, year = {2008}, month = {2008/10//}, pages = {221 - 224}, abstract = {Compressed sensing (CS) suggests that a signal, sparse in some basis, can be recovered from a small number of random projections. In this paper, we apply the CS theory on sparse background-subtracted silhouettes and show the usefulness of such an approach in various multi-view estimation problems. The sparsity of the silhouette images corresponds to sparsity of object parameters (location, volume etc.) in the scene. We use random projections (compressed measurements) of the silhouette images for directly recovering object parameters in the scene coordinates. To keep the computational requirements of this recovery procedure reasonable, we tessellate the scene into a bunch of non-overlapping lines and perform estimation on each of these lines. Our method is scalable in the number of cameras and utilizes very few measurements for transmission among cameras. We illustrate the usefulness of our approach for multi-view tracking and 3-D voxel reconstruction problems.}, keywords = {3D, background-subtracted, coding;, Estimation, image, problems;multi-view, projections;silhouette, reconstruction;CS, reconstruction;video, sensing;multi-view, silhouettes;image, sparsity;sparse, theory;compressed, tracking;random, voxel}, doi = {10.1109/ICIP.2008.4711731}, author = {Reddy, D. and Sankaranarayanan,A. C and Cevher, V. and Chellapa, Rama} } @article {12569, title = {Compressive sensing for background subtraction}, journal = {Computer Vision{\textendash}ECCV 2008}, year = {2008}, month = {2008///}, pages = {155 - 168}, abstract = {Compressive sensing (CS) is an emerging field that provides a framework for image recovery using sub-Nyquist sampling rates. The CS theory shows that a signal can be reconstructed from a small set of random projections, provided that the signal is sparse in some basis, e.g., wavelets. In this paper, we describe a method to directly recover background subtracted images using CS and discuss its applications in some communication constrained multi-camera computer vision problems. We show how to apply the CS theory to recover object silhouettes (binary background subtracted images) when the objects of interest occupy a small portion of the camera view, i.e., when they are sparse in the spatial domain. We cast the background subtraction as a sparse approximation problem and provide different solutions based on convex optimization and total variation. In our method, as opposed to learning the background, we learn and adapt a low dimensional compressed representation of it, which is sufficient to determine spatial innovations; object silhouettes are then estimated directly using the compressive samples without any auxiliary image reconstruction. We also discuss simultaneous appearance recovery of the objects using compressive measurements. In this case, we show that it may be necessary to reconstruct one auxiliary image. To demonstrate the performance of the proposed algorithm, we provide results on data captured using a compressive single-pixel camera. We also illustrate that our approach is suitable for image coding in communication constrained problems by using data captured by multiple conventional cameras to provide 2D tracking and 3D shape reconstruction results with compressive measurements.}, author = {Cevher, V. and Sankaranarayanan, A. and Duarte, M. and Reddy, D. and Baraniuk, R. and Chellapa, Rama} } @conference {12555, title = {Compressive wireless arrays for bearing estimation}, booktitle = {Acoustics, Speech and Signal Processing, 2008. ICASSP 2008. IEEE International Conference on}, year = {2008}, month = {2008/04/31/4}, pages = {2497 - 2500}, abstract = {Joint processing of sensor array outputs improves the performance of parameter estimation and hypothesis testing problems beyond the sum of the individual sensor processing results. When the sensors have high data sampling rates, arrays are tethered, creating a disadvantage for their deployment and also limiting their aperture size. In this paper, we develop the signal processing algorithms for randomly deployable wireless sensor arrays that are severely constrained in communication bandwidth. We focus on the acoustic bearing estimation problem and show that when the target bearings are modeled as a sparse vector in the angle space, low dimensional random projections of the microphone signals can be used to determine multiple source bearings by solving an l 1-norm minimization problem. Field data results are shown where only 10 bits of information is passed from each microphone to estimate multiple target bearings.}, keywords = {acoustic, algorithms;sparse, arrays;acoustic, arrays;hypothesis, bandwidth;compressive, bearing, Estimation, estimation;signal, estimation;sparse, matrices;vectors;wireless, minimization, networks;, problem;communication, problem;microphone, problems;joint, PROCESSING, processing;array, processing;direction-of-arrival, processing;l1-norm, sensor, signal, signals;parameter, Testing, vector;wireless, wireless}, doi = {10.1109/ICASSP.2008.4518155}, author = {Cevher, V. and Gurbuz, A.C. and McClellan, J.H. and Chellapa, Rama} } @article {12567, title = {Computational Vision Approaches for Event Modeling}, journal = {Understanding Events}, volume = {1}, year = {2008}, month = {2008///}, pages = {473 - 522}, abstract = {Event modeling systems provide a semantic interpretation of sequences of pixels that are captured by a video camera. The design of a practical system has to take into account the following three main factors: low-level preprocessing limitations, computational and storage complexity of the event model, and user interaction. The hidden Markov model (HMM) and its variants have been widely used to model both speech and video signals. Computational efficiency of the Baum-Welch and the Viterbi algorithms has been a leading reason for the popularity of the HMM. Since the objective is to detect events in video sequences that are meaningful to humans, one might want to provide space in the design loop for a user who can specify events of interest. This chapter explores this using semantic approaches that not only use features extracted from raw video streams but also incorporate metadata and ontologies of activities. It presents three approaches for applications such as event recognition: anomaly detection, temporal segmentation, and ontology evaluation. The three approaches discussed are statistical methods based on HMMs, formal grammars, and ontologies. The effectiveness of these approaches is illustrated using video sequences captured both indoors and outdoors: the indoor UCF human action dataset, the TSA airport tarmac surveillance dataset, and the bank monitoring dataset.}, author = {Chellapa, Rama and Cuntoor, N.P. and Joo, S.W. and V.S. Subrahmanian and Turaga,P.} } @article {12549, title = {A Constrained Probabilistic Petri Net Framework for Human Activity Detection in Video}, journal = {Multimedia, IEEE Transactions on}, volume = {10}, year = {2008}, month = {2008/10//}, pages = {982 - 996}, abstract = {Recognition of human activities in restricted settings such as airports, parking lots and banks is of significant interest in security and automated surveillance systems. In such settings, data is usually in the form of surveillance videos with wide variation in quality and granularity. Interpretation and identification of human activities requires an activity model that a) is rich enough to handle complex multi-agent interactions, b) is robust to uncertainty in low-level processing and c) can handle ambiguities in the unfolding of activities. We present a computational framework for human activity representation based on Petri nets. We propose an extension-Probabilistic Petri Nets (PPN)-and show how this model is well suited to address each of the above requirements in a wide variety of settings. We then focus on answering two types of questions: (i) what are the minimal sub-videos in which a given activity is identified with a probability above a certain threshold and (ii) for a given video, which activity from a given set occurred with the highest probability? We provide the PPN-MPS algorithm for the first problem, as well as two different algorithms (naive PPN-MPA and PPN-MPA) to solve the second. Our experimental results on a dataset consisting of bank surveillance videos and an unconstrained TSA tarmac surveillance dataset show that our algorithms are both fast and provide high quality results.}, keywords = {activity, dataset;automated, detection;human, interactions;security, net;human, nets;image, Petri, probabilistic, processing;multiagent, processing;video, representation;low-level, representation;video, signal, Surveillance, surveillance;, systems;constrained, systems;surveillance, tarmac, TSA, videos;Petri}, isbn = {1520-9210}, doi = {10.1109/TMM.2008.2001369}, author = {Albanese, M. and Chellapa, Rama and Moscato, V. and Picariello, A. and V.S. Subrahmanian and Turaga,P. and Udrea,O.} } @conference {13123, title = {Context and observation driven latent variable model for human pose estimation}, booktitle = {Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on}, year = {2008}, month = {2008/06//}, pages = {1 - 8}, abstract = {Current approaches to pose estimation and tracking can be classified into two categories: generative and discriminative. While generative approaches can accurately determine human pose from image observations, they are computationally expensive due to search in the high dimensional human pose space. On the other hand, discriminative approaches do not generalize well, but are computationally efficient. We present a hybrid model that combines the strengths of the two in an integrated learning and inference framework. We extend the Gaussian process latent variable model (GPLVM) to include an embedding from observation space (the space of image features) to the latent space. GPLVM is a generative model, but the inclusion of this mapping provides a discriminative component, making the model observation driven. Observation Driven GPLVM (OD-GPLVM) not only provides a faster inference approach, but also more accurate estimates (compared to GPLVM) in cases where dynamics are not sufficient for the initialization of search in the latent space. We also extend OD-GPLVM to learn and estimate poses from parameterized actions/gestures. Parameterized gestures are actions which exhibit large systematic variation in joint angle space for different instances due to difference in contextual variables. For example, the joint angles in a forehand tennis shot are function of the height of the ball (Figure 2). We learn these systematic variations as a function of the contextual variables. We then present an approach to use information from scene/objects to provide context for human pose estimation for such parameterized actions.}, keywords = {estimation;, estimation;image, Gaussian, gestures;pose, latent, learning;parameterized, model;human, observations;integrated, pose, process, processes;gesture, processing;pose, recognition;image, tracking;Gaussian, variable}, doi = {10.1109/CVPR.2008.4587511}, author = {Gupta,A. and Chen,T. and Chen,F. and Kimber,D. and Davis, Larry S.} } @article {12906, title = {Covariability of Vibrio Cholerae Microdiversity and Environmental Parameters}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {74}, year = {2008}, month = {2008/05/01/}, pages = {2915 - 2920}, abstract = {Fine-scale diversity of natural bacterial assemblages has been attributed to neutral radiation because correspondence between bacterial phylogenetic signals in the natural environment and environmental parameters had not been detected. Evidence that such correspondence occurs is provided for Vibrio cholerae, establishing a critical role for environmental parameters in bacterial diversity.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.02139-07}, url = {http://aem.asm.org/content/74/9/2915}, author = {Zo,Young-Gun and Chokesajjawatee,Nipa and Arakawa,Eiji and Watanabe,Haruo and Huq,Anwar and Rita R Colwell} } @conference {18692, title = {The Deployment of a Darknet on an Organization-Wide Network: An Empirical Analysis}, year = {2008}, month = {2008/12//}, pages = {59 - 68}, abstract = {Darknet sensors have the interesting property of collecting only suspicious traffic, including misconfiguration, backscatter and malicious traffic. The type of traffic collected highly depends on two parameters: the size and the location of the darknet sensor. The goals of this paper are to study empirically the relationship between these two parameters and to try to increase the volume of attackers detected by a given darknet sensor. Our empirical results reveal that on average, on a daily basis, 485 distinct external source IP addresses perform a TCP scan on one of the two /16 networks of our organizationpsilas network. Moreover, a given darknet sensor of 77 IP addresses deployed in the same /16 network collects on average attack traffic from 26\% of these attackers.}, keywords = {attack traffic, backscatter, darknet sensors, external source IP address, malicious traffic, organization network, organization-wide network, TCP scan, telecommunication congestion control, transmission control protocol, Transport protocols}, doi = {10.1109/HASE.2008.54}, author = {Berthier,R. and Michel Cukier} } @article {12901, title = {Determination of Clonality and Relatedness of Vibrio Cholerae Isolates by Genomic Fingerprinting, Using Long-Range Repetitive Element Sequence-Based PCR}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {74}, year = {2008}, month = {2008/09/01/}, pages = {5392 - 5401}, abstract = {A high-throughput method which is applicable for rapid screening, identification, and delineation of isolates of Vibrio cholerae, sensitive to genome variation, and capable of providing phylogenetic inferences enhances environmental monitoring of this bacterium. We have developed and optimized a method for genomic fingerprinting of V. cholerae based on long-range PCR. The method uses a primer set directed to enterobacterial repetitive intergenic consensus sequences, a high-fidelity DNA polymerase, and analysis via conventional agarose gel electrophoresis. Long (\~{}10 kb), highly reproducible amplicons were generated from V. cholerae isolates, including those from different geographical locations and historical strains isolated during the period 1931-2000. The amplicons yielded reduced variability in their densitometric band patterns to <=10\% and clonal distinction at <90\% similarity. Rapid band-matching analysis was accomplished for fingerprints with >=90\% similarity, discriminating O serotypes and biotypes (classical versus El Tor) as well as pathogenic and nonpathogenic strains. Compared to genome similarity measured by DNA-DNA hybridization, the results showed good correlation (r = 0.7; P < 0.001), with five times less measurement error and without bias. The method permits both phylogenetic inference and clonal differentiation of individual V. cholerae strains, enables robust, high-throughput analysis, and does not require specialized equipment to perform. With access to a curated public database furnished with appropriate analytical software applications, the method should prove useful in large-scale multilaboratory surveys, especially those designed to detect specific pathogens in the natural environment.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.00151-08}, url = {http://aem.asm.org/content/74/17/5392}, author = {Chokesajjawatee,Nipa and Zo,Young-Gun and Rita R Colwell} } @conference {18565, title = {Distinguishing persistent failures from transient losses}, booktitle = {Proceedings of the 2008 ACM CoNEXT Conference}, series = {CoNEXT {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {50:1{\textendash}50:2 - 50:1{\textendash}50:2}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Network tomography is a promising technique to identify the location of of IP faults. The goal of tomography is to infer the status of network internal characteristics based on end-to-end observations. In particular, binary tomography identifies the set of failed links from end-to-end path meausrments. Upon detecting the failure of one or more of the monitored paths, a monitor sends its measurements to a central coordinator. The coordinator then runs the binary tomography algorithm, which takes as input the topology of the network and the status (i.e., up or down) of all monitored paths and finds the minimum set of links that explain the observations.}, isbn = {978-1-60558-210-8}, doi = {10.1145/1544012.1544062}, url = {http://doi.acm.org/10.1145/1544012.1544062}, author = {Cunha,{\'I}talo and Teixeira,Renata and Feamster, Nick and Diot,Christophe} } @article {12904, title = {Dual role colonization factors connecting Vibrio cholerae{\textquoteright}s lifestyles in human and aquatic environments open new perspectives for combating infectious diseases}, journal = {Current Opinion in Biotechnology}, volume = {19}, year = {2008}, month = {2008/06//}, pages = {254 - 259}, abstract = {Vibrio cholerae exhibits two distinctive lifestyles, one inside the milieu of the human intestine and the other in the aquatic environment. Recently, the existence of V. cholerae ligands involved in colonization of both human intestine and environmental chitin surfaces via the same binding specificity has been shown. Such molecules, here named {\textquoteleft}dual role colonization factors (DRCFs){\textquoteright}, are example of a tight connection between the two V. cholerae{\textquoteright}s lifestyles. It is suggested that DRCFs and, more generally, bacterial factors and pathways having roles in pathogenesis and in the out of the human body life may be promising targets for development of novel prophylactic or therapeutic interventions that may also affect V. cholerae fitness in its environmental reservoirs.}, isbn = {0958-1669}, doi = {10.1016/j.copbio.2008.04.002}, url = {http://www.sciencedirect.com/science/article/pii/S0958166908000426}, author = {Vezzulli,Luigi and Guzm{\'a}n,Carlos A and Rita R Colwell and Pruzzo,Carla} } @article {18205, title = {Dynamic Resource Allocation for Robust Distributed Multi-Point Video Conferencing}, journal = {Multimedia, IEEE Transactions on}, volume = {10}, year = {2008}, month = {2008/08//}, pages = {910 - 925}, abstract = {This paper proposes a distributed multi-point video conferencing system over packet erasure channels, where the aggregation of multiple video streams and resource allocation are performed in a distributed manner. Video stream combiners, which are located in different geographical areas and serve as portals for conferees, aggregate incoming streams supplied by local users with other streams aggregated from nearby video stream combiners. A packet-division multiple-access (PDMA)-based error protection scheme is proposed to be performed at each video stream combiner to minimize the maximal expected video distortion among aggregated streams. The proposed error protection scheme for multi-stream aggregation also supports user preference. In order to deliver video streams to end users with different preferred quality, a consensus algorithm is proposed to adaptively perform resource allocation based on user preference. Simulation results show that the proposed multi-stream aggregation and error protection scheme has significant gains over traditional multi-stream error protection schemes for a multi-point video conferencing system.}, keywords = {allocation;error, channels;packet-division, communication;, conferencing, conferencing;multi-access, distributed, dynamic, erasure, error, multiple-access-based, multipoint, Protection, resource, scheme;multi-point, scheme;robust, schemes;packet, streams;multistream, system;multiple, systems;teleconferencing;video, video}, isbn = {1520-9210}, doi = {10.1109/TMM.2008.922846}, author = {Chen,Meng and Su,Guan-Ming and M. Wu} } @inbook {19607, title = {Effective Visualization of File System Access-Control}, booktitle = {Visualization for Computer Security}, series = {Lecture Notes in Computer Science}, year = {2008}, month = {2008/01/01/}, pages = {18 - 25}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {In this paper, we present a visual representation of access control permissions in a standard hierarchical file system. Our visualization of file permissions leverages treemaps, a popular graphical representation of hierarchical data. In particular, we present a visualization of access control for the NTFS file system that can help a non-expert user understand and manipulate file system permissions in a simple and effective way. While our examples are based on NTFS, our approach can be used for many other hierarchical file systems as well.}, keywords = {Computer Communication Networks, Computer Imaging, Vision, Pattern Recognition and Graphics, data mining and knowledge discovery, Data Structures, Cryptology and Information Theory, Visualization}, isbn = {978-3-540-85931-4, 978-3-540-85933-8}, url = {http://link.springer.com/chapter/10.1007/978-3-540-85933-8_2}, author = {Heitzmann, Alexander and Palazzi, Bernardo and Charalampos Papamanthou and Tamassia, Roberto}, editor = {Goodall, John R. and Conti, Gregory and Ma, Kwan-Liu} } @conference {15648, title = {Embedding and similarity search for point sets under translation}, booktitle = {Proceedings of the twenty-fourth annual symposium on Computational geometry}, series = {SCG {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {320 - 327}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Pattern matching in point sets is a well studied problem with numerous applications. We assume that the point sets may contain outliers (missing or spurious points) and are subject to an unknown translation. We define the distance between any two point sets to be the minimum size of their symmetric difference over all translations of one set relative to the other. We consider the problem in the context of similarity search. We assume that a large database of point sets is to be preprocessed so that given any query point set, the closest matches in the database can be computed efficiently. Our approach is based on showing that there is a randomized algorithm that computes a translation-invariant embedding of any point set of size at most n into the L_1 metric, so that with high probability, distances are subject to a distortion that is O(log2 n).}, keywords = {EMBEDDING, point pattern matching, randomized algorithms, Similarity Search}, isbn = {978-1-60558-071-5}, doi = {10.1145/1377676.1377731}, url = {http://doi.acm.org/10.1145/1377676.1377731}, author = {Cho,Minkyoung and Mount, Dave} } @article {16063, title = {Enhancing In-Car Navigation Systems with Personal Experience}, journal = {Transportation Research Record: Journal of the Transportation Research Board}, volume = {2064}, year = {2008}, month = {2008/12/01/}, pages = {33 - 42}, abstract = {Computers are extremely powerful for data processing but less adept at handling problems that involve subjective reasoning. People, on the other hand, are good at such tasks. A framework is presented for adding subjective human experience to in-car navigation systems. People often rely on personal experience when planning trips, choosing the route that is fastest, prettiest, or recommended by a friend. A set of methods was developed to help people record personal driving history, add textual annotations describing subjective experiences, and share data with friends and family or even the broader community. Users can then learn from personal data or harness the multiplicity of individual experiences to enjoy new routes. This approach can be used in conjunction with traditional in-car navigation systems.}, doi = {10.3141/2064-06}, url = {http://dx.doi.org/10.3141/2064-06}, author = {Bederson, Benjamin B. and Clamage,Aaron and Plaisant, Catherine} } @article {12913, title = {Environmental signatures associated with cholera epidemics}, journal = {Proceedings of the National Academy of Sciences}, volume = {105}, year = {2008}, month = {2008///}, pages = {17676 - 17676}, abstract = {The causative agent of cholera, Vibrio cholerae, has been shown to be autochthonous to riverine, estuarine, and coastal waters along with its host, the copepod, a significant member of the zooplankton community. Temperature, salinity, rainfall and plankton have proven to be important factors in the ecology of V. cholerae, influencing the transmission of the disease in those regions of the world where the human population relies on untreated water as a source of drinking water. In this study, the pattern of cholera outbreaks during 1998{\textendash}2006 in Kolkata, India, and Matlab, Bangladesh, and the earth observation data were analyzed with the objective of developing a prediction model for cholera. Satellite sensors were used to measure chlorophyll a concentration (CHL) and sea surface temperature (SST). In addition, rainfall data were obtained from both satellite and in situ gauge measurements. From the analyses, a statistically significant relationship between the time series for cholera in Kolkata, India, and CHL and rainfall anomalies was determined. A statistically significant one month lag was observed between CHL anomaly and number of cholera cases in Matlab, Bangladesh. From the results of the study, it is concluded that ocean and climate patterns are useful predictors of cholera epidemics, with the dynamics of endemic cholera being related to climate and/or changes in the aquatic ecosystem. When the ecology of V. cholerae is considered in predictive models, a robust early warning system for cholera in endemic regions of the world can be developed for public health planning and decision making.ecology epidemiology microbiology remote sensing }, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0809654105}, url = {http://www.pnas.org/content/105/46/17676}, author = {Constantin de Magny,G. and Murtugudde,R. and Sapiano,M. R. P. and Nizam,A. and Brown,C. W. and Busalacchi,A. J. and Yunus,M. and Nair,G. B. and Gil,A. I. and Lanata,C. F. and Rita R Colwell} } @article {12908, title = {Environmental Vibrio spp., isolated in Mozambique, contain a polymorphic group of integrative conjugative elements and class 1 integrons}, journal = {FEMS Microbiology Ecology}, volume = {64}, year = {2008}, month = {2008/04/01/}, pages = {45 - 54}, abstract = {Circulation of mobile genetic elements linked to drug resistance spread was studied in Vibrio strains isolated from surface urban water (river and sea) and shellfish samples in 2002{\textendash}2003 in Maputo, Mozambique. Class 1 integrons and integrating conjugative elements (ICE) were investigated by PCR and mating experiments in strains of major health interest: 10 Vibrio cholerae, six Vibrio parahaemolyticus, two Vibrio alginolyticus and one Vibrio fluvialis. Resistance to at least two antibiotics (predominantly β-lactams) was detected in all the strains, with additional resistances to sulfamethoxazole, spectinomycin, streptomycin and/or trimethoprim. Class 1 integrons contributed partially to the expression of drug resistance and were found in five isolates: four V. cholerae (blaP1 cassette, one strain also contained the dfrA15 cassette) and one V. alginolyticus (aadA2 cassette). ICEs, apparently devoid of resistance genes, were found in eight V. cholerae, three V. parahaemolyticus and one V. fluvialis isolates. A wide variability was observed by molecular characterization of ICEs. Five ICEs were included in the SXT/R391 family and seven ICEs were not classified. Our results indicate that the SXT/R391 family and related ICEs comprise a large class of polymorphic genetic elements widely circulating in environmental Vibrio strains in Africa, beside those evidently linked to drug resistance in clinical isolates.}, keywords = {ICE, integron, Mozambique, Vibrio}, isbn = {1574-6941}, doi = {10.1111/j.1574-6941.2008.00455.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6941.2008.00455.x/full}, author = {Taviani,Elisa and Ceccarelli,Daniela and Lazaro,Nivalda and Bani,Stefania and Cappuccinelli,Piero and Rita R Colwell and Colombo,Mauro M.} } @article {12971, title = {Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming with an Application to Phylogenetic Analysis of Gene Expression}, volume = {1142}, year = {2008}, month = {2008///}, institution = {Department of Statistics, University of Wisconsin}, abstract = {We present a novel method for estimating tree-structured covariance matrices directly fromobserved continuous data. A representation of these classes of matrices as linear combinations of rank-one matrices indicating object partitions is used to formulate estimation as instances of well-studied numerical optimization problems. In particular, we present estimation based on projection where the covariance estimate is the nearest tree-structured covariance matrix to an observed sample covariance matrix. The problem is posed as a linear or quadratic mixed-integer program (MIP) where a setting of the integer variables in the MIP specifies a set of tree topologies of the structured covariance matrix. We solve these problems to optimality using efficient and robust existing MIP solvers. We also show that the least squares distance method of Fitch and Margoliash (1967) can be formulated as a quadratic MIP and thus solved exactly using existing, robust branch-and-bound MIP solvers. Our motivation for this method is the discovery of phylogenetic structure directly from gene expression data. Recent studies have adapted traditional phylogenetic comparative anal- ysis methods to expression data. Typically, these methods first estimate a phylogenetic tree from genomic sequence data and subsequently analyze expression data. A covariance matrix constructed from the sequence-derived tree is used to correct for the lack of independence in phy- logenetically related taxa. However, recent results have shown that the hierarchical structure of sequence-derived tree estimates are highly sensitive to the genomic region chosen to build them. To circumvent this difficulty, we propose a stable method for deriving tree-structured covariance matrices directly from gene expression as an exploratory step that can guide investigators in their modelling choices for these types of comparative analysis. We present a case study in phylogenetic analysis of expression in yeast gene families. Our method is able to corroborate the presence of phylogenetic structure in the response of expression in a subset of the gene families under particular experimental conditions. Additionally, when used in conjunction with transcription factor occupancy data, our methods show that alternative modelling choices should be considered when creating sequence-derived trees for this comparative analysis. }, author = {Corrada Bravo, Hector and Eng,K. H and Keles,S. and Wahba,G. and Wright,S.} } @article {16066, title = {Evaluating Visual Analytics at the 2007 VAST Symposium Contest}, journal = {Computer Graphics and Applications, IEEE}, volume = {28}, year = {2008}, month = {2008/04//march}, pages = {12 - 21}, abstract = {In this article, we report on the contest{\textquoteright}s data set and tasks, the judging criteria, the winning tools, and the overall lessons learned in the competition. We believe that by organizing these contests, we{\textquoteright}re creating useful resources for researchers and are beginning to understand how to better evaluate VA tools. Competitions encourage the community to work on difficult problems, improve their tools, and develop baselines for others to build or improve upon. We continue to evolve a collection of data sets, scenarios, and evaluation methodologies that reflect the richness of the many VA tasks and applications.}, keywords = {2007, analytics, analytics;data, and, Contest;Visual, Science, Symposium, Technology;data, VAST, visualisation;, visualization;visual}, isbn = {0272-1716}, doi = {10.1109/MCG.2008.27}, author = {Plaisant, Catherine and Grinstein,G. and Scholtz,J. and Whiting,M. and O{\textquoteright}Connell,T. and Laskowski,S. and Chien,L. and Tat,A. and Wright,W. and Gorg,C. and Zhicheng Liu and Parekh,N. and Singhal,K. and Stasko,J.} } @article {12834, title = {Executable Specifications for Real-Time Distributed Systems}, journal = {Electronic Notes in Theoretical Computer Science}, volume = {203}, year = {2008}, month = {2008/06/05/}, pages = {3 - 17}, abstract = {One of the challenges in designing distributed, embedded systems is the paucity of formal, executable specification notations that provide support for both real-time and asynchronous communication. This paper describes a timed architecture design language (Timed Architecture Interaction Diagrams or TAID) that, by virtue of its formal, executable semantics, combines the benefits of synchronous specification notations with the advantages of traditional architecture description languages. In addition, TAID provides support for a variety of temporal inter-process communication (IPC) primitives as a native feature of the language, so that the encapsulated communication behavior (captured by real-time {\^a}{\texteuro}{\oe}buses{\^a}{\texteuro} in TAID) may be re-used across designs and serve as specifications for more detailed model implementations.}, keywords = {distributed systems, Formal Methods, real-time, Simulations, Software architecture}, isbn = {1571-0661}, doi = {10.1016/j.entcs.2008.05.007}, url = {http://www.sciencedirect.com/science/article/pii/S1571066108003216}, author = {Ray,Arnab and Cleaveland, Rance} } @inbook {12996, title = {Expanding the reach of Grid computing: combining Globus- and BOINC-based systems}, booktitle = {Grids for Bioinformatics and Computational BiologyGrids for Bioinformatics and Computational Biology}, series = {Wiley Book Series on Bioinformatics: Computational Techniques and Engineering}, year = {2008}, month = {2008///}, pages = {71 - 85}, publisher = {Wiley-Interscience}, organization = {Wiley-Interscience}, address = {Hoboken}, author = {Myers,D. S and Bazinet,A. L and Cummings, Michael P.}, editor = {Talbi,E-G and Zomaya,AY} } @article {18670, title = {Experiences with building an intrusion-tolerant group communication system}, journal = {Software: Practice and Experience}, volume = {38}, year = {2008}, month = {2008///}, pages = {639 - 666}, abstract = {There are many group communication systems (GCSs) that provide consistent group membership and reliable, ordered multicast properties in the presence of crash faults. However, relatively few GCS implementations are able to provide these properties in the presence of malicious faults resulting from intrusions. We describe the systematic transformation of a crash-tolerant GCS, namely C-Ensemble, into an intrusion-tolerant GCS, the ITUA GCS. To perform the transformation, we devised intrusion-tolerant versions of key group communication protocols. We then inserted implementations of the protocols into C-Ensemble and made significant changes to the rest of the C-Ensemble protocol stack to make the stack intrusion tolerant. We quantify the cost of providing intrusion-tolerant group communication in two ways. First, we quantify the implementation effort by presenting a detailed analysis of the amount of change required to the original C-Ensemble system. In doing so, we provide insight into the choice of building an intrusion-tolerant GCS from scratch versus building one by leveraging a crash-tolerant implementation. Second, we quantify the run-time performance cost of tolerating intrusions by presenting results from an experimental evaluation of the main intrusion-tolerant microprotocols. The results are analyzed to identify the parts that contribute the most overhead while providing intrusion tolerance during both normal operation and recovery from intrusions. Copyright {\textcopyright} 2007 John Wiley \& Sons, Ltd.}, keywords = {distributed protocols, experimental evaluation, Fault tolerance, Group communication, intrusion tolerance}, isbn = {1097-024X}, doi = {10.1002/spe.848}, url = {http://onlinelibrary.wiley.com/doi/10.1002/spe.848/abstract}, author = {Ramasamy,HariGovind V. and Pandey,Prashant and Michel Cukier and Sanders,William H.} } @conference {14696, title = {Fable: A Language for Enforcing User-defined Security Policies}, booktitle = {IEEE Symposium on Security and Privacy, 2008. SP 2008}, year = {2008}, month = {2008/05/18/22}, pages = {369 - 383}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper presents FABLE, a core formalism for a programming language in which programmers may specify security policies and reason that these policies are properly enforced. In FABLE, security policies can be expressed by associating security labels with the data or actions they protect. Programmers define the semantics of labels in a separate part of the program called the enforcement policy. FABLE prevents a policy from being circumvented by allowing labeled terms to be manipulated only within the enforcement policy; application code must treat labeled values abstractly. Together, these features facilitate straightforward proofs that programs implementing a particular policy achieve their high-level security goals. FABLE is flexible enough to implement a wide variety of security policies, including access control, information flow, provenance, and security automata. We have implemented FABLE as part of the LINKS web programming language; we call the resulting language SELlNKS. We report on our experience using SELlNKS to build two substantial applications, a wiki and an on-line store, equipped with a combination of access control and provenance policies. To our knowledge, no existing framework enables the enforcement of such a wide variety of security policies with an equally high level of assurance.}, keywords = {Access control, Automata, Collaborative work, Communication system security, Computer languages, computer security, Data security, enforcement policy, FABLE, Government, high-level security goals, information flow, Information security, Language-based security, programming languages, Programming profession, provenance, security automata, security labels, security of data, user-defined security policies, verified enforcement, Web programming language}, isbn = {978-0-7695-3168-7}, doi = {10.1109/SP.2008.29}, author = {Swamy,N. and Corcoran,B.J. and Hicks, Michael W.} } @conference {12554, title = {Factorized variational approximations for acoustic multi source localization}, booktitle = {Acoustics, Speech and Signal Processing, 2008. ICASSP 2008. IEEE International Conference on}, year = {2008}, month = {2008/04/31/4}, pages = {2409 - 2412}, abstract = {Estimation based on received signal strength (RSS) is crucial in sensor networks for sensor localization, target tracking, etc. In this paper, we present a Gaussian approximation of the Chi distribution that is applicable to general RSS source localization problems in sensor networks. Using our Gaussian approximation, we provide a factorized variational Bayes (VB) approximation to the location and power posterior of multiple sources using a sensor network. When the source signal and the sensor noise have uncorrelated Gaussian distributions, we demonstrate that the envelope of the sensor output can be accurately modeled with a multiplicative Gaussian noise model. In turn, our factorized VB approximations decrease the computational complexity and provide computational robustness as the number of targets increases. Simulations are provided to demonstrate the effectiveness of the proposed approximations.}, keywords = {approximation;acoustic, approximation;Bayes, approximation;multisensor, approximation;variational, Bayes, Chi, detection;wireless, distribution;Gaussian, localization;factorized, localization;sensor, methods;Gaussian, multisource, networks;, networks;stochastic, processes;acoustic, sensor, signal, strength;sensor, systems;object, tracking;received, variational}, doi = {10.1109/ICASSP.2008.4518133}, author = {Cevher, V. and Sankaranarayanan,A. C and Chellapa, Rama} } @conference {15317, title = {Fast, easy, and cheap: Construction of statistical machine translation models with MapReduce}, booktitle = {Proceedings of the Third Workshop on Statistical Machine Translation}, year = {2008}, month = {2008///}, pages = {199 - 207}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, abstract = {In recent years, the quantity of parallel train-ing data available for statistical machine trans- lation has increased far more rapidly than the performance of individual computers, re- sulting in a potentially serious impediment to progress. Parallelization of the model- building algorithms that process this data on computer clusters is fraught with challenges such as synchronization, data exchange, and fault tolerance. However, the MapReduce programming paradigm has recently emerged as one solution to these issues: a powerful functional abstraction hides system-level de- tails from the researcher, allowing programs to be transparently distributed across potentially very large clusters of commodity hardware. We describe MapReduce implementations of two algorithms used to estimate the parame- ters for two word alignment models and one phrase-based translation model, all of which rely on maximum likelihood probability esti- mates. On a 20-machine cluster, experimental results show that our solutions exhibit good scaling characteristics compared to a hypo- thetical, optimally-parallelized version of cur- rent state-of-the-art single-core tools. }, author = {Dyer,C. and Cordova,A. and Mont,A. and Jimmy Lin} } @inbook {18675, title = {Finding Corrupted Computers Using Imperfect Intrusion Prevention System Event Data}, booktitle = {Computer Safety, Reliability, and Security}, series = {Lecture Notes in Computer Science}, volume = {5219}, year = {2008}, month = {2008///}, pages = {221 - 234}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {With the increase of attacks on the Internet, a primary concern for organizations is how to protect their network. The objectives of a security team are 1) to prevent external attackers from launching successful attacks against organization computers that could become compromised, 2) to ensure that organization computers are not vulnerable (e.g., fully patched) so that in either case the organization computers do not start launching attacks. The security team can monitor and block malicious activity by using devices such as intrusion prevention systems. However, in large organizations, such monitoring devices could record a high number of events. The contributions of this paper are 1) to introduce a method that ranks potentially corrupted computers based on imperfect intrusion prevention system event data, and 2) to evaluate the method based on empirical data collected at a large organization of about 40,000 computers. The evaluation is based on the judgment of a security expert of which computers were indeed corrupted. On the one hand, we studied how many computers classified as of high concern or of concern were indeed corrupted (i.e., true positives). On the other hand, we analyzed how many computers classified as of lower concern were in fact corrupted (i.e., false negatives).}, keywords = {Computer science}, isbn = {978-3-540-87697-7}, url = {http://www.springerlink.com/content/4767u3017r613822/abstract/}, author = {Chrun,Danielle and Michel Cukier and Sneeringer,Gerry}, editor = {Harrison,Michael and Sujan,Mark-Alexander} } @conference {14331, title = {Flowers or a robot army?: encouraging awareness \& activity with personal, mobile displays}, booktitle = {Proceedings of the 10th international conference on Ubiquitous computing}, series = {UbiComp {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {54 - 63}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Personal, mobile displays, such as those on mobile phones, are ubiquitous, yet for the most part, underutilized. We present results from a field experiment that investigated the effectiveness of these displays as a means for improving awareness of daily life (in our case, self-monitoring of physical activity). Twenty-eight participants in three experimental conditions used our UbiFit system for a period of three months in their day-to-day lives over the winter holiday season. Our results show, for example, that participants who had an awareness display were able to maintain their physical activity level (even during the holidays), while the level of physical activity for participants who did not have an awareness display dropped significantly. We discuss our results and their general implications for the use of everyday mobile devices as awareness displays.}, keywords = {ambient display, awareness, calm technology, field experiment, fitness, glanceable display, mobile phone, personal mobile display, persuasive technology, physical activity}, isbn = {978-1-60558-136-1}, doi = {10.1145/1409635.1409644}, url = {http://doi.acm.org/10.1145/1409635.1409644}, author = {Consolvo,Sunny and Klasnja,Predrag and McDonald,David W. and Avrahami,Daniel and Jon Froehlich and LeGrand,Louis and Libby,Ryan and Mosher,Keith and Landay,James A.} } @conference {12106, title = {A Framework for Software Engineering Experimental Replications}, booktitle = {Engineering of Complex Computer Systems, 2008. ICECCS 2008. 13th IEEE International Conference on}, year = {2008}, month = {2008/04/31/3}, pages = {203 - 212}, abstract = {Experimental replications are very important to the advancement of empirical software engineering. Replications are one of the key mechanisms to confirm previous experimental findings. They are also used to transfer experimental knowledge, to train people, and to expand a base of experimental evidence. Unfortunately, experimental replications are difficult endeavors. It is not easy to transfer experimental know-how and experimental findings. Based on our experience, this paper discusses this problem and proposes a Framework for Improving the Replication of Experiments (FIRE). The FIRE addresses knowledge sharing issues both at the intra-group (internal replications) and inter-group (external replications) levels. It encourages coordination of replications in order to facilitate knowledge transfer for lower cost, higher quality replications and more generalizable results.}, keywords = {engineering, engineering;, evidence;experimental, experimental, Experiments;experimental, for, Framework, Improving, knowledge, of, replication, replication;software, sharing;software, the, transfer;knowledge}, doi = {10.1109/ICECCS.2008.38}, author = {Mendonca,M.G. and Maldonado,J.C. and de Oliveira,M.C.F. and Carver, J. and Fabbri,C.P.F. and Shull, F. and Travassos,G.H. and Hohn,E.N. and Basili, Victor R.} } @article {12563, title = {From Videos to Verbs: Mining Videos for Activities using a cascade of dynamical systems (Supplemental Material)}, journal = {Relation}, volume = {10}, year = {2008}, month = {2008///}, pages = {9944 - 9944}, author = {Turaga, P.K. and Veeraraghavan,A. and Chellapa, Rama} } @article {12975, title = {A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE}, journal = {Evolution}, volume = {62}, year = {2008}, month = {2008/09/01/}, pages = {2411 - 2422}, abstract = {We introduce a statistic, the genealogical sorting index (gsi), for quantifying the degree of exclusive ancestry of labeled groups on a rooted genealogy and demonstrate its application. The statistic is simple, intuitive, and easily calculated. It has a normalized range to facilitate comparisons among different groups, trees, or studies and it provides information on individual groups rather than a composite measure for all groups. It naturally handles polytomies and accommodates measures of uncertainty in phylogenetic relationships. We use coalescent simulations to explore the behavior of the gsi across a range of divergence times, with the mean value increasing to 1, the maximum value when exclusivity within a group reached monophyly. Simulations also demonstrate that the power to reject the null hypothesis of mixed genealogical ancestry increased markedly as sample size increased, and that the gsi provides a statistically more powerful measure of divergence than FST. Applications to data from published studies demonstrated that the gsi provides a useful way to detect significant exclusivity even when groups are not monophyletic. Although we describe this statistic in the context of divergence, it is more broadly applicable to quantify and assess the significance of clustering of observations in labeled groups on any tree.}, keywords = {Ancestral polymorphism, congruence, exclusivity, genealogy, lineage sorting, monophyly, paraphyly, Phylogeny, polyphyly, speciation, species}, isbn = {1558-5646}, doi = {10.1111/j.1558-5646.2008.00442.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2008.00442.x/abstract}, author = {Cummings, Michael P. and Neel,Maile C and Shaw,Kerry L} } @conference {19448, title = {Getting to Green: Understanding Resource Consumption in the Home}, booktitle = {UbiComp {\textquoteright}08}, series = {UbiComp {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {242 - 251}, publisher = {ACM}, organization = {ACM}, abstract = {Rising global energy demands, increasing costs and limited natural resources mean that householders are more conscious about managing their domestic resource consumption. Yet, the question of what tools Ubicomp researchers can create for residential resource management remains open. To begin to address this omission, we present a qualitative study of 15 households and their current management practices around the water, electricity and natural gas systems in the home. We find that in-the-moment resource consumption is mostly invisible to householders and that they desire more real-time information to help them save money, keep their homes comfortable and be environmentally friendly. Designing for domestic sustainability therefore turns on improving the visibility of resource production and consumption costs as well as supporting both individuals and collectives in behavior change. Domestic sustainability also highlights the caveat of potentially creating a green divide by making resource management available only to those who can afford the technologies to support being green. Finally, we suggest that the Ubicomp community can contribute to the domestic and broader sustainability agenda by incorporating green values in designs and highlight the challenge of collecting data on being green.}, keywords = {domestic conservation, residential resource consumption, Sustainability}, isbn = {978-1-60558-136-1}, url = {http://doi.acm.org/10.1145/1409635.1409668}, author = {Marshini Chetty and Tran, David and Grinter, Rebecca E.} } @article {12903, title = {Global impact of Vibrio cholerae interactions with chitin}, journal = {Environmental Microbiology}, volume = {10}, year = {2008}, month = {2008/06/01/}, pages = {1400 - 1410}, abstract = {The interaction of Vibrio cholerae with chitin exemplifies for microbial ecology a successful bacteria{\textendash}substrate interaction with complex and significant influence on the lifestyle of the bacterium. Chitin is one of the most abundant polymers on earth and possibly the most abundant in the aquatic environment, where its association with V.~cholerae has provided the microorganism with a number of advantages, including food availability, adaptation to environmental nutrient gradients, tolerance to stress and protection from predators. Emergent properties of V.~cholerae{\textendash}chitin interactions occur at multiple hierarchical levels in the environment and include cell metabolic and physiological responses e.g. chemotaxis, cell multiplication, induction of competence, biofilm formation, commensal and symbiotic relationship with higher organisms, cycling of nutrients, and pathogenicity for humans and aquatic animals. As factors mediating virulence of V.~cholerae for humans and aquatic animals derive from mechanisms of adaptation to its environment, at different levels of hierarchical scale, V.~cholerae interactions with chitin represent a useful model for examination of the role of primary habitat selection in the development of traits that have been identified as virulence factors in human disease.}, isbn = {1462-2920}, doi = {10.1111/j.1462-2920.2007.01559.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2007.01559.x/full}, author = {Pruzzo,Carla and Vezzulli,Luigi and Rita R Colwell} } @article {12565, title = {Hardware and Software Systems for Image and Video Processing-Algorithmic and Architectural Optimizations for Computationally Efficient Particle Filtering}, journal = {IEEE Transactions on Image Processing}, volume = {17}, year = {2008}, month = {2008///}, pages = {737 - 748}, author = {Sankaranarayanan,A. C and Srivastava, A. and Chellapa, Rama} } @conference {19450, title = {Hci for community and international development}, booktitle = {SIGCHI EA {\textquoteright}08}, series = {CHI EA {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {3909 - 3912}, publisher = {ACM}, organization = {ACM}, abstract = {This workshop explores the challenges in applying, extending and inventing appropriate methods and contributions of Human Computer Interaction (HCI) to International economic and community Development. We address interaction design for parts of the world that are often marginalized by the Global North as well as people in the Global North who are themselves similarly marginalized by poverty or other barriers. We hope to extend the boundaries of the field of Human Computer Interaction by spurring a discussion on how existing methods and practices can be adapted and modified, and how new practices can be developed, to deal with the unique challenges posed by these contexts.}, keywords = {community design, ict4d, information and communication technology, international development, participatory design, ucd4id, User centered design}, isbn = {978-1-60558-012-8}, url = {http://doi.acm.org/10.1145/1358628.1358954}, author = {Thomas, John and Dearden, Andy and Dray, Susan and Light, Ann and Best, Michael and Arkin, Nuray and Maunder, Andrew and Kam, Mathew and Marshini Chetty and Sambasivan, Nithya and Buckhalter, Celeste and Krishnan, Gaurishankar} } @article {15550, title = {Improved approximation bounds for planar point pattern matching}, journal = {Algorithmica}, volume = {50}, year = {2008}, month = {2008///}, pages = {175 - 207}, abstract = {We analyze the performance of simple algorithms for matching two planar point sets under rigid transformations so as to minimize the directed Hausdorff distance between the sets. This is a well studied problem in computational geometry. Goodrich, Mitchell, and Orletsky presented a very simple approximation algorithm for this problem, which computes transformations based on aligning pairs of points. They showed that their algorithm achieves an approximation ratio of 4. We introduce a modification to their algorithm, which is based on aligning midpoints rather than endpoints. This modification has the same simplicity and running time as theirs, and we show that it achieves a better approximation ratio of roughly 3.14. We also analyze the approximation ratio in terms of a instance-specific parameter that is based on the ratio between diameter of the pattern set to the optimum Hausdorff distance. We show that as this ratio increases (as is common in practical applications) the approximation ratio approaches 3 in the limit. We also investigate the performance of the algorithm by Goodrich et al. as a function of this ratio, and present nearly matching lower bounds on the approximation ratios of both algorithms.}, doi = {10.1007/s00453-007-9059-9}, author = {Cho,M. and Mount, Dave} } @conference {16843, title = {Indexing planar point quartets via geometric attributes}, booktitle = {Proceedings of the 16th ACM SIGSPATIAL international conference on Advances in geographic information systems}, series = {GIS {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {71:1{\textendash}71:4 - 71:1{\textendash}71:4}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {An index is devised to support position-independent search for images containing quartets of icons. Point quartets exist that do not unambiguously map to quadrilaterals, however, four points do unambiguously determine a set of six interpoint line segments. Values for the "size", "shape", and "orientation" attributes of an icon quartet can be derived as functions of this interpoint line set, and can be used to construct a point-based index, in which each point quartet maps to a single point in the resulting hyperdimensional index space. Orientation can be represented by a single, spatially closed dimension. However, assignment of a reference direction for quartets possessing a k-fold rotational symmetry presents a significant challenge. Methods are described for determining shape and orientation attributes for point quartets, and for mapping these attributes onto a set of attribute axes to form a combined index. The orientation computation supplies, as a byproduct, one component of the shape attribute. All attributes are continuous with respect to small variations in the indexed point quartets.}, isbn = {978-1-60558-323-5}, doi = {10.1145/1463434.1463516}, url = {http://doi.acm.org/10.1145/1463434.1463516}, author = {Cranston,Charles B. and Samet, Hanan} } @article {12829, title = {An instrumentation-based approach to controller model validation}, journal = {Model-Driven Development of Reliable Automotive Services}, year = {2008}, month = {2008///}, pages = {84 - 97}, author = {Cleaveland, Rance and Smolka,S. and Sims,S.} } @conference {13264, title = {A Java3D framework for inspecting and segmenting 3D models}, booktitle = {Proceedings of the 13th international symposium on 3D web technology}, series = {Web3D {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {67 - 74}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Models of 3D objects have become widely accessible in several disciplines within academia and industry, spanning from scientific visualization to entertainment. In the last few years, 3D models are often organized into digital libraries accessible over the network, and thus semantic annotation of such models becomes an important issue. A fundamental step in annotating a 3D model is to segment it into meaningful parts. In this work, we present a Java3D framework for inspecting and segmenting 3D objects represented in X3D format. In particular, we present a combination of segmentation and merging techniques for producing a feasible decomposition of the boundary of a 3D object. We represent such decomposition as a graph, that we call the segmentation graph which is the basis for semantic annotation. We describe also the interface we have developed to allow visualization and browsing of both the decomposition and the segmentation graph in order to understand the topological structure of the resulting decomposition.}, keywords = {Java3D, object manipulation, Object segmentation, shape semantics, X3D}, isbn = {978-1-60558-213-9}, doi = {10.1145/1394209.1394225}, url = {http://doi.acm.org/10.1145/1394209.1394225}, author = {De Floriani, Leila and Papaleo,Laura and Carissimi,Nicol{\'o}} } @inbook {13024, title = {The Lattice Project: a Grid research and production environment combining multiple Grid computing models}, booktitle = {Distributed \& Grid Computing {\textemdash} Science Made Transparent for Everyone. Principles, Applications and Supporting CommunitiesDistributed \& Grid Computing {\textemdash} Science Made Transparent for Everyone. Principles, Applications and Supporting Communities}, year = {2008}, month = {2008///}, pages = {2 - 13}, publisher = {Rechenkraft.net}, organization = {Rechenkraft.net}, address = {Marburg}, author = {Bazinet,A. L and Cummings, Michael P.}, editor = {Weber,MHW} } @conference {12543, title = {Learning action dictionaries from video}, booktitle = {Image Processing, 2008. ICIP 2008. 15th IEEE International Conference on}, year = {2008}, month = {2008/10//}, pages = {1704 - 1707}, abstract = {Summarizing the contents of a video containing human activities is an important problem in computer vision and has important applications in automated surveillance systems. Summarizing a video requires one to identify and learn a {\textquoteright}vocabulary{\textquoteright} of action-phrases corresponding to specific events and actions occurring in the video. We propose a generative model for dynamic scenes containing human activities as a composition of independent action-phrases - each of which is derived from an underlying vocabulary. Given a long video sequence, we propose a completely unsupervised approach to learn the vocabulary. Once the vocabulary is learnt, a video segment can be decomposed into a collection of phrases for summarization. We then describe methods to learn the correlations between activities and sequentiality of events. We also propose a novel method for building invariances to spatial transforms in the summarization scheme.}, keywords = {(artificial, action, action-phrases;learning, automated, decomposition;video, dictionaries;spatial, intelligence);video, segment, segmentation;learning, sequence;computer, Surveillance, surveillance;, systems;computer, transforms;video, vision;image, vision;independent}, doi = {10.1109/ICIP.2008.4712102}, author = {Turaga,P. and Chellapa, Rama} } @article {12542, title = {Machine Recognition of Human Activities: A Survey}, journal = {Circuits and Systems for Video Technology, IEEE Transactions on}, volume = {18}, year = {2008}, month = {2008/11//}, pages = {1473 - 1488}, abstract = {The past decade has witnessed a rapid proliferation of video cameras in all walks of life and has resulted in a tremendous explosion of video content. Several applications such as content-based video annotation and retrieval, highlight extraction and video summarization require recognition of the activities occurring in the video. The analysis of human activities in videos is an area with increasingly important consequences from security and surveillance to entertainment and personal archiving. Several challenges at various levels of processing-robustness against errors in low-level processing, view and rate-invariant representations at midlevel processing and semantic representation of human activities at higher level processing-make this problem hard to solve. In this review paper, we present a comprehensive survey of efforts in the past couple of decades to address the problems of representation, recognition, and learning of human activities from video and related applications. We discuss the problem at two major levels of complexity: 1) "actions" and 2) "activities." "Actions" are characterized by simple motion patterns typically executed by a single human. "Activities" are more complex and involve coordinated actions among a small number of humans. We will discuss several approaches and classify them according to their ability to handle varying degrees of complexity as interpreted above. We begin with a discussion of approaches to model the simplest of action classes known as atomic or primitive actions that do not require sophisticated dynamical modeling. Then, methods to model actions with more complex dynamics are discussed. The discussion then leads naturally to methods for higher level representation of complex activities.}, keywords = {activity;low-level, annotation;human, cameras;video, content-based, factors;image, processing;machine, processing;rate-invariant, recognition;image, recognition;midlevel, representation;image, representation;video, representations;semantic, retrieval;human, sequences;, summarization;content-based, video}, isbn = {1051-8215}, doi = {10.1109/TCSVT.2008.2005594}, author = {Turaga,P. and Chellapa, Rama and V.S. Subrahmanian and Udrea,O.} } @inbook {12915, title = {The marine environment and human health: the cholera model}, booktitle = {Global Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease EmergenceGlobal Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease Emergence}, year = {2008}, month = {2008///}, publisher = {National Academies Press}, organization = {National Academies Press}, isbn = {9780309124027}, author = {Rita R Colwell}, editor = {Relman,David} } @article {14921, title = {The Maryland Large-Scale Integrated Neurocognitive Architecture}, year = {2008}, month = {2008/03//}, institution = {University of Maryland College Park}, abstract = {Recent progress in neural computation, high performance computing, neuroscience and cognitive science suggests that an effort to produce a general-purpose, adaptive machine intelligence is likely to yield a qualitatively more powerful system than those currently existing. Here we outline our progress in developing a framework for creating such a large-scale machine intelligence, or neurocognitive architecture that is based on the modularity, dynamics and plasticity of the human brain. We successfully implemented three intermediate-scale parts of such a system, and these are described. Based on this experience, we concluded that for the short term, optimal results would be obtained by using a hybrid design including neural, symbolic AI, and artificial life methods. We propose a three-tiered architecture that integrates these different methods, and describe a prototype mini-Roboscout that we implemented and evaluated based on this architecture. We also examined, via computational experiments, the effectiveness of genetic programming as a design tool for recurrent neural networks, and the speed-up obtained for adaptive neural networks when they are executed on a graphical processing unit. We conclude that the implementation of a large-scale neurocognitive architecture is feasible, and outline a roadmap for proceeding.}, keywords = {*COMPUTATIONS, *HYBRID SYSTEMS, *NEURAL NETS, *NEUROCOGNITIVE ARCHITECTURE, ADAPTIVE SYSTEMS, Artificial intelligence, BRAIN, Cognition, COMPUTER PROGRAMMING, COMPUTER PROGRAMMING AND SOFTWARE, HYBRID AI, Machine intelligence, MECHANICAL ORGANS, MODULAR CONSTRUCTION, NERVOUS SYSTEM, PE61101E, PLASTIC PROPERTIES, PROCESSING EQUIPMENT, RECURRENT NEURAL NETWORK}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA481261}, author = {Reggia, James A. and Tagamets,M. and Contreras-Vidal,J. and Jacobs, David W. and Weems,S. and Naqvi,W. and Yang,C.} } @article {14569, title = {Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development}, journal = {Development}, volume = {135}, year = {2008}, month = {2008///}, pages = {2729 - 2738}, abstract = {CTCF is a multifunctional nuclear factor involved in epigenetic regulation. Despite recent advances that include the systematic discovery of CTCF-binding sites throughout the mammalian genome, the in vivo roles of CTCF in adult tissues and during embryonic development are largely unknown. Using transgenic RNAi, we depleted maternal stores of CTCF from growing mouse oocytes, and identified hundreds of misregulated genes. Moreover, our analysis suggests that CTCF predominantly activates or derepresses transcription in oocytes. CTCF depletion causes meiotic defects in the egg, and mitotic defects in the embryo that are accompanied by defects in zygotic gene expression, and culminate in apoptosis. Maternal pronuclear transfer and CTCF mRNA microinjection experiments indicate that CTCF is a mammalian maternal effect gene, and that persistent transcriptional defects rather than persistent chromosomal defects perturb early embryonic development. This is the first study detailing a global and essential role for CTCF in mouse oocytes and preimplantation embryos.}, doi = {10.1242/dev.024539}, url = {http://dev.biologists.org/content/135/16/2729.abstract}, author = {Wan,Le-Ben and Pan,Hua and Hannenhalli, Sridhar and Cheng,Yong and Ma,Jun and Fedoriw,Andrew and Lobanenkov,Victor and Latham,Keith E. and Schultz,Richard M. and Bartolomei,Marisa S.} } @article {12557, title = {Mixed state models for automatic target recognition and behavior analysis in video sequences}, journal = {Proceedings of SPIE}, volume = {6967}, year = {2008}, month = {2008/04/03/}, pages = {69670Q-69670Q-11 - 69670Q-69670Q-11}, abstract = {Mixed state or hybrid state space systems are useful tools for various problems in computer vision. These systems model complicated system dynamics as a mixture of inherently simple sub-systems, with an additional mechanism to switch between the sub-systems. This approach of modeling using simpler systems allows for ease in learning the parameters of the system and in solving the inference problem. In this paper, we study the use of such mixed state space systems for problems in recognition and behavior analysis in video sequences. We begin with a dynamical system formulation for recognition of faces from a video. This system is used to introduce the simultaneous tracking and recognition paradigm that allows for improved performance in both tracking and recognition. We extend this framework to design a second system for verification of vehicles across non-overlapping views using structural and textural fingerprints for characterizing the identity of the target. Finally, we show the use of such modeling for tracking and behavior analysis of bees from video.}, isbn = {0277786X}, doi = {doi:10.1117/12.777766}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/6967/1/69670Q_1?isAuthorized=no}, author = {Chellapa, Rama and Sankaranarayanan,Aswin C. and Veeraraghavan,Ashok} } @article {12851, title = {Model Based Design Verification: A Monitor Based Approach}, volume = {2008-01-0741}, year = {2008}, month = {2008/04//}, institution = {SAE International}, address = {Warrendale, PA}, abstract = {This paper assesses the utility of an automated functional verification methodology in the design of a body electronics application. The use of design models as detailed specifications for software is gaining steady acceptance in the automotive industry because of the advantages it offers in terms of rapid system prototyping and automatic code generation. This paper argues that such modeling effort can also be used to provide support for design verification, so that errors may be pinpointed before they find their way into code, when they become much harder and more expensive to isolate, diagnose and repair.}, url = {http://papers.sae.org/2008-01-0741}, author = {Ackermann,Chris and Ray,Arnab and Cleaveland, Rance and Heit,J{\"u}rgen and Martin,Christopher and Shelton,Charles} } @article {12544, title = {Model Driven Segmentation of Articulating Humans in Laplacian Eigenspace}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {30}, year = {2008}, month = {2008/10//}, pages = {1771 - 1785}, abstract = {We propose a general approach using Laplacian Eigenmaps and a graphical model of the human body to segment 3D voxel data of humans into different articulated chains. In the bottom-up stage, the voxels are transformed into a high-dimensional (6D or less) Laplacian Eigenspace (LE) of the voxel neighborhood graph. We show that LE is effective at mapping voxels on long articulated chains to nodes on smooth 1D curves that can be easily discriminated, and prove these properties using representative graphs. We fit 1D splines to voxels belonging to different articulated chains such as the limbs, head and trunk, and determine the boundary between splines using the spline fitting error. A top-down probabilistic approach is then used to register the segmented chains, utilizing their mutual connectivity and individual properties. Our approach enables us to deal with complex poses such as those where the limbs form loops. We use the segmentation results to automatically estimate the human body models. While we use human subjects in our experiments, the method is fairly general and can be applied to voxel-based segmentation of any articulated object composed of long chains. We present results on real and synthetic data that illustrate the usefulness of this approach.}, keywords = {3D voxel data segmentation, algorithms, Anatomic;Pattern Recognition, Artificial intelligence, Automated;Reproducibility of Results;Sensitivity and Specificity;Whole Body Imaging;, Computer simulation, Computer-Assisted;Imaging, curve fitting, Eigenvalues and eigenfunctions, graph theory, human articulation, human body graphical model, human motion analysis, HUMANS, Image Enhancement, Image Interpretation, Image motion analysis, image registration, Image segmentation, Laplace transforms, Laplacian eigenspace transform, model driven segmentation, probability, representative graph, skeleton registration, Smoothing methods, solid modelling, spline fitting error, splines (mathematics), Three-Dimensional;Joints;Models, top-down probabilistic approach, voxel neighborhood graph}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2007.70823}, author = {Sundaresan, A. and Chellapa, Rama} } @conference {12550, title = {Modeling shape and textural variations in aging faces}, booktitle = {Automatic Face Gesture Recognition, 2008. FG {\textquoteright}08. 8th IEEE International Conference on}, year = {2008}, month = {2008/09//}, pages = {1 - 8}, abstract = {We propose a two fold approach towards modeling facial aging in adults. Firstly, we develop a shape transformation model that is formulated as a physically-based parametric muscle model that captures the subtle deformations facial features undergo with age. The model implicitly accounts for the physical properties and geometric orientations of the individual facial muscles. Next, we develop an image gradient based texture transformation function that characterizes facial wrinkles and other skin artifacts often observed during different ages. Facial growth statistics (both in terms of shape and texture) play a crucial role in developing the aforementioned transformation models. From a database that comprises of pairs of age separated face images of many individuals, we extract age-based facial measurements across key fiducial features and further, study textural variations across ages. We present experimental results that illustrate the applications of the proposed facial aging model in tasks such as face recognition and facial appearance prediction across aging.}, keywords = {Aging, analysis;, faces;image, function;face, gradient;modeling, model;textural, recognition;image, shape;shape, texture;statistical, transformation, variations;texture}, doi = {10.1109/AFGR.2008.4813337}, author = {Ramanathan,N. and Chellapa, Rama} } @article {12976, title = {A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13}, journal = {J Mol Evol}, volume = {67}, year = {2008}, month = {2008/12//}, pages = {581 - 593}, abstract = {The homeobox gene Hoxa-13 codes for a transcription factor involved in multiple functions, including body axis and hand/foot development in tetrapods. In this study we investigate whether the loss of one function (e.g., limb loss in snakes) left a molecular footprint in exon 1 of Hoxa-13 that could be associated with the release of functional constraints caused by limb loss. Fragments of the Hoxa-13 exon 1 were sequenced from 13 species and analyzed, with additional published sequences of the same region, using relative rates and likelihood-ratio tests. Five amino acid sites in exon 1 of Hoxa-13 were detected as evolving under positive selection in the stem lineage of snakes. To further investigate whether there is an association between limb loss and sequence variation in Hoxa-13, we used the random forest method on an alignment that included shark, basal fish lineages, and "eu-tetrapods" such as mammals, turtle, alligator, and birds. The random forest method approaches the problem as one of classification, where we seek to predict the presence or absence of autopodium based on amino acid variation in Hoxa-13 sequences. Different alignments tested were associated with similar error rates (18.42\%). The random forest method suggested that phenotypic states (autopodium present and absent) can often be correctly predicted based on Hoxa-13 sequences. Basal, nontetrapod gnat-hostomes that never had an autopodium were consistently classified as limbless together with the snakes, while eu-tetrapods without any history of limb loss in their phylogeny were also consistently classified as having a limb. Misclassifications affected mostly lizards, which, as a group, have a history of limb loss and limb re-evolution, and the urodele and caecilian in our sample. We conclude that a molecular footprint can be detected in Hoxa-13 that is associated with the lack of an autopodium; groups with classification ambiguity (lizards) are characterized by a history of repeated limb loss and possible limb re-evolution.}, doi = {10.1007/s00239-008-9156-7}, author = {Kohlsdorf,T and Cummings, Michael P. and Lynch,VJ and Stopper,GF and Takahashi,K and Wagner,GP} } @conference {19457, title = {More Than Meets the Eye: Transforming the User Experience of Home Network Management}, booktitle = {Proceedings of the 7th ACM conference on Designing interactive systems}, series = {DIS {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {455 - 464}, publisher = {ACM}, organization = {ACM}, abstract = {As computing migrates from the workplace to the home, householders must tackle problems of home network maintenance. Often they lack the technical knowledge or motivation to complete these tasks, making the user experience of home network maintenance frustrating. In response to these difficulties, many householders rely on handwritten reminders or interactive networking tools that are ill-suited for the home environment. In this paper, we seek to understand how to design better home network management tools through a study of sketches created by 40 people in 18 households. In our study, we obtained information about householders{\textquoteright} knowledge, practices and needs with respect to home networking. Based on our results, we present guidelines for transforming the user experience of home network management.}, keywords = {home networks, sketching, troubleshooting}, isbn = {978-1-60558-002-9}, url = {http://doi.acm.org/10.1145/1394445.1394494}, author = {Poole, Erika Shehan and Marshini Chetty and Grinter, Rebecca E. and Edwards, W. Keith} } @conference {12556, title = {Multi-biometric cohort analysis for biometric fusion}, booktitle = {Acoustics, Speech and Signal Processing, 2008. ICASSP 2008. IEEE International Conference on}, year = {2008}, month = {2008/04/31/4}, pages = {5224 - 5227}, abstract = {Biometric matching decisions have traditionally been made based solely on a score that represents the similarity of the query biometric to the enrolled biometric(s) of the claimed identity. Fusion schemes have been proposed to benefit from the availability of multiple biometric samples (e.g., multiple samples of the same fingerprint) or multiple different biometrics (e.g., face and fingerprint). These commonly adopted fusion approaches rarely make use of the large number of non-matching biometric samples available in the database in the form of other enrolled identities or training data. In this paper, we study the impact of combining this information with the existing fusion methodologies in a cohort analysis framework. Experimental results are provided to show the usefulness of such a cohort-based fusion of face and fingerprint biometrics.}, keywords = {(access, analysis;biometrics, biometric, biometrics;fingerprint, biometrics;multi-biometric, cohort, control);face, data;, decisions;face, fusion;biometric, identification;security, MATCHING, of, recognition;fingerprint}, doi = {10.1109/ICASSP.2008.4518837}, author = {Aggarwal,G. and Ratha,N. K and Bolle, R.M. and Chellapa, Rama} } @conference {13311, title = {Multi-Scale 3D Morse Complexes}, booktitle = {Computational Sciences and Its Applications, 2008. ICCSA {\textquoteright}08. International Conference on}, year = {2008}, month = {2008/07/30/3}, pages = {441 - 451}, abstract = {Morse theory studies the relationship between the topology of a manifold M and the critical points of a scalar function f defined over M. Morse and Morse-Smale complexes, defined by critical points and integral lines of f, induce a subdivision of M into regions of uniform gradient flow, representing the morphology of M in a compact way. Function f can be simplified by canceling its critical points in pairs, thus simplifying the morphological representation of M, given by Morse and Morse-Smale complexes of f. Here, we propose a compact representation for the two Morse complexes in 3D, which is based on encoding the incidence relations of their cells, and on exploiting the duality among the complexes. We define cancellation operations, and their inverse expansion operations, on the Morse complexes and on their dual representation. We propose a multi-scale representation of the Morse complexes which provides a description of such complexes, and thus of the morphology of a 3D scalar field, at different levels of abstraction. This representation allows us also to perform selective refinement operations to extract description of the complexes which varies in different parts of the domain, thus improving efficiency on large data sets, and eliminating the noise in the data through topology simplification.}, keywords = {(mathematics);inverse, 3D, analysis;duality, complexes;topology;data, computing;topology;, critical, expansion, lines;inverse, morphology;mathematics, Morse, operations;morphology;multi-scale, points;duality;integral, problems;mathematical}, doi = {10.1109/ICCSA.2008.10}, author = {Comic,L. and De Floriani, Leila} } @article {12900, title = {New records of phytoplankton for Bangladesh. 2. Cryptophyceae and Synurophyceae}, journal = {Bangladesh Journal of Botany}, volume = {36}, year = {2008}, month = {2008/11/05/}, abstract = {This study presents two species of Rhodomonas, four species of Chroomonas, six species of Cryptomonas and Cryptochrysis minor, Cyanomonas coeruleus, Chrysodidymus synuroideus and Mallomonas akrokomos. These species have been reported from some ponds of Mathbaria in Pirojpur and Bakerganj of Barisal district in Bangladesh.}, isbn = {0253-5416}, doi = {10.3329/bjb.v36i1.1549}, url = {http://www.banglajol.info/bd/index.php/BJB/article/viewArticle/1549}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasmin,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @article {12902, title = {New records of phytoplankton for Bangladesh. 5. Euglena, Euglenocapsa}, journal = {Bangladesh Journal of Plant Taxonomy}, volume = {15}, year = {2008}, month = {2008/06/16/}, abstract = {This study presents 20 taxa of the genus Euglena and one species of the rare euglenoid genus Euglenocapsa. All these taxa are reported for the first time from some pond ecosystems of Mathbaria in Pirojpur and Bakerganj of Barisal districts of Bangladesh.}, isbn = {1028-2092}, doi = {10.3329/bjpt.v15i1.910}, url = {http://www.banglajol.info/index.php/BJPT/article/viewArticle/910}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasmin,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @article {12899, title = {New records of phytoplankton for Bangladesh. 7. Phacus spp.}, journal = {Bangladesh Journal of Botany}, volume = {37}, year = {2008}, month = {2008/11/05/}, abstract = {Thirteen species of Phacus hitherto not reported from Bangladesh have been described and illustrated. Freshwater ponds at southern districts of Pirojpur and Barisal revealed these presence of the species.}, isbn = {0253-5416}, doi = {10.3329/bjb.v37i1.1564}, url = {http://www.banglajol.info/bd/index.php/BJB/article/viewArticle/1564}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasmin,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @article {12897, title = {New records of phytoplankton for Bangladesh. 8. Trachelomonas Ehr. (Euglenophyceae)}, journal = {Bangladesh Journal of Botany}, volume = {37}, year = {2008}, month = {2008/12/19/}, abstract = {Investigation of pelagic plankton communities from some freshwater ponds of Pirojpur and Barisal districts revealed the presence of 17 species under the genus Trachelomonas Ehr. for the first time in Bangladesh.}, isbn = {0253-5416}, doi = {10.3329/bjb.v37i2.1719}, url = {http://www.banglajol.info/bd/index.php/BJB/article/viewArticle/1719}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasmin,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @conference {12548, title = {A Non-generative Approach for Face Recognition Across Aging}, booktitle = {Biometrics: Theory, Applications and Systems, 2008. BTAS 2008. 2nd IEEE International Conference on}, year = {2008}, month = {2008/10//undefin}, pages = {1 - 6}, abstract = {Human faces undergo a lot of change in appearance as they age. Though facial aging has been studied for decades, it is only recently that attempts have been made to address the problem from a computational point of view. Most of these early efforts follow a simulation approach in which matching is performed by synthesizing face images at the target age. Given the innumerable different ways in which a face can potentially age, the synthesized aged image may not be similar to the actual aged image. In this paper, we bypass the synthesis step and directly analyze the drifts of facial features with aging from a purely matching perspective. Our analysis is based on the observation that facial appearance changes in a coherent manner as people age. We provide measures to capture this coherency in feature drifts. Illustrations and experimental results show the efficacy of such an approach for matching faces across age progression.}, keywords = {appearance;nongenerative, approach;face, Face, image, matching;, recognition;facial, recognition;image, synthesis;face}, doi = {10.1109/BTAS.2008.4699331}, author = {Biswas,S. and Aggarwal,G. and Ramanathan,N. and Chellapa, Rama} } @article {12545, title = {Object Detection, Tracking and Recognition for Multiple Smart Cameras}, journal = {Proceedings of the IEEE}, volume = {96}, year = {2008}, month = {2008/10//}, pages = {1606 - 1624}, abstract = {Video cameras are among the most commonly used sensors in a large number of applications, ranging from surveillance to smart rooms for videoconferencing. There is a need to develop algorithms for tasks such as detection, tracking, and recognition of objects, specifically using distributed networks of cameras. The projective nature of imaging sensors provides ample challenges for data association across cameras. We first discuss the nature of these challenges in the context of visual sensor networks. Then, we show how real-world constraints can be favorably exploited in order to tackle these challenges. Examples of real-world constraints are (a) the presence of a world plane, (b) the presence of a three-dimiensional scene model, (c) consistency of motion across cameras, and (d) color and texture properties. In this regard, the main focus of this paper is towards highlighting the efficient use of the geometric constraints induced by the imaging devices to derive distributed algorithms for target detection, tracking, and recognition. Our discussions are supported by several examples drawn from real applications. Lastly, we also describe several potential research problems that remain to be addressed.}, keywords = {algorithm;geometric, analysis;image, association;distributed, camera;visual, cameras;, cameras;object, colour, constraints;imaging, data, detection;object, detection;sensor, detection;three-dimiensional, fusion;target, model;video, network;distributed, recognition;object, scene, sensor, sensor;multiple, sensors;geometry;image, sensors;object, smart, texture;intelligent, tracking;target, tracking;video}, isbn = {0018-9219}, doi = {10.1109/JPROC.2008.928758}, author = {Sankaranarayanan,A. C and Veeraraghavan,A. and Chellapa, Rama} } @article {12910, title = {Occurrence and Expression of Luminescence in Vibrio Cholerae}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {74}, year = {2008}, month = {2008/02/01/}, pages = {708 - 715}, abstract = {Several species of the genus Vibrio, including Vibrio cholerae, are bioluminescent or contain bioluminescent strains. Previous studies have reported that only 10\% of V. cholerae strains are luminescent. Analysis of 224 isolates of non-O1/non-O139 V. cholerae collected from Chesapeake Bay, MD, revealed that 52\% (116/224) were luminescent when an improved assay method was employed and 58\% (130/224) of isolates harbored the luxA gene. In contrast, 334 non-O1/non-O139 V. cholerae strains isolated from two rural provinces in Bangladesh yielded only 21 (6.3\%) luminescent and 35 (10.5\%) luxA+ isolates. An additional 270 clinical and environmental isolates of V. cholerae serogroups O1 and O139 were tested, and none were luminescent or harbored luxA. These results indicate that bioluminescence may be a trait specific for non-O1/non-O139 V. cholerae strains that frequently occur in certain environments. Luminescence expression patterns of V. cholerae were also investigated, and isolates could be grouped based on expression level. Several strains with defective expression of the lux operon, including natural K variants, were identified.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.01537-07}, url = {http://aem.asm.org/content/74/3/708}, author = {Grim,Christopher J. and Taviani,Elisa and Alam,Munirul and Huq,Anwar and Sack,R. Bradley and Rita R Colwell} } @conference {12570, title = {An ontology based approach for activity recognition from video}, booktitle = {Proceedings of the 16th ACM international conference on Multimedia}, series = {MM {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {709 - 712}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Representation and recognition of human activities is an important problem for video surveillance and security applications. Considering the wide variety of settings in which surveillance systems are being deployed, it is necessary to create a common knowledge-base or ontology of human activities. Most current attempts at ontology design in computer vision for human activities have been empirical in nature. In this paper, we present a more systematic approach to address the problem of designing ontologies for visual activity recognition. We draw on general ontology design principles and adapt them to the specific domain of human activity ontologies. Then, we discuss qualitative evaluation principles and provide several examples from existing ontologies and how they can be improved upon. Finally, we demonstrate quantitatively in terms of recognition performance, the efficacy and validity of our approach for bank and airport tarmac surveillance domains.}, keywords = {activity ontologies, visual surveillance}, isbn = {978-1-60558-303-7}, doi = {10.1145/1459359.1459466}, url = {http://doi.acm.org/10.1145/1459359.1459466}, author = {Akdemir,Umut and Turaga,Pavan and Chellapa, Rama} } @conference {12560, title = {Optimal Multi-View Fusion of Object Locations}, booktitle = {Motion and video Computing, 2008. WMVC 2008. IEEE Workshop on}, year = {2008}, month = {2008/01//}, pages = {1 - 8}, abstract = {In surveillance applications, it is common to have multiple cameras observing targets exhibiting motion on a ground plane. Tracking and estimation of the location of a target on the plane becomes an important inference problem. In this paper, we study the problem of combining estimates of location obtained from multiple cameras. We model the relation between the uncertainty in the location estimation to the position and location of the camera with respect to the plane (which is encoded by a 2D projective transformation). This is addressed by a theoretical study of the properties of a random variable under a projective transformation and analysis of the geometric setting when the moments of the transformed random variable exist. In this context, we prove that ground plane tracking near the horizon line is often inaccurate. Using suitable approximations to compute the moments, a minimum variance estimator is designed to fuse the multi-camera location estimates. Finally, we present experimental results that illustrate the importance of such modeling in location estimation and tracking.}, keywords = {control;surveillance;tracking;, detection;position, estimates;optimal, estimation;location, estimation;multicamera, estimation;object, estimator;motion, fusion;surveillance;cameras;estimation, location, multiview, theory;motion, tracking;minimum, variance}, doi = {10.1109/WMVC.2008.4544048}, author = {Sankaranarayanan,A. C and Chellapa, Rama} } @article {12568, title = {Pose and Illumination Issues in Face-and Gait-Based Identification}, journal = {Advances in Biometrics}, year = {2008}, month = {2008///}, pages = {307 - 322}, abstract = {Although significant work has been done in the field of face- and gait- based recognition, the performance of the state-of-the-art recognition algorithms is not good enough to be effective in operational systems. Most algorithms do reasonably well for controlled images but are susceptible to changes in illumination conditions and pose. This has shifted the focus of research to more challenging tasks of obtaining better performance for uncontrolled realistic scenarios. In this chapter, we discuss several recent advances made to achieve this goal.}, author = {Chellapa, Rama and Aggarwal,G.} } @article {12564, title = {Recognition of Humans and their Activities using Statistical analysis on Stiefel and Grassmann Manifolds}, journal = {Red}, volume = {7}, year = {2008}, month = {2008///}, pages = {643 - 643}, abstract = {Many applications in computer vision involve learning and recognition of patterns from exemplars which lie on certainmanifolds. Given a database of examples and a query, the following two questions are usually addressed {\textendash} a) what is the {\textquoteleft}closest{\textquoteright} example to the query in the database ? b) what is the {\textquoteleft}most probable{\textquoteright} class to which the query belongs ? The answer to the first question involves study of the geometric properties of the manifold, which then leads to appropriate definitions of distance metrics on the manifold (geodesics etc). The answer to the second question involves statistical modeling of inter- and intra-class variations on the manifold. In this paper, we concern ourselves with two related manifolds that often appear in several vision applications {\textendash} the Stiefel Manifold and the Grassmann Manifold. We describe statistical modeling and inference tools on these manifolds which result in significant improvements in performance over traditional distance-based classifiers. We illustrate applications to video-based face recognition and activity recognition. }, author = {Turaga,P. and Veeraraghavan,A. and Chellapa, Rama} } @article {13016, title = {Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence}, journal = {Syst Biol}, volume = {57}, year = {2008}, month = {2008/12//}, pages = {920 - 938}, abstract = {This study attempts to resolve relationships among and within the four basal arthropod lineages (Pancrustacea, Myriapoda, Euchelicerata, Pycnogonida) and to assess the widespread expectation that remaining phylogenetic problems will yield to increasing amounts of sequence data. Sixty-eight regions of 62 protein-coding nuclear genes (approximately 41 kilobases (kb)/taxon) were sequenced for 12 taxonomically diverse arthropod taxa and a tardigrade outgroup. Parsimony, likelihood, and Bayesian analyses of total nucleotide data generally strongly supported the monophyly of each of the basal lineages represented by more than one species. Other relationships within the Arthropoda were also supported, with support levels depending on method of analysis and inclusion/exclusion of synonymous changes. Removing third codon positions, where the assumption of base compositional homogeneity was rejected, altered the results. Removing the final class of synonymous mutations{\textendash}first codon positions encoding leucine and arginine, which were also compositionally heterogeneous{\textendash}yielded a data set that was consistent with a hypothesis of base compositional homogeneity. Furthermore, under such a data-exclusion regime, all 68 gene regions individually were consistent with base compositional homogeneity. Restricting likelihood analyses to nonsynonymous change recovered trees with strong support for the basal lineages but not for other groups that were variably supported with more inclusive data sets. In a further effort to increase phylogenetic signal, three types of data exploration were undertaken. (1) Individual genes were ranked by their average rate of nonsynonymous change, and three rate categories were assigned{\textendash}fast, intermediate, and slow. Then, bootstrap analysis of each gene was performed separately to see which taxonomic groups received strong support. Five taxonomic groups were strongly supported independently by two or more genes, and these genes mostly belonged to the slow or intermediate categories, whereas groups supported only by a single gene region tended to be from genes of the fast category, arguing that fast genes provide a less consistent signal. (2) A sensitivity analysis was performed in which increasing numbers of genes were excluded, beginning with the fastest. The number of strongly supported nodes increased up to a point and then decreased slightly. Recovery of Hexapoda required removal of fast genes. Support for Mandibulata (Pancrustacea + Myriapoda) also increased, at times to "strong" levels, with removal of the fastest genes. (3) Concordance selection was evaluated by clustering genes according to their ability to recover Pancrustacea, Euchelicerata, or Myriapoda and analyzing the three clusters separately. All clusters of genes recovered the three concordance clades but were at times inconsistent in the relationships recovered among and within these clades, a result that indicates that the a priori concordance criteria may bias phylogenetic signal in unexpected ways. In a further attempt to increase support of taxonomic relationships, sequence data from 49 additional taxa for three slow genes (i.e., EF-1 alpha, EF-2, and Pol II) were combined with the various 13-taxon data sets. The 62-taxon analyses supported the results of the 13-taxon analyses and provided increased support for additional pancrustacean clades found in an earlier analysis including only EF-1 alpha, EF-2, and Pol II.}, doi = {10.1080/10635150802570791}, author = {Regier,J. C and Shultz,J. W and Ganley,A. R.D and Hussey,A. and Shi,D. and Ball,B. and Zwick,A. and Stajich,J. E and Cummings, Michael P. and Martin,J. W and Cunningham,CW} } @article {12180, title = {A review of overview+ detail, zooming, and focus+ context interfaces}, journal = {ACM Computing Surveys (CSUR)}, volume = {41}, year = {2008}, month = {2008///}, pages = {1 - 31}, author = {Cockburn,A. and Karlson,A. and Bederson, Benjamin B.} } @conference {12541, title = {A Scalable Projective Bundle Adjustment Algorithm using the L infinity Norm}, booktitle = {Computer Vision, Graphics Image Processing, 2008. ICVGIP {\textquoteright}08. Sixth Indian Conference on}, year = {2008}, month = {2008/12//}, pages = {79 - 86}, abstract = {The traditional bundle adjustment algorithm for structure from motion problem has a computational complexity of O((m+n)3) per iteration and memory requirement of O(mn(m+n)), where m is the number of cameras and n is the number of structure points. The sparse version of bundle adjustment has a computational complexity of O(m3+mn) per iteration and memory requirement of O(mn). Here we propose an algorithm that has a computational complexity of O(mn(radicm+radicn)) per iteration and memory requirement of O(max(m,n)). The proposed algorithm is based on minimizing the Linfin norm of reprojection error. It alternately estimates the camera and structure parameters, thus reducing the potentially large scale optimization problem to many small scale subproblems each of which is a quasi-convex optimization problem and hence can be solved globally. Experiments using synthetic and real data show that the proposed algorithm gives good performance in terms of minimizing the reprojection error and also has a good convergence rate.}, keywords = {adjustment, algorithm;structure, bundle, complexity;convex, complexity;iteration, error;scalable, estimation;, estimation;cameras;computational, Linfin, method;large, methods;parameter, norm;camera;computational, OPTIMIZATION, parameter, problem;memory, problem;projection, problem;reprojection, programming;image, projective, reconstruction;iterative, reconstruction;quasiconvex, requirement;motion, scale}, doi = {10.1109/ICVGIP.2008.51}, author = {Mitra, K. and Chellapa, Rama} } @article {14853, title = {Searching the world{\textquoteright}s herbaria: A system for visual identification of plant species}, journal = {Computer Vision{\textendash}ECCV 2008}, year = {2008}, month = {2008///}, pages = {116 - 129}, abstract = {We describe a working computer vision system that aids in the identification of plant species. A user photographs an isolated leaf on a blank background, and the system extracts the leaf shape and matches it to the shape of leaves of known species. In a few seconds, the system displays the top matching species, along with textual descriptions and additional images. This system is currently in use by botanists at the Smithsonian Institution National Museum of Natural History. The primary contributions of this paper are: a description of a working computer vision system and its user interface for an important new application area; the introduction of three new datasets containing thousands of single leaf images, each labeled by species and verified by botanists at the US National Herbarium; recognition results for two of the three leaf datasets; and descriptions throughout of practical lessons learned in constructing this system.}, doi = {10.1007/978-3-540-88693-8_9}, author = {Belhumeur,P. and Chen,D. and Feiner,S. and Jacobs, David W. and Kress,W. and Ling,H. and Lopez,I. and Ramamoorthi,R. and Sheorey,S. and White,S.} } @article {12907, title = {Seasonal Cholera from Multiple Small Outbreaks, Rural Bangladesh}, journal = {Emerging Infectious DiseasesEmerg Infect Dis}, volume = {14}, year = {2008}, month = {2008/05//}, pages = {831 - 833}, abstract = {Clinical and environmental Vibrio cholerae organisms collected from February 2004 through April 2005 were systematically isolated from 2 rural Bangladeshi locales. Their genetic relatedness was evaluated at 5 loci that contained a variable number of tandem repeats (VNTR). The observed minimal overlap in VNTR patterns between the 2 communities was consistent with sequential, small outbreaks from local sources.}, isbn = {1080-6040}, doi = {10.3201/eid1405.071116}, author = {Stine,O. Colin and Alam,Munirul and Tang,Li and Nair,G. Balakrish and Siddique,A. Kasem and Faruque,Shah M. and Huq,Anwar and Rita R Colwell and Sack,R. Bradley and Morris,J. Glenn} } @article {14098, title = {Sequence diversity and evolution of multigene families in Trypanosoma cruzi}, journal = {Molecular and Biochemical Parasitology}, volume = {157}, year = {2008}, month = {2008/01//}, pages = {65 - 72}, abstract = {Several copies of genes belonging to three multigene families present in the genome of Trypanosoma cruzi were sequenced and comparatively analyzed across six different strains of the parasite belonging to the T. cruzi I lineage (Colombiana, Silvio X10 and Dm28c), the T. cruzi II lineage (Esmeraldo and JG) and a hybrid strain (CL Brener). For all three gene families analyzed, our results support the division in T. cruzi I and II lineages. Furthermore, in agreement with its hybrid nature, sequences derived from the CL Brener clone clustered together with T. cruzi II sequences as well as with a third group of sequences. Paralogous sequences encoding Amastin, an amastigote surface glycoprotein and TcAG48, an antigenic RNA binding protein, which are clustered in the parasite genome, present higher intragenomic variability in T. cruzi II and CL Brener strains, when compared to T. cruzi I strains. Paralogous sequences derived from the TcADC gene family, which encode various isoforms of adenylyl cyclases and are dispersed throughout the T. cruzi genome, exhibit similar degree of variability in all strains, except in the CL Brener strain, in which the sequences were more divergent. Several factors including mutation rates and gene conversion mechanisms, acting differently within the T. cruzi population, may contribute to create such distinct levels of sequence diversity in multigene families that are clustered in the T. cruzi genome.}, keywords = {Amastin, Gene conversion, Genetic diversity, Multigene families, Trypanosoma cruzi}, isbn = {0166-6851}, doi = {16/j.molbiopara.2007.10.002}, url = {http://www.sciencedirect.com/science/article/pii/S0166685107002769}, author = {Cerqueira,Gustavo C. and Bartholomeu,Daniella C. and DaRocha,Wanderson D. and Hou,Lihua and Freitas-Silva,Danielle M. and Machado,Carlos Renato and El-Sayed, Najib M. and Teixeira,Santuza M.R.} } @article {13120, title = {Sequential Kernel Density Approximation and Its Application to Real-Time Visual Tracking}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {30}, year = {2008}, month = {2008/07//}, pages = {1186 - 1197}, abstract = {Visual features are commonly modeled with probability density functions in computer vision problems, but current methods such as a mixture of Gaussians and kernel density estimation suffer from either the lack of flexibility by fixing or limiting the number of Gaussian components in the mixture or large memory requirement by maintaining a nonparametric representation of the density. These problems are aggravated in real-time computer vision applications since density functions are required to be updated as new data becomes available. We present a novel kernel density approximation technique based on the mean-shift mode finding algorithm and describe an efficient method to sequentially propagate the density modes over time. Although the proposed density representation is memory efficient, which is typical for mixture densities, it inherits the flexibility of nonparametric methods by allowing the number of components to be variable. The accuracy and compactness of the sequential kernel density approximation technique is illustrated by both simulations and experiments. Sequential kernel density approximation is applied to online target appearance modeling for visual tracking, and its performance is demonstrated on a variety of videos.}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;Statistical Distributions;Subtraction Technique;, Computer-Assisted;Models, Gaussian estimation;kernel density estimation;mean-shift mode finding algorithm;online target appearance modeling;probability density function;real-time computer vision application;real-time visual tracking;sequential kernel density approximation;visual f, Statistical;Motion;Pattern Recognition}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2007.70771}, author = {Han,Bohyung and Comaniciu, D. and Zhu,Ying and Davis, Larry S.} } @article {14574, title = {Sex and Age Dimorphism of Myocardial Gene Expression in Nonischemic Human Heart Failure}, journal = {Circulation: Cardiovascular Genetics}, volume = {1}, year = {2008}, month = {2008/12/01/}, pages = {117 - 125}, abstract = {Background{\textemdash} We report the first comprehensive analysis of gene expression differences by sex and age in left ventricular samples from 102 patients with dilated cardiomyopathy.Methods and Results{\textemdash} Gene expression data (HG-U133A gene chip, Affymetrix) were analyzed from 30 females and 72 males from 3 separate centers. More than 1800 genes displayed sexual dimorphism in the heart (adjusted P value <0.05). A significant number of these genes were highly represented in gene ontology pathways involved in ion transport and G-protein-coupled receptor signaling. Localization of these genes revealed enrichment on both the sex chromosomes as well as chromosomes 3, 4, and 14. The second goal of this study was to determine the effect of age on gene expression. Within the female cohort, >140 genes were differentially expressed in the <55 years age group compared with the >55 years age group. These genes were highly represented in gene ontology pathways involved in DNA damage. In contrast, zero genes in the male cohort <55 years met statistical significance when compared with the >55 years age group.Conclusions{\textemdash} Gene expression in dilated cardiomyopathy displayed evidence of sexual dimorphism similar to other somatic tissues and age dimorphism within the female cohort.}, doi = {10.1161/CIRCGENETICS.108.802652}, url = {http://circgenetics.ahajournals.org/content/1/2/117.abstract}, author = {Fermin,David R. and Barac,Ana and Lee,Sangjin and Polster,Sean P. and Hannenhalli, Sridhar and Bergemann,Tracy L. and Grindle,Suzanne and Dyke,David B. and Pagani,Francis and Miller,Leslie W. and Tan,Sarah and dos Remedios,Cris and Cappola,Thomas P. and Margulies,Kenneth B. and Hall,Jennifer L.} } @article {12559, title = {Shape-and-Behavior Encoded Tracking of Bee Dances}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {30}, year = {2008}, month = {2008/03//}, pages = {463 - 476}, abstract = {Behavior analysis of social insects has garnered impetus in recent years and has led to some advances in fields like control systems and flight navigation. Manual labeling of insect motions required for analyzing the behaviors of insects requires significant investment of time and effort. In this paper, we propose certain general principles that help in simultaneous automatic tracking and behavior analysis, with applications in tracking bees and recognizing specific behaviors that they exhibit. The state space for tracking is defined using the position, orientation, and current behavior of the insect being tracked. The position and the orientation are parameterized using a shape model, whereas the behavior is explicitly modeled using a three-tier hierarchical motion model. The first tier (dynamics) models the local motions exhibited, and the models built in this tier act as a vocabulary for behavior modeling. The second tier is a Markov motion model built on top of the local motion vocabulary, which serves as the behavior model. The third tier of the hierarchy models the switching between behaviors, and this is also modeled as a Markov model. We address issues in learning the three-tier behavioral model, in discriminating between models, and in detecting and modeling abnormal behaviors. Another important aspect of this work is that it leads to joint tracking and behavior analysis instead of the traditional "track-and-then-recognize" approach. We apply these principles for tracking bees in a hive while they are executing the waggle dance and the round dance.}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;Social Behavior;, Computer-Assisted;Imaging, Markov model;bee dance;behavior analysis;shape model;social insect;three-tier hierarchical motion model;tracking;video sequence;waggle dance;Markov processes;image sequences;optical tracking;video signal processing;zoology;Algorithms;Animal Communication;, Three-Dimensional;Information Storage and Retrieval;Male;Pattern Recognition}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2007.70707}, author = {Veeraraghavan,A. and Chellapa, Rama and Srinivasan, M.} } @article {12914, title = {Silent Sputnik}, journal = {BioScience}, volume = {58}, year = {2008}, month = {2008///}, pages = {3 - 3}, isbn = {0006-3568}, doi = {10.1641/B580101}, url = {http://www.bioone.org/doi/abs/10.1641/B580101}, author = {Rita R Colwell} } @article {12911, title = {A simple binomial test for estimating sequencing errors in public repository 16S rRNA sequences}, journal = {Journal of Microbiological Methods}, volume = {72}, year = {2008}, month = {2008/02//}, pages = {166 - 179}, abstract = {Sequences in public databases may contain a number of sequencing errors. A double binomial model describing the distribution of indel-excluded similarity coefficients (S) among repeatedly sequenced 16S rRNA was previously developed and it produced a confidence interval of S useful for testing sequence identity among sequences of 400-bp length. We characterized patterns in sequencing errors found in nearly complete 16S rRNA sequences of Vibrionaceae as highly variable in reported sequence length and containing a small number of indels. To accommodate these characteristics, a simple binomial model for distribution of the similarity coefficient (H) that included indels was derived from the double binomial model for S. The model showed good fit to empirical data. By using either a pre-determined or bootstrapping estimated standard probability of base matching, we were able to use the exact binomial test to determine the relative level of sequencing error for a given pair of duplicated sequences. A limitation of the method is the requirement that duplicated sequences for the same template sequence be paired, but this can be overcome by using only conserved regions of 16S rRNA sequences and pairing a given sequence with its highest scoring BLAST search hit from the nr database of GenBank.}, keywords = {16S rRNA, Binomial model, Sequence similarity coefficient, Sequencing error, SSU rRNA}, isbn = {0167-7012}, doi = {10.1016/j.mimet.2007.11.013}, url = {http://www.sciencedirect.com/science/article/pii/S0167701207003910}, author = {Zo,Young-Gun and Rita R Colwell} } @conference {12551, title = {Statistical analysis on Stiefel and Grassmann manifolds with applications in computer vision}, booktitle = {Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on}, year = {2008}, month = {2008/06//}, pages = {1 - 8}, abstract = {Many applications in computer vision and pattern recognition involve drawing inferences on certain manifold-valued parameters. In order to develop accurate inference algorithms on these manifolds we need to a) understand the geometric structure of these manifolds b) derive appropriate distance measures and c) develop probability distribution functions (pdf) and estimation techniques that are consistent with the geometric structure of these manifolds. In this paper, we consider two related manifolds - the Stiefel manifold and the Grassmann manifold, which arise naturally in several vision applications such as spatio-temporal modeling, affine invariant shape analysis, image matching and learning theory. We show how accurate statistical characterization that reflects the geometry of these manifolds allows us to design efficient algorithms that compare favorably to the state of the art in these very different applications. In particular, we describe appropriate distance measures and parametric and non-parametric density estimators on these manifolds. These methods are then used to learn class conditional densities for applications such as activity recognition, video based face recognition and shape classification.}, keywords = {algorithm;learning, analysis;computer, analysis;statistical, analysis;video, based, classification;image, classification;spatio-temporal, distribution, distributions;, Face, functions;shape, Grassmann, invariant, manifold;activity, manifold;Stiefel, matching;inference, matching;spatiotemporal, measures;estimation, modeling;statistical, parameters;pattern, phenomena;statistical, recognition;affine, recognition;computer, recognition;probability, SHAPE, structure;image, technique;geometric, theory;manifold-valued, vision;distance, vision;image}, doi = {10.1109/CVPR.2008.4587733}, author = {Turaga,P. and Veeraraghavan,A. and Chellapa, Rama} } @conference {12546, title = {Stochastic fusion of multi-view gradient fields}, booktitle = {Image Processing, 2008. ICIP 2008. 15th IEEE International Conference on}, year = {2008}, month = {2008/10//}, pages = {1324 - 1327}, abstract = {Image gradients form powerful cues in a host of vision and graphics applications. In this paper, we consider multiple views of a textured planar scene and consider the problem of estimating the scene texture map using these multi-view inputs. Modeling each camera view as a projective transformation of the scene, we show that the problem is equivalent to that of studying the effect of noise (and the projective imaging) on the gradient fields induced by this texture map. We show that these noisy gradient fields can be modeled as complete observers of the scene radiance. Further, the corrupting noise can be shown to be additive and linear, although spatially varying. However, the specific form of the noise term can be exploited to design linear estimators that fuse the gradient fields obtained from each of the individual views. The fused gradient field forms a robust estimate of the scene gradients and can be used for scene reconstruction.}, keywords = {application;brightness;cameras;gradient, application;image, camera, estimators;multiview, fields;projective, fusion;image, fusion;textured, gradient, gradients;linear, gradients;scene, imaging;scene, map;stochastic, methods;image, noise;graphics, planar, radiance;scene, reconstruction;image, reconstruction;scene, scene;vision, TEXTURE, texture;, view;corrupting}, doi = {10.1109/ICIP.2008.4712007}, author = {Sankaranarayanan,A. C and Chellapa, Rama} } @article {12540, title = {Synthesis of Silhouettes and Visual Hull Reconstruction for Articulated Humans}, journal = {Multimedia, IEEE Transactions on}, volume = {10}, year = {2008}, month = {2008/12//}, pages = {1565 - 1577}, abstract = {In this paper, we propose a complete framework for improved synthesis and understanding of the human pose from a limited number of silhouette images. It combines the active image-based visual hull (IBVH) algorithm and a contour-based body part segmentation technique. We derive a simple, approximate algorithm to decide the extrinsic parameters of a virtual camera, and synthesize the turntable image collection of the person using the IBVH algorithm by actively moving the virtual camera on a properly computed circular trajectory around the person. Using the turning function distance as the silhouette similarity measurement, this approach can be used to generate the desired pose-normalized images for recognition applications. In order to overcome the inability of the visual hull (VH) method to reconstruct concave regions, we propose a contour-based human body part localization algorithm to segment the silhouette images into convex body parts. The body parts observed from the virtual view are generated separately from the corresponding body parts observed from the input views and then assembled together for a more accurate VH reconstruction. Furthermore, the obtained turntable image collection helps to improve the body part segmentation and identification process. By using the inner distance shape context (IDSC) measurement, we are able to estimate the body part locations more accurately from a synthesized view where we can localize the body part more precisely. Experiments show that the proposed algorithm can greatly improve body part segmentation and hence shape reconstruction results.}, keywords = {active, algorithm;articulated, algorithm;inner, body, camera;visual, collection;virtual, computation;contour-based, Context, detection;image, distance, distance;turntable, estimation;shape, function, hull, human, image, image;approximate, localization, measurement;silhouette, measurement;turning, part, pose;circular, reality;, recognition;virtual, reconstruction;approximation, reconstruction;image, segmentation, segmentation;pose, SHAPE, similarity, synthesis;silhouette, technique;human, theory;cameras;edge, Trajectory}, isbn = {1520-9210}, doi = {10.1109/TMM.2008.2007321}, author = {Yue,Zhanfeng and Chellapa, Rama} } @article {12912, title = {Transesterification activity of a novel lipase from Acinetobacter venetianus RAG-1}, journal = {Antonie van Leeuwenhoek}, volume = {94}, year = {2008}, month = {2008///}, pages = {621 - 625}, abstract = {Transesterification activity and the industrial potential of a novel lipase prepared from Acinetobacter ventiatus RAG-1 were evaluated. Purified lipase samples were dialyzed against pH 9.0 buffer in a single optimization step prior to lyophilization. The enzyme and organic phase were pre-equilibrated (separately) to the same thermodynamic water activities (a w) ranging from a w 0.33 to 0.97. Production of 1-octyl butyrate by lipase-catalyzed transesterification of vinyl butyrate with 1-octanol in hexane was monitored by gas chromatography. Production of 1-octyl butyrate and initial rate of reaction depended on water activity. Product synthesis and rate of transesterification increased sharply with increase from a w 0.33 to 0.55. Highest product concentration (218 mM) and rate of reaction (18.7 μmol h-1 {\textperiodcentered} 10 μg protein) were measured at a w 0.86. Transesterification activity in hexane represented 32\% of comparable hydrolytic activity in aqueous buffer.}, doi = {10.1007/s10482-008-9276-5}, author = {Snellman,E. A. and Rita R Colwell} } @article {18448, title = {Understanding the High-Performance-Computing Community: A Software Engineer{\textquoteright}s Perspective}, journal = {Software, IEEE}, volume = {25}, year = {2008}, month = {2008/08//july}, pages = {29 - 36}, abstract = {Computational scientists developing software for HPC systems face unique software engineering issues. Attempts to transfer SE technologies to this domain must take these issues into account.}, keywords = {community;software, computational, engineering;, engineering;software, Science, software;high-performance-computing}, isbn = {0740-7459}, doi = {10.1109/MS.2008.103}, author = {Basili, Victor R. and Carver, J. C and Cruzes, D. and Hochstein, L. M and Hollingsworth, Jeffrey K and Shull, F. and Zelkowitz, Marvin V} } @conference {18682, title = {On the Use of Security Metrics Based on Intrusion Prevention System Event Data: An Empirical Analysis}, year = {2008}, month = {2008/12//}, pages = {49 - 58}, abstract = {With the increasing number of attacks on the Internet, a primary concern for organizations is the protection of their network. To do so, organizations install security devices such as intrusion prevention systems to monitor network traffic. However, data that are collected by these devices are often imperfect. The contribution of this paper is to try to define some practical metrics based on imperfect data collected by an intrusion prevention system. Since attacks greatly differ, we propose to group the attacks into several attack type groups. We then define a set of metrics for each attack type group. We introduce an approach that consists in analyzing the evolution of these metrics per attack type group by focusing on outliers in order to give an insight into an organizationpsilas security. The method is assessed for an organization of about 40,000 computers. The results were encouraging: outliers could be related to security issues that, in some cases, had not been previously flagged.}, keywords = {empirical analysis, Internet, Internet attack group, intrusion prevention system event data, network traffic monitoring, organization security metrics, security of data}, doi = {10.1109/HASE.2008.52}, author = {Chrun,D. and Michel Cukier and Sneeringer,G.} } @article {12909, title = {Vibrio cholerae non-O1, non-O139 strains isolated before 1992 from Varanasi, India are multiple drug resistant, contain intSXT, dfr18 and aadA5 genes}, journal = {Environmental Microbiology}, volume = {10}, year = {2008}, month = {2008/04/01/}, pages = {866 - 873}, abstract = {In this study, we report the presence of the SXT element and Class I integron in Vibrio cholerae non-O1, non-O139 strains isolated from Varanasi, India. Isolates were resistant to cotrimoxazole, trimethoprim and/or streptomycin, furazolidone and ampicillin. None contained plasmids. Polymerase chain reaction (PCR) and DNA sequencing revealed the presence of antibiotic resistance gene cassettes, aadA1, aadA2, aadA5 and dfrA15, in the Class I integron and SXT, an integrative conjugative element containing dfr18, sulII and strAB, in three and six of the isolates respectively. Conjugation experiments, followed by PCR analysis of transconjugants, provided evidence for the transferable nature of intSXT and associated antibiotic resistance gene cassettes. This is the first report of the occurrence of SXT ICE, dfr18, sulII, strAB and aadA5 genes in environmental V.~cholerae non-O1, non-O139 strains from Varanasi, India, that had been isolated before 1992.}, isbn = {1462-2920}, doi = {10.1111/j.1462-2920.2007.01502.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2007.01502.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Mohapatra,Harapriya and Mohapatra,Saswat S. and Mantri,Chinmay K. and Rita R Colwell and Singh,Durg V.} } @article {12566, title = {Video stabilization and mosaicing}, journal = {The Essential Guide to Video Processing,}, year = {2008}, month = {2008///}, pages = {109 - 138}, author = {Ramachandran, M. and Veeraraghavan,A. and Chellapa, Rama} } @conference {16765, title = {Virtual access points for vehicular networks}, booktitle = {Proceedings of the 1st international conference on MOBILe Wireless MiddleWARE, Operating Systems, and Applications}, year = {2008}, month = {2008///}, pages = {14 - 14}, author = {Frangiadakis,N. and C{\^a}mara,D. and Filali,F. and Loureiro,A. A.F and Roussopoulos, Nick} } @inbook {16072, title = {Visualizing Functional Data with an Application to eBay{\textquoteright}s Online Auctions}, booktitle = {Handbook of Data VisualizationHandbook of Data Visualization}, series = {Springer Handbooks of Computational Statistics}, year = {2008}, month = {2008///}, pages = {873 - 898}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Technological advances in the measurement, collection, and storage of data have led tomore andmore complex data structures. Examples of such structures include measurements of the behavior of individuals over time, digitized two- or three-dimensional images of the brain, and recordings of three- or even four-dimensional movements of objects traveling through space and time. Such data, although recorded in a discrete fashion, are usually thought of as continuous objects that are represented by functional relationships. This gave rise to functional data analysis (FDA), which was made popular by the monographs of Ramsay and Silverman (1997, 2002), where the center of interest is a set of curves, shapes, objects, or, more generally, a set of functional observations , in contrast to classical statistics where interest centers on a set of data vectors. In that sense, functional data is not only different from the data structure studied in classical statistics, but it actually generalizes it. Many of these new data structures require new statistical methods to unveil the information that they carry.}, isbn = {978-3-540-33037-0}, url = {http://dx.doi.org/10.1007/978-3-540-33037-0_34}, author = {Chen,Chun-houh and H{\"a}rdle,Wolfgang and Unwin,Antony and Jank,Wolfgang and Shmueli,Galit and Plaisant, Catherine and Shneiderman, Ben} } @article {15706, title = {A Weighted GCV Method for Lanczos Hybrid Regularization}, journal = {Electronic Transactions on Numerical Analysis}, volume = {28}, year = {2008}, month = {2008///}, pages = {149 - 167}, url = {http://etna.mcs.kent.edu/vol.28.2007-2008/pp149-167.dir/pp149-167.pdfhttp://etna.mcs.kent.edu/vol.28.2007-2008/pp149-167.dir/pp149-167.pdf}, author = {Chung,Julianne and Nagy,James G. and O{\textquoteright}Leary, Dianne P.} } @article {14894, title = {Appearance Characterization of Linear Lambertian Objects, Generalized Photometric Stereo, and Illumination-Invariant Face Recognition}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {29}, year = {2007}, month = {2007/02//}, pages = {230 - 245}, abstract = {Traditional photometric stereo algorithms employ a Lambertian reflectance model with a varying albedo field and involve the appearance of only one object. In this paper, we generalize photometric stereo algorithms to handle all appearances of all objects in a class, in particular the human face class, by making use of the linear Lambertian property. A linear Lambertian object is one which is linearly spanned by a set of basis objects and has a Lambertian surface. The linear property leads to a rank constraint and, consequently, a factorization of an observation matrix that consists of exemplar images of different objects (e.g., faces of different subjects) under different, unknown illuminations. Integrability and symmetry constraints are used to fully recover the subspace bases using a novel linearized algorithm that takes the varying albedo field into account. The effectiveness of the linear Lambertian property is further investigated by using it for the problem of illumination-invariant face recognition using just one image. Attached shadows are incorporated in the model by a careful treatment of the inherent nonlinearity in Lambert{\textquoteright}s law. This enables us to extend our algorithm to perform face recognition in the presence of multiple illumination sources. Experimental results using standard data sets are presented}, keywords = {albedo field;appearance characterization;generalized photometric stereo algorithms;illumination-invariant face recognition;linear Lambertian objects;observation matrix factorization;face recognition;matrix decomposition;Algorithms;Artificial Intelligence;, Automated;Photogrammetry;Reproducibility of Results;Sensitivity and Specificity;, Computer-Assisted;Information Storage and Retrieval;Lighting;Linear Models;Pattern Recognition}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2007.25}, author = {Zhou,S. K and Aggarwal,G. and Chellapa, Rama and Jacobs, David W.} } @conference {18660, title = {Applying Software Reliability Models on Security Incidents}, year = {2007}, month = {2007/11//}, pages = {159 - 168}, abstract = {Computer and network security incidents have increasing financial consequences as demand for network accessibility and connectivity to resources continues to rise. These security incidents can lead to direct financial losses either through data theft of personal and/or proprietary information as well as a reputational damage which may negatively impact stock prices or consumer confidence in a company. This paper examines a large set of security incident data using tools from the software reliability community. We look at applying Non-Homogenous Poisson Process (NHPP) models as a method for describing the reliability growth process. We examine the full set of incidents as well as subsets of the data based on incident types. We look at using the Laplace test to guide selection of the appropriate models. Then, based on the trend results, we apply various NHPP models (i.e., Goel-Okumutu, S-Shaped, Duane, and K-Stage Curve) to illustrate the relevance of using these models to fit the incident data and to predict future incidents.}, keywords = {computer security incidents, consumer confidence, data theft, network security incidents, nonhomogenous Poisson process, reliability growth process, reputational damage, security of data, software reliability, stock prices}, doi = {10.1109/ISSRE.2007.29}, author = {Condon,E. and Michel Cukier and He,Tao} } @article {18663, title = {Archetypal behavior in computer security}, journal = {Journal of Systems and Software}, volume = {80}, year = {2007}, month = {2007/10//}, pages = {1594 - 1606}, abstract = {The purpose of this study is to understand observed behavior and to diagnose and find solutions to issues encountered in organizational computer security using a systemic approach, namely system archetypes. In this paper we show the feasibility of archetypes application and the benefits of simulation. We developed a model and simulation of some aspects of security based on system dynamics principles. The system dynamics simulation model can be used in support of decision-making, training, and teaching regarding the mitigation of computer security risks. In this paper, we combine two archetypes and show the computer security relevance of such combinations. Presented are instances of the archetypes {\textquotedblleft}Escalation{\textquotedblright}, in which an organization must continuously increase its efforts to counter additional attacker effort; and {\textquotedblleft}Limits to Growth{\textquotedblright}, in which the gains from an organization{\textquoteright}s security efforts plateau or decline due to its limited capacity for security-related tasks. We describe a scenario where these archetypes (individually and combined) can help in diagnosis and understanding, and present simulation of {\textquotedblleft}what-if{\textquotedblright} scenarios suggesting how an organization might remedy these problems and maximize its gains from security efforts.}, keywords = {Attacks and countermeasures, Escalation, Limits to Growth, Organization computer security, System archetypes, System dynamics, System dynamics modeling and simulation}, isbn = {0164-1212}, doi = {10.1016/j.jss.2007.01.046}, url = {http://www.sciencedirect.com/science/article/pii/S0164121207000155}, author = {Rosenfeld,Shalom N. and Rus,Ioana and Michel Cukier} } @article {12916, title = {Association of Vibrio Cholerae O1 El Tor and O139 Bengal with the Copepods Acartia Tonsa and Eurytemora Affinis}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {73}, year = {2007}, month = {2007/12/15/}, pages = {7926 - 7933}, abstract = {The association of Vibrio cholerae with zooplankton has been suggested as an important factor in transmission of human epidemic cholera, and the ability to colonize zooplankton surfaces may play a role in the temporal variation and predominance of the two different serogroups (V. cholerae O1 El Tor and O139) in the aquatic environment. To date, interactions between specific serogroups and species of plankton remain poorly understood. Laboratory microcosm experiments were carried out to compare quantitatively the colonization of two copepod species, Acartia tonsa and Eurytemora affinis, by each of the epidemic serogroups. V. cholerae O1 consistently achieved higher abundances than V. cholerae O139 in colonizing adults of each copepod species as well as the multiple life stages of E. affinis. This difference in colonization may be significant in the general predominance of V. cholerae O1 in cholera epidemics in rural Bangladesh where water supplies are taken directly from the environment.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.01238-07}, url = {http://aem.asm.org/content/73/24/7926}, author = {Rawlings,Tonya K. and Ruiz,Gregory M. and Rita R Colwell} } @conference {13034, title = {A Bayesian model for discovering typological implications}, booktitle = {ANNUAL MEETING-ASSOCIATION FOR COMPUTATIONAL LINGUISTICS}, volume = {45}, year = {2007}, month = {2007///}, pages = {65 - 65}, author = {Daum{\'e}, Hal and Campbell,L.} } @article {12981, title = {Biased data reduce efficiency and effectiveness of conservation reserve networks}, journal = {Ecology Letters}, volume = {10}, year = {2007}, month = {2007/05/01/}, pages = {364 - 374}, abstract = {Complementarity-based reserve selection algorithms efficiently prioritize sites for biodiversity conservation, but they are data-intensive and most regions lack accurate distribution maps for the majority of species. We explored implications of basing conservation planning decisions on incomplete and biased data using occurrence records of the plant family Proteaceae in South Africa. Treating this high-quality database as {\textquoteleft}complete{\textquoteright}, we introduced three realistic sampling biases characteristic of biodiversity databases: a detectability sampling bias and two forms of roads sampling bias. We then compared reserve networks constructed using complete, biased, and randomly sampled data. All forms of biased sampling performed worse than both the complete data set and equal-effort random sampling. Biased sampling failed to detect a median of 1{\textendash}5\% of species, and resulted in reserve networks that were 9{\textendash}17\% larger than those designed with complete data. Spatial congruence and the correlation of irreplaceability scores between reserve networks selected with biased and complete data were low. Thus, reserve networks based on biased data require more area to protect fewer species and identify different locations than those selected with randomly sampled or complete data.}, keywords = {Bias, biodiversity conservation, complementarity, efficiency, marxan, rarity, reserve networks, reserve selection algorithms, species detection}, isbn = {1461-0248}, doi = {10.1111/j.1461-0248.2007.01025.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2007.01025.x/abstract}, author = {Grand,Joanna and Cummings, Michael P. and Rebelo,Tony G and Ricketts,Taylor H and Neel,Maile C} } @article {12982, title = {Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences}, journal = {Future Generation Comp Syst}, volume = {23}, year = {2007}, month = {2007/03//}, pages = {497 - 509}, abstract = {Life science research is becoming evermore computationally intensive. Hence, from a computational resource perspective, Grid computing provides a logical approach to meeting many of the computational needs of life science research. However, there are several barriers to the widespread use of Grid computing in life sciences. In this paper, we attempt to address one particular barrier: the difficulty of using Grid computing by life scientists. Life science research often involves connecting multiple applications together to form a workflow. This process of constructing a workflow is complex. When combined with the difficulty of using Grid services, composing a meaningful workflow using Grid services can present a challenge to life scientists. Our proposed solution is a Semantic Web-enabled computing environment, called Bio-STEER. In BioSTEER, bioinformatics Grid services are mapped to Semantic Web services, described in OWL-S. We also defined an ontology in OWL to model bioinformatics applications. A graphical user interface helps to construct a scientific workflow by showing a list of services that are semantically sound: that is, the output of one service is semantically compatible with the input of the connecting service. Bio-STEER can help users take full advantaue of Grid services through a user-friendly graphical user interface (GUI), which allows them to easily construct the workflows they need. (c) 2006 Elsevier B.V. All rights reserved.}, keywords = {client/server;, distributed, environments;, integrated, interface, management;, semantics;, services;, systems;, user, web-base, workflow}, doi = {DOI 10.1016/j.future.2006.07.011}, author = {Lee,S. and Wang,T. D and Hashmi,N. and Cummings, Michael P.} } @conference {12921, title = {Bridging art and science with creativity support tools}, booktitle = {Proceedings of the 6th ACM SIGCHI conference on Creativity \& cognition}, series = {C\&C {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {309 - 309}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {978-1-59593-712-4}, doi = {10.1145/1254960.1255044}, url = {http://doi.acm.org/10.1145/1254960.1255044}, author = {Shneiderman, Ben and Rita R Colwell and Diamond,Sara and Greenhalgh,Paul and Wulf,William} } @inbook {15722, title = {Bridging the ROUGE/Human Evaluation Gap in Multi-Document Summarization}, booktitle = {Document Understanding Conference DUC 2007Document Understanding Conference DUC 2007}, year = {2007}, month = {2007/04/26/}, publisher = {HLT-NAACL}, organization = {HLT-NAACL}, address = {Rochester, NY}, author = {Conroy,John M. and Schlesinger,Judith D. and O{\textquoteright}Leary, Dianne P.} } @article {15156, title = {Chosen-ciphertext security from identity-based encryption}, journal = {SIAM Journal on Computing}, volume = {36}, year = {2007}, month = {2007///}, pages = {1301 - 1328}, abstract = {We propose simple and efficient CCA-secure public-key encryption schemes (i.e., schemessecure against adaptive chosen-ciphertext attacks) based on any identity-based encryption (IBE) scheme. Our constructions have ramifications of both theoretical and practical interest. First, our schemes give a new paradigm for achieving CCA-security; this paradigm avoids {\textquotedblleft}proofs of well-formedness{\textquotedblright} that have been shown to underlie previous constructions. Second, instantiating our construction using known IBE constructions we obtain CCA-secure encryption schemes whose performance is competitive with the most efficient CCA-secure schemes to date. Our techniques extend naturally to give an efficient method for securing IBE schemes (even hierarchical ones) against adaptive chosen-ciphertext attacks. Coupled with previous work, this gives the first efficient constructions of CCA-secure IBE schemes. }, author = {Boneh,D. and Canetti,R. and Halevi,S. and Katz, Jonathan} } @conference {12593, title = {Coarse-to-Fine Event Model for Human Activities}, booktitle = {Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on}, volume = {1}, year = {2007}, month = {2007/04//}, pages = {I-813 -I-816 - I-813 -I-816}, abstract = {We analyze coarse-to-fine hierarchical representation of human activities in video sequences. It can be used for efficient video browsing and activity recognition. Activities are modeled using a sequence of instantaneous events. Events in activities can be represented in a coarse-to-fine hierarchy in several ways, i.e., there may not be a unique hierarchical structure. We present five criteria and quantitative measures for evaluating their effectiveness. The criteria are minimalism, stability, consistency, accessibility and applicability. It is desirable to develop activity models that rank highly on these criteria at all levels of hierarchy. In this paper, activities are represented as sequence of event probabilities computed using the hidden Markov model framework. Two aspects of hierarchies are analyzed: the effect of reduced frame rate on the accuracy of events detected at a finer scale; and the effect of reduced spatial resolution on activity recognition. Experiments using the UCF indoor human action dataset and the TSA airport tarmac surveillance dataset show encouraging results}, keywords = {action, activities;spatial, airport, browsing;video, dataset;activity, dataset;UCF, event, framework;human, human, indoor, Markov, model, model;event, models;image, probabilities;hidden, processing;, recognition;coarse-to-fine, reduction;video, representation;image, resolution, resolution;image, sequences;hidden, sequences;stability;video, signal, Surveillance, tarmac, TSA}, doi = {10.1109/ICASSP.2007.366032}, author = {Cuntoor, N.P. and Chellapa, Rama} } @article {14103, title = {Cofactor-independent phosphoglycerate mutase is an essential gene in procyclic form Trypanosoma brucei}, journal = {Parasitology research}, volume = {100}, year = {2007}, month = {2007///}, pages = {887 - 892}, author = {Djikeng,A. and Raverdy,S. and Foster, Jeffrey S. and Bartholomeu,D. and Zhang,Y. and El-Sayed, Najib M. and Carlow,C.} } @article {14666, title = {Combining provenance and security policies in a web-based document management system}, journal = {On-line Proceedings of the Workshop on Principles of Provenance (PrOPr)}, year = {2007}, month = {2007///}, author = {Corcoran,B.J. and Swamy,N. and Hicks, Michael W.} } @conference {18646, title = {A Comparison between Internal and External Malicious Traffic}, year = {2007}, month = {2007///}, pages = {109 - 114}, abstract = {This paper empirically compares malicious traffic originating inside an organization (i.e., internal traffic) with malicious traffic originating outside an organization (i.e., external traffic). Two honeypot target computers were deployed to collect malicious traffic data over a period of fifteen weeks. In the first study we showed that there was a weak correlation between internal and external traffic based on the number of malicious connections. Since the type of malicious activity is linked to the port that was targeted, we focused on the most frequently targeted ports. We observed that internal malicious traffic often contained different malicious content compared to that of external traffic. In the third study, we discovered that the volume of malicious traffic was linked to the day of the week. We showed that internal and external malicious activities differ: where the external malicious activity is quite stable over the week, the internal traffic varied as a function of the users{\textquoteright} activity profile.}, keywords = {Computer networks, Data analysis, external traffic, honeypot target computers, internal traffic, malicious traffic data, security of data, user activity profile}, doi = {10.1109/ISSRE.2007.32}, author = {Michel Cukier and Panjwani,S.} } @article {14327, title = {Conducting In Situ Evaluations for and With Ubiquitous Computing Technologies}, journal = {International Journal of Human-Computer Interaction}, volume = {22}, year = {2007}, month = {2007///}, pages = {103 - 118}, abstract = {Abstract To evaluate ubiquitous computing technologies, which may be embedded in the environment, embedded in objects, worn, or carried by the user throughout everyday life, it is essential to use methods that accommodate the often unpredictable, real-world environments in which the technologies are used. This article discusses how we have adapted and applied traditional methods from psychology and human-computer interaction, such as Wizard of Oz and Experience Sampling, to be more amenable to the in situ evaluations of ubiquitous computing applications, particularly in the early stages of design. The way that ubiquitous computing technologies can facilitate the in situ collection of self-report data is also discussed. Although the focus is on ubiquitous computing applications and tools for their assessment, it is believed that the in situ evaluation tools that are proposed will be generally useful for field trials of other technology, applications, or formative studies that are concerned with collecting data in situ.Abstract To evaluate ubiquitous computing technologies, which may be embedded in the environment, embedded in objects, worn, or carried by the user throughout everyday life, it is essential to use methods that accommodate the often unpredictable, real-world environments in which the technologies are used. This article discusses how we have adapted and applied traditional methods from psychology and human-computer interaction, such as Wizard of Oz and Experience Sampling, to be more amenable to the in situ evaluations of ubiquitous computing applications, particularly in the early stages of design. The way that ubiquitous computing technologies can facilitate the in situ collection of self-report data is also discussed. Although the focus is on ubiquitous computing applications and tools for their assessment, it is believed that the in situ evaluation tools that are proposed will be generally useful for field trials of other technology, applications, or formative studies that are concerned with collecting data in situ. }, isbn = {1044-7318}, doi = {10.1080/10447310709336957}, url = {http://www.tandfonline.com/doi/abs/10.1080/10447310709336957}, author = {Consolvo,Sunny and Harrison,Beverly and Smith,Ian and Chen,Mike Y. and Everitt,Katherine and Jon Froehlich and Landay,James A.} } @conference {15462, title = {Covering array sampling of input event sequences for automated gui testing}, booktitle = {Proceedings of the twenty-second IEEE/ACM international conference on Automated software engineering}, series = {ASE {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {405 - 408}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a new automated technique to generate test cases for GUIs by using covering arrays (CAs). The key motivation is to generate long GUI event sequences that are systematically sampled at a particular coverage strength. CAs, to date, have not been effectively used in sampling event driven systems such as GUIs which maintain state. We leverage a "stateless" abstraction of GUIs that allows us to use CAs. Once the CAs have been generated, we reuse the abstractions to reinsert ordering relationships between GUI events, thereby creating executable test cases. A feasibility study on a well-studied GUI-based application shows that the new technique is able to detect a large number of previously undetected faults}, keywords = {covering arrays, event driven software, GUI testing}, isbn = {978-1-59593-882-4}, doi = {10.1145/1321631.1321695}, url = {http://doi.acm.org/10.1145/1321631.1321695}, author = {Xun Yuan and Cohen,Myra and Memon, Atif M.} } @article {12922, title = {Creating a nationwide wireless detection sensor network for chemical, biological and radiological threats}, journal = {Gentag White Paper}, year = {2007}, month = {2007///}, author = {Rita R Colwell and Peeters,J.} } @conference {17582, title = {Cross-layer latency minimization in wireless networks with SINR constraints}, booktitle = {Proceedings of the 8th ACM international symposium on Mobile ad hoc networking and computing}, series = {MobiHoc {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {110 - 119}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Recently, there has been substantial interest in the design of cross-layer protocols for wireless networks. These protocols optimize certain performance metric(s) of interest (e.g. latency, energy, rate) by jointly optimizing the performance of multiple layers of the protocol stack. Algorithm designers often use geometric-graph-theoretic models for radio interference to design such cross-layer protocols. In this paper we study the problem of designing cross-layer protocols for multi-hop wireless networks using a more realistic Signal to Interference plus Noise Ratio (SINR) model for radio interference. The following cross-layer latency minimization problem is studied: Given a set V of transceivers, and a set of source-destination pairs, (i) choose power levels for all the transceivers, (ii) choose routes for all connections, and (iii) construct an end-to-end schedule such that the SINR constraints are satisfied at each time step so as to minimize the make-span of the schedule (the time by which all packets have reached their respective destinations). We present a polynomial-time algorithm with provable worst-case performance guarantee for this cross-layer latency minimization problem. As corollaries of the algorithmic technique we show that a number of variants of the cross-layer latency minimization problem can also be approximated efficiently in polynomial time. Our work extends the results of Kumar et al. (Proc. SODA, 2004) and Moscibroda et al. (Proc. MOBIHOC, 2006). Although our algorithm considers multiple layers of the protocol stack, it can naturally be viewed as compositions of tasks specific to each layer --- this allows us to improve the overall performance while preserving the modularity of the layered structure.}, keywords = {cross-layer design, end-to-end scheduling, Interference, SINR model, Wireless networks}, isbn = {978-1-59593-684-4}, doi = {10.1145/1288107.1288123}, url = {http://doi.acm.org/10.1145/1288107.1288123}, author = {Chafekar,Deepti and Kumar,V. S. Anil and Marathe,Madhav V. and Parthasarathy,Srinivasan and Srinivasan, Aravind} } @article {12326, title = {Dataflow-based mapping of computer vision algorithms onto FPGAs}, journal = {EURASIP Journal on Embedded Systems}, volume = {2007}, year = {2007}, month = {2007///}, pages = {29 - 29}, author = {Sen,M. and Corretjer,I. and Haim,F. and Saha,S. and Schlessman,J. and Lv,T. and Bhattacharyya, Shuvra S. and Wolf,W.} } @booklet {19446, title = {Description of Computer Science Higher Education in Sub-Saharan Africa: Initial Explorations}, year = {2007}, month = {2007///}, abstract = {Many countries in Sub-Saharan Africa (SSA) are in need oftechnology innovators who are equipped to leverage technologies in locally relevant domains such as health, government and education. To create skilled graduates who can build and shape locally relevant technologies, higher education institutes in Africa must have Computer Science (CS) education programs that meet local needs, for example, to satisfy the demand for entrepreneurs to build industry and strengthen an economy. This paper characterizes the current state of CS education in SSA in order to identify opportunities for addressing education challenges and to make suggestions that may improve the Information and Communication Technology (ICT) infrastructure in this region. We present the results of a survey of CS educators in SSA institutions of higher education, which was aimed at exploring the issues they face. In addition to the continued chronic under-funding of SSA education, we found that universities in SSA have smaller departments, less focus on Human Computer Interaction (HCI) and offer a variety of courses aside from undergraduate Bachelors degrees. We discuss directions to improve CS curricula through investing in locally tailored courses and changing perceptions of the value of SSA CS higher education programs, standards and educators. Further, we reflect on the challenges of conducting research on SSA. We conclude that further research in this area is needed to build on the ideas we offer here to continue to strengthen CS higher education in SSA. }, keywords = {Sub-Saharan Africa, Undergraduate computing education}, doi = {Technical Report}, url = {https://smartech.gatech.edu/handle/1853/20060}, author = {Marshini Chetty and Buckhalter, Celeste and Best, Michael L. and Grinter, Rebecca E. and Guzdial, Mark} } @conference {16079, title = {Discovering interesting usage patterns in text collections: integrating text mining with visualization}, booktitle = {Proceedings of the sixteenth ACM conference on Conference on information and knowledge management}, series = {CIKM {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {213 - 222}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper addresses the problem of making text mining results more comprehensible to humanities scholars, journalists, intelligence analysts, and other researchers, in order to support the analysis of text collections. Our system, FeatureLens1, visualizes a text collection at several levels of granularity and enables users to explore interesting text patterns. The current implementation focuses on frequent itemsets of n-grams, as they capture the repetition of exact or similar expressions in the collection. Users can find meaningful co-occurrences of text patterns by visualizing them within and across documents in the collection. This also permits users to identify the temporal evolution of usage such as increasing, decreasing or sudden appearance of text patterns. The interface could be used to explore other text features as well. Initial studies suggest that FeatureLens helped a literary scholar and 8 users generate new hypotheses and interesting insights using 2 text collections.}, keywords = {digital humanities, frequent closed itemsets, n-grams, text mining, user interface}, isbn = {978-1-59593-803-9}, doi = {10.1145/1321440.1321473}, url = {http://doi.acm.org/10.1145/1321440.1321473}, author = {Don,Anthony and Zheleva,Elena and Gregory,Machon and Tarkan,Sureyya and Auvil,Loretta and Clement,Tanya and Shneiderman, Ben and Plaisant, Catherine} } @inbook {19567, title = {Distribution-Free Testing Lower Bounds for Basic Boolean Functions}, booktitle = {Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques}, series = {Lecture Notes in Computer Science}, year = {2007}, month = {2007/01/01/}, pages = {494 - 508}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {In the distribution-free property testing model, the distance between functions is measured with respect to an arbitrary and unknown probability distribution \mathcal{D} over the input domain. We consider distribution-free testing of several basic Boolean function classes over {0,1} n , namely monotone conjunctions, general conjunctions, decision lists, and linear threshold functions. We prove that for each of these function classes, Ω((n/logn)1/5) oracle calls are required for any distribution-free testing algorithm. Since each of these function classes is known to be distribution-free properly learnable (and hence testable) using Θ(n) oracle calls, our lower bounds are within a polynomial factor of the best possible.}, keywords = {Algorithm Analysis and Problem Complexity, Discrete Mathematics in Computer Science, Numeric Computing}, isbn = {978-3-540-74207-4, 978-3-540-74208-1}, url = {http://link.springer.com/chapter/10.1007/978-3-540-74208-1_36}, author = {Dana Dachman-Soled and Servedio, Rocco A.}, editor = {Charikar, Moses and Jansen, Klaus and Reingold, Omer and Rolim, Jos{\'e} D. P.} } @article {16257, title = {Draft Genome of the Filarial Nematode Parasite Brugia Malayi}, journal = {Science}, volume = {317}, year = {2007}, month = {2007/09/21/}, pages = {1756 - 1760}, abstract = {Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the \~{}90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict \~{}11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during \~{}350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1145406}, url = {http://www.sciencemag.org/content/317/5845/1756}, author = {Ghedin,Elodie and Wang,Shiliang and Spiro,David and Caler,Elisabet and Zhao,Qi and Crabtree,Jonathan and Allen,Jonathan E and Delcher,Arthur L. and Guiliano,David B and Miranda-Saavedra,Diego and Angiuoli,Samuel V and Creasy,Todd and Amedeo,Paolo and Haas,Brian and El-Sayed, Najib M. and Wortman,Jennifer R. and Feldblyum,Tamara and Tallon,Luke and Schatz,Michael and Shumway,Martin and Koo,Hean and Salzberg,Steven L. and Schobel,Seth and Pertea,Mihaela and Pop, Mihai and White,Owen and Barton,Geoffrey J and Carlow,Clotilde K. S and Crawford,Michael J and Daub,Jennifer and Dimmic,Matthew W and Estes,Chris F and Foster,Jeremy M and Ganatra,Mehul and Gregory,William F and Johnson,Nicholas M and Jin,Jinming and Komuniecki,Richard and Korf,Ian and Kumar,Sanjay and Laney,Sandra and Li,Ben-Wen and Li,Wen and Lindblom,Tim H and Lustigman,Sara and Ma,Dong and Maina,Claude V and Martin,David M. A and McCarter,James P and McReynolds,Larry and Mitreva,Makedonka and Nutman,Thomas B and Parkinson,John and Peregr{\'\i}n-Alvarez,Jos{\'e} M and Poole,Catherine and Ren,Qinghu and Saunders,Lori and Sluder,Ann E and Smith,Katherine and Stanke,Mario and Unnasch,Thomas R and Ware,Jenna and Wei,Aguan D and Weil,Gary and Williams,Deryck J and Zhang,Yinhua and Williams,Steven A and Fraser-Liggett,Claire and Slatko,Barton and Blaxter,Mark L and Scott,Alan L} } @conference {12588, title = {Efficient Indexing For Articulation Invariant Shape Matching And Retrieval}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 8}, abstract = {Most shape matching methods are either fast but too simplistic to give the desired performance or promising as far as performance is concerned but computationally demanding. In this paper, we present a very simple and efficient approach that not only performs almost as good as many state-of-the-art techniques but also scales up to large databases. In the proposed approach, each shape is indexed based on a variety of simple and easily computable features which are invariant to articulations and rigid transformations. The features characterize pairwise geometric relationships between interest points on the shape, thereby providing robustness to the approach. Shapes are retrieved using an efficient scheme which does not involve costly operations like shape-wise alignment or establishing correspondences. Even for a moderate size database of 1000 shapes, the retrieval process is several times faster than most techniques with similar performance. Extensive experimental results are presented to illustrate the advantages of our approach as compared to the best in the field.}, keywords = {alignment;image, articulation, geometric, invariant, matching;image, matching;indexing;invariant, relationships;shape-wise, retrieval;indexing;, retrieval;pairwise, SHAPE}, doi = {10.1109/CVPR.2007.383227}, author = {Biswas,S. and Aggarwal,G. and Chellapa, Rama} } @conference {18654, title = {An empirical study of filesystem activity following a SSH compromise}, year = {2007}, month = {2007/12//}, pages = {1 - 5}, abstract = {Monitoring filesystem data is a common method used to detect attacks. Once a computer is compromised, attackers will likely alter files, add new files or delete existing files. The changes that attackers make may target any part of the filesystem, including metadata along with files (e.g., permissions, ownerships and inodes). In this paper, we describe an empirical study that focused on SSH compromised attacks. First statistical data on the number of files targeted and the associated activity (e.g., read, write, delete, ownership and rights) is reported. Then, we refine the analysis to identify and understand patterns in the attack activity.}, keywords = {attack activity, filesystem activity, filesystem data monitoring, intrusion detection systems evaluation, meta data, metadata, security of data, SSH compromised attacks}, doi = {10.1109/ICICS.2007.4449675}, author = {Molina,J. and Gordon,J. and Chorin,X. and Michel Cukier} } @conference {12584, title = {Epitomic Representation of Human Activities}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 8}, abstract = {We introduce an epitomic representation for modeling human activities in video sequences. A video sequence is divided into segments within which the dynamics of objects is assumed to be linear and modeled using linear dynamical systems. The tuple consisting of the estimated system matrix, statistics of the input signal and the initial state value is said to form an epitome. The system matrices are decomposed using the Iwasawa matrix decomposition to isolate the effect of rotation, scaling and projective action on the state vector. "We demonstrate the usefulness of the proposed representation and decomposition for activity recognition using the TSA airport surveillance dataset and the UCF indoor human action dataset.}, keywords = {action, activities, airport, dataset;epitomic, dataset;UCF, decomposition;modelling;statistics;video, decomposition;TSA, dynamical, human, indoor, Iwasawa, matrix, matrix;human, modeling;input, processing;, representation;estimated, sequences;image, sequences;matrix, signal, statistics;linear, Surveillance, system, systems;video}, doi = {10.1109/CVPR.2007.383135}, author = {Cuntoor, N.P. and Chellapa, Rama} } @article {12600, title = {Estimation of contour motion and deformation for nonrigid object tracking}, journal = {Journal of the Optical Society of America AJ. Opt. Soc. Am. A}, volume = {24}, year = {2007}, month = {2007///}, pages = {2109 - 2121}, abstract = {We present an algorithm for nonrigid contour tracking in heavily cluttered background scenes. Based on the properties of nonrigid contour movements, a sequential framework for estimating contour motion and deformation is proposed. We solve the nonrigid contour tracking problem by decomposing it into three subproblems: motion estimation, deformation estimation, and shape regulation. First, we employ a particle filter to estimate the global motion parameters of the affine transform between successive frames. Then we generate a probabilistic deformation map to deform the contour. To improve robustness, multiple cues are used for deformation probability estimation. Finally, we use a shape prior model to constrain the deformed contour. This enables us to retrieve the occluded parts of the contours and accurately track them while allowing shape changes specific to the given object types. Our experiments show that the proposed algorithm significantly improves the tracker performance.}, keywords = {Motion detection, VISION}, doi = {10.1364/JOSAA.24.002109}, url = {http://josaa.osa.org/abstract.cfm?URI=josaa-24-8-2109}, author = {Jie Shao and Porikli,Fatih and Chellapa, Rama} } @article {16261, title = {Evolution of genes and genomes on the Drosophila phylogeny}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007/11/08/}, pages = {203 - 218}, abstract = {Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.}, isbn = {0028-0836}, doi = {10.1038/nature06341}, url = {http://www.nature.com/nature/journal/v450/n7167/full/nature06341.html}, author = {Clark,Andrew G. and Eisen,Michael B. and Smith,Douglas R. and Bergman,Casey M. and Oliver,Brian and Markow,Therese A. and Kaufman,Thomas C. and Kellis,Manolis and Gelbart,William and Iyer,Venky N. and Pollard,Daniel A. and Sackton,Timothy B. and Larracuente,Amanda M. and Singh,Nadia D. and Abad,Jose P. and Abt,Dawn N. and Adryan,Boris and Aguade,Montserrat and Akashi,Hiroshi and Anderson,Wyatt W. and Aquadro,Charles F. and Ardell,David H. and Arguello,Roman and Artieri,Carlo G. and Barbash,Daniel A. and Barker,Daniel and Barsanti,Paolo and Batterham,Phil and Batzoglou,Serafim and Begun,Dave and Bhutkar,Arjun and Blanco,Enrico and Bosak,Stephanie A. and Bradley,Robert K. and Brand,Adrianne D. and Brent,Michael R. and Brooks,Angela N. and Brown,Randall H. and Butlin,Roger K. and Caggese,Corrado and Calvi,Brian R. and Carvalho,A. Bernardo de and Caspi,Anat and Castrezana,Sergio and Celniker,Susan E. and Chang,Jean L. and Chapple,Charles and Chatterji,Sourav and Chinwalla,Asif and Civetta,Alberto and Clifton,Sandra W. and Comeron,Josep M. and Costello,James C. and Coyne,Jerry A. and Daub,Jennifer and David,Robert G. and Delcher,Arthur L. and Delehaunty,Kim and Do,Chuong B. and Ebling,Heather and Edwards,Kevin and Eickbush,Thomas and Evans,Jay D. and Filipski,Alan and Findei|[szlig]|,Sven and Freyhult,Eva and Fulton,Lucinda and Fulton,Robert and Garcia,Ana C. L. and Gardiner,Anastasia and Garfield,David A. and Garvin,Barry E. and Gibson,Greg and Gilbert,Don and Gnerre,Sante and Godfrey,Jennifer and Good,Robert and Gotea,Valer and Gravely,Brenton and Greenberg,Anthony J. and Griffiths-Jones,Sam and Gross,Samuel and Guigo,Roderic and Gustafson,Erik A. and Haerty,Wilfried and Hahn,Matthew W. and Halligan,Daniel L. and Halpern,Aaron L. and Halter,Gillian M. and Han,Mira V. and Heger,Andreas and Hillier,LaDeana and Hinrichs,Angie S. and Holmes,Ian and Hoskins,Roger A. and Hubisz,Melissa J. and Hultmark,Dan and Huntley,Melanie A. and Jaffe,David B. and Jagadeeshan,Santosh and Jeck,William R. and Johnson,Justin and Jones,Corbin D. and Jordan,William C. and Karpen,Gary H. and Kataoka,Eiko and Keightley,Peter D. and Kheradpour,Pouya and Kirkness,Ewen F. and Koerich,Leonardo B. and Kristiansen,Karsten and Kudrna,Dave and Kulathinal,Rob J. and Kumar,Sudhir and Kwok,Roberta and Lander,Eric and Langley,Charles H. and Lapoint,Richard and Lazzaro,Brian P. and Lee,So-Jeong and Levesque,Lisa and Li,Ruiqiang and Lin,Chiao-Feng and Lin,Michael F. and Lindblad-Toh,Kerstin and Llopart,Ana and Long,Manyuan and Low,Lloyd and Lozovsky,Elena and Lu,Jian and Luo,Meizhong and Machado,Carlos A. and Makalowski,Wojciech and Marzo,Mar and Matsuda,Muneo and Matzkin,Luciano and McAllister,Bryant and McBride,Carolyn S. and McKernan,Brendan and McKernan,Kevin and Mendez-Lago,Maria and Minx,Patrick and Mollenhauer,Michael U. and Montooth,Kristi and Mount, Stephen M. and Mu,Xu and Myers,Eugene and Negre,Barbara and Newfeld,Stuart and Nielsen,Rasmus and Noor,Mohamed A. F. and O{\textquoteright}Grady,Patrick and Pachter,Lior and Papaceit,Montserrat and Parisi,Matthew J. and Parisi,Michael and Parts,Leopold and Pedersen,Jakob S. and Pesole,Graziano and Phillippy,Adam M and Ponting,Chris P. and Pop, Mihai and Porcelli,Damiano and Powell,Jeffrey R. and Prohaska,Sonja and Pruitt,Kim and Puig,Marta and Quesneville,Hadi and Ram,Kristipati Ravi and Rand,David and Rasmussen,Matthew D. and Reed,Laura K. and Reenan,Robert and Reily,Amy and Remington,Karin A. and Rieger,Tania T. and Ritchie,Michael G. and Robin,Charles and Rogers,Yu-Hui and Rohde,Claudia and Rozas,Julio and Rubenfield,Marc J. and Ruiz,Alfredo and Russo,Susan and Salzberg,Steven L. and Sanchez-Gracia,Alejandro and Saranga,David J. and Sato,Hajime and Schaeffer,Stephen W. and Schatz,Michael C and Schlenke,Todd and Schwartz,Russell and Segarra,Carmen and Singh,Rama S. and Sirot,Laura and Sirota,Marina and Sisneros,Nicholas B. and Smith,Chris D. and Smith,Temple F. and Spieth,John and Stage,Deborah E. and Stark,Alexander and Stephan,Wolfgang and Strausberg,Robert L. and Strempel,Sebastian and Sturgill,David and Sutton,Granger and Sutton,Granger G. and Tao,Wei and Teichmann,Sarah and Tobari,Yoshiko N. and Tomimura,Yoshihiko and Tsolas,Jason M. and Valente,Vera L. S. and Venter,Eli and Venter,J. Craig and Vicario,Saverio and Vieira,Filipe G. and Vilella,Albert J. and Villasante,Alfredo and Walenz,Brian and Wang,Jun and Wasserman,Marvin and Watts,Thomas and Wilson,Derek and Wilson,Richard K. and Wing,Rod A. and Wolfner,Mariana F. and Wong,Alex and Wong,Gane Ka-Shu and Wu,Chung-I and Wu,Gabriel and Yamamoto,Daisuke and Yang,Hsiao-Pei and Yang,Shiaw-Pyng and Yorke,James A. and Yoshida,Kiyohito and Zdobnov,Evgeny and Zhang,Peili and Zhang,Yu and Zimin,Aleksey V. and Baldwin,Jennifer and Abdouelleil,Amr and Abdulkadir,Jamal and Abebe,Adal and Abera,Brikti and Abreu,Justin and Acer,St Christophe and Aftuck,Lynne and Alexander,Allen and An,Peter and Anderson,Erica and Anderson,Scott and Arachi,Harindra and Azer,Marc and Bachantsang,Pasang and Barry,Andrew and Bayul,Tashi and Berlin,Aaron and Bessette,Daniel and Bloom,Toby and Blye,Jason and Boguslavskiy,Leonid and Bonnet,Claude and Boukhgalter,Boris and Bourzgui,Imane and Brown,Adam and Cahill,Patrick and Channer,Sheridon and Cheshatsang,Yama and Chuda,Lisa and Citroen,Mieke and Collymore,Alville and Cooke,Patrick and Costello,Maura and D{\textquoteright}Aco,Katie and Daza,Riza and Haan,Georgius De and DeGray,Stuart and DeMaso,Christina and Dhargay,Norbu and Dooley,Kimberly and Dooley,Erin and Doricent,Missole and Dorje,Passang and Dorjee,Kunsang and Dupes,Alan and Elong,Richard and Falk,Jill and Farina,Abderrahim and Faro,Susan and Ferguson,Diallo and Fisher,Sheila and Foley,Chelsea D. and Franke,Alicia and Friedrich,Dennis and Gadbois,Loryn and Gearin,Gary and Gearin,Christina R. and Giannoukos,Georgia and Goode,Tina and Graham,Joseph and Grandbois,Edward and Grewal,Sharleen and Gyaltsen,Kunsang and Hafez,Nabil and Hagos,Birhane and Hall,Jennifer and Henson,Charlotte and Hollinger,Andrew and Honan,Tracey and Huard,Monika D. and Hughes,Leanne and Hurhula,Brian and Husby,M Erii and Kamat,Asha and Kanga,Ben and Kashin,Seva and Khazanovich,Dmitry and Kisner,Peter and Lance,Krista and Lara,Marcia and Lee,William and Lennon,Niall and Letendre,Frances and LeVine,Rosie and Lipovsky,Alex and Liu,Xiaohong and Liu,Jinlei and Liu,Shangtao and Lokyitsang,Tashi and Lokyitsang,Yeshi and Lubonja,Rakela and Lui,Annie and MacDonald,Pen and Magnisalis,Vasilia and Maru,Kebede and Matthews,Charles and McCusker,William and McDonough,Susan and Mehta,Teena and Meldrim,James and Meneus,Louis and Mihai,Oana and Mihalev,Atanas and Mihova,Tanya and Mittelman,Rachel and Mlenga,Valentine and Montmayeur,Anna and Mulrain,Leonidas and Navidi,Adam and Naylor,Jerome and Negash,Tamrat and Nguyen,Thu and Nguyen,Nga and Nicol,Robert and Norbu,Choe and Norbu,Nyima and Novod,Nathaniel and O{\textquoteright}Neill,Barry and Osman,Sahal and Markiewicz,Eva and Oyono,Otero L. and Patti,Christopher and Phunkhang,Pema and Pierre,Fritz and Priest,Margaret and Raghuraman,Sujaa and Rege,Filip and Reyes,Rebecca and Rise,Cecil and Rogov,Peter and Ross,Keenan and Ryan,Elizabeth and Settipalli,Sampath and Shea,Terry and Sherpa,Ngawang and Shi,Lu and Shih,Diana and Sparrow,Todd and Spaulding,Jessica and Stalker,John and Stange-Thomann,Nicole and Stavropoulos,Sharon and Stone,Catherine and Strader,Christopher and Tesfaye,Senait and Thomson,Talene and Thoulutsang,Yama and Thoulutsang,Dawa and Topham,Kerri and Topping,Ira and Tsamla,Tsamla and Vassiliev,Helen and Vo,Andy and Wangchuk,Tsering and Wangdi,Tsering and Weiand,Michael and Wilkinson,Jane and Wilson,Adam and Yadav,Shailendra and Young,Geneva and Yu,Qing and Zembek,Lisa and Zhong,Danni and Zimmer,Andrew and Zwirko,Zac and Jaffe,David B. and Alvarez,Pablo and Brockman,Will and Butler,Jonathan and Chin,CheeWhye and Gnerre,Sante and Grabherr,Manfred and Kleber,Michael and Mauceli,Evan and MacCallum,Iain} } @article {19072, title = {Evolution of genes and genomes on the Drosophila phylogeny}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007}, pages = {203 - 218}, author = {Clark, A.G. and Eisen,M. B and Smith,D. R and Bergman, C.M. and Oliver, B. and Markow, T.A. and Kaufman, T.C. and Kellis, M. and Gelbart, W. and Iyer, V.N. and others} } @article {12599, title = {Face and Gesture Recognition-Appearance Characterization of Linear Lambertian Objects, Generalized Photometric Stereo, and Illumination-Invariant Face Recognition}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {29}, year = {2007}, month = {2007///}, pages = {230 - 245}, author = {Zhou,S. K and Aggarwal,G. and Chellapa, Rama and Jacobs, David W.} } @conference {12576, title = {Fast Bilinear SfM with Side Information}, booktitle = {Computer Vision, 2007. ICCV 2007. IEEE 11th International Conference on}, year = {2007}, month = {2007/10//}, pages = {1 - 8}, abstract = {We study the beneficial effect of side information on the Structure from Motion (SfM) estimation problem. The side information that we consider is measurement of a {\textquoteright}reference vector{\textquoteright} and distance from fixed plane perpendicular to that reference vector. Firstly, we show that in the presence of this information, the SfM equations can be rewritten similar to a bilinear form in its unknowns. Secondly, we describe a fast iterative estimation procedure to recover the structure of both stationary scenes and moving objects that capitalizes on this information. We also provide a refinement procedure in order to tackle incomplete or noisy side information. We characterize the algorithm with respect to its reconstruction accuracy, memory requirements and stability. Finally, we describe two classes of commonly occurring real-world scenarios in which this algorithm will be effective: (a) presence of a dominant ground plane in the scene and (b) presence of an inertial measurement unit on board. Experiments using both real data and rigorous simulations show the efficacy of the algorithm.}, keywords = {bilinear, Estimation, estimation;, estimation;reference, information;image, methods;motion, procedure;motion, procedure;side, reconstruction;iterative, recovery;image, structure, vector;refinement}, doi = {10.1109/ICCV.2007.4408874}, author = {Ramachandran, M. and Veeraraghavan,A. and Chellapa, Rama} } @conference {18674, title = {Filesystem activity following a SSH compromise: an empirical study of file sequences}, series = {ICISC{\textquoteright}07}, year = {2007}, month = {2007///}, pages = {144 - 155}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {Berlin, Heidelberg}, abstract = {A common method used to detect intrusions is monitoring filesystem data. Once a computer is compromised, an attacker may alter files, add new files or delete existing ones. Attackers may target any part of the filesystem, including metadata along with files (e.g., permissions, ownerships and inodes). In this paper, we will describe an empirical study that focused on computer attack activity after a SSH compromise. Statistical data will be provided on the number of files targeted and the associated activity (e.g., read, write, delete, ownership and rights). We extend this analysis to include the sequence of files and activities targeted. We focused on the most frequent sequences of consecutive files and activities, then explored in greater detail the longer sequences using state machines. Finally, we developed a simple state machine representing three major observed attack activities (i.e., reconnaissance, malware download and password change) with the number of transitions and time for each transition. The analysis of individual and sequences of files and activities will help to better understand attack activity patterns resulting in more efficient intrusion detection.}, keywords = {filesystem data, host intrusion detection systems, intrusion detection systems evaluation, SSH compromises}, isbn = {3-540-76787-8, 978-3-540-76787-9}, url = {http://dl.acm.org/citation.cfm?id=1775532.1775548}, author = {Molina,Jesus and Chorin,Xavier and Michel Cukier} } @article {15120, title = {A forward-secure public-key encryption scheme}, journal = {Journal of Cryptology}, volume = {20}, year = {2007}, month = {2007///}, pages = {265 - 294}, abstract = {Cryptographic computations are often carried out on insecure devices for which the threat of key exposure represents a serious concern. Forward security allows one to mitigate the damage caused by exposure of secret keys. In a forward-secure scheme, secret keys are updated at regular periods of time; exposure of the secret key corresponding to a given time period does not enable an adversary to "break" the scheme (in the appropriate sense) for any prior time period. We present the first constructions of (non-interactive) forward-secure public-key encryption schemes. Our main construction achieves security against chosen-plaintext attacks in the standard model, and all parameters of the scheme are poly-logarithmic in the total number of time periods. Some variants and extensions of this scheme are also given. We also introduce the notion of binary tree encryption and construct a binary tree encryption scheme in the standard model. Our construction implies the first hierarchical identity-based encryption scheme in the standard model. (The notion of security we achieve, however, is slightly weaker than that achieved by some previous constructions in the random oracle model.)}, doi = {10.1007/s00145-006-0442-5}, author = {Canetti,R. and Halevi,S. and Katz, Jonathan} } @conference {12583, title = {From Videos to Verbs: Mining Videos for Activities using a Cascade of Dynamical Systems}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 8}, abstract = {Clustering video sequences in order to infer and extract activities from a single video stream is an extremely important problem and has significant potential in video indexing, surveillance, activity discovery and event recognition. Clustering a video sequence into activities requires one to simultaneously recognize activity boundaries (activity consistent subsequences) and cluster these activity subsequences. In order to do this, we build a generative model for activities (in video) using a cascade of dynamical systems and show that this model is able to capture and represent a diverse class of activities. We then derive algorithms to learn the model parameters from a video stream and also show how a single video sequence may be clustered into different clusters where each cluster represents an activity. We also propose a novel technique to build affine, view, rate invariance of the activity into the distance metric for clustering. Experiments show that the clusters found by the algorithm correspond to semantically meaningful activities.}, keywords = {activities, clustering;image, clustering;video, extraction;dynamical, mining;video, processing;, sequence, sequences;pattern, signal, stream;video, systems;single, video}, doi = {10.1109/CVPR.2007.383170}, author = {Turaga, P.K. and Veeraraghavan,A. and Chellapa, Rama} } @article {16590, title = {Functional connectivity in fMRI: A modeling approach for estimation and for relating to local circuits}, journal = {Neuroimage}, volume = {34}, year = {2007}, month = {2007///}, pages = {1093 - 1107}, author = {Winder,R. and Cortes,C. R and Reggia, James A. and Tagamets,M. A} } @article {14581, title = {GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo}, journal = {Development}, volume = {134}, year = {2007}, month = {2007/01/01/}, pages = {189 - 198}, abstract = {In vitro studies have suggested that members of the GATA and Nkx transcription factor families physically interact, and synergistically activate pulmonary epithelial- and cardiac-gene promoters. However, the relevance of this synergy has not been demonstrated in vivo. We show that Gata6-Titf1 (Gata6-Nkx2.1) double heterozygous (G6-Nkx DH) embryos and mice have severe defects in pulmonary epithelial differentiation and distal airway development, as well as reduced phospholipid production. The defects in G6-Nkx DH embryos and mice are similar to those observed in human neonates with respiratory distress syndromes, including bronchopulmonary dysplasia, and differential gene expression analysis reveals essential developmental pathways requiring synergistic regulation by both Gata6 and Titf1 (Nkx2.1). These studies indicate that Gata6 and Nkx2.1 act in a synergistic manner to direct pulmonary epithelial differentiation and development in vivo, providing direct evidence that interactions between these two transcription factor families are crucial for the development of the tissues in which they are co-expressed.}, doi = {10.1242/dev.02720}, url = {http://dev.biologists.org/content/134/1/189.abstract}, author = {Zhang,Yuzhen and Rath,Nibedita and Hannenhalli, Sridhar and Wang,Zhishan and Cappola,Thomas and Kimura,Shioko and Atochina-Vasserman,Elena and Lu,Min Min and Beers,Michael F. and Morrisey,Edward E.} } @conference {12580, title = {Gaussian Approximations for Energy-Based Detection and Localization in Sensor Networks}, booktitle = {Statistical Signal Processing, 2007. SSP {\textquoteright}07. IEEE/SP 14th Workshop on}, year = {2007}, month = {2007/08//}, pages = {655 - 659}, abstract = {Energy-based detection and estimation are crucial in sensor networks for sensor localization, target tracking, etc. In this paper, we present novel Gaussian approximations that are applicable to general energy-based source detection and localization problems in sensor networks. Using our approximations, we derive receiver operating characteristics curves and Cramer-Rao bounds, and we provide a factorized variational Bayes approximation to the location and source energy posterior for centralized or decentralized estimation. When the source signal and the sensor noise have uncorrelated Gaussian distributions, we demonstrate that the envelope of the sensor output can be accurately modeled with a multiplicative Gaussian noise model, which results in smaller estimation biases than the other Gaussian models typically used in the literature. We also prove that additive Gaussian noise models result in negatively biased speed estimates under the same signal assumptions, which can be circumvented by the proposed approximations.}, doi = {10.1109/SSP.2007.4301340}, author = {Cevher,Volkan and Chellapa, Rama and McClellan,James H.} } @article {15279, title = {Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses}, journal = {Emerging Infectious DiseasesEmerg Infect Dis}, volume = {13}, year = {2007}, month = {2007/05//}, pages = {713 - 718}, abstract = {Although linked, these viruses are distinct from earlier outbreak strains., To better understand the ecology and epidemiology of the highly pathogenic avian influenza virus in its transcontinental spread, we sequenced and analyzed the complete genomes of 36 recent influenza A (H5N1) viruses collected from birds in Europe, northern Africa, and southeastern Asia. These sequences, among the first complete genomes of influenza (H5N1) viruses outside Asia, clearly depict the lineages now infecting wild and domestic birds in Europe and Africa and show the relationships among these isolates and other strains affecting both birds and humans. The isolates fall into 3 distinct lineages, 1 of which contains all known non-Asian isolates. This new Euro-African lineage, which was the cause of several recent (2006) fatal human infections in Egypt and Iraq, has been introduced at least 3 times into the European-African region and has split into 3 distinct, independently evolving sublineages. One isolate provides evidence that 2 of these sublineages have recently reassorted.}, isbn = {1080-6040}, doi = {10.3201/eid1305.070013}, author = {Salzberg,Steven L. and Kingsford, Carl and Cattoli,Giovanni and Spiro,David J. and Janies,Daniel A. and Aly,Mona Mehrez and Brown,Ian H. and Couacy-Hymann,Emmanuel and De Mia,Gian Mario and Dung,Do Huu and Guercio,Annalisa and Joannis,Tony and Ali,Ali Safar Maken and Osmani,Azizullah and Padalino,Iolanda and Saad,Magdi D. and Savi{\'c},Vladimir and Sengamalay,Naomi A. and Yingst,Samuel and Zaborsky,Jennifer and Zorman-Rojs,Olga and Ghedin,Elodie and Capua,Ilaria} } @article {13002, title = {Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services}, journal = {Future Generation Comp Syst}, volume = {23}, year = {2007}, month = {2007///}, pages = {517 - 522}, abstract = {The Grid Services Base Library (GSBL) is a procedural application programming interface (API) that abstracts many of the high-level functions performed by Globus Grid services, thus dramatically lowering the barriers to writing Grid services. The library has been extensively tested and used for computational biology research in a Globus Toolkit-based Grid system, in which no fewer than twenty Grid services written with this API are deployed.}, author = {Bazinet,A. L and Myers,D. S and Fuetsch,J. and Cummings, Michael P.} } @conference {19449, title = {Grow and Know: Understanding Record-keeping Needs for Tracking the Development of Young Children}, booktitle = {SIGCHI {\textquoteright}07}, series = {CHI {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {1351 - 1360}, publisher = {ACM}, organization = {ACM}, abstract = {From birth through age five, children undergo rapid development and learn skills that will influence them their entire lives. Regular visits to the pediatrician and detailed record-keeping can ensure that children are progressing and can identify early warning signs of developmental delay or disability. However, new parents are often overwhelmed with new responsibilities, and we believe there is an opportunity for computing technology to assist in this process. In this paper, we present a qualitative study aimed at uncovering some specific needs for record-keeping and analysis for new parents and their network of caregivers. Through interviews and focus groups, we have confirmed assumptions about the rationales parents have and the functions required for using technology for record-keeping. We also identify new themes, potential prototypes, and design guidelines for this domain.}, keywords = {children, design requirements, developmental delay, healthcare, qualitative study}, isbn = {978-1-59593-593-9}, url = {http://doi.acm.org/10.1145/1240624.1240830}, author = {Kientz, Julie A. and Arriaga, Rosa I. and Marshini Chetty and Hayes, Gillian R. and Richardson, Jahmeilah and Patel, Shwetak N. and Abowd, Gregory D.} } @article {12579, title = {Guest Editorial: Special Issue on Human Detection and Recognition}, journal = {Information Forensics and Security, IEEE Transactions on}, volume = {2}, year = {2007}, month = {2007/09//}, pages = {489 - 490}, abstract = {The 12 regular papers and three correspondences in this special issue focus on human detection and recognition. The papers represent gait, face (3-D, 2-D, video), iris, palmprint, cardiac sounds, and vulnerability of biometrics and protection against the spoof attacks.}, isbn = {1556-6013}, doi = {10.1109/TIFS.2007.905740}, author = {Bhanu, B. and Ratha,N. K and Kumar, V. and Chellapa, Rama and Bigun, J.} } @conference {19451, title = {HCI4D: hci challenges in the global south}, booktitle = {SIGCHI EA {\textquoteright}07}, series = {CHI EA {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {2327 - 2332}, publisher = {ACM}, organization = {ACM}, abstract = {While researchers have designed user-centered systems for the Global South, fewer have discussed the unique challenges facing HCI projects. In this paper, we describe methodological and practical challenges for HCI research and practice in the Global South.}, keywords = {global south, hci, methodologies}, isbn = {978-1-59593-642-4}, url = {http://doi.acm.org/10.1145/1240866.1241002}, author = {Marshini Chetty and Grinter, Rebecca E.} } @article {13437, title = {Heuristic Search and Information Visualization Methods for School Redistricting}, journal = {AI Magazine}, volume = {28}, year = {2007}, month = {2007/09/15/}, pages = {59 - 59}, abstract = {We describe an application of AI search and information visualization techniques to the problem of school redistricting, in which students are assigned to home schools within a county or school district. This is a multicriteria optimization problem in which competing objectives, such as school capacity, busing costs, and socioeconomic distribution, must be considered. Because of the complexity of the decision-making problem, tools are needed to help end users generate, evaluate, and compare alternative school assignment plans. A key goal of our research is to aid users in finding multiple qualitatively different redistricting plans that represent different trade-offs in the decision space. We present heuristic search methods that can be used to find a set of qualitatively different plans, and give empirical results of these search methods on population data from the school district of Howard County, Maryland. We show the resulting plans using novel visualization methods that we have developed for summarizing and comparing alternative plans.}, isbn = {0738-4602}, doi = {10.1609/aimag.v28i3.2055}, url = {https://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/2055}, author = {desJardins, Marie and Bulka,Blazej and Carr,Ryan and Jordan,Eric and Rheingans,Penny} } @article {15959, title = {HIV risk behaviors among female IDUs in developing and transitional countries}, journal = {BMC Public Health}, volume = {7}, year = {2007}, month = {2007///}, author = {Charles,C. and Des Jarlais Don,P. T and Gerry,S.} } @inbook {19453, title = {How Smart Homes Learn: The Evolution of the Networked Home and Household}, booktitle = {UbiComp 2007: Ubiquitous Computing}, series = {Lecture Notes in Computer Science}, year = {2007}, month = {2007/01/01/}, pages = {127 - 144}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Despite a growing desire to create smart homes, we know little about how networked technologies interact with a house{\textquoteright}s infrastructure. In this paper, we begin to close this gap by presenting findings from a study that examined the relationship between home networking and the house itself{\textemdash}and the work that results for householders as a consequence of this interaction. We discuss four themes that emerged: an ambiguity in understanding the virtual boundaries created by wireless networks, the home network control paradox, a new home network access paradox, and the relationship between increased responsibilities and the possibilities of wireless networking.}, keywords = {Computer Communication Networks, computers and society, home networking, Information Systems Applications (incl.Internet), infrastructure, smart home, software engineering, Systems and Data Security, User Interfaces and Human Computer Interaction}, isbn = {978-3-540-74852-6, 978-3-540-74853-3}, url = {http://link.springer.com/chapter/10.1007/978-3-540-74853-3_8}, author = {Marshini Chetty and Sung, Ja-Young and Grinter, Rebecca E.}, editor = {Krumm, John and Abowd, Gregory D. and Seneviratne, Aruna and Strang, Thomas} } @conference {12585, title = {Human Identification using Gait and Face}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 2}, abstract = {In general the visual-hull approach for performing integrated face and gait recognition requires at least two cameras. In this paper we present experimental results for fusion of face and gait for the single camera case. We considered the NIST database which contains outdoor face and gait data for 30 subjects. In the NIST database, subjects walk along an inverted Sigma pattern. In (A. Kale, et al., 2003), we presented a view-invariant gait recognition algorithm for the single camera case along with some experimental evaluations. In this chapter we present the results of our view-invariant gait recognition algorithm in (A. Kale, et al., 2003) on the NIST database. The algorithm is based on the planar approximation of the person which is valid when the person walks far away from the camera. In (S. Zhou et al., 2003), an algorithm for probabilistic recognition of human faces from video was proposed and the results were demonstrated on the NIST database. Details of these methods can be found in the respective papers. We give an outline of the fusion strategy here.}, keywords = {algorithm;visual-hull, analysis;image, approach;cameras;face, approximation;probabilistic, database;camera;face, databases;, fusion;face, fusion;human, fusion;probability;video, Gait, identification;planar, NIST, processing;visual, recognition, recognition;gait, recognition;view-invariant, signal}, doi = {10.1109/CVPR.2007.383523}, author = {Chellapa, Rama and Roy-Chowdhury, A.K. and Kale, A.} } @article {12573, title = {Hybrid Detectors for Subpixel Targets}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {29}, year = {2007}, month = {2007/11//}, pages = {1891 - 1903}, abstract = {Subpixel detection is a challenging problem in hyperspectral imagery analysis. Since the target size is smaller than the size of a pixel, detection algorithms must rely solely on spectral information. A number of different algorithms have been developed over the years to accomplish this task, but most detectors have taken either a purely statistical or a physics-based approach to the problem. We present two new hybrid detectors that take advantage of these approaches by modeling the background using both physics and statistics. Results demonstrate improved performance over the well-known AMSD and ACE subpixel algorithms in experiments that include multiple targets, images, and area types - especially when dealing with weak targets in complex backgrounds.}, keywords = {ACE subpixel algorithm;AMSD subpixel algorithm;hybrid detectors;hyperspectral imagery analysis;physics;statistics;subpixel target detection;subspace detection;object detection;spectral analysis;statistical analysis;target tracking;Algorithms;Artificial In, Automated;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Computer-Assisted;, Computer-Assisted;Models, Computer-Assisted;Pattern Recognition, Statistical;Image Enhancement;Image Interpretation, Statistical;Numerical Analysis}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2007.1104}, author = {Broadwater, J. and Chellapa, Rama} } @article {12590, title = {Hyperstereo algorithms for the perception of terrain drop-offs}, journal = {Proceedings of SPIE}, volume = {6557}, year = {2007}, month = {2007/04/27/}, pages = {65570L-65570L-10 - 65570L-65570L-10}, abstract = {The timely detection of terrain drop-offs is critical for safe and efficient off-road mobility, whether with human drivers or with terrain navigation systems that use autonomous machine-vision. In this paper, we propose a joint tracking and detection machine-vision approach for accurate and efficient terrain drop-off detection and localization. We formulate the problem using a hyperstereo camera system and build an elevation map using the range map obtained from a stereo algorithm. A terrain drop-off is then detected with the use of optimal drop-off detection filters applied to the range map. For more robust results, a method based on multi-frame fusion of terrain drop-off evidence is proposed. Also presented is a fast, direct method that does not employ stereo disparity mapping. We compared our algorithm{\textquoteright}s detection of terrain drop-offs with time-code data from human observers viewing the same video clips in stereoscopic 3D. The algorithm detected terrain drop-offs an average of 9 seconds sooner, or 12m farther, than the human observers. This suggests that passive image-based hyperstereo machine-vision may be useful as an early warning system for off-road mobility.}, isbn = {0277786X}, doi = {doi:10.1117/12.721066}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/6557/1/65570L_1?isAuthorized=no}, author = {Mohananchettiar,Arunkumar and Cevher,Volkan and CuQlock-Knopp,Grayson and Chellapa, Rama and Merritt,John} } @conference {12582, title = {In Situ Evaluation of Tracking Algorithms Using Time Reversed Chains}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 8}, abstract = {Automatic evaluation of visual tracking algorithms in the absence of ground truth is a very challenging and important problem. In the context of online appearance modeling, there is an additional ambiguity involving the correctness of the appearance model. In this paper, we propose a novel performance evaluation strategy for tracking systems based on particle filter using a time reversed Markov chain. Starting from the latest observation, the time reversed chain is propagated back till the starting time t = 0 of the tracking algorithm. The posterior density of the time reversed chain is also computed. The distance between the posterior density of the time reversed chain (at t = 0) and the prior density used to initialize the tracking algorithm forms the decision statistic for evaluation. It is postulated that when the data is generated true to the underlying models, the decision statistic takes a low value. We empirically demonstrate the performance of the algorithm against various common failure modes in the generic visual tracking problem. Finally, we derive a small frame approximation that allows for very efficient computation of the decision statistic.}, keywords = {(numerical, algorithm;Markov, chain;tracking, decision, density;time, detection;particle, Evaluation, evaluation;object, filter;performance, Filtering, Markov, methods);tracking;visual, processes;decision, reversed, servoing;, situ, statistics;in, strategy;posterior, systems;visual, theory;object, tracking, tracking;particle}, doi = {10.1109/CVPR.2007.382992}, author = {Wu,Hao and Sankaranarayanan,A. C and Chellapa, Rama} } @conference {14334, title = {Increasing the breadth: applying sensors, inference and self-report in field studies with the MyExperience tool}, booktitle = {Proceedings of the 1st international workshop on System evaluation for mobile platforms}, series = {MobiEval {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {27 - 27}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {In situ evaluation, context-aware systems, experience sampling method (ESM), field studies, Mobile computing, toolkits}, isbn = {978-1-59593-762-9}, doi = {10.1145/1247721.1247727}, url = {http://doi.acm.org/10.1145/1247721.1247727}, author = {Jon Froehlich and Chen,Mike Y. and Consolvo,Sunny and Harrison,Beverly and Landay,James A.} } @conference {16847, title = {Indexing Point Triples Via Triangle Geometry}, booktitle = {Data Engineering, 2007. ICDE 2007. IEEE 23rd International Conference on}, year = {2007}, month = {2007/04//}, pages = {936 - 945}, abstract = {Database search for images containing icons with specific mutual spatial relationships can be facilitated by an appropriately structured index. For the case of images containing subsets each of which consist of three icons, the one-to-one correspondence between (distinct) point triples and triangles allows the use of such triangle attributes as position, size, orientation, and "shape" in constructing a point-based index, in which each triangle maps to a single point in a resulting hyperdimensional index space. Size (based on the triangle perimeter) can be represented by a single linear dimension. The abstract "shape" of a triangle induces a space that is inherently two-dimensional, and a number of alternative definitions of a basis for this space are examined. Within a plane, orientation reduces to rotation, and (after assignment of a reference direction for the triangle) can be represented by a single, spatially closed dimension. However, assignment of a reference direction for triangles possessing a k-fold rotational symmetry presents a significant challenge. Methods are described for characterizing shape and orientation of triangles, and for mapping these attributes onto a set of linear axes to form a combined index. The shape attribute is independent of size, orientation, and position, and the characterization of shape and orientation is stable with respect to small variations in the indexed triangles.}, keywords = {database, databases;, dimension;spatial, geometry;database, hyperdimensional, index, index;single, index;triangle, indexing;query, linear, point;k-fold, processing;visual, relationships;structured, rotational, search;indexing, space;image, symmetry;point-based}, doi = {10.1109/ICDE.2007.367939}, author = {Cranston,C.B. and Samet, Hanan} } @article {12575, title = {Jmin-image based color-texture segmentation using watershed and hierarchical clustering}, journal = {Proceedings of the 8th International Symposium on Mathematical Morphology}, volume = {2}, year = {2007}, month = {2007/10//undefin}, pages = {35 - 36}, author = {Santos, T.T. and Morimoto, CH and Chellapa, Rama} } @conference {12595, title = {Joint Acoustic-Video Fingerprinting of Vehicles, Part I}, booktitle = {Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on}, volume = {2}, year = {2007}, month = {2007/04//}, pages = {II-745 -II-748 - II-745 -II-748}, abstract = {We address vehicle classification and measurement problems using acoustic and video sensors. In this paper, we show how to estimate a vehicle{\textquoteright}s speed, width, and length by jointly estimating its acoustic wave-pattern using a single passive sensor that records the vehicle{\textquoteright}s drive-by noise. The acoustic wave-pattern is approximated using three envelope shape (ES) components, which approximate the shape of the received signal{\textquoteright}s power envelope. We incorporate the parameters of the ES components along with the estimates of the vehicle engine RPM and number of cylinders to create a vehicle profile vector that forms an intuitive discriminatory feature space. In the companion paper, we discuss vehicle classification and mensuration based on silhouette extraction and wheel detection, using a video sensor. Vehicle speed estimation and classification results are provided using field data.}, keywords = {acoustic, acoustic-video, components;joint, detection;acoustic, estimation;video, fingerprinting;passive, processing;, processing;acoustic, sensor;vehicle, sensors;acoustic, sensors;wheel, SHAPE, signal, speed, transducers;video, wave-pattern;envelope}, doi = {10.1109/ICASSP.2007.366343}, author = {Cevher, V. and Chellapa, Rama and McClellan, J.H.} } @conference {12594, title = {Joint Acoustic-Video Fingerprinting of Vehicles, Part II}, booktitle = {Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on}, volume = {2}, year = {2007}, month = {2007/04//}, pages = {II-749 -II-752 - II-749 -II-752}, abstract = {In this second paper, we first show how to estimate the wheelbase length of a vehicle using line metrology in video. We then address the vehicle fingerprinting problem using vehicle silhouettes and color invariants. We combine the acoustic metrology and classification results discussed in Part I with the video results to improve estimation performance and robustness. The acoustic video fusion is achieved in a Bayesian framework by assuming conditional independence of the observations of each modality. For the metrology density functions, Laplacian approximations are used for computational efficiency. Experimental results are given using field data}, keywords = {acoustic-video, analysis;video, approximations;acoustic, Bayesian, colour, density, efficiency;joint, estimation;Bayes, fingerprinting;metrology, framework;Laplacian, functions;performance, fusion;color, identification;image, invariants;computational, methods;acoustic, metrology;acoustic, processing;, processing;fingerprint, signal, video}, doi = {10.1109/ICASSP.2007.366344}, author = {Cevher, V. and Guo, F. and Sankaranarayanan,A. C and Chellapa, Rama} } @conference {12581, title = {Kernel fully constrained least squares abundance estimates}, booktitle = {Geoscience and Remote Sensing Symposium, 2007. IGARSS 2007. IEEE International}, year = {2007}, month = {2007/07//}, pages = {4041 - 4044}, abstract = {A critical step for fitting a linear mixing model to hyperspectral imagery is the estimation of the abundances. The abundances are the percentage of each end member within a given pixel; therefore, they should be non-negative and sum to one. With the advent of kernel based algorithms for hyperspectral imagery, kernel based abundance estimates have become necessary. This paper presents such an algorithm that estimates the abundances in the kernel feature space while maintaining the non-negativity and sum-to-one constraints. The usefulness of the algorithm is shown using the AVIRIS Cuprite, Nevada image.}, keywords = {abundance, algorithm;kernel, analysis;, AVIRIS, based, constrained, constraint;feature, constraint;spectral, estimates;linear, extraction;geophysical, feature, fully, image;hyperspectral, imagery;kernel, least, mixing, model;nonnegativity, processing;geophysical, processing;multidimensional, processing;spectral, signal, space;kernel, squares, techniques;image, unmixing;sum-to-one}, doi = {10.1109/IGARSS.2007.4423736}, author = {Broadwater, J. and Chellapa, Rama and Banerjee, A. and Burlina, P.} } @conference {12592, title = {Markerless Monocular Tracking of Articulated Human Motion}, booktitle = {Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on}, volume = {1}, year = {2007}, month = {2007/04//}, pages = {I-693 -I-696 - I-693 -I-696}, abstract = {This paper presents a method for tracking general 3D general articulated human motion using a single camera with unknown calibration data. No markers, special clothes, or devices are assumed to be attached to the subject. In addition, both the camera and the subject are allowed to move freely, so that long-term view-independent human motion tracking and recognition are possible. We exploit the fact that the anatomical structure of the human body can be approximated by an articulated blob model. The optical flow under scaled orthographic projection is used to relate the spatial-temporal intensity change of the image sequence to the human motion parameters. These motion parameters are obtained by solving a set of linear equations to achieve global optimization. The correctness and robustness of the proposed method are demonstrated using Tai Chi sequences}, keywords = {analysis;image, blob, camera;spatial-temporal, Chi, equations;markerless, flow;scaled, human, intensity;cameras;gait, model;articulated, monocular, MOTION, motion;global, optimization;human, orthographic, projection;single, recognition;image, sequence;linear, sequences;anatomical, sequences;optimisation;, structure;articulated, Tai, tracking;optical}, doi = {10.1109/ICASSP.2007.366002}, author = {Liu,Haiying and Chellapa, Rama} } @conference {13828, title = {Measuring variability in sentence ordering for news summarization}, booktitle = {Proceedings of the Eleventh European Workshop on Natural Language Generation}, series = {ENLG {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {81 - 88}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {The issue of sentence ordering is an important one for natural language tasks such as multi-document summarization, yet there has not been a quantitative exploration of the range of acceptable sentence orderings for short texts. We present results of a sentence reordering experiment with three experimental conditions. Our findings indicate a very high degree of variability in the orderings that the eighteen subjects produce. In addition, the variability of reorderings is significantly greater when the initial ordering seen by subjects is different from the original summary. We conclude that evaluation of sentence ordering should use multiple reference orderings. Our evaluation presents several metrics that might prove useful in assessing against multiple references. We conclude with a deeper set of questions: (a) what sorts of independent assessments of quality of the different reference orderings could be made and (b) whether a large enough test set would obviate the need for such independent means of quality assessment.}, url = {http://dl.acm.org/citation.cfm?id=1610163.1610177}, author = {Madnani,Nitin and Passonneau,Rebecca and Ayan,Necip Fazil and Conroy,John M. and Dorr, Bonnie J and Klavans,Judith L. and O{\textquoteright}Leary, Dianne P. and Schlesinger,Judith D.} } @article {12596, title = {Method of three-dimensional object reconstruction from a video sequence using a generic model}, volume = {10/644,817}, year = {2007}, month = {2007/02/27/}, abstract = {In a novel method of 3D modeling of an object from a video sequence using an SfM algorithm and a generic object model, the generic model is incorporated after the SfM algorithm generates a 3D estimate of the object model purely and directly from the input video sequence. An optimization framework provides for comparison of the local trends of the 3D estimate and the generic model so that the errors in the 3D estimate are corrected. The 3D estimate is obtained by fusing intermediate 3D reconstructions of pairs of frames of the video sequence after computing the uncertainty of the two frame solutions. The quality of the fusion algorithm is tracked using a rate-distortion function. In order to combine the generic model with the 3D estimate, an energy function minimization procedure is applied to the 3D estimate. The optimization is performed using a Metropolis-Hasting sampling strategy.}, url = {http://www.google.com/patents?id=4At_AAAAEBAJ}, author = {Chellapa, Rama and Chowdhury,Amit K. Roy and Srinivasan,Sridhar}, editor = {University of Maryland} } @article {14088, title = {Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni}, journal = {BMC Genomics}, volume = {8}, year = {2007}, month = {2007///}, pages = {181 - 181}, abstract = {BACKGROUND:The parasitic trematode Schistosoma mansoni is one of the major causative agents of Schistosomiasis, a disease that affects approximately 200 million people, mostly in developing countries. Since much of the pathology is associated with eggs laid by the female worm, understanding the mechanisms involved in oogenesis and sexual maturation is an important step towards the discovery of new targets for effective drug therapy. It is known that the adult female worm only develops fully in the presence of a male worm and that the rates of oviposition and maturation of eggs are significantly increased by mating. In order to study gene transcripts associated with sexual maturation and oviposition, we compared the gene expression profiles of sexually mature and immature parasites using DNA microarrays.RESULTS:For each experiment, three amplified RNA microarray hybridizations and their dye swaps were analyzed. Our results show that 265 transcripts are differentially expressed in adult females and 53 in adult males when mature and immature worms are compared. Of the genes differentially expressed, 55\% are expressed at higher levels in paired females while the remaining 45\% are more expressed in unpaired ones and 56.6\% are expressed at higher levels in paired male worms while the remaining 43.4\% are more expressed in immature parasites. Real-time RT-PCR analysis validated the microarray results. Several new maturation associated transcripts were identified. Genes that were up-regulated in single-sex females were mostly related to energy generation (i.e. carbohydrate and protein metabolism, generation of precursor metabolites and energy, cellular catabolism, and organelle organization and biogenesis) while genes that were down-regulated related to RNA metabolism, reactive oxygen species metabolism, electron transport, organelle organization and biogenesis and protein biosynthesis.CONCLUSION:Our results confirm previous observations related to gene expression induced by sexual maturation in female schistosome worms. They also increase the list of S. mansoni maturation associated transcripts considerably, therefore opening new and exciting avenues for the study of the conjugal biology and development of new drugs against schistosomes.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-8-181}, url = {http://www.biomedcentral.com/1471-2164/8/181}, author = {Waisberg,Michael and Lobo,Francisco and Cerqueira,Gustavo and Passos,Liana and Carvalho,Omar and Franco,Gloria and El-Sayed, Najib M.} } @article {12598, title = {Mixed-state models for nonstationary multiobject activities}, journal = {EURASIP J. Appl. Signal Process.}, volume = {2007}, year = {2007}, month = {2007/01//}, pages = {106 - 106}, abstract = {We present a mixed-state space approach for modeling and segmenting human activities. The discrete-valued component of the mixed state represents higher-level behavior while the continuous state models the dynamics within behavioral segments. A basis of behaviors based on generic properties of motion trajectories is chosen to characterize segments of activities. A Viterbi-based algorithm to detect boundaries between segments is described. The usefulness of the proposed approach for temporal segmentation and anomaly detection is illustrated using the TSA airport tarmac surveillance dataset, the bank monitoring dataset, and the UCF database of human actions.}, isbn = {1110-8657}, doi = {10.1155/2007/65989}, url = {http://dx.doi.org/10.1155/2007/65989}, author = {Cuntoor,Naresh P. and Chellapa, Rama} } @conference {18586, title = {MobCast: Overlay Architecture for Seamless IP Mobility using Scalable Anycast Proxies}, booktitle = {Wireless Communications and Networking Conference, 2007.WCNC 2007. IEEE}, year = {2007}, month = {2007/03//}, pages = {3872 - 3876}, abstract = {We propose a routing overlay system, MobCast, for simple and efficient routing to mobile hosts. Mobcast nodes advertise the same address space at each proxy location, and each mobile host is assigned a "universal" IP address from this address space, so packets sent to a mobile host{\textquoteright}s universal IP address automatically go to the nearest proxy on the overlay. The overlay then delivers the packets to the mobile host. Our architecture enables seamless mobility for both micro and macro mobility. While our initial design is not as mature as Mobile IP, it shows great promise to solve the traditional problems of ingress routing, firewalls, NATs, and rapid mobility with much lower complexity. We present our design as a scalable and deployable alternative to mobile IP. In this paper, we focus on describing the MobCast system architecture. We form our arguments for scalability, handoff-speed, and simplicity, and give our initial results for scalability. We postpone a detailed discussion of MobCast{\textquoteright}s security model for future work.}, keywords = {address space, handoff-speed, IP networks, MobCast, mobile hosts, mobile radio, overlay architecture, proxy location, routing overlay system, scalable anycast proxies, seamless IP mobility, telecommunication network routing, universal IP address}, doi = {10.1109/WCNC.2007.708}, author = {Lee,C.P. and Attrey,K. and Caballero,C. and Feamster, Nick and Mihail,M. and Copeland,J.A.} } @conference {18002, title = {Models for advancing PRAM and other algorithms into parallel programs for a PRAM-On-Chip platform}, booktitle = {IN HANDBOOK OF PARALLEL COMPUTING: MODELS, ALGORITHMS AND APPLICATIONS, EDITORS}, year = {2007}, month = {2007///}, publisher = {CRC Press}, organization = {CRC Press}, abstract = {A bold vision that guided this work is as follows: (i) a parallel algorithms and programming course could become a standard course in every undergraduate computer science program, and (ii) this course could be coupled with a so-called PRAM-On-Chip architecture {\textemdash} a commodity high-end multi-core computer architecture. In fact, the current paper is a tutorial on how to convert PRAM algorithms intoefficient PRAM-On-Chip programs. Coupled with a text on PRAM algorithms as well as an available PRAM-On-Chip tool-chain, comprising a compiler and a simulator, the paper provides the missing link for upgrading a standard theoretical PRAM algorithms class to a parallel algorithms and programming class. Having demonstrated that such a course could cover similar programming projects and material to what is covered by a typical first serial algorithms and programming course, the paper suggests that parallel programming in the emerging multi-core era does not need to be more difficult than serial programming. If true, a powerful answer to the so-called parallel programming open problem is being provided. This open problem is currently the main stumbling block for the industry in getting the upcoming generation of multi-core architectures to improve single task completion time using easy-to-program application programmer interfaces. Known constraints of this open problem, such as backwards compatibility on serial code, are also addressed by the overall approach. More concretely, a widely used methodology for advancing parallel algorithmic thinking into parallel algorithms is revisited, and is extended into a methodology for advancing parallel algorithms to PRAM-On-Chip programs. A performance cost model for the PRAM-On-Chip is also presented. It uses as complexity metrics the length of sequence of round trips to memory (LSRTM) and queuing delay (QD) from memory access queues, in addition to standard PRAM computation costs. Highlighting the importance of LSRTM in determining performance is another contribution of the paper. Finally, some alternatives to PRAM algorithms, which, on one hand, are easier-to-think, but, on the other hand, suppress more architecture details, are also discussed. }, author = {Vishkin, Uzi and Caragea,George C. and Lee,Bryant} } @conference {19036, title = {Multi-Dimensional Range Query over Encrypted Data}, year = {2007}, month = {2007}, pages = {350 - 364}, abstract = {We design an encryption scheme called multi-dimensional range query over encrypted data (MRQED), to address the privacy concerns related to the sharing of network audit logs and various other applications. Our scheme allows a network gateway to encrypt summaries of network flows before submitting them to an untrusted repository. When network intrusions are suspected, an authority can release a key to an auditor, allowing the auditor to decrypt flows whose attributes (e.g., source and destination addresses, port numbers, etc.) fall within specific ranges. However, the privacy of all irrelevant flows are still preserved. We formally define the security for MRQED and prove the security of our construction under the decision bilinear Diffie-Hellman and decision linear assumptions in certain bilinear groups. We study the practical performance of our construction in the context of network audit logs. Apart from network audit logs, our scheme also has interesting applications for financial audit logs, medical privacy, untrusted remote storage, etc. In particular, we show that MRQED implies a solution to its dual problem, which enables investors to trade stocks through a broker in a privacy-preserving manner.}, keywords = {auditing, cryptography, data privacy, decision bilinear Diffie-Hellman, decision linear assumptions, encrypted data, multi-dimensional range query, network audit logs, network gateway, network intrusions}, author = {Elaine Shi and Bethencourt, J. and Chan, T.-H.H. and Song, Dawn and Perrig, A.} } @article {12571, title = {A Multiple-Hypothesis Approach for Multiobject Visual Tracking}, journal = {Image Processing, IEEE Transactions on}, volume = {16}, year = {2007}, month = {2007/11//}, pages = {2849 - 2854}, abstract = {In multiple-object tracking applications, it is essential to address the problem of associating targets and observation data. For visual tracking of multiple targets which involves objects that split and merge, a target may be associated with multiple measurements and many targets may be associated with a single measurement. The space of such data association is exponential in the number of targets and exhaustive enumeration is impractical. We pose the association problem as a bipartite graph edge covering problem given the targets and the object detection information. We propose an efficient method of maintaining multiple association hypotheses with the highest probabilities over all possible histories of associations. Our approach handles objects entering and exiting the field of view, merging and splitting objects, as well as objects that are detected as fragmented parts. Experimental results are given for tracking multiple players in a soccer game and for tracking people with complex interaction in a surveillance setting. It is shown through quantitative evaluation that our method tracks through varying degrees of interactions among the targets with high success rate.}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, bipartite graph edge covering problem;data association;multiobject visual tracking;multiple measurements;multiple-hypothesis approach;multiple-object tracking;object detection;graph theory;object detection;probability;target tracking;Algorithms;Artificial, Computer-Assisted;Motion;Numerical Analysis, Computer-Assisted;Pattern Recognition, Computer-Assisted;Subtraction Technique;}, isbn = {1057-7149}, doi = {10.1109/TIP.2007.906254}, author = {Joo,Seong-Wook and Chellapa, Rama} } @conference {14338, title = {MyExperience: a system for in situ tracing and capturing of user feedback on mobile phones}, booktitle = {Proceedings of the 5th international conference on Mobile systems, applications and services}, series = {MobiSys {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {57 - 70}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper presents MyExperience, a system for capturing both objective and subjective in situ data on mobile computing activities. MyExperience combines the following two techniques: 1) passive logging of device usage, user context, and environmental sensor readings, and 2) active context-triggered user experience sampling to collect in situ, subjective user feedback. MyExperience currently runs on mobile phones and supports logging of more than 140 event types, including: 1) device usage such as communication, application usage, and media capture, 2) user context such as calendar appointments, and 3) environmental sensing such as Bluetooth and GPS. In addition, user experience sampling can be targeted to moments of interest by triggering off sensor readings. We present several case studies of field deployments on people{\textquoteright}s personal phones to demonstrate how MyExperience can be used effectively to understand how people use and experience mobile technology.}, keywords = {context-aware systems, experience sampling method (ESM), field studies, in situ evaluation, Mobile computing, SmartPhones, toolkit, usage logging, user surveys, user-centered design}, isbn = {978-1-59593-614-1}, doi = {10.1145/1247660.1247670}, url = {http://doi.acm.org/10.1145/1247660.1247670}, author = {Jon Froehlich and Chen,Mike Y. and Consolvo,Sunny and Harrison,Beverly and Landay,James A.} } @book {18596, title = {NETB{\textquoteright}07: Proceedings of the 3rd USENIX international workshop on Networking meets databases}, year = {2007}, month = {2007///}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, editor = {Cooper,Brian and Feamster, Nick} } @article {12918, title = {New records of phytoplankton for Bangladesh. 3. Volvocales}, journal = {Bangladesh Journal of Plant Taxonomy}, volume = {14}, year = {2007}, month = {2007/12/01/}, abstract = {This study presents 21 species of Chlamydomonas, four species of Carteria, two species of each of Nephroselmis, Pyramidomonas and Scherffelia, and Collodictyon triciliatum, Polytoma minus, Tetrachloridium ? allorgei and Tetraselmis cordiformis. These species have been reported from some ponds of Mathbaria of Pirojpur and Bakerganj of Barisal districts in Bangladesh.}, isbn = {1028-2092}, doi = {10.3329/bjpt.v14i1.518}, url = {http://www.banglajol.info/bd/index.php/BJPT/article/viewArticle/518}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasmin,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @article {12917, title = {New records of phytoplankton for Bangladesh. 4. Chlorococcales}, journal = {Bangladesh Journal of Plant Taxonomy}, volume = {14}, year = {2007}, month = {2007/12/02/}, abstract = {This study presents three species from each of Schroederia, Monoraphidium and Ankistrodesmus, two species and one variety of Dictyosphaerium, two varieties of Pediastrum, and Tetraedron arthrodesmiforme var. contorta, Chlorotetraedron polymorphum, Myrmecia aquatica, Oocystis tainoensis, Nephrocytium spirale, Kirchneriella irregularis, Coelastrum indicum and Scenedesmus similagineus. These taxa have been reported from some ponds of Mathbaria of Pirojpur and Bakerganj of Barisal Districts in Bangladesh.}, isbn = {1028-2092}, doi = {10.3329/bjpt.v14i2.528}, url = {http://www.banglajol.info/bd/index.php/BJPT/article/viewArticle/528}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasim,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @conference {12970, title = {Optimizing mpf queries}, booktitle = {Proceedings of the 2007 ACM SIGMOD international conference on Management of data - SIGMOD {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {701 - 701}, address = {Beijing, China}, doi = {10.1145/1247480.1247558}, url = {http://dl.acm.org/citation.cfm?id=1247558}, author = {Corrada Bravo, Hector and Ramakrishnan,Raghu} } @article {18642, title = {Password Changes: Empirical Results}, journal = {Computers and Software Engineering}, year = {2007}, month = {2007///}, abstract = {This paper focuses on a detailed analysis of oneaspect of password evolution based on empirical data: password changes. Passwords can be divided into weak and strong based on how easy it is to crack them. We present a model of password changes and analyze passwords collected during 21 months from a large network of an average of 770 users. The results include tracking the percentage of users with weak passwords over time and the percentage of users changing between weak and strong passwords. Based on the data analysis, the distribution of users switching between weak and strong passwords was characterized and two parameters of the model were estimated. }, url = {http://isastorganization.org/ISAST_CS_1_2007.pdf$\#$page=10}, author = {Michel Cukier and Sharma,A.} } @article {12577, title = {Pose-Encoded Spherical Harmonics for Face Recognition and Synthesis Using a Single Image}, journal = {EURASIP Journal on Advances in Signal Processing}, volume = {2008}, year = {2007}, month = {2007/09/25/}, pages = {748483 - 748483}, abstract = {Face recognition under varying pose is a challenging problem, especially when illumination variations are also present. In this paper, we propose to address one of the most challenging scenarios in face recognition. That is, to identify a subject from a test image that is acquired under different pose and illumination condition from only one training sample (also known as a gallery image) of this subject in the database. For example, the test image could be semifrontal and illuminated by multiple lighting sources while the corresponding training image is frontal under a single lighting source. Under the assumption of Lambertian reflectance, the spherical harmonics representation has proved to be effective in modeling illumination variations for a fixed pose. In this paper, we extend the spherical harmonics representation to encode pose information. More specifically, we utilize the fact that 2D harmonic basis images at different poses are related by close-form linear transformations, and give a more convenient transformation matrix to be directly used for basis images. An immediate application is that we can easily synthesize a different view of a subject under arbitrary lighting conditions by changing the coefficients of the spherical harmonics representation. A more important result is an efficient face recognition method, based on the orthonormality of the linear transformations, for solving the above-mentioned challenging scenario. Thus, we directly project a nonfrontal view test image onto the space of frontal view harmonic basis images. The impact of some empirical factors due to the projection is embedded in a sparse warping matrix; for most cases, we show that the recognition performance does not deteriorate after warping the test image to the frontal view. Very good recognition results are obtained using this method for both synthetic and challenging real images.}, isbn = {1687-6180}, doi = {10.1155/2008/748483}, url = {http://asp.eurasipjournals.com/content/2008/1/748483}, author = {Yue,Zhanfeng and Zhao,Wenyi and Chellapa, Rama} } @article {12795, title = {Priority and abstraction in process algebra}, journal = {Information and Computation}, volume = {205}, year = {2007}, month = {2007/09//}, pages = {1426 - 1458}, abstract = {More than 15 years ago, Cleaveland and Hennessy proposed an extension of the process algebra CCS in which some actions may take priority over others. The theory was equipped with a behavioral congruence based on strong bisimulation.This article gives a full account of the challenges in, and the solutions employed for, defining a semantic theory of observation congruence for this process algebra. A full-abstraction result is presented whose proof relies on a novel approach based on successive approximations for identifying the largest congruence contained in an intuitive but na{\~A}{\textasciimacron}ve equivalence. Prioritized observation congruence is also characterized equationally for the class of finite processes, while its utility for system verification is demonstrated by an illustrative example. }, keywords = {Axiomatization, Bisimulation, Full abstraction, Observation congruence, Priority, Process algebra}, isbn = {0890-5401}, doi = {10.1016/j.ic.2007.05.001}, url = {http://www.sciencedirect.com/science/article/pii/S0890540107000624}, author = {Cleaveland, Rance and L{\~A}{\textonequarter}ttgen,Gerald and Natarajan,V.} } @conference {18688, title = {Profiling Attacker Behavior Following SSH Compromises}, year = {2007}, month = {2007/06//}, pages = {119 - 124}, abstract = {This practical experience report presents the results of an experiment aimed at building a profile of attacker behavior following a remote compromise. For this experiment, we utilized four Linux honeypot computers running SSH with easily guessable passwords. During the course of our research, we also determined the most commonly attempted usernames and passwords, the average number of attempted logins per day, and the ratio of failed to successful attempts. To build a profile of attacker behavior, we looked for specific actions taken by the attacker and the order in which they occurred. These actions were: checking the configuration, changing the password, downloading a file, installing/running rogue code, and changing the system configuration.}, keywords = {Linux, Linux honeypot computers, profiling attacker behavior, remote compromise, rogue code, security of data, SSH compromises, system configuration}, doi = {10.1109/DSN.2007.76}, author = {Ramsbrock,D. and Berthier,R. and Michel Cukier} } @inbook {18418, title = {Protocols in the use of empirical software engineering artifacts}, booktitle = {Empirical Software EngineeringEmpirical Software Engineering}, volume = {12}, year = {2007}, month = {2007///}, pages = {107 - 119}, publisher = {Springer}, organization = {Springer}, abstract = {If empirical software engineering is to grow as a valid scientific endeavor, the ability to acquire, use, share, and compare data collected from a variety of sources must be encouraged. This is necessary to validate the formal models being developed within computer science. However, within the empirical software engineering community this has not been easily accomplished. This paper analyses experiences from a number of projects, and defines the issues, which include the following: (1) How should data, testbeds, and artifacts be shared? (2) What limits should be placed on who can use them and how? How does one limit potential misuse? (3) What is the appropriate way to credit the organization and individual that spent the effort collecting the data, developing the testbed, and building the artifact? (4) Once shared, who owns the evolved asset? As a solution to these issues, the paper proposes a framework for an empirical software engineering artifact agreement. Such an agreement is intended to address the needs for both creator and user of such artifacts and should foster a market in making available and using such artifacts. If this framework for sharing software engineering artifacts is commonly accepted, it should encourage artifact owners to make the artifacts accessible to others (gaining credit is more likely and misuse is less likely). It may be easier for other researchers to request artifacts since there will be a well-defined protocol for how to deal with relevant matters.}, author = {Basili, Victor R. and Zelkowitz, Marvin V and Sj{\o}berg,D. I.K and Johnson,P. and Cowling,A. J} } @article {15790, title = {QCS: A system for querying, clustering and summarizing documents}, journal = {Information Processing \& Management}, volume = {43}, year = {2007}, month = {2007/11//}, pages = {1588 - 1605}, abstract = {Information retrieval systems consist of many complicated components. Research and development of such systems is often hampered by the difficulty in evaluating how each particular component would behave across multiple systems. We present a novel integrated information retrieval system{\textemdash}the Query, Cluster, Summarize (QCS) system{\textemdash}which is portable, modular, and permits experimentation with different instantiations of each of the constituent text analysis components. Most importantly, the combination of the three types of methods in the QCS design improves retrievals by providing users more focused information organized by topic.We demonstrate the improved performance by a series of experiments using standard test sets from the Document Understanding Conferences (DUC) as measured by the best known automatic metric for summarization system evaluation, ROUGE. Although the DUC data and evaluations were originally designed to test multidocument summarization, we developed a framework to extend it to the task of evaluation for each of the three components: query, clustering, and summarization. Under this framework, we then demonstrate that the QCS system (end-to-end) achieves performance as good as or better than the best summarization engines. Given a query, QCS retrieves relevant documents, separates the retrieved documents into topic clusters, and creates a single summary for each cluster. In the current implementation, Latent Semantic Indexing is used for retrieval, generalized spherical k-means is used for the document clustering, and a method coupling sentence {\textquotedblleft}trimming{\textquotedblright} and a hidden Markov model, followed by a pivoted QR decomposition, is used to create a single extract summary for each cluster. The user interface is designed to provide access to detailed information in a compact and useful format. Our system demonstrates the feasibility of assembling an effective IR system from existing software libraries, the usefulness of the modularity of the design, and the value of this particular combination of modules. }, keywords = {clustering, Information retrieval, latent semantic indexing, Sentence trimming, Summarization, TEXT PROCESSING}, isbn = {0306-4573}, doi = {10.1016/j.ipm.2007.01.003}, url = {http://www.sciencedirect.com/science/article/pii/S0306457307000246}, author = {Dunlavy,Daniel M. and O{\textquoteright}Leary,Dianne P. and Conroy,John M. and Schlesinger,Judith D.} } @inbook {12601, title = {Recognizing Faces Across Age Progression}, booktitle = {Face Biometrics for Personal IdentificationFace Biometrics for Personal Identification}, series = {Signals and Communication Technology}, year = {2007}, month = {2007///}, pages = {27 - 42}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, isbn = {978-3-540-49346-4}, url = {http://dx.doi.org/10.1007/978-3-540-49346-4_3}, author = {Ramanathan,Narayanan and Chellapa, Rama}, editor = {Hammoud,Riad and Abidi,Besma and Abidi,Mongi} } @article {12919, title = {Recovery in culture of viable but nonculturable Vibrio parahaemolyticus: regrowth or resuscitation?}, journal = {The ISME Journal}, volume = {1}, year = {2007}, month = {2007/05/10/}, pages = {111 - 120}, abstract = {The objective of this study was to explore the recovery of culturability of viable but nonculturable (VBNC) Vibrio parahaemolyticus after temperature upshift and to determine whether regrowth or resuscitation occurred. A clinical strain of V. parahaemolyticus Vp5 was rendered VBNC by exposure to artificial seawater (ASW) at 4{\textdegree}C. Aliquots of the ASW suspension of cells (0.1, 1 and 10 ml) were subjected to increased temperatures of 20{\textdegree}C and 37{\textdegree}C. Culturability of the cells in the aliquots was monitored for colony formation on a rich medium and changes in morphology were measured by scanning (SEM) and transmission (TEM) electron microscopy. Samples of VBNC cells were fixed and examined by SEM, revealing a heterogeneous population comprising small cells and larger, flattened cells. Forty-eight hours after temperature upshift to 20{\textdegree}C or 37{\textdegree}C, both elongation and division by binary fission of the cells were observed, employing SEM and TEM, but only in the 10-ml aliquots. The results suggest that a portion of VBNC cells is able to undergo cell division. It is concluded that a portion of VBNC cells of V. parahaemolyticus subjected to cold temperatures remain viable. After temperature upshift, regrowth of those cells, rather than resuscitation of all bacteria of the initial inoculum, appears to be responsible for recovery of culturability of VBNC cells of V. parahaemolyticus. Nutrient in filtrates of VBNC cells is hypothesized to allow growth of the temperature-responsive cells, with cell division occurring via binary fission, but also including an atypical, asymmetric cell division.}, keywords = {ecophysiology, ecosystems, environmental biotechnology, geomicrobiology, ISME J, microbe interactions, microbial communities, microbial ecology, microbial engineering, microbial epidemiology, microbial genomics, microorganisms}, isbn = {1751-7362}, doi = {10.1038/ismej.2007.1}, url = {http://www.nature.com/ismej/journal/v1/n2/full/ismej20071a.html}, author = {Coutard,Fran|[ccedil]|ois and Crassous,Philippe and Droguet,Micka|[euml]|l and Gobin,Eric and Rita R Colwell and Pommepuy,Monique and Hervio-Heath,Dominique} } @conference {12574, title = {Robust Visual Tracking Using the Time-Reversibility Constraint}, booktitle = {Computer Vision, 2007. ICCV 2007. IEEE 11th International Conference on}, year = {2007}, month = {2007/10//}, pages = {1 - 8}, abstract = {Visual tracking is a very important front-end to many vision applications. We present a new framework for robust visual tracking in this paper. Instead of just looking forward in the time domain, we incorporate both forward and backward processing of video frames using a novel time-reversibility constraint. This leads to a new minimization criterion that combines the forward and backward similarity functions and the distances of the state vectors between the forward and backward states of the tracker. The new framework reduces the possibility of the tracker getting stuck in local minima and significantly improves the tracking robustness and accuracy. Our approach is general enough to be incorporated into most of the current tracking algorithms. We illustrate the improvements due to the proposed approach for the popular KLT tracker and a search based tracker. The experimental results show that the improved KLT tracker significantly outperforms the original KLT tracker. The time-reversibility constraint used for tracking can be incorporated to improve the performance of optical flow, mean shift tracking and other algorithms.}, keywords = {backward, constraint;video, criterion;state, forward, frame, KLT, processing;, processing;video, processing;visual, signal, tracker;minimization, tracking;minimisation;video, vectors;time-reversibility}, doi = {10.1109/ICCV.2007.4408956}, author = {Wu,Hao and Chellapa, Rama and Sankaranarayanan,A. C and Zhou,S. K} } @article {14099, title = {Schistosoma mansoni genome: Closing in on a final gene set}, journal = {Experimental Parasitology}, volume = {117}, year = {2007}, month = {2007/11//}, pages = {225 - 228}, abstract = {The Schistosoma mansoni genome sequencing consortium has recently released the latest versions of the genome assembly as well as an automated preliminary gene structure annotation. The combined datasets constitute a vast resource for researchers to exploit in a variety of post-genomic studies with an emphasis of transcriptomic and proteomic tools. Here we present an innovative method used for combining diverse sources of evidence including ab initio gene predictions, protein and transcript sequence homologies, and cross-genome sequence homologies between S. mansoni and Schistosoma japonicum to define a comprehensive list of protein-coding genes.}, keywords = {Annotation, Gene finding, Genome, Schistosoma mansoni}, isbn = {0014-4894}, doi = {16/j.exppara.2007.06.005}, url = {http://www.sciencedirect.com/science/article/pii/S0014489407001683}, author = {Haas,Brian J. and Berriman,Matthew and Hirai,Hirohisa and Cerqueira,Gustavo G. and LoVerde,Philip T. and El-Sayed, Najib M.} } @conference {17780, title = {Sentiment analysis: Adjectives and adverbs are better than adjectives alone}, booktitle = {Proceedings of the International Conference on Weblogs and Social Media (ICWSM)}, year = {2007}, month = {2007///}, abstract = {Most past work on determining the strength of subjective expres-sions within a sentence or a document use specific parts of speech such as adjectives, verbs and nouns. To date, there is almost no work on the use of adverbs in sentiment analysis, nor has there been any work on the use of adverb-adjective combinations (AACs). We propose an AAC-based sentiment analysis technique that uses a lin- guistic analysis of adverbs of degree. We define a set of general axioms (based on a classification of adverbs of degree into five cat- egories) that all adverb scoring techniques must satisfy. Instead of aggregating scores of both adverbs and adjectives using simple scor- ing functions, we propose an axiomatic treatment of AACs based on the linguistic classification of adverbs. Three specific AAC scor- ing methods that satisfy the axioms are presented. We describe the results of experiments on an annotated set of 200 news articles (an- notated by 10 students) and compare our algorithms with some exist- ing sentiment analysis algorithms. We show that our results lead to higher accuracy based on Pearson correlation with human subjects. }, author = {Benamara,F. and Cesarano,C. and Picariello, A. and Reforgiato,D. and V.S. Subrahmanian} } @article {12572, title = {Signal Processing for Biometric Systems [DSP Forum]}, journal = {Signal Processing Magazine, IEEE}, volume = {24}, year = {2007}, month = {2007/11//}, pages = {146 - 152}, abstract = {This IEEE signal processing magazine (SPM) forum discuses signal processing applications, technologies, requirements, and standardization of biometric systems. The forum members bring their expert insights into issues such as biometric security, privacy, and multibiometric and fusion techniques. The invited forum members are Prof. Anil K. Jain of Michigan State University, Prof. Rama Chellappa of the University of Maryland, Dr. Stark C. Draper of theUniversity of Wisconsin in Madison, Prof. Nasir Memon of Polytechnic University, and Dr. P. Jonathon Phillips of the National Institute of Standards and Technology. The moderator of the forum is Dr. Anthony Vetro of Mitsubishi Electric Research Labs, and associate editor of SPM.}, keywords = {(access, biometric, control);security;signal, forum;signal, magazine, PROCESSING, processing;, security;biometric, standardization;fusion, systems, technique;multibiometric, technique;signal, technology;biometrics}, isbn = {1053-5888}, doi = {10.1109/MSP.2007.905886}, author = {Jain, A.K. and Chellapa, Rama and Draper, S.C. and Memon, N. and Phillips,P.J. and Vetro, A.} } @conference {12591, title = {Simulation and Analysis of Human Walking Motion}, booktitle = {Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on}, volume = {1}, year = {2007}, month = {2007/04//}, pages = {I-797 -I-800 - I-797 -I-800}, abstract = {Simulation and analysis of human walking motion has applications in surveillance and healthcare. In this paper we discuss an approach for modeling human walking motion using a mechanical model in the form of a kinematic chain consisting of rigid links and revolute joints. Our goal is to discriminate different types of walking motions using information such as joint torque and angle sequences extracted from the model. The angle sequences are initially extracted using 3D geometry. From these angle sequences we extract the torque sequences using a recursive Newton Euler inverse dynamics algorithm. Time series models and dynamic time warping of the torque and angle sequences are used to characterize and discriminate different walking patterns. A forward dynamics algorithm is also presented for synthesizing different walking sequences like limping from a normal walking torque sequence}, keywords = {3D, algorithm;revolute, analysis;image, chain;mechanical, DYNAMICS, Euler, extraction;image, geometry;angle, inverse, joints;rigid, links;surveillance;time, method;feature, model;recursive, models;torque, MOTION, motion;kinematic, Newton, patterns;Newton, problems;time, sequences;dynamic, sequences;inverse, sequences;walking, series, series;time, simulation;torque;, TIME, walking, warp, warping;healthcare;human}, doi = {10.1109/ICASSP.2007.366028}, author = {Nandy, K. and Chellapa, Rama} } @article {16080, title = {Something that is interesting is interesting then: Using text minig and visualizations to aid interpreting repetition in Gertrude Stein{\textquoteright}s The Making of Americans}, journal = {Proceedings of the Digital Humanities Conference}, year = {2007}, month = {2007///}, pages = {40 - 44}, author = {Clement,T. and Don,A. and Plaisant, Catherine and Auvil,L. and Pape,G. and Goren,V.} } @article {17779, title = {Story creation from heterogeneous data sources}, journal = {Multimedia Tools and Applications}, volume = {33}, year = {2007}, month = {2007///}, pages = {351 - 377}, abstract = {There are numerous applications where there is a need to rapidly infer a story about a given subject from a given set of potentially heterogeneous data sources. In this paper, we formally define a story to be a set of facts about a given subject that satisfies a {\textquotedblleft}story length{\textquotedblright} constraint. An optimal story is a story that maximizes the value of an objective function measuring the goodness of a story. We present algorithms to extract stories from text and other data sources. We also develop an algorithm to compute an optimal story, as well as three heuristic algorithms to rapidly compute a suboptimal story. We run experiments to show that constructing stories can be efficiently performed and that the stories constructed by these heuristic algorithms are high quality stories. We have built a prototype STORY system based on our model{\textemdash}we briefly describe the prototype as well as one application in this paper.}, doi = {10.1007/s11042-007-0100-4}, author = {Fayzullin,M. and V.S. Subrahmanian and Albanese, M. and Cesarano,C. and Picariello, A.} } @article {12586, title = {Super-Resolution of Face Images Using Kernel PCA-Based Prior}, journal = {Multimedia, IEEE Transactions on}, volume = {9}, year = {2007}, month = {2007/06//}, pages = {888 - 892}, abstract = {We present a learning-based method to super-resolve face images using a kernel principal component analysis-based prior model. A prior probability is formulated based on the energy lying outside the span of principal components identified in a higher-dimensional feature space. This is used to regularize the reconstruction of the high-resolution image. We demonstrate with experiments that including higher-order correlations results in significant improvements}, keywords = {analysis;learning-based, analysis;probability;, component, Face, image, method;prior, model;face, principal, probability, recognition;image, reconstruction;image, reconstruction;kernel, resolution;principal, super-resolution;high-resolution}, isbn = {1520-9210}, doi = {10.1109/TMM.2007.893346}, author = {Chakrabarti,Ayan and Rajagopalan, AN and Chellapa, Rama} } @conference {12589, title = {Symmetric Objects are Hardly Ambiguous}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 7}, abstract = {Given any two images taken under different illumination conditions, there always exist a physically realizable object which is consistent with both the images even if the lighting in each scene is constrained to be a known point light source at infinity. In this paper, we show that images are much less ambiguous for the class of bilaterally symmetric Lambertian objects. In fact, the set of such objects can be partitioned into equivalence classes such that it is always possible to distinguish between two objects belonging to different equivalence classes using just one image per object. The conditions required for two objects to belong to the same equivalence class are very restrictive, thereby leading to the conclusion that images of symmetric objects are hardly ambiguous. The observation leads to an illumination-invariant matching algorithm to compare images of bilaterally symmetric Lambertian objects. Experiments on real data are performed to show the implications of the theoretical result even when the symmetry and Lambertian assumptions are not strictly satisfied.}, keywords = {algorithm;symmetric, bilaterally, images;image, Lambertian, MATCHING, matching;, objects, objects;illumination-invariant, objects;symmetric, symmetric}, doi = {10.1109/CVPR.2007.383289}, author = {Aggarwal,G. and Biswas,S. and Chellapa, Rama} } @article {12587, title = {Target Tracking Using a Joint Acoustic Video System}, journal = {Multimedia, IEEE Transactions on}, volume = {9}, year = {2007}, month = {2007/06//}, pages = {715 - 727}, abstract = {In this paper, a multitarget tracking system for collocated video and acoustic sensors is presented. We formulate the tracking problem using a particle filter based on a state-space approach. We first discuss the acoustic state-space formulation whose observations use a sliding window of direction-of-arrival estimates. We then present the video state space that tracks a target{\textquoteright}s position on the image plane based on online adaptive appearance models. For the joint operation of the filter, we combine the state vectors of the individual modalities and also introduce a time-delay variable to handle the acoustic-video data synchronization issue, caused by acoustic propagation delays. A novel particle filter proposal strategy for joint state-space tracking is introduced, which places the random support of the joint filter where the final posterior is likely to lie. By using the Kullback-Leibler divergence measure, it is shown that the joint operation of the filter decreases the worst case divergence of the individual modalities. The resulting joint tracking filter is quite robust against video and acoustic occlusions due to our proposal strategy. Computer simulations are presented with synthetic and field data to demonstrate the filter{\textquoteright}s performance}, keywords = {(numerical, acoustic, adaptive, appearance, approach;synchronization;time-delay, data, delay;acoustic, divergence;acoustic, estimate;joint, estimation;hidden, feature, filter;sliding, Filtering, fusion;multitarget, fusion;synchronisation;target, highways;direction-of-arrival, Kullback-Leibler, methods);sensor, model;particle, processing;, processing;automated, propagation, removal;optical, signal, system;multimodal, tracking;acoustic, tracking;direction-of-arrival, tracking;occlusion;online, tracking;particle, tracking;video, variable;visual, video, window;state-space}, isbn = {1520-9210}, doi = {10.1109/TMM.2007.893340}, author = {Cevher, V. and Sankaranarayanan,A. C and McClellan, J.H. and Chellapa, Rama} } @article {13918, title = {A theoretical model of children{\textquoteright}s storytelling using physically-oriented technologies (SPOT)}, journal = {Journal of Educational Multimedia and Hypermedia}, volume = {16}, year = {2007}, month = {2007///}, pages = {389 - 389}, author = {Guha,M.L. and Druin, Allison and Montemayor,J. and Chipman,G. and Farber,A.} } @article {12920, title = {Ultrastructure of coccoid viable but non-culturable Vibrio cholerae}, journal = {Environmental Microbiology}, volume = {9}, year = {2007}, month = {2007/02/01/}, pages = {393 - 402}, abstract = {Morphology of viable but non-culturable Vibrio cholerae was monitored for 2~years by scanning and transmission electron microscopy. Morphological changes included very small coccoid forms, after extended incubation at 4{\textdegree}C and room temperature, and sequential transformation from curved rods to irregular (\~{}1~μm) rods to \~{}0.8~μm coccoid cells and, ultimately, to tiny coccoid forms (0.07{\textendash}0.4~μm). Irregular rod-shaped and coccoid cells were equally distributed in microcosms during the first 30{\textendash}60~days of incubation at both temperatures, but only coccoid cells were observed after incubation for 60~days at 4{\textdegree}C. When V.~cholerae O1 and O139, maintained for 30{\textendash}60~days at both temperatures, were heated to 45{\textdegree}C for 60~s, after serial passage through 0.45~μm and 0.1~μm filters, and plating on Luria{\textendash}Bertania (LB) agar, only cells larger than 1~μm yielded colonies on LB agar. Approximately 0.1\% of heat-treated cultures were culturable. Cell division in the smallest coccoid cells was observed, yielding daughter cells of equal size, whereas other coccoid cells revealed bleb-like, cell wall evagination, followed by transfer of nuclear material. Coccoid cells of V.~cholerae O1 and O139 incubated at 4{\textdegree}C for more than 1~year remained substrate responsive and antigenic.}, isbn = {1462-2920}, doi = {10.1111/j.1462-2920.2006.01150.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01150.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Chaiyanan,Saipin and Chaiyanan,Sitthipan and Grim,Christopher and Maugel,Timothy and Huq,Anwar and Rita R Colwell} } @conference {18611, title = {Usage-based dhcp lease time optimization}, booktitle = {Proceedings of the 7th ACM SIGCOMM conference on Internet measurement}, series = {IMC {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {71 - 76}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The Dynamic Host Configuration Protocol (DHCP) is used to dynamically allocate address space to hosts on a local area network. Despite its widespread usage, few studies exist on DHCP usage patterns, and even less is known about the importance of setting the lease time (the time that a client retains ownership over some IP address) to an appropriate value. Lease time can greatly affect the tradeoff between address space utilization and the number of both renewal messages and client session expirations. In this paper, using a DHCP trace for 5 weekdays from the Georgia Tech campus network, we present the largest known study of DHCP utilization. We also explore how various strategies for setting lease times can dramatically reduce the number of renewals and expirations without prohibitively increasing address space utilization.}, keywords = {dhcp, network management, OPTIMIZATION, usage}, isbn = {978-1-59593-908-1}, doi = {10.1145/1298306.1298315}, url = {http://doi.acm.org/10.1145/1298306.1298315}, author = {Khadilkar,Manas and Feamster, Nick and Sanders,Matt and Clark,Russ} } @conference {14846, title = {Using Stereo Matching for 2-D Face Recognition Across Pose}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 8}, abstract = {We propose using stereo matching for 2-D face recognition across pose. We match one 2-D query image to one 2-D gallery image without performing 3-D reconstruction. Then the cost of this matching is used to evaluate the similarity of the two images. We show that this cost is robust to pose variations. To illustrate this idea we built a face recognition system on top of a dynamic programming stereo matching algorithm. The method works well even when the epipolar lines we use do not exactly fit the viewpoints. We have tested our approach on the PIE dataset. In all the experiments, our method demonstrates effective performance compared with other algorithms.}, keywords = {2D, estimation;stereo, Face, gallery, image, image;2D, image;dynamic, matching;dynamic, matching;pose, processing;, programming;face, programming;pose, query, recognition;2D, recognition;image, variation;stereo}, doi = {10.1109/CVPR.2007.383111}, author = {Castillo,C. D and Jacobs, David W.} } @article {12923, title = {Viable but nonculturable Vibrio cholerae O1 in biofilms in the aquatic environment and their role in cholera transmission}, journal = {Proceedings of the National Academy of Sciences}, volume = {104}, year = {2007}, month = {2007///}, pages = {17801 - 17801}, abstract = {Vibrio cholerae persists in aquatic environments predominantly in a nonculturable state. In this study coccoid, nonculturable V. cholerae O1 in biofilms maintained for 495 days in Mathbaria, Bangladesh, pond water became culturable upon animal passage. Culturability, biofilm formation, and the wbe, ctxA, and rstR2 genes were monitored by culture, direct fluorescent antibody (DFA), and multiplex PCR. DFA counts were not possible after formation of biofilm. Furthermore, wbe, but not ctxA, were amplifiable, even after incubation for 54 and 68 days at room temperature (≈25{\textdegree}C) and 4{\textdegree}C, respectively, when no growth was detectable. Slower biofilm formation and extended culturability were observed for cultures incubated at 4{\textdegree}C, compared with ≈25{\textdegree}C, suggesting biofilm production to be temperature dependent and linked to loss of culturability. Small colonies appearing after incubation in microcosms for 54 and 68 days at 25{\textdegree}C and 4{\textdegree}C, respectively, were wbe positive and ctxA and rstR2 negative, indicating loss of bacteriophage CTXΦ. The coccoid V. cholerae O1 observed as free cells in microcosms incubated for 495 days could not be cultured, but biofilms in the same microcosms yielded culturable cells. It is concluded that biofilms can act as a reservoir for V. cholerae O1 between epidemics because of its long-term viability in biofilms. In contrast to biofilms produced in Mathbaria pond water, V. cholerae O1 in biofilms present in cholera stools and incubated under identical conditions as the Mathbaria pond water biofilms could not be cultured after 2 months, indicating that those V. cholerae cells freshly discharged into the environment are significantly less robust than cells adapted to environmental conditions.Bangladesh bacteriophage CTXΦ DFA multiplex-PCR ctxA }, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0705599104}, url = {http://www.pnas.org/content/104/45/17801}, author = {Alam,M. and Sultana,M. and Nair,G. B. and Siddique,A. K. and Hasan,N. A. and Sack,R. B. and Sack,D. A. and Ahmed,K. U. and Sadique,A. and Watanabe,H. and Rita R Colwell} } @conference {12578, title = {Video Biometrics}, booktitle = {Image Analysis and Processing, 2007. ICIAP 2007. 14th International Conference on}, year = {2007}, month = {2007/09//}, pages = {363 - 370}, abstract = {A strong requirement to come up with secure and user- friendly ways to authenticate and identify people, to safeguard their rights and interests, has probably been the main guiding force behind biometrics research. Though a vast amount of research has been done to recognize humans based on still images, the problem is still far from solved for unconstrained scenarios. This has led to an increased interest in using video for the task of biometric recognition. Not only does video provide more information, but also is more suitable for recognizing humans in general surveillance scenarios. Other than the multitude of still frames, video makes it possible to characterize biometrics based on inherent dynamics like gait which is not possible with still images. In this paper, we describe several recent algorithms to illustrate the usefulness of videos to identify humans. A brief discussion on remaining challenges is also included.}, keywords = {(access, analysis;video, biometrics;biometrics, control);face, dynamics;ofbiometric, images;surveillance, inherent, MOTION, processing;, recognition;image, recognition;still, scenarios;unconstrained, scenarios;video, signal}, doi = {10.1109/ICIAP.2007.4362805}, author = {Chellapa, Rama and Aggarwal,G.} } @inbook {12623, title = {Acquisition of Articulated Human Body Models Using Multiple Cameras}, booktitle = {Articulated Motion and Deformable ObjectsArticulated Motion and Deformable Objects}, series = {Lecture Notes in Computer Science}, volume = {4069}, year = {2006}, month = {2006///}, pages = {78 - 89}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Motion capture is an important application in different areas such as biomechanics, computer animation, and human-computer interaction. Current motion capture methods typically use human body models in order to guide pose estimation and tracking. We model the human body as a set of tapered super-quadrics connected in an articulated structure and propose an algorithm to automatically estimate the parameters of the model using video sequences obtained from multiple calibrated cameras. Our method is based on the fact that the human body is constructed of several articulated chains that can be visualised as essentially 1-D segments embedded in 3-D space and connected at specific joint locations. The proposed method first computes a voxel representation from the images and maps the voxels to a high dimensional space in order to extract the 1-D structure. A bottom-up approach is then suggested in order to build a parametric (spline-based) representation of a general articulated body in the high dimensional space followed by a top-down probabilistic approach that registers the segments to the known human body model. We then present an algorithm to estimate the parameters of our model using the segmented and registered voxels.}, isbn = {978-3-540-36031-5}, url = {http://dx.doi.org/10.1007/11789239_9}, author = {Sundaresan,Aravind and Chellapa, Rama}, editor = {Perales,Francisco and Fisher,Robert} } @conference {12617, title = {An Adaptive Threshold Method for Hyperspectral Target Detection}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {5}, year = {2006}, month = {2006/05//}, pages = {V - V}, abstract = {In this paper, we present a new approach to automatically determine a detector threshold. This research problem is especially important in hyperspectral target detection as targets are typically very similar to the background. While a number of methods exist to determine the threshold, these methods require either large amounts of data or make simplifying assumptions about the background distribution. We use a method called inverse blind importance sampling which requires few samples and makes no a-priori assumptions about the background statistics. Results show the promise of this algorithm to determine thresholds for fixed false alarm densities in hyperspectral detectors}, keywords = {adaptive, blind, detection;, detection;inverse, importance, method;background, processing;importance, sampling;geophysical, sampling;object, signal, statistics;hyperspectral, target, threshold}, doi = {10.1109/ICASSP.2006.1661497}, author = {Broadwater, J. and Chellapa, Rama} } @article {19020, title = {Anonymous multi-attribute encryption with range query and conditional decryption}, year = {2006}, month = {2006}, institution = {Carnegie Mellon University}, abstract = {We introduce the concept of Anonymous Multi-Attribute Encryption with Range Query and Con-ditional Decryption (AMERQCD). In AMERQCD, a plaintext is encrypted under a point in multi- dimensional space. To a computationally bounded adversary, the ciphertext hides both the plaintext and the point under which it is encrypted. In a range query, a master key owner releases the decryp- tion key for an arbitrary hyper-rectangle in space, thus allowing decryption of ciphertexts previ- ously encrypted under any point within the hyper-rectangle. However, a computationally bounded adversary cannot learn any information on ciphertexts outside the range covered by the decryption key (except the fact that they do not lie within this range). We give an efficient construction based on the Decision Bilinear Diffie-Hellman (D-BDH) and Decision Linear (D-Linear) assumption. }, isbn = {CMU-CS-06-135}, doi = {Technical Report}, url = {http://reports-archive.adm.cs.cmu.edu/anon/anon/home/ftp/2006/CMU-CS-06-135.pdf}, author = {Bethencourt, J. and Chan, H. and Perrig, A. and Elaine Shi and Song,D.} } @conference {13357, title = {Approximate Data Collection in Sensor Networks using Probabilistic Models}, booktitle = {Proceedings of the 22nd International Conference on Data Engineering, 2006. ICDE {\textquoteright}06}, year = {2006}, month = {2006/04/03/07}, pages = {48 - 48}, publisher = {IEEE}, organization = {IEEE}, abstract = {Wireless sensor networks are proving to be useful in a variety of settings. A core challenge in these networks is to minimize energy consumption. Prior database research has proposed to achieve this by pushing data-reducing operators like aggregation and selection down into the network. This approach has proven unpopular with early adopters of sensor network technology, who typically want to extract complete "dumps" of the sensor readings, i.e., to run "SELECT *" queries. Unfortunately, because these queries do no data reduction, they consume significant energy in current sensornet query processors. In this paper we attack the "SELECT " problem for sensor networks. We propose a robust approximate technique called Ken that uses replicated dynamic probabilistic models to minimize communication from sensor nodes to the network{\textquoteright}s PC base station. In addition to data collection, we show that Ken is well suited to anomaly- and event-detection applications. A key challenge in this work is to intelligently exploit spatial correlations across sensor nodes without imposing undue sensor-to-sensor communication burdens to maintain the models. Using traces from two real-world sensor network deployments, we demonstrate that relatively simple models can provide significant communication (and hence energy) savings without undue sacrifice in result quality or frequency. Choosing optimally among even our simple models is NPhard, but our experiments show that a greedy heuristic performs nearly as well as an exhaustive algorithm.}, keywords = {Batteries, Biological system modeling, Biosensors, data mining, Databases, Energy consumption, Intelligent networks, Intelligent sensors, Robustness, Wireless sensor networks}, isbn = {0-7695-2570-9}, doi = {10.1109/ICDE.2006.21}, author = {Chu,D. and Deshpande, Amol and Hellerstein,J. M and Wei Hong} } @article {18653, title = {An architecture for adaptive intrusion-tolerant applications}, journal = {Software: Practice and Experience}, volume = {36}, year = {2006}, month = {2006///}, pages = {1331 - 1354}, abstract = {Applications that are part of a mission-critical information system need to maintain a usable level of key services through ongoing cyber-attacks. In addition to the well-publicized denial of service (DoS) attacks, these networked and distributed applications are increasingly threatened by sophisticated attacks that attempt to corrupt system components and violate service integrity. While various approaches have been explored to deal with DoS attacks, corruption-inducing attacks remain largely unaddressed. We have developed a collection of mechanisms based on redundancy, Byzantine fault tolerance, and adaptive middleware that help distributed, object-based applications tolerate corruption-inducing attacks. In this paper, we present the ITUA architecture, which integrates these mechanisms in a framework for auto-adaptive intrusion-tolerant systems, and we describe our experience in using the technology to defend a critical application that is part of a larger avionics system as an example. We also motivate the adaptive responses that are key to intrusion tolerance, and explain the use of the ITUA architecture to support them in an architectural framework. Copyright {\textcopyright} 2006 John Wiley \& Sons, Ltd.}, keywords = {adaptive defense, adaptive middleware, Byzantine fault tolerance, intrusion tolerance, redundancy, survivability architecture}, isbn = {1097-024X}, doi = {10.1002/spe.747}, url = {http://onlinelibrary.wiley.com/doi/10.1002/spe.747/abstract}, author = {Pal,Partha and Rubel,Paul and Atighetchi,Michael and Webber,Franklin and Sanders,William H. and Seri,Mouna and Ramasamy,HariGovind and Lyons,James and Courtney,Tod and Agbaria,Adnan and Michel Cukier and Gossett,Jeanna and Keidar,Idit} } @conference {18664, title = {Assessing the Attack Threat due to IRC Channels}, year = {2006}, month = {2006/06//}, pages = {467 - 472}, abstract = {This practical experience report presents the results of an investigation into the threat of attacks associated with the chat medium IRC. A combination of simulated users (i.e., bots), some configured with scripts that simulated conversations, and regular users were used. The average number of attacks per day a user on IRC can expect, the effect of channel activity, gender based on the name, and network type on the number of attacks were determined. The social structure of IRC channels and the types of users that use it were analyzed. The results indicate that attacks through IRC channels come from human users selecting targets rather than automated scripts targeting every user in a channel}, keywords = {attack threat assessment, channel activity, client-server systems, computer crime, intrusion-resilient channels, IRC channels, IRC protocols, Protocols, telecommunication channels, telecommunication security}, doi = {10.1109/DSN.2006.12}, author = {Meyer,R. and Michel Cukier} } @conference {12615, title = {Attribute Grammar-Based Event Recognition and Anomaly Detection}, booktitle = {Computer Vision and Pattern Recognition Workshop, 2006. CVPRW {\textquoteright}06. Conference on}, year = {2006}, month = {2006/06//}, pages = {107 - 107}, abstract = {We propose to use attribute grammars for recognizing normal events and detecting abnormal events in a video. Attribute grammars can describe constraints on features (attributes) in addition to the syntactic structure of the input. Events are recognized using an extension of the Earley parser that handles attributes and concurrent event threads. Abnormal events are detected when the input does not follow syntax of the grammar or the attributes do not satisfy the constraints in the attribute grammar to some degree. We demonstrate the effectiveness of our method for the task of recognizing normal events and detecting anomalies in a parking lot.}, doi = {10.1109/CVPRW.2006.32}, author = {Joo,Seong-Wook and Chellapa, Rama} } @inbook {15719, title = {Back to Basics: CLASSY 2006}, booktitle = {DUC 06 Conference ProceedingsDUC 06 Conference Proceedings}, year = {2006}, month = {2006///}, publisher = {U.S. National Inst. of Standards and Technology}, organization = {U.S. National Inst. of Standards and Technology}, abstract = {The IDA/CCS summarization system, CLASSY, underwent significant change for this year{\textquoteright}sDUC. Two changes made processing simpler and faster: 1) we eliminated the use of a POS (part of speech) tagger for sentence splitting and to assist sentence trimming, and 2) we simplified the scoring of sentences for inclusion in the summary by introducing a new {\textquotedblleft}approximate oracle{\textquotedblright} score. An additional change introduced a modest amount of extra computation: we ordered sentences in the summary using a new Traveling Salesperson (TSP) formulation. These changes improved ROUGE scores on the DUC 2005 data from last year and gave strong performance in the DUC 2006 competition. }, url = {\tt http://duc.nist.gov/}, author = {Conroy,John M. and Schlesinger,Judith D. and O{\textquoteright}Leary, Dianne P. and Goldstein,Jade} } @conference {13894, title = {A case study of tangible flags: a collaborative technology to enhance field trips}, booktitle = {Proceedings of the 2006 conference on Interaction design and children}, year = {2006}, month = {2006///}, pages = {1 - 8}, author = {Chipman,G. and Druin, Allison and Beer,D. and Fails,J. A and Guha,M.L. and Simms,S.} } @article {18173, title = {Classification-based spatial error concealment for visual communications}, journal = {EURASIP J. Appl. Signal Process.}, volume = {2006}, year = {2006}, month = {2006/01//}, pages = {257 - 257}, abstract = {In an error-prone transmission environment, error concealment is an effective technique to reconstruct the damaged visual content. Due to large variations of image characteristics, different concealment approaches are necessary to accommodate the different nature of the lost image content. In this paper, we address this issue and propose using classification to integrate the state-of-the-art error concealment techniques. The proposed approach takes advantage of multiple concealment algorithms and adaptively selects the suitable algorithm for each damaged image area. With growing awareness that the design of sender and receiver systems should be jointly considered for efficient and reliable multimedia communications, we proposed a set of classification-based block concealment schemes, including receiver-side classification, sender-side attachment, and sender-side embedding. Our experimental results provide extensive performance comparisons and demonstrate that the proposed classification-based error concealment approaches outperform the conventional approaches.}, isbn = {1110-8657}, doi = {10.1155/ASP/2006/13438}, url = {http://dx.doi.org/10.1155/ASP/2006/13438}, author = {Chen,Meng and Yefeng Zheng and M. Wu} } @inbook {15727, title = {CLASSYArabic and English Multi-Document Summarization}, booktitle = {Multi-Lingual Summarization Evaluation 2006Multi-Lingual Summarization Evaluation 2006}, year = {2006}, month = {2006///}, url = {http://www.isi.edu/ cyl/MTSE2006/MSE2006/papers/index.htmlhttp://www.isi.edu/ cyl/MTSE2006/MSE2006/papers/index.html}, author = {Conroy,John M. and O{\textquoteright}Leary, Dianne P. and Schlesinger,Judith D.} } @article {17533, title = {Community-oriented network measurement infrastructure (CONMI) workshop report}, journal = {ACM SIGCOMM Computer Communication Review}, volume = {36}, year = {2006}, month = {2006/04/28/}, pages = {41 - 41}, isbn = {01464833}, doi = {10.1145/1129582.1129594}, url = {http://dl.acm.org/citation.cfm?id=1129594}, author = {claffy,kc and Crovella,Mark and Friedman,Timur and Shannon,Colleen and Spring, Neil} } @article {18971, title = {Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis}, journal = {BMC Genomics}, volume = {7}, year = {2006}, month = {2006/12/28/}, pages = {327 - 327}, abstract = {Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice) and Arabidopsis thaliana (Arabidopsis). Additionally, these two plant species have extensive cDNA and expressed sequence tag (EST) libraries. We employed the Program to Assemble Spliced Alignments (PASA) to identify and analyze alternatively spliced isoforms in both species.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-7-327}, url = {http://www.biomedcentral.com/1471-2164/7/327/abstract}, author = {Campbell,Matthew A. and Haas,Brian J. and Hamilton,John P. and Mount, Stephen M. and Buell,C. Robin} } @inbook {12640, title = {Computer Vision, Statistics in}, booktitle = {Encyclopedia of Statistical SciencesEncyclopedia of Statistical Sciences}, year = {2006}, month = {2006///}, publisher = {John Wiley \& Sons, Inc.}, organization = {John Wiley \& Sons, Inc.}, abstract = {Computer Vision (CV) broadly refers to the discipline where extraction of useful 2D and/or 3D information from one or more images is of interest. Useful information could consist of features such as edges, lines, curves and textures, or information about depth, motion, object descriptions, etc. CV problems are usually ill-posed inverse problems. Since the image data is usually obtained from sensors such as video cameras, infrared, radar, etc., the information extraction processes often have to deal with data that is corrupted by noise from the sensors and the environment. Statistics can help in obtaining robust and accurate solutions to these inverse problems by modeling the noise processes. We present here a broad overview of the applications of statistics to different computer vision problems and explain in detail two particular applications, tracking and motion analysis, where statistical approaches have been used very successfully.}, keywords = {Computer vision, sampling, Statistics, structure from motion, tracking}, isbn = {9780471667193}, url = {http://onlinelibrary.wiley.com/doi/10.1002/0471667196.ess3129/abstract}, author = {Chellapa, Rama and Chowdhury,Amit K. Roy} } @conference {12376, title = {Configuration and representation of large-scale dataflow graphs using the dataflow interchange format}, booktitle = {Proceedings of the IEEE Workshop on Signal Processing Systems, Banff, Canada}, year = {2006}, month = {2006///}, pages = {10 - 15}, author = {Corretjer,I. and Hsu,C. and Bhattacharyya, Shuvra S.} } @conference {12427, title = {Content-based search techniques for searching CAD databases}, booktitle = {CAD Conference}, year = {2006}, month = {2006///}, abstract = {The popularity of 3D CAD systems is resulting in large assembly and part databases being createdby product development organizations. Over the last few years several content-based techniques have emerged to search these databases. Ability to perform content-based searches on CAD databases is expected to help the designers and manufacturing engineers in many different ways. Representative examples include part-family formation, redesign suggestion generation, supplier selection, cost estimation, tooling design, machine selection, stock selection, and design reuse. This paper covers the following three topics. First, it presents an overview of different types of part search techniques. Second, it presents an overview of the different aspects of assembly search techniques. Finally, it identifies the open challenges in these areas and outlines future research directions. }, author = {Gupta, Satyandra K. and Cardone, Antonio and Deshmukh,A.} } @article {16315, title = {Covering arrays for efficient fault characterization in complex configuration spaces}, journal = {IEEE Transactions on Software Engineering}, year = {2006}, month = {2006///}, pages = {20 - 34}, author = {Yilmaz,C. and Cohen,M. B and Porter, Adam} } @article {17042, title = {Creativity Support Tools: Report From a U.S. National Science Foundation Sponsored Workshop}, journal = {International Journal of Human-Computer Interaction}, volume = {20}, year = {2006}, month = {2006///}, pages = {61 - 77}, abstract = {Creativity support tools is a research topic with high risk but potentially very high payoff. The goal is to develop improved software and user interfaces that empower users to be not only more productive but also more innovative. Potential users include software and other engineers, diverse scientists, product and graphic designers, architects, educators, students, and many others. Enhanced interfaces could enable more effective searching of intellectual resources, improved collaboration among teams, and more rapid discovery processes. These advanced interfaces should also provide potent support in hypothesis formation, speedier evaluation of alternatives, improved understanding through visualization, and better dissemination of results. For creative endeavors that require composition of novel artifacts (e.g., computer programs, scientific papers, engineering diagrams, symphonies, artwork), enhanced interfaces could facilitate exploration of alternatives, prevent unproductive choices, and enable easy backtracking. This U.S. National Science Foundation sponsored workshop brought together 25 research leaders and graduate students to share experiences, identify opportunities, and formulate research challenges. Two key outcomes emerged: (a) encouragement to evaluate creativity support tools through multidimensional in-depth longitudinal case studies and (b) formulation of 12 principles for design of creativity support tools.Creativity support tools is a research topic with high risk but potentially very high payoff. The goal is to develop improved software and user interfaces that empower users to be not only more productive but also more innovative. Potential users include software and other engineers, diverse scientists, product and graphic designers, architects, educators, students, and many others. Enhanced interfaces could enable more effective searching of intellectual resources, improved collaboration among teams, and more rapid discovery processes. These advanced interfaces should also provide potent support in hypothesis formation, speedier evaluation of alternatives, improved understanding through visualization, and better dissemination of results. For creative endeavors that require composition of novel artifacts (e.g., computer programs, scientific papers, engineering diagrams, symphonies, artwork), enhanced interfaces could facilitate exploration of alternatives, prevent unproductive choices, and enable easy backtracking. This U.S. National Science Foundation sponsored workshop brought together 25 research leaders and graduate students to share experiences, identify opportunities, and formulate research challenges. Two key outcomes emerged: (a) encouragement to evaluate creativity support tools through multidimensional in-depth longitudinal case studies and (b) formulation of 12 principles for design of creativity support tools. }, isbn = {1044-7318}, doi = {10.1207/s15327590ijhc2002_1}, url = {http://www.tandfonline.com/doi/abs/10.1207/s15327590ijhc2002_1}, author = {Shneiderman, Ben and Fischer,Gerhard and Czerwinski,Mary and Resnick,Mitch and Myers,Brad and Candy,Linda and Edmonds,Ernest and Eisenberg,Mike and Giaccardi,Elisa and Hewett,Tom and Jennings,Pamela and Kules,Bill and Nakakoji,Kumiyo and Nunamaker,Jay and Pausch,Randy and Selker,Ted and Sylvan,Elisabeth and Terry,Michael} } @conference {18186, title = {Cross-Path PDMA-Based Error Protection for Streaming Multiuser Video over Multiple Paths}, booktitle = {Image Processing, 2006 IEEE International Conference on}, year = {2006}, month = {2006/10//}, pages = {21 - 24}, abstract = {In this paper, we consider aggregating multiple video streams and transmitting the merged stream over multiple error-prone paths. We propose a novel multi-stream error protection scheme based on packet division multiplexing access (PDMA) and cross-path forward error coding. Compared with the traditional time division multiplexing access (TDMA)-based error protection scheme, the proposed scheme outperforms 1.43 1.88 dB for the averaged PSNR of all received streams}, keywords = {access;error, codes;forward, coding;multiple, coding;video, correction, correction;multi-access, division, error, error-prone, forward, multiplexing, path;multistream, PDMA;cross-path, Protection, scheme;multiuser, streaming;, streaming;packet, systems;video, video}, doi = {10.1109/ICIP.2006.313151}, author = {Su,Guan-Ming and Chen,Meng and M. Wu} } @inbook {12925, title = {Detection, Isolation, and Identification of Vibrio cholerae from the Environment}, booktitle = {Current Protocols in MicrobiologyCurrent Protocols in Microbiology}, year = {2006}, month = {2006/09/01/}, pages = {6A.5.1-6A.5.38 - 6A.5.1-6A.5.38}, publisher = {John Wiley \& Sons, Inc.}, organization = {John Wiley \& Sons, Inc.}, keywords = {culturable, DETECTION, Environment, identification, isolation, nonculturable, viable, Vibrio cholerae}, isbn = {9780471729259}, url = {http://onlinelibrary.wiley.com/doi/10.1002/9780471729259.mc06a05s02/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Huq,Anwar and Grim,Christopher and Rita R Colwell and Nair,G. Balakrish} } @article {14922, title = {Development of a Large-Scale Integrated Neurocognitive Architecture Part 1: Conceptual Framework}, volume = {UMIACS-TR-2006-33}, year = {2006}, month = {2006/06/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {The idea of creating a general purpose machine intelligence that capturesmany of the features of human cognition goes back at least to the earliest days of artificial intelligence and neural computation. In spite of more than a half-century of research on this issue, there is currently no existing approach to machine intelligence that comes close to providing a powerful, general-purpose human-level intelligence. However, substantial progress made during recent years in neural computation, high performance computing, neuroscience and cognitive science suggests that a renewed effort to produce a general purpose and adaptive machine intelligence is timely, likely to yield qualitatively more powerful approaches to machine intelligence than those currently existing, and certain to lead to substantial progress in cognitive science, AI and neural computation. In this report, we outline a conceptual framework for the long-term development of a large-scale machine intelligence that is based on the modular organization, dynamics and plasticity of the human brain. Some basic design principles are presented along with a review of some of the relevant existing knowledge about the neurobiological basis of cognition. Three intermediate-scale prototypes for parts of a larger system are successfully implemented, providing support for the effectiveness of several of the principles in our framework. We conclude that a human-competitive neuromorphic system for machine intelligence is a viable long- term goal, but that for the short term, substantial integration with more standard symbolic methods as well as substantial research will be needed to make this goal achievable. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/3665}, author = {Reggia, James A. and Tagamets,Malle and Contreras-Vidal,Jose and Weems,Scott and Jacobs, David W. and Winder,Ransom and Chabuk,Timur} } @article {14920, title = {Development of a Large-Scale Integrated Neurocognitive Architecture - Part 2: Design and Architecture}, volume = {UMIACS-TR-2006-43}, year = {2006}, month = {2006/10//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {In Part 1 of this report, we outlined a framework for creating an intelligent agentbased upon modeling the large-scale functionality of the human brain. Building on those results, we begin Part 2 by specifying the behavioral requirements of a large-scale neurocognitive architecture. The core of our long-term approach remains focused on creating a network of neuromorphic regions that provide the mechanisms needed to meet these requirements. However, for the short term of the next few years, it is likely that optimal results will be obtained by using a hybrid design that also includes symbolic methods from AI/cognitive science and control processes from the field of artificial life. We accordingly propose a three-tiered architecture that integrates these different methods, and describe an ongoing computational study of a prototype {\textquoteright}mini-Roboscout{\textquoteright} based on this architecture. We also examine the implications of some non-standard computational methods for developing a neurocognitive agent. This examination included computational experiments assessing the effectiveness of genetic programming as a design tool for recurrent neural networks for sequence processing, and experiments measuring the speed-up obtained for adaptive neural networks when they are executed on a graphical processing unit (GPU) rather than a conventional CPU. We conclude that the implementation of a large-scale neurocognitive architecture is feasible, and outline a roadmap for achieving this goal. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/3957}, author = {Reggia, James A. and Tagamets,M. and Contreras-Vidal,J. and Jacobs, David W. and Weems,S. and Naqvi,W. and Winder,R. and Chabuk,T. and Jung,J. and Yang,C.} } @conference {13540, title = {DOCLIB: a Software Library for Document Processing}, booktitle = {International Conference on Document Recognition and Retrieval XIII}, year = {2006}, month = {2006///}, pages = {1 - 9}, publisher = {San Jose, CA}, organization = {San Jose, CA}, abstract = {Most researchers would agree that research in the field of document processing can benefit tremendously from a common software library through which institutions are able to develop and share research-related software and applications across academic, business, and government domains. However, despite several attempts in the past, the research community still lacks a widely-accepted standard software library for document processing. This paper describes a new library called DOCLIB, which tries to overcome the drawbacks of earlier approaches. Many of DOCLIB{\textquoteright}s features are unique either in themselves or in their combination with others, e.g. the factory concept for support of different image types, the juxtaposition of image data and metadata, or the add-on mechanism. We cherish the hope that DOCLIB serves the needs of researchers better than previous approaches and will readily be accepted by a larger group of scientists.}, author = {Jaeger,Stefan and Zhu,Guangyu and David Doermann and Chen,Kevin and Sampat,Summit} } @inbook {12634, title = {Early Recognition Approaches}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {35 - 43}, abstract = {The earliest approaches concerned recognition within small populations, with the volume of data limited largely by the computational resources available then. As illustrated by Fig. 4.1, many sought to derive a human silhouette from an image and, as common in pattern recognition, and then to derive a description which can be associated with the identity of the subject. This gives a {\textquoteleft}statistical{\textquoteright} approach to automatic gait recognition wherein the image sequence is described as a whole, and neither by a model- nor by a motion-based approach, but one which describes the motion content. Given that techniques to separate a moving object from its background have been developed for many years (especially in surveillance) there existed a selection of approaches to derive the silhouette of the moving subject, an example silhouette extraction from the image of Fig. 4.1(a) is shown in Fig. 4.1(b). What was then needed was approaches to process the sequence of silhouettes so as to derive a gait signature {\textemdash} a set of numbers to represent a subject{\textquoteright}s identity. A selection of signatures is shown in Fig. 4.1(c) which are displayed in a 3-dimensional space for visualization purposes only (the signature usually has more dimensions than this). These signatures represent ten of walking subjects with four instances of each subject. In this case the signatures derived from the four instances mostly cluster well, representing a good recognition rate. Accordingly, the target of the early approaches was to process video data of the form of Fig. 4.1(a) to obtain silhouettes of the form of Fig. 4.1(b) so as to derive signatures for recognition performance analysis.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @conference {12643, title = {Edge Suppression by Gradient Field Transformation Using Cross-Projection Tensors}, booktitle = {Computer Vision and Pattern Recognition, 2006 IEEE Computer Society Conference on}, volume = {2}, year = {2006}, month = {2006///}, pages = {2301 - 2308}, abstract = {We propose a new technique for edge-suppressing operations on images. We introduce cross projection tensors to achieve affine transformations of gradient fields. We use these tensors, for example, to remove edges in one image based on the edge-information in a second image. Traditionally, edge suppression is achieved by setting image gradients to zero based on thresholds. A common application is in the Retinex problem, where the illumination map is recovered by suppressing the reflectance edges, assuming it is slowly varying. We present a class of problems where edge-suppression can be a useful tool. These problems involve analyzing images of the same scene under variable illumination. Instead of resetting gradients, the key idea in our approach is to derive local tensors using one image and to transform the gradient field of another image using them. Reconstructed image from the modified gradient field shows suppressed edges or textures at the corresponding locations. All operations are local and our approach does not require any global analysis. We demonstrate the algorithm in the context of several applications such as (a) recovering the foreground layer under varying illumination, (b) estimating intrinsic images in non-Lambertian scenes, (c) removing shadows from color images and obtaining the illumination map, and (d) removing glass reflections.}, doi = {10.1109/CVPR.2006.106}, author = {Agrawal,A. and Raskar, R. and Chellapa, Rama} } @article {12930, title = {Effect of transport at ambient temperature on detection and isolation of Vibrio cholerae from environmental samples}, journal = {Applied and environmental microbiology}, volume = {72}, year = {2006}, month = {2006///}, pages = {2185 - 2190}, abstract = {It has long been assumed that prolonged holding of environmental samples at the ambient air temperature prior to bacteriological analysis is detrimental to isolation and detection of Vibrio cholerae, the causative agent of pandemic cholera. The present study was aimed at understanding the effect of transporting environmental samples at the ambient air temperature on isolation and enumeration of V. cholerae. For water and plankton samples held at ambient temperatures ranging from 31{\textdegree}C to 35{\textdegree}C for 20 h, the total counts did not increase significantly but the number of culturable V. cholerae increased significantly compared to samples processed within 1 h of collection, as measured by culture, acridine orange direct count, direct fluorescent-antibody-direct viable count (DFA-DVC), and multiplex PCR analyses. For total coliform counts, total bacterial counts, and DFA-DVC counts, the numbers did not increase significantly, but the culturable plate counts for V. cholerae increased significantly after samples were held at the ambient temperature during transport to the laboratory for analysis. An increase in the recovery of V. cholerae O1 and improved detection of V. cholerae O1 rfb and ctxA also occurred when samples were enriched after they were kept for 20 h at the ambient temperature during transport. Improved detection and isolation of toxigenic V. cholerae from freshwater ecosystems can be achieved by holding samples at the ambient temperature, an observation that has significant implications for tracking this pathogen in diverse aquatic environments.}, author = {Alam,M. and Sadique,A. and Bhuiyan,N. A. and Nair,G. B. and Siddique,A. K. and Sack,D. A. and Ahsan,S. and Huq,A. and Sack,R. B. and Rita R Colwell and others} } @conference {16876, title = {Efficient position-independent iconic search using an R-theta index}, booktitle = {Proceedings of the 14th annual ACM international symposium on Advances in geographic information systems}, series = {GIS {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {27 - 34}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {An iconic image database is a collection of symbolic images where each image is a collection of labeled point features called icons. A method is presented to support fast position-independent similarity search in an iconic database for symbolic images where the similarity condition involves finding icon pairs that satisfy a specific spatial relationship. This is achieved by introducing an index data structure based on r-θ space, which corresponds to the Cartesian product of separation (i.e., inter-icon distance) and (some representation of) relative spatial orientation. In this space, each pairing of two icons is represented by a single point, and all pairs with the same separation and relative orientation (regardless of absolute position) map to the same point. Similarly, all icon pairs with the same separation but different relative orientations map to points on a line parallel to the θ axis, while all pairs with different separations but the same relative orientation map to points on a line parallel to the r axis. Using such an index, database search for icon pairs with a given spatial relationship or range is accomplished by examining the subarea of the index space into which desired pairs would map. This r-θ index space can be organized using well-known spatial database techniques, such as quadtrees or R-trees. Although the size of such an index grows only linearly with respect to the number of images in the collection, it grows quadratically with the average number of icons in an image. A scheme is described to reduce the size of the index by pruning away a subset of the pairs, at the cost of incurring additional work when searching the database. This pruning is governed by a parameter φ, whose variation provides a continuous range of trade-offs between index size and search time.}, keywords = {iconic database, position-independent, spatial indexing}, isbn = {1-59593-529-0}, doi = {10.1145/1183471.1183478}, url = {http://doi.acm.org/10.1145/1183471.1183478}, author = {Cranston,Charles B. and Samet, Hanan} } @article {15932, title = {Enhancing reinforcement learning with metacognitive monitoring and control for improved perturbation tolerance}, journal = {Journal of Experimental and Theoretical Artificial Intelligence}, volume = {18}, year = {2006}, month = {2006///}, pages = {387 - 411}, author = {Anderson,M. L and Oates,T. and Chong,W. and Perlis, Don} } @inbook {14424, title = {Entity Resolution in Graphs}, booktitle = {Mining Graph DataMining Graph Data}, year = {2006}, month = {2006/04/10/}, pages = {311 - 344}, publisher = {John Wiley \& Sons, Inc.}, organization = {John Wiley \& Sons, Inc.}, abstract = {This chapter contains sections titled:Introduction Related Work Motivating Example for Graph-Based Entity Resolution Graph-Based Entity Resolution: Problem Formulation Similarity Measures for Entity Resolution Graph-Based Clustering for Entity Resolution Experimental Evaluation Conclusion References }, keywords = {entity resolution in graphs, graph-based clustering for entity resolution, graph-based entity resolution problem}, isbn = {9780470073049}, url = {http://onlinelibrary.wiley.com/doi/10.1002/9780470073049.ch13/summary}, author = {Bhattacharya,Indrajit and Getoor, Lise}, editor = {Cook,Diane J. and Holder,Lawrence B.} } @conference {15852, title = {Evaluation of Multilingual and Multi-modal Information Retrieval-Seventh Workshop of the Cross-Language Evaluation Forum, CLEF 2006, Alicante, Spain, September 19-21, 2006, Revised Selected Papers}, booktitle = {Seventh Workshop of the Cross-Language Evaluation Forum, CLEF 2006}, year = {2006}, month = {2006///}, address = {Alicante, Spain}, author = {Peters,C. and Clough,P. and Gey,F. and Karlgren,J. and Magnini,B. and Oard, Douglas and De Rijke,M. and Stempfhuber,M.} } @article {14068, title = {Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements}, journal = {Molecular and Biochemical Parasitology}, volume = {145}, year = {2006}, month = {2006/02//}, pages = {158 - 170}, abstract = {The ingi and L1Tc non-LTR retrotransposons - which constitute the ingi clade - are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5{\textquoteright}-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.}, keywords = {Degenerate retroelement, Evolution, Ingi, L1Tc, Leishmania major, Non-LTR retrotransposon, Retroposon, Trypanosoma brucei, Trypanosoma cruzi}, isbn = {0166-6851}, doi = {16/j.molbiopara.2005.09.017}, url = {http://www.sciencedirect.com/science/article/pii/S0166685105002963}, author = {Bringaud,Fr{\'e}d{\'e}ric and Ghedin,Elodie and Blandin,Ga{\"e}lle and Bartholomeu,Daniella C. and Caler,Elisabet and Levin,Mariano J. and Baltz,Th{\'e}o and El-Sayed, Najib M.} } @article {12135, title = {Experiments to understand HPC time to development}, journal = {CTWatch Quarterly}, year = {2006}, month = {2006///}, abstract = {In order to understand how high performance computing (HPC) programs are developed, a series of experiments, using students in graduate level HPC classes, have been conducted at many universities in the US. In this paper we discuss the general process of conducting those experiments, give some of the early results of those experiments, and describe a web-based process we are developing that will allow us to run additional experiments at other universities and laboratories that will be easier to conduct and generate results that more accurately reflect the process of building HPC programs.}, keywords = {hackystat, HPC, publications-journals}, url = {http://csdl.ics.hawaii.edu/techreports/06-08/06-08.pdf}, author = {Hochstein, Lorin and Nakamura,Taiga and Basili, Victor R. and Asgari, Sima and Zelkowitz, Marvin V and Hollingsworth, Jeffrey K and Shull, Forrest and Carver,Jeffrey and Voelp,Martin and Zazworka, Nico and Johnson,Philip} } @article {14435, title = {Exploiting independence for branch operations in Bayesian learning of C\&RTs}, journal = {Probabilistic, Logical and Relational Learning-Towards a Synthesis}, year = {2006}, month = {2006///}, abstract = {In this paper we extend a methodology for Bayesian learning via MCMC, with the ability to grow arbitrarily long branches in C\&RT models. We are able to do so by exploiting independence in the model construction process. The ability to grow branches rather than single nodes has been noted as desirable in the literature. The most singular feature of the underline methodology used here in comparison to other approaches is the coupling of the prior and the proposal. The main contribution of this paper is to show how taking advantage of independence in the coupled process, can allow branch growing and swapping for proposal models.}, author = {Angelopoulos,N. and Cussens,J. and De Raedt,L. and Dietterich,T. and Getoor, Lise and Muggleton,S. H} } @conference {16087, title = {Exploring erotics in Emily Dickinson{\textquoteright}s correspondence with text mining and visual interfaces}, booktitle = {Proceedings of the 6th ACM/IEEE-CS joint conference on Digital libraries}, series = {JCDL {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {141 - 150}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a system to support humanities scholars in their interpretation of literary work. It presents a user interface and web architecture that integrates text mining, a graphical user interface and visualization, while attempting to remain easy to use by non specialists. Users can interactively read and rate documents found in a digital libraries collection, prepare training sets, review results of classification algorithms and explore possible indicators and explanations. Initial evaluation steps suggest that there is a rationale for "provocational" text mining in literary interpretation.}, keywords = {case studies, humanities, literary criticism, text mining, user interface, Visualization}, isbn = {1-59593-354-9}, doi = {10.1145/1141753.1141781}, url = {http://doi.acm.org/10.1145/1141753.1141781}, author = {Plaisant, Catherine and Rose,James and Yu,Bei and Auvil,Loretta and Kirschenbaum,Matthew G. and Smith,Martha Nell and Clement,Tanya and Lord,Greg} } @book {12641, title = {Face Processing: Advanced Modeling and Methods}, year = {2006}, month = {2006///}, publisher = {Academic Press/Elsevier}, organization = {Academic Press/Elsevier}, author = {Chellapa, Rama and Zhao, W.} } @article {12603, title = {Face Verification Across Age Progression}, journal = {Image Processing, IEEE Transactions on}, volume = {15}, year = {2006}, month = {2006/11//}, pages = {3349 - 3361}, abstract = {Human faces undergo considerable amounts of variations with aging. While face recognition systems have been proven to be sensitive to factors such as illumination and pose, their sensitivity to facial aging effects is yet to be studied. How does age progression affect the similarity between a pair of face images of an individual? What is the confidence associated with establishing the identity between a pair of age separated face images? In this paper, we develop a Bayesian age difference classifier that classifies face images of individuals based on age differences and performs face verification across age progression. Further, we study the similarity of faces across age progression. Since age separated face images invariably differ in illumination and pose, we propose preprocessing methods for minimizing such variations. Experimental results using a database comprising of pairs of face images that were retrieved from the passports of 465 individuals are presented. The verification system for faces separated by as many as nine years, attains an equal error rate of 8.5\%}, keywords = {age, Aging, Bayesian, classification;, classification;face, classifier;age, difference, effects;preprocessing, Face, image, images;error, methods;Bayes, methods;error, progression;age, rate;face, recognition, recognition;image, separated, statistics;face, systems;face, verification;facial}, isbn = {1057-7149}, doi = {10.1109/TIP.2006.881993}, author = {Ramanathan,N. and Chellapa, Rama} } @conference {12626, title = {Finding Gait in Space and Time}, booktitle = {Pattern Recognition, 2006. ICPR 2006. 18th International Conference on}, volume = {4}, year = {2006}, month = {2006///}, pages = {586 - 589}, abstract = {We describe an approach to characterize the signatures generated by walking humans in spatio-temporal domain. To describe the computational model for this periodic pattern, we take the mathematical theory of geometry group theory, which is widely used in crystallographic structure research. Both empirical and theoretical analyses prove that spatio-temporal helical patterns generated by legs belong to the Frieze Groups because they can be characterized by a repetitive motif along the direction of walking. The theory is applied to an automatic detection-and-tracking system capable of counting heads and handling occlusion by recognizing such patterns. Experimental results for videos acquired from both static and moving ground sensors are presented. Our algorithm demonstrates robustness to non-rigid human deformation as well as background clutter}, keywords = {analysis;, analysis;geometry, analysis;group, characterization;occlusion, counting;mathematical, detection-and-tracking, domain;spatiotemporal, Frieze, group, groups;automatic, handling;pattern, helical, humans;computer, MOTION, pattern;spatiotemporal, patterns;walking, recognition;periodic, signature, system;computer, theory;head, theory;image, theory;motion, vision;gait}, doi = {10.1109/ICPR.2006.562}, author = {Yang Ran and Chellapa, Rama and Qinfen Zheng} } @conference {13370, title = {Flow algorithms for two pipelined filter ordering problems}, booktitle = {Proceedings of the twenty-fifth ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems}, series = {PODS {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {193 - 202}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Pipelined filter ordering is a central problem in database query optimization, and has received renewed attention recently in the context of environments such as the web, continuous high-speed data streams and sensor networks. We present algorithms for two natural extensions of the classical pipelined filter ordering problem: (1) a distributional type problem where the filters run in parallel and the goal is to maximize throughput, and (2) an adversarial type problem where the goal is to minimize the expected value of multiplicative regret. We show that both problems can be solved using similar flow algorithms, which find an optimal ordering scheme in time O(n2), where n is the number of filters. Our algorithm for (1) improves on an earlier O(n3 log n) algorithm of Kodialam.}, keywords = {flow algorithms, Pipelined filter ordering, Query optimization, selection ordering}, isbn = {1-59593-318-2}, doi = {10.1145/1142351.1142379}, url = {http://doi.acm.org/10.1145/1142351.1142379}, author = {Condon,Anne and Deshpande, Amol and Hellerstein,Lisa and Wu,Ning} } @article {12613, title = {From sample similarity to ensemble similarity: probabilistic distance measures in reproducing kernel Hilbert space}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {28}, year = {2006}, month = {2006/06//}, pages = {917 - 929}, abstract = {This paper addresses the problem of characterizing ensemble similarity from sample similarity in a principled manner. Using a reproducing kernel as a characterization of sample similarity, we suggest a probabilistic distance measure in the reproducing kernel Hilbert space (RKHS) as the ensemble similarity. Assuming normality in the RKHS, we derive analytic expressions for probabilistic distance measures that are commonly used in many applications, such as Chernoff distance (or the Bhattacharyya distance as its special case), Kullback-Leibler divergence, etc. Since the reproducing kernel implicitly embeds a nonlinear mapping, our approach presents a new way to study these distances whose feasibility and efficiency is demonstrated using experiments with synthetic and real examples. Further, we extend the ensemble similarity to the reproducing kernel for ensemble and study the ensemble similarity for more general data representations.}, keywords = {Automated;Sample Size;Signal Processing, Bhattacharyya distance;Chernoff distance;Gram matrix;Kullback-Leibler divergence;data representations;ensemble similarity characterization;nonlinear mapping;probabilistic distance measures;reproducing kernel Hilbert space;sample similarity characterizatio, Computer-Assisted;, Statistical;Pattern Recognition}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2006.120}, author = {Zhou,S. K and Chellapa, Rama} } @conference {12622, title = {The Function Space of an Activity}, booktitle = {Computer Vision and Pattern Recognition, 2006 IEEE Computer Society Conference on}, volume = {1}, year = {2006}, month = {2006///}, pages = {959 - 968}, abstract = {An activity consists of an actor performing a series of actions in a pre-defined temporal order. An action is an individual atomic unit of an activity. Different instances of the same activity may consist of varying relative speeds at which the various actions are executed, in addition to other intra- and inter- person variabilities. Most existing algorithms for activity recognition are not very robust to intra- and inter-personal changes of the same activity, and are extremely sensitive to warping of the temporal axis due to variations in speed profile. In this paper, we provide a systematic approach to learn the nature of such time warps while simultaneously allowing for the variations in descriptors for actions. For each activity we learn an $\#$145;average $\#$146; sequence that we denote as the nominal activity trajectory. We also learn a function space of time warpings for each activity separately. The model can be used to learn individualspecific warping patterns so that it may also be used for activity based person identification. The proposed model leads us to algorithms for learning a model for each activity, clustering activity sequences and activity recognition that are robust to temporal, intra- and inter-person variations. We provide experimental results using two datasets.}, doi = {10.1109/CVPR.2006.304}, author = {Veeraraghavan,A. and Chellapa, Rama and Roy-Chowdhury, A.K.} } @article {14611, title = {Functional Analysis of Hes-1 in Preadipocytes}, journal = {Molecular EndocrinologyMolecular Endocrinology}, volume = {20}, year = {2006}, month = {2006/03/01/}, pages = {698 - 705}, abstract = {Notch signaling blocks differentiation of 3T3-L1 preadipocytes, and this can be mimicked by constitutive expression of the Notch target gene Hes-1. Although considered initially to function only as a repressor, recent evidence indicates that Hes-1 can also activate transcription. We show here that the domains of Hes-1 needed to block adipogenesis coincide with those necessary for transcriptional repression. HRT1, another basic-helix-loop-helix protein and potential Hes-1 partner, was also induced by Notch in 3T3-L1 cells but did not block adipogenesis, suggesting that Hes-1 functions primarily as a homodimer or possibly as a heterodimer with an unknown partner. Purification of Hes-1 identified the Groucho/transducin-like enhancer of split family of corepressors as the only significant Hes-1 interacting proteins in vivo. An evaluation of global gene expression in preadipocytes identified approximately 200 Hes-1-responsive genes comprising roughly equal numbers of up-regulated and down-regulated genes. However, promoter analyses indicated that the down-regulated genes were significantly more likely to contain Hes-1 binding sites, indicating that Hes-1 is more likely to repress transcription of its direct targets. We conclude that Notch most likely blocks adipogenesis through the induction of Hes-1 homodimers, which repress transcription of key target genes.}, isbn = {0888-8809, 1944-9917}, doi = {10.1210/me.2005-0325}, url = {http://mend.endojournals.org/content/20/3/698}, author = {Ross,David A and Hannenhalli, Sridhar and Tobias,John W and Cooch,Neil and Shiekhattar,Ramin and Kadesch,Tom} } @inbook {12635, title = {Further Gait Developments}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {135 - 149}, abstract = {Human gait characteristics are best analyzed when presented in its canonical view (side view). The dynamics behind an individual{\textquoteright}s gait, the quasi-periodicity of an individual{\textquoteright}s gait etc. which contribute significantly towards establishing his/her identity are more evident when the canonical view of human gait is presented. Thus, the availability of such a canonical view is crucial to the success of many gait recognition systems. We observe that in surveillance applications a non-canonical view of an individual{\textquoteright}s gait is captured more often and this necessitates developing gait recognition algorithms that are view invariant. When individuals walk at an angle oblique to the camera, the performance of gait recognition systems suffers due to the gradual change in the individual{\textquoteright}s height and stride length as captured by the camera.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @inbook {12631, title = {Future Challenges}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {151 - 170}, abstract = {Although a large number of gait recognition algorithms have been reported, it should be noted that gait recognition is still in its infancy. This is because previous work was mainly implemented under some simplified and controlled conditions, e.g., no occlusion during human walking, relatively plain background, the lack of view generality except [142, 103, 102], etc (see Table 8.1). Although reporting good recognition performance, most existing algorithms were usually evaluated on a small and non-realistic database. Further, recognition rates have not yet far reached a possible upper bound even under the above two conditions.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @inbook {12632, title = {Gait Databases}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {17 - 34}, abstract = {Naturally, the success and evolution of a new application relies largely on the dataset used for evaluation. The early gait databases were collected about 10 years before the time of writing. Then, computers had little power and memory costs were comparatively high. Clearly, this was before digital video and acquisition was based on analogue camcorder technology which resulted in frames being digitized individually. Since techniques were in their infancy, as in face recognition, early databases only had few subjects. The idea then was to determine whether recognition could be achieved at all {\textemdash} or not. At that stage we were not interested in the ramifications of recognition. There were two early databases which were developed independently: the UCSD data was recorded outdoors and the Southampton data was indoors, with subjects wearing special trousers. The current databases are considerably more advanced, but certainly benefited in their development for the early approaches.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @article {12160, title = {The Goal Question Metric Approach}, journal = {5th ACM-IEEE International Symposium on Empirical Software Engineering (ISESE{\textquoteright}06)}, year = {2006}, month = {2006///}, author = {Basili, Victor R. and Caldiera,G. and Rombach,H. D} } @conference {13436, title = {Heuristic search and information visualization methods for school redistricting}, booktitle = {Proceedings of the 18th conference on Innovative applications of artificial intelligence - Volume 2}, series = {IAAI{\textquoteright}06}, year = {2006}, month = {2006///}, pages = {1774 - 1781}, publisher = {AAAI Press}, organization = {AAAI Press}, abstract = {We describe an application of AI search and information visualization techniques to the problem of school redistricting, in which students are assigned to home schools within a county or school district. This is a multicriteria optimization problem in which competing objectives must be considered, such as school capacity, busing costs, and socioeconomic distribution. Because of the complexity of the decision-making problem, tools are needed to help end users generate, evaluate, and compare alternative school assignment plans. A key goal of our research is to aid users in finding multiple qualitatively different redistricting plans that represent different tradeoffs in the decision space.We present heuristic search methods that can be used to find a set of qualitatively different plans, and give empirical results of these search methods on population data from the school district of Howard County, Maryland. We show the resulting plans using novel visualization methods that we have developed for summarizing and comparing alternative plans. }, isbn = {978-1-57735-281-5}, url = {http://dl.acm.org/citation.cfm?id=1597122.1597136}, author = {desJardins, Marie and Bulka,Blazej and Carr,Ryan and Hunt,Andrew and Rathod,Priyang and Rheingans,Penny} } @article {12814, title = {High-confidence medical device software and systems}, journal = {Computer}, volume = {39}, year = {2006}, month = {2006/04//}, pages = {33 - 38}, abstract = {Given the shortage of caregivers and the increase in an aging US population, the future of US healthcare quality does not look promising and definitely is unlikely to be cheaper. Advances in health information systems and healthcare technology offer a tremendous opportunity for improving the quality of care while reducing costs. The development and production of medical device software and systems is a crucial issue, both for the US economy and for ensuring safe advances in healthcare delivery. As devices become increasingly smaller in physical terms but larger in software terms, the design, testing, and eventual Food and Drug Administration (FDA) device approval is becoming much more expensive for medical device manufacturers both in terms of time and cost. Furthermore, the number of devices that have recently been recalled due to software and hardware problems is increasing at an alarming rate. As medical devices are becoming increasingly networked, ensuring even the same level of health safety seems a challenge.}, keywords = {Aging, biomedical equipment, Clinical software engineering, Costs, FDA device, Food and Drug Administration device, health and safety, health care, health information system, health safety, healthcare delivery, Healthcare technology, Information systems, medical computing, medical device manufacturing, medical device software development, medical device systems development, medical information systems, Medical services, Medical software, Medical tests, networked medical devices, Production systems, Software design, Software safety, Software systems, Software testing, US healthcare quality}, isbn = {0018-9162}, doi = {10.1109/MC.2006.127}, author = {Lee,I. and Pappas,G. J and Cleaveland, Rance and Hatcliff,J. and Krogh,B. H and Lee,P. and Rubin,H. and Sha,L.} } @book {12628, title = {Human identification based on gait}, year = {2006}, month = {2006///}, publisher = {Springer Science \& Business}, organization = {Springer Science \& Business}, abstract = {Biometrics now affect many people{\textquoteright}s lives, and is the focus of much academic research and commercial development. Gait is one of the most recent biometrics, with its own unique advantages. Gait recognizes people by the way they walk and run, analyzes movement, which in turn implies analyzing sequences of images. This professional book introduces developments from the laboratories of very distinguished researchers within this relatively new area of biometrics and clearly establishes human gait as a biometric. Human Identification Based on Gait provides a snapshot of all the biometric work in human identification by gait (all major centers for research are indicated in this book). To complete the picture, studies are included from medicine, psychology and other areas wherein we find not only justification for the use of gait as a biometric, but also pointers to techniques and to analysis. Human Identification Based on Gait is designed for a professional audience, composed of researchers and practitioners in industry. This book is also suitable as a secondary text for graduate-level students in computer science.}, keywords = {Biometric identification, Computers / Computer Graphics, Computers / Computer Science, Computers / Computer Vision \& Pattern Recognition, Computers / General, Computers / Information Technology, Computers / Programming / Software Development, Computers / Software Development \& Engineering / Systems Analysis \& Design, Gait in humans, Medical / Physiology, Social Science / Anthropology / Physical}, isbn = {9780387244242}, author = {Nixon,Mark S. and Tan,Tieniu and Chellapa, Rama} } @conference {15543, title = {Image Registration and Fusion Studies for the Integration of Multiple Remote Sensing Data}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {5}, year = {2006}, month = {2006/05//}, pages = {V - V}, abstract = {The future of remote sensing will see the development of spacecraft formations, and with this development will come a number of complex challenges such as maintaining precise relative position and specified attitudes. At the same time, there will be increasing needs to understand planetary system processes and build accurate prediction models. One essential technology to accomplish these goals is the integration of multiple source data. For this integration, image registration and fusion represent the first steps and need to be performed with very high accuracy. In this paper, we describe studies performed in both image registration and fusion, including a modular framework that was built to describe registration algorithms, a Web-based image registration toolbox, and the comparison of several image fusion techniques using data from the EO-1/ALI and Hyperion sensors}, keywords = {ALI, EO-1, fusion studies, geophysical signal processing, Hyperion sensors, image registration, Internet, multiple remote sensing data, multiple source data, Remote sensing, Web-based image registration toolbox}, doi = {10.1109/ICASSP.2006.1661494}, author = {Le Moigne,J. and Cole-Rhodes,A. and Eastman,R. and Jain,P. and Joshua,A. and Memarsadeghi,N. and Mount, Dave and Netanyahu,N. and Morisette,J. and Uko-Ozoro,E.} } @conference {12620, title = {Integrated Motion Detection and Tracking for Visual Surveillance}, booktitle = {Computer Vision Systems, 2006 ICVS {\textquoteright}06. IEEE International Conference on}, year = {2006}, month = {2006/01//}, pages = {28 - 28}, abstract = {Visual surveillance systems have gained a lot of interest in the last few years. In this paper, we present a visual surveillance system that is based on the integration of motion detection and visual tracking to achieve better performance. Motion detection is achieved using an algorithm that combines temporal variance with background modeling methods. The tracking algorithm combines motion and appearance information into an appearance model and uses a particle filter framework for tracking the object in subsequent frames. The systems was tested on a large ground-truthed data set containing hundreds of color and FLIR image sequences. A performance evaluation for the system was performed and the average evaluation results are reported in this paper.}, doi = {10.1109/ICVS.2006.35}, author = {Abdelkader, M.F. and Chellapa, Rama and Qinfen Zheng and Chan, A.L.} } @inbook {12637, title = {Integrating Video Information over Time. Example: Face Recognition from Video}, booktitle = {Cognitive Vision SystemsCognitive Vision Systems}, series = {Lecture Notes in Computer Science}, volume = {3948}, year = {2006}, month = {2006///}, pages = {127 - 144}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The ability to integrate information over time in order to come to a conclusion is a strength of cognitive systems. It allows the system, e.g., to 1 verify insecure observations: This is the case when data is noisy or of low-quality, or if conditions in general are non-optimal. 2 exploit general knowledge about spatio-temporal relations: This allows the system to exploit the specific dynamics of an object as an additional feature for, e.g., recognition, interpretation and prediction of actions of other agents. 3 In general, using dynamics allows the system to recursively generate and verify hypotheses for object and scene interpretation and to generate warnings when {\textquoteleft}implausible{\textquoteright} hypotheses occur or to circumvent them altogether. We have studied the effectiveness of temporal integration for recognition purposes by using the face recognition as an example study case. Face recognition is a prominent problem and has been studied more extensively than almost any other recognition problem. An observation is that face recognition works well in ideal conditions. If those conditions, however, are not met, then all present algorithms break down disgracefully. This problem appears to be general to all vision techniques that intend to extract visual information out of low-SNR image data. It is exactly a strength of cognitive systems that they are able to cope with non-ideal situations. In this chapter we will deal with this problem.}, isbn = {978-3-540-33971-7}, url = {http://dx.doi.org/10.1007/11414353_9}, author = {Kr{\"u}ger,Volker and Zhou,Shaohua and Chellapa, Rama}, editor = {Christensen,Henrik and Nagel,Hans-Hellmut} } @conference {12611, title = {Invariant Geometric Representation of 3D Point Clouds for Registration and Matching}, booktitle = {Image Processing, 2006 IEEE International Conference on}, year = {2006}, month = {2006/10//}, pages = {1209 - 1212}, abstract = {Though implicit representations of surfaces have often been used for various computer graphics tasks like modeling and morphing of objects, it has rarely been used for registration and matching of 3D point clouds. Unlike in graphics, where the goal is precise reconstruction, we use isosurfaces to derive a smooth and approximate representation of the underlying point cloud which helps in generalization. Implicit surfaces are generated using a variational interpolation technique. Implicit function values on a set of concentric spheres around the 3D point cloud of object are used as features for matching. Geometric-invariance is achieved by decomposing implicit values based feature set into various spherical harmonics. The decomposition provides a compact representation of 3D point clouds while achieving rotation invariance}, keywords = {3D, cloud;computer, function, geometric, graphics;geophysical, graphics;image, Interpolation, matching;image, point, processing;image, reconstruction;image, registration;image, registration;implicit, representation;interpolation;, representation;variational, signal, technique;clouds;computer, value;invariant}, doi = {10.1109/ICIP.2006.312542}, author = {Biswas,S. and Aggarwal,G. and Chellapa, Rama} } @article {18013, title = {Issues in writing a parallel compiler starting from a serial compiler}, year = {2006}, month = {2006///}, institution = {draft. Technical report, University of Maryland Institute for Advanced Compuer Studies}, author = {Tzannes,A. and Barua,R. and Caragea,G. and Vishkin, Uzi} } @inbook {12639, title = {Key Frame-Based Activity Representation Using Antieigenvalues}, booktitle = {Computer Vision {\textendash} ACCV 2006Computer Vision {\textendash} ACCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3852}, year = {2006}, month = {2006///}, pages = {499 - 508}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Many activities may be characterized by a sequence of key frames that are related to important changes in motion rather than dominant characteristics that persist over a long sequence of frames. To detect such changes, we define a transformation operator at every time instant, which relates the past to the future states. One of the useful quantities associated with numerical range of an operator is the eigenvalue. In the literature, eigenvalue-based approaches have been studied extensively for many modeling tasks. These rely on gross properties of the data and are not suitable to detect subtle changes. We propose an antieigenvalue {\textendash} based measure to detect key frames. Antieigenvalues depend critically on the turning of the operator, whereas eigenvalues represent the amount of dilation along the eigenvector directions aligned with the direction of maximum variance. We demonstrate its application to activity modeling and recognition using two datasets: a motion capture dataset and the UCF human action dataset.}, isbn = {978-3-540-31244-4}, url = {http://dx.doi.org/10.1007/11612704_50}, author = {Cuntoor,Naresh and Chellapa, Rama}, editor = {Narayanan,P. and Nayar,Shree and Shum,Heung-Yeung} } @article {18856, title = {Machining feature-based similarity assessment algorithms for prismatic machined parts}, journal = {Computer-Aided Design}, volume = {38}, year = {2006}, month = {2006/09//}, pages = {954 - 972}, abstract = {This paper presents algorithms for identifying machined parts in a database that are similar to a given query part based on machining features. In this paper we only consider parts that are machined on 3-axis machining centers. We utilize reduced feature vectors consisting of machining feature access directions, feature types, feature volumes, feature dimensional tolerances and feature group cardinality as a basis for assessing shape similarity. We have defined a distance function between two sets of reduced feature vectors to assess the similarity between them from the machining effort point of view. To assess the similarity between the two parts, one set of reduced feature vectors is transformed in space using rigid body transformations with respect to the other set such that the distance between them is minimized. The distance between the two sets of aligned reduced feature vectors is used as a measure of similarity between the two parts. The existing machined parts are rank ordered based on the value of the distance with respect to the query part. The cost of previously machined parts that have a very small distance from the query part can be used as a basis for estimating the cost of machining the new part.}, keywords = {Feature vector alignment, Machining features, Similarity assessment}, isbn = {0010-4485}, doi = {10.1016/j.cad.2006.08.001}, url = {http://www.sciencedirect.com/science/article/pii/S0010448506001369}, author = {Cardone, Antonio and Gupta, Satyandra K. and Deshmukh,Abhijit and Karnik,Mukul} } @article {12636, title = {Measuring human movement for biomechanical applications using markerless motion capture}, journal = {Proceedings of SPIE}, volume = {6056}, year = {2006}, month = {2006///}, pages = {60560R - 60560R}, abstract = {Modern biomechanical and clinical applications require the accurate capture of normal and pathological humanmovement without the artifacts associated with standard marker-based motion capture techniques such as soft tissue artifacts and the risk of artificial stimulus of taped-on or strapped-on markers. In this study, the need for new markerless human motion capture methods is discussed in view of biomechanical applications. Three different approaches for estimating human movement from multiple image sequences were explored. The first two approaches tracked a 3D articulated model in 3D representations constructed from the image sequences, while the third approach tracked a 3D articulated model in multiple 2D image planes. The three methods are systematically evaluated and results for real data are presented. The role of choosing appropriate technical equipment and algorithms for accurate markerless motion capture is critical. The implementation of this new methodology offers the promise for simple, time-efficient, and potentially more meaningful assessments of human movement in research and clinical practice. }, author = {M{\"u}ndermann, L. and Corazza, S. and Chaudhari, A.M. and Andriacchi, T.P. and Sundaresan, A. and Chellapa, Rama} } @article {16006, title = {The metacognitive loop I: Enhancing reinforcement learning with metacognitive monitoring and control for improved perturbation tolerance}, journal = {Journal of Experimental \& Theoretical Artificial Intelligence}, volume = {18}, year = {2006}, month = {2006///}, pages = {387 - 411}, author = {Anderson,M. L and Oates,T. and Chong,W. and Perlis, Don} } @article {12602, title = {Method and System for Object Surveillance and Real Time Activity Recognition}, volume = {12/086,118}, year = {2006}, month = {2006/12/05/}, abstract = {Method and system for objects surveillance and real-time activity recognition is based on analysis of spatio-temporal images of individuals under surveillance where a spatio-temporal volume occupied by each individual is decomposed by crossing the same at specific heights to form 2-dimensional slices, each containing representation of trajectory of the motion of corresponding portions of the individual body. The symmetry of the trajectories (Gait DNA) is analyzed and classified to generate data indicative of a type of activity of the individual based on the symmetry or asymmetry of the Gait DNA in each 2-dimensional slice. An effective occlusion handling ability is implemented which permits to restore the occluded silhouette of an individual.}, url = {http://www.google.com/patents?id=IArMAAAAEBAJ}, author = {Yang Ran and Chellapa, Rama and Qinfen Zheng} } @conference {12928, title = {Microbial diversity in the era of genomics}, booktitle = {SYMPOSIA-SOCIETY FOR GENERAL MICROBIOLOGY}, volume = {66}, year = {2006}, month = {2006///}, pages = {1 - 1}, author = {Rita R Colwell} } @conference {12838, title = {Model based verification and validation of distributed control architectures}, booktitle = {Proceedings of Convergence Convergence International Congress and Exposition on Transportation Electronics, Detroit, USA}, year = {2006}, month = {2006///}, author = {Ray,A. and Cleaveland, Rance and Jiang,S. and Fuhrman,T.} } @inbook {12633, title = {Model-Based Approaches}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {107 - 133}, abstract = {The model based approaches aim to derive the movement of the torso and/or the legs. The distinction of a structural approach is one which uses static parameters illustrated in Fig. 6.1(a) whereas a model can be the (relative) motion of the angles (α, β, and ϕ) between the limbs, shown in Fig. 6.1(b). As earlier, these angles can also be measured relative to vertical.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @conference {12614, title = {Modeling Age Progression in Young Faces}, booktitle = {Computer Vision and Pattern Recognition, 2006 IEEE Computer Society Conference on}, volume = {1}, year = {2006}, month = {2006/06//}, pages = {387 - 394}, abstract = {We propose a craniofacial growth model that characterizes growth related shape variations observed in human faces during formative years. The model draws inspiration from the $\#$145;revised $\#$146; cardioidal strain transformation model proposed in psychophysical studies related to craniofacial growth. The model takes into account anthropometric evidences collected on facial growth and hence is in accordance with the observed growth patterns in human faces across years. We characterize facial growth by means of growth parameters defined over facial landmarks often used in anthropometric studies. We illustrate how the age-based anthropometric constraints on facial proportions translate into linear and non-linear constraints on facial growth parameters and propose methods to compute the optimal growth parameters. The proposed craniofacial growth model can be used to predict one $\#$146;s appearance across years and to perform face recognition across age progression. This is demonstrated on a database of age separated face images of individuals under 18 years of age.}, doi = {10.1109/CVPR.2006.187}, author = {Ramanathan,N. and Chellapa, Rama} } @article {18643, title = {Modeling and Simulation of the Escalation Archetype in Computer Security}, journal = {Symposium on Simulation Software Security (SSSS 06)}, volume = {38}, year = {2006}, month = {2006///}, pages = {495 - 495}, abstract = {To support decision-making for mitigating computer security risks, we developed and used a system dynamics model of security aspects of an enterprise system. We describe the notion of archetypes in general and the escalation archetype specifically, showing how it can arise in computer security. We show the effects of this instance of escalation through simulation of our model, consider the effects of changes in the simulation, and discuss the prognoses drawn from the archetype literature and their applicability to security.}, url = {https://www.scs.org/confernc/springsim/springsim06/prelimProgram/ssss/2.html}, author = {Rosenfeld,S. N. and Rus,I. and Michel Cukier} } @conference {18679, title = {Modeling the Symptomatic Fixes Archetype in Enterprise Computer Security}, volume = {1}, year = {2006}, month = {2006/09//}, pages = {178 - 188}, abstract = {To support decision-making for security-risk mitigation and the appropriate selection of security countermeasures, we propose a system dynamics model of the security aspects of an enterprise system. We developed such an executable model, incorporating the concept of archetypes. We present here one archetype for computer security, namely symptomatic fixes (or shifting the burden). Using simulation, we show one instance of how this archetype can be used for recognizing and diagnosing typical situations, as well as for fixing problems. The global effects of changes and behavioral trends are examined, and other instances of symptomatic fixes in security are described as well}, keywords = {business data processing, decision making, decision-making, enterprise computer security, human factors, security of data, security-risk mitigation, symptomatic fixes archetype modeling, system dynamics model, system modeling}, doi = {10.1109/COMPSAC.2006.62}, author = {Rosenfeld,S. N. and Rus,I. and Michel Cukier} } @article {18011, title = {Models for Advancing PRAM and Other Algorithms into Parallel Programs for a PRAM-On-Chip Platform}, year = {2006}, month = {2006/05/18/}, abstract = {A bold vision that guided this work is as follows: (i) a parallel algorithms and programming course could become a standard course in every undergraduate computer science program, and (ii) this course could be coupled with a so-called PRAM-On-Chip architecture --- a commodity high-end multi-core computer architecture.In fact, the current paper is a tutorial on how to convert PRAM algorithms into efficient PRAM-On-Chip programs. Coupled with a text on PRAM algorithms as well as an available PRAM-On-Chip tool-chain, comprising a compiler and a simulator, the paper provides the missing link for upgrading a standard theoretical PRAM algorithms class to a parallel algorithms and programming class. Having demonstrated that such a course could cover similar programming projects and material to what is covered by a typical first serial algorithms and programming course, the paper suggests that parallel programming in the emerging multi-core era does not need to be more difficult than serial programming. If true, a powerful answer to the so-called parallel programming open problem is being provided. This open problem is currently the main stumbling block for the industry in getting the upcoming generation of multi-core architectures to improve single task completion time using easy-to-program application programmer interfaces. Known constraints of this open problem, such as backwards compatibility on serial code, are also addressed by the overall approach. More concretely, a widely used methodology for advancing parallel algorithmic thinking into parallel algorithms is revisited, and is extended into a methodology for advancing parallel algorithms to PRAM-On-Chip programs. A performance cost model for the PRAM-On-Chip is also presented. It uses as complexity metrics the length of sequence of round trips to memory (LSRTM) and queuing delay (QD) from memory access queues, in addition to standard PRAM computation costs. Highlighting the importance of LSRTM in determining performance is another contribution of the paper. Finally, some alternatives to PRAM algorithms, which, on one hand, are easier-to-think, but, on the other hand, suppress more architecture details, are also discussed. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/3338}, author = {Vishkin, Uzi and Caragea,George C. and Lee,Bryant} } @article {14081, title = {Molecular Characterization of Serine-, Alanine-, and Proline-Rich Proteins of Trypanosoma cruzi and Their Possible Role in Host Cell Infection}, journal = {Infect. Immun.}, volume = {74}, year = {2006}, month = {2006/03/01/}, pages = {1537 - 1546}, abstract = {We previously reported the isolation of a novel protein gene family, termed SAP (serine-, alanine-, and proline-rich protein), from Trypanosoma cruzi. Aided by the availability of the completed genome sequence of T. cruzi, we have now identified 39 full-length sequences of SAP, six pseudogenes and four partial genes. SAPs share a central domain of about 55 amino acids and can be divided into four groups based on their amino (N)- and carboxy (C)-terminal sequences. Some SAPs have conserved N- and C-terminal domains encoding a signal peptide and a glycosylphosphatidylinositol anchor addition site, respectively. Analysis of the expression of SAPs in metacyclic trypomastigotes by two-dimensional electrophoresis and immunoblotting revealed that they are likely to be posttranslationally modified in vivo. We have also demonstrated that some SAPs are shed into the extracellular medium. The recombinant SAP exhibited an adhesive capacity toward mammalian cells, where binding was dose dependent and saturable, indicating a possible ligand-receptor interaction. SAP triggered the host cell Ca2+ response required for parasite internalization. A cell invasion assay performed in the presence of SAP showed inhibition of internalization of the metacyclic forms of the CL strain. Taken together, these results show that SAP is involved in the invasion of mammalian cells by metacyclic trypomastigotes, and they confirm the hypothesis that infective trypomastigotes exploit an arsenal of surface glycoproteins and shed proteins to induce signaling events required for their internalization.}, doi = {

10.1128/IAI.74.3.1537-1546.2006

}, url = {http://iai.asm.org/cgi/content/abstract/74/3/1537}, author = {Baida,Renata C. P. and Santos,Marcia R. M. and Carmo,Mirian S. and Yoshida,Nobuko and Ferreira,Danielle and Ferreira,Alice Teixeira and El Sayed,Najib M. and Andersson,Bjorn and da Silveira,Jose Franco} } @conference {12616, title = {Motion Based Correspondence for 3D Tracking of Multiple Dim Objects}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {2}, year = {2006}, month = {2006/05//}, pages = {II - II}, abstract = {Tracking multiple objects in a video is a demanding task that is frequently encountered in several systems such as surveillance and motion analysis. Ability to track objects in 3D requires the use of multiple cameras. While tracking multiple objects using multiples video cameras, establishing correspondence between objects in the various cameras is a nontrivial task. Specifically, when the targets are dim or are very far away from the camera, appearance cannot be used in order to establish this correspondence. Here, we propose a technique to establish correspondence across cameras using the motion features extracted from the targets, even when the relative position of the cameras is unknown. Experimental results are provided for the problem of tracking multiple bees in natural flight using two cameras. The reconstructed 3D flight paths of the bees show some interesting flight patterns}, keywords = {3D, analysis;motion, analysis;video, based, cameras;feature, correspondence;motion, dim, extraction;image, extraction;multiple, features, MOTION, objects;video, processing;, signal, tracking;motion}, doi = {10.1109/ICASSP.2006.1660431}, author = {Veeraraghavan,A. and Srinivasan, M. and Chellapa, Rama and Baird, E. and Lamont, R.} } @conference {12619, title = {Moving Object Verification from Airborne Video}, booktitle = {Computer Vision Systems, 2006 ICVS {\textquoteright}06. IEEE International Conference on}, year = {2006}, month = {2006/01//}, pages = {29 - 29}, abstract = {This paper presents an end-to-end verification system for moving objects in airborne video. Lacking prior training data, the object information is collected on the fly from a short real-time learning sequence. Using a sample selection module, the system selects samples from the learning sequence and stores them in an exemplar database. To handle appearance change due to potentially large aspect angle variations, a homography-based view synthesis method is used to generate a novel view of each image in the exemplar database at the same pose as the query object in each frame of a query sequence. A spatial match score is obtained using a Distance Transform to compare the novel view and query object. After looping over all query frames, the set of match scores is passed to a temporal analysis module to examine the behavior of the query object, and calculate a final likelihood. Very good verification performance is achieved over thousands of trials for both color and infrared video sequences using the proposed system.}, doi = {10.1109/ICVS.2006.42}, author = {Yue,Zhanfeng and Chellapa, Rama and Guarino, D.} } @inbook {12624, title = {Multi-camera Tracking of Articulated Human Motion Using Motion and Shape Cues}, booktitle = {Computer Vision {\textendash} ACCV 2006Computer Vision {\textendash} ACCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3852}, year = {2006}, month = {2006///}, pages = {131 - 140}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present a framework and algorithm for tracking articulated motion for humans. We use multiple calibrated cameras and an articulated human shape model. Tracking is performed using motion cues as well as image-based cues (such as silhouettes and {\textquotedblleft}motion residues{\textquotedblright} hereafter referred to as spatial cues,) as opposed to constructing a 3D volume image or visual hulls. Our algorithm consists of a predictor and corrector: the predictor estimates the pose at the t + 1 using motion information between images at t and t + 1. The error in the estimated pose is then corrected using spatial cues from images at t + 1. In our predictor, we use robust multi-scale parametric optimisation to estimate the pixel displacement for each body segment. We then use an iterative procedure to estimate the change in pose from the pixel displacement of points on the individual body segments. We present a method for fusing information from different spatial cues such as silhouettes and {\textquotedblleft}motion residues{\textquotedblright} into a single energy function. We then express this energy function in terms of the pose parameters, and find the optimum pose for which the energy is minimised.}, isbn = {978-3-540-31244-4}, url = {http://dx.doi.org/10.1007/11612704_14}, author = {Sundaresan,Aravind and Chellapa, Rama}, editor = {Narayanan,P. and Nayar,Shree and Shum,Heung-Yeung} } @article {17309, title = {Nuclear Envelope Dystrophies Show a Transcriptional Fingerprint Suggesting Disruption of Rb{\textendash}MyoD Pathways in Muscle Regeneration}, journal = {BrainBrain}, volume = {129}, year = {2006}, month = {2006/04/01/}, pages = {996 - 1013}, abstract = {Mutations of lamin A/C (LMNA) cause a wide range of human disorders, including progeria, lipodystrophy, neuropathies and autosomal dominant Emery{\textendash}Dreifuss muscular dystrophy (EDMD). EDMD is also caused by X-linked recessive loss-of-function mutations of emerin, another component of the inner nuclear lamina that directly interacts with LMNA. One model for disease pathogenesis of LMNA and emerin mutations is cell-specific perturbations of the mRNA transcriptome in terminally differentiated cells. To test this model, we studied 125 human muscle biopsies from 13 diagnostic groups (125 U133A, 125 U133B microarrays), including EDMD patients with LMNA and emerin mutations. A Visual and Statistical Data Analyzer (VISDA) algorithm was used to statistically model cluster hierarchy, resulting in a tree of phenotypic classifications. Validations of the diagnostic tree included permutations of U133A and U133B arrays, and use of two probe set algorithms (MAS5.0 and MBEI). This showed that the two nuclear envelope defects (EDMD LMNA, EDMD emerin) were highly related disorders and were also related to fascioscapulohumeral muscular dystrophy (FSHD). FSHD has recently been hypothesized to involve abnormal interactions of chromatin with the nuclear envelope. To identify disease-specific transcripts for EDMD, we applied a leave-one-out (LOO) cross-validation approach using LMNA patient muscle as a test data set, with reverse transcription{\textendash}polymerase chain reaction (RT{\textendash}PCR) validations in both LMNA and emerin patient muscle. A high proportion of top-ranked and validated transcripts were components of the same transcriptional regulatory pathway involving Rb1 and MyoD during muscle regeneration (CRI-1, CREBBP, Nap1L1, ECREBBP/p300), where each was specifically upregulated in EDMD. Using a muscle regeneration time series (27 time points) we develop a transcriptional model for downstream consequences of LMNA and emerin mutations. We propose that key interactions between the nuclear envelope and Rb and MyoD fail in EDMD at the point of myoblast exit from the cell cycle, leading to poorly coordinated phosphorylation and acetylation steps. Our data is consistent with mutations of nuclear lamina components leading to destabilization of the transcriptome in differentiated cells.}, keywords = {EDMD = Emery{\textendash}Dreifuss muscular dystrophy, emerin, Emery-Dreifuss muscular dystrophy, FSHD = fascioscapulohumeral muscular dystrophy, IDG = individual discriminatory genes, JDG = jointly discriminatory genes, lamin A/C, LGMD = limb-girdle muscular dystrophy, LOO = leave-one-out, RT{\textendash}PCR = reverse transcription{\textendash}polymerase chain reaction; VISDA = Visual and Statistical Data Analyzer, Skeletal muscle, wFC = weighted Fisher criterion}, isbn = {0006-8950, 1460-2156}, doi = {10.1093/brain/awl023}, url = {http://brain.oxfordjournals.org/content/129/4/996}, author = {Bakay,Marina and Wang,Zuyi and Melcon,Gisela and Schiltz,Louis and Xuan,Jianhua and Zhao,Po and Sartorelli,Vittorio and Seo,Jinwook and Pegoraro,Elena and Angelini,Corrado and Shneiderman, Ben and Escolar,Diana and Chen,Yi-Wen and Winokur,Sara T and Pachman,Lauren M and Fan,Chenguang and Mandler,Raul and Nevo,Yoram and Gordon,Erynn and Zhu,Yitan and Dong,Yibin and Wang,Yue and Hoffman,Eric P} } @article {12150, title = {Observations about software development for high end computing}, journal = {CTWatch Quarterly}, volume = {2}, year = {2006}, month = {2006///}, pages = {33 - 38}, abstract = {In this paper, we have summarized our findings from a series of case studies conducted with ten ASC and MP Codes as a series of observations. Due to different environments in which each code is developed, some of the observations are consistent across code teams while others vary across code teams. Overall, we found high consistency among the ASC Codes and the MP Codes. Due to the different environments and foci of these projects, this result is both surprising and positive. In addition, despite the fact that a large majority of the developers on these teams have little or no formal training in software engineering, they have been able to make use of some basic software engineering principles. Further education and motivation could increase the use of these principles and further increase the quality of scientific and engineering software that has already demonstrated its value.Based on the positive results thus far, we have plans to conduct additional case studies to gather more data in support of or in contradiction to the observations presented in this paper. In future case studies, we will strive to investigate codes from additional domains, thereby allowing broader, more inclusive conclusions to be drawn. }, author = {Carver, J. C and Hochstein, L. M and Kendall,R. P and Nakamura, T. and Zelkowitz, Marvin V and Basili, Victor R. and Post,D. E} } @book {12929, title = {Oceans And Health: Pathogens In The Marine Environment}, year = {2006}, month = {2006///}, publisher = {Springer}, organization = {Springer}, abstract = {The release of non-disinfected wastewaters into the marine environment is a common worldwide practice, in under-developed as well as in highly developed countries. Consequently, the seas are constantly infused with wastewater bacteria, among them highly pathogenic ones. In view of the public health significance of this phenomenon, it is surprising how little is actually known concerning the fate of such bacteria once they enter the sea. While numerous studies have addressed the effects of various environmental parameters on colony formation, many of them actually ignore the fact that bacteria can retain viability and infectivity while losing colony-forming ability. Only in recent years have efforts also been directed at unraveling the mechanisms determining bacterial sensitivity or survival under these conditions. This, therefore, is one subject of Oceans and Health: Pathogens in the Marine Environment: the survival, infectivity, pathogenicity and viability of enteric bacteria in the sea. Chapters also detail the public health aspects of wastewater release, civil engineering and economic considerations, other sources of pathogens, and much more.}, keywords = {Electronic books, Marine microbiology, Medical / Epidemiology, Medical / Microbiology, Nature / Animals / Marine Life, Pathogenic microorganisms, Science / Environmental Science, Science / Life Sciences / Biology, Science / Life Sciences / Marine Biology, Science / Life Sciences / Microbiology, Seawater/ microbiology}, isbn = {9780387237084}, author = {Belkin,Shimshon and Rita R Colwell} } @conference {17788, title = {Opinion Analysis in Document Databases}, booktitle = {Proc. AAAI Spring Symposium on Computational Approaches to Analyzing Weblogs, Stanford, CA}, year = {2006}, month = {2006///}, abstract = {There are numerous applications in which we would like toassess what opinions are being expressed in text documents. Forr example, Martha Stewart{\textquoteright}s company may have wished to assess the degree of harshness of news articles about her in the recent past. Likewise, a World Bank official may wish to as- sess the degree of criticism of a proposed dam in Bangladesh. The ability to gauge opinion on a given topic is therefore of critical interest. In this paper, we develop a suite of algo- rithms which take as input, a set D of documents as well as a topic t, and gauge the degree of opinion expressed about topic t in the set D of documents. Our algorithms can return both a number (larger the number, more positive the opinion) as well as a qualitative opinion (e.g. harsh, complimentary). We as- sess the accuracy of these algorithms via human experiments and show that the best of these algorithms can accurately re- flect human opinions. We have also conducted performance experiments showing that our algorithms are computationally fast. }, author = {Cesarano,C. and Dorr, Bonnie J and Picariello, A. and Reforgiato,D. and Sagoff,A. and V.S. Subrahmanian} } @article {15348, title = {A parallel implicit method for the direct numerical simulation of wall-bounded compressible turbulence}, journal = {Journal of Computational Physics}, volume = {215}, year = {2006}, month = {2006///}, pages = {153 - 171}, abstract = {A new second-order accurate implicit temporal numerical scheme for the direct numerical simulation of turbulent flows is presented. The formulation of the implicit method and the corresponding tunable parameters are introduced. The numerical simulation results are compared with the results given by explicit Runge{\textendash}Kutta schemes, theoretical results, and published experimental and numerical data. An assessment of the accuracy and performance of the method to simulate turbulent flows is made for temporally decaying isotropic turbulence and subsonic and supersonic turbulent boundary layers. Whereas no significant advantage over typical explicit time integration methods are found for the incompressible flows; it is shown that the implicit scheme yields significant reduction in computer cost while assuring time-accurate solutions for compressible turbulence simulations.}, keywords = {direct numerical simulation, Implicit time integration, Wall-bounded turbulent flow}, isbn = {0021-9991}, doi = {10.1016/j.jcp.2005.10.017}, url = {http://www.sciencedirect.com/science/article/pii/S0021999105004833}, author = {Martin, M.P and Candler,Graham V.} } @article {13178, title = {PDR: A Performance Evaluation Method for Foreground-Background Segmentation Algorithms}, journal = {EURASIP Journal on Applied Signal Processing}, year = {2006}, month = {2006///}, abstract = {We introduce a performance evaluation methodologycalled Perturbation Detection Rate (PDR) analysis for measuring performance of foreground-background seg- mentation. It has some advantages over the commonly used Receiver Operation Characteristics (ROC) analy- sis. Specifically, it does not require foreground targets or knowledge of foreground distributions. It measures the sensitivity of a background subtraction algorithm in detecting possible low contrast targets against the background as a function of contrast, also depending on how well the model captures mixed (moving) back- ground events. We compare four background subtrac- tion algorithms using the methodology. The experimen- tal results show how PDR is used to measure perfor- mance with respect to detection sensitivity in interest- ing low contrast regions. }, author = {Kim,K. and Chalidabhongse,T.H. and Harwood,D. and Davis, Larry S.} } @article {12607, title = {Physics-Based Detectors Applied to Long-Wave Infrared Hyperspectral Data}, year = {2006}, month = {2006/11//}, institution = {CENTER FOR AUTOMATION RESEARCH, UNIVERSITY OF MARYLAND COLLEGE PARK}, abstract = {Long-wave infrared (LWIR) hyperspectral image (HSI) data presents an interesting challenge for automatic target detection algorithms. LWIR HSI data is useful for both day and night operations, but weak signatures like disturbed soil can be problematic for standard matched-filter techniques. In this paper, we augment the standard matched-filter techniques with physics-based information particular to HSI data. Our results show that these physics-based detectors provide improved detection performance with quick processing times.}, keywords = {*HYPERSPECTRAL IMAGERY, algorithms, AUTOMATIC, DETECTION, FAR INFRARED RADIATION, LOW STRENGTH, Matched filters, MILITARY OPERATIONS, NIGHT, OPTICS, SIGNATURES, SOILS, SPECTROMETERS, TARGET DETECTION}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA481339}, author = {Broadwater,Joshua and Chellapa, Rama} } @article {12270, title = {Postmodern internetwork architecture}, journal = {ITTC-FY2006-TR-45030-01, Information and Telecommunication Center, The University of Kansas}, year = {2006}, month = {2006/02//}, abstract = {Network-layer innovation has proven surprisingly difficult, in part because internetworking protocols ignore com-peting economic interests and because a few protocols dominate, enabling layer violations that entrench technologies. Many shortcomings of today{\textquoteright}s internetwork layer result from its inflexibility with respect to the policies of the stake- holders: users and service providers. The consequences of these failings are well-known: various hacks, layering violations, and overloadings are introduced to enforce policies and attempt to get the upper hand in various {\textquotedblleft}tus- sles{\textquotedblright}. The result is a network that is increasingly brittle, hostile to innovation, vulnerable to attack, and insensitive to concerns about accountability and privacy. Our project aims to design, implement, and evaluate through daily use a minimalist internetwork layer and aux- iliary functionality that anticipates tussles and allows them to be played out in policy space, as opposed to in the packet-forwarding path. We call our approach postmodern internetwork architecture, because it is a reaction against many established network layer design concepts. The overall goal of the project is to make a larger portion of the network design space accessible without sacrificing the economy of scale offered by the unified Internet. We will use the postmodern architecture to explore basic architectural questions. These include: {\textbullet} What mechanisms should be supported by the network such that any foreseeable policy requirement can be explicitly addressed? {\textbullet} To what extent can routing and forwarding be isolated from each other while maintaining an efficient and usable network? {\textbullet} What forms of identity should be visible within the network, and what forms of accountability do different identities enable? {\textbullet} What mechanisms are needed to enable efficient access to cross-layer information and mechanisms such that lower layers can express their characteristics and upper layers can exert control downward? We plan to build and evaluate a complete end-to-end networking layer to help us understand feasible solutions to these questions. The Internet has fulfilled the potential of a complete generation of networking research by producing a global platform for innovation, commerce, and democracy. Unfortunately, the Internet also amply demonstrates the com- plexity and architectural ugliness that ensue when competing interests vie for benefits beyond those envisioned in the original design. This project is about redesigning the waist of the architectural hourglass to foster innovation, enhance security and accountability, and accomodate competing interests. }, author = {Bhattacharjee, Bobby and Calvert,K. and Griffioen,J. and Spring, Neil and Sterbenz,J. P.G} } @article {12612, title = {Principal components null space analysis for image and video classification}, journal = {Image Processing, IEEE Transactions on}, volume = {15}, year = {2006}, month = {2006/07//}, pages = {1816 - 1830}, abstract = {We present a new classification algorithm, principal component space analysis (PCNSA), which is designed for classification problems like object recognition where different classes have unequal and nonwhite noise covariance matrices. PCNSA first obtains a principal components subspace (PCA space) for the entire data. In this PCA space, it finds for each class "i", an Mi-dimensional subspace along which the class{\textquoteright} intraclass variance is the smallest. We call this subspace an approximate space (ANS) since the lowest variance is usually "much smaller" than the highest. A query is classified into class "i" if its distance from the class{\textquoteright} mean in the class{\textquoteright} ANS is a minimum. We derive upper bounds on classification error probability of PCNSA and use these expressions to compare classification performance of PCNSA with that of subspace linear discriminant analysis (SLDA). We propose a practical modification of PCNSA called progressive-PCNSA that also detects "new" (untrained classes). Finally, we provide an experimental comparison of PCNSA and progressive PCNSA with SLDA and PCA and also with other classification algorithms-linear SVMs, kernel PCA, kernel discriminant analysis, and kernel SLDA, for object recognition and face recognition under large pose/expression variation. We also show applications of PCNSA to two classification problems in video-an action retrieval problem and abnormal activity detection.}, keywords = {approximate null space;classification error probability;face recognition;image classification;object recognition;principal components null space analysis;subspace linear discriminant analysis;video classification;image classification;principal component a, Automated;Principal Component Analysis;Signal Processing, Computer-Assisted;Information Storage and Retrieval;Models, Computer-Assisted;Video Recording;, Statistical;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2006.873449}, author = {Vaswani, N. and Chellapa, Rama} } @article {12837, title = {Probabilistic I/O automata: Theories of two equivalences}, journal = {CONCUR 2006{\textendash}Concurrency Theory}, year = {2006}, month = {2006///}, pages = {343 - 357}, author = {Stark,E. and Cleaveland, Rance and Smolka,S.} } @conference {16472, title = {Query Rewriting in the Semantic Web7}, booktitle = {Data Engineering Workshops, 22nd International Conference on}, year = {2006}, month = {2006///}, pages = {7 - 7}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {The widespread explosion of Web accessible resources has lead to a new challenge of locating all relevant resources and identifying the best ones to answer a query. This challenge has to address the difficult task of ranking the resources based on user needs, as well as the more expensive computational task of determining all the solutions to answer a query. In this paper, we define a Top K problem for query rewriting on the Semantic Web. We first introduce a three level data model composed of the ontology level, the physical level of the physical resources, and the data level composed of the entries in the different resources. We present a query language for Top K navigational queries over ontology concepts. We then sketch the outline of an efficient search algorithm to compute an approximation of the Top K rewriting options to produce source paths among the physical resources. We briefly discuss the results of an experimental study}, isbn = {0-7695-2571-7}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICDEW.2006.124}, author = {Vidal,Maria Esther and Raschid, Louiqa and Marquez,Natalia and Cardenas,Marelis and Yao Wu} } @conference {12610, title = {Recognition of Multi-Object Events Using Attribute Grammars}, booktitle = {Image Processing, 2006 IEEE International Conference on}, year = {2006}, month = {2006/10//}, pages = {2897 - 2900}, abstract = {We present a method for representing and recognizing visual events using attribute grammars. In contrast to conventional grammars, attribute grammars are capable of describing features that are not easily represented by finite symbols. Our approach handles multiple concurrent events involving multiple entities by associating unique object identification labels with multiple event threads. Probabilistic parsing and probabilistic conditions on the attributes are used to achieve a robust recognition system. We demonstrate the effectiveness of our method for the task of recognizing vehicle casing in parking lots and events occurring in an airport tarmac}, keywords = {attribute, event, grammar;multiobject, grammars;image, identification, label;probabilistic, parsing;attribute, recognition;object, recognition;probability;, representation;object}, doi = {10.1109/ICIP.2006.313035}, author = {Joo,Seong-Wook and Chellapa, Rama} } @conference {19459, title = {Reflecting on Health: A System for Students to Monitor Diet and Exercise}, booktitle = {SIGCHI EA {\textquoteright}06}, series = {CHI EA {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {1807 - 1812}, publisher = {ACM}, organization = {ACM}, abstract = {Using an iterative design process, we designed and evaluated a system for college students to encourage the development and maintenance of healthy diet and exercise habits. The system has three components: a camera phone application to support photographic diet and exercise journaling, an automatic workout tracking application for exercise machines in the gym, and a visualization application to support users as they reflect on their diet and exercise activities.}, keywords = {diet, exercise, journaling, mobile phone, Visualization}, isbn = {1-59593-298-4}, url = {http://doi.acm.org/10.1145/1125451.1125794}, author = {Brown, Brandon and Marshini Chetty and Grimes, Andrea and Harmon, Ellie} } @article {14641, title = {Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection}, journal = {PLoS PathogPLoS Pathog}, volume = {2}, year = {2006}, month = {2006/06/23/}, pages = {e60 - e60}, abstract = {Retroviruses differ in their preferences for sites for viral DNA integration in the chromosomes of infected cells. Human immunodeficiency virus (HIV) integrates preferentially within active transcription units, whereas murine leukemia virus (MLV) integrates preferentially near transcription start sites and CpG islands. We investigated the viral determinants of integration-site selection using HIV chimeras with MLV genes substituted for their HIV counterparts. We found that transferring the MLV integrase (IN) coding region into HIV (to make HIVmIN) caused the hybrid to integrate with a specificity close to that of MLV. Addition of MLV gag (to make HIVmGagmIN) further increased the similarity of target-site selection to that of MLV. A chimeric virus with MLV Gag only (HIVmGag) displayed targeting preferences different from that of both HIV and MLV, further implicating Gag proteins in targeting as well as IN. We also report a genome-wide analysis indicating that MLV, but not HIV, favors integration near DNase I{\textendash}hypersensitive sites (i.e., +/- 1 kb), and that HIVmIN and HIVmGagmIN also favored integration near these features. These findings reveal that IN is the principal viral determinant of integration specificity; they also reveal a new role for Gag-derived proteins, and strengthen models for integration targeting based on tethering of viral IN proteins to host proteins.}, doi = {10.1371/journal.ppat.0020060}, url = {UR - http://dx.plos.org/10.1371/journal.ppat.0020060,http://dx.plos.org/10.1371/journal.ppat.0020060}, author = {Lewinski,Mary K and Yamashita,Masahiro and Emerman,Michael and Ciuffi,Angela and Marshall,Heather and Crawford,Gregory and Collins,Francis and Shinn,Paul and Leipzig,Jeremy and Hannenhalli, Sridhar and Berry,Charles C and Ecker,Joseph R and Bushman,Frederic D.} } @article {12618, title = {Robust ego-motion estimation and 3-D model refinement using surface parallax}, journal = {Image Processing, IEEE Transactions on}, volume = {15}, year = {2006}, month = {2006/05//}, pages = {1215 - 1225}, abstract = {We present an iterative algorithm for robustly estimating the ego-motion and refining and updating a coarse depth map using parametric surface parallax models and brightness derivatives extracted from an image pair. Given a coarse depth map acquired by a range-finder or extracted from a digital elevation map (DEM), ego-motion is estimated by combining a global ego-motion constraint and a local brightness constancy constraint. Using the estimated camera motion and the available depth estimate, motion of the three-dimensional (3-D) points is compensated. We utilize the fact that the resulting surface parallax field is an epipolar field, and knowing its direction from the previous motion estimates, estimate its magnitude and use it to refine the depth map estimate. The parallax magnitude is estimated using a constant parallax model (CPM) which assumes a smooth parallax field and a depth based parallax model (DBPM), which models the parallax magnitude using the given depth map. We obtain confidence measures for determining the accuracy of the estimated depth values which are used to remove regions with potentially incorrect depth estimates for robustly estimating ego-motion in subsequent iterations. Experimental results using both synthetic and real data (both indoor and outdoor sequences) illustrate the effectiveness of the proposed algorithm.}, keywords = {3D model refinement, algorithms, Artificial intelligence, Automated;Subtraction Technique;, Computer-Assisted;Imaging, constant parallax model, depth based parallax model, digital elevation map, epipolar field, Image Enhancement, Image Interpretation, iterative algorithm, iterative methods, Motion estimation, robust ego-motion estimation, smooth parallax field, surface parallax, Three-Dimensional;Information Storage and Retrieval;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2005.864167}, author = {Agrawal,A. and Chellapa, Rama} } @conference {15246, title = {A robust maximum completion time measure for scheduling}, booktitle = {Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm}, series = {SODA {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {324 - 333}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {One popular measure for evaluating the performance of scheduling algorithms, is the maximum response time of any job (makespan). Typically the objective is to find a schedule that minimizes the maximum response time over all jobs. One drawback of this measure is that a relatively small number of jobs in the request set could cause the maximum response time to be very high. Thus, this measure reflects local rather than global properties of the request set. In this paper we consider a robust generalization of this measure. Our goal is to minimize T, such that a given fraction of jobs can be scheduled with a response time of at most T. We demonstrate the applicability of this measure in the context of broadcast scheduling. We show that in the online setting no constant factor online approximation is possible for the problem of minimizing the maximum response time for a given fraction of jobs in the context of broadcast scheduling. We give a factor 5, polynomial time offline approximation algorithm for the problem of minimizing the maximum response time for a given fraction of jobs in the context of broadcast scheduling.}, isbn = {0-89871-605-5}, doi = {10.1145/1109557.1109594}, url = {http://doi.acm.org/10.1145/1109557.1109594}, author = {Charikar,Moses and Khuller, Samir} } @article {12926, title = {Seasonal Cholera Caused by Vibrio Cholerae Serogroups O1 and O139 in the Coastal Aquatic Environment of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {72}, year = {2006}, month = {2006/06/01/}, pages = {4096 - 4104}, abstract = {Since Vibrio cholerae O139 first appeared in 1992, both O1 El Tor and O139 have been recognized as the epidemic serogroups, although their geographic distribution, endemicity, and reservoir are not fully understood. To address this lack of information, a study of the epidemiology and ecology of V. cholerae O1 and O139 was carried out in two coastal areas, Bakerganj and Mathbaria, Bangladesh, where cholera occurs seasonally. The results of a biweekly clinical study (January 2004 to May 2005), employing culture methods, and of an ecological study (monthly in Bakerganj and biweekly in Mathbaria from March 2004 to May 2005), employing direct and enrichment culture, colony blot hybridization, and direct fluorescent-antibody methods, showed that cholera is endemic in both Bakerganj and Mathbaria and that V. cholerae O1, O139, and non-O1/non-O139 are autochthonous to the aquatic environment. Although V. cholerae O1 and O139 were isolated from both areas, most noteworthy was the isolation of V. cholerae O139 in March, July, and September 2004 in Mathbaria, where seasonal cholera was clinically linked only to V. cholerae O1. In Mathbaria, V. cholerae O139 emerged as the sole cause of a significant outbreak of cholera in March 2005. V. cholerae O1 reemerged clinically in April 2005 and established dominance over V. cholerae O139, continuing to cause cholera in Mathbaria. In conclusion, the epidemic potential and coastal aquatic reservoir for V. cholerae O139 have been demonstrated. Based on the results of this study, the coastal ecosystem of the Bay of Bengal is concluded to be a significant reservoir for the epidemic serogroups of V. cholerae.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.00066-06}, url = {http://aem.asm.org/content/72/6/4096}, author = {Alam,Munirul and Hasan,Nur A. and Sadique,Abdus and Bhuiyan,N. A. and Ahmed,Kabir U. and Nusrin,Suraia and Nair,G. Balakrish and Siddique,A. K. and Sack,R. Bradley and Sack,David A. and Huq,Anwar and Rita R Colwell} } @conference {12625, title = {Segmentation and Probabilistic Registration of Articulated Body Models}, booktitle = {Pattern Recognition, 2006. ICPR 2006. 18th International Conference on}, volume = {2}, year = {2006}, month = {2006///}, pages = {92 - 96}, abstract = {There are different approaches to pose estimation and registration of different body parts using voxel data. We propose a general bottom-up approach in order to segment the voxels into different body parts. The voxels are first transformed into a high dimensional space which is the eigenspace of the Laplacian of the neighbourhood graph. We exploit the properties of this transformation and fit splines to the voxels belonging to different body segments in eigenspace. The boundary of the splines is determined by examination of the error in spline fitting. We then use a probabilistic approach to register the segmented body segments by utilizing their connectivity and prior knowledge of the general structure of the subjects. We present results on real data, containing both simple and complex poses. While we use human subjects in our experiment, the method is fairly general and can be applied to voxel-based registration of any articulated or non-rigid object composed of primarily 1-D parts}, keywords = {(mathematics);, and, approach;eigenspace;image, articulated, body, data;voxel-based, eigenfunctions;graph, estimation;probabilistic, fitting;voxel, graph;pose, models;bottom-up, registration;eigenvalues, registration;image, registration;spline, segmentation;neighbourhood, segmentation;probability;splines, theory;image}, doi = {10.1109/ICPR.2006.1034}, author = {Sundaresan, A. and Chellapa, Rama} } @inbook {15806, title = {Sentence Trimming and Selection: Mixing and Matching}, booktitle = {DUC 06 Conference Proceedings}, year = {2006}, month = {2006///}, publisher = {U.S. National Inst. of Standards and Technology}, organization = {U.S. National Inst. of Standards and Technology}, abstract = {We describe how components from two distinct multi-document summarization systems were combined. Twenty four possible combinations of components were considered. We observed some contrasts between conservative and aggressive sentence compression (i.e., trimming) in the context of multi-document summarization. }, url = {http://duc.nist.gov/}, author = {Zajic, David and Dorr, Bonnie J and Jimmy Lin and O{\textquoteright}Leary, Dianne P. and Conroy,John M. and Schlesinger,Judith D.} } @article {12924, title = {Septaplex PCR assay for rapid identification of Vibrio cholerae including detection of virulence and int SXT genes}, journal = {FEMS Microbiology Letters}, volume = {265}, year = {2006}, month = {2006/12/01/}, pages = {208 - 214}, abstract = {In this study, we describe a septaplex PCR assay for rapid identification of Vibrio cholerae including detection of the virulence and intsxt genes. Conditions were optimized to amplify fragments of ISRrRNA (encoding for 16S{\textendash}23S rRNA gene, Intergenic spacer regions), O1rfb (O1 serogroup specific rfb), O139rfb (O139 serogroup specific rfb), ctxA (cholera toxin subunit A), tcpA (toxin coregulated pilus), and intsxt (sxt integron) simultaneously in a single PCR. The septaplex PCR was evaluated using 211 strains of V. cholerae and six water samples for in situ testing. PCR results were correlated with genotype data obtained by individual PCR and slot-blot assays. The one-step PCR described here can be used to identify V. cholerae accurately and rapidly. Also, the virulence and intsxt genes can be simultaneously detected, providing a useful method for monitoring pathogenic, intsxt-positive and nonpathogenic, intsxt-negative V. cholerae serogroups both in the environment and clinical settings.}, keywords = {DETECTION, intsxt, septaplex PCR, Vibrio cholerae, virulence}, isbn = {1574-6968}, doi = {10.1111/j.1574-6968.2006.00491.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2006.00491.x/full}, author = {Mantri,Chinmay K. and Mohapatra,Saswat S. and Ramamurthy,Thandavarayan and Ghosh,Raikamal and Rita R Colwell and Singh,Durg V.} } @conference {19367, title = {Shape Similarity Assessment Based On Face Alignment Using Attributed Applied Vectors.}, booktitle = {CAD Conference}, year = {2006}, author = {Cardone, Antonio and Gupta, Satyandra K.} } @conference {12608, title = {Shape-Regulated Particle Filtering for Tracking Non-Rigid Objects}, booktitle = {Image Processing, 2006 IEEE International Conference on}, year = {2006}, month = {2006/10//}, pages = {2813 - 2816}, abstract = {This paper presents an active contour based algorithm for tracking non-rigid objects in heavily cluttered scenes. We decompose the non-rigid contour tracking problem into three subproblems: 2D motion estimation, deformation detection, and shape regulation. First, we employ a particle filter to estimate the affine transform parameters between successive frames. Second, by using a dynamic object model, we generate a probabilistic map of deformation to reshape its contour. Finally, we project the updated model onto a trained shape subspace to constrain deformations to be within possible object appearances. Our experiments show that the proposed algorithm significantly improves the performance of the tracker}, keywords = {(numerical, 2D, algorithm;affine, based, contour, detection;dynamic, detection;motion, detection;parameter, estimation;active, estimation;object, estimation;particle, Filtering, filtering;probabilistic, filters;, map;shape-regulation;affine, methods);tracking, model;nonrigid, MOTION, object, scenes;deformation, tracking;parameter, transform;cluttered, transforms;clutter;edge}, doi = {10.1109/ICIP.2006.312993}, author = {Jie Shao and Chellapa, Rama and Porikli, F.} } @article {16084, title = {Shared family calendars: Promoting symmetry and accessibility}, journal = {ACM Trans. Comput.-Hum. Interact.}, volume = {13}, year = {2006}, month = {2006/09//}, pages = {313 - 346}, abstract = {We describe the design and use of a system facilitating the sharing of calendar information between remotely located, multi-generational family members. Most previous work in this area involves software enabling younger family members to monitor their parents. We have found, however, that older adults are equally if not more interested in the activities of younger family members. The major obstacle preventing them from participating in information sharing is the technology itself. Therefore, we developed a multi-layered interface approach that offers simple interaction to older users. In our system, users can choose to enter information into a computerized calendar or write it by hand on digital paper calendars. All of the information is automatically shared among everyone in the distributed family. By making the interface more accessible to older users, we promote symmetrical sharing of information among both older and younger family members. We present our participatory design process, describe the user interface, and report on an exploratory field study in three households of an extended family.}, keywords = {calendar, digital paper, elderly, family technology, Home, layered interface, privacy, universal usability}, isbn = {1073-0516}, doi = {10.1145/1183456.1183458}, url = {http://doi.acm.org/10.1145/1183456.1183458}, author = {Plaisant, Catherine and Clamage,Aaron and Hutchinson,Hilary Browne and Bederson, Benjamin B. and Druin, Allison} } @inbook {12629, title = {Silhouette-Based Approaches}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {45 - 105}, abstract = {Of the current approaches, most are based on analysis of silhouettes. This is like the earlier analysis which concerned abstracting a walking subject from the background and then deriving set of measurements that describe the shape and motion of that silhouette in a sequence of images. This is similar in approach the classic computer vision approach to recognize objects by using shape descriptions of objects derived, say, by optimal thresholding.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @conference {12830, title = {A Software Architectural Approach to Security by Design}, booktitle = {Computer Software and Applications Conference, 2006. COMPSAC {\textquoteright}06. 30th Annual International}, volume = {2}, year = {2006}, month = {2006/09/17/21}, pages = {83 - 86}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper shows how an architecture description notation that has support for timed events can be used to provide a meta-language for specifying exact communication semantics. The advantages of such an approach is that a designer is made fully aware of the ramifications of her design choices so that an attacker can no longer take advantage of hidden assumptions}, keywords = {architecture description notation, Clocks, communication semantics, Computer architecture, computer crime, computer security, Connectors, Costs, Degradation, Delay, Educational institutions, security design, security of data, Software architecture, software engineering}, isbn = {0-7695-2655-1}, doi = {10.1109/COMPSAC.2006.102}, author = {Ray,A. and Cleaveland, Rance} } @article {13864, title = {SParseval: Evaluation metrics for parsing speech}, journal = {Proc. LREC}, year = {2006}, month = {2006///}, abstract = {While both spoken and written language processing stand to benefit from parsing, the standard Parseval metrics (Black et al., 1991) andtheir canonical implementation (Sekine and Collins, 1997) are only useful for text. The Parseval metrics are undefined when the words input to the parser do not match the words in the gold standard parse tree exactly, and word errors are unavoidable with automatic speech recognition (ASR) systems. To fill this gap, we have developed a publicly available tool for scoring parses that implements a variety of metrics which can handle mismatches in words and segmentations, including: alignment-based bracket evaluation, alignment-based dependency evaluation, and a dependency evaluation that does not require alignment. We describe the different metrics, how to use the tool, and the outcome of an extensive set of experiments on the sensitivity of the metrics. }, author = {Roark,B. and Harper,M. and Charniak,E. and Dorr, Bonnie J and Johnson,M. and Kahn,J. and Liu,Y. and Ostendorf,M. and Hale,J. and Krasnyanskaya,A. and others} } @article {12605, title = {Special Issue on Biometrics: Algorithms and Applications}, journal = {Proceedings of the IEEE}, volume = {94}, year = {2006}, month = {2006/11//}, pages = {1912 - 1914}, isbn = {0018-9219}, doi = {10.1109/JPROC.2006.886016}, author = {Chellapa, Rama and Phillips, J. and Reynolds, D.} } @conference {12609, title = {Stabilization and Mosaicing of Airborne Videos}, booktitle = {Image Processing, 2006 IEEE International Conference on}, year = {2006}, month = {2006/10//}, pages = {345 - 348}, abstract = {We present an algorithm for stabilizing low-quality and low-resolution video sequences obtained from UAVs and MAVs flying over a predominantly planar terrain. The problem is important for the processing of videos captured from airborne platforms where most of the image region gives little information about the image-motion. The algorithm consists of approximately aligning the images using phase correlation, then refining the transformation parameters using available optical flow measurements and finally performing a minimization of the image difference by carefully selecting the image regions to make the iterations converge. In the second part of the paper, we describe an algorithm for camera ego-motion estimation by incorporating available metadata along with the video sequence. The availability of metadata such as IMU measurements provides a good initial solution for the camera orientation and helps the iterations converge faster by reducing the search space}, keywords = {airborne, analysis;image, cameras;, convergence;low-resolution, ego-motion, estimation;iterations, flow, measurement;video, mosaicing;camera, MOTION, resolution;image, segmentation;image, sequence;optical, sequences;video, stabilization;image, video, Videos}, doi = {10.1109/ICIP.2006.313164}, author = {Ramachandran, M. and Chellapa, Rama} } @conference {18649, title = {A Statistical Analysis of Attack Data to Separate Attacks}, year = {2006}, month = {2006/06//}, pages = {383 - 392}, abstract = {This paper analyzes malicious activity collected from a test-bed, consisting of two target computers dedicated solely to the purpose of being attacked, over a 109 day time period. We separated port scans, ICMP scans, and vulnerability scans from the malicious activity. In the remaining attack data, over 78\% (i.e., 3,677 attacks) targeted port 445, which was then statistically analyzed. The goal was to find the characteristics that most efficiently separate the attacks. First, we separated the attacks by analyzing their messages. Then we separated the attacks by clustering characteristics using the K-Means algorithm. The comparison between the analysis of the messages and the outcome of the K-Means algorithm showed that 1) the mean of the distributions of packets, bytes and message lengths over time are poor characteristics to separate attacks and 2) the number of bytes, the mean of the distribution of bytes and message lengths as a function of the number packets are the best characteristics for separating attacks}, keywords = {attack data statistical analysis, attack separation, computer crime, Data analysis, data mining, ICMP scans, K-Means algorithm, pattern clustering, port scans, statistical analysis, vulnerability scans}, doi = {10.1109/DSN.2006.9}, author = {Michel Cukier and Berthier,R. and Panjwani,S. and Tan,S.} } @article {12604, title = {Structure From Planar Motion}, journal = {Image Processing, IEEE Transactions on}, volume = {15}, year = {2006}, month = {2006/11//}, pages = {3466 - 3477}, abstract = {Planar motion is arguably the most dominant type of motion in surveillance videos. The constraints on motion lead to a simplified factorization method for structure from planar motion when using a stationary perspective camera. Compared with methods for general motion , our approach has two major advantages: a measurement matrix that fully exploits the motion constraints is formed such that the new measurement matrix has a rank of at most 3, instead of 4; the measurement matrix needs similar scalings, but the estimation of fundamental matrices or epipoles is not needed. Experimental results show that the algorithm is accurate and fairly robust to noise and inaccurate calibration. As the new measurement matrix is a nonlinear function of the observed variables, a different method is introduced to deal with the directional uncertainty in the observed variables. Differences and the dual relationship between planar motion and planar object are also clarified. Based on our method, a fully automated vehicle reconstruction system has been designed}, keywords = {algebra;road, analysis;matrix, camera;surveillance, directional, matrix;planar, MOTION, motion;stationary, perspective, processing;, reconstruction, signal, system;image, uncertainty;measurement, vehicles;surveillance;video, videos;vehicle}, isbn = {1057-7149}, doi = {10.1109/TIP.2006.881943}, author = {Li,Jian and Chellapa, Rama} } @inbook {12630, title = {Subjects Allied to Gait}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {5 - 15}, abstract = {There is considerable support for the notion that each person{\textquoteright}s gait is unique. As we shall see, it has been observed in literature that people can be recognized by the way they walk. The same notion has been observed in medicine and biomechanics, though not in the context of biometrics but more as an assertion of individuality. Perhaps driven by these notions, though without reference to them, there has been work in psychology on the human ability to recognize each other by using gait. Those suffering myopia often state that they can use gait as a way of recognizing people. There is other evidence too, which suggests that each person{\textquoteright}s gait is unique. People have also studied walking from medical and biomechanical perspectives, and this gives insight into how its properties can change which is of general interest in any biometrie deployment. We shall start with literature, with definitions of meaning.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @conference {15825, title = {Topic-focused multi-document summarization using an approximate oracle score}, booktitle = {Proceedings of the COLING/ACL on Main conference poster sessions}, series = {COLING-ACL {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {152 - 159}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {We consider the problem of producing a multi-document summary given a collection of documents. Since most successful methods of multi-document summarization are still largely extractive, in this paper, we explore just how well an extractive method can perform. We introduce an "oracle" score, based on the probability distribution of unigrams in human summaries. We then demonstrate that with the oracle score, we can generate extracts which score, on average, better than the human summaries, when evaluated with ROUGE. In addition, we introduce an approximation to the oracle score which produces a system with the best known performance for the 2005 Document Understanding Conference (DUC) evaluation.}, url = {http://dl.acm.org/citation.cfm?id=1273073.1273093}, author = {Conroy,John M. and Schlesinger,Judith D. and O{\textquoteright}Leary, Dianne P.} } @article {12927, title = {Toxigenic Vibrio Cholerae in the Aquatic Environment of Mathbaria, Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {72}, year = {2006}, month = {2006/04/01/}, pages = {2849 - 2855}, abstract = {Toxigenic Vibrio cholerae, rarely isolated from the aquatic environment between cholera epidemics, can be detected in what is now understood to be a dormant stage, i.e., viable but nonculturable when standard bacteriological methods are used. In the research reported here, biofilms have proved to be a source of culturable V. cholerae, even in nonepidemic periods. Biweekly environmental surveillance for V. cholerae was carried out in Mathbaria, an area of cholera endemicity adjacent to the Bay of Bengal, with the focus on V. cholerae O1 and O139 Bengal. A total of 297 samples of water, phytoplankton, and zooplankton were collected between March and December 2004, yielding eight V. cholerae O1 and four O139 Bengal isolates. A combination of culture methods, multiplex-PCR, and direct fluorescent antibody (DFA) counting revealed the Mathbaria aquatic environment to be a reservoir for V. cholerae O1 and O139 Bengal. DFA results showed significant clumping of the bacteria during the interepidemic period for cholera, and the fluorescent micrographs revealed large numbers of V. cholerae O1 in thin films of exopolysaccharides (biofilm). A similar clumping of V. cholerae O1 was also observed in samples collected from Matlab, Bangladesh, where cholera also is endemic. Thus, the results of the study provided in situ evidence for V. cholerae O1 and O139 in the aquatic environment, predominantly as viable but nonculturable cells and culturable cells in biofilm consortia. The biofilm community is concluded to be an additional reservoir of cholera bacteria in the aquatic environment between seasonal epidemics of cholera in Bangladesh.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.72.4.2849-2855.2006}, url = {http://aem.asm.org/content/72/4/2849}, author = {Alam,Munirul and Sultana,Marzia and Nair,G. Balakrish and Sack,R. Bradley and Sack,David A. and Siddique,A. K. and Ali,Afsar and Huq,Anwar and Rita R Colwell} } @article {14585, title = {Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure}, journal = {Circulation}, volume = {114}, year = {2006}, month = {2006///}, pages = {1269 - 1276}, abstract = {Background{\textemdash} Specific transcription factors (TFs) modulate cardiac gene expression in murine models of heart failure, but their relevance in human subjects remains untested. We developed and applied a computational approach called transcriptional genomics to test the hypothesis that a discrete set of cardiac TFs is associated with human heart failure.Methods and Results{\textemdash} RNA isolates from failing (n=196) and nonfailing (n=16) human hearts were hybridized with Affymetrix HU133A arrays, and differentially expressed heart failure genes were determined. TF binding sites overrepresented in the -5-kb promoter sequences of these heart failure genes were then determined with the use of public genome sequence databases. Binding sites for TFs identified in murine heart failure models (MEF2, NKX, NF-AT, and GATA) were significantly overrepresented in promoters of human heart failure genes (P<0.002; false discovery rate 2\% to 4\%). In addition, binding sites for FOX TFs showed substantial overrepresentation in both advanced human and early murine heart failure (P<0.002 and false discovery rate <4\% for each). A role for FOX TFs was supported further by expression of FOXC1, C2, P1, P4, and O1A in failing human cardiac myocytes at levels similar to established hypertrophic TFs and by abundant FOXP1 protein in failing human cardiac myocyte nuclei.Conclusions{\textemdash} Our results provide the first evidence that specific TFs identified in murine models (MEF2, NKX, NFAT, and GATA) are associated with human heart failure. Moreover, these data implicate specific members of the FOX family of TFs (FOXC1, C2, P1, P4, and O1A) not previously suggested in heart failure pathogenesis. These findings provide a crucial link between animal models and human disease and suggest a specific role for FOX signaling in modulating the hypertrophic response of the heart to stress in humans.}, doi = {10.1161/CIRCULATIONAHA.106.632430}, url = {http://circ.ahajournals.org/content/114/12/1269.abstract}, author = {Hannenhalli, Sridhar and Putt,Mary E. and Gilmore,Joan M. and Wang,Junwen and Parmacek,Michael S. and Epstein,Jonathan A. and Morrisey,Edward E. and Margulies,Kenneth B. and Cappola,Thomas P.} } @article {14085, title = {Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region}, journal = {BMC Genomics}, volume = {7}, year = {2006}, month = {2006///}, pages = {60 - 60}, abstract = {BACKGROUND:The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification.RESULTS:We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5{\textquoteright}-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2.CONCLUSION:The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-7-60}, url = {http://www.biomedcentral.com/1471-2164/7/60}, author = {Westenberger,Scott and Cerqueira,Gustavo and El-Sayed, Najib M. and Zingales,Bianca and Campbell,David and Sturm,Nancy} } @book {12621, title = {Unconstrained face recognition}, year = {2006}, month = {2006///}, publisher = {Springer Science \& Business}, organization = {Springer Science \& Business}, abstract = {Face recognition has been actively studied over the past decade and continues to be a big research challenge. Just recently, researchers have begun to investigate face recognition under unconstrained conditions. Unconstrained Face Recognition provides a comprehensive review of this biometric, especially face recognition from video, assembling a collection of novel approaches that are able to recognize human faces under various unconstrained situations. The underlying basis of these approaches is that, unlike conventional face recognition algorithms, they exploit the inherent characteristics of the unconstrained situation and thus improve the recognition performance when compared with conventional algorithms.Unconstrained Face Recognition is structured to meet the needs of a professional audience of researchers and practitioners in industry. This volume is also suitable for advanced-level students in computer science.}, keywords = {Computer science, Computer vision, Computers / Computer Graphics, Computers / Computer Science, Computers / Computer Vision \& Pattern Recognition, Computers / General, Computers / Image Processing, Computers / Information Technology, Computers / Information Theory, Computers / Interactive \& Multimedia, Computers / Security / Cryptography, Computers / User Interfaces, Data encryption (Computer science), Data structures (Computer science), Electronic books, Human face recognition (Computer science), IMAGE PROCESSING, Image processing - Digital techniques, multimedia systems, Optical pattern recognition, Science / Life Sciences / Biology}, isbn = {9780387264073}, author = {Zhou,S. Kevin and Chellapa, Rama and Zhao,Wenyi} } @article {12606, title = {Vehicle Fingerprinting Using Drive-By Sounds}, year = {2006}, month = {2006/11//}, institution = {CENTER FOR AUTOMATION RESEARCH, UNIVERSITY OF MARYLAND COLLEGE PARK}, abstract = {We estimate a vehicle{\textquoteright}s speed, width, and length by jointly estimating its acoustic wave-pattern using a single passive acoustic sensor that records the vehicle{\textquoteright}s drive-by noise. The acoustic wave-pattern is estimated using three envelope shape (ES) components, which approximate the shape of the received signal{\textquoteright}s power envelope. We incorporate the parameters of the ES components along with estimates of the vehicle engine RPM and number of cylinders to form a vehicle profile vector. This vector provides a compressed statistics that can be used for vehicle identification and classification. Vehicle speed estimation and classification results are provided using field data.}, keywords = {*ACOUSTIC DETECTORS, *GROUND VEHICLES, *SIGNAL PROCESSING, ACOUSTIC DETECTION AND DETECTORS, AMPLITUDE, Interference, PASSIVE SYSTEMS, spatial distribution, STATISTICAL PROCESSES, SURFACE TRANSPORTATION AND EQUIPMENT, SYMPOSIA, WAVE PROPAGATION}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA481471}, author = {Cevher, V. and Chellapa, Rama and Gurbuz, A.C. and Shah, F. and McClellan, J.H.} } @inbook {12638, title = {Video Mensuration Using a Stationary Camera}, booktitle = {Computer Vision {\textendash} ECCV 2006Computer Vision {\textendash} ECCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3953}, year = {2006}, month = {2006///}, pages = {164 - 176}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper presents a method for video mensuration using a single stationary camera. The problem we address is simple, i.e., the mensuration of any arbitrary line segment on the reference plane using multiple frames with minimal calibration. Unlike previous solutions that are based on planar rectification, our approach is based on fitting the image of multiple concentric circles on the plane. Further, the proposed method aims to minimize the error in mensuration. Hence we can calculate the mensuration of the line segments not lying on the reference plane. Using an algorithm for detecting and tracking wheels of an automobile, we have implemented a fully automatic system for wheel base mensuration. The mensuration results are accurate enough that they can be used to determine the vehicle classes. Furthermore, we measure the line segment between any two points on the vehicle and plot them in top and side views.}, isbn = {978-3-540-33836-9}, url = {http://dx.doi.org/10.1007/11744078_13}, author = {Guo,Feng and Chellapa, Rama}, editor = {Leonardis,Ale{\v s} and Bischof,Horst and Pinz,Axel} } @article {12627, title = {View Invariance for Human Action Recognition}, journal = {International Journal of Computer Vision}, volume = {66}, year = {2006}, month = {2006///}, pages = {83 - 101}, abstract = {This paper presents an approach for viewpoint invariant human action recognition, an area that has received scant attention so far, relative to the overall body of work in human action recognition. It has been established previously that there exist no invariants for 3D to 2D projection. However, there exist a wealth of techniques in 2D invariance that can be used to advantage in 3D to 2D projection. We exploit these techniques and model actions in terms of view-invariant canonical body poses and trajectories in 2D invariance space, leading to a simple and effective way to represent and recognize human actions from a general viewpoint. We first evaluate the approach theoretically and show why a straightforward application of the 2D invariance idea will not work. We describe strategies designed to overcome inherent problems in the straightforward approach and outline the recognition algorithm. We then present results on 2D projections of publicly available human motion capture data as well on manually segmented real image sequences. In addition to robustness to viewpoint change, the approach is robust enough to handle different people, minor variabilities in a given action, and the speed of aciton (and hence, frame-rate) while encoding sufficient distinction among actions.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1007/s11263-005-3671-4}, author = {Parameswaran,Vasu and Chellapa, Rama} } @article {13183, title = {View-invariant estimation of height and stride for gait recognition}, journal = {Biometric Authentication}, year = {2006}, month = {2006///}, pages = {155 - 167}, abstract = {We present a parametric method to automatically identify people in monocular low-resolution video by estimating the height and stride parameters of their walking gait. Stride parameters (stride length and cadence) are functions of body height, weight, and gender. Previous work has demonstrated effective use of these biometrics for identification and verification of people. In this paper, we show that performance is significantly improved by using height as an additional discriminant feature. Height is estimated by robustly segmenting the person from the background and fitting their apparent height to a time-dependent model. This method is correspondence-free and works with low-resolution images of people. It is also view-invariant, albeit performance is optimal in near fronto-parallel configurations. Identification accuracy is estimated at 47\% for fronto-parallel sequences of 41 people, and 65\% for non-fronto-parallel sequences of 17 people, compared with 18\% and 51\%, respectively, when only stride and cadence are used.}, author = {BenAbdelkader,C. and Cutler, R. and Davis, Larry S.} } @article {19462, title = {VoIP deregulation in South Africa: Implications for underserviced areas}, journal = {Telecommunications Policy}, volume = {30}, year = {2006}, month = {2006/06//}, pages = {332 - 344}, abstract = {Several statutory restrictions have recently been lifted on the use of Voice over Internet Protocol (VoIP) in South Africa. Previously, VoIP could only be utilised by the incumbent telecommunications operator, Telkom, the Second National Operator (SNO) and under serviced area licensees (USALs). This means new opportunities and cost savings for both network service providers and consumers. However, in rural and remote regions, further liberalisation is required so that service providers can take advantage of wireless technologies to provide connectivity in these areas. This paper discusses the legislative environment in South Africa and around the world with respect to VoIP and Wireless Fidelity (WiFi). In addition, examples are provided of how these technologies have been combined to provide last mile solutions around the world and particularly in South Africa. The paper concludes that further liberalisation in the telecommunications environment in South Africa is required if the goal of providing affordable access in rural areas is to be attained. Specifically, it is recommended that wireless technologies be deregulated since the combination of VoIP and WiFi may benefit rural areas. Also, the paper finds that USALs may not be the right model for underserviced areas in South Africa. Lastly, it is apparent that applications drive development and dictate which technologies are relevant for rural areas.}, keywords = {South Africa, VoIP, WiFi}, isbn = {0308-5961}, url = {http://www.sciencedirect.com/science/article/pii/S0308596106000231}, author = {Marshini Chetty and Blake, Edwin and McPhie, Ewan} } @inbook {19210, title = {Voting with Your Feet: An Investigative Study of the Relationship Between Place Visit Behavior and Preference}, booktitle = {UbiComp 2006: Ubiquitous Computing}, series = {Lecture Notes in Computer Science}, volume = {4206}, year = {2006}, month = {2006}, pages = {333 - 350}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Real world recommendation systems, personalized mobile search, and online city guides could all benefit from data on personal place preferences. However, collecting explicit rating data of locations as users travel from place to place is impractical. This paper investigates the relationship between explicit place ratings and implicit aspects of travel behavior such as visit frequency and travel time. We conducted a four-week study with 16 participants using a novel sensor-based experience sampling tool, called My Experience (Me), which we developed for mobile phones. Over the course of the study Me was used to collect 3,458 in-situ questionnaires on 1,981 place visits. Our results show that, first, sensor-triggered experience sampling is a useful methodology for collecting targeted information in situ. Second, despite the complexities underlying travel routines and visit behavior, there exist positive correlations between place preference and automatically detectable features like visit frequency and travel time. And, third, we found that when combined, visit frequency and travel time result in stronger correlations with place rating than when measured individually. Finally, we found no significant difference in place ratings due to the presence of others.}, isbn = {978-3-540-39634-5}, url = {http://dx.doi.org/10.1007/11853565_20}, author = {Jon Froehlich and Chen,Mike and Smith,Ian and Potter,Fred}, editor = {Dourish,Paul and Friday,Adrian} } @inbook {12642, title = {What Is the Range of Surface Reconstructions from a Gradient Field?}, booktitle = {Computer Vision {\textendash} ECCV 2006Computer Vision {\textendash} ECCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3951}, year = {2006}, month = {2006///}, pages = {578 - 591}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We propose a generalized equation to represent a continuum of surface reconstruction solutions of a given non-integrable gradient field. We show that common approaches such as Poisson solver and Frankot-Chellappa algorithm are special cases of this generalized equation. For a N {\texttimes} N pixel grid, the subspace of all integrable gradient fields is of dimension N 2 {\textendash} 1. Our framework can be applied to derive a range of meaningful surface reconstructions from this high dimensional space. The key observation is that the range of solutions is related to the degree of anisotropy in applying weights to the gradients in the integration process. While common approaches use isotropic weights, we show that by using a progression of spatially varying anisotropic weights, we can achieve significant improvement in reconstructions. We propose (a) α-surfaces using binary weights, where the parameter α allows trade off between smoothness and robustness, (b) M-estimators and edge preserving regularization using continuous weights and (c) Diffusion using affine transformation of gradients. We provide results on photometric stereo, compare with previous approaches and show that anisotropic treatment discounts noise while recovering salient features in reconstructions.}, isbn = {978-3-540-33832-1}, url = {http://dx.doi.org/10.1007/11744023_45}, author = {Agrawal,Amit and Raskar,Ramesh and Chellapa, Rama}, editor = {Leonardis,Ale{\v s} and Bischof,Horst and Pinz,Axel} } @article {12672, title = {3D face modeling from monocular video sequences}, journal = {Face Processing: Advanced Modeling and Methods}, year = {2005}, month = {2005///}, abstract = {In this chapter we present two algorithms for 3D face modeling from a monocular video sequence. The firstmethod is based on Structure from Motion (SfM), while the second one relies on contour adaptation over time. The SfM based method incorporates statistical measures of quality of the 3D estimate into the reconstruction algorithm. The initial multi-frame SfM estimate is smoothed using a generic face model in an energy function minimization framework. Such a strategy avoids excessively biasing the final 3D estimate towards the generic model. The second method relies on matching a generic 3D face model to the outer contours of a face in the input video sequence, and integrating this strategy over all the frames in the sequence. It consists of an edge-based head pose estimation step, followed by global and local deformations of the generic face model in order to adapt it to the actual 3D face. This contour adaptation approach is able to separate the geometric subtleties of the human head from the variations in shading and texture, and it does not rely on finding accurate point correspondences across frames. Detailed experimental evaluation of both the methods along with reconstructed 3D models is presented. }, author = {Roy-Chowdhury, A. and Chellapa, Rama and Gupta, R.} } @inbook {12679, title = {3D Facial Pose Tracking in Uncalibrated Videos}, booktitle = {Pattern Recognition and Machine IntelligencePattern Recognition and Machine Intelligence}, series = {Lecture Notes in Computer Science}, volume = {3776}, year = {2005}, month = {2005///}, pages = {515 - 520}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper presents a method to recover the 3D configuration of a face in each frame of a video. The 3D configuration consists of the 3 translational parameters and the 3 orientation parameters which correspond to the yaw, pitch and roll of the face, which is important for applications like face modeling, recognition, expression analysis, etc. The approach combines the structural advantages of geometric modeling with the statistical advantages of a particle-filter based inference. The face is modeled as the curved surface of a cylinder which is free to translate and rotate arbitrarily. The geometric modeling takes care of pose and self-occlusion while the statistical modeling handles moderate occlusion and illumination variations. Experimental results on multiple datasets are provided to show the efficacy of the approach. The insensitivity of our approach to calibration parameters (focal length) is also shown.}, isbn = {978-3-540-30506-4}, url = {http://dx.doi.org/10.1007/11590316_81}, author = {Aggarwal,Gaurav and Veeraraghavan,Ashok and Chellapa, Rama}, editor = {Pal,Sankar and Bandyopadhyay,Sanghamitra and Biswas,Sambhunath} } @article {15168, title = {Adaptively-secure, non-interactive public-key encryption}, journal = {Theory of Cryptography}, year = {2005}, month = {2005///}, pages = {150 - 168}, abstract = {Adaptively-secure encryption schemes ensure secrecy even in the presence of an adversary who can corrupt parties in an adaptive manner based on public keys, ciphertexts, and secret data of already-corrupted parties. Ideally, an adaptively-secure encryption scheme should, like standard public-key encryption, allow arbitrarily-many parties to use a single encryption key to securely encrypt arbitrarily-many messages to a given receiver who maintains only a single short decryption key. However, it is known that these requirements are impossible to achieve: no non-interactive encryption scheme that supports encryption of an unbounded number of messages and uses a single, unchanging decryption key can be adaptively secure. Impossibility holds even if secure data erasure is possible.We show that this limitation can be overcome by updating the decryption key over time and making some mild assumptions about the frequency of communication between parties. Using this approach, we construct adaptively-secure, completely non-interactive encryption schemes supporting secure encryption of arbitrarily-many messages from arbitrarily-many senders. Our schemes additionally provide forward security and security against chosen-ciphertext attacks. }, doi = {10.1007/978-3-540-30576-7_9}, author = {Canetti,R. and Halevi,S. and Katz, Jonathan} } @conference {12650, title = {An algebraic approach to surface reconstruction from gradient fields}, booktitle = {Computer Vision, 2005. ICCV 2005. Tenth IEEE International Conference on}, volume = {1}, year = {2005}, month = {2005/10//}, pages = {174 - 181 Vol. 1 - 174 - 181 Vol. 1}, abstract = {Several important problems in computer vision such as shape from shading (SFS) and photometric stereo (PS) require reconstructing a surface from an estimated gradient field, which is usually non-integrable, i.e. have non-zero curl. We propose a purely algebraic approach to enforce integrability in discrete domain. We first show that enforcing integrability can be formulated as solving a single linear system Ax =b over the image. In general, this system is under-determined. We show conditions under which the system can be solved and a method to get to those conditions based on graph theory. The proposed approach is non-iterative, has the important property of local error confinement and can be applied to several problems. Results on SFS and PS demonstrate the applicability of our method.}, keywords = {algebra;, algebraic, approach;, Computer, confinement;, discrete, domain, error, field;, from, gradient, graph, image, integrability;, linear, local, methods;, photometric, reconstruction;, shading;, SHAPE, stereo;, surface, system;, theory;, vision;}, doi = {10.1109/ICCV.2005.31}, author = {Agrawal,A. and Chellapa, Rama and Raskar, R.} } @article {12813, title = {An Algebraic Theory Of Boundary Crossing Transitions}, journal = {Electronic Notes in Theoretical Computer Science}, volume = {115}, year = {2005}, month = {2005/01/18/}, pages = {69 - 88}, abstract = {This paper gives a process-algebraic semantics for the hierarchical state machine (HSM) fragment of Statecharts, in which state transitions are permitted to cross state boundaries. Although frowned upon by researchers as promoting unstructured modeling, such transitions are used extensively in practice to model parameterized start states and conditional exit states. The purpose of this work is to develop a compositional semantics for HSMs that may be fit together with compositional semantic accounts for Statecharts without boundary-crossing transitions in order to arrive at a compositional theory for virtually the whole Statecharts language. Our technical development consists of a process algebra for HSMs that is equipped with an operational semantics, an argument that bisimulation is a congruence for the algebra, a syntax-directed translation procedure for HSMs into the process algebra, and an equational axiomatization of the algebra.}, keywords = {Compositional Semantics, Formal Methods, Process algebra, Statecharts}, isbn = {1571-0661}, doi = {10.1016/j.entcs.2004.09.029}, url = {http://www.sciencedirect.com/science/article/pii/S1571066104053186}, author = {Ray,Arnab and Cleaveland, Rance and Skou,Arne} } @conference {12648, title = {Algorithmic and architectural design methodology for particle filters in hardware}, booktitle = {Computer Design: VLSI in Computers and Processors, 2005. ICCD 2005. Proceedings. 2005 IEEE International Conference on}, year = {2005}, month = {2005/10//}, pages = {275 - 280}, abstract = {In this paper, we present algorithmic and architectural methodology for building particle filters in hardware. Particle filtering is a new paradigm for filtering in presence of nonGaussian nonlinear state evolution and observation models. This technique has found wide-spread application in tracking, navigation, detection problems especially in a sensing environment. So far most particle filtering implementations are not lucrative for real time problems due to excessive computational complexity involved. In this paper, we re-derive the particle filtering theory to make it more amenable to simplified VLSI implementations. Furthermore, we present and analyze pipelined architectural methodology for designing these computational blocks. Finally, we present an application using the bearing only tracking problem and evaluate the proposed architecture and algorithmic methodology.}, keywords = {(numerical, algorithmic, architectural, architectures;, bearing, complexity;, computational, design, digital, evolution;, Filtering, filtering;, filters;, implementation;, methodology;, methods);, nonGaussian, nonlinear, only, Parallel, particle, pipeline, pipelined, problem;, processing;, state, tracking, VLSI, VLSI;}, doi = {10.1109/ICCD.2005.20}, author = {Sankaranarayanan,A. C and Chellapa, Rama and Srivastava, A.} } @conference {12649, title = {Appearance modeling under geometric context}, booktitle = {Computer Vision, 2005. ICCV 2005. Tenth IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/10//}, pages = {1252 -1259 Vol. 2 - 1252 -1259 Vol. 2}, abstract = {We propose a unified framework based on a general definition of geometric transform (GeT) for modeling appearance. GeT represents the appearance by applying designed functionals over certain geometric sets. We show that image warping, Radon transform, trace transform, etc. are special cases of our definition. Moreover, three different types of GeTs are designed to handle deformation, articulation and occlusion and applied to fingerprinting the appearance inside a contour. They include the contour-driven GeT, the feature curve based GeT and selecting functionals to model the appearance inside the convex hull of the contour. A multi-resolution representation that combines both shape and appearance information is also proposed. We apply our approach to image synthesis and object recognition. The proposed approach produces promising results when applied to fingerprinting the appearance of human and body parts despite the challenges due to articulated motion and deformations}, keywords = {based, curve, geometry;image, GeT;convex, GeT;fingerprinting;geometric, hull;feature, information;trace, modeling;contour-driven, Radon, recognition;, recognition;shape, representation;object, synthesis;image, transform;appearance, transform;image, transform;Radon, transforms;computational, warping;multi-resolution}, doi = {10.1109/ICCV.2005.38}, author = {Li,Jian and Zhou,S. K and Chellapa, Rama} } @conference {12673, title = {An architectural level design methodology for embedded face detection}, booktitle = {Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis}, series = {CODES+ISSS {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {136 - 141}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Face detection and recognition research has attracted great attention in recent years. Automatic face detection has great potential in a large array of application areas, including banking and security system access control, video surveillance, and multimedia information retrieval. In this paper, we discuss an architectural level design methodology for implementation of an embedded face detection system on a reconfigurable system on chip. We present models for performance estimation and validate these models with experimental values obtained from implementing our system on an FPGA platform. This modeling approach is shown to be efficient, accurate, and intuitive for designers to work with. Using this approach, we present several design options that trade-off various architectural features.}, keywords = {design space exploration, Face detection, platforms, reconfigurable, system-level models}, isbn = {1-59593-161-9}, doi = {10.1145/1084834.1084872}, url = {http://doi.acm.org/10.1145/1084834.1084872}, author = {Kianzad,V. and Saha,S. and Schlessman,J. and Aggarwal,G. and Bhattacharyya, Shuvra S. and Wolf,W. and Chellapa, Rama} } @conference {14325, title = {Are GSM phones THE solution for localization?}, booktitle = {Mobile Computing Systems and Applications, 2006. WMCSA{\textquoteright}06. Proceedings. 7th IEEE Workshop on}, year = {2005}, month = {2005///}, pages = {34 - 42}, author = {Varshavsky,A. and Chen,M.Y. and de Lara,E. and Jon Froehlich and Haehnel,D. and Hightower,J. and LaMarca,A. and Potter,F. and Sohn,T. and Tang,K. and others} } @conference {18665, title = {Automated checking for Windows host vulnerabilities}, year = {2005}, month = {2005/11//}, pages = {10 pp. -148 - 10 pp. -148}, abstract = {Evaluation of computing system security requires knowledge of the vulnerabilities present in the system and of potential attacks against the system. Vulnerabilities can be classified based on their location as application vulnerabilities, network vulnerabilities, or host vulnerabilities. This paper describes Ferret-Windows, a new software tool for checking host vulnerabilities on the Windows platforms. This tool helps system administrators by quickly finding vulnerabilities that are present on a host. It is designed and implemented in a modular way: a plug-in module is used for each vulnerability checked, and each possible output format is specified by a plug-in module. Moreover, several vulnerability fixing plug-in modules exist to help users remove specific vulnerabilities. As a result, Ferret-Windows is extensible, and can easily be kept up-to-date through the addition of checks for new vulnerabilities as they are identified. Finally, Ferret-Windows is a freely available open-source software}, keywords = {application vulnerabilities, computing system security, Ferret-Windows software tool, host vulnerabilities, network vulnerabilities, open-source software, operating systems (computers), plug-in module, program diagnostics, security of data, software reliability, software tools, system attacks, Windows host vulnerability checking, Windows platforms}, doi = {10.1109/ISSRE.2005.11}, author = {Tamizi,M. and Weinstein,M. and Michel Cukier} } @conference {12655, title = {Average relative radiance transform for subpixel detection}, booktitle = {Geoscience and Remote Sensing Symposium, 2005. IGARSS {\textquoteright}05. Proceedings. 2005 IEEE International}, volume = {5}, year = {2005}, month = {2005/07//}, pages = {3565 - 3568}, doi = {10.1109/IGARSS.2005.1526617}, author = {Broadwater, J. and Meth, R. and Chellapa, Rama} } @article {12656, title = {Background learning for robust face recognition with PCA in the presence of clutter}, journal = {Image Processing, IEEE Transactions on}, volume = {14}, year = {2005}, month = {2005/06//}, pages = {832 - 843}, abstract = {We propose a new method within the framework of principal component analysis (PCA) to robustly recognize faces in the presence of clutter. The traditional eigenface recognition (EFR) method, which is based on PCA, works quite well when the input test patterns are faces. However, when confronted with the more general task of recognizing faces appearing against a background, the performance of the EFR method can be quite poor. It may miss faces completely or may wrongly associate many of the background image patterns to faces in the training set. In order to improve performance in the presence of background, we argue in favor of learning the distribution of background patterns and show how this can be done for a given test image. An eigenbackground space is constructed corresponding to the given test image and this space in conjunction with the eigenface space is used to impart robustness. A suitable classifier is derived to distinguish nonface patterns from faces. When tested on images depicting face recognition in real situations against cluttered background, the performance of the proposed method is quite good with fewer false alarms.}, keywords = {Automated;Principal Component Analysis;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Biological;Models, Computer-Assisted;Information Storage and Retrieval;Models, Computer-Assisted;Subtraction Technique;, PCA;background learning;clutter;eigenface recognition method;face recognition;linear discriminant;principal component analysis;clutter;eigenvalues and eigenfunctions;face recognition;learning (artificial intelligence);principal component analysis;Algorith, Statistical;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2005.847288}, author = {Rajagopalan, AN and Chellapa, Rama and Koterba, N.T.} } @article {12661, title = {Bayesian algorithms for simultaneous structure from motion estimation of multiple independently moving objects}, journal = {Image Processing, IEEE Transactions on}, volume = {14}, year = {2005}, month = {2005/01//}, pages = {94 - 109}, abstract = {The problem of simultaneous structure from motion estimation for multiple independently moving objects from a monocular image sequence is addressed. Two Bayesian algorithms are presented for solving this problem using the sequential importance sampling (SIS) technique. The empirical posterior distribution of object motion and feature separation parameters is approximated by weighted samples. The first algorithm addresses the problem when only two moving objects are present. A singular value decomposition (SVD)-based sample clustering algorithm is shown to be capable of separating samples related to different objects. A pair of SIS procedures is used to track the posterior distribution of the motion parameters. In the second algorithm, a balancing step is added into the SIS procedure to preserve samples of low weights so that all objects have enough samples to propagate empirical motion distributions. By using the proposed algorithms, the relative motions of all the moving objects with respect to the camera can be simultaneously estimated. Both algorithms have been tested on synthetic and real- image sequences. Improved results have been achieved.}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Bayesian algorithm;clustering algorithm;empirical posterior distribution;feature separation parameter;monocular image sequence;motion estimation;multiple independently moving object;object motion;real-image sequence;sequential importance sampling techniqu, Biological;Models, Computer-Assisted;Imaging, Computer-Assisted;Pattern Recognition, Computer-Assisted;Subtraction Technique;Video Recording;Walking;, Statistical;Movement;Numerical Analysis, Three-Dimensional;Information Storage and Retrieval;Models}, isbn = {1057-7149}, doi = {10.1109/TIP.2004.837551}, author = {Qian,Gang and Chellapa, Rama and Qinfen Zheng} } @inbook {12669, title = {Beyond one still image: Face recognition from multiple still images or a video sequence}, booktitle = {Face ProcessingFace Processing}, year = {2005}, month = {2005///}, pages = {547 - 575}, publisher = {Academic Press}, organization = {Academic Press}, address = {Burlington}, abstract = {While face recognition (FR) from a single still image has been extensively studied over a decade, FR based on a group of still images (also referred to as multiple still images) or a video sequence is an emerging topic. This is mainly evidenced by the growing increase in the literature. For instance, a research initiative called Face Recognition Grand Challenge [1] has been organized. One specific challenge directly addresses the use of multiple still images to improve the recognition accuracy significantly [3]. Recently a workshop jointly held with CVPR 2004 was devoted to face processing in video [2]. It is predictable that, with the ubiquity of video sequences, face recognition based on video sequences will become more and more popular.}, isbn = {978-0-12-088452-0}, url = {http://www.sciencedirect.com/science/article/pii/B9780120884520500182}, editor = {Zhao,Wenyi and Chellapa, Rama} } @article {18939, title = {Bootstrapping parsers via syntactic projection across parallel texts}, journal = {Nat. Lang. Eng.}, volume = {11}, year = {2005}, month = {2005/09//}, pages = {311 - 325}, abstract = {Broad coverage, high quality parsers are available for only a handful of languages. A prerequisite for developing broad coverage parsers for more languages is the annotation of text with the desired linguistic representations (also known as {\textquotedblleft}treebanking{\textquotedblright}). However, syntactic annotation is a labor intensive and time-consuming process, and it is difficult to find linguistically annotated text in sufficient quantities. In this article, we explore using parallel text to help solving the problem of creating syntactic annotation in more languages. The central idea is to annotate the English side of a parallel corpus, project the analysis to the second language, and then train a stochastic analyzer on the resulting noisy annotations. We discuss our background assumptions, describe an initial study on the {\textquotedblleft}projectability{\textquotedblright} of syntactic relations, and then present two experiments in which stochastic parsers are developed with minimal human intervention via projection from English.}, isbn = {1351-3249}, doi = {10.1017/S1351324905003840}, url = {http://dx.doi.org/10.1017/S1351324905003840}, author = {Hwa,Rebecca and Resnik, Philip and Weinberg, Amy and Cabezas,Clara and Kolak,Okan} } @article {17002, title = {Building a Coherent Data Pipeline in Microarray Data Analyses: Optimization of Signal/Noise Ratios Using an Interactive Visualization Tool and a Novel Noise Filtering Method (2003)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {Motivation: Sources of uncontrolled noise strongly influence data analysis in microarray studies, yet signal/noise ratios are rarely considered in microarray data analyses. We hypothesized that different research projects would have different sources and levels of confounding noise, and built an interactive visual analysis tool to test and define parameters in Affymetrix analyses that optimize the ratio of signal (desired biological variable) versus noise (confounding uncontrolled variables). Results: Five probe set algorithms were studied with and without statistical weighting of probe sets using Microarray Suite (MAS) 5.0 probe set detection p values. The signal/noise optimization method was tested in two large novel microarray datasets with different levels of confounding noise; a 105 sample U133A human muscle biopsy data set (11 groups) (extensive noise), and a 40 sample U74A inbred mouse lung data set (8 groups) (little noise). Success was measured using F-measure value of success of unsupervised clustering into appropriate biological groups (signal). We show that both probe set signal algorithm and probe set detection p-value weighting have a strong effect on signal/noise ratios, and that the different methods performed quite differently in the two data sets. Among the signal algorithms tested, dChip difference model with p-value weighting was the most consistent at maximizing the effect of the target biological variables on data interpretation of the two data sets. Availability: The Hierarchical Clustering Explorer 2.0 is [url=http://www.cs.umd.edu/hcil/hce/]available[/url] online and the improved version of the Hierarchical Clustering Explorer 2.0 with p-value weighting and Fmeasure is available upon request to the first author. Murine arrays (40 samples) are publicly available at the [url=http://microarray.cnmcresearch.org/pgadatatable.asp]PEPR resource.[/url] (Chen et al., 2004).}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6511}, author = {Seo,Jinwook and Bakay,Marina and Chen,Yi-Wen and Hilmer,Sara and Shneiderman, Ben and Hoffman,Eric P} } @article {16110, title = {The Challenge of Personal Information Management}, journal = {INTERACT{\textquoteright}05: Communicating Naturally through Computers (Adjunct Proceedings)}, year = {2005}, month = {2005///}, author = {Dix,A. and Jones,W. and Czerwinski,M. and Teevan,J. and Plaisant, Catherine and Moran,TP} } @conference {13910, title = {Child{\textquoteright}s play: a comparison of desktop and physical interactive environments}, booktitle = {Proceedings of the 2005 conference on Interaction design and children}, year = {2005}, month = {2005///}, pages = {48 - 55}, author = {Fails,J. A and Druin, Allison and Guha,M.L. and Chipman,G. and Simms,S. and Churaman,W.} } @article {12935, title = {Cholera: the killer from the deep}, journal = {The Biochemist}, year = {2005}, month = {2005///}, abstract = {The current international attention to the importance ofcombating infectious diseases can provide the opportunity for a multidisciplinary approach that joins medicine with many other scientific and technological disciplines. Science and technology are major forces that have the potential to balance the world{\textquoteright}s inequities. The connection between cholera and the environment provides a paradigm for this perspective. }, author = {Rita R Colwell} } @conference {14777, title = {Combining self-reported and automatic data to improve programming effort measurement}, booktitle = {Proceedings of the 10th European software engineering conference held jointly with 13th ACM SIGSOFT international symposium on Foundations of software engineering}, series = {ESEC/FSE-13}, year = {2005}, month = {2005///}, pages = {356 - 365}, publisher = {ACM}, organization = {ACM}, address = {Lisbon, Portugal}, abstract = {Measuring effort accurately and consistently across subjects in a programming experiment can be a surprisingly difficult task. In particular, measures based on self-reported data may differ significantly from measures based on data which is recorded automatically from a subject{\textquoteright}s computing environment. Since self-reports can be unreliable, and not all activities can be captured automatically, a complete measure of programming effort should incorporate both classes of data. In this paper, we show how self-reported and automatic effort can be combined to perform validation and to measure total programming effort.}, keywords = {effort, experimentation, human factors, manual approaches, measurement, process metrics, verification}, isbn = {1-59593-014-0}, doi = {10.1145/1081706.1081762}, author = {Hochstein, Lorin and Basili, Victor R. and Zelkowitz, Marvin V and Hollingsworth, Jeffrey K and Carver, Jeff} } @article {14078, title = {Comparative Genomics of Trypanosomatid Parasitic Protozoa}, journal = {Science}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {404 - 409}, abstract = {A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that{\textemdash}along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions{\textemdash}have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.}, doi = {10.1126/science.1112181}, url = {http://www.sciencemag.org/content/309/5733/404.abstract}, author = {El-Sayed, Najib M. and Myler,Peter J. and Blandin,Ga{\"e}lle and Berriman,Matthew and Crabtree,Jonathan and Aggarwal,Gautam and Caler,Elisabet and Renauld,Hubert and Worthey,Elizabeth A. and Hertz-Fowler,Christiane and Ghedin,Elodie and Peacock,Christopher and Bartholomeu,Daniella C. and Haas,Brian J. and Tran,Anh-Nhi and Wortman,Jennifer R. and Alsmark,U. Cecilia M. and Angiuoli,Samuel and Anupama,Atashi and Badger,Jonathan and Bringaud,Frederic and Cadag,Eithon and Carlton,Jane M. and Cerqueira,Gustavo C. and Creasy,Todd and Delcher,Arthur L. and Djikeng,Appolinaire and Embley,T. Martin and Hauser,Christopher and Ivens,Alasdair C. and Kummerfeld,Sarah K. and Pereira-Leal,Jose B. and Nilsson,Daniel and Peterson,Jeremy and Salzberg,Steven L. and Shallom,Joshua and Silva,Joana C. and Sundaram,Jaideep and Westenberger,Scott and White,Owen and Melville,Sara E. and Donelson,John E. and Andersson,Bj{\"o}rn and Stuart,Kenneth D. and Hall,Neil} } @article {16920, title = {A Comparison of Voice Controlled and Mouse Controlled Web Browsing (2000)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {Voice controlled web browsers allow users to navigate by speaking the text of a link or an associated number instead of clicking with a mouse. One such browser is Conversa, by Conversational Computing. This within subjects study with 18 subjects compared voice browsing with traditional mouse-based browsing. It attempted to identify which of three common hypertext forms (linear slide show, grid/tiled map, and hierarchical menu) are well suited to voice navigation, and whether voice navigation is helped by numbering links. The study shows that voice control adds approximately 50 percent to the performance time for certain types of tasks. Subjective satisfaction measures indicate that for voice browsing, textual links are preferable to numbered links.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6475}, author = {Christian,Kevin and Kules,Bill and Shneiderman, Ben and Youssef,Adel} } @conference {12370, title = {Computer vision on FPGAs: Design methodology and its application to gesture recognition}, booktitle = {Computer Vision and Pattern Recognition-Workshops, 2005. CVPR Workshops. IEEE Computer Society Conference on}, year = {2005}, month = {2005///}, pages = {133 - 133}, author = {Sen,M. and Corretjer,I. and Haim,F. and Saha,S. and Bhattacharyya, Shuvra S. and Schlessman,J. and Wolf,W.} } @article {12931, title = {Critical Factors Influencing the Occurrence of Vibrio Cholerae in the Environment of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {71}, year = {2005}, month = {2005/08/01/}, pages = {4645 - 4654}, abstract = {The occurrence of outbreaks of cholera in Africa in 1970 and in Latin America in 1991, mainly in coastal communities, and the appearance of the new serotype Vibrio cholerae O139 in India and subsequently in Bangladesh have stimulated efforts to understand environmental factors influencing the growth and geographic distribution of epidemic Vibrio cholerae serotypes. Because of the severity of recent epidemics, cholera is now being considered by some infectious disease investigators as a {\textquotedblleft}reemerging{\textquotedblright} disease, prompting new work on the ecology of vibrios. Epidemiological and ecological surveillance for cholera has been under way in four rural, geographically separated locations in Bangladesh for the past 4 years, during which both clinical and environmental samples were collected at biweekly intervals. The clinical epidemiology portion of the research has been published (Sack et al., J. Infect. Dis. 187:96-101, 2003). The results of environmental sampling and analysis of the environmental and clinical data have revealed significant correlations of water temperature, water depth, rainfall, conductivity, and copepod counts with the occurrence of cholera toxin-producing bacteria (presumably V. cholerae). The lag periods between increases or decreases in units of factors, such as temperature and salinity, and occurrence of cholera correlate with biological parameters, e.g., plankton population blooms. The new information on the ecology of V. cholerae is proving useful in developing environmental models for the prediction of cholera epidemics.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.71.8.4645-4654.2005}, url = {http://aem.asm.org/content/71/8/4645}, author = {Huq,Anwar and Sack,R. Bradley and Nizam,Azhar and Longini,Ira M. and Nair,G. Balakrish and Ali,Afsar and Morris,J. Glenn and Khan,M. N. Huda and Siddique,A. Kasem and Yunus,Mohammed and Albert,M. John and Sack,David A. and Rita R Colwell} } @article {12989, title = {Data sharing in ecology and evolution}, journal = {Trends in Ecology \& Evolution}, volume = {20}, year = {2005}, month = {2005/07//}, pages = {362 - 363}, isbn = {0169-5347}, doi = {10.1016/j.tree.2005.04.023}, url = {http://www.sciencedirect.com/science/article/pii/S0169534705001308}, author = {Parr,Cynthia S. and Cummings, Michael P.} } @conference {18560, title = {Design and implementation of a routing control platform}, booktitle = {Proceedings of the 2nd conference on Symposium on Networked Systems Design \& Implementation - Volume 2}, series = {NSDI{\textquoteright}05}, year = {2005}, month = {2005///}, pages = {15 - 28}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {The routers in an Autonomous System (AS) must distribute the information they learn about how to reach external destinations. Unfortunately, today{\textquoteright}s internal Border Gateway Protocol (iBGP) architectures have serious problems: a "full mesh" iBGP configuration does not scale to large networks and "route reflection" can introduce problems such as protocol oscillations and persistent loops. Instead, we argue that a Routing Control Platform (RCP) should collect information about external destinations and internal topology and select the BGP routes for each router in an AS. RCP is a logically-centralized platform, separate from the IP forwarding plane, that performs route selection on behalf of routers and communicates selected routes to the routers using the unmodified iBGP protocol. RCP provides scalability without sacrificing correctness. In this paper, we present the design and implementation of an RCP prototype on commodity hardware. Using traces of BGP and internal routing data from a Tier-1 backbone, we demonstrate that RCP is fast and reliable enough to drive the BGP routing decisions for a large network. We show that RCP assigns routes correctly, even when the functionality is replicated and distributed, and that networks using RCP can expect comparable convergence delays to those using today{\textquoteright}s iBGP architectures.}, url = {http://dl.acm.org/citation.cfm?id=1251203.1251205}, author = {Caesar,Matthew and Caldwell,Donald and Feamster, Nick and Rexford,Jennifer and Shaikh,Aman and van der Merwe,Jacobus} } @inbook {14211, title = {Detecting Independent 3D Movement}, booktitle = {Handbook of Geometric ComputingHandbook of Geometric Computing}, year = {2005}, month = {2005///}, pages = {383 - 401}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, isbn = {978-3-540-28247-1}, url = {http://dx.doi.org/10.1007/3-540-28247-5_12}, author = {Corrochano,Eduardo Bayro and Ogale, Abhijit S. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {17079, title = {Determining Causes and Severity of End-User Frustration (2002)}, year = {2005}, month = {2005///}, abstract = {While computers are beneficial to individuals and society, frequently, users encounter frustrating experiences when using computers. This study attempts to measure, through 111 participants, the frequency, cause, and the level of severity of frustrating experiences. The data showed that frustrating experiences happen on a frequent basis. The applications in which the frustrating experiences happened most frequently were web browsing, e-mail, and word processing. The most-cited causes of frustrating experiences were error messages, dropped network connections, long download times, and hard-to-find features. The time lost due to frustrating experiences ranged from 47-53\% of time spent on a computer depending on the location and study method. After discarding extreme cases the time lost was still above 38\%. These disturbing results should be a basis for future study.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6493}, author = {Ceaparu,Irina and Lazar,Jonathan and Bessiere,Katie and Robinson,John and Shneiderman, Ben} } @conference {13539, title = {DOCLIB: A document processing research tool}, booktitle = {Symposium on Document Image Understanding Technology}, year = {2005}, month = {2005///}, pages = {159 - 163}, abstract = {Often, valuable document processing intellectual capital is lost due to staff transitions or project restructuring prior to technology transfer. Furthermore, hardware and software integrity, dependencies, and compatibility are critical components that often impede technology migration. While many open source tools attempt to mitigate these issues, they do not always address specific design needs and tailored-process that Government organizations must adhere to. This paper addresses the need for a common document processing research vehicle through which institutions can develop and share research-related software and applications across academic, business, and Government domains.}, author = {Chen,Kevin and Jaeger,Stefan and Zhu,Guangyu and David Doermann} } @conference {12852, title = {Efficient temporal-logic query checking for presburger systems}, booktitle = {Proceedings of the 20th IEEE/ACM international Conference on Automated software engineering}, series = {ASE {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {24 - 33}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper develops a framework for solving temporal-logic query-checking problems for a class of infinite-state system models that compute with integer-valued variables (so-called Presburger systems, in which Presburger formulas are used to define system behavior). The temporal-logic query checking problem may be formulated as follows: given a model and a temporal logic formula with placeholders, compute a set of assignments of formulas to placeholders such that the resulting temporal formula is satisfied by the given model. Temporal-logic query checking has proved useful as a means for requirements and design understanding; existing work, however, has focused only on propositional temporal logic and finite-state systems.Our method is based on a symbolic model-checking technique that relies on proof search. The paper first introduces this model-checking approach and then shows how it can be adapted to solving the temporal queries in which formulas may contain integer variables. We also present experimental results showing the computational efficacy of our approach.}, keywords = {Formal Methods, Model checking, on-the-fly symbolic model checking, Presburger systems, query checking}, isbn = {1-58113-993-4}, doi = {10.1145/1101908.1101915}, url = {http://doi.acm.org/10.1145/1101908.1101915}, author = {Zhang,Dezhuang and Cleaveland, Rance} } @conference {12664, title = {Ego-Motion Estimation and 3D Model Refinement in Scenes with Varying Illumination}, booktitle = {Application of Computer Vision, 2005. WACV/MOTIONS {\textquoteright}05 Volume 1. Seventh IEEE Workshops on}, volume = {2}, year = {2005}, month = {2005/01//}, pages = {140 - 146}, abstract = {We present an iterative algorithm for robustly estimating the ego-motion and refining and updating a coarse depth map using surface parallax and a generalized dynamic image (GDI) model. Given a coarse depth map acquired by a range-finder or extracted from a Digital Elevation Map (DEM), we first estimate the ego-motion by combining a global ego-motion constraint and a local GDI model. Using the estimated camera motion and the available depth estimate, motion of the 3D points is compensated. We utilize the fact that the resulting surface parallax field is an epipolar field and constrain its direction using the previous motion estimates. We then estimate the magnitude of the parallax field and the GDI model parameters locally and use them to refine the depth map estimates. We use a tensor based approach to formulate the depth refinement procedure as an eigen-value problem and obtain confidence measures for determining the accuracy of the estimated depth values. These confidence measures are used to remove regions with potentially incorrect depth estimates for robustly estimating ego-motion in the next iteration. Experimental results using both synthetic and real data are presented. Comparisons with results obtained using a brightness constancy (BC) model show that the proposed algorithm works significantly better when time-varying illumination changes are present in the scene.}, doi = {10.1109/ACVMOT.2005.45}, author = {Agrawal,Amit K and Chellapa, Rama} } @inbook {16105, title = {Evaluation Methodologies for Visual Analytics}, booktitle = {Illuminating the Path: The Research and Development Agenda for Visual AnalyticsIlluminating the Path: The Research and Development Agenda for Visual Analytics}, year = {2005}, month = {2005///}, pages = {150 - 157}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, keywords = {file-import-09-03-18}, url = {http://nvac.pnl.gov/agenda.stm$\#$book}, author = {Laskowski,S. and Plaisant, Catherine}, editor = {Thomas,James and Cook,Kristin} } @article {15441, title = {An evolutionary testbed for software technology evaluation}, journal = {Innovations in Systems and Software Engineering}, volume = {1}, year = {2005}, month = {2005///}, pages = {3 - 11}, abstract = {Empirical evidence and technology evaluation are needed to close the gap between the state of the art and the state of the practice in software engineering. However, there are difficulties associated with evaluating technologies based on empirical evidence: insufficient specification of context variables, cost of experimentation, and risks associated with trying out new technologies. In this paper, we propose the idea of an evolutionary testbed for addressing these problems. We demonstrate the utility of the testbed in empirical studies involving two different research technologies applied to the testbed, as well as the results of these studies. The work is part of NASArsquos High Dependability Computing Project (HDCP), in which we are evaluating a wide range of new technologies for improving the dependability of NASA mission-critical systems.}, doi = {10.1007/s11334-005-0007-z}, author = {Lindvall,M. and Rus,I. and Shull, F. and Zelkowitz, Marvin V and Donzelli,P. and Memon, Atif M. and Basili, Victor R. and Costa,P. and Tvedt,R. and Hochstein, L.} } @article {12794, title = {Executable requirements specifications using triggered message sequence charts}, journal = {Distributed Computing and Internet Technology}, year = {2005}, month = {2005///}, pages = {482 - 493}, author = {Sengupta,B. and Cleaveland, Rance} } @conference {18657, title = {An experimental evaluation to determine if port scans are precursors to an attack}, year = {2005}, month = {2005/07/01/june}, pages = {602 - 611}, abstract = {This paper describes an experimental approach to determine the correlation between port scans and attacks. Discussions in the security community often state that port scans should be considered as precursors to an attack. However, very few studies have been conducted to quantify the validity of this hypothesis. In this paper, attack data were collected using a test-bed dedicated to monitoring attackers. The data collected consist of port scans, ICMP scans, vulnerability scans, successful attacks and management traffic. Two experiments were performed to validate the hypothesis of linking port scans and vulnerability scans to the number of packets observed per connection. Customized scripts were then developed to filter the collected data and group them on the basis of scans and attacks between a source and destination IP address pair. The correlation of the filtered data groups was assessed. The analyzed data consists of forty-eight days of data collection for two target computers on a heavily utilized subnet.}, keywords = {attack data collection, computer crime, filtered data groups, ICMP scans, IP address, IP networks, management traffic, port scans, telecommunication security, Telecommunication traffic, vulnerability scans}, doi = {10.1109/DSN.2005.18}, author = {Panjwani,S. and Tan,S. and Jarrin,K.M. and Michel Cukier} } @article {16111, title = {Extending the Utility of Treemaps with Flexible Hierarchy (2004)}, year = {2005}, month = {2005///}, abstract = {Treemaps is a visualization technique for presenting hierarchical information on two dimensional displays. Prior implementations limit the visualization to pre-defined static hierarchies. Flexible hierarchy, a new capability of Treemap 4.0, enables users to define various hierarchies through dynamically selecting a series of data attributes so that they can discover patterns, clusters and outliers. This paper describes the design and implementation issues of flexible hierarchy. It then reports on a usability study which led to enhancements to the interface.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6514}, author = {Chintalapani,Gouthami and Plaisant, Catherine and Shneiderman, Ben} } @conference {12651, title = {Face recognition in the presence of multiple illumination sources}, booktitle = {Computer Vision, 2005. ICCV 2005. Tenth IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/10//}, pages = {1169 -1176 Vol. 2 - 1169 -1176 Vol. 2}, abstract = {Most existing face recognition algorithms work well for controlled images but are quite susceptible to changes in illumination and pose. This has led to the rise of analysis-by-synthesis approaches due to their inherent potential to handle these external factors. Though these approaches work quite well, most of them assume that the face is illuminated by a single light source which is usually not true in realistic conditions. In this paper, we propose an algorithm to recognize faces illuminated by arbitrarily placed, multiple light sources. The algorithm does not need to know the number of light sources and works extremely well even while recognizing faces illuminated by different number of light sources. Results using this algorithm are reported on multiple-illumination datasets generated from PIE by T. Sim, et al. (2003) and Yale Face Database B by W. Zhao, et al. (2003). We also highlight the importance of the hard non-linearity in the Lambert{\textquoteright}s law which is often ignored, probably to linearize the estimation process}, keywords = {approach;estimation, illumination, Lambert, law;analysis-by-synthesis, nonlinearity;multiple, process;face, recognition;hard, recognition;light, source;face, sources;}, doi = {10.1109/ICCV.2005.92}, author = {Aggarwal,G. and Chellapa, Rama} } @conference {12662, title = {A Factorization Method for Structure from Planar Motion}, booktitle = {Application of Computer Vision, 2005. WACV/MOTIONS {\textquoteright}05 Volume 1. Seventh IEEE Workshops on}, volume = {2}, year = {2005}, month = {2005/01//}, pages = {154 - 159}, abstract = {We propose a factorization method for structure from planar motion using a stationary perspective camera. Compared with [A factorization based algorithm for multi-image projective structure and motion] for general motion, our work has three major differences: a different measurement matrix specialized for planar motion is formed. The measurement matrix has a rank of at most 3, instead of 4; the measurement matrix needs similar scalings, but estimation of fundamental matrices or epipoles is not needed; we have an Euclidean reconstruction instead of a projective reconstruction. The camera is not required to be calibrated. A simple semi-automatic calibration method using vanishing points and lines is sufficient. Experimental results show that the algorithm is accurate and fairly robust to noise and inaccurate calibration.}, doi = {10.1109/ACVMOT.2005.4}, author = {Li,Jian and Chellapa, Rama} } @article {12820, title = {Fast generic model-checking for data-based systems}, journal = {Formal Techniques for Networked and Distributed Systems-FORTE 2005}, year = {2005}, month = {2005///}, pages = {83 - 97}, author = {Zhang,D. and Cleaveland, Rance} } @conference {12815, title = {Fast on-the-fly parametric real-time model checking}, booktitle = {Real-Time Systems Symposium, 2005. RTSS 2005. 26th IEEE International}, year = {2005}, month = {2005///}, pages = {10{\textendash}pp - 10{\textendash}pp}, author = {Zhang,D. and Cleaveland, Rance} } @article {17167, title = {Finding Governmental Statistical Data on the Web: Three Empirical Studies of the FedStats Topics Page (2003)}, year = {2005}, month = {2005///}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6509}, author = {Ceaparu,Irina and Shneiderman, Ben} } @article {12969, title = {A framework for set-oriented computation in inductive logic programming and its application in generalizing inverse entailment}, journal = {Inductive Logic Programming}, year = {2005}, month = {2005///}, pages = {69 - 86}, author = {Corrada Bravo, Hector and Page,D. and Ramakrishnan,R. and Shavlik,J. and Costa,V. S} } @inbook {12678, title = {Fusing Depth and Video Using Rao-Blackwellized Particle Filter}, booktitle = {Pattern Recognition and Machine IntelligencePattern Recognition and Machine Intelligence}, series = {Lecture Notes in Computer Science}, volume = {3776}, year = {2005}, month = {2005///}, pages = {521 - 526}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We address the problem of fusing sparse and noisy depth data obtained from a range finder with features obtained from intensity images to estimate ego-motion and refine 3D structure of a scene using a Rao-Blackwellized particle filter. For scenes with low depth variability, the algorithm shows an alternate way of performing Structure from Motion (SfM) starting with a flat depth map. Instead of using 3D depths, we formulate the problem using 2D image domain parallax and show that conditioned on non-linear motion parameters, the parallax magnitude with respect to the projection of the vanishing point forms a linear subsystem independent of camera motion and their distributions can be analytically integrated. Thus, the structure is obtained by estimating parallax with respect to the given depths using a Kalman filter and only the ego-motion is estimated using a particle filter. Hence, the required number of particles becomes independent of the number of feature points which is an improvement over previous algorithms. Experimental results on both synthetic and real data show the effectiveness of our approach.}, isbn = {978-3-540-30506-4}, url = {http://dx.doi.org/10.1007/11590316_82}, author = {Agrawal,Amit and Chellapa, Rama}, editor = {Pal,Sankar and Bandyopadhyay,Sanghamitra and Biswas,Sambhunath} } @article {12674, title = {Gait-based human identification using appearance matching}, journal = {Optical and Digital Techniques for Information Security}, year = {2005}, month = {2005///}, pages = {271 - 295}, abstract = {In this chapter, we present an appearance-based approach for recognizing human gait. Given the gait video of an individual, the images are binarized and the width of the outer contour of the silhouette of that individual is obtained for each image frame. Several gait features are derived from this basic width vector. Temporally ordered sequences of the feature vectors are then used to represent the gait of a person. While matching the feature templates for recognition, dynamic time-warping (DTW), which is a nonlinear time-normalization technique, is used to deal with naturally occurring changes in the walking speeds of individuals. The performance of the proposed method is tested on indoor as well as outdoor gait databases, and the efficacy of different gait features and their noise resilience is studied. The experiments also demonstrate the effect of change in the viewing angle and frame rate of data capture on the accuracy of gait recognition.}, author = {Kale, A. and Cuntoor, N. and Yegnanarayana,B. and Rajagopalan, A. and Chellapa, Rama} } @conference {18394, title = {Generating testable hypotheses from tacit knowledge for high productivity computing}, booktitle = {Proceedings of the second international workshop on Software engineering for high performance computing system applications}, series = {SE-HPCS {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {17 - 21}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this research, we are developing our understanding of how the high performance computing community develops effective parallel implementations of programs by collecting the folklore within the community. We use this folklore as the basis for a series of experiments, which we expect, will validate or negate these assumptions.}, keywords = {folklore elicitation, high productivity development time experimental studies, hypothesis generation, tacit knowledge solicitation, testable hypotheses}, isbn = {1-59593-117-1}, doi = {10.1145/1145319.1145325}, url = {http://doi.acm.org/10.1145/1145319.1145325}, author = {Asgari, Sima and Hochstein, Lorin and Basili, Victor R. and Zelkowitz, Marvin V and Hollingsworth, Jeffrey K and Carver, Jeff and Shull, Forrest} } @article {14092, title = {The genome of the African trypanosome Trypanosoma brucei}, journal = {Science}, volume = {309}, year = {2005}, month = {2005///}, pages = {416 - 416}, author = {Berriman,M. and Ghedin,E. and Hertz-Fowler,C. and Blandin,G. and Renauld,H. and Bartholomeu,D. C and Lennard,N. J and Caler,E. and Hamlin,N. E and Haas,B. and others} } @article {14071, title = {The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease}, journal = {Science}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {409 - 415}, abstract = {Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50\% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.}, doi = {10.1126/science.1112631}, url = {http://www.sciencemag.org/content/309/5733/409.abstract}, author = {El-Sayed, Najib M. and Myler,Peter J. and Bartholomeu,Daniella C. and Nilsson,Daniel and Aggarwal,Gautam and Tran,Anh-Nhi and Ghedin,Elodie and Worthey,Elizabeth A. and Delcher,Arthur L. and Blandin,Ga{\"e}lle and Westenberger,Scott J. and Caler,Elisabet and Cerqueira,Gustavo C. and Branche,Carole and Haas,Brian and Anupama,Atashi and Arner,Erik and {\r A}slund,Lena and Attipoe,Philip and Bontempi,Esteban and Bringaud,Fr{\'e}d{\'e}ric and Burton,Peter and Cadag,Eithon and Campbell,David A. and Carrington,Mark and Crabtree,Jonathan and Darban,Hamid and da Silveira,Jose Franco and de Jong,Pieter and Edwards,Kimberly and Englund,Paul T. and Fazelina,Gholam and Feldblyum,Tamara and Ferella,Marcela and Frasch,Alberto Carlos and Gull,Keith and Horn,David and Hou,Lihua and Huang,Yiting and Kindlund,Ellen and Klingbeil,Michele and Kluge,Sindy and Koo,Hean and Lacerda,Daniela and Levin,Mariano J. and Lorenzi,Hernan and Louie,Tin and Machado,Carlos Renato and McCulloch,Richard and McKenna,Alan and Mizuno,Yumi and Mottram,Jeremy C. and Nelson,Siri and Ochaya,Stephen and Osoegawa,Kazutoyo and Pai,Grace and Parsons,Marilyn and Pentony,Martin and Pettersson,Ulf and Pop, Mihai and Ramirez,Jose Luis and Rinta,Joel and Robertson,Laura and Salzberg,Steven L. and Sanchez,Daniel O. and Seyler,Amber and Sharma,Reuben and Shetty,Jyoti and Simpson,Anjana J. and Sisk,Ellen and Tammi,Martti T. and Tarleton,Rick and Teixeira,Santuza and Van Aken,Susan and Vogt,Christy and Ward,Pauline N. and Wickstead,Bill and Wortman,Jennifer and White,Owen and Fraser,Claire M. and Stuart,Kenneth D. and Andersson,Bj{\"o}rn} } @article {16291, title = {The Genome Sequence of Trypanosoma Cruzi, Etiologic Agent of Chagas Disease}, journal = {ScienceScience}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {409 - 415}, abstract = {Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50\% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1112631}, url = {http://www.sciencemag.org/content/309/5733/409}, author = {El-Sayed, Najib M. and Myler,Peter J. and Bartholomeu,Daniella C. and Nilsson,Daniel and Aggarwal,Gautam and Tran,Anh-Nhi and Ghedin,Elodie and Worthey,Elizabeth A. and Delcher,Arthur L. and Blandin,Ga{\"e}lle and Westenberger,Scott J. and Caler,Elisabet and Cerqueira,Gustavo C. and Branche,Carole and Haas,Brian and Anupama,Atashi and Arner,Erik and {\r A}slund,Lena and Attipoe,Philip and Bontempi,Esteban and Bringaud,Fr{\'e}d{\'e}ric and Burton,Peter and Cadag,Eithon and Campbell,David A. and Carrington,Mark and Crabtree,Jonathan and Darban,Hamid and da Silveira,Jose Franco and de Jong,Pieter and Edwards,Kimberly and Englund,Paul T. and Fazelina,Gholam and Feldblyum,Tamara and Ferella,Marcela and Frasch,Alberto Carlos and Gull,Keith and Horn,David and Hou,Lihua and Huang,Yiting and Kindlund,Ellen and Klingbeil,Michele and Kluge,Sindy and Koo,Hean and Lacerda,Daniela and Levin,Mariano J. and Lorenzi,Hernan and Louie,Tin and Machado,Carlos Renato and McCulloch,Richard and McKenna,Alan and Mizuno,Yumi and Mottram,Jeremy C. and Nelson,Siri and Ochaya,Stephen and Osoegawa,Kazutoyo and Pai,Grace and Parsons,Marilyn and Pentony,Martin and Pettersson,Ulf and Pop, Mihai and Ramirez,Jose Luis and Rinta,Joel and Robertson,Laura and Salzberg,Steven L. and Sanchez,Daniel O. and Seyler,Amber and Sharma,Reuben and Shetty,Jyoti and Simpson,Anjana J. and Sisk,Ellen and Tammi,Martti T. and Tarleton,Rick and Teixeira,Santuza and Van Aken,Susan and Vogt,Christy and Ward,Pauline N. and Wickstead,Bill and Wortman,Jennifer and White,Owen and Fraser,Claire M. and Stuart,Kenneth D. and Andersson,Bj{\"o}rn} } @article {14616, title = {Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription}, journal = {Journal of VirologyJ. Virol.}, volume = {79}, year = {2005}, month = {2005/06/01/}, pages = {6610 - 6619}, abstract = {We have investigated regulatory sequences in noncoding human DNA that are associated with repression of an integrated human immunodeficiency virus type 1 (HIV-1) promoter. HIV-1 integration results in the formation of precise and homogeneous junctions between viral and host DNA, but integration takes place at many locations. Thus, the variation in HIV-1 gene expression at different integration sites reports the activity of regulatory sequences at nearby chromosomal positions. Negative regulation of HIV transcription is of particular interest because of its association with maintaining HIV in a latent state in cells from infected patients. To identify chromosomal regulators of HIV transcription, we infected Jurkat T cells with an HIV-based vector transducing green fluorescent protein (GFP) and separated cells into populations containing well-expressed (GFP-positive) or poorly expressed (GFP-negative) proviruses. We then determined the chromosomal locations of the two classes by sequencing 971 junctions between viral and cellular DNA. Possible effects of endogenous cellular transcription were characterized by transcriptional profiling. Low-level GFP expression correlated with integration in (i) gene deserts, (ii) centromeric heterochromatin, and (iii) very highly expressed cellular genes. These data provide a genome-wide picture of chromosomal features that repress transcription and suggest models for transcriptional latency in cells from HIV-infected patients.}, isbn = {0022-538X, 1098-5514}, doi = {10.1128/JVI.79.11.6610-6619.2005}, url = {http://jvi.asm.org/content/79/11/6610}, author = {Lewinski,M. K and Bisgrove,D. and Shinn,P. and Chen,H. and Hoffmann,C. and Hannenhalli, Sridhar and Verdin,E. and Berry,C. C and Ecker,J. R and Bushman,F. D} } @article {14566, title = {Genome-wide analysis of retroviral DNA integration}, journal = {Nat Rev MicroNat Rev Micro}, volume = {3}, year = {2005}, month = {2005/11//}, pages = {848 - 858}, isbn = {1740-1526}, doi = {10.1038/nrmicro1263}, url = {http://dx.doi.org/10.1038/nrmicro1263}, author = {Bushman,Frederic and Lewinski,Mary and Ciuffi,Angela and Barr,Stephen and Leipzig,Jeremy and Hannenhalli, Sridhar and Hoffmann,Christian} } @article {12934, title = {Global microbial ecology of Vibrio cholerae}, journal = {Oceans and health: pathogens in the marine environment}, year = {2005}, month = {2005///}, pages = {297 - 305}, abstract = {The disease cholera can no longer be considered a simple equation of bacteria and human host, but represents a complex network that includes global weather patterns, aquatic reservoirs, phages, zooplankton, collective behavior of surface-attached cells, an adaptable genome, and the deep sea inter alia. This interesting characterization emerges from a view of biological systems termed biocomplexity (Colwell, 2002a, b). The holistic approach to understanding cholera integrates contributions from experts in many fields, with multiple points of view, in models for prediction, prevention, and treatment of the disease that Vibrio cholerae causes. The spiral form shown in Figure 12.1 symbolizes the nonlinear manner in which the many parts of such a model interact. It also shows that these interactions often occur across many different scales.}, doi = {10.1007/0-387-23709-7_12}, author = {Rita R Colwell} } @article {13001, title = {Grid computing}, journal = {EDUCAUSE Review}, volume = {40}, year = {2005}, month = {2005///}, pages = {116 - 117}, author = {Cummings, Michael P. and Huskamp,J. C} } @article {17187, title = {Help! I{\textquoteright}m Lost: User Frustration in Web Navigation (2003)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {Computers can be valuable tools, and networked resources via the Internet can be beneficial to many different populations and communities. Unfortunately, when people are unable to reach their task goals due to frustrating experiences, this can hinder the effectiveness of technology. This research summary provides information about the user frustration research that has been performed at the University of Maryland and Towson University. Causes of user frustration are discussed in this research summary, along with the surprising finding that nearly one-third to one-half of the time spent in front of the computer is wasted due to frustrating experiences. Furthermore, when interfaces are planned to be deceptive and confusing, this}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6508}, author = {Lazar,Jonathan and Bessiere,Katie and Ceaparu,Irina and Robinson,John and Shneiderman, Ben} } @conference {16668, title = {The Hiero machine translation system: Extensions, evaluation, and analysis}, booktitle = {Proceedings of the conference on Human Language Technology and Empirical Methods in Natural Language Processing}, year = {2005}, month = {2005///}, pages = {779 - 786}, author = {Chiang,D. and Lopez,A. and Madnani,N. and Monz,C. and Resnik, Philip and Subotin,M.} } @article {12658, title = {Human action-recognition using mutual invariants}, journal = {Computer Vision and Image Understanding}, volume = {98}, year = {2005}, month = {2005/05//}, pages = {294 - 324}, abstract = {Static and temporally varying 3D invariants are proposed for capturing the spatio-temporal dynamics of a general human action to enable its representation in a compact, view-invariant manner. Two variants of the representation are presented and studied: (1) a restricted-3D version, whose theory and implementation are simple and efficient but which can be applied only to a restricted class of human action, and (2) a full-3D version, whose theory and implementation are more complex but which can be applied to any general human action. A detailed analysis of the two representations is presented. We show why a straightforward implementation of the key ideas does not work well in the general case, and present strategies designed to overcome inherent weaknesses in the approach. What results is an approach for human action modeling and recognition that is not only invariant to viewpoint, but is also robust enough to handle different people, different speeds of action (and hence, frame rate) and minor variabilities in a given action, while encoding sufficient distinction among actions. Results on 2D projections of human motion capture and on manually segmented real image sequences demonstrate the effectiveness of the approach.}, keywords = {Human action-recognition, Model based invariants, Mutual invariants, View invariance}, isbn = {1077-3142}, doi = {10.1016/j.cviu.2004.09.002}, url = {http://www.sciencedirect.com/science/article/pii/S107731420400147X}, author = {Parameswaran,Vasu and Chellapa, Rama} } @inbook {12677, title = {Image Sequence Stabilization, Mosaicking, and Superresolution}, booktitle = {Handbook of Image and Video Processing (Second Edition)Handbook of Image and Video Processing (Second Edition)}, year = {2005}, month = {2005///}, pages = {309-VII - 309-VII}, publisher = {Academic Press}, organization = {Academic Press}, address = {Burlington}, abstract = {A sequence of temporal images gathered from a single sensor adds a whole new dimension to two-dimensional (2D) image data. Availability of an image sequence permits the measurement of quantities such as subpixel intensities, camera motion and depth, and detection and tracking of moving objects. In turn, the processing of image sequences necessitates the development of sophisticated techniques to extract this information. With the recent availability of powerful yet inexpensive computers, data storage systems, and image acquisition devices, image sequence analysis has transitioned from an esoteric research domain to a practical area with significant commercial interest.}, isbn = {978-0-12-119792-6}, url = {http://www.sciencedirect.com/science/article/pii/B9780121197926500826}, author = {Chellapa, Rama and Srinivasan, S. and Aggarwal,G. and Veeraraghavan,A.}, editor = {Al Bovik} } @article {12660, title = {Image-based face recognition under illumination and pose variations}, journal = {Journal of the Optical Society of America AJ. Opt. Soc. Am. A}, volume = {22}, year = {2005}, month = {2005/02/01/}, pages = {217 - 229}, abstract = {We present an image-based method for face recognition across different illuminations and poses, where the term image-based means that no explicit prior three-dimensional models are needed. As face recognition under illumination and pose variations involves three factors, namely, identity, illumination, and pose, generalizations in all these three factors are desired. We present a recognition approach that is able to generalize in the identity and illumination dimensions and handle a given set of poses. Specifically, the proposed approach derives an identity signature that is illumination- and pose-invariant, where the identity is tackled by means of subspace encoding, the illumination is characterized with a Lambertian reflectance model, and the given set of poses is treated as a whole. Experimental results using the Pose, Illumination, and Expression (PIE) database demonstrate the effectiveness of the proposed approach.}, keywords = {illumination, pattern recognition}, doi = {10.1364/JOSAA.22.000217}, url = {http://josaa.osa.org/abstract.cfm?URI=josaa-22-2-217}, author = {Zhou,Shaohua Kevin and Chellapa, Rama} } @article {15555, title = {Improved approximation bounds for planar point pattern matching}, journal = {Algorithms and Data Structures}, year = {2005}, month = {2005///}, pages = {432 - 443}, abstract = {We consider the well known problem of matching two planar point sets under rigid transformations so as to minimize the directed Hausdorff distance. This is a well studied problem in computational geometry. Goodrich, Mitchell, and Orletsky [GMO94] presented a very simple approximation algorithm for this problem, which computes transformations based on aligning pairs of points. They showed that their algorithm achieves an approximation ratio of 4. We consider a minor modification to their algorithm, which is based on aligning midpoints rather than endpoints. We show that this algorithm achieves an approximation ratio not greater than 3.13. Our analysis is sensitive to the ratio between the diameter of the pattern set and the Hausdorff distance, and we show that the approximation ratio approaches 3 in the limit. Finally, we provide lower bounds that show that our approximation bounds are nearly tight.}, doi = {10.1007/11534273_38}, author = {Cho,M. and Mount, Dave} } @article {17228, title = {Improving Web-based Civic Information Access: A Case Study of the 50 US States (2002)}, year = {2005}, month = {2005///}, abstract = {An analysis of the home pages of all fifty U. S. states reveals great variety in key design features that influence efficacy. Some states had excessively large byte counts that would slow users connected by commonly-used 56K modems. Many web sites had low numbers of or poorly organized links that would make it hard for citizens to find what they were interested in. Features such as search boxes, privacy policies, online help, or contact information need to be added by several states. Our analysis concludes with ten recommendations and finds many further opportunities for individual states to improve their websites. However still greater benefits will come through collaboration among the states that would lead to consistency, appropriate tagging, and common tools.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6494}, author = {Ceaparu,Irina and Shneiderman, Ben} } @conference {12803, title = {An integrated framework for scenarios and state machines}, booktitle = {Integrated Formal Methods}, year = {2005}, month = {2005///}, pages = {366 - 385}, author = {Sengupta,B. and Cleaveland, Rance} } @article {17247, title = {Interactive Color Mosaic and Dendogram Displays for Signal/Noise Optimization in Microarray Data Analysis (2003)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {Data analysis and visualization is strongly influenced by noise and noise filters. There are multiple sources of oisein microarray data analysis, but signal/noise ratios are rarely optimized, or even considered. Here, we report a noise analysis of a novel 13 million oligonucleotide dataset - 25 human U133A (~500,000 features) profiles of patient muscle biposies. We use our recently described interactive visualization tool, the Hierarchical Clustering Explorer (HCE) to systemically address the effect of different noise filters on resolution of arrays into orrectbiological groups (unsupervised clustering into three patient groups of known diagnosis). We varied probe set interpretation methods (MAS 5.0, RMA), resent callfilters, and clustering linkage methods, and investigated the results in HCE. HCE interactive features enabled us to quickly see the impact of these three variables. Dendrogram displays showed the clustering results systematically, and color mosaic displays provided a visual support for the results. We show that each of these three variables has a strong effect on unsupervised clustering. For this dataset, the strength of the biological variable was maximized, and noise minimized, using MAS 5.0, 10\% present call filter, and Average Group Linkage. We propose a general method of using interactive tools to identify the optimal signal/noise balance or the optimal combination of these three variables to maximize the effect of the desired biological variable on data interpretation.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6506}, author = {Seo,Jinwook and Bakay,Marina and Zhao,Po and Chen,Yi-Wen and Clarkson,Priscilla and Shneiderman, Ben and Hoffman,Eric P} } @article {12675, title = {Interpretation of state sequences in HMM for activity representation}, journal = {Proc. IEEE Conf. Acoustic Speech and Signal Processing}, volume = {2}, year = {2005}, month = {2005///}, pages = {709 - 712}, abstract = {We propose a method for activity representation based on seman-tic events, using the HMM framework. For every time instant, the probability of event occurrence is computed by exploring a subset of state sequences. The idea is that while activity trajectories may have large variations at the data or the state levels, they may ex- hibit similarities at the event level. Our experiments show the ap- plication of these events to activity recognition in an office envi- ronment and to anomalous trajectory detection using surveillance video data. }, author = {Cuntoor, N.P. and Yegnanarayana,B. and Chellapa, Rama} } @conference {13198, title = {Kernel-based Bayesian filtering for object tracking}, booktitle = {Computer Vision and Pattern Recognition, 2005. CVPR 2005. IEEE Computer Society Conference on}, volume = {1}, year = {2005}, month = {2005/06//}, pages = {227 - 234 vol. 1 - 227 - 234 vol. 1}, abstract = {Particle filtering provides a general framework for propagating probability density functions in nonlinear and non-Gaussian systems. However, the algorithm is based on a Monte Carlo approach and sampling is a problematic issue, especially for high dimensional problems. This paper presents a new kernel-based Bayesian filtering framework, which adopts an analytic approach to better approximate and propagate density functions. In this framework, the techniques of density interpolation and density approximation are introduced to represent the likelihood and the posterior densities by Gaussian mixtures, where all parameters such as the number of mixands, their weight, mean, and covariance are automatically determined. The proposed analytic approach is shown to perform sampling more efficiently in high dimensional space. We apply our algorithm to real-time tracking problems, and demonstrate its performance on real video sequences as well as synthetic examples.}, keywords = {approach;, approximation;, Bayes, Bayesian, Carlo, density, detection;, filtering;, functions;, Gaussian, interpolation;, kernel-based, methods;, mixtures;, Monte, nonGaussian, nonlinear, object, particle, probability, probability;, processes;, recognition;, sampling, sampling;, sequences;, system;, tracking;, video}, doi = {10.1109/CVPR.2005.199}, author = {Han,Bohyung and Zhu,Ying and Comaniciu, D. and Davis, Larry S.} } @article {13006, title = {Magic bullets and golden rules: data sampling in molecular phylogenetics}, journal = {Zoology (Jena)}, volume = {108}, year = {2005}, month = {2005///}, pages = {329 - 336}, abstract = {Data collection for molecular phylogenetic studies is based on samples of both genes and taxa. In an ideal world, with no limitations to resources, as many genes could be sampled as deemed necessary to address phylogenetic problems. Given limited resources in the real world, inadequate (in terms of choice of genes or number of genes) sequences or restricted taxon sampling can adversely affect the reliability or information gained in phylogenetics. Recent empirical and simulation-based studies of data sampling in molecular phylogenetics have reached differing conclusions on how to deal with these problems. Some advocated sampling more genes, others more taxa. There is certainly no {\textquoteright}magic bullet{\textquoteright} that will fit all phylogenetic problems, and no specific {\textquoteright}golden rules{\textquoteright} have been deduced, other than that single genes may not always contain sufficient phylogenetic information. However, several general conclusions and suggestions can be made. One suggestion is that the determination of a multiple, but moderate number (e.g., 6-10) of gene sequences might take precedence over sequencing a larger set of genes and thereby permit the sampling of more taxa for a phylogenetic study.}, doi = {10.1016/j.zool.2005.09.006}, author = {Cummings, Michael P. and Meyer,A.} } @conference {12646, title = {Markerless Motion Capture using Multiple Cameras}, booktitle = {Computer Vision for Interactive and Intelligent Environment, 2005}, year = {2005}, month = {2005/11//}, pages = {15 - 26}, abstract = {Motion capture has important applications in different areas such as biomechanics, computer animation, and human-computer interaction. Current motion capture methods use passive markers that are attached to different body parts of the subject and are therefore intrusive in nature. In applications such as pathological human movement analysis, these markers may introduce an unknown artifact in the motion, and are, in general, cumbersome. We present computer vision based methods for performing markerless human motion capture. We model the human body as a set of super-quadrics connected in an articulated structure and propose algorithms to estimate the parameters of the model from video sequences. We compute a volume data (voxel) representation from the images and combine bottom-up approach with top down approach guided by our knowledge of the model. We propose a tracking algorithm that uses this model to track human pose. The tracker uses an iterative framework akin to an Iterated Extended Kalman Filter to estimate articulated human motion using multiple cues that combine both spatial and temporal information in a novel manner. We provide preliminary results using data collected from 8-16 cameras. The emphasis of our work is on models and algorithms that are able to scale with respect to the requirement for accuracy. Our ultimate objective is to build an end-to-end system that can integrate the above mentioned components into a completely automated markerless motion capture system.}, doi = {10.1109/CVIIE.2005.13}, author = {Sundaresan, A. and Chellapa, Rama} } @article {12645, title = {Matching shape sequences in video with applications in human movement analysis}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {27}, year = {2005}, month = {2005/12//}, pages = {1896 - 1909}, abstract = {We present an approach for comparing two sequences of deforming shapes using both parametric models and nonparametric methods. In our approach, Kendall{\textquoteright}s definition of shape is used for feature extraction. Since the shape feature rests on a non-Euclidean manifold, we propose parametric models like the autoregressive model and autoregressive moving average model on the tangent space and demonstrate the ability of these models to capture the nature of shape deformations using experiments on gait-based human recognition. The nonparametric model is based on dynamic time-warping. We suggest a modification of the dynamic time-warping algorithm to include the nature of the non-Euclidean space in which the shape deformations take place. We also show the efficacy of this algorithm by its application to gait-based human recognition. We exploit the shape deformations of a person{\textquoteright}s silhouette as a discriminating feature and provide recognition results using the nonparametric model. Our analysis leads to some interesting observations on the role of shape and kinematics in automated gait-based person authentication.}, keywords = {Automated;Photography;Reproducibility of Results;Sensitivity and Specificity;Subtraction Technique;Video Recording;, autoregressive moving average model;deforming shapes;dynamic time-warping;feature extraction;gait-based human recognition;human movement analysis;matching shape sequences;video;autoregressive moving average processes;feature extraction;image matching;imag, Biological;Models, Computer-Assisted;Imaging, Statistical;Movement;Pattern Recognition, Three-Dimensional;Leg;Models}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2005.246}, author = {A,Veeraraghavan and Roy-Chowdhury, A.K. and Chellapa, Rama} } @conference {12659, title = {A method for converting a smiling face to a neutral face with applications to face recognition}, booktitle = {Acoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP {\textquoteright}05). IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/03//}, pages = {ii/977 - ii/980 Vol. 2 - ii/977 - ii/980 Vol. 2}, abstract = {The human face displays a variety of expressions, like smile, sorrow, surprise, etc. All these expressions constitute nonrigid motions of various features of the face. These expressions lead to a significant change in the appearance of a facial image which leads to a drop in the recognition accuracy of a face-recognition system trained with neutral faces. There are other factors like pose and illumination which also lead to performance drops. Researchers have proposed methods to tackle the effects of pose and illumination; however, there has been little work on how to tackle expressions. We attempt to address the issue of expression invariant face-recognition. We present preprocessing steps for converting a smiling face to a neutral face. We expect that this would in turn make the vector in the feature space to be closer to the correct vector in the gallery, in an appearance-based face recognition. This conjecture is supported by our recognition results which demonstrate that the accuracy goes up if we include the expression-normalization block.}, keywords = {appearance-based, Expression, Face, face;, feature, invariant, motion;, neutral, nonrigid, normalization;, recognition;, smiling}, doi = {10.1109/ICASSP.2005.1415570}, author = {Ramachandran, M. and Zhou,S. K and Jhalani, D. and Chellapa, Rama} } @conference {14986, title = {Mitigating risk of data loss in preservation environments}, booktitle = {Mass Storage Systems and Technologies, 2005. Proceedings. 22nd IEEE / 13th NASA Goddard Conference on}, year = {2005}, month = {2005/04//}, pages = {39 - 48}, abstract = {Preservation environments manage digital records for time periods that are much longer than that of a single vendor product. A primary requirement is the preservation of the authenticity and integrity of the digital records while simultaneously minimizing the cost of long-term storage, as the data is migrated onto successive generations of technology. The emergence of low-cost storage hardware has made it possible to implement innovative software systems that minimize risk of data loss and preserve authenticity and integrity. This paper describes software mechanisms in use in current persistent archives and presents an example based upon the NARA research prototype persistent archive.}, keywords = {archives;, authentication;, authenticity;, computing;, data, databases;, digital, distributed, environment;, Grid, integrity;, management;, message, objects;, persistent, preservation, record, risk, storage}, doi = {10.1109/MSST.2005.20}, author = {Moore,R.W. and JaJa, Joseph F. and Chadduck,R.} } @article {13307, title = {Morse-Smale decompositions for modeling terrain knowledge}, journal = {Spatial Information Theory}, year = {2005}, month = {2005///}, pages = {426 - 444}, abstract = {In this paper, we describe, analyze and compare techniques for extracting spatial knowledge from a terrain model. Specifically, we investigate techniques for extracting a morphological representation from a terrain model based on an approximation of a Morse-Smale complex. A Morse-Smale complex defines a decomposition of a topographic surface into regions with vertices at the critical points and bounded by integral lines which connect passes to pits and peaks. This provides a terrain representation which encompasses the knowledge on the salient characteristics of the terrain. We classify the various techniques for computing a Morse-Smale complexe based on the underlying terrain model, a Regular Square Grid (RSG) or a Triangulated Irregular Network (TIN), and based on the algorithmic approach they apply. Finally, we discuss hierarchical terrain representations based on a Morse-Smale decomposition.}, doi = {10.1007/11556114_27}, author = {{\v C}omi{\'c},L. and De Floriani, Leila and Papaleo,L.} } @inbook {12670, title = {Moving Object Detection and Compression in IR Sequences}, booktitle = {Computer Vision Beyond the Visible SpectrumComputer Vision Beyond the Visible Spectrum}, series = {Advances in Pattern Recognition}, year = {2005}, month = {2005///}, pages = {141 - 165}, publisher = {Springer London}, organization = {Springer London}, abstract = {We consider the problem of remote surveillance using infrared (IR) sensors. The aim is to use IR image sequences to detect moving objects (humans or vehicles), and to transmit a few {\textquotedblleft}best-view images{\textquotedblright} of every new object that is detected. Since the available bandwidth is usually low, if the object chip is big, it needs to be compressed before being transmitted. Due to low computational power of computing devices attached to the sensor, the algorithms should be computationally simple. We present two approaches for object detection {\textemdash} one which specifically solves the more difficult long-range object detection problem, and the other for objects at short range. For objects at short range, we also present techniques for selecting a single best-view object chip and computationally simple techniques for compressing it to very low bit rates due to the channel bandwidth constraint. A fast image chip compression scheme implemented in the wavelet domain by combining a non-iterative zerotree coding method with 2D-DPCM for both low-and high-frequency subbands is presented. Comparisons with some existing schemes are also included. The object detection and compression algorithms have been implemented in C/C++ and their performance has been evaluated using the Hitachi{\textquoteright}s SH4 platform with software simulation.}, isbn = {978-1-84628-065-8}, url = {http://dx.doi.org/10.1007/1-84628-065-6_5}, author = {Vaswani,Namrata and Agrawal,Amit and Qinfen Zheng and Chellapa, Rama}, editor = {Bhanu,Bir and Pavlidis,Ioannis} } @conference {12665, title = {Moving Object Segmentation and Dynamic Scene Reconstruction Using Two Frames}, booktitle = {Acoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP {\textquoteright}05). IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005//18/23}, pages = {705 - 708}, keywords = {3D, analysis;, constraints;, dynamic, ego-motion, estimation;, flow, image, images;, independent, INTENSITY, least, mean, median, method;, methods;, model;, MOTION, motion;, moving, object, of, parallax, parallax;, parametric, processing;, reconstruction;, scene, segmentation;, signal, squares, squares;, static, structure;, subspace, surface, translational, two-frame, unconstrained, video}, doi = {10.1109/ICASSP.2005.1415502}, author = {Agrawala, Ashok K. and Chellapa, Rama} } @article {14027, title = {Neuromimetic sound representation for percept detection and manipulation}, journal = {EURASIP Journal on Applied Signal Processing}, volume = {9}, year = {2005}, month = {2005///}, pages = {1350 - 1350}, abstract = {The acoustic wave received at the ears is processed by the human auditory system to separate different sounds along the intensity,pitch, and timbre dimensions. Conventional Fourier-based signal processing, while endowed with fast algorithms, is unable to easily represent a signal along these attributes. In this paper, we discuss the creation of maximally separable sounds in auditory user interfaces and use a recently proposed cortical sound representation, which performs a biomimetic decomposition of an acoustic signal, to represent and manipulate sound for this purpose. We briefly overview algorithms for obtaining, manipulating, and inverting a cortical representation of a sound and describe algorithms for manipulating signal pitch and timbre separately. The algorithms are also used to create sound of an instrument between a {\textquotedblleft}guitar{\textquotedblright} and a {\textquotedblleft}trumpet.{\textquotedblright} Excellent sound quality can be achieved if processing time is not a concern, and intelligible signals can be reconstructed in reasonable processing time (about ten seconds of computational time for a one-second signal sampled at 8 kHz). Work on bringing the algorithms into the real-time processing domain is ongoing. }, author = {Zotkin,Dmitry N and Chi,T. and Shamma,S.A. and Duraiswami, Ramani} } @conference {12644, title = {Non-Stationary "Shape Activities"}, booktitle = {Decision and Control, 2005 and 2005 European Control Conference. CDC-ECC {\textquoteright}05. 44th IEEE Conference on}, year = {2005}, month = {2005/12//}, pages = {1521 - 1528}, abstract = {The changing configuration of a group of moving landmarks can be modeled as a moving and deforming shape. The landmarks defining the shape could be moving objects(people/vehicles/robots) or rigid components of an articulated shape like the human body. In past work, the term "shape activity" has been used to denote a particular stochastic model for shape deformation. Dynamical models have been proposed for characterizing stationary shape activities (assume constant mean shape). In this work we define stochastic dynamic models for non-stationary shape activities and show that the stationary shape activity model follows as a special case of this. Most activities performed by a group of moving landmarks (here, objects) are not stationary and hence this more general model is needed. We also define a piecewise stationary model with non-stationary transitions which can be used to segment out and track a sequence of activities. Noisy observations coming from these models can be tracked using a particle filter. We discuss applications of our framework to abnormal activity detection, tracking and activity sequence segmentation.}, doi = {10.1109/CDC.2005.1582374}, author = {Vaswani, N. and Chellapa, Rama} } @article {16399, title = {Path dependence and the validation of agent-based spatial models of land use}, journal = {International Journal of Geographical Information Science}, volume = {19}, year = {2005}, month = {2005///}, pages = {153 - 174}, author = {Corresponding,D.G.B. and Page,S and Riolo,R and Zellner,M and Rand, William} } @article {12933, title = {Pathogenic Vibrio species in the marine and estuarine environment}, journal = {Oceans and health: pathogens in the marine environment}, year = {2005}, month = {2005///}, pages = {217 - 252}, abstract = {The genus Vibrio includes more than 30 species, at least 12 of which are pathogenic to humans and/or have been associated with foodborne diseases (Chakraborty et al., 1997). Among these species, Vibrio cholerae, serogroups O1 and O139, are the most important, since they are associated with epidemic and pandemic diarrhea outbreaks in many parts of the world (Centers for Disease Control and Prevention, 1995; Kaper et al., 1995). However, other species of vibrios capable of causing diarrheal disease in humans have received greater attention in the last decade. These include Vibrio parahaemolyticus, a leading cause of foodborne disease outbreaks in Japan and Korea (Lee et al., 2001), Vibrio vulnificus, Vibrio alginolyticus, Vibrio damsela, Vibrio fluvialis, Vibrio furnissii, Vibrio hollisae, Vibrio metschnikovii, and Vibrio mimicus (Altekruse et al., 2000; H{\o}i et al., 1997). In the USA, Vibrio species have been estimated to be the cause of about 8000 illnesses annually (Mead et al., 1999).}, doi = {10.1007/0-387-23709-7_9}, author = {Pruzzo,C. and Huq,A. and Rita R Colwell and Donelli,G.} } @inbook {12676, title = {Pattern Recognition in Video}, booktitle = {Pattern Recognition and Machine IntelligencePattern Recognition and Machine Intelligence}, series = {Lecture Notes in Computer Science}, volume = {3776}, year = {2005}, month = {2005///}, pages = {11 - 20}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Images constitute data that live in a very high dimensional space, typically of the order of hundred thousand dimensions. Drawing inferences from correlated data of such high dimensions often becomes intractable. Therefore traditionally several of these problems like face recognition, object recognition, scene understanding etc. have been approached using techniques in pattern recognition. Such methods in conjunction with methods for dimensionality reduction have been highly popular and successful in tackling several image processing tasks. Of late, the advent of cheap, high quality video cameras has generated new interests in extending still image-based recognition methodologies to video sequences. The added temporal dimension in these videos makes problems like face and gait-based human recognition, event detection, activity recognition addressable. Our research has focussed on solving several of these problems through a pattern recognition approach. Of course, in video streams patterns refer to both patterns in the spatial structure of image intensities around interest points and temporal patterns that arise either due to camera motion or object motion. In this paper, we discuss the applications of pattern recognition in video to problems like face and gait-based human recognition, behavior classification, activity recognition and activity based person identification.}, isbn = {978-3-540-30506-4}, url = {http://dx.doi.org/10.1007/11590316_2}, author = {Chellapa, Rama and Veeraraghavan,Ashok and Aggarwal,Gaurav}, editor = {Pal,Sankar and Bandyopadhyay,Sanghamitra and Biswas,Sambhunath} } @inbook {12666, title = {Pose-Encoded Spherical Harmonics for Robust Face Recognition Using a Single Image}, booktitle = {Analysis and Modelling of Faces and GesturesAnalysis and Modelling of Faces and Gestures}, series = {Lecture Notes in Computer Science}, volume = {3723}, year = {2005}, month = {2005///}, pages = {229 - 243}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Face recognition under varying pose is a challenging problem, especially when illumination variations are also present. Under Lambertian model, spherical harmonics representation has proved to be effective in modelling illumination variations for a given pose. In this paper, we extend the spherical harmonics representation to encode pose information. More specifically, we show that 2D harmonic basis images at different poses are related by close-form linear combinations. This enables an analytic method for generating new basis images at a different pose which are typically required to handle illumination variations at that particular pose. Furthermore, the orthonormality of the linear combinations is utilized to propose an efficient method for robust face recognition where only one set of front-view basis images per subject is stored. In the method, we directly project a rotated testing image onto the space of front-view basis images after establishing the image correspondence. Very good recognition results have been demonstrated using this method.}, isbn = {978-3-540-29229-6}, url = {http://dx.doi.org/10.1007/11564386_18}, author = {Yue,Zhanfeng and Zhao,Wenyi and Chellapa, Rama}, editor = {Zhao,Wenyi and Gong,Shaogang and Tang,Xiaoou} } @article {12667, title = {Pose-normalized view synthesis from silhouettes}, journal = {IEEE Intl. Conf. on Acoustics, Speech, and Signal Processing (ICASSP)}, year = {2005}, month = {2005///}, abstract = {In this paper, we introduce an active view synthesis approachfrom silhouettes. With the virtual camera moving on a properly se- lected circular trajectory around an object of interest, we achieve a collection of virtual views of the object, which is equivalent to the case that the object is on a rotating turntable and captured by a static camera whose optical axis is parallel to the turntable. We show how to derive the virtual camera{\textquoteright}s extrinsic parameters at each position on the trajectory. Using the turning function dis- tance as the silhouette similarity measurement, this approach can be used to generate the desired pose-normalized images for recog- nition applications. }, author = {Yue, Z. and Chellapa, Rama} } @article {12769, title = {Probabilistic temporal logics via the modal mu-calculus}, journal = {Theoretical Computer Science}, volume = {342}, year = {2005}, month = {2005/09/07/}, pages = {316 - 350}, abstract = {This paper presents a mu-calculus-based modal logic for describing properties of reactive probabilistic labeled transition systems (RPLTSs) and develops a model-checking algorithm for determining whether or not states in finite-state RPLTSs satisfy formulas in the logic. The logic is based on the distinction between (probabilistic) {\^a}{\texteuro}{\oe}systems{\^a}{\texteuro} and (nonprobabilistic) {\^a}{\texteuro}{\oe}observations{\^a}{\texteuro}: using the modal mu-calculus, one may specify sets of observations, and the semantics of our logic then enable statements to be made about the measures of such sets at various system states. The logic may be used to encode a variety of probabilistic modal and temporal logics; in addition, the model-checking problem for it may be reduced to the calculation of solutions to systems of non-linear equations. Finally, the logic induces an equivalence on RPLTSs that coincides with accepted notions of probabilistic bisimulation in the literature.}, keywords = {Model-checking, Probabilistic bisimulation, Probabilistic temporal logic, Probabilistic transition systems, reactive systems}, isbn = {0304-3975}, doi = {10.1016/j.tcs.2005.03.048}, url = {http://www.sciencedirect.com/science/article/pii/S0304397505001829}, author = {Cleaveland, Rance and Iyer,S. Purushothaman and Narasimha,Murali} } @article {13206, title = {Real-time foreground-background segmentation using codebook model}, journal = {Real-time imaging}, volume = {11}, year = {2005}, month = {2005///}, pages = {172 - 185}, author = {Kim,K. and Chalidabhongse,T.H. and Harwood,D. and Davis, Larry S.} } @article {12663, title = {Recognition of Humans and Their Activities Using Video}, journal = {Synthesis Lectures on Image, Video, and Multimedia Processing}, volume = {1}, year = {2005}, month = {2005/01//}, pages = {1 - 173}, abstract = {The recognition of humans and their activities from video sequences is currently a very active area of research because of its applications in video surveillance, design of realistic entertainment systems, multimedia communications, and medical diagnosis. In this lecture, we discuss the use of face and gait signatures for human identification and recognition of human activities from video sequences. We survey existing work and describe some of the more well-known methods in these areas. We also describe our own research and outline future possibilities.In the area of face recognition, we start with the traditional methods for image-based analysis and then describe some of the more recent developments related to the use of video sequences, 3D models, and techniques for representing variations of illumination. We note that the main challenge facing researchers in this area is the development of recognition strategies that are robust to changes due to pose, illumination, disguise, and aging. Gait recognition is a more recent area of research in video understanding, although it has been studied for a long time in psychophysics and kinesiology. The goal for video scientists working in this area is to automatically extract the parameters for representation of human gait. We describe some of the techniques that have been developed for this purpose, most of which are appearance based. We also highlight the challenges involved in dealing with changes in viewpoint and propose methods based on image synthesis, visual hull, and 3D models. In the domain of human activity recognition, we present an extensive survey of various methods that have been developed in different disciplines like artificial intelligence, image processing, pattern recognition, and computer vision. We then outline our method for modeling complex activities using 2D and 3D deformable shape theory. The wide application of automatic human identification and activity recognition methods will require the fusion of different modalities like face and gait, dealing with the problems of pose and illumination variations, and accurate computation of 3D models. The last chapter of this lecture deals with these areas of future research. }, isbn = {1559-8136, 1559-8144}, doi = {10.2200/S00002ED1V01Y200508IVM001}, url = {http://www.morganclaypool.com/doi/abs/10.2200/S00002ED1V01Y200508IVM001}, author = {Chellapa, Rama and Roy-Chowdhury,Amit K. and Zhou,S. Kevin} } @inbook {16114, title = {Representing Unevenly-Spaced Time Series Data for Visualization and Interactive Exploration}, booktitle = {Human-Computer Interaction - INTERACT 2005Human-Computer Interaction - INTERACT 2005}, series = {Lecture Notes in Computer Science}, volume = {3585}, year = {2005}, month = {2005///}, pages = {835 - 846}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Visualizing time series is useful to support discovery of relations and patterns in financial, genomic, medical and other applications. Often, measurements are equally spaced over time. We discuss the challenges of unevenly-spaced time series and present fourrepresentationmethods: sampled events, aggregated sampled events, event index and interleaved event index. We developed these methods while studying eBay auction data with TimeSearcher. We describe the advantages, disadvantages, choices for algorithms and parameters, and compare the different methods for different tasks. Interaction issues such as screen resolution, response time for dynamic queries, and learnability are governed by these decisions.}, isbn = {978-3-540-28943-2}, url = {http://dx.doi.org/10.1007/11555261_66}, author = {Aris,Aleks and Shneiderman, Ben and Plaisant, Catherine and Shmueli,Galit and Jank,Wolfgang}, editor = {Costabile,Maria and Patern{\`o},Fabio} } @inbook {17656, title = {Scheduling on Unrelated Machines Under Tree-Like Precedence Constraints}, booktitle = {Approximation, Randomization and Combinatorial Optimization. Algorithms and TechniquesApproximation, Randomization and Combinatorial Optimization. Algorithms and Techniques}, series = {Lecture Notes in Computer Science}, volume = {3624}, year = {2005}, month = {2005///}, pages = {609 - 609}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present polylogarithmic approximations for the R | prec | C max and R | prec |∑ j w j C j problems, when the precedence constraints are {\textquotedblleft}treelike{\textquotedblright} {\textendash} i.e., when the undirected graph underlying the precedences is a forest. We also obtain improved bounds for the weighted completion time and flow time for the case of chains with restricted assignment {\textendash} this generalizes the job shop problem to these objective functions. We use the same lower bound of {\textquotedblleft}congestion+dilation{\textquotedblright}, as in other job shop scheduling approaches. The first step in our algorithm for the R | prec | C max problem with treelike precedences involves using the algorithm of Lenstra, Shmoys and Tardos to obtain a processor assignment with the congestion + dilation value within a constant factor of the optimal. We then show how to generalize the random delays technique of Leighton, Maggs and Rao to the case of trees. For the weighted completion time, we show a certain type of reduction to the makespan problem, which dovetails well with the lower bound we employ for the makespan problem. For the special case of chains, we show a dependent rounding technique which leads to improved bounds on the weighted completion time and new bicriteria bounds for the flow time.}, isbn = {978-3-540-28239-6}, url = {http://dx.doi.org/10.1007/11538462_13}, author = {Kumar, V. and Marathe,Madhav and Parthasarathy,Srinivasan and Srinivasan, Aravind}, editor = {Chekuri,Chandra and Jansen,Klaus and Rolim,Jos{\'e} and Trevisan,Luca} } @article {12775, title = {Secure requirements elicitation through triggered message sequence charts}, journal = {Distributed Computing and Internet Technology}, year = {2005}, month = {2005///}, pages = {273 - 282}, author = {Ray,A. and Sengupta,B. and Cleaveland, Rance} } @article {12647, title = {"Shape Activity": a continuous-state HMM for moving/deforming shapes with application to abnormal activity detection}, journal = {Image Processing, IEEE Transactions on}, volume = {14}, year = {2005}, month = {2005/10//}, pages = {1603 - 1616}, abstract = {The aim is to model "activity" performed by a group of moving and interacting objects (which can be people, cars, or different rigid components of the human body) and use the models for abnormal activity detection. Previous approaches to modeling group activity include co-occurrence statistics (individual and joint histograms) and dynamic Bayesian networks, neither of which is applicable when the number of interacting objects is large. We treat the objects as point objects (referred to as "landmarks") and propose to model their changing configuration as a moving and deforming "shape" (using Kendall{\textquoteright}s shape theory for discrete landmarks). A continuous-state hidden Markov model is defined for landmark shape dynamics in an activity. The configuration of landmarks at a given time forms the observation vector, and the corresponding shape and the scaled Euclidean motion parameters form the hidden-state vector. An abnormal activity is then defined as a change in the shape activity model, which could be slow or drastic and whose parameters are unknown. Results are shown on a real abnormal activity-detection problem involving multiple moving objects.}, keywords = {abnormal activity detection;activity recognition;co-occurrence statistics;continuous-state hidden Markov model;dynamic Bayesian networks;hidden-state vector;particle filtering;scaled Euclidean motion parameter;shape deforming;belief networks;filtering the, Automated;Subtraction Technique;Video Recording;, Biological;Models, Computer-Assisted;Information Storage and Retrieval;Markov Chains;Models, Statistical;Movement;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2005.852197}, author = {Vaswani, N. and Roy-Chowdhury, A.K. and Chellapa, Rama} } @article {17841, title = {A simulation and data analysis system for large-scale, data-driven oil reservoir simulation studies}, journal = {Concurrency and Computation: Practice and Experience}, volume = {17}, year = {2005}, month = {2005///}, pages = {1441 - 1467}, author = {Kurc, T. and Catalyurek,U. and Zhang,X. and Saltz, J. and Martino,R. and Wheeler,M. and Peszy{\'n}ska,M. and Sussman, Alan and Hansen,C. and Sen,M. and others} } @article {17368, title = {Social and Psychological Influences on Computer User Frustration (Newhagen book chapter, 2002)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {As computer usage has proliferated, so has user frustration. Even devoted and knowledgeable users encounter annoying delays, incomprehensible messages, incompatible files, and indecipherable menus. The frustration generated by these problems can be personally disturbing and socially disruptive. Psychological and social perspectives on frustration may clarify the relationships among variables such as personality types, cultural factors, goal attainment, workplace anger, and computer anxiety. These perspectives may also help designers, managers, and users understand the range of responses to frustration, which could lead to effective interventions such as redesign of software, improved training, better online help, user discipline, and even resetting of national research priorities.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6497}, author = {Bessiere,Katie and Ceaparu,Irina and Lazar,Jonathan and Robinson,John and Shneiderman, Ben} } @article {12654, title = {Statistical bias in 3-D reconstruction from a monocular video}, journal = {Image Processing, IEEE Transactions on}, volume = {14}, year = {2005}, month = {2005/08//}, pages = {1057 - 1062}, abstract = {The present state-of-the-art in computing the error statistics in three-dimensional (3-D) reconstruction from video concentrates on estimating the error covariance. A different source of error which has not received much attention is the fact that the reconstruction estimates are often significantly statistically biased. In this paper, we derive a precise expression for the bias in the depth estimate, based on the continuous (differentiable) version of structure from motion (SfM). Many SfM algorithms, or certain portions of them, can be posed in a linear least-squares (LS) framework Ax=b. Examples include initialization procedures for bundle adjustment or algorithms that alternately estimate depth and camera motion. It is a well-known fact that the LS estimate is biased if the system matrix A is noisy. In SfM, the matrix A contains point correspondences, which are always difficult to obtain precisely; thus, it is expected that the structure and motion estimates in such a formulation of the problem would be biased. Existing results on the minimum achievable variance of the SfM estimator are extended by deriving a generalized Cramer-Rao lower bound. A detailed analysis of the effect of various camera motion parameters on the bias is presented. We conclude by presenting the effect of bias compensation on reconstructing 3-D face models from rendered images.}, keywords = {3D face models, 3D video reconstruction, algorithms, artifacts, Artificial intelligence, Automated;Signal Processing, bias compensation, bundle adjustment, camera motion estimation, Computer simulation, Computer-Assisted;Imaging, Computer-Assisted;Subtraction Technique;Video Recording;, depth estimate, error covariance estimation, error statistics, generalized Cramer-Rao lower bound, Image Enhancement, Image Interpretation, Image reconstruction, initialization procedures, least squares approximations, linear least-squares framework, monocular video, motion compensation, Motion estimation, statistical bias, Statistical;Pattern Recognition, structure from motion algorithms, Three-Dimensional;Information Storage and Retrieval;Models, video signal processing}, isbn = {1057-7149}, doi = {10.1109/TIP.2005.849775}, author = {Roy-Chowdhury, A.K. and Chellapa, Rama} } @article {12668, title = {Synthesis of novel views of moving objects in airborne video}, journal = {Proc. British Machine Vision Conference}, year = {2005}, month = {2005///}, pages = {290 - 299}, abstract = {This paper presents a method for synthesizing novel views of movingobjects in airborne video. The object of interest is tracked using an appear- ance based visual tracking method. The on-object point correspondence is then built and used to estimate the homography induced by the ground plane. With known camera focal length, the surface normal to the ground plane and the camera motion between two views are factored out from the homography. In order to assure robustness of surface normal estimation, a rank one con- straint is applied to decompose a matrix which contains the homographies from multiple frame pairs. Given a desired viewing direction, the novel im- age of the object is generated by warping the reference frame using the new homography between the desired viewpoint and the reference frame. Exper- imental results show that the method is robust and errors due to small depth variations of the object is negligible. }, author = {Yue, Z. and Chellapa, Rama} } @article {12932, title = {Temperature-Driven Campylobacter Seasonality in England and Wales}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {71}, year = {2005}, month = {2005/01/01/}, pages = {85 - 92}, abstract = {Campylobacter incidence in England and Wales between 1990 and 1999 was examined in conjunction with weather conditions. Over the 10-year interval, the average annual rate was determined to be 78.4 {\textpm} 15.0 cases per 100,000, with an upward trend. Rates were higher in males than in females, regardless of age, and highest in children less than 5 years old. Major regional differences were detected, with the highest rates in Wales and the southwest and the lowest in the southeast. The disease displayed a seasonal pattern, and increased campylobacter rates were found to be correlated with temperature. The most marked seasonal effect was observed for children under the age of 5. The seasonal pattern of campylobacter infections indicated a linkage with environmental factors rather than food sources. Therefore, public health interventions should not be restricted to food-borne approaches, and the epidemiology of the seasonal peak in human campylobacter infections may best be understood through studies in young children.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.71.1.85-92.2005}, url = {http://aem.asm.org/content/71/1/85}, author = {Louis,Val{\'e}rie R. and Gillespie,Iain A. and O{\textquoteright}Brien,Sarah J. and Russek-Cohen,Estelle and Pearson,Andrew D. and Rita R Colwell} } @article {12671, title = {Tracking Algorithm Using Background-Foreground Motion Models and Multiple Cues}, journal = {ICASSP apos}, year = {2005}, month = {2005///}, pages = {233 - 236}, abstract = {We present a stochastic tracking algorithm for surveillance videoswhere targets are dim and of low resolution. Our tracker is mainly based on the particle filter algorithm. Two important novel fea- tures of the tracker include: A motion model consisting of both background and foreground motion parameters is built. Multiple cues are adaptively integrated in a system observation model when estimating the likelihood functions. Based on these features, the accuracy and robustness of the tracker has been improved, which is very important for surveillance problems. We present the results of applying the proposed algorithm to many videos. }, author = {Shao, J. and Zhou,S. K and Chellapa, Rama} } @conference {12652, title = {Tracking objects in video using motion and appearance models}, booktitle = {Image Processing, 2005. ICIP 2005. IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/09//}, pages = {II - 394-7 - II - 394-7}, abstract = {This paper proposes a visual tracking algorithm that combines motion and appearance in a statistical framework. It is assumed that image observations are generated simultaneously from a background model and a target appearance model. This is different from conventional appearance-based tracking, that does not use motion information. The proposed algorithm attempts to maximize the likelihood ratio of the tracked region, derived from appearance and background models. Incorporation of motion in appearance based tracking provides robust tracking, even when the target violates the appearance model. We show that the proposed algorithm performs well in tracking targets efficiently over long time intervals.}, keywords = {algorithm;, analysis;, appearance, background, estimation;, image, likelihood, maximum, model;, models;, MOTION, object, processing;, signal, target, tracking, tracking;, video, visual}, doi = {10.1109/ICIP.2005.1530075}, author = {Sankaranarayanan,A. C and Chellapa, Rama and Qinfen Zheng} } @article {14072, title = {Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock}, journal = {Environmental Microbiology}, volume = {7}, year = {2005}, month = {2005/06/01/}, pages = {789 - 797}, abstract = {Temperature shock of the hyperthermophilic methanarchaeon Methanococcus jannaschii from its optimal growth temperature of 85{\textdegree}C to 65{\textdegree}C and 95{\textdegree}C resulted in different transcriptional responses characteristic of both the direction of shock (heat or cold shock) and whether the shock was lethal. Specific outcomes of lethal heat shock to 95{\textdegree}C included upregulation of genes encoding chaperones, and downregulation of genes encoding subunits of the H+ transporting ATP synthase. A gene encoding an α subunit of a putative prefoldin was also upregulated, which may comprise a novel element in the protein processing pathway in M. jannaschii. Very different responses were observed upon cold shock to 65{\textdegree}C. These included upregulation of a gene encoding an RNA helicase and other genes involved in transcription and translation, and upregulation of genes coding for proteases and transport proteins. Also upregulated was a gene that codes for an 18~kDa FKBP-type PPIase, which may facilitate protein folding at low temperatures. Transcriptional profiling also revealed several hypothetical proteins that respond to temperature stress conditions.}, isbn = {1462-2920}, doi = {10.1111/j.1462-2920.2005.00751.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2005.00751.x/abstract}, author = {Boonyaratanakornkit,Boonchai B and Simpson,Anjana J. and Whitehead,Timothy A and Fraser,Claire M. and El-Sayed, Najib M. and Clark,Douglas S} } @conference {12657, title = {UMD Experiments with FRGC Data}, booktitle = {Computer Vision and Pattern Recognition - Workshops, 2005. CVPR Workshops. IEEE Computer Society Conference on}, year = {2005}, month = {2005/06//}, pages = {172 - 172}, abstract = {Although significant work has been done in the field of face recognition, the performance of state-of-the art face recognition algorithms is not good enough to be effective in operational systems. Though most algorithms work well for controlled images, they are quite susceptible to changes in illumination and pose. Face Recognition Grand Challenge (FRGC) is an effort to examine such issues to suitably guide future research in the area. This paper describes the efforts made at UMD in this direction. We present our results on several experiments suggested in FRGC. We believe that though pattern classification techniques play an extremely significant role in automatic face recognition under controlled conditions, physical modeling is required to generalize across varying situations. Accordingly, we describe a generative approach to recognize faces across varying illumination. Unlike most current methods, our method does not ignore shadows. Instead we use them to our benefit by modeling attached shadows in our formulation.}, doi = {10.1109/CVPR.2005.586}, author = {Aggarwal,G. and Biswas,S. and Chellapa, Rama} } @article {15087, title = {Universally composable password-based key exchange}, journal = {Advances in Cryptology{\textendash}Eurocrypt 2005}, year = {2005}, month = {2005///}, pages = {557 - 557}, abstract = {We propose and realize a definition of security for password-based key exchange within the framework of universally composable (UC) security, thus providing security guarantees under arbitrary composition with other protocols. In addition, our definition captures some aspects of the problem that were not adequately addressed by most prior notions. For instance, it does not assume any underlying probability distribution on passwords, nor does it assume independence between passwords chosen by different parties. We also formulate a definition of password-based secure channels, and show that such a definition is achievable given password-based key exchange.Our protocol realizing the new definition of password-based key exchange is in the common reference string model and relies on standard number-theoretic assumptions. The components of our protocol can be instantiated to give a relatively efficient solution which is conceivably usable in practice. We also show that it is impossible to satisfy our definition in the {\textquotedblleft}plain{\textquotedblright} model (e.g., without a common reference string). }, doi = {10.1007/11426639_24}, author = {Canetti,R. and Halevi,S. and Katz, Jonathan and Lindell,Y. and MacKenzie,P.} } @article {17465, title = {User Frustration with Technology in the Workplace (2004)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {When hard to use computers cause users to become frustrated, it can affect workplace productivity, user mood, and interactions with other co-workers. Previous research has examined the frustration that graduate students and their families face in using computers. To learn more about the causes and effects of user frustration with computers in the workplace, we collected modified time diaries from 50 workplace users, who spent an average of 5.1 hours on the computer. In this experiment, users reported wasting on average, 42-43\% of their time on the computer due to frustrating experiences. The causes of the frustrating experiences, the time lost due to the frustrating experiences, and the effects of the frustrating experiences on the mood of the users are discussed in this paper. Implications for designers, managers, users, information technology staff, and policymakers are discussed.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6515}, author = {Lazar,Jonathan and Jones,Adam and Bessiere,Katie and Ceaparu,Irina and Shneiderman, Ben} } @article {12431, title = {Using Iterative Strategies for Aligning Attributed Points in Space}, volume = {ISR-TR-2005-2}, year = {2005}, month = {2005///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {Signatures based on shape features are expected to be useful for several similarity assessment applications. Such signatures can extract the relevant shape information needed for similarity assessment and ignore the shape information not needed for a particular application.

Since different feature-based models are created in different coordinate systems, in order to compute distance between two sets of features, one needs to include geometric transformations for aligning features. Optimal alignment is the alignment that results in the minimum distance between two sets of features. In general, features can be viewed as attributed points in space. Hence, we need to develop techniques for aligning attributed points in space.

This report introduces iterative strategies for optimally aligning attributed points in space. Iterative strategies presented in this report involve successively applying algorithms that perform alignment under restricted rigid body transformations (e.g., rotations only or translations only) to solve point alignment problems that require higher dimension transformations (e.g., combinations rotations and translations). Our preliminary experimental results show that the idea of using of iterative strategies to solve higher dimension attributed point alignment problems is promising and can be used to perform feature-based shape similarity assessment.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/6467}, author = {Cardone, Antonio and Gupta, Satyandra K. and Mount, Dave} } @inbook {16108, title = {Visualizing Missing Data: Graph Interpretation User Study}, booktitle = {Human-Computer Interaction - INTERACT 2005}, series = {Lecture Notes in Computer Science}, volume = {3585}, year = {2005}, month = {2005///}, pages = {861 - 872}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Most visualization tools fail to provide support for missing data. In this paper, we identify sources of missing data and describe three levels of impact missing data can have on the visualization: perceivable, invisible or propagating. We then report on a user study with 30 participants that compared three design variants. A between-subject graph interpretation study provides strong evidence for the need of indicating the presence of missing information, and some direction for addressing the problem.}, isbn = {978-3-540-28943-2}, url = {http://dx.doi.org/10.1007/11555261_68}, author = {Eaton,Cyntrica and Plaisant, Catherine and Drizd,Terence}, editor = {Costabile,Maria and Patern{\`o},Fabio} } @conference {12706, title = {3D model refinement using surface-parallax}, booktitle = {Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP {\textquoteright}04). IEEE International Conference on}, volume = {3}, year = {2004}, month = {2004/05//}, pages = {iii - 285-8 vol.3 - iii - 285-8 vol.3}, abstract = {We present an approach to update and refine coarse 3D models of urban environments from a sequence of intensity images using surface parallax. This generalizes the plane-parallax recovery methods to surface-parallax using arbitrary surfaces. A coarse and potentially incomplete depth map of the scene obtained from a digital elevation map (DEM) is used as a reference surface which is refined and updated using this approach. The reference depth map is used to estimate the camera motion and the motion of the 3D points on the reference surface is compensated. The resulting parallax, which is an epipolar field, is estimated using an adaptive windowing technique and used to obtain the refined depth map.}, keywords = {3D, adaptive, arbitrary, camera, coarse, compensation;, Computer, DEM;, depth, digital, ELEVATION, environments;, epipolar, estimation;, field;, image, incomplete, INTENSITY, map;, model, MOTION, parallax;, plane-parallax, reconstruction;, recovery;, refinement;, sequence;, sequences;, surface, surfaces;, urban, vision;, windowing;}, doi = {10.1109/ICASSP.2004.1326537}, author = {Agrawala, Ashok K. and Chellapa, Rama} } @article {12713, title = {3d modelling of human motion using kinematic chains and multiple cameras for tracking}, journal = {Proc. of Eighth International Symposium on the}, year = {2004}, month = {2004///}, author = {Sundaresan, A. and RoyChowdhury, A. and Chellapa, Rama} } @conference {12978, title = {Abstracting workflows: unifying bioinformatics task conceptualization and specification through Semantic Web services}, booktitle = {W3C Workshop on Semantic Web for Life Sciences}, year = {2004}, month = {2004///}, address = {Cambridge, Massachusetts USA}, author = {Hashmi,N. and Lee,S. and Cummings, Michael P.} } @article {12941, title = {Acinetobacter lipases: molecular biology, biochemical properties and biotechnological potential}, journal = {Journal of industrial microbiology \& biotechnology}, volume = {31}, year = {2004}, month = {2004///}, pages = {391 - 400}, abstract = {Lipases (EC 3.1.1.3) have received increased attention recently, evidenced by the increasing amount of information about lipases in the current literature. The renewed interest in this enzyme class is due primarily to investigations of their role in pathogenesis and their increasing use in biotechnological applications [38]. Also, many microbial lipases are available as commercial products, the majority of which are used in detergents, cosmetic production, food flavoring, and organic synthesis. Lipases are valued biocatalysts because they act under mild conditions, are highly stable in organic solvents, show broad substrate specificity, and usually show high regio- and/or stereo-selectivity in catalysis. A number of lipolytic strains of Acinetobacter have been isolated from a variety of sources and their lipases possess many biochemical properties similar to those that have been developed for biotechnological applications. This review discusses the biology of lipase expression in Acinetobacter, with emphasis on those aspects relevant to potential biotechnology applications.}, doi = {10.1007/s10295-004-0167-0}, author = {Snellman,E. A. and Rita R Colwell} } @inbook {15129, title = {Adaptively-Secure, Non-Interactive Public-Key Encryption}, booktitle = {Model reduction methods for vector autoregressive processes}, year = {2004}, month = {2004///}, pages = {150 - 150}, author = {Canetti,R. and Halevi,S. and Katz, Jonathan} } @article {12710, title = {Appearance tracking using adaptive models in a particle filter}, journal = {Proc. of 6th Asian Conference on Computer Vision (ACCV)}, year = {2004}, month = {2004///}, abstract = {The particle filter is a popular tool for visual tracking. Usually, the appearance model is eitherfixed or rapidly changing and the motion model is simply a random walk with fixed noise vari- ance. Also, the number of particles used is typically fixed. All these factors make the visual tracker unstable. To stabilize the tracker, we propose the following measures: an observation model arising from an adaptive noise variance, and adaptive number of particles. The adaptive- velocity is computed via a first-order linear predictor using the previous particle configuration. Tracking under occlusion is accomplished using robust statistics. Experimental results on track- ing visual objects in long video sequences such as vehicles, tank, and human faces demonstrate the effectiveness and robustness of our algorithm. }, author = {Zhou, S. and Chellapa, Rama and Moghaddam, B.} } @conference {12703, title = {Appearance-based tracking and recognition using the 3D trilinear tensor}, booktitle = {Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP {\textquoteright}04). IEEE International Conference on}, volume = {3}, year = {2004}, month = {2004/05//}, pages = {iii - 613-16 vol.3 - iii - 613-16 vol.3}, abstract = {The paper presents an appearance-based adaptive algorithm for simultaneous tracking and recognition by generalizing the transformation model to 3D perspective transformation. A trilinear tensor operator is used to represent the 3D geometrical structure. The tensor is estimated by predicting the corresponding points using the existing affine-transformation based algorithm. The estimated tensor is used to synthesize novel views to update the appearance templates. Some experimental results using airborne video are presented.}, keywords = {3D, adaptive, affine-transformation, airborne, algorithm;, appearance, appearance-based, based, estimation;, geometrical, image, mathematical, novel, object, operator;, operators;, perspective, prediction;, processing;, recognition;, representation;, signal, structure, synthesis;, template, tensor, tensor;, tensors;, tracking;, transformation;, trilinear, updating;, video, video-based, video;, view}, doi = {10.1109/ICASSP.2004.1326619}, author = {Jie Shao and Zhou,S. K and Chellapa, Rama} } @article {12979, title = {Applying permutation tests to tree-based statistical models: extending the R package rpart}, volume = {2004-24}, year = {2004}, month = {2004///}, institution = {University of Maryland Institute for Advanced Computer Studies}, abstract = {Tree-based statistical models are useful for evaluating relationships between predictor and response variables and for generating predictions when the response is unknown. However, current methods of constructing tree-based models do not provide a probabilistic assessment of the models produced. Here we describe our work to use permutation tests to quantitatively estimate the probability of tree-based statistical models. We have extended the rpart (recursive partitioning) package of the R system for statistical data analysis. This extension, rpart.permutation, executes the permutations in parallel, using MPI (Message Passing Interface) to greatly decrease the time necessary to complete the analysis.}, author = {Cummings, Michael P. and Myers,D. S and Mangelson,M} } @conference {14811, title = {Automated cluster-based Web service performance tuning}, booktitle = {13th IEEE International Symposium on High performance Distributed Computing, 2004. Proceedings}, year = {2004}, month = {2004/06/04/6}, pages = {36 - 44}, publisher = {IEEE}, organization = {IEEE}, abstract = {Active harmony provides a way to automate performance tuning. We apply the Active Harmony system to improve the performance of a cluster-based web service system. The performance improvement cannot easily be achieved by tuning individual components for such a system. The experimental results show that there is no single configuration for the system that performs well for all kinds of workloads. By tuning the parameters, Active Harmony helps the system adapt to different workloads and improve the performance up to 16\%. For scalability, we demonstrate how to reduce the time when tuning a large system with many tunable parameters. Finally an algorithm is proposed to automatically adjust the structure of cluster-based web systems, and the system throughput is improved up to 70\% using this technique.}, keywords = {Active Harmony system, automated performance tuning, business, cluster-based Web service system, Clustering algorithms, Computer science, Educational institutions, electronic commerce, Internet, Middleware, performance evaluation, scalability, Throughput, Transaction databases, Web server, Web services, workstation clusters}, isbn = {0-7695-2175-4}, doi = {10.1109/HPDC.2004.1323484}, author = {Chung,I. -H and Hollingsworth, Jeffrey K} } @conference {13213, title = {Background modeling and subtraction by codebook construction}, booktitle = {Image Processing, 2004. ICIP {\textquoteright}04. 2004 International Conference on}, volume = {5}, year = {2004}, month = {2004/10//}, pages = {3061 - 3064 Vol. 5 - 3061 - 3064 Vol. 5}, abstract = {We present a new fast algorithm for background modeling and subtraction. Sample background values at each pixel are quantized into codebooks which represent a compressed form of background model for a long image sequence. This allows us to capture structural background variation due to periodic-like motion over a long period of time under limited memory. Our method can handle scenes containing moving backgrounds or illumination variations (shadows and highlights), and it achieves robust detection for compressed videos. We compared our method with other multimode modeling techniques.}, keywords = {(signal);, analysis;, background, codebook, coding;, colour, compression;, construction;, data, image, modeling, modeling;, MOTION, multimode, quantisation, representation;, sequence;, sequences;, subtraction;, technique;, video}, doi = {10.1109/ICIP.2004.1421759}, author = {Kim,Kyungnam and Chalidabhongse,T.H. and Harwood,D. and Davis, Larry S.} } @article {12689, title = {Bayesian self-calibration of a moving camera}, journal = {Computer Vision and Image Understanding}, volume = {95}, year = {2004}, month = {2004/09//}, pages = {287 - 316}, abstract = {In this paper, a Bayesian self-calibration approach using sequential importance sampling (SIS) is proposed. Given a set of feature correspondences tracked through an image sequence, the joint posterior distributions of both camera extrinsic and intrinsic parameters as well as the scene structure are approximated by a set of samples and their corresponding weights. The critical motion sequences are explicitly considered in the design of the algorithm. The probability of the existence of the critical motion sequence is inferred from the sample and weight set obtained from the SIS procedure. No initial guess for the calibration parameters is required. The proposed approach has been extensively tested on both synthetic and real image sequences and satisfactory performance has been observed.}, keywords = {self-calibration, Sequential Monte Carlo methods, structure from motion, video analysis}, isbn = {1077-3142}, doi = {10.1016/j.cviu.2004.03.009}, url = {http://www.sciencedirect.com/science/article/pii/S1077314204000396}, author = {Qian,Gang and Chellapa, Rama} } @article {12973, title = {A book like its cover}, journal = {Heredity}, volume = {93}, year = {2004}, month = {2004/08/01/}, pages = {234 - 235}, abstract = {An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News \& Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field.}, keywords = {animal and plant breeding, biometrical and statistical genetics, cytogenetics, ecological, eukaryotes, Genetics, Genomics, human population genetics, population and evolutionary genetics, post-genomics}, isbn = {0018-067X}, doi = {10.1038/sj.hdy.6800475}, url = {http://www.nature.com/hdy/journal/v93/n2/full/6800475a.html}, author = {Cummings, Michael P.} } @conference {14774, title = {Challenges in Measuring HPCS Learner Productivity in an Age of Ubiquitous Computing: The HPCS Program}, booktitle = {In Proceedings of ICSE Workshop on High Productivity Computing. May 2004}, year = {2004}, month = {2004///}, author = {Asgari, S. and Basili, Victor R. and Carver, J. and Hochstein, L. and Hollingsworth, Jeffrey K and Zelkowitz, Marvin V} } @article {14852, title = {Characterization of human faces under illumination variations using rank, integrability, and symmetry constraints}, journal = {Computer Vision-ECCV 2004}, year = {2004}, month = {2004///}, pages = {588 - 601}, abstract = {Photometric stereo algorithms use a Lambertian reflectance model with a varying albedo field and involve the appearances of only one object. This paper extends photometric stereo algorithms to handle all the appearances of all the objects in a class, in particular the class of human faces. Similarity among all facial appearances motivates a rank constraint on the albedos and surface normals in the class. This leads to a factorization of an observation matrix that consists of exemplar images of different objects under different illuminations, which is beyond what can be analyzed using bilinear analysis. Bilinear analysis requires exemplar images of different objects under same illuminations. To fully recover the class-specific albedos and surface normals, integrability and face symmetry constraints are employed. The proposed linear algorithm takes into account the effects of the varying albedo field by approximating the integrability terms using only the surface normals. As an application, face recognition under illumination variation is presented. The rank constraint enables an algorithm to separate the illumination source from the observed appearance and keep the illuminant-invariant information that is appropriate for recognition. Good recognition results have been obtained using the PIE dataset.}, doi = {10.1007/978-3-540-24670-1_45}, author = {Zhou, S. and Chellapa, Rama and Jacobs, David W.} } @article {15078, title = {Chosen-ciphertext security from identity-based encryption}, journal = {Advances in Cryptology-Eurocrypt 2004}, year = {2004}, month = {2004///}, pages = {207 - 222}, abstract = {We propose a simple and efficient construction of a CCA-secure public-key encryption scheme from any CPA-secure identity-based encryption (IBE) scheme. Our construction requires the underlying IBE scheme to satisfy only a relatively {\textquotedblleft}weak{\textquotedblright} notion of security which is known to be achievable without random oracles; thus, our results provide a new approach for constructing CCA-secure encryption schemes in the standard model. Our approach is quite different from existing ones; in particular, it avoids non-interactive proofs of {\textquotedblleft}well-formedness{\textquotedblright} which were shown to underlie most previous constructions. Furthermore, applying our conversion to some recently-proposed IBE schemes results in CCA-secure schemes whose efficiency makes them quite practical.Our technique extends to give a simple and reasonably efficient method for securing any binary tree encryption (BTE) scheme against adaptive chosen-ciphertext attacks. This, in turn, yields more efficient CCA-secure hierarchical identity-based and forward-secure encryption schemes in the standard model. }, doi = {10.1007/978-3-540-24676-3_13}, author = {Canetti,R. and Halevi,S. and Katz, Jonathan} } @conference {12693, title = {Classification probability analysis of principal component space analysis}, booktitle = {Pattern Recognition, 2004. ICPR 2004. Proceedings of the 17th International Conference on}, volume = {1}, year = {2004}, month = {2004/08//}, pages = {240 - 243 Vol.1 - 240 - 243 Vol.1}, abstract = {In a previous paper, we have presented a new linear classification algorithm, principal component space analysis (PCNSA) which is designed for problems like object recognition where different classes have unequal and non-white noise covariance matrices. PCNSA first obtains a principal components space (PCA space) for the entire data and in this PCA space, it finds for each class "i", an Mi dimensional subspace along which the class{\textquoteright}s intra-class variance is the smallest. We call this subspace an approximate space (ANS) since the lowest variance is usually "much smaller" than the highest. A query is classified into class "i" if its distance from the class{\textquoteright}s mean in the class{\textquoteright}s ANS is a minimum. In this paper, we discuss the PCNSA algorithm more precisely and derive tight upper bounds on its classification error probability. We use these expressions to compare classification performance of PCNSA with that of subspace linear discriminant analysis (SLDA).}, keywords = {algorithm;, analysis;, approximate, classification, classification;, component, covariance, discriminant, error, intraclass, linear, matrices;, matrix;, noise;, nonwhite, object, pattern, PCA;, principal, probability;, recognition;, space, space;, statistics;, subspace, variance;}, doi = {10.1109/ICPR.2004.1334068}, author = {Vaswani, N. and Chellapa, Rama} } @conference {12716, title = {Contour-based 3D Face Modeling from a Monocular Video}, booktitle = {Proceedings of the British Machine Vision Conference}, year = {2004}, month = {2004///}, pages = {39.1-39.10 - 39.1-39.10}, publisher = {British Machine Vision Association}, organization = {British Machine Vision Association}, abstract = {In this paper, we present a novel 3D face modeling approach from a monoc-ular video captured using a conventional camera. The proposed algorithm relies on matching a generic 3D face model to the outer contours of the face to be modeled and a few of its internal features. At the first stage of the method, we estimate the head pose by comparing the edges extracted from video frames, with the contours extracted from a generic face model. Next, the generic face model is adapted to the actual 3D face by global and local deformations. An affine model is used for global deformation. The 3D model is locally deformed by computing the optimal perturbations of a sparse set of control points using a stochastic search optimization method. The deforma- tions are integrated over a set of poses in the video sequence, leading to an accurate 3D model. }, isbn = {1-901725-25-1}, doi = {10.5244/C.18.39}, url = {http://www.bmva.org/bmvc/2004/papers/paper_136.html}, author = {Gupta, H. and Roy Chowdhury, A.K. and Chellapa, Rama} } @conference {16311, title = {Covering arrays for efficient fault characterization in complex configuration spaces}, booktitle = {ACM SIGSOFT Software Engineering Notes}, volume = {29}, year = {2004}, month = {2004///}, pages = {45 - 54}, author = {Yilmaz,C. and Cohen,M. B and Porter, Adam} } @article {14481, title = {Data sciences technology for homeland security information management and knowledge discovery}, journal = {Report of the DHS Workshop Data Sciences, Jointly Released by Sandia National Laboratories and Lawrence Livermore National Laboratory, Alexandria, Va}, year = {2004}, month = {2004///}, author = {Kolda,T. and Brown,D and Corones,J. and Critchlow,T. and Eliassi-Rad,T. and Getoor, Lise and Hendrickson,B. and Kumar, V. and Lambert,D. and Matarazzo,C.} } @article {12210, title = {DateLens: A fisheye calendar interface for PDAs}, journal = {ACM Transactions on Computer-Human Interaction (TOCHI)}, volume = {11}, year = {2004}, month = {2004///}, pages = {90 - 119}, author = {Bederson, Benjamin B. and Clamage,A. and Czerwinski,M.P. and Robertson,G.G.} } @article {17078, title = {Determining Causes and Severity of End-User Frustration}, journal = {International Journal of Human-Computer Interaction}, volume = {17}, year = {2004}, month = {2004///}, pages = {333 - 356}, abstract = {Although computers are beneficial to individuals and society, frequently users encounter frustrating experiences when using computers. This study represents an attempt to measure, in 111 participants, the frequency, the cause, and the level of severity of frustrating experiences. The data show that frustrating experiences happen on a frequent basis. The applications in which the frustrating experiences happened most frequently were Web browsing, e-mail, and word processing. The most-cited causes of frustrating experiences were error messages, dropped network connections, long download times, and hard-to-find features. The time lost due to frustrating experiences ranged from 47\% to 53\% of time spent on a computer, depending on the location and study method. After extreme cases were discarded, the time lost was still above 38\%. These disturbing results should be a basis for future study.Although computers are beneficial to individuals and society, frequently users encounter frustrating experiences when using computers. This study represents an attempt to measure, in 111 participants, the frequency, the cause, and the level of severity of frustrating experiences. The data show that frustrating experiences happen on a frequent basis. The applications in which the frustrating experiences happened most frequently were Web browsing, e-mail, and word processing. The most-cited causes of frustrating experiences were error messages, dropped network connections, long download times, and hard-to-find features. The time lost due to frustrating experiences ranged from 47\% to 53\% of time spent on a computer, depending on the location and study method. After extreme cases were discarded, the time lost was still above 38\%. These disturbing results should be a basis for future study. }, isbn = {1044-7318}, doi = {10.1207/s15327590ijhc1703_3}, url = {http://www.tandfonline.com/doi/abs/10.1207/s15327590ijhc1703_3}, author = {Ceaparu,Irina and Lazar,Jonathan and Bessiere,Katie and Robinson,John and Shneiderman, Ben} } @conference {19447, title = {Developing Locally Relevant Software Applications for Rural Areas: A South African Example}, booktitle = {SAICSIT {\textquoteright}04}, series = {SAICSIT {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {239 - 243}, publisher = {South African Institute for Computer Scientists and Information Technologists}, organization = {South African Institute for Computer Scientists and Information Technologists}, abstract = {The digital divide between rural and urban areas within developing countries is vast. We investigate how to address this divide by introducing Information and Communication Technologies (ICTs) into remote rural areas. Our aim is to discover how to create locally relevant software applications with appropriate content for these areas. We use a user centred design approach and a modified software development lifecyle that is participatory, iterative and cyclical. This process is based on principles from Participatory Design and Action Research. This paper presents our initial experience of developing a telemedicine application for a rural village in the Eastern Cape Province of South Africa using this process. We present an overview of the methodology, describe the software application we have developed and cite several challenges we have faced. Finally we conclude that an inter-organisational and inter-disciplinary approach is needed to develop software for remote areas.}, keywords = {action research, design, human factors, participatory design, telemedicine}, url = {http://dl.acm.org/citation.cfm?id=1035053.1035083}, author = {Marshini Chetty and Tucker, William and Blake, Edwin} } @article {12681, title = {Dimensionality Estimation in Hyperspectral Imagery Using Minimum Description Length}, year = {2004}, month = {2004/12//}, institution = {MARYLAND UNIV COLLEGE PARK CENTER FOR AUTOMATION RESEARCH}, abstract = {Numerous algorithms have been developed for hyperspectral automatic target recognition (ATR) applications. Many of these algorithms require estimation of a background subspace. The estimation of the background subspace has been addressed using multiple methods. but most of these methods assume a-priori knowledge of the background dimensionality. In order to automate the estimation of the background subspace. we present an algorithm based on minimum description length (MDL) that can identify the background dimension. Results show that the MDL criterion estimates the proper dimension of the background for ATR applications.}, keywords = {*ALGORITHMS, *HYPERSPECTRAL IMAGERY, *TARGET DETECTION, *TARGET RECOGNITION, AUTOMATIC, BURIED OBJECTS, COMPONENT REPORTS, MINE DETECTION, NUMERICAL MATHEMATICS, SURFACE TARGETS., SYMPOSIA, TARGET DIRECTION, RANGE AND POSITION FINDING}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA431643}, author = {Broadwater,Joshua B and Meth,Reuven and Chellapa, Rama} } @article {12817, title = {Distributed prototyping from validated specifications}, journal = {Journal of Systems and Software}, volume = {70}, year = {2004}, month = {2004/03//}, pages = {275 - 298}, abstract = {We present vpl2cxx, a translator that automatically generates efficient, fully distributed C++ code from high-level system models specified in the mathematically well-founded VPL design language. As the Concurrency Workbench of the New Century (CWB-NC) verification tool includes a front-end for VPL, designers may use the full range of automatic verification and simulation checks provided by this tool on their VPL system designs before invoking the translator, thereby generating distributed prototypes from validated specifications. Besides being fully distributed, the code generated by vpl2cxx is highly readable and portable to a host of execution environments and real-time operating systems (RTOSes). This is achieved by encapsulating all generated code dealing with low-level interprocess communication issues in a library for synchronous communication, which in turn is built upon the adaptive communication environment (ACE) client-server network programming interface. Finally, example applications show that the performance of the generated code is very good, especially for prototyping purposes. We discuss two such examples, including the RETHER real-time Ethernet protocol for voice and video applications.}, isbn = {0164-1212}, doi = {10.1016/S0164-1212(03)00074-8}, url = {http://www.sciencedirect.com/science/article/pii/S0164121203000748}, author = {Hansel,David and Cleaveland, Rance and Smolka,Scott A.} } @article {12990, title = {Divergent Gene Copies in the Asexual Class Bdelloidea (Rotifera) Separated Before the Bdelloid Radiation or Within Bdelloid Families}, journal = {Proceedings of the National Academy of Sciences of the United States of AmericaPNAS}, volume = {101}, year = {2004}, month = {2004/02/10/}, pages = {1622 - 1625}, abstract = {Rotifers of the asexual class Bdelloidea are unusual in possessing two or more divergent copies of every gene that has been examined. Phylogenetic analysis of the heat-shock gene hsp82 and the TATA-box-binding protein gene tbp in multiple bdelloid species suggested that for each gene, each copy belonged to one of two lineages that began to diverge before the bdelloid radiation. Such gene trees are consistent with the two lineages having descended from former alleles that began to diverge after meiotic segregation ceased or from subgenomes of an alloploid ancestor of the bdelloids. However, the original analyses of bdelloid gene-copy divergence used only a single outgroup species and were based on parsimony and neighbor joining. We have now used maximum likelihood and Bayesian inference methods and, for hsp82, multiple outgroups in an attempt to produce more robust gene trees. Here we report that the available data do not unambiguously discriminate between gene trees that root the origin of hsp82 and tbp copy divergence before the bdelloid radiation and those which indicate that the gene copies began to diverge within bdelloid families. The remarkable presence of multiple diverged gene copies in individual genomes is nevertheless consistent with the loss of sex in an ancient ancestor of bdelloids.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.2136686100}, url = {http://www.pnas.org/content/101/6/1622}, author = {Welch,David B. Mark and Cummings, Michael P. and Hillis,David M and Meselson,Matthew} } @article {12297, title = {Efficient peer-to-peer namespace searches}, journal = {University of Maryland, College Park, MD, Tech. Rep. CSTR-4568}, year = {2004}, month = {2004///}, abstract = {In this paper we describe new methods for efficient and exact search (keyword and full-text) in distributed namespaces. Our methods can be used in conjunction with existing distributed lookup schemes, such as Distributed Hash Tables, and distributed directories. We describe how indexes for implementing distributed searches can be efficiently created, located, and stored. We describe techniques for creating approximate indexes that can be used to bound the space requirement at individual hosts; such techniques are particularly useful for full-text searches that may require a very large number of individual indexes to be created and maintained. Our methods use a new distributed data structure called the view tree. View trees can be used to efficiently cache and locate results from prior queries. We describe how view trees are created, and maintained. We present experimental results, using large namespaces and realistic data, showing that the techniques introduced in this paper can reduce search overheads (both network and processing costs) by more than an order of magnitude.}, author = {Gopalakrishnan,V. and Bhattacharjee, Bobby and Chawathe,S. and Keleher,P.} } @conference {12131, title = {Empirical-based estimation of the effect on software dependability of a technique for architecture conformance verification}, booktitle = {Proceedings of the ICSE 2004 Workshop on Architecting Dependable Systems, Edinburgh, UK}, year = {2004}, month = {2004///}, abstract = {The High Dependability Computing Program (HDCP)project is a NASA initiative for increasing dependability of software-based systems. It researches achieving high dependability by introducing new technologies. We focus on the evaluation of the effectiveness of technologies with respect to dependability. We employ empirical evaluation methods along with evaluation testbeds. In this paper, our technology evaluation approach is described. A testbed representative of air traffic control applications is used. An experiment to evaluate a technology to for identification of architectural violations is presented. }, author = {Asgari, S. and Basili, Victor R. and Costa,P. and Donzelli,P. and Hochstein, L. and Lindvall,M. and Rus,I. and Shull, F. and Tvedt,R. and Zelkowitz, Marvin V} } @conference {17155, title = {Extending the utility of treemaps with flexible hierarchy}, booktitle = {Eighth International Conference on Information Visualisation, 2004. IV 2004. Proceedings}, year = {2004}, month = {2004/07/14/16}, pages = {335 - 344}, publisher = {IEEE}, organization = {IEEE}, abstract = {Treemaps are a visualization technique for presenting hierarchical information on two-dimensional displays. Prior implementations limit the visualization to pre-defined static hierarchies. Flexible hierarchy, a new capability of Treemap 4.0, enables users to define various hierarchies through dynamically selecting a series of data attributes so that they can discover patterns, clusters and outliers. This work describes the design and implementation issues of flexible hierarchy. It then reports on a usability study, which led to enhancements to the interface.}, keywords = {2D displays, Computer displays, Computer science, data visualisation, Data visualization, Educational institutions, flexible hierarchy, graphical user interface, Graphical user interfaces, hierarchical information, Nominations and elections, Switches, Tree data structures, Tree graphs, Treemap 4.0, Two dimensional displays, usability, visualization technique}, isbn = {0-7695-2177-0}, doi = {10.1109/IV.2004.1320166}, author = {Chintalapani,G. and Plaisant, Catherine and Shneiderman, Ben} } @conference {12685, title = {Facial similarity across age, disguise, illumination and pose}, booktitle = {Image Processing, 2004. ICIP {\textquoteright}04. 2004 International Conference on}, volume = {3}, year = {2004}, month = {2004/10//}, pages = {1999 - 2002 Vol. 3 - 1999 - 2002 Vol. 3}, abstract = {Illumination, pose variations, disguises, aging effects and expression variations are some of the key factors that affect the performance of face recognition systems. Face recognition systems have always been studied from a recognition perspective. Our emphasis is on deriving a measure of similarity between faces. The similarity measure provides insights into the role each of the above mentioned variations play in affecting the performance of face recognition systems. In the process of computing the similarity measure between faces, we suggest a framework to compensate for pose variations and introduce the notion of {\textquoteright}half-faces{\textquoteright} to circumvent the problem of non-uniform illumination. We used the similarity measure to retrieve similar faces from a database containing multiple images of individuals. Moreover, we devised experiments to study the effect age plays in affecting facial similarity. In conclusion, the similarity measure helps in studying the significance facial features play in affecting the performance of face recognition systems.}, keywords = {Aging, database, databases;, disguise;, effect;, Expression, Face, half-face;, illumination;, image, lighting;, pose, recognition, recognition;, retrieval;, system;, variation;, visual}, doi = {10.1109/ICIP.2004.1421474}, author = {Ramanathan,N. and Chellapa, Rama and Roy Chowdhury, A.K.} } @conference {18673, title = {Ferret: a host vulnerability checking tool}, year = {2004}, month = {2004/03//}, pages = {389 - 394}, abstract = {Evaluation of computing system security requires knowledge of the vulnerabilities present in the system and of potential attacks against the system. Vulnerabilities can be classified based on their location as application vulnerabilities, network vulnerabilities, or host vulnerabilities. We describe Ferret, a new software tool for checking host vulnerabilities. Ferret helps system administrators by quickly finding vulnerabilities that are present on a host. It is designed and implemented in a modular way: a different plug-in module is used for each vulnerability checked, and each possible output format is specified by a plug-in module. As a result, Ferret is extensible, and can easily be kept up-to-date through addition of checks for new vulnerabilities as they are discovered; the modular approach also makes it easy to provide specific configurations of Ferret tailored to specific operating systems or use environments. Ferret is a freely available open-source software implemented in Perl.}, keywords = {Ferret software tool, host vulnerability checking tool, open-source software, Perl, plug-in module, program verification, security auditing tool, security evaluation, security of data, software tools}, doi = {10.1109/PRDC.2004.1276595}, author = {Sharma,Anil and Martin,J.R. and Anand,N. and Michel Cukier and Sanders,W. H.} } @article {12998, title = {Few amino acid positions in {\i}t rpoB are associated with most of the rifampin resistance in {\i}t Mycobacterium tuberculosis}, journal = {BMC Bioinformatics}, volume = {5}, year = {2004}, month = {2004/09//}, pages = {137 - 137}, abstract = {BACKGROUND: Mutations in rpoB, the gene encoding the beta subunit of DNA-dependent RNA polymerase, are associated with rifampin resistance in Mycobacterium tuberculosis. Several studies have been conducted where minimum inhibitory concentration (MIC, which is defined as the minimum concentration of the antibiotic in a given culture medium below which bacterial growth is not inhibited) of rifampin has been measured and partial DNA sequences have been determined for rpoB in different isolates of M. tuberculosis. However, no model has been constructed to predict rifampin resistance based on sequence information alone. Such a model might provide the basis for quantifying rifampin resistance status based exclusively on DNA sequence data and thus eliminate the requirements for time consuming culturing and antibiotic testing of clinical isolates. RESULTS: Sequence data for amino acid positions 511-533 of rpoB and associated MIC of rifampin for different isolates of M. tuberculosis were taken from studies examining rifampin resistance in clinical samples from New York City and throughout Japan. We used tree-based statistical methods and random forests to generate models of the relationships between rpoB amino acid sequence and rifampin resistance. The proportion of variance explained by a relatively simple tree-based cross-validated regression model involving two amino acid positions (526 and 531) is 0.679. The first partition in the data, based on position 531, results in groups that differ one hundredfold in mean MIC (1.596 micrograms/ml and 159.676 micrograms/ml). The subsequent partition based on position 526, the most variable in this region, results in a > 354-fold difference in MIC. When considered as a classification problem (susceptible or resistant), a cross-validated tree-based model correctly classified most (0.884) of the observations and was very similar to the regression model. Random forest analysis of the MIC data as a continuous variable, a regression problem, produced a model that explained 0.861 of the variance. The random forest analysis of the MIC data as discrete classes produced a model that correctly classified 0.942 of the observations with sensitivity of 0.958 and specificity of 0.885. CONCLUSIONS: Highly accurate regression and classification models of rifampin resistance can be made based on this short sequence region. Models may be better with improved (and consistent) measurements of MIC and more sequence data.}, doi = {10.1186/1471-2105-5-137}, author = {Cummings, Michael P. and Segal,M. R} } @article {17165, title = {Finding governmental statistical data on the Web: A study of categorically organized links for the FedStats topics page}, journal = {Journal of the American Society for Information Science and Technology}, volume = {55}, year = {2004}, month = {2004/09/01/}, pages = {1008 - 1015}, abstract = {More than 100 U.S. governmental agencies offer links through FedStats, a centralized Web site that facilitates access to statistical tables, reports, and agencies. This and similar large collections need appropriate interfaces to guide the general public to easily and successfully find information they seek. This paper summarizes the results of 3 empirical studies of alternate organization concepts of the FedStats Topics Web page. Each study had 15 participants. The evolution from 645 alphabetically organized links, to 549 categorically organized links, to 215 categorically organized links tied to portal pages produced a steady rise in successful task completion from 15.6 to 24.4 to 42.2\%. User satisfaction also increased. We make recommendations based on these data and our observations of users.}, isbn = {1532-2890}, doi = {10.1002/asi.20052}, url = {http://onlinelibrary.wiley.com/doi/10.1002/asi.20052/abstract}, author = {Ceaparu,Irina and Shneiderman, Ben} } @article {17166, title = {Finding Governmental Statistical Data on the Web: Three Empirical Studies of the FedStats Topics Page}, journal = {Journal of the American Society for Information Science and Technology}, volume = {55}, year = {2004}, month = {2004///}, pages = {1008 - 1015}, abstract = {Governmental agencies provide statistical data on their web sites. These large collections of data need appropriate interfaces that would guide the general public, as well as the researchers, to easily and successfully find information they seek. This paper summarizes the results of three empirical studies with 15 users in each group of the FedStats Topics web page. The evolution from 645 alphabetically organized links, to 549 categorically organized links, to 215 categorically organized links tied to portal pages produced a steady rise in successful task completion from 15 \% to 28 \% to 42\%. User satisfaction also increased. We make recommendations based on these data and our observations of users.}, author = {Ceaparu,Irina and Shneiderman, Ben} } @article {12805, title = {Formal Modeling Of Middleware-based Distributed Systems}, journal = {Electronic Notes in Theoretical Computer Science}, volume = {108}, year = {2004}, month = {2004/12/13/}, pages = {21 - 37}, abstract = {Effective design of middleware-based systems requires modeling notations that allow the use of process-interaction schemes provided by different middleware packages directly in designs. Traditional design notations typically only support a fixed class of interprocess interaction schemes, and designers wishing to use them for modeling middleware-based systems must devote significant effort to encoding the middleware primitives in the notation. In this paper, we demonstrate how a new graphical design notation, Architectural Interaction Diagrams (AIDs), which provides parameterized support for different interaction schemes, may be used to model a real-life middleware-based system like the Event Heap coordination infrastructure of the i-Room ubiquitous computing environment.}, keywords = {distributed systems, Formal Methods, Middleware, Software architecture}, isbn = {1571-0661}, doi = {10.1016/j.entcs.2004.01.010}, url = {http://www.sciencedirect.com/science/article/pii/S1571066104051989}, author = {Ray,Arnab and Cleaveland, Rance} } @inbook {12943, title = {Free-Living to Freewheeling: The Evolution of Vibrio cholerae from Innocence to Infamy}, booktitle = {Infectious Disease and Host-Pathogen EvolutionInfectious Disease and Host-Pathogen Evolution}, year = {2004}, month = {2004///}, pages = {198 - 198}, publisher = {Cambridge University Press}, organization = {Cambridge University Press}, isbn = {9780521820660}, author = {Rita R Colwell and Faruque,S. M. and Nair,G. B.}, editor = {Dronamraju,Krishna R.} } @conference {12704, title = {Fusion of gait and face for human identification}, booktitle = {Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP {\textquoteright}04). IEEE International Conference on}, volume = {5}, year = {2004}, month = {2004/05//}, pages = {V - 901-4 vol.5 - V - 901-4 vol.5}, abstract = {Identification of humans from arbitrary view points is an important requirement for different tasks including perceptual interfaces for intelligent environments, covert security and access control etc. For optimal performance, the system must use as many cues as possible and combine them in meaningful ways. In this paper, we discuss fusion of face and gait cues for the single camera case. We present a view invariant gait recognition algorithm for gait recognition. We employ decision fusion to combine the results of our gait recognition algorithm and a face recognition algorithm based on sequential importance sampling. We consider two fusion scenarios: hierarchical and holistic. The first involves using the gait recognition algorithm as a filter to pass on a smaller set of candidates to the face recognition algorithm. The second involves combining the similarity scores obtained individually from the face and gait recognition algorithms. Simple rules like the SUM, MIN and PRODUCT are used for combining the scores. The results of fusion experiments are demonstrated on the NIST database which has outdoor gait and face data of 30 subjects.}, keywords = {access, algorithm;, analysis;, combining, control;, covert, cues;, data, decision, Environment, Face, fusion;, Gait, hierarchical, holistic, human, identification;, importance, intelligent, interfaces;, invariant, perceptual, recognition, recognition;, rules;, sampling;, score, scores;, security;, sensor, sequential, similarity, view}, doi = {10.1109/ICASSP.2004.1327257}, author = {Kale, A. and Roy Chowdhury, A.K. and Chellapa, Rama} } @article {13223, title = {Gait recognition using image self-similarity}, journal = {EURASIP J. Appl. Signal Process.}, volume = {2004}, year = {2004}, month = {2004/01//}, pages = {572 - 585}, abstract = {Gait is one of the few biometrics that can be measured at a distance, and is hence useful for passive surveillance as well as biometric applications. Gait recognition research is still at its infancy, however, and we have yet to solve the fundamental issue of finding gait features which at once have suffcient discrimination power and can be extracted robustly and accurately from low-resolution video. This paper describes a novel gait recognition technique based on the image self-similarity of a walking person. We contend that the similarity plot encodes a projection of gait dynamics. It is also correspondence-free, robust to segmentation noise, and works well with low-resolution video. The method is tested on multiple data sets of varying sizes and degrees of diffculty. Performance is best for fronto-parallel viewpoints, whereby a recognition rate of 98\% is achieved for a data set of 6 people, and 70\% for a data set of 54 people.}, keywords = {behavioral biometrics, gait recognition, human identification at a distance, human movement analysis, pattern recognition}, isbn = {1110-8657}, doi = {10.1155/S1110865704309236}, url = {http://dx.doi.org/10.1155/S1110865704309236}, author = {BenAbdelkader,Chiraz and Cutler,Ross G. and Davis, Larry S.} } @article {12715, title = {Gait-based human identification from a monocular video sequence}, journal = {Handbook on Pattern Recognition and Computer Vision}, year = {2004}, month = {2004///}, abstract = {Human gait is a spatio-temporal phenomenon that characterizes the motion char-acteristics of an individual. It is possible to detect and measure gait even in low- resolution video. In this chapter, we discuss algorithms for identifying people by their gait from a monocular video sequence. Human identification using gait, sim- ilar to text-based speaker identification, involves different individuals performing the same task and a template-matching approach is suitable for such problems. In situations where the amount of training data is limited, we demonstrate the utility of a simple width feature for gait recognition. By virtue of their determin- istic nature, template matching methods have limited noise resilience. In order to deal with noise we introduce a systematic approach to gait recognition by building representations for the structural and dynamic components of gait using exemplars and hidden Markov models (HMMs). The above methods assume that an exact side-view of the subject is available in the probe sequence. For the case when the person walks at an arbitrary angle far away from the camera we present a view invariant gait recognition algorithm which is based on synthesizing a side view of a person from an arbitrary monocular view. }, author = {Kale, A. and Sundaresan, A. and Roy Chowdhury, A.K. and Chellapa, Rama} } @article {14876, title = {Generalized photometric stereo and its application to face recognition}, journal = {International Journal of Computer Vision}, year = {2004}, month = {2004///}, abstract = {Most photometric stereo algorithms employ a Lambertian reflectance model witha varying albedo field and involve the appearances of only one object. The recovered albedos and surface normals are object-specific and appearances not belonging to the object cannot be easily handled. We generalize photometric stereo algorithms to handle all appearances of all objects in a class, in particular the human face class, by assuming that albedos and surface normals of all objects in the class be rank-constrained, i.e. lie in a subspace. Rank constraints lead us to a factorization of an observation matrix that consists of exemplar images of different objects under different illuminations. To fully recover the subspace bases or class- specific albedos and surface normals, we employ integrability and face symmetry constraints and propose a linearized algorithm. This algorithm takes into account the effects of the varying albedo field by approximating the integrability terms using only the surface normals. We then apply our generalized photometric stereo algorithm for recognizing faces under illumination variations. As far as recognition is concerned, we can utilize a bootstrap set which is just a collection of 2D image observations to avoid an explicit requirement that 3D information be available. We obtain good recognition results using the PIE database. }, author = {Zhou, S. and Chellapa, Rama and Jacobs, David W.} } @article {18648, title = {A global-state-triggered fault injector for distributed system evaluation}, journal = {Parallel and Distributed Systems, IEEE Transactions on}, volume = {15}, year = {2004}, month = {2004/07//}, pages = {593 - 605}, abstract = {Validation of the dependability of distributed systems via fault injection is gaining importance because distributed systems are being increasingly used in environments with high dependability requirements. The fact that distributed systems can fail in subtle ways that depend on the state of multiple parts of the system suggests that a global-state-based fault injection mechanism should be used to validate them. However, global-state-based fault injection is challenging since it is very difficult in practice to maintain the global state of a distributed system at runtime with minimal intrusion into the system execution. We present Loki, a global-state-based fault injector, which has been designed with the goals of low intrusion, high precision, and high flexibility. Loki achieves these goals by utilizing the ideas of partial view of global state, optimistic synchronization, and offline analysis. In Loki, faults are injected based on a partial, view of the global state of the system, and a post-runtime analysis is performed to place events and injections into a single global timeline and to discard experiments with incorrect fault injections. Finally, the experiments with correct fault injections are used to estimate user-specified performance and dependability measures. A flexible measure language has been designed that facilitates the specification of a wide range of measures.}, keywords = {distributed processing, distributed system evaluation, fault tolerant computing, global-state-based fault injection mechanism, Loki, offline clock synchronization, performance evaluation, post-runtime analysis, Synchronisation, system recovery, user-specified performance}, isbn = {1045-9219}, doi = {10.1109/TPDS.2004.14}, author = {Chandra,Ramesh and Lefever,R.M. and Joshi,K.R. and Michel Cukier and Sanders,W. H.} } @conference {12691, title = {A hybrid algorithm for subpixel detection in hyperspectral imagery}, booktitle = {Geoscience and Remote Sensing Symposium, 2004. IGARSS {\textquoteright}04. Proceedings. 2004 IEEE International}, volume = {3}, year = {2004}, month = {2004/09//}, pages = {1601 -1604 vol.3 - 1601 -1604 vol.3}, abstract = {Numerous subpixel detection algorithms utilizing structured backgrounds have been developed over the past few years. These range from detection schemes based on spectral unmixing to generalized likelihood ratio tests. Spectral unmixing algorithms such as the Fully Constrained Least Squares (FCLS) algorithm have the advantage of physically modeling the interactions of spectral signatures based on reflectance/emittance spectroscopy. Generalized likelihood ratio tests like the Adaptive Matched Subspace Detector (AMSD) have the advantage of identifying targets that are statistically different from the background. Therefore, a hybrid detector based on both AMSD and FCLS was developed to take advantage of each detector{\textquoteright}s strengths. Results demonstrate that the hybrid detector achieved the lowest false alarm rates while also producing meaningful abundance estimates}, keywords = {alarm, algorithm;abundance, algorithm;Fully, algorithm;hybrid, algorithm;statistical, AMSD;Adaptive, analysis;structured, approximations;maximum, backgrounds;subpixel, constrained, detection;alarm, detection;target, Detector;FCLS, detector;hyperspectral, estimation;, estimation;emittance, identification;adaptive, imagery;reflectance, least, likelihood, Matched, matching;least, processing;geophysical, rate;generalized, ratio, signal, signatures;spectral, spectra;false, spectra;spectral, squares, subspace, systems;geophysical, techniques;image, tests;hybrid, unmixing}, doi = {10.1109/IGARSS.2004.1370633}, author = {Broadwater, J. and Meth, R. and Chellapa, Rama} } @article {12690, title = {Identification of humans using gait}, journal = {Image Processing, IEEE Transactions on}, volume = {13}, year = {2004}, month = {2004/09//}, pages = {1163 - 1173}, abstract = {We propose a view-based approach to recognize humans from their gait. Two different image features have been considered: the width of the outer contour of the binarized silhouette of the walking person and the entire binary silhouette itself. To obtain the observation vector from the image features, we employ two different methods. In the first method, referred to as the indirect approach, the high-dimensional image feature is transformed to a lower dimensional space by generating what we call the frame to exemplar (FED) distance. The FED vector captures both structural and dynamic traits of each individual. For compact and effective gait representation and recognition, the gait information in the FED vector sequences is captured in a hidden Markov model (HMM). In the second method, referred to as the direct approach, we work with the feature vector directly (as opposed to computing the FED) and train an HMM. We estimate the HMM parameters (specifically the observation probability B) based on the distance between the exemplars and the image features. In this way, we avoid learning high-dimensional probability density functions. The statistical nature of the HMM lends overall robustness to representation and recognition. The performance of the methods is illustrated using several databases.}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, binary silhouette;frame to exemplar distance;gait databases;gait recognition;hidden Markov model;human identification;image features;observation probability;observation vector;hidden Markov models;image recognition;image representation;image sequences;pro, Biological;Models, Computer-Assisted;Models, Computer-Assisted;Subtraction Technique;Task Performance and Analysis;Video Recording;, Statistical;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2004.832865}, author = {Kale, A. and Sundaresan, A. and Rajagopalan, AN and Cuntoor, N.P. and Roy-Chowdhury, A.K. and Kruger, V. and Chellapa, Rama} } @conference {12428, title = {Identifying similar parts for assisting cost estimation of prismatic machined parts}, booktitle = {ASME Design for Manufacturing Conference, Salt Lake City, Utah}, year = {2004}, month = {2004///}, author = {Cardone, Antonio and Gupta,S.K. and Karnik,M.} } @conference {12701, title = {Illuminating light field: image-based face recognition across illuminations and poses}, booktitle = {Automatic Face and Gesture Recognition, 2004. Proceedings. Sixth IEEE International Conference on}, year = {2004}, month = {2004/05//}, pages = {229 - 234}, abstract = {We present an image-based method for face recognition across different illuminations and different poses, where the term {\textquoteright}image-based{\textquoteright} means that only 2D images are used and no explicit 3D models are needed. As face recognition across illuminations and poses involves three factors, namely identity, illumination, and pose, generalizations from known identities to novel identities, from known illuminations to novel illuminations, and from known poses to unknown poses are desired. Our approach, called the illuminating light field, derives an identity signature that is invariant to illuminations and poses, where a subspace encoding is assumed for the identity, a Lambertain reflectance model for the illumination, and a light field model for the poses. Experimental results using the PIE database demonstrate the effectiveness of the proposed approach.}, keywords = {Face, field;, illuminating, image-based, Lambertain, light, lighting;, model;, multidimensional, poses;, processing;, recognition;, reflectance, reflectivity;, signal}, doi = {10.1109/AFGR.2004.1301536}, author = {Zhou,Shaohua and Chellapa, Rama} } @article {14880, title = {Illumination, Reflectance, and Reflection-Characterization of Human Faces under Illumination Variations Using Rank, Integrability, and Symmetry Constraints}, journal = {Lecture Notes in Computer Science}, volume = {3021}, year = {2004}, month = {2004///}, pages = {588 - 601}, author = {Zhou,S. K and Chellapa, Rama and Jacobs, David W.} } @article {13227, title = {Improved Multiuser Detectors Employing Genetic Algorithms in a Space-Time Block Coded System, Yinggang Du and Kam Tai Chan}, journal = {Signal}, volume = {2004}, year = {2004}, month = {2004///}, pages = {640 - 648}, author = {Self-Similarity,G.R.U.I. and BenAbdelkader,C. and Cutler,R.G. and Davis, Larry S. and Local,F.R.U. and Global Features,J.H. and Yuen, P.C. and Lai,JH and Li,C.} } @article {13229, title = {Incremental density approximation and kernel-based bayesian filtering for object tracking}, journal = {IEEE Computer Society Conference on Computer Vision and Pattern Recognition}, volume = {1}, year = {2004}, month = {2004///}, abstract = {Statistical density estimation techniques are used in manycomputer vision applications such as object tracking, back- ground subtraction, motion estimation and segmentation. The particle filter (Condensation) algorithm provides a gen- eral framework for estimating the probability density func- tions (pdf) of general non-linear and non-Gaussian systems. However, since this algorithm is based on a Monte Carlo ap- proach, where the density is represented by a set of random samples, the number of samples is problematic, especially for high dimensional problems. In this paper, we propose an alternative to the classical particle filter in which the un- derlying pdf is represented with a semi-parametric method based on a mode finding algorithm using mean-shift. A mode propagation technique is designed for this new representa- tion for tracking applications. A quasi-random sampling method [14] in the measurement stage is used to improve performance, and sequential density approximation for the measurements distribution is performed for efficient compu- tation. We apply our algorithm to a high dimensional color- based tracking problem, and demonstrate its performance by showing competitive results with other trackers. }, author = {Han,B. and Comaniciu, D. and Zhu,Y. and Davis, Larry S.} } @article {12937, title = {Infectious disease and environment: cholera as a paradigm for waterborne disease}, journal = {International Microbiology}, volume = {7}, year = {2004}, month = {2004/12//}, pages = {285 - 289}, isbn = {1139-6709}, url = {http://scielo.isciii.es/scielo.php?pid=S1139-67092004000400008\&script=sci_arttext}, author = {Rita R Colwell} } @article {12698, title = {An information theoretic criterion for evaluating the quality of 3-D reconstructions from video}, journal = {Image Processing, IEEE Transactions on}, volume = {13}, year = {2004}, month = {2004/07//}, pages = {960 - 973}, abstract = {Even though numerous algorithms exist for estimating the three-dimensional (3-D) structure of a scene from its video, the solutions obtained are often of unacceptable quality. To overcome some of the deficiencies, many application systems rely on processing more data than necessary, thus raising the question: how is the accuracy of the solution related to the amount of data processed by the algorithm? Can we automatically recognize situations where the quality of the data is so bad that even a large number of additional observations will not yield the desired solution? Previous efforts to answer this question have used statistical measures like second order moments. They are useful if the estimate of the structure is unbiased and the higher order statistical effects are negligible, which is often not the case. This paper introduces an alternative information-theoretic criterion for evaluating the quality of a 3-D reconstruction. The accuracy of the reconstruction is judged by considering the change in mutual information (MI) (termed as the incremental MI) between a scene and its reconstructions. An example of 3-D reconstruction from a video sequence using optical flow equations and known noise distribution is considered and it is shown how the MI can be computed from first principles. We present simulations on both synthetic and real data to demonstrate the effectiveness of the proposed criterion.}, keywords = {3D reconstruction, algorithms, Artificial intelligence, Automated;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Computer Graphics, Computer-Assisted;Imaging, Computer-Assisted;Software Validation;Subtraction Technique;Video Recording;, Image Enhancement, Image Interpretation, Image reconstruction, Image sequences, information theoretic criterion, Mutual information, NOISE, noise distribution, optical flow equations, second order moments, statistical analysis, Three-Dimensional;Information Storage and Retrieval;Information Theory;Movement;Pattern Recognition, Video sequences, video signal processing}, isbn = {1057-7149}, doi = {10.1109/TIP.2004.827240}, author = {Roy-Chowdhury, A.K. and Chellapa, Rama} } @article {17260, title = {Interactively Optimizing Signal-to-Noise Ratios in Expression Profiling: Project-Specific Algorithm Selection and Detection P-Value Weighting in Affymetrix Microarrays}, journal = {BioinformaticsBioinformatics}, volume = {20}, year = {2004}, month = {2004/11/01/}, pages = {2534 - 2544}, abstract = {Motivation: The most commonly utilized microarrays for mRNA profiling (Affymetrix) include {\textquoteleft}probe sets{\textquoteright} of a series of perfect match and mismatch probes (typically 22 oligonucleotides per probe set). There are an increasing number of reported {\textquoteleft}probe set algorithms{\textquoteright} that differ in their interpretation of a probe set to derive a single normalized {\textquoteleft}signal{\textquoteright} representative of expression of each mRNA. These algorithms are known to differ in accuracy and sensitivity, and optimization has been done using a small set of standardized control microarray data. We hypothesized that different mRNA profiling projects have varying sources and degrees of confounding noise, and that these should alter the choice of a specific probe set algorithm. Also, we hypothesized that use of the Microarray Suite (MAS) 5.0 probe set detection p-value as a weighting function would improve the performance of all probe set algorithms.Results: We built an interactive visual analysis software tool (HCE2W) to test and define parameters in Affymetrix analyses that optimize the ratio of signal (desired biological variable) versus noise (confounding uncontrolled variables). Five probe set algorithms were studied with and without statistical weighting of probe sets using the MAS 5.0 probe set detection p-values. The signal-to-noise ratio optimization method was tested in two large novel microarray datasets with different levels of confounding noise, a 105 sample U133A human muscle biopsy dataset (11 groups: mutation-defined, extensive noise), and a 40 sample U74A inbred mouse lung dataset (8 groups: little noise). Performance was measured by the ability of the specific probe set algorithm, with and without detection p-value weighting, to cluster samples into the appropriate biological groups (unsupervised agglomerative clustering with F-measure values). Of the total random sampling analyses, 50\% showed a highly statistically significant difference between probe set algorithms by ANOVA [F(4,10) > 14, p < 0.0001], with weighting by MAS 5.0 detection p-value showing significance in the mouse data by ANOVA [F(1,10) > 9, p < 0.013] and paired t-test [t(9) = -3.675, p = 0.005]. Probe set detection p-value weighting had the greatest positive effect on performance of dChip difference model, ProbeProfiler and RMA algorithms. Importantly, probe set algorithms did indeed perform differently depending on the specific project, most probably due to the degree of confounding noise. Our data indicate that significantly improved data analysis of mRNA profile projects can be achieved by optimizing the choice of probe set algorithm with the noise levels intrinsic to a project, with dChip difference model with MAS 5.0 detection p-value continuous weighting showing the best overall performance in both projects. Furthermore, both existing and newly developed probe set algorithms should incorporate a detection p-value weighting to improve performance. Availability: The Hierarchical Clustering Explorer 2.0 is available at http://www.cs.umd.edu/hcil/hce/. Murine arrays (40 samples) are publicly available at the PEPR resource (http://microarray.cnmcresearch.org/pgadatatable.asp; http://pepr.cnmcresearch.org; Chen et al., 2004). }, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/bth280}, url = {http://bioinformatics.oxfordjournals.org/content/20/16/2534}, author = {Seo,Jinwook and Bakay,Marina and Chen,Yi-Wen and Hilmer,Sara and Shneiderman, Ben and Hoffman,Eric P} } @conference {12700, title = {Intra-personal kernel space for face recognition}, booktitle = {Automatic Face and Gesture Recognition, 2004. Proceedings. Sixth IEEE International Conference on}, year = {2004}, month = {2004/05//}, pages = {235 - 240}, abstract = {Intra-personal space modeling proposed by Moghaddam et al. has been successfully applied in face recognition. In their work the regular principal subspaces are derived from the intra-personal spacce using a principal componen analysis and embedded in a probabilistic formulation. In this paper, we derive the principal subspace from the intro-personal kernel space by developing a probabilistic analysis for kernel principal components for face recognition. We test this algorithm on a subset of the FERET database with illumination and facial expression variations. The recognition performance demonstrates its advantage over other traditional subspace approaches.}, keywords = {analysis;, component, Expression, Face, facial, illumination, intra-personal, Kernel, lighting;, principal, probabilistic, probability;, recognition;, space;, variation;}, doi = {10.1109/AFGR.2004.1301537}, author = {Zhou,Shaohua and Chellapa, Rama and Moghaddam, B.} } @article {12707, title = {Kullback-Leibler distance between two Gaussian densities in reproducing kernel Hilbert space}, journal = {IEEE Intl. Symp. Information Theory}, year = {2004}, month = {2004///}, author = {Zhou,S. K and Chellapa, Rama} } @inbook {15766, title = {Left-Brain/Right-Brain Multi-Document Summarization}, booktitle = {DUC 04 Conference ProceedingsDUC 04 Conference Proceedings}, year = {2004}, month = {2004///}, publisher = {U.S. National Inst. of Standards and Technology}, organization = {U.S. National Inst. of Standards and Technology}, url = {\tt http://duc.nist.gov/}, author = {Conroy,John M. and Schlesinger,Judith D. and Goldstein,Jade and O{\textquoteright}Leary, Dianne P.} } @article {15861, title = {Mandarin-English Information (MEI): investigating translingual speech retrieval}, journal = {Computer Speech \& Language}, volume = {18}, year = {2004}, month = {2004/04//}, pages = {163 - 179}, abstract = {This paper describes the Mandarin{\^a}{\texteuro}{\textquotedblleft}English Information (MEI) project, where we investigated the problem of cross-language spoken document retrieval (CL-SDR), and developed one of the first English{\^a}{\texteuro}{\textquotedblleft}Chinese CL-SDR systems. Our system accepts an entire English news story (text) as query, and retrieves relevant Chinese broadcast news stories (audio) from the document collection. Hence, this is a cross-language and cross-media retrieval task. We applied a multi-scale approach to our problem, which unifies the use of phrases, words and subwords in retrieval. The English queries are translated into Chinese by means of a dictionary-based approach, where we have integrated phrase-based translation with word-by-word translation. Untranslatable named entities are transliterated by a novel subword translation technique. The multi-scale approach can be divided into three subtasks {\^a}{\texteuro}{\textquotedblleft} multi-scale query formulation, multi-scale audio indexing (by speech recognition) and multi-scale retrieval. Experimental results demonstrate that the use of phrase-based translation and subword translation gave performance gains, and multi-scale retrieval outperforms word-based retrieval.}, keywords = {English{\^a}{\texteuro}{\textquotedblleft}Chinese cross-language spoken document retrieval, Multi-scale spoken document retrieval}, isbn = {0885-2308}, doi = {10.1016/j.csl.2003.09.003}, url = {http://www.sciencedirect.com/science/article/pii/S0885230803000524}, author = {Meng,Helen M. and Chen,Berlin and Khudanpur,Sanjeev and Levow,Gina-Anne and Lo,Wai-Kit and Oard, Douglas and Schone,Patrick and Tang,Karen and Wang,Hsin-Min and Wang,Jianqiang} } @conference {13902, title = {Mixing ideas: a new technique for working with young children as design partners}, booktitle = {Proceedings of the 2004 conference on Interaction design and children: building a community}, year = {2004}, month = {2004///}, pages = {35 - 42}, author = {Guha,M.L. and Druin, Allison and Chipman,G. and Fails,J. A and Simms,S. and Farber,A.} } @conference {12683, title = {Multiple view tracking of humans modelled by kinematic chains}, booktitle = {Image Processing, 2004. ICIP {\textquoteright}04. 2004 International Conference on}, volume = {2}, year = {2004}, month = {2004/10//}, pages = {1009 - 1012 Vol.2 - 1009 - 1012 Vol.2}, abstract = {We use a kinematic chain to model human body motion. We estimate the kinematic chain motion parameters using pixel displacements calculated from video sequences obtained from multiple calibrated cameras to perform tracking. We derive a linear relation between the 2D motion of pixels in terms of the 3D motion parameters of various body parts using a perspective projection model for the cameras, a rigid body motion model for the base body and the kinematic chain model for the body parts. An error analysis of the estimator is provided, leading to an iterative algorithm for calculating the motion parameters from the pixel displacements. We provide experimental results to demonstrate the accuracy of our formulation. We also compare our iterative algorithm to the noniterative algorithm and discuss its robustness in the presence of noise.}, keywords = {3D, algorithm;, analysis;, body, calibrated, cameras;, chain, displacement;, error, estimation;, human, image, iterative, kinematic, kinematics;, methods;, model;, MOTION, motion;, multiple, parameters;, perspective, Pixel, processing;, projection, sequences;, signal, tracking;, video, view}, doi = {10.1109/ICIP.2004.1419472}, author = {Sundaresan, A. and Chellapa, Rama and RoyChowdhury, R.} } @conference {12692, title = {Multiple-exemplar discriminant analysis for face recognition}, booktitle = {Pattern Recognition, 2004. ICPR 2004. Proceedings of the 17th International Conference on}, volume = {4}, year = {2004}, month = {2004/08//}, pages = {191 - 194 Vol.4 - 191 - 194 Vol.4}, abstract = {Face recognition is characteristically different from regular pattern recognition and, therefore, requires a different discriminant analysis other than linear discriminant analysis(LDA). LDA is a single-exemplar method in the sense that each class during classification is represented by a single exemplar, i.e., the sample mean of the class. We present a multiple-exemplar discriminant analysis (MEDA) where each class is represented using several exemplars or even the whole available sample set. The proposed approach produces improved classification results when tested on a subset of FERET database where LDA is ineffective.}, keywords = {analysis;, database;, databases;, discriminant, Face, FERET, multiple-exemplar, recognition;, visual}, doi = {10.1109/ICPR.2004.1333736}, author = {Zhou,S. K and Chellapa, Rama} } @article {13308, title = {Multi-resolution modeling, visualization and streaming of volume meshes}, journal = {Eurographics 2004, Tutorials 2: Multi-resolution Modeling, Visualization and Streaming of Volume Meshes}, year = {2004}, month = {2004///}, author = {Cignoni,P. and De Floriani, Leila and Lindstrom,P. and Pascucci,V. and Rossignac,J. and Silva,C.} } @conference {18729, title = {New directions in design for manufacturing}, year = {2004}, month = {2004///}, pages = {1 - 9}, abstract = {This paper gives an overview of research that is expandingthe domain of design for manufacturing (DFM) into new and important areas. This paper covers DFM and concurrent engineering, DFM for conceptual design, DFM for embodiment design, DFM for detailed design, design for production, platform design for reducing time-to-market, design for system quality, design for life cycle costs, and design for environment. The paper concludes with some general guidelines that suggest how manufacturing firms can develop useful, effective DFM tools. }, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.198.8706\&rep=rep1\&type=pdf}, author = {Herrmann,J.W. and Cooper,J. and Gupta,S.K. and Hayes,C. C. and Ishii,K. and Kazmer,D. and Sandborn,P. A. and Wood,W. H.} } @conference {17805, title = {Oasys: An opinion analysis system}, booktitle = {AAAI Spring symposium on Computational Approaches to Analyzing Weblogs}, year = {2004}, month = {2004///}, abstract = {There are numerous applications in which we would like toassess what opinions are being expressed in text documents. For example, Martha Stewart{\textquoteright}s company may have wished to assess the degree of harshness of news articles about her in the recent past. Likewise, a World Bank official may wish to as- sess the degree of criticism of a proposed dam in Bangladesh. The ability to gauge opinion on a given topic is therefore of critical interest. In this paper, we develop a suite of algo- rithms which take as input, a set D of documents as well as a topic t, and gauge the degree of opinion expressed about topic t in the set D of documents. Our algorithms can return both a number (larger the number, more positive the opinion) as well as a qualitative opinion (e.g. harsh, complimentary). We as- sess the accuracy of these algorithms via human experiments and show that the best of these algorithms can accurately re- flect human opinions. We have also conducted performance experiments showing that our algorithms are computationally fast. }, author = {Cesarano,C. and Dorr, Bonnie J and Picariello, A. and Reforgiato,D. and Sagoff,A. and V.S. Subrahmanian} } @article {12939, title = {Occurrence and distribution of Vibrio cholerae in the coastal environment of Peru}, journal = {Environmental Microbiology}, volume = {6}, year = {2004}, month = {2004/07/01/}, pages = {699 - 706}, abstract = {The occurrence and distribution of Vibrio cholerae in sea water and plankton along the coast of Peru were studied from October 1997 to June 2000, and included the 1997{\textendash}98 El Ni{\~n}o event. Samples were collected at four sites in coastal waters off Peru at monthly intervals. Of 178 samples collected and tested, V. cholerae O1 was cultured from 10 (5.6\%) samples, and V. cholerae O1 was detected by direct fluorescent antibody assay in 26 out of 159 samples tested (16.4\%). Based on the number of cholera cases reported in Peru from 1997 to 2000, a significant correlation was observed between cholera incidence and elevated sea surface temperature (SST) along the coast of Peru (P~<~0.001). From the results of this study, coastal sea water and zooplankton are concluded to be a reservoir for V. cholerae in Peru. The climate{\textendash}cholera relationship observed for the 1997{\textendash}98 El Ni{\~n}o year suggests that an early warning system for cholera risk can be established for Peru and neighbouring Latin American countries.}, isbn = {1462-2920}, doi = {10.1111/j.1462-2920.2004.00601.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2004.00601.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Gil,Ana I. and Louis,Val{\'e}rie R. and Rivera,Irma N. G. and Lipp,Erin and Huq,Anwar and Lanata,Claudio F. and Taylor,David N. and Russek-Cohen,Estelle and Choopun,Nipa and Sack,R. Bradley and Rita R Colwell} } @article {12938, title = {Pandemic strains of O3:K6 Vibrio parahaemolyticus in the aquatic environment of Bangladesh}, journal = {Canadian Journal of Microbiology}, volume = {50}, year = {2004}, month = {2004/10//}, pages = {827 - 834}, abstract = {A total of 1500 environmental strains of Vibrio parahaemolyticus, isolated from the aquatic environment of Bangladesh, were screened for the presence of a major V. parahaemolyticus virulence factor, the thermostable direct haemolysin (tdh) gene, by the colony blot hybridization method using a digoxigenin-labeled tdh gene probe. Of 1500 strains, 5 carried the tdh sequence, which was further confirmed by PCR using primers specific for the tdh gene. Examination by PCR confirmed that the 5 strains were V. parahamolyticus and lacked the thermostable direct haemolysin-related haemolysin (trh) gene, the alternative major virulence gene known to be absent in pandemic strains. All 5 strains gave positive Kanagawa phenomenon reaction with characteristic beta-haemolysis on Wagatsuma agar medium. Southern blot analysis of the HindIII-digested chromosomal DNA demonstrated, in all 5 strains, the presence of 2 tdh genes common to strains positive for Kanagawa phenomenon. However, the 5 strains were found to belong to 3 different serotypes (O3:K29, O4:K37, and O3:K6). The 2 with pandemic serotype O3:K6 gave positive results in group-specific PCR and ORF8 PCR assays, characteristics unique to the pandemic clone. Clonal variations among the 5 isolates were analyzed by comparing RAPD and ribotyping patterns. Results showed different patterns for the 3 serotypes, but the pattern was identical among the O3:K6 strains. This is the first report on the isolation of pandemic O3:K6 strains of V. parahaemolyticus from the aquatic environment of Bangladesh.}, url = {http://umd.library.ingentaconnect.com/content/nrc/cjm/2004/00000050/00000010/art00007}, author = {Islam,M. S. and Tasmin,Rizwana and Khan,Sirajul I. s l a m and Bakht,Habibul B. M. and Mahmood,Zahid H. a y a t and Rahman,M. Z. i a u r and Bhuiyan,Nurul A. m i n and Nishibuchi,Mitsuaki and Nair,G. B. a l a k r i s h and Sack,R. B. r a d l e y and Huq,Anwar and Rita R Colwell and Sack,David A.} } @article {12940, title = {Polylysogeny and prophage induction by secondary infection in Vibrio cholerae}, journal = {Environmental Microbiology}, volume = {6}, year = {2004}, month = {2004/07/01/}, pages = {760 - 763}, abstract = {Strains of Vibrio cholerae O1, biotypes El Tor and classical, were infected with a known temperate phage (ΦP15) and monitored over a 15-day period for prophage induction. Over the course of the experiment two morphologically and three genomically distinct virus-like particles were observed from the phage-infected El Tor strain by transmission electron microscopy and field inversion gel electrophoresis, respectively, whereas only one phage, ΦP15, was observed from the infected classical strain. In the uninfected El Tor culture one prophage was spontaneously induced after 6~days. No induction in either strain was observed after treatment with mitomycin C. Data indicate that El Tor biotypes of V. cholerae may be polylysogenic and that secondary infection can promote multiple prophage induction. These traits may be important in the transfer of genetic material among V. cholerae by providing an environmentally relevant route for multiple prophage propagation and transmission.}, isbn = {1462-2920}, doi = {10.1111/j.1462-2920.2004.00603.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2004.00603.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Espeland,Eric M. and Lipp,Erin K. and Huq,Anwar and Rita R Colwell} } @article {12712, title = {Pose-normailzed view synthesis of a symmetric object using a single image}, journal = {Proceedings of the 6th Asian Conference on Computer Vision (ACCV{\textquoteright}04)}, year = {2004}, month = {2004///}, pages = {915 - 920}, abstract = {Object recognition under varying pose is a challenging prob-lem, especially when illumination variations are also present. In this paper, we propose a pose-normalized view synthe- sis method under varying illuminations for symmetric ob- jects. For a given non-frontal view of a symmetric object under non-frontal illumination, the mirror image of the orig- inal view is equivalent to the view when the object rotates around the Y -axis by the same angle as the original view but in the opposite direction, and under opposite illumina- tion condition in the X direction. Exploiting the bilateral symmetry of the object, we generate the mirror view of the object under the same illumination condition as the original view on a pixel-by-pixel basis. The frontal view under the same illumination is then easily obtained using view mor- phing techniques. }, author = {Yue, Z. and Chellapa, Rama} } @article {12080, title = {Proactive key distribution using neighbor graphs}, journal = {IEEE Wireless Communications}, volume = {11}, year = {2004}, month = {2004/02//}, pages = {26 - 36}, abstract = {User mobility in wireless data networks is increasing because of technological advances, and the desire for voice and multimedia applications. These applications, however, require that handoffs between base stations (or access points) be fast to maintain the quality of the connections. In this article we introduce a novel data structure, the neighbor graph, that dynamically captures the mobility topology of a wireless network. We show how neighbor graphs can be utilized to obtain a 99 percent reduction in the authentication time of an IEEE 802.11 handoff (full EAP-TLS) by proactively distributing necessary key material one hop ahead of the mobile user. We also present a reactive method for fast authentication that requires only firmware changes to access points and hence can easily be deployed on existing wireless networks.}, keywords = {access points, Authentication, authentication time, Base stations, Communication system security, Delay, graph theory, GSM, IEEE 802.11 handoff, Land mobile radio cellular systems, Message authentication, mobile radio, Multiaccess communication, neighbor graph, Network topology, Roaming, telecommunication security, Telephone sets, user mobility, Wi-Fi networks, wireless data networks, Wireless LAN, Wireless networks}, isbn = {1536-1284}, doi = {10.1109/MWC.2004.1269714}, author = {Mishra,A. and Min Ho Shin and Petroni,N. L. and Clancy,T. C and Arbaugh, William A.} } @article {12709, title = {Probabilistic analysis of kernel principal components}, journal = {NIPS}, year = {2004}, month = {2004///}, abstract = {This paper presents a probabilistic analysis of kernel principal compo-nents by unifying the theory of probabilistic principal component analy- sis and kernel principal component analysis. It is shown that, while the kernel component enhances the nonlinear modeling power, the proba- bilistic structure offers (i) a mixture model for nonlinear data structure containing nonlinear sub-structures, and (ii) an effective classification scheme. It turns out that the original loading matrix is replaced by a newly defined empirical loading matrix. The expectation/maximization algorithm for learning parameters of interest is also presented. }, author = {Zhou, S. and Chellapa, Rama and Moghaddam, B.} } @conference {12695, title = {Probabilistic identity characterization for face recognition}, booktitle = {Computer Vision and Pattern Recognition, 2004. CVPR 2004. Proceedings of the 2004 IEEE Computer Society Conference on}, volume = {2}, year = {2004}, month = {2004/07/02/june}, pages = {II-805 - II-812 Vol.2 - II-805 - II-812 Vol.2}, abstract = {We present a general framework for characterizing the object identity in a single image or a group of images with each image containing a transformed version of the object, with applications to face recognition. In terms of the transformation, the group is made of either many still images or frames of a video sequence. The object identity is either discrete- or continuous-valued. This probabilistic framework integrates all the evidence of the set and handles the localization problem, illumination and pose variations through subspace identity encoding. Issues and challenges arising in this framework are addressed and efficient computational schemes are presented. Good face recognition results using the PIE database are reported.}, keywords = {characterization;, database, database;, encoding;, Face, identity, identity;, image, localization, management, object, PIE, probabilistic, problem;, recognition;, sequence;, sequences;, subspace, systems;, video}, doi = {10.1109/CVPR.2004.1315247}, author = {Zhou,S. K and Chellapa, Rama} } @article {16122, title = {Project portfolio earned value management using treemaps}, journal = {Proceedings of the Project Management Institute Research Conference}, year = {2004}, month = {2004///}, abstract = {Project portfolio management deals with organizing and managing a set of projects in anorganization. Each organization has its own way of managing the portfolio that meets its business goals. One of the main challenges is to track project performance across the entire portfolio in a timely and effective manner. It allows managers to diagnose performance trends and identify projects in need of attention, giving them the opportunity to take management action in a timely fashion. In this paper, we investigate the use of Earned Value Management (EVM) for tracking project performance across the portfolio, and explore the benefits of an interactive visualization technique called Treemaps to display project performance metrics for the entire portfolio on a single screen. }, author = {Cable,J. H and Ordonez,J. F and Chintalapani,G. and Plaisant, Catherine} } @article {15794, title = {Reconstructing Images of Bar Codes for Construction Site Object Recognition}, journal = {Automation in Construction (Elsevier)}, volume = {13}, year = {2004}, month = {2004///}, pages = {21 - 35}, author = {Gilsinn,David E. and Cheok,Geraldine S. and O{\textquoteright}Leary, Dianne P.} } @conference {12686, title = {Robust Bayesian cameras motion estimation using random sampling}, booktitle = {Image Processing, 2004. ICIP {\textquoteright}04. 2004 International Conference on}, volume = {2}, year = {2004}, month = {2004/10//}, pages = {1361 - 1364 Vol.2 - 1361 - 1364 Vol.2}, abstract = {In this paper, we propose an algorithm for robust 3D motion estimation of wide baseline cameras from noisy feature correspondences. The posterior probability density function of the camera motion parameters is represented by weighted samples. The algorithm employs a hierarchy coarse-to-fine strategy. First, a coarse prior distribution of camera motion parameters is estimated using the random sample consensus scheme (RANSAC). Based on this estimate, a refined posterior distribution of camera motion parameters can then be obtained through importance sampling. Experimental results using both synthetic and real image sequences indicate the efficacy of the proposed algorithm.}, keywords = {3D, baseline, Bayesian, CAMERAS, cameras;, coarse-to-fine, consensus, density, estimation;, feature, function;, hierarchy, image, images;, importance, matching;, MOTION, posterior, probability, probability;, processing;, random, RANSAC;, real, realistic, sample, sampling;, scheme;, sequences;, stereo, strategy;, synthetic, wide}, doi = {10.1109/ICIP.2004.1419754}, author = {Qian, G. and Chellapa, Rama and Qinfen Zheng} } @conference {12687, title = {Robust ego-motion estimation and 3D model refinement using depth based parallax model}, booktitle = {Image Processing, 2004. ICIP {\textquoteright}04. 2004 International Conference on}, volume = {4}, year = {2004}, month = {2004/10//}, pages = {2483 - 2486 Vol. 4 - 2483 - 2486 Vol. 4}, abstract = {We present an iterative algorithm for robustly estimating the ego-motion and refining and updating a coarse, noisy and partial depth map using a depth based parallax model and brightness derivatives extracted from an image pair. Given a coarse, noisy and partial depth map acquired by a range-finder or obtained from a Digital Elevation Map (DFM), we first estimate the ego-motion by combining a global ego-motion constraint and a local brightness constancy constraint. Using the estimated camera motion and the available depth map estimate, motion of the 3D points is compensated. We utilize the fact that the resulting surface parallax field is an epipolar field and knowing its direction from the previous motion estimates, estimate its magnitude and use it to refine the depth map estimate. Instead of assuming a smooth parallax field or locally smooth depth models, we locally model the parallax magnitude using the depth map, formulate the problem as a generalized eigen-value analysis and obtain better results. In addition, confidence measures for depth estimates are provided which can be used to remove regions with potentially incorrect (and outliers in) depth estimates for robustly estimating ego-motion in the next iteration. Results on both synthetic and real examples are presented.}, keywords = {3D, algorithm;, analysis;, and, based, camera;, coarse, compensation;, DEM;, depth, digital, ego-motion, eigen-value, eigenfunctions;, eigenvalues, ELEVATION, epipolar, estimation;, extraction;, feature, field;, iteration, iterative, map;, method;, methods;, model, model;, MOTION, parallax, partial, range-finding;, refinement;, refining;, surface}, doi = {10.1109/ICIP.2004.1421606}, author = {Agrawala, Ashok K. and Chellapa, Rama} } @conference {12702, title = {Robust two-camera tracking using homography}, booktitle = {Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP {\textquoteright}04). IEEE International Conference on}, volume = {3}, year = {2004}, month = {2004/05//}, pages = {iii - 1-4 vol.3 - iii - 1-4 vol.3}, abstract = {The paper introduces a two view tracking method which uses the homography relation between the two views to handle occlusions. An adaptive appearance-based model is incorporated in a particle filter to realize robust visual tracking. Occlusion is detected using robust statistics. When there is occlusion in one view, the homography from this view to other views is estimated from previous tracking results and used to infer the correct transformation for the occluded view. Experimental results show the robustness of the two view tracker.}, keywords = {Carlo, filter;, filters;, frame, framework;, homography;, image, method;, methods;, Monte, nonlinear, occlusions;, optical, particle, processing;, robust, sequences;, sequential, signal, statistics;, tracking, tracking;, two, two-camera, video, view, visual}, doi = {10.1109/ICASSP.2004.1326466}, author = {Yue,Zhanfeng and Zhou,S. K and Chellapa, Rama} } @conference {12696, title = {Role of shape and kinematics in human movement analysis}, booktitle = {Computer Vision and Pattern Recognition, 2004. CVPR 2004. Proceedings of the 2004 IEEE Computer Society Conference on}, volume = {1}, year = {2004}, month = {2004/07/02/june}, pages = {I-730 - I-737 Vol.1 - I-730 - I-737 Vol.1}, abstract = {Human gait and activity analysis from video is presently attracting a lot of attention in the computer vision community. In this paper we analyze the role of two of the most important cues in human motion-shape and kinematics. We present an experimental framework whereby it is possible to evaluate the relative importance of these two cues in computer vision based recognition algorithms. In the process, we propose a new gait recognition algorithm by computing the distance between two sequences of shapes that lie on a spherical manifold. In our experiments, shape is represented using Kendall{\textquoteright}s definition of shape. Kinematics is represented using a Linear Dynamical system We place particular emphasis on human gait. Our conclusions show that shape plays a role which is more significant than kinematics in current automated gait based human identification algorithms. As a natural extension we study the role of shape and kinematics in activity recognition. Our experiments indicate that we require models that contain both shape and kinematics in order to perform accurate activity classification. These conclusions also allow us to explain the relative performance of many existing methods in computer-based human activity modeling.}, keywords = {activity, algorithm;, algorithms;, analysis;, autoregressive, average, based, classification;, community;, Computer, definition;, dynamical, extraction;, feature, Gait, hidden, human, identification, image, Kendall, linear, manifold;, Markov, modeling;, models;, MOTION, Movement, moving, processes;, recognition, sequences;, SHAPE, spherical, system;, VISION, vision;}, doi = {10.1109/CVPR.2004.1315104}, author = {Veeraraghavan,A. and Chowdhury, A.R. and Chellapa, Rama} } @article {13020, title = {Section-level relationships of North American {\i}t Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions}, journal = {BMC Evol Biol}, volume = {4}, year = {2004}, month = {2004/06//}, pages = {15 - 15}, abstract = {BACKGROUND: The North American Agalinis are representatives of a taxonomically difficult group that has been subject to extensive taxonomic revision from species level through higher sub-generic designations (e.g., subsections and sections). Previous presentations of relationships have been ambiguous and have not conformed to modern phylogenetic standards (e.g., were not presented as phylogenetic trees). Agalinis contains a large number of putatively rare taxa that have some degree of taxonomic uncertainty. We used DNA sequence data from three chloroplast genes to examine phylogenetic relationships among sections within the genus Agalinis Raf. (=Gerardia), and between Agalinis and closely related genera within Orobanchaceae. RESULTS: Maximum likelihood analysis of sequences data from rbcL, ndhF, and matK gene regions (total aligned length 7323 bp) yielded a phylogenetic tree with high bootstrap values for most branches. Likelihood ratio tests showed that all but a few branch lengths were significantly greater than zero, and an additional likelihood ratio test rejected the molecular clock hypothesis. Comparisons of substitution rates between gene regions based on linear models of pairwise distance estimates between taxa show both ndhF and matK evolve more rapidly than rbcL, although the there is substantial rate heterogeneity within gene regions due in part to rate differences among codon positions. CONCLUSIONS: Phylogenetic analysis supports the monophyly of Agalinis, including species formerly in Tomanthera, and this group is sister to a group formed by the genera Aureolaria, Brachystigma, Dasistoma, and Seymeria. Many of the previously described sections within Agalinis are polyphyletic, although many of the subsections appear to form natural groups. The analysis reveals a single evolutionary event leading to a reduction in chromosome number from n = 14 to n = 13 based on the sister group relationship of section Erectae and section Purpureae subsection Pedunculares. Our results establish the evolutionary distinctiveness of A. tenella from the more widespread and common A. obtusifolia. However, further data are required to clearly resolve the relationship between A. acuta and A. tenella.}, doi = {10.1186/1471-2148-4-15}, author = {Neel,M. C and Cummings, Michael P.} } @article {13325, title = {Selective refinement queries for volume visualization of unstructured tetrahedral meshes}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {10}, year = {2004}, month = {2004///}, pages = {29 - 45}, abstract = {We address the problem of the efficient visualization of large irregular volume data sets by exploiting a multiresolution model based on tetrahedral meshes. Multiresolution models, also called Level-Of-Detail (LOD) models, allow encoding the whole data set at a virtually continuous range of different resolutions. We have identified a set of queries for extracting meshes at variable resolution from a multiresolution model, based on field values, domain location, or opacity of the transfer function. Such queries allow trading off between resolution and speed in visualization. We define a new compact data structure for encoding a multiresolution tetrahedral mesh built through edge collapses to support selective refinement efficiently and show that such a structure has a storage cost from 3 to 5.5 times lower than standard data structures used for tetrahedral meshes. The data structures and variable resolution queries have been implemented together with state-of-the art visualization techniques in a system for the interactive visualization of three-dimensional scalar fields defined on tetrahedral meshes. Experimental results show that selective refinement queries can support interactive visualization of large data sets.}, keywords = {Automated;Signal Processing, Computer-Assisted;Imaging, Computer-Assisted;User-Computer Interface;, data structure;geometric modeling;interactive visualization;large data sets;multiresolution model;selective refinement queries;unstructured tetrahedral meshes;variable resolution queries;volume data visualization;data visualisation;mesh generation;query p, Three-Dimensional;Online Systems;Pattern Recognition}, isbn = {1077-2626}, doi = {10.1109/TVCG.2004.1260756}, author = {Cignoni,P. and De Floriani, Leila and Magillo,P. and Puppo,E. and Scopigno,R.} } @article {15273, title = {A semidefinite programming approach to side chain positioning with new rounding strategies}, journal = {INFORMS Journal on Computing}, volume = {16}, year = {2004}, month = {2004///}, pages = {380 - 392}, author = {Chazelle,B. and Kingsford, Carl and Singh,M.} } @article {13230, title = {Sequential kernel density approximation through mode propagation: applications to background modeling}, journal = {Proc. ACCV}, volume = {2004}, year = {2004}, month = {2004///}, abstract = {Density-based modeling of visual features is very commonin computer vision, either by using non-parametric techniques or through representing the underlying density function as a weighted sum of Gaussians. A number of real-time tasks such as background modeling or modeling the appearance of a moving target require sequential density estimation, where new data is incorporated in the model as it becomes avail- able. Nevertheless, current methods for updating the den- sity function either lack flexibility, by fixing the number of Gaussians in the mixture, or require large memory amounts, by maintaining a non-parametric representation of the den- sity. This paper presents an efficient method for recursive density approximation that relies on the propagation of the density modes. At each time step, the modes of the density are re-estimated and a Gaussian component is assigned to each mode. The covariance of each component is derived from the Hessian matrix estimated at the mode location. To detect the modes we employ the variable-bandwidth mean shift. While the proposed density representation is mem- ory efficient (which is typical for mixture densities), it in- herits the flexibility of non-parametric methods, by allow- ing the number of modes to adapt in time. We show that the same mode propagation principle applies for subspaces derived from eigen analysis. Extensive experimental back- ground modeling results demonstrate the performance of the method. }, author = {Han,B. and Comaniciu, D. and Davis, Larry S.} } @article {17657, title = {SESSION 2: STREAMING}, journal = {Proceedings of the 14th International Workshop on Network and Operating Systems Support for Digital Audio and Video: NOSSDAV 2003: June 16-18, 2004, Cork, Ireland}, year = {2004}, month = {2004///}, pages = {3 - 3}, author = {Banerjee,S. and Lee,S. and Braud,R. and Bhattacharjee, Bobby and Srinivasan, Aravind and Chu,Y. and Zhang,H. and Sinha,R. and Papadopoulos,C. and Boustead,P. and others} } @article {13021, title = {Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA}, journal = {BMC Bioinformatics}, volume = {5}, year = {2004}, month = {2004/09//}, pages = {132 - 132}, abstract = {BACKGROUND: RNA editing is the process whereby an RNA sequence is modified from the sequence of the corresponding DNA template. In the mitochondria of land plants, some cytidines are converted to uridines before translation. Despite substantial study, the molecular biological mechanism by which C-to-U RNA editing proceeds remains relatively obscure, although several experimental studies have implicated a role for cis-recognition. A highly non-random distribution of nucleotides is observed in the immediate vicinity of edited sites (within 20 nucleotides 5{\textquoteright} and 3{\textquoteright}), but no precise consensus motif has been identified. RESULTS: Data for analysis were derived from the the complete mitochondrial genomes of Arabidopsis thaliana, Brassica napus, and Oryza sativa; additionally, a combined data set of observations across all three genomes was generated. We selected datasets based on the 20 nucleotides 5{\textquoteright} and the 20 nucleotides 3{\textquoteright} of edited sites and an equivalently sized and appropriately constructed null-set of non-edited sites. We used tree-based statistical methods and random forests to generate models of C-to-U RNA editing based on the nucleotides surrounding the edited/non-edited sites and on the estimated folding energies of those regions. Tree-based statistical methods based on primary sequence data surrounding edited/non-edited sites and estimates of free energy of folding yield models with optimistic re-substitution-based estimates of approximately 0.71 accuracy, approximately 0.64 sensitivity, and approximately 0.88 specificity. Random forest analysis yielded better models and more exact performance estimates with approximately 0.74 accuracy, approximately 0.72 sensitivity, and approximately 0.81 specificity for the combined observations. CONCLUSIONS: Simple models do moderately well in predicting which cytidines will be edited to uridines, and provide the first quantitative predictive models for RNA edited sites in plant mitochondria. Our analysis shows that the identity of the nucleotide -1 to the edited C and the estimated free energy of folding for a 41 nt region surrounding the edited C are the most important variables that distinguish most edited from non-edited sites. However, the results suggest that primary sequence data and simple free energy of folding calculations alone are insufficient to make highly accurate predictions.}, doi = {10.1186/1471-2105-5-132}, author = {Cummings, Michael P. and Myers,D. S} } @conference {12684, title = {Simultaneous background and foreground modeling for tracking in surveillance video}, booktitle = {Image Processing, 2004. ICIP {\textquoteright}04. 2004 International Conference on}, volume = {2}, year = {2004}, month = {2004/10//}, pages = {1053 - 1056 Vol.2 - 1053 - 1056 Vol.2}, abstract = {We present a stochastic tracking algorithm for surveillance video where targets are dim and at low resolution. The algorithm builds motion models for both background and foreground by integrating motion and intensity information. Some other merits of the algorithm include adaptive selection of feature points for scene description and defining proper cost functions for displacement estimation. The experimental results show tracking robustness and precision in a challenging video sequences.}, keywords = {algorithm;, analysis;, background-foreground, displacement, estimation;, image, information;, INTENSITY, modeling;, MOTION, processes;, processing;, resolution;, sequences;, signal, Stochastic, Surveillance, surveillance;, tracking, tracking;, video}, doi = {10.1109/ICIP.2004.1419483}, author = {Shao, J. and Zhou,S. K and Chellapa, Rama} } @article {12171, title = {SlideBar: Analysis of a linear input device}, journal = {Behaviour \& Information Technology}, volume = {23}, year = {2004}, month = {2004///}, pages = {1 - 9}, author = {Chipman,L.E. and Bederson, Benjamin B. and Golbeck,J.} } @inbook {17367, title = {Social and psychological influences on computer user frustration}, booktitle = {Media access: Social and psychological dimensions of new technology useMedia access: Social and psychological dimensions of new technology use}, year = {2004}, month = {2004///}, pages = {91 - 103}, author = {Bessiere,K. and Ceaparu,I. and Lazar,J. and Robinson,J. and Shneiderman, Ben} } @article {12714, title = {Structure from Motion Using Sequential Monte Carlo Methods}, journal = {International Journal of Computer Vision}, volume = {59}, year = {2004}, month = {2004///}, pages = {5 - 31}, abstract = {In this paper, the structure from motion (SfM) problem is addressed using sequential Monte Carlo methods. A new SfM algorithm based on random sampling is derived to estimate the posterior distributions of camera motion and scene structure for the perspective projection camera model. Experimental results show that challenging issues in solving the SfM problem, due to erroneous feature tracking, feature occlusion, motion/structure ambiguity, mixed-domain sequences, mismatched features, and independently moving objects, can be well modeled and effectively addressed using the proposed method.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1023/B:VISI.0000020669.68126.4b}, author = {Qian,Gang and Chellapa, Rama} } @conference {14761, title = {Studying code development for high performance computing: the HPCS program}, booktitle = {First International Workshop On Software Engineering for High Performance Computing System Applications}, year = {2004}, month = {2004///}, pages = {32 - 32}, author = {Carver, J. and Asgari, S. and Basili, Victor R. and Hochstein, L. and Hollingsworth, Jeffrey K and Shull, F. and Zelkowitz, Marvin V} } @conference {12694, title = {A system identification approach for video-based face recognition}, booktitle = {Pattern Recognition, 2004. ICPR 2004. Proceedings of the 17th International Conference on}, volume = {4}, year = {2004}, month = {2004/08//}, pages = {175 - 178 Vol.4 - 175 - 178 Vol.4}, abstract = {The paper poses video-to-video face recognition as a dynamical system identification and classification problem. We model a moving face as a linear dynamical system whose appearance changes with pose. An autoregressive and moving average (ARMA) model is used to represent such a system. The choice of ARMA model is based on its ability to take care of the change in appearance while modeling the dynamics of pose, expression etc. Recognition is performed using the concept of sub space angles to compute distances between probe and gallery video sequences. The results obtained are very promising given the extent of pose, expression and illumination variation in the video data used for experiments.}, keywords = {and, autoregressive, average, dynamical, Face, gallery, identification;, image, linear, model;, moving, processes;, processing;, recognition;, sequences;, signal, system, system;, video, video-based}, doi = {10.1109/ICPR.2004.1333732}, author = {Aggarwal,G. and Chowdhury, A.K.R. and Chellapa, Rama} } @inbook {12944, title = {A Tangled Bank: Reflections on the Tree of Life and Human Health}, booktitle = {Assembling the Tree of LifeAssembling the Tree of Life}, year = {2004}, month = {2004///}, pages = {18 - 18}, publisher = {Oxford University Press}, organization = {Oxford University Press}, isbn = {9780195172348}, author = {Rita R Colwell} } @article {13909, title = {Tools for children to create physical interactive storyrooms}, journal = {Computers in Entertainment (CIE)}, volume = {2}, year = {2004}, month = {2004///}, pages = {12 - 12}, author = {Montemayor,J. and Druin, Allison and Chipman,G. and Farber,A. and Guha,M.L.} } @article {18725, title = {Ubistatins Inhibit Proteasome-Dependent Degradation by Binding the Ubiquitin Chain}, journal = {Science}, volume = {306}, year = {2004}, month = {2004/10/01/}, pages = {117 - 120}, abstract = {To identify previously unknown small molecules that inhibit cell cycle machinery, we performed a chemical genetic screen in Xenopus extracts. One class of inhibitors, termed ubistatins, blocked cell cycle progression by inhibiting cyclin B proteolysis and inhibited degradation of ubiquitinated Sic1 by purified proteasomes. Ubistatins blocked the binding of ubiquitinated substrates to the proteasome by targeting the ubiquitin-ubiquitin interface of Lys48-linked chains. The same interface is recognized by ubiquitin-chain receptors of the proteasome, indicating that ubistatins act by disrupting a critical protein-protein interaction in the ubiquitin-proteasome system.}, doi = {10.1126/science.1100946}, url = {http://www.sciencemag.org/cgi/content/abstract/sci;306/5693/117}, author = {Verma,Rati and Peters,Noel R. and D{\textquoteright}Onofrio,Mariapina and Tochtrop,Gregory P. and Sakamoto,Kathleen M. and Varadan,Ranjani and Zhang,Mingsheng and Coffino,Philip and Fushman, David and Deshaies,Raymond J. and King,Randall W.} } @article {12792, title = {Unit verification: the CARA experience}, journal = {International Journal on Software Tools for Technology Transfer (STTT)}, volume = {5}, year = {2004}, month = {2004///}, pages = {351 - 369}, author = {Ray,A. and Cleaveland, Rance} } @article {12942, title = {Variation of toxigenic Vibrio cholerae O1 in the aquatic environment of Bangladesh and its correlation with the clinical strains}, journal = {Microbiology and immunology}, volume = {48}, year = {2004}, month = {2004///}, pages = {773 - 777}, author = {Islam,M. S. and Talukder,K. A. and Khan,N. H. and Mahmud,Z. H. and Rahman,M. Z. and Nair,G. B. and Siddique,A. K. M. and Yunus,M. and Sack,D. A. and Sack,R. B. and Rita R Colwell} } @conference {12705, title = {Vehicle detection and tracking using acoustic and video sensors}, booktitle = {Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP {\textquoteright}04). IEEE International Conference on}, volume = {3}, year = {2004}, month = {2004/05//}, pages = {iii - 793-6 vol.3 - iii - 793-6 vol.3}, abstract = {Multimodal sensing has attracted much attention in solving a wide range of problems, including target detection, tracking, classification, activity understanding, speech recognition, etc. In surveillance applications, different types of sensors, such as video and acoustic sensors, provide distinct observations of ongoing activities. We present a fusion framework using both video and acoustic sensors for vehicle detection and tracking. In the detection phase, a rough estimate of target direction-of-arrival (DOA) is first obtained using acoustic data through beam-forming techniques. This initial DOA estimate designates the approximate target location in video. Given the initial target position, the DOA is refined by moving target detection using the video data. Markov chain Monte Carlo techniques are then used for joint audio-visual tracking. A novel fusion approach has been proposed for tracking, based on different characteristics of audio and visual trackers. Experimental results using both synthetic and real data are presented. Improved tracking performance has been observed by fusing the empirical posterior probability density functions obtained using both types of sensors.}, keywords = {acoustic, applications;, audio, audio-visual, beam-forming, Carlo, chain, density, detection;, direction-of-arrival, DOA, empirical, estimation;, framework;, functions;, fusion, fusion;, joint, Markov, methods;, Monte, moving, multimodal, object, optical, posterior, probability, probability;, processes;, processing;, sensing;, sensor, sensors;, signal, Surveillance, surveillance;, systems;, target, techniques;, tracking;, vehicle, video}, doi = {10.1109/ICASSP.2004.1326664}, author = {Chellapa, Rama and Qian,Gang and Qinfen Zheng} } @article {12936, title = {Viable but Nonculturable Vibrio Cholerae O1 in the Aquatic Environment of Argentina}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {70}, year = {2004}, month = {2004/12/01/}, pages = {7481 - 7486}, abstract = {In Argentina, as in other countries of Latin America, cholera has occurred in an epidemic pattern. Vibrio cholerae O1 is native to the aquatic environment, and it occurs in both culturable and viable but nonculturable (VNC) forms, the latter during interepidemic periods. This is the first report of the presence of VNC V. cholerae O1 in the estuarine and marine waters of the R{\'\i}o de la Plata and the Argentine shelf of the Atlantic Ocean, respectively. Employing immunofluorescence and PCR methods, we were able to detect reservoirs of V. cholerae O1 carrying the virulence-associated genes ctxA and tcpA. The VNC forms of V. cholerae O1 were identified in samples of water, phytoplankton, and zooplankton; the latter organisms were mainly the copepods Acartia tonsa, Diaptomus sp., Paracalanus crassirostris, and Paracalanus parvus. We found that under favorable conditions, the VNC form of V. cholerae can revert to the pathogenic, transmissible state. We concluded that V. cholerae O1 is a resident of Argentinean waters, as has been shown to be the case in other geographic regions of the world.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.70.12.7481-7486.2004}, url = {http://aem.asm.org/content/70/12/7481}, author = {Binsztein,Norma and Costagliola,Marcela C. and Pichel,Mariana and Jurquiza,Ver{\'o}nica and Ram{\'\i}rez,Fernando C. and Akselman,Rut and Vacchino,Marta and Huq,Anwarul and Rita R Colwell} } @article {12680, title = {Video-Based Automatic Target Recognition}, year = {2004}, month = {2004/12//}, institution = {MARYLAND UNIV COLLEGE PARK CENTER FOR AUTOMATION RESEARCH}, abstract = {We present an approach for vehicle classification in IR video sequences by integrating detection, tracking and recognition. The method has two steps. First, the moving target is automatically detected using a detection algorithm. Next, we perform simultaneous tracking and recognition using an appearance-model based particle filter. The tracking result is evaluated at each frame. Low confidence in tracking performance initiates a new cycle of detection, tracking and classification. We demonstrate the robustness of the proposed method using outdoor IR video sequences.}, keywords = {*SEQUENCES(MATHEMATICS), *TARGET RECOGNITION, *VEHICLES, *VIDEO RECORDING, algorithms, AUTOMATIC TRACKING., COMPONENT REPORTS, MOVING TARGETS, SURFACE TRANSPORTATION AND EQUIPMENT, SYMPOSIA, TARGET CLASSIFICATION, TARGET DIRECTION, RANGE AND POSITION FINDING, tracking, VIDEO SIGNALS}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA431617}, author = {Zhou,S. K and Chellapa, Rama and Mei,Xue and Wu,Hao and Qinfen Zheng} } @conference {12697, title = {View independent human body pose estimation from a single perspective image}, booktitle = {Computer Vision and Pattern Recognition, 2004. CVPR 2004. Proceedings of the 2004 IEEE Computer Society Conference on}, volume = {2}, year = {2004}, month = {2004/07/02/june}, pages = {II-16 - II-22 Vol.2 - II-16 - II-22 Vol.2}, abstract = {Recovering the 3D coordinates of various joints of the human body from an image is a critical first step for several model-based human tracking and optical motion capture systems. Unlike previous approaches that have used a restrictive camera model or assumed a calibrated camera, our work deals with the general case of a perspective uncalibrated camera and is thus well suited for archived video. The input to the system is an image of the human body and correspondences of several body landmarks, while the output is the set of 3D coordinates of the landmarks in a body-centric coordinate system. Using ideas from 3D model based invariants, we set up a polynomial system of equations in the unknown head pitch, yaw and roll angles. If we are able to make the often-valid assumption that the torso twist is small, there are finite numbers of solutions to the head-orientation that can be computed readily. Once the head orientation is computed, the epipolar geometry of the camera is recovered, leading to solutions to the 3D joint positions. Results are presented on synthetic and real images.}, keywords = {3D, analysis;, biomechanics;, body, body-centric, camera;, capture, coordinate, coordinates;, detection;, epipolar, equation, estimation;, geometry;, human, image, image;, images;, model-based, models;, MOTION, object, optical, perspective, physiological, polynomial, polynomials;, pose, real, single, synthetic, system;, systems;, torso, tracking;, twist;, uncalibrated}, doi = {10.1109/CVPR.2004.1315139}, author = {Parameswaran, V. and Chellapa, Rama} } @article {12682, title = {Visual tracking and recognition using appearance-adaptive models in particle filters}, journal = {IEEE Transactions on Image Processing}, volume = {13}, year = {2004}, month = {2004/11//}, pages = {1491 - 1506}, abstract = {We present an approach that incorporates appearance-adaptive models in a particle filter to realize robust visual tracking and recognition algorithms. Tracking needs modeling interframe motion and appearance changes, whereas recognition needs modeling appearance changes between frames and gallery images. In conventional tracking algorithms, the appearance model is either fixed or rapidly changing, and the motion model is simply a random walk with fixed noise variance. Also, the number of particles is typically fixed. All these factors make the visual tracker unstable. To stabilize the tracker, we propose the following modifications: an observation model arising from an adaptive appearance model, an adaptive velocity motion model with adaptive noise variance, and an adaptive number of particles. The adaptive-velocity model is derived using a first-order linear predictor based on the appearance difference between the incoming observation and the previous particle configuration. Occlusion analysis is implemented using robust statistics. Experimental results on tracking visual objects in long outdoor and indoor video sequences demonstrate the effectiveness and robustness of our tracking algorithm. We then perform simultaneous tracking and recognition by embedding them in a particle filter. For recognition purposes, we model the appearance changes between frames and gallery images by constructing the intra- and extrapersonal spaces. Accurate recognition is achieved when confronted by pose and view variations.}, keywords = {adaptive filters, adaptive noise variance, algorithms, appearance-adaptive model, Artificial intelligence, Cluster Analysis, Computer Graphics, Computer simulation, Feedback, Filtering, first-order linear predictor, hidden feature removal, HUMANS, Image Enhancement, Image Interpretation, Computer-Assisted, image recognition, Information Storage and Retrieval, Kinematics, Laboratories, Male, Models, Biological, Models, Statistical, MOTION, Movement, Noise robustness, Numerical Analysis, Computer-Assisted, occlusion analysis, Particle filters, Particle tracking, Pattern Recognition, Automated, Predictive models, Reproducibility of results, robust statistics, Sensitivity and Specificity, Signal Processing, Computer-Assisted, State estimation, statistical analysis, Subtraction Technique, tracking, Training data, visual recognition, visual tracking}, isbn = {1057-7149}, doi = {10.1109/TIP.2004.836152}, author = {Zhou,Shaohua Kevin and Chellapa, Rama and Moghaddam, B.} } @article {12189, title = {Visualizations for taxonomic and phylogenetic trees}, journal = {Bioinformatics}, volume = {20}, year = {2004}, month = {2004///}, pages = {2997 - 2997}, author = {Parr,C.S. and Lee,B. and Campbell,D. and Bederson, Benjamin B.} } @article {12699, title = {Wide baseline image registration with application to 3-D face modeling}, journal = {Multimedia, IEEE Transactions on}, volume = {6}, year = {2004}, month = {2004/06//}, pages = {423 - 434}, abstract = {Establishing correspondence between features in two images of the same scene taken from different viewing angles is a challenging problem in image processing and computer vision. However, its solution is an important step in many applications like wide baseline stereo, three-dimensional (3-D) model alignment, creation of panoramic views, etc. In this paper, we propose a technique for registration of two images of a face obtained from different viewing angles. We show that prior information about the general characteristics of a face obtained from video sequences of different faces can be used to design a robust correspondence algorithm. The method works by matching two-dimensional (2-D) shapes of the different features of the face (e.g., eyes, nose etc.). A doubly stochastic matrix, representing the probability of match between the features, is derived using the Sinkhorn normalization procedure. The final correspondence is obtained by minimizing the probability of error of a match between the entire constellation of features in the two sets, thus taking into account the global spatial configuration of the features. The method is applied for creating holistic 3-D models of a face from partial representations. Although this paper focuses primarily on faces, the algorithm can also be used for other objects with small modifications.}, keywords = {2D, 3D, algorithm;, baseline, biometrics;, Computer, configuration;, correspondence, doubly, error, extraction;, Face, feature, holistic, image, matching;, matrix;, minimization;, modeling;, models;, normalization, probability, probability;, procedure;, processes;, processing;, recognition;, registration;, representation;, sequences;, shapes;, Sinkhorn, spatial, statistics;, Stochastic, video, vision;, wide}, isbn = {1520-9210}, doi = {10.1109/TMM.2004.827511}, author = {Roy-Chowdhury, A.K. and Chellapa, Rama and Keaton, T.} } @article {12955, title = {A 4-Year Study of the Epidemiology of Vibrio Cholerae in Four Rural Areas of Bangladesh}, journal = {Journal of Infectious DiseasesJ Infect Dis.}, volume = {187}, year = {2003}, month = {2003/01/01/}, pages = {96 - 101}, abstract = {How Vibrio cholerae spreads around the world and what determines its seasonal peaks in endemic areas are not known. These features of cholera have been hypothesized to be primarily the result of environmental factors associated with aquatic habitats that can now be identified. Since 1997, fortnightly surveillance in 4 widely separated geographic locations in Bangladesh has been performed to identify patients with cholera and to collect environmental data. A total of 5670 patients (53\% <5 years of age) have been studied; 14.3\% had cholera (10.4\% due to V. cholerae O1 El Tor, 3.8\% due to O139). Both serogroups were found in all locations; outbreaks were seasonal and often occurred simultaneously. Water-use patterns showed that bathing and washing clothes in tube-well water was significantly protective in two of the sites. These data will be correlated with environmental factors, to develop a model for prediction of cholera outbreaks}, isbn = {0022-1899, 1537-6613}, doi = {10.1086/345865}, url = {http://jid.oxfordjournals.org/content/187/1/96}, author = {Sack,R. Bradley and Siddique,A. Kasem and Longini,Ira M. and Nizam,Azhar and Yunus,Md and M. Sirajul Islam and Morris,Jr and Ali,Afsar and Huq,Anwar and Nair,G. Balakrish and Qadri,Firdausi and Faruque,Shah M. and Sack,David A. and Rita R Colwell} } @article {12719, title = {Accurate dense optical flow estimation using adaptive structure tensors and a parametric model}, journal = {Image Processing, IEEE Transactions on}, volume = {12}, year = {2003}, month = {2003/10//}, pages = {1170 - 1180}, abstract = {An accurate optical flow estimation algorithm is proposed in this paper. By combining the three-dimensional (3D) structure tensor with a parametric flow model, the optical flow estimation problem is converted to a generalized eigenvalue problem. The optical flow can be accurately estimated from the generalized eigenvectors. The confidence measure derived from the generalized eigenvalues is used to adaptively adjust the coherent motion region to further improve the accuracy. Experiments using both synthetic sequences with ground truth and real sequences illustrate our method. Comparisons with classical and recently published methods are also given to demonstrate the accuracy of our algorithm.}, keywords = {3D, accuracy;, adaptive, and, coherent, confidence, dense, eigenfunctions;, eigenvalue, eigenvalues, eigenvectors;, estimation;, flow, generalized, ground, image, measure;, model;, MOTION, optical, parameter, parametric, problem;, real, region;, sequences;, structure, synthetic, tensor;, tensors;, three-dimensional, truth;}, isbn = {1057-7149}, doi = {10.1109/TIP.2003.815296}, author = {Liu,Haiying and Chellapa, Rama and Rosenfeld, A.} } @article {12745, title = {Activity modeling and recognition using shape theory}, journal = {Behavior Representation in Modeling and Simulation}, year = {2003}, month = {2003///}, abstract = {Understanding activities arising out of the interactions of aconfiguration of moving objects is an important problem in video understanding, with applications in surveillance and monitoring, animation, medicine, etc. In this paper, we in- troduce a novel method for activity modeling based on the observation that that every activity has with it an associated structure characterized by a non-rigid shape and a dynamic model that characterizes the variations in the structure as the activity unfolds. We propose two mathematical models to characterize the non-rigid shape and its dynamics. In our first approach, we propose to model an activity by the polygonal shape formed by joining the locations of these point masses at any time , and its deformation over time. This uses the statistical shape theory of Kendall. The second approach models the trajectories of each separate class of moving objects in 3D shape space, and thus can identify dif- ferent kinds of activities. It is based on the factorization the- orem for matrices, which has been used before in computer vision for structure estimation. Deviations from the learned normal shape for each activity is used to identify abnormal ones. We demonstrate the applicability of our algorithms using real-life video sequences in an airport surveillance environment. We are able to identify the major activities that take place in that setting and detect abnormal ones. }, author = {Chellapa, Rama and Vaswani, N. and Chowdhury, A.K.R.} } @conference {12729, title = {Activity recognition using the dynamics of the configuration of interacting objects}, booktitle = {Computer Vision and Pattern Recognition, 2003. Proceedings. 2003 IEEE Computer Society Conference on}, volume = {2}, year = {2003}, month = {2003/06//}, pages = {II - 633-40 vol.2 - II - 633-40 vol.2}, abstract = {Monitoring activities using video data is an important surveillance problem. A special scenario is to learn the pattern of normal activities and detect abnormal events from a very low resolution video where the moving objects are small enough to be modeled as point objects in a 2D plane. Instead of tracking each point separately, we propose to model an activity by the polygonal {\textquoteright}shape{\textquoteright} of the configuration of these point masses at any time t, and its deformation over time. We learn the mean shape and the dynamics of the shape change using hand-picked location data (no observation noise) and define an abnormality detection statistic for the simple case of a test sequence with negligible observation noise. For the more practical case where observation (point locations) noise is large and cannot be ignored, we use a particle filter to estimate the probability distribution of the shape given the noisy observations up to the current time. Abnormality detection in this case is formulated as a change detection problem. We propose a detection strategy that can detect both {\textquoteright}drastic{\textquoteright} and {\textquoteright}slow{\textquoteright} abnormalities. Our framework can be directly applied for object location data obtained using any type of sensors - visible, radar, infrared or acoustic.}, keywords = {2D, abnormal, abnormality, abnormality;, acoustic, activity, analysis;, change;, Computer, configuration, configuration;, data;, DETECTION, detection;, distribution;, drastic, dynamics;, event;, filter;, hand-picked, image, infrared, interacting, learning;, location, low, mean, model;, monitoring;, MOTION, moving, noise;, noisy, object, object;, observation, observation;, particle, pattern, plane;, point, polygonal, probability, probability;, problem;, processing;, radar, recognition;, resolution, sensor;, sensors;, sequence;, SHAPE, shape;, signal, slow, statistic;, strategy;, Surveillance, surveillance;, target, test, tracking;, video, video;, visible, vision;}, doi = {10.1109/CVPR.2003.1211526}, author = {Vaswani, N. and RoyChowdhury, A. and Chellapa, Rama} } @article {18652, title = {An adaptive quality of service aware middleware for replicated services}, journal = {Parallel and Distributed Systems, IEEE Transactions on}, volume = {14}, year = {2003}, month = {2003/11//}, pages = {1112 - 1125}, abstract = {A dependable middleware should be able to adaptively share the distributed resources it manages in order to meet diverse application requirements, even when the quality of service (QoS) is degraded due to uncertain variations in load and unanticipated failures. We have addressed this issue in the context of a dependable middleware that adaptively manages replicated servers to deliver a timely and consistent response to time-sensitive client applications. These applications have specific temporal and consistency requirements, and can tolerate a certain degree of relaxed consistency in exchange for better response time. We propose a flexible QoS model that allows clients to specify their timeliness and consistency constraints. We also propose an adaptive framework that dynamically selects replicas to service a client{\textquoteright}s request based on the prediction made by probabilistic models. These models use the feedback from online performance monitoring of the replicas to provide probabilistic guarantees for meeting a client{\textquoteright}s QoS specification. The experimental results we have obtained demonstrate the role of feedback and the efficacy of simple analytical models for adaptively sharing the available replicas among the users under different workload scenarios.}, keywords = {distributed resource sharing, Middleware, online performance monitoring, probabilistic modeling, QoS specification, quality of service, replica consistency, replicated services, resource allocation, time-sensitive client applications, timeliness constraints}, isbn = {1045-9219}, doi = {10.1109/TPDS.2003.1247672}, author = {Krishnamurthy,Sudha and Sanders,W. H. and Michel Cukier} } @conference {12723, title = {Adaptive visual tracking and recognition using particle filters}, booktitle = {Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {2}, year = {2003}, month = {2003/07//}, pages = {II - 349-52 vol.2 - II - 349-52 vol.2}, abstract = {This paper presents an improved method for simultaneous tracking and recognition of human faces from video, where a time series model is used to resolve the uncertainties in tracking and recognition. The improvements mainly arise from three aspects: (i) modeling the inter-frame appearance changes within the video sequence using an adaptive appearance model and an adaptive-velocity motion model; (ii) modeling the appearance changes between the video frames and gallery images by constructing intra- and extra-personal spaces; and (iii) utilization of the fact that the gallery images are in frontal views. By embedding them in a particle filter, we are able to achieve a stabilized tracker and an accurate recognizer when confronted by pose and illumination variations.}, keywords = {adaptive, adaptive-velocity, appearance, extra-personal, Filtering, filters;, image, intra-personal, model;, MOTION, particle, processing;, recognition;, sequence;, sequences;, series, signal, spaces;, theory;, TIME, tracking;, video, visual}, doi = {10.1109/ICME.2003.1221625}, author = {Zhou,Shaohua and Chellapa, Rama and Moghaddam, B.} } @inbook {12738, title = {Airborne Video Registration for Activity Monitoring}, booktitle = {Video RegistrationVideo Registration}, series = {The Kluwer International Series in Video Computing}, volume = {5}, year = {2003}, month = {2003///}, pages = {130 - 143}, publisher = {Springer US}, organization = {Springer US}, abstract = {The analysis of ground activities involving vehicles and humans is of interest in airborne surveillance applications. The high spatiotemporal resolution of a video camera makes it the sensor of choice for such applications. In the past, video sensors were not preferred, precisely because of the high volume of data generated, which had to be processed manually for the most part. Further, the moving platform gives rise to numerous false alarms.}, isbn = {978-1-4615-0459-7}, url = {http://dx.doi.org/10.1007/978-1-4615-0459-7_6}, author = {Shekhar,Chandra and Chellapa, Rama}, editor = {Shah,Mubarak and Kumar,Rakesh and Shah,Mubarak} } @article {12956, title = {ANNUAL REVIEW \& FORECAST REPORTS-THE OCEANS: TO PROTECT AND TO PLOW}, journal = {Sea Technology}, volume = {44}, year = {2003}, month = {2003///}, pages = {33 - 34}, author = {Rita R Colwell} } @conference {12721, title = {An appearance based approach for human and object tracking}, booktitle = {Image Processing, 2003. ICIP 2003. Proceedings. 2003 International Conference on}, volume = {2}, year = {2003}, month = {2003/09//}, pages = {II - 85-8 vol.3 - II - 85-8 vol.3}, abstract = {A system for tracking humans and detecting human-object interactions in indoor environments is described. A combination of correlogram and histogram information is used to model object and human color distributions. Humans and objects are detected using a background subtraction algorithm. The models are built on the fly and used to track them on a frame by frame basis. The system is able to detect when people merge into groups and segment them during occlusion. Identities are preserved during the sequence, even if a person enters and leaves the scene. The system is also able to detect when a person deposits or removes an object from the scene. In the first case the models are used to track the object retroactively in time. In the second case the objects are tracked for the rest of the sequence. Experimental results using indoor video sequences are presented.}, keywords = {algorithm;, analysis;, background, basis;, by, Color, colour, correlogram, detection;, distributions;, frame, histogram, human, image, information;, object, processing;, segmentation;, sequences;, signal, subtraction, tracking;, video}, doi = {10.1109/ICIP.2003.1246622}, author = {Capellades,M. B and David Doermann and DeMenthon,D. and Chellapa, Rama} } @article {18661, title = {AQuA: an adaptive architecture that provides dependable distributed objects}, journal = {Computers, IEEE Transactions on}, volume = {52}, year = {2003}, month = {2003/01//}, pages = {31 - 50}, abstract = {Building dependable distributed systems from commercial off-the-shelf components is of growing practical importance. For both cost and production reasons, there is interest in approaches and architectures that facilitate building such systems. The AQuA architecture is one such approach; its goal is to provide adaptive fault tolerance to CORBA applications by replicating objects. The AQuA architecture allows application programmers to request desired levels of dependability during applications{\textquoteright} runtimes. It provides fault tolerance mechanisms to ensure that a CORBA client can always obtain reliable services, even if the CORBA server object that provides the desired services suffers from crash failures and value faults. AQuA includes a replicated dependability manager that provides dependability management by configuring the system in response to applications{\textquoteright} requests and changes in system resources due to faults. It uses Maestro/Ensemble to provide group communication services. It contains a gateway to intercept standard CORBA IIOP messages to allow any standard CORBA application to use AQuA. It provides different types of replication schemes to forward messages reliably to the remote replicated objects. All of the replication schemes ensure strong, data consistency among replicas. This paper describes the AQuA architecture and presents, in detail, the active replication pass-first scheme. In addition, the interface to the dependability manager and the design of the dependability manager replication are also described. Finally, we describe performance measurements that were conducted for the active replication pass-first scheme, and we present results from our study of fault detection, recovery, and blocking times.}, keywords = {active replication pass-first scheme, adaptive architecture, adaptive fault tolerance, AQuA, CORBA, data consistency, data integrity, dependable distributed objects, distributed object management, performance measurements, quality of service, replicated dependability manager, replication schemes, software fault tolerance, system resources}, isbn = {0018-9340}, doi = {10.1109/TC.2003.1159752}, author = {Ren,Yansong and Bakken,D. E. and Courtney,T. and Michel Cukier and Karr,D. A. and Rubel,P. and Sabnis,C. and Sanders,W. H. and Schantz,R.E. and Seri,M.} } @conference {12801, title = {Architectural Interaction Diagrams: AIDs for System Modeling}, booktitle = {Software Engineering, International Conference on}, year = {2003}, month = {2003///}, pages = {396 - 396}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper develops a modeling paradigm called Architectural Interaction Diagrams, or AIDs, for the high-level design of systems containing concurrent, interacting components. The novelty of AIDs is that they introduce interaction mechanisms, or buses, as first-class entities into the modeling vocabulary. Users then have the capability, in their modeling, of using buses whose behavior captures interaction at a higher level of abstraction than that afforded by modeling notations such as Message Sequence Charts or process algebra, which typically provide only one fixed interaction mechanism. This paper defines AIDs formally by giving them an operational semantics that describes how buses combine subsystem transitions into system-level transitions. This semantics enables AIDs to be simulated; to incorporate subsystems given in different modeling notations into a single system model; and to use testing, debugging and model checking early in the system design cycle in order to catch design errors before they are implemented.}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICSE.2003.1201218}, author = {Ray,Arnab and Cleaveland, Rance} } @article {15239, title = {Bistro: a scalable and secure data transfer service for digital government applications}, journal = {Communications of the ACM}, volume = {46}, year = {2003}, month = {2003/01//}, pages = {50 - 51}, abstract = {Government at all levels is a major collector and provider of data.Our project focuses on the collection of data over wide-area networks (WANs) and addresses the scalability issues that arise in the context of Internet-based massive data collection applications. Furthermore, security, due to the need for privacy and integrity of the data, is a central issue for data collection applications that use a public infrastructure such as the Internet. Numerous digital government applications require data collection over WANs [5].One compelling example of such an application is the Internal Revenue Service{\textquoteright}s electronic submission of income tax forms. Other digital government applications include collecting census data, federal statistics, and surveys; gathering and tallying of electronic votes; collecting crime data for the U.S. Justice department; collecting data from sensors for disaster response applications; collecting data from geological surveys; collecting electronic filings of patents, permits, and securities (for SEC) applications; grant proposals and contract bids submissions; and so on. All these applications have scalability and security needs in common.The poor performance that may be experienced by current digital government users, given the existing state of technology (as in Figure 1a), is largely due to how (independent) data transfers using TCP/IP work over the Internet. TCP/IP is good at equally sharing bandwidth between data streams, which in large-scale applications can lead to poor performance for individual clients (as they receive only a very small share of this bandwidth). Given that TCP/IP is here to stay for the foreseeable future, what is needed is a scalable yet cost- effective solution that can be easily deployed over the existing Internet technology.We are designing and developing a system called Bistro, which addresses the scalability needs of digital government data collection applications while allowing them to share the same infrastructure and resources efficiently, cost-effectively, and securely [1]. Bistro{\textquoteright}s basic approach is to introduce intermediate hosts---bistros---which allow replacement of a traditionally "synchronized client push" approach with a "nonsynchronized combination of client-push and server-pull" approach (as depicted in Figure 1b). This in turn allows spreading of the workload on the destination server and the network over time, with subsequent elimination of hot spots as well as significant improvements in performance for both clients and servers. Our ongoing research [2, 4] indicates that orders of magnitude of improvement can be achieved with the Bistro architecture and the corresponding data collection algorithms it affords.Bistro{\textquoteright}s design allows for a gradual deployment and experimentation over the Internet (by simply downloading Bistro server software and installing it on public servers). Bistro{\textquoteright}s security protocol and trust structure [3] are designed such that only encrypted data travels through (not necessarily trusted) bistros. This means a government agency does not need to trust bistros installed by other agencies or commercial institutions. At the same time, these (untrusted) bistros can significantly improve the agency{\textquoteright}s data collection performance. Each application (within each agency) can have its own scalability, security, fault tolerance, and other data collection needs, and these applications and agencies can still share available resources, if so desired, across all Bistro servers.We believe an appropriately designed single infrastructure such as Bistro can address all digital government wide-area data collection needs in a scalable, secure, and cost-effective manner. (For more information, see bourbon.usc.edu/iml/bistro/.}, isbn = {0001-0782}, doi = {10.1145/602421.602448}, url = {http://doi.acm.org/10.1145/602421.602448}, author = {Golubchik,Leana and Cheng,William C. and Chou,Cheng-Fu and Khuller, Samir and Samet, Hanan and Wan,C. Justin} } @article {16899, title = {Bistro: a scalable and secure data transfer service for digital government applications}, journal = {Commun. ACM}, volume = {46}, year = {2003}, month = {2003/01//}, pages = {50 - 51}, abstract = {Government at all levels is a major collector and provider of data.Our project focuses on the collection of data over wide-area networks (WANs) and addresses the scalability issues that arise in the context of Internet-based massive data collection applications. Furthermore, security, due to the need for privacy and integrity of the data, is a central issue for data collection applications that use a public infrastructure such as the Internet. Numerous digital government applications require data collection over WANs [5].One compelling example of such an application is the Internal Revenue Service{\textquoteright}s electronic submission of income tax forms. Other digital government applications include collecting census data, federal statistics, and surveys; gathering and tallying of electronic votes; collecting crime data for the U.S. Justice department; collecting data from sensors for disaster response applications; collecting data from geological surveys; collecting electronic filings of patents, permits, and securities (for SEC) applications; grant proposals and contract bids submissions; and so on. All these applications have scalability and security needs in common.The poor performance that may be experienced by current digital government users, given the existing state of technology (as in Figure 1a), is largely due to how (independent) data transfers using TCP/IP work over the Internet. TCP/IP is good at equally sharing bandwidth between data streams, which in large-scale applications can lead to poor performance for individual clients (as they receive only a very small share of this bandwidth). Given that TCP/IP is here to stay for the foreseeable future, what is needed is a scalable yet cost- effective solution that can be easily deployed over the existing Internet technology.We are designing and developing a system called Bistro, which addresses the scalability needs of digital government data collection applications while allowing them to share the same infrastructure and resources efficiently, cost-effectively, and securely [1]. Bistro{\textquoteright}s basic approach is to introduce intermediate hosts---bistros---which allow replacement of a traditionally "synchronized client push" approach with a "nonsynchronized combination of client-push and server-pull" approach (as depicted in Figure 1b). This in turn allows spreading of the workload on the destination server and the network over time, with subsequent elimination of hot spots as well as significant improvements in performance for both clients and servers. Our ongoing research [2, 4] indicates that orders of magnitude of improvement can be achieved with the Bistro architecture and the corresponding data collection algorithms it affords.Bistro{\textquoteright}s design allows for a gradual deployment and experimentation over the Internet (by simply downloading Bistro server software and installing it on public servers). Bistro{\textquoteright}s security protocol and trust structure [3] are designed such that only encrypted data travels through (not necessarily trusted) bistros. This means a government agency does not need to trust bistros installed by other agencies or commercial institutions. At the same time, these (untrusted) bistros can significantly improve the agency{\textquoteright}s data collection performance. Each application (within each agency) can have its own scalability, security, fault tolerance, and other data collection needs, and these applications and agencies can still share available resources, if so desired, across all Bistro servers.We believe an appropriately designed single infrastructure such as Bistro can address all digital government wide-area data collection needs in a scalable, secure, and cost-effective manner. (For more information, see bourbon.usc.edu/iml/bistro/.}, isbn = {0001-0782}, doi = {10.1145/602421.602448}, url = {http://doi.acm.org/10.1145/602421.602448}, author = {Golubchik,Leana and Cheng,William C. and Chou,Cheng-Fu and Khuller, Samir and Samet, Hanan and Wan,C. Justin} } @article {16996, title = {Bringing Treasures to the Surface: Previews and Overviews in a Prototype for the Library of Congress National Digital Library}, journal = {The craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {388 - 388}, author = {Marchionini,A.S. and Nation,D. and Karasik,S. and Cronnell,T. and Shneiderman, Ben and Spotfire,V.D.M.U. and Bederson, Benjamin B. and Data,T.S. and Hochheiser,H. and Shneiderman, Ben and others} } @article {12951, title = {Characterization of a Vibrio cholerae phage isolated from the coastal water of Peru}, journal = {Environmental Microbiology}, volume = {5}, year = {2003}, month = {2003/04/25/}, pages = {350 - 354}, abstract = {A Vibrio cholerae bacteriophage, family Myoviridae, was isolated from seawater collected from the coastal water of Lima, Peru. Genome size was estimated to be 29~kbp. The temperate phage was specific to V. cholerae and infected 12/13 V. cholerae O1 strains and half of the four non-O1/non-O139 strains tested in this study. Vibrio cholerae O139 strains were resistant to infection and highest infection rates were obtained in low nutrient media amended with NaCl or prepared using seawater as diluent.}, isbn = {1462-2920}, doi = {10.1046/j.1462-2920.2003.00411.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1462-2920.2003.00411.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Talledo,Miguel and Rivera,Irma N. G. and Lipp,Erin K. and Neale,Angela and Karaolis,David and Huq,Anwar and Rita R Colwell} } @conference {18172, title = {Classification-based spatial error concealment for images}, booktitle = {Image Processing, 2003. ICIP 2003. Proceedings. 2003 International Conference on}, volume = {2}, year = {2003}, month = {2003/09//}, pages = {II - 675-8 vol.3 - II - 675-8 vol.3}, abstract = {This paper presents a new, classification-based spatial error concealment algorithm for images. The proposed scheme takes advantage of two state-of-the-art concealment schemes and adaptively selects a better suitable concealment scheme for each corrupted block. Using a support vector machine (SVM) classifier, our proposed approach outperforms the prior art in terms of the concealment quality and has moderate computational complexity.}, keywords = {algorithm;, classification-based, classification;, classifier;, complexity;, computational, concealment, error, image, Machine;, machines;, moderate, scheme;, spatial, state-of-the-art, Support, SVM, vector}, doi = {10.1109/ICIP.2003.1246770}, author = {Chen,M. and Wu,M. and Zheng,Y.} } @inbook {15728, title = {Clustering and Summarizing Medline Abstracts}, booktitle = {BISTI 2003 Symposium on Digital Biology: The Emerging ParadigmBISTI 2003 Symposium on Digital Biology: The Emerging Paradigm}, year = {2003}, month = {2003///}, publisher = {U.S. National Institutes of Health Biomedical Information Science and Technology Initiative (BISTI)}, organization = {U.S. National Institutes of Health Biomedical Information Science and Technology Initiative (BISTI)}, author = {Dunlavy,Daniel M. and Conroy,John M. and O{\textquoteright}Leary,Timothy J and O{\textquoteright}Leary, Dianne P.} } @article {13911, title = {A collaborative digital library for children}, journal = {Journal of Computer Assisted Learning}, volume = {19}, year = {2003}, month = {2003///}, pages = {239 - 248}, author = {Druin, Allison and Revelle,G. and Bederson, Benjamin B. and Hourcade,J. P and Farber,A. and Lee,J. and Campbell,D.} } @conference {12734, title = {Combining multiple evidences for gait recognition}, booktitle = {Acoustics, Speech, and Signal Processing, 2003. Proceedings. (ICASSP {\textquoteright}03). 2003 IEEE International Conference on}, volume = {3}, year = {2003}, month = {2003/04//}, pages = {III - 33-6 vol.3 - III - 33-6 vol.3}, abstract = {In this paper, we systematically analyze different components of human gait, for the purpose of human identification. We investigate dynamic features such as the swing of the hands/legs, the sway of the upper body and static features like height, in both frontal and side views. Both probabilistic and non-probabilistic techniques are used for matching the features. Various combination strategies may be used depending upon the gait features being combined. We discuss three simple rules: the Sum, Product and MIN rules that are relevant to our feature sets. Experiments using four different datasets demonstrate that fusion can be used as an effective strategy in recognition.}, keywords = {analysis;, dynamic, evidences;, extraction;, feature, features;, frontal, Gait, height;, human, identification;, image, MIN, multiple, nonprobabilistic, probabilistic, Product, recognition;, rules;, sets;, side, static, Sum, sway;, swing;, techniques;, views;}, doi = {10.1109/ICASSP.2003.1199100}, author = {Cuntoor, N. and Kale, A. and Chellapa, Rama} } @article {12985, title = {Comparing bootstrap and posterior probability values in the four-taxon case}, journal = {Syst Biol}, volume = {52}, year = {2003}, month = {2003/08//}, pages = {477 - 487}, abstract = {Assessment of the reliability of a given phylogenetic hypothesis is an important step in phylogenetic analysis. Historically, the nonparametric bootstrap procedure has been the most frequently used method for assessing the support for specific phylogenetic relationships. The recent employment of Bayesian methods for phylogenetic inference problems has resulted in clade support being expressed in terms of posterior probabilities. We used simulated data and the four-taxon case to explore the relationship between nonparametric bootstrap values (as inferred by maximum likelihood) and posterior probabilities (as inferred by Bayesian analysis). The results suggest a complex association between the two measures. Three general regions of tree space can be identified: (1) the neutral zone, where differences between mean bootstrap and mean posterior probability values are not significant, (2) near the two-branch corner, and (3) deep in the two-branch corner. In the last two regions, significant differences occur between mean bootstrap and mean posterior probability values. Whether bootstrap or posterior probability values are higher depends on the data in support of alternative topologies. Examination of star topologies revealed that both bootstrap and posterior probability values differ significantly from theoretical expectations; in particular, there are more posterior probability values in the range 0.85-1 than expected by theory. Therefore, our results corroborate the findings of others that posterior probability values are excessively high. Our results also suggest that extrapolations from single topology branch-length studies are unlikely to provide any general conclusions regarding the relationship between bootstrap and posterior probability values.}, author = {Cummings, Michael P. and Handley,S. A and Myers,D. S and Reed,D. L and Rokas,A. and Winka,K.} } @article {12301, title = {Deno: a decentralized, peer-to-peer object-replication system for weakly connected environments}, journal = {Computers, IEEE Transactions on}, volume = {52}, year = {2003}, month = {2003/07//}, pages = {943 - 959}, abstract = {This paper presents the design, implementation, and evaluation of the replication framework of Deno, a decentralized, peer-to-peer object-replication system targeted for weakly connected environments. Deno uses weighted voting for availability and pair-wise, epidemic information flow for flexibility. This combination allows the protocols to operate with less than full connectivity, to easily adapt to changes in group membership, and to make few assumptions about the underlying network topology. We present two versions of Deno{\textquoteright}s protocol that differ in the consistency levels they support. We also propose security extensions to handle a class of malicious actions that involve misrepresentation of protocol information. Deno has been implemented and runs on top of Linux and Win32 platforms. We use the Deno prototype to characterize the performance of the Deno protocols and extensions. Our study reveals several interesting results that provide fundamental insight into the benefits of decentralization and the mechanics of epidemic protocols.}, keywords = {actions;, connected, consistency, data, data;, databases;, decentralized, Deno;, distributed, environments;, epidemic, group, levels;, Linux;, malicious, management;, membership;, network, object, object-replication, of, operating, peer-to-peer, protocols;, replicated, replication;, Security, security;, synchronisation;, system;, systems;, topology;, Unix;, voting;, weakly, weighted, Win32;}, isbn = {0018-9340}, doi = {10.1109/TC.2003.1214342}, author = {Cetintemel,U. and Keleher,P. J and Bhattacharjee, Bobby and Franklin,M.J.} } @article {16905, title = {Digital Government-Bistro: A Scalable and Secure Data Transfer Service for Digital Government Applications}, journal = {Communications of the ACM-Association for Computing Machinery-CACM}, volume = {46}, year = {2003}, month = {2003///}, pages = {50 - 51}, author = {Golubchik,L. and Cheng,W. C and Chou,C. F and Khuller, Samir and Samet, Hanan and Wan,Y. C.J} } @article {12948, title = {Direct Detection of Vibrio Cholerae and ctxA in Peruvian Coastal Water and Plankton by PCR}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {69}, year = {2003}, month = {2003/06/01/}, pages = {3676 - 3680}, abstract = {Seawater and plankton samples were collected over a period of 17 months from November 1998 to March 2000 along the coast of Peru. Total DNA was extracted from water and from plankton grouped by size into two fractions (64 μm to 202 μm and >202 μm). All samples were assayed for Vibrio cholerae, V. cholerae O1, V. cholerae O139, and ctxA by PCR. Of 50 samples collected and tested, 33 (66.0\%) were positive for V. cholerae in at least one of the three fractions. Of these, 62.5\% (n = 32) contained V. cholerae O1; ctxA was detected in 25\% (n = 20) of the V. cholerae O1-positive samples. None were positive for V. cholerae O139. Thus, PCR was successfully employed in detecting toxigenic V. cholerae directly in seawater and plankton samples and provides evidence for an environmental reservoir for this pathogen in Peruvian coastal waters.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.69.6.3676-3680.2003}, url = {http://aem.asm.org/content/69/6/3676}, author = {Lipp,Erin K. and Rivera,Irma N. G. and Gil,Ana I. and Espeland,Eric M. and Choopun,Nipa and Louis,Val{\'e}rie R. and Russek-Cohen,Estelle and Huq,Anwar and Rita R Colwell} } @article {17844, title = {Driving scientific applications by data in distributed environments}, journal = {Computational Science{\textemdash}ICCS 2003}, year = {2003}, month = {2003///}, pages = {713 - 713}, author = {Saltz, J. and Catalyurek,U. and Kurc, T. and Gray,M. and Hastings,S. and Langella,S. and Narayanan,S. and Martino,R. and Bryant,S. and Peszynska,M. and others} } @article {12950, title = {Effect of treatment on the dynamics of circulating hypodermin C in cattle naturally infested with Hypoderma lineatum (Diptera: Oestridae)}, journal = {Veterinary Parasitology}, volume = {113}, year = {2003}, month = {2003/05/01/}, pages = {263 - 272}, abstract = {An antigen capture ELISA, using a murine monoclonal antibody recognising recombinant hypodermin C (rHyC), was used to evaluate the influence of early treatment with eprinomectin (Eprinex{\textregistered}) or fenthion (Spotton{\textregistered}) on the kinetics of circulating hypodermin C in calves naturally infested with Hypoderma lineatum. No viable larvae were collected from treated animals, whereas a variable number of warbles were found in control animals. Treatment provoked a decrease in circulating HyC levels that was significant 9 days post-treatment (p.t.). Circulating antigen levels in the treated cattle remained detectable for approximately 99 days p.t. In contrast, control animals had no detectable antigen at 64 days p.t., 42 days earlier than in the treated animals. These results suggest that larvae were either gradually killed, resulting in slow release of antigen or they were encapsulated, leading to the slow liberation of antigen. Kinetics of circulating HyC did not differ among the two insecticide treatments. Antibodies persisted, in all groups, throughout the 120-day study. These results suggest that the antigen capture ELISA will be useful as a technique for detecting successful treatment of cattle grub infestations and for the detection of new infestations in previously infested cattle.}, keywords = {Capture ELISA, Cattle-arthropoda, Control methods-arthropoda, Eprinomectin, Fenthion, Hypoderma spp.}, isbn = {0304-4017}, doi = {10.1016/S0304-4017(03)00084-0}, url = {http://www.sciencedirect.com/science/article/pii/S0304401703000840}, author = {Douglas D Colwell and Panadero-Fontan,Rosario and L{\'o}pez-Sandez,Ceferino and Parra-Fernandez,Francisco and Paz-Silva,A and S{\'a}nchez-Andrade,Rita and D{\i}́ez-Ba{\~n}os,Pablo} } @article {12992, title = {Effectiveness of conservation targets in capturing genetic diversity}, journal = {Conserv Biol}, volume = {17}, year = {2003}, month = {2003/02//}, pages = {219 - 229}, abstract = {Any conservation actions that preserve some populations and not others will have genetic consequences. We used empirical data from four rare plant taxa to assess these consequences in terms of how well allele numbers ( all alleles and alleles occurring at a frequency openface>0.05 in any population ) and expected heterozygosity are represented when different numbers of populations are conserved. We determined sampling distributions for these three measures of genetic diversity using Monte Carlo methods. We assessed the proportion of alleles included in the number of populations considered adequate for conservation, needed to capture all alleles, and needed to meet an accepted standard of genetic-diversity conservation of having a 90-95\% probability of including all common alleles. We also assessed the number of populations necessary to obtain values of heterozygosity within +/-10\% of the value obtained from all populations. Numbers of alleles were strongly affected by the number of populations sampled. Heterozygosity was only slightly less sensitive to numbers of populations than were alleles. On average, currently advocated conservation intensities represented 67-83\% of all alleles and 85-93\% of common alleles. The smallest number of populations to include all alleles ranged from 6 to 17 ( 42-57\% ), but <0.2\% of 1000 samples of these numbers of populations included them all. It was necessary to conserve 16-29 ( 53-93\% ) of the sampled populations to meet the standard for common alleles. Between 20\% and 64\% of populations were needed to reliably represent species-level heterozygosity. Thus, higher percentages of populations are needed than are currently considered adequate to conserve genetic diversity if populations are selected without genetic data.}, author = {Neel,M. C and Cummings, Michael P.} } @conference {16772, title = {Efficient dissemination of aggregate data over the wireless web}, booktitle = {International Workshop on the Web and Databases (WebDB)}, year = {2003}, month = {2003///}, pages = {93 - 98}, author = {Sharaf,M. A and Sismanis,Y. and Labrinidis,A. and Chrysanthis,P. and Roussopoulos, Nick} } @article {12305, title = {Efficient peer-to-peer searches using result-caching}, journal = {Peer-to-Peer Systems II}, year = {2003}, month = {2003///}, pages = {225 - 236}, abstract = {Existing peer-to-peer systems implement a single function well: data lookup. There is now a wealth of research describing how to reliably disseminate, and to later retrieve, data in a scalable and load-balanced manner.}, author = {Bhattacharjee, Bobby and Chawathe,S. and Gopalakrishnan,V. and Keleher,P. and Silaghi,B.} } @article {12129, title = {Eight lessons learned during COTS-based systems maintenance}, journal = {Software, IEEE}, volume = {20}, year = {2003}, month = {2003/10//sept}, pages = {94 - 96}, abstract = {To make better decisions relative to CBSs, we need empirical knowledge. To gain this knowledge, we must more fully understand the lifecycle processes people use when harnessing COTS packages. The initial findings reported here are but the first step in our attempts to capture this empirical knowledge. We plan to continue collecting data and investigating the phenomenology of COTS-based systems.}, keywords = {COTS, COTS-based, cycle, life, lifecycle, Maintenance, maintenance;, object-oriented, packages;, phase;, processes;, programming;, reusability;, software, systems}, isbn = {0740-7459}, doi = {10.1109/MS.2003.1231161}, author = {Reifer,D.J. and Basili, Victor R. and Boehm,B.W. and Clark,B.} } @article {12952, title = {Emergence and Evolution of Vibrio Cholerae O139}, journal = {Proceedings of the National Academy of SciencesPNAS}, volume = {100}, year = {2003}, month = {2003/02/04/}, pages = {1304 - 1309}, abstract = {The emergence of Vibrio cholerae O139 Bengal during 1992{\textendash}1993 was associated with large epidemics of cholera in India and Bangladesh and, initially, with a total displacement of the existing V. cholerae O1 strains. However, the O1 strains reemerged in 1994 and initiated a series of disappearance and reemergence of either of the two serogroups that was associated with temporal genetic and phenotypic changes sustained by the strains. Since the initial emergence of the O139 vibrios, new variants of the pathogen derived from multiple progenitors have been isolated and characterized. The clinical and epidemiological characteristics of these strains have been studied. Rapid genetic reassortment in O139 strains appears to be a response to the changing epidemiology of V. cholerae O1 and also a strategy for persistence in competition with strains of the O1 serogroup. The emergence of V. cholerae O139 has provided a unique opportunity to witness genetic changes in V. cholerae that may be associated with displacement of an existing serogroup by a newly emerging one and, thus, provide new insights into the epidemiology of cholera. The genetic changes and natural selection involving both environmental and host factors are likely to influence profoundly the genetics, epidemiology, and evolution of toxigenic V. cholerae, not only in the Ganges Delta region of India and Bangladesh, but also in other areas of endemic and epidemic cholera.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0337468100}, url = {http://www.pnas.org/content/100/3/1304}, author = {Faruque,Shah M. and Sack,David A. and Sack,R. Bradley and Rita R Colwell and Takeda,Yoshifumi and Nair,G. Balakrish} } @conference {18656, title = {An experimental evaluation of correlated network partitions in the Coda distributed file system}, year = {2003}, month = {2003/10//}, pages = {273 - 282}, abstract = {Experimental evaluation is an important way to assess distributed systems, and fault injection is the dominant technique in this area for the evaluation of a system{\textquoteright}s dependability. For distributed systems, network failure is an important fault model. Physical network failures often have far-reaching effects, giving rise to multiple correlated failures as seen by higher-level protocols. This paper presents an experimental evaluation, using the Loki fault injector, which provides insight into the impact that correlated network partitions have on the Coda distributed file system. In this evaluation, Loki created a network partition between two Coda file servers, during which updates were made at each server to the same replicated data volume. Upon repair of the partition, a client requested directory resolution to converge the diverging replicas. At various stages of the resolution, Loki invoked a second correlated network partition, thus allowing us to evaluate its impact on the system{\textquoteright}s correctness, performance, and availability.}, keywords = {client-server systems, Coda distributed file system, correlated network partitions, distributed file systems, experimental evaluation, fault model, Loki fault injector, multiple correlated failures, network failure, Network topology, performance evaluation, replicated data, replicated databases, software fault tolerance, system performance evaluation}, doi = {10.1109/RELDIS.2003.1238077}, author = {Lefever,R.M. and Michel Cukier and Sanders,W. H.} } @article {12717, title = {Face recognition: A literature survey}, journal = {ACM Comput. Surv.}, volume = {35}, year = {2003}, month = {2003/12//}, pages = {399 - 458}, abstract = {As one of the most successful applications of image analysis and understanding, face recognition has recently received significant attention, especially during the past several years. At least two reasons account for this trend: the first is the wide range of commercial and law enforcement applications, and the second is the availability of feasible technologies after 30 years of research. Even though current machine recognition systems have reached a certain level of maturity, their success is limited by the conditions imposed by many real applications. For example, recognition of face images acquired in an outdoor environment with changes in illumination and/or pose remains a largely unsolved problem. In other words, current systems are still far away from the capability of the human perception system.This paper provides an up-to-date critical survey of still- and video-based face recognition research. There are two underlying motivations for us to write this survey paper: the first is to provide an up-to-date review of the existing literature, and the second is to offer some insights into the studies of machine recognition of faces. To provide a comprehensive survey, we not only categorize existing recognition techniques but also present detailed descriptions of representative methods within each category. In addition, relevant topics such as psychophysical studies, system evaluation, and issues of illumination and pose variation are covered.}, keywords = {face recognition, person identification}, isbn = {0360-0300}, doi = {10.1145/954339.954342}, url = {http://doi.acm.org/10.1145/954339.954342}, author = {Zhao, W. and Chellapa, Rama and Phillips,P.J. and Rosenfeld, A.} } @article {12726, title = {Face reconstruction from monocular video using uncertainty analysis and a generic model}, journal = {Computer Vision and Image Understanding}, volume = {91}, year = {2003}, month = {2003/07//}, pages = {188 - 213}, abstract = {Reconstructing a 3D model of a human face from a monocular video sequence is an important problem in computer vision, with applications to recognition, surveillance, multimedia, etc. However, the quality of 3D reconstructions using structure from motion (SfM) algorithms is often not satisfactory. One of the reasons is the poor quality of the input video data. Hence, it is important that 3D face reconstruction algorithms take into account the statistics representing the quality of the video. Also, because of the structural similarities of most faces, it is natural that the performance of these algorithms can be improved by using a generic model of a face. Most of the existing work using this approach initializes the reconstruction algorithm with this generic model. The problem with this approach is that the algorithm can converge to a solution very close to this initial value, resulting in a reconstruction which resembles the generic model rather than the particular face in the video which needs to be modeled. In this paper, we propose a method of 3D reconstruction of a human face from video in which the 3D reconstruction algorithm and the generic model are handled separately. We show that it is possible to obtain a reasonably good 3D SfM estimate purely from the video sequence, provided the quality of the input video is statistically assessed and incorporated into the algorithm. The final 3D model is obtained after combining the SfM estimate and the generic model using an energy function that corrects for the errors in the estimate by comparing the local regions in the two models. The main advantage of our algorithm over others is that it is able to retain the specific features of the face in the video sequence even when these features are different from those of the generic model and it does so even as the quality of the input video varies. The evolution of the 3D model through the various stages of the algorithm and an analysis of its accuracy are presented.}, keywords = {Energy function minimization, Face modeling, Generic model, stochastic approximation, structure from motion, uncertainty analysis}, isbn = {1077-3142}, doi = {10.1016/S1077-3142(03)00079-1}, url = {http://www.sciencedirect.com/science/article/pii/S1077314203000791}, author = {Roy Chowdhury,Amit K. and Chellapa, Rama} } @conference {12731, title = {A Factorization Approach for Activity Recognition}, booktitle = {Computer Vision and Pattern Recognition Workshop, 2003. CVPRW {\textquoteright}03. Conference on}, volume = {4}, year = {2003}, month = {2003/06//}, pages = {41 - 41}, abstract = {Understanding activities arising out of the interactions of a configuration of moving objects is an important problem in video understanding, with applications in surveillance and monitoring. A special situation is when the objects are small enough to be represented as points on a 2D plane. In this paper, we introduce a novel method of representing the activity by the deformations of the point configuration in a properly defined shape space. Instead of inferring about the activity directly from the motion tracks of the individual points, we propose to model an activity by the polygonal shape formed by joining the locations of these point masses at any time t, and its deformation as the activity unfolds. Given the locations of the 2D points over a sequence of frames in the video, the factorization theorem for matrices is used to obtain a set of basis shapes for each activity. An unknown activity can now be recognized by projecting onto these basis shapes. Also, once a specific activity is recognized, the deviations from it can be modeled by the deformations from the basis shape. This is used to identify an abnormal activity. We demonstrate the applicability of our algorithm using real-life video sequences in an airport surveillance environment. We are able to identify the major activities that take place in that setting and detect abnormal ones.}, doi = {10.1109/CVPRW.2003.10040}, author = {Chowdhury,Amit K. Roy and Chellapa, Rama} } @article {12740, title = {Fast two-frame multiscale dense optical flow estimation using discrete wavelet filters}, journal = {Journal of the Optical Society of America AJ. Opt. Soc. Am. A}, volume = {20}, year = {2003}, month = {2003///}, pages = {1505 - 1515}, abstract = {A multiscale algorithm with complexity O(N) (where N is the number of pixels in one image) using wavelet filters is proposed to estimate dense optical flow from two frames. Hierarchical image representation by wavelet decomposition is integrated with differential techniques in a new multiscale framework. It is shown that if a compactly supported wavelet basis with one vanishing moment is carefully selected, hierarchical image, first-order derivative, and corner representations can be obtained from the wavelet decomposition. On the basis of this result, three of the four components of the wavelet decomposition are employed to estimate dense optical flow with use of only two frames. This overcomes the {\textquotedblleft}flattening-out{\textquotedblright} problem in traditional pyramid methods, which produce large errors when low-texture regions become flat at coarse levels as a result of blurring. A two-dimensional affine motion model is used to formulate the optical flow problem as a linear system, with all resolutions simultaneously (i.e., coarse-and-fine) rather than the traditional coarse-to-fine approach, which unavoidably propagates errors from the coarse level. This not only helps to improve the accuracy but also makes the hardware implementation of our algorithm simple. Experiments on different types of image sequences, together with quantitative and qualitative comparisons with several other optical flow methods, are given to demonstrate the effectiveness and the robustness of our algorithm.}, keywords = {digital image processing, Image analysis, optical flow}, doi = {10.1364/JOSAA.20.001505}, url = {http://josaa.osa.org/abstract.cfm?URI=josaa-20-8-1505}, author = {Liu,Haiying and Chellapa, Rama and Rosenfeld,Azriel} } @conference {18340, title = {Footloose: a case for physical eventual consistency and selective conflict resolution}, booktitle = {Mobile Computing Systems and Applications, 2003. Proceedings. Fifth IEEE Workshop on}, year = {2003}, month = {2003///}, pages = {170 - 179}, publisher = {IEEE}, organization = {IEEE}, abstract = {Users are increasingly inundated with small devices with communication and storage capabilities. Unfortunately, the user is still responsible for reconciling all of the devices whenever a change is made. We present Footloose, a user-centered data store that can share data and reconcile conflicts across diverse devices. Footloose is an optimistic system based on physical eventual consistency: consistency based on the movement of devices, and selective conflict resolution, which allows conflicts to flow through devices that cannot resolve the conflict to devices that can. Using these techniques, Footloose can present consistent views of data on the devices closest to the user without user interaction.}, isbn = {0-7695-1995-4}, doi = {10.1109/MCSA.2003.1240778}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1240778}, author = {Paluska and Saff and Yeh and Chen} } @article {18638, title = {Formal verification of an intrusion-tolerant group membership protocol}, journal = {IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS E SERIES D}, volume = {86}, year = {2003}, month = {2003///}, pages = {2612 - 2622}, abstract = {The traditional approach for establishing thecorrectness of group communication protocols is through rigor- ous arguments. While this is a valid approach, the likelihood of subtle errors in the design and implementation of such complex distributed protocols is not negligible. The use of formal verifi- cation methods has been widely advocated to instill confidence in the correctness of protocols. In this paper, we describe how we used the SPIN model checker to formally verify a group mem- bership protocol that is part of an intrusion-tolerant group com- munication system. We describe how we successfully tackled the state-space explosion problem by determining the right abstrac- tion level for formally specifying the protocol. The verification exercise not only formally showed that the protocol satisfies its correctness claims, but also provided information that will help us make the protocol more efficient without violating correctness. key words: intrusion tolerance, group communication systems, validation, formal methods }, url = {https://www.perform.csl.illinois.edu/Papers/USAN_papers/03RAM01.pdf}, author = {Ramasamy,H. V. and Michel Cukier and Sanders,W. H.} } @article {15095, title = {A forward-secure public-key encryption scheme}, journal = {Advances in Cryptology{\textemdash}Eurocrypt 2003}, year = {2003}, month = {2003///}, pages = {646 - 646}, abstract = {Cryptographic computations are often carried out on insecure devices for which the threat of key exposure represents a serious and realistic concern. In an effort to mitigate the damage caused by exposure of secret data (e.g., keys) stored on such devices, the paradigm of forward security was introduced. In a forward-secure scheme, secret keys are updated at regular periods of time; furthermore, exposure of a secret key corresponding to a given time period does not enable an adversary to {\textquotedblleft}break{\textquotedblright} the scheme (in the appropriate sense) for any prior time period. A number of constructions of forward-secure digital signature schemes, key-exchange protocols, and symmetric-key schemes are known.We present the first constructions of a (non-interactive) forward-secure public-key encryption scheme. Our main construction achieves security against chosen plaintext attacks under the decisional bilinear Diffie-Hellman assumption in the standard model. It is practical, and all complexity parameters grow at most logarithmically with the total number of time periods. The scheme can also be extended to achieve security against chosen ciphertext attacks. }, doi = {10.1007/3-540-39200-9_16}, author = {Canetti,R. and Halevi,S. and Katz, Jonathan} } @article {12947, title = {From terabytes to insights}, journal = {Communications of the ACM}, volume = {46}, year = {2003}, month = {2003/07//}, pages = {25 - 27}, abstract = {For scientists and engineers tapping the NSF{\textquoteright}s high-performance cyberinfrastructure, the path to wisdom follows a route both miraculous and familiar.}, isbn = {0001-0782}, doi = {10.1145/792704.792724}, url = {http://doi.acm.org/10.1145/792704.792724}, author = {Rita R Colwell} } @inbook {12741, title = {Gait Analysis for Human Identification}, booktitle = {Audio- and Video-Based Biometric Person AuthenticationAudio- and Video-Based Biometric Person Authentication}, series = {Lecture Notes in Computer Science}, volume = {2688}, year = {2003}, month = {2003///}, pages = {1058 - 1058}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Human gait is an attractive modality for recognizing people at a distance. In this paper we adopt an appearance-based approach to the problem of gait recognition. The width of the outer contour of the binarized silhouette of a walking person is chosen as the basic image feature. Different gait features are extracted from the width vector such as the dowsampled, smoothed width vectors, the velocity profile etc. and sequences of such temporally ordered feature vectors are used for representing a person{\textquoteright}s gait. We use the dynamic time-warping (DTW) approach for matching so that non-linear time normalization may be used to deal with the naturally-occuring changes in walking speed. The performance of the proposed method is tested using different gait databases.}, isbn = {978-3-540-40302-9}, url = {http://dx.doi.org/10.1007/3-540-44887-X_82}, author = {Kale, A. and Cuntoor, N. and Yegnanarayana,B. and Rajagopalan, AN and Chellapa, Rama}, editor = {Kittler,Josef and Nixon,Mark} } @article {13000, title = {Genetic consequences of ecological reserve design guidelines: An empirical investigation}, journal = {Conserv Genet}, volume = {4}, year = {2003}, month = {2003///}, pages = {427 - 439}, abstract = {We assessed the genetic diversity consequences of applying ecological reserve design guidelines to four federally-listed globally-rare plant species. Consequences were measured using two metrics: proportion of all alleles and of common alleles included in reserves. Common alleles were defined as those alleles having a frequency of greater than or equal to0.05 in at least one population. Four conservation professionals applied ecological reserve guidelines to choose specific populations of each species for inclusion in reserves of size 1 to N - 1, where N is the total number of populations of each species. Information regarding genetic diversity was not used in selecting populations. The resulting reserve designs were compared to random designs, and the agreement among experts was assessed using Kendall{\textquoteright}s coefficient of concordance. Application of ecological reserve design guidelines proved mostly ineffective in capturing more genetic diversity than is captured selecting populations randomly. Meeting established targets for genetic diversity, such as one advocated by the Center for Plant Conservation, required larger numbers of populations than are suggested to be sufficient. Relative performance of expert designs differed among species and was dependent on whether the proportion of all alleles or of common alleles was used as a measure of diversity. Furthermore there was no significant concordance among experts in order in which populations were incorporated into reserves as experts differed in priority they placed on individual guidelines.}, keywords = {albens;, Astragulus, Bernardino, conservation, conservation;, design;, diversity;, Erigeron, Eriogonum, genetic, genetics;, goodmaniana;, Mountains, ovalifolium, Oxytheca, parishii, parishii;, plant, reserve, San, var., vineum;}, author = {Neel,M. C and Cummings, Michael P.} } @article {16290, title = {The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria}, journal = {Nature}, volume = {423}, year = {2003}, month = {2003/05/01/}, pages = {81 - 86}, abstract = {Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax1. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identify additional genes that might contribute to virulence, we analysed the complete sequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute to pathogenicity{\textemdash}including haemolysins, phospholipases and iron acquisition functions{\textemdash}and identified numerous surface proteins that might be important targets for vaccines and drugs. Almost all these putative chromosomal virulence and surface proteins have homologues in Bacillus cereus, highlighting the similarity of B. anthracis to near-neighbours that are not associated with anthrax4. By performing a comparative genome hybridization of 19 B. cereus and Bacillus thuringiensis strains against a B. anthracis DNA microarray, we confirmed the general similarity of chromosomal genes among this group of close relatives. However, we found that the gene sequences of pXO1 and pXO2 were more variable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis.}, isbn = {0028-0836}, doi = {10.1038/nature01586}, url = {http://www.nature.com/nature/journal/v423/n6935/full/nature01586.html}, author = {Read,Timothy D. and Peterson,Scott N. and Tourasse,Nicolas and Baillie,Les W. and Paulsen,Ian T. and Nelson,Karen E. and Tettelin,Herv|[eacute]| and Fouts,Derrick E. and Eisen,Jonathan A. and Gill,Steven R. and Holtzapple,Erik K. and |[Oslash]|kstad,Ole Andreas and Helgason,Erlendur and Rilstone,Jennifer and Wu,Martin and Kolonay,James F. and Beanan,Maureen J. and Dodson,Robert J. and Brinkac,Lauren M. and Gwinn,Michelle and DeBoy,Robert T. and Madpu,Ramana and Daugherty,Sean C. and Durkin,A. Scott and Haft,Daniel H. and Nelson,William C. and Peterson,Jeremy D. and Pop, Mihai and Khouri,Hoda M. and Radune,Diana and Benton,Jonathan L. and Mahamoud,Yasmin and Jiang,Lingxia and Hance,Ioana R. and Weidman,Janice F. and Berry,Kristi J. and Plaut,Roger D. and Wolf,Alex M. and Watkins,Kisha L. and Nierman,William C. and Hazen,Alyson and Cline,Robin and Redmond,Caroline and Thwaite,Joanne E. and White,Owen and Salzberg,Steven L. and Thomason,Brendan and Friedlander,Arthur M. and Koehler,Theresa M. and Hanna,Philip C. and Kolst|[oslash]|,Anne-Brit and Fraser,Claire M.} } @article {17185, title = {HCIL Technical Report Listing (1993-2002)}, journal = {The craft of information visualization: readings and reflections}, volume = {27}, year = {2003}, month = {2003///}, pages = {393 - 393}, author = {Ceaparu,I. and Druin, Allison and Guimbretiere,F. and Manipulation,D. and Shneiderman, Ben and Westerlurid,B. and Keogh,E. and Hochheiser,H. and Shrieidemian,B. and Shneidemiari,B. and others} } @article {17188, title = {Help! I{\textquoteright}m lost: User frustration in web navigation}, journal = {IT \& Society}, volume = {1}, year = {2003}, month = {2003///}, pages = {18 - 26}, abstract = {Computers can be valuable tools, and networked resources via the Internet can be beneficial to many different populations and communities. Unfortunately, when people are unable to reach their task goals due to frustrating experiences, this can hinder the effectiveness of technology. This research summary provides information about the user frustration research that has been performed at the University of Maryland and Towson University. Causes of user frustration are discussed in this research summary, along with the surprising finding that nearly one-third to one-half of the time spent in front of the computer is wasted due to frustrating experiences. Furthermore, when interfaces are planned to be deceptive and confusing, this can lead to increased frustration. Implications for designers and users are discussed.}, author = {Lazar,J. and Bessiere,K. and Ceaparu,I. and Robinson,J. and Shneiderman, Ben} } @conference {12720, title = {A hidden Markov model based framework for recognition of humans from gait sequences}, booktitle = {Image Processing, 2003. ICIP 2003. Proceedings. 2003 International Conference on}, volume = {2}, year = {2003}, month = {2003/09//}, pages = {II - 93-6 vol.3 - II - 93-6 vol.3}, abstract = {In this paper we propose a generic framework based on hidden Markov models (HMMs) for recognition of individuals from their gait. The HMM framework is suitable, because the gait of an individual can be visualized as his adopting postures from a set, in a sequence which has an underlying structured probabilistic nature. The postures that the individual adopts can be regarded as the states of the HMM and are typical to that individual and provide a means of discrimination. The framework assumes that, during gait, the individual transitions between N discrete postures or states but it is not dependent on the particular feature vector used to represent the gait information contained in the postures. The framework, thus, provides flexibility in the selection of the feature vector. The statistical nature of the HMM lends robustness to the model. In this paper we use the binarized background-subtracted image as the feature vector and use different distance metrics, such as those based on the L1 and L2 norms of the vector difference, and the normalized inner product of the vectors, to measure the similarity between feature vectors. The results we obtain are better than the baseline recognition rates reported before.}, keywords = {analysis;, background-subtracted, binarized, discrete, distance, feature, Gait, hidden, human, image, image;, Markov, metrics;, model;, models;, postures;, recognition;, sequences;, vector;}, doi = {10.1109/ICIP.2003.1246624}, author = {Sundaresan,Aravind and RoyChowdhury,Amit and Chellapa, Rama} } @inbook {17237, title = {Innovating the Interaction}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {295 - 295}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, address = {San Francisco}, isbn = {978-1-55860-915-0}, author = {Bederson, Benjamin B. and Plaisant, Catherine and Mushlin,R. and Snyder,A. and Li,J. and Heller,D. and Shneiderman, Ben and Hochheiser,H. and Fekete,J. D and Czenvinski,M.} } @conference {12782, title = {The integrated CWB-NC/PIOAtool for functional verification and performance analysis of concurrent systems}, booktitle = {Proceedings of the 9th international conference on Tools and algorithms for the construction and analysis of systems}, year = {2003}, month = {2003///}, pages = {431 - 436}, author = {Zhang,D. and Cleaveland, Rance and Stark,E. W} } @conference {17248, title = {Interactive color mosaic and dendrogram displays for signal/noise optimization in microarray data analysis}, booktitle = {Multimedia and Expo, 2003. ICME{\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {3}, year = {2003}, month = {2003///}, pages = {III{\textendash}461 - III{\textendash}461}, abstract = {Data analysis and visualization is strongly influenced by noise and noise filters. There are multiple sources of oisein microarray data analysis, but signal/noise ratios are rarely optimized, or even considered. Here, we report a noise analysis of a novel 13 million oligonucleotide dataset - 25 human U133A (~500,000 features) profiles of patient muscle biposies. We use our recently described interactive visualization tool, the Hierarchical Clustering Explorer (HCE) to systemically address the effect of different noise filters on resolution of arrays into orrectbiological groups (unsupervised clustering into three patient groups of known diagnosis). We varied probe set interpretation methods (MAS 5.0, RMA), resent callfilters, and clustering linkage methods, and investigated the results in HCE. HCE interactive features enabled us to quickly see the impact of these three variables. Dendrogram displays showed the clustering results systematically, and color mosaic displays provided a visual support for the results. We show that each of these three variables has a strong effect on unsupervised clustering. For this dataset, the strength of the biological variable was maximized, and noise minimized, using MAS 5.0, 10\% present call filter, and Average Group Linkage. We propose a general method of using interactive tools to identify the optimal signal/noise balance or the optimal combination of these three variables to maximize the effect of the desired biological variable on data interpretation.}, author = {Seo,J. and Bakay,M. and Zhao,P. and Chen,Y.W. and Clarkson,P. and Shneiderman, Ben and Hoffman,E.P.} } @article {13299, title = {Interactive Visualization of Large Tetrahedral Meshes through Selective Refinement}, journal = {IEEE Transactions on Visualization and Computer Graphics}, year = {2003}, month = {2003///}, abstract = {In this paper, we address the problem of the efficient visualization of very largeirregular volume datasets. To this aim, we exploit a multiresolution representation based on a domain decomposition into tetrahedral cells. A new compact data struc- ture is described which encodes the whole dataset at a virtually continuous range of different resolutions, with a storage cost six times lower than a standard data struc- ture for tetrahedral meshes. Such structure supports on-line selective refinement to focus resolution on areas that the user considers more critical, based on either field values, or domain location, or opacity of the transfer function. Selective refinement is used to trade-off between resolution and speed in visualization, according to user needs and hardware constraints. These features have been implemented in a new system, called TAn2 (Tetrahedra Analyzer), for the interactive visualization of three- dimensional scalar fields defined on very large tetrahedral meshes. Multiresolution representation and selective refinement make the system fully scalable with respect to the size of the dataset and to hardware requirements. }, author = {Cignoni,P. and De Floriani, Leila and Magillo,P. and Puppo,E. and Scopigno,R. and di Genova,U.} } @article {15769, title = {Machine and Human Performance for Single- and Multi-Document Summarization}, journal = {IEEE Intelligent Systems (special issue on Natural Language Processing)}, volume = {18}, year = {2003}, month = {2003///}, pages = {46 - 54}, url = {http://csdl.computer.org/comp/mags/ex/2003/01/x1toc.htmhttp://csdl.computer.org/comp/mags/ex/2003/01/x1toc.htm}, author = {Schlesinger,Judith D. and Conroy,John M. and Okurowski,Mary Ellen and O{\textquoteright}Leary, Dianne P.} } @article {12946, title = {Method of DNA extraction and application of multiplex polymerase chain reaction to detect toxigenic Vibrio cholerae O1 and O139 from aquatic ecosystems}, journal = {Environmental Microbiology}, volume = {5}, year = {2003}, month = {2003/07/01/}, pages = {599 - 606}, abstract = {Vibrio cholerae is a free-living bacterium found in water and in association with plankton. V. cholerae non-O1/non-O139 strains are frequently isolated from aquatic ecosystems worldwide. Less frequently isolated are V. cholerae O1 and V. cholerae O139, the aetiological agents of cholera. These strains have two main virulence-associated factors, cholera toxin (CT) and toxin co-regulated pilus (TCP). By extracting total DNA from aquatic samples, the presence of pathogenic strains can be determined quickly and used to improve a microbiological risk assessment for cholera in coastal areas. Some methods suggested for DNA extraction from water samples are not applicable to all water types. We describe here a method for DNA extraction from coastal water and a multiplex polymerase chain reaction (PCR) for O1 and O139 serogroups. DNA extraction was successfully accomplished from 117 sea water samples collected from coastal areas of Per{\'u}, Brazil and the USA. DNA concentration in all samples varied from 20~ng to 480~{\textmu}g~{\textmu}l-1. The sensitivity of the DNA extraction method was 100 V. cholerae cells in 250~ml of water. The specificity of multiplex O1/O139 PCR was investigated by analysing 120 strains of V. cholerae, Vibrio and other Bacteria species. All V. cholerae O1 and O139 tested were positive. For cholera surveillance of aquatic environments and ballast water, total DNA extraction, followed by V. cholerae PCR, and O1/O139 serogroup and tcpA/ctxA genes by multiplex PCR offers an efficient system, permitting risk analysis for cholera in coastal areas.}, isbn = {1462-2920}, doi = {10.1046/j.1462-2920.2003.00443.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1462-2920.2003.00443.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Rivera,Irma N. G. and Lipp,Erin K. and Gil,Ana and Choopun,Nipa and Huq,Anwar and Rita R Colwell} } @article {13007, title = {Necessity is the mother of invention: a simple grid computing system using commodity tools}, journal = {J Parallel Distr Com}, volume = {63}, year = {2003}, month = {2003/05//}, pages = {578 - 589}, abstract = {Access to sufficient resources is a barrier to scientific progress for many researchers facing large computational problems. Gaining access to large-scale resources (i.e., university-wide or federally supported computer centers) can be difficult, given their limited availability, particular architectures, and request/review/approval cycles. Simultaneously, researchers often find themselves with access to workstations and older clusters overlooked by their owners in favor of newer hardware. Software to tie these resources into a coherent Grid, however, has been problematic. Here, we describe our experiences building a Grid computing system to conduct a large-scale simulation study using "borrowed" computing resources distributed over a wide area. Using standard software components, we have produced a Grid computing system capable of coupling several hundred processors spanning multiple continents and administrative domains. We believe that this system fills an important niche between a closely coupled local system and a heavyweight, highly customized wide area system. (C) 2003 Elsevier Science (USA). All rights reserved.}, keywords = {Apache;, computing;, distributed, Grid, HTTP;, Java;, Linux;, Perl;, SQL;, Unix;, XML-RPC}, doi = {DOI 10.1016/S0743-7315(03)00004-2}, author = {Myers,D. S and Cummings, Michael P.} } @article {12737, title = {A particle filtering approach to abnormality detection in nonlinear systems and its application to abnormal activity detection}, journal = {3rd Int{\textquoteright}l Workshop on Statistical and Computational Theories of Vision, Nice, France}, year = {2003}, month = {2003///}, abstract = {We study abnormality detection in partially observed nonlinear dynamic systems tracked usingparticle filters. An {\textquoteleft}abnormality{\textquoteright} is defined as a change in the system model, which could be drastic or gradual, with the parameters of the changed system unknown. If the change is drastic the particle filter will lose track rapidly and the increase in tracking error can be used to detect the change. In this paper we propose a new statistic for detecting {\textquoteleft}slow{\textquoteright} changes or abnormalities which do not cause the particle filter to lose track for a long time. In a previous work, we have proposed a partially observed nonlinear dynamical system for modeling the configuration dynamics of a group of interacting point objects and formulated abnormal activity detection as a change detection problem. We show here results for abnormal activity detection comparing our proposed change detection strategy with others used in literature. }, author = {Vaswani, N. and Chellapa, Rama} } @article {12954, title = {Pathogenic Potential of Environmental Vibrio Cholerae Strains Carrying Genetic Variants of the Toxin-Coregulated Pilus Pathogenicity Island}, journal = {Infection and ImmunityInfect. Immun.}, volume = {71}, year = {2003}, month = {2003/02/01/}, pages = {1020 - 1025}, abstract = {The major virulence factors of toxigenic Vibrio cholerae are cholera toxin (CT), which is encoded by a lysogenic bacteriophage (CTXΦ), and toxin-coregulated pilus (TCP), an essential colonization factor which is also the receptor for CTXΦ. The genes for the biosynthesis of TCP are part of a larger genetic element known as the TCP pathogenicity island. To assess their pathogenic potential, we analyzed environmental strains of V. cholerae carrying genetic variants of the TCP pathogenicity island for colonization of infant mice, susceptibility to CTXΦ, and diarrheagenicity in adult rabbits. Analysis of 14 environmental strains, including 3 strains carrying a new allele of the tcpA gene, 9 strains carrying a new allele of the toxT gene, and 2 strains carrying conventional tcpA and toxT genes, showed that all strains colonized infant mice with various efficiencies in competition with a control El Tor biotype strain of V. cholerae O1. Five of the 14 strains were susceptible to CTXΦ, and these transductants produced CT and caused diarrhea in adult rabbits. These results suggested that the new alleles of the tcpA and toxT genes found in environmental strains of V. cholerae encode biologically active gene products. Detection of functional homologs of the TCP island genes in environmental strains may have implications for understanding the origin and evolution of virulence genes of V. cholerae.}, isbn = {0019-9567, 1098-5522}, doi = {10.1128/IAI.71.2.1020-1025.2003}, url = {http://iai.asm.org/content/71/2/1020}, author = {Faruque,Shah M. and Kamruzzaman,M. and Meraj,Ismail M. and Chowdhury,Nityananda and Nair,G. Balakrish and Sack,R. Bradley and Rita R Colwell and Sack,David A.} } @inbook {15786, title = {Performance of a Three-Stage System for Multi-Document Summarization}, booktitle = {DUC 03 Conference ProceedingsDUC 03 Conference Proceedings}, year = {2003}, month = {2003///}, publisher = {U.S. National Inst. of Standards and Technology}, organization = {U.S. National Inst. of Standards and Technology}, url = {http://duc.nist.gov/http://duc.nist.gov/}, author = {Dunlavy,Daniel M. and Conroy,John M. and Schlesinger,Judith D. and Goodman,Sarah A. and Okurowski,Mary Ellen and O{\textquoteright}Leary, Dianne P. and Halteren,Hans van} } @article {12945, title = {Persistence of adhesive properties in Vibrio cholerae after long-term exposure to sea water}, journal = {Environmental Microbiology}, volume = {5}, year = {2003}, month = {2003/10/01/}, pages = {850 - 858}, abstract = {The effect of exposure to artificial sea water (ASW) on the ability of classical Vibrio cholerae O1 cells to interact with chitin-containing substrates and human intestinal cells was studied. Incubation of vibrios in ASW at 5{\textdegree}C and 18{\textdegree}C resulted in two kinds of cell responses: the viable but non-culturable (VBNC) state (i.e.~<0.1 colony forming unit ml-1) at 5{\textdegree}C, and starvation (i.e. maintenance of culturability of the population) at 18{\textdegree}C. The latter remained rod shaped and, after 40~days{\textquoteright} incubation, presented a 47{\textendash}58\% reduction in the number of cells attached to chitin, a 48{\textendash}53\% reduction in the number of bacteria adhering to copepods, and a 48{\textendash}54\% reduction in the number of bacteria adhering to human cultured intestinal cells, compared to control cells not suspended in ASW. Bacteria suspended in ASW at 5{\textdegree}C became coccoid and, after 40~days, showed 34{\textendash}42\% fewer cells attached to chitin, 52{\textendash}55\% fewer adhering to copep-ods, and 45{\textendash}48\% fewer cells adhering to intestinal cell monolayers, compared to controls. Sarkosyl-insoluble membrane proteins that bind chitin particles were isolated and analysed by SDS-PAGE. After 40~days incubation in ASW at both 5{\textdegree}C and 18{\textdegree}C vibrios expressed chitin-binding ligands similar to bacteria harvested in the stationary growth phase. It is concluded that as vibrios do not lose adhesive properties after long-term exposure to ASW, it is important to include methods for VBNC bacteria when testing environmental and clinical samples for purposes of public health safety.}, isbn = {1462-2920}, doi = {10.1046/j.1462-2920.2003.00498.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1462-2920.2003.00498.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Pruzzo,Carla and Tarsi,Renato and Del Mar Lle{\`o},Maria and Signoretto,Caterina and Zampini,Massimiliano and Pane,Luigi and Rita R Colwell and Canepari,Pietro} } @article {13254, title = {A perturbation method for evaluating background subtraction algorithms}, journal = {Joint IEEE International Workshop on Visual Surveillance and Performance Evaluation of Tracking and Surveillance (VS-PETS)}, year = {2003}, month = {2003///}, abstract = {We introduce a performance evaluation methodology calledPerturbation Detection Rate (PDR) analysis, for measuring performance of background subtraction (BGS) algorithms. It has some advantages over the commonly used Receiver Operation Characteristics (ROC) analysis. Specifically, it does not require foreground targets or knowledge of fore- ground distributions. It measures the sensitivity of a BGS algorithm in detecting low contrast targets against back- ground as a function of contrast, also depending on how well the model captures mixed (moving) background events. We compare four algorithms having similarities and differ- ences. Three are in [2, 3, 5] while the fourth is recently de- veloped, called Codebook BGS. The latter algorithm quan- tizes sample background values at each pixel into code- books which represent a compressed form of background model for a long image sequence. }, author = {Chalidabhongse,T.H. and Kim,K. and Harwood,D. and Davis, Larry S.} } @article {13010, title = {Phylogenetic analysis reveals five independent transfers of the chloroplast gene {\i}t rbcL to the mitochondrial genome in angiosperms}, journal = {Curr Genet}, volume = {43}, year = {2003}, month = {2003/05//}, pages = {131 - 138}, abstract = {We used the chloroplast gene rbcL as a model to study the frequency and relative timing of transfer of chloroplast sequences to the mitochondrial genome. Southern blot survey of 20 mitochondrial DNAs confirmed three previously reported groups of plants containing rbcL in their mitochondrion, while PCR studies identified a new mitochondrial rbcL. Published and newly determined mitochondrial and chloroplast rbcL sequences were used to reconstruct rbcL phylogeny. The results imply five or six separate interorganellar transfers of rbcL among the angiosperms examined, and hundreds of successful transfers across all flowering plants. By taxonomic criteria, the crucifer transfer is the most ancient, two separate transfers within the grass family are of intermediate ancestry, and the morning-glory transfer is most recent. All five mitochondrial copies of rbcL examined exhibit insertion and/or deletion events that disrupt the reading frame (three are grossly truncated); and all are elevated in the proportion of nonsynonymous substitutions, providing clear evidence that these sequences are pseudogenes.}, doi = {10.1007/s00294-003-0378-3}, author = {Cummings, Michael P. and Nugent,J. M and Olmstead,R. G and Palmer,J. D} } @article {12949, title = {Predictability of Vibrio Cholerae in Chesapeake Bay}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {69}, year = {2003}, month = {2003/05/01/}, pages = {2773 - 2785}, abstract = {Vibrio cholerae is autochthonous to natural waters and can pose a health risk when it is consumed via untreated water or contaminated shellfish. The correlation between the occurrence of V. cholerae in Chesapeake Bay and environmental factors was investigated over a 3-year period. Water and plankton samples were collected monthly from five shore sampling sites in northern Chesapeake Bay (January 1998 to February 2000) and from research cruise stations on a north-south transect (summers of 1999 and 2000). Enrichment was used to detect culturable V. cholerae, and 21.1\% (n = 427) of the samples were positive. As determined by serology tests, the isolates, did not belong to serogroup O1 or O139 associated with cholera epidemics. A direct fluorescent-antibody assay was used to detect V. cholerae O1, and 23.8\% (n = 412) of the samples were positive. V. cholerae was more frequently detected during the warmer months and in northern Chesapeake Bay, where the salinity is lower. Statistical models successfully predicted the presence of V. cholerae as a function of water temperature and salinity. Temperatures above 19{\textdegree}C and salinities between 2 and 14 ppt yielded at least a fourfold increase in the number of detectable V. cholerae. The results suggest that salinity variation in Chesapeake Bay or other parameters associated with Susquehanna River inflow contribute to the variability in the occurrence of V. cholerae and that salinity is a useful indicator. Under scenarios of global climate change, increased climate variability, accompanied by higher stream flow rates and warmer temperatures, could favor conditions that increase the occurrence of V. cholerae in Chesapeake Bay.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.69.5.2773-2785.2003}, url = {http://aem.asm.org/content/69/5/2773}, author = {Louis,Val{\'e}rie R. and Russek-Cohen,Estelle and Choopun,Nipa and Rivera,Irma N. G. and Gangle,Brian and Jiang,Sunny C. and Rubin,Andrea and Patz,Jonathan A. and Huq,Anwar and Rita R Colwell} } @article {12722, title = {Probabilistic recognition of human faces from video}, journal = {Computer Vision and Image Understanding}, volume = {91}, year = {2003}, month = {2003/07//}, pages = {214 - 245}, abstract = {Recognition of human faces using a gallery of still or video images and a probe set of videos is systematically investigated using a probabilistic framework. In still-to-video recognition, where the gallery consists of still images, a time series state space model is proposed to fuse temporal information in a probe video, which simultaneously characterizes the kinematics and identity using a motion vector and an identity variable, respectively. The joint posterior distribution of the motion vector and the identity variable is estimated at each time instant and then propagated to the next time instant. Marginalization over the motion vector yields a robust estimate of the posterior distribution of the identity variable. A computationally efficient sequential importance sampling (SIS) algorithm is developed to estimate the posterior distribution. Empirical results demonstrate that, due to the propagation of the identity variable over time, a degeneracy in posterior probability of the identity variable is achieved to give improved recognition. The gallery is generalized to videos in order to realize video-to-video recognition. An exemplar-based learning strategy is adopted to automatically select video representatives from the gallery, serving as mixture centers in an updated likelihood measure. The SIS algorithm is applied to approximate the posterior distribution of the motion vector, the identity variable, and the exemplar index, whose marginal distribution of the identity variable produces the recognition result. The model formulation is very general and it allows a variety of image representations and transformations. Experimental results using images/videos collected at UMD, NIST/USF, and CMU with pose/illumination variations illustrate the effectiveness of this approach for both still-to-video and video-to-video scenarios with appropriate model choices.}, keywords = {Exemplar-based learning, face recognition, sequential importance sampling, Still-to-video, Time series state space model, Video-to-video}, isbn = {1077-3142}, doi = {10.1016/S1077-3142(03)00080-8}, url = {http://www.sciencedirect.com/science/article/pii/S1077314203000808}, author = {Zhou,Shaohua and Krueger,Volker and Chellapa, Rama} } @article {12788, title = {A process-algebraic language for probabilistic I/O automata}, journal = {CONCUR 2003-Concurrency Theory}, year = {2003}, month = {2003///}, pages = {193 - 207}, author = {Stark,E. W and Cleaveland, Rance and Smolka,S. A} } @conference {14543, title = {Random MAX SAT, random MAX CUT, and their phase transitions}, booktitle = {Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms}, year = {2003}, month = {2003///}, pages = {364 - 373}, author = {Coppersmith,D. and Gamarnik,D. and Hajiaghayi, Mohammad T. and Sorkin,G. B} } @conference {12718, title = {Rank constrained recognition under unknown illuminations}, booktitle = {Analysis and Modeling of Faces and Gestures, 2003. AMFG 2003. IEEE International Workshop on}, year = {2003}, month = {2003/10//}, pages = {11 - 18}, abstract = {Recognition under illumination variations is a challenging problem. The key is to successfully separate the illumination source from the observed appearance. Once separated, what remains is invariant to illuminant and appropriate for recognition. Most current efforts employ a Lambertian reflectance model with varying albedo field ignoring both attached and cast shadows, but restrict themselves by using object-specific samples, which undesirably deprives them of recognizing new objects not in the training samples. Using rank constraints on the albedo and the surface normal, we accomplish illumination separation in a more general setting, e.g., with class-specific samples via a factorization approach. In addition, we handle shadows (both attached and cast ones) by treating them as missing values, and resolve the ambiguities in the factorization method by enforcing integrability. As far as recognition is concerned, a bootstrap set which is just a collection of two-dimensional image observations can be utilized to avoid the explicit requirement that three-dimensional information be available. Our approaches produce good recognition results as shown in our experiments using the PIE database.}, keywords = {albedo, approach;, constrained, database;, databases;, decomposition;, factorization, field;, illumination, image;, information;, Lambertian, lighting;, model;, object, object-specific, PIE, rank, recognition;, reflectance, samples;, singular, three-dimensional, two-dimensional, value, variations;, visual}, doi = {10.1109/AMFG.2003.1240818}, author = {Zhou, S. and Chellapa, Rama} } @article {15019, title = {Recovery of a Digital Image Collection Through the SDSC/UMD/NARA Prototype Persistent Archive}, volume = {UMIACS-TR-2003-105}, year = {2003}, month = {2003/11/25/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {The San Diego Supercomputer Center (SDSC), the University of Maryland, and theNational Archives and Records Administration (NARA) are collaborating on building a pilot persistent archive using and extending data grid and digital library technologies. The current prototype consists of node servers at SDSC, University of Maryland, and NARA, connected through the Storage Request Broker (SRB) data grid middleware, and currently holds several terabytes of NARA selected collections. In particular, a historically important image collection that was on the verge of becoming inaccessible was fully restored and ingested into our pilot system. In this report, we describe the methodology behind our approach to fully restore this image collection and the process used to ingest it into the prototype persistent archive. (UMIACS-TR-2003-105) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1321}, author = {Smorul,Mike and JaJa, Joseph F. and McCall,Fritz and Brown,Susan Fitch and Moore,Reagan and Marciano,Richard and Chen,Sheau-Yen and Lopez,Rick and Chadduck,Robert} } @article {12953, title = {Reduction of Cholera in Bangladeshi Villages by Simple Filtration}, journal = {Proceedings of the National Academy of SciencesPNAS}, volume = {100}, year = {2003}, month = {2003/02/04/}, pages = {1051 - 1055}, abstract = {Based on results of ecological studies demonstrating that Vibrio cholerae, the etiological agent of epidemic cholera, is commensal to zooplankton, notably copepods, a simple filtration procedure was developed whereby zooplankton, most phytoplankton, and particulates >20 μm were removed from water before use. Effective deployment of this filtration procedure, from September 1999 through July 2002 in 65 villages of rural Bangladesh, of which the total population for the entire study comprised ≈133,000 individuals, yielded a 48\% reduction in cholera (P < 0.005) compared with the control.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0237386100}, url = {http://www.pnas.org/content/100/3/1051}, author = {Rita R Colwell and Huq,Anwar and M. Sirajul Islam and K. M. A. Aziz and Yunus,M. and N. Huda Khan and A. Mahmud and Sack,R. Bradley and Nair,G. B. and J. Chakraborty and Sack,David A. and E. Russek-Cohen} } @article {12153, title = {Replicated studies: building a body of knowledge about software reading techniques}, journal = {SERIES ON SOFTWARE ENGINEERING AND KNOWLEDGE ENGINEERING}, volume = {12}, year = {2003}, month = {2003///}, pages = {39 - 84}, author = {Shull, F. and Carver, J. and Travassos,G.H. and Maldonado,J.C. and Conradi,R. and Basili, Victor R.} } @inbook {12739, title = {Robust Face Recognition in the Presence of Clutter}, booktitle = {Audio- and Video-Based Biometric Person AuthenticationAudio- and Video-Based Biometric Person Authentication}, series = {Lecture Notes in Computer Science}, volume = {2688}, year = {2003}, month = {2003///}, pages = {1062 - 1062}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We propose a new method within the framework of principal component analysis to robustly recognize faces in the presence of clutter. The traditional eigenface recognition method performs poorly when confronted with the more general task of recognizing faces appearing against a background. It misses faces completely or throws up many false alarms. We argue in favor of learning the distribution of background patterns and show how this can be done for a given test image. An eigenbackground space is constructed and this space in conjunction with the eigenface space is used to impart robustness in the presence of background. A suitable classifier is derived to distinguish non-face patterns from faces. When tested on real images, the performance of the proposed method is found to be quite good.}, isbn = {978-3-540-40302-9}, url = {http://dx.doi.org/10.1007/3-540-44887-X_1}, author = {Rajagopalan, AN and Chellapa, Rama and Koterba,Nathan}, editor = {Kittler,Josef and Nixon,Mark} } @article {14819, title = {A search engine for 3D models}, journal = {ACM Trans. Graph.}, volume = {22}, year = {2003}, month = {2003/01//}, pages = {83 - 105}, abstract = {As the number of 3D models available on the Web grows, there is an increasing need for a search engine to help people find them. Unfortunately, traditional text-based search techniques are not always effective for 3D data. In this article, we investigate new shape-based search methods. The key challenges are to develop query methods simple enough for novice users and matching algorithms robust enough to work for arbitrary polygonal models. We present a Web-based search engine system that supports queries based on 3D sketches, 2D sketches, 3D models, and/or text keywords. For the shape-based queries, we have developed a new matching algorithm that uses spherical harmonics to compute discriminating similarity measures without requiring repair of model degeneracies or alignment of orientations. It provides 46 to 245\% better performance than related shape-matching methods during precision--recall experiments, and it is fast enough to return query results from a repository of 20,000 models in under a second. The net result is a growing interactive index of 3D models available on the Web (i.e., a Google for 3D models).}, keywords = {Search engine, shape matching, shape representation, shape retrieval}, isbn = {0730-0301}, doi = {10.1145/588272.588279}, url = {http://doi.acm.org/10.1145/588272.588279}, author = {Funkhouser,Thomas and Min,Patrick and Kazhdan,Michael and Chen,Joyce and Halderman,Alex and Dobkin,David and Jacobs, David W.} } @article {15953, title = {Seven days in the life of a robotic agent}, journal = {Innovative Concepts for Agent-Based Systems}, year = {2003}, month = {2003///}, pages = {243 - 256}, author = {Chong,W. and O{\textquoteright}Donovan-Anderson,M. and Okamoto,Y. and Perlis, Don} } @conference {12725, title = {Shape and motion driven particle filtering for human body tracking}, booktitle = {Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {3}, year = {2003}, month = {2003/07//}, pages = {III - 61-4 vol.3 - III - 61-4 vol.3}, abstract = {In this paper, we propose a method to recover 3D human body motion from a video acquired by a single static camera. In order to estimate the complex state distribution of a human body, we adopt the particle filtering framework. We present the human body using several layers of representation and compose the whole body step by step. In this way, more effective particles are generated and ineffective particles are removed as we process each layer. In order to deal with the rotational motion, the frequency of rotation is obtained using a preprocessing operation. In the preprocessing step, the variance of the motion field at each image is computed, and the frequency of rotation is estimated. The estimated frequency is used for the state update in the algorithm. We successfully track the movement of figure skaters in TV broadcast image sequence, and recover the 3D shape and motion of the skater.}, keywords = {3D, body, broadcast, camera;, cameras;, estimation;, Filtering, framework;, human, image, MOTION, motion;, particle, processing;, rotational, sequence;, sequences;, signal, single, static, theory;, tracking;, TV, video}, doi = {10.1109/ICME.2003.1221248}, author = {Yamamoto, T. and Chellapa, Rama} } @conference {12732, title = {Simultaneous tracking and recognition of human faces from video}, booktitle = {Acoustics, Speech, and Signal Processing, 2003. Proceedings. (ICASSP {\textquoteright}03). 2003 IEEE International Conference on}, volume = {3}, year = {2003}, month = {2003/04//}, pages = {III - 225-8 vol.3 - III - 225-8 vol.3}, abstract = {The paper investigates the interaction between tracking and recognition of human faces from video under a framework proposed earlier (Shaohua Zhou et al., Proc. 5th Int. Conf. on Face and Gesture Recog., 2002; Shaohua Zhou and Chellappa, R., Proc. European Conf. on Computer Vision, 2002), where a time series model is used to resolve the uncertainties in both tracking and recognition. However, our earlier efforts employed only a simple likelihood measurement in the form of a Laplacian density to deal with appearance changes between frames and between the observation and gallery images, yielding poor accuracies in both tracking and recognition when confronted by pose and illumination variations. The interaction between tracking and recognition was not well understood. We address the interdependence between tracking and recognition using a series of experiments and quantify the interacting nature of tracking and recognition.}, keywords = {appearance, changes;, density;, Face, human, illumination, Laplacian, model;, optical, pose, processing;, recognition;, series, series;, signal, TIME, tracking;, variations;, video, video;}, doi = {10.1109/ICASSP.2003.1199148}, author = {Zhou,Shaohua and Chellapa, Rama} } @conference {12208, title = {Starting an intergenerational technology design team: a case study}, booktitle = {Proceedings of the 2003 conference on Interaction design and children}, series = {IDC {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {51 - 58}, publisher = {ACM}, organization = {ACM}, address = {Preston, England}, abstract = {This paper presents a case study of the first three months of a new intergenerational design team with children ages 10--13. It discusses the research and design methods used for working with children of this age group, the challenges and opportunities of starting a new team, and the lessons learned.}, keywords = {children, cooperative inquiry, design methods, educational applications, intergenerational design teams, participatory design}, isbn = {1-58113-732-X}, doi = {10.1145/953536.953545}, author = {Knudtzon,Kendra and Druin, Allison and Kaplan,Nancy and Summers,Kathryn and Chisik,Yoram and Kulkarni,Rahul and Moulthrop,Stuart and Weeks,Holly and Bederson, Benjamin B.} } @conference {12744, title = {Statistical bias and the accuracy of 3d reconstruction from video}, booktitle = {in International Journal of Computer Vision}, year = {2003}, month = {2003///}, abstract = {The present state of the art in determining the error statistics in3D reconstruction from video concentrates on estimating the error covariance. A different source of error which has not received much attention in the computer vision community, but has been noted by psychophysicists, is the fact "that it is hard to explain ... the existence of systematic biases in observers{\textquoteright} magnitude estimation of perceived depth" (Todd, 1998). In this paper, we prove that the depth estimate is statistically biased, derive a precise expression for it, and hypothesize that our analysis can be a possible explanation for the experimental observations. Many structure from motion (SfM) algorithms that reconstruct a scene from a video sequence pose the problem in a linear least squares framework Ax = b. It is a well- known fact that the least squares estimate is biased if the system matrix A is noisy. In SfM, the matrix A contains the image coordinates, which are always difficult to obtain precisely; thus it is expected that the structure and motion estimates in such a formulation of the problem would be biased. Though previous authors have analyzed the bias in 3D motion estimation from stereo, to the best of our knowledge, the statistical bias in 3D reconstruction from video has not been studied in the vision community. We show that even with a perfect motion estimate, the depth estimate is statistically biased. Existing results on the minimum achievable variance of the estimator are extended by deriving a generalized Cramer-Rao lower bound. Through simulations, we demonstrate the effects of camera motion parameters on the bias and give numerical examples to highlight the importance of compensating for it. }, author = {Chowdhury, A.R. and Chellapa, Rama} } @conference {12730, title = {Statistical Error Propagation in 3D Modeling From Monocular Video}, booktitle = {Computer Vision and Pattern Recognition Workshop, 2003. CVPRW {\textquoteright}03. Conference on}, volume = {8}, year = {2003}, month = {2003/06//}, pages = {89 - 89}, abstract = {A significant portion of recent research in computer vision has focused on issues related to sensitivity and robustness of existing techniques. In this paper, we study the classical structure from motion problem and analyze how the statistics representing the quality of the input video propagates through the reconstruction algorithm and affects the quality of the output reconstruction. Specifically, we show that it is possible to derive analytical expressions of the first and second order statistics (bias and error covariance) of the solution as a function of the statistics of the input. We concentrate on the case of reconstruction from a monocular video, where the small baseline makes any algorithm very susceptible to noise in the motion estimates from the video sequence. We derive an expression relating the error covariance of the reconstruction to the error covariance of the feature tracks in the input video. This is done using the implicit function theorem of real analysis and does not require strong statistical assumptions. Next, we prove that the 3D reconstruction is statistically biased, derive an expression for it and show that it is numerically significant. Combining these two results, we also establish a new bound on the minimum error in the depth reconstruction. We present the numerical significance of these analytical results on real video data.}, doi = {10.1109/CVPRW.2003.10092}, author = {RoyChowdhury,Amit and Chellapa, Rama} } @article {12736, title = {Statistical physical model for foliage clutter in ultra-wideband synthetic aperture radar images}, journal = {Journal of the Optical Society of America AThe Journal of the Optical Society of America A}, volume = {20}, year = {2003}, month = {2003/01/01/}, pages = {32 - 39}, abstract = {Analyzing foliage-penetrating (FOPEN) ultra-wideband synthetic aperture radar (SAR) images is a challenging problem owing to the noisy and impulsive nature of foliage clutter. Indeed, many target-detection algorithms for FOPEN SAR data are characterized by high false-alarm rates. In this work, a statistical{\textendash}physical model for foliage clutter is proposed that explains the presence of outliers in the data and suggests the use of symmetric alpha-stable (SαS) distributions for accurate clutter modeling. Furthermore, with the use of general assumptions of the noise sources and propagation conditions, the proposed model relates the parameters of the SαS model to physical parameters such as the attenuation coefficient and foliage density.}, keywords = {IMAGE PROCESSING, Remote sensing and sensors}, doi = {10.1364/JOSAA.20.000032}, url = {http://josaa.osa.org/abstract.cfm?URI=josaa-20-1-32}, author = {Banerjee,Amit and Chellapa, Rama} } @conference {12733, title = {Statistical shape theory for activity modeling}, booktitle = {Acoustics, Speech, and Signal Processing, 2003. Proceedings. (ICASSP {\textquoteright}03). 2003 IEEE International Conference on}, volume = {3}, year = {2003}, month = {2003/04//}, pages = {III - 493-6 vol.3 - III - 493-6 vol.3}, abstract = {Monitoring activities in a certain region from video data is an important surveillance problem. The goal is to learn the pattern of normal activities and detect unusual ones by identifying activities that deviate appreciably from the typical ones. We propose an approach using statistical shape theory based on the shape model of D.G. Kendall et al. (see "Shape and Shape Theory", John Wiley and Sons, 1999). In a low resolution video, each moving object is best represented as a moving point mass or particle. In this case, an activity can be defined by the interactions of all or some of these moving particles over time. We model this configuration of the particles by a polygonal shape formed from the locations of the points in a frame and the activity by the deformation of the polygons in time. These parameters are learned for each typical activity. Given a test video sequence, an activity is classified as abnormal if the probability for the sequence (represented by the mean shape and the dynamics of the deviations), given the model, is below a certain threshold The approach gives very encouraging results in surveillance applications using a single camera and is able to identify various kinds of abnormal behavior.}, keywords = {abnormal, activities, activity, analysis;, behavior;, classification;, data;, image, mass;, matching;, modeling;, monitoring;, moving, normal, particle;, pattern, pattern;, point, polygonal, probability;, problem;, processing;, sequence;, sequences;, SHAPE, shape;, signal, statistical, Surveillance, surveillance;, theory;, video}, doi = {10.1109/ICASSP.2003.1199519}, author = {Vaswani, N. and Chowdhury, A.R. and Chellapa, Rama} } @article {12743, title = {Stochastic Approximation and Rate-Distortion Analysis for Robust Structure and Motion Estimation}, journal = {International Journal of Computer Vision}, volume = {55}, year = {2003}, month = {2003///}, pages = {27 - 53}, abstract = {Recent research on structure and motion recovery has focused on issues related to sensitivity and robustness of existing techniques. One possible reason is that in practical applications, the underlying assumptions made by existing algorithms are often violated. In this paper, we propose a framework for 3D reconstruction from short monocular video sequences taking into account the statistical errors in reconstruction algorithms. Detailed error analysis is especially important for this problem because the motion between pairs of frames is small and slight perturbations in its estimates can lead to large errors in 3D reconstruction. We focus on the following issues: physical sources of errors, their experimental and theoretical analysis, robust estimation techniques and measures for characterizing the quality of the final reconstruction. We derive a precise relationship between the error in the reconstruction and the error in the image correspondences. The error analysis is used to design a robust, recursive multi-frame fusion algorithm using {\textquotedblleft}stochastic approximation{\textquotedblright} as the framework since it is capable of dealing with incomplete information about errors in observations. Rate-distortion analysis is proposed for evaluating the quality of the final reconstruction as a function of the number of frames and the error in the image correspondences. Finally, to demonstrate the effectiveness of the algorithm, examples of depth reconstruction are shown for different video sequences.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1023/A:1024488407740}, author = {Chowdhury,Amit K. Roy and Chellapa, Rama} } @article {12430, title = {A Survey of Shape Similarity Assessment Algorithms for Product Design and Manufacturing Applications}, journal = {Journal of Computing and Information Science in EngineeringJ. Comput. Inf. Sci. Eng.}, volume = {3}, year = {2003}, month = {2003/06/00/}, pages = {109 - 118}, keywords = {CAD, computational geometry, production engineering computing, spatial reasoning}, doi = {10.1115/1.1577356}, url = {http://link.aip.org/link/?CIS/3/109/1}, author = {Cardone, Antonio and Gupta, Satyandra K. and Karnik,Mukul} } @article {18749, title = {A system for generating process and material selection advice during embodiment design of mechanical components}, journal = {Journal of manufacturing systems}, volume = {22}, year = {2003}, month = {2003///}, pages = {28 - 45}, abstract = {This paper describes a systematic approach to material and process selection during theembodiment design of mechanical components and a system for generating process and material selection advice. Quite often during the embodiment design stage, design requirements are not precisely defined. Therefore, the system described in this paper accounts for imprecision in design requirements during generation and evaluation of alternative process sequences and material options. To reduce the computational effort, the system uses a depth-first branch-and- bound search algorithm. This aids in exploring promising process sequences and material options that can be used to meet the given set of design requirements. Various process sequences and material options are evaluated by using a commercial cost estimation tool. }, url = {ftp://ftp.eng.umd.edu/:/home/glue/s/k/skgupta/backup/pub/Publication/JMS03_Gupta.pdf}, author = {Gupta,S.K. and Chen,Y. and Feng,S. and Sriram,R.} } @conference {16139, title = {Technology probes: inspiring design for and with families}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, series = {CHI {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {17 - 24}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We describe a new method for use in the process of co-designing technologies with users called technology probes. Technology probes are simple, flexible, adaptable technologies with three interdisciplinary goals: the social science goal of understanding the needs and desires of users in a real-world setting, the engineering goal of field-testing the technology, and the design goal of inspiring users and researchers to think about new technologies. We present the results of designing and deploying two technology probes, the messageProbe and the videoProbe, with diverse families in France, Sweden, and the U.S. We conclude with our plans for creating new technologies for and with families based on our experiences.}, keywords = {computer mediated communication, ethnography, Home, participatory design and cooperative design}, isbn = {1-58113-630-7}, doi = {10.1145/642611.642616}, url = {http://doi.acm.org/10.1145/642611.642616}, author = {Hutchinson,Hilary and Mackay,Wendy and Westerlund,Bo and Bederson, Benjamin B. and Druin, Allison and Plaisant, Catherine and Beaudouin-Lafon,Michel and Conversy,St{\'e}phane and Evans,Helen and Hansen,Heiko and Roussel,Nicolas and Eiderb{\"a}ck,Bj{\"o}rn} } @article {13344, title = {TelegraphCQ: An architectural status report}, journal = {IEEE Data Engineering Bulletin}, volume = {26}, year = {2003}, month = {2003///}, pages = {11 - 18}, author = {Krishnamurthy, S. and Chandrasekaran,S. and Cooper,O. and Deshpande, Amol and Franklin,M.J. and Hellerstein,J. M and Hong,W. and Madden,S. and Reiss,F. and Shah,M. A} } @conference {13405, title = {TelegraphCQ: continuous dataflow processing}, booktitle = {Proceedings of the 2003 ACM SIGMOD international conference on Management of data}, series = {SIGMOD {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {668 - 668}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {1-58113-634-X}, doi = {10.1145/872757.872857}, url = {http://doi.acm.org/10.1145/872757.872857}, author = {Chandrasekaran,Sirish and Cooper,Owen and Deshpande, Amol and Franklin,Michael J. and Hellerstein,Joseph M. and Wei Hong and Krishnamurthy,Sailesh and Madden,Samuel R. and Reiss,Fred and Shah,Mehul A.} } @conference {12728, title = {Towards a view invariant gait recognition algorithm}, booktitle = {Proceedings. IEEE Conference on Advanced Video and Signal Based Surveillance, 2003.}, year = {2003}, month = {2003/07//}, pages = {143 - 150}, abstract = {Human gait is a spatio-temporal phenomenon and typifies the motion characteristics of an individual. The gait of a person is easily recognizable when extracted from a side-view of the person. Accordingly, gait-recognition algorithms work best when presented with images where the person walks parallel to the camera image plane. However, it is not realistic to expect this assumption to be valid in most real-life scenarios. Hence, it is important to develop methods whereby the side-view can be generated from any other arbitrary view in a simple, yet accurate, manner. This is the main theme of the paper. We show that if the person is far enough from the camera, it is possible to synthesize a side view (referred to as canonical view) from any other arbitrary view using a single camera. Two methods are proposed for doing this: (i) using the perspective projection model; (ii) using the optical flow based structure from motion equations. A simple camera calibration scheme for this method is also proposed. Examples of synthesized views are presented. Preliminary testing with gait recognition algorithms gives encouraging results. A by-product of this method is a simple algorithm for synthesizing novel views of a planar scene.}, keywords = {(access, algorithm;, analysis;, Biometrics, biometrics;, Calibration, calibration;, camera, canonical, control);, equations;, flow;, Gait, gait;, human, image, invariant, model;, MOTION, optical, perspective, phenomenon;, projection, recognition, scheme;, sequences;, spatio-temporal, view, view;}, doi = {10.1109/AVSS.2003.1217914}, author = {Kale, A. and Chowdhury, A.K.R. and Chellapa, Rama} } @conference {12840, title = {Towards formal but flexible scenarios}, booktitle = {2nd International Workshop on Scenarios and State Machines: Models, Algorithms and Tools}, year = {2003}, month = {2003///}, author = {Sengupta,B. and Cleaveland, Rance} } @conference {12839, title = {TRIM: A tool for triggered message sequence charts}, booktitle = {Computer Aided Verification}, year = {2003}, month = {2003///}, pages = {106 - 109}, author = {Sengupta,B. and Cleaveland, Rance} } @article {17449, title = {Understanding Computer User Frustration: Measuring and Modeling the Disruption from Poor Designs}, journal = {Technical Reports from UMIACS}, year = {2003}, month = {2003/01/21/}, abstract = {User frustration in the use of information and computing technology is apervasive and persistent problem. When computers crash, network congestion causes delays, and poor user interfaces trigger confusion there are dramatic consequences for individuals, organizations, and society. These frustrations not only cause personal dissatisfaction and loss of self-efficacy, but may disrupt workplaces, slow learning, and reduce participation in local and national communities. We propose a Computing Frustration Model with incident specific and individual variables to guide research. Our study of 108 computer users shows high levels of frustration and loss of 1/3 to 1/2 of time spent. The importance of the users{\textquoteright} goals and the severity of the disruption were correlated with frustration. Those who had strong self-efficacy, indicated by a willingness to stick to solving the problem, reported lower levels of frustration. Implications for users, software developers, managers, and policymakers are discussed. Keywords: user frustration, user interface design, training, helpdesk, computer experience, computer anxiety (UMIACS-TR-2002-89) (HCIL-TR-2002-18) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1233}, author = {Bessiere,Katie and Ceaparu,Irina and Lazar,Jonathan and Robinson,John and Shneiderman, Ben} } @conference {12299, title = {On the use of flow migration for handling short-term overloads}, booktitle = {Global Telecommunications Conference, 2003. GLOBECOM {\textquoteright}03. IEEE}, volume = {6}, year = {2003}, month = {2003/12//}, pages = {3108 - 3112 vol.6 - 3108 - 3112 vol.6}, abstract = {In this work, we investigate flow migration as a mechanism to sustain QoS to network users during short-term overloads in the context of an MPLS IP network. We experiment with three different control techniques: static long-term optimal mapping of flows to LSPs; on-line locally optimal mapping of flows to LSPs at flow set-up time; and dynamic flow migration in response to transient congestion. These techniques are applicable over different timescales, have different run-time overheads, and require different levels of monitoring and control software inside the network. We present results both from detailed simulations and a complete implementation using software IP routers. We use voice-over-IP as our test application, and show that if end-to-end quality is to be maintained during short unpredictable bursts of high load, then a fast-timescale control such as migration is required.}, keywords = {computing;, CONGESTION, congestion;, CONTROL, control;, dynamic, end-to-end, engineering, fast-timescale, flow, Internet, IP, label, long-term, mapping;, migration;, MPLS, multiprotocol, network, network;, networks;, of, optimal, overloads;, protocol;, QoS;, QUALITY, quality;, routers;, routing;, service;, set-up, short-term, software, software;, static, switching;, Telecommunication, telephony;, time;, transient, voice-over-IP;}, doi = {10.1109/GLOCOM.2003.1258807}, author = {Kuo,Kuo-Tung and Phuvoravan,S. and Bhattacharjee, Bobby and Jun La,R. and Shayman,M. and Chang,Hyeong Soo} } @conference {16123, title = {Using Visualization Tools to Gain Insight Into Your Data}, booktitle = {SPE Annual Technical Conference and Exhibition}, year = {2003}, month = {2003/10//}, publisher = {Society of Petroleum Engineers}, organization = {Society of Petroleum Engineers}, abstract = {When the term {\textquoteleft}visualization{\textquoteright} is used in the oil and gas industry, it is usually referring to the viewing of complex geologic structures in three-dimensional space. This paper illustrates insights gained by applying interactive visual environments to petroleum industry data that has traditionally been presented in spreadsheets, line graphs, and bar charts. Two information visualization tools, Treemap and SpaceTree, will be shown applied to a variety of oilfield related data.}, isbn = {9781555631529}, doi = {10.2118/84439-MS}, url = {http://www.onepetro.org/mslib/servlet/onepetropreview?id=00084439}, author = {Plaisant, Catherine and Chintalapani,G. and Lukehart,C. and Schiro,D. and Ryan,J.} } @conference {12727, title = {Video based rendering of planar dynamic scenes}, booktitle = {Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {1}, year = {2003}, month = {2003/07//}, pages = {I - 477-80 vol.1 - I - 477-80 vol.1}, abstract = {In this paper, we propose a method to synthesize arbitrary views of a planar scene from a monocular video sequence of it. The 3-D direction of motion of the object is robustly estimated from the video sequence. Given this direction any other view of the object can be synthesized through a perspective projection approach, under assumptions of planarity. If the distance of the object from the camera is large, a planar approximation is reasonable even for non-planar scenes. Such a method has many important applications, one of them being gait recognition where a side view of the person is required. Our method can be used to synthesize the side-view of the person in case he/she does not present a side view to the camera. Since the planarity assumption is often an approximation, the effects of non-planarity can lead to inaccuracies in rendering and needs to be corrected for. Regions where this happens are examined and a simple technique based on weak perspective approximation is proposed to offset rendering inaccuracies. Examples of synthesized views using our method and performance evaluation are presented.}, keywords = {(computer, 3D, analysis;, approximation;, based, camera;, cameras;, direction;, dynamic, graphics);, image, monocular, MOTION, perspective, planar, processing;, rendering, rendering;, scenes;, sequence;, sequences;, signal, video, weak}, doi = {10.1109/ICME.2003.1220958}, author = {Kale, A. and Chowdhury, A.K.R. and Chellapa, Rama} } @article {12742, title = {VIDEO SYNTHESIS OF ARBITRARY VIEWS FOR APPROXIMATELY PLANAR SCENES}, journal = {IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS SPEECH AND SIGNAL PROCESSING}, volume = {3}, year = {2003}, month = {2003///}, author = {Chowdhury, A.R. and Kale, A. and Chellapa, Rama} } @conference {12735, title = {Video synthesis of arbitrary views for approximately planar scenes}, booktitle = {Acoustics, Speech, and Signal Processing, 2003. Proceedings. (ICASSP {\textquoteright}03). 2003 IEEE International Conference on}, volume = {3}, year = {2003}, month = {2003/04//}, pages = {III - 497-500 vol.3 - III - 497-500 vol.3}, abstract = {In this paper, we propose a method to synthesize arbitrary views of a planar scene, given a monocular video sequence. The method is based on the availability of knowledge of the angle between the original and synthesized views. Such a method has many important applications, one of them being gait recognition. Gait recognition algorithms rely on the availability of an approximate side-view of the person. From a realistic viewpoint, such an assumption is impractical in surveillance applications and it is of interest to develop methods to synthesize a side view of the person, given an arbitrary view. For large distances from the camera, a planar approximation for the individual can be assumed. In this paper, we propose a perspective projection approach for recovering the direction of motion of the person purely from the video data, followed by synthesis of a new video sequence at a different angle. The algorithm works purely in the image and video domain, though 3D structure plays an implicit role in its theoretical justification. Examples of synthesized views using our method and performance evaluation are presented.}, keywords = {(access, 3D, applications;, approach;, approximately, approximation;, arbitrary, Biometrics, control);, data;, direction, estimation;, evaluation;, Gait, image, monocular, MOTION, performance, perspective, planar, processing;, projection, recognition;, recovery;, scenes;, sequence;, sequences;, side, signal, structure;, Surveillance, surveillance;, synthesis;, synthesized, video, view, views;}, doi = {10.1109/ICASSP.2003.1199520}, author = {Chowdhury, A.K.R. and Kale, A. and Chellapa, Rama} } @conference {12724, title = {View synthesis of articulating humans using visual hull}, booktitle = {Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {1}, year = {2003}, month = {2003/07//}, pages = {I - 489-92 vol.1 - I - 489-92 vol.1}, abstract = {In this paper, we present a method, which combines image-based visual hull and human body part segmentation for overcoming the inability of the visual hull method to reconstruct concave regions. The virtual silhouette image corresponding to the given viewing direction is first produced with image-based visual hull. Human body part localization technique is used to segment the input images and the rendered virtual silhouette image into convex body parts. The body parts in the virtual view are generated separately from the corresponding body parts in the input views and then assembled together. The previously rendered silhouette image is used to locate the corresponding body parts in input views and avoid the unconnected or squeezed regions in the assembled final view. Experiments show that this method can improve the reconstruction of concave regions for human postures and texture mapping.}, keywords = {analysis;, body, convex, gesture, hull;, human, image, image-based, image;, mapping;, MOTION, part, parts;, postures;, recognition;, reconstruction;, segmentation;, silhouette, synthesis;, TEXTURE, texture;, view, virtual, visual}, doi = {10.1109/ICME.2003.1220961}, author = {Yue,Zhanfeng and Liang Zhao and Chellapa, Rama} } @article {17849, title = {The virtual microscope}, journal = {IEEE Transactions on Information Technology in Biomedicine}, volume = {7}, year = {2003}, month = {2003/12//}, pages = {230 - 248}, abstract = {We present the design and implementation of the virtual microscope, a software system employing a client/server architecture to provide a realistic emulation of a high power light microscope. The system provides a form of completely digital telepathology, allowing simultaneous access to archived digital slide images by multiple clients. The main problem the system targets is storing and processing the extremely large quantities of data required to represent a collection of slides. The virtual microscope client software runs on the end user{\textquoteright}s PC or workstation, while database software for storing, retrieving and processing the microscope image data runs on a parallel computer or on a set of workstations at one or more potentially remote sites. We have designed and implemented two versions of the data server software. One implementation is a customization of a database system framework that is optimized for a tightly coupled parallel machine with attached local disks. The second implementation is component-based, and has been designed to accommodate access to and processing of data in a distributed, heterogeneous environment. We also have developed caching client software, implemented in Java, to achieve good response time and portability across different computer platforms. The performance results presented show that the Virtual Microscope systems scales well, so that many clients can be adequately serviced by an appropriately configured data server.}, keywords = {biomedical optical imaging, client software, client/server architecture, Computer architecture, Computer Graphics, computer platforms, Computer simulation, Concurrent computing, configured data server, data server software, database management systems, database software, Database systems, digital slide images, digital telepathology, diseases, emulation, Environment, Equipment Design, Equipment Failure Analysis, high power light microscope, Image databases, Image Enhancement, Image Interpretation, Computer-Assisted, Image retrieval, Information retrieval, Information Storage and Retrieval, java, local disks, microscope image data, Microscopy, multiple clients, optical microscopy, PACS, software, Software design, software system, Software systems, Systems Integration, Telepathology, User-Computer Interface, virtual microscope design, Virtual reality, Workstations}, isbn = {1089-7771}, doi = {10.1109/TITB.2004.823952}, author = {Catalyurek,U. and Beynon,M. D and Chang,Chialin and Kurc, T. and Sussman, Alan and Saltz, J.} } @inbook {16131, title = {The World{\textquoteright}s Information in Digital Libraries}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {149 - 149}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, isbn = {978-1-55860-915-0}, author = {Plaisant, Catherine and Marchimini,G. and Bruns,T. and Komlodi,A. and Campbell,L. and Rose,A. and Ding,G.M. and Beale Jr,J. and Nolet,V. and Shneiderman, Ben and others} } @conference {12765, title = {3D face reconstruction from video using a generic model}, booktitle = {Multimedia and Expo, 2002. ICME {\textquoteright}02. Proceedings. 2002 IEEE International Conference on}, volume = {1}, year = {2002}, month = {2002///}, pages = {449 - 452 vol.1 - 449 - 452 vol.1}, abstract = {Reconstructing a 3D model of a human face from a video sequence is an important problem in computer vision, with applications to recognition, surveillance, multimedia etc. However, the quality of 3D reconstructions using structure from motion (SfM) algorithms is often not satisfactory. One common method of overcoming this problem is to use a generic model of a face. Existing work using this approach initializes the reconstruction algorithm with this generic model. The problem with this approach is that the algorithm can converge to a solution very close to this initial value, resulting in a reconstruction which resembles the generic model rather than the particular face in the video which needs to be modeled. We propose a method of 3D reconstruction of a human face from video in which the 3D reconstruction algorithm and the generic model are handled separately. A 3D estimate is obtained purely from the video sequence using SfM algorithms without use of the generic model. The final 3D model is obtained after combining the SfM estimate and the generic model using an energy function that corrects for the errors in the estimate by comparing local regions in the two models. The optimization is done using a Markov chain Monte Carlo (MCMC) sampling strategy. The main advantage of our algorithm over others is that it is able to retain the specific features of the face in the video sequence even when these features are different from those of the generic model. The evolution of the 3D model through the various stages of the algorithm is presented.}, keywords = {3D, algorithm;, algorithms;, analysis;, Carlo, chain, Computer, Face, from, function;, generic, human, image, Markov, MCMC, methods;, model;, Monte, MOTION, optimisation;, OPTIMIZATION, processes;, processing;, recognition;, reconstruction, reconstruction;, sampling;, sequence;, sequences;, SfM, signal, structure, surveillance;, video, vision;}, doi = {10.1109/ICME.2002.1035815}, author = {Chowdhury, A.R. and Chellapa, Rama and Krishnamurthy, S. and Vo, T.} } @conference {14795, title = {Active Harmony: Towards Automated Performance Tuning}, booktitle = {Supercomputing, ACM/IEEE 2002 Conference}, year = {2002}, month = {2002/11//}, pages = {44 - 44}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we present the Active Harmony automated runtime tuning system. We describe the interface used by programs to make applications tunable. We present the Library Specification Layer which helps program library developers expose multiple variations of the same API using different algorithms.The Library Specification Language helps to select the most appropriate program library to tune the overall performance. We also present the optimization algorithm used to adjust parameters in the application and the libraries. Finally, we present results that show how the system is able to tune several real applications. The automated tuning system is able to tune the application parameers to within a few percent of the best value after evaluating only 11 out of over 1,700 possible configurations.}, keywords = {Application software, Automatic control, Computational modeling, Computer science, Computerized monitoring, Control systems, grid computing, Runtime library, software libraries, Specification languages}, isbn = {0-7695-1524-X}, doi = {10.1109/SC.2002.10062}, author = {Tapus, C. and I-Hsin Chung and Hollingsworth, Jeffrey K} } @conference {18651, title = {An adaptive framework for tunable consistency and timeliness using replication}, year = {2002}, month = {2002///}, pages = {17 - 26}, abstract = {One well-known challenge in using replication to service multiple clients concurrently is that of delivering a timely and consistent response to the clients. In this paper, we address this problem in the context of client applications that have specific temporal and consistency requirements. These applications can tolerate a certain degree of relaxed consistency, in exchange for better response time. We propose a flexible QoS model that allows these clients to specify their temporal and consistency constraints. In order to select replicas to serve these clients, we need to control of the inconsistency of the replicas, so that we have a large enough pool of replicas with the appropriate state to meet a client{\textquoteright}s timeliness, consistency, and dependability requirements. We describe an adaptive framework that uses lazy update propagation to control the replica inconsistency and employs a probabilistic approach to select replicas dynamically to service a client, based on its QoS specification. The probabilistic approach predicts the ability of a replica to meet a client{\textquoteright}s QoS specification by using the performance history collected by monitoring the replicas at runtime. We conclude with experimental results based on our implementation.}, keywords = {adaptive framework, concurrent multiple client service, consistency requirements, dependability requirements, distributed object management, flexible QoS model, lazy update propagation, performance history, probabilistic approach, Protocols, quality of service, replication, temporal requirements, timely consistent response, tunable consistency, tunable timeliness}, doi = {10.1109/DSN.2002.1028882}, author = {Krishnamurthy, S. and Sanders,W. H. and Michel Cukier} } @article {12966, title = {Analysis of 16S-23S rRNA intergenic spacer of Vibrio cholerae and Vibrio mimicus for detection of these species}, journal = {METHODS IN MOLECULAR BIOLOGY}, volume = {179}, year = {2002}, month = {2002///}, pages = {171 - 178}, doi = {10.1385/1-59259-238-4:171}, author = {Chun,J. and Rivera,I. N. G. and Rita R Colwell} } @article {14097, title = {Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray}, journal = {Molecular and Biochemical Parasitology}, volume = {123}, year = {2002}, month = {2002/08/28/}, pages = {115 - 123}, abstract = {A microarray comprising 21[punctuation space]024 different PCR products spotted on glass slides was constructed for gene expression studies on Trypanosoma brucei. The arrayed fragments were generated from a T. brucei shotgun clone library, which had been prepared from randomly sheared and size-fractionated genomic DNA. For the identification of stage-specific gene activity, total RNA from in vitro cultures of the human, long slender form and the insect, procyclic form of the parasite was labelled and hybridised to the microarray. Approximately 75\% of the genomic fragments produced a signal and about 2\% exhibited significant differences between the transcript levels in the bloodstream and procyclic forms. A few results were confirmed by Northern blot analysis or reverse-transcription and PCR. Three hundred differentially regulated clones have been selected for sequencing. So far, of 33 clones that showed about 2-fold or more over-expression in bloodstream forms, 15 contained sequences similar to those of VSG expression sites and at least six others appeared non-protein-coding. Of 29 procyclic-specific clones, at least eight appeared not to be protein-coding. A surprisingly large proportion of known regulated genes was already identified in this small sample, and some new ones were found, illustrating the utility of genomic arrays.}, keywords = {Expression, Gene, Microarray, Regulation, Trypanosoma brucei}, isbn = {0166-6851}, doi = {16/S0166-6851(02)00138-X}, url = {http://www.sciencedirect.com/science/article/pii/S016668510200138X}, author = {Diehl,Susanne and Diehl,Frank and El-Sayed, Najib M. and Clayton,Christine and Hoheisel,J{\"o}rg D.} } @inbook {16960, title = {An Augmented Visual Query Mechanism for Finding Patterns in Time Series Data}, booktitle = {Flexible Query Answering SystemsFlexible Query Answering Systems}, series = {Lecture Notes in Computer Science}, volume = {2522}, year = {2002}, month = {2002///}, pages = {240 - 250}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Relatively few query tools exist for data exploration and pattern identification in time series data sets. In previous work we introduced Timeboxes . Timeboxes are rectangular, direct-manipulation queries for studying time-series datasets. We demonstrated how Timeboxes can be used to support interactive exploration via dynamic queries, along with overviews of query results and drag-and-drop support for query-by-example. In this paper, we extend our work by introducing Variable Time Timeboxes (VTT). VTTs are a natural generalization of Timeboxes, which permit the specification of queries that allow a degree of uncertainty in the time axis. We carefully motivate the need for these more expressive queries, and demonstrate the utility of our approach on several data sets.}, isbn = {978-3-540-00074-7}, url = {http://dx.doi.org/10.1007/3-540-36109-X_19}, author = {Keogh,Eamonn and Hochheiser,Harry and Shneiderman, Ben}, editor = {Carbonell,Jaime and Siekmann,J{\"o}rg and Andreasen,Troels and Christiansen,Henning and Motro,Amihai and Legind Larsen,Henrik} } @article {12759, title = {A Bayesian Approach to Simultaneous Motion Estimation of Multiple Independently Moving Objects}, journal = {INTERNATIONAL CONFERENCE ON PATTERN RECOGNITION}, volume = {16}, year = {2002}, month = {2002///}, pages = {309 - 314}, abstract = {In this paper, the problem of simultaneous motion estima-tion of multiple independently moving objects is addressed. A novel Bayesian approach is designed for solving this prob- lem using the sequential importance sampling (SIS) method. In the proposed algorithm, a balancing step is added into the SIS procedure to preserve samples of low weights so that all objects have enough samples to propagate empirical motion distributions. By using the proposed algorithm, the relative motions of all moving objects with respect to camera can be simultaneously estimated . This algorithm has been tested on both synthetic and real image sequences. Improved re- sults have been achieved. }, author = {Qian, G. and Chellapa, Rama and Zheng,Q.} } @conference {12753, title = {Bayesian methods for face recognition from video}, booktitle = {Acoustics, Speech, and Signal Processing (ICASSP), 2002 IEEE International Conference on}, volume = {4}, year = {2002}, month = {2002/05//}, pages = {IV-4068 -IV-4071 - IV-4068 -IV-4071}, abstract = {Face recognition (FR) from video necessitates simultaneously solving two asks, recognition and tracking. To accommodate the video, a time series state space model is introduced in a Bayesian approach. Given this model, the goal reduces to estimating the posterior distribution of the state vector given the observations up to the present. The Sequential Importance Sampling (SIS) technique is invoked to generate a numerical solution to this model. However, the ultimate goal is to estimate the posterior distribution of the identity of humans for recognition purposes. Presented here are two methods to approximate the above distribution under different experimental scenarios.}, doi = {10.1109/ICASSP.2002.5745551}, author = {Chellapa, Rama and Zhou,Shaohua and Li,Baoxin} } @conference {12758, title = {Bayesian structure from motion using inertial information}, booktitle = {Image Processing. 2002. Proceedings. 2002 International Conference on}, volume = {3}, year = {2002}, month = {2002///}, pages = {III-425 - III-428 vol.3 - III-425 - III-428 vol.3}, abstract = {A novel approach to Bayesian structure from motion (SfM) using inertial information and sequential importance sampling (SIS) is presented. The inertial information is obtained from camera-mounted inertial sensors and is used in the Bayesian SfM approach as prior knowledge of the camera motion in the sampling algorithm. Experimental results using both synthetic and real images show that, when inertial information is used, more accurate results can be obtained or the same estimation accuracy can be obtained at a lower cost.}, keywords = {3D, analysis;, Bayes, Bayesian, camera, estimation;, image, images;, importance, inertial, information;, methods;, MOTION, motion;, parameter, processing;, real, reconstruction;, sampling;, scene, sensors;, sequence;, sequences;, sequential, signal, structure-from-motion;, synthetic, systems;, video}, doi = {10.1109/ICIP.2002.1038996}, author = {Qian,Gang and Chellapa, Rama and Qinfen Zheng} } @article {12964, title = {Characterization of Pseudoalteromonas citrea and P. nigrifaciens Isolated from Different Ecological Habitats Based on REP-PCR Genomic Fingerprints}, journal = {Systematic and Applied Microbiology}, volume = {25}, year = {2002}, month = {2002///}, pages = {275 - 283}, abstract = {SummaryDNA primers corresponding to conserved repetitive interspersed genomic motifs and PCR were used to show that REP, ERIC and BOX-like DNA sequences are present in marine, oxidative, Gram-negative Pseudoalteromonas strains. REP, ERIC and BOX-PCR were used for rapid molecular characterization of both the type species of the genus and environmental strains isolated from samples collected in different geographical areas. PCR-generated genomic fingerprint patterns were found to be both complex and strain specific. Analysis of the genotypic structure of phenotypically diverse P. citrea revealed a geographic clustering of Far Eastern brown-pigmented, agar-digesting strains of this species. Marine isolates of P. nigrifaciens with 67{\textendash}70\% DNA relatedness generated genomic patterns different from those of the type strain and formed a separate cluster. It is concluded that REP, ERIC and BOX-PCR are effective in generating strain specific patterns that can be used to elucidate geographic distribution, with these genomic patterns providing a valuable biogeographic criterion. }, keywords = {biogeography, BOX-PCR, ERIC, Pseudoalteromonas, REP}, isbn = {0723-2020}, doi = {10.1078/0723-2020-00103}, url = {http://www.sciencedirect.com/science/article/pii/S0723202004701125}, author = {Ivanova,Elena P. and Matte,Glavur R. and Matte,Maria H. and Coenye,Tom and Huq,Anwarul and Rita R Colwell} } @conference {17009, title = {CHI@20: fighting our way from marginality to power}, booktitle = {CHI {\textquoteright}02 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {688 - 691}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The Special Interest Group on Computer Human Interaction (SIGCHI) has had a successful history of 20 years of growth in its numbers and influence. To help guide the continued evolution of the academic discipline and professional community, we invite several senior members to offer their visions for what the field of CHI actually accomplished over the past several decades, and what do we still need to accomplish? What do we need to do differently/ better/smarter? What haven{\textquoteright}t we tried because the technology, the money or the will wasn{\textquoteright}t there in the past, but perhaps is now.The CHI field is more than just technology. We understand that our work can have a profound effect on individuals, families, neighborhoods, corporations, and countries. We know that we can influence education, commerce, healthcare, and government. How can we contribute to bridging the digital divides in developed and developing countries? What agendas can we offer for the academic, research, industrial, and civic spheres for the next 20 years? How can we be more ambitious? How can we truly serve human needs.}, keywords = {education, future vision, Human-computer interaction, practice, professional, THEORY, usability engineering}, isbn = {1-58113-454-1}, doi = {10.1145/506443.506548}, url = {http://doi.acm.org/10.1145/506443.506548}, author = {Shneiderman, Ben and Card,Stuart and Norman,Donald A. and Tremaine,Marilyn and Waldrop,M. Mitchell} } @inbook {14598, title = {Combinatorial Algorithms for Design of DNA Arrays}, booktitle = {Chip TechnologyChip Technology}, series = {Advances in Biochemical Engineering/Biotechnology}, volume = {77}, year = {2002}, month = {2002///}, pages = {1 - 19}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Optimal design of DNA arrays requires the development of algorithms with two-fold goals: reducing the effects caused by unintended illumination ( border length minimization problem ) and reducing the complexity of masks ( mask decomposition problem ). We describe algorithms that reduce the number of rectangles in mask decomposition by 20{\textendash}30\% as compared to a standard array design under the assumption that the arrangement of oligonucleotides on the array is fixed. This algorithm produces provably optimal solution for all studied real instances of array design. We also address the difficult problem of finding an arrangement which minimizes the border length and come up with a new idea of threading that significantly reduces the border length as compared to standard designs.}, isbn = {978-3-540-43215-9}, url = {http://dx.doi.org/10.1007/3-540-45713-5_1}, author = {Hannenhalli, Sridhar and Hubbell,Earl and Lipshutz,Robert and Pevzner,Pavel}, editor = {Hoheisel,J{\"o}rg and Brazma,A. and B{\"u}ssow,K. and Cantor,C. and Christians,F. and Chui,G. and Diaz,R. and Drmanac,R. and Drmanac,S. and Eickhoff,H. and Fellenberg,K. and Hannenhalli, Sridhar and Hoheisel,J. and Hou,A. and Hubbell,E. and Jin,H. and Jin,P. and Jurinke,C. and Konthur,Z. and K{\"o}ster,H. and Kwon,S. and Lacy,S. and Lehrach,H. and Lipshutz,R. and Little,D. and Lueking,A. and McGall,G. and Moeur,B. and Nordhoff,E. and Nyarsik,L. and Pevzner,P. and Robinson,A. and Sarkans,U. and Shafto,J. and Sohail,M. and Southern,E. and Swanson,D. and Ukrainczyk,T. and van den Boom,D. and Vilo,J. and Vingron,M. and Walter,G. and Xu,C.} } @booklet {19440, title = {A Comparison of Unified Modelling Language (UML) and Specification and Description Language (SDL)}, year = {2002}, month = {2002/03/01/}, abstract = {This report serves as a basic introduction to the formal specification languages UML and SDL. It also includes a comparison of the two languages.}, keywords = {D.2 SOFTWARE ENGINEERING}, doi = {Departmental Technical Report}, url = {http://pubs.cs.uct.ac.za/archive/00000054/}, author = {Marshini Chetty} } @inbook {18914, title = {On the Complexity of Plan Adaptation by Derivational Analogy in a Universal Classical Planning Framework}, booktitle = {Advances in Case-Based Reasoning}, series = {Lecture Notes in Computer Science}, volume = {2416}, year = {2002}, month = {2002///}, pages = {199 - 206}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In this paper we present an algorithm called DerUCP, which can be regarded as a general model for plan adaptation using Derivational Analogy. Using DerUCP, we show that previous results on the complexity of plan adaptation do not apply to Derivational Analogy. We also show that Derivational Analogy can potentially produce exponential reductions in the size of the search space generated by a planning system.}, keywords = {Computer science}, isbn = {978-3-540-44109-0}, url = {http://www.springerlink.com/content/db2mr13j90mfrcaw/abstract/}, author = {Au,Tsz-Chiu and Mu{\~n}oz-Avila,H{\'e}ctor and Nau, Dana S.}, editor = {Craw,Susan and Preece,Alun} } @conference {18645, title = {A configurable CORBA gateway for providing adaptable system properties}, year = {2002}, month = {2002///}, url = {https://www.perform.csl.illinois.edu/Papers/USAN_papers/02SER01.pdf}, author = {Seri,M. and Courtney,T. and Michel Cukier and Gupta,V. and Krishnmamurthy,S. and Lyons,J. and Ramasamy,H. and Ren,J. and Sanders,W. H.} } @article {12125, title = {COTS-based software development: Processes and open issues}, journal = {Journal of Systems and Software}, volume = {61}, year = {2002}, month = {2002/04/01/}, pages = {189 - 199}, abstract = {The work described in this paper is an investigation of the COTS-based software development within a particular NASA environment, with an emphasis on the processes used. Fifteen projects using a COTS-based approach were studied and their actual process was documented. This process is evaluated to identify essential differences in comparison to traditional software development. The main differences, and the activities for which projects require more guidance, are requirements definition and COTS selection, high level design, integration and testing. Starting from these empirical observations, a new process and set of guidelines for COTS-based development are developed and briefly presented.}, keywords = {Commercial off-the-shelf, Component-based, COTS, empirical study, Software development process}, isbn = {0164-1212}, doi = {10.1016/S0164-1212(01)00147-9}, url = {http://www.sciencedirect.com/science/article/pii/S0164121201001479}, author = {Morisio,M and Seaman,C.B and Basili, Victor R. and Parra,A.T and Kraft,S.E and Condon,S.E} } @article {14672, title = {Cyclone: A safe dialect of C}, journal = {USENIX Annual Technical Conference}, year = {2002}, month = {2002///}, pages = {275 - 288}, abstract = {Cyclone is a safe dialect of C. It has been designed from the ground up to prevent the buffer overflows, format string attacks, and memory management errors that are common in C programs, while retaining C{\textquoteright}s syntax and semantics. This paper examines safety violations enabled by C{\textquoteright}s design, and shows how Cyclone avoids them, without giving up C{\textquoteright}s hallmark control over low-level details such as data representation and memory management.}, author = {Jim,T. and Morrisett,G. and Grossman,D. and Hicks, Michael W. and Cheney,J. and Wang, Y.} } @article {12958, title = {Detection of Cytotoxin-Hemolysin mRNA in Nonculturable Populations of Environmental and Clinical Vibrio Vulnificus Strains in Artificial Seawater}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {68}, year = {2002}, month = {2002/11/01/}, pages = {5641 - 5646}, abstract = {The objective of this study was to develop a molecular detection method that better estimates the potential risk associated with the presence of Vibrio vulnificus. For that purpose, we applied seminested reverse transcription-PCR (RT-PCR) to viable but nonculturable (VBNC) populations of V. vulnificus and targeted the cytotoxin-hemolysin virulence gene vvhA. Three strains, two environmental, IF Vv10 and IF Vv18, and one clinical, C7184, were used in this study. Artificial seawater, inoculated with mid-log-phase cells, was maintained at 4{\textdegree}C. VBNC cells resulted after 3, 6, and 14 days for C7184, IF Vv18, and IF Vv10, respectively. Our data indicate that seminested RT-PCR is sensitive for the detection of vvhA mRNA in artificial seawater when exclusively nonculturable bacteria are present. This is the first report of the expression of a toxin gene in VBNC V. vulnificus. Moreover, vvhA transcripts were shown to persist in nonculturable populations over a 4.5-month period, with a progressive decline of the signal over time. This result indicates that special attention should be given to the presence of potentially pathogenic VBNC cells in environmental samples when assessing public health risk.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.68.11.5641-5646.2002}, url = {http://aem.asm.org/content/68/11/5641}, author = {Fischer-Le Saux,Marion and Hervio-Heath,Dominique and Loaec,Solen and Rita R Colwell and Pommepuy,Monique} } @article {12959, title = {Effects of Global Climate on Infectious Disease: The Cholera Model}, journal = {Clinical Microbiology ReviewsClin. Microbiol. Rev.}, volume = {15}, year = {2002}, month = {2002/10/01/}, pages = {757 - 770}, abstract = {Recently, the role of the environment and climate in disease dynamics has become a subject of increasing interest to microbiologists, clinicians, epidemiologists, and ecologists. Much of the interest has been stimulated by the growing problems of antibiotic resistance among pathogens, emergence and/or reemergence of infectious diseases worldwide, the potential of bioterrorism, and the debate concerning climate change. Cholera, caused by Vibrio cholerae, lends itself to analyses of the role of climate in infectious disease, coupled to population dynamics of pathogenic microorganisms, for several reasons. First, the disease has a historical context linking it to specific seasons and biogeographical zones. In addition, the population dynamics of V. cholerae in the environment are strongly controlled by environmental factors, such as water temperature, salinity, and the presence of copepods, which are, in turn, controlled by larger-scale climate variability. In this review, the association between plankton and V. cholerae that has been documented over the last 20 years is discussed in support of the hypothesis that cholera shares properties of a vector-borne disease. In addition, a model for environmental transmission of cholera to humans in the context of climate variability is presented. The cholera model provides a template for future research on climate-sensitive diseases, allowing definition of critical parameters and offering a means of developing more sophisticated methods for prediction of disease outbreaks.}, isbn = {0893-8512, 1098-6618}, doi = {10.1128/CMR.15.4.757-770.2002}, url = {http://cmr.asm.org/content/15/4/757}, author = {Lipp,Erin K. and Huq,Anwar and Rita R Colwell} } @conference {17838, title = {Efficient Manipulation of Large Datasets on Heterogeneous Storage Systems}, booktitle = {Parallel and Distributed Processing Symposium, International}, volume = {2}, year = {2002}, month = {2002///}, pages = {0084 - 0084}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {In this paper we are concerned with the efficient use of a collection of disk-based storage systems and computing platforms in a heterogeneous setting for retrieving and processing large scientific datasets. We demonstrate, in the context of a data-intensive visualization application, how heterogeneity affects performance and show a set of optimization techniques that can be used to improve performance in a component-based framework. In particular, we examine the application of parallelism via transparent copies of application components in the pipelined processing of data.}, keywords = {component-based frameworks, data-intensive computing, load balancing}, isbn = {0-7695-1573-8}, doi = {http://doi.ieeecomputersociety.org/10.1109/IPDPS.2002.1015655}, author = {Beynon,Michael D. and Sussman, Alan and Kurc,Tahsin and Catalyurek,Umit and Saltz,Joel} } @article {18385, title = {Empirical findings in agile methods}, journal = {Extreme Programming and Agile Methods{\textemdash}XP/Agile Universe 2002}, year = {2002}, month = {2002///}, pages = {81 - 92}, abstract = {In recent years, the use of, interest in, and controversy about Agile methodologies have realized dramatic growth. Anecdotal evidence is rising regarding the effectiveness of agile methodologies in certain environments and for specified projects. However, collection and analysis of empirical evidence of this effectiveness and classification of appropriate environments for Agile projects has not been conducted. Researchers from four institutions organized an eWorkshop to synchronously and virtually discuss and gather experiences and knowledge from eighteen Agile experts spread across the globe. These experts characterized Agile Methods and communicated experiences using these methods on small to very large teams. They discussed the importance of staffing Agile teams with highly skilled developers. They shared common success factors and identified warning signs of problems in Agile projects. These and other findings and heuristics gathered through this valuable exchange can be useful to researchers and to practitioners as they establish an experience base for better decision making.}, doi = {10.1007/3-540-45672-4_19}, author = {Lindvall,M. and Basili, Victor R. and Boehm,B. and Costa,P. and Dangle,K. and Shull, F. and Tesoriero,R. and Williams,L. and Zelkowitz, Marvin V} } @article {18974, title = {Evidence for a Plastid Origin of Plant Ethylene Receptor Genes}, journal = {Plant PhysiologyPlant Physiol.}, volume = {130}, year = {2002}, month = {2002/09/01/}, pages = {10 - 14}, isbn = {0032-0889, 1532-2548}, doi = {10.1104/pp.005397}, url = {http://www.plantphysiol.org/content/130/1/10}, author = {Mount, Stephen M. and Chang,Caren} } @conference {12843, title = {Evidence-based model checking}, booktitle = {Computer Aided Verification}, year = {2002}, month = {2002///}, pages = {641 - 680}, author = {Tan,L. and Cleaveland, Rance} } @conference {17889, title = {Executing Multiple Pipelined Data Analysis Operations in the Grid}, booktitle = {SC Conference}, year = {2002}, month = {2002///}, pages = {54 - 54}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Processing of data in many data analysis applications can be represented as an acyclic, coarse grain data flow, from data sources to the client. This paper is concerned with scheduling of multiple data analysis operations, each of which is represented as a pipelined chain of processing on data. We define the scheduling problem for effectively placing components onto Grid resources, and propose two scheduling algorithms. Experimental results are presented using a visualization application.}, doi = {http://doi.ieeecomputersociety.org/10.1109/SC.2002.10015}, author = {Spencer,Matthew and Ferreira,Renato and Beynon,Michael and Kurc,Tahsin and Catalyurek,Umit and Sussman, Alan and Saltz,Joel} } @conference {12763, title = {An experimental evaluation of linear and kernel-based methods for face recognition}, booktitle = {Applications of Computer Vision, 2002. (WACV 2002). Proceedings. Sixth IEEE Workshop on}, year = {2002}, month = {2002///}, pages = {13 - 18}, abstract = {In this paper we present the results of a comparative study of linear and kernel-based methods for face recognition. The methods used for dimensionality reduction are Principal Component Analysis (PCA), Kernel Principal Component Analysis (KPCA), Linear Discriminant Analysis (LDA) and Kernel Discriminant Analysis (KDA). The methods used for classification are Nearest Neighbor (NN) and Support Vector Machine (SVM). In addition, these classification methods are applied on raw images to gauge the performance of these dimensionality reduction techniques. All experiments have been performed on images from UMIST Face Database.}, keywords = {analysis;, classification;, component, discriminant, Face, image, Kernel, linear, Machine;, nearest, neighbor;, principal, recognition;, Support, vector}, doi = {10.1109/ACV.2002.1182137}, author = {Gupta, H. and Agrawala, Ashok K. and Pruthi, T. and Shekhar, C. and Chellapa, Rama} } @inbook {18671, title = {Experimental Evaluation of the Unavailability Induced by a Group Membership Protocol}, booktitle = {Dependable Computing EDCC-4}, series = {Lecture Notes in Computer Science}, volume = {2485}, year = {2002}, month = {2002///}, pages = {644 - 648}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Group communication is an important paradigm for building highly available distributed systems. However, group membership operations often require the system to block message traffic, causing system services to become unavailable. This makes it important to quantify the unavailability induced by membership operations. This paper experimentally evaluates the blocking behavior of the group membership protocol of the Ensemble group communication system using a novel global-state-based fault injection technique. In doing so, we demonstrate how a layered distributed protocol such as the Ensemble group membership protocol can be modeled in terms of a state machine abstraction, and show how the resulting global state space can be used to specify fault triggers and define important measures on the system. Using this approach, we evaluate the cost associated with important states of the protocol under varying workload and group size. We also evaluate the sensitivity of the protocol to the occurrence of a second correlated crash failure during its operation.}, keywords = {Computer science}, isbn = {978-3-540-00012-9}, url = {http://www.springerlink.com/content/mnkd4upqr14w2r7e/abstract/}, author = {Joshi,Kaustubh and Michel Cukier and Sanders,William}, editor = {Bondavalli,Andrea and Thevenod-Fosse,Pascale} } @conference {12749, title = {Face recognition from video: a CONDENSATION approach}, booktitle = {Automatic Face and Gesture Recognition, 2002. Proceedings. Fifth IEEE International Conference on}, year = {2002}, month = {2002/05//}, pages = {221 - 226}, abstract = {The aim of this work is to investigate how to exploit the temporal information in a video sequence for the task of face recognition. Following the approach in (Li and Chellappa, 2000), we propose a probabilistic model parameterized by a tracking state vector and a recognizing identity variable, simultaneously characterizing the kinematics and identity of humans. We then invoke a CONDENSATION (Isard and Blake, 1996) approach to provide a numerical solution to the model. Once the joint posterior distribution of the state vector and the identity variable is estimated, we marginalize it over the state vector to yield a robust estimate of the posterior distribution of the identity variable. Due to the propagation of identity and dynamics, a degeneracy in the posterior distribution of the identity variable is achieved to give improved recognition. This evolving behavior is characterized using changes in entropy. The effectiveness of this approach is illustrated using experimental results on low-resolution video data.}, keywords = {algorithm;experimental, approach;Sequential, CONDENSATION, data;probabilistic, distribution;kinematics;low-resolution, importance, information;tracking, model;state, posterior, recognition;image, recognition;joint, resolution;image, results;face, sampling, sampling;probability;, sequence;face, sequences;importance, state, vector;temporal, vector;video, video}, doi = {10.1109/AFGR.2002.1004158}, author = {Zhou,Shaohua and Krueger, V. and Chellapa, Rama} } @conference {18676, title = {Formal specification and verification of a group membership protocol for an intrusion-tolerant group communication system}, year = {2002}, month = {2002/12//}, pages = {9 - 18}, abstract = {We describe a group membership protocol that is part of an intrusion-tolerant group communication system, and present an effort to use formal tools to model and validate our protocol. We describe in detail the most difficult part of the validation exercise, which was the determination of the right level of abstraction of the protocol for formally specifying the protocol. The validation exercise not only formally showed that the protocol satisfies its correctness claims, but also provided information that will help us make the protocol more efficient without violating correctness.}, keywords = {computer network reliability, distributed processing, distributed systems, fault tolerant computing, formal specification, formal verification, group membership protocol, intrusion-tolerant group communication system, PROMELA, Protocols}, doi = {10.1109/PRDC.2002.1185613}, author = {Ramasamy,H. V. and Michel Cukier and Sanders,W. H.} } @inbook {12965, title = {Fulfilling the promise of marine biotechnology}, booktitle = {Marine biotechnology in the twenty-first century: problems, promise, and productsMarine biotechnology in the twenty-first century: problems, promise, and products}, year = {2002}, month = {2002///}, pages = {39 - 39}, publisher = {National Academies Press}, organization = {National Academies Press}, isbn = {9780309083423}, author = {Rita R Colwell}, editor = {National Research Council (U S. ) Committee on Marine Biotechnology: Biomedical Applications of Marine Natural Products} } @article {12752, title = {A generic approach to simultaneous tracking and verification in video}, journal = {Image Processing, IEEE Transactions on}, volume = {11}, year = {2002}, month = {2002/05//}, pages = {530 - 544}, abstract = {A generic approach to simultaneous tracking and verification in video data is presented. The approach is based on posterior density estimation using sequential Monte Carlo methods. Visual tracking, which is in essence a temporal correspondence problem, is solved through probability density propagation, with the density being defined over a proper state space characterizing the object configuration. Verification is realized through hypothesis testing using the estimated posterior density. In its most basic form, verification can be performed as follows. Given a measurement vector Z and two hypotheses H1 and H0, we first estimate posterior probabilities P(H0|Z) and P(H1|Z), and then choose the one with the larger posterior probability as the true hypothesis. Several applications of the approach are illustrated by experiments devised to evaluate its performance. The idea is first tested on synthetic data, and then experiments with real video sequences are presented, illustrating vehicle tracking and verification, human (face) tracking and verification, facial feature tracking, and image sequence stabilization.}, keywords = {approach;, Carlo, configuration;, correspondence, data;, density, density;, estimated, estimation;, evaluation;, extraction;, Face, facial, feature, generic, human, hypothesis, image, measurement, methods;, Monte, object, performance, posterior, probability, probability;, problem;, processing;, propagation;, recognition;, road, sequence, sequences;, sequential, signal, space;, stabilization;, state, synthetic, temporal, testing;, tracking;, vector;, vehicle, vehicles;, verification;, video, visual}, isbn = {1057-7149}, doi = {10.1109/TIP.2002.1006400}, author = {Li,Baoxin and Chellapa, Rama} } @article {12822, title = {Generic tools for verifying concurrent systems}, journal = {Science of Computer Programming}, volume = {42}, year = {2002}, month = {2002/01//}, pages = {39 - 47}, abstract = {Despite the enormous strides made in automatic verification technology over the past decade and a half, tools such as model checkers remain relatively underused in the development of software. One reason for this is that the bewildering array of specification and verification formalisms complicates the development and adoption by users of relevant tool support. This paper proposes a remedy to this state of affairs in the case of finite-state concurrent systems by describing an approach to developing customizable yet efficient verification tools.}, keywords = {Model checking, Operational semantics, Process algebra, Specification, verification, Verification tools}, isbn = {0167-6423}, doi = {10.1016/S0167-6423(01)00033-8}, url = {http://www.sciencedirect.com/science/article/pii/S0167642301000338}, author = {Cleaveland, Rance and Sims,Steven T.} } @article {16270, title = {Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii}, journal = {Nature}, volume = {419}, year = {2002}, month = {2002/10/03/}, pages = {512 - 519}, abstract = {Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.}, isbn = {0028-0836}, doi = {10.1038/nature01099}, url = {http://www.nature.com/nature/journal/v419/n6906/full/nature01099.html}, author = {Carlton,Jane M. and Angiuoli,Samuel V and Suh,Bernard B. and Kooij,Taco W. and Pertea,Mihaela and Silva,Joana C. and Ermolaeva,Maria D. and Allen,Jonathan E and Jeremy D Selengut and Koo,Hean L. and Peterson,Jeremy D. and Pop, Mihai and Kosack,Daniel S. and Shumway,Martin F. and Bidwell,Shelby L. and Shallom,Shamira J. and Aken,Susan E. van and Riedmuller,Steven B. and Feldblyum,Tamara V. and Cho,Jennifer K. and Quackenbush,John and Sedegah,Martha and Shoaibi,Azadeh and Cummings,Leda M. and Florens,Laurence and Yates,John R. and Raine,J. Dale and Sinden,Robert E. and Harris,Michael A. and Cunningham,Deirdre A. and Preiser,Peter R. and Bergman,Lawrence W. and Vaidya,Akhil B. and Lin,Leo H. van and Janse,Chris J. and Waters,Andrew P. and Smith,Hamilton O. and White,Owen R. and Salzberg,Steven L. and Venter,J. Craig and Fraser,Claire M. and Hoffman,Stephen L. and Gardner,Malcolm J. and Carucci,Daniel J.} } @article {12962, title = {Genomic profiles of clinical and environmental isolates of Vibrio cholerae O1 in cholera-endemic areas of Bangladesh}, journal = {Proceedings of the National Academy of Sciences}, volume = {99}, year = {2002}, month = {2002///}, pages = {12409 - 12409}, abstract = {Diversity, relatedness, and ecological interactions of toxigenic Vibrio cholerae O1 populations in two distinctive habitats, the human intestine and the aquatic environment, were analyzed. Twenty environmental isolates and 42 clinical isolates were selected for study by matching serotype, geographic location of isolation in Bangladesh, and season of isolation. Genetic profiling was done by enterobacterial repetitive intergenic consensus sequence{\textendash}PCR, optimized for profiling by using the fully sequenced V. cholerae El Tor N16961 genome. Five significant clonal clusters of haplotypes were found from 57 electrophoretic types. Isolates from different areas or habitats intermingled in two of the five significant clusters. Frequencies of haplotypes differed significantly only between the environmental populations (exact test; P < 0.05). Analysis of molecular variance yielded a population genetic structure reflecting the differentiating effects of geographic area, habitat, and sampling time. Although a parameter confounding the latter differences explained 9\% of the total molecular variance in the entire population (P < 0.01), the net effect of habitat and time could not be separated because of the small number of environmental isolates included in the study. Five subpopulations from a single area were determined, and from these we were able to estimate a relative differentiating effect of habitat, which was small compared with the effect of temporal change. In conclusion, the resulting population structure supports the hypothesis that spatial and temporal fluctuations in the composition of toxigenic V. cholerae populations in the aquatic environment can cause shifts in the dynamics of the disease.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.192426499}, url = {http://www.pnas.org/content/99/19/12409}, author = {Zo,Y. G. and Rivera,I. N. G. and E. Russek-Cohen and Islam,M. S. and Siddique,A. K. and Yunus,M. and Sack,R. B. and Huq,A. and Rita R Colwell} } @conference {12746, title = {A hierarchical approach for obtaining structure from two-frame optical flow}, booktitle = {Motion and Video Computing, 2002. Proceedings. Workshop on}, year = {2002}, month = {2002/12//}, pages = {214 - 219}, abstract = {A hierarchical iterative algorithm is proposed for extracting structure from two-frame optical flow. The algorithm exploits two facts: one is that in many applications, such as face and gesture recognition, the depth variation of the visible surface of an object in a scene is small compared to the distance between the optical center and the object; the other is that the time aliasing problem is alleviated at the coarse level for any two-frame optical flow estimate so that the estimate tends to be more accurate. A hierarchical representation for the relationship between the optical flow, depth, and the motion parameters is derived, and the resulting non-linear system is iteratively solved through two linear subsystems. At the coarsest level, the surface of the object tends to be flat, so that the inverse depth tends to be a constant, which is used as the initial depth map. Inverse depth and motion parameters are estimated by the two linear subsystems at each level and the results are propagated to finer levels. Error analysis and experiments using both computer-rendered images and real images demonstrate the correctness and effectiveness of our algorithm.}, keywords = {algorithm;, aliasing;, analysis;, computer-rendered, depth, depth;, error, estimation;, extraction;, Face, feature, flow;, gesture, hierarchical, image, images;, inverse, iterative, methods;, MOTION, nonlinear, optical, parameter, processing;, real, recognition;, sequences;, signal, structure-from-motion;, system;, systems;, TIME, two-frame, variation;, video}, doi = {10.1109/MOTION.2002.1182239}, author = {Liu,Haiying and Chellapa, Rama and Rosenfeld, A.} } @article {12386, title = {High-level synthesis of DSP applications using adaptive negative cycle detection}, journal = {EURASIP J. Appl. Signal Process.}, volume = {2002}, year = {2002}, month = {2002/01//}, pages = {893 - 907}, abstract = {The problem of detecting negative weight cycles in a graph is examined in the context of the dynamic graph structures that arise in the process of high level synthesis (HLS). The concept of adaptive negative cycle detection is introduced, in which a graph changes over time and negative cycle detection needs to be done periodically, but not necessarily after every individual change. We present an algorithm for this problem, based on a novel extension of the well-known Bellman-Ford algorithm that allows us to adapt existing cycle information to the modified graph, and show by experiments that our algorithm significantly outperforms previous incremental approaches for dynamic graphs. In terms of applications, the adaptive technique leads to a very fast implementation of Lawlers algorithm for the computation of the maximum cycle mean (MCM) of a graph, especially for a certain form of sparse graph. Such sparseness often occurs in practical circuits and systems, as demonstrated, for example, by the ISCAS 89/93 benchmarks. The application of the adaptive technique to design-space exploration (synthesis) is also demonstrated by developing automated search techniques for scheduling iterative data-flow graphs.}, keywords = {adaptive performance estimation, dynamic graphs, maximum cycle mean, negative cycle detection}, isbn = {1110-8657}, url = {http://dl.acm.org/citation.cfm?id=1283100.1283192}, author = {Chandrachoodan,Nitin and Bhattacharyya, Shuvra S. and Liu,K. J.R} } @conference {13931, title = {How young can our design partners be}, booktitle = {Proceedings of the Participatory Design Conference}, year = {2002}, month = {2002///}, pages = {272 - 277}, author = {Farber,A. and Druin, Allison and Chipman,G. and Julian,D. and Somashekhar,S.} } @conference {12762, title = {Identification of humans using gait}, booktitle = {IEEE Transactions on Image Processing}, year = {2002}, month = {2002///}, abstract = {We propose a view-based approach to recognize humans from their gait. Two different imagefeatures have been considered: the width of the outer contour of the binarized silhouette of the walking person and the entire binary silhouette itself. To obtain the observation vector from the image features we employ two different methods. In the first method referred to as the indirect approach, the high-dimensional image feature is transformed to a lower-dimensional space by generating what we call the Frame to Exemplar (FED) distance. The FED vector captures both structural and dynamic traits of each individual. For compact and effective gait representation and recognition, the gait information in the FED vector sequences is captured in a hidden Markov model (HMM). In the second method referred to as the direct approach, we work with the feature vector directly (as opposed to computing the FED) and train an HMM. We estimate the HMM parameters (specifically the observation probability B) based on the distance between the exemplars and the image features. In this way we avoid learning high-dimensional probability density functions. The statistical nature of the HMM lends overall robustness to representation and recognition. The performance of the methods is illustrated using several databases. }, author = {Kale, A. and Rajagopalan, AN and Cuntoor, N. and Krueger, V. and Chellapa, Rama} } @inbook {12757, title = {Image-based face recognition: Issues and methods}, booktitle = {Image recognition and classification: algorithms, systems, and applicationsImage recognition and classification: algorithms, systems, and applications}, year = {2002}, month = {2002///}, pages = {375 - 402}, publisher = {CRC Press}, organization = {CRC Press}, isbn = {9780824707835}, author = {Zhao, W.Y. and Chellapa, Rama} } @conference {17227, title = {Improving Web-based civic information access: a case study of the 50 US states}, booktitle = {2002 International Symposium on Technology and Society, 2002. (ISTAS{\textquoteright}02)}, year = {2002}, month = {2002///}, pages = {275 - 282}, publisher = {IEEE}, organization = {IEEE}, abstract = {An analysis of the home pages of all fifty US states reveals great variety in key design features that influence efficacy. Some states had excessively large byte counts that would slow users connected by commonly-used 56 K modems. Many web sites had low numbers of or poorly organized links that would make it hard for citizens to find what they were interested in. Features such as search boxes, privacy policies, online help, or contact information need to be added by several states. Our analysis concludes with ten recommendations and finds many further opportunities for individual states to improve their Websites. However still greater benefits will come through collaboration among the states that would lead to consistency, appropriate tagging, and common tools.}, keywords = {Computer aided software engineering, Computer science, contact information, Educational institutions, government data processing, Guidelines, home page design features, information resources, Laboratories, Modems, Navigation, online help, privacy, privacy policies, search boxes, Tagging, Uniform resource locators, US states, USA, User interfaces, Web sites, Web-based civic information access}, isbn = {0-7803-7284-0}, doi = {10.1109/ISTAS.2002.1013826}, author = {Ceaparu,I. and Shneiderman, Ben} } @article {12963, title = {In vitro adhesion to human cells by viable but nonculturable Enterococcus faecalis}, journal = {Current microbiology}, volume = {45}, year = {2002}, month = {2002///}, pages = {105 - 110}, abstract = {The ability of viable but nonculturable (VBNC) Enterococcus faecalis to adhere to Caco-2 and Girardi heart cultured cells and to urinary tract epithelial cells (ECs) was studied. Enterococci were harvested during the vegetative growth phase (early exponential and stationary), in the VBNC state, and after recovery of the ability to divide. VBNC bacteria maintained their adherence capability but the efficiency of attachment was reduced by about 50 to 70\%, depending on the target cell employed. The decrease was transient, since enterococci that regained their culturability showed adherence values similar to those observed for actively growing cells. Analysis of the invasive properties of E. faecalis revealed that the VBNC state caused a decrease in the number of bacteria that entered the cultured HEK cells as a result of the reduction in the number of adhering bacteria. These results highlight the importance of studies of the VBNC phenomenon, with respect to both microbial survival in the environment and the impact on human health.}, doi = {10.1007/s00284-001-0089-2}, author = {Pruzzo,C. and Tarsi,R. and Lle{\`o},M. M. and Signoretto,C. and Zampini,M. and Rita R Colwell and Canepari,P.} } @article {17230, title = {In Web we trust: establishing strategic trust among online customers}, journal = {E-Service: new directions in theory and practice}, year = {2002}, month = {2002///}, pages = {90 - 107}, abstract = {Electronic commerce (e-commerce) provides an important chance for established large companies to gain more customers as well as for new small companies to have a good start and rapid growth. However, establishing trust between customers and companies through web interface, a key component of successful e-service, is not as easy as through human-buyer-human-seller interaction. In the past few years, a number of experiments have been conducted in order to determine the factors that influence customers{\textquoteright} trust in online businesses. The goal of our experiment was to establish which features that appear on commercial websites are trust-inducing. Our study focused on three independent variables: customer service (limited and extensive), testimonial (self and external) and security features representation (graphics and text). We designed the homepages of eight web sites with all combinations of treatments of the three independent variables. Each of the 52 subjects reviewed all the eight homepages and gave them a relative rank of trustworthiness. After the experiment subjects answered additional e-trust related questions. The experiment results and the survey support the belief that specific customer service commitments, third party testimonials and graphic security representations are important in establishing strategic trust among on-line customers.}, author = {Ceaparu,I. and Demner,D. and Hung,E. and Zhao,H. and Shneiderman, Ben} } @book {19352, title = {Level of Detail for 3D Graphics}, year = {2002}, month = {2002}, publisher = {Elsevier Science Inc.}, organization = {Elsevier Science Inc.}, address = {New York, NY, USA}, abstract = {Level of detail (LOD) techniques are increasingly used by professional real-time developers to strike the balance between breathtaking virtual worlds and smooth, flowing animation. Level of Detail for 3D Graphics brings together, for the first time, the mechanisms, principles, practices, and theory needed by every graphics developer seeking to apply LOD methods.Continuing advances in level of detail management have brought this powerful technology to the forefront of 3D graphics optimization research. This book, written by the very researchers and developers who have built LOD technology, is both a state-of-the-art chronicle of LOD advances and a practical sourcebook, which will enable graphics developers from all disciplines to apply these formidable techniques to their own work. }, isbn = {1558608389}, author = {Luebke, David and Watson, Benjamin and Cohen, Jonathan D. and Reddy, Martin and Varshney, Amitabh} } @article {12748, title = {Optimal edge-based shape detection}, journal = {Image Processing, IEEE Transactions on}, volume = {11}, year = {2002}, month = {2002/11//}, pages = {1209 - 1227}, abstract = {We propose an approach to accurately detecting two-dimensional (2-D) shapes. The cross section of the shape boundary is modeled as a step function. We first derive a one-dimensional (1-D) optimal step edge operator, which minimizes both the noise power and the mean squared error between the input and the filter output. This operator is found to be the derivative of the double exponential (DODE) function, originally derived by Ben-Arie and Rao (1994). We define an operator for shape detection by extending the DODE filter along the shape{\textquoteright}s boundary contour. The responses are accumulated at the centroid of the operator to estimate the likelihood of the presence of the given shape. This method of detecting a shape is in fact a natural extension of the task of edge detection at the pixel level to the problem of global contour detection. This simple filtering scheme also provides a tool for a systematic analysis of edge-based shape detection. We investigate how the error is propagated by the shape geometry. We have found that, under general assumptions, the operator is locally linear at the peak of the response. We compute the expected shape of the response and derive some of its statistical properties. This enables us to predict both its localization and detection performance and adjust its parameters according to imaging conditions and given performance specifications. Applications to the problem of vehicle detection in aerial images, human facial feature detection, and contour tracking in video are presented.}, keywords = {1D, 2D, aerial, analysis;, boundary, conditions;, contour, cross, detection;, DODE, double, edge, edge-based, error, error;, exponential, extraction;, facial, feature, filter, filter;, Filtering, function;, geometry;, global, human, images;, imaging, localization, mean, methods;, NOISE, operator;, optimal, optimisation;, output;, performance;, pixel;, power;, propagation;, properties;, section;, SHAPE, square, squared, statistical, step, theory;, tracking;, two-dimensional, vehicle, video;}, isbn = {1057-7149}, doi = {10.1109/TIP.2002.800896}, author = {Moon, H. and Chellapa, Rama and Rosenfeld, A.} } @conference {18683, title = {Passive replication schemes in AQuA}, year = {2002}, month = {2002/12//}, pages = {125 - 130}, abstract = {Building large-scale distributed object-oriented systems that provide multidimensional quality of service (QoS) in terms of fault tolerance, scalability, and performance is challenging. In order to meet this challenge, we need an architecture that can ensure that applications{\textquoteright} requirements can be met while providing reusable technologies and software solutions. This paper describes techniques, based on the AQuA architecture, that enhance the applications{\textquoteright} dependability and scalability by introducing two types of group members and a novel passive replication scheme. In addition, we describe how to make the management structure itself dependable by using the passive replication scheme. Finally, we provide performance measurements for the passive replication scheme.}, keywords = {AQuA architecture, distributed object management, Fault tolerance, group members, large-scale distributed object-oriented systems, management structure, multidimensional quality of service, passive replication scheme, performance measurements, reusable technologies, scalability, software fault tolerance, software performance evaluation, software reusability, software solutions}, doi = {10.1109/PRDC.2002.1185628}, author = {Ren,Yansong and Rubel,P. and Seri,M. and Michel Cukier and Sanders,W. H. and Courtney,T.} } @article {12754, title = {Performance analysis of a simple vehicle detection algorithm}, journal = {Image and Vision Computing}, volume = {20}, year = {2002}, month = {2002/01/01/}, pages = {1 - 13}, abstract = {We have performed an end-to-end analysis of a simple model-based vehicle detection algorithm for aerial parking lot images. We constructed a vehicle detection operator by combining four elongated edge operators designed to collect edge responses from the sides of a vehicle. We derived the detection and localization performance of this algorithm, and verified them by experiments. Performance degradation due to different camera angles and illuminations was also examined using simulated images. Another important aspect of performance characterization {\textemdash} whether and how much prior information about the scene improves performance {\textemdash} was also investigated. As a statistical diagnostic tool for the detection performance, a computational approach employing bootstrap was used.}, keywords = {Aerial image, Bootstrap, empirical evaluation, Performance analysis, Vehicle detection}, isbn = {0262-8856}, doi = {10.1016/S0262-8856(01)00059-2}, url = {http://www.sciencedirect.com/science/article/pii/S0262885601000592}, author = {Moon, H. and Chellapa, Rama and Rosenfeld, A.} } @conference {18684, title = {Performance evaluation of a probabilistic replica selection algorithm}, year = {2002}, month = {2002///}, pages = {119 - 127}, abstract = {When executing time-sensitive distributed applications, a middleware that provides dependability and timeliness is faced with the important problem of preventing timing failures both under normal conditions and when the quality of service is degraded due to replica failures and transient overload on the server. To address this problem, we have designed a probabilistic model-based replica selection algorithm that allows a middleware to choose a set of replicas to service a client based on their ability to meet a client{\textquoteright}s timeliness requirements. This selection is done based on the prediction made by a probabilistic model that uses the performance history of replicas as inputs. In this paper, we describe the experiments we have conducted to evaluate the ability of this dynamic selection algorithm to meet a client{\textquoteright}s timing requirements, and compare it with that of a static and round-robin selection scheme under different scenarios}, keywords = {client-server systems, Dependability, distributed object management, dynamic selection algorithm, Middleware, probabilistic model, probabilistic model-based replica selection algorithm, probability, quality of service, real-time systems, replica failures, round-robin selection scheme, static scheme, time-sensitive distributed applications, timeliness, timing failures, transient overload}, doi = {10.1109/WORDS.2002.1000044}, author = {Krishnamurthy, S. and Sanders,W. H. and Michel Cukier} } @conference {18685, title = {Performance evaluation of a QoS-aware framework for providing tunable consistency and timeliness}, year = {2002}, month = {2002///}, pages = {214 - 223}, abstract = {Strong replica consistency models ensure that the data delivered by a replica always includes the latest updates, although this may result in poor response times. On the other hand, weak replica consistency models provide quicker access to information, but do not usually provide guarantees about the degree of staleness in the data they deliver. In order to support emerging distributed applications that are characterized by high concurrency demands, an increasing shift towards dynamic content, and timely delivery, we need quality of service models that allow us to explore the intermediate space between these two extreme approaches to replica consistency. Further, for better support of time-sensitive applications that can tolerate relaxed consistency in exchange for better responsiveness, we need to understand how the desired level of consistency affects the timeliness of a response. The QoS model we have developed to realize these objectives considers both timeliness and consistency, and treats consistency along two dimensions: order and staleness. We evaluate experimentally the framework we have developed to study the timeliness/consistency tradeoffs for replicated services and present experimental results that compare these tradeoffs in the context of sequential and FIFO ordering.}, keywords = {client-server systems, Computer networks, CORBA-based middleware, distributed applications, distributed object management, Network servers, QoS, quality of service, replica consistency, replicated services, server replicas, timeliness}, doi = {10.1109/IWQoS.2002.1006589}, author = {Krishnamurthy, S. and Sanders,W. H. and Michel Cukier} } @conference {17886, title = {Persistent caching in a multiple query optimization framework}, booktitle = {Proceedings of the 6th Workshop on Languages, Compilers, and Run-Time Systems for Scalable Computers}, year = {2002}, month = {2002///}, abstract = {This paper focuses on persistent caching in multi-client en-vironments, which aims to improve the performance of a data server by caching on disk query results that can be expensive to produce. We present and evaluate extensions to an existing multi-query optimization framework, called MQO, to incorporate persistent caching capabilities. }, author = {Andrade,H. and Kurc, T. and Catalyurek,U. and Sussman, Alan and Saltz, J.} } @article {13009, title = {Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala)}, journal = {Mol Phylogenet Evol}, volume = {23}, year = {2002}, month = {2002/05//}, pages = {288 - 292}, abstract = {Members of phylum Acanthocephala are parasites of vertebrates and arthropods and are distributed worldwide. The phylum has traditionally been divided into three classes, Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala; a fourth class, Polyacanthocephala, has been recently proposed. However, erection of this new class, based on morphological characters, has been controversial. We sequenced the near complete 18S rRNA gene of Polyacanthorhynchus caballeroi (Polyacanthocephala) and Rhadinorhynchus sp. (Palaeacanthocephala); these sequences were aligned with another 21 sequences of acanthocephalans representing the three widely recognized classes of the phylum and with 16 sequences from outgroup taxa. Phylogenetic relationships inferred by maximum-likelihood and maximum-parsimony analyses showed Archiacanthocephala as the most basal group within the phylum, whereas classes Polyacanthocephala + Eoacanthocephala formed a monophyletic clade, with Palaeacanthocephala as its sister group. These results are consistent with the view of Polyacanthocephala representing an independent class within Acanthocephala.}, doi = {10.1016/S1055-7903(02)00020-9}, author = {Garc{\'\i}a-Varela,M and Cummings, Michael P. and P{\'e}rez-Ponce de Le{\'o}n,G. and Gardner,S. L and Laclette,J. P} } @conference {13906, title = {Physical Programming: Designing Tools for Children to Create Physical Interactive}, booktitle = {Proceedings: SIGCHI}, year = {2002}, month = {2002///}, author = {Montemayor,J. and Druin, Allison and Farber,A. and Simms,S. and Churaman,W.} } @inbook {12755, title = {Probabilistic Human Recognition from Video}, booktitle = {Computer Vision {\textemdash} ECCV 2002Computer Vision {\textemdash} ECCV 2002}, series = {Lecture Notes in Computer Science}, volume = {2352}, year = {2002}, month = {2002///}, pages = {173 - 183}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper presents a method for incorporating temporal information in a video sequence for the task of human recognition. A time series state space model, parameterized by a tracking state vector and a recognizing identity variable , is proposed to simultaneously characterize the kinematics and identity. Two sequential importance sampling (SIS) methods, a brute-force version and an efficient version, are developed to provide numerical solutions to the model. The joint distribution of both state vector and identity variable is estimated at each time instant and then propagated to the next time instant. Marginalization over the state vector yields a robust estimate of the posterior distribution of the identity variable. Due to the propagation of identity and kinematics, a degeneracy in posterior probability of the identity variable is achieved to give improved recognition. This evolving behavior is characterized using changes in entropy . The effectiveness of this approach is illustrated using experimental results on low resolution face data and upper body data.}, isbn = {978-3-540-43746-8}, url = {http://dx.doi.org/10.1007/3-540-47977-5_45}, author = {Zhou,Shaohua and Chellapa, Rama}, editor = {Heyden,Anders and Sparr,Gunnar and Nielsen,Mads and Johansen,Peter} } @conference {12766, title = {Probabilistic recognition of human faces from video}, booktitle = {Image Processing. 2002. Proceedings. 2002 International Conference on}, volume = {1}, year = {2002}, month = {2002///}, pages = {I-41 - I-44 vol.1 - I-41 - I-44 vol.1}, abstract = {Most present face recognition approaches recognize faces based on still images. We present a novel approach to recognize faces in video. In that scenario, the face gallery may consist of still images or may be derived from a videos. For evidence integration we use classical Bayesian propagation over time and compute the posterior distribution using sequential importance sampling. The probabilistic approach allows us to handle uncertainties in a systematic manner. Experimental results using videos collected by NIST/USF and CMU illustrate the effectiveness of this approach in both still-to-video and video-to-video scenarios with appropriate model choices.}, keywords = {Bayes, Bayesian, CMU;, distribution;, Face, faces;, gallery;, handling;, human, image, images;, importance, likelihood;, methods;, NIST/USF;, observation, posterior, probabilistic, probability;, processing;, propagation;, recognition;, sampling;, sequential, signal, still, Still-to-video, Uncertainty, video, Video-to-video}, doi = {10.1109/ICIP.2002.1037954}, author = {Chellapa, Rama and Kruger, V. and Zhou,Shaohua} } @conference {18635, title = {Probabilistic validation of intrusion tolerance}, year = {2002}, month = {2002///}, pages = {78 - 79}, url = {https://www.perform.csl.illinois.edu/Papers/USAN_papers/02SAN02.pdf}, author = {Sanders,W. H. and Michel Cukier and Webber,F. and Pal,P. and Watro,R.} } @article {17865, title = {Processing large-scale multi-dimensional data in parallel and distributed environments}, journal = {Parallel Computing}, volume = {28}, year = {2002}, month = {2002/05//}, pages = {827 - 859}, abstract = {Analysis of data is an important step in understanding and solving a scientific problem. Analysis involves extracting the data of interest from all the available raw data in a dataset and processing it into a data product. However, in many areas of science and engineering, a scientist{\textquoteright}s ability to analyze information is increasingly becoming hindered by dataset sizes. The vast amount of data in scientific datasets makes it a difficult task to efficiently access the data of interest, and manage potentially heterogeneous system resources to process the data. Subsetting and aggregation are common operations executed in a wide range of data-intensive applications. We argue that common runtime and programming support can be developed for applications that query and manipulate large datasets. This paper presents a compendium of frameworks and methods we have developed to support efficient execution of subsetting and aggregation operations in applications that query and manipulate large, multi-dimensional datasets in parallel and distributed computing environments.}, keywords = {Data-intensive applications, Distributed computing, Multi-dimensional datasets, PARALLEL PROCESSING, Runtime systems}, isbn = {0167-8191}, doi = {10.1016/S0167-8191(02)00097-2}, url = {http://www.sciencedirect.com/science/article/pii/S0167819102000972}, author = {Beynon,Michael and Chang,Chialin and Catalyurek,Umit and Kurc,Tahsin and Sussman, Alan and Andrade,Henrique and Ferreira,Renato and Saltz,Joel} } @article {12957, title = {Purification and properties of the extracellular lipase, LipA, of Acinetobacter sp. RAG-1}, journal = {European Journal of Biochemistry}, volume = {269}, year = {2002}, month = {2002/12/01/}, pages = {5771 - 5779}, abstract = {An extracellular lipase, LipA, extracted from Acinetobacter sp. RAG-1 grown on hexadecane was purified and properties of the enzyme investigated. The enzyme is released into the growth medium during the transition to stationary phase. The lipase was harvested from cells grown to stationary phase, and purified with 22\% yield and > 10-fold purification. The protein demonstrates little affinity for anion exchange resins, with contaminating proteins removed by passing crude supernatants over a Mono Q column. The lipase was bound to a butyl Sepharose column and eluted in a Triton~X-100 gradient. The molecular mass (33~kDa) was determined employing SDS/PAGE. LipA was found to be stable at pH~5.8{\textendash}9.0, with optimal activity at 9.0. The lipase remained active at temperatures up to 70~{\textdegree}C, with maximal activity observed at 55~{\textdegree}C. LipA is active against a wide range of fatty acid esters of p-nitrophenyl, but preferentially attacks medium length acyl chains (C6, C8). The enzyme demonstrates hydrolytic activity in emulsions of both medium and long chain triglycerides, as demonstrated by zymogram analysis. RAG-1 lipase is stabilized by Ca2+, with no loss in activity observed in preparations containing the cation, compared to a 70\% loss over 30~h without Ca2+. The lipase is strongly inhibited by EDTA, Hg2+, and Cu2+, but shows no loss in activity after incubation with other metals or inhibitors examined in this study. The protein retains more than 75\% of its initial activity after exposure to organic solvents, but is rapidly deactivated by pyridine. RAG-1 lipase offers potential for use as a biocatalyst.}, keywords = {Acinetobacter sp. RAG-1, LipA, lipase, protein purification, zymogram}, isbn = {1432-1033}, doi = {10.1046/j.1432-1033.2002.03235.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1432-1033.2002.03235.x/full}, author = {Snellman,Erick A. and Sullivan,Elise R. and Rita R Colwell} } @conference {18690, title = {Quantifying the cost of providing intrusion tolerance in group communication systems}, year = {2002}, month = {2002///}, pages = {229 - 238}, abstract = {Group communication systems that provide consistent group membership and reliable, ordered multicast properties in the presence of faults resulting from malicious intrusions have not been analyzed extensively to quantify the cost of tolerating these intrusions. This paper attempts to quantify this cost by presenting results from an experimental evaluation of three new intrusion-tolerant microprotocols that have been added to an existing crash-fault-tolerant group communication system. The results are analyzed to identify the parts that contribute the most overhead during provision of intrusion tolerance at the group communication system level.}, keywords = {consistent group membership, crash-fault-tolerant group communication system, cryptography, finite state machines, groupware, intrusion-tolerant microprotocols, malicious intrusions, multicast communication, reliable ordered multicast properties, security of data, Transport protocols}, doi = {10.1109/DSN.2002.1028904}, author = {Ramasamy,H. V. and Pandey,P. and Lyons,J. and Michel Cukier and Sanders,W. H.} } @conference {12761, title = {Quasi-invariants for human action representation and recognition}, booktitle = {Pattern Recognition, 2002. Proceedings. 16th International Conference on}, volume = {1}, year = {2002}, month = {2002///}, pages = {307 - 310 vol.1 - 307 - 310 vol.1}, abstract = {Although human action recognition has been the subject of much research in the past, the issue of viewpoint invariance has received scarce attention. In this paper, we present an approach to detect human action with a high tolerance to viewpoint change. Canonical body poses are modeled in a view invariant manner to enable detection from a general viewpoint. While there exist no invariants for 3D to 2D projection, there exists a wealth of techniques in 2D invariance that can be used to advantage in 3D to 2D projection. We employ 2D invariants to recognize canonical poses of the human body leading to an effective way to represent and recognize human action which we evaluate theoretically and experimentally on 2D projections of publicly available human motion capture data.}, keywords = {2D, action, analysis;, body, canonical, change, human, image, invariance;, MOTION, poses;, quasi-invariants;, recognition;, representation;, tolerance;, viewpoint}, doi = {10.1109/ICPR.2002.1044699}, author = {Parameswaran, V. and Chellapa, Rama} } @proceedings {15793, title = {Reconstructing Images of Bar Codes for Construction Site Object Recognition}, year = {2002}, month = {2002/09//}, author = {Gilsinn,David E. and Cheok,Geraldine S. and O{\textquoteright}Leary, Dianne P.} } @article {14726, title = {Region-based memory management in cyclone}, journal = {SIGPLAN Not.}, volume = {37}, year = {2002}, month = {2002/05//}, pages = {282 - 293}, abstract = {Cyclone is a type-safe programming language derived from C. The primary design goal of Cyclone is to let programmers control data representation and memory management without sacrificing type-safety. In this paper, we focus on the region-based memory management of Cyclone and its static typing discipline. The design incorporates several advancements, including support for region subtyping and a coherent integration with stack allocation and a garbage collector. To support separate compilation, Cyclone requires programmers to write some explicit region annotations, but a combination of default annotations, local type inference, and a novel treatment of region effects reduces this burden. As a result, we integrate C idioms in a region-based framework. In our experience, porting legacy C to Cyclone has required altering about 8\% of the code; of the changes, only 6\% (of the 8\%) were region annotations.}, isbn = {0362-1340}, doi = {10.1145/543552.512563}, url = {http://doi.acm.org/10.1145/543552.512563}, author = {Grossman,Dan and Morrisett,Greg and Jim,Trevor and Hicks, Michael W. and Wang,Yanling and Cheney,James} } @conference {12756, title = {A robust algorithm for probabilistic human recognition from video}, booktitle = {Pattern Recognition, 2002. Proceedings. 16th International Conference on}, volume = {1}, year = {2002}, month = {2002///}, pages = {226 - 229 vol.1 - 226 - 229 vol.1}, abstract = {Human recognition from video requires solving the two tasks, recognition and tracking, simultaneously. This leads to a parameterized time series state space model, representing both motion and identity of the human. Sequential Monte Carlo (SMC) algorithms, like Condensation, can be developed to offer numerical solutions to this model. However in outdoor environments, the solution is more likely to diverge from the foreground, causing failures in both recognition and tracking. In this paper we propose an approach for tackling this problem by incorporating the constraint of temporal continuity in the observations. Experimental results demonstrate improvements over its Condensation counterpart.}, keywords = {algorithm;, algorithms;, Carlo, continuity;, human, image, methods;, model;, Monte, parameterized, probabilistic, recognition;, robust, sequential, series, series;, space, state, state-space, temporal, TIME}, doi = {10.1109/ICPR.2002.1044661}, author = {Zhou,Shaohua and Chellapa, Rama} } @article {12961, title = {Simple Procedure for Rapid Identification of Vibrio Cholerae from the Aquatic Environment}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {68}, year = {2002}, month = {2002/02/01/}, pages = {995 - 998}, abstract = {Biochemical tests commonly used to screen for Vibrio cholerae in environmental samples were evaluated, and we found that a combination of alkaline peptone enrichment followed by streaking on thiosulfate citrate bile salts sucrose agar and testing for arginine dihydrolase activity and esculin hydrolysis was an effective rapid technique to screen for aquatic environmental V. cholerae. This technique provided 100\% sensitivity and >=70\% specificity.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.68.2.995-998.2002}, url = {http://aem.asm.org/content/68/2/995}, author = {Choopun,Nipa and Louis,Val{\'e}rie and Huq,Anwar and Rita R Colwell} } @article {17925, title = {State of the art in data representation for visualization}, journal = {IEEE Visualization Tutorial}, year = {2002}, month = {2002///}, author = {Chen,B. and Kaufman,A. and Mueller,K. and Varshney, Amitabh} } @article {12760, title = {Structure from Motion/Stereoscopic Vision/Surface Geometry/Shape-Bayesian Self-Calibration of a Moving Camera}, journal = {Lecture Notes in Computer Science}, volume = {2351}, year = {2002}, month = {2002///}, pages = {277 - 293}, author = {Qian, G. and Chellapa, Rama} } @conference {12750, title = {Towards a criterion for evaluating the quality of 3D reconstructions}, booktitle = {Acoustics, Speech, and Signal Processing (ICASSP), 2002 IEEE International Conference on}, volume = {4}, year = {2002}, month = {2002/05//}, pages = {IV-3321 -IV-3324 - IV-3321 -IV-3324}, abstract = {Even though numerous algorithms exist for estimating the structure of a scene from its video, the solutions obtained are often of unacceptable quality. To overcome some of the deficiencies, many application systems rely on processing more information than necessary with the hope that the redundancy will help improve the quality. This raises the question about how the accuracy of the solution is related to the amount of information processed by the algorithm. Can we define the accuracy of the solution precisely enough that we automatically recognize situations where the quality of the data is so bad that even a large number of additional observations will not yield the desired solution? This paper proposes an information theoretic criterion for evaluating the quality of a 3D reconstruction in terms of the statistics of the observed parameters (i.e. the image correspondences). The accuracy of the reconstruction is judged by considering the change in mutual information (or equivalently the conditional differential entropy) between a scene and its reconstructions and its effectiveness is shown through simulations.}, doi = {10.1109/ICASSP.2002.5745364}, author = {Roy Chowdhury,Amit K. and Chellapa, Rama} } @article {12827, title = {Triggered message sequence charts}, journal = {ACM SIGSOFT Software Engineering Notes}, volume = {27}, year = {2002}, month = {2002/11/01/}, pages = {167 - 167}, isbn = {01635948}, doi = {10.1145/605466.605492}, url = {http://dl.acm.org/citation.cfm?id=605492}, author = {Sengupta,Bikram and Cleaveland, Rance} } @conference {12751, title = {Two-frame multi-scale optical flow estimation using wavelet decomposition}, booktitle = {Acoustics, Speech, and Signal Processing (ICASSP), 2002 IEEE International Conference on}, volume = {4}, year = {2002}, month = {2002/05//}, pages = {IV-3588 -IV-3591 - IV-3588 -IV-3591}, abstract = {A multi-scale algorithm using wavelet decomposition is proposed to estimate dense optical flow using only two frames. Hierarchical image representation by wavelet decomposition is used to exploit the assumption of local rigid motion in a new multi-scale framework. It is shown that if a wavelet basis with one vanishing moment is carefully selected, we can get hierarchical images, edges, and comers from the wavelet decomposition. Based on this result, all the components of the wavelet decomposition are used to estimate relatively accurate optical flow even under the inadequate image sampling condition, and overcome the $\#$x201C;flattening-out $\#$x201D; problem in traditional pyramid methods, which produce high errors when low-texture regions become flat at coarse levels due to blurring. Local affine transforms are also used to speed up flow estimation. Experiments on different types of image sequences together with quantitative and qualitative comparisons with several other optical flow methods are given to demonstrate the effectiveness and robustness of our algorithm.}, doi = {10.1109/ICASSP.2002.5745431}, author = {Liu,Haiying and Rosenfeld,Azriel and Chellapa, Rama} } @inbook {15826, title = {Understanding Machine Performance in the Context of Human Performance for Multi-document Summarization}, booktitle = {DUC 02 Conference ProceedingsDUC 02 Conference Proceedings}, year = {2002}, month = {2002///}, publisher = {U.S. National Inst. of Standards and Technology}, organization = {U.S. National Inst. of Standards and Technology}, abstract = {We present a discussion of our summarization algorithm -- both single and multi-document -- along with a discussion of the evaluation experiments we have undertaken, what we have learned from them, and how we intend to utilize this information.}, url = {http://duc.nist.gov/http://duc.nist.gov/}, author = {Schlesinger,J.D. and Okurowski,M. E. and Conroy,J.M. and O{\textquoteright}Leary, Dianne P. and Taylor,A. and Hobbs,J. and Wilson,H. T.} } @article {12764, title = {View-Based Recognition of Military Vehicles in Ladar Imagery Using CAD Model Matching}, journal = {OPTICAL ENGINEERING-NEW YORK-MARCEL DEKKER INCORPORATED-}, volume = {78}, year = {2002}, month = {2002///}, pages = {151 - 188}, author = {Der, S.Z. and Zheng,Q. and Redman, B. and Chellapa, Rama and Mahmoud, H.} } @article {12960, title = {A voyage of discovery: cholera, climate and complexity}, journal = {Environmental Microbiology}, volume = {4}, year = {2002}, month = {2002/04/23/}, pages = {67 - 69}, isbn = {1462-2920}, doi = {10.1046/j.1462-2920.2002.00270.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1462-2920.2002.00270.x/abstract}, author = {Rita R Colwell} } @article {17670, title = {Wavelength rerouting in optical networks, or the Venetian Routing problem}, journal = {Journal of Algorithms}, volume = {45}, year = {2002}, month = {2002/11//}, pages = {93 - 125}, abstract = {Wavelength rerouting has been suggested as a viable and cost-effective method to improve the blocking performance of wavelength-routed wavelength-division multiplexing (WDM) networks. This method leads to the following combinatorial optimization problem, dubbed Venetian Routing. Given a directed multigraph G along with two vertices s and t and a collection of pairwise arc-disjoint paths, we wish to find an st-path which arc-intersects the smallest possible number of the given paths. In this paper we prove the computational hardness of this problem even in various special cases, and present several approximation algorithms for its solution. In particular we show a non-trivial connection between Venetian Routing and Label Cover.}, keywords = {Approximation algorithms, Label Cover, Optical networks, Shortest paths, Wavelength rerouting, Wavelength-division multiplexing}, isbn = {0196-6774}, doi = {10.1016/S0196-6774(02)00214-6}, url = {http://www.sciencedirect.com/science/article/pii/S0196677402002146}, author = {Caprara,Alberto and Italiano,Giuseppe F. and Mohan,G. and Panconesi,Alessandro and Srinivasan, Aravind} } @conference {18453, title = {What we have learned about fighting defects}, booktitle = {Software Metrics, 2002. Proceedings. Eighth IEEE Symposium on}, year = {2002}, month = {2002///}, pages = {249 - 258}, abstract = {The Center for Empirically Based Software Engineering helps improve software development by providing guidelines for selecting development techniques, recommending areas for further research, and supporting software engineering education. A central activity toward achieving this goal has been the running of "e- Workshops" that capture expert knowledge with a minimum of overhead effort to formulate heuristics on a particular topic. The resulting heuristics are a useful summary of the current state of knowledge in an area based on expert opinion. This paper discusses the results to date of a series of e-Workshops on software defect reduction. The original discussion items are presented along with an encapsulated summary of the expert discussion. The reformulated heuristics can be useful both to researchers (for pointing out gaps in the current state of the knowledge requiring further investigation) and to practitioners (for benchmarking or setting expectations about development practices).}, keywords = {based, Center, Computer, defect, development;, education;, electronic, Empiric, engineering, engineering;, eWorkshops;, for, heuristics;, reduction;, Science, software, workshops;}, doi = {10.1109/METRIC.2002.1011343}, author = {Shull, F. and Basili, Victor R. and Boehm,B. and Brown,A. W and Costa,P. and Lindvall,M. and Port,D. and Rus,I. and Tesoriero,R. and Zelkowitz, Marvin V} } @conference {12747, title = {Wide baseline image registration using prior information}, booktitle = {Multimedia Signal Processing, 2002 IEEE Workshop on}, year = {2002}, month = {2002/12//}, pages = {37 - 40}, abstract = {Establishing correspondence between features in two images of the same scene taken from different viewing angles in a challenging problem in image processing and computer vision. However, its solution is an important step in many applications like wide baseline stereo, 3D model alignment, creation of panoramic views etc. In this paper, we propose a technique for registration of two images of a face obtained from different viewing angles. We show that prior information about the general characteristics of a face obtained from video sequences of different faces can be used to design a robust correspondence algorithm. The method works by matching 2D shapes of the different features of the face. A doubly stochastic matrix, representing the probability of match between the features, is derived using the Sinkhorn normalization procedure. The final correspondence is obtained by minimizing the probability of error of a match between the entire constellations of features in the two sets, thus taking into account the global spatial configuration of the features. The method is applied for creating holistic 3D models of a face from partial representations. Although this paper focuses primarily on faces, the algorithm can also be used for other objects with small modifications.}, keywords = {2D, 3D, algorithm;, alignment;, angles;, baseline, Computer, configuration;, constellation;, correspondence, creation;, doubly, error, extraction;, Face, feature, global, holistic, image, images;, matching;, matrix;, model, models;, normalization, panoramic, probability;, procedure;, processes;, processing;, registration;, robust, sequences;, SHAPE, signal, Sinkhorn, spatial, statistics;, stereo;, Stochastic, video, view, viewing, vision;, wide}, doi = {10.1109/MMSP.2002.1203242}, author = {Chowdhury, AM and Chellapa, Rama and Keaton, T.} } @article {18650, title = {An adaptive algorithm for tolerating value faults and crash failures}, journal = {Parallel and Distributed Systems, IEEE Transactions on}, volume = {12}, year = {2001}, month = {2001/02//}, pages = {173 - 192}, abstract = {The AQuA architecture provides adaptive fault tolerance to CORBA applications by replicating objects and providing a high-level method that an application can use to specify its desired level of dependability. This paper presents the algorithms that AQUA uses, when an application{\textquoteright}s dependability requirements can change at runtime, to tolerate both value faults in applications and crash failures simultaneously. In particular, we provide an active replication communication scheme that maintains data consistency among replicas, detects crash failures, collates the messages generated by replicated objects, and delivers the result of each vote. We also present an adaptive majority voting algorithm that enables the correct ongoing vote while both the number of replicas and the majority size dynamically change. Together, these two algorithms form the basis of the mechanism for tolerating and recovering from value faults and crash failures in AQuA}, keywords = {active replication communication, adaptive algorithm, adaptive fault tolerance, adaptive majority voting algorithm, AQuA architecture, client-server systems, CORBA, crash failures, data consistency, data integrity, Dependability, distributed object management, fault tolerant computing, objects replication, value faults}, isbn = {1045-9219}, doi = {10.1109/71.910872}, author = {Ren,Yansong and Michel Cukier and Sanders,W. H.} } @conference {12335, title = {Adaptive negative cycle detection in dynamic graphs}, booktitle = {Circuits and Systems, 2001. ISCAS 2001. The 2001 IEEE International Symposium on}, volume = {5}, year = {2001}, month = {2001///}, pages = {163 - 166}, author = {Chandrachoodan,N. and Bhattacharyya, Shuvra S. and Liu,K. J.R} } @conference {15646, title = {Algorithms for facility location problems with outliers}, booktitle = {Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms}, series = {SODA {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {642 - 651}, publisher = {Society for Industrial and Applied Mathematics}, organization = {Society for Industrial and Applied Mathematics}, address = {Philadelphia, PA, USA}, abstract = {Facility location problems are traditionally investigated with the assumption that all the clients are to be provided service. A significant shortcoming of this formulation is that a few very distant clients, called outliers, can exert a disproportionately strong influence over the final solution. In this paper we explore a generalization of various facility location problems (K-center, K-median, uncapacitated facility location etc) to the case when only a specified fraction of the customers are to be served. What makes the problems harder is that we have to also select the subset that should get service. We provide generalizations of various approximation algorithms to deal with this added constraint.}, isbn = {0-89871-490-7}, url = {http://dl.acm.org/citation.cfm?id=365411.365555}, author = {Charikar,Moses and Khuller, Samir and Mount, Dave and Narasimhan,Giri} } @conference {18164, title = {Analysis of attacks on SDMI audio watermarks}, booktitle = {Acoustics, Speech, and Signal Processing, 2001. Proceedings. (ICASSP {\textquoteright}01). 2001 IEEE International Conference on}, volume = {3}, year = {2001}, month = {2001///}, pages = {1369 -1372 vol.3 - 1369 -1372 vol.3}, abstract = {This paper explains and analyzes the successful attacks submitted by the authors on four audio watermark proposals during a 3-week SDMI public challenge. Our analysis points out some weaknesses in the watermark techniques currently under SDMI consideration and suggests directions for further improvement. The paper also discusses the framework and strategies for analyzing the robustness and security of watermarking systems as well as the difficulty, uniqueness, and unrealistic expectations of the attack setup}, keywords = {attacks;watermark, audio, coding;copy, digital, encapsulation;, Initiative;attack, Music, protection;data, SDMI, setup;robustness;security;successful, watermarks;Secure, weaknesses;audio}, doi = {10.1109/ICASSP.2001.941183}, author = {M. Wu and Craver,S. and Felten,E.W. and Liu,B.} } @conference {15353, title = {Assessment of the k-epsilon turbulence model for compressible flows using direct simulation data}, booktitle = {39th AIAA Aerospace Sciences Meeting and Exhibit}, year = {2001}, month = {2001///}, address = {Reno, NV}, abstract = {We evaluate the k-epsilon turbulence model using direct numerical simulation (DNS) data of a Mach 4 boundary layer. We find that the low Reynolds number damping functions for the Reynolds stress must be corrected by the density ratio to match the DNS data. We present the budget of the k equation and assess the modeling of the various source terms. The models for all the source terms, except for the production and dilatational dissipation terms, are found to be adequate. Finally, we present the solenoidal dissipation rate equation and compute its budget using the boundary layer data. We compare this equation with the dissipation rate equation in an incompressible flow to show the equivalence between the two equations. This is the basis for modeling the solenoidal dissipation equation. However, an additional term in the equation due to variation of fluid viscosity needs to be modeled.}, author = {Sinha,K. and Candler,G. V and Martin, M.P} } @conference {18318, title = {Attentive toys}, booktitle = {International Conference on Multimedia and Expo}, volume = {22}, year = {2001}, month = {2001///}, pages = {25 - 25}, author = {Haritaoglu,I. and Cozzi,A. and Koons,D. and Flickner,M. and Zotkin,Dmitry N and Yacoob,Yaser} } @conference {12823, title = {Automated Validation of Software Models}, booktitle = {Automated Software Engineering, International Conference on}, year = {2001}, month = {2001///}, pages = {91 - 91}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper describes the application of an automated verification tool to a software model developed at Ford. Ford already has in place an advanced model-based software development framework that employs the Matlab?, Simulink?, and Stateflow? modeling tools. During this project we applied the invariant checker Salsa to a Simulink?/ Stateflow? model of automotive software to check for nondeterminism, missing cases, dead code, and redundant code. During the analysis, a number of anomalies were detected that had not been found during manual review. We argue that the detection and correction of these problems demonstrates a cost-effective application of formal verification that elevates our level of confidence in the model.}, isbn = {0-7695-1426-X}, doi = {http://doi.ieeecomputersociety.org/10.1109/ASE.2001.989794}, author = {Sims,Steve and Cleaveland, Rance and Butts,Ken and Ranville,Scott} } @article {12123, title = {Building an Experience Base for Software Engineering: A report on the first CeBASE eWorkshop}, journal = {Product Focused Software Process Improvement}, year = {2001}, month = {2001///}, pages = {110 - 125}, abstract = {New information is obtained by research and disseminated by papers in conferences and journals. The synthesis of knowledge depends upon social discourse among the experts in a given domain to discuss the impact of this new information. Meetings among such experts are, however, expensive and time consuming. In this paper we discuss the organization of CeBASE, a center whose goal is the collection and dissemination of empirically-based software engineering knowledge, and the concept of the online workshop or eWorkshop as a way to use the Internet to minimize the needs of face-to-face meetings. We discuss the design of our eWorkshop and give the results of one eWorkshop that discussed the impact of defect reduction strategies.We want to thank Barry Boehm, Scott Henninger, Rayford Vaughn, Winsor Brown, Dan Port and Michael Frey as well as all participants for their contribution to the success of the eWorkshop. We also want to thank students at USC and UMD for their contribution in testing the system and Jennifer Dix for proof reading this paper. }, doi = {10.1007/3-540-44813-6_13}, author = {Basili, Victor R. and Tesoriero,R. and Costa,P. and Lindvall,M. and Rus,I. and Shull, F. and Zelkowitz, Marvin V} } @article {15872, title = {CLEF experiments at Maryland: Statistical stemming and backoff translation}, journal = {Cross-Language Information Retrieval and Evaluation}, year = {2001}, month = {2001///}, pages = {176 - 187}, author = {Oard, Douglas and Levow,G.A. and Cabezas,C.} } @article {14671, title = {Cyclone User{\textquoteright}s Manual, Version 0.1. 3}, journal = {Computer Science Technical Reports}, year = {2001}, month = {2001/11/16/undef}, abstract = {The current version of this manual should be available at http://www.cs.cornell.edu/projects/cyclone/ and http://www.research.att.com/projects/cyclone/. The version here describes Cyclone Version 0.1.3, although minor changes may have occurred before the release.}, author = {Grossman,D. and Morrisett,G. and Jim,T. and Hicks, Michael W. and Wang, Y. and Cheney,J.} } @article {17882, title = {Distributed processing of very large datasets with DataCutter}, journal = {Parallel Computing}, volume = {27}, year = {2001}, month = {2001/10//}, pages = {1457 - 1478}, abstract = {We describe a framework, called DataCutter, that is designed to provide support for subsetting and processing of datasets in a distributed and heterogeneous environment. We illustrate the use of DataCutter with several data-intensive applications from diverse fields, and present experimental results.}, keywords = {Component architectures, Data analysis, Distributed computing, Multi-dimensional datasets, Runtime systems}, isbn = {0167-8191}, doi = {10.1016/S0167-8191(01)00099-0}, url = {http://www.sciencedirect.com/science/article/pii/S0167819101000990}, author = {Beynon,Michael D. and Kurc,Tahsin and Catalyurek,Umit and Chang,Chialin and Sussman, Alan and Saltz,Joel} } @conference {18647, title = {A dynamic replica selection algorithm for tolerating timing faults}, year = {2001}, month = {2001/07//}, pages = {107 - 116}, abstract = {Server replication is commonly used to improve the fault tolerance and response time of distributed services. An important problem when executing time-critical applications in a replicated environment is that of preventing timing failures by dynamically selecting the replicas that can satisfy a client{\textquoteright}s timing requirement, even when the quality of service is degraded due to replica failures and excess load on the server. We describe the approach we have used to solve this problem in AQuA, a CORBA-based middleware that transparently replicates objects across a local area network. The approach we use estimates a replica{\textquoteright}s response time distribution based on performance measurements regularly broadcast by the replica. An online model uses these measurements to predict the probability with which a replica can prevent a timing failure for a client. A selection algorithm then uses this prediction to choose a subset of replicas that can together meet the client{\textquoteright}s timing constraints with at least the probability requested by the client. We conclude with experimental results based on our implementation.}, keywords = {AQuA, client, client-server systems, CORBA-based middleware, distributed object management, distributed services, dynamic replica selection algorithm, fault tolerant computing, local area network, Local area networks, quality of service, replica failures, response time, server replication, time-critical applications, timing failures, timing fault tolerance}, doi = {10.1109/DSN.2001.941397}, author = {Krishnamurthy, S. and Sanders,W. H. and Michel Cukier} } @conference {12828, title = {Efficient Model Checking Via Buchi Tableau Automata*}, booktitle = {Computer aided verification: 13th International conference, CAV 2001, Paris, France, July 18-22, 2001: proceedings}, volume = {2102}, year = {2001}, month = {2001///}, pages = {38 - 38}, author = {Bhat,G. S and Cleaveland, Rance and Groce,A.} } @article {12847, title = {Equivalence and preorder checking for finite-state systems}, journal = {Handbook of Process Algebra}, year = {2001}, month = {2001///}, pages = {391 - 424}, author = {Cleaveland, Rance and Sokolsky,O.} } @conference {12120, title = {An experience management system for a software engineering research organization}, booktitle = {Software Engineering Workshop, 2001. Proceedings. 26th Annual NASA Goddard}, year = {2001}, month = {2001///}, pages = {29 - 35}, abstract = {Most businesses rely on the fact that their employees possess relevant knowledge and that they can apply it to the task at hand. The problem is that this knowledge is not owned by the organization. It is owned and controlled by its employees. Maintaining an appropriate level of knowledge in the organization is a very important issue. It is, however, not an easy task for most organizations, and it is particularly problematic for software organizations, which are human- and knowledge-intensive. Knowledge management is a relatively new area that has attempted to address these problems. This paper introduces an approach called the "knowledge dust-to-pearls" approach. This approach addresses some of the issues with knowledge management by providing low-barrier mechanisms to "jump start" the experience base. This approach allows the experience base to become more useful more quickly than traditional approaches. This paper describes the approach and gives an example of its use at the Fraunhofer Center for Experimental Software Engineering, Maryland, USA}, keywords = {and, approach;knowledge, base;experience, Center, control;knowledge, data, development, dust-to-pearls, engineering, Engineering;business, engineering;software, experimental, for, Fraunhofer, houses;, knowledge;employee, knowledge;experience, level, maintenance;knowledge, management, management;knowledge, management;software, mechanisms;software, organization;software, organizational, organizations;administrative, organizations;knowledge, organizations;low-barrier, ownership;knowledge-intensive, processing;personnel;research, research, software, system;human-intensive}, doi = {10.1109/SEW.2001.992652}, author = {Basili, Victor R. and Costa,P. and Lindvall,M. and Mendonca,M. and Seaman,C. and Tesoriero,R. and Zelkowitz, Marvin V} } @inbook {17594, title = {Experimental Analysis of Algorithms for Bilateral-Contract Clearing Mechanisms Arising in Deregulated Power Industry}, booktitle = {Algorithm EngineeringAlgorithm Engineering}, series = {Lecture Notes in Computer Science}, volume = {2141}, year = {2001}, month = {2001///}, pages = {172 - 184}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We consider the bilateral contract satisfaction problem arising from electrical power networks due to the proposed deregulation of the electric utility industry in the USA. Given a network and a (multi)set of pairs of vertices (contracts) with associated demands, the goal is to find the maximum number of simultaneously satisfiable contracts. We study how four different algorithms perform in fairly realistic settings; we use an approximate electrical power network from Colorado. Our experiments show that three heuristics outperform a theoretically better algorithm. We also test the algorithms on four types of scenarios that are likely to occur in a deregulated marketplace. Our results show that the networks that are adequate in a regulated marketplace might be inadequate for satisfying all the bilateral contracts in a deregulated industry.}, isbn = {978-3-540-42500-7}, url = {http://dx.doi.org/10.1007/3-540-44688-5_14}, author = {Barrett,Chris and Cook,Doug and Hicks,Gregory and Faber,Vance and Marathe,Achla and Marathe,Madhav and Srinivasan, Aravind and Sussmann,Yoram and Thornquist,Heidi}, editor = {Brodal,Gerth and Frigioni,Daniele and Marchetti-Spaccamela,Alberto} } @conference {15949, title = {Handling uncertainty with active logic}, booktitle = {In Proceedings, AAAI Fall Symposium on Uncertainty in Computation}, year = {2001}, month = {2001///}, author = {Bhatia,M. and Chi,P. and Chong,W. and Josyula,D. P and Okamoto,Y. and Perlis, Don and Purang,K.} } @article {17903, title = {Haptic and aural rendering of a virtual milling process}, journal = {ASME 2001 Design Engineering Technical Conference and Computers and Information in Engineering Conference, Pittsburgh, PA}, year = {2001}, month = {2001///}, pages = {105 - 113}, author = {Chang,C. F and Varshney, Amitabh and Ge,Q. J} } @inbook {17921, title = {Hierarchical image-based and polygon-based rendering for large-scale visualizations}, booktitle = {Hierarchical and Geometrical Methods in Scientific VisualizationHierarchical and Geometrical Methods in Scientific Visualization}, year = {2001}, month = {2001///}, publisher = {Springer}, organization = {Springer}, isbn = {9783540433132}, author = {Chang,C. F and Varshney, Amitabh and Ge,Q. J} } @conference {17858, title = {A hypergraph-based workload partitioning strategy for parallel data aggregation}, booktitle = {Proceedings of the Eleventh SIAM Conference on Parallel Processing for Scientific Computing}, year = {2001}, month = {2001///}, author = {Chang,C. and Kurc, T. and Sussman, Alan and Catalyurek,U. and Saltz, J.} } @conference {12139, title = {Implementing the Experience Factory concepts as a set of Experience Bases}, booktitle = {Proc. 13th Int{\textquoteright}l Conf. Software Eng. and Knowledge Eng}, year = {2001}, month = {2001///}, pages = {102 - 109}, abstract = {This talk takes the Experience Factory concept, which was originally developed as organizational support for softwaredevelopment and generalizes it to organizational support for any aspect of a business, e.g., business practices. The Experience Factory supports the evolution of processes and other forms of knowledge, based upon experiences within the organization, and related knowledge gathered from outside the organization. It then discusses how you might design an appropriate experience base for the particular set of organizational needs determined to be of importance. Specific examples are given in developing experience bases for specific organizations and it discusses the Experience Management System (EMS) currently being evolved and how it has been applied. }, author = {Basili, Victor R. and Lindvall,M. and Costa,P.} } @article {18852, title = {Integrated Microelectromechanical System (MEMS) Inertial Measurement Unit (IMIMU)}, year = {2001}, month = {2001/12//}, institution = {CARNEGIE-MELLON UNIVERSITY}, abstract = {Processes, designs and design tools are developed to enable the monolithic integration of arrays of inertial microsensors with electronics. Accelerometers and gyroscopes, fabricated in a single CMOS process, are functional and demonstrate a single chip IMU. Two integrated post CMOS micro-machining processes are demonstrated. Thin-film microstructures are defined from the metal-dielectric stack of a conventional process. In the second process, a back-side silicon etch, followed by front-side DRIE produces bulk silicon microstructures. Accelerometer and gyroscope designs are developed with accompanying low noise electronic circuitry. Noise performance was limited to 1/f circuit noise. The chip output sensibility is set by the interface circuit design. A thermally stabilized accelerometer and circuit design is demonstrated using embedded polysilicon resistors as temperature sensors and heaters in a closed loop. Nested gyroscope topologies are demonstrated with a lateral MEMS accelerometer used as a coriolis acceleration sensor. Modeling and simulation tools that simultaneously consider the electromechanical transducer and the electronic circuit to predict system performance are developed. Electrical, electromechanical and mechanical parasitics required to enable predictive lumped parameter simulation are identified and can be extracted, enabling a designer to confidently estimate design performance prior to fabrication. Generic physics-based fault models for surface-micromachined actuators and sensors are developed that enable effective testing, diagnosis and design for manufacturability.}, keywords = {*ELECTROMECHANICAL DEVICES, *GYROSCOPES, *INERTIAL MEASUREMENT UNITS, *INERTIAL NAVIGATION, *MICROELECTROMECHANICAL SYSTEMS, ACCELEROMETERS, BULK MATERIALS, CHIPS(ELECTRONICS), CIRCUITS, CLOSED LOOP SYSTEMS, CORIOLIS EFFECT, Detectors, DIELECTRICS, ELECTRICAL AND ELECTRONIC EQUIPMENT, EMBEDDING, METALS, MICROSENSORS., MICROSTRUCTURE, MONOLITHIC STRUCTURES(ELECTRONICS), NAVIGATION AND GUIDANCE, PARASITES, PE63739E, PERFORMANCE(ENGINEERING), POLYSILICONS, RESISTORS, SILICON, TEMPERATURE SENSITIVE ELEMENTS, THERMAL STABILITY, THIN FILMS, tools, Topology, WUAFRLE1170030}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA399565}, author = {Fedder,Gary K. and Blanton,Shawn and Carley,L. R. and Gupta, Satyandra K. and Koester,David} } @conference {18634, title = {Intrusion tolerance approaches in ITUA}, volume = {64}, year = {2001}, month = {2001///}, url = {http://www.dist-systems.bbn.com/papers/2001/ICDSN/01CUK01.pdf}, author = {Michel Cukier and Lyons,J. and Pandey,P. and Ramasamy,H. V. and Sanders,W. H. and Pal,P. and Webber,F. and Schantz,R. and Loyall,J. and Watro,R.} } @conference {15899, title = {Mandarin-English Information (MEI): investigating translingual speech retrieval}, booktitle = {Proceedings of the first international conference on Human language technology research}, series = {HLT {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {1 - 7}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This paper describes the Mandarin-English Information (MEI) project, where we investigated the problem of cross-language spoken document retrieval (CL-SDR), and developed one of the first English-Chinese CL-SDR systems. Our system accepts an entire English news story (text) as query, and retrieves relevant Chinese broadcast news stories (audio) from the document collection. Hence this is a cross-language and cross-media retrieval task. We applied a multi-scale approach to our problem, which unifies the use of phrases, words and subwords in retrieval. The English queries are translated into Chinese by means of a dictionary-based approach, where we have integrated phrase-based translation with word-by-word translation. Untranslatable named entities are transliterated by a novel subword translation technique. The multi-scale approach can be divided into three subtasks -- multi-scale query formulation, multi-scale audio indexing (by speech recognition) and multi-scale retrieval. Experimental results demonstrate that the use of phrase-based translation and subword translation gave performance gains, and multi-scale retrieval outperforms word-based retrieval.}, keywords = {cross-language, English-Chinese, spoken document retrieval}, doi = {10.3115/1072133.1072202}, url = {http://dx.doi.org/10.3115/1072133.1072202}, author = {Meng,Helen and Chen,Berlin and Khudanpur,Sanjeev and Levow,Gina-Anne and Lo,Wai-Kit and Oard, Douglas and Schone,Patrick and Tang,Karen and Wang,Hsin-Min and Wang,Jianqiang} } @conference {17873, title = {Performance optimization for data intensive grid applications}, booktitle = {Active Middleware Services, 2001. Third Annual International Workshop on}, year = {2001}, month = {2001///}, pages = {97 - 105}, author = {Beynon,M. D and Sussman, Alan and Catalyurek,U. and Kurc, T. and Saltz, J.} } @article {18265, title = {Reading between the lines: Lessons from the SDMI challenge}, journal = {Proceedings of the 10th USENIX Security Symposium}, year = {2001}, month = {2001///}, pages = {13 - 17}, abstract = {The Secure Digital Music Initiative is a consortium ofparties interested in preventing piracy of digital music, and to this end they are developing architectures for con- tent protection on untrusted platforms. SDMI recently held a challenge to test the strength of four watermark- ing technologies, and two other security technologies. No documentation explained the implementations of the technologies, and neither watermark embedding nor de- tecting software was directly accessible to challenge par- ticipants. We nevertheless accepted the challenge, and explored the inner workings of the technologies. We re- port on our results here. }, author = {Craver,S.A. and Wu,M. and Liu,B. and Stubblefield,A. and Swartzlander,B. and Wallach,D.S. and Dean,D. and Felten,E.W.} } @article {13015, title = {Relating amino acid sequence to phenotype: analysis of peptide-binding data}, journal = {Biometrics}, volume = {57}, year = {2001}, month = {2001/06//}, pages = {632 - 642}, abstract = {We illustrate data analytic concerns that arise in the context of relating genotype, as represented by amino acid sequence, to phenotypes (outcomes). The present application examines whether peptides that bind to a particular major histocompatibility complex (MHC) class I molecule have characteristic amino acid sequences. However, the concerns identified and addressed are considerably more general. It is recognized that simple rules for predicting binding based solely on preferences for specific amino acids in certain (anchor) positions of the peptide{\textquoteright}s amino acid sequence are generally inadequate and that binding is potentially influenced by all sequence positions as well as between-position interactions. The desire to elucidate these more complex prediction rules has spawned various modeling attempts, the shortcomings of which provide motivation for the methods adopted here. Because of (i) this need to model between-position interactions, (ii) amino acids constituting a highly (20) multilevel unordered categorical covariate, and (iii) there frequently being numerous such covariates (i.e., positions) comprising the sequence, standard regression/classification techniques are problematic due to the proliferation of indicator variables required for encoding the sequence position covariates and attendant interactions. These difficulties have led to analyses based on (continuous) properties (e.g., molecular weights) of the amino acids. However, there is potential information loss in such an approach if the properties used are incomplete and/or do not capture the mechanism underlying association with the phenotype. Here we demonstrate that handling unordered categorical covariates with numerous levels and accompanying interactions can be done effectively using classification trees and recently devised bump-hunting methods. We further tackle the question of whether observed associations are attributable to amino acid properties as well as addressing the assessment and implications of between-position covariation.}, author = {Segal,M. R and Cummings, Michael P. and Hubbard,A. E} } @article {18710, title = {Rescuing a destabilized protein fold through backbone cyclization}, journal = {Journal of Molecular Biology}, volume = {308}, year = {2001}, month = {2001/05/18/}, pages = {1045 - 1062}, abstract = {We describe the physicochemical characterization of various circular and linear forms of the \~{}60 residue N-terminal Src homology 3 (SH3) domain from the murine c-Crk adapter protein. Structural, dynamic, thermodynamic, kinetic and biochemical studies reveal that backbone circularization does not prevent the adoption of the natural folded structure in any of the circular proteins. Both the folding and unfolding rate of the protein increased slightly upon circularization. Circularization did not lead to a significant thermodynamic stabilization of the full-length protein, suggesting that destabilizing enthalpic effects (e.g. strain) negate the expected favorable entropic contribution to overall stability. In contrast, we find circularization results in a dramatic stabilization of a truncated version of the SH3 domain lacking a key glutamate residue. The ability to rescue the destabilized mutant indicates that circularization may be a useful tool in protein engineering programs geared towards generating minimized proteins.}, keywords = {circular protein, ligation, SH3 domain}, isbn = {0022-2836}, doi = {10.1006/jmbi.2001.4631}, url = {http://www.sciencedirect.com/science/article/pii/S0022283601946315}, author = {Camarero,Julio A and Fushman, David and Sato,Satoshi and Giriat,Izabela and Cowburn,David and Raleigh,Daniel P and Muir,Tom W} } @article {15296, title = {The role of a natural language conversational interface in online sales: A case study}, journal = {International Journal of Speech Technology}, volume = {4}, year = {2001}, month = {2001///}, pages = {285 - 295}, abstract = {This paper describes the evaluation of a natural language dialog-based navigation system (HappyAssistant) that helps users access e-commerce sites to find relevant information about products and services. The prototype system leverages technologies in natural language processing and human-computer interaction to create a faster and more intuitive way of interacting with websites, especially for less experienced users. The result of a comparative study shows that users prefer the natural language-enabled navigation two to one over the menu driven navigation. In addition, the study confirmed the efficiency of using natural language dialog in terms of the number of clicks and the amount of time required to obtain the relevant information. In the case study, as compared to the menu driven system, the average number of clicks used in the natural language system was reduced by 63.2\% and the average time was reduced by 33.3\%.}, doi = {10.1023/A:1011316909641}, author = {Chai,J. and Jimmy Lin and Zadrozny,W. and Ye,Y. and Stys-Budzikowska,M. and Horvath,V. and Kambhatla,N. and Wolf,C.} } @article {18271, title = {Rotation, scale, and translation resilient public watermarking for images using a log-polar fourier transform}, year = {2001}, month = {2001/08/28/}, abstract = {A method for detecting a watermark signal in digital image data. The detecting method includes the steps of: computing a log-polar Fourier transform of the image data to obtain a log-polar Fourier spectrum; projecting the log-polar Fourier spectrum down to a lower dimensional space to obtain an extracted signal; comparing the extracted signal to a target watermark signal; and declaring the presence or absence of the target watermark signal in the image data based on the comparison. Also provided is a method for inserting a watermark signal in digital image data to obtain a watermarked image. The inserting method includes the steps of: computing a log-polar Fourier transform of the image data to obtain a log-polar Fourier spectrum; projecting the log-polar Fourier spectrum down to a lower dimensional space to obtain an extracted signal; modifying the extracted signal such that it is similar to a target watermark; performing a one-to-many mapping of the modified signal back to...}, url = {http://www.google.com/patents?id=v4AIAAAAEBAJ}, author = {Bloom,Jeffrey A. and Cox,Ingemar J. and Miller,Matthew L. and M. Wu and Lin,Ching-Yung and Lui,Yui Man}, editor = {Signafy, Inc.} } @article {18272, title = {Rotation, scale, and translation resilient watermarking for images}, journal = {Image Processing, IEEE Transactions on}, volume = {10}, year = {2001}, month = {2001/05//}, pages = {767 - 782}, abstract = {Many electronic watermarks for still images and video content are sensitive to geometric distortions. For example, simple rotation, scaling, and/or translation (RST) of an image can prevent blind detection of a public watermark. In this paper, we propose a watermarking algorithm that is robust to RST distortions. The watermark is embedded into a one-dimensional (1-D) signal obtained by taking the Fourier transform of the image, resampling the Fourier magnitudes into log-polar coordinates, and then summing a function of those magnitudes along the log-radius axis. Rotation of the image results in a cyclical shift of the extracted signal. Scaling of the image results in amplification of the extracted signal, and translation of the image has no effect on the extracted signal. We can therefore compensate for rotation with a simple search, and compensate for scaling by using the correlation coefficient as the detection measure. False positive results on a database of 10 000 images are reported. Robustness results on a database of 2000 images are described. It is shown that the watermark is robust to rotation, scale, and translation. In addition, we describe tests examining the watermarks resistance to cropping and JPEG compression}, keywords = {axis;one-dimensional, coding;security, coefficient;cropping;cyclical, compression;RST, coordinates;log-radius, data;, detection;correlation, distortions;blind, distortions;images;log-polar, encapsulation;image, Fourier, images;translation, magnitudes;Fourier, measure;geometric, of, protection;data, resilient, shift;detection, signal;public, transform;JPEG, transforms;copy, watermark;resampling;rotation;scale;search;still, watermarking;video;Fourier}, isbn = {1057-7149}, doi = {10.1109/83.918569}, author = {Lin,C.-Y. and Wu,M. and Bloom,J.A. and Cox,I.J. and Miller,M.L. and Lui,Y.M.} } @inbook {14728, title = {Safe and Flexible Dynamic Linking of Native Code}, booktitle = {Types in Compilation}, series = {Lecture Notes in Computer Science}, volume = {2071}, year = {2001}, month = {2001///}, pages = {147 - 176}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present the design and implementation of the first complete framework for flexible and safe dynamic linking of native code. Our approach extends Typed Assembly Language with a primitive for loading and typechecking code, which is flexible enough to support a variety of linking strategies, but simple enough that it does not significantly expand the trusted computing base. Using this primitive, along with the ability to compute with types, we show that we can program many existing dynamic linking approaches. As a concrete demonstration, we have used our framework to implement dynamic linking for a type-safe dialect of C, closely modeled after the standard linking facility for Unix C programs. Aside from the unavoidable cost of verification, our implementation performs comparably with the standard, untyped approach.}, isbn = {978-3-540-42196-2}, url = {http://dx.doi.org/10.1007/3-540-45332-6_6}, author = {Hicks, Michael W. and Weirich,Stephanie and Crary,Karl}, editor = {Harper,Robert} } @article {12800, title = {Simulation revisited}, journal = {Tools and Algorithms for the Construction and Analysis of Systems}, year = {2001}, month = {2001///}, pages = {480 - 495}, author = {Tan,L. and Cleaveland, Rance} } @article {13863, title = {Spanish Language Processing at University of Maryland: Building Infrastructure for Multilingual Applications}, year = {2001}, month = {2001///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {We describe here our construction of lexical resources, tool creation, building of an alignedparallel corpus, and an approach to automatic treebank creation that we have been de- veloping using Spanish data, based on projection of English syntactic dependency infor- mation across a parallel corpus. }, author = {Cabezas,C. and Dorr, Bonnie J and Resnik, Philip} } @conference {16708, title = {Supervised sense tagging using support vector machines}, booktitle = {Proceedings of the Second International Workshop on Evaluating Word Sense Disambiguation Systems (SENSEVAL-2)}, year = {2001}, month = {2001///}, pages = {59 - 62}, author = {Cabezas,C. and Resnik, Philip and Stevens,J.} } @article {16158, title = {Understanding Manufacturing Systems with a Learning Historian for User-Directed Experimentation}, volume = {CS-TR-4243}, year = {2001}, month = {2001///}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {This paper describes a learning historian to improve user-directed experimentation withdiscrete event simulation models of manufacturing systems. In user-directed experimentation, an analyst conducts simulation runs to estimate system performance. Then the analyst modifies the simulation model to evaluate other possibilities. An important characteristic is the ad hoc nature of the experimentation, as the analyst forms and runs new trials based on the results from previous trials. Through user-directed experimentation designers compare alternatives and students learn the relationships between input parameters and performance measures. Recording and reviewing previous trials while using simulation models enhances their benefits, transforming trial-and-error into learning. The learning historian combines a graphical user interface, a discrete event simulation model, and dynamic data visualization. Usability studies indicate that the learning historian is a usable and useful tool because it allows users to concentrate more on understanding system behavior than on operating simulation software. }, author = {Chipman,G. and Plaisant, Catherine and Gahagan,S. and Herrmann,J.W. and Hewitt,S. and Reaves,L.} } @article {17842, title = {Visualization of large data sets with the Active Data Repository}, journal = {IEEE Computer Graphics and Applications}, volume = {21}, year = {2001}, month = {2001/08//Jul}, pages = {24 - 33}, abstract = {We implement ray-casting-based volume rendering and isosurface rendering methods using the Active Data Repository (ADR) for visualizing out-of-core data sets. We have developed the ADR object-oriented framework to provide support for applications that employ range queries with user-defined mapping and aggregation operations on large-scale multidimensional data. ADR targets distributed-memory parallel machines with one or more disks attached to each node. It is designed as a set of modular services implemented in C++, which can be customized for application-specific processing. The ADR runtime system supports common operations such as memory management, data retrieval, and scheduling of processing across a parallel machine}, keywords = {active data repository, ADR runtime system, Algorithm design and analysis, application-specific processing, C++, data mining, data retrieval, data visualisation, Data visualization, distributed-memory parallel machines, Indexing, Information retrieval, isosurface rendering, Isosurfaces, large data sets, large-scale multidimensional data, Memory management, modular services, out-of-core data sets, parallel machine, Parallel machines, Partitioning algorithms, ray-casting-based volume rendering, Rendering (computer graphics), Runtime, software libraries, storage management}, isbn = {0272-1716}, doi = {10.1109/38.933521}, author = {Kurc, T. and Catalyurek,U. and Chang,Chialin and Sussman, Alan and Saltz, J.} } @conference {18292, title = {What can we reasonably expect from watermarks?}, booktitle = {Applications of Signal Processing to Audio and Acoustics, 2001 IEEE Workshop on the}, year = {2001}, month = {2001///}, pages = {223 - 226}, abstract = {Digital watermarking has been positioned as a solution to copyright protection of digital music, and some doubt exists about its ability to perform in this regard. A survey of watermarking applications assesses the technology{\textquoteright}s potential for copy protection, as well as other digital audio applications}, keywords = {applications;audio, applications;digital, audio, coding;copy, data;, databases;music, hashing;steganography;watermarking, music;digital, of, protection;copyright, protection;copyright;music;security, protection;digital, watermarking;copy, watermarking;forensic, watermarking;music}, doi = {10.1109/ASPAA.2001.969583}, author = {Craver,S.A. and M. Wu and Liu,B.} } @article {13353, title = {Adaptive query processing: Technology in evolution}, journal = {IEEE Data Engineering Bulletin}, volume = {23}, year = {2000}, month = {2000///}, pages = {7 - 18}, abstract = {As query engines are scaled and federated, they must cope with highly unpredictable and changeableenvironments. In the Telegraph project, we are attempting to architect and implement a continuously adaptive query engine suitable for global-area systems, massive parallelism, and sensor networks. To set the stage for our research, we present a survey of prior work on adaptive query processing, focusing on three characterizations of adaptivity: the frequency of adaptivity, the effects of adaptivity, and the extent of adaptivity. Given this survey, we sketch directions for research in the Telegraph project. }, author = {Hellerstein,J. M and Franklin,M.J. and Chandrasekaran,S. and Deshpande, Amol and Hildrum,K. and Madden,S. and Raman,V. and Shah,M. A} } @conference {15336, title = {Assessment of Temperature Fluctuation Models for RANS Simulations of Hypersonic Reacting Flows}, booktitle = {38th AIAA Aerospace Sciences Meeting and Exhibit}, year = {2000}, month = {2000///}, address = {Reno, NV}, abstract = {Turbulence-chemistry interactions play an important role in various fluid flow problems. In a hypersonic boundary layer, these interactions can alter the surface heating rate of the vehicle by modifying the temperature profile across the layer. The effect of these interactions is accounted for in a Reynolds-averaged Navier Stokes (RANS) simulation using a probability density function (PDF) of the temperature distribution. In this paper, two presumed PDF models are considered, namely, the Martin and Candler model and the Gaffney et al. model, and their accuracy is assessed by comparing to direct numerical simulation (DNS) of homogeneous isotropic turbulence. TheMartin and Candler model reproduces the turbulence-chemistry interactions in the flow correctly whereas the Gaffney model overpredicts the temperature fluctuations.}, author = {Sinha,K. and Martin, M.P and Candler,G. V} } @article {12974, title = {A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity}, journal = {Molecular Biology and EvolutionMol Biol Evol}, volume = {17}, year = {2000}, month = {2000/12/01/}, pages = {1776 - 1788}, abstract = {Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling. Despite the recent development of powerful genome technologies capable of producing sequence data in large quantities (witness the recently completed first draft of the human genome), there has been relatively little change in how evolutionary studies are conducted. The application of genomic methods to evolutionary biology is a challenge, in part because gene segments from different organisms are manipulated separately, requiring individual purification, cloning, and sequencing. We suggest that a feasible approach to collecting genome-scale data sets for evolutionary biology (i.e., evolutionary genomics) may consist of combination of DNA samples prior to cloning and sequencing, followed by computational reconstruction of the original sequences. This approach will allow the full benefit of automated protocols developed by genome projects to be realized; taxon sampling levels can easily increase to thousands for targeted genomes and genomic regions. Sequence diversity at this level will dramatically improve the quality and accuracy of phylogenetic inference, as well as the accuracy and resolution of comparative evolutionary studies. In particular, it will be possible to make accurate estimates of normal evolution in the context of constant structural and functional constraints (i.e., site-specific substitution probabilities), along with accurate estimates of changes in evolutionary patterns, including pairwise coevolution between sites, adaptive bursts, and changes in selective constraints. These estimates can then be used to understand and predict the effects of protein structure and function on sequence evolution and to predict unknown details of protein structure, function, and functional divergence. In order to demonstrate the practicality of these ideas and the potential benefit for functional genomic analysis, we describe a pilot project we are conducting to simultaneously sequence large numbers of vertebrate mitochondrial genomes.}, isbn = {0737-4038, 1537-1719}, url = {http://mbe.oxfordjournals.org/content/17/12/1776}, author = {Pollock,David D and Eisen,Jonathan A. and Doggett,Norman A and Cummings, Michael P.} } @article {15724, title = {Chromosome Identification Using Hidden Markov Models: Comparison with Neural Networks, Singular Value Decomposition, Principal Components Analysis, and Fisher Discriminant Analysis}, journal = {Laboratory Investigation}, volume = {80}, year = {2000}, month = {2000/11/01/}, pages = {1629 - 1641}, abstract = {The analysis of G-banded chromosomes remains the most important tool available to the clinical cytogeneticist. The analysis is laborious when performed manually, and the utility of automated chromosome identification algorithms has been limited by the fact that classification accuracy of these methods seldom exceeds about 80\% in routine practice. In this study, we use four new approaches to automated chromosome identification {\textemdash} singular value decomposition (SVD), principal components analysis (PCA), Fisher discriminant analysis (FDA), and hidden Markov models (HMM) {\textemdash} to classify three well-known chromosome data sets (Philadelphia, Edinburgh, and Copenhagen), comparing these approaches with the use of neural networks (NN). We show that the HMM is a particularly robust approach to identification that attains classification accuracies of up to 97\% for normal chromosomes and retains classification accuracies of up to 95\% when chromosome telomeres are truncated or small portions of the chromosome are inverted. This represents a substantial improvement of the classification accuracy for normal chromosomes, and a doubling in classification accuracy for truncated chromosomes and those with inversions, as compared with NN-based methods. HMMs thus appear to be a promising approach for the automated identification of both normal and abnormal G-banded chromosomes.}, keywords = {addiction disorders, anxiety, depression, psychopharmacology, schizophrenia}, isbn = {0023-6837}, doi = {10.1038/labinvest.3780173}, url = {http://www.nature.com/labinvest/journal/v80/n11/full/3780173a.html}, author = {Conroy,John M. and Kolda,Tamara G. and O{\textquoteright}Leary, Dianne P. and O{\textquoteright}Leary,Timothy J} } @article {17576, title = {Combinatorial Problems Arising in Deregulated Electrical Power Industry: Survey and Future Directions}, journal = {NONCONVEX OPTIMIZATION AND ITS APPLICATIONS}, volume = {42}, year = {2000}, month = {2000///}, pages = {138 - 162}, author = {Cook,D. and Hicks,G. and Faber,V. and Marathe,M. V and Srinivasan, Aravind and Sussmann,Y. J and Thornquist,H.} } @conference {18032, title = {Communication complexity of document exchange}, booktitle = {Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms}, series = {SODA {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {197 - 206}, publisher = {Society for Industrial and Applied Mathematics}, organization = {Society for Industrial and Applied Mathematics}, address = {Philadelphia, PA, USA}, isbn = {0-89871-453-2}, url = {http://dl.acm.org/citation.cfm?id=338219.338252}, author = {Cormode,Graham and Paterson,Mike and Sahinalp,S{\"u}leyman Cenk and Vishkin, Uzi} } @conference {15287, title = {Comparative Evaluation of a Natural Language Dialog Based System and a Menu-Driven System for Information Access: A Case Study}, booktitle = {In Proceedings of the International Conference on Multimedia Information Retrieval (RIAO 2000)}, year = {2000}, month = {2000///}, abstract = {This paper describes the evaluation of a natural language dialog based navigation system (HappyAssistant) thathelps users access e-commerce sites to find relevant information about products and services. The prototype system leverages technologies in natural language processing and human computer interaction to create a faster and more intuitive way of interacting with websites, especially for the less experienced users. The result of a comparative study shows that users prefer the natural language enabled navigation two to one over the menu driven navigation. In addition, the study confirmed the efficiency of using natural language dialog in terms of the number of clicks and the amount of time required to obtain the relevant information. In the case study, comparing to the menu driven system, the average number of clicks used in the natural language system was reduced by 63.2\% and the average time was reduced by 33.3\%. }, author = {Chai,J. and Jimmy Lin and Zadrozny,W. and Ye,Y. and Budzikowska,M. and Horvath,V. and Kambhatla,N. and Wolf,C.} } @conference {16919, title = {A comparison of voice controlled and mouse controlled web browsing}, booktitle = {Proceedings of the fourth international ACM conference on Assistive technologies}, series = {Assets {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {72 - 79}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {human-computer, interaction, User interfaces, voice browsers, voice recognition, web browsing}, isbn = {1-58113-313-8}, doi = {10.1145/354324.354345}, url = {http://doi.acm.org/10.1145/354324.354345}, author = {Christian,Kevin and Kules,Bill and Shneiderman, Ben and Youssef,Adel} } @book {12848, title = {A compositional approach to statecharts semantics}, volume = {25}, year = {2000}, month = {2000///}, publisher = {ACM}, organization = {ACM}, author = {L\{\"u}ttgen,G. and Von Der Beeck,M. and Cleaveland, Rance} } @conference {18636, title = {Dynamic node management and measure estimation in a state-driven fault injector}, year = {2000}, month = {2000///}, pages = {248 - 261}, abstract = {Validation of distributed systems using fault injectionis difficult because of their inherent complexity, lack of a global clock, and lack of an easily accessible notion of a global state. To address these challenges, the Loki fault injector injects faults based on a partial view of the global state of a distributed system, and performs a post-runtime analysis using an off-line clock synchronization algorithm to determine whether the faults were properly injected. In this paper, we first describe an enhanced runtime architecture for the Loki fault injector and then present a new method for obtaining measures in Loki. The enhanced runtime allows dynamic entry and exit of nodes in the system. It also offers more efficient multicast of notification messages and more efficient communication between state machines on the same host, and is more scalable than the previous runtime. We then detail a new and flexible method for obtaining a wide range of performance and dependability measures in Loki. }, url = {https://www.perform.csl.illinois.edu/Papers/USAN_papers/00CHA01.pdf}, author = {Chandra,R. and Michel Cukier and Lefever,R. and Sanders,W. and others} } @article {15547, title = {Efficient expected-case algorithms for planar point location}, journal = {Algorithm Theory-SWAT 2000}, year = {2000}, month = {2000///}, pages = {537 - 543}, doi = {10.1007/3-540-44985-X_31}, author = {Arya,S. and Cheng,S. W and Mount, Dave and Ramesh,H.} } @article {12810, title = {GCCS: A graphical coordination language for system specification}, journal = {Coordination Languages and Models}, year = {2000}, month = {2000///}, pages = {207 - 212}, author = {Cleaveland, Rance and Du,X. and Smolka,S.} } @article {18960, title = {The genome sequence of Drosophila melanogaster}, journal = {Science}, volume = {287}, year = {2000}, month = {2000///}, pages = {2185 - 2185}, abstract = {The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the \~{}120-megabase euchromatic portion of theDrosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes \~{}13,600 genes, somewhat fewer than the smaller Caenorhabditis elegansgenome, but with comparable functional diversity.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.287.5461.2185}, url = {http://www.sciencemag.org/content/287/5461/2185}, author = {Adams,M.D. and Celniker,S.E. and Holt,R.A. and Evans,C.A. and Gocayne,J.D. and Amanatides,P.G. and Scherer,S.E. and Li,P.W. and Hoskins,R.A. and Galle,R.F. and others} } @article {17603, title = {Improved Algorithms via Approximations of Probability Distributions}, journal = {Journal of Computer and System Sciences}, volume = {61}, year = {2000}, month = {2000/08//}, pages = {81 - 107}, abstract = {We present two techniques for constructing sample spaces that approximate probability distributions. The first is a simple method for constructing the small-bias probability spaces introduced by Naor and Naor. We show how to efficiently combine this construction with the method of conditional probabilities to yield improved parallel algorithms for problems such as set discrepancy, finding large cuts in graphs, and finding large acyclic subgraphs. The second is a construction of small probability spaces approximating general independent distributions which are of smaller size than the constructions of Even, Goldreich, Luby, Nisan, and Veli{\v c}kovi{\'c}.}, keywords = {derandomization, discrepancy, explicit constructions, graph coloring, Parallel algorithms, small sample spaces}, isbn = {0022-0000}, doi = {10.1006/jcss.1999.1695}, url = {http://www.sciencedirect.com/science/article/pii/S0022000099916951}, author = {Chari,Suresh and Rohatgi,Pankaj and Srinivasan, Aravind} } @conference {14844, title = {In search of illumination invariants}, booktitle = {Computer Vision and Pattern Recognition, 2000. Proceedings. IEEE Conference on}, volume = {1}, year = {2000}, month = {2000///}, pages = {254 -261 vol.1 - 254 -261 vol.1}, abstract = {We consider the problem of determining functions of an image of an object that are insensitive to illumination changes. We first show that for an object with Lambertian reflectance there are no discriminative functions that are invariant to illumination. This result leads as to adopt a probabilistic approach in which we analytically determine a probability distribution for the image gradient as a function of the surface{\textquoteright}s geometry and reflectance. Our distribution reveals that the direction of the image gradient is insensitive to changes in illumination direction. We verify this empirically by constructing a distribution for the image gradient from more than 20 million samples of gradients in a database of 1,280 images of 20 inanimate objects taken under varying lighting condition. Using this distribution we develop an illumination insensitive measure of image comparison and test it on the problem of face recognition}, keywords = {comparison;image, gradient;face, invariants;image, Lambertian, recognition;, recognition;illumination, recognition;object, reflectance;face}, doi = {10.1109/CVPR.2000.855827}, author = {Chen,H. F and Belhumeur,P. N. and Jacobs, David W.} } @article {14523, title = {An inverse method for the acoustic detection, localization and determination of the shape evolution of a bubble}, journal = {Inverse Problems}, volume = {16}, year = {2000}, month = {2000///}, pages = {1741 - 1741}, author = {Gumerov, Nail A. and Chahine,G. L} } @conference {18678, title = {Loki: a state-driven fault injector for distributed systems}, year = {2000}, month = {2000///}, pages = {237 - 242}, abstract = {Distributed applications can fail in subtle ways that depend on the state of multiple parts of a system. This complicates the validation of such systems via fault injection, since it suggests that faults should be injected based on the global state of the system. In Loki, fault injection is performed based on a partial view of the global state of a distributed system, i.e. faults injected in one node of the system can depend on the state of other nodes. Once faults are injected, a post-runtime analysis, using off-line clock synchronization, is used to place events and injections on a single global timeline and to determine whether the intended faults were properly injected. Finally, experiments containing successful fault injections are used to estimate the specified measures. In addition to briefly reviewing the concepts behind Loki and its organization, we detail Loki{\textquoteright}s user interface. In particular, we describe the graphical user interfaces for specifying state machines and faults, for executing a campaign and for verifying whether the faults were properly injected}, keywords = {campaign execution, computer testing, distributed applications failure, distributed processing, distributed system validation, Fault diagnosis, fault event placement, fault specification, global system state, global timeline, Graphical user interfaces, Loki, off-line clock synchronization, post-runtime analysis, specified measures estimation, state machine specification, state-driven fault injection, Synchronisation}, doi = {10.1109/ICDSN.2000.857544}, author = {Chandra,R. and Lefever,R.M. and Michel Cukier and Sanders,W. H.} } @article {15942, title = {Meta-reasoning for intelligent dialog repair}, year = {2000}, month = {2000///}, institution = {Technical report, University of Maryland}, abstract = {Under consideration for other conferences (specify)? We present a logical approach and implmentation of a real-time rational agent for dialogue management, which includes an ability to represent, reason about, and repair (both implicitly and explicitly) incoherence in dialogue. We exemplify a target problem of negative feedback in action directive subdialogues, with an ability to make reference resolution sensitive to dialogue context and like intentions. The resulting system is able to behave more sensibly in several situations than earlier dialogue management systems in these same conditions. Meta-reasoning for intelligent dialog repair We present a logical approach and implmentation of a real-time rational agent for dialogue management, which includes an ability to represent, reason about, and repair (both implicitly and explicitly) incoherence in dialogue. We exemplify a target problem of negative feedback in action directive subdialogues, with an ability to make reference resolution sensitive to dialogue context and like intentions. The resulting system is able to behave more sensibly in several situations than earlier dialogue management systems in these same conditions.}, author = {Purang,K. and Traum,D. and Purushothaman,D. and Chong,W. and Okamato,Y. and Perlis, Don} } @conference {17880, title = {Optimizing retrieval and processing of multi-dimensional scientific datasets}, booktitle = {Parallel and Distributed Processing Symposium, 2000. IPDPS 2000. Proceedings. 14th International}, year = {2000}, month = {2000///}, pages = {405 - 410}, publisher = {IEEE}, organization = {IEEE}, abstract = {We have developed the Active Data Repository (ADR), an infrastructure that integrates storage, retrieval, and processing of large multi-dimensional scientific datasets on distributed memory parallel machines with multiple disks attached to each node. In earlier work, we proposed three strategies for processing range queries within the ADR framework. Our experimental results show that the relative performance of the strategies changes under varying application characteristics and machine configurations. In this work we investigate approaches to guide and automate the selection of the best strategy for a given application and machine configuration. We describe analytical models to predict the relative performance of the strategies where input data elements are uniformly distributed in the attribute space of the output dataset, restricting the output dataset to be a regular d-dimensional array}, keywords = {active data repository, Area measurement, Computer science, Data analysis, distributed memory parallel machines, Educational institutions, Information retrieval, Information Storage and Retrieval, infrastructure, Microscopy, Microwave integrated circuits, multi-dimensional scientific datasets retrieval, PARALLEL PROCESSING, Pathology, range queries, regular d-dimensional array, Satellites, Tomography}, isbn = {0-7695-0574-0}, doi = {10.1109/IPDPS.2000.846013}, author = {Chang,Chialin and Kurc, T. and Sussman, Alan and Saltz, J.} } @article {13011, title = {Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences}, journal = {J Mol Evol}, volume = {50}, year = {2000}, month = {2000/06//}, pages = {532 - 540}, abstract = {Acanthocephala (thorny-headed worms) is a phylum of endoparasites of vertebrates and arthropods, included among the most phylogenetically basal tripoblastic pseudocoelomates. The phylum is divided into three classes: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These classes are distinguished by morphological characters such as location of lacunar canals, persistence of ligament sacs in females, number and type of cement glands in males, number and size of proboscis hooks, host taxonomy, and ecology. To understand better the phylogenetic relationships within Acanthocephala, and between Acanthocephala and Rotifera, we sequenced the nearly complete 18S rRNA genes of nine species from the three classes of Acanthocephala and four species of Rotifera from the classes Bdelloidea and Monogononta. Phylogenetic relationships were inferred by maximum-likelihood analyses of these new sequences and others previously determined. The analyses showed that Acanthocephala is the sister group to a clade including Eoacanthocephala and Palaeacanthocephala. Archiacanthocephala exhibited a slower rate of evolution at the nucleotide level, as evidenced by shorter branch lengths for the group. We found statistically significant support for the monophyly of Rotifera, represented in our analysis by species from the clade Eurotatoria, which includes the classes Bdelloidea and Monogononta. Eurotatoria also appears as the sister group to Acanthocephala.}, author = {Garc{\'\i}a-Varela,M and P{\'e}rez-Ponce de Le{\'o}n,G. and de la Torre,P and Cummings, Michael P. and Sarma,SS and Laclette,J. P} } @article {13012, title = {Phylogenetic relationships of {\i}t Phytophthora species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI}, journal = {Mycol Res}, volume = {104}, year = {2000}, month = {2000/09//}, pages = {1055 - 1061}, abstract = {Phylogenetic relationships among Phytophthora species were investigated by sequence analysis of the internal transcribed spacer region I of the ribosomal DNA repeat unit. The extensive collection of isolates included taxa from all six morphological groups recognized by Waterhouse (1963) including molecular groups previously identified using isozymes and mtDNA restriction fragment length polymorphisms. Similar to previous studies, the inferred relationships indicated that molecular groups of P. cryptooea/drechsleri-like and P. megasperma-like taxa are polyphyletic. Morphological groups V and VI, which are differentiated by the presence of amphigynous or paragynous antheridia, are not monophyletic: species of the two groups are interspersed in the tree. Species with papillate and semi-papillate sporangia (groups I-IV) clustered together and this cluster was distinct from those of species with non-papillate sporangia. There was no congruence between the mode of antheridial attachment, sporangial caducity, or homo- or heterothallic habit and the molecular grouping of the species. Our study provides evidence that the antheridial position together with homo- or heterothallic habit does not reflect phylogenetic relationships within Phytophthora. Consequently, confirming studies done previously (Cooke \& Duncan 1997), this study provides evidence that the morphological characters used in Phytophthora taxonomy are of limited value for deducing phylogenetic relationships, because they exhibit convergent evolution.}, author = {F{\"o}rster,H and Cummings, Michael P. and Coffey,M. D} } @article {16490, title = {Producing Interoperable Queries for Relational and Object-Oriented Databases}, journal = {Journal of Intelligent Information Systems}, volume = {14}, year = {2000}, month = {2000///}, pages = {51 - 75}, author = {Chang,Y. H and Raschid, Louiqa} } @conference {17532, title = {Receiver based management of low bandwidth access links}, booktitle = {IEEE INFOCOM 2000. Nineteenth Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings}, volume = {1}, year = {2000}, month = {2000///}, pages = {245-254 vol.1 - 245-254 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we describe a receiver-based congestion control policy that leverages TCP flow control mechanisms to prioritize mixed traffic loads across access links. We manage queueing at the access link to: (1) improve the response time of interactive network applications; (2) reduce congestion-related packet losses; while (3) maintaining high throughput for bulk-transfer applications. Our policy controls queue length by manipulating receive socket buffer sizes. We have implemented this solution in a dynamically loadable Linux kernel module, and tested it over low-bandwidth links. Our approach yields a 7-fold improvement in packet latency over an unmodified system while maintaining 94\% link utilization. In the common case, congestion-related packet losses at the access link can be eliminated. Finally, by prioritizing short flows, we show that our system reduces the time to download a complex Web page during a large background transfer by a factor of two}, keywords = {Bandwidth, buffer storage, bulk-transfer applications, complex Web page, congestion control policy, Delay, dynamically loadable Linux kernel module, information resources, interactive network, Internet, Kernel, link utilization, Linux, low-bandwidth access links, mixed traffic load, packet latency, queue length, queueing theory, receive socket buffer sizes, receiver-based management, response time, short flow prioritizing, Size control, Sockets, subscriber loops, TCP flow control, telecommunication congestion control, telecommunication network management, Telecommunication traffic, Testing, Throughput, Transport protocols, Unix, Web pages}, isbn = {0-7803-5880-5}, doi = {10.1109/INFCOM.2000.832194}, author = {Spring, Neil and Chesire,M. and Berryman,M. and Sahasranaman,V. and Anderson,T. and Bershad,B.} } @article {18270, title = {Rotation, scale, and translation resilient public watermarking for images}, journal = {PROC SPIE INT SOC OPT ENG}, volume = {3971}, year = {2000}, month = {2000///}, pages = {90 - 98}, abstract = {Many electronic watermarks for still images and video content are sensitive to geometric distortions. For example,simple rotation, scaling, and/or translation (RST) of an image can prevent detection of a public watermark. In this paper, we propose a watermarking algorithm that is robust to RST distortions. The watermark is embedded into a 1-dimensional signal obtained by first taking the Fourier transform of the image, resampling the Fourier magnitudes into log-polar coordinates, and then summing a function of those magnitudes along the log-radius axis. If the image is rotated, the resulting signal is cyclically shifted. If it is scaled, the signal is multiplied by some value. And if the image is translated, the signal is unaffected. We can therefore compensate for rotation with a simple search, and for scaling by using the correlation coefficient for the detection metric. False positive results on a database of 10,000 images are reported. Robustness results on a database of 2,000 images are described. It is shown that the watermark is robust to rotation, scale and translation. In addition, the algorithm shows resistance to cropping. }, author = {Lin,C.Y. and Wu,M. and Bloom,J.A. and Cox,I.J. and Miller,M.L. and Lui,Y.M.} } @article {14727, title = {Safe and Flexible Dynamic Linking of Native Code}, year = {2000}, month = {2000/01/01/}, abstract = {We present the design and implementation of a framework for flexible and safe dynamic linking of native code. Our approach extends Typed Assembly Language with a primitive for loading and typechecking code, which is flexible enough to support a variety of linking strategies, but simple enough that it does not significantly expand the trusted computing base. Using this primitive, along with the ability to compute with types, we show that we can program many existing dynamic linking approaches. As a concrete demonstration, we have used our framework to implement dynamic linking for a type-safe dialect of C, closely modeled after the standard linking facility for Unix C programs. Aside from the unavoidable cost of verification, our implementation performs comparably with the standard, untyped approach.}, url = {http://repository.upenn.edu/cis_reports/137}, author = {Crary,Karl and Hicks, Michael W. and Weirich,Stephanie} } @article {12808, title = {A semantic theory for heterogeneous system design}, journal = {FST TCS 2000: Foundations of Software Technology and Theoretical Computer Science}, year = {2000}, month = {2000///}, pages = {312 - 324}, author = {Cleaveland, Rance and L\{\"u}ttgen,G.} } @article {15337, title = {Subgrid-scale models for compressible large-eddy simulations}, journal = {Theoretical and Computational Fluid Dynamics}, volume = {13}, year = {2000}, month = {2000///}, pages = {361 - 376}, author = {Martin, M.P and Piomelli,U. and Candler,G. V} } @article {16633, title = {The temporal correlation hypothesis for self-organizing feature maps}, journal = {International Journal of Systems Science}, volume = {31}, year = {2000}, month = {2000///}, pages = {911 - 921}, author = {Chen,Y. and Reggia, James A.} } @article {15351, title = {Toward the large-eddy simulation over a hypersonic elliptical cross-section cone}, journal = {AIAA Paper No. 00-2311}, year = {2000}, month = {2000///}, author = {Martin, M.P and Weirs,G. and Candler,G. V and Piomelli,U. and Johnson,H. and Nompelis,I.} } @inbook {13477, title = {Using Feature Hierarchies in Bayesian Network Learning}, booktitle = {Abstraction, Reformulation, and Approximation}, series = {Lecture Notes in Computer Science}, volume = {1864}, year = {2000}, month = {2000///}, pages = {260 - 270}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In recent years, researchers in statistics and the UAI community have developed an impressive body of theory and algorithmic machinery for learning Bayesian networks from data. Learned Bayesian networks can be used for pattern discovery, prediction, diagnosis, and density estimation tasks. Early pioneering work in this area includes [ 5 , 9 , 10 , 13 ]. The algorithm that has emerged as the current most popular approach is a simple greedy hill-climbing algorithm that searches the space of candidate structures, guided by a network scoring function (either Bayesian or Minimum Description Length (MDL)-based). The search begins with an initial candidate network (typically the empty network, which has no edges), and then considers making small local changes such as adding, deleting, or reversing an edge in the network.}, isbn = {978-3-540-67839-7}, url = {http://dx.doi.org/10.1007/3-540-44914-0_16}, author = {desJardins, Marie and Getoor,Lise and Koller,Daphne}, editor = {Choueiry,Berthe and Walsh,Toby} } @inbook {17671, title = {Wavelength Rerouting in Optical Networks, or the Venetian Routing Problem}, booktitle = {Approximation Algorithms for Combinatorial Optimization}, series = {Lecture Notes in Computer Science}, volume = {1913}, year = {2000}, month = {2000///}, pages = {71 - 84}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Wavelength rerouting has been suggested as a viable and cost-effective method to improve the blocking performance of wavelength-routed Wavelength-Division Multiplexing (WDM) networks. This method leads to the following combinatorial optimization problem, dubbed Venetian Routing. Given a directed multigraph G along with two vertices s and t and a collection of pairwise arc-disjoint paths, we wish to find an st -path which arc-intersects the smallest possible number of such paths. In this paper we prove the computational hardness oft his problem even in various special cases, and present several approximation algorithms for its solution. In particular we show a non-trivial connection between Venetian Routing and Label Cover.}, isbn = {978-3-540-67996-7}, url = {http://dx.doi.org/10.1007/3-540-44436-X_9}, author = {Caprara,Alberto and Italiano,Giuseppe and Mohan,G. and Panconesi,Alessandro and Srinivasan, Aravind}, editor = {Jansen,Klaus and Khuller, Samir} } @conference {18761, title = {A web-based process/material advisory system}, year = {2000}, month = {2000///}, abstract = {This paper describes a web-based process/material advisorysystem that can be used during conceptual design. Given a set of design requirements for a part during conceptual design stage, our system produces process sequences that can meet the design requirements. Quite often during conceptual design stage, design requirements are not precisely defined. Therefore, we allow users to describe design requirements in terms of parameter ranges. Parameter ranges are used to capture uncertainties in design requirements. Our system accounts for uncertainties in design requirements in generating and evaluating process/material combinations. Our system uses a two step algorithm. During the first step, we generate a material/process option tree. This tree represents various process/material options that can be used to meet the given set of design requirements. During the second step, we evaluate various alternative process/material options using a depth first branch and bound algorithm to identify and recommend the least expensive process/material combination to the designer. Our system can be accessed on the World Wide Web using a standard browser. Our system allows designs to consider a wide variety of process/material options during the conceptual design stage and allows them to find the most cost-effective combination. By selecting the process/material combination during the early design stages, designers can ensure that the detailed design is compatible with all of the process constraints for the selected process. }, url = {http://www.mel.nist.gov/msidlibrary/doc/imece_feng.pdf}, author = {Chen,Y. S. and Gupta,S.K. and Feng,S.} } @article {16916, title = {1D, 2D, 3D}, journal = {Readings in information visualization}, year = {1999}, month = {1999///}, pages = {57 - 61}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @article {16958, title = {Alternate geometry}, journal = {Readings in information visualization}, year = {1999}, month = {1999///}, pages = {381 - 381}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @article {16977, title = {Applications and implications}, journal = {Readings in information visualization}, year = {1999}, month = {1999///}, pages = {625 - 635}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @article {16991, title = {Bifocal lens}, journal = {Readings in information visualization}, year = {1999}, month = {1999///}, pages = {331 - 332}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @conference {18666, title = {Building dependable distributed applications using AQUA}, year = {1999}, month = {1999///}, pages = {189 - 196}, abstract = {Building dependable distributed systems using ad hoc methods is a challenging task. Without proper support, an application programmer must face the daunting requirement of having to provide fault tolerance at the application level, in addition to dealing with the complexities of the distributed application itself. This approach requires a deep knowledge of fault tolerance on the part of the application designer, and has a high implementation cost. What is needed is a systematic approach to providing dependability to distributed applications. Proteus, part of the AQuA architecture, fills this need and provides facilities to make a standard distributed CORBA application dependable, with minimal changes to an application. Furthermore, it permits applications to specify, either directly or via the Quality Objects (QuO) infrastructure, the level of dependability they expect of a remote object, and will attempt to configure the system to achieve the requested dependability level. Our previous papers have focused on the architecture and implementation of Proteus. This paper describes how to construct dependable applications using the AQuA architecture, by describing the interface that a programmer is presented with and the graphical monitoring facilities that it provides}, keywords = {ad hoc methods, application programmer, AQuA, complexities, computational complexity, dependable distributed applications, distributed CORBA application, distributed object management, Fault tolerance, fault tolerant computing, proteus}, doi = {10.1109/HASE.1999.809494}, author = {Ren,J. and Michel Cukier and Rubel,P. and Sanders,W. H. and Bakken,D. E. and Karr,D. A.} } @conference {18639, title = {Building dependable distributed objects with the AQuA architecture}, year = {1999}, month = {1999///}, pages = {17 - 18}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.16.2819\&rep=rep1\&type=pdf}, author = {Michel Cukier and Ren,J. and Rubel,P. and Bakken,D. E. and Karr,D. A.} } @book {13528, title = {Content-Based Access to Multimedia Information: From Technology Trends to Sate of the Art}, year = {1999}, month = {1999///}, publisher = {Kluwer}, organization = {Kluwer}, author = {Perry,B. and Chang,S-K. and Dinsmore,J. and David Doermann and Rosenfeld, A. and Stevens,S.} } @article {18668, title = {Coverage estimation methods for stratified fault-injection}, journal = {Computers, IEEE Transactions on}, volume = {48}, year = {1999}, month = {1999/07//}, pages = {707 - 723}, abstract = {This paper addresses the problem of estimating fault tolerance coverage through statistical processing of observations collected in fault-injection experiments. In an earlier paper, venous estimators based on simple sampling in the complete fault/activity input space and stratified sampling in a partitioned space were studied; frequentist confidence limits were derived based on a normal approximation. In this paper, the validity of this approximation is analyzed. The theory of confidence regions is introduced to estimate coverage without approximation when stratification is used. Three statistics are considered for defining confidence regions. It is shown that one-a vectorial statistic-is often more conservative than the other two. However, only the vectorial statistic is computationally tractable. We then consider Bayesian estimation methods for stratified sampling. Two methods are presented to obtain an approximation of the posterior distribution of the coverage by calculating its moments. The moments are then used to identify the type of the distribution in the Pearson distribution system, to estimate its parameters, and to obtain the coverage confidence limit. Three hypothetical example systems are used to compare the validity and the conservatism of the frequentist and Bayesian estimations}, keywords = {Bayes methods, Bayesian estimations, confidence regions, coverage estimation methods, fault tolerance coverage, fault tolerant computing, frequentist confidence limits, parameter estimation, parameters estimation, Pearson distribution system, statistical processing, stratified fault-injection, stratified sampling, vectorial statistic}, isbn = {0018-9340}, doi = {10.1109/12.780878}, author = {Michel Cukier and Powell,D. and Ariat,J.} } @article {17055, title = {Departments-Book Preview-Readings in Information Visualization: Using Vision to Think}, journal = {Interactions}, volume = {6}, year = {1999}, month = {1999///}, pages = {51 - 51}, author = {Card,S.K. and Mackinlay,J. and Shneiderman, Ben} } @inbook {17100, title = {Dynamic queries}, booktitle = {Readings in information visualizationReadings in information visualization}, year = {1999}, month = {1999///}, pages = {235 - 235}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @article {12767, title = {On the evolution of reactive components: A process-algebraic approach}, journal = {Lecture notes in computer science}, year = {1999}, month = {1999///}, pages = {161 - 175}, author = {M\{\"u}ller-Olm,M. and Steffen,B. and Cleaveland, Rance} } @conference {18672, title = {Fault injection based on a partial view of the global state of a distributed system}, year = {1999}, month = {1999///}, pages = {168 - 177}, abstract = {This paper describes the basis for and preliminary implementation of a new fault injector, called Loki, developed specifically for distributed systems. Loki addresses issues related to injecting correlated faults in distributed systems. In Loki, fault injection is performed based on a partial view of the global state of an application. In particular, facilities are provided to pass user-specified state information between nodes to provide a partial view of the global state in order to try to inject complex faults successfully. A post-runtime analysis, using an off-line clock synchronization and a bounding technique, is used to place events and injections on a single global time-line and determine whether the intended faults were properly injected. Finally, observations containing successful fault injections are used to estimate specified dependability measures. In addition to describing the details of our new approach, we present experimental results obtained from a preliminary implementation in order to illustrate Loki{\textquoteright}s ability to inject complex faults predictably}, keywords = {bounding technique, clock synchronization, distributed programming, distributed software systems, fault injection, Loki, post-runtime analysis, program testing, program verification, software reliability, Synchronisation}, doi = {10.1109/RELDIS.1999.805093}, author = {Michel Cukier and Chandra,R. and Henke,D. and Pistole,J. and Sanders,W. H.} } @inbook {17170, title = {Fisheye views}, booktitle = {Readings in information visualizationReadings in information visualization}, year = {1999}, month = {1999///}, pages = {311 - 311}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @inbook {17172, title = {Focus+ context}, booktitle = {Readings in information visualizationReadings in information visualization}, year = {1999}, month = {1999///}, pages = {306 - 309}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @article {12999, title = {Genes and other samples of DNA sequence data for phylogenetic inference}, journal = {The Biological Bulletin}, volume = {196}, year = {1999}, month = {1999/06//}, pages = {345 - 350}, author = {Cummings, Michael P. and Otto,S. P and Wakeley,J.} } @article {18704, title = {Impact of Cl- and Na+ ions on simulated structure and dynamics of βARK1 PH domain}, journal = {Proteins: Structure, Function, and Bioinformatics}, volume = {35}, year = {1999}, month = {1999///}, pages = {206 - 217}, abstract = {A nonzero net charge of proteins at pH 7 is usually compensated by the addition of charge-balancing counter ions during molecular dynamics simulation, which reduces electrostatic interactions. For highly charged proteins, like the βARK1 PH domain used here, it seems reasonable to also add explicit salt ions. To assess the impact of explicit salt ions, two molecular dynamics simulations of solvated βARK1 PH domain have been carried out with different numbers of Cl- and Na+ ions, based on the Cornell et al. force field and the Ewald summation, which was used in the treatment of long-range electrostatic interactions. Initial positions of ions were obtained from the AMBER CION program. Increasing the number of ions alters the average structure in loop regions, as well as the fluctuation amplitudes of dihedral angles. We found unnaturally strong interactions between side chains in the absence of salt ions. The presence of salt ions reduces these electrostatic interactions. The time needed for the equilibration of the ionic environment around the protein, after initial placement of ions close to oppositely charged side chains, is in the nanosecond time range, which can be shortened by using a higher ionic strength. Our results also suggest selecting those methods that do not place the ions initially close to the protein surface. Proteins 1999;35:206{\textendash}217. {\textcopyright} 1999 Wiley-Liss, Inc.}, keywords = {counter ions, electrostatic interaction, equilibration, GRK2 PH domain, hydrogen bonds, ionic solvent, ionic strength, molecular dynamics simulation, Proteins}, isbn = {1097-0134}, doi = {10.1002/(SICI)1097-0134(19990501)35:2<206::AID-PROT7>3.0.CO;2-A}, url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0134(19990501)35:2<206::AID-PROT7>3.0.CO;2-A/abstract}, author = {Pfeiffer,Stefania and Fushman, David and Cowburn,David} } @article {17235, title = {Information workspaces}, journal = {Readings in information visualization}, year = {1999}, month = {1999///}, pages = {513 - 514}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @article {17236, title = {Infosphere, workspace, tools, objects}, journal = {Readings in information visualization}, year = {1999}, month = {1999///}, pages = {463 - 464}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @conference {17874, title = {Infrastructure for building parallel database systems for multi-dimensional data}, booktitle = {IPPS}, year = {1999}, month = {1999///}, pages = {582 - 582}, author = {Chang,C. and Ferreira,R. and Sussman, Alan and Saltz, J.} } @inbook {17245, title = {Interaction}, booktitle = {Readings in information visualizationReadings in information visualization}, year = {1999}, month = {1999///}, pages = {231 - 234}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco}, isbn = {1-55860-533-9}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @inbook {17246, title = {Interactive analysis}, booktitle = {Readings in information visualizationReadings in information visualization}, year = {1999}, month = {1999///}, pages = {261 - 262}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco}, isbn = {1-55860-533-9}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @inbook {17262, title = {Internet and Infosphere}, booktitle = {Readings in information visualizationReadings in information visualization}, year = {1999}, month = {1999///}, pages = {465 - 468}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco}, isbn = {1-55860-533-9}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @inbook {15765, title = {Latent Semantic Indexing via a Semi-Discrete Matrix Decomposition}, booktitle = {The Mathematics of Information Coding, Extraction and DistributionThe Mathematics of Information Coding, Extraction and Distribution}, year = {1999}, month = {1999///}, pages = {73 - 80}, publisher = {Springer-Verlag IMA Volumes in Math. and Its Applics.}, organization = {Springer-Verlag IMA Volumes in Math. and Its Applics.}, address = {New York}, abstract = {With the electronic storage of documents comes the possibility of building search engines that can automatically choose documents relevant to a given set of topics. In information retrieval, we wish to match queries with relevant documents. Documents can be represented by the terms that appear within them, but literal matching of terms does not necessarily retrieve all relevant documents. There are a number of information retrieval systems based on inexact matches. Latent Semantic Indexing represents documents by approximations and tends to cluster documents on similar topics even if their term profiles are somewhat different. This approximate representation is usually accomplished using a low-rank singular value decomposition (SVD) approximation. In this paper, we use an alternate decomposition, the semi-discrete decomposition (SDD). For equal query times, the SDD does as well as the SVD and uses less than one-tenth the storage for the MEDLINE test set.}, author = {Kolda,Tamara G. and O{\textquoteright}Leary, Dianne P.}, editor = {Cybenko,George and O{\textquoteright}Leary, Dianne P. and Rissanen,Jorma} } @article {12779, title = {Local model checking and protocol analysis}, journal = {International Journal on Software Tools for Technology Transfer (STTT)}, volume = {2}, year = {1999}, month = {1999///}, pages = {219 - 241}, author = {Du,X. and Smolka,S. A and Cleaveland, Rance} } @conference {17302, title = {Multiple dimensions> 3}, booktitle = {Readings in information visualization}, year = {1999}, month = {1999///}, pages = {93 - 95}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco}, isbn = {1-55860-533-9}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @inbook {14712, title = {Network Programming Using PLAN}, booktitle = {Internet Programming LanguagesInternet Programming Languages}, series = {Lecture Notes in Computer Science}, volume = {1686}, year = {1999}, month = {1999///}, pages = {127 - 143}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present here a methodology for programming active networks in the environment defined by our new language PLAN (Packet Language for Active Networks). This environment presumes a two-level architecture consisting of: 1. active packets carrying PLAN code; and 2. downloadable, node-resident services written in more general-purpose languages. We present several examples which illustrate how these two features can be combined to implement various network functions.}, isbn = {978-3-540-66673-8}, url = {http://dx.doi.org/10.1007/3-540-47959-7_7}, author = {Hicks, Michael W. and Kakkar,Pankaj and Moore,Jonathan and Gunter,Carl and Nettles,Scott}, editor = {Bal,Henri and Belkhouche,Boumediene and Cardelli,Luca} } @article {17855, title = {Object-relational queries into multidimensional databases with the active data repository}, journal = {Parallel Processing Letters}, volume = {9}, year = {1999}, month = {1999///}, pages = {173 - 195}, author = {Ferreira,R. and Kurc, T. and Beynon, M. and Chang,C. and Sussman, Alan and Saltz,J. H} } @inbook {17317, title = {Overview+ detail}, booktitle = {Readings in information visualizationReadings in information visualization}, year = {1999}, month = {1999///}, pages = {285 - 286}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @conference {17323, title = {Physical data}, booktitle = {Readings in information visualization}, year = {1999}, month = {1999///}, pages = {37 - 38}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco}, isbn = {1-55860-533-9}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @article {12790, title = {A practical approach to implementing real-time semantics}, journal = {Annals of Software Engineering}, volume = {7}, year = {1999}, month = {1999///}, pages = {127 - 155}, author = {Bhat,G. and Cleaveland, Rance and L\{\"u}ttgen,G.} } @book {15334, title = {A Priori Test of SGS Models in Compressible Turbulence}, year = {1999}, month = {1999///}, publisher = {Army High Performance Computing Research Center}, organization = {Army High Performance Computing Research Center}, author = {Martin, M.P and Piomelli,U. and Candler,G. V and Center,Army High Performance Computing Research and Minnesota,University of} } @conference {18689, title = {Proteus: a flexible infrastructure to implement adaptive fault tolerance in AQuA}, year = {1999}, month = {1999/11//}, pages = {149 - 168}, abstract = {Building dependable distributed systems from commercial off-the-shelf components is of growing practical importance. For both cost and production reasons, there is interest in approaches and architectures that facilitate building such systems. The AQuA architecture is one such approach; its goal is to provide adaptive fault tolerance to CORBA applications by replicating objects, providing a high-level method for applications to specify their desired dependability, and providing a dependability manager that attempts to reconfigure a system at runtime so that dependability requests are satisfied. This paper describes how dependability is provided in AQuA. In particular it describes Proteus, the part of AQuA that dynamically manages replicated distributed objects to make them dependable. Given a dependability request, Proteus chooses a fault tolerance approach and reconfigures the system to try to meet the request. The infrastructure of Proteus is described in this paper, along with its use in implementing active replication and a simple dependability policy}, keywords = {adaptive fault tolerance, AQuA, commercial off-the-shelf components, CORBA applications, cost, dependable distributed systems, distributed object management, object replication, proteus, reconfigurable architectures, Runtime, Software architecture, software fault tolerance}, doi = {10.1109/DCFTS.1999.814294}, author = {Sabnis,C. and Michel Cukier and Ren,J. and Rubel,P. and Sanders,W. H. and Bakken,D. E. and Karr,D.} } @conference {17871, title = {Querying Very Large Multi-dimensional Datasets in ADR}, booktitle = {In Proceedings of SC99: High Performance Networking and Computing}, year = {1999}, month = {1999///}, author = {Chialin,T. K and Kurc, T. and Chang,C. and Ferreira,R. and Sussman, Alan and Saltz, J.} } @book {17339, title = {Readings in Information Visualization: Using Vision to Think}, year = {1999}, month = {1999/01/25/}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, abstract = {This groundbreaking book defines the emerging field of information visualization and offers the first-ever collection of the classic papers of the discipline, with introductions and analytical discussions of each topic and paper. The authors{\textquoteright} intention is to present papers that focus on the use of visualization to discover relationships, using interactive graphics to amplify thought. This book is intended for research professionals in academia and industry; new graduate students and professors who want to begin work in this burgeoning field; professionals involved in financial data analysis, statistics, and information design; scientific data managers; and professionals involved in medical, bioinformatics, and other areas.* Full-color reproduction throughout* Author power team - an exciting and timely collaboration between the field{\textquoteright}s pioneering, most-respected names* The only book on Information Visualization with the depth necessary for use as a text or as a reference for the information professional* Text includes the classic source papers as well as a collection of cutting edge work}, keywords = {Computer Graphics, Computers / Computer Engineering, Computers / Computer Graphics, Computers / Computer Graphics / General, Computers / Computer Science, Computers / General, Computers / Information Technology, Computers / Information Theory, Computers / Intelligence (AI) \& Semantics, Computers / Social Aspects / Human-Computer Interaction, IMAGE PROCESSING, Information display systems, Information Visualization, Psychology / General, Visualization}, isbn = {9781558605336}, author = {Card,Stuart K. and Mackinlay,Jock D. and Shneiderman, Ben} } @article {13465, title = {Reports on the AAAI Fall Symposia}, journal = {AI Magazine}, volume = {20}, year = {1999}, month = {1999/09/15/}, pages = {87 - 87}, abstract = {The Association for the Advancement of Artificial Intelligence (AAAI) held its 1998 Fall Symposium Series on 23 to 25 October at the Omni Rosen Hotel in Orlando, Florida. This article contains summaries of seven of the symposia that were conducted: (1) Cognitive Robotics; (2) Distributed, Continual Planning; (3) Emotional and Intelligent: The Tangled Knot of Cognition; (4) Integrated Planning for Autonomous Agent Architectures; (5) Planning with Partially Observable Markov Decision Processes; (6) Reasoning with Visual and Diagrammatic Representations; and (7) Robotics and Biology: Developing Connections.}, isbn = {0738-4602}, doi = {10.1609/aimag.v20i3.1470}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/1470}, author = {De Giacomo,Giuseppe and desJardins, Marie and Canamero,Dolores and Wasson,Glenn and Littman,Michael and Allwein,Gerard and Marriott,Kim and Meyer,Bernd and Webb,Barbara and Consi,Tom} } @book {19005, title = {The RNA World}, year = {1999}, month = {1999///}, publisher = {Cold Spring Harbor Laboratory Press}, organization = {Cold Spring Harbor Laboratory Press}, address = {Cold Spring Harbor, New York}, author = {Woodson,Sarah A. and Mount, Stephen M.}, editor = {Gesteland,Raymond F. and Cech,Thomas R. and Atkins,John F.} } @conference {18158, title = {A rotation, scale and translation resilient public watermark}, booktitle = {Acoustics, Speech, and Signal Processing, 1999. Proceedings., 1999 IEEE International Conference on}, volume = {4}, year = {1999}, month = {1999/03//}, pages = {2065 vol.4 - 2065 vol.4}, abstract = {Summary form only given. Watermarking algorithms that are robust to the common geometric transformations of rotation, scale and translation (RST) have been reported for cases in which the original unwatermarked content is available at the detector so as to allow the transformations to be inverted. However, for public watermarks the problem is significantly more difficult since there is no original content to register with. Two classes of solution have been proposed. The first embeds a registration pattern into the content while the second seeks to apply detection methods that are invariant to these geometric transformations. This paper describes a public watermarking method which is invariant (or bares a simple relation) to the common geometric transforms of rotation, scale, and translation. It is based on the Fourier-Mellin transform which has previously been suggested. We extend this work, using a variation based on the Radon transform. The watermark is inserted into a projection of the image. The properties of this projection are such that RST transforms produce simple or no effects on the projection waveform. When a watermark is inserted into a projection, the signal must eventually be back projected to the original image dimensions. This is a one to many mapping that allows for considerable flexibility in the watermark insertion process. We highlight some theoretical and practical issues that affect the implementation of an RST invariant watermark. Finally, we describe preliminary experimental results}, keywords = {algorithms;Fourier, coding;, coding;image, data;transform, dimensions;projection, Fourier-Mellin, image, invariant, methods;detector;experimental, of, pattern;rotation, projection;mapping;original, public, registration;security, resilient, results;geometric, transform;detection, transform;RST, transformations;image, transforms;image, transforms;Radon, watermark;RST, watermark;scale, watermark;translation, watermark;watermarking, waveform;registration}, doi = {10.1109/ICASSP.1999.758337}, author = {Wu,M. and Miller,M.L. and Bloom,J.A. and Cox,I.J.} } @article {18715, title = {Solution Structure of the Proapoptotic Molecule BID: A Structural Basis for Apoptotic Agonists and Antagonists}, journal = {Cell}, volume = {96}, year = {1999}, month = {1999/03/05/}, pages = {625 - 634}, abstract = {Members of the BCL2 family of proteins are key regulators of programmed cell death, acting either as apoptotic agonists or antagonists. Here we describe the solution structure of BID, presenting the structure of a proapoptotic BCL2 family member. An analysis of sequence/structure of BCL2 family members allows us to define a structural superfamily, which has implications for general mechanisms for regulating proapoptotic activity. It appears two criteria must be met for proapoptotic function within the BCL2 family: targeting of molecules to intracellular membranes, and exposure of the BH3 death domain. BID{\textquoteright}s activity is regulated by a Caspase 8{\textendash}mediated cleavage event, exposing the BH3 domain and significantly changing the surface charge and hydrophobicity, resulting in a change of cellular localization.}, isbn = {0092-8674}, doi = {10.1016/S0092-8674(00)80573-5}, url = {http://www.sciencedirect.com/science/article/pii/S0092867400805735}, author = {McDonnell,James M and Fushman, David and Milliman,Curt L. and Korsmeyer,Stanley J. and Cowburn,David} } @conference {12774, title = {Statecharts via process algebra}, booktitle = {CONCUR{\textquoteright}99: concurrency theory: 10th International Conference, Eindhoven, the Netherlands, August 24-27, 1999: proceedings}, year = {1999}, month = {1999///}, pages = {399 - 399}, author = {Liittgen,G. and Cleaveland, Rance} } @article {15354, title = {Subgrid-scale model for the temperature fluctuations in reacting hypersonic turbulent flows}, journal = {Physics of Fluids}, volume = {11}, year = {1999}, month = {1999///}, pages = {2765 - 2765}, author = {Martin, M.P and Candler,G. V} } @inbook {17399, title = {Text in 1D}, booktitle = {Readings in information visualizationReadings in information visualization}, year = {1999}, month = {1999///}, pages = {411 - 412}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco}, isbn = {1-55860-533-9}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @inbook {17400, title = {Text in 2D}, booktitle = {Readings in information visualizationReadings in information visualization}, year = {1999}, month = {1999///}, pages = {431 - 431}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco}, isbn = {1-55860-533-9}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @inbook {17401, title = {Text in 3D}, booktitle = {Readings in information visualizationReadings in information visualization}, year = {1999}, month = {1999///}, pages = {440 - 441}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco}, isbn = {1-55860-533-9}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @inbook {17402, title = {Text in 3D+ time}, booktitle = {Readings in information visualizationReadings in information visualization}, year = {1999}, month = {1999///}, pages = {451 - 451}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco}, isbn = {1-55860-533-9}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @article {12845, title = {A Theory of Efficiency for Markovian Processes}, journal = {University of Bologna}, year = {1999}, month = {1999///}, author = {Bernardo,M. and Cleaveland, Rance} } @article {17482, title = {Using vision to think}, journal = {Readings in information visualization: using vision to think}, year = {1999}, month = {1999///}, pages = {579 - 581}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @conference {17504, title = {Visually enhanced objects}, booktitle = {Readings in information visualization}, year = {1999}, month = {1999///}, pages = {561 - 561}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco}, isbn = {1-55860-533-9}, author = {Card,S.K. and Mackinlay,J.D. and Shneiderman, Ben} } @article {14181, title = {3D motion and shape representations in visual servo control}, journal = {The International Journal of Robotics Research}, volume = {17}, year = {1998}, month = {1998///}, pages = {4 - 4}, author = {Ferm{\"u}ller, Cornelia and Cheong, L. F and Aloimonos, J.} } @conference {15634, title = {Approximation algorithms for multiple-tool miling}, booktitle = {Proceedings of the fourteenth annual symposium on Computational geometry}, series = {SCG {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {297 - 306}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-973-4}, doi = {10.1145/276884.276918}, url = {http://doi.acm.org/10.1145/276884.276918}, author = {Arya,Sunil and Cheng,Siu-Wing and Mount, Dave} } @conference {18662, title = {AQuA: an adaptive architecture that provides dependable distributed objects}, booktitle = {Seventeenth IEEE Symposium on Reliable Distributed Systems}, year = {1998}, month = {1998/10//}, pages = {245 - 253}, abstract = {Dependable distributed systems are difficult to build. This is particularly true if they have dependability requirements that change during the execution of an application, and are built with commercial off-the-shelf hardware. In that case, fault tolerance must be achieved using middleware software, and mechanisms must be provided to communicate the dependability requirements of a distributed application to the system and to adapt the system{\textquoteright}s configuration to try to achieve the desired dependability. The AQuA architecture allows distributed applications to request a desired level of availability using the Quality Objects (QuO) framework and includes a dependability manager that attempts to meet requested availability levels by configuring the system in response to outside requests and changes in system resources due to faults. The AQuA architecture uses the QuO runtime to process and invoke availability requests, the Proteus dependability manager to configure the system in response to faults and availability requests, and the Ensemble protocol stack to provide group communication services. Furthermore, a CORBA interface is provided to application objects using the AQuA gateway. The gateway provides a mechanism to translate between process-level communication, as supported by Ensemble, and IIOP messages, understood by Object Request Brokers. Both active and passive replication are supported, and the replication type to use is chosen based on the performance and dependability requirements of particular distributed applications}, keywords = {adaptive architecture, AQuA, availability requests, client-server systems, commercial off-the-shelf hardware, CORBA, dependability manager, dependability requirements, dependable distributed objects, distributed object management, Ensemble protocol stack, Fault tolerance, group communication services, middleware software, Object Request Brokers, process-level communication, proteus, Quality Objects, replication, software fault tolerance, Software quality}, doi = {10.1109/RELDIS.1998.740506}, author = {Cukier, Michel and Ren,J. and Sabnis,C. and Henke,D. and Pistole,J. and Sanders,W. H. and Bakken,D. E. and Berman,M.E. and Karr,D. A. and Schantz,R.E.} } @article {16570, title = {Cellular automata models of self-replicating systems}, journal = {Advances in Computers}, volume = {47}, year = {1998}, month = {1998///}, pages = {141 - 183}, author = {Reggia, James A. and Chou,H. H. and Lohn,J. D} } @article {17864, title = {The design and evaluation of a high-performance earth science database}, journal = {Parallel Computing}, volume = {24}, year = {1998}, month = {1998/01//}, pages = {65 - 89}, abstract = {Earth scientists have encountered two major obstacles in their attempts to use remotely sensed imagery to analyze the earth{\textquoteright}s land cover dynamics. First, the volume of data involved is very large and second, significant preprocessing is needed before the data can be used. This is particularly so for studies that analyze global trends using data sets that cover multiple years. In this paper, we present the design of an earth science database as well as our early experiences with it. The primary design goal of this database is to facilitate efficient access to and preprocessing of large volumes of satellite data. Our initial design assumed that the main bottleneck in the system would be retrieving data from the disks. However, experimental results show that precise identification of all the data values corresponding to a query can take a significant amount of time. The problem is even more pronounced in designing the system to attempt to minimize time spent performing I/O. We therefore discuss a major redesign of the system that includes a reworking of the indexing scheme and a reorganization of the data on disks. Experimental results show that the redesigned system performs significantly better than the original system, providing interactive response times for local queries.}, keywords = {Communication, High-performance I/O, load balancing, scalability, Scientific databases}, isbn = {0167-8191}, doi = {10.1016/S0167-8191(97)00117-8}, url = {http://www.sciencedirect.com/science/article/pii/S0167819197001178}, author = {Shock,Carter T. and Chang,Chialin and Moon,Bongki and Acharya,Anurag and Davis, Larry S. and Saltz,Joel and Sussman, Alan} } @article {16183, title = {The Design of a Telepathology Workstation: Exploring Remote Images}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {Dynamic telepathology uses a tele-operated microscope to allowpathologists to view samples at a remote location. However, time delays introduced by remote operation have made use of a commercial dynamic telepathology system difficult and frustrating. This paper describes experiments to evaluate and redesign the user interface. We also make recomendations for further automation to support the pathology process and increase the usefulness of the system. Copyright, 1994, by David Carr, Catherine Plaisant, and Hiroaki Hasegawa All rights reserved (Also cross-referenced as CAR-TR-708) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/408}, author = {Carr,David and Plaisant, Catherine and Hasegawa,Hiroaki} } @article {16176, title = {Designing a real-time telepathology workstation to mitigate communication delays}, journal = {Interacting with Computers}, volume = {11}, year = {1998}, month = {1998/12/01/}, pages = {33 - 52}, abstract = {Dynamic telepathology uses a teleoperated microscope to allow pathologists to view samples at a remote location. However, time delays introduced by remote operation have made use of a commercial dynamic telepathology system difficult and frustrating. This paper describes the iterative redesign of the user interface. We redesigned the interface, conducted experiments to evaluate the improvements, and then redesigned the user interface based on the results.Our work shows that predictive displays and local maps improve user control of the microscope and increase user comfort with the system. It also indicates that some degree of automation is necessary to support the navigation process and increase the overall usefulness of the system. Therefore, we also make recommendations for further automation to support the telepathology process and increase the usefulness of the system. While performed on a specific device using a dedicated communications system, the same problems would be encountered in other environments. For example, Internet-based systems that enable remote control or require browsing of large images will need to compensate for time delays and can benefit from our experience with the telepathology application. }, keywords = {Iterative design, Predictive displays, Remote control, Supervisory control, Telepathology, Time delays}, isbn = {0953-5438}, doi = {10.1016/S0953-5438(98)00032-0}, url = {http://www.sciencedirect.com/science/article/pii/S0953543898000320}, author = {Carr,David and Plaisant, Catherine and Hasegawa,Hiroaki} } @article {14910, title = {Determining the similarity of deformable shapes}, journal = {Vision Research}, volume = {38}, year = {1998}, month = {1998/08//}, pages = {2365 - 2385}, abstract = {Determining the similarity of two shapes is a significant task in both machine and human vision systems that must recognize or classify objects. The exact properties of human shape similarity judgements are not well understood yet, and this task is particularly difficult in domains where the shapes are not related by rigid transformations. In this paper we identify a number of possibly desirable properties of a shape similarity method, and determine the extent to which these properties can be captured by approaches that compare local properties of the contours of the shapes, through elastic matching. Special attention is devoted to objects that possess articulations, i.e. articulated parts. Elastic matching evaluates the similarity of two shapes as the sum of local deformations needed to change one shape into another. We show that similarities of part structure can be captured by such an approach, without the explicit computation of part structure. This may be of importance, since although parts appear to play a significant role in visual recognition, it is difficult to stably determine part structure. We also show novel results about how one can evaluate smooth and polyhedral shapes with the same method. Finally, we describe shape similarity effects that cannot be handled by current approaches.}, isbn = {0042-6989}, doi = {10.1016/S0042-6989(98)00043-1}, url = {http://www.sciencedirect.com/science/article/pii/S0042698998000431}, author = {Basri,Ronen and Costa,Luiz and Geiger,Davi and Jacobs, David W.} } @conference {17832, title = {Digital dynamic telepathology{\textendash}the Virtual Microscope.}, booktitle = {Proceedings of the AMIA Symposium}, year = {1998}, month = {1998///}, pages = {912 - 912}, author = {Afework,A. and Beynon,M. D and Bustamante,F. and Cho,S. and Demarzo,A. and Ferreira,R. and Miller,R. and Silberman,M. and Saltz, J. and Sussman, Alan and others} } @article {17946, title = {Double quaternions for motion interpolation}, journal = {Proceedings of the ASME Design Engineering Technical Conference}, year = {1998}, month = {1998///}, abstract = {This paper describes the concept of double quaternions, anextension of quaternions, and shows how they can be used for ef- fective three-dimensional motion interpolation. Motion interpo- lation using double quaternions has several advantages over the method of interpolating rotation and translation independently and then combining the results. First, double quaternions pro- vide a conceptual framework that allows one to handle rotational and translational components in a unified manner. Second, re- sults obtained by using double quaternions are coordinate frame invariant. Third, double quaternions allow a natural way to trade- off robustness against accuracy. Fourth, double quaternions, be- ing a straightforward extension of quaternions, can be integrated into several existing systems that currently use quaternions with translational components, with a only small coding effort. }, author = {Ge,Q. J and Varshney, Amitabh and Menon,J. P and Chang,C. F} } @conference {14521, title = {Dynamics of bubbles in conditions of gas hydrate formation}, booktitle = {8th International Offshore and Polar Engineering Conference, Montreal, Canada}, year = {1998}, month = {1998///}, author = {Gumerov, Nail A. and Chahine,G. L} } @article {14215, title = {Effects of Errors in the Viewing Geometry on Shape Estimation}, journal = {Computer Vision and Image Understanding}, volume = {71}, year = {1998}, month = {1998/09//}, pages = {356 - 372}, abstract = {A sequence of images acquired by a moving sensor contains information about the three-dimensional motion of the sensor and the shape of the imaged scene. Interesting research during the past few years has attempted to characterize the errors that arise in computing 3D motion (egomotion estimation) as well as the errors that result in the estimation of the scene{\textquoteright}s structure (structure from motion). Previous research is characterized by the use of optic flow or correspondence of features in the analysis as well as by the employment of particular algorithms and models of the scene in recovering expressions for the resulting errors. This paper presents a geometric framework that characterizes the relationship between 3D motion and shape in the presence of errors. We examine how the three-dimensional space recovered by a moving monocular observer, whose 3D motion is estimated with some error, is distorted. We characterize the space of distortions by its level sets, that is, we characterize the systematic distortion via a family of iso-distortion surfaces, which describes the locus over which the depths of points in the scene in view are distorted by the same multiplicative factor. The framework introduced in this way has a number of applications: Since the visible surfaces have positive depth (visibility constraint), by analyzing the geometry of the regions where the distortion factor is negative, that is, where the visibility constraint is violated, we make explicit situations which are likely to give rise to ambiguities in motion estimation, independent of the algorithm used. We provide a uniqueness analysis for 3D motion analysis from normal flow. We study the constraints on egomotion, object motion, and depth for an independently moving object to be detectable by a moving observer, and we offer a quantitative account of the precision needed in an inertial sensor for accurate estimation of 3D motion.}, isbn = {1077-3142}, doi = {10.1006/cviu.1997.0649}, url = {http://www.sciencedirect.com/science/article/pii/S1077314297906494}, author = {LoongFah Cheong and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {11952, title = {Effects of Errors in the Viewing Geometry on Shape Estimation* 1,* 2}, journal = {Computer Vision and Image Understanding}, volume = {71}, year = {1998}, month = {1998///}, pages = {356 - 372}, author = {Cheong, L. F and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {13767, title = {Evaluation of EuroWordNet-and LCS-based lexical resources for machine translation}, journal = {Proceedings from First International Conference on Language Resources \& Evaluation}, year = {1998}, month = {1998///}, pages = {393 - 398}, abstract = {We evaluate two types of lexical resources with respect to their applicability to interlingual machine translation: (1) a EuroWordNet-based database of bilingual links between Spanish and English words; and (2) a repository of semantically classified verbs with their corresponding Lexical Conceptual Structure (LCS) representations. We examine the utility of these two resources for the task of lexical selection in machine translation. Our approach uses a coarse-grained graph-matching scheme that selects target-language words based on their LCS representation. The final selection of target-language terms is based on a finer-grained linking into the EuroWordNet-based repository. }, author = {Dorr, Bonnie J and Marti,A. and Castellon,I.} } @article {15367, title = {Extension of Spherical Harmonic Method to RF Transient Regime}, journal = {Simulation of semiconductor processes and devices 1998: SISPAD 98}, year = {1998}, month = {1998///}, pages = {42 - 42}, abstract = {The space and time dependent electron Boltzmann transport equation (BTE)is solved sclf-consistently with the Poisson and transient hole current-continuity equation. A transient Spherical Harmonic expansion method is used to solve the BTE. By this method we can efficiently solve the BTE in the RF regime to observe how the complete distribution function responds to a rapid transient. Calculations on a BJT, which give the time dependent distribution function over a large energy range 0-3eV, throughout the device, as well as average quantities, require only 40 minutes CPU time on an Alpha workstation. }, author = {Lin,C. K. and Goldsman,N. and Chang,C. H. and Mayergoyz, Issak D and Aronowitz,S. and Dong,J. and Belova,N.} } @article {18640, title = {Frequentist and Bayesian Coverage Estimations for Stratified Fault-Injection}, journal = {DEPENDABLE COMPUTING AND FAULT TOLERANT SYSTEMS}, volume = {11}, year = {1998}, month = {1998///}, pages = {43 - 62}, abstract = {This paper addresses the problem of estimating the coverage of fault tolerancethrough statistical processing of observations collected in fault-injection experiments. In an earlier paper, we have studied various frequentist estimation methods based on simple sampling in the whole fault/activity input space and stratified sampling in a partitioned space. In this paper, Bayesian estimation methods are introduced for stratified sampling. Two methods are presented to obtain an approximation of the posterior distribution of the coverage by calculating its moments. The moments are then used to identify the type of the distribution in the Pearson distribution system, to estimate its parameters and to obtain the coverage confidence limit. Two hypothetical example systems are used to compare the validity and the conservatism of the Bayesian and frequentist estimations. It is shown that one Bayesian estimation method is valid for both examples and that its estimations are much less conservative than the frequentist ones. However, the Bayesian estimations for stratified sampling are still conservative compared to estimations for simple sampling. }, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.29.6784\&rep=rep1\&type=pdf}, author = {Michel Cukier and Arlat,J. and Powell,D.} } @article {20053, title = {Genetic nomenclature for Trypanosoma and Leishmania.}, journal = {Mol Biochem Parasitol}, volume = {97}, year = {1998}, month = {1998 Nov 30}, pages = {221-4}, keywords = {Animals, Leishmania, Terminology as Topic, Trypanosoma}, issn = {0166-6851}, author = {Clayton, C and Adams, M and Almeida, R and Baltz, T and Barrett, M and Bastien, P and Belli, S and Beverley, S and Biteau, N and Blackwell, J and Blaineau, C and Boshart, M and Bringaud, F and Cross, G and Cruz, A and Degrave, W and Donelson, J and El-Sayed, N and Fu, G and Ersfeld, K and Gibson, W and Gull, K and Ivens, A and Kelly, J and Vanhamme, L} } @article {14102, title = {Genetic nomenclature for Trypanosoma and Leishmania.}, journal = {Molecular and biochemical parasitology}, volume = {97}, year = {1998}, month = {1998///}, pages = {221 - 221}, author = {Clayton,C. and Adams,M. and Almeida,R. and Baltz,T. and Barrett,M. and Bastien,P. and Belli,S. and Beverley,S. and Biteau,N. and Blackwell,J. and others} } @conference {12781, title = {Infinite Probabilistic and Nonprobabilistic Testing*}, booktitle = {Foundations of software technology and theoretical computer science: 18th Conference, Chennai, India, December 17-19, 1998: proceedings}, year = {1998}, month = {1998///}, pages = {209 - 209}, author = {Kumar,K. N and Cleaveland, Rance and Smolka,S. A} } @inbook {17618, title = {Low-bandwidth routing and electrical power networks}, booktitle = {Automata, Languages and ProgrammingAutomata, Languages and Programming}, series = {Lecture Notes in Computer Science}, volume = {1443}, year = {1998}, month = {1998///}, pages = {604 - 615}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Given a graph G and a (multi-)set of pairs of vertices in it, the classical NP-hard maximum edge-disjoint-paths problem (MDP) is to connect as many of the given pairs as possible using pairwise edge-disjoint paths in G . We study a relative of this problem: we have a network with fixed link capacities that may have to service large demands when necessary. In particular, individual demands are allowed to exceed capacities, and thus flows for some request pairs necessarily have to be split into different flow-paths. This is the framework for computational problems arising from: (i) electrical power networks due to the proposed deregulation of the electric utility industry in the USA, and (ii) applications such as real-time Internet services (e.g., telephone, fax, video). We show that these problems come in a few variants, some efficiently solvable and many NP -hard; we also present approximation algorithms for many of the NP -hard variants presented. Some of our approximation algorithms benefit from certain improved tail estimates that we derive; the latter also yield improved approximations for a family of packing integer programs.}, isbn = {978-3-540-64781-2}, url = {http://dx.doi.org/10.1007/BFb0055088}, author = {Cook,Doug and Faber,Vance and Marathe,Madhav and Srinivasan, Aravind and Sussmann,Yoram}, editor = {Larsen,Kim and Skyum,Sven and Winskel,Glynn} } @article {13008, title = {Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley ({\i}t Hordeum vulgare ssp. {\i}t spontaneum): an evaluation of the background selection hypothesis}, journal = {Proc Natl Acad Sci USA}, volume = {95}, year = {1998}, month = {1998/05//}, pages = {5637 - 5642}, abstract = {The background selection hypothesis predicts a reduction in nucleotide site diversity and an excess of rare variants, owing to linkage associations with deleterious alleles. This effect is expected to be amplified in species that are predominantly self-fertilizing. To examine the predictions of the background selection hypothesis in self-fertilizing species, we sequenced 1,362 bp of adh1, a gene for alcohol dehydrogenase (Adh; alcohol:NAD+ oxidoreductase, EC 1.1.1.1), in a sample of 45 accessions of wild barley, Hordeum vulgare ssp. spontaneum, drawn from throughout the species range. The region sequenced included 786 bp of exon sequence (part of exon 4, all of exons 5-9, and part of exon 10) and 576 bp of intron sequence (all of introns 4-9). There were 19 sites polymorphic for nucleotide substitutions, 8 in introns, and 11 in exons. Of the 11 nucleotide substitutions in codons, 4 were synonymous and 7 were nonsynonymous, occurring uniquely in the sample. There was no evidence of recombination in the region studied, and the estimated effective population size (Ne) based on synonymous sites was approximately 1.8-4.2 x 10(5). Several tests reveal that the pattern of nonsynonymous substitutions departs significantly from neutral expectations. However, the data do not appear to be consistent with recovery from a population bottleneck, recent population expansion, selective sweep, or strong positive selection. Though several features of the data are consistent with background selection, the distributions of polymorphic synonymous and intron sites are not perturbed toward a significant excess of rare alleles as would be predicted by background selection.}, author = {Cummings, Michael P. and Clegg,M. T} } @article {13013, title = {Phylogenetic relationships of platyhelminthes based on 18S ribosomal gene sequences}, journal = {Mol Phylogenet Evol}, volume = {10}, year = {1998}, month = {1998/08//}, pages = {1 - 10}, abstract = {Nucleotide sequences of 18S ribosomal RNA from 71 species of Platyhelminthes, the flatworms, were analyzed using maximum likelihood, and the resulting phylogenetic trees were compared with previous phylogenetic hypotheses. Analyses including 15 outgroup species belonging to eight other phyla show that Platyhelminthes are monophyletic with the exception of a sequence putatively from Acoela sp., Lecithoepitheliata, Polycladida, Tricladida, Trematoda (Aspidobothrii + Digenea), Monogenea, and Cestoda (Gyrocotylidea + Amphilinidea + Eucestoda) are monophyletic groups. Catenulids form the sister group to the rest of platyhelminths, whereas a complex clade formed by Acoela, Tricladida, "Dalyellioida", and perhaps "Typhloplanoida" is sister to Neodermata. "Typhloplanoida" does not appear to be monophyletic; Fecampiida does not appear to belong within "Dalyellioida," nor Kalyptorhynchia within "Typhloplanoida." Trematoda is the sister group to the rest of Neodermata, and Monogenea is sister group to Cestoda. Within Trematoda, Aspidobothrii is the sister group of Digenea and Heronimidae is the most basal family in Digenea. Our trees support the hypothesis that parasitism evolved at least twice in Platyhelminthes, once in the ancestor to Neodermata and again in the ancestor of Fecampiida, independently to the ancestor of putatively parasitic "Dalyellioida."}, doi = {10.1006/mpev.1997.0483}, author = {Campos,A. and Cummings, Michael P. and Reyes,J. L and Laclette,J. P} } @article {13014, title = {Pigment composition of putatively achlorophyllous angiosperms}, journal = {Plant Syst Evol}, volume = {210}, year = {1998}, month = {1998///}, pages = {105 - 111}, abstract = {Chlorophyll and carotenoid pigment composition was determined for ten species of putatively achlorophyllous angiosperms using high-performance liquid chromatography. Four families were represented: Lennoaceae (Pholisma arenarium); Monotropaceae (Allotropa virgata, Monotropa uniflora, Pterospora andromedea, Sarcodes sanguinea); Orobanchaceae (Epifagus virginiana, Orobanche cooperi, O. uniflora); Orchidaceae (Cephalanthera austinae, Corallorhiza maculata). Chlorophyll a was detected in all tars, but chlorophyll b was only detected in Corallorhiza maculata. The relative amount of chlorophyll and chlorophyll-related pigments in these plants is greatly reduced compared to fully autotrophic angiosperms.}, keywords = {Angiospermae, Lennoaceae, Monotropaceae, Orchidaceae; Lennoaceae; Monotropaceae; Orobanchaceae; Orchidaceae; chlorophyll; carotenoid; pigment; high-performance liquid chromatography, Orobanchaceae}, author = {Cummings, Michael P. and Welschmeyer,N. A} } @article {12778, title = {Probabilistic resource failure in real-time process algebra}, journal = {CONCUR{\textquoteright}98 Concurrency Theory}, year = {1998}, month = {1998///}, pages = {465 - 472}, author = {Philippou,A. and Cleaveland, Rance and Lee,I. and Smolka,S. and Sokolsky,O.} } @article {16609, title = {Problem solving during artificial selection of self-replicating loops* 1}, journal = {Physica D: Nonlinear Phenomena}, volume = {115}, year = {1998}, month = {1998///}, pages = {293 - 312}, author = {Chou,H. H. and Reggia, James A.} } @article {15021, title = {Scalable Data Parallel Algorithms for Texture Synthesis and Compression using Gibbs Random Fields}, volume = {UMIACS-TR-93-80}, year = {1998}, month = {1998/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This paper introduces scalable data parallel algorithms for image processing. Focusing on Gibbs and Markov Random Field model representation for textures, we present parallel algorithms for texture synthesis, compression, and maximum likelihood parameter estimation, currently implemented on Thinking Machines CM-2 and CM-5. Use of fine-grained, data parallel processing techniques yields real-time algorithms for texture synthesis and compression that are substantially faster than the previously known sequential implementations. Although current implementations are on Connection Machines, the methodology presented here enables machine independent scalable algorithms for a number of problems in image processing and analysis. (Also cross-referenced as UMIACS-TR-93-80.) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/596}, author = {Bader,David A. and JaJa, Joseph F. and Chellapa, Rama} } @article {11919, title = {Scheduling Aperiodic and Sporadic Tasks in Hard Real-Time Systems}, journal = {Technical Reports from UMIACS, UMIACS-TR-97-44}, year = {1998}, month = {1998/10/15/}, abstract = {The stringent timing constraints as well as the functional correctnessare essential requirements of hard real-time systems. In such systems, scheduling plays a very important role in satisfying these constraints. The priority based scheduling schemes have been used commonly due to the simplicity of the scheduling algorithm. However, in the presence of task interdependencies and complex timing constraints, such scheduling schemes may not be appropriate due to the lack of an efficient mechanism to schedule them and to carry out the schedulability analysis. In contrast, the time based scheduling scheme may be used to schedule a set of tasks with greater degree of schedulability achieved at a cost of higher complexity of off-line scheduling. One of the drawbacks of currently available scheduling schemes, however, is known to be their inflexibility in dynamic environments where dynamic processes exist, such as aperiodic and sporadic processes. We develop and analyze scheduling schemes which efficiently provide the flexibility required in real-time systems for scheduling processes arriving dynamically. This enables static hard periodic processes and dynamic processes(aperiodic or sporadic) to be jointly scheduled. (Also cross-referenced as UMIACS-TR-97-44) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/900}, author = {Choi,Seonho and Agrawala, Ashok K.} } @article {16627, title = {Self-replicating structures: evolution, emergence, and computation}, journal = {Artificial Life}, volume = {4}, year = {1998}, month = {1998///}, pages = {283 - 302}, author = {Reggia, James A. and Lohn,J. D and Chou,H. H.} } @article {18714, title = {Solution structure and dynamics of the bioactive retroviral M domain from rous sarcoma virus}, journal = {Journal of Molecular Biology}, volume = {279}, year = {1998}, month = {1998/06/19/}, pages = {921 - 928}, abstract = {A biologically active construct of the retroviral M domain from the avian Rous sarcoma virus is defined and its solution structure described. This M domain is fully active in budding and infectivity without myristylation. In spite of a sequence homology level that suggests no relationship among M domains and the family of matrix proteins in mammalian retroviruses, the conserved structural elements of a central core allow an M domain sequence motif to be described for all retroviruses. The surface of the M domain has a highly clustered positive patch comprised of sequentially distant residues. An analysis of the backbone dynamics, incorporating rotational anisotropy, is used to estimate the thermodynamics of proposed domain oligomerization.}, keywords = {heteronuclear NMR spectroscopy, protein dynamics, RSV matrix protein, sequence homology, three-dimensional structure}, isbn = {0022-2836}, doi = {10.1006/jmbi.1998.1788}, url = {http://www.sciencedirect.com/science/article/pii/S0022283698917880}, author = {McDonnell,James M and Fushman, David and Cahill,Sean M. and Zhou,Wenjun and Wolven,Amy and Wilson,Carol B and Nelle,Timothy D and Resh,Marilyn D and Wills,John and Cowburn,David} } @article {18723, title = {The Solution Structure and Dynamics of the Pleckstrin Homology Domain of G Protein-coupled Receptor Kinase 2 (β-Adrenergic Receptor Kinase 1) A BINDING PARTNER OF Gβγ SUBUNITS}, journal = {Journal of Biological ChemistryJ. Biol. Chem.}, volume = {273}, year = {1998}, month = {1998/01/30/}, pages = {2835 - 2843}, abstract = {The solution structure of an extended pleckstrin homology (PH) domain from the β-adrenergic receptor kinase is obtained by high resolution NMR. The structure establishes that the β-adrenergic receptor kinase extended PH domain has the same fold and topology as other PH domains, and there are several unique features, most notably an extended C-terminal α-helix that behaves as a molten helix, and a surface charge polarity that is extensively modified by positive residues in the extended α-helix and the C terminus. These observations complement biochemical evidence that the C-terminal portion of this PH domain participates in protein-protein interactions with Gβγ subunits. This suggests that the C-terminal segment of the PH domain may function to mediate protein-protein interactions with the targets of PH domains.}, isbn = {0021-9258, 1083-351X}, doi = {10.1074/jbc.273.5.2835}, url = {http://www.jbc.org/content/273/5/2835}, author = {Fushman, David and Najmabadi-Haske,Taraneh and Cahill,Sean and Zheng,Jie and LeVine,Harry and Cowburn,David} } @article {17375, title = {Sorting out searching: a user-interface framework for text searches}, journal = {Communications of the ACM}, volume = {41}, year = {1998}, month = {1998/04//}, pages = {95 - 98}, isbn = {0001-0782}, doi = {10.1145/273035.273069}, url = {http://doi.acm.org/10.1145/273035.273069}, author = {Shneiderman, Ben and Byrd,Donald and Croft,W. Bruce} } @article {17833, title = {T2}, journal = {ACM SIGMOD Record}, volume = {27}, year = {1998}, month = {1998/03/01/}, pages = {58 - 66}, isbn = {01635808}, doi = {10.1145/273244.273264}, url = {http://dl.acm.org/citation.cfm?id=273264}, author = {Chang,Chialin and Acharya,Anurag and Sussman, Alan and Saltz,Joel} } @book {13028, title = {Trends in the Early Careers of Life Scientists}, year = {1998}, month = {1998///}, publisher = {National Academy Press}, organization = {National Academy Press}, address = {Washington, DC}, author = {Tilghman,S and Astin,HS and Brinkley,W and Chilton,MD and Cummings, Michael P. and Ehrenberg,RG and Fox,MF and Glenn,K and Green,PJ and Hans,S and Kelman,A and LaPidus,J and Levin,B and McIntosh,JR and Riecken,H and Stephen,PE} } @article {13029, title = {Trends in the early careers of life scientists - Preface and executive summary}, journal = {Mol Biol Cell}, volume = {9}, year = {1998}, month = {1998/11//}, pages = {3007 - 3015}, author = {Tilghman,S and Astin,HS and Brinkley,W and Chilton,MD and Cummings, Michael P. and Ehrenberg,RG and Fox,MF and Glenn,K and Green,PJ and Hans,S and Kelman,A and LaPidus,J and Levin,B and McIntosh,JR and Riecken,H and Stephen,PE} } @conference {14468, title = {Utility elicitation as a classification problem}, booktitle = {Proceedings of the Fourteenth conference on Uncertainty in artificial intelligence}, series = {UAI{\textquoteright}98}, year = {1998}, month = {1998///}, pages = {79 - 88}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco, CA, USA}, abstract = {We investigate the application of classification techniques to utility elicitation. In a decision problem, two sets of parameters must generally be elicited: the probabilities and the utilities. While the prior and conditional probabilities in the model do not change from user to user, the utility models do. Thus it is necessary to elicit a utility model separately for each new user. Elicitation is long and tedious, particularly if the outcome space is large and not decomposable. There are two common approaches to utility function elicitation. The first is to base the determination of the user{\textquoteright}s utility function solely on elicitation of qualitative preferences. The second makes assumptions about the form and decomposability of the utility function. Here we take a different approach: we attempt to identify the new user{\textquoteright}s utility function based on classification relative to a database of previously collected utility functions. We do this by identifying clusters of utility functions that minimize an appropriate distance measure. Having identified the clusters, we develop a classification scheme that requires many fewer and simpler assessments than full utility elicitation and is more robust than utility elicitation based solely on preferences. We have tested our algorithm on a small database of utility functions in a prenatal diagnosis domain and the results are quite promising.}, isbn = {1-55860-555-X}, url = {http://dl.acm.org/citation.cfm?id=2074094.2074104}, author = {Chajewska,Urszula and Getoor, Lise and Norman,Joseph and Shahar,Yuval} } @article {17914, title = {Walkthroughs of complex environments using image-based simplification}, journal = {Computers \& Graphics}, volume = {22}, year = {1998}, month = {1998/02/25/}, pages = {55 - 69}, abstract = {We present an image-based technique to accelerate the navigation in complex static environments. We perform an image-space simplification of each sample of the scene taken at a particular viewpoint and dynamically combine these simplified samples to produce images for arbitrary viewpoints. Since the scene is converted into a bounded complexity representation in the image space, with the base images rendered beforehand, the rendering speed is relatively insensitive to the complexity of the scene. The proposed method correctly simulates the kinetic depth effect (parallax), occlusion, and can resolve the missing visibility information. This paper describes a suitable representation for the samples, a specific technique for simplifying them, and different morphing methods for combining the sample information to reconstruct the scene. We use hardware texture mapping to implement the image-space warping and hardware affine transformations to compute the view-dependent warping function.}, keywords = {image-based rendering, image morphing, virtual walkthroughs, visibility, image compositing}, isbn = {0097-8493}, doi = {10.1016/S0097-8493(97)00083-6}, url = {http://www.sciencedirect.com/science/article/pii/S0097849397000836}, author = {Darsa,L. and Costa,B. and Varshney, Amitabh} } @conference {17269, title = {Is the Web really different from everything else?}, booktitle = {CHI 98 conference summary on Human factors in computing systems}, series = {CHI {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {92 - 93}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {design, user experience, World Wide Web}, isbn = {1-58113-028-7}, doi = {10.1145/286498.286545}, url = {http://doi.acm.org/10.1145/286498.286545}, author = {Shneiderman, Ben and Nielsen,Jakob and Butler,Scott and Levi,Michael and Conrad,Frederick} } @article {12771, title = {An algebraic theory of multiple clocks}, journal = {CONCUR{\textquoteright}97: Concurrency Theory}, year = {1997}, month = {1997///}, pages = {166 - 180}, author = {Cleaveland, Rance and L\{\"u}ttgen,G. and Mendler,M.} } @conference {16195, title = {Bringing treasures to the surface: iterative design for the Library of Congress National Digital Library Program}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, series = {CHI {\textquoteright}97}, year = {1997}, month = {1997///}, pages = {518 - 525}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {browse, design process, digital libraries, dynamic query, java, preview, search, web design}, isbn = {0-89791-802-9}, doi = {10.1145/258549.259009}, url = {http://doi.acm.org/10.1145/258549.259009}, author = {Plaisant, Catherine and Marchionini,Gary and Bruns,Tom and Komlodi,Anita and Campbell,Laura} } @conference {15693, title = {Challenges in sending large radiology images over military communications channels}, booktitle = {Proceedings of SPIE}, volume = {3035}, year = {1997}, month = {1997///}, pages = {230 - 230}, author = {Cleary,K.R. and Levine,B.A. and Norton,G.S. and Mundur,P.V.} } @article {17012, title = {Clarifying search: A user-interface framework for text searches}, journal = {D-lib magazine}, volume = {3}, year = {1997}, month = {1997///}, pages = {18 - 20}, abstract = {Current user interfaces for textual database searching leave much to be desired: individually, they are often confusing, and as a group, they are seriously inconsistent. We propose a four- phase framework for user-interface design: the framework provides common structure and terminology for searching while preserving the distinct features of individual collections and search mechanisms. Users will benefit from faster learning, increased comprehension, and better control, leading to more effective searches and higher satisfaction.}, author = {Shneiderman, Ben and Byrd,D. and Croft, W.B.} } @article {16549, title = {A computational model of acute focal cortical lesions}, journal = {Stroke}, volume = {28}, year = {1997}, month = {1997///}, pages = {101 - 101}, author = {Goodall,S. and Reggia, James A. and Chen,Y. and Ruppin,E. and Whitney,C.} } @conference {17048, title = {Data models, visual representations, metaphors: how to solve the puzzle? (panel)}, booktitle = {Proceedings of the third IFIP WG2.6 working conference on Visual database systems 3 (VDB-3)}, year = {1997}, month = {1997///}, pages = {177 - 182}, publisher = {Chapman \& Hall, Ltd.}, organization = {Chapman \& Hall, Ltd.}, address = {London, UK, UK}, keywords = {data model, metaphor, visual representation}, isbn = {0-412-72170-8}, url = {http://dl.acm.org/citation.cfm?id=265394.265440}, author = {Catarci,T. and Costabile,M. F. and Cruz,I. F. and Ioannidis,Y. and Shneiderman, Ben} } @article {12791, title = {Dynamic priorities for modeling real-time}, journal = {Proc. of the Formal Description Techniques and Protocol Specification, Testing and Verification (FORTE X/PSTV XVII{\textquoteright}97)}, year = {1997}, month = {1997///}, pages = {321 - 336}, author = {Bhat,G. and Cleaveland, Rance and L\{\"u}ttgen,G.} } @article {14473, title = {Effective redundant constraints for online scheduling}, journal = {PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE}, year = {1997}, month = {1997///}, pages = {302 - 307}, abstract = {The use of heuristics as a means to improve constraint solverperformance has been researched widely. However, most work has been on problem-independent heuristics (e.g., vari- able and value ordering), and has focused on offline prob- lems (e.g., one-shot constraint satisfaction). In this paper, we present an online scheduling problem for which we are developing a real-time scheduling algorithm. While we can and do use generic heuristics in the scheduler, here we fo- cus on the use of domain-specific redundant constraints to ef- fectively approximate optimal offline solutions. We present a taxonomy of redundant domain constraints, and examine their impact on the effectiveness of the scheduler. We also describe several techniques for generating redundant con- straints, which can be applied to a large class of job shop scheduling problems. }, author = {Getoor, Lise and Ottosson,G. and Fromherz,M. and Carlson,B.} } @article {16569, title = {Emergence of self-replicating structures in cellular automata space}, journal = {Physica D}, volume = {110}, year = {1997}, month = {1997///}, pages = {252 - 276}, author = {Reggia, James A. and Chou,H. H.} } @article {17934, title = {Enabling virtual reality for large-scale mechanical CAD datasets}, journal = {Proceedings of ASME Design Engineering Technical Conferences, Sept}, volume = {14}, year = {1997}, month = {1997///}, pages = {17 - 17}, abstract = {Reconciling scene realism with interactivity has emerged asone of the most important areas in making virtual reality fea- sible for large-scale mechanical CAD datasets consisting of sev- eral millions of primitives. This paper surveys our research and related work for achieving interactivity without sacrificing real- ism in virtual reality walkthroughs and flythroughs of polygonal CAD datasets. We outline our recent work on efficient genera- tion of triangle strips from polygonal models that takes advan- tage of compression of connectivity information. This results in substantial savings in rendering, transmission, and storage. We outline our work on genus-reducing simplifications as well as real-time view-dependent simplifications that allow on-the-fly selection amongst multiple levels of detail, based upon lighting and viewing parameters. Our method allows multiple levels of detail to coexist on the same object at different regions and to merge seamlessly without any cracks or shading artifacts. We also present an overview of our work on hardware-assisted image- based rendering that allows interactive exploration of computer- generated scenes. }, author = {Varshney, Amitabh and El-Sana,J. and Evans,F. and Darsa,L. and Costa,B. and Skiena,S.} } @article {13023, title = {The evolution of plant nuclear genes}, journal = {Proc Natl Acad Sci USA}, volume = {94}, year = {1997}, month = {1997/07//}, pages = {7791 - 7798}, abstract = {We analyze the evolutionary dynamics of three of the best-studied plant nuclear multigene families. The data analyzed derive from the genes that encode the small subunit of ribulose-1,5-bisphosphate carboxylase (rbcS), the gene family that encodes the enzyme chalcone synthase (Chs), and the gene family that encodes alcohol dehydrogenases (Adh). In addition, we consider the limited evolutionary data available on plant transposable elements. New Chs and rbcS genes appear to be recruited at about 10 times the rate estimated for Adh genes, and this is correlated with a much smaller average gene family size for Adh genes. In addition, duplication and divergence in function appears to be relatively common for Chs genes in flowering plant evolution. Analyses of synonymous nucleotide substitution rates for Adh genes in monocots reject a linear relationship with clock time. Replacement substitution rates vary with time in a complex fashion, which suggests that adaptive evolution has played an important role in driving divergence following gene duplication events. Molecular population genetic studies of Adh and Chs genes reveal high levels of molecular diversity within species. These studies also reveal that inter- and intralocus recombination are important forces in the generation allelic novelties. Moreover, illegitimate recombination events appear to be an important factor in transposable element loss in plants. When we consider the recruitment and loss of new gene copies, the generation of allelic diversity within plant species, and ectopic exchange among transposable elements, we conclude that recombination is a pervasive force at all levels of plant evolution.}, author = {Clegg,M. T and Cummings, Michael P. and Durbin,M. L} } @inbook {14265, title = {The geometry of visual space distortion}, booktitle = {Algebraic Frames for the Perception-Action CycleAlgebraic Frames for the Perception-Action Cycle}, series = {Lecture Notes in Computer Science}, volume = {1315}, year = {1997}, month = {1997///}, pages = {249 - 277}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The encounter of perception and action happens at the intermediate representations of space-time. In many of the computational models employed in the past, it has been assumed that a metric representation of physical space can be derived by visual means. Psychophysical experiments, as well as computational considerations, can convince us that the perception of space and shape has a much more complicated nature, and that only a distorted version of actual, physical space can be computed. This paper develops a computational geometric model that explains why such distortion might take place. The basic idea is that, both in stereo and motion, we perceive the world from multiple views. Given the rigid transformation between the views and the properties of the image correspondence, the depth of the scene can be obtained. Even a slight error in the rigid transformation parameters causes distortion of the computed depth of the scene. The unified framework introduced here describes this distortion in computational terms. We characterize the space of distortions by its level sets, that is, we characterize the systematic distortion via a family of iso-distortion surfaces which describes the locus over which depths are distorted by some multiplicative factor. Clearly, functions of the distorted space exhibiting some sort of invariance, produce desirable representations for biological and artificial systems [13]. Given that humans{\textquoteright} estimation of egomotion or estimation of the extrinsic parameters of the stereo apparatus is likely to be imprecise, the framework is used to explain a number of psychophysical experiments on the perception of depth from motion or stereo.}, isbn = {978-3-540-63517-8}, url = {http://dx.doi.org/10.1007/BFb0017872}, author = {Ferm{\"u}ller, Cornelia and LoongFah Cheong and Aloimonos, J.}, editor = {Sommer,Gerald and Koenderink,Jan} } @article {18722, title = {The main-chain dynamics of the dynamin pleckstrin homology (PH) domain in solution: analysis of 15N relaxation with monomer/dimer equilibration}, journal = {Journal of Molecular Biology}, volume = {266}, year = {1997}, month = {1997/02/14/}, pages = {173 - 194}, abstract = {The backbone dynamics of the pleckstrin homology (PH) domain from dynamin were studied by 15N NMR relaxation (R1 and R2) and steady state heteronuclear 15N {1H} nuclear Overhauser effect measurements at 500 and 600 MHz, at protein concentrations of 1.7 mM and 300 μM, and by molecular dynamics (MD) simulations. The analysis was performed using the model-free approach. The method was extended in order to account for observed partial (equilibrium) dimerization of the protein at NMR concentrations. A model is developed that takes into account both rapid monomer-dimer exchange and anisotropy of the over-all rotation of the dimer. The data show complex dynamics of the dynamin PH domain. Internal motions in elements of the secondary structure are restricted, as inferred from the high value of the order parameter (S2 \~{} 0.9) and from the local correlation time \<100 ps. Of the four extended loop regions that are disordered in the NMR-derived solution structure of the protein, loops β1/β2 and β5/β6 are involved in a large-amplitude (S2 down to 0.2 to 0.3) subnanosecond to nanosecond time-scale motion. Reorientation of the loops β3/β4 and β6/β7, in contrast, is restricted, characterized by the values of order parameter S2 \~{} 0.9 more typical of the protein core. These loops, however, are involved in much slower processes of motion resulting in a conformational exchange on a microsecond to submillisecond time scale. The motions of the terminal regions (residues 1 to 10, 122 to 125) are practically unrestricted (S2 down to 0.05, characteristic times in nanosecond time scale), suggesting that these parts of the sequence do not participate in the protein fold. The analysis shows a larger sensitivity of the 15N relaxation data to protein microdynamic parameters (S2, τloc) when protein molecular mass (τc) increases. The use of negative values of the steady state 15N{1H} NOEs as an indicator of the residues not belonging to the folded structure is suggested. The amplitudes of local motion observed in the MD simulation are in a good agreement with the NMR data for the amide NH groups located in the protein core.}, keywords = {dynamin, monomer/dimer equilibration, NMR relaxation, pleckstrin homology domain, protein dynamics}, isbn = {0022-2836}, doi = {10.1006/jmbi.1996.0771}, url = {http://www.sciencedirect.com/science/article/pii/S0022283696907718}, author = {Fushman, David and Cahill,Sean and Cowburn,David} } @article {13608, title = {Multiscale Document Page Segmentation Using Soft Decision Integration}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, year = {1997}, month = {1997///}, pages = {92 - 96}, author = {Etemad,K. and David Doermann and Chellapa, Rama} } @conference {17936, title = {Navigating static environments using image-space simplification and morphing}, booktitle = {Proceedings of the 1997 symposium on Interactive 3D graphics}, series = {I3D {\textquoteright}97}, year = {1997}, month = {1997///}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-884-3}, doi = {10.1145/253284.253298}, url = {http://doi.acm.org/10.1145/253284.253298}, author = {Darsa,Lucia and Costa Silva,Bruno and Varshney, Amitabh} } @article {17729, title = {Perturbation analysis for the QR decomposition}, journal = {SIAM Journal on Matrix Analysis and Applications}, volume = {18}, year = {1997}, month = {1997///}, pages = {775 - 791}, author = {Chang,X. C. and Paige,C. C. and Stewart, G.W.} } @conference {18687, title = {Probabilistic verification of a synchronous round-based consensus protocol}, year = {1997}, month = {1997/10//}, pages = {165 - 174}, abstract = {Consensus protocols are used in a variety of reliable distributed systems, including both safety-critical and business-critical applications. The correctness of a consensus protocol is usually shown, by making assumptions about the environment in which it executes, and then proving properties about the protocol. But proofs about a protocol{\textquoteright}s behavior are only as good as the assumptions which were made to obtain them, and violation of these assumptions can lead to unpredicted and serious consequences. We present a new approach for the probabilistic verification of synchronous round based consensus protocols. In doing so, we make stochastic assumptions about the environment in which a protocol operates, and derive probabilities of proper and non proper behavior. We thus can account for the violation of assumptions made in traditional proof techniques. To obtain the desired probabilities, the approach enumerates possible states that can be reached during an execution of the protocol, and computes the probability of achieving the desired properties for a given fault and network environment. We illustrate the use of this approach via the evaluation of a simple consensus protocol operating under a realistic environment which includes performance, omission, and crash failures}, keywords = {business-critical applications, consensus protocol correctness, crash failures, formal verification, network environment, probabilistic verification, probabilities, probability, program verification, proper behavior, protocol behavior, Protocols, realistic environment, reliable distributed systems, safety-critical applications, simple consensus protocol, software reliability, stochastic assumptions, synchronous round based consensus protocol, synchronous round based consensus protocols, traditional proof techniques}, doi = {10.1109/RELDIS.1997.632812}, author = {Duggal,H.S. and Michel Cukier and Sanders,W. H.} } @inbook {11921, title = {Regulation of Cable Television}, booktitle = {The Froehlich/Kent Encyclopedia of Telecommunications: Volume 15-Radio Astronomy to Submarine Cable SystemsThe Froehlich/Kent Encyclopedia of Telecommunications: Volume 15-Radio Astronomy to Submarine Cable Systems}, volume = {15}, year = {1997}, month = {1997///}, pages = {84 - 84}, author = {Agrawala, Ashok K. and CILINGIROGLU,A. and Lee,S.} } @article {13019, title = {Satellite DNA repeat sequence variation is low in three species of burying beetles in the genus {\i}t Nicrophorus (Coleoptera: Silphidae)}, journal = {Mol Biol Evol}, volume = {14}, year = {1997}, month = {1997/11//}, pages = {1088 - 1095}, abstract = {Three satellite DNA families were identified in three species of burying beetles, Nicrophorus orbicollis, N. marginatus, and N. americanus. Southern hybridization and nucleotide sequence analysis of individual randomly cloned repeats shows that these satellite DNA families are highly abundant in the genome, are composed of unique repeats, and are species-specific. The repeats do not have identifiable core elements or substructures that are similar in all three families, and most interspecific sequence similarity is confined to homopolymeric runs of A and T. Satellite DNA from N. marginatus and N. americanus show single-base-pair indels among repeats, but single-nucleotide substitutions characterize most of the repeat variability. Although the repeat units are of similar lengths (342, 350, and 354 bp) and A + T composition (65\%, 71\%, and 71\%, respectively), the average nucleotide divergence among sequenced repeats is very low (0.18\%, 1.22\%, and 0.71\%, respectively). Transition/transversion ratios from the consensus sequence are 0.20, 0.69, and 0.70, respectively.}, author = {King,L. M and Cummings, Michael P.} } @conference {17848, title = {Scheduling in a high performance remote-sensing data server}, booktitle = {Proceedings of the Eighth SIAM Conference on Parallel Processing for Scientific Computing. SIAM}, year = {1997}, month = {1997///}, author = {Chang,C. and Sussman, Alan and Saltz, J.} } @conference {13862, title = {Spanish EuroWordNet and LCS-Based Interlingual MT}, booktitle = {IN PROCEEDINGS OF THE MT SUMMIT WORKSHOP ON INTERLINGUAS IN MT}, year = {1997}, month = {1997///}, abstract = {We present a machine translation framework in which the interlingua -- Lexical Conceptual Structure (LCS) -- is coupled with a definitional component that includes bilingual (EuroWordNet) links between words in the source and target languages. While the links between individual words are language-specific, the LCS is designed to be a language-independent, compositional representation. We take the view that the two types of information -- shallower, transfer-like knowledge as well as deeper, compositional knowledge -- can be reconciled in interlingual machine translation, the former for overcoming the intractability of LCS-based lexical selection, and the latter for relating the underlying semantics of two words cross-linguistically. We describe the acquisition process for these two information types and present results of hand-verification of the acquired lexicon. Finally, we demonstrate the utility of the two information types in interlingual MT.}, author = {Dorr, Bonnie J and Marti,M. Antonia and Castellon,Irene} } @article {13655, title = {Symbolic Compression and Processing of Document Images}, volume = {LAMP-TR-004,CFAR-TR-849,CS-TR-3734}, year = {1997}, month = {1997/01//}, institution = {University of Maryland, College Park}, abstract = {In this paper we describe a compression and representation scheme which exploits the component-level redundancy found within a document image. The approach identifies patterns which appear repeatedly, represents similar patterns with a single prototype, stores the location of pattern instances and codes the residuals between the prototypes and the pattern instances. Using a novel encoding scheme, we provide a representation which facilitates scalable lossy compression and progressive transmission, and supports document image analysis in the compressed domain. We motivate the approach, provide details of the encoding procedures, report compression results and describe a class of document image understanding tasks which operate on the compressed representation.}, author = {Kia,Omid and David Doermann and Rosenfeld,Azriel and Chellapa, Rama} } @conference {17856, title = {Titan: a High-Performance Remote-sensing Database}, booktitle = {In Proceedings of the 1997 International Conference on Data Engineering}, year = {1997}, month = {1997///}, author = {Bongki,C. C and Chang,C. and Moon,B. and Acharya, A. and Shock,C. and Sussman, Alan and Saltz, J.} } @inbook {14269, title = {Toward motion picture grammars}, booktitle = {Computer Vision {\textemdash} ACCV{\textquoteright}98Computer Vision {\textemdash} ACCV{\textquoteright}98}, series = {Lecture Notes in Computer Science}, volume = {1352}, year = {1997}, month = {1997///}, pages = {283 - 290}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We are interested in processing video data for the purpose of solving a variety of problems in video search, analysis, indexing, browsing and compression. Instead of concentrating on a particular problem, in this paper we present a framework for developing video applications. Our basic thesis is that video data can be represented at a higher level of abstraction as a string generated by a grammar, termed motion picture grammar. The rules of that grammar relate different spatiotemporal representations of the video content and, in particular, representations of action.}, isbn = {978-3-540-63931-2}, url = {http://dx.doi.org/10.1007/3-540-63931-4_228}, author = {Bolle,Ruud and Aloimonos, J. and Ferm{\"u}ller, Cornelia}, editor = {Chin,Roland and Pong,Ting-Chuen} } @article {13891, title = {Using WordNet to Posit Hierarchical Structure in Levin{\textquoteright}s Verb Classes}, year = {1997}, month = {1997///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {In this paper we report on experiments using WordNet synset tags to evaluate the seman-tic properties of the verb classes cataloged by Levin 1993. This paper represents ongoing research begun at the University of Pennsylvania (Rosenzweig et al. 1997, Palmer et al. 1997) and the University of Maryland (Dorr and Jones 1996b, 1996d, 1996e). Using WordNet sense tags to constrain the intersection of Levin classes, we avoid spurious class intersections introduced by homonymy and polysemy (run a bath, run a mile). By adding class intersections based on a single shared sense-tagged word, we minimize the impact of the non-exhaustiveness of Levin{\textquoteright}s database (Dorr and Olsen 1996, Dorr to appear). By examining the syntactic properties of the intersective classes, we provide a clearer picture of the relationship between WordNet/EuroWordNet and the LCS interlingua for machine translation and other NLP applications. }, author = {Olsen,M.B. and Dorr, Bonnie J and Clark,D.J.} } @conference {15040, title = {The vegetation canopy lidar mission}, booktitle = {Proceedings of Land Satellite Information in the Next Decade, II: Sources and Applications. Bethesda (MD): American Society of Photogrammetry and Remote Sensing}, year = {1997}, month = {1997///}, pages = {100 - 112}, abstract = {The Vegetation Canopy Lidar (VCL) is the first selected mission of NASA{\textquoteright}s new EarthSystem Science Pathfinder program. The principal goal of VCL is the characterization of the three-dimensional structure of the earth; in particular, canopy vertical and horizontal structure and land surface topography. Its primary science objectives are: landcover characterization for terrestrial ecosystem modeling, monitoring and prediction; landcover characterization for climate modeling and prediction; and, production of a global reference data set of topographic spot heights and transects. VCL will provide unique data sets for understanding important environ- mental issues including climatic change and variability, biotic erosion and sustainable landuse, and will dramatically improve our estimation of global biomass and carbon stocks, fractional forest cover, forest extent and condition. It will also provide canopy data critical for biodiversity, natural hazard, and climate studies. Scheduled for launch in early 2000, VCL is an active lidar remote sensing system consisting of a five-beam instrument with 25 m contiguous along track resolution. The five beams are in a circular configuration 8 km across and each beam traces a separate ground track spaced 2 km apart, eventually producing 2 km coverage between 65{\textdegree} N and S. VCL{\textquoteright}s core measurement objectives are: (1) canopy top heights; (2) vertical distribution of intercepted surfaces (e.g. leaves and branches); and, (3) ground surface topographic elevations. These measurements are used to derive a variety of science data products including canopy heights, canopy vertical distribution, and ground elevations gridded monthly at 1{\textdegree} resolution and every 6 months at 2 km resolution, as well as a 2 km fractional forest cover product. }, author = {Dubayah, R. and Blair,J. B. and Bufton,J. L. and Clark,D. B. and JaJa, Joseph F. and Knox,R. and Luthcke,S. B. and Prince,S. and Weishampel,J.} } @article {14275, title = {Visual space distortion}, journal = {Biological Cybernetics}, volume = {77}, year = {1997}, month = {1997///}, pages = {323 - 337}, abstract = {We are surrounded by surfaces that we perceive by visual means. Understanding the basic principles behind this perceptual process is a central theme in visual psychology, psychophysics, and computational vision. In many of the computational models employed in the past, it has been assumed that a metric representation of physical space can be derived by visual means. Psychophysical experiments, as well as computational considerations, can convince us that the perception of space and shape has a much more complicated nature, and that only a distorted version of actual, physical space can be computed. This paper develops a computational geometric model that explains why such distortion might take place. The basic idea is that, both in stereo and motion, we perceive the world from multiple views. Given the rigid transformation between the views and the properties of the image correspondence, the depth of the scene can be obtained. Even a slight error in the rigid transformation parameters causes distortion of the computed depth of the scene. The unified framework introduced here describes this distortion in computational terms. We characterize the space of distortions by its level sets, that is, we characterize the systematic distortion via a family of iso-distortion surfaces which describes the locus over which depths are distorted by some multiplicative factor. Given that humans{\textquoteright} estimation of egomotion or estimation of the extrinsic parameters of the stereo apparatus is likely to be imprecise, the framework is used to explain a number of psychophysical experiments on the perception of depth from motion or stereo.}, isbn = {0340-1200}, url = {http://dx.doi.org/10.1007/s004220050393}, author = {Ferm{\"u}ller, Cornelia and LoongFah Cheong and Aloimonos, J.} } @conference {12802, title = {An algebraic theory of process efficiency}, booktitle = {, Eleventh Annual IEEE Symposium on Logic in Computer Science, 1996. LICS {\textquoteright}96. Proceedings}, year = {1996}, month = {1996/07/27/30}, pages = {63 - 72}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper presents a testing-based semantic theory for reasoning about the efficiency of concurrent systems as measured in terms of the amount of their internal activity. The semantic preorders are given an algebraic characterization, and their optimality is established by means of a full abstractness result. They are also shown to subsume existing bisimulation-based efficiency preorders. An example is provided to illustrate the utility of this approach}, keywords = {algebraic characterization, algebraic specification, algebraic theory, bisimulation-based efficiency preorders, Calculus, calculus of communicating systems, Carbon capture and storage, Computer science, concurrent systems, formal logic, formal specification, full abstractness result, internal activity, optimality, process efficiency, reasoning, semantic preorders, System testing, testing-based semantic theory}, isbn = {0-8186-7463-6}, doi = {10.1109/LICS.1996.561304}, author = {Natarajan,V. and Cleaveland, Rance} } @article {16562, title = {Alignment of coexisting cortical maps in a motor control model}, journal = {Neural computation}, volume = {8}, year = {1996}, month = {1996///}, pages = {731 - 755}, author = {Chen,Y. and Reggia, James A.} } @article {13525, title = {Compressed-domain document retrieval and analysis}, journal = {SPIE Conference of Multimedia Storage and Archiving Systems}, volume = {2916}, year = {1996}, month = {1996/11/01/}, pages = {176 - 187}, abstract = {In this paper, we first describe a structural compression technique which has been designed to facilitate document text image storage, retrieval, and processing. This technique provides an efficient representation of textural images and lends itself to lossy compression, progressive transmission, direct access to sub-regions of the document and document processing in the compressed domain. We describe a data structure which can be used to efficiently store the compressed information, provide algorithms for creating and manipulating it, and present results of document processing on images compressed form the University of Washington database.}, isbn = {0277786X}, doi = {doi:10.1117/12.257287}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/2916/1/176_1?isAuthorized=no}, author = {Kia,Omid E and David Doermann and Chellapa, Rama} } @conference {12844, title = {The Concurrency Factory: A development environment for concurrent systems}, booktitle = {Computer Aided Verification}, year = {1996}, month = {1996///}, pages = {398 - 401}, author = {Cleaveland, Rance and Lewis,P. and Smolka,S. and Sokolsky,O.} } @inbook {14213, title = {Directions of motion fields are hardly ever ambiguous}, booktitle = {Computer Vision {\textemdash} ECCV {\textquoteright}96Computer Vision {\textemdash} ECCV {\textquoteright}96}, series = {Lecture Notes in Computer Science}, volume = {1065}, year = {1996}, month = {1996///}, pages = {119 - 128}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Recent literature [7, 10, 11, 9, 13, 17] provides a number of results regarding uniqueness aspects of motion fields and exact image displacements due to 3-D rigid motion. Here instead of the full motion field we consider only the direction of the motion field due to a rigid motion and ask what can we say about the three-dimensional motion information contained in it. This paper provides a geometric analysis of this question based solely on the fact that the depth of the surfaces in view is positive (i.e. that the surface in view is in front of the camera). With this analysis we thus offer a theoretical foundation for image constraints employing only the sign of flow in various directions and provide a solid basis for their utilization in addressing 3D dynamic vision problems.}, isbn = {978-3-540-61123-3}, url = {http://dx.doi.org/10.1007/3-540-61123-1_132}, author = {Brodsky, Tomas and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Buxton,Bernard and Cipolla,Roberto} } @article {12991, title = {DNA sequence variation in the ribosomal internal transcribed spacer region of freshwater {\i}t Cladophora species (Chlorophyta)}, journal = {J Phycol}, volume = {32}, year = {1996}, month = {1996/12//}, pages = {1035 - 1042}, abstract = {Freshwater species of Cladophora (Chlorophyta) are globally distributed and occupy an unusually wide range of ecological habitats. Delineating species is difficult because most easily observed morphological traits are highly variable and because sexual reproduction has not been clearly documented. Synthesizing ecological data on freshwater Cladophora species is problematic because it is unclear whether freshwater Cladophora species comprise many genetically distinct species or a few ecologically and morphologically variable and / or plastic species. We determined nucleotide sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal cistron of freshwater Cladophora species from a wide range of habitats and geographic locations. We compared these sequences to those derived from culture collections of C. fracta and C. glomerata, the two most commonly reported freshwater Cladophora species. Cladophora fracta and C. glomerata had very similar ITS sequences (95.3\%). All other sequences were identical to those from the C. fracta or C. glomerata culture collections with the exception of one California sample that was similar to both C. fracta (95.6\%) and C. glomerata (92.4\%). ITS genotypes did not correlate with morphology or geography. This analysis shows that common freshwater Cladophora species comprise very few (possibly one) ecologically and morphologically variable species.}, keywords = {algae;, Chlorophyta;, Cladophora;, diversity;, freshwater, genetic, internal, spacer, transcribed}, author = {Marks,J. C and Cummings, Michael P.} } @conference {15346, title = {Effect of Chemical Reactions on Decaying Isotropic Turbulence}, booktitle = {APS Meeting Abstracts}, volume = {1}, year = {1996}, month = {1996///}, author = {Martin, M.P and Candler,G. V} } @conference {15355, title = {Effect of chemical reactions on the decay of isotropic homogeneous turbulence}, booktitle = {AIAA Fluid Dynamics Conference}, volume = {96}, year = {1996}, month = {1996///}, pages = {131 - 131}, address = {New Orleans, LA}, abstract = {Direct numerical simulations, (DNS), are usedto simulate the decay of an isotopic, turbulent, chemically-reacting flow at high temperatures. The independent parameters that govern the physical pro- cess are introduced. The different effects from each of the parameters in the flow are explained by using the results from the DNS. It is found that there is a feedback mechanism between the chemical reactions and the turbulent motion. This feedback is positive for exothermic reactions and negative for endother- mic reactions. }, author = {Aguirre,M and Candler,G. V and Martin, M.P} } @article {16546, title = {Effects of varying parameters on properties of self-organizing feature maps}, journal = {Neural Processing Letters}, volume = {4}, year = {1996}, month = {1996///}, pages = {53 - 59}, author = {Cho,S. and Jang,M. and Reggia, James A.} } @article {16379, title = {Efficient distribution analysis via graph contraction}, journal = {Languages and Compilers for Parallel Computing}, year = {1996}, month = {1996///}, pages = {377 - 391}, author = {Sheffler,T. and Schreiber,R. and Pugh, William and Gilbert,J. and Chatterjee,S.} } @article {12831, title = {Efficient local model-checking for fragments of the modal $\mu$-calculus}, journal = {Tools and Algorithms for the Construction and Analysis of Systems}, year = {1996}, month = {1996///}, pages = {107 - 126}, author = {Bhat,G. and Cleaveland, Rance} } @conference {12799, title = {Efficient model checking via the equational μ-calculus}, booktitle = {, Eleventh Annual IEEE Symposium on Logic in Computer Science, 1996. LICS {\textquoteright}96. Proceedings}, year = {1996}, month = {1996/07/27/30}, pages = {304 - 312}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper studies the use of an equational variant of the modal μ-calculus as a unified framework for efficient temporal logic model checking. In particular we show how an expressive temporal logic, CTL*, may be efficiently translated into the μ-calculus. Using this translation, one may then employ μ-calculus model-checking techniques, including on-the-fly procedures, BDD-based algorithms and compositional model-checking approaches, to determine if systems satisfy formulas in CTL*}, keywords = {Automata, BDD-based algorithms, Boolean functions, Calculus, compositional model-checking approaches, computational complexity, Computer science, CTL*, Data structures, Encoding, equational variant, equational μ-calculus, Equations, expressive temporal logic, Logic, Maintenance, modal μ-calculus, Model checking, on-the-fly procedures, Surges, temporal logic, temporal logic model checking, unified framework}, isbn = {0-8186-7463-6}, doi = {10.1109/LICS.1996.561358}, author = {Bhat,G. and Cleaveland, Rance} } @article {18644, title = {Estimation of time-dependent coverage}, volume = {96466}, year = {1996}, month = {1996///}, institution = {LAAS-CNRS: Laboratory for analysis and architecture of systems}, address = {Toulouse, France}, abstract = {It is well-known that the dependability that can be achieved by a fault-tolerant systemis particularly sensitive to both the asymptotic value of coverage and to the time distribution of coverage. However, most previous work on coverage evaluation by statistical processing of the results of fault-injection experiments has only been concerned with estimating asymptotic coverage. In this paper, we tackle the problem of estimating the parameters of models that also account for coverage latency. After discussing some data sets resulting from fault-injection experiments on practical systems, we propose a series of coverage latency models that might be considered to account for the observed phenomena in a system dependability evaluation. We consider both exponential and non-exponential models, and assess their pertinence by means of a sensitivity study. We confirm previous results that latency can have an extremely important effect on the achievable dependability. We also show that the shape of the latency distribution has only a minor impact in the practical case of systems with high asymptotic coverage. A simple action model based on an exponential latency distribution is therefore proposed. We show how worst-case confidence limits can be obtained for the parameters of this action model and study the effects of data truncation that are unavoidable in any practical measurements of latency. We conclude by a critical assessment of the proposed estimation technique and a demonstration of its application to practical data sets. }, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.48.8253\&rep=rep1\&type=pdf}, author = {Arlat,D. P. M. C. J. and Crouzet,Y.} } @article {12994, title = {Evolutionary biology of parasitic platyhelminths: The role of molecular phylogenetics}, journal = {Parasitol Today}, volume = {12}, year = {1996}, month = {1996/02//}, pages = {66 - 71}, abstract = {As our appreciation of the diversity within the flatworms has grown, so too has our curiosity about the ways in which these varied creatures are related to one another. In particular, the parasitic groups (trematodes, cestodes and monogeneans have been the focus of enquiry. Until recently, morphology, anatomy and life histories have provided the raw data for building hypotheses on relationships. Now, ultrastructural evidence, and most recently, molecular data from nucleic acid sequences, have been brought to bear on the topic. Here, David Blair, Andr{\'e}s Campos, Michael Cummings and Juan Pedro Laclette discuss the ways in which molecular data, in particular, are helping us recognize the various lineages of flatworms.}, author = {Blair,D and Campos,A. and Cummings, Michael P. and Laclette,J. P} } @conference {17860, title = {A high performance image database system for remotely sensed imagery}, booktitle = {Euro-Par{\textquoteright}96 Parallel Processing}, year = {1996}, month = {1996///}, pages = {109 - 122}, author = {Shock,C. and Chang,C. and Davis, Larry S. and Goward,S. and Saltz, J. and Sussman, Alan} } @article {18703, title = {Identification of the Binding Site for Acidic Phospholipids on the PH Domain of Dynamin: Implications for Stimulation of GTPase Activity}, journal = {Journal of Molecular Biology}, volume = {255}, year = {1996}, month = {1996/01/12/}, pages = {14 - 21}, abstract = {It has recently been suggested that pleckstrin homology (PH) domains bind specifically to phospholipids, with phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) being most strongly bound. This observation suggests that PH domains may be responsible for membrane association of proteins in which they occur. Further, this membrane association may be regulated by enzymes that modify lipid head groups to which PH domains may bind. We have studied the binding of phospholipids to the PH domain of human dynamin, a 100 kDa GTPase that is involved in the initial stages of endocytosis. We describe a rapid method for screening PH domain/ligand interactions that gives precise binding constants. We confirm that PtdIns(4,5)P2can bind to dynamin PH domain, although not in an aggregated state. Using NMR spectroscopy, we have mapped a specific site on the surface of dynamin PH domain of which binding of gIns(1,4,5)P3(the head-group skeleton of PtdIns(4,5)P2) occurs. The relative affinity of acidic phospholipids for dynamin PH domain correlates with their ability to activate the GTPase of dynamin. We propose, therefore, that the interaction of these phospholipids with dynamin is likely to occurviathe PH domain. Given the fact that PH domains are often found in pro- teins associated with GTPase activity, or in guanine nucleotide exchange factors, we suggest that one role of PH domains may be to couple phosphatidylinositol signalling to GTP hydrolysis.}, keywords = {Fluorescence, ligand binding, NMR, PH domain, phospholipid}, isbn = {0022-2836}, doi = {10.1006/jmbi.1996.0002}, url = {http://www.sciencedirect.com/science/article/pii/S0022283696900029}, author = {Zheng,Jie and Cahill,Sean M. and Lemmon,Mark A. and Fushman, David and Schlessinger,Joseph and Cowburn,David} } @inbook {13005, title = {Inferring phylogenies from DNA sequence data: The effects of sampling}, booktitle = {New Uses for New PhylogeniesNew Uses for New Phylogenies}, year = {1996}, month = {1996///}, pages = {103 - 115}, publisher = {Oxford University Press}, organization = {Oxford University Press}, author = {Otto,S. P and Cummings, Michael P. and Wakeley,J.}, editor = {Harvey,PH and Leigh Brown,AJ and Maynard Smith,J and Nee,S} } @book {14225, title = {Interaction between 3D Shape and Motion: Theory and Applications}, year = {1996}, month = {1996/06//}, publisher = {Computer Vision Laboratory, University of Maryland}, organization = {Computer Vision Laboratory, University of Maryland}, abstract = {Research during the past few years has attempted to characterize the errors that arise in computing 3D motion (egomotion estimation) and in a scene{\textquoteright}s structure (structure from motion) from a sequence of images acquired by a moving sensor. This paper presents a new geometric framework that characterizes how the three-dimensional space recovered by a moving monocular observer, whose 3D motion is estimated with some error, is distorted. We characterize the space of distortions by its level sets, that is, by a family of iso-distortion surfaces, each of which describes the locus over which the depths of points in the scene are distorted by the same multiplicative factor. By analyzing the geometry of the regions where the distortion factor is negative, that is, where the visibility constraint is violated, we make explicit situations which are likely to give rise to ambiguities in motion estimation. We also apply our approach to a uniqueness analysis for 3D motion analysis from normal flow; we study the constraints on egomotion, object motion and depth for an independently moving object to be detectable by a moving observer; and we offer a quantitative account of the precision needed in an inertial sensor for accurate estimation of 3D motion.}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J. and Cheong,L.} } @article {12785, title = {Modeling and verifying distributed systems using priorities: A case study}, journal = {Software - Concepts and Tools}, volume = {17}, year = {1996}, month = {1996///}, pages = {50 - 62}, author = {Cleaveland, Rance and Natarajan,V. and Sims,S. and Luettgen,G.} } @conference {12835, title = {The NCSU concurrency workbench}, booktitle = {Computer Aided Verification}, year = {1996}, month = {1996///}, pages = {394 - 397}, author = {Cleaveland, Rance and Sims,S.} } @conference {12818, title = {Predictability of real-time systems: a process-algebraic approach}, booktitle = {Real-Time Systems Symposium, IEEE International}, year = {1996}, month = {1996///}, pages = {82 - 82}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper presents a testing-based semantic preorder that relates real-time systems given in the process description language TPL on the basis of the predictability of their timing behavior. This predictability is measured in terms of the amount of variability present in processes{\textquoteright} "activity-completion times". The semantic preorder is shown to coincide with an already existing, well-investigated implementation relation for TPL-the must-preorder. The optimality of our relation is also established by means of a full abstraction result. An example is provided to illustrate the utility of this work.}, keywords = {process algebra; real time systems predictability; process algebra; testing-based semantic preorder; process description language; tpl; timing behavior; variability; activity-completion times; semantic preorder; must-preorder; optimality}, doi = {http://doi.ieeecomputersociety.org/10.1109/REAL.1996.563703}, author = {Natarajan,V. and Cleaveland, Rance} } @article {12824, title = {Priorities for modeling and verifying distributed systems}, journal = {Tools and Algorithms for the Construction and Analysis of Systems}, year = {1996}, month = {1996///}, pages = {278 - 297}, author = {Cleaveland, Rance and L\{\"u}ttgen,G. and Natarajan,V. and Sims,S.} } @article {12804, title = {A process algebra with distributed priorities}, journal = {CONCUR{\textquoteright}96: Concurrency Theory}, year = {1996}, month = {1996///}, pages = {34 - 49}, author = {Cleaveland, Rance and L\{\"u}ttgen,G. and Natarajan,V.} } @article {12826, title = {Semantic theories and system design}, journal = {ACM Computing Surveys (CSUR)}, volume = {28}, year = {1996}, month = {1996///}, pages = {41 - 41}, author = {Cleaveland, Rance} } @conference {17940, title = {Simplification envelopes}, booktitle = {Proceedings of the 23rd annual conference on Computer graphics and interactive techniques}, series = {SIGGRAPH {\textquoteright}96}, year = {1996}, month = {1996///}, pages = {119 - 128}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {geometric modeling, hierarchical approximation, levels-of-detail generation, model simplification, offsets, shape approximation}, isbn = {0-89791-746-4}, doi = {10.1145/237170.237220}, url = {http://doi.acm.org/10.1145/237170.237220}, author = {Cohen,Jonathan and Varshney, Amitabh and Manocha,Dinesh and Turk,Greg and Weber,Hans and Agarwal,Pankaj and Brooks,Frederick and Wright,William} } @inbook {14259, title = {Spatiotemporal representations for visual navigation}, booktitle = {Computer Vision {\textemdash} ECCV {\textquoteright}96Computer Vision {\textemdash} ECCV {\textquoteright}96}, series = {Lecture Notes in Computer Science}, volume = {1064}, year = {1996}, month = {1996///}, pages = {671 - 684}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The study of visual navigation problems requires the integration of visual processes with motor control. Most essential in approaching this integration is the study of appropriate spatio-temporal representations which the system computes from the imagery and which serve as interfaces to all motor activities. Since representations resulting from exact quantitative reconstruction have turned out to be very hard to obtain, we argue here for the necessity of representations which can be computed easily, reliably and in real time and which recover only the information about the 3D world which is really needed in order to solve the navigational problems at hand. In this paper we introduce a number of such representations capturing aspects of 3D motion and scene structure which are used for the solution of navigational problems implemented in visual servo systems. In particular, the following three problems are addressed: (a) to change the robot{\textquoteright}s direction of motion towards a fixed direction, (b) to pursue a moving target while keeping a certain distance from the target, and (c) to follow a wall-like perimeter. The importance of the introduced representations lies in the following: \&$\#$x96; They can be extracted using minimal visual information, in particular the sign of flow measurements or the the first order spatiotemporal derivatives of the image intensity function. In that sense they are direct representations needing no intermediate level of computation such as correspondence. \&$\#$x96; They are global in the sense that they represent how three-dimensional information is globally encoded in them. Thus, they are robust representations since local errors do not affect them. \&$\#$x96; Usually, from sequences of images, three-dimensional quantities such as motion and shape are computed and used as input to control processes. The representations discussed here are given directly as input to the control procedures, thus resulting in a real time solution.}, isbn = {978-3-540-61122-6}, url = {http://dx.doi.org/10.1007/BFb0015577}, author = {LoongFah Cheong and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Buxton,Bernard and Cipolla,Roberto} } @inbook {18680, title = {On stratified sampling for high coverage estimations}, booktitle = {Dependable Computing {\textemdash} EDCC-2}, series = {Lecture Notes in Computer Science}, volume = {1150}, year = {1996}, month = {1996///}, pages = {35 - 54}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper addresses the problem of estimating the coverage of a fault tolerance mechanism through statistical processing of observations collected in faultinjection experiments. In an earlier paper, several techniques for sampling the fault/activity input space of a fault tolerance mechanism were presented. Various estimators based on simple sampling in the whole space and stratified sampling in a partitioned space were studied; confidence limits were derived based on a normal approximation. In this paper, the validity of this approximation is analyzed, especially for high coverage systems. The theory of confidence regions is then introduced to estimate the coverage without approximation when, for practical reasons, stratification is used. Three statistics are considered for defining confidence regions. It is shown that one of these statistics {\textemdash} a vectorial statistic {\textemdash} is often more conservative than the other two. However, only the vectorial statistic is computationally tractable. The results obtained are compared with those based on approximation by means of three hypothetical example systems.}, keywords = {Computer science}, isbn = {978-3-540-61772-3}, url = {http://www.springerlink.com/content/7t2w2u472601h730/abstract/}, author = {Powell,David and Michel Cukier and Arlat,Jean}, editor = {Hlawiczka,Andrzej and Silva,Jo{\~a}o and Simoncini,Luca} } @article {12841, title = {Verification of an active control system using temporal process algebra}, journal = {Engineering with computers}, volume = {12}, year = {1996}, month = {1996///}, pages = {46 - 61}, author = {Elseaidy,W. M and Baugh,J. W. and Cleaveland, Rance} } @conference {16205, title = {Where is information visualization technology going?}, booktitle = {Proceedings of the 9th annual ACM symposium on User interface software and technology}, series = {UIST {\textquoteright}96}, year = {1996}, month = {1996///}, pages = {75 - 77}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-798-7}, doi = {10.1145/237091.237101}, url = {http://doi.acm.org/10.1145/237091.237101}, author = {Hasco{\"e}t-Zizi,Mountaz and Ahlberg,Chris and Korfhage,Robert and Plaisant, Catherine and Chalmers,Matthew and Rao,Ramana} } @conference {12033, title = {3D motion representations in visual servo control}, booktitle = {Proceedings of International Symposium on Computer Vision, 1995}, year = {1995}, month = {1995/11/21/23}, pages = {61 - 66}, publisher = {IEEE}, organization = {IEEE}, abstract = {A new approach to visual servoing and vision-guided robotics is introduced. This approach uses visual information for autonomous behavior. It amounts to using robust, global spatiotemporal representations easily extracted from the dynamic imagery. Specifically, the geometrical patterns of normal flows are used as the input to the servo mechanism. It is shown that the positions of these patterns are related to the three dimensional motion parameters. By locating the positions of these patterns, we can solve a variety of navigational problems with little computational effort}, keywords = {3D motion representations, autonomous behavior, CAMERAS, computational effort, Computer vision, dynamic imagery, global spatiotemporal representations, image representation, Mobile robots, motion control, Navigation, navigational problems, Optical computing, Robot kinematics, Robot sensing systems, robot vision, Robot vision systems, Robotics and automation, servomechanisms, Servosystems, Spatiotemporal phenomena, vision-guided robotics, visual information, visual servo control, visual servoing}, isbn = {0-8186-7190-4}, doi = {10.1109/ISCV.1995.476978}, author = {Ferm{\"u}ller, Cornelia and LoongFah Cheong and Aloimonos, J.} } @article {12809, title = {Divergence and fair testing}, journal = {Automata, Languages and Programming}, year = {1995}, month = {1995///}, pages = {648 - 659}, author = {Natarajan,V. and Cleaveland, Rance} } @conference {12787, title = {Efficient on-the-fly model checking for CTL}, booktitle = {, Tenth Annual IEEE Symposium on Logic in Computer Science, 1995. LICS {\textquoteright}95. Proceedings}, year = {1995}, month = {1995/06/26/29}, pages = {388 - 397}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper gives an on-the-fly algorithm for determining whether a finite-state system satisfies a formula in the temporal logic CTL. The time complexity of our algorithm matches that of the best existing {\textquotedblleft}global algorithm{\textquotedblright} for model checking in this logic, and it performs as well as the best known global algorithms for the sublogics CTL and LTL. In contrast with these approaches, however, our routine constructs the state space of the system under consideration in a need-driven fashion and will therefore perform better in practice}, keywords = {Algorithm design and analysis, Automata, computational complexity, Computer science, CTL, Encoding, finite automata, finite-state system, global algorithm, Logic, LTL, on-the-fly model checking, Performance analysis, Safety, State-space methods, sublogic, temporal logic, time complexity}, isbn = {0-8186-7050-9}, doi = {10.1109/LICS.1995.523273}, author = {Bhat,G. and Cleaveland, Rance and Grumberg,O.} } @article {17142, title = {Evaluating Spatial and Textual Style of Displays}, journal = {Institute for Systems Research Technical Reports}, year = {1995}, month = {1995///}, abstract = {The next generation of Graphic User Interfaces (GUIs) will offer rapid access to perceptually-rich, information abundant, and cognitively consistent interfaces. These new GUIs will be subjected to usability tests and expert reviews, plus new analysis methods and novel metrics to help guide designers. We have developed and tested first generation concordance tools to help developers to review terminology, capitalization, and abbreviation. We have also developed a dialog box summary table to help developers spot patterns and identify possible inconsistencies in layout, color fonts, font size, font style, and ordering of widgets. In this study we also explored the use of metrics such as widget counts, balance, alignment, density, and aspect ratios to provide further clues about where redesigns might be appropriate. Preliminary experience with several commercial projects is encouraging.}, keywords = {human-computer interaction, Systems Integration Methodology}, url = {http://drum.lib.umd.edu/handle/1903/5639}, author = {Shneiderman, Ben and Chimera,Richard and Jog,Ninog and Stimart,Ren and White,David} } @article {12825, title = {A front-end generator for verification tools}, journal = {Tools and Algorithms for the Construction and Analysis of Systems}, year = {1995}, month = {1995///}, pages = {153 - 173}, author = {Cleaveland, Rance and Madelaine,E. and Sims,S.} } @article {12849, title = {Generating diagnostic information for behavioral preorders}, journal = {Distributed computing}, volume = {9}, year = {1995}, month = {1995///}, pages = {61 - 75}, author = {Celikkan,U. and Cleaveland, Rance} } @article {14615, title = {Genome Sequence Comparison and Scenarios for Gene Rearrangements: A Test Case}, journal = {Genomics}, volume = {30}, year = {1995}, month = {1995/11//}, pages = {299 - 311}, abstract = {As large portions of related genomes are being sequenced, methods for comparing complete or nearly complete genomes, as opposed to comparing individual genes, are becoming progressively more important. A major, widespread phenomenon in genome evolution is the rearrangement of genes and gene blocks. There is, however, no consistent method for genome sequence comparison combined with the reconstruction of the evolutionary history of highly rearranged genomes. We developed a schema for genome sequence comparison that includes three successive steps: (i) comparison of all proteins encoded in different genomes and generation of genomic similarity plots; (ii) construction of an alphabet of conserved genes and gene blocks; and (iii) generation of most parsimonious genome rearrangement scenarios. The approach is illustrated by a comparison of the herpesvirus genomes that constitute the largest set of relatively long, complete genome sequences available to date. Herpesviruses have from 70 to about 200 genes; comparison of the amino acid sequences encoded in these genes results in an alphabet of about 30 conserved genes comprising 7 conserved blocks that are rearranged in the genomes of different herpesviruses. Algorithms to analyze rearrangements of multiple genomes were developed and applied to the derivation of most parsimonious scenarios of herpesvirus evolution under different evolutionary models. The developed approaches to genome comparison will be applicable to the comparative analysis of bacterial and eukaryotic genomes as soon as their sequences become available.}, isbn = {0888-7543}, doi = {10.1006/geno.1995.9873}, url = {http://www.sciencedirect.com/science/article/pii/S0888754385798734}, author = {Hannenhalli, Sridhar and Chappey,Colombe and Koonin,Eugene V. and Pevzner,Pavel A.} } @book {17211, title = {Human-Computer Interaction Laboratory 1995 Video Reports}, year = {1995}, month = {1995///}, publisher = {University of Maryland at College Park, Human/Computer Interaction Laboratory}, organization = {University of Maryland at College Park, Human/Computer Interaction Laboratory}, author = {Plaisant, Catherine and Morrison,S. and Skokowski,C. and Reesch,J. and Shneiderman, Ben and Laboratory,University of Maryland at College Park. Human/Computer Interaction and Channel,F.} } @article {17222, title = {Image-browser taxonomy and guidelines for designers}, journal = {IEEE Software}, volume = {12}, year = {1995}, month = {1995/03//}, pages = {21 - 32}, abstract = {In many applications users must browse large images. Most designers merely use two one-dimensional scroll bars or ad hoc designs for two-dimensional scroll bars. However, the complexity of two-dimensional browsing suggests that more careful analysis, design, and evaluation might lead to significant improvements. Our exploration of existing 2D browsers has led us to identify many features and a wide variety of tasks performed with the browsers. We introduce an informal specification technique to describe 2D browsers and a task taxonomy, suggest design features and guidelines, and assess existing strategies. We focus on the tools to explore a selected image and so do not cover techniques to browse a series of images or to browse large-image databases}, keywords = {analysis, Computer Graphics, design, designer guidelines, Equations, Europe, Evaluation, Formal specifications, Graphical user interfaces, Guidelines, IMAGE PROCESSING, image-browser taxonomy, informal specification technique, Laboratories, large image browsing, Layout, Road transportation, selected image exploration, SHAPE, Software design, task taxonomy, Taxonomy, tools, two-dimensional browsing, user interface management systems, visual databases}, isbn = {0740-7459}, doi = {10.1109/52.368260}, author = {Plaisant, Catherine and Carr,D. and Shneiderman, Ben} } @article {16457, title = {Interoperable query processing from object to relational schemas based on a parameterized canonical representation}, journal = {Int. J. Cooperative Inf. Syst.}, volume = {4}, year = {1995}, month = {1995///}, pages = {81 - 120}, author = {Raschid, Louiqa and Chang,Y.} } @conference {12031, title = {Iso-distortion contours and egomotion estimation}, booktitle = {Proceedings of International Symposium on Computer Vision, 1995}, year = {1995}, month = {1995/11/21/23}, pages = {55 - 60}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper introduces the framework of iso-distortion contour to deal with the problem of depth distortion due to erroneous motion estimates, and various related aspects such as the effectiveness of the visibility constraint. The framework can also be used to inquire the uniqueness aspect of normal flow. Future work will examine the implications of the iso-distortion contours for the problem of multiple frame integration}, keywords = {Automation, Computer vision, Degradation, depth distortion, Educational institutions, egomotion estimation, Equations, erroneous motion estimates, Error analysis, HUMANS, Image sequences, iso-distortion contours, Laboratories, Layout, Motion estimation, Robustness, visibility constraint}, isbn = {0-8186-7190-4}, doi = {10.1109/ISCV.1995.476977}, author = {LoongFah Cheong and Aloimonos, J.} } @conference {14981, title = {Land cover dynamics investigation using parallel computers}, booktitle = {Geoscience and Remote Sensing Symposium, 1995. IGARSS {\textquoteright}95. {\textquoteright}Quantitative Remote Sensing for Science and Applications{\textquoteright}, International}, volume = {1}, year = {1995}, month = {1995//10/14}, pages = {332 -334 vol.1 - 332 -334 vol.1}, abstract = {A comprehensive and highly interdisciplinary research program is being carried out to investigate global land cover dynamics in heterogeneous parallel computing environments. Some of the problems are addressed including atmospheric correction, mixture modeling, image classifications by Markovian random fields and by segmentation, global image/map databases, object oriented parallel programming and parallel/IO. During the initial two years project, significant progress has been made in all of these areas}, keywords = {; geographic information system; geophysical measurement technique; geophysics computing; image classification; image map database; image segmentation; land cover dynamics; land surface; mixture modeling; object oriented programming; optical imaging; para, GIS; IR imaging; Markovian random fields; atmospheric correction}, doi = {10.1109/IGARSS.1995.520273}, author = {Liang, S. and Davis, Larry S. and Townshend,J. and Chellapa, Rama and DeFries, R. and Dubayah, R. and Goward,S. and JaJa, Joseph F. and Krishnamachar, S. and Roussopoulos, Nick and Saltz, J. and Samet, Hanan and Shock,T. and Srinivasan, M.} } @article {12768, title = {Optimality in abstractions of model checking}, journal = {Static Analysis}, year = {1995}, month = {1995///}, pages = {51 - 63}, author = {Cleaveland, Rance and Iyer,P. and Yankelevich,D.} } @article {14816, title = {The Paradyn parallel performance measurement tool}, journal = {Computer}, volume = {28}, year = {1995}, month = {1995/11//}, pages = {37 - 46}, abstract = {Paradyn is a tool for measuring the performance of large-scale parallel programs. Our goal in designing a new performance tool was to provide detailed, flexible performance information without incurring the space (and time) overhead typically associated with trace-based tools. Paradyn achieves this goal by dynamically instrumenting the application and automatically controlling this instrumentation in search of performance problems. Dynamic instrumentation lets us defer insertion until the moment it is needed (and remove it when it is no longer needed); Paradyn{\textquoteright}s Performance Consultant decides when and where to insert instrumentation}, keywords = {Aerodynamics, Automatic control, automatic instrumentation control, Debugging, dynamic instrumentation, flexible performance information, high level languages, insertion, Instruments, large-scale parallel program, Large-scale systems, measurement, Paradyn parallel performance measurement tool, Parallel machines, parallel programming, Performance Consultant, Programming profession, scalability, software performance evaluation, software tools}, isbn = {0018-9162}, doi = {10.1109/2.471178}, author = {Miller, B. P and Callaghan, M. D and Cargille, J. M and Hollingsworth, Jeffrey K and Irvin, R. B and Karavanic, K. L and Kunchithapadam, K. and Newhall, T.} } @article {17648, title = {Randomness-Optimal Unique Element Isolation with Applications to Perfect Matching and Related Problems}, journal = {SIAM Journal on Computing}, volume = {24}, year = {1995}, month = {1995///}, pages = {1036 - 1036}, abstract = {In this paper, we precisely characterize the randomness complexity of the unique element isolation problem, a crucial step in the $RNC$ algorithm for perfect matching by Mulmuley, Vazirani, and Vazirani [Combinatorica, 7 (1987), pp. 105{\textendash}113] and in several other applications. Given a set $S$ and an unknown family $\mathcal{F} \subseteq 2^{S}$ with $|\mathcal{F}| \leq Z$, we present a scheme for assigning polynomially bounded weights to the elements of $S$ using only $O(\log Z + \log |S|)$ random bits, such that the minimum weight set in $\mathcal{F}$ is unique with high probability. This generalizes the solution of Mulmuley, Vazirani, and Vazirani, who use $O(S \log S)$ bits, independent of $Z$. We also provide a matching lower bound for the randomness complexity of this problem. The new weight assignment scheme yields a randomness-efficient $RNC^{2}$ algorithm for perfect matching which uses $O(\log Z + \log n)$ random bits, where $Z$ is any given upper bound on the number of perfect matchings in the input graph. This generalizes the result of Grigoriev and Karpinski [Proc. IEEE Symposium on Foundations of computer Science, 1987, pp. 166{\textendash}172], who presentan $NC^{3}$ algorithm when $Z$ is polynomial and improves the running time in this case. The worst-case randomness complexity of our algorithm is $O(n \log (m/n))$ random bits improving on the previous bound of $O(m \log n)$. Our scheme also gives randomness-efficient solutions for several problems where unique element isolation is used, such as $RNC$ algorithms for variants of matching and basic problems on linear matroids. We obtain a randomness-efficient random reduction from SAT to USAT, the language of uniquely satisfiable formulas, which can be derandomized in the case of languages in Few $P$ to yield new proofs of the results Few $P \subseteq \oplus P$ and Few $P \subseteq C_{=} P$.}, isbn = {00975397}, doi = {10.1137/S0097539793250330}, url = {http://link.aip.org/link/SMJCAT/v24/i5/p1036/s1\&Agg=doi}, author = {Chari,Suresh and Rohatgi,Pankaj and Srinivasan, Aravind} } @article {13018, title = {Sampling properties of DNA sequence data in phylogenetic analysis}, journal = {Mol Biol Evol}, volume = {12}, year = {1995}, month = {1995/09//}, pages = {814 - 822}, abstract = {We inferred phylogenetic trees from individual genes and random samples of nucleotides from the mitochondrial genomes of 10 vertebrates and compared the results to those obtained by analyzing the whole genomes. Individual genes are poor samples in that they infrequently lead to the whole-genome tree. A large number of nucleotide sites is needed to exactly determine the whole-genome tree. A relatively small number of sites, however, often results in a tree close to the whole-genome tree. We found that blocks of contiguous sites were less likely to lead to the whole-genome tree than samples composed of sites drawn individually from throughout the genome. Samples of contiguous sites are not representative of the entire genome, a condition that violates a basic assumption of the bootstrap method as it is applied in phylogenetic studies.}, author = {Cummings, Michael P. and Otto,S. P and Wakeley,J.} } @article {15022, title = {Scalable data parallel algorithms for texture synthesis using Gibbs random fields}, journal = {Image Processing, IEEE Transactions on}, volume = {4}, year = {1995}, month = {1995/10//}, pages = {1456 - 1460}, abstract = {This article introduces scalable data parallel algorithms for image processing. Focusing on Gibbs and Markov random field model representation for textures, we present parallel algorithms for texture synthesis, compression, and maximum likelihood parameter estimation, currently implemented on Thinking Machines CM-2 and CM-5. The use of fine-grained, data parallel processing techniques yields real-time algorithms for texture synthesis and compression that are substantially faster than the previously known sequential implementations. Although current implementations are on Connection Machines, the methodology presented enables machine-independent scalable algorithms for a number of problems in image processing and analysis}, keywords = {algorithms;maximum, algorithms;parallel, algorithms;scalable, algorithms;texture, analysis;image, CM-2;Thinking, CM-5;fine-grained, compression;image, compression;texture, Connection, data, estimation;model, estimation;parallel, field;Thinking, fields;Markov, likelihood, machine, Machines;Gibbs, machines;random, Parallel, parameter, processes;, processes;data, processing;image, processing;machine-independent, random, representation;real-time, scalable, synthesis;Markov, texture;maximum}, isbn = {1057-7149}, doi = {10.1109/83.465111}, author = {Bader, D.A. and JaJa, Joseph F. and Chellapa, Rama} } @article {13413, title = {AAAI 1994 Spring Symposium Series Reports}, journal = {AI Magazine}, volume = {15}, year = {1994}, month = {1994/09/15/}, pages = {22 - 22}, isbn = {0738-4602}, doi = {10.1609/aimag.v15i3.1101}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/1101}, author = {Woods,William and Uckun,Sendar and Kohane,Isaac and Bates,Joseph and Hulthage,Ingemar and Gasser,Les and Hanks,Steve and Gini,Maria and Ram,Ashwin and desJardins, Marie and Johnson,Peter and Etzioni,Oren and Coombs,David and Whitehead,Steven} } @article {18964, title = {An Atlas of Drosophila Genes: Sequences and Molecular Features}, journal = {Journal of Heredity}, volume = {85}, year = {1994}, month = {1994///}, pages = {495 - 496}, author = {Maroni,G. and Mount, Stephen M. and Cavener,DR and Cavener,BA and Sharp,PM and Lloyd,AT and Schaeffer,SW} } @article {18060, title = {On the detection of robust curves}, journal = {CVGIP: Graphical Models and Image Processing}, volume = {56}, year = {1994}, month = {1994///}, pages = {189 - 204}, author = {Cole,R. and Vishkin, Uzi} } @conference {13546, title = {Document page decomposition by integration of distributed soft decisions}, booktitle = {International Conference on Neural Networks}, year = {1994}, month = {1994///}, pages = {4022 - 4027}, author = {Etemad,K. and David Doermann and Chellapa, Rama} } @conference {14760, title = {Dynamic program instrumentation for scalable performance tools}, booktitle = {Scalable High-Performance Computing Conference, 1994., Proceedings of the}, year = {1994}, month = {1994/05//}, pages = {841 - 850}, publisher = {IEEE}, organization = {IEEE}, abstract = {Presents a new technique called {\textquoteleft}dynamic instrumentation{\textquoteright} that provides efficient, scalable, yet detailed data collection for large-scale parallel applications. Our approach is unique because it defers inserting any instrumentation until the application is in execution. We can insert or change instrumentation at any time during execution by modifying the application{\textquoteright}s binary image. Only the instrumentation required for the currently selected analysis or visualization is inserted. As a result, our technique collects several orders of magnitude less data than traditional data collection approaches. We have implemented a prototype of our dynamic instrumentation on the CM-5, and present results for several real applications. In addition, we include recommendations to operating system designers, compiler writers, and computer architects about the features necessary to permit efficient monitoring of large-scale parallel systems}, keywords = {Application software, binary image, compiler writing, Computer architecture, Computer displays, Computerized monitoring, Concurrent computing, data acquisition, data collection, data visualisation, Data visualization, dynamic program instrumentation, efficient monitoring, executing program, Instruments, large-scale parallel applications, Large-scale systems, operating system design, Operating systems, parallel programming, program analysis, program diagnostics, program visualization, Programming profession, Sampling methods, scalable performance tools, software tools}, isbn = {0-8186-5680-8}, doi = {10.1109/SHPCC.1994.296728}, author = {Hollingsworth, Jeffrey K and Miller, B. P and Cargille, J.} } @article {16970, title = {An exploratory evaluation of three interfaces for browsing large hierarchical tables of contents}, journal = {ACM Trans. Inf. Syst.}, volume = {12}, year = {1994}, month = {1994/10//}, pages = {383 - 406}, abstract = {Three different interfaces were used to browse a large (1296 items) table of contents. A fully expanded stable interface, expand/contract interface, and multipane interface were studied in a between-groups experiment with 41 novice participants. Nine timed fact retrieval tasks were performed; each task is analyzed and discussed separately. We found that both the expand/contract and multipane interfaces produced significantly faster times than the stable interface for many tasks using this large hierarchy; other advantages of the expand/contract and multipane interfaces over the stable interface are discussed. The animation characteristics of the expand/contract interface appear to play a major role. Refinements to the multipane and expand/contract interfaces are suggested. A predictive model for measuring navigation effort of each interface is presented.}, keywords = {Browsing, hierarchies, table of contents, User interfaces}, isbn = {1046-8188}, doi = {10.1145/185462.185483}, url = {http://doi.acm.org/10.1145/185462.185483}, author = {Chimera,Richard and Shneiderman, Ben} } @article {16595, title = {An extended cellular space method for simulating autocatalytic oligonucleotides}, journal = {Computers \& chemistry}, volume = {18}, year = {1994}, month = {1994///}, pages = {33 - 43}, author = {Chou,H. H. and Reggia, James A. and Navarro-Gonzalez,R. and Wu,J.} } @conference {14896, title = {Finding structurally consistent motion correspondences}, booktitle = {Pattern Recognition, 1994. Vol. 1 - Conference A: Computer Vision Image Processing., Proceedings of the 12th IAPR International Conference on}, volume = {1}, year = {1994}, month = {1994/10//}, pages = {650 -653 vol.1 - 650 -653 vol.1}, abstract = {Much work on deriving scene structure and motion from features assumes as input a set of tracked image features that share a common 3D motion. Producing this input requires segmenting independent motions, and detecting image features that do not correspond to 3D features, originating instead, for example in occlusion boundaries or specularities. We derive a linear program that tells when a set of tracked points might have come from 3D points that share a single motion, assuming affine motion and bounded error. We can also use linear programming to place conservative bounds on the structure of the scene that corresponds to tracked points. We implement and test this algorithm on real images}, keywords = {3D, boundaries;, common, consistent, correspondences;, estimation;, features;, image, independent, linear, MOTION, motion;, occlusion, programming;, scene, segmentation;, specularities;, structurally, structure;, tracked}, doi = {10.1109/ICPR.1994.576388}, author = {Jacobs, David W. and Chennubhotla,C.} } @article {12816, title = {Fully abstract characterizations of testing preorders for probabilistic processes}, journal = {CONCUR{\textquoteright}94: Concurrency Theory}, year = {1994}, month = {1994///}, pages = {497 - 512}, author = {Yuen,S. and Cleaveland, Rance and Dayar,Z. and Smolka,S.} } @conference {17876, title = {High performance computing for land cover dynamics}, booktitle = {Pattern Recognition, 1994. Vol. 3-Conference C: Signal Processing, Proceedings of the 12th IAPR International Conference on}, year = {1994}, month = {1994///}, pages = {234 - 238}, author = {Parulekar,R. and Davis, Larry S. and Chellapa, Rama and Saltz, J. and Sussman, Alan and Townshend,J.} } @article {16215, title = {Image Browsers: Taxonomy, Guidelines, and Informal Specifications}, journal = {Institute for Systems Research Technical Reports}, year = {1994}, month = {1994///}, abstract = {Image browsing is necessary in numerous applications. Designers have merely used two one-dimensional scroll bars or they have made ad hoc designs for a two-dimensional scroll bar. However, the complexity of two-dimensional browsing suggests that more careful analysis, design, and evaluation might lead to significant improvements. We present a task taxonomy for image browsing, suggest design features and guidelines, assess existing strategies, and introduce an informal specification}, keywords = {Graphics, Systems Integration, use interface}, url = {http://drum.lib.umd.edu/handle/1903/5591}, author = {Plaisant, Catherine and Carr,David A and Shneiderman, Ben} } @conference {11924, title = {Integrated approaches for improving the effectiveness of Plan Reuse (A Progress Report)}, booktitle = {ARPA/Rome Laboratory knowledge-based planning and scheduling initiative: workshop proceedings: Tuscon, Arizona, February 21-24, 1994}, year = {1994}, month = {1994///}, pages = {325 - 325}, author = {Kambhampati,S. and Ihrig,L. and Katukam,S. and Chen,J. and Hendler,J. A and Agrawala, Ashok K.} } @article {16594, title = {Map formation in proprioceptive cortex.}, journal = {International journal of neural systems}, volume = {5}, year = {1994}, month = {1994///}, pages = {87 - 87}, author = {Cho,S. and Reggia, James A.} } @article {11925, title = {Mission-oriented replication of periodic tasks in real-time distributed systems}, journal = {Computer Science Technical Report Series; Vol. CS-TR-3256}, year = {1994}, month = {1994///}, pages = {24 - 24}, author = {Cheng,S. T and Hwang,S. I and Agrawala, Ashok K.} } @conference {16559, title = {Modeling brain adaptation to focal damage.}, booktitle = {Proceedings of the Annual Symposium on Computer Application in Medical Care}, year = {1994}, month = {1994///}, pages = {860 - 860}, author = {Goodall,S. and Reggia, James A. and Cho,S.} } @conference {12850, title = {An operational framework for value-passing processes}, booktitle = {Proceedings of the 21st ACM SIGPLAN-SIGACT symposium on Principles of programming languages}, series = {POPL {\textquoteright}94}, year = {1994}, month = {1994///}, pages = {326 - 338}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper develops a semantic framework for concurrent languages with value passing. An operation analogous to substitution in the \&lgr;-calculus is given, and a semantics is given for a value-passing version of Milner{\textquoteright}s Calculus of Communicating Systems (CCS). An operational equivalence is then defined and shown to coincide with Milner{\textquoteright}s (early) bisimulation equivalence. We also show how semantics maybe given for languages with asynchronous communication primitives. In contrast with existing approaches to value passing, this semantics does not reduce data exchange to pure synchronization over (potentially infinite) families of ports indexed by data, and it avoids variable renamings that are not local to processes engaged in communication.}, isbn = {0-89791-636-0}, doi = {10.1145/174675.177941}, url = {http://doi.acm.org/10.1145/174675.177941}, author = {Cleaveland, Rance and Yankelevich,Daniel} } @conference {13621, title = {Page Segmentation Using Decision Integration and Wavelet Packet Basis}, booktitle = {ICPR}, year = {1994}, month = {1994///}, pages = {345 - 349}, author = {Etemad,K. and David Doermann and Chellapa, Rama} } @inbook {18049, title = {On a parallel-algorithms method for string matching problems (overview)}, booktitle = {Algorithms and ComplexityAlgorithms and Complexity}, series = {Lecture Notes in Computer Science}, volume = {778}, year = {1994}, month = {1994///}, pages = {22 - 32}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, keywords = {Computer, Science}, isbn = {978-3-540-57811-6}, url = {http://dx.doi.org/10.1007/3-540-57811-0_3}, author = {Sahinalp,Suleyman and Vishkin, Uzi}, editor = {Bonuccelli,M. and Crescenzi,P. and Petreschi,R.} } @article {13845, title = {Query transformation techniques for interoperable query processing in cooperative information systems}, journal = {Proceedings of the Second International Conference on Cooperative Information Systems (CoopIS94), May}, year = {1994}, month = {1994///}, pages = {17 - 20}, author = {Raschid, Louiqa and Chang,Y. and Dorr, Bonnie J} } @conference {14881, title = {Segmenting independently moving, noisy points}, booktitle = {Motion of Non-Rigid and Articulated Objects, 1994., Proceedings of the 1994 IEEE Workshop on}, year = {1994}, month = {1994/11//}, pages = {96 - 103}, abstract = {There has been much work on using point features tracked through a video sequence to determine structure and motion. In many situations, to use this work, we must first isolate subsets of points that share a common motion. This is hard because we must distinguish between independent motions and apparent deviations from a single motion due to noise. We propose several methods of searching for point-sets with consistent 3D motions. We analyze the potential sensitivity of each method for detecting independent motions, and experiment with each method on a real image sequence}, keywords = {3D, common, consistent, estimation;, features;, image, independently, linear, MOTION, motion;, moving, noisy, point, points;, programming;, real, segmentation;, sequence;, sequences;, video}, doi = {10.1109/MNRAO.1994.346249}, author = {Jacobs, David W. and Chennubhotla,C.} } @article {13022, title = {Slipped-strand mispairing in a plastid gene: {\i}t rpoC2 in grasses (Poaceae)}, journal = {Mol Biol Evol}, volume = {11}, year = {1994}, month = {1994/01//}, pages = {1 - 8}, abstract = {An exception to the generally conservative nature of plastid gene evolution is the gene coding for the beta" subunit of RNA polymerase, rpoC2. Previous work by others has shown that maize and rice have an insertion in the coding region of rpoC2, relative to spinach and tobacco. To assess the distribution of this extra coding sequence, we surveyed a broad phylogenetic sample comprising 55 species from 17 angiosperm families by using Southern hybridization. The extra coding sequence is restricted to the grasses (Poaceae). DNA sequence analysis of 11 species from all five subfamilies within the grass family demonstrates that the extra sequence in the coding region of rpoC2 is a repetitive array that exhibits more than a twofold increase in nucleotide substitution, as well as a large number of insertion/deletion events, relative to the adjacent flanking sequences. The structure of the array suggests that slipped-strand mispairing causes the repeated motifs and adds to the mechanisms through which the coding sequence of plastid genes are known to evolve. Phylogenetic analyses based on the sequence data from grass species support several relationships previously suggested by morphological work, but they are ambiguous about broad relationships within the family.}, author = {Cummings, Michael P. and King,L. M and Kellogg,E. A} } @inbook {18691, title = {Software reliability analysis of three successive generations of a Switching System}, booktitle = {Dependable Computing {\textemdash} EDCC-1}, series = {Lecture Notes in Computer Science}, volume = {852}, year = {1994}, month = {1994///}, pages = {471 - 490}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Most current approaches to software reliability evaluation are based on data collected on a single generation of products. However, many applications are developed through improvements of the existing software: to the families of products are added various generations as the need for new functionalities arises. Experimental studies dealing with the analysis of data collected on families of products are seldom reported. In this paper, we analyze the data (failure and correction reports) collected on the software of three successive generations of the Brazilian Switching System {\textemdash} TROPICO-R, during validation and operation. A comparative analysis of the three products is done and the main results are outlined. Emphasis is placed on the evolution of the software and the corresponding failures and corrected faults. The analysis addresses: i) the modifications introduced on system components, ii) the distribution of failures and corrected faults in the components and the functions fulfilled by the system, and iii) the evolution of the failure intensity functions.}, keywords = {Computer science}, isbn = {978-3-540-58426-1}, url = {http://www.springerlink.com/content/f71g30v177521471/abstract/}, author = {Ka{\^a}niche,M. and Kanoun,K. and Michel Cukier and Martini,M.}, editor = {Echtle,Klaus and Hammer,Dieter and Powell,David} } @conference {16316, title = {Tool support for tailored software prototyping}, booktitle = {Assessment of Quality Software Development Tools, 1994, Proceedings., Third Symposium on}, year = {1994}, month = {1994///}, pages = {171 - 181}, author = {Chen,C. and Porter, Adam and Purtilo,J.} } @inbook {13879, title = {Transforming queries from a relational schema to an object schema: A prototype based on F-logic}, booktitle = {Methodologies for Intelligent SystemsMethodologies for Intelligent Systems}, series = {Lecture Notes in Computer Science}, volume = {869}, year = {1994}, month = {1994///}, pages = {154 - 163}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, isbn = {978-3-540-58495-7}, url = {http://dx.doi.org/10.1007/3-540-58495-1_16}, author = {Chang,Yahui and Raschid, Louiqa and Dorr, Bonnie J}, editor = {Ras,Zbigniew and Zemankova,Maria} } @article {13027, title = {Transmission patterns of eukaryotic transposable elements - arguments for and against horizontal transfer}, journal = {Trends Ecol Evol}, volume = {9}, year = {1994}, month = {1994/04//}, pages = {141 - 145}, abstract = {Recent studies have demonstrated that several classes of transposable elements are widely distributed within eukaryotes. Horizontal transmission of these transposable elements has often been invoked in order to explain the observed variation and relationships within and between species. These same patterns of variation and relationships, however, may originate from processes that do not involve the lateral transfer of genetic material across species.}, author = {Cummings, Michael P.} } @article {16216, title = {Usability Experiments for the Redesign of a Telepathology Workstation}, volume = {CS-TR-3270}, year = {1994}, month = {1994///}, institution = {Technical Report CS-TR-3270, University of Maryland}, abstract = {Dynamic telepathology uses a remotely controlled microscope to allow a pathologist to viewsamples at a remote location. However, time delays introduced by remote operation have made use of a commercial dynamic telepathology system difficult and frustrating. This paper describes experiments to evaluate and redesign the user interface. We also make recommendations for further automation to support the pathology process and increase the usefulness of the system. }, author = {Carr,D. and Plaisant, Catherine and Hasegawa,H.} } @conference {12783, title = {Verifying an intelligent structural control system: a case study}, booktitle = {Real-Time Systems Symposium, 1994., Proceedings.}, year = {1994}, month = {1994/12/07/9}, pages = {271 - 275}, publisher = {IEEE}, organization = {IEEE}, abstract = {Describes the formal verification of the timing properties of the design of an intelligent structural control system using the Concurrency Workbench, an automatic verification tool for finite-state processes. The high-level design of the system is first given in Modechart, a graphical specification language for real-time systems, and then translated into a temporal process algebra supported by the Workbench. The facilities provided by this tool are then used to analyze the system and ultimately show it to be correct}, keywords = {automatic verification tool, case study, Concurrency Workbench, Distributed computing, Distributed control, distributed processing, finite automata, finite-state processes, formal verification, graphical specification language, high-level design, intelligent control, intelligent structural control system verification, Logic, Modechart, Process algebra, Real time systems, real-time systems, Specification languages, structural engineering computing, temporal logic, temporal process algebra, time-varying systems, Timing, timing properties, visual languages}, isbn = {0-8186-6600-5}, doi = {10.1109/REAL.1994.342708}, author = {Elseaidy,W. M and Cleaveland, Rance and Baugh,J. W.} } @conference {17497, title = {Visualization in the information highway}, booktitle = {Proceedings of the conference on Visualization {\textquoteright}94}, series = {VIS {\textquoteright}94}, year = {1994}, month = {1994///}, pages = {4 - 7}, publisher = {IEEE Computer Society Press}, organization = {IEEE Computer Society Press}, address = {Los Alamitos, CA, USA}, isbn = {0-7803-2521-4}, url = {http://dl.acm.org/citation.cfm?id=951087.951091}, author = {Gershon,Nahum and Card,Stuart K. and Roth,Steven F. and Shneiderman, Ben} } @conference {12811, title = {Analyzing concurrent systems using the Concurrency Workbench}, booktitle = {Functional Programming, Concurrency, Simulation and Automated Reasoning}, year = {1993}, month = {1993///}, pages = {129 - 144}, author = {Cleaveland, Rance} } @article {12780, title = {The concurrency workbench: a semantics-based tool for the verification of concurrent systems}, journal = {ACM Transactions on Programming Languages and Systems}, volume = {15}, year = {1993}, month = {1993/01/01/}, pages = {36 - 72}, isbn = {01640925}, doi = {10.1145/151646.151648}, url = {http://dl.acm.org/citation.cfm?id=151648}, author = {Cleaveland, Rance and Parrow,Joachim and Steffen,Bernhard} } @book {14133, title = {Costs of Solving the Discrete Convection-diffusion Equation by Relaxation Methods}, year = {1993}, month = {1993///}, publisher = {University of Maryland}, organization = {University of Maryland}, author = {Chernesky, M. P and Elman, Howard} } @conference {14576, title = {A distributed algorithm for ear decomposition}, booktitle = {, Fifth International Conference on Computing and Information, 1993. Proceedings ICCI {\textquoteright}93}, year = {1993}, month = {1993/05/27/29}, pages = {180 - 184}, publisher = {IEEE}, organization = {IEEE}, abstract = {A distributed algorithm for finding an ear decomposition of an asynchronous communication network with n nodes and m links is presented. At the completion of the algorithm either the ears are correctly labeled or the nodes are informed that there exists no ear decomposition. First we present a novel algorithm to check the existence of an ear decomposition which uses O(m) messages. We also present two other algorithms, one which is time-optimal and the other which is message-optimal to determine the actual ears and their corresponding numbers after determining the existence of an ear decomposition}, keywords = {Asynchronous communication, asynchronous communication network, Automata, Communication networks, computational complexity, Computer networks, Computer science, decomposition graph, distributed algorithm, distributed algorithms, Distributed computing, Ear, ear decomposition, graph theory, message-optimal, network decomposition, sorting, Testing, time-optimal}, isbn = {0-8186-4212-2}, doi = {10.1109/ICCI.1993.315382}, author = {Hannenhalli, Sridhar and Perumalla,K. and Chandrasekharan,N. and Sridhar,R.} } @conference {16220, title = {Exploring remote images: a telepathology workstation}, booktitle = {Proceedings of the INTERACT {\textquoteright}93 and CHI {\textquoteright}93 conference on Human factors in computing systems}, series = {CHI {\textquoteright}93}, year = {1993}, month = {1993///}, pages = {518{\textendash} - 518{\textendash}}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-575-5}, doi = {10.1145/169059.169488}, url = {http://doi.acm.org/10.1145/169059.169488}, author = {Plaisant, Catherine and Carr,David A and Hasegawa,Hiroaki} } @article {12784, title = {A generalized approach to real-time schedulability analysis}, journal = {IEEE Real-Time Systems Newsletter}, volume = {9}, year = {1993}, month = {1993///}, pages = {98 - 103}, author = {Fredette,A. N and Cleaveland, Rance} } @conference {13800, title = {Interoperable query processing with multiple heterogeneous knowledge servers}, booktitle = {Proceedings of the second international conference on Information and knowledge management}, series = {CIKM {\textquoteright}93}, year = {1993}, month = {1993///}, pages = {461 - 470}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-626-3}, doi = {10.1145/170088.170395}, url = {http://doi.acm.org/10.1145/170088.170395}, author = {Raschid, Louiqa and Chang,Yahui and Dorr, Bonnie J} } @article {17267, title = {Investigating touchscreen typing: the effect of keyboard size on typing speed}, journal = {Behaviour \& Information Technology}, volume = {12}, year = {1993}, month = {1993///}, pages = {17 - 22}, abstract = {Abstract Two studies investigated the effect keyboard size has on typing speed and error rates for touchscreen keyboards using the lift-off strategy. A cursor appeared when users touched the screen and a key was selected when they lifted their finger from the screen. Four keyboard sizes were investigated ranging from 24.6 cm to 6.8 cm wide. Results indicate that novices can type approximately 10 words per minute (WPM) on the smallest keyboard and 20 WPM on the largest. Experienced users improved to 21 WPM on the smallest keyboard and 32 WPM on the largest. These results indicate that, although slower, small touchscreen keyboards can be used for limited data entry when the presence of a regular keyboard is not practical. Applications include portable pocket-sized or palmtop computers, messaging systems, and personal information resources. Results also suggest the increased importance of experience on these smaller keyboards. Research directions are suggested.Abstract Two studies investigated the effect keyboard size has on typing speed and error rates for touchscreen keyboards using the lift-off strategy. A cursor appeared when users touched the screen and a key was selected when they lifted their finger from the screen. Four keyboard sizes were investigated ranging from 24.6 cm to 6.8 cm wide. Results indicate that novices can type approximately 10 words per minute (WPM) on the smallest keyboard and 20 WPM on the largest. Experienced users improved to 21 WPM on the smallest keyboard and 32 WPM on the largest. These results indicate that, although slower, small touchscreen keyboards can be used for limited data entry when the presence of a regular keyboard is not practical. Applications include portable pocket-sized or palmtop computers, messaging systems, and personal information resources. Results also suggest the increased importance of experience on these smaller keyboards. Research directions are suggested. }, isbn = {0144-929X}, doi = {10.1080/01449299308924362}, url = {http://www.tandfonline.com/doi/abs/10.1080/01449299308924362}, author = {Sears,Andrew and REVIS,DOREEN and SWATSKI,JANET and CRITTENDEN,ROB and Shneiderman, Ben} } @article {16571, title = {Learning competition and cooperation}, journal = {Neural computation}, volume = {5}, year = {1993}, month = {1993///}, pages = {242 - 259}, author = {Cho,S. and Reggia, James A.} } @article {12770, title = {A linear-time model-checking algorithm for the alternation-free modal mu-calculus}, journal = {Formal methods in system design}, volume = {2}, year = {1993}, month = {1993///}, pages = {121 - 147}, author = {Cleaveland, Rance and Steffen,B.} } @article {16541, title = {Multiple disorder diagnosis with adaptive competitive neural networks}, journal = {Artificial intelligence in medicine}, volume = {5}, year = {1993}, month = {1993///}, pages = {469 - 487}, author = {Cho,S. and Reggia, James A.} } @conference {12812, title = {An operational semantics of value passing}, booktitle = {Proceedings 2nd North American Process Algebra Workshop, Ithaca, New York}, year = {1993}, month = {1993///}, author = {Cleaveland, Rance} } @article {14115, title = {Ordering Effects on Relaxation Methods Applied to the Discrete One- Dimensional Convection-Diffusion Equation}, journal = {SIAM Journal on Numerical Analysis}, volume = {30}, year = {1993}, month = {1993/10/01/}, pages = {1268 - 1290}, abstract = {The authors present an analysis of relaxation methods for the one-dimensional discrete convection-diffusion equation based on norms of the iteration matrices. In contrast to standard analytic techniques that use spectral radii, these results show how the performance of iterative solvers is affected by directions of flow associated with the underlying operator, and by orderings of the discrete grid points. In particular, for problems of size n, relaxation against the flow incurs a latency of approximately n steps in which convergence is slow, and red-black relaxation incurs a latency of approximately n/2 steps. There is no latency associated with relaxation that follows that flow. These results are largely independent of the choice of discretization.}, isbn = {0036-1429}, url = {http://www.jstor.org/stable/2158237}, author = {Elman, Howard and Chernesky, Michael P.} } @conference {17325, title = {Potentials and limitations of pen-based computers}, booktitle = {Proceedings of the 1993 ACM conference on Computer science}, series = {CSC {\textquoteright}93}, year = {1993}, month = {1993///}, pages = {536 - 539}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {There are four possible genres of input devices that can be attached to personal workstations; keyboard, mouse, pen, and voice. For investigating potentials and limitations of pen-based computers, we propose to compare those four categories as different types of man-machine communication channel.Even though arrow keys allow a limited scope of 2D capability in keyboard usage, the primary use of a keyboard is typing. Typing generates a linear sequence of discrete characters. The maximum speed of typing is roughly 10 characters per second, hence the bandwidth of 100 (10{\texttimes}10) bps. A mouse is used primarily for pointing (menu item/object selection) and then for dragging (moving and re-sizing objects). Mouse pointing generates a discrete information of a point location on a 2D (planer) plane with the maximum speed of 2 clicking per second. Each pointing may generate 20 bits of information with the bandwidth of 40 (2{\texttimes}20) bps. Mouse dragging generates a continuous geometric pattern in 2D. Assuming the maximum rate of 40 selections per second in the eight (3 bits) possible directions of dragging, the bandwidth of mouse dragging peaks at 120 (40{\texttimes}3) bps. The usage of pen on a planer flat surface of LCD unit can be divided into scribing and tapping. By scribing we mean a generation of continuous pen strokes forming a character, a gesture, or a picture. Scribing includes drawing and gesturing. Tapping corresponds to a mouse clicking. Tapping may be considered as a special kind of gesture as in the PenPoint operating system. The bandwidth of scribing can be calculated in the same manner as for mouse dragging. With the maximum rate of 100 selections of direction per second for pen, scribing may produce strokes with the speed of 300 (100{\texttimes}3) bps. The bandwidth of pen tapping is almost the same as that of a mouse clicking except that a selection of a point is easier by a pen (3 tappings per second) than by a mouse (2 clickings per second). Talking through a microphone generates a linear sequence of continuous speech with a high degree of redundancy. Using the CELP speech compression algorithm, the bandwidth of normal speech can be reduced to 4800 bps. By vocal signaling we mean a generation of a sequence of discrete messages each of which consists of different pitches and loudness levels. The maximum rate of signaling could be 5 messages per second with 10 differentiable pitches and 10 levels of loudness producing the bandwidth of 35 (5{\texttimes}7) bps. Note that mouse dragging, pen scribing, and voice talking, each produces continuous data objects. Only after quantization by sampling, the data objects can be represented by discrete data structure. By precision we mean the degree of ease in duplicating the identical information using the same input technology. Keyboard is a high precision device because there is no difficulty in generating the same character over and over again. Drawing by a mouse is more difficult than drawing by a pen, because pen is easier to control than mouse. Precision of voice is low because it is difficult to duplicate the sound of the same pitch and the same volume. By latency we mean the set-up time necessary to start generating a stream of information. The latency of using keyboard and mouse is larger than the latency of using pen and voice. By translation we mean a process of converting the information generated by the input device into a sequence of discrete symbols, i.e., a transduction of a continuous data type to a discrete data type. Translation for a keyboard is not necessary. Translation of a mouse click on a menu item requires a finite table look-up which is rather simple operation. Translation of pen scribing and mouse dragging involves a handwriting recognition algorithm which is still a difficult problem at present time. Voice recognition is a very difficult problem. With the assumption that real-time translation is feasible for handwriting recognition and speech recognition, the efficiency of input device for text entry can be measured by how many characters can be entered in a second (cps). A simulated keyboard on CRT is used for entering text by a mouse. Long handwriting on a pen computer is used for a pen. When personal workstations become down-sized, the physical dimension of an input/output device becomes a dominant factor for the mobility of workstations. Keyboard and mouse are portable but intrusive. Wireless pen is mobile and less intrusive. Voice can be ubiquitous but intrusive. One conclusion we can draw from the above analysis is that pen is mightier than mouse. A pen can replace a mouse any time any place. However, keyboard, pen, and voice have different strong points and weak points. They compensate with each other. Therefore, we predict that future workstations will carry multi-modal user-interface with any combination of keyboard, pen, and voice. }, isbn = {0-89791-558-5}, doi = {10.1145/170791.171171}, url = {http://doi.acm.org/10.1145/170791.171171}, author = {Citrin,Wayne and Halbert,Dan and Hewitt,Carl and Meyrowitz,Norm and Shneiderman, Ben} } @article {13844, title = {Query mapping and transformation techniques for problem solving with multiple knowledge servers}, journal = {Proceedings of the Second International Conference on Information and Knowledge Management (CIKM-93)}, year = {1993}, month = {1993///}, abstract = {This paper describes a technique for infor-mation mediation when multiple heterogeneous knowl- edge and data servers are to be accessed during query processing. One problem is building an intelligent in- terface between each knowledge server (KS) and its processor (KP); and the second is to provide interoper- ability among multiple KP/KS so that a query may be answered using information from multiple sources. We present example scenarios which highlight these prob- lems and then outline query mapping and transforma- tion techniques that are applicable. The techniques for solving the interoperability problems involve rep- resentations in some canonical form. This includes a canonical representation (CR) corresponding to each KP/KS pair and a merged CR (MCR) to represent the mapping among the CRs. The MCR and CRs include relevant information obtained from a source query, and heterogeneous mapping (het-map) information, for all possible mappings among the multiple servers. The knowledge in the canonical form must be represented so that it can be easily accessed during query transfor- mation. We use an example of translating queries from an object schema to a relational schema to illustrate typical knowledge that must be represented in some canonical form. We use a high level logical language, F-logic, to represent the heterogeneous mapping (het- map) and query transformation information as a set of declarative rules, in the canonical form. }, author = {Raschid, Louiqa and Chang,Y. and Dorr, Bonnie J} } @conference {12796, title = {RTSL: a language for real-time schedulability analysis}, booktitle = {Real-Time Systems Symposium, 1993., Proceedings.}, year = {1993}, month = {1993/12/01/3}, pages = {274 - 283}, publisher = {IEEE}, organization = {IEEE}, abstract = {The paper develops a generalized approach to schedulability analysis that is mathematically founded in a process algebra called RTSL. Within RTSL one may describe the functional behavior, timing behavior, timing constraints (or deadlines), and scheduling discipline for real-time systems. The formal semantics of RTSL then allows the reachable state space of finite state systems to be automatically generated and searched for timing exceptions. We provide a generalized schedulability analysis technique to perform this state-based analysis}, keywords = {Algebra, Algorithm design and analysis, Dynamic scheduling, Failure analysis, finite state machines, finite state systems, formal logic, formal semantics, functional behavior, generalized approach, generalized schedulability analysis technique, Process algebra, Processor scheduling, reachable state space, Real time systems, real-time schedulability analysis, Real-Time Specification Language, real-time systems, RTSL, scheduling, Scheduling algorithm, scheduling discipline, Specification languages, state-based analysis, State-space methods, Time factors, Timing, timing behavior, timing constraints, timing exceptions}, isbn = {0-8186-4480-X}, doi = {10.1109/REAL.1993.393489}, author = {Fredette,A. N and Cleaveland, Rance} } @article {16513, title = {Simple systems that exhibit template-directed replication}, journal = {Science}, volume = {259}, year = {1993}, month = {1993///}, pages = {1282 - 1287}, author = {Reggia, James A. and Armentrout,S. L and Chou,H. H. and Peng,Y.} } @article {17466, title = {User interface consistency: an evaluation of original and revised interfaces for a videodisk library}, journal = {Sparks of innovation in human-computer interaction}, year = {1993}, month = {1993///}, pages = {259 - 259}, author = {Chimera,R. and Shneiderman, Ben} } @article {18369, title = {An application of decision theory for the evaluation of software prototypes}, journal = {Journal of Systems and Software}, volume = {19}, year = {1992}, month = {1992///}, pages = {27 - 39}, author = {C{\'a}rdenas,S. R and Tian,J. and Zelkowitz, Marvin V} } @conference {12798, title = {Computing diagnostic tests for incorrect processes}, booktitle = {Proc. IFIP WG6. 1 12th Intl. Symp. on Protocol Specification, Testing, and Verification}, year = {1992}, month = {1992///}, pages = {263 - 278}, author = {Celikkan,U. and Cleaveland, Rance} } @article {12987, title = {copia-like retrotransposons are ubiquitous among plants}, journal = {Proc Natl Acad Sci USA}, volume = {89}, year = {1992}, month = {1992/08//}, pages = {7124 - 7128}, abstract = {Transposable genetic elements are assumed to be a feature of all eukaryotic genomes. Their identification, however, has largely been haphazard, limited principally to organisms subjected to molecular or genetic scrutiny. We assessed the phylogenetic distribution of copia-like retrotransposons, a class of transposable element that proliferates by reverse transcription, using a polymerase chain reaction assay designed to detect copia-like element reverse transcriptase sequences. copia-like retrotransposons were identified in 64 plant species as well as the photosynthetic protist Volvox carteri. The plant species included representatives from 9 of 10 plant divisions, including bryophytes, lycopods, ferns, gymnosperms, and angiosperms. DNA sequence analysis of 29 cloned PCR products and of a maize retrotransposon cDNA confirmed the identity of these sequences as copia-like reverse transcriptase sequences, thereby demonstrating that this class of retrotransposons is a ubiquitous component of plant genomes.}, author = {Voytas,D. F and Cummings, Michael P. and Koniczny,A. and Ausubel,F. M and Rodermel,S. R} } @article {12988, title = {Copia-like retrotransposons in plants: a brief introduction}, journal = {The Plant Genetics Newsletter}, volume = {8}, year = {1992}, month = {1992///Summer}, pages = {38 - 41}, author = {Cummings, Michael P.} } @article {16231, title = {The effects of time delays on a telepathology user interface.}, journal = {Proceedings of the Annual Symposium on Computer Application in Medical CareProc Annu Symp Comput Appl Med Care}, year = {1992}, month = {1992///}, pages = {256 - 260}, abstract = {Telepathology enables a pathologist to examine physically distant tissue samples by microscope operation over a communication link. Communication links can impose time delays which cause difficulties in controlling the remote device. Such difficulties were found in a microscope teleoperation system. Since the user interface is critical to pathologist{\textquoteright}s acceptance of telepathology, we redesigned the user interface for this system, built two different versions (a keypad whose movement commands operated by specifying a start command followed by a stop command and a trackball interface whose movement commands were incremental and directly proportional to the rotation of the trackball). We then conducted a pilot study to determine the effect of time delays on the new user interfaces. In our experiment, the keypad was the faster interface when the time delay is short. There was no evidence to favor either the keypad or trackball when the time delay was longer. Inexperienced participants benefitted by allowing them to move long distances over the microscope slide by dragging the field-of-view indicator on the touchscreen control panel. The experiment suggests that changes could be made to the trackball interface which would improve its performance.}, isbn = {0195-4210}, author = {Carr,D. and Hasegawa,H. and Lemmon,D. and Plaisant, Catherine} } @conference {14587, title = {Efficient algorithms for computing matching and chromatic polynomials on series-parallel graphs}, booktitle = {, Fourth International Conference on Computing and Information, 1992. Proceedings. ICCI {\textquoteright}92}, year = {1992}, month = {1992/05/28/30}, pages = {42 - 45}, publisher = {IEEE}, organization = {IEEE}, abstract = {The authors present efficient algorithms for computing the matching polynomial and chromatic polynomial of a series-parallel graph in O(n3) and O(n2) time respectively. Their algorithm for computing the matching polynomial generalizes an existing result from Lovasz, Plummer (1986) and the chromatic polynomial algorithm improves the result given by Hunt, Ravi, Stearn (1988) from O(n4) time}, keywords = {chromatic polynomials, computational complexity, Computer science, graph colouring, graph theory, matching polynomial, Polynomials, series-parallel graphs, Terminology, Tree data structures, Tree graphs}, isbn = {0-8186-2812-X}, doi = {10.1109/ICCI.1992.227709}, author = {Chandrasekharan,N. and Hannenhalli, Sridhar} } @conference {16588, title = {Learning visual coordinate transformations with competition}, booktitle = {Neural Networks, 1992. IJCNN., International Joint Conference on}, volume = {4}, year = {1992}, month = {1992///}, pages = {49 - 54}, author = {Cho,S. and Reggia, James A.} } @article {15603, title = {A parallel algorithm for enclosed and enclosing triangles}, journal = {International Journal of Computational Geometry and Applications}, volume = {2}, year = {1992}, month = {1992///}, pages = {191 - 214}, abstract = {We consider the problems of computing the largest area triangle enclosed within a given n-sided convex polygon and the smallest area triangle which encloses a given convex polygon. We show that these problems are closely related by presenting a single sequential linear time algorithm which essentially solves both problems simultaneously. We also present a cost-optimal parallel algorithm that solves both of these problems in O(log log n) time using n/log log n processors on a CRCW PRAM. In order to achieve these bounds we develop new techniques for the design of parallel algorithms for computational problems involving the rotating calipers method.}, doi = {10.1142/S0218195992000123}, author = {Chandran,S. and Mount, Dave} } @article {15549, title = {Parallel computational geometry of rectangles}, journal = {Algorithmica}, volume = {7}, year = {1992}, month = {1992///}, pages = {25 - 49}, abstract = {Rectangles in a plane provide a very useful abstraction for a number of problems in diverse fields. In this paper we consider the problem of computing geometric properties of a set of rectangles in the plane. We give parallel algorithms for a number of problems usingn processors wheren is the number of upright rectangles. Specifically, we present algorithms for computing the area, perimeter, eccentricity, and moment of inertia of the region covered by the rectangles inO(logn) time. We also present algorithms for computing the maximum clique and connected components of the rectangles inO(logn) time. Finally, we give algorithms for finding the entire contour of the rectangles and the medial axis representation of a givenn {\texttimes} n binary image inO(n) time. Our results are faster than previous results and optimal (to within a constant factor).}, doi = {10.1007/BF01758750}, author = {Chandran,S. and Kim,S. K and Mount, Dave} } @article {17830, title = {PARTI primitives for unstructured and block structured problems}, journal = {Computing Systems in Engineering}, volume = {3}, year = {1992}, month = {1992///}, pages = {73 - 86}, abstract = {This paper describes a set of primitives (PARTI) developed to efficiently execute unstructured and block structured problems on distributed memory parallel machines. We present experimental data from a three-dimensional unstructured Euler solver run on the Intel Touchstone Delta to demonstrate the usefulness of our methods.}, isbn = {0956-0521}, doi = {10.1016/0956-0521(92)90096-2}, url = {http://www.sciencedirect.com/science/article/pii/0956052192900962}, author = {Sussman, Alan and Saltz, J. and Das,R. and Gupta,S. and Mavriplis,D. and Ponnusamy,R. and Crowley,K.} } @conference {16228, title = {Remote manipulation interfaces the case of a telepathology workstation}, booktitle = {Posters and short talks of the 1992 SIGCHI conference on Human factors in computing systems}, series = {CHI {\textquoteright}92}, year = {1992}, month = {1992///}, pages = {65 - 65}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Telemedicine is the practice of medicine over communication links. The physician being consulted and the patient are in two different locations. A first telepathology system has been developed by Corabi Telemetrics. It allows a pathologist to render a diagnosis by examining tissue samples or body fluids under a remotely located microscope.}, doi = {10.1145/1125021.1125082}, url = {http://doi.acm.org/10.1145/1125021.1125082}, author = {Plaisant, Catherine and Carr,David A} } @article {16650, title = {Simple systems exhibiting self-directed replication: annex of transition functions and software documentation}, year = {1992}, month = {1992///}, institution = {University of Maryland at College Park}, address = {College Park, MD, USA}, author = {Reggia, James A. and Chou,Hui-Hsien and Armentrout,Steven L. and Peng,Yun} } @article {12776, title = {Testing preorders for probabilistic processes}, journal = {Automata, Languages and Programming}, year = {1992}, month = {1992///}, pages = {708 - 719}, author = {Cleaveland, Rance and Smolka,S. and Zwarico,A.} } @article {15050, title = {VLSI Implementation of Real-Time Parallel DCT/DST Lattice Structures for Video}, volume = {ISR-TR-1992-34}, year = {1992}, month = {1992///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {The alternate use [1] of the discrete cosine transform (DCT) and the discrete sine transform (DST) can achieve a higher data compression rate and less block effect in image processing. A parallel lattice structure that can dually generate the 1-D DCT and DST is proposed. We also develop a fully-pipelined 2-D DCT lattice architecture that consists of two 1-D DCT/DST arrays without transposition. Both architectures are ideally suited for VLSI implementation because they are modular, regular, and have only local interconnections. the VLSI implementation of the lattice module using the distributed arithmetic approach is described. This realization of the lattice module using 2 um CMOS technology can achieve an 80Mb/s data rate.}, keywords = {Parallel architectures, Signal processing, Systems Integration, VLSI architectures}, url = {http://drum.lib.umd.edu/handle/1903/5216}, author = {Chiu,Ching-Te and Kolagotla,Ravi K. and Liu,K. J. Ray and JaJa, Joseph F.} } @article {16229, title = {When an Intermediate View Matters a 2D-browser Experiment}, journal = {Institute for Systems Research Technical Reports}, year = {1992}, month = {1992///}, abstract = {The browsing of two dimensional images can be found in a large number of application. When the image to be viewed is much larger than the screen available, a two dimensional browser has to be provided to allow users to access all parts of the image. We show the diversity of tasks and systems available and the need for 2D browser design guidelines. In the context of a microscope image browser, we investigate one common technique consisting of a global view of the whole image, coupled to a detailed, magnified view of part of the image. In particular we look at the benefits of providing an intermediate view when the detail- to-overview ratio over 20:1. Our experience is also a good example of a real world application for which added features and added hardware need to be justified.}, keywords = {Human computer interaction, Supervisory control, Systems Integration}, url = {http://drum.lib.umd.edu/handle/1903/5300}, author = {Plaisant, Catherine and Carr,David A and Hasegawa,Hiroaki} } @article {18080, title = {Approximate parallel scheduling. II. Applications to logarithmic-time optimal parallel graph algorithms}, journal = {Information and Computation}, volume = {92}, year = {1991}, month = {1991///}, pages = {1 - 47}, author = {Cole,R. and Vishkin, Uzi} } @article {16622, title = {Competitive activation mechanisms in connectionist models}, journal = {Advances in control networks and large-scale parallel distributed processing models}, volume = {1}, year = {1991}, month = {1991///}, pages = {119 - 119}, author = {Reggia, James A. and Sutton,G. and Cho,S.} } @article {12819, title = {Computing behavioural relations, logically}, journal = {Automata, Languages and Programming}, year = {1991}, month = {1991///}, pages = {127 - 138}, author = {Cleaveland, Rance and Steffen,B.} } @conference {17054, title = {Demonstrational interfaces: Coming soon?}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems: Reaching through technology}, series = {CHI {\textquoteright}91}, year = {1991}, month = {1991///}, pages = {393 - 396}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-383-3}, doi = {10.1145/108844.108966}, url = {http://doi.acm.org/10.1145/108844.108966}, author = {Myers,Brad A. and Cypher,Allen and Maulsby,David and Smith,David C. and Shneiderman, Ben} } @article {17137, title = {ESP{\textquoteright}91 Panel on The Best of ESP}, journal = {Empirical studies of programmers: fourth workshop}, year = {1991}, month = {1991///}, pages = {1 - 1}, author = {Zweben,S. and Curtis,B. and Shneiderman, Ben} } @book {12786, title = {Gdr: A visualization tool for graph algorithms}, year = {1991}, month = {1991///}, publisher = {Citeseer}, organization = {Citeseer}, author = {Stallmann,M. and Cleaveland, Rance and Hebbar,P.} } @article {18362, title = {A management tool for evaluation of software design}, journal = {Software Engineering, IEEE Transactions on}, volume = {17}, year = {1991}, month = {1991/09//}, pages = {961 - 971}, abstract = {A model for evaluating software designs based on extending the functional model of program verification with concepts from economic decision theory has been proposed. The authors describe the method, and discuss a prototype implementation of a tool, called Selector, which implements this technique. It is suggested that a system like Selector can be used in two ways: as a decision support system for management to be used in the process of making choices among various alternatives; and as a prototyping investigative system for proposing and answering a series of {\textquoteleft}what if{\textquoteright} scenarios. The proposed model depends on a risk analysis, of each potential solution and aspects of decision theory to modify the evaluation strategy. The model depends on equilibrium probabilities for generating answers}, keywords = {analysis;software, decision, designs;decision, investigative, model;management, probabilities;evaluation, prototyping;software, Selector;decision, strategy;functional, Support, system;economic, system;risk, systems;program, theory;equilibrium, tool;program, tools;, verification;prototyping, verification;software}, isbn = {0098-5589}, doi = {10.1109/32.92916}, author = {Cardenas-Garcia,S. and Zelkowitz, Marvin V} } @conference {14835, title = {Model group indexing for recognition}, booktitle = {Computer Vision and Pattern Recognition, 1991. Proceedings CVPR {\textquoteright}91., IEEE Computer Society Conference on}, year = {1991}, month = {1991/06//}, pages = {4 - 9}, abstract = {It is shown that an index space can be a powerful tool for reducing the image-model match search by a factor of kG-3 , but only when accompanied by some mechanism, such as grouping, that prevents the system from having to consider all matches between image groups of size G and model groups of size G. It is also shown that if image groups are to index a single point at recognition time, then the index space must contain pointers to each model group over a 2-D sheet, and should therefore be 2G-4 dimensional. A simple indexing system has been implemented to demonstrate these concepts, and a series of experiments have been conducted to investigate the tradeoffs between space and time. They indicate that the speedups are achievable, but require a large amount of space}, keywords = {2-D, dimensional;image, group, groups;image-model, indexing;pattern, lookup;, match, pattern, recognition;data, recognition;pointers;computer, search;index, sheet;2G-4, space;indexing, structures;table, system;model, vision;computerised}, doi = {10.1109/CVPR.1991.139652}, author = {Clemens,D. T and Jacobs, David W.} } @article {15006, title = {Parallel Algorithms for Channel Routing in the Knock-Knee Model}, journal = {SIAM Journal on Computing}, volume = {20}, year = {1991}, month = {1991///}, pages = {228 - 245}, abstract = {The channel routing problem of a set of two-terminal nets in the knock-knee model is considered. A new approach to route all the nets within $d$ tracks, where $d$ is the density, such that the corresponding layout can be realized with three layers is developed. The routing and the layer assignment algorithms run in $O(\log n)$ time with $n / \log n$ processors on the CREW PRAM model under the reasonable assumption that all terminals lie in the range $[1,N]$, where $N = O(n)$.}, keywords = {channel routing, Layout, left-edge algorithm, line packing, Parallel algorithms, VLSI design}, doi = {10.1137/0220014}, url = {http://link.aip.org/link/?SMJ/20/228/1}, author = {JaJa, Joseph F. and Chang,Shing-Chong} } @article {13017, title = {Review of Fundamentals of Molecular Evolution, by Li. W.-H. and D. Graur}, journal = {Cladistics}, volume = {7}, year = {1991}, month = {1991///}, pages = {310 - 312}, author = {Cummings, Michael P.} } @article {18441, title = {The role for executable specifications in system maintenance}, journal = {Information Sciences}, volume = {57{\textendash}58}, year = {1991}, month = {1991/09//}, pages = {347 - 359}, abstract = {As software becomes increasingly complex, two attributes of the system life cycle are taking on more important roles. We need the ability to formally specify the functionality of the systems we build in order to minimize costly development problems and, with long life times, we need the ability to enhance existing systems with new features in order to prolong their usefulness. This enhancement process also needs a mechanism for formally defining any new functionality on data objects placed upon the system. This paper describes the AS* research project which is addressing this issue. AS* is a language-independent specification language embedded within an existing programming language for the purpose of providing extensions to existing systems. This paper discusses the designs of AS*, the structure of the prototype implementation and describes some early experiences using the system.}, isbn = {0020-0255}, doi = {10.1016/0020-0255(91)90086-A}, url = {http://www.sciencedirect.com/science/article/pii/002002559190086A}, author = {Zelkowitz, Marvin V and Cardenas,Sergio} } @article {14888, title = {Space and time bounds on indexing 3D models from 2D images}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {13}, year = {1991}, month = {1991/10//}, pages = {1007 - 1017}, abstract = {Model-based visual recognition systems often match groups of image features to groups of model features to form initial hypotheses, which are then verified. In order to accelerate recognition considerably, the model groups can be arranged in an index space (hashed) offline such that feasible matches are found by indexing into this space. For the case of 2D images and 3D models consisting of point features, bounds on the space required for indexing and on the speedup that such indexing can achieve are demonstrated. It is proved that, even in the absence of image error, each model must be represented by a 2D surface in the index space. This places an unexpected lower bound on the space required to implement indexing and proves that no quantity is invariant for all projections of a model into the image. Theoretical bounds on the speedup achieved by indexing in the presence of image error are also determined, and an implementation of indexing for measuring this speedup empirically is presented. It is found that indexing can produce only a minimal speedup on its own. However, when accompanied by a grouping operation, indexing can provide significant speedups that grow exponentially with the number of features in the groups}, keywords = {2D, bounds;time, bounds;visual, extraction;grouping, features;model, features;model-based, images;3D, indexing;feature, model, operation;image, pattern, picture, processing;, recognition, recognition;computerised, recognition;space, systems;computerised}, isbn = {0162-8828}, doi = {10.1109/34.99235}, author = {Clemens,D. T and Jacobs, David W.} } @article {12977, title = {A superfamily of {\i}t Arabidopsis thaliana retrotransposons}, journal = {Genetics}, volume = {127}, year = {1991}, month = {1991/04//}, pages = {801 - 809}, abstract = {We describe a superfamily of Arabidopsis thaliana retrotransposable elements that consists of at least ten related families designated Ta1-Ta10. The Ta1 family has been described previously. Two genomic clones representing the Ta2 and Ta3 elements were isolated from an A. thaliana (race Landsberg erecta) lambda library using sequences derived from the reverse transcriptase region of Ta1 as hybridization probes. Nucleotide sequence analysis showed that the Ta1, Ta2 and Ta3 families share greater than 75\% amino acid identity in pairwise comparisons of their reverse transcriptase and RNase H genes. In addition to Ta1, Ta2 and Ta3, we identified seven other related retrotransposon families in Landsberg erecta, Ta4-Ta10, using degenerate primers and the polymerase chain reaction to amplify a highly conserved region of retrotransposon-encoded reverse transcriptase. One to two copies of elements Ta2-Ta10 are present in the genomes of the A. thaliana races Landsberg erecta and Columbia indicating that the superfamily comprises at least 0.1\% of the A. thaliana genome. The nucleotide sequences of the reverse transcriptase regions of the ten element families place them in the category of copia-like retrotransposons and phylogenetic analysis of the amino acid sequences suggests that horizontal transfer may have played a role in their evolution.}, author = {Konieczny,A and Voytas,D. F and Cummings, Michael P. and Ausubel,F. M} } @conference {12836, title = {A theory of testing for real-time}, booktitle = {, Proceedings of Sixth Annual IEEE Symposium on Logic in Computer Science, 1991. LICS {\textquoteright}91}, year = {1991}, month = {1991/07/15/18}, pages = {110 - 119}, publisher = {IEEE}, organization = {IEEE}, abstract = {A framework for generating testing preorders that relate processes on the basis of their timing behavior as well as their degree of relative nondeterminism is developed. The basic concepts of transition systems and testing are reviewed, and timed testing, which takes account of the delay exhibited by a process as it attempts to pass a test, is introduced. The framework is then applied to two different scenarios. In the first, relations are constructed that relate processes on the basis of all timing considerations. In the second, relations are constructed that relate processes on the basis of their relative speeds. In both cases, alternative denotational characterizations of the resulting preorders are presented, and examples are given to illustrate the utility of the approach}, keywords = {Algebra, Character generation, Computer science, Delay, formal logic, Licenses, nondeterminism, Process control, Protocols, Real time systems, real-time, System testing, testing preorders, testing theory, timed testing, Timing, timing behavior, transition systems}, isbn = {0-8186-2230-X}, doi = {10.1109/LICS.1991.151635}, author = {Cleaveland, Rance and Zwarico,A. E} } @article {15047, title = {VLSI architectures for multidimensional transforms}, journal = {Computers, IEEE Transactions on}, volume = {40}, year = {1991}, month = {1991/09//}, pages = {1053 - 1057}, abstract = {The authors propose a family of VLSI architectures with area-time tradeoffs for computing (N times;N times; . . . times;N) d-dimensional linear separable transforms. For fixed-precision arithmetic with b bits, the architectures have an area A=O(Nd+2a) and computation time T=O(dNd/2-ab ), and achieve the AT2 bound of AT2=O(n2b 2) for constant d, where n=Nd and O lt;a les;d/2}, keywords = {architecture;, architectures;, arithmetic;, complexity;, computational, Computer, digital, fixed-precision, linear, multidimensional, separable, transforms;, VLSI}, isbn = {0018-9340}, doi = {10.1109/12.83648}, author = {Chakrabarti,C. and JaJa, Joseph F.} } @article {15048, title = {VLSI architectures for template matching and block matching}, journal = {Parallel architectures and algorithms for image understanding}, year = {1991}, month = {1991///}, pages = {3 - 27}, author = {Chakrabarti,C. and JaJa, Joseph F.} } @conference {12832, title = {On automatically distinguishing inequivalent processes}, booktitle = {Workshop on Computer-Aided Verification}, year = {1990}, month = {1990///}, author = {Cleaveland, Rance} } @conference {12772, title = {The concurrency workbench}, booktitle = {Automatic Verification Methods for Finite State Systems}, year = {1990}, month = {1990///}, pages = {24 - 37}, author = {Cleaveland, Rance and Parrow,J. and Steffen,B.} } @conference {16542, title = {Diagnostic reasoning at multiple levels of abstraction}, booktitle = {AI Systems in Government Conference, 1990. Proceedings., Fifth Annual}, year = {1990}, month = {1990///}, pages = {168 - 175}, author = {Chu,B. T.B and Reggia, James A.} } @conference {18388, title = {Evaluation criteria for functional specifications}, booktitle = {Proceedings of the 12th international conference on Software engineering}, series = {ICSE {\textquoteright}90}, year = {1990}, month = {1990///}, pages = {26 - 33}, publisher = {IEEE Computer Society Press}, organization = {IEEE Computer Society Press}, address = {Los Alamitos, CA, USA}, isbn = {0-89791-349-3}, url = {http://dl.acm.org/citation.cfm?id=100296.100299}, author = {Cardenas,S. and Zelkowitz, Marvin V} } @article {12993, title = {Evolution of avocados as revealed by DNA restriction fragment variation}, journal = {J Hered}, volume = {81}, year = {1990}, month = {1990/06//May}, pages = {183 - 188}, abstract = {Individuals representing the genus {\i}t Persea, subgenus {\i}t Persea were assayed for restriction fragment length polymorphisms in their chloroplast genome, nuclear ribosomal DNA, and the genes coding for the enzyme cellulase. The subgenus {\i}t Persea appears to consist of {\i}t P. schiedeana and a separate taxon containing the remaining species. {\i}t P. americana does not appear to be a monophyletic group. If {\i}t P. americana is to be maintained as a species containing var. {\i}t americana, var. {\i}t drymifolia, and var. {\i}t guatemalensis, then our data suggest that it should also contain varieties corresponding to {\i}t P. floccosa, {\i}t P. nubigena, and {\i}t P. steyermarkii. {\i}t P. americana var. {\i}t guatemalensis appears to have originated as a hybrid between {\i}t P. steyermarkii and {\i}t P. nubigena. The root-rot-resistant cultivar G755A is a hybrid progeny of {\i}t P. schiedeana and {\i}t P. americana var. guatemalensis. The three varieties of {\i}t P. americana were all distinguished by mutations.}, author = {Furnier,GR and Cummings, Michael P. and Clegg,M. T} } @article {14791, title = {IPS-2: the second generation of a parallel program measurement system}, journal = {IEEE Transactions on Parallel and Distributed Systems}, volume = {1}, year = {1990}, month = {1990/04//}, pages = {206 - 217}, abstract = {IPS, a performance measurement system for parallel and distributed programs, is currently running on its second implementation. IPS{\textquoteright}s model of parallel programs uses knowledge about the semantics of a program{\textquoteright}s structure to provide two important features. First, IPS provides a large amount of performance data about the execution of a parallel program, and this information is organized so that access to it is easy and intuitive. Secondly, IPS provides performance analysis techniques that help to guide the programmer automatically to the location of program bottlenecks. The first implementation of IPS was a testbed for the basic design concepts, providing experience with a hierarchical program and measurement model, interactive program analysis, and automatic guidance techniques. It was built on the Charlotte distributed operating system. The second implementation, IPS-2, extends the basic system with new instrumentation techniques, an interactive and graphical user interface, and new automatic guidance analysis techniques. This implementation runs on 4.3BSD UNIX systems, on the VAX, DECstation, Sun 4, and Sequent Symmetry multiprocessor}, keywords = {4.3BSD UNIX systems, automatic guidance techniques, Automatic testing, Charlotte distributed operating system, CPA, DECstation, design concepts, distributed programs, graphical user interface, Graphical user interfaces, Instruments, interactive program analysis, IPS-2, measurement, message systems, network operating systems, Operating systems, parallel program measurement system, parallel programming, parallel programs, Performance analysis, performance analysis techniques, performance evaluation, performance measurement system, Power system modeling, program bottlenecks, program diagnostics, Programming profession, semantics, Sequent Symmetry multiprocessor, shared-memory systems, software tools, Springs, Sun, Sun 4, Unix, VAX}, isbn = {1045-9219}, doi = {10.1109/71.80132}, author = {Miller, B. P and Clark, M. and Hollingsworth, Jeffrey K and Kierstead, S. and Lim,S. -S and Torzewski, T.} } @conference {16652, title = {Modeling diagnostic problem-solving at multiple levels of abstraction}, booktitle = {Artificial Intelligence Applications, 1990., Sixth Conference on}, year = {1990}, month = {1990/05//}, pages = {55 -61 vol.1 - 55 -61 vol.1}, abstract = {A precise domain-independent computational model for diagnostic problem-solving at multiple levels of abstraction is presented. The knowledge representation framework allows causal knowledge to be represented in a precise yet natural way that reflects a human diagnostician{\textquoteright}s experience in guiding diagnostic reasoning at multiple levels of abstraction. The inference mechanism clearly defines how to form plausible diagnostic hypotheses guided by explicit causal links and the principle of parsimonious covering. It permits the efficient formation of high-level diagnostic hypotheses while at the same time ensuring that all plausible diagnostic alternatives will be considered if one wishes to reason at sufficiently detailed levels. A prototype implementation is described to demonstrate that the proposed inference model is natural for capturing a small but representative fragment of medical causal knowledge, and, with the addition of reasonable heuristics, that the inference mechanism exhibits desirable problem-solving behavior}, keywords = {causal knowledge, diagnostic problem-solving, diagnostic reasoning, domain-independent computational model, explicit causal links, heuristic programming, heuristics, inference mechanism, inference mechanisms, knowledge capture, knowledge representation, knowledge representation framework, medical knowledge, multiple abstraction levels, parsimonious covering, plausible diagnostic hypotheses, problem solving}, doi = {10.1109/CAIA.1990.89171}, author = {Chu,B.-T.B. and Reggia, James A.} } @article {12821, title = {A preorder for partial process specifications}, journal = {CONCUR{\textquoteright}90 Theories of Concurrency: Unification and Extension}, year = {1990}, month = {1990///}, pages = {141 - 151}, author = {Cleaveland, Rance and Steffen,B.} } @article {12777, title = {Priorities in process algebras}, journal = {Information and Computation}, volume = {87}, year = {1990}, pages = {58 - 77}, abstract = {An operational semantics for an algebraic theory of concurrency that incorporates a notion of priority into the definition of the execution of actions is developed. An equivalence based on strong observational equivalence is defined and shown to be a congruence, and a complete axiomatization is given for finite terms. Several examples higlight the novelty and usefulness of our approach.}, isbn = {0890-5401}, doi = {10.1016/0890-5401(90)90059-Q}, url = {http://www.sciencedirect.com/science/article/pii/089054019090059Q}, author = {Cleaveland, Rance and Hennessy,Matthew} } @article {13025, title = {The structure, distribution and evolution of the {\i}t Ta1 retrotransposable element family of {\i}t Arabidopsis thaliana}, journal = {Genetics}, volume = {126}, year = {1990}, month = {1990/11//}, pages = {713 - 721}, abstract = {The Ta1 elements are a low copy number, copia-like retrotransposable element family of Arabidopsis thaliana. Six Ta1 insertions comprise all of the Ta1 element copies found in three geographically diverse A. thaliana races. These six elements occupy three distinct target sites: Ta1-1 is located on chromosome 5 and is common to all three races (Col-0, Kas-1 and La-0). Ta1-2 is present in two races on chromosome 4 (Kas-1 and La-0), and Ta1-3, also located on chromosome 4, is present only in one race (La-0). The six Ta1 insertions share greater than 96\% nucleotide identity, yet are likely to be incapable of further transposition due to deletions or nucleotide changes that alter either the coding capacity of the elements or conserved protein domains required for retrotransposition. Nucleotide sequence comparisons of these elements and the distribution of Ta1 among 12 additional A. thaliana geographical races suggest that Ta1-1 predated the global dispersal of A. thaliana. As the species spread throughout the world, two additional transposition events occurred which gave rise first to Ta1-2 and finally to Ta1-3.}, author = {Voytas,D. F and Konieczny,A and Cummings, Michael P. and Ausubel,F. M} } @article {15033, title = {Systolic architectures for the computation of the discrete Hartley and the discrete cosine transforms based on prime factor decomposition}, journal = {Computers, IEEE Transactions on}, volume = {39}, year = {1990}, month = {1990/11//}, pages = {1359 - 1368}, abstract = {Two-dimensional systolic array implementations for computing the discrete Hartley transform (DHT) and the discrete cosine transform (DCT) when the transform size N is decomposable into mutually prime factors are proposed. The existing two-dimensional formulations for DHT and DCT are modified, and the corresponding algorithms are mapped into two-dimensional systolic arrays. The resulting architecture is fully pipelined with no control units. The hardware design is based on bit serial left to right MSB (most significant bit) to LSB (least significant bit) binary arithmetic}, keywords = {architectures;, architectures;two-dimensional, arithmetic;discrete, arrays;fast, binary, cosine, decomposition;systolic, design;prime, factor, Fourier, Hartley;discrete, systolic, transforms;hardware, transforms;parallel}, isbn = {0018-9340}, doi = {10.1109/12.61045}, author = {Chakrabarti,C. and JaJa, Joseph F.} } @article {12807, title = {Tableau-based model checking in the propositional mu-calculus}, journal = {Acta Informatica}, volume = {27}, year = {1990}, month = {1990///}, pages = {725 - 747}, author = {Cleaveland, Rance} } @conference {12833, title = {Testing equivalence as a bisimulation equivalence}, booktitle = {Automatic Verification Methods for Finite State Systems}, year = {1990}, month = {1990///}, pages = {11 - 23}, author = {Cleaveland, Rance and Hennessy,M.} } @conference {12797, title = {When is {\textquoteleft}partial{\textquoteright} adequate? A logic-based proof technique using partial specifications}, booktitle = {Logic in Computer Science, 1990. LICS {\textquoteright}90, Proceedings., Fifth Annual IEEE Symposium on e}, year = {1990}, month = {1990/06/04/7}, pages = {440 - 449}, publisher = {IEEE}, organization = {IEEE}, abstract = {A technique is presented for ascertaining when a (finite-state) partial process specification is adequate, in the sense of being specified enough, for contexts in which it is to be used. The method relies on the automatic generation of a modal formula from the partial specification; if the remainder of the network satisfies this formula, then any process that meets the specification is guaranteed to ensure correct behavior of the overall system. Using the results, the authors develop compositional proof rules for establishing the correctness of networks of parallel processes and illustrate their use with several examples}, keywords = {Calculus, Carbon capture and storage, compositional proof rules, Computer science, Concurrent computing, Context, correctness, formal specification, logic-based proof technique, modal formula, parallel processes, partial process specification, partial specifications, specification adequacy, State-space methods, Technological innovation}, isbn = {0-8186-2073-0}, doi = {10.1109/LICS.1990.113768}, author = {Cleaveland, Rance and Steffen,B.} } @article {18086, title = {Faster optimal parallel prefix sums and list ranking}, journal = {Information and Computation}, volume = {81}, year = {1989}, month = {1989///}, pages = {334 - 352}, author = {Cole,R. and Vishkin, Uzi} } @article {14130, title = {Fourier Analysis of Iterative Methods for Elliptic Problems}, journal = {SIAM Review}, volume = {31}, year = {1989}, month = {1989/03/01/}, pages = {20 - 49}, abstract = {This paper presents a Fourier method for analyzing stationary iterative methods and preconditioners for discretized elliptic boundary value problems. As in the von Neumann stability analysis of hyperbolic and parabolic problems, the approach is easier to apply, reveals more details about convergence properties than about standard techniques, and can be applied in a systematic way to a wide class of numerical methods. Although the analysis is applicable only to periodic problems, the results essentially reproduce those of classical convergence and condition number analysis for problems with other boundary conditions, such as the Dirichlet problem. In addition, they give suggestive new evidence of the strengths and weaknesses of methods such as incomplete factorization preconditioners in the Dirichlet case.}, isbn = {0036-1445}, url = {http://www.jstor.org/stable/2030846}, author = {Chan, Tony F. and Elman, Howard} } @article {16648, title = {Functional and psychosocial effects of multimodality limb-sparing therapy in patients with soft tissue sarcomas}, journal = {Journal of Clinical Oncology}, volume = {7}, year = {1989}, month = {1989///}, pages = {1217 - 1217}, author = {Chang,A. E and Steinberg,S. M and Culnane,M. and Lampert,M. H and Reggia, James A. and Simpson,C. G and Hicks,J. E and White,D. E and Yang,J. J and Glatstein,E.} } @article {15003, title = {Optimal parallel algorithms for one-layer routing}, year = {1989}, month = {1989///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, author = {Chang,S. C. and JaJa, Joseph F. and Ryu,K. W.} } @conference {12793, title = {A semantics based verification tool for finite state systems}, booktitle = {Proceedings of the IFIP WG6}, volume = {1}, year = {1989}, month = {1989///}, pages = {287 - 302}, author = {Cleaveland, Rance and Parrow,J. and Steffen,B.} } @article {18097, title = {The accelerated centroid decomposition technique for optimal parallel tree evaluation in logarithmic time}, journal = {Algorithmica}, volume = {3}, year = {1988}, month = {1988///}, pages = {329 - 346}, author = {Cole,R. and Vishkin, Uzi} } @article {18095, title = {Approximate parallel scheduling. Part I: The basic technique with applications to optimal parallel list ranking in logarithmic time}, journal = {SIAM Journal on Computing}, volume = {17}, year = {1988}, month = {1988///}, pages = {128 - 128}, author = {Cole,R. and Vishkin, Uzi} } @article {17117, title = {Ecological studies of professional programmers}, journal = {Commun. ACM}, volume = {31}, year = {1988}, month = {1988/11//}, pages = {1256 - 1258}, abstract = {For over two decades, software psychology researchers have been developing insights to software productivity and quality by investigating builders and users of software. This research has been diverse in both its approach and its impacts. It has introduced systematic behavioral measurement into the software development process and into research on new software techniques and technologies, and has also opened up new social and cognitive interpretations of software processes [5, 12].We now see evidence of a new thrust in software psychology coming to the fore, one in which usability researchers are direct participants in the definition and creation of new software artifacts. We call this paradigm Ecological Design, to emphasize (1) that realistic software situations are being confronted on their own terms, and (2) that the work is directed toward design results, not merely toward evaluation and description in the service of design goals. The reorientation towards studying teamwork was prompted in 1971 by Weinberg and followed by a few researchers at that time, but the movement has accelerated with the recent and intense interest in computer supported collaborative work [15]. This was apparent in the papers presented at the two workshops on Empirical Studies of Programmers [10, 13]. An accompanying shift has also occurred in the software engineering community. The traditional waterfall model of software development with the precise specification of a provable topdown design is giving way to newer exploratory styles of program development that emphasize rapid prototyping and iterative refinement. The shift from product to process also puts greater emphasis on team organization, group processes, management policies, reusability, development tools, design methods, debugging strategies, and maintenance [6]. The three papers in this special section exemplify this new paradigm. Rosson, Maass, and Kellogg and Curtis, Krasner, and Iscoe describe highly qualitative studies of professional designers that produced specific technical proposals for improving software tools and the coordination of project management, an assessment of major bottlenecks, and a new framework for thinking about software design as a learning and communication process. Soloway, Pinto, Letovsky, Littman, and Lampert describe the design and exploration of software documentation that grew out of similarly qualitative studies of program maintenance. We caution that this research paradigm is still in its infancy: setting design requirements and developing prototypes are not traditional activities of psychological researchers. These roles are still emerging, still being reconciled with the earlier paradigms. The particular projects highlighted here are only the beginning; the field continues to evolve, as more researchers are attracted, as more topics are explored, as more methods are developed. Thus, despite the shortcomings of any particular project, the trajectory of this paradigm seems clear to us: it is the development of ideas that directly impact productivity and quality in software. Indeed, part of our intention in presenting this special section is to encourage more and more rapid development of the new paradigm. }, isbn = {0001-0782}, doi = {10.1145/50087.214900}, url = {http://doi.acm.org/10.1145/50087.214900}, author = {Shneiderman, Ben and Carroll,John M.} } @conference {16962, title = {An empirical comparison of pie vs. linear menus}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, series = {CHI {\textquoteright}88}, year = {1988}, month = {1988///}, pages = {95 - 100}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Menus are largely formatted in a linear fashion listing items from the top to bottom of the screen or window. Pull down menus are a common example of this format. Bitmapped computer displays, however, allow greater freedom in the placement, font, and general presentation of menus. A pie menu is a format where the items are placed along the circumference of a circle at equal radial distances from the center. Pie menus gain over traditional linear menus by reducing target seek time, lowering error rates by fixing the distance factor and increasing the target size in Fitts{\textquoteright}s Law, minimizing the drift distance after target selection, and are, in general, subjectively equivalent to the linear style.}, isbn = {0-201-14237-6}, doi = {10.1145/57167.57182}, url = {http://doi.acm.org/10.1145/57167.57182}, author = {Callahan,J. and Hopkins,D. and Weiser,M. and Shneiderman, Ben} } @article {15002, title = {Optimal Architectures for Multidimensional Transforms}, volume = {ISR-TR-1988-39}, year = {1988}, month = {1988///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {Multidimensional transforms have widespread applications in computer vision, pattern analysis and image processing. The only existing optimal architecture for computing multidimensional DFT on data of size n = Nd requires very large rotator units of area O(n^2) and pipeline-time O(log n). In this paper we propose a family of optimal architectures with areatime trade-offs for computing multidimensional transforms. The large rotator unit is replaced by a combination of a small rotator unit, a transpose unit and a block rotator unit. The combination has an area of O(N^(d+2a)) and a pipeline time of O(N^(d/2-a)log n), for 0 < a < d/2. We apply this scheme to design optimal architectures for two-dimensional DFT, DHT and DCT. The computation is made efficient by mapping each of the one-dimensional transforms involved into two dimensions.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/4770}, author = {Chakrabarti,Chaitali and JaJa, Joseph F.} } @conference {18096, title = {Optimal parallel algorithms for expression tree evaluation and list ranking}, booktitle = {VLSI Algorithms and Architectures}, year = {1988}, month = {1988///}, pages = {91 - 100}, author = {Cole,R. and Vishkin, Uzi} } @article {15004, title = {Optimal Systolic Designs for the Computation of the Discrete Hartley and the Discrete Cosine Transforms}, year = {1988}, month = {1988///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {In this paper, we propose new algorithms for computing the Discrete Hartley and the Discrete Cosine Transform. The algorithms are based on iterative applications of the modified small n algorithms of DFT. The one dimensional transforms are mapped into two dimensions first and then implemented on two dimensional systolic arrays. Pipelined bit serial architectures operating on left to right LSB to MSB binary arithmetic is the basis of the hardware design. Different hardware schemes for implementing these transforms are studied. We show that our schemes achieve a substantial speed-up over existing schemes.}, keywords = {*ALGORITHMS, *BINARY ARITHMETIC, Computer architecture, DCT(DISCRETE COSINE TRANSFORM), DISCRETE FOURIER TRANSFORMS, ITERATIONS, NUMERICAL MATHEMATICS, TWO DIMENSIONAL}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA452389}, author = {Chakrabarti,Chaitali and JaJa, Joseph F.} } @article {15014, title = {Parallel Algorithms for Wiring Module Pins to Frame Pads}, year = {1988}, month = {1988///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {We present fast and efficient parallel algorithms for several problems related to wiring a set of pins on a module to a set of pads lying on the houndary of a chip. The one-layer model is used to perform the wiring. Our basic model of parallel processing is the CREW-PRAM model which is characterized by the presence of an unlimited number processors sharing the main memory. Concurrent reads are allowed while concurrent writes are not. All our algorithms use 0(n) processors, where n is the input length. Our algorithms have fast implementations on other parallel models such as the mesh or the hypercube.}, keywords = {*ALGORITHMS, *PARALLEL PROCESSING, COMPUTER PROGRAMMING AND SOFTWARE, efficiency, INPUT, LAYERS, length, MEMORY DEVICES, MODELS, MODULAR CONSTRUCTION, NUMERICAL MATHEMATICS, PARALLEL ORIENTATION, PINS, WIRE}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA452383}, author = {Chang,Shing-Chong and JaJa, Joseph F.} } @article {12789, title = {Type theory and concurrency}, journal = {International Journal of Parallel Programming}, volume = {17}, year = {1988}, month = {1988///}, pages = {153 - 206}, author = {Cleaveland, Rance and Panangaden,P.} } @article {15615, title = {A united approach to finding enclosing and enclosed triangles}, journal = {Proceedings of 26th Allerton Conference on Communication, Control and Computing}, year = {1988}, month = {1988///}, author = {Mount, Dave and Chandran,S.} } @article {16370, title = {ALEX-an Alexical Programming Language}, volume = {TR87-835}, year = {1987}, month = {1987///}, institution = {Cornell University}, abstract = {ALEX is an experimental language for high-level parallel programming. It is a testbed for exploring various non-traditional ways of expressing algorithmic ideas, making extensive use of high-resolution color graphics. The language itself is not a programming language in the traditional sense, since there is no lexical syntax. This paper discusses the basic design of the ALEX user interface.}, url = {http://hdl.handle.net/1813/6675}, author = {Kozen,D. and Teitelbaum,T. and Chen,W. Z and Field,J. H and Pugh, William and Vander Zanden,B. T} } @conference {17029, title = {Computer-supported cooperative work (panel): is this REALLY a new field of research?}, booktitle = {Proceedings of the SIGCHI/GI conference on Human factors in computing systems and graphics interface}, series = {CHI {\textquoteright}87}, year = {1987}, month = {1987///}, pages = {227 - 228}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-213-6}, doi = {10.1145/29933.275634}, url = {http://doi.acm.org/10.1145/29933.275634}, author = {Greif,Irene and Curtis,Bill and Krasner,Herb and Malone,Thomas W. and Shneiderman, Ben} } @article {15595, title = {Shared memory algorithms and the medial axis transform}, journal = {IEEE Workshop on Computer Architecture for PAMI}, year = {1987}, month = {1987///}, pages = {44 - 50}, author = {Chandran,S. and Mount, Dave} } @article {17384, title = {Subjective user evaluation of CF PASCAL programming tools}, journal = {Department of Computer Science and Human-Computer Interaction Laboratory Working Paper}, year = {1987}, month = {1987///}, abstract = {This study investigated subjective evaluations of two programming environments: 1) SUPPORT, an interactive programming environment with a syntax directed editor on a personal computer and 2) a batch run environment on a large mainframe computer. Participants were students in a 15 week introductory computer science course. In Part 1, one group of 128 first used SUPPORT, while another group of 85 programmed on a mainframe environment. After 6 weeks they were given an evaluative questionnaire and then switched programming environments. In Part 2, 68 used SUPPORT and 60 used the mainframe. At the twelfth week of the course, they were given two questionnaires, one evaluating the environment they had used in the last 6 weeks and one comparing both enviro nments. A measure of programming performance (exam and programming project grades) was also collected. SUPPORT was predicted to reduce the burden of remembering syntactic details resulting in better performance and higher subjective evaluations. Unexpectedly, the SUPPORT users did not earn statistically significantly higher grades. Furthermore, participants expressed a preference for the mainframe over SUPPORT. Specific items on the questionnaires were used to diagnose the strengths and weaknesses of each environment. Designers of syntax directed editors should focus on reducing the syntactic burden not only in programming , but also in the user interface of these tools.}, author = {Chin,JP and Norman,K. L and Shneiderman, Ben} } @article {18115, title = {The accelerated centroid decomposition technique for optimal parallel tree evaluation in logarithmic time, Ultracomputer Note-108}, year = {1986}, month = {1986///}, institution = {TR-242, Department of Computer Science, Courant Institute NYU}, author = {Cole,R. and Vishkin, Uzi} } @conference {18112, title = {Approximate and exact parallel scheduling with applications to list, tree and graph problems}, booktitle = {27th Annual Symposium on Foundations of Computer Science}, year = {1986}, month = {1986///}, pages = {478 - 491}, author = {Cole,R. and Vishkin, Uzi} } @conference {18113, title = {Approximate scheduling, exact scheduling, and applications to parallel algorithms}, booktitle = {Proceedings Symposium on Foundations of Computer Science}, year = {1986}, month = {1986///}, pages = {478 - 491}, author = {Cole,R. and Vishkin, Uzi} } @conference {18114, title = {Deterministic coin tossing and accelerating cascades: micro and macro techniques for designing parallel algorithms}, booktitle = {Proceedings of the eighteenth annual ACM symposium on Theory of computing}, year = {1986}, month = {1986///}, pages = {206 - 219}, author = {Cole,R. and Vishkin, Uzi} } @article {18111, title = {Deterministic coin tossing with applications to optimal parallel list ranking}, journal = {Information and Control}, volume = {70}, year = {1986}, month = {1986///}, pages = {32 - 53}, author = {Cole,R. and Vishkin, Uzi} } @book {12004, title = {Detection of Surface Orientation and Motion from Texture: The Case of Planes}, year = {1985}, month = {1985///}, publisher = {Dept. of Computer Science, University of Rochester}, organization = {Dept. of Computer Science, University of Rochester}, author = {Aloimonos, J. and Chou, P. B and Science, University of Rochester. Dept. of Computer} } @article {18122, title = {Solving NP-hard problems in [] almost trees{\textquoteright}: Vertex cover}, journal = {Discrete applied mathematics}, volume = {10}, year = {1985}, month = {1985///}, pages = {27 - 45}, author = {Coppersmith,D. and Vishkin, Uzi} } @conference {16755, title = {A timed petri net methodolgoy for specifying real-time system timing requirements}, booktitle = {International Workshop on Timed Petri Nets}, year = {1985}, month = {1985///}, pages = {24 - 31}, author = {Coolahan Jr,J. E and Roussopoulos, Nick} } @article {18405, title = {Monitoring an Ada software development}, journal = {ACM SIG Ada Letters}, volume = {IV}, year = {1984}, month = {1984/07//}, pages = {32 - 39}, isbn = {1094-3641}, doi = {10.1145/998401.998402}, url = {http://doi.acm.org/10.1145/998401.998402}, author = {Basili, Victor R. and Chang,Shih and Gannon,John and Katz,Elizabeth and Panlilio-Yap,N. Monina and Ramsey,Connie Loggia and Zelkowitz, Marvin V and Bailey,John and Kruesi,Elizabeth and Sheppard,Sylvia} } @article {16788, title = {Timing Requirements for Time-Driven Systems Using Augmented Petri Nets}, journal = {IEEE Transactions on Software Engineering}, volume = {SE-9}, year = {1983}, month = {1983/09//}, pages = {603 - 616}, abstract = {A methodology for the statement of timing requirements is presented for a class of embedded computer systems. The notion of a "time-driven" system is introduced which is formalized using a Petri net model augmented with timing information. Several subclasses of time-driven systems are defined with increasing levels of complexity. By deriving the conditions under which the Petri net model can be proven to be safe in the presence of time, timing requirements for modules in the system can be obtained. Analytical techniques are developed for proving safeness in the presence of time for the net constructions used in the defined subclasses of time-driven systems.}, keywords = {Application software, Concurrent computing, Control systems, Embedded computing, Embedded system, Helium, Modeling methodology, performance specifications, Petri nets, Power system modeling, Real time systems, real-time systems, Timing, timing requirements}, isbn = {0098-5589}, doi = {10.1109/TSE.1983.235261}, author = {Coolahan,J. E. and Roussopoulos, Nick} } @conference {18142, title = {A complexity theory for unbounded fan-in parallelism}, booktitle = {23rd Annual Symposium on Foundations of Computer Science}, year = {1982}, month = {1982///}, pages = {1 - 13}, author = {Chandra,A. K and Stockmeyer,L. J and Vishkin, Uzi} } @conference {18450, title = {Use of cluster analysis to evaluate software engineering methodologies}, booktitle = {Proceedings of the 5th international conference on Software engineering}, series = {ICSE {\textquoteright}81}, year = {1981}, month = {1981///}, pages = {117 - 123}, publisher = {IEEE Press}, organization = {IEEE Press}, address = {Piscataway, NJ, USA}, abstract = {The development of quantitative measures to evaluate software development techniques is necessary if we are going to develop appropriate methodologies for software production. Data is collected by the Software Engineering Laboratory at NASA Goddard Space Flight Center on developing medium scale projects of up to ten man years effort. In this study, cluster analysis was used on this collected data and several measures are proposed. These measurements are objective, quantifiable, are the results of the methodology, and most important, seem relevant.}, isbn = {0-89791-146-6}, url = {http://dl.acm.org/citation.cfm?id=800078.802523}, author = {Chen,Eric and Zelkowitz, Marvin V} } @conference {16770, title = {Systematic Derivation of Software Requirements}, booktitle = {Proceedings of the 1st International Conference on the Entity-Relationship Approach to Systems Analysis and Design}, year = {1980}, month = {1980///}, pages = {403 - 404}, author = {Yeh,R. Y and Roussopoulos, Nick and Chang,P.} } @article {15775, title = {Numerical Solution of Nonlinear Elliptic Partial Differential Equations by a Generalized Conjugate Gradient Method}, journal = {Computing}, volume = {19}, year = {1978}, month = {1978///}, pages = {321 - 339}, abstract = {We have studied previously a generalized conjugate gradient method for solving sparse positive-definite systems of linear equations arising from the discretization of elliptic partial-differential boundary-value problems. Here, extensions to the nonlinear case are considered. We split the original discretized operator into the sum of two operators, one of which corresponds to a more easily solvable system of equations, and accelerate the associated iteration based on this splitting by (nonlinear) conjugate gradients. The behavior of the method is illustrated for the minimal surface equation with splittings corresponding to nonlinear SSOR, to approximate factorization of the Jacobian matrix, and to elliptic operators suitable for use with fast direct methods. The results of numerical experiments are given as well for a mildy nonlinear example, for which, in the corresponding linear case, the finite termination property of the conjugate gradient algorithm is crucial.}, author = {Concus,Paul and Golub, Gene H. and O{\textquoteright}Leary, Dianne P.} } @inbook {15701, title = {A Generalized Conjugate Gradient Method for the Numerical Solution of Elliptic Partial Differential Equations}, booktitle = {Sparse Matrix ComputationsSparse Matrix Computations}, year = {1976}, month = {1976///}, pages = {309 - 332}, publisher = {Academic Press}, organization = {Academic Press}, address = {New York}, abstract = {We consider a generalized conjugate gradient method for solvingsparse, symmetric, positive-definite systems of linear equations, principally those arising from the discretization of boundary value problems for elliptic partial differential equations. The method is based on splitting off from the original coefficient matrix a symmetric, positive-definiteonethat corresponds to a more easily solvable system of equations, and then accelerating the associated iteration using conjugate gradients. Optimality and convergence properties are presented, and the relation to other methods is discussed. Several splittings for which the method seems particularly effective are also discussed, and for some, numerical examples are given }, author = {Concus,Paul and Golub, Gene H. and O{\textquoteright}Leary, Dianne P.}, editor = {Bunch,James R. and Rose,Donald J.} } @article {16724, title = {TORUS: A step towards bridging the gap between data bases and the casual user}, journal = {Information Systems}, volume = {2}, year = {1976}, month = {1976///}, pages = {49 - 64}, abstract = {This paper describes TORUS, a natural language understanding system that serves as a front end to a data base management system in order to facilitate communication with casual users. The system employs a semantic network to store knowledge about a data base of student files. This knowledge is used to find the meaning of each input statement, to decide what action to take with respect to the data base, and to select information that must be output in response to the input statement. A prototype version of TORUS has been implemented.}, isbn = {0306-4379}, doi = {16/0306-4379(76)90009-0}, url = {http://www.sciencedirect.com/science/article/pii/0306437976900090}, author = {Mylopoulos,J. and Borgida,A. and Cohen,P. and Roussopoulos, Nick and Tsotsos,J. and Wong,H.} } @conference {16721, title = {TORUS-a natural language understanding system for data management}, booktitle = {Proceedings of the Fourth International Conference on Artificial Intelligence}, year = {1975}, month = {1975///}, pages = {414 - 421}, author = {Mylopoulos,J. and Borgida,A. and Cohen,P. and Roussopoulos, Nick and Tsotsos,J. and Wong,H.} }