@article {19692, title = {Evaluating Regularized Anchor Words}, journal = {mimno.infosci.cornell.edu}, year = {Submitted}, abstract = {Abstract We perform a comprehensive examination of the recently proposed anchor method for topic model inference using topic interpretability and held-out likelihood measures. After measuring the sensitivity to the anchor selection process, we incorporate L2 and Beta ...}, url = {http://mimno.infosci.cornell.edu/nips2013ws/nips2013tm_submission_27.pdf}, author = {Nguyen, T and Hu, Y and Jordan Boyd-Graber} } @article {19690, title = {Topic Models for Translation Domain Adaptation}, journal = {mimno.infosci.cornell.edu}, year = {Submitted}, abstract = {Abstract Topic models have been successfully applied in domain adaptation for translation models. However, previous works applied topic models only on source side and ignored the relations between source and target languages in machine translation. This paper ...}, url = {http://mimno.infosci.cornell.edu/nips2013ws/nips2013tm_submission_19.pdf}, author = {Hu, Y and Zhai, K and Edelman, V and Jordan Boyd-Graber} } @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 {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 {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} } @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 {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 {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 {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 {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} } @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 {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.} } @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 {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 {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 {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} } @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 {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.} } @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 {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 {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 {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 {19684, title = {Argviz: Interactive Visualization of Topic Dynamics in Multi-party Conversations}, journal = {Human Language Technologies: The 2013 Annual Conference of the North American Chapter of the Association for Computational Linguistics}, year = {2013}, month = {2013/00/01}, abstract = {Abstract We introduce an efficient, interactive framework{\textemdash}Argviz{\textemdash}for experts to analyze the dynamic topical structure of multi-party conversations. Users inject their needs, expertise, and insights into models via iterative topic refinement. The refined topics feed into a ...}, url = {https://www.aclweb.org/anthology-new/N/N13/N13-3.pdf$\#$page=42}, author = {Nguyen, V A and Hu, Y and Jordan Boyd-Graber} } @article {19685, title = {Binary to Bushy: Bayesian Hierarchical Clustering with the Beta Coalescent}, year = {2013}, month = {2013/00/01}, pages = {1079 - 1087}, abstract = {Abstract Discovering hierarchical regularities in data is a key problem in interacting with large datasets, modeling cognition, and encoding knowledge. A previous Bayesian solution-- -Kingman{\textquoteright}s coalescent---provides a convenient probabilistic model for data represented ...}, url = {http://papers.nips.cc/paper/5161-binary-to-bushy-bayesian-hierarchical-clustering-with-the-beta-coalescent}, author = {Hu, Yuening and Jordan Boyd-Graber and Daume III, Hal and Ying, Z Irene} } @conference {19215, title = {Combining Crowdsourcing and Google Street View to Identify Street-level Accessibility Problems}, booktitle = {CHI 2013 To Appear}, year = {2013}, month = {2013}, abstract = {Poorly maintained sidewalks, missing curb ramps, and other obstacles pose considerable accessibility challenges; however, there are currently few if any, mechanisms to determine accessible areas of a city a priori. In this paper, we investigate the feasibility of using untrained crowd workers from Amazon Mechanical Turk (turkers) to find, label, and assess sidewalk accessibility problems in Google Street View imagery. We report on two studies: Study 1 examines the feasibility of this labeling task with six dedicated labelers including three wheelchair users; Study 2 investigates the comparative performance of turkers. In all, we collected 13,379 labels and 19,189 verification labels from a total of 402 turkers We show that turkers are capable of determining the presence of an accessibility problem with 81\% accuracy. With simple quality control methods, this number increases to 93\%. Our work demonstrates a promising new, highly scalable method for acquiring knowledge about sidewalk accessibility. }, author = {Hara, K. and Le, V. and Jon Froehlich} } @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 {19705, title = {Exploring Early Solutions for Automatically Identifying Inaccessible Sidewalks in the Physical World Using Google Street View}, journal = {HCIC 2013}, year = {2013}, month = {2013/00/01}, abstract = {Abstract Poorly maintained sidewalks , missing curb ramps, and other obstacles pose considerable accessibility challenges. Although pedestrian-and bicycle-oriented maps and associated routing algorithms continue to improve, there has been a lack of work focusing ...}, url = {http://www.cs.umd.edu/~jonf/publications/Hara_ExploringEarlySolutionsForAutomaticallyIdentifyingInaccessibleSidewalksInThePhysicalWorldUsingGoogleStreetView_HCIC2013.pdf}, author = {Hara, K and Le, V and Sun, J and Jacobs, D and Jon Froehlich} } @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} } @conference {19213, title = {Mind the Theoretical Gap: Interpreting, Using, and Developing Behavioral Theory in HCI Research}, booktitle = {CHI 2013 To Appear}, year = {2013}, month = {2013}, author = {Hekler, E. B. and Klasnja,P. and Jon Froehlich and Buman, M. P.} } @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 {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 {19716, title = {TIGRFAMs and Genome Properties in 2013.}, journal = {Nucleic Acids Res}, volume = {41}, year = {2013}, month = {2013 Jan}, pages = {D387-95}, abstract = {

TIGRFAMs, available online at http://www.jcvi.org/tigrfams is a database of protein family definitions. Each entry features a seed alignment of trusted representative sequences, a hidden Markov model (HMM) built from that alignment, cutoff scores that let automated annotation pipelines decide which proteins are members, and annotations for transfer onto member proteins. Most TIGRFAMs models are designated equivalog, meaning they assign a specific name to proteins conserved in function from a common ancestral sequence. Models describing more functionally heterogeneous families are designated subfamily or domain, and assign less specific but more widely applicable annotations. The Genome Properties database, available at http://www.jcvi.org/genome-properties, specifies how computed evidence, including TIGRFAMs HMM results, should be used to judge whether an enzymatic pathway, a protein complex or another type of molecular subsystem is encoded in a genome. TIGRFAMs and Genome Properties content are developed in concert because subsystems reconstruction for large numbers of genomes guides selection of seed alignment sequences and cutoff values during protein family construction. Both databases specialize heavily in bacterial and archaeal subsystems. At present, 4284 models appear in TIGRFAMs, while 628 systems are described by Genome Properties. Content derives both from subsystem discovery work and from biocuration of the scientific literature.

}, keywords = {Databases, Protein, Genome, Archaeal, Genome, Bacterial, Genomics, Internet, Markov chains, Molecular Sequence Annotation, Proteins, sequence alignment}, issn = {1362-4962}, doi = {10.1093/nar/gks1234}, author = {Haft, Daniel H and Jeremy D Selengut and Richter, Roland A and Harkins, Derek and Basu, Malay K and Beck, Erin} } @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 {19723, title = {Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification.}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 Jan}, pages = {36-48}, abstract = {

Multiple new prokaryotic C-terminal protein-sorting signals were found that reprise the tripartite architecture shared by LPXTG and PEP-CTERM: motif, TM helix, basic cluster. Defining hidden Markov models were constructed for all. PGF-CTERM occurs in 29 archaeal species, some of which have more than 50 proteins that share the domain. PGF-CTERM proteins include the major cell surface protein in Halobacterium, a glycoprotein with a partially characterized diphytanylglyceryl phosphate linkage near its C terminus. Comparative genomics identifies a distant exosortase homolog, designated archaeosortase A (ArtA), as the likely protein-processing enzyme for PGF-CTERM. Proteomics suggests that the PGF-CTERM region is removed. Additional systems include VPXXXP-CTERM/archeaosortase B in two of the same archaea and PEF-CTERM/archaeosortase C in four others. Bacterial exosortases often fall into subfamilies that partner with very different cohorts of extracellular polymeric substance biosynthesis proteins; several species have multiple systems. Variant systems include the VPDSG-CTERM/exosortase C system unique to certain members of the phylum Verrucomicrobia, VPLPA-CTERM/exosortase D in several alpha- and deltaproteobacterial species, and a dedicated (single-target) VPEID-CTERM/exosortase E system in alphaproteobacteria. Exosortase-related families XrtF in the class Flavobacteria and XrtG in Gram-positive bacteria mark distinctive conserved gene neighborhoods. A picture emerges of an ancient and now well-differentiated superfamily of deeply membrane-embedded protein-processing enzymes. Their target proteins are destined to transit cellular membranes during their biosynthesis, during which most undergo additional posttranslational modifications such as glycosylation.

}, keywords = {Amino Acid Sequence, Aminoacyltransferases, Archaeal Proteins, Bacterial Proteins, Cell Membrane, Cysteine Endopeptidases, Gene Expression Regulation, Archaeal, Gene Expression Regulation, Bacterial, Gene Expression Regulation, Enzymologic, Molecular Sequence Data, Protein Processing, Post-Translational}, issn = {1098-5530}, doi = {10.1128/JB.06026-11}, author = {Haft, Daniel H and Payne, Samuel H and Jeremy D Selengut} } @article {13505, title = {Automatic Authentication of Banknotes}, journal = {IEEE Transactions on Information Forensics \& Security}, year = {2012}, month = {2012///}, abstract = {In this paper, we address the problem of the automatic authentication of paper currency. Indian banknotes are used to show how a system can be developed for discriminating counterfeit notes from genuine notes. Image processing and pattern recognition techniques are designed to carefully analyze embedded security features. Experiments conducted on forensic samples show that a high precision low cost machine can be developed to address this problem. The analysis of current security features{\textquoteright} ability to protect against counterfeiting also suggest topics that should be considered in designing future currency notes.}, author = {Roy,Ankush and Halder,Biswaiit and Garain,Utpal and David Doermann} } @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 {19135, title = {Bioinformatics for the Human Microbiome Project}, journal = {PLoS Computational Biology}, volume = {8}, year = {2012}, month = {11/2012}, pages = {e1002779}, doi = {10.1371/journal.pcbi.1002779}, author = {Gevers, Dirk and Pop, Mihai and Schloss, Patrick D. and Huttenhower, Curtis} } @conference {18334, title = {Co-designing an e-health tutorial for older adults}, booktitle = {Proceedings of the 2012 iConference}, series = {iConference {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {240 - 247}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Older adults{\textquoteright} ability to access and use electronic health information is generally low, requiring innovative approaches for improvement. An integrated e-tutorial overlays instructions onto Websites. The literature suggests integrated e-tutorials are more effective than paper or video-based tutorials for younger people, but little is known about their effectiveness for older adults. This study explores the applicability of an integrated e-health tutorial for older adults. An integrated e-tutorial, the Online Tutorial Overlay Presenter (OnTOP), added an instructional overlay to the NIHSeniorHealth.gov Website. Overlay features were examined in seven participatory design sessions with seven older adults. Participatory design techniques were used to elicit participants{\textquoteright} preferences for tutorial features. Three themes emerged: 1) using contextual cues; 2) tailoring to the learner{\textquoteright}s literacy level; and 3) enhancing interfaces with multimedia cues. These findings improved the design features of OnTOP. They also generated empirical evidence about the effects of multimedia learning among older adults.}, keywords = {e-health literacy, health information seeking, integrated e-tutorial, participatory design}, isbn = {978-1-4503-0782-6}, doi = {10.1145/2132176.2132207}, url = {http://doi.acm.org/10.1145/2132176.2132207}, author = {Xie,Bo and Tom Yeh and Walsh,Greg and Watkins,Ivan and Huang,Man} } @article {13065, title = {Density-Based Multifeature Background Subtraction with Support Vector Machine}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {34}, year = {2012}, month = {2012/05//}, pages = {1017 - 1023}, abstract = {Background modeling and subtraction is a natural technique for object detection in videos captured by a static camera, and also a critical preprocessing step in various high-level computer vision applications. However, there have not been many studies concerning useful features and binary segmentation algorithms for this problem. We propose a pixelwise background modeling and subtraction technique using multiple features, where generative and discriminative techniques are combined for classification. In our algorithm, color, gradient, and Haar-like features are integrated to handle spatio-temporal variations for each pixel. A pixelwise generative background model is obtained for each feature efficiently and effectively by Kernel Density Approximation (KDA). Background subtraction is performed in a discriminative manner using a Support Vector Machine (SVM) over background likelihood vectors for a set of features. The proposed algorithm is robust to shadow, illumination changes, spatial variations of background. We compare the performance of the algorithm with other density-based methods using several different feature combinations and modeling techniques, both quantitatively and qualitatively.}, keywords = {algorithm;density-based, application;illumination, approximation;object, background, camera;support, change;kernel, Computer, density, detection;pixelwise, detection;support, extraction;image, feature;background, generative, Haar-like, likelihood, machine;Haar, machines;vectors;, modeling, multifeature, segmentation, segmentation;object, subtraction, technique;discriminative, technique;high-level, techniques;spatial, transforms;cameras;computer, variation;spatio-temporal, variation;static, vector, vector;binary, VISION, vision;feature}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2011.243}, author = {Han,Bohyung and Davis, Larry 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 {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.} } @conference {14906, title = {Dynamic changes in motivation in collaborative citizen-science projects}, booktitle = {Proceedings of the ACM 2012 conference on Computer Supported Cooperative Work}, series = {CSCW {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {217 - 226}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Online citizen science projects engage volunteers in collecting, analyzing, and curating scientific data. Existing projects have demonstrated the value of using volunteers to collect data, but few projects have reached the full collaborative potential of scientists and volunteers. Understanding the shared and unique motivations of these two groups can help designers establish the technical and social infrastructures needed to promote effective partnerships. We present findings from a study of the motivational factors affecting participation in ecological citizen science projects. We show that volunteers are motivated by a complex framework of factors that dynamically change throughout their cycle of work on scientific projects; this motivational framework is strongly affected by personal interests as well as external factors such as attribution and acknowledgment. Identifying the pivotal points of motivational shift and addressing them in the design of citizen-science systems will facilitate improved collaboration between scientists and volunteers.}, keywords = {citizen science, Collaboration, crowdsourcing, ecology, motivation, scientists, volunteers}, isbn = {978-1-4503-1086-4}, doi = {10.1145/2145204.2145238}, url = {http://doi.acm.org/10.1145/2145204.2145238}, author = {Rotman,Dana and Preece,Jenny and Hammock,Jen and Procita,Kezee and Hansen,Derek and Parr,Cynthia and Lewis,Darcy and Jacobs, David W.} } @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} } @article {12422, title = {Efficient Tree-Based Topic Modeling}, journal = {Association for Computational Linguistics}, year = {2012}, month = {2012///}, abstract = {Topic modeling with a tree-based prior has been used for a variety of applications be- cause it can encode correlations between words that traditional topic modeling cannot. How- ever, its expressive power comes at the cost of more complicated inference. We extend the SPARSELDA (Yao et al., 2009) inference scheme for latent Dirichlet allocation (LDA) to tree-based topic models. This sampling scheme computes the exact conditional distri- bution for Gibbs sampling much more quickly than enumerating all possible latent variable assignments. We further improve performance by iteratively refining the sampling distribution only when needed. Experiments show that the proposed techniques dramatically improve the computation time.}, author = {Hu,Yuening and Jordan Boyd-Graber} } @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.} } @conference {19217, title = {A feasibility study of crowdsourcing and google street view to determine sidewalk accessibility}, year = {2012}, month = {2012}, pages = {273 - 274}, publisher = {ACM}, organization = {ACM}, isbn = {1450313213}, author = {Hara, K. and Le, V. and Jon Froehlich} } @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 {19718, title = {Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.}, journal = {ISME J}, volume = {6}, year = {2012}, month = {2012 Jun}, pages = {1186-99}, abstract = {

Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition.

}, keywords = {Computational Biology, Gammaproteobacteria, Genome, Bacterial, Genomic Library, metagenomics, Oceans and Seas, Phylogeny, plankton, Rhodopsin, RNA, Ribosomal, 16S, Seawater}, issn = {1751-7370}, doi = {10.1038/ismej.2011.189}, author = {Dupont, Chris L and Rusch, Douglas B and Yooseph, Shibu and Lombardo, Mary-Jane and Richter, R Alexander and Valas, Ruben and Novotny, Mark and Yee-Greenbaum, Joyclyn and Jeremy D Selengut and Haft, Dan H and Halpern, Aaron L and Lasken, Roger S and Nealson, Kenneth and Friedman, Robert and Venter, J Craig} } @article {17249, title = {Interactive Dynamics for Visual Analysis}, journal = {Queue - Micoprocessors}, volume = {10}, year = {2012}, month = {2012/02//}, pages = {30:30{\textendash}30:55 - 30:30{\textendash}30:55}, abstract = {A taxonomy of tools that support the fluent and flexible use of visualizations}, isbn = {1542-7730}, doi = {10.1145/2133416.2146416}, url = {http://doi.acm.org/10.1145/2133416.2146416}, author = {Heer,Jeffrey and Shneiderman, Ben} } @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 {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 {17673, title = {Mobile Data Offloading through Opportunistic Communications and Social Participation}, journal = {Mobile Computing, IEEE Transactions on}, volume = {11}, year = {2012}, month = {2012/05//}, pages = {821 - 834}, abstract = {3G networks are currently overloaded, due to the increasing popularity of various applications for smartphones. Offloading mobile data traffic through opportunistic communications is a promising solution to partially solve this problem, because there is almost no monetary cost for it. We propose to exploit opportunistic communications to facilitate information dissemination in the emerging Mobile Social Networks (MoSoNets) and thus reduce the amount of mobile data traffic. As a case study, we investigate the target-set selection problem for information delivery. In particular, we study how to select the target set with only k users, such that we can minimize the mobile data traffic over cellular networks. We propose three algorithms, called Greedy, Heuristic, and Random, for this problem and evaluate their performance through an extensive trace-driven simulation study. Our simulation results verify the efficiency of these algorithms for both synthetic and real-world mobility traces. For example, the Heuristic algorithm can offload mobile data traffic by up to 73.66 percent for a real-world mobility trace. Moreover, to investigate the feasibility of opportunistic communications for mobile phones, we implement a proof-of-concept prototype, called Opp-off, on Nokia N900 smartphones, which utilizes their Bluetooth interface for device/service discovery and content transfer.}, keywords = {3G mobile communication, 3G networks, Bluetooth interface, cellular networks, cellular radio, content transfer, device/service discovery, graph theory, greedy algorithm, heuristic algorithm, information delivery, information dissemination, mobile data offloading, mobile data traffic, mobile phones, mobile social networks, MoSoNets, Nokia N900 smartphones, Opp-off, opportunistic communications, random algorithm, real-world mobility traces, smart phones, social networking (online), social participation, target-set selection problem, telecommunication network routing, Telecommunication traffic, trace-driven simulation study}, isbn = {1536-1233}, doi = {10.1109/TMC.2011.101}, author = {Han,Bo and Hui,Pan and Kumar,V. S.A and Marathe,M. V and Shao,Jianhua and Srinivasan, Aravind} } @conference {12423, title = {Modeling Images using Transformed Indian Buffet Processes}, booktitle = {International Conference of Machine Learning}, year = {2012}, month = {2012///}, abstract = {Latent feature models are attractive for image modeling, since images generally contain mul- tiple objects. However, many latent feature models ignore that objects can appear at dif- ferent locations or require pre-segmentation of images. While the transformed Indian buffet process (tIBP) provides a method for modeling transformation-invariant features in unsegmented binary images, its current form is inappropriate for real images because of its computational cost and modeling assumptions. We combine the tIBP with likelihoods appropriate for real images and develop an efficient inference, using the cross- correlation between images and features, that is theoretically and empirically faster than existing inference techniques. Our method discovers rea- sonable components and achieve effective image reconstruction in natural images.}, author = {Zhai,Ke and Hu,Yuening and Williamson,Sinead and Jordan Boyd-Graber} } @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.} } @article {14415, title = {Organizing User Search Histories}, journal = {Knowledge and Data Engineering, IEEE Transactions on}, volume = {24}, year = {2012}, month = {2012/05//}, pages = {912 - 925}, abstract = {Users are increasingly pursuing complex task-oriented goals on the web, such as making travel arrangements, managing finances, or planning purchases. To this end, they usually break down the tasks into a few codependent steps and issue multiple queries around these steps repeatedly over long periods of time. To better support users in their long-term information quests on the web, search engines keep track of their queries and clicks while searching online. In this paper, we study the problem of organizing a user{\textquoteright}s historical queries into groups in a dynamic and automated fashion. Automatically identifying query groups is helpful for a number of different search engine components and applications, such as query suggestions, result ranking, query alterations, sessionization, and collaborative search. In our approach, we go beyond approaches that rely on textual similarity or time thresholds, and we propose a more robust approach that leverages search query logs. We experimentally study the performance of different techniques, and showcase their potential, especially when combined together.}, keywords = {alteration;query, analysis;user, engines;search, engines;text, goal;textual, group, historical, History, identification;query, information, interfaces;, log;sessionization;task-oriented, organization;query, processing;search, query, query;user, quest;query, ranking;search, search, search;long-term, similarity;time, suggestion;result, threshold;user, Web;collaborative}, isbn = {1041-4347}, doi = {10.1109/TKDE.2010.251}, author = {Hwang,Heasoo and Lauw,H. W and Getoor, Lise and Ntoulas,A.} } @article {19254, title = {Prototyping scalable digital signal processing systems for radio astronomy using dataflow models}, journal = {Radio Science}, volume = {47}, year = {2012}, month = {2012}, pages = {n/a - n/a}, abstract = {There is a growing trend toward using high-level tools for design and implementation of radio astronomy digital signal processing (DSP) systems. Such tools, for example, those from the Collaboration for Astronomy Signal Processing and Electronics Research (CASPER), are usually platform-specific, and lack high-level, platform-independent, portable, scalable application specifications. This limits the designer{\textquoteright}s ability to experiment with designs at a high-level of abstraction and early in the development cycle. We address some of these issues using a model-based design approach employing dataflow models. We demonstrate this approach by applying it to the design of a tunable digital downconverter (TDD) used for narrow-bandwidth spectroscopy. Our design is targeted toward an FPGA platform, called theInterconnect Break-out Board (IBOB), that is available from the CASPER. We use the term TDD to refer to a digital downconverter for which the decimation factor and center frequency can be reconfigured without the need for regenerating the hardware code. Such a design is currently not available in the CASPER DSP library. The work presented in this paper focuses on two aspects. First, we introduce and demonstrate a dataflow-based design approach using thedataflow interchange format (DIF) tool for high-level application specification, and we integrate this approach with the CASPER tool flow. Secondly, we explore the trade-off between the flexibility of TDD designs and the low hardware cost of fixed-configuration digital downconverter (FDD) designs that use the available CASPER DSP library. We further explore this trade-off in the context of a two-stage downconversion scheme employing a combination of TDD or FDD designs.}, keywords = {dataflow models, digital downconverter, Digital signal processing, model-based design, radio astronomy, rapid prototyping}, isbn = {1944-799X}, url = {http://onlinelibrary.wiley.com/doi/10.1029/2011RS004924/abstract}, author = {Sane, N. and Ford, J. and Harris, A. I. and Bhattacharyya, Shuvra S.} } @article {15108, title = {Quid Pro Quo-tocols: Strengthening Semi-Honest Protocols with Dual Execution}, journal = {IEEE Symposium on Security and Privacy}, year = {2012}, month = {2012///}, abstract = {Known protocols for secure two-party computa-tion that are designed to provide full security against malicious behavior are significantly less efficient than protocols intended only to thwart semi-honest adversaries. We present a concrete design and implementation of protocols achieving security guarantees that are much stronger than are possible with semi-honest protocols, at minimal extra cost. Specifically, we consider protocols in which a malicious adversary may learn a single (arbitrary) bit of additional information about the honest party{\textquoteright}s input. Correctness of the honest party{\textquoteright}s output is still guaranteed. Adapting prior work of Mohassel and Franklin, the basic idea in our protocols is to conduct two separate runs of a (specific) semi-honest, garbled-circuit protocol, with the parties swapping roles, followed by an inexpensive secure equality test. We provide a rigorous definition and prove that this protocol leaks no more than one additional bit against a malicious adversary. In addition, we propose some heuristic enhancements to reduce the overall information a cheating adversary learns. Our experiments show that protocols meeting this security level can be implemented at cost very close to that of protocols that only achieve semi-honest security. Our results indicate that this model enables the large-scale, practical applications possible within the semi-honest security model, while providing stronger security guarantees. }, author = {Huang,Y. and Katz, Jonathan and Evans,D.} } @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.} } @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} } @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} } @article {19717, title = {Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.}, journal = {PLoS Negl Trop Dis}, volume = {6}, year = {2012}, month = {2012}, pages = {e1853}, abstract = {

The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010(T) and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics.

}, keywords = {DNA, Bacterial, Evolution, Molecular, Gene Transfer, Horizontal, Genome, Bacterial, Genomic islands, HUMANS, Leptospira, Molecular Sequence Data, Multigene Family, Prophages, Sequence Analysis, DNA, Virulence factors}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0001853}, author = {Ricaldi, Jessica N and Fouts, Derrick E and Jeremy D Selengut and Harkins, Derek M and Patra, Kailash P and Moreno, Angelo and Lehmann, Jason S and Purushe, Janaki and Sanka, Ravi and Torres, Michael and Webster, Nicholas J and Vinetz, Joseph M and Matthias, Michael A} } @article {19181, title = {Ability-based design: Concept, principles and examples}, journal = {ACM Transactions on Accessible Computing (TACCESS)}, volume = {3}, year = {2011}, month = {2011}, author = {Wobbrock,J.O. and Kane,S.K. and Gajos,K.Z. and Harada,S. and Jon Froehlich} } @article {14592, title = {Accelerated evolution of 3{\textquoteright}avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1}, journal = {BMC Evolutionary Biology}, volume = {11}, year = {2011}, month = {2011/10/15/}, pages = {302 - 302}, abstract = {The forkhead transcription factor gene E1 (FOXE1) plays an important role in regulation of thyroid development, palate formation and hair morphogenesis in mammals. However, avian FOXE1 genes have not been characterized and as such, codon evolution of FOXE1 orthologs in a broader evolutionary context of mammals and birds is not known.}, isbn = {1471-2148}, doi = {10.1186/1471-2148-11-302}, url = {http://www.biomedcentral.com/1471-2148/11/302}, author = {Yaklichkin,Sergey Yu and Darnell,Diana K and Pier,Maricela V and Antin,Parker B and Hannenhalli, Sridhar} } @conference {16042, title = {Active progress bars: facilitating the switch to temporary activities}, 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 = {1963 - 1968}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this paper, we seek to find a better way of effective task management when a progress bar interrupts user{\textquoteright}s primary activity. We propose to augment progress bars with user controlled functionalities facilitating the switch to temporary activities. We detail a taxonomy of waiting period contexts and possible temporary tasks, then report on 5 participatory design, and a follow-up survey of 96 respondents. Finally we describe an early prototype of active progress bars, and report on initial use.}, keywords = {Frustration, participatory design, progress bars, task switching}, isbn = {978-1-4503-0268-5}, doi = {10.1145/1979742.1979883}, url = {http://doi.acm.org/10.1145/1979742.1979883}, author = {Hurter,Christophe and Girouard,Audrey and Riche,Nathalie and Plaisant, Catherine} } @article {19279, title = {Analysis of SystemC actor networks for efficient synthesis}, journal = {ACM Trans. Embed. Comput. Syst.}, volume = {10}, year = {2011}, month = {2011}, pages = {18:1 - 18:34}, abstract = {Applications in the signal processing domain are often modeled by dataflow graphs. Due to heterogeneous complexity requirements, these graphs contain both dynamic and static dataflow actors. In previous work, we presented a generalized clustering approach for these heterogeneous dataflow graphs in the presence of unbounded buffers. This clustering approach allows the application of static scheduling methodologies for static parts of an application during embedded software generation for multiprocessor systems. It systematically exploits the predictability and efficiency of the static dataflow model to obtain latency and throughput improvements. In this article, we present a generalization of this clustering technique to dataflow graphs with bounded buffers, therefore enabling synthesis for embedded systems without dynamic memory allocation. Furthermore, a case study is given to demonstrate the performance benefits of the approach.}, keywords = {actor-oriented design, clustering, Dataflow analysis, scheduling}, isbn = {1539-9087}, url = {http://doi.acm.org/10.1145/1880050.1880054}, author = {Falk, Joachim and Zebelein, Christian and Keinert, Joachim and Haubelt, Christian and Teich, Juergen and Bhattacharyya, Shuvra S.} } @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 {17566, title = {Article 28 (28 pages)-New Constructive Aspects of the Lov{\'a}sz Local Lemma}, journal = {Journal of the ACM-Association for ComputingMachinery}, volume = {58}, year = {2011}, month = {2011///}, author = {Haeupler,B. and Saha,B. and Srinivasan, Aravind} } @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} } @article {18795, title = {A Case Study in Optimization of Gait and Physical Parameters for a Snake-Inspired Robot Based on a Rectilinear Gait}, journal = {Journal of mechanisms and robotics}, volume = {3}, year = {2011}, month = {2011///}, abstract = {Physical parameters of the constituent modules and gait parameters affect the overall performance of snake-inspired robots. Hence, a system-level optimization model needs to concurrently optimize the module parameters and the gait. Incorporating a physics-based model of rectilinear gaits in the system-level optimization model is a computationally challenging problem. This paper presents a case study to illustrate how metamodels of the precomputed optimal rectilinear gaits can be utilized to reduce the complexity of the system-level optimization model. An example is presented to illustrate the importance of concurrently optimizing the module parameters and the gait to obtain the optimal performance for a given mission.}, isbn = {1942-4302}, url = {http://cat.inist.fr/?aModele=afficheN\&cpsidt=23978760}, author = {Hopkins,James K. and Spranklin,Brent W. and Gupta, Satyandra K.} } @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} } @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 {15126, title = {Complete Fairness in Secure Two-Party Computation}, journal = {Journal of the ACM}, volume = {58}, year = {2011}, month = {2011/12//}, pages = {24:1{\textendash}24:37 - 24:1{\textendash}24:37}, abstract = {In the setting of secure two-party computation, two mutually distrusting parties wish to compute some function of their inputs while preserving, to the extent possible, various security properties such as privacy, correctness, and more. One desirable property is fairness which guarantees, informally, that if one party receives its output, then the other party does too. Cleve [1986] showed that complete fairness cannot be achieved in general without an honest majority. Since then, the accepted folklore has been that nothing non-trivial can be computed with complete fairness in the two-party setting. We demonstrate that this folklore belief is false by showing completely fair protocols for various nontrivial functions in the two-party setting based on standard cryptographic assumptions. We first show feasibility of obtaining complete fairness when computing any function over polynomial-size domains that does not contain an {\textquotedblleft}embedded XOR{\textquotedblright}; this class of functions includes boolean AND/OR as well as Yao{\textquoteright}s {\textquotedblleft}millionaires{\textquoteright} problem{\textquotedblright}. We also demonstrate feasibility for certain functions that do contain an embedded XOR, though we prove a lower bound showing that any completely fair protocol for such functions must have round complexity super-logarithmic in the security parameter. Our results demonstrate that the question of completely fair secure computation without an honest majority is far from closed.}, keywords = {cryptography, fairness, secure computation}, isbn = {0004-5411}, doi = {10.1145/2049697.2049698}, url = {http://doi.acm.org/10.1145/2049697.2049698}, author = {Gordon,S. Dov and Hazay,Carmit and Katz, Jonathan and Lindell,Yehuda} } @article {18335, title = {Co-designing contextual tutorials for older adults on searching health information on the internet}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {48}, year = {2011}, month = {2011/01/01/}, pages = {1 - 4}, abstract = {Evidence in the literature suggests an integrated e-tutorial is more effective than a paper- or video-based tutorial among younger people. Yet, relatively little is known about the effectiveness of an integrated e-tutorial on the older population. This study explored the applicability of an integrated e-tutorial to an older population, focusing on the content area of e-health literacy. A specific integrated e- tutorial, the Online Tutorial Overlay Presenter (OnTOP), was used to add an overlay to the NIHSeniorHealth.gov Website. Features of the overlay were examined thoroughly in seven 2-hour-long participatory design sessions with ten older adults. Several participatory design techniques were used to elicit participants{\textquoteright} preferences for design features of the OnTOP tutorial. These techniques included drawing on the board, voice recording and integration, and peer instruction. Three major themes emerged: 1) using contextual cues to facilitate learning; 2) tailoring to accommodate the learner{\textquoteright}s literacy level; and 3) enhancing existing interfaces with multimedia cues. These findings improved the design of OnTOP. They also contribute to the multimedia learning literature, generating empirical evidence about the effects of multimedia learning among the understudied older adult population.}, isbn = {1550-8390}, doi = {10.1002/meet.2011.14504801160}, url = {http://onlinelibrary.wiley.com/doi/10.1002/meet.2011.14504801160/abstract}, author = {Xie,Bo and Tom Yeh and Walsh,Greg and Watkins,Ivan and Huang,Man} } @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.} } @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} } @inbook {14676, title = {Directed Symbolic Execution}, booktitle = {Static AnalysisStatic Analysis}, series = {Lecture Notes in Computer Science}, volume = {6887}, year = {2011}, month = {2011///}, pages = {95 - 111}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In this paper, we study the problem of automatically finding program executions that reach a particular target line. This problem arises in many debugging scenarios; for example, a developer may want to confirm that a bug reported by a static analysis tool on a particular line is a true positive. We propose two new directed symbolic execution strategies that aim to solve this problem: shortest-distance symbolic execution (SDSE) uses a distance metric in an interprocedural control flow graph to guide symbolic execution toward a particular target; and call-chain-backward symbolic execution (CCBSE) iteratively runs forward symbolic execution, starting in the function containing the target line, and then jumping backward up the call chain until it finds a feasible path from the start of the program. We also propose a hybrid strategy, Mix-CCBSE, which alternates CCBSE with another (forward) search strategy. We compare these three with several existing strategies from the literature on a suite of six GNU Coreutils programs. We find that SDSE performs extremely well in many cases but may fail badly. CCBSE also performs quite well, but imposes additional overhead that sometimes makes it slower than SDSE. Considering all our benchmarks together, Mix-CCBSE performed best on average, combining to good effect the features of its constituent components.}, isbn = {978-3-642-23701-0}, url = {http://dx.doi.org/10.1007/978-3-642-23702-7_11}, author = {Ma,Kin-Keung and Yit Phang,Khoo and Foster, Jeffrey S. and Hicks, Michael W.}, editor = {Yahav,Eran} } @conference {14679, title = {Dynamic Enforcement of Knowledge-Based Security Policies}, booktitle = {Computer Security Foundations Symposium (CSF), 2011 IEEE 24th}, year = {2011}, month = {2011/06/27/29}, pages = {114 - 128}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper explores the idea of knowledge-based security policies, which are used to decide whether to answer queries over secret data based on an estimation of the querier{\textquoteright}s (possibly increased) knowledge given the results. Limiting knowledge is the goal of existing information release policies that employ mechanisms such as noising, anonymization, and redaction. Knowledge-based policies are more general: they increase flexibility by not fixing the means to restrict information flow. We enforce a knowledge-based policy by explicitly tracking a model of a querier{\textquoteright}s belief about secret data, represented as a probability distribution, and denying any query that could increase knowledge above a given threshold. We implement query analysis and belief tracking via abstract interpretation using a novel probabilistic polyhedral domain, whose design permits trading off precision with performance while ensuring estimates of a querier{\textquoteright}s knowledge are sound. Experiments with our implementation show that several useful queries can be handled efficiently, and performance scales far better than would more standard implementations of probabilistic computation based on sampling.}, keywords = {abstract interpretation, belief networks, belief tracking, Data models, dynamic enforcement, Facebook, information flow, knowledge based systems, knowledge-based security, knowledge-based security policy, privacy, probabilistic computation, probabilistic logic, probabilistic polyhedral domain, probabilistic polyhedron, probability, query analysis, Security, security of data, semantics, Waste materials}, isbn = {978-1-61284-644-6}, doi = {10.1109/CSF.2011.15}, author = {Mardziel,P. and Magill,S. and Hicks, Michael W. and Srivatsa,M.} } @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.} } @conference {19022, title = {Efficient and secure threshold-based event validation for vanets}, year = {2011}, month = {2011}, abstract = {Determining whether the number of vehicles reporting anevent is above a threshold is an important mechanism for VANETs, because many applications rely on a threshold number of notifications to reach agreement among vehicles, to determine the validity of an event, or to prevent the abuse of emergency alarms. We present the first efficient and se- cure threshold-based event validation protocol for VANETs. Quite counter-intuitively, we found that the z-smallest ap- proach offers the best tradeoff between security and effi- ciency since other approaches perform better for probabilis- tic counting. Analysis and simulation shows that our pro- tocol provides > 99\% accuracy despite the presence of at- tackers, collection and distribution of alerts in less than 1 second, and negligible impact on network performance. }, url = {http://www.eecs.berkeley.edu/~elaines/docs/hsiao_wisec2011.pdf}, author = {Hsiao, H. C. and Studer, A. and Dubey, R. and Elaine Shi and Perrig, A.} } @article {15130, title = {Efficient privacy-preserving biometric identification}, journal = {Network and Distributed System Security Symposium}, year = {2011}, month = {2011///}, abstract = {We present an efficient matching protocol that can be usedin many privacy-preserving biometric identification systems in the semi-honest setting. Our most general technical con- tribution is a new backtracking protocol that uses the by- product of evaluating a garbled circuit to enable efficient oblivious information retrieval. We also present a more ef- ficient protocol for computing the Euclidean distances of vectors, and optimized circuits for finding the closest match between a point held by one party and a set of points held by another. We evaluate our protocols by implementing a practical privacy-preserving fingerprint matching system. }, author = {Huang,Y. and Malka,L. and Evans,D. and Katz, Jonathan} } @article {15113, title = {Efficient Secure Computation with Garbled Circuits}, journal = {Information Systems Security}, year = {2011}, month = {2011///}, pages = {28 - 48}, abstract = {Secure two-party computation enables applications in which participants compute the output of a function that depends on their private inputs, without revealing those inputs or relying on any trusted third party. In this paper, we show the potential of building privacy-preserving applications using garbled circuits, a generic technique that until recently was believed to be too inefficient to scale to realistic problems. We present a Java-based framework that uses pipelining and circuit-level optimizations to build efficient and scalable privacy-preserving applications. Although the standard garbled circuit protocol assumes a very week, honest-but-curious adversary, techniques are available for converting such protocols to resist stronger adversaries, including fully malicious adversaries. We summarize approaches to producing malicious-resistant secure computations that reduce the costs of transforming a protocol to be secure against stronger adversaries. In addition, we summarize results on ensuring fairness, the property that either both parties receive the result or neither party does. Several open problems remain, but as theory and pragmatism advance, secure computation is approaching the point where it offers practical solutions for a wide variety of important problems.}, doi = {10.1007/978-3-642-25560-1_2}, author = {Huang,Y. and Shen,C. and Evans,D. and Katz, Jonathan and Shelat,A.} } @article {17128, title = {Electronic medical records: usability challenges and opportunities}, journal = {Interactions}, volume = {18}, year = {2011}, month = {2011///}, pages = {48 - 49}, author = {Hochheiser,H. and Shneiderman, Ben} } @article {14608, title = {Epigenomic and RNA structural correlates of polyadenylation}, journal = {RNA Biology}, volume = {8}, year = {2011}, month = {2011/05/01/}, pages = {529 - 537}, abstract = {Polyadenylation (poly(A)) of mRNA plays a critical role in regulating gene expression. Identifying the sequence, structural, and epigenomic determinants of poly(A) site usage is an important long term goal. Several cis elements that mediate poly(A) regulation have been identified. Highly used poly(A) sites are also known to have a greater nucleosome occupancy in the immediate downstream. However, a detailed exploration of additional epigenomic and mRNA structural correlates of poly(A) site usage has not been reported. Importantly, functional interaction between sequence, structure, and the epigenome in determining the poly(A) site usage is not known. We show that highly used poly(A) sites are positively associated with an mRNA structure that is energetically more favorable and one that better exposes a critical polyadenylation cis element. In exploring potential interplay between RNA and chromatin structure, we found that a stronger nucleosome occupancy downstream of poly(A) site strongly correlated with (1) a more favorable mRNA structure, and (2) a greater accumulation of RNA Polymerase II (PolII) at the poly(A) site. Further analysis suggested a causal relationship pointing from PolII accumulation to a stable RNA structure. Additionally, we found that distinct patterns of histone modifications characterize poly(A) sites and these epigenetic patterns alone can distinguish true poly(A) sites with ~76\% accuracy and also discriminate between high and low usage poly(A) sites with ~74\% accuracy. Our results suggest a causative link between chromatin structure and mRNA structure whereby a compacted chromatin downstream of the poly(A) site slows down the elongating transcript, thus facilitating the folding of nascent mRNA in a favorable structure at poly(A) site during transcription. Additionally we report hitherto unknown epigenomic correlates for poly(A) site usage.}, isbn = {1547-6286}, doi = {10.4161/rna.8.3.15194}, url = {http://www.landesbioscience.com/journals/rnabiology/article/15194/}, author = {Khaladkar,Mugdha and Smyda,Mark and Hannenhalli, Sridhar} } @article {14690, title = {Evaluating Dynamic Software Update Safety Using Systematic Testing}, journal = {IEEE Transactions on Software Engineering}, volume = {PP}, year = {2011}, pages = {1 - 1}, abstract = {Dynamic software updating (DSU) systems patch programs on the fly without incurring downtime. To avoid failures due to the updating process itself, many DSU systems employ timing restrictions. However, timing restrictions are theoretically imperfect, and their practical effectiveness is an open question. This paper presents the first significant empirical evaluation of three popular timing restrictions: activeness safety (AS), which prevents updates to active functions; con-freeness safety (CFS), which only allows modifications to active functions when doing so is provably type-safe; and manual identification of the event-handling loops during which an update may occur. We evaluated these timing restrictions using a series of DSU patches to three programs: OpenSSH, vsftpd, and ngIRCd. We systematically applied updates at each distinct update point reached during execution of a suite of system tests for these programs to determine which updates pass and which fail. We found that all three timing restrictions prevented most failures, but only manual identification allowed none. Further, although CFS and AS allowed many more update points, manual identification still supported updates with minimal delay. Finally, we found that manual identification required the least developer effort. Overall, we conclude that manual identification is most effective.}, keywords = {and serviceability, Availability, Computer Systems Organization, Delay, Manuals, Performance of Systems, reliability, Safety, servers, software, software engineering, Test execution, Testing and Debugging}, isbn = {0098-5589}, doi = {10.1109/TSE.2011.101}, author = {Hayden,C. and Smith,E. and Hardisty,E. and Hicks, Michael W. and Foster, Jeffrey S.} } @conference {17144, title = {EventGraphs: Charting Collections of Conference Connections}, booktitle = {2011 44th Hawaii International Conference on System Sciences (HICSS)}, year = {2011}, month = {2011/01/04/7}, pages = {1 - 10}, publisher = {IEEE}, organization = {IEEE}, abstract = {EventGraphs are social media network diagrams of conversations related to events, such as conferences. Many conferences now communicate a common "hashtag" or keyword to identify messages related to the event. EventGraphs help make sense of the collections of connections that form when people follow, reply or mention one another and a keyword. This paper defines EventGraphs, characterizes different types, and shows how the social media network analysis add-in NodeXL supports their creation and analysis. The structural patterns to look for in EventGraphs are highlighted and design ideas for their improvement are discussed.}, keywords = {conference connections, Conferences, Data visualization, EventGraphs, hashtag, measurement, Media, message identification, multimedia computing, NodeXL, Real time systems, social media network diagrams, social networking (online), Twitter}, isbn = {978-1-4244-9618-1}, doi = {10.1109/HICSS.2011.196}, author = {Hansen,D. and Smith,M. A and Shneiderman, Ben} } @article {14691, title = {Evolution in Action: Using Active Networking to Evolve Network Support for Mobility}, journal = {IFIP Lecture Notes in Computer Science (LNCS)}, volume = {2546}, year = {2011}, month = {2011///}, pages = {146 - 161}, abstract = {key early objective of Active Networking (AN) was to support on-the-fly network evolution. Although AN has been used relatively extensively to build application-customized protocols and even whole networking systems, demonstrations of evolution have been limited.}, author = {Hicks, Michael W. and Nettles,S. and Seong-Kyu,S. and Shannon,S.} } @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} } @article {15184, title = {Faster secure two-party computation using garbled circuits}, journal = {USENIX Security Symposium}, year = {2011}, month = {2011///}, abstract = {Secure two-party computation enables two parties toevaluate a function cooperatively without revealing to ei- ther party anything beyond the function{\textquoteright}s output. The garbled-circuit technique, a generic approach to secure two-party computation for semi-honest participants, was developed by Yao in the 1980s, but has been viewed as being of limited practical significance due to its in- efficiency. We demonstrate several techniques for im- proving the running time and memory requirements of the garbled-circuit technique, resulting in an implemen- tation of generic secure two-party computation that is significantly faster than any previously reported while also scaling to arbitrarily large circuits. We validate our approach by demonstrating secure computation of cir- cuits with over 109 gates at a rate of roughly 10 {\textmu}s per garbled gate, and showing order-of-magnitude improve- ments over the best previous privacy-preserving proto- cols for computing Hamming distance, Levenshtein dis- tance, Smith-Waterman genome alignment, and AES. }, author = {Huang,Y. and Evans,D. and Katz, Jonathan and Malka,L.} } @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 {14619, title = {Genome-Wide Survey of Natural Selection on Functional, Structural, and Network Properties of Polymorphic Sites in Saccharomyces Paradoxus}, journal = {Molecular Biology and EvolutionMol Biol Evol}, volume = {28}, year = {2011}, month = {2011/09/01/}, pages = {2615 - 2627}, abstract = {Background. To characterize the genetic basis of phenotypic evolution, numerous studies have identified individual genes that have likely evolved under natural selection. However, phenotypic changes may represent the cumulative effect of similar evolutionary forces acting on functionally related groups of genes. Phylogenetic analyses of divergent yeast species have identified functional groups of genes that have evolved at significantly different rates, suggestive of differential selection on the functional properties. However, due to environmental heterogeneity over long evolutionary timescales, selection operating within a single lineage may be dramatically different, and it is not detectable via interspecific comparisons alone. Moreover, interspecific studies typically quantify selection on protein-coding regions using the Dn/Ds ratio, which cannot be extended easily to study selection on noncoding regions or synonymous sites. The population genetic-based analysis of selection operating within a single lineage ameliorates these limitations. Findings. We investigated selection on several properties associated with genes, promoters, or polymorphic sites, by analyzing the derived allele frequency spectrum of single nucleotide polymorphisms (SNPs) in 28 strains of Saccharomyces paradoxus. We found evidence for significant differential selection between many functionally relevant categories of SNPs, underscoring the utility of function-centric approaches for discovering signatures of natural selection. When comparable, our findings are largely consistent with previous studies based on interspecific comparisons, with one notable exception: our study finds that mutations from an ancient amino acid to a relatively new amino acid are selectively disfavored, whereas interspecific comparisons have found selection against ancient amino acids. Several of our findings have not been addressed through prior interspecific studies: we find that synonymous mutations from preferred to unpreferred codons are selected against and that synonymous SNPs in the linker regions of proteins are relatively less constrained than those within protein domains. Conclusions. We present the first global survey of selection acting on various functional properties in S. paradoxus. We found that selection pressures previously detected over long evolutionary timescales have also shaped the evolution of S. paradoxus. Importantly, we also make novel discoveries untenable via conventional interspecific analyses.}, keywords = {derived allele frequency, Evolution, natural selection, yeast}, isbn = {0737-4038, 1537-1719}, doi = {10.1093/molbev/msr085}, url = {http://mbe.oxfordjournals.org/content/28/9/2615}, author = {Vishnoi,Anchal and Sethupathy,Praveen and Simola,Daniel and Plotkin,Joshua B. and Hannenhalli, Sridhar} } @conference {17181, title = {Group-in-a-Box Layout for Multi-faceted Analysis of Communities}, 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 = {354 - 361}, publisher = {IEEE}, organization = {IEEE}, abstract = {Communities in social networks emerge from interactions among individuals and can be analyzed through a combination of clustering and graph layout algorithms. These approaches result in 2D or 3D visualizations of clustered graphs, with groups of vertices representing individuals that form a community. However, in many instances the vertices have attributes that divide individuals into distinct categories such as gender, profession, geographic location, and similar. It is often important to investigate what categories of individuals comprise each community and vice-versa, how the community structures associate the individuals from the same category. Currently, there are no effective methods for analyzing both the community structure and the category-based partitions of social graphs. We propose Group-In-a-Box (GIB), a meta-layout for clustered graphs that enables multi-faceted analysis of networks. It uses the tree map space filling technique to display each graph cluster or category group within its own box, sized according to the number of vertices therein. GIB optimizes visualization of the network sub-graphs, providing a semantic substrate for category-based and cluster-based partitions of social graphs. We illustrate the application of GIB to multi-faceted analysis of real social networks and discuss desirable properties of GIB using synthetic datasets.}, keywords = {Algorithm design and analysis, category based social graph partitions, clustered graphs, clustering, Clustering algorithms, Communities, data visualisation, force-directed, gender, geographic location, graph layout algorithms, graph theory, group-in-a-box, group-in-a-box layout, Image edge detection, Layout, meta-layout, multifaceted community analysis, network subgraph visualization, network visualization, pattern clustering, profession, semantic substrates, Social network services, social networking (online), social networks, treemap space filling technique, Visualization}, isbn = {978-1-4577-1931-8}, doi = {10.1109/PASSAT/SocialCom.2011.139}, author = {Rodrigues,E.M. and Milic-Frayling,N. and Smith,M. and Shneiderman, Ben and Hansen,D.} } @conference {17184, title = {HCI for peace: from idealism to concrete steps}, booktitle = {PART 2 {\textemdash}{\textemdash}{\textemdash}{\textendash} Proceedings of the 2011 annual conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {613 - 616}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This panel will contribute diverse perspectives on the use of computer technology to promote peace and prevent armed conflict. These perspectives include: the use of social media to promote democracy and citizen participation, the role of computers in helping people communicate across division lines in zones of conflict, how persuasive technology can promote peace, and how interaction design can play a role in post-conflict reconciliation.}, keywords = {cyprus, peace, persuasive technology, post-conflict reconciliation, social media, value sensitive design, war}, doi = {10.1145/1979482.1979493}, url = {http://doi.acm.org/10.1145/1979482.1979493}, author = {Hourcade,Juan Pablo and Bullock-Rest,Natasha E. and Friedman,Batya and Nelson,Mark and Shneiderman, Ben and Zaphiris,Panayiotis} } @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} } @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 {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 {19689, title = {Interactive topic modeling}, year = {2011}, month = {2011/00/19}, pages = {248 - 257}, publisher = {Association for Computational Linguistics}, abstract = {Abstract Topic models have been used extensively as a tool for corpus exploration, and a cottage industry has developed to tweak topic models to better encode human intuitions or to better model data. However, creating such extensions requires expertise in machine ...}, url = {http://dl.acm.org/citation.cfm?id=2002472.2002505}, author = {Hu, Yuening and Jordan Boyd-Graber and Satinoff, Brianna} } @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} } @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 {14702, title = {Lightweight monadic programming in ML}, booktitle = {Proceedings of the 16th ACM SIGPLAN international conference on Functional programming}, series = {ICFP {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {15 - 27}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Many useful programming constructions can be expressed as monads. Examples include probabilistic modeling, functional reactive programming, parsing, and information flow tracking, not to mention effectful functionality like state and I/O. In this paper, we present a type-based rewriting algorithm to make programming with arbitrary monads as easy as using ML{\textquoteright}s built-in support for state and I/O. Developers write programs using monadic values of type m τ as if they were of type τ, and our algorithm inserts the necessary binds, units, and monad-to-monad morphisms so that the program type checks. Our algorithm, based on Jones{\textquoteright} qualified types, produces principal types. But principal types are sometimes problematic: the program{\textquoteright}s semantics could depend on the choice of instantiation when more than one instantiation is valid. In such situations we are able to simplify the types to remove any ambiguity but without adversely affecting typability; thus we can accept strictly more programs. Moreover, we have proved that this simplification is efficient (linear in the number of constraints) and coherent: while our algorithm induces a particular rewriting, all related rewritings will have the same semantics. We have implemented our approach for a core functional language and applied it successfully to simple examples from the domains listed above, which are used as illustrations throughout the paper.}, keywords = {coercion, coherence, monad, rewriting, type}, isbn = {978-1-4503-0865-6}, doi = {10.1145/2034773.2034778}, url = {http://doi.acm.org/10.1145/2034773.2034778}, author = {Swamy,Nikhil and Guts,Nataliya and Leijen,Daan and Hicks, Michael W.} } @article {14705, title = {LOCKSMITH: Practical static race detection for C}, journal = {ACM Trans. Program. Lang. Syst.}, volume = {33}, year = {2011}, month = {2011/01//}, pages = {3:1{\textendash}3:55 - 3:1{\textendash}3:55}, abstract = {Locksmith is a static analysis tool for automatically detecting data races in C programs. In this article, we describe each of Locksmith{\textquoteright}s component analyses precisely, and present systematic measurements that isolate interesting trade-offs between precision and efficiency in each analysis. Using a benchmark suite comprising stand-alone applications and Linux device drivers totaling more than 200,000 lines of code, we found that a simple no-worklist strategy yielded the most efficient interprocedural dataflow analysis; that our sharing analysis was able to determine that most locations are thread-local, and therefore need not be protected by locks; that modeling C structs and void pointers precisely is key to both precision and efficiency; and that context sensitivity yields a much more precise analysis, though with decreased scalability. Put together, our results illuminate some of the key engineering challenges in building Locksmith and data race detection analyses in particular, and constraint-based program analyses in general.}, keywords = {context sensitivity, contextual effects, correlation inference, Data race, locksmith, race detection, sharing analysis, static analysis}, isbn = {0164-0925}, doi = {10.1145/1889997.1890000}, url = {http://doi.acm.org/10.1145/1889997.1890000}, author = {Pratikakis,Polyvios and Foster, Jeffrey S. and Hicks, Michael W.} } @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} } @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} } @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} } @article {16039, title = {Medication Reconciliation: Work Domain Ontology, Prototype Development, and a Predictive Model}, journal = {AMIA Annual Symposium ProceedingsAMIA Annu Symp Proc}, volume = {2011}, year = {2011}, month = {2011///}, pages = {878 - 887}, abstract = {Medication errors can result from administration inaccuracies at any point of care and are a major cause for concern. To develop a successful Medication Reconciliation (MR) tool, we believe it necessary to build a Work Domain Ontology (WDO) for the MR process. A WDO defines the explicit, abstract, implementation-independent description of the task by separating the task from work context, application technology, and cognitive architecture. We developed a prototype based upon the WDO and designed to adhere to standard principles of interface design. The prototype was compared to Legacy Health System{\textquoteright}s and Pre-Admission Medication List Builder MR tools via a Keystroke-Level Model analysis for three MR tasks. The analysis found the prototype requires the fewest mental operations, completes tasks in the fewest steps, and completes tasks in the least amount of time. Accordingly, we believe that developing a MR tool, based upon the WDO and user interface guidelines, improves user efficiency and reduces cognitive load.}, isbn = {1942-597X}, author = {Markowitz,Eliz and Bernstam,Elmer V. and Herskovic,Jorge and Zhang,Jiajie and Shneiderman, Ben and Plaisant, Catherine and Johnson,Todd R.} } @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 {13303, title = {Modeling Multiresolution 3D Scalar Fields through Regular Simplex Bisection}, journal = {Scientific Visualization: Interactions, Features, Metaphors}, volume = {2}, year = {2011}, month = {2011///}, pages = {360 - 377}, abstract = {We review modeling techniques for multiresolution three-dimensional scalar fields based on a dis-cretization of the field domain into nested tetrahedral meshes generated through regular simplex bisection. Such meshes are described through hierarchical data structures and their representa- tion is characterized by the modeling primitive used. The primary conceptual distinction among the different approaches proposed in the literature is whether they treat tetrahedra or clusters of tetrahedra, called diamonds, as the modeling primitive. We first focus on representations for the modeling primitive and for nested meshes. Next, we survey the applications of these meshes to modeling multiresolution 3D scalar fields, with an emphasis on interactive visualization. We also consider the relationship of such meshes to octrees. Finally, we discuss directions for further research }, author = {Weiss,K. and De Floriani, Leila and Hagen,H.} } @conference {17299, title = {Motivation for Participation in Online Neighborhood Watch Communities: An Empirical Study Involving Invitation Letters}, 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 = {760 - 765}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper presents a three-part experiment designed to investigate the motivations of users of a community safety and neighborhood watch social networking website. The experiment centers around an intervention into the invitation system that current users employ to invite nonmembers to join the site, and involves several versions of an invitation email which differ by expressing one of four possible motivations for using such a site. The research presented investigates how potential users{\textquoteright} choice of whether or not to join the site is affected by the use case presented by the invitation. It also includes an investigation of the motivations of current users of the site, as reported in an online survey. The experiment yielded no significant difference in responses to the emails. Overall, invitations that included a specific motivation slightly outperformed those which did not, but not to a statistically significant degree. We conclude that although users have specific motivations for using the site, as reported in the survey, attempting to increase response rates to invitation emails by suggesting use cases of the site is surprisingly unlikely to be successful.}, keywords = {Art, Communities, community safety, Electronic mail, Interviews, invitation email, invitations, motivation, neighborhood watch, Online communities, online neighborhood watch communities, online survey, participation, Safety, Security, social media, Social network services, social networking (online), social networking Website}, isbn = {978-1-4577-1931-8}, doi = {10.1109/PASSAT/SocialCom.2011.108}, author = {Violi,N. and Shneiderman, Ben and Hanson,A. and Rey,P. J} } @article {14709, title = {MultiOtter: Multiprocess Symbolic Execution}, journal = {Technical Reports of the Computer Science Department}, year = {2011}, month = {2011///}, abstract = {Symbolic execution can be an effective technique for exploring large numbers of program paths, but it has generally been applied to programs running in isolation, whose inputs are files or command-line arguments. Programs that take inputs from other programs---servers, for example---have been beyond the reach of symbolic execution. To address this, we developed a multiprocess symbolic executor called MultiOtter, along with an implementation of many of the POSIX functions, such as socket and select, that interactive programs usually rely on. However, that is just a first step. Next, we must determine what symbolic inputs to feed to an interactive program to make multiprocess symbolic execution effective. Providing completely unconstrained symbolic values causes symbolic execution to spend too much time exploring uninteresting paths, such as paths to handle invalid inputs. MultiOtter allows us to generate inputs that conform to a context-free grammar, similar to previous work, but it also enables new input generation capabilities because we can now run arbitrary programs concurrently with the program being studied. As examples, we symbolically executed a key-value store server, redis, and an FTP server, vsftpd, each with a variety of inputs, including symbolic versions of tests from redis{\textquoteright}s test suite and wget as a client for vsftpd. We report the coverage provided by symbolic execution with various forms of symbolic input, showing that different testing goals require different degrees of symbolic inputs.}, author = {Turpie,J. and Reisner,E. and Foster, Jeffrey S. and Hicks, Michael W.} } @article {19268, title = {Multithreaded Simulation for Synchronous Dataflow Graphs}, journal = {ACM Trans. Des. Autom. Electron. Syst.}, volume = {16}, year = {2011}, month = {2011}, pages = {25:1 - 25:23}, abstract = {For system simulation, Synchronous DataFlow (SDF) has been widely used as a core model of computation in design tools for digital communication and signal processing systems. The traditional approach for simulating SDF graphs is to compute and execute static schedules in single-processor desktop environments. Nowadays, however, multicore processors are increasingly popular desktop platforms for their potential performance improvements through thread-level parallelism. Without novel scheduling and simulation techniques that explicitly explore thread-level parallelism for executing SDF graphs, current design tools gain only minimal performance improvements on multicore platforms. In this article, we present a new multithreaded simulation scheduler, called MSS, to provide simulation runtime speedup for executing SDF graphs on multicore processors. MSS strategically integrates graph clustering, intracluster scheduling, actor vectorization, and intercluster buffering techniques to construct InterThread Communication (ITC) graphs at compile-time. MSS then applies efficient synchronization and dynamic scheduling techniques at runtime for executing ITC graphs in multithreaded environments. We have implemented MSS in the Advanced Design System (ADS) from Agilent Technologies. On an Intel dual-core, hyper-threading (4 processing units) processor, our results from this implementation demonstrate up to 3.5 times speedup in simulating modern wireless communication systems (e.g., WCDMA3G, CDMA 2000, WiMax, EDGE, and Digital TV).}, keywords = {multithreaded simulation, scheduling, Synchronous dataflow}, isbn = {1084-4309}, url = {http://doi.acm.org/10.1145/1970353.1970358}, author = {Chia-Jui Hsu and Pino, Jos{\'e} Luis and Bhattacharyya, Shuvra S.} } @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 {14902, title = {Odd Leaf Out: Improving Visual Recognition with Games}, booktitle = {Privacy, security, risk and trust (passat), 2011 ieee third international conference on and 2011 ieee third international conference on social computing (socialcom)}, year = {2011}, month = {2011/10//}, pages = {87 - 94}, abstract = {A growing number of projects are solving complex computational and scientific tasks by soliciting human feedback through games. Many games with a purpose focus on generating textual tags for images. In contrast, we introduce a new game, Odd Leaf Out, which provides players with an enjoyable and educational game that serves the purpose of identifying misclassification errors in a large database of labeled leaf images. The game uses a novel mechanism to solicit useful information from players{\textquoteright} incorrect answers. A study of 165 players showed that game data can be used to identify mislabeled leaves much more quickly than would have been possible using a computer vision algorithm alone. Domain novices and experts were equally good at identifying mislabeled images, although domain experts enjoyed the game more. We discuss the successes and challenges of this new game, which can be applied to other domains with labeled image datasets.}, keywords = {algorithm;educational, classification;object, computational, computing;botany;computer, datasets;misclassification, errors;scientific, feedback;labeled, game;human, games;computer, games;image, image, leaf, Odd, Out;complex, recognition;, recognition;biology, tags;visual, tasks;computer, tasks;textual, VISION}, doi = {10.1109/PASSAT/SocialCom.2011.225}, author = {Hansen,D. L and Jacobs, David W. and Lewis,D. and Biswas,A. and Preece,J. and Rotman,D. and Stevens,E.} } @article {15069, title = {Private Set Intersection: Are Garbled Circuits Better than Custom Protocols?}, journal = {19th Network and Distributed Security Symposium}, year = {2011}, month = {2011///}, abstract = {Cryptographic protocols for Private Set Intersection (PSI)are the basis for many important privacy-preserving ap- plications. Over the past few years, intensive research has been devoted to designing custom protocols for PSI based on homomorphic encryption and other public-key tech- niques, apparently due to the belief that solutions using generic approaches would be impractical. This paper ex- plores the validity of that belief. We develop three classes of protocols targeted to different set sizes and domains, all based on Yao{\textquoteright}s generic garbled-circuit method. We then compare the performance of our protocols to the fastest custom PSI protocols in the literature. Our results show that a careful application of garbled circuits leads to solu- tions that can run on million-element sets on typical desk- tops, and that can be competitive with the fastest custom protocols. Moreover, generic protocols like ours can be used directly for performing more complex secure com- putations, something we demonstrate by adding a simple information-auditing mechanism to our PSI protocols. }, author = {Huang,Y. and Evans,D. and Katz, Jonathan} } @article {19722, title = {ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process.}, journal = {BMC Bioinformatics}, volume = {12}, year = {2011}, month = {2011}, pages = {434}, abstract = {

BACKGROUND: Phylogenetic profiling is a technique of scoring co-occurrence between a protein family and some other trait, usually another protein family, across a set of taxonomic groups. In spite of several refinements in recent years, the technique still invites significant improvement. To be its most effective, a phylogenetic profiling algorithm must be able to examine co-occurrences among protein families whose boundaries are uncertain within large homologous protein superfamilies.

RESULTS: Partial Phylogenetic Profiling (PPP) is an iterative algorithm that scores a given taxonomic profile against the taxonomic distribution of families for all proteins in a genome. The method works through optimizing the boundary of each protein family, rather than by relying on prebuilt protein families or fixed sequence similarity thresholds. Double Partial Phylogenetic Profiling (DPPP) is a related procedure that begins with a single sequence and searches for optimal granularities for its surrounding protein family in order to generate the best query profiles for PPP. We present ProPhylo, a high-performance software package for phylogenetic profiling studies through creating individually optimized protein family boundaries. ProPhylo provides precomputed databases for immediate use and tools for manipulating the taxonomic profiles used as queries.

CONCLUSION: ProPhylo results show universal markers of methanogenesis, a new DNA phosphorothioation-dependent restriction enzyme, and efficacy in guiding protein family construction. The software and the associated databases are freely available under the open source Perl Artistic License from ftp://ftp.jcvi.org/pub/data/ppp/.

}, keywords = {algorithms, Archaea, Archaeal Proteins, DNA, Methane, Phylogeny, software}, issn = {1471-2105}, doi = {10.1186/1471-2105-12-434}, author = {Basu, Malay K and Jeremy D Selengut and Haft, Daniel H} } @article {16038, title = {Reducing Missed Laboratory Results: Defining Temporal Responsibility, Generating User Interfaces for Test Process Tracking, and Retrospective Analyses to Identify Problems}, journal = {AMIA Annual Symposium ProceedingsAMIA Annu Symp Proc}, volume = {2011}, year = {2011}, month = {2011///}, pages = {1382 - 1391}, abstract = {Researchers have conducted numerous case studies reporting the details on how laboratory test results of patients were missed by the ordering medical providers. Given the importance of timely test results in an outpatient setting, there is limited discussion of electronic versions of test result management tools to help clinicians and medical staff with this complex process. This paper presents three ideas to reduce missed results with a system that facilitates tracking laboratory tests from order to completion as well as during follow-up: (1) define a workflow management model that clarifies responsible agents and associated time frame, (2) generate a user interface for tracking that could eventually be integrated into current electronic health record (EHR) systems, (3) help identify common problems in past orders through retrospective analyses.}, isbn = {1942-597X}, author = {Tarkan,Sureyya and Plaisant, Catherine and Shneiderman, Ben and Hettinger,A. Zachary} } @article {14639, title = {Regulation of Lung Endoderm Progenitor Cell Behavior by miR302/367}, journal = {DevelopmentDevelopment}, volume = {138}, year = {2011}, month = {2011/04/01/}, pages = {1235 - 1245}, abstract = {The temporal and spatial control of organ-specific endoderm progenitor development is poorly understood. miRNAs affect cell function by regulating programmatic changes in protein expression levels. We show that the miR302/367 cluster is a target of the transcription factor Gata6 in mouse lung endoderm and regulates multiple aspects of early lung endoderm progenitor development. miR302/367 is expressed at early stages of lung development, but its levels decline rapidly as development proceeds. Gain- and loss-of-function studies show that altering miR302/367 expression disrupts the balance of lung endoderm progenitor proliferation and differentiation, as well as apical-basal polarity. Increased miR302/367 expression results in the formation of an undifferentiated multi-layered lung endoderm, whereas loss of miR302/367 activity results in decreased proliferation and enhanced lung endoderm differentiation. miR302/367 coordinates the balance between proliferation and differentiation, in part, through direct regulation of Rbl2 and Cdkn1a, whereas apical-basal polarity is controlled by regulation of Tiam1 and Lis1. Thus, miR302/367 directs lung endoderm development by coordinating multiple aspects of progenitor cell behavior, including proliferation, differentiation and apical-basal polarity.}, keywords = {Lung, MicroRNA, mouse, Progenitor}, isbn = {0950-1991, 1477-9129}, doi = {10.1242/dev.061762}, url = {http://dev.biologists.org/content/138/7/1235}, author = {Tian,Ying and Zhang,Yuzhen and Hurd,Laura and Hannenhalli, Sridhar and Liu,Feiyan and Lu,Min Min and Morrisey,Edward E.} } @article {16033, title = {Research Directions in Data Wrangling: Visualizations and Transformations for Usable and Credible Data}, journal = {Information VisualizationInformation Visualization}, volume = {10}, year = {2011}, month = {2011/10/01/}, pages = {271 - 288}, abstract = {In spite of advances in technologies for working with data, analysts still spend an inordinate amount of time diagnosing data quality issues and manipulating data into a usable form. This process of {\textquoteleft}data wrangling{\textquoteright} often constitutes the most tedious and time-consuming aspect of analysis. Though data cleaning and integration arelongstanding issues in the database community, relatively little research has explored how interactive visualization can advance the state of the art. In this article, we review the challenges and opportunities associated with addressing data quality issues. We argue that analysts might more effectively wrangle data through new interactive systems that integrate data verification, transformation, and visualization. We identify a number of outstanding research questions, including how appropriate visual encodings can facilitate apprehension of missing data, discrepant values, and uncertainty; how interactive visualizations might facilitate data transform specification; and how recorded provenance and social interaction might enable wider reuse, verification, and modification of data transformations.}, keywords = {data cleaning, data quality, data transformation, Uncertainty, Visualization}, isbn = {1473-8716, 1473-8724}, doi = {10.1177/1473871611415994}, url = {http://ivi.sagepub.com/content/10/4/271}, author = {Kandel,Sean and Heer,Jeffrey and Plaisant, Catherine and Kennedy,Jessie and Van Ham,Frank and Riche,Nathalie Henry and Weaver,Chris and Lee,Bongshin and Brodbeck,Dominique and Buono,Paolo} } @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} } @conference {13940, title = {Scalable fast multipole methods on distributed heterogeneous architectures}, booktitle = {High Performance Computing, Networking, Storage and Analysis (SC), 2011 International Conference for}, year = {2011}, month = {2011/11//}, pages = {1 - 12}, abstract = {We fundamentally reconsider implementation of the Fast Multipole Method (FMM) on a computing node with a heterogeneous CPU-GPU architecture with multicore CPU(s) and one or more GPU accelerators, as well as on an interconnected cluster of such nodes. The FMM is a divide- and-conquer algorithm that performs a fast N-body sum using a spatial decomposition and is often used in a time- stepping or iterative loop. Using the observation that the local summation and the analysis-based translation parts of the FMM are independent, we map these respectively to the GPUs and CPUs. Careful analysis of the FMM is performed to distribute work optimally between the multicore CPUs and the GPU accelerators. We first develop a single node version where the CPU part is parallelized using OpenMP and the GPU version via CUDA. New parallel algorithms for creating FMM data structures are presented together with load balancing strategies for the single node and distributed multiple-node versions. Our implementation can perform the N-body sum for 128M particles on 16 nodes in 4.23 seconds, a performance not achieved by others in the literature on such clusters.}, keywords = {accelerators;OpenMP;analysis, algorithm;iterative, and, architecture;CUDA;FMM, architectures;, architectures;divide-and-conquer, based, conquer, CPU-GPU, CPU;scalable, data, fast, heterogeneous, loop;data, loop;multicore, methods;graphics, methods;multiprocessing, methods;time, multipole, parts;distributed, PROCESSING, stepping, structures;divide, structures;GPU, systems;parallel, translation, units;iterative}, author = {Hu,Qi and Gumerov, Nail A. and Duraiswami, Ramani} } @conference {14736, title = {State transfer for clear and efficient runtime updates}, booktitle = {2011 IEEE 27th International Conference on Data Engineering Workshops (ICDEW)}, year = {2011}, month = {2011/04/11/16}, pages = {179 - 184}, publisher = {IEEE}, organization = {IEEE}, abstract = {Dynamic software updating (DSU), the practice of updating software while it executes, is a lively area of research. The DSU approach most prominent in both commercial and research systems is in-place updating, in which patches containing program modifications are loaded into a running process. However, in-place updating suffers from several problems: it requires complex tool support, it may adversely affect the performance of normal execution, it requires challenging reasoning to understand the behavior of an updated program, and it requires extra effort to modify program state to be compatible with an update. This paper presents preliminary work investigating the potential for state transfer updating to address these problems. State transfer updates work by launching a new process running the updated program version and transferring program state from the running process to the updated version. In this paper, we describe the use and implementation of Ekiden, a new state transfer updating library for C/C++ programs. Ekiden seeks to redress the difficulties of in-place updating, and we report on our experience updating VSFTPD using Ekiden. This initial experience suggests that state transfer provides the availability benefits of in-place DSU approaches while addressing many of their shortcomings.}, keywords = {C++ language, C++ program, Cognition, complex tool support, dynamic software updating, efficient runtime update, in-place DSU approach, Libraries, Operating systems, program modification, Program processors, program transfer, program version, Runtime, servers, software libraries, Software maintenance, state transfer update, Steady-state, updating library, VSFTPD}, isbn = {978-1-4244-9195-7}, doi = {10.1109/ICDEW.2011.5767632}, author = {Hayden,C.M. and Smith,E. K and Hicks, Michael W. and Foster, Jeffrey S.} } @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.} } @article {13949, title = {Toward improved aeromechanics simulations using recent advancements in scientific computing}, journal = {Proceedings 67th Annual Forum of the American Helicopter Society}, year = {2011}, month = {2011///}, pages = {3 - 5}, author = {Hu,Q. and Syal,M. and Gumerov, Nail A. and Duraiswami, Ramani and Leishman,J.G.} } @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.} } @article {14646, title = {Transcriptional Regulation Via TF-Modifying Enzymes: An Integrative Model-Based Analysis}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {39}, year = {2011}, month = {2011/07/01/}, pages = {e78-e78 - e78-e78}, abstract = {Transcription factor activity is largely regulated through post-translational modification. Here, we report the first integrative model of transcription that includes both interactions between transcription factors and promoters, and between transcription factors and modifying enzymes. Simulations indicate that our method is robust against noise. We validated our tool on a well-studied stress response network in yeast and on a STAT1-mediated regulatory network in human B cells. Our work represents a significant step toward a comprehensive model of gene transcription.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/gkr172}, url = {http://nar.oxfordjournals.org/content/39/12/e78}, author = {Everett,Logan J and Jensen,Shane T and Hannenhalli, Sridhar} } @conference {13412, title = {A trust model for supply chain management}, booktitle = {The 10th International Conference on Autonomous Agents and Multiagent Systems-Volume 3}, year = {2011}, month = {2011///}, pages = {1375 - 1376}, author = {Haghpanah,Y. and desJardins, Marie and others} } @article {13076, title = {Vehicle Detection Using Partial Least Squares}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {33}, year = {2011}, month = {2011/06//}, pages = {1250 - 1265}, abstract = {Detecting vehicles in aerial images has a wide range of applications, from urban planning to visual surveillance. We describe a vehicle detector that improves upon previous approaches by incorporating a very large and rich set of image descriptors. A new feature set called Color Probability Maps is used to capture the color statistics of vehicles and their surroundings, along with the Histograms of Oriented Gradients feature and a simple yet powerful image descriptor that captures the structural characteristics of objects named Pairs of Pixels. The combination of these features leads to an extremely high-dimensional feature set (approximately 70,000 elements). Partial Least Squares is first used to project the data onto a much lower dimensional subspace. Then, a powerful feature selection analysis is employed to improve the performance while vastly reducing the number of features that must be calculated. We compare our system to previous approaches on two challenging data sets and show superior performance.}, keywords = {aerial images;color probability maps;oriented gradients feature;partial least squares;powerful feature selection analysis;urban planning;vehicle detection;visual surveillance;gradient methods;image colour analysis;least squares approximations;road vehicle, Automated;}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2010.182}, author = {Kembhavi,A. and Harwood,D. and Davis, Larry S.} } @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} } @article {14660, title = {Adapting Scrum to Managing a Research Group}, journal = {Technical Reports of the Computer Science Department}, year = {2010}, month = {2010/09/18/undef}, abstract = {Score is an adaptation of the Scrum agile software development methodology to the task of managing Ph.D. students in an academic research group. This paper describes Score, conceived in October 2006, and our experience using it. We have found that Score enables us---faculty and students---to be more efficient and thereby more productive, and enhances the cohesion of our research group.}, author = {Hicks, Michael W. and Foster, Jeffrey S.} } @article {13094, title = {Advanced tracking systems: computational approaches to be introduced to new series}, journal = {Augmented vision \& reality}, volume = {1}, year = {2010}, month = {2010///}, abstract = {Modern visual tracking systems implement a computational process that is often divided into several modules such as localization, tracking, recognition, behavior analysis and classification of events. This book will focus on recent advances in computational approaches for detection and tracking of human body, road boundaries and lane markers as well as on recognition of human activities, drowsiness and distraction state. This book is composed of seven distinct parts. Part I covers people localization algorithms in video sequences. Part II describes successful approaches for tracking people and bodyparts. The third part focuses on tracking of pedestrian and vehicles in outdoor images. Part IV describes recent methods to track lane markers and road boundaries. In part V, methods to track head, hand and facial features are reviewed. The last two parts cover the topics of automatic recognition and classification of activity, gesture, behavior, drowsiness and visual distraction state of humans.}, author = {HAMMOUD,R. and Porikli, F. and Davis, Larry S.} } @article {14374, title = {AI Theory and Practice: A Discussion on Hard Challenges and Opportunities Ahead}, journal = {AI Magazine}, volume = {31}, year = {2010}, month = {2010/07/28/}, pages = {103 - 114}, abstract = {AI Theory and Practice: A Discussion on Hard Challenges and Opportunities Ahead}, isbn = {0738-4602}, doi = {10.1609/aimag.v31i3.2293}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/2293}, author = {Horvitz,Eric and Getoor, Lise and Guestrin,Carlos and Hendler,James and Konstan,Joseph and Subramanian,Devika and Wellman,Michael and Kautz,Henry} } @book {16975, title = {Analyzing Social Media Networks with NodeXL}, year = {2010}, month = {2010/08/27/}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, abstract = {"Analyzing Social Media Networks with NodeXL provides a much needed resource for the social media research community, as it describes network theory, provides compelling examples using data sources like Twitter and Flickr, and highlights how to use a free sophisticated tool for analysis. This is the perfect book for anyone trying to analyze the behavior of online social networks and beyond." ---Adam Perer, Research Scientist, IBM Research "This book provides a basic introduction to social network analysis, followed by practical instruction and examples on gathering data from online sources, importing into Excel, and then analyzing the data through Excel. The book will be important for promoting research in the area for those in information science, sociology, cultural studies, virtual community, and e-commerce."---Caroline Haythornthwaite, PhD, Professor, Graduate School of Library and Information Science, University of Illinois at Urbana-Champaign Businesses, entrepreneurs, individuals, and government agencies alike are looking to social network analysis (SNA) tools for insight into trends, connections, and fluctuations in social media. Microsoft{\textquoteright}s NodeXL is a free, open-source SNA plug-in for use with Excel. It provides instant graphical representation of relationships of complex networked data. But it goes further than other SNA tools - NodeXL was developed by a multidisciplinary team of experts that bring together information studies, computer science, sociology, human-computer interaction, and over 20 years of visual analytic theory and information visualization into a simple tool anyone can use. This makes NodeXL of interest not only to end-users but also to researchers and students studying visual and network analytics and their application in the real world.}, keywords = {Business \& Economics / Marketing / Research, Computers / Computer Science, Computers / Data Processing, Computers / Database Management / Data Mining, Computers / General, Computers / Information Theory, Computers / Interactive \& Multimedia, Computers / Social Aspects / General, Computers / Social Aspects / Human-Computer Interaction, Computers / User Interfaces, data mining, Data mining - Computer programs, Data mining/ Computer programs, Information Visualization, Information visualization - Computer programs, Information visualization/ Computer programs, NodeXL, online social networks, Social Science / General, Social Science / Reference, Social Science / Sociology / General, Technology \& Engineering / General, Technology \& Engineering / Social Aspects, Webometrics, Webometrics - Computer programs, Webometrics/ Computer programs}, isbn = {9780123822291}, author = {Hansen,Derek and Shneiderman, Ben and Smith,Marc A.} } @book {19357, title = {Analyzing Social Media Networks with NodeXL: Insights from a Connected World}, year = {2010}, month = {2010}, pages = {302}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, abstract = {Businesses, entrepreneurs, individuals, and government agencies alike are looking to social network analysis (SNA) tools for insight into trends, connections, and fluctuations in social media. Microsoft{\textquoteright}s NodeXL is a free, open-source SNA plug-in for use with Excel. It provides instant graphical representation of relationships of complex networked data. But it goes further than other SNA tools -- NodeXL was developed by a multidisciplinary team of experts that bring together information studies, computer science, sociology, human-computer interaction, and over 20 years of visual analytic theory and information visualization into a simple tool anyone can use. This makes NodeXL of interest not only to end-users but also to researchers and students studying visual and network analytics and their application in the real world. In Analyzing Social Media Networks with NodeXL, members of the NodeXL development team up to provide readers with a thorough and practical guide for using the tool while also explaining the development behind each feature. Blending the theoretical with the practical, this book applies specific SNA instructions directly to NodeXL, but the theory behind the implementation can be applied to any SNA. To learn more about Analyzing Social Media Networks and NodeXL, visit the companion site at www.mkp.com/nodexl*Walks you through NodeXL, while explaining the theory and development behind each step, providing takeaways that can apply to any SNA *Demonstrates how visual analytics research can be applied to SNA tools for the mass market *Includes case studies from researchers who use NodeXL on popular networks like email, Facebook, Twitter, and wikis}, keywords = {Computers / Computer Science, Computers / General, Computers / Social Aspects / General, Computers / Social Aspects / Human-Computer Interaction, Computers / User Interfaces}, isbn = {9780123822307}, author = {Hansen,Derek and Shneiderman, Ben and Smith,Marc A.} } @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} } @conference {15849, title = {Assessor error in stratified evaluation}, booktitle = {Proceedings of the 19th ACM international conference on Information and knowledge management}, year = {2010}, month = {2010///}, pages = {539 - 548}, author = {Webber,W. and Oard, Douglas and Scholer,F. and Hedin,B.} } @article {15165, title = {Bounds on the efficiency of black-box commitment schemes}, journal = {Theoretical Computer Science}, volume = {411}, year = {2010}, month = {2010/03/04/}, pages = {1251 - 1260}, abstract = {Constructions of cryptographic primitives based on general assumptions (e.g., one-way functions) tend to be less efficient than constructions based on specific (e.g., number-theoretic) assumptions. This has prompted a recent line of research aimed at investigating the best possible efficiency of (black-box) cryptographic constructions based on general assumptions. Here, we present bounds on the efficiency of statistically-binding commitment schemes constructed using black-box access to one-way permutations; our bounds are tight for the case of perfectly-binding schemes. Our bounds hold in an extension of the Impagliazzo{\textendash}Rudich model: we show that any construction beating our bounds would imply the unconditional existence of a one-way function (from which a statistically-binding commitment scheme could be constructed {\textquotedblleft}from scratch{\textquotedblright}).}, keywords = {Commitment schemes, cryptography}, isbn = {0304-3975}, doi = {10.1016/j.tcs.2009.10.021}, url = {http://www.sciencedirect.com/science/article/pii/S0304397509007737}, author = {Horvitz,Omer and Katz, Jonathan} } @conference {17572, title = {Cellular traffic offloading through opportunistic communications: a case study}, booktitle = {Proceedings of the 5th ACM workshop on Challenged networks}, series = {CHANTS {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {31 - 38}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Due to the increasing popularity of various applications for smartphones, 3G networks are currently overloaded by mobile data traffic. Offloading cellular traffic through opportunistic communications is a promising solution to partially solve this problem, because there is no monetary cost for it. As a case study, we investigate the target-set selection problem for information delivery in the emerging Mobile Social Networks (MoSoNets). We propose to exploit opportunistic communications to facilitate the information dissemination and thus reduce the amount of cellular traffic. In particular, we study how to select the target set with only k users, such that we can minimize the cellular data traffic. In this scenario, initially the content service providers deliver information over cellular networks to only users in the target set. Then through opportunistic communications, target-users will further propagate the information among all the subscribed users. Finally, service providers will send the information to users who fail to receive it before the delivery deadline (i.e., delay-tolerance threshold). We propose three algorithms, called Greedy, Heuristic, and Random, for this problem and evaluate their performance through an extensive trace-driven simulation study. The simulation results verify the efficiency of these algorithms for both synthetic and real-world mobility traces. For example, the Heuristic algorithm can offload cellular traffic by up to 73.66\% for a real-world mobility trace.}, keywords = {cellular traffic offloading, mobile social networks, opportunistic communications, target-set selection}, isbn = {978-1-4503-0139-8}, doi = {10.1145/1859934.1859943}, url = {http://doi.acm.org/10.1145/1859934.1859943}, author = {Han,Bo and Hui,Pan and Kumar,V. S. Anil and Marathe,Madhav V. and Guanhong Pei and Srinivasan, Aravind} } @conference {16500, title = {Challenges in personalized authority flow based ranking of social media}, booktitle = {Proceedings of the 19th ACM international conference on Information and knowledge management}, year = {2010}, month = {2010///}, pages = {1409 - 1412}, author = {Sayyadi,H. and Edmonds,J. and Hristidis,V. and Raschid, Louiqa} } @conference {13905, title = {Children{\textquoteright}s roles using keyword search interfaces at home}, booktitle = {Proceedings of the 28th international conference on Human factors in computing systems}, year = {2010}, month = {2010///}, pages = {413 - 422}, author = {Druin, Allison and Foss,E. and Hutchinson,H. and Golub,E. and Hatley,L.} } @conference {13937, title = {Clear Panels: a technique to design mobile application interactivity}, booktitle = {Proceedings of the 8th ACM Conference on Designing Interactive Systems}, year = {2010}, month = {2010///}, pages = {360 - 363}, author = {Brown,Q. and Bonsignore,E. and Hatley,L. and Druin, Allison and Walsh,G. and Foss,E. and Brewer,R. and Hammer,J. and Golub,E.} } @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} } @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} } @article {14602, title = {Correlated Changes Between Regulatory Cis Elements and Condition-Specific Expression in Paralogous Gene Families}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {38}, year = {2010}, month = {2010/01/01/}, pages = {738 - 749}, abstract = {Gene duplication is integral to evolution, providing novel opportunities for organisms to diversify in function. One fundamental pathway of functional diversification among initially redundant gene copies, or paralogs, is via alterations in their expression patterns. Although the mechanisms underlying expression divergence are not completely understood, transcription factor binding sites and nucleosome occupancy are known to play a significant role in the process. Previous attempts to detect genomic variations mediating expression divergence in orthologs have had limited success for two primary reasons. First, it is inherently challenging to compare expressions among orthologs due to variable trans-acting effects and second, previous studies have quantified expression divergence in terms of an overall similarity of expression profiles across multiple samples, thereby obscuring condition-specific expression changes. Moreover, the inherently inter-correlated expressions among homologs present statistical challenges, not adequately addressed in many previous studies. Using rigorous statistical tests, here we characterize the relationship between cis element divergence and condition-specific expression divergence among paralogous genes in Saccharomyces cerevisiae. In particular, among all combinations of gene family and TFs analyzed, we found a significant correlation between TF binding and the condition-specific expression patterns in over 20\% of the cases. In addition, incorporating nucleosome occupancy reveals several additional correlations. For instance, our results suggest that GAL4 binding plays a major role in the expression divergence of the genes in the sugar transporter family. Our work presents a novel means of investigating the cis regulatory changes potentially mediating expression divergence in paralogous gene families under specific conditions.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/gkp989}, url = {http://nar.oxfordjournals.org/content/38/3/738}, author = {Singh,Larry N. and Hannenhalli, Sridhar} } @article {15261, title = {Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs}, journal = {Research in Computational Molecular Biology}, year = {2010}, month = {2010///}, pages = {456 - 472}, abstract = {In this paper, we focus on finding complex annotation patterns representing novel and interesting hypotheses from gene annotation data. We define a generalization of the densest subgraph problem by adding an additional distance restriction (defined by a separate metric) to the nodes of the subgraph. We show that while this generalization makes the problem NP-hard for arbitrary metrics, when the metric comes from the distance metric of a tree, or an interval graph, the problem can be solved optimally in polynomial time. We also show that the densest subgraph problem with a specified subset of vertices that have to be included in the solution can be solved optimally in polynomial time. In addition, we consider other extensions when not just one solution needs to be found, but we wish to list all subgraphs of almost maximum density as well. We apply this method to a dataset of genes and their annotations obtained from The Arabidopsis Information Resource (TAIR). A user evaluation confirms that the patterns found in the distance restricted densest subgraph for a dataset of photomorphogenesis genes are indeed validated in the literature; a control dataset validates that these are not random patterns. Interestingly, the complex annotation patterns potentially lead to new and as yet unknown hypotheses. We perform experiments to determine the properties of the dense subgraphs, as we vary parameters, including the number of genes and the distance.}, doi = {10.1007/978-3-642-12683-3_30}, author = {Saha,B. and Hoch,A. and Khuller, Samir and Raschid, Louiqa and Zhang,X. N} } @article {14545, title = {Deploying sensor networks with guaranteed fault tolerance}, journal = {IEEE/ACM Transactions on Networking (TON)}, volume = {18}, year = {2010}, month = {2010///}, pages = {216 - 228}, author = {Bredin,J. L and Demaine,E. D and Hajiaghayi, Mohammad T. and Rus,D.} } @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.} } @article {18539, title = {Don{\textquoteright}t Configure the Network, Program It! Domain-Specific Programming Languages for Network Systems}, volume = {YALEU/DCS/RR-1432}, year = {2010}, month = {2010///}, institution = {Yale University}, abstract = {Network operators must configure networks to accomplish critical, complex, and often conflicting requirements: they must ensure good performance while maintaining security, and satisfy contractual obligations while ensuring profitable use of interdomain connections. Unfortunately, today they have no choice but to implement these high-level goals by configuring hundreds of individual network devices. These interact in complex and unexpected ways, often resulting in misconfigurations or downtime. We propose a new approach: rather than configure individual network devices, operators should program the network holistically, according to high-level policies. Towards this goal, we present Nettle, a system for clearly and concisely expressing network requirements together with mechanisms to control the network accordingly. At the lowest level, we rely on OpenFlow switches for programmable network hardware. On top of this layer, we build an extensible family of embedded domain-specific languages (EDSLs), each aimed at different operational concerns and provide convenient ways to sensibly combine expressions in these languages. We present a case study demonstrating a DSL for networks that provides fine-grained, dynamic access control policies.}, author = {Feamster, Nick and Voellmy,A. and Agarwal,A. and Hudak,P. and Burnett,S. and Launchbury,J.} } @conference {12221, title = {Don{\textquoteright}t love thy nearest neighbor}, booktitle = {Proceedings of the 9th international conference on Peer-to-peer systems}, series = {IPTPS{\textquoteright}10}, year = {2010}, month = {2010///}, pages = {5 - 5}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, url = {http://dl.acm.org/citation.cfm?id=1863145.1863150}, author = {Lumezanu,Cristian and Levin,Dave and Han,Bo and Spring, Neil and Bhattacharjee, Bobby} } @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 {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 {15882, title = {Evaluation of information retrieval for E-discovery}, journal = {Artificial Intelligence and Law}, volume = {18}, year = {2010}, month = {2010/08/10/}, pages = {347 - 386}, isbn = {0924-8463, 1572-8382}, doi = {10.1007/s10506-010-9093-9}, url = {http://www.springerlink.com/content/m700w2k26n264u01/}, author = {Oard, Douglas and Baron,Jason R. and Hedin,Bruce and Lewis,David D. and Tomlinson,Stephen} } @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 {17174, title = {From bowling alone to tweeting together: technology-mediated social participation}, journal = {Interactions}, volume = {17}, year = {2010}, month = {2010///}, pages = {64 - 67}, author = {Hochheiser,H. and Shneiderman, Ben} } @article {12219, title = {A general framework for efficient geographic routing in wireless networks}, journal = {Computer Networks}, volume = {54}, year = {2010}, month = {2010/04/08/}, pages = {844 - 861}, abstract = {We propose a new link metric called normalized advance (NADV) for geographic routing in multihop wireless networks. NADV selects neighbors with the optimal trade-off between proximity and link cost. Coupled with the local next hop decision in geographic routing, NADV enables an adaptive and efficient cost-aware routing strategy. Depending on the objective or message priority, applications can use the NADV framework to minimize various types of link cost.We present efficient methods for link cost estimation and perform detailed experiments in simulated environments. Our results show that NADV outperforms current schemes in many aspects: for example, in high noise environments with frequent packet losses, the use of NADV leads to 81\% higher delivery ratio. When compared to centralized routing under certain settings, geographic routing using NADV finds paths whose cost is close to the optimum. We also conducted experiments in Emulab testbed and the results demonstrate that our proposed approach performs well in practice. }, keywords = {Geographic routing, Link cost estimation, Routing metric, Wireless multihop networks}, isbn = {1389-1286}, doi = {10.1016/j.comnet.2009.09.013}, url = {http://www.sciencedirect.com/science/article/pii/S1389128609002904}, author = {Lee,Seungjoon and Bhattacharjee, Bobby and Banerjee,Suman and Han,Bo} } @article {14584, title = {Genetic and Physiological Activation of Osmosensitive Gene Expression Mimics Transcriptional Signatures of Pathogen Infection in C. elegans}, journal = {PLoS ONEPLoS ONE}, volume = {5}, year = {2010}, month = {2010/02/02/}, pages = {e9010 - e9010}, abstract = {The soil-dwelling nematode C. elegans is a powerful system for comparative molecular analyses of environmental stress response mechanisms. Infection of worms with bacterial and fungal pathogens causes the activation of well-characterized innate immune transcriptional programs in pathogen-exposed hypodermal and intestinal tissues. However, the pathophysiological events that drive such transcriptional responses are not understood. Here, we show that infection-activated transcriptional responses are, in large part, recapitulated by either physiological or genetic activation of the osmotic stress response. Microarray profiling of wild type worms exposed to non-lethal hypertonicity identified a suite of genes that were also regulated by infection. Expression profiles of five different osmotic stress resistant (osr) mutants under isotonic conditions reiterated the wild type transcriptional response to osmotic stress and also showed substantial similarity to infection-induced gene expression under isotonic conditions. Computational, transgenic, and functional approaches revealed that two GATA transcription factors previously implicated in infection-induced transcriptional responses, elt-2 and elt-3, are also essential for coordinated tissue-specific activation of osmosensitive gene expression and promote survival under osmotically stressful conditions. Together, our data suggest infection and osmotic adaptation share previously unappreciated transcriptional similarities which might be controlled via regulation of tissue-specific GATA transcription factors.}, doi = {10.1371/journal.pone.0009010}, url = {http://dx.doi.org/10.1371/journal.pone.0009010}, author = {Rohlfing,Anne-Katrin and Miteva,Yana and Hannenhalli, Sridhar and Lamitina,Todd} } @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 {13958, title = {GPUML: Graphical processors for speeding up kernel machines}, journal = {Workshop on High Performance Analytics-Algorithms, Implementations, and Applications}, year = {2010}, month = {2010///}, abstract = {Algorithms based on kernel methods play a central rolein statistical machine learning. At their core are a num- ber of linear algebra operations on matrices of kernel functions which take as arguments the training and test- ing data. These range from the simple matrix-vector product, to more complex matrix decompositions, and iterative formulations of these. Often the algorithms scale quadratically or cubically, both in memory and op- erational complexity, and as data sizes increase, kernel methods scale poorly. We use parallelized approaches on a multi-core graphical processor (GPU) to partially address this lack of scalability. GPUs are used to scale three different classes of problems, a simple kernel- matrix-vector product, iterative solution of linear sys- tems of kernel function and QR and Cholesky decom- position of kernel matrices. Application of these accel- erated approaches in scaling several kernel based learn- ing approaches are shown, and in each case substantial speedups are obtained. The core software is released as an open source package, GPUML. }, author = {Srinivasan,B.V. and Hu,Q. and Duraiswami, Ramani} } @article {14622, title = {Hopx and Hdac2 Interact to Modulate Gata4 Acetylation and Embryonic Cardiac Myocyte Proliferation}, journal = {Developmental Cell}, volume = {19}, year = {2010}, month = {2010/09/14/}, pages = {450 - 459}, abstract = {SummaryRegulation of chromatin structure via histone modification has recently received intense attention. Here,~we demonstrate that the chromatin-modifying enzyme histone deacetylase 2 (Hdac2) functions with a small homeodomain factor, Hopx, to mediate deacetylation of Gata4, which is expressed by cardiac progenitor cells and plays critical roles in the regulation of cardiogenesis. In the absence of Hopx and Hdac2 in mouse embryos, Gata4 hyperacetylation is associated with a marked increase in~cardiac myocyte proliferation, upregulation of Gata4 target genes, and perinatal lethality. Hdac2 physically interacts with Gata4, and this interaction is stabilized by Hopx. The ability of Gata4 to transactivate cell cycle genes is impaired by Hopx/Hdac2-mediated deacetylation, and this effect is abrogated by loss of Hdac2-Gata4 interaction. These results suggest that Gata4 is a nonhistone target of Hdac2-mediated deacetylation and that Hdac2, Hopx, and Gata4 coordinately regulate cardiac myocyte proliferation during embryonic development. }, isbn = {1534-5807}, doi = {10.1016/j.devcel.2010.08.012}, url = {http://www.sciencedirect.com/science/article/pii/S1534580710003874}, author = {Trivedi,Chinmay M. and Zhu,Wenting and Wang,Qiaohong and Jia,Cheng and Kee,Hae Jin and Li,Li and Hannenhalli, Sridhar and Epstein,Jonathan A.} } @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} } @conference {16692, title = {Improving translation via targeted paraphrasing}, booktitle = {Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing}, year = {2010}, month = {2010///}, pages = {127 - 137}, author = {Resnik, Philip and Buzek,O. and Hu,C. and Kronrod,Y. and Quinn,A. and Bederson, Benjamin B.} } @article {13798, title = {Interlingual Annotation of Parallel Text Corpora: A New Framework for Annotation and Evaluation}, journal = {Natural Language Engineering}, volume = {16}, year = {2010}, month = {2010///}, pages = {197 - 243}, abstract = {This paper focuses on an important step in the creation of a system of meaning representation and the development of semantically annotated parallel corpora, for use in applications such as machine translation, question answering, text summarization, and information retrieval. The work described below constitutes the first effort of any kind to annotate multiple translations of foreign-language texts with interlingual content. Three levels of representation are introduced: deep syntactic dependencies (IL0), intermediate semantic representations (IL1), and a normalized representation that unifies conversives, nonliteral language, and paraphrase (IL2). The resulting annotated, multilingually induced, parallel corpora will be useful as an empirical basis for a wide range of research, including the development and evaluation of interlingual NLP systems and paraphrase-extraction systems as well as a host of other research and development efforts in theoretical and applied linguistics, foreign language pedagogy, translation studies, and other related disciplines.}, doi = {10.1017/S1351324910000070}, author = {Dorr, Bonnie J and Passonneau,Rebecca J. and Farwell,David and Green,Rebecca and Habash,Nizar and Helmreich,Stephen and Hovy,Eduard and Levin,Lori and Miller,Keith J. and Mitamura,Teruko and Rambow,Owen and Siddharthan,Advaith} } @article {18522, title = {An Internet Wide View into DNS Lookup Patterns}, year = {2010}, month = {2010///}, institution = {VeriSign Labs, School of Computer Science, Georgia Tech}, abstract = {This paper analyzes the DNS lookup patterns from a largeauthoritative top-level domain server and characterizes how the lookup patterns for unscrupulous domains may differ from those for legitimate domains. We examine domains for phishing attacks and spam and malware related domains, and see how these lookup patterns vary in terms of both their temporal and spatial characteristics. We find that malicious domains tend to exhibit more variance in the networks that look up these domains, and we also find that these domains become popular considerably more quickly after their initial registration time. We also note that miscreant domains ex- hibit distinct clusters, in terms to the networks that look up these domains. The distinct spatial and temporal character- istics of these domains, and their tendency to exhibit simi- lar lookup behavior, suggests that it may be possible to ulti- mately develop more effective blacklisting techniques based on these differing lookup patterns. }, author = {Hao,S. and Feamster, Nick and Pandrangi,R.} } @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} } @article {12144, title = {Linking Software Development and Business Strategy Through Measurement}, journal = {Computer}, volume = {43}, year = {2010}, month = {2010/04//}, pages = {57 - 65}, abstract = {The GQM+Strategies approach extends the goal/question/metric paradigm for measuring the success or failure of goals and strategies, adding enterprise-wide support for determining action on the basis of measurement results. An organization can thus integrate its measurement program across all levels.}, keywords = {approach;business, aspects;software, development;organisational, engineering;, GQM+Strategies, program;software, strategy;enterprise, support;measurement, wide}, isbn = {0018-9162}, doi = {10.1109/MC.2010.108}, author = {Basili, Victor R. and Lindvall,M. and Regardie,M. and Seaman,C. and Heidrich,J. and Munch,J. and Rombach,D. and Trendowicz,A.} } @conference {12223, title = {Maranello: practical partial packet recovery for 802.11}, booktitle = {Proceedings of the 7th USENIX conference on Networked systems design and implementation}, series = {NSDI{\textquoteright}10}, year = {2010}, month = {2010///}, pages = {14 - 14}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {Partial packet recovery protocols attempt to repair corrupted packets instead of retransmitting them in their entirety. Recent approaches have used physical layer confidence estimates or additional error detection codes embedded in each transmission to identify corrupt bits, or have applied forward error correction to repair without such explicit knowledge. In contrast to these approaches, our goal is a practical design that simultaneously: (a) requires no extra bits in correct packets, (b) reduces recovery latency, except in rare instances, (c) remains compatible with existing 802.11 devices by obeying timing and backoff standards, and (d) can be incrementally deployed on widely available access points and wireless cards. In this paper, we design, implement, and evaluate Maranello, a novel partial packet recovery mechanism for 802.11. In Maranello, the receiver computes checksums over blocks in corrupt packets and bundles these checksums into a negative acknowledgment sent when the sender expects to receive an acknowledgment. The sender then retransmits only those blocks for which the checksum is incorrect, and repeats this partial retransmission until it receives an acknowledgment. Successful transmissions are not burdened by additional bits and the receiver needs not infer which bits were corrupted. We implemented Maranello using OpenFWWF (open source firmware for Broadcom wireless cards) and deployed it in a small testbed. We compare Maranello to alternative recovery protocols using a trace-driven simulation and to 802.11 using a live implementation under various channel conditions. To our knowledge, Maranello is the first partial packet recovery design to be implemented in commonly available firmware.}, url = {http://dl.acm.org/citation.cfm?id=1855711.1855725}, author = {Han,Bo and Schulman,Aaron and Gringoli,Francesco and Spring, Neil and Bhattacharjee, Bobby and Nava,Lorenzo and Ji,Lusheng and Lee,Seungjoon and Miller,Robert} } @article {18239, title = {Method for fingerprinting multimedia content}, volume = {11/326,313}, year = {2010}, month = {2010/10/12/}, abstract = {To identify participants in collusion directed to altering a digital fingerprint embedded in multimedia content, an ECC based fingerprinting technique establishes a code symbol for each of a plurality of segments of digital data forming the multimedia content. The code symbols are concatenated to form a fingerprint signal, which is subdivided into a plurality of subsegments for each segment in the digital data. The subsegments are permuted and embedded into the digital data. When a suspicious copy of the multimedia content is discovered, the permuted fingerprint signal is extracted from the content and inversely permuted to form a test fingerprint. The identity of one of the colluders is determined by correlation with characteristics of the codeword originally assigned to the user. The determination of identity may be enhanced by the addition of group data embedded as an additional fingerprint in the digital data. Joint consideration of coding and embedding provide benefits over...}, url = {http://www.google.com/patents?id=GXnXAAAAEBAJ}, author = {He,Shan and M. Wu}, editor = {University of Maryland} } @article {14629, title = {Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction}, journal = {Algorithms for Molecular Biology}, volume = {5}, year = {2010}, month = {2010/01/04/}, pages = {4 - 4}, abstract = {Functionally related genes tend to be correlated in their expression patterns across multiple conditions and/or tissue-types. Thus co-expression networks are often used to investigate functional groups of genes. In particular, when one of the genes is a transcription factor (TF), the co-expression-based interaction is interpreted, with caution, as a direct regulatory interaction. However, any particular TF, and more importantly, any particular regulatory interaction, is likely to be active only in a subset of experimental conditions. Moreover, the subset of expression samples where the regulatory interaction holds may be marked by presence or absence of a modifier gene, such as an enzyme that post-translationally modifies the TF. Such subtlety of regulatory interactions is overlooked when one computes an overall expression correlation.}, isbn = {1748-7188}, doi = {10.1186/1748-7188-5-4}, url = {http://www.almob.org/content/5/1/4}, author = {Hansen,Matthew and Everett,Logan and Singh,Larry and Hannenhalli, Sridhar} } @article {17625, title = {Mobile data offloading in metropolitan area networks}, journal = {SIGMOBILE Mob. Comput. Commun. Rev.}, volume = {14}, year = {2010}, month = {2010/11//}, pages = {28 - 30}, abstract = {Cellular networks, especially 3G networks, are currently overloaded with mobile data traffic. It is thus imperative to develop novel communication architectures and protocols for this problem. In this paper, we propose to exploit the delay-tolerant nature of non-realtime applications to offload mobile data traffic through opportunistic communications and WiFi networks. We argue that it is necessary for cellular network operators, WiFi service providers, and end-users to cooperate to make the offloading more effective. We also present several preliminary experiment results about the work we have been conducting, which show that it is promising to offload mobile data traffic in metropolitan area networks.}, isbn = {1559-1662}, doi = {10.1145/1942268.1942279}, url = {http://doi.acm.org/10.1145/1942268.1942279}, author = {Han,Bo and Hui,Pan and Srinivasan, Aravind} } @conference {12407, title = {Modeling perspective using adaptor grammars}, booktitle = {Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing}, series = {EMNLP {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {284 - 292}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Strong indications of perspective can often come from collocations of arbitrary length; for example, someone writing get the government out of my X is typically expressing a conservative rather than progressive viewpoint. However, going beyond unigram or bigram features in perspective classification gives rise to problems of data sparsity. We address this problem using nonparametric Bayesian modeling, specifically adaptor grammars (Johnson et al., 2006). We demonstrate that an adaptive na{\"\i}ve Bayes model captures multiword lexical usages associated with perspective, and establishes a new state-of-the-art for perspective classification results using the Bitter Lemons corpus, a collection of essays about mid-east issues from Israeli and Palestinian points of view.}, url = {http://dl.acm.org/citation.cfm?id=1870658.1870686}, author = {Hardisty,Eric A. and Jordan Boyd-Graber and Resnik, Philip} } @article {13093, title = {Multi-Camera Tracking with Adaptive Resource Allocation}, journal = {International Journal of Computer Vision}, year = {2010}, month = {2010///}, pages = {1 - 14}, author = {Han,B. and Joo, S.W. and Davis, Larry S.} } @conference {17633, title = {New Constructive Aspects of the Lovasz Local Lemma}, booktitle = {2010 51st Annual IEEE Symposium on Foundations of Computer Science (FOCS)}, year = {2010}, month = {2010/10/23/26}, pages = {397 - 406}, publisher = {IEEE}, organization = {IEEE}, abstract = {The Lov{\textquoteright}{a}sz Local Lemma (LLL) is a powerful tool that gives sufficient conditions for avoiding all of a given set of {\textquoteleft}{\textquoteleft}bad{\textquoteright}{\textquoteright} events, with positive probability. A series of results have provided algorithms to efficiently construct structures whose existence is non-constructively guaranteed by the LLL, culminating in the recent breakthrough of Moser \& Tardos. We show that the output distribution of the Moser-Tardos algorithm well-approximates the emph{conditional LLL-distribution} {\textendash} the distribution obtained by conditioning on all bad events being avoided. We show how a known bound on the probabilities of events in this distribution can be used for further probabilistic analysis and give new constructive and non-constructive results. We also show that when an LLL application provides a small amount of slack, the number of resamplings of the Moser-Tardos algorithm is nearly linear in the number of underlying independent variables (not events!), and can thus be used to give efficient constructions in cases where the underlying proof applies the LLL to super-polynomially many events. Even in cases where finding a bad event that holds is computationally hard, we show that applying the algorithm to avoid a polynomial-sized {\textquoteleft}{\textquoteleft}core{\textquoteright}{\textquoteright} subset of bad events leads to a desired outcome with high probability. We demonstrate this idea on several applications. We give the first constant-factor approximation algorithm for the Santa Claus problem by making an LLL-based proof of Feige constructive. We provide Monte Carlo algorithms for acyclic edge coloring, non-repetitive graph colorings, and Ramsey-type graphs. In all these applications the algorithm falls directly out of the non-constructive LLL-based proof. Our algorithms are very simple, often provide better bounds than previous algorithms, and are in several cases the first efficient algorithms known. As a second type of application we consider settings beyond the critical dependency threshold of the LLL: - - avoiding all bad events is impossible in these cases. As the first (even non-constructive) result of this kind, we show that by sampling from the LLL-distribution of a selected smaller core, we can avoid a fraction of bad events that is higher than the expectation. MAX $k$-SAT is an example of this.}, keywords = {acyclic edge coloring, Algorithm design and analysis, Approximation algorithms, Approximation methods, computational complexity, Computer science, constant factor approximation algorithm, graph colouring, Linearity, Lovasz Local Lemma, MAX k-SAT, Monte Carlo Algorithm, Monte Carlo methods, Moser-Tardos algorithm, nonrepetitive graph coloring, output distribution, polynomial sized core subset, Polynomials, Probabilistc Method, probabilistic analysis, probabilistic logic, probability, Ramsey type graph, Sampling methods, Santa Claus Problem}, isbn = {978-1-4244-8525-3}, doi = {10.1109/FOCS.2010.45}, author = {Haeupler,B. and Saha,B. and Srinivasan, Aravind} } @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 {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} } @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 {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} } @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} } @inbook {14638, title = {Regulating the Regulators: Modulators of Transcription Factor Activity}, booktitle = {Computational Biology of Transcription Factor BindingComputational Biology of Transcription Factor Binding}, series = {Methods in Molecular Biology}, volume = {674}, year = {2010}, month = {2010///}, pages = {297 - 312}, publisher = {Humana Press}, organization = {Humana Press}, abstract = {Gene transcription is largely regulated by DNA-binding transcription factors ( TFs ). However, the TF activity itself is modulated via, among other things, post-translational modifications ( PTMs ) by specific modification enzymes in response to cellular stimuli. TF-PTMs thus serve as {\textquotedblleft}molecular switchboards{\textquotedblright} that map upstream signaling events to the downstream transcriptional events. An important long-term goal is to obtain a genome-wide map of {\textquotedblleft}regulatory triplets{\textquotedblright} consisting of a TF, target gene, and a modulator gene that specifically modulates the regulation of the target gene by the TF. A variety of genome-wide data sets can be exploited by computational methods to obtain a rough map of regulatory triplets, which can guide directed experiments. However, a prerequisite to developing such computational tools is a systematic catalog of known instances of regulatory triplets. We first describe PTM-Switchboard, a recent database that stores triplets of genes such that the ability of one gene (the TF) to regulate a target gene is dependent on one or more PTMs catalyzed by a third gene, the modifying enzyme. We also review current computational approaches to infer regulatory triplets from genome-wide data sets and conclude with a discussion of potential future research. PTM-Switchboard is accessible at http://cagr.pcbi.upenn.edu/PTMswitchboard /}, isbn = {978-1-60761-854-6}, url = {http://dx.doi.org/10.1007/978-1-60761-854-6_19}, author = {Everett,Logan and Hansen,Matthew and Hannenhalli, Sridhar}, editor = {Ladunga,Istvan} } @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.} } @article {14373, title = {REPORTS AI Theory and Practice: A Discussion on Hard Challenges and Opportunities Ahead}, journal = {AI Magazine}, volume = {31}, year = {2010}, month = {2010///}, pages = {87 - 87}, author = {Horvitz,E. and Getoor, Lise and Guestrin,C. and Hendler,J. and Kautz,H. and Konstan,J. and Subramanian,D. and Wellman,M.} } @article {18711, title = {Reversible Post-Translational Carboxylation Modulates the Enzymatic Activity of N-Acetyl-l-ornithine Transcarbamylase}, journal = {Biochemistry}, volume = {49}, year = {2010}, month = {2010///}, pages = {6887 - 6895}, abstract = {N-Acetyl-l-ornithine transcarbamylase (AOTCase), rather than ornithine transcarbamylase (OTCase), is the essential carbamylase enzyme in the arginine biosynthesis of several plant and human pathogens. The specificity of this unique enzyme provides a potential target for controlling the spread of these pathogens. Recently, several crystal structures of AOTCase from Xanthomonas campestris (xc) have been determined. In these structures, an unexplained electron density at the tip of the Lys302 side chain was observed. Using 13C NMR spectroscopy, we show herein that Lys302 is post-translationally carboxylated. The structure of wild-type AOTCase in a complex with the bisubstrate analogue Nδ-(phosphonoacetyl)-Nα-acetyl-l-ornithine (PALAO) indicates that the carboxyl group on Lys302 forms a strong hydrogen bonding network with surrounding active site residues, Lys252, Ser253, His293, and Glu92 from the adjacent subunit either directly or via a water molecule. Furthermore, the carboxyl group is involved in binding N-acetyl-l-ornithine via a water molecule. Activity assays with the wild-type enzyme and several mutants demonstrate that the post-translational modification of lysine 302 has an important role in catalysis.N-Acetyl-l-ornithine transcarbamylase (AOTCase), rather than ornithine transcarbamylase (OTCase), is the essential carbamylase enzyme in the arginine biosynthesis of several plant and human pathogens. The specificity of this unique enzyme provides a potential target for controlling the spread of these pathogens. Recently, several crystal structures of AOTCase from Xanthomonas campestris (xc) have been determined. In these structures, an unexplained electron density at the tip of the Lys302 side chain was observed. Using 13C NMR spectroscopy, we show herein that Lys302 is post-translationally carboxylated. The structure of wild-type AOTCase in a complex with the bisubstrate analogue Nδ-(phosphonoacetyl)-Nα-acetyl-l-ornithine (PALAO) indicates that the carboxyl group on Lys302 forms a strong hydrogen bonding network with surrounding active site residues, Lys252, Ser253, His293, and Glu92 from the adjacent subunit either directly or via a water molecule. Furthermore, the carboxyl group is involved in binding N-acetyl-l-ornithine via a water molecule. Activity assays with the wild-type enzyme and several mutants demonstrate that the post-translational modification of lysine 302 has an important role in catalysis. }, isbn = {0006-2960}, doi = {10.1021/bi1007386}, url = {http://dx.doi.org/10.1021/bi1007386}, author = {Li,Yongdong and Yu,Xiaolin and Ho,Jeremy and Fushman, David and Allewell,Norma M. and Tuchman,Mendel and Shi,Dashuang} } @article {17950, title = {Saliency Guided Summarization of Molecular Dynamics Simulations}, journal = {Scientific Visualization: Advanced Concepts}, volume = {1}, year = {2010}, month = {2010///}, pages = {321 - 335}, abstract = {We present a novel method to measure saliency in molecular dynamics simulation data. This saliency measure is based on a multiscale center-surround mechanism, which is fast and efficient to compute. We explore the use of the saliency function to guide the selection of representative and anomalous timesteps for summarization of simulations. To this end, we also introduce a multiscale keyframe selection procedure which automatically provides keyframes representing the simulation at varying levels of coarseness. We compare our saliency guided keyframe approach against other methods, and show that it consistently selects superior keyframes as measured by their predictive power in reconstructing the simulation.}, author = {Patro,R. and Ip,C. Y and Varshney, Amitabh and Hagen,H.} } @conference {15283, title = {Scaling Populations of a Genetic Algorithm for Job Shop Scheduling Problems Using MapReduce}, booktitle = {Cloud Computing Technology and Science (CloudCom), 2010 IEEE Second International Conference on}, year = {2010}, month = {2010///}, pages = {780 - 785}, abstract = {Inspired by Darwinian evolution, a genetic algorithm (GA) approach is one popular heuristic method for solving hard problems such as the Job Shop Scheduling Problem (JSSP), which is one of the hardest problems lacking efficient exact solutions today. It is intuitive that the population size of a GA may greatly affect the quality of the solution, but it is unclear what are the effects of having population sizes that are significantly greater than typical experiments. The emergence of MapReduce, a framework running on a cluster of computers that aims to provide large-scale data processing, offers great opportunities to investigate this issue. In this paper, a GA is implemented to scale the population using MapReduce. Experiments are conducted on a large cluster, and population sizes up to 107 are inspected. It is shown that larger population sizes not only tend to yield better solutions, but also require fewer generations. Therefore, it is clear that when dealing with a hard problem such as JSSP, an existing GA can be improved by massively scaling up populations with MapReduce, so that the solution can be parallelized and completed in reasonable time.}, keywords = {algorithm;job, algorithms;job, computing;genetic, data, large-scale, MapReduce;cloud, problems;parallel, processing;, processing;cloud, scheduling, scheduling;parallel, shop}, doi = {10.1109/CloudCom.2010.18}, author = {Di-Wei Huang and Jimmy Lin} } @article {14733, title = {SCORE: agile research group management}, journal = {Commun. ACM}, volume = {53}, year = {2010}, month = {2010/10//}, pages = {30 - 31}, abstract = {Adapting agile software development methodology toward more efficient management of academic research groups.}, isbn = {0001-0782}, doi = {10.1145/1831407.1831421}, url = {http://doi.acm.org/10.1145/1831407.1831421}, author = {Hicks, Michael W. and Foster, Jeffrey S.} } @article {14734, title = {Serializing C intermediate representations for efficient and portable parsing}, journal = {Software: Practice and Experience}, volume = {40}, year = {2010}, month = {2010/03/01/}, pages = {225 - 238}, abstract = {C static analysis tools often use intermediate representations (IRs) that organize program data in a simple, well-structured manner. However, the C parsers that create IRs are slow, and because they are difficult to write, only a few implementations exist, limiting the languages in which a C static analysis can be written. To solve these problems, we investigate two language-independent, on-disk representations of C IRs: one using XML and the other using an Internet standard binary encoding called eXternal Data Representation (XDR). We benchmark the parsing speeds of both options, finding the XML to be about a factor of 2 slower than parsing C and the XDR over 6 times faster. Furthermore, we show that the XML files are far too large at 19 times the size of C source code, whereas XDR is only 2.2 times the C size. We also demonstrate the portability of our XDR system by presenting a C source code querying tool in Ruby. Our solution and the insights we gained from building it will be useful to analysis authors and other clients of C IRs. We have made our software freely available for download at http://www.cs.umd.edu/projects/PL/scil/. Copyright {\textcopyright} 2010 John Wiley\&Sons, Ltd.}, keywords = {C, intermediate representations, parsing, static analysis, XDR, XML}, isbn = {1097-024X}, doi = {10.1002/spe.954}, url = {http://onlinelibrary.wiley.com/doi/10.1002/spe.954/abstract}, author = {Meister,Jeffrey A and Foster, Jeffrey S. and Hicks, Michael W.} } @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} } @conference {19296, title = {Simulating dynamic communication systems using the core functional dataflow model}, booktitle = {2010 IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP)}, year = {2010}, month = {2010}, pages = {1538 - 1541}, abstract = {The latest communication technologies invariably consist of modules with dynamic behavior. There exists a number of design tools for communication system design with their foundation in dataflow modeling semantics. These tools must not only support the functional specification of dynamic communication modules and subsystems but also provide accurate estimation of resource requirements for efficient simulation and implementation. We explore this trade-off - between flexible specification of dynamic behavior and accurate estimation of resource requirements - using a representative application employing an adaptive modulation scheme. We propose an approach for precise modeling of such applications based on a recently-introduced form of dynamic dataflow called core functional dataflow. From our proposed modeling approach, we show how parameterized looped schedules can be generated and analyzed to simulate applications with low run-time overhead as well as guaranteed bounded memory execution. We demonstrate our approach using the Advanced Design System from Agilent Technologies, Inc., which is a commercial tool for design and simulation of communication systems.}, keywords = {adaptive modulation, Analytical models, Application software, Computational modeling, core functional dataflow model, Dataflow, dataflow modeling semantics, design tools, Digital signal processing, dynamic communication systems, functional specification, Hardware, modeling and simulation, Power system modeling, Predictive models, Processor scheduling, Production, Signal processing, software tools, wireless communication}, author = {Sane, N. and Chia-Jui Hsu and Pino,J. L and Bhattacharyya, Shuvra S.} } @article {19725, title = {Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function.}, journal = {BMC Bioinformatics}, volume = {11}, year = {2010}, month = {2010}, pages = {52}, abstract = {

BACKGROUND: Comparative genomics methods such as phylogenetic profiling can mine powerful inferences from inherently noisy biological data sets. We introduce Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL), a method that applies the Partial Phylogenetic Profiling (PPP) approach locally within a protein sequence to discover short sequence signatures associated with functional sites. The approach is based on the basic scoring mechanism employed by PPP, namely the use of binomial distribution statistics to optimize sequence similarity cutoffs during searches of partitioned training sets.

RESULTS: Here we illustrate and validate the ability of the SIMBAL method to find functionally relevant short sequence signatures by application to two well-characterized protein families. In the first example, we partitioned a family of ABC permeases using a metabolic background property (urea utilization). Thus, the TRUE set for this family comprised members whose genome of origin encoded a urea utilization system. By moving a sliding window across the sequence of a permease, and searching each subsequence in turn against the full set of partitioned proteins, the method found which local sequence signatures best correlated with the urea utilization trait. Mapping of SIMBAL "hot spots" onto crystal structures of homologous permeases reveals that the significant sites are gating determinants on the cytosolic face rather than, say, docking sites for the substrate-binding protein on the extracellular face. In the second example, we partitioned a protein methyltransferase family using gene proximity as a criterion. In this case, the TRUE set comprised those methyltransferases encoded near the gene for the substrate RF-1. SIMBAL identifies sequence regions that map onto the substrate-binding interface while ignoring regions involved in the methyltransferase reaction mechanism in general. Neither method for training set construction requires any prior experimental characterization.

CONCLUSIONS: SIMBAL shows that, in functionally divergent protein families, selected short sequences often significantly outperform their full-length parent sequence for making functional predictions by sequence similarity, suggesting avenues for improved functional classifiers. When combined with structural data, SIMBAL affords the ability to localize and model functional sites.

}, keywords = {algorithms, Amino Acid Sequence, Gene Expression Profiling, Molecular Sequence Data, Phylogeny, Proteins, Sequence Analysis, Protein, Structure-Activity Relationship}, issn = {1471-2105}, doi = {10.1186/1471-2105-11-52}, author = {Jeremy D Selengut and Rusch, Douglas B and Haft, Daniel H} } @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.} } @article {13087, title = {SPECIAL SECTION ON SHAPE ANALYSIS AND ITS APPLICATIONS IN IMAGE UNDERSTANDING}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {32}, year = {2010}, month = {2010///}, pages = {0162 - 8828}, author = {Srivastava, A. and Damon,J.N. and Dryden,I.L. and Jermyn,I.H. and Das,S. and Vaswani, N. and Huckemann,S. and Hotz,T. and Munk,A. and Lin,Z. and others} } @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.} } @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.} } @article {18284, title = {System and Method for Confidentiality-Preserving Rank-Ordered Search}, volume = {12/608,724}, year = {2010}, month = {2010/06/10/}, abstract = {A confidentiality preserving system and method for performing a rank-ordered search and retrieval of contents of a data collection. The system includes at least one computer system including a search and retrieval algorithm using term frequency and/or similar features for rank-ordering selective contents of the data collection, and enabling secure retrieval of the selective contents based on the rank-order. The search and retrieval algorithm includes a baseline algorithm, a partially server oriented algorithm, and/or a fully server oriented algorithm. The partially and/or fully server oriented algorithms use homomorphic and/or order preserving encryption for enabling search capability from a user other than an owner of the contents of the data collection. The confidentiality preserving method includes using term frequency for rank-ordering selective contents of the data collection, and retrieving the selective contents based on the rank-order.}, url = {http://www.google.com/patents?id=kInVAAAAEBAJ}, author = {Swaminathan,Ashwin and Mao,Yinian and Su,Guan-Ming and Gou,Hongmei and Varna,Avinash L. and He,Shan and M. Wu and Oard, Douglas} } @inbook {17395, title = {Technology-Mediated Social Participation: Deep Science and Extreme Technology}, booktitle = {Active Media TechnologyActive Media Technology}, series = {Lecture Notes in Computer Science}, volume = {6335}, year = {2010}, month = {2010///}, pages = {1 - 4}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The dramatic success of social media such as Facebook, Twitter, YouTube, Flickr, blogs, and traditional discussion groups empowers individuals to become active in local and global communities. With modest redesign, these technologies can be harnessed to support national priorities such as healthcare/wellness, disaster response, community safety, energy sustainability, etc. This talk describes a research agenda for these topics that develops deep science questions and extreme technology challenges.}, isbn = {978-3-642-15469-0}, url = {http://dx.doi.org/10.1007/978-3-642-15470-6_1}, author = {Shneiderman, Ben}, editor = {An,Aijun and Lingras,Pawan and Petty,Sheila and Huang,Runhe} } @article {19724, title = {Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.}, journal = {J Bacteriol}, volume = {192}, year = {2010}, month = {2010 Nov}, pages = {5788-98}, abstract = {

Regimens targeting Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), require long courses of treatment and a combination of three or more drugs. An increase in drug-resistant strains of M. tuberculosis demonstrates the need for additional TB-specific drugs. A notable feature of M. tuberculosis is coenzyme F(420), which is distributed sporadically and sparsely among prokaryotes. This distribution allows for comparative genomics-based investigations. Phylogenetic profiling (comparison of differential gene content) based on F(420) biosynthesis nominated many actinobacterial proteins as candidate F(420)-dependent enzymes. Three such families dominated the results: the luciferase-like monooxygenase (LLM), pyridoxamine 5{\textquoteright}-phosphate oxidase (PPOX), and deazaflavin-dependent nitroreductase (DDN) families. The DDN family was determined to be limited to F(420)-producing species. The LLM and PPOX families were observed in F(420)-producing species as well as species lacking F(420) but were particularly numerous in many actinobacterial species, including M. tuberculosis. Partitioning the LLM and PPOX families based on an organism{\textquoteright}s ability to make F(420) allowed the application of the SIMBAL (sites inferred by metabolic background assertion labeling) profiling method to identify F(420)-correlated subsequences. These regions were found to correspond to flavonoid cofactor binding sites. Significantly, these results showed that M. tuberculosis carries at least 28 separate F(420)-dependent enzymes, most of unknown function, and a paucity of flavin mononucleotide (FMN)-dependent proteins in these families. While prevalent in mycobacteria, markers of F(420) biosynthesis appeared to be absent from the normal human gut flora. These findings suggest that M. tuberculosis relies heavily on coenzyme F(420) for its redox reactions. This dependence and the cofactor{\textquoteright}s rarity may make F(420)-related proteins promising drug targets.

}, keywords = {Actinobacteria, Amino Acid Sequence, Binding Sites, Coenzymes, Flavonoids, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genome, Bacterial, molecular biology, Molecular Sequence Data, Molecular Structure, Mycobacterium tuberculosis, Phylogeny, Protein Conformation, Riboflavin}, issn = {1098-5530}, doi = {10.1128/JB.00425-10}, author = {Jeremy D Selengut and Haft, Daniel H} } @conference {13475, title = {Using a Trust Model in Decision Making for Supply Chain Management}, booktitle = {Workshops at the Twenty-Fourth AAAI Conference on Artificial Intelligence}, year = {2010}, month = {2010///}, author = {Haghpanah,Y. and desJardins, Marie and others} } @article {17749, title = {Using Generalized Annotated Programs to Solve Social Network Optimization Problems}, journal = {ICLP}, year = {2010}, month = {2010///}, abstract = {Reasoning about social networks (labeled, directed, weighted graphs) is be-coming increasingly important and there are now models of how certain phenomena (e.g. adoption of products/services by consumers, spread of a given disease) {\textquotedblleft}diffuse{\textquotedblright} through the network. Some of these diffusion models can be expressed via generalized annotated programs (GAPs). In this paper, we consider the following problem: suppose we have a given goal to achieve (e.g. maximize the expected number of adoptees of a product or minimize the spread of a disease) and suppose we have limited resources to use in trying to achieve the goal (e.g. give out a few free plans, provide medication to key people in the SN) - how should these resources be used so that we optimize a given objective function related to the goal? We define a class of social network optimization problems (SNOPs) that supports this type of reasoning. We formalize and study the complexity of SNOPs and show how they can be used in conjunction with existing economic and disease diffusion models. }, author = {Shakarian,P. and V.S. Subrahmanian and Sapino,M. L and Hermenegildo,M. and Schaub,T.} } @article {14757, title = {Viewpoint Adapting agile software development methodology toward more efficient management of academic research groups.}, journal = {Communications of the ACM}, volume = {53}, year = {2010}, month = {2010///}, pages = {30 - 30}, author = {Hicks, Michael W. and Foster, Jeffrey S.} } @inbook {17503, title = {Visualizing Threaded Conversation Networks: Mining Message Boards and Email Lists for Actionable Insights}, booktitle = {Active Media TechnologyActive Media Technology}, series = {Lecture Notes in Computer Science}, volume = {6335}, year = {2010}, month = {2010///}, pages = {47 - 62}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Analyzing complex online relationships is a difficult job, but new information visualization tools are enabling a wider range of users to make actionable insights from the growing volume of online data. This paper describes the challenges and methods for conducting analyses of threaded conversations such as found in enterprise message boards, email lists, and forums. After defining threaded conversation, we characterize the types of networks that can be extracted from them. We then provide 3 mini case studies to illustrate how actionable insights for community managers can be gained by applying the network analysis metrics and visualizations available in the free, open source NodeXL tool, which is a powerful, yet easy-to-use tool embedded in Excel 2007/2010.}, isbn = {978-3-642-15469-0}, url = {http://dx.doi.org/10.1007/978-3-642-15470-6_7}, author = {Hansen,Derek and Shneiderman, Ben and Smith,Marc}, editor = {An,Aijun and Lingras,Pawan and Petty,Sheila and Huang,Runhe} } @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} } @conference {15456, title = {Workshop on experimental evaluation of software and systems in computer science (Evaluate 2010)}, booktitle = {Proceedings of the ACM international conference companion on Object oriented programming systems languages and applications companion}, series = {SPLASH {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {291 - 292}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We call ourselves {\textquoteright}computer scientists{\textquoteright}, but are we scientists? If we are scientists, then we must practice the scientific method. This includes a solid experimental evaluation. In our experience, our experimental methodology is ad hoc at best, and nonexistent at worst. This workshop brings together experts from different areas of computer science to discuss, explore, and attempt to identify the principles of sound experimental evaluation}, keywords = {Evaluation, METHODOLOGY}, isbn = {978-1-4503-0240-1}, doi = {10.1145/1869542.1869618}, url = {http://doi.acm.org/10.1145/1869542.1869618}, author = {Blackburn,Steven M. and Diwan,Amer and Hauswirth,Matthias and Memon, Atif M. and Sweeney,Peter F.} } @article {14650, title = {Young Proteins Experience More Variable Selection Pressures Than Old Proteins}, journal = {Genome ResearchGenome Res.}, volume = {20}, year = {2010}, month = {2010/11/01/}, pages = {1574 - 1581}, abstract = {It is well known that young proteins tend to experience weaker purifying selection and evolve more quickly than old proteins. Here, we show that, in addition, young proteins tend to experience more variable selection pressures over time than old proteins. We demonstrate this pattern in three independent taxonomic groups: yeast, Drosophila, and mammals. The increased variability of selection pressures on young proteins is highly significant even after controlling for the fact that young proteins are typically shorter and experience weaker purifying selection than old proteins. The majority of our results are consistent with the hypothesis that the function of a young gene tends to change over time more readily than that of an old gene. At the same time, our results may be caused in part by young genes that serve constant functions over time, but nevertheless appear to evolve under changing selection pressures due to depletion of adaptive mutations. In either case, our results imply that the evolution of a protein-coding sequence is partly determined by its age and origin, and not only by the phenotypic properties of the encoded protein. We discuss, via specific examples, the consequences of these findings for understanding of the sources of evolutionary novelty.}, isbn = {1088-9051, 1549-5469}, doi = {10.1101/gr.109595.110}, url = {http://genome.cshlp.org/content/20/11/1574}, author = {Vishnoi,Anchal and Kryazhimskiy,Sergey and Bazykin,Georgii A and Hannenhalli, Sridhar and Plotkin,Joshua B.} } @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} } @conference {12229, title = {All Bits Are Not Equal - A Study of IEEE 802.11 Communication Bit Errors}, booktitle = {INFOCOM 2009, IEEE}, year = {2009}, month = {2009/04//}, pages = {1602 - 1610}, abstract = {In IEEE 802.11 Wireless LAN (WLAN) systems, techniques such as acknowledgement, retransmission, and transmission rate adaptation, are frame-level mechanisms designed for combating transmission errors. Recently sub-frame level mechanisms such as frame combining have been proposed by the research community. In this paper, we present results obtained from our bit error study for identifying sub-frame error patterns because we believe that identifiable bit error patterns can potentially introduce new opportunities in channel coding, network coding, forward error correction (FEC), and frame combining mechanisms. We have constructed a number of IEEE 802.11 wireless LAN testbeds and conducted extensive experiments to study the characteristics of bit errors and their location distribution. Conventional wisdom dictates that bit error probability is the result of channel condition and ought to follow corresponding distribution. However our measurement results identify three repeatable bit error patterns that are not induced by channel conditions. We have verified that such error patterns are present in WLAN transmissions in different physical environments and across different wireless LAN hardware platforms. We also discuss our current hypotheses for the reasons behind these bit error probability patterns and how identifying these patterns may help improving WLAN transmission robustness.}, keywords = {802.11, bit, coding;error, coding;forward, coding;subframe, combining, Communication, correction;frame, correction;wireless, error, errors;channel, errors;wireless, IEEE, LAN;, LAN;channel, mechanisms;network, patterns;transmission, statistics;forward}, doi = {10.1109/INFCOM.2009.5062078}, author = {Han,Bo and Ji,Lusheng and Lee,Seungjoon and Bhattacharjee, Bobby and Miller,R.R.} } @conference {11902, title = {Approximate kernel matrix computation on GPUs forlarge scale learning applications}, booktitle = {Proceedings of the 23rd international conference on Supercomputing}, series = {ICS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {511 - 512}, publisher = {ACM}, organization = {ACM}, address = {Yorktown Heights, NY, USA}, abstract = {Kernel-based learning methods require quadratic space and time complexities to compute the kernel matrix. These complexities limit the applicability of kernel methods to large scale problems with millions of data points. In this paper, we introduce a novel representation of kernel matrices on Graphics Processing Units (GPU). The novel representation exploits the sparseness of the kernel matrix to address the space complexity problem. It also respects the guidelines for memory access on GPUs, which are critical for good performance, to address the time complexity problem. Our representation utilizes the locality preserving properties of space filling curves to obtain a band approximation of the kernel matrix. To prove the validity of the representation, we use Affinity Propagation, an unsupervised clustering algorithm, as an example of kernel methods. Experimental results show a 40x speedup of AP using our representation without degradation in clustering performance.}, keywords = {affinity propagation, algorithms, arrays, gpu, kernel methods, parallel programming, performance, space filling curves, sparse matrices}, isbn = {978-1-60558-498-0}, doi = {10.1145/1542275.1542355}, author = {Hussein,Mohamed E and Abd-Almageed, Wael} } @conference {15136, title = {Attacking cryptographic schemes based on "perturbation polynomials"}, booktitle = {Proceedings of the 16th ACM conference on Computer and communications security}, series = {CCS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {1 - 10}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We show attacks on several cryptographic schemes that have recently been proposed for achieving various security goals in sensor networks. Roughly speaking, these schemes all use "perturbation polynomials" to add "noise" to polynomialbased systems that offer information-theoretic security, in an attempt to increase the resilience threshold while maintaining efficiency. We show that the heuristic security arguments given for these modified schemes do not hold, and that they can be completely broken once we allow even a slight extension of the parameters beyond those achieved by the underlying information-theoretic schemes. Our attacks apply to the key predistribution scheme of Zhang et al. (MobiHoc 2007), the access-control schemes of Subramanian et al. (PerCom 2007), and the authentication schemes of Zhang et al. (INFOCOM 2008). Our results cast doubt on the viability of using "perturbation polynomials" for designing secure cryptographic schemes.}, keywords = {pairwise key establishment, random perturbation polynomial, sensor network security}, isbn = {978-1-60558-894-0}, doi = {10.1145/1653662.1653664}, url = {http://doi.acm.org/10.1145/1653662.1653664}, author = {Albrecht,Martin and Gentry,Craig and Halevi,Shai and Katz, Jonathan} } @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 {12227, title = {Channel Access Throttling for Improving WLAN QoS}, booktitle = {Sensor, Mesh and Ad Hoc Communications and Networks, 2009. SECON {\textquoteright}09. 6th Annual IEEE Communications Society Conference on}, year = {2009}, month = {2009/06//}, pages = {1 - 9}, abstract = {The de facto QoS channel access method for the IEEE 802.11 Wireless LANs is the Enhanced Distributed Channel Access (EDCA) mechanism, which differentiates transmission treatments for data frames belonging to different traffic categories with four different levels of channel access priority. In this paper, we propose extending EDCA with Channel Access Throttling (CAT) for more flexible and efficient QoS support. By assigning different member stations different channel access parameters, CAT differentiates channel access priorities not between traffic categories but between member stations. Then by dynamically changing the channel access parameters of each member station based on a pre-computed schedule, CAT enables EDCA WLANs the benefits of scheduled access QoS. We also present evaluation results of CAT obtained from both simulations and experiments conducted using off-the-shelf WLAN hardware and open-source device driver. Our results show that CAT can proportionally partition channel capacity, significantly improve performance of multimedia applications, effectively achieve performance protection for admitted flows, and increase per cell VoIP call capacity by up to 41\%.}, keywords = {802.11, access, area, call, capacity;data, capacity;quality, capacity;WLAN, categories;transmission, channel, device, distributed, driver;quality, facto, frames;de, IEEE, LAN;, LAN;VoIP, local, mechanism;member, method;enhanced, multimedia, network;wireless, networks;channel, of, parameters;channel, priority;channel, QoS, QoS;channel, service;telecommunication, service;traffic, standards;telecommunication, stations;open-source, throttling;channel, traffic;wireless, treatments;wireless, wireless}, doi = {10.1109/SAHCN.2009.5168915}, author = {Han,Bo and Ji,Lusheng and Lee,Seungjoon and Miller,R.R. and Bhattacharjee, Bobby} } @conference {12226, title = {Channel Access Throttling for Overlapping BSS Management}, booktitle = {Communications, 2009. ICC {\textquoteright}09. IEEE International Conference on}, year = {2009}, month = {2009/06//}, pages = {1 - 6}, abstract = {Multiple co-channel WLAN BSSes (i.e., WLAN cells) overlapping in coverage are generally considered undesirable because members of the OBSSes compete for channel access, which typically increases the contention level of wireless medium access and reduces overall system performance. In this paper, we propose to use channel access throttling (CAT) for managing Wireless LAN radio resources for overlapping BSSes (OBSSes). CAT provides an access point (AP) of each BSS with a mechanism to control channel access parameters of its member stations on the fly. By coordinating the CAT operations of the OBSS APs, we can enable privileged channel access to an individual BSS at a particular time, for example, by assigning high priority access parameters to member stations associated with the BSS. By controlling how much each BSS may be given the privileged channel access, we can also achieve a proportional partitioning of channel capacity among OBSSes. We present evaluation results obtained from both simulations and experiments using testbed built with commercial off-the-shelf (COTS) WLAN hardware and open-source device driver. Our results show that with CAT, not only can we proportionally partition channel capacity among the OBSSes, but also improve channel utilization efficiency and increase overall capacity.}, keywords = {access, access;cellular, allocation;channel, BSS, capacity;computer, capacity;proportional, cell;open-source, channel, channels;, co-channel, device, driver;overlapping, efficiency;high-priority, LAN;wireless, management;partition, management;wireless, medium, network, parameters;multiple, partitioning;radio, radio;channel, resources;wireless, throttling;channel, utilization, WLAN}, doi = {10.1109/ICC.2009.5198815}, author = {Han,Bo and Ji,Lusheng and Lee,Seungjoon and Miller,R.R. and Bhattacharjee, Bobby} } @conference {13276, title = {Classification of non-manifold singularities from transformations of 2-manifolds}, booktitle = {Shape Modeling and Applications, 2009. SMI 2009. IEEE International Conference on}, year = {2009}, month = {2009/06//}, pages = {179 - 184}, abstract = {Non-manifold models are frequently encountered in engineering simulations and design as well as in computer graphics. However, these models lack shape characterization for modelling and searching purposes. Topological properties act as a kernel for deriving key features of objects. Here we propose a classification for the non-manifold singularities of non-manifold objects through continuous shape transformations of 2-manifolds without boundary up to the creation of non-manifold singularities. As a result, the non-manifold objects thus created can be categorized and contribute to the definition of a general purpose taxonomy for non-manifold shapes.}, keywords = {classification;search, Computer, graphic;continuous, graphics;pattern, model;nonmanifold, problems;topology;, property;computer, SHAPE, singularity;topological, transformation;nonmanifold}, doi = {10.1109/SMI.2009.5170146}, author = {Leon,J.-C. and De Floriani, Leila and Hetroy,F.} } @conference {14208, title = {Combining powerful local and global statistics for texture description}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition, 2009. CVPR 2009}, year = {2009}, month = {2009/06/20/25}, pages = {573 - 580}, publisher = {IEEE}, organization = {IEEE}, abstract = {A texture descriptor is proposed, which combines local highly discriminative features with the global statistics of fractal geometry to achieve high descriptive power, but also invariance to geometric and illumination transformations. As local measurements SIFT features are estimated densely at multiple window sizes and discretized. On each of the discretized measurements the fractal dimension is computed to obtain the so-called multifractal spectrum, which is invariant to geometric transformations and illumination changes. Finally to achieve robustness to scale changes, a multi-scale representation of the multifractal spectrum is developed using a framelet system, that is, a redundant tight wavelet frame system. Experiments on classification demonstrate that the descriptor outperforms existing methods on the UIUC as well as the UMD high-resolution dataset.}, keywords = {Computer science, discretized measurements, fractal geometry, Fractals, geometric transformations, global statistics, Histograms, illumination transformations, image classification, image resolution, Image texture, lighting, local measurements SIFT features, local statistics, MATHEMATICS, multifractal spectrum, multiscale representation, Power engineering and energy, Power engineering computing, Robustness, Solids, Statistics, texture description, UMD high-resolution dataset, wavelet frame system, Wavelet transforms}, isbn = {978-1-4244-3992-8}, doi = {10.1109/CVPR.2009.5206741}, author = {Yong Xu and Si-Bin Huang and Hui Ji and Ferm{\"u}ller, Cornelia} } @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} } @article {13104, title = {A Comprehensive Evaluation Framework and a Comparative Study for Human Detectors}, journal = {Intelligent Transportation Systems, IEEE Transactions on}, volume = {10}, year = {2009}, month = {2009/09//}, pages = {417 - 427}, abstract = {We introduce a framework for evaluating human detectors that considers the practical application of a detector on a full image using multisize sliding-window scanning. We produce detection error tradeoff (DET) curves relating the miss detection rate and the false-alarm rate computed by deploying the detector on cropped windows and whole images, using, in the latter, either image resize or feature resize. Plots for cascade classifiers are generated based on confidence scores instead of on variation of the number of layers. To assess a method{\textquoteright}s overall performance on a given test, we use the average log miss rate (ALMR) as an aggregate performance score. To analyze the significance of the obtained results, we conduct 10-fold cross-validation experiments. We applied our evaluation framework to two state-of-the-art cascade-based detectors on the standard INRIA person dataset and a local dataset of near-infrared images. We used our evaluation framework to study the differences between the two detectors on the two datasets with different evaluation methods. Our results show the utility of our framework. They also suggest that the descriptors used to represent features and the training window size are more important in predicting the detection performance than the nature of the imaging process, and that the choice between resizing images or features can have serious consequences.}, keywords = {classification;infrared, classifier;comprehensive, curve;INRIA, dataset;average, DET, DETECTION, detection;, detector;image, error, Evaluation, framework;cropped, image;image, imaging;object, log, miss, person, rate;cascade, rate;feature, rate;multisize, resize;human, resize;miss, scanning;near-infrared, sliding-window, tradeoff;false-alarm, window;detection}, isbn = {1524-9050}, doi = {10.1109/TITS.2009.2026670}, author = {Hussein,M. and Porikli, F. and Davis, Larry S.} } @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 {13279, title = {Computing and visualizing a graph-based decomposition for non-manifold shapes}, journal = {Graph-Based Representations in Pattern Recognition}, year = {2009}, month = {2009///}, pages = {62 - 71}, abstract = {Modeling and understanding complex non-manifold shapes is a key issue in shape analysis and retrieval. The topological structure of a non-manifold shape can be analyzed through its decomposition into a collection of components with a simpler topology. Here, we consider a decomposition of a non-manifold shape into components which are almost manifolds, and we present a novel graph representation which highlights the non-manifold singularities shared by the components as well as their connectivity relations. We describe an algorithm for computing the decomposition and its associated graph representation. We present a new tool for visualizing the shape decomposition and its graph as an effective support to modeling, analyzing and understanding non-manifold shapes.}, doi = {10.1007/978-3-642-02124-4_7}, author = {De Floriani, Leila and Panozzo,D. and Hui,A.} } @conference {13097, title = {Concurrent transition and shot detection in football videos using Fuzzy Logic}, booktitle = {Image Processing (ICIP), 2009 16th IEEE International Conference on}, year = {2009}, month = {2009/11//}, pages = {4341 - 4344}, abstract = {Shot detection is a fundamental step in video processing and analysis that should be achieved with high degree of accuracy. In this paper, we introduce a unified algorithm for shot detection in sports video using fuzzy logic as a powerful inference mechanism. Fuzzy logic overcomes the problems of hard cut thresholds and the need to large training data used in previous work. The proposed algorithm integrates many features like color histogram, edgeness, intensity variance, etc. Membership functions to represent different features and transitions between shots have been developed to detect different shot boundary and transition types. We address the detection of cut, fade, dissolve, and wipe shot transitions. The results show that our algorithm achieves high degree of accuracy.}, keywords = {analysis;inference, boundary;shot, Color, colour, detection;sports, functions;shot, histogram;concurrent, logic;image, logic;inference, mechanism;intensity, mechanisms;sport;video, processing;, processing;videonanalysis;fuzzy, signal, transition;edgeness;football, variance;membership, video;video, videos;fuzzy}, doi = {10.1109/ICIP.2009.5413648}, author = {Refaey,M.A. and Elsayed,K.M. and Hanafy,S.M. and Davis, Larry S.} } @article {13701, title = {A cost-effective lexical acquisition process for large-scale thesaurus translation}, journal = {Language resources and evaluation}, volume = {43}, year = {2009}, month = {2009///}, pages = {27 - 40}, abstract = {Thesauri and controlled vocabularies facilitate access to digital collections by explicitly representing the underlying principles of organization. Translation of such resources into multiple languages is an important component for providing multilingual access. However, the specificity of vocabulary terms in most thesauri precludes fully-automatic translation using general-domain lexical resources. In this paper, we present an efficient process for leveraging human translations to construct domain-specific lexical resources. This process is illustrated on a thesaurus of 56,000 concepts used to catalog a large archive of oral histories. We elicited human translations on a small subset of concepts, induced a probabilistic phrase dictionary from these translations, and used the resulting resource to automatically translate the rest of the thesaurus. Two separate evaluations demonstrate the acceptability of the automatic translations and the cost-effectiveness of our approach.}, author = {Jimmy Lin and Murray,G. C and Dorr, Bonnie J and Haji{\v c},J. and Pecina,P.} } @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.} } @article {14603, title = {CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features}, journal = {Genome Biology}, volume = {10}, year = {2009}, month = {2009/11/18/}, pages = {R131 - R131}, abstract = {CTCF (CCCTC-binding factor) is an evolutionarily conserved zinc finger protein involved in diverse functions ranging from negative regulation of MYC, to chromatin insulation of the beta-globin gene cluster, to imprinting of the Igf2 locus. The 11 zinc fingers of CTCF are known to differentially contribute to the CTCF-DNA interaction at different binding sites. It is possible that the differences in CTCF-DNA conformation at different binding sites underlie CTCF{\textquoteright}s functional diversity. If so, the CTCF binding sites may belong to distinct classes, each compatible with a specific functional role.}, isbn = {1465-6906}, doi = {10.1186/gb-2009-10-11-r131}, url = {http://genomebiology.com/2009/10/11/R131}, author = {Essien,Kobby and Vigneau,Sebastien and Apreleva,Sofia and Singh,Larry N. and Bartolomei,Marisa S. and Hannenhalli, Sridhar} } @conference {18563, title = {Detecting spammers with SNARE: spatio-temporal network-level automatic reputation engine}, booktitle = {Proceedings of the 18th conference on USENIX security symposium}, series = {SSYM{\textquoteright}09}, year = {2009}, month = {2009///}, pages = {101 - 118}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {Users and network administrators need ways to filter email messages based primarily on the reputation of the sender. Unfortunately, conventional mechanisms for sender reputation--notably, IP blacklists--are cumbersome to maintain and evadable. This paper investigates ways to infer the reputation of an email sender based solely on network-level features, without looking at the contents of a message. First, we study first-order properties of network-level features that may help distinguish spammers from legitimate senders. We examine features that can be ascertained without ever looking at a packet{\textquoteright}s contents, such as the distance in IP space to other email senders or the geographic distance between sender and receiver. We derive features that are lightweight, since they do not require seeing a large amount of email from a single IP address and can be gleaned without looking at an email{\textquoteright}s contents--many such features are apparent from even a single packet. Second, we incorporate these features into a classification algorithm and evaluate the classifier{\textquoteright}s ability to automatically classify email senders as spammers or legitimate senders. We build an automated reputation engine, SNARE, based on these features using labeled data from a deployed commercial spam-filtering system. We demonstrate that SNARE can achieve comparable accuracy to existing static IP blacklists: about a 70\%detection rate for less than a 0.3\%false positive rate. Third, we show how SNARE can be integrated into existing blacklists, essentially as a first-pass filter.}, url = {http://dl.acm.org/citation.cfm?id=1855768.1855775}, author = {Hao,Shuang and Syed,Nadeem Ahmed and Feamster, Nick and Gray,Alexander G. and Krasser,Sven} } @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} } @conference {14677, title = {Directing JavaScript with arrows}, booktitle = {Proceedings of the 5th symposium on Dynamic languages}, series = {DLS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {49 - 58}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {JavaScript programmers make extensive use of event-driven programming to help build responsive web applications. However, standard approaches to sequencing events are messy, and often lead to code that is difficult to understand and maintain. We have found that arrows, a generalization of monads, are an elegant solution to this problem. Arrows allow us to easily write asynchronous programs in small, modular units of code, and flexibly compose them in many different ways, while nicely abstracting the details of asynchronous program composition. In this paper, we present Arrowlets, a new JavaScript library that offers arrows to the everyday JavaScript programmer. We show how to use Arrowlets to construct a variety of state machines, including state machines that branch and loop. We also demonstrate how Arrowlets separate computation from composition with examples such as a drag-and-drop handler and a bubblesort animation.}, keywords = {arrowlets, arrows, events, javascript, web programming}, isbn = {978-1-60558-769-1}, doi = {10.1145/1640134.1640143}, url = {http://doi.acm.org/10.1145/1640134.1640143}, author = {Khoo,Yit Phang and Hicks, Michael W. and Foster, Jeffrey S. and Sazawal,Vibha} } @conference {17585, title = {Distributed Strategies for Channel Allocation and Scheduling in Software-Defined Radio Networks}, booktitle = {IEEE INFOCOM 2009}, year = {2009}, month = {2009/04/19/25}, pages = {1521 - 1529}, publisher = {IEEE}, organization = {IEEE}, abstract = {Equipping wireless nodes with multiple radios can significantly increase the capacity of wireless networks, by making these radios simultaneously transmit over multiple non-overlapping channels. However, due to the limited number of radios and available orthogonal channels, designing efficient channel assignment and scheduling algorithms in such networks is a major challenge. In this paper, we present provably-good distributed algorithms for simultaneous channel allocation of individual links and packet-scheduling, in software-defined radio (SDR) wireless networks. Our distributed algorithms are very simple to implement, and do not require any coordination even among neighboring nodes. A novel access hash function or random oracle methodology is one of the key drivers of our results. With this access hash function, each radio can know the transmitters{\textquoteright} decisions for links in its interference set for each time slot without introducing any extra communication overhead between them. Further, by utilizing the inductive-scheduling technique, each radio can also backoff appropriately to avoid collisions. Extensive simulations demonstrate that our bounds are valid in practice.}, keywords = {access hash function, Channel allocation, channel assignment algorithm, channel capacity, collision avoidance, Computer science, cryptography, distributed algorithm, distributed algorithms, Educational institutions, inductive-scheduling technique, Interference, interference set, packet scheduling algorithm, Peer to peer computing, Radio network, radio networks, radiofrequency interference, random oracle methodology, scheduling, Scheduling algorithm, simultaneous channel allocation, software radio, software-defined radio wireless network capacity, telecommunication congestion control, telecommunication security, Throughput, wireless channels, Wireless networks}, isbn = {978-1-4244-3512-8}, doi = {10.1109/INFCOM.2009.5062069}, author = {Han,Bo and Kumar,V. S.A and Marathe,M. V and Parthasarathy,S. and Srinivasan, Aravind} } @article {17095, title = {Do you know the way to SNA?: A process model for analyzing and visualizing social media data}, journal = {University of Maryland Tech Report: HCIL-2009-17}, year = {2009}, month = {2009///}, abstract = {Traces of activity left by social media users can shed lighton individual behavior, social relationships, and community efficacy. Tools and processes to analyze social traces are essential for enabling practitioners to study and nurture meaningful and sustainable social interaction. Yet such tools and processes remain in their infancy. We conducted a study of 15 graduate students who were learning to apply Social Network Analysis (SNA) to data from online communities. Based on close observations of their emergent practices, we derived the Network Analysis and Visualization (NAV) process model and identified stages where intervention from peers, experts, and an SNA tool were most useful. We show how the NAV model informs the design of SNA tools and services, education practices, and support for social media practitioners. }, author = {Hansen,D. L and Rotman,D. and Bonsignore,E. and Milic-Frayling,N. and Rodrigues,E.M. and Smith,M. and Shneiderman, Ben} } @conference {14684, title = {Dynamic software updates: a VM-centric approach}, booktitle = {Proceedings of the 2009 ACM SIGPLAN conference on Programming language design and implementation}, series = {PLDI {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {1 - 12}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Software evolves to fix bugs and add features. Stopping and restarting programs to apply changes is inconvenient and often costly. Dynamic software updating (DSU) addresses this problem by updating programs while they execute, but existing DSU systems for managed languages do not support many updates that occur in practice and are inefficient. This paper presents the design and implementation of Jvolve, a DSU-enhanced Java VM. Updated programs may add, delete, and replace fields and methods anywhere within the class hierarchy. Jvolve implements these updates by adding to and coordinating VM classloading, just-in-time compilation, scheduling, return barriers, on-stack replacement, and garbage collection. Jvolve, is safe: its use of bytecode verification and VM thread synchronization ensures that an update will always produce type-correct executions. Jvolve is flexible: it can support 20 of 22 updates to three open-source programs--Jetty web server, JavaEmailServer, and CrossFTP server--based on actual releases occurring over 1 to 2 years. Jvolve is efficient: performance experiments show that incurs no overhead during steady-state execution. These results demonstrate that this work is a significant step towards practical support for dynamic updates in virtual machines for managed languages.}, keywords = {dynamic software updating, garbage collection, virtual machine technology}, isbn = {978-1-60558-392-1}, doi = {10.1145/1542476.1542478}, url = {http://doi.acm.org/10.1145/1542476.1542478}, author = {Subramanian,Suriya and Hicks, Michael W. and McKinley,Kathryn S.} } @article {14683, title = {Dynamic software updates for Java: A VM-centric approach}, journal = {Proceedings of the ACM Conference on Programming Language Design and Implementation (PLDI)}, year = {2009}, month = {2009///}, abstract = {Software evolves to fix bugs and add features, but stopping andrestarting existing programs to take advantage of these changes can be inconvenient and costly. Dynamic software updating (DSU) addresses these problems by updating programs while they run. The challenge is to develop DSU infrastructure that is flexible, safe, and efficient{\textemdash}DSU should enable updates that are likely to occur in practice, and updated programs should be as reliable and as efficient as those started from scratch. This paper presents the design and implementation of a JVM we call JVOLVE that is enhanced with DSU support. The pa- per{\textquoteright}s key insight is that flexible, safe, and efficient DSU can be supported by naturally extending existing VM services. By piggybacking on classloading and garbage collection, JVOLVE can flexibly support additions and replacements of fields and methods anywhere within the class hierarchy, and in a manner that may alter class signatures. By utilizing bytecode verifi- cation and thread synchronization support, JVOLVE can ensure that an applied update will never violate type-safety. Finally, by employing JIT compilation, all DSU-related overhead be- fore or after an update can be effectively eliminated. Using JVOLVE, we successfully applied dynamic continuous updates corresponding to 20 of the 22 releases that occurred over nearly two years{\textquoteright} time, one update per release, for three open-source programs, Jetty web server, JavaEmailServer, and CrossFTP server. Our results indicate that the VM is well-suited to sup- port practical DSU services. }, author = {Subramanian,S. and Hicks, Michael W. and McKinley,K.S.} } @conference {11907, title = {Efficient band approximation of Gram matrices for large scale kernel methods on GPUs}, booktitle = {Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis}, series = {SC {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {31:1{\textendash}31:10 - 31:1{\textendash}31:10}, publisher = {ACM}, organization = {ACM}, address = {Portland, Oregon}, abstract = {Kernel-based methods require O(N2) time and space complexities to compute and store non-sparse Gram matrices, which is prohibitively expensive for large scale problems. We introduce a novel method to approximate a Gram matrix with a band matrix. Our method relies on the locality preserving properties of space filling curves, and the special structure of Gram matrices. Our approach has several important merits. First, it computes only those elements of the Gram matrix that lie within the projected band. Second, it is simple to parallelize. Third, using the special band matrix structure makes it space efficient and GPU-friendly. We developed GPU implementations for the Affinity Propagation (AP) clustering algorithm using both our method and the COO sparse representation. Our band approximation is about 5 times more space efficient and faster to construct than COO. AP gains up to 6x speedup using our method without any degradation in its clustering performance.}, keywords = {affinity propagation, algorithms, gpu}, isbn = {978-1-60558-744-8}, doi = {10.1145/1654059.1654091}, author = {Hussein,Mohamed and Abd-Almageed, Wael} } @conference {14689, title = {Efficient systematic testing for dynamically updatable software}, booktitle = {Proceedings of the 2nd International Workshop on Hot Topics in Software Upgrades}, series = {HotSWUp {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {9:1{\textendash}9:5 - 9:1{\textendash}9:5}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Recent years have seen significant advances in dynamic software updating (DSU) systems, which allow programs to be patched on the fly. However, a significant challenge remains: How can we ensure the act of applying a patch does not itself introduce errors? In this paper, we address this problem by presenting a new systematic testing methodology for updatable programs. Our idea is to transform standard system tests into update tests that execute as before, but each transformed test applies a patch at a different update point during execution. To mitigate the increase in the number of tests, we developed an algorithm for test suite minimization that finds a subset of update points that, if fully tested, yields the equivalent to full update point coverage. We implemented our approach and evaluated it on OpenSSH and vsftpd, two widely used server applications. We found that minimization is highly effective, reducing the number of update tests required for full coverage by 93\%.}, isbn = {978-1-60558-723-3}, doi = {10.1145/1656437.1656449}, url = {http://doi.acm.org/10.1145/1656437.1656449}, author = {Hayden,Christopher M and Hardisty,Eric A. and Hicks, Michael W. and Foster, Jeffrey S.} } @conference {14278, title = {Efficient systematic testing for dynamically updatable software}, booktitle = {Proceedings of the 2nd International Workshop on Hot Topics in Software Upgrades}, year = {2009}, month = {2009///}, pages = {9 - 9}, author = {Hayden,C.M. and Hardisty,E.A. and Hicks, Michael W. and Foster, Jeffrey S.} } @article {15057, title = {Encryption Algorithm Based on Circle Property}, journal = {Jisuanji Gongcheng/ Computer Engineering}, volume = {35}, year = {2009}, month = {2009///}, pages = {180 - 182}, author = {Ge,L.N. and He,Z.H. and Zhuolin Jiang} } @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 {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 {14577, title = {The evolution of Fox genes and their role in development and disease}, journal = {Nature reviews. GeneticsNat Rev Genet}, volume = {10}, year = {2009}, month = {2009/04//}, pages = {233 - 240}, abstract = {The forkhead box (Fox) family of transcription factors, which originated in unicellular eukaryotes, has expanded over time through multiple duplication events, and sometimes through gene loss, to over 40 members in mammals. Fox genes have evolved to acquire a specialized function in many key biological processes. Mutations in Fox genes have a profound effect on human disease, causing phenotypes as varied as cancer, glaucoma and language disorders. We summarize the salient features of the evolution of the Fox gene family and highlight the diverse contribution of various Fox subfamilies to developmental processes, from organogenesis to speech acquisition.}, isbn = {1471-0056}, doi = {10.1038/nrg2523}, author = {Hannenhalli, Sridhar and Kaestner,Klaus H.} } @article {18213, title = {Fingerprinting Compressed Multimedia Signals}, journal = {Information Forensics and Security, IEEE Transactions on}, volume = {4}, year = {2009}, month = {2009/09//}, pages = {330 - 345}, abstract = {Digital fingerprinting is a technique to deter unauthorized redistribution of multimedia content by embedding a unique identifying signal in each legally distributed copy. The embedded fingerprint can later be extracted and used to trace the originator of an unauthorized copy. A group of users may collude and attempt to create a version of the content that cannot be traced back to any of them. As multimedia data is commonly stored in compressed form, this paper addresses the problem of fingerprinting compressed signals. Analysis is carried out to show that due to the quantized nature of the host signal and the embedded fingerprint, directly extending traditional fingerprinting techniques for uncompressed signals to the compressed case leads to low collusion resistance. To overcome this problem and improve the collusion resistance, a new technique for fingerprinting compressed signals called Anti-Collusion Dither (ACD) is proposed, whereby a random dither signal is added to the compressed host before embedding so as to make the effective host signal appear more continuous. The proposed technique is shown to reduce the accuracy with which attackers can estimate the host signal, and from an information theoretic perspective, the proposed ACD technique increases the maximum number of users that can be supported by the fingerprinting system under a given attack. Both analytical and experimental studies confirm that the proposed technique increases the probability of identifying a guilty user and can approximately quadruple the collusion resistance compared to conventional Gaussian fingerprinting.}, keywords = {coding;, coding;copy, collusion;digital, communication;video, compression;digital, compression;video, dither;collusion, domain, fingerprinting;anti-collusion, fingerprinting;multimedia, Gaussian, management;multimedia, protection;data, resistance;compressed, rights}, isbn = {1556-6013}, doi = {10.1109/TIFS.2009.2025860}, author = {Varna,A.L. and He,Shan and Swaminathan,A. and M. Wu} } @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} } @conference {16485, title = {Flexible and efficient querying and ranking on hyperlinked data sources}, booktitle = {Proceedings of the 12th International Conference on Extending Database Technology: Advances in Database Technology}, year = {2009}, month = {2009///}, pages = {553 - 564}, author = {Varadarajan,R. and Hristidis,V. and Raschid, Louiqa and Vidal,M. E and Ib{\'a}\ nez,L. and Rodr{\'\i}guez-Drumond,H.} } @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 {13780, title = {Generating surveys of scientific paradigms}, journal = {Proceedings of HLT-NAACL}, year = {2009}, month = {2009///}, abstract = {The number of research publications in var-ious disciplines is growing exponentially. Researchers and scientists are increasingly finding themselves in the position of having to quickly understand large amounts of tech- nical material. In this paper we present the first steps in producing an automatically gen- erated, readily consumable, technical survey. Specifically we explore the combination of citation information and summarization tech- niques. Even though prior work (Teufel et al., 2006) argues that citation text is unsuitable for summarization, we show that in the frame- work of multi-document survey creation, cita- tion texts can play a crucial role. }, author = {Mohammad,S. and Dorr, Bonnie J and Egan,M. and Hassan,A. and Muthukrishan,P. and Qazvinian,V. and Radev,D. and Zajic, David} } @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} } @article {14553, title = {Hat guessing games}, journal = {SIAM review}, volume = {51}, year = {2009}, month = {2009///}, pages = {399 - 413}, author = {Butler,S. and Hajiaghayi, Mohammad T. and Kleinberg,R. D and Leighton,T.} } @article {18222, title = {High-Fidelity Data Embedding for Image Annotation}, journal = {Image Processing, IEEE Transactions on}, volume = {18}, year = {2009}, month = {2009/02//}, pages = {429 - 435}, abstract = {High fidelity is a demanding requirement for data hiding, especially for images with artistic or medical value. This correspondence proposes a high-fidelity image watermarking for annotation with robustness to moderate distortion. To achieve the high fidelity of the embedded image, we introduce a visual perception model that aims at quantifying the local tolerance to noise for arbitrary imagery. Based on this model, we embed two kinds of watermarks: a pilot watermark that indicates the existence of the watermark and an information watermark that conveys a payload of several dozen bits. The objective is to embed 32 bits of metadata into a single image in such a way that it is robust to JPEG compression and cropping. We demonstrate the effectiveness of the visual model and the application of the proposed annotation technology using a database of challenging photographic and medical images that contain a large amount of smooth regions.}, keywords = {Automated;Product Labeling;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Computer-Assisted;, Computer-Assisted;Information Storage and Retrieval;Pattern Recognition, JPEG compression;JPEG cropping;arbitrary imagery;data hiding;high-fidelity data embedding;image annotation;image watermarking;medical images;photographic images;data compression;image coding;watermarking;Algorithms;Computer Graphics;Documentation;Image En}, isbn = {1057-7149}, doi = {10.1109/TIP.2008.2008733}, author = {He,Shan and Kirovski,D. and M. Wu} } @conference {13892, title = {How children search the internet with keyword interfaces}, booktitle = {Proceedings of the 8th International Conference on Interaction Design and Children}, year = {2009}, month = {2009///}, pages = {89 - 96}, author = {Druin, Allison and Foss,E. and Hatley,L. and Golub,E. and Guha,M.L. and Fails,J. and Hutchinson,H.} } @conference {13099, title = {Human detection using partial least squares analysis}, booktitle = {Computer Vision, 2009 IEEE 12th International Conference on}, year = {2009}, month = {2009/10/29/2}, pages = {24 - 31}, abstract = {Significant research has been devoted to detecting people in images and videos. In this paper we describe a human detection method that augments widely used edge-based features with texture and color information, providing us with a much richer descriptor set. This augmentation results in an extremely high-dimensional feature space (more than 170,000 dimensions). In such high-dimensional spaces, classical machine learning algorithms such as SVMs are nearly intractable with respect to training. Furthermore, the number of training samples is much smaller than the dimensionality of the feature space, by at least an order of magnitude. Finally, the extraction of features from a densely sampled grid structure leads to a high degree of multicollinearity. To circumvent these data characteristics, we employ Partial Least Squares (PLS) analysis, an efficient dimensionality reduction technique, one which preserves significant discriminative information, to project the data onto a much lower dimensional subspace (20 dimensions, reduced from the original 170,000). Our human detection system, employing PLS analysis over the enriched descriptor set, is shown to outperform state-of-the-art techniques on three varied datasets including the popular INRIA pedestrian dataset, the low-resolution gray-scale DaimlerChrysler pedestrian dataset, and the ETHZ pedestrian dataset consisting of full-length videos of crowded scenes.}, doi = {10.1109/ICCV.2009.5459205}, author = {Schwartz,William Robson and Kembhavi,Aniruddha and Harwood,David and Davis, Larry S.} } @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 {14560, title = {Improved approximation algorithms for prize-collecting Steiner tree and TSP}, booktitle = {2009 50th Annual IEEE Symposium on Foundations of Computer Science}, year = {2009}, month = {2009///}, pages = {427 - 436}, author = {Archer,A. and Bateni,M. H and Hajiaghayi, Mohammad T. and Karloff,H.} } @conference {16604, title = {Improving rule extraction from neural networks by modifying hidden layer representations}, booktitle = {Neural Networks, 2009. IJCNN 2009. International Joint Conference on}, year = {2009}, month = {2009///}, pages = {1316 - 1321}, author = {Huynh,T. Q and Reggia, James A.} } @inbook {13797, title = {Interlingual annotation of multilingual text corpora and FrameNet}, booktitle = {Multilingual FrameNets in Computational LexicographyMultilingual FrameNets in Computational Lexicography}, volume = {200}, year = {2009}, month = {2009/07/14/}, pages = {287 - 318}, publisher = {Mouton de Gruyter}, organization = {Mouton de Gruyter}, address = {Berlin, New York}, isbn = {978-3-11-021296-9, 978-3-11-021297-6}, url = {http://www.degruyter.com/view/books/9783110212976/9783110212976.4.287/9783110212976.4.287.xml}, author = {Farwell,David and Dorr, Bonnie J and Habash,Nizar and Helmreich,Stephen and Hovy,Eduard and Green,Rebecca and Levin,Lori and Miller,Keith and Mitamura,Teruko and Rambow,Owen and Reeder,Flo and Siddharthan,Advaith}, editor = {Bisang,Walter and Hock,Hans Henrich and Winter,Werner and Boas,Hans C.} } @conference {15913, title = {Inverse halftoning using a shearlet representation}, booktitle = {Proceedings of SPIE}, volume = {7446}, year = {2009}, month = {2009///}, pages = {74460C - 74460C}, author = {Easley,G. R and Patel, Vishal M. and Healy Jr,D.M.} } @conference {14628, title = {Mimosa: mixture model of co-expression to detect modulators of regulatory interaction}, booktitle = {Proceedings of the 9th international conference on Algorithms in bioinformatics}, series = {WABI{\textquoteright}09}, year = {2009}, month = {2009///}, pages = {133 - 144}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {Berlin, Heidelberg}, abstract = {Functionally related genes tend to be correlated in their expression patterns across multiple conditions and/or tissue-types. Thus co-expression networks are often used to investigate functional groups of genes. In particular, when one of the genes is a transcription factor (TF), the co-expression-based interaction is interpreted, with caution, as a direct regulatory interaction. However, any particular TF, and more importantly, any particular regulatory interaction, is likely to be active only in a subset of experimental conditions. Moreover, the subset of expression samples where the regulatory interaction holds may be marked by presence or absence of a modifier gene, such as an enzyme that post-translationally modifies the TF. Such subtlety of regulatory interactions is overlooked when one computes an overall expression correlation. Here we present a novel mixture modeling approach where a TF-Gene pair is presumed to be significantly correlated (with unknown coefficient) in a (unknown) subset of expression samples. The parameters of the model are estimated using a Maximum Likelihood approach. The estimated mixture of expression samples is then mined to identify genes potentially modulating the TF-Gene interaction. We have validated our approach using synthetic data and on three biological cases in cow and in yeast. While limited in some ways, as discussed, the work represents a novel approach to mine expression data and detect potential modulators of regulatory interactions.}, isbn = {3-642-04240-6, 978-3-642-04240-9}, url = {http://dl.acm.org/citation.cfm?id=1812906.1812918}, author = {Hansen,Matthew and Everett,Logan and Singh,Larry and Hannenhalli, Sridhar} } @conference {14337, title = {Mobile Living Labs 09: Methods and Tools for Evaluation in the Wild}, booktitle = {Proceedings of the 11th International Conference on Human-Computer Interaction with Mobile Devices and Services}, series = {MobileHCI {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {107:1{\textendash}107:2 - 107:1{\textendash}107:2}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In a Mobile Living Lab, mobile devices are used to evaluate concepts and prototypes in real-life settings. In other words, the lab is brought to the people. This workshop provides a forum for researchers and practitioners to share experiences and issues with methods and tools for Mobile Living Labs. In particular, we seek to bring together people who have applied methods for Mobile Living Labs and people who build tools for those methods.The aim of the workshop is twofold. First, to make an up-to-date overview of current methods and tools for conducting user studies in Mobile Living Labs -- highlighting their individual strengths and weaknesses. Second, to uncover challenges that are not adequately addressed by current methods and tools and to come up with ideas and requirements that could fill this gap thus serving as beacons for further research and development in this area. }, keywords = {field study, in-situ evaluation, living labs, methods, mobile, tools, user experience}, isbn = {978-1-60558-281-8}, doi = {10.1145/1613858.1613981}, url = {http://doi.acm.org/10.1145/1613858.1613981}, author = {ter Hofte,Henri and Jensen,Kasper L{\o}vborg and Nurmi,Petteri and Jon Froehlich} } @article {14630, title = {Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons}, journal = {Genome Biology}, volume = {10}, year = {2009}, month = {2009/07/01/}, pages = {R72 - R72}, abstract = {Hundreds of proteins modulate neurotransmitter release and synaptic plasticity during neuronal development and in response to synaptic activity. The expression of genes in the pre- and post-synaptic neurons is under stringent spatio-temporal control, but the mechanism underlying the neuronal expression of these genes remains largely unknown.}, isbn = {1465-6906}, doi = {10.1186/gb-2009-10-7-r72}, url = {http://genomebiology.com/2009/10/7/R72}, author = {Liu,Rui and Hannenhalli, Sridhar and Bucan,Maja} } @conference {13113, title = {Multiple instance Feature for robust part-based object detection}, booktitle = {Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on}, year = {2009}, month = {2009///}, pages = {405 - 412}, author = {Lin,Z. and Hua,G. and Davis, Larry S.} } @conference {14564, title = {Network-aware forward caching}, booktitle = {Proceedings of the 18th international conference on World wide web}, series = {WWW {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {291 - 300}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper proposes and evaluates a Network Aware Forward Caching approach for determining the optimal deployment strategy of forward caches to a network. A key advantage of this approach is that we can reduce the network costs associated with forward caching to maximize the benefit obtained from their deployment. We show in our simulation that a 37\% increase to net benefits could be achieved over the standard method of full cache deployment to cache all POPs traffic. In addition, we show that this maximal point occurs when only 68\% of the total traffic is cached. Another contribution of this paper is the analysis we use to motivate and evaluate this problem. We characterize the Internet traffic of 100K subscribers of a US residential broadband provider. We use both layer 4 and layer 7 analysis to investigate the traffic volumes of the flows as well as study the general characteristics of the applications used. We show that HTTP is a dominant protocol and account for 68\% of the total downstream traffic and that 34\% of that traffic is multimedia. In addition, we show that multimedia content using HTTP exhibits a 83\% annualized growth rate and other HTTP traffic has a 53\% growth rate versus the 26\% over all annual growth rate of broadband traffic. This shows that HTTP traffic will become ever more dominent and increase the potential caching opportunities. Furthermore, we characterize the core backbone traffic of this broadband provider to measure the distance travelled by content and traffic. We find that CDN traffic is much more efficient than P2P content and that there is large skew in the Air Miles between POP in a typical network. Our findings show that there are many opportunties in broadband provider networks to optimize how traffic is delivered and cached.}, keywords = {caching, Web}, isbn = {978-1-60558-487-4}, doi = {10.1145/1526709.1526749}, url = {http://doi.acm.org/10.1145/1526709.1526749}, author = {Erman,Jeffrey and Gerber,Alexandre and Hajiaghayi, Mohammad T. and Pei,Dan and Spatscheck,Oliver} } @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} } @conference {13098, title = {Object detection via boosted deformable features}, booktitle = {Image Processing (ICIP), 2009 16th IEEE International Conference on}, year = {2009}, month = {2009/11//}, pages = {1445 - 1448}, abstract = {It is a common practice to model an object for detection tasks as a boosted ensemble of many models built on features of the object. In this context, features are defined as subregions with fixed relative locations and extents with respect to the object{\textquoteright}s image window. We introduce using deformable features with boosted ensembles. A deformable features adapts its location depending on the visual evidence in order to match the corresponding physical feature. Therefore, deformable features can better handle deformable objects. We empirically show that boosted ensembles of deformable features perform significantly better than boosted ensembles of fixed features for human detection.}, keywords = {boosted, detection;object, detection;statistics;, detection;visual, ensembles;deformable, evidence;feature, extraction;object, features;human}, doi = {10.1109/ICIP.2009.5414561}, author = {Hussein,M. and Porikli, F. and Davis, Larry S.} } @article {14713, title = {Passive aggressive measurement with MGRP}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {39}, year = {2009}, month = {2009/08//}, pages = {279 - 290}, abstract = {We present the Measurement Manager Protocol (MGRP), an in-kernel service that schedules and transmits probes on behalf of active measurement tools. Unlike prior measurement services, MGRP transparently piggybacks application packets inside the often significant amounts of empty padding contained in typical probes. Using MGRP thus combines the modularity, flexibility, and accuracy of standalone active measurement tools with the lower overhead of passive measurement techniques. Microbenchmark experiments show that the resulting bandwidth savings makes it possible to measure the network accurately, but faster and more aggressively than without piggybacking, and with few ill effects to piggybacked application or competing traffic. When using MGRP to schedule measurements on behalf of MediaNet, an overlay service that adaptively schedules media streams, we show MediaNet can achieve significantly higher streaming rates under the same network conditions.}, keywords = {active, available bandwidth, kernel module, passive, piggybacking, probing, streaming, transport protocol}, isbn = {0146-4833}, doi = {10.1145/1594977.1592601}, url = {http://doi.acm.org/10.1145/1594977.1592601}, author = {Papageorge,Pavlos and McCann,Justin and Hicks, Michael W.} } @article {13115, title = {PERCEPTION AND NAVIGATION FOR AUTONOMOUS VEHICLES}, journal = {IEEE Transactions on intelligent transportation systems}, volume = {10}, year = {2009}, month = {2009///}, pages = {417 - 427}, abstract = {We introduce a framework for evaluating human detectors that considers the practical application of a detector on a full image using multisize sliding-window scanning. We produce detection error tradeoff (DET) curves relating the miss detection rate and the false-alarm rate computed by deploying the detector on cropped windows and whole images, using, in the latter, either image resize or feature resize. Plots for cascade classifiers are generated based on confidence scores instead of on variation of the number of layers. To assess a method{\textquoteright}s overall performance on a given test, we use the average log miss rate (ALMR) as an aggregate performance score. To analyze the significance of the obtained results, we conduct 10-fold cross-validation experiments. We applied our evaluation framework to two state-of-the-art cascade-based detectors on the standard INRIA Person dataset and a local dataset of near-infrared images. We used our evaluation framework to study the differences between the two detectors on the two datasets with different evaluation methods. Our results show the utility of our framework. They also suggest that the descriptors used to represent features and the training window size are more important in predicting the detection performance than the nature of the imaging process, and that the choice between resizing images or features can have serious consequences.}, author = {Hussein,M. and Porikli, F. and Davis, Larry S.} } @inbook {18916, title = {Planning for Interactions among Autonomous Agents}, booktitle = {Programming Multi-Agent Systems}, series = {Lecture Notes in Computer Science}, volume = {5442}, year = {2009}, month = {2009///}, pages = {1 - 23}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {AI planning research has traditionally focused on offline pl- anning for static single-agent environments. In environments where an agent needs to plan its interactions with other autonomous agents, planning is much more complicated, because the actions of the other agents can induce a combinatorial explosion in the number of contingencies that the planner will need to consider. This paper discusses several ways to alleviate the combinatorial explosion, and illustrates their use in several different kinds of multi-agent planning domains.}, keywords = {Computer science}, isbn = {978-3-642-03277-6}, url = {http://www.springerlink.com/content/j258015ux2p38383/abstract/}, author = {Au,Tsz-Chiu and Kuter,Ugur and Nau, Dana S.}, editor = {Hindriks,Koen and Pokahr,Alexander and Sardina,Sebastian} } @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 {13109, title = {Probabilistic fusion-based parameter estimation for visual tracking}, journal = {Computer Vision and Image Understanding}, volume = {113}, year = {2009}, month = {2009/04//}, pages = {435 - 445}, abstract = {In object tracking, visual features may not be discriminative enough to estimate high dimensional motion parameters accurately, and complex motion estimation is computationally expensive due to a large search space. To tackle these problems, a reasonable strategy is to track small components within the target independently in lower dimensional motion parameter spaces (e.g., translation only) and then estimate the overall high dimensional motion (e.g., translation, scale and rotation) by statistically integrating the individual tracking results. Although tracking each component in a lower dimensional space is more reliable and faster, it is not trivial to combine the local motion information and estimate global parameters in a robust way because the individual component motions are frequently inconsistent. We propose a robust fusion algorithm to estimate the complex motion parameters using variable-bandwidth mean-shift. By employing correlation-based uncertainty modeling and fusion of individual components, the motion parameter that is robust to outliers can be detected with variable-bandwidth density-based fusion (VBDF) algorithm. In addition, we describe a method to update target appearance model for each component adaptively based on the component motion consistency. We present various tracking results and compare the performance of our algorithm with others using real video sequences.}, keywords = {Component-based tracking, Density-based fusion, Mean-shift, visual tracking}, isbn = {1077-3142}, doi = {10.1016/j.cviu.2008.11.003}, url = {http://www.sciencedirect.com/science/article/pii/S1077314208001872}, author = {Han,Bohyung and Davis, Larry S.} } @article {14588, title = {PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes}, journal = {Nucleic Acids ResearchNucleic Acids Research}, volume = {37}, year = {2009}, month = {2009/01//}, pages = {D66-D71 - D66-D71}, isbn = {0305-1048}, doi = {10.1093/nar/gkn731}, url = {http://nar.oxfordjournals.org/content/37/suppl_1/D66.short}, author = {Everett,L. and Vo,A. and Hannenhalli, Sridhar} } @article {15116, title = {Reducing complexity assumptions for statistically-hiding commitment}, journal = {Journal of cryptology}, volume = {22}, year = {2009}, month = {2009///}, pages = {283 - 310}, abstract = {We revisit the following question: what are the minimal assumptions needed to construct statistically-hiding commitment schemes? Naor et al. show how to construct such schemes based on any one-way permutation. We improve upon this by showing a construction based on any approximable preimage-size one-way function. These are one-way functions for which it is possible to efficiently approximate the number of pre-images of a given output. A special case is the class of regular one-way functions where all points in the image of the function have the same (known) number of pre-images.We also prove two additional results related to statistically-hiding commitment. First, we prove a (folklore) parallel composition theorem showing, roughly speaking, that the statistical hiding property of any such commitment scheme is amplified exponentially when multiple independent parallel executions of the scheme are carried out. Second, we show a compiler which transforms any commitment scheme which is statistically hiding against an honest-but-curious receiver into one which is statistically hiding even against a malicious receiver. }, doi = {10.1007/s00145-007-9012-8}, author = {Haitner,I. and Horvitz,O. and Katz, Jonathan and Koo,C. Y and Morselli,R. and Shaltiel,R.} } @conference {15856, title = {Replication and automation of expert judgments: Information engineering in legal e-discovery}, booktitle = {IEEE International Conference on Systems, Man and Cybernetics, 2009. SMC 2009}, year = {2009}, month = {2009/10/11/14}, pages = {102 - 107}, publisher = {IEEE}, organization = {IEEE}, abstract = {The retrieval of digital evidence responsive to discovery requests in civil litigation, known in the United States as {\~A}‚{\^A}{\textquestiondown}e-discovery,{\~A}‚{\^A}{\textquestiondown} presents several important and understudied conditions and challenges. Among the most important of these are (i) that the definition of responsiveness that governs the search effort can be learned and made explicit through effective interaction with the responding party, (ii) that the governing definition of responsiveness is generally complex, deriving both from considerations of subject-matter relevance and from considerations of litigation strategy, and (iii) that the result of the search effort is a set (rather than a ranked list) of documents, and sometimes a quite large set, that is turned over to the requesting party and that the responding party certifies to be an accurate and complete response to the request. This paper describes the design of an {\~A}‚{\^A}{\textquestiondown}interactive task{\~A}‚{\^A}{\textquestiondown} for the text retrieval conference{\textquoteright}s legal track that had the evaluation of the effectiveness of e-discovery applications at the {\~A}‚{\^A}{\textquestiondown}responsive review{\~A}‚{\^A}{\textquestiondown} task as its goal. Notable features of the 2008 interactive task were high-fidelity human-system task modeling, authority control for the definition of {\~A}‚{\^A}{\textquestiondown}responsiveness,{\~A}‚{\^A}{\textquestiondown} and relatively deep sampling for estimation of type 1 and type 2 errors (expressed as {\~A}‚{\^A}{\textquestiondown}precision{\~A}‚{\^A}{\textquestiondown} and {\~A}‚{\^A}{\textquestiondown}recall{\~A}‚{\^A}{\textquestiondown}). The paper presents a critical assessment of the strengths and weaknesses of the evaluation design from the perspectives of reliability, reusability, and cost-benefit tradeoffs.}, keywords = {authorisation, authority control, Automation, civil litigation, CYBERNETICS, Delay, digital evidence retrieval, discovery request, Educational institutions, expert judgment automation, Human computer interaction, Human-machine cooperation and systems, human-system task modeling, information engineering, Information retrieval, interactive task, Law, law administration, legal e-discovery, Legal factors, PROBES, Production, Protocols, search effort, Search methods, text analysis, text retrieval conference legal track, United States, USA Councils, User modeling}, isbn = {978-1-4244-2793-2}, doi = {10.1109/ICSMC.2009.5346118}, author = {Hedin,B. and Oard, Douglas} } @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} } @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 {14743, title = {The ruby intermediate language}, journal = {SIGPLAN Not.}, volume = {44}, year = {2009}, month = {2009/10//}, pages = {89 - 98}, abstract = {Ruby is a popular, dynamic scripting language that aims to "feel natural to programmers" and give users the "freedom to choose" among many different ways of doing the same thing. While this arguably makes programming in Ruby easier, it makes it hard to build analysis and transformation tools that operate on Ruby source code. In this paper, we present the Ruby Intermediate Language (RIL), a Ruby front-end and intermediate representation that addresses these. RIL includes an extensible GLR parser for Ruby, and an automatic translation into an easy-to-analyze intermediate form. This translation eliminates redundant language constructs, unravels the often subtle ordering among side effecting operations, and makes implicit interpreter operations explicit. We also describe several additional useful features of RIL, such as a dynamic instrumentation library for profiling source code and a dataflow analysis engine. We demonstrate the usefulness of RIL by presenting a static and dynamic analysis to eliminate null pointer errors in Ruby programs. We hope that RIL{\textquoteright}s features will enable others to more easily build analysis tools for Ruby, and that our design will inspire the of similar frameworks for other dynamic languages.}, keywords = {intermediate language, profile guided anlaysis, ril, ruby}, isbn = {0362-1340}, doi = {10.1145/1837513.1640148}, url = {http://doi.acm.org/10.1145/1837513.1640148}, author = {Furr,Michael and An,Jong-hoon (David) and Foster, Jeffrey S. and Hicks, Michael W.} } @article {14730, title = {Safe and timely updates to multi-threaded programs}, journal = {SIGPLAN Not.}, volume = {44}, year = {2009}, month = {2009/06//}, pages = {13 - 24}, abstract = {Many dynamic updating systems have been developed that enable a program to be patched while it runs, to fix bugs or add new features. This paper explores techniques for supporting dynamic updates to multi-threaded programs, focusing on the problem of applying an update in a timely fashion while still producing correct behavior. Past work has shown that this tension of safety versus timeliness can be balanced for single-threaded programs. For multi-threaded programs, the task is more difficult because myriad thread interactions complicate understanding the possible program states to which a patch could be applied. Our approach allows the programmer to specify a few program points (e.g., one per thread) at which a patch may be applied, which simplifies reasoning about safety. To improve timeliness, a combination of static analysis and run-time support automatically expands these few points to many more that produce behavior equivalent to the originals. Experiments with thirteen realistic updates to three multi-threaded servers show that we can safely perform a dynamic update within milliseconds when more straightforward alternatives would delay some updates indefinitely.}, keywords = {dynamic software updating, multi-threading, update safety, update timeliness}, isbn = {0362-1340}, doi = {10.1145/1543135.1542479}, url = {http://doi.acm.org/10.1145/1543135.1542479}, author = {Neamtiu,Iulian and Hicks, Michael W.} } @article {13114, title = {Scene it or not? incremental multiple kernel learning for object detection}, journal = {Proceedings of the International Conference on Computer Vision}, year = {2009}, month = {2009///}, author = {Kembhavi,A. and Siddiquie,B. and Miezianko,R. and McCloskey,S. and Davis, Larry S. and Schwartz, W.R. and Harwood,D. and Gupta,A. and Farrell,R. and Luo,Y. and others} } @conference {14562, title = {Scheduling to minimize staleness and stretch in real-time data warehouses}, booktitle = {Proceedings of the twenty-first annual symposium on Parallelism in algorithms and architectures}, year = {2009}, month = {2009///}, pages = {29 - 38}, author = {Bateni,M. H and Golab,L. and Hajiaghayi, Mohammad T. and Karloff,H.} } @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} } @article {13271, title = {A set of tools for Representing, Decomposing and Visualizing non manifold Cellular Complexes}, volume = {DISI-TR-09-06}, year = {2009}, month = {2009///}, institution = {Department of Computer Science and Information Science, University of Genoa}, abstract = {Modeling and understanding complex non-manifold shapes is a key issue in shape analysis and retrieval. The topological structure of a non-manifold shape can be analyzed through its decomposition into a collection of components with a simpler topology. Here, we consider a decomposition of a non-manifold shape into components which are almost manifolds, and we present a novel graph representation which highlights the non-manifold singularities shared by the components as well as their connectivity relations. We describe an algorithm for computing the decomposition and its associated graph representation. We present a new tool for visualizing the shape decomposition and its graph as an effective support to modeling, analyzing and understanding non-manifold shapes. We describe a new data structure for non-manifold simplicial complex that we used in our decomposition software and we provide a complete description of all functionalities of the library we developed.}, author = {De Floriani, Leila and Panozzo,D. and Hui,A.} } @article {15909, title = {Shearlet-Based Deconvolution}, journal = {IEEE Transactions on Image Processing}, volume = {18}, year = {2009}, month = {2009/12//}, pages = {2673 - 2685}, abstract = {In this paper, a new type of deconvolution algorithm is proposed that is based on estimating the image from a shearlet decomposition. Shearlets provide a multidirectional and multiscale decomposition that has been mathematically shown to represent distributed discontinuities such as edges better than traditional wavelets. Constructions such as curvelets and contourlets share similar properties, yet their implementations are significantly different from that of shearlets. Taking advantage of unique properties of a new M-channel implementation of the shearlet transform, we develop an algorithm that allows for the approximation inversion operator to be controlled on a multiscale and multidirectional basis. A key improvement over closely related approaches such as ForWaRD is the automatic determination of the threshold values for the noise shrinkage for each scale and direction without explicit knowledge of the noise variance using a generalized cross validation (GCV). Various tests show that this method can perform significantly better than many competitive deconvolution algorithms.}, keywords = {approximation inversion operator, contourlets, curvelets, Deconvolution, distributed discontinuities, generalized cross validation, image restoration, M-channel implementation, shearlet-based deconvolution, shearlets, Wavelet transforms, wavelets}, isbn = {1057-7149}, doi = {10.1109/TIP.2009.2029594}, author = {Patel, Vishal M. and Easley,G. R and Healy,D. M} } @conference {14738, title = {Static type inference for Ruby}, booktitle = {Proceedings of the 2009 ACM symposium on Applied Computing}, series = {SAC {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {1859 - 1866}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Many general-purpose, object-oriented scripting languages are dynamically typed, which provides flexibility but leaves the programmer without the benefits of static typing, including early error detection and the documentation provided by type annotations. This paper describes Diamondback Ruby (DRuby), a tool that blends Ruby{\textquoteright}s dynamic type system with a static typing discipline. DRuby provides a type language that is rich enough to precisely type Ruby code we have encountered, without unneeded complexity. When possible, DRuby infers static types to discover type errors in Ruby programs. When necessary, the programmer can provide DRuby with annotations that assign static types to dynamic code. These annotations are checked at run time, isolating type errors to unverified code. We applied DRuby to a suite of benchmarks and found several bugs that would cause run-time type errors. DRuby also reported a number of warnings that reveal questionable programming practices in the benchmarks. We believe that DRuby takes a major step toward bringing the benefits of combined static and dynamic typing to Ruby and other object-oriented languages.}, keywords = {Contracts, dynamic typing, ruby, Type inference}, isbn = {978-1-60558-166-8}, doi = {10.1145/1529282.1529700}, url = {http://doi.acm.org/10.1145/1529282.1529700}, author = {Furr,Michael and An,Jong-hoon (David) and Foster, Jeffrey S. and Hicks, Michael W.} } @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 {18808, title = {A survey of snake-inspired robot designs}, journal = {Bioinspiration \& Biomimetics}, volume = {4}, year = {2009}, month = {2009/06/01/}, pages = {021001 - 021001}, abstract = {Body undulation used by snakes and the physical architecture of a snake body may offer significant benefits over typical legged or wheeled locomotion designs in certain types of scenarios. A large number of research groups have developed snake-inspired robots to exploit these benefits. The purpose of this review is to report different types of snake-inspired robot designs and categorize them based on their main characteristics. For each category, we discuss their relative advantages and disadvantages. This review will assist in familiarizing a newcomer to the field with the existing designs and their distinguishing features. We hope that by studying existing robots, future designers will be able to create new designs by adopting features from successful robots. The review also summarizes the design challenges associated with the further advancement of the field and deploying snake-inspired robots in practice.}, isbn = {1748-3182, 1748-3190}, doi = {10.1088/1748-3182/4/2/021001}, url = {http://iopscience.iop.org/1748-3182/4/2/021001}, author = {Hopkins,James K. and Spranklin,Brent W. and Gupta, Satyandra K.} } @article {13868, title = {Symbolic-to-statistical hybridization: extending generation-heavy machine translation}, journal = {Machine Translation}, volume = {23}, year = {2009}, month = {2009///}, pages = {23 - 63}, abstract = {The last few years have witnessed an increasing interest in hybridizing surface-based statistical approaches and rule-based symbolic approaches to machine translation (MT). Much of that work is focused on extending statistical MT systems with symbolic knowledge and components. In the brand of hybridization discussed here, we go in the opposite direction: adding statistical bilingual components to a symbolic system. Our base system is Generation-heavy machine translation (GHMT), a primarily symbolic asymmetrical approach that addresses the issue of Interlingual MT resource poverty in source-poor/target-rich language pairs by exploiting symbolic and statistical target-language resources. GHMT{\textquoteright}s statistical components are limited to target-language models, which arguably makes it a simple form of a hybrid system . We extend the hybrid nature of GHMT by adding statistical bilingual components. We also describe the details of retargeting it to Arabic{\textendash}English MT. The morphological richness of Arabic brings several challenges to the hybridization task. We conduct an extensive evaluation of multiple system variants. Our evaluation shows that this new variant of GHMT{\textemdash}a primarily symbolic system extended with monolingual and bilingual statistical components{\textemdash}has a higher degree of grammaticality than a phrase-based statistical MT system, where grammaticality is measured in terms of correct verb-argument realization and long-distance dependency translation.}, isbn = {0922-6567}, url = {http://dx.doi.org/10.1007/s10590-009-9056-7}, author = {Habash,Nizar and Dorr, Bonnie J and Monz,Christof} } @article {15058, title = {Target Tracking Based on Nonparametric Clustering and Multi-Scale Images}, journal = {JSCUT (Natural Science Edition)}, volume = {37}, year = {2009}, month = {2009///}, pages = {34 - 41}, abstract = {In order to track a target in space and scale in a complex background,a target tracking algorithm based on the nonparametric clustering and multi-scale images is presented.In this algorithm,first,a modified nonparame-tric color-clustering method is employed to adaptively partition the color space of a tracked object,and the Gaussian function is used to model the spatial information of each bin of the color histogram.Next,the Bhattacharyya coefficient is adopted to derive a function describing the similarity between the target model and the target candidate.Then,a coarse-to-fine approach of multi-scale images is employed to implement the spatial location of the tracked object.Finally,the derived automatic bandwidth selection method of kernel function is applied to obtain the scale of the tracked object.Experimental results show that the proposed algorithm outperforms the classical mean shift tracker.}, author = {Shao-fa,J.Z.L. and Hong-li,J.X.Z.} } @article {14657, title = {A Testing Based Empirical Study of Dynamic Software Update Safety Restrictions}, journal = {Technical Reports of the Computer Science Department}, year = {2009}, month = {2009/10/16/}, abstract = {Recent years have seen significant advances in dynamic softwareupdating (DSU) systems, which allow programs to be patched on the fly. Most DSU systems employ automatic safety checks to avoid applying a patch if doing so may lead to incorrect behavior. This paper presents what we believe is the first comprehensive empirical evaluation of the two most significant DSU safety checks: activeness safety (AS), which disallows patches that modify functions on the stack, and con-freeness safety (CFS), which allows modifications to active functions, but only when doing so will be type safe. To measure the checks{\textquoteright} effectiveness, we tested them against three years of updates to Open-SSH and vsftpd. We performed this testing using a novel DSU testing methodology that systematically applies updates throughout the execution of a test suite. After testing updates to both applications in this way, we tracked how often the safety checks allow updates and which updates result in test failures. We found that updating without safety checks produced many failures, and that both AS and CFS dramatically reduced, but did not fully eliminate, these failures. CFS yielded more failures than AS, but AS was more restrictive than CFS, disallowing far more successful updates. Our results suggest that neither AS nor CFS is likely suitable for general-purpose DSU on its own. Indeed, we found that selecting update points manually could avoid all failures while still permitting sufficient updates. Our results present a challenge and important insights for future work: to discover safe and sufficient update points fully automatically. }, url = {http://drum.lib.umd.edu/handle/1903/9802}, author = {Hayden,Christopher M and Hardisty,Eric A. and Hicks, Michael W. and Foster, Jeffrey S.} } @conference {14740, title = {Tests to the left of me, types to the right: how not to get stuck in the middle of a ruby execution}, booktitle = {Proceedings for the 1st workshop on Script to Program Evolution}, series = {STOP {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {14 - 16}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Ruby is a popular dynamic scripting language that permits terse, expressive code, but provides no static checks to detect errors before running the program. To address this, we have developed Diamond-back Ruby (DRuby), a tool that blends the benefits of static and dynamic typing. This paper briefly describes the main features of DRuby, which we will present in a tool demonstration. The presentation will concentrate on the development of a small, statically typed Ruby program, illustrating how DRuby might be used in practice. The audience will learn about some of the practical design decisions that went into DRuby, and how to use it to develop a type-safe Ruby program.}, isbn = {978-1-60558-543-7}, doi = {10.1145/1570506.1570508}, url = {http://doi.acm.org/10.1145/1570506.1570508}, author = {Furr,Michael and An,Jong-hoon (David) and Foster, Jeffrey S. and Hicks, Michael W.} } @conference {14658, title = {A theory of typed coercions and its applications}, booktitle = {Proceedings of the 14th ACM SIGPLAN international conference on Functional programming}, series = {ICFP {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {329 - 340}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {A number of important program rewriting scenarios can be recast as type-directed coercion insertion. These range from more theoretical applications such as coercive subtyping and supporting overloading in type theories, to more practical applications such as integrating static and dynamically typed code using gradual typing, and inlining code to enforce security policies such as access control and provenance tracking. In this paper we give a general theory of type-directed coercion insertion. We specifically explore the inherent tradeoff between expressiveness and ambiguity--the more powerful the strategy for generating coercions, the greater the possibility of several, semantically distinct rewritings for a given program. We consider increasingly powerful coercion generation strategies, work out example applications supported by the increased power (including those mentioned above), and identify the inherent ambiguity problems of each setting, along with various techniques to tame the ambiguities.}, keywords = {coercion insertion, gradual typing, nonambiguity, provenance, type-directed translation}, isbn = {978-1-60558-332-7}, doi = {10.1145/1596550.1596598}, url = {http://doi.acm.org/10.1145/1596550.1596598}, author = {Swamy,Nikhil and Hicks, Michael W. and Bierman,Gavin M.} } @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 {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} } @article {18529, title = {Towards an Internet Connectivity Market}, volume = {GT-CS-09-01}, year = {2009}, month = {2009///}, institution = {Georgia Institute of Technology}, abstract = {Today{\textquoteright}s Internet achieves end-to-end connectivity through bilateral contracts between neighboring networks; unfortunately, this {\textquotedblleft}one size fits all{\textquotedblright} connectivity results in less efficient paths, unsold capacity and unmet demand, and sometimes catastrophic market failures that result in global disconnectivity. This paper presents the design and evaluation of MINT, a Market for Internet Transit. MINT is a connectivity market and corresponding set of protocols that allows ISPs to offer path segments on an open market. Edge networks bid for end-to-end paths, and a mediator matches bids for paths to collections of path segments that form end-to-end paths. MINT can be deployed using protocols that are present in today{\textquoteright}s routers, and it operates in parallel with the existing routing infrastructure and connectivity market. We present MINT{\textquoteright}s market model and protocol design; evaluate how MINT improves efficiency, the utility of edge networks, and the profits of transit networks; and how MINT can operate at Internet scale.}, url = {http://hdl.handle.net/1853/30622}, author = {Feamster, Nick and Hassan,U. and Sundaresan,S. and Valancius,V. and Johari,R. and Vazirani,V.} } @article {14301, title = {Triaging Checklists: a Substitute for a PhD in Static Analysis}, journal = {Evaluation and Usability of Programming Languages and Tools (PLATEAU) PLATEAU 2009}, year = {2009}, month = {2009///}, abstract = {Static analysis tools have achieved great success in recentyears in automating the process of detecting defects in soft- ware. However, these sophisticated tools have yet to gain widespread adoption, since many of these tools remain too difficult to understand and use. In previous work, we dis- covered that even with an effective code visualization tool, users still found it hard to determine if warnings reported by these tools were true errors or false warnings. The fun- damental problem users face is to understand enough of the underlying algorithm to determine if a warning is caused by imprecision in the algorithm, a challenge that even experts with PhDs may take a while to achieve. In our current work, we propose to use triaging checklists to provide users with systematic guidance to identify false warnings by taking into account specific sources of imprecision in the particular tool. Additionally, we plan to provide checklist assistants, which is a library of simple analyses designed to aid users in an- swering checklist questions. }, author = {Phang,K.Y. and Foster, Jeffrey S. and Hicks, Michael W. and Sazawal,V.} } @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.} } @conference {13888, title = {Using citations to generate surveys of scientific paradigms}, booktitle = {Proceedings of Human Language Technologies: The 2009 Annual Conference of the North American Chapter of the Association for Computational Linguistics}, series = {NAACL {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {584 - 592}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {The number of research publications in various disciplines is growing exponentially. Researchers and scientists are increasingly finding themselves in the position of having to quickly understand large amounts of technical material. In this paper we present the first steps in producing an automatically generated, readily consumable, technical survey. Specifically we explore the combination of citation information and summarization techniques. Even though prior work (Teufel et al., 2006) argues that citation text is unsuitable for summarization, we show that in the framework of multi-document survey creation, citation texts can play a crucial role.}, isbn = {978-1-932432-41-1}, url = {http://dl.acm.org/citation.cfm?id=1620754.1620839}, author = {Mohammad,Saif and Dorr, Bonnie J and Egan,Melissa and Hassan,Ahmed and Muthukrishan,Pradeep and Qazvinian,Vahed and Radev,Dragomir and Zajic, David} } @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 {14756, title = {Verified enforcement of stateful information release policies}, journal = {SIGPLAN Not.}, volume = {43}, year = {2009}, month = {2009/02//}, pages = {21 - 31}, abstract = {Many organizations specify information release policies to describe the terms under which sensitive information may be released to other organizations. This paper presents a new approach for ensuring that security-critical software correctly enforces its information release policy. Our approach has two parts. First, an information release policy is specified as a security automaton written in a new language called AIR. Second, we enforce an AIR policy by translating it into an API for programs written in lAIR, a core formalism for a functional programming language. lAIR uses a novel combination of dependent, affine, and singleton types to ensure that the API is used correctly. As a consequence we can certify that programs written in lAIR meet the requirements of the original AIR policy specification.}, keywords = {affine types, certified evaluation, declassification, dependent types, singleton types, state modifying policies}, isbn = {0362-1340}, doi = {10.1145/1513443.1513448}, url = {http://doi.acm.org/10.1145/1513443.1513448}, author = {Swamy,Nikhil and Hicks, Michael W.} } @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.} } @article {15838, title = {Access to recorded interviews}, journal = {Journal on Computing and Cultural Heritage}, volume = {1}, year = {2008}, month = {2008/06/01/}, pages = {1 - 27}, isbn = {15564673}, doi = {10.1145/1367080.1367083}, url = {http://dl.acm.org/citation.cfm?id=1367083}, author = {Jong,Franciska De and Oard, Douglas and Heeren,Willemijn and Ordelman,Roeland} } @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 {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} } @article {12158, title = {The ASC-Alliance Projects: A Case Study of Large-Scale Parallel Scientific Code Development}, journal = {Computer}, volume = {41}, year = {2008}, month = {2008/03//}, pages = {50 - 58}, abstract = {Computational scientists face many challenges when developing software that runs on large-scale parallel machines. However, software-engineering researchers haven{\textquoteright}t studied their software development processes in much detail. To better understand the nature of software development in this context, the authors examined five large-scale computational science software projects operated at the five ASC-Alliance centers.}, keywords = {ASC-Alliance, code, development;large-scale, development;parallel, engineering;, machines;software, Parallel, projects;computational, scale, Science, scientific, scientists;large, software, systems;parallel}, isbn = {0018-9162}, doi = {10.1109/MC.2008.101}, author = {Hochstein, L. and Basili, Victor R.} } @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} } @conference {16329, title = {CiCUTS: Combining System Execution Modeling Tools with Continuous Integration Environments}, booktitle = {Engineering of Computer-Based Systems, IEEE International Conference on the}, year = {2008}, month = {2008///}, pages = {66 - 75}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {System execution modeling (SEM) tools provide an effective means to evaluate the quality of service (QoS) of enterprise distributed real-time and embedded (DRE) systems. SEM tools facilitate testing and resolving performance issues throughout the entire development life-cycle, rather than waiting until final system integration. SEM tools have not historically focused on effective testing. New techniques are therefore needed to help bridge the gap between the early integration capabilities of SEM tools and testing so developers can focus on resolving strategic integration and performance issues, as opposed to wrestling with tedious and error-prone low-level testing concerns. This paper provides two contributions to research on using SEM tools to address enterprise DRE system integration challenges. First, we evaluate several approaches for combining continuous integration environments with SEM tools and describe CiCUTS, which combines the CUTS SEM tool with the CruiseControl .NET continuous integration environment. Second, we present a case study that shows how CiCUTS helps reduce the time and effort required to manage and execute integration tests that evaluate QoS metrics for a representative DRE system from the domain of shipboard computing. The results of our case study show that CiCUTS helps developers and testers ensure the performance of an example enterprise DRE system is within its QoS specifications throughout development, instead of waiting until system integration time to evaluate QoS.}, keywords = {continuous integration, integration testing, serialized phasing, system execution modeling}, isbn = {978-0-7695-3141-0}, doi = {http://doi.ieeecomputersociety.org/10.1109/ECBS.2008.20}, author = {Hill,James H. and Schmidt,Douglas C. and Porter, Adam and Slaby,John M.} } @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 {14599, title = {Computational Analysis of Constraints on Noncoding Regions, Coding Regions and Gene Expression in Relation to Plasmodium Phenotypic Diversity}, journal = {PLoS ONEPLoS ONE}, volume = {3}, year = {2008}, month = {2008///}, pages = {e3122 - e3122}, abstract = {Malaria-causing Plasmodium species exhibit marked differences including host choice and preference for invading particular cell types. The genetic bases of phenotypic differences between parasites can be understood, in part, by investigating constraints on gene expression and genic sequences, both coding and regulatory.We investigated the evolutionary constraints on sequence and expression of parasitic genes by applying comparative genomics approaches to 6 Plasmodium genomes and 2 genome-wide expression studies. We found that the coding regions of Plasmodium transcription factor and sexual development genes are relatively less constrained, as are those of genes encoding CCCH zinc fingers and invasion proteins, which all play important roles in these parasites. Transcription factors and genes with stage-restricted expression have conserved upstream regions and so do several gene classes critical to the parasite{\textquoteright}s lifestyle, namely, ion transport, invasion, chromatin assembly and CCCH zinc fingers. Additionally, a cross-species comparison of expression patterns revealed that Plasmodium-specific genes exhibit significant expression divergence. Overall, constraints on Plasmodium{\textquoteright}s protein coding regions confirm observations from other eukaryotes in that transcription factors are under relatively lower constraint. Proteins relevant to the parasite{\textquoteright}s unique lifestyle also have lower constraint on their coding regions. Greater conservation between Plasmodium species in terms of promoter motifs suggests tight regulatory control of lifestyle genes. However, an interspecies divergence in expression patterns of these genes suggests that either expression is controlled via genomic or epigenomic features not encoded in the proximal promoter sequence, or alternatively, the combinatorial interactions between motifs confer species-specific expression patterns. }, doi = {10.1371/journal.pone.0003122}, url = {UR - http://dx.doi.org/10.1371/journal.pone.0003122,http://dx.doi.org/10.1371/journal.pone.0003122}, author = {Essien,Kobby and Hannenhalli, Sridhar and Stoeckert,Christian J.} } @conference {13741, title = {Computing word-pair antonymy}, booktitle = {Proceedings of the Conference on Empirical Methods in Natural Language Processing}, series = {EMNLP {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {982 - 991}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Knowing the degree of antonymy between words has widespread applications in natural language processing. Manually-created lexicons have limited coverage and do not include most semantically contrasting word pairs. We present a new automatic and empirical measure of antonymy that combines corpus statistics with the structure of a published thesaurus. The approach is evaluated on a set of closest-opposite questions, obtaining a precision of over 80\%. Along the way, we discuss what humans consider antonymous and how antonymy manifests itself in utterances.}, url = {http://dl.acm.org/citation.cfm?id=1613715.1613843}, author = {Mohammad,Saif and Dorr, Bonnie J and Hirst,Graeme} } @conference {14669, title = {Contextual effects for version-consistent dynamic software updating and safe concurrent programming}, booktitle = {Proceedings of the 35th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages}, series = {POPL {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {37 - 49}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper presents a generalization of standard effect systems that we call contextual effects. A traditional effect system computes the effect of an expression e. Our system additionally computes the effects of the computational context in which e occurs. More specifically, we computethe effect of the computation that has already occurred(the prior effect) and the effect of the computation yet to take place (the future effect). Contextual effects are useful when the past or future computation of the program is relevant at various program points. We present two substantial examples. First, we show how prior and future effects can be used to enforce transactional version consistency(TVC), a novel correctness property for dynamic software updates. TV Censures that programmer-designated transactional code blocks appear to execute entirely at the same code version, even if a dynamic update occurs in the middle of the block. Second, we show how future effects can be used in the analysis of multi-threaded programs to find thread-shared locations. This is an essential step in applications such as data race detection.}, keywords = {computation effects, contextual effects, data race detection, dynamic software updating, type and effect systems, version consistency}, isbn = {978-1-59593-689-9}, doi = {10.1145/1328438.1328447}, url = {http://doi.acm.org/10.1145/1328438.1328447}, author = {Neamtiu,Iulian and Hicks, Michael W. and Foster, Jeffrey S. and Pratikakis,Polyvios} } @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} } @inbook {19030, title = {Delegating Capabilities in Predicate Encryption Systems}, booktitle = {Automata, Languages and Programming}, series = {Lecture Notes in Computer Science}, volume = {5126}, year = {2008}, month = {2008}, pages = {560 - 578}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In predicate encryption systems, given a capability, one can evaluate one or more predicates on the plaintext encrypted, while all other information about the plaintext remains hidden. We consider the role of delegation in such predicate encryption systems. Suppose Alice has a capability, and she wishes to delegate to Bob a more restrictive capability allowing the decryption of a subset of the information Alice can learn about the plaintext encrypted. We formally define delegation in predicate encryption systems, propose a new security definition for delegation, and give an efficient construction supporting conjunctive queries. The security of our construction can be reduced to the general 3-party Bilinear Diffie-Hellman assumption, and the Bilinear Decisional Diffie-Hellman assumption in composite order bilinear groups.}, keywords = {Computer science}, isbn = {978-3-540-70582-6}, url = {http://www.springerlink.com/content/w320422h15050004/abstract/}, author = {Elaine Shi and Waters,Brent}, editor = {Aceto,Luca and Damg{\r a}rd,Ivan and Goldberg,Leslie and Halld{\'o}rsson,Magn{\'u}s and Ing{\'o}lfsd{\'o}ttir,Anna and Walukiewicz,Igor} } @article {14678, title = {Directing javascript with arrows (functional pearl)}, year = {2008}, month = {2008///}, abstract = {JavaScript, being a single-threaded language, makes extensive use of event-driven programming to enable responsive web applications. However, standard approaches to sequencing events are messy, and often lead to code that is difficult to understand and maintain. We have found that arrows, a generalization of monads, are an elegant solution to this problem. Arrows allow us to easily write asynchronous programs in small, modular units of code, and flexibly compose them in many different ways, while nicely abstracting the details of asynchronous program composition. In particular, we show how to use arrows to construct a variety of state machines, such as autoscrollers and drag-and-drop handlers.}, author = {Khoo,Y.P. and Hicks, Michael W. and Foster, Jeffrey S. and Sazawal,V.} } @article {18961, title = {The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)}, journal = {Nature}, volume = {452}, year = {2008}, month = {2008///}, pages = {991 - 996}, abstract = {Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3 draft genome sequence of {\textquoteright}SunUp{\textquoteright} papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica{\textquoteright}s distinguishing morpho-physiological, medicinal and nutritional properties.}, isbn = {0028-0836}, doi = {10.1038/nature06856}, url = {http://www.nature.com/nature/journal/v452/n7190/full/nature06856.html}, author = {Ming,R. and Hou,S. and Feng,Y. and Yu,Q. and Dionne-Laporte,A. and Saw,J.H. and Senin,P. and Wang,W. and Ly,B.V. and Lewis,K.L.T. and others} } @article {14681, title = {Dynamic Rebinding for Marshalling and Update, Via Redex-Time and Destruct-Time Reduction}, journal = {Journal of Functional Programming}, volume = {18}, year = {2008}, month = {2008///}, pages = {437 - 502}, abstract = {Most programming languages adopt static binding, but for distributed programming an exclusive reliance on static binding is too restrictive: dynamic binding is required in various guises, for example, when a marshalled value is received from the network, containing identifiers that must be rebound to local resources. Typically, it is provided only by ad hoc mechanisms that lack clean semantics. In this paper, we adopt a foundational approach, developing core dynamic rebinding mechanisms as extensions to the simply typed call-by-value λ calculus. To do so, we must first explore refinements of the call-by-value reduction strategy that delay instantiation, to ensure computations make use of the most recent versions of rebound definitions. We introduce redex-time and destruct-time strategies. The latter forms the basis for a λmarsh calculus that supports dynamic rebinding of marshalled values, while remaining as far as possible statically typed. We sketch an extension of λmarsh with concurrency and communication, giving examples showing how wrappers for encapsulating untrusted code can be expressed. Finally, we show that a high-level semantics for dynamic updating can also be based on the destruct-time strategy, defining a λupdate calculus with simple primitives to provide type-safe updating of running code. We show how the ideas of this simple calculus extend to more real-world, module-level dynamic updating in the style of Erlang. We thereby establish primitives and a common semantic foundation for a variety of real-world dynamic rebinding requirements.}, doi = {10.1017/S0956796807006600}, author = {Sewell,Peter and Stoyle,Gareth and Hicks, Michael W. and Bierman,Gavin and Wansbrough,Keith} } @article {18518, title = {A Dynamic Reputation Service for Spotting Spammers}, volume = {GT-CS-08-09}, year = {2008}, month = {2008///}, institution = {School of Computer Science, Georgia Tech}, abstract = {This paper presents the design, implementation, evalu-ation, and initial deployment of SpamSpotter, the first open, large-scale, real-time reputation system for filtering spam. Existing blacklists (e.g., SpamHaus) have trouble keeping pace with spammers{\textquoteright} increasing ability to send spam from {\textquotedblleft}fresh{\textquotedblright} IP addresses, and filters based purely on content are easily evadable. In contrast, SpamSpotter dynamically classifies email senders in real time based on their global sending behavior, rather than based on ephemeral features such as an IP address or the content of the message. In implementing SpamSpotter, we address significant challenges involving both dynamism (i.e., de- termining when to {\textquotedblleft}retrain{\textquotedblright} our dynamic classification algorithms) and scale (i.e., maintaining fast, accurate per- formance in the face of tremendous email message vol- ume). We have evaluated the performance and accuracy of SpamSpotter using traces from a large email-hosting provider and a spam appliance vendor that receives 300 million messages a day. Our evaluation shows that SpamSpotter is scalable, fast, and accurate. SpamSpotter is also operational today: it will currently answer queries from existing spam filtering software (e.g., SpamAssas- sin) with only minor configuration changes. }, author = {Ramachandran,A. and Hao,S. and Khandelwal,H. and Feamster, Nick and Vempala,S.} } @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 {19601, title = {Efficient Integrity Checking of Untrusted Network Storage}, booktitle = {StorageSS {\textquoteright}08 Proceedings of the 4th ACM International Workshop on Storage Security and Survivability }, series = {StorageSS {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {43 - 54}, publisher = {ACM}, organization = {ACM}, abstract = {Outsourced storage has become more and more practical in recent years. Users can now store large amounts of data in multiple servers at a relatively low price. An important issue for outsourced storage systems is to design an efficient scheme to assure users that their data stored at remote servers has not been tampered with. This paper presents a general method and a practical prototype application for verifying the integrity of files in an untrusted network storage service. The verification process is managed by an application running in a trusted environment (typically on the client) that stores just one cryptographic hash value of constant size, corresponding to the "digest" of an authenticated data structure. The proposed integrity verification service can work with any storage service since it is transparent to the storage technology used. Experimental results show that our integrity verification method is efficient and practical for network storage systems.}, keywords = {authenticated data structures, data integrity, Security, untrusted outsourced storage}, isbn = {978-1-60558-299-3}, url = {http://doi.acm.org/10.1145/1456469.1456479}, author = {Heitzmann, Alexander and Palazzi, Bernardo and Charalampos Papamanthou and Tamassia, Roberto} } @inbook {12117, title = {An Environment for Conducting Families of Software Engineering Experiments}, booktitle = {Software Development}, volume = {Volume 74}, year = {2008}, month = {2008///}, pages = {175 - 200}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {The classroom is a valuable resource for conducting software engineering experiments. However, coordinating a family of experiments in classroom environments presents a number of challenges to researchers. Understanding how to run such experiments, developing procedures to collect accurate data, and collecting data that is consistent across multiple studies are major problems. This paper describes an environment, the Experiment Manager that simplifies the process of collecting, managing, and sanitizing data from classroom experiments, while minimizing disruption to natural subject behavior. We have successfully used this environment to study the impact of parallel programming languages in the high-performance computing domain on programmer productivity at multiple universities across the United States.}, isbn = {0065-2458}, url = {http://www.sciencedirect.com/science/article/pii/S0065245808006050}, author = {Hochstein, Lorin and Nakamura,Taiga and Shull, Forrest and Zazworka, Nico and Basili, Victor R. and Zelkowitz, Marvin V}, editor = {Zelkowitz, Marvin V} } @article {14609, title = {Eukaryotic Transcription Factor Binding Sites{\textemdash}modeling and Integrative Search Methods}, journal = {BioinformaticsBioinformatics}, volume = {24}, year = {2008}, month = {2008/06/01/}, pages = {1325 - 1331}, abstract = {A comprehensive knowledge of transcription factor binding sites (TFBS) is important for a mechanistic understanding of transcriptional regulation as well as for inferring gene regulatory networks. Because the DNA motif recognized by a transcription factor is typically short and degenerate, computational approaches for identifying binding sites based only on the sequence motif inevitably suffer from high error rates. Current state-of-the-art techniques for improving computational identification of binding sites can be broadly categorized into two classes: (1) approaches that aim to improve binding motif models by extracting maximal sequence information from experimentally determined binding sites and (2) approaches that supplement binding motif models with additional genomic or other attributes (such as evolutionary conservation). In this review we will discuss recent attempts to improve computational identification of TFBS through these two types of approaches and conclude with thoughts on future development.Contact: sridharh@pcbi.upenn.edu }, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/btn198}, url = {http://bioinformatics.oxfordjournals.org/content/24/11/1325}, author = {Hannenhalli, Sridhar} } @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.} } @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 {13369, title = {Flow Algorithms for Parallel Query Optimization}, booktitle = {IEEE 24th International Conference on Data Engineering, 2008. ICDE 2008}, year = {2008}, month = {2008/04/07/12}, pages = {754 - 763}, publisher = {IEEE}, organization = {IEEE}, abstract = {We address the problem of minimizing the response time of a multi-way join query using pipelined (inter-operator) parallelism, in a parallel or a distributed environment. We observe that in order to fully exploit the parallelism in the system, we must consider a new class of ";interleaving"; plans, where multiple query plans are used simultaneously to minimize the response time of a query (or to maximize the tuple-throughput of the system). We cast the query planning problem in this environment as a ";flow maximization problem";, and present polynomial-time algorithms that (statically) find the optimal set of plans to use for a given query, for a large class of multi-way join queries. Our proposed algorithms also naturally extend to query optimization over web services. Finally we present an extensive experimental evaluation that demonstrates both the need to consider such plans in parallel query processing and the effectiveness of our algorithms.}, keywords = {Casting, computational complexity, Cost function, Databases, Delay, distributed environment, Educational institutions, flow maximization algorithm, Interleaved codes, interoperator parallelism, minimisation, multiway join query response time minimization problem, parallel database, Parallel databases, parallel query optimization, Partitioning algorithms, pipeline processing, pipelined parallelism, polynomial-time algorithm, query planning problem, Query processing, Web service, Web services}, isbn = {978-1-4244-1836-7}, doi = {10.1109/ICDE.2008.4497484}, author = {Deshpande, Amol and Hellerstein,L.} } @inbook {14698, title = {Formalizing Soundness of Contextual Effects}, booktitle = {Theorem Proving in Higher Order LogicsTheorem Proving in Higher Order Logics}, series = {Lecture Notes in Computer Science}, volume = {5170}, year = {2008}, month = {2008///}, pages = {262 - 277}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {A contextual effect system generalizes standard type and effect systems: where a standard effect system computes the effect of an expression e , a contextual effect system additionally computes the prior and future effect of e , which characterize the behavior of computation prior to and following, respectively, the evaluation of e . This paper describes the formalization and proof of soundness of contextual effects, which we mechanized using the Coq proof assistant. Contextual effect soundness is an unusual property because the prior and future effect of a term e depends not on e itself (or its evaluation), but rather on the evaluation of the context in which e appears. Therefore, to state and prove soundness we must {\textquotedblleft}match up{\textquotedblright} a subterm in the original typing derivation with the possibly-many evaluations of that subterm during the evaluation of the program, in a way that is robust under substitution. We do this using a novel typed operational semantics. We conjecture that our approach could prove useful for reasoning about other properties of derivations that rely on the context in which that derivation appears.}, isbn = {978-3-540-71065-3}, url = {http://dx.doi.org/10.1007/978-3-540-71067-7_22}, author = {Pratikakis,Polyvios and Foster, Jeffrey S. and Hicks, Michael W. and Neamtiu,Iulian}, editor = {Mohamed,Otmane and Mu{\~n}oz,C{\'e}sar and Tahar,Sofi{\`e}ne} } @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 {14612, title = {Functional Diversification of Paralogous Transcription Factors via Divergence in DNA Binding Site Motif and in Expression}, journal = {PLoS ONEPLoS ONE}, volume = {3}, year = {2008}, month = {2008/06/04/}, pages = {e2345 - e2345}, abstract = {Gene duplication is a major driver of evolutionary innovation as it allows for an organism to elaborate its existing biological functions via specialization or diversification of initially redundant gene paralogs. Gene function can diversify in several ways. Transcription factor gene paralogs in particular, can diversify either by changes in their tissue-specific expression pattern or by changes in the DNA binding site motif recognized by their protein product, which in turn alters their gene targets. The relationship between these two modes of functional diversification of transcription factor paralogs has not been previously investigated, and is essential for understanding adaptive evolution of transcription factor gene families.Based on a large set of human paralogous transcription factor pairs, we show that when the DNA binding site motifs of transcription factor paralogs are similar, the expressions of the genes that encode the paralogs have diverged, so in general, at most one of the paralogs is highly expressed in a tissue. Moreover, paralogs with diverged DNA binding site motifs tend to be diverged in their function. Conversely, two paralogs that are highly expressed in a tissue tend to have dissimilar DNA binding site motifs. We have also found that in general, within a paralogous family, tissue-specific decrease in gene expression is more frequent than what is expected by chance. While previous investigations of paralogous gene diversification have only considered coding sequence divergence, by explicitly quantifying divergence in DNA binding site motif, our work presents a new paradigm for investigating functional diversification. Consistent with evolutionary expectation, our quantitative analysis suggests that paralogous transcription factors have survived extinction in part, either through diversification of their DNA binding site motifs or through alterations in their tissue-specific expression levels. }, doi = {10.1371/journal.pone.0002345}, url = {UR - http://dx.plos.org/10.1371/journal.pone.0002345,http://dx.plos.org/10.1371/journal.pone.0002345}, author = {Singh,Larry N. and Hannenhalli, Sridhar} } @article {14617, title = {Genome-Wide Analysis of Natural Selection on Human Cis-Elements}, journal = {PLoS ONEPLoS ONE}, volume = {3}, year = {2008}, month = {2008///}, pages = {e3137 - e3137}, abstract = {It has been speculated that the polymorphisms in the non-coding portion of the human genome underlie much of the phenotypic variability among humans and between humans and other primates. If so, these genomic regions may be undergoing rapid evolutionary change, due in part to natural selection. However, the non-coding region is a heterogeneous mix of functional and non-functional regions. Furthermore, the functional regions are comprised of a variety of different types of elements, each under potentially different selection regimes.Using the HapMap and Perlegen polymorphism data that map to a stringent set of putative binding sites in human proximal promoters, we apply the Derived Allele Frequency distribution test of neutrality to provide evidence that many human-specific and primate-specific binding sites are likely evolving under positive selection. We also discuss inherent limitations of publicly available human SNP datasets that complicate the inference of selection pressures. Finally, we show that the genes whose proximal binding sites contain high frequency derived alleles are enriched for positive regulation of protein metabolism and developmental processes. Thus our genome-scale investigation provides evidence for positive selection on putative transcription factor binding sites in human proximal promoters. }, doi = {10.1371/journal.pone.0003137}, url = {UR - http://dx.doi.org/10.1371/journal.pone.0003137,http://dx.doi.org/10.1371/journal.pone.0003137}, author = {Sethupathy,Praveen and Giang,Hoa and Plotkin,Joshua B. and Hannenhalli, Sridhar} } @article {14620, title = {Guest Editors{\textquoteright} Introduction to the Special Section on Algorithms in Bioinformatics}, journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {5}, year = {2008}, month = {2008/12//Oct}, pages = {482 - 483}, keywords = {Abstracts, Algorithm design and analysis, Bioinformatics, Biological system modeling, biology computing, Computational Biology, Computational modeling, Computer science, Genomics, sequences}, isbn = {1545-5963}, doi = {10.1109/TCBB.2008.116}, author = {Giancarlo,Raffaele and Hannenhalli, Sridhar} } @article {14788, title = {Hardware monitors for dynamic page migration}, journal = {Journal of Parallel and Distributed Computing}, volume = {68}, year = {2008}, month = {2008/09//}, pages = {1186 - 1200}, abstract = {In this paper, we first introduce a profile-driven online page migration scheme and investigate its impact on the performance of multithreaded applications. We use centralized lightweight, inexpensive plug-in hardware monitors to profile the memory access behavior of an application, and then migrate pages to memory local to the most frequently accessing processor. We also investigate the use of several other potential sources of data gathered from hardware monitors and compare their effectiveness to using data from centralized hardware monitors. In particular, we investigate the effectiveness of using cache miss profiles, Translation Lookaside Buffer (TLB) miss profiles and the content of the on-chip TLBs using the valid bit information. Moreover, we also introduce a modest hardware feature, called Address Translation Counters (ATC), and compare its effectiveness with other sources of hardware profiles.Using the Dyninst runtime instrumentation combined with hardware monitors, we were able to add page migration capabilities to a Sun Fire 6800 server without having to modify the operating system kernel, or to re-compile application programs. Our dynamic page migration scheme reduced the total number of non-local memory accesses of applications by up to 90\% and improved the execution times up to 16\%. We also conducted a simulation based study and demonstrated that cache miss profiles gathered from on-chip CPU monitors, which are typically available in current microprocessors, can be effectively used to guide dynamic page migrations in applications. }, keywords = {Address translation counters, cc-NUMA systems, Dynamic page migration, Full system simulation, Hardware performance monitors, High performance computing, Multiprocessor systems, OpenMP applications, Runtime optimization}, isbn = {0743-7315}, doi = {16/j.jpdc.2008.05.006}, url = {http://www.sciencedirect.com/science/article/pii/S0743731508001020}, author = {Tikir, Mustafa M. and Hollingsworth, Jeffrey K} } @article {13297, title = {Identification of Form Features in Non-Manifold Shapes Through a Decomposition Approach}, journal = {ASME Conference Proceedings}, volume = {2008}, year = {2008}, month = {2008///}, pages = {293 - 300}, abstract = {In Computer-Aided Design (CAD), the idealization process reduces the complexity of the model of a solid object, thus resulting in a simplified representation which captures only the essential elements of its shape. Form features extraction is a relevant issue in order to recover semantic information from an idealized object model, since such information is typically lost during the idealization process. An idealized model is usually composed of non-manifold parts, whose topology carries significant structural information about the object shape. To this aim, we define form features for non-manifold object by extending the taxonomy of form features provided by STEP [19]. We describe an approach for the identification of features, which interact with non-manifold singularities in the object, based on a decomposition of a non-manifold object into nearly manifold components and on the properties of the graph representing such decomposition.}, doi = {10.1115/ESDA2008-59566}, url = {http://link.aip.org/link/abstract/ASMECP/v2008/i48371/p293/s1}, author = {De Floriani, Leila and Hui,Annie and Giannini,Franca} } @inbook {14700, title = {Implicit Flows: Can{\textquoteright}t Live with {\textquoteleft}Em, Can{\textquoteright}t Live without {\textquoteleft}Em}, booktitle = {Information Systems SecurityInformation Systems Security}, series = {Lecture Notes in Computer Science}, volume = {5352}, year = {2008}, month = {2008///}, pages = {56 - 70}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Verifying that programs trusted to enforce security actually do so is a practical concern for programmers and administrators. However, there is a disconnect between the kinds of tools that have been successfully applied to real software systems (such as taint mode in Perl and Ruby), and information-flow compilers that enforce a variant of the stronger security property of noninterference. Tools that have been successfully used to find security violations have focused on explicit flows of information, where high-security information is directly leaked to output. Analysis tools that enforce noninterference also prevent implicit flows of information, where high-security information can be inferred from a program{\textquoteright}s flow of control. However, these tools have seen little use in practice, despite the stronger guarantees that they provide. To better understand why, this paper experimentally investigates the explicit and implicit flows identified by the standard algorithm for establishing noninterference. When applied to implementations of authentication and cryptographic functions, the standard algorithm discovers many real implicit flows of information, but also reports an extremely high number of false alarms, most of which are due to conservative handling of unchecked exceptions (e.g., null pointer exceptions). After a careful analysis of all sources of true and false alarms, due to both implicit and explicit flows, the paper concludes with some ideas to improve the false alarm rate, toward making stronger security analysis more practical.}, isbn = {978-3-540-89861-0}, url = {http://dx.doi.org/10.1007/978-3-540-89862-7_4}, author = {King,Dave and Hicks,Boniface and Hicks, Michael W. and Jaeger,Trent}, editor = {Sekar,R. and Pujari,Arun} } @conference {13122, title = {Kernel integral images: A framework for fast non-uniform filtering}, booktitle = {Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on}, year = {2008}, month = {2008/06//}, pages = {1 - 8}, abstract = {Integral images are commonly used in computer vision and computer graphics applications. Evaluation of box filters via integral images can be performed in constant time, regardless of the filter size. Although Heckbert (1986) extended the integral image approach for more complex filters, its usage has been very limited, in practice. In this paper, we present an extension to integral images that allows for application of a wide class of non-uniform filters. Our approach is superior to Heckbertpsilas in terms of precision requirements and suitability for parallelization. We explain the theoretical basis of the approach and instantiate two concrete examples: filtering with bilinear interpolation, and filtering with approximated Gaussian weighting. Our experiments show the significant speedups we achieve, and the higher accuracy of our approach compared to Heckbertpsilas.}, keywords = {approximated, equations;interpolation;, filtering;bilinear, filtering;kernel, Gaussian, graphics;computer, images;approximation, integral, interpolation;computer, nonuniform, processing;integral, theory;filtering, theory;image, vision;fast, weighting}, doi = {10.1109/CVPR.2008.4587641}, author = {Hussein,M. and Porikli, F. and Davis, Larry S.} } @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 {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 {14708, title = {Modular Information Hiding and Type-Safe Linking for C}, journal = {IEEE Transactions on Software Engineering}, volume = {34}, year = {2008}, month = {2008/06//May}, pages = {357 - 376}, abstract = {This paper presents CMod, a novel tool that provides a sound module system for C. CMod works by enforcing four rules that are based on principles of modular reasoning and on current programming practice. CMod{\textquoteright}s rules flesh out the convention that .h header files are module interfaces and .c source files are module implementations. Although this convention is well-known, existing explanations of it are incomplete, omitting important subtleties needed for soundness. In contrast, we have proven formally that CMod{\textquoteright}s rules enforce both information hiding and type-safe linking. To use CMod, the programmer develops and builds their software as usual, redirecting the compiler and linker to CMod{\textquoteright}s wrappers. We evaluated CMod by applying it to 30 open source programs, totaling more than one million LoC. Violations to CMod{\textquoteright}s rules revealed more than a thousand information hiding errors, dozens of typing errors, and hundreds of cases that, although not currently bugs, make programming mistakes more likely as the code evolves. At the same time, programs generally adhere to the assumptions underlying CMod{\textquoteright}s rules, and so we could fix rule violations with a modest effort. We conclude that CMod can effectively support modular programming in C: it soundly enforces type-safe linking and information-hiding while being largely compatible with existing practice.}, keywords = {C language, CMOD, Code design, Coding Tools and Techniques, compiler, data encapsulation, Information hiding, modular information hiding, modular reasoning, modules, object-oriented programming, open source programs, packages, program compilers, public domain software, reliability, software reusability, type-safe linking}, isbn = {0098-5589}, doi = {10.1109/TSE.2008.25}, author = {Srivastava,S. and Hicks, Michael W. and Foster, Jeffrey S. and Jenkins,P.} } @article {18247, title = {Mpeg recompression detection based on block artifacts}, journal = {Proc. of SPIE Electronic Imaging, Security, Steganography, and Watermarking of Multimedia Contents}, volume = {6819}, year = {2008}, month = {2008///}, abstract = {With sophisticated video editing technologies, it is becoming increasingly easy to tamper digital video withoutleaving visual clues. One of the common tampering operations on video is to remove some frames and then re-encode the resulting video. In this paper, we propose a new method for detecting this type of tampering by exploring the temporal patterns of the block artifacts in video sequences. We show that MPEG compression introduces different block artifacts into various types of frames and that the strength of the block artifacts as a function over time has a regular pattern for a given group of pictures (GOP) structure. When some frames are removed from an MPEG video file and the file is then recompressed, the block artifacts introduced by the previous compression would remain and affect the average of block artifact strength of the recompressed one in such a way that depends on the number of deleted frames and the type of GOP used previously. We propose a feature curve to reveal the compression history of an MPEG video file with a given GOP structure, and use it as evidence to detect tampering. Experimental results evaluated on common video benchmark clips demonstrate the effectiveness of the proposed method. }, author = {Luo,W. and Wu,M. and Huang,J.} } @article {18707, title = {Mutations in the Hydrophobic Core of Ubiquitin Differentially Affect Its Recognition by Receptor Proteins}, journal = {Journal of Molecular Biology}, volume = {375}, year = {2008}, month = {2008/01/25/}, pages = {979 - 996}, abstract = {Ubiquitin (Ub) is one of the most highly conserved signaling proteins in eukaryotes. In carrying out its myriad functions, Ub conjugated to substrate proteins interacts with dozens of receptor proteins that link the Ub signal to various biological outcomes. Here we report mutations in conserved residues of Ub{\textquoteright}s hydrophobic core that have surprisingly potent and specific effects on molecular recognition. Mutant Ubs bind tightly to the Ub-associated domain of the receptor proteins Rad23 and hHR23A but fail to bind the Ub-interacting motif present in the receptors Rpn10 and S5a. Moreover, chains assembled on target substrates with mutant Ubs are unable to support substrate degradation by the proteasome in vitro or sustain viability of yeast cells. The mutations have relatively little effect on Ub{\textquoteright}s overall structure but reduce its rigidity and cause a slight displacement of the C-terminal β-sheet, thereby compromising association with Ub-interacting motif but not with Ub-associated domains. These studies emphasize an unexpected role for Ub{\textquoteright}s core in molecular recognition and suggest that the diversity of protein{\textendash}protein interactions in which Ub engages placed enormous constraints on its evolvability.}, keywords = {hydrophobic core mutation, molecular recognition, proteasomal degradation, ubiquitin, ubiquitin receptors}, isbn = {0022-2836}, doi = {10.1016/j.jmb.2007.11.016}, url = {http://www.sciencedirect.com/science/article/pii/S0022283607014763}, author = {Haririnia,Aydin and Verma,Rati and Purohit,Nisha and Twarog,Michael Z. and Deshaies,Raymond J. and Bolon,Dan and Fushman, David} } @article {13045, title = {Name translation in statistical machine translation: Learning when to transliterate}, journal = {Proceedings of ACL-08: HLT}, year = {2008}, month = {2008///}, pages = {389 - 397}, author = {Hermjakob,U. and Knight,K. and Daum{\'e}, Hal} } @conference {15916, title = {A new multiresolution generalized directional filter bank design and application in image enhancement}, booktitle = {15th IEEE International Conference on Image Processing, 2008. ICIP 2008}, year = {2008}, month = {2008/10//}, pages = {2816 - 2819}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we present an image enhancement technique based on a new multiscale generalized directional filter bank design. The design presented is a shift-invariant overcomplete representation, which is well suited to extracting geometric features such as edges. Special cases of this design method can be made to reduce to different and improved implementations of the shearlet and the contourlet transforms, which are known to represent certain classes of images optimally. Use of this new filter bank design has proven itself competitive in image restoration for noisy images and is well suited for distinguishing noise from weak edges. Experimental results show that our unique image enhancement technique out-performs wavelet and contourlet based enhancement methods.}, keywords = {Algorithm design and analysis, Approximation error, Channel bank filters, contourlet transform, Design methodology, Discrete transforms, Feature extraction, Filter bank, Frequency, geometric feature extraction, Image Enhancement, IMAGE PROCESSING, image resolution, image restoration, Multidimensional digital filters, Multidimensional systems, multiresolution generalized directional filter bank design, shearlet transform, shift-invariant overcomplete representation, transforms, Wavelet transforms}, isbn = {978-1-4244-1765-0}, doi = {10.1109/ICIP.2008.4712380}, author = {Patel, Vishal M. and Easley,G. R and Healy,D. M} } @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} } @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} } @inbook {19642, title = {Optimal Cryptographic Hardness of Learning Monotone Functions}, booktitle = {Automata, Languages and Programming}, series = {Lecture Notes in Computer Science}, year = {2008}, month = {2008/01/01/}, pages = {36 - 47}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {A wide range of positive and negative results have been established for learning different classes of Boolean functions from uniformly distributed random examples. However, polynomial-time algorithms have thus far been obtained almost exclusively for various classes of monotone functions, while the computational hardness results obtained to date have all been for various classes of general (nonmonotone) functions. Motivated by this disparity between known positive results (for monotone functions) and negative results (for nonmonotone functions), we establish strong computational limitations on the efficient learnability of various classes of monotone functions. We give several such hardness results which are provably almost optimal since they nearly match known positive results. Some of our results show cryptographic hardness of learning polynomial-size monotone circuits to accuracy only slightly greater than 1/2+1/n--√1/2 + 1/\sqrt{n} ; this accuracy bound is close to optimal by known positive results (Blum et al., FOCS {\textquoteright}98). Other results show that under a plausible cryptographic hardness assumption, a class of constant-depth, sub-polynomial-size circuits computing monotone functions is hard to learn; this result is close to optimal in terms of the circuit size parameter by known positive results as well (Servedio, Information and Computation {\textquoteright}04). Our main tool is a complexity-theoretic approach to hardness amplification via noise sensitivity of monotone functions that was pioneered by O{\textquoteright}Donnell (JCSS {\textquoteright}04).}, keywords = {Data structures, Data Structures, Cryptology and Information Theory, Discrete Mathematics in Computer Science, Numeric Computing, Software Engineering/Programming and Operating Systems, Theory of computation}, isbn = {978-3-540-70574-1, 978-3-540-70575-8}, url = {http://link.springer.com/chapter/10.1007/978-3-540-70575-8_4}, author = {Dana Dachman-Soled and Lee, Homin K. and Malkin, Tal and Servedio, Rocco A. and Wan, Andrew and Wee, Hoeteck}, editor = {Aceto, Luca and Damg{\r a}rd, Ivan and Goldberg, Leslie Ann and Halld{\'o}rsson, Magn{\'u}s M. and Ing{\'o}lfsd{\'o}ttir, Anna and Walukiewicz, Igor} } @conference {14714, title = {Path projection for user-centered static analysis tools}, booktitle = {Proceedings of the 8th ACM SIGPLAN-SIGSOFT workshop on Program analysis for software tools and engineering}, series = {PASTE {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {57 - 63}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The research and industrial communities have made great strides in developing sophisticated defect detection tools based on static analysis. To date most of the work in this area has focused on developing novel static analysis algorithms, but has neglected study of other aspects of static analysis tools, particularly user interfaces. In this work, we present a novel user interface toolkit called Path Projection that helps users visualize, navigate, and understand program paths, a common component of many tools{\textquoteright} error reports. We performed a controlled user study to measure the benefit of Path Projection in triaging error reports from Locksmith, a data race detection tool for C. We found that Path Projection improved participants{\textquoteright} time to complete this task without affecting accuracy, while participants felt Path Projection was useful and strongly preferred it to a more standard viewer.}, isbn = {978-1-60558-382-2}, doi = {10.1145/1512475.1512488}, url = {http://doi.acm.org/10.1145/1512475.1512488}, author = {Khoo,Yit Phang and Foster, Jeffrey S. and Hicks, Michael W. and Sazawal,Vibha} } @article {12109, title = {A pilot study to compare programming effort for two parallel programming models}, journal = {Journal of Systems and Software}, volume = {81}, year = {2008}, month = {2008/11//}, pages = {1920 - 1930}, abstract = {ContextWriting software for the current generation of parallel systems requires significant programmer effort, and the community is seeking alternatives that reduce effort while still achieving good performance. Objective Measure the effect of parallel programming models (message-passing vs. PRAM-like) on programmer effort. Design, setting, and subjects One group of subjects implemented sparse-matrix dense-vector multiplication using message-passing (MPI), and a second group solved the same problem using a PRAM-like model (XMTC). The subjects were students in two graduate-level classes: one class was taught MPI and the other was taught XMTC. Main outcome measures Development time, program correctness. Results Mean XMTC development time was 4.8\&$\#$xa0;h less than mean MPI development time (95\% confidence interval, 2.0{\textendash}7.7), a 46\% reduction. XMTC programs were more likely to be correct, but the difference in correctness rates was not statistically significant (p\&$\#$xa0;=\&$\#$xa0;.16). Conclusions XMTC solutions for this particular problem required less effort than MPI equivalents, but further studies are necessary which examine different types of problems and different levels of programmer experience. }, keywords = {effort, empirical study, Message-passing, MPI, parallel programming, PRAM, XMT}, isbn = {0164-1212}, doi = {10.1016/j.jss.2007.12.798}, url = {http://www.sciencedirect.com/science/article/pii/S0164121208000125}, author = {Hochstein, Lorin and Basili, Victor R. and Vishkin, Uzi and Gilbert,John} } @article {18594, title = {Practical issues with using network tomography for fault diagnosis}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {38}, year = {2008}, month = {2008/09//}, pages = {53 - 58}, abstract = {This paper investigates the practical issues in applying network tomography to monitor failures. We outline an approach for selecting paths to monitor, detecting and confirming the existence of a failure, correlating multiple independent observations into a single failure event, and applying existing binary networking tomography algorithms to identify failures. We evaluate the ability of network tomography algorithms to correctly detect and identify failures in a controlled environment on the VINI testbed.}, keywords = {Environment, Fault detection, network tomography}, isbn = {0146-4833}, doi = {10.1145/1452335.1452343}, url = {http://doi.acm.org/10.1145/1452335.1452343}, author = {Huang,Yiyi and Feamster, Nick and Teixeira,Renata} } @inbook {17668, title = {The Randomized Coloring Procedure with Symmetry-Breaking}, booktitle = {Automata, Languages and ProgrammingAutomata, Languages and Programming}, series = {Lecture Notes in Computer Science}, volume = {5125}, year = {2008}, month = {2008///}, pages = {306 - 319}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {A basic randomized coloring procedure has been used in probabilistic proofs to obtain remarkably strong results on graph coloring. These results include the asymptotic version of the List Coloring Conjecture due to Kahn, the extensions of Brooks{\textquoteright} Theorem to sparse graphs due to Kim and Johansson, and Luby{\textquoteright}s fast parallel and distributed algorithms for graph coloring. The most challenging aspect of a typical probabilistic proof is showing adequate concentration bounds for key random variables. In this paper, we present a simple symmetry-breaking augmentation to the randomized coloring procedure that works well in conjunction with Azuma{\textquoteright}s Martingale Inequality to easily yield the requisite concentration bounds. We use this approach to obtain a number of results in two areas: frugal coloring and weighted equitable coloring . A β-frugal coloring of a graph G is a proper vertex-coloring of G in which no color appears more than β times in any neighborhood. Let G = ( V , E ) be a vertex-weighted graph with weight function w : V {\textrightarrow}[0, 1] and let W = ∑ v ∈ V w ( v ). A weighted equitable coloring of G is a proper k -coloring such that the total weight of every color class is {\textquotedblleft}large{\textquotedblright}, i.e., {\textquotedblleft}not much smaller{\textquotedblright} than W / k ; this notion is useful in obtaining tail bounds for sums of dependent random variables.}, isbn = {978-3-540-70574-1}, url = {http://dx.doi.org/10.1007/978-3-540-70575-8_26}, author = {Pemmaraju,Sriram and Srinivasan, Aravind}, editor = {Aceto,Luca and Damg{\r a}rd,Ivan and Goldberg,Leslie and Halld{\'o}rsson,Magn{\'u}s and Ing{\'o}lfsd{\'o}ttir,Anna and Walukiewicz,Igor} } @conference {12173, title = {Readability of scanned books in digital libraries}, booktitle = {Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems}, year = {2008}, month = {2008///}, pages = {705 - 714}, author = {Quinn,A.J. and Hu,C. and Arisaka,T. and Rose,A. and Bederson, Benjamin B.} } @article {16390, title = {Reciprocity between the cerebellum and the cerebral cortex: Nonlinear dynamics in microscopic modules for generating voluntary motor commands}, journal = {Complexity}, volume = {14}, year = {2008}, month = {2008/11/01/}, pages = {29 - 45}, abstract = {The cerebellum and basal ganglia are reciprocally connected with the cerebral cortex, forming many loops that function as distributed processing modules. Here we present a detailed model of one microscopic loop between the motor cortex and the cerebellum, and we show how small arrays of these microscopic loops (CB modules) can be used to generate biologically plausible motor commands for controlling movement. A fundamental feature of CB modules is the presence of positive feedback loops between the cerebellar nucleus and the motor cortex. We use nonlinear dynamics to model one microscopic loop and to investigate its bistable properties. Simulations demonstrate an ability to program a motor command well in advance of command generation and an ability to vary command duration. However, control of command intensity is minimal, which could interfere with the control of movement velocity. To assess these hypotheses, we use a minimal nonlinear model of the neuromuscular (NM) system that translates motor commands into actual movements. Simulations of the combined CB-NM modular model indicate that movement duration is readily controlled, whereas velocity is poorly controlled. We then explore how an array of eight CB-NM modules can be used to control the direction and endpoint of a planar movement. In actuality, thousands of such microscopic loops function together as an array of adjustable pattern generators for programming and regulating the composite motor commands that control limb movements. We discuss the biological plausibility and limitations of the model. We also discuss ways in which an agent-based representation can take advantage of the modularity in order to model this complex system. {\textcopyright} 2008 Wiley Periodicals, Inc. Complexity, 2008}, keywords = {agent-based modeling, cerebellum, equilibrium point control, motor command, motor cortex, Movement, neural network, nonlinear dynamics}, isbn = {1099-0526}, doi = {10.1002/cplx.20241}, url = {http://onlinelibrary.wiley.com/doi/10.1002/cplx.20241/abstract}, author = {Wang,Jun and Dam,Gregory and Yildirim,Sule and Rand, William and Wilensky,Uri and Houk,James C.} } @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 {16070, title = {Searching Electronic Health Records for Temporal Patterns in Patient Histories: A Case Study with Microsoft Amalga}, journal = {AMIA Annual Symposium ProceedingsAMIA Annu Symp Proc}, volume = {2008}, year = {2008}, month = {2008///}, pages = {601 - 605}, abstract = {As electronic health records (EHR) become more widespread, they enable clinicians and researchers to pose complex queries that can benefit immediate patient care and deepen understanding of medical treatment and outcomes. However, current query tools make complex temporal queries difficult to pose, and physicians have to rely on computer professionals to specify the queries for them. This paper describes our efforts to develop a novel query tool implemented in a large operational system at the Washington Hospital Center (Microsoft Amalga, formerly known as Azyxxi). We describe our design of the interface to specify temporal patterns and the visual presentation of results, and report on a pilot user study looking for adverse reactions following radiology studies using contrast.}, isbn = {1942-597X}, author = {Plaisant, Catherine and Lam,Stanley and Shneiderman, Ben and Smith,Mark S. and Roseman,David and Marchand,Greg and Gillam,Michael and Feied,Craig and Handler,Jonathan and Rappaport,Hank} } @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.} } @conference {18865, title = {System-Level Optimization Model for a Snake-Inspired Robot Based on a Rectilinear Gait}, year = {2008}, month = {2008///}, pages = {913 - 924}, publisher = {ASME}, organization = {ASME}, abstract = {Physical parameters of modules and gait parameters affect the overall snake-inspired robot performance. Hence the system-level optimization model has to concurrently optimize the module parameters and the gait. The equations of motion associated with the rectilinear gait are quite complex due to the changing topology of the rectilinear gait. Embedding these equations in the system-level optimization model leads to a computationally challenging formulation. This paper presents a system-level optimization model that utilizes a hierarchical optimization approach and meta-models of the pre-computed optimal gaits to reduce the complexity of the optimization model. This approach enabled us to use an experimentally validated physics-based model of the rectilinear gait and yet at the same time enabled us to create a system-level optimization model with a manageable complexity. A detailed case study is presented to show the importance of concurrently optimizing the module parameters and the gait using our model to obtain the optimal performance for a given mission.}, isbn = {978-0-7918-4326-0}, doi = {10.1115/DETC2008-49972}, url = {http://link.aip.org/link/ASMECP/v2008/i43260/p913/s1\&Agg=doi}, author = {Hopkins,James K. and Spranklin,Brent W. and Gupta, Satyandra K.} } @conference {15430, title = {Test case generator for GUITAR}, booktitle = {Companion of the 30th international conference on Software engineering}, series = {ICSE Companion {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {959 - 960}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {As GUIs become more popular, the need for GUI testing tools becomes greater. Many current GUI test generation techniques require proprietary tools and can be hard to use to their fullest potential. This paper outlines a new test case generation strategy, which enables testers to automatically produce cases in a widely used format. We hope that this strategy will encourage more complete GUI testing.}, keywords = {code coverage, event-flow, Graphical user interfaces, gui ripping, integration tree, jfcunit, junit, Test Case Generation}, isbn = {978-1-60558-079-1}, doi = {10.1145/1370175.1370207}, url = {http://doi.acm.org/10.1145/1370175.1370207}, author = {Hackner,Daniel R. and Memon, Atif M.} } @article {14591, title = {A Tutorial of the Poisson Random Field Model in Population Genetics}, journal = {Advances in Bioinformatics}, volume = {2008}, year = {2008}, month = {2008///}, pages = {1 - 9}, abstract = {Population genetics is the study of allele frequency changes driven by various evolutionary forces such as mutation, natural selection, and random genetic drift. Although natural selection is widely recognized as a bona-fide phenomenon, the extent to which it drives evolution continues to remain unclear and controversial. Various qualitative techniques, or so-called {\textquotedblleft}tests of neutrality{\textquotedblright}, have been introduced to detect signatures of natural selection. A decade and a half ago, Stanley Sawyer and Daniel Hartl provided a mathematical framework, referred to as the Poisson random field (PRF), with which to determine quantitatively the intensity of selection on a particular gene or genomic region. The recent availability of large-scale genetic polymorphism data has sparked widespread interest in genome-wide investigations of natural selection. To that end, the original PRF model is of particular interest for geneticists and evolutionary genomicists. In this article, we will provide a tutorial of the mathematical derivation of the original Sawyer and Hartl PRF model.}, isbn = {1687-8027, 1687-8035}, doi = {10.1155/2008/257864}, url = {http://www.hindawi.com/journals/abi/2008/257864/}, author = {Sethupathy,Praveen and Hannenhalli, Sridhar} } @article {13127, title = {UMD_VDT, an Integration of Detection and Tracking Methods for Multiple Human Tracking}, journal = {Multimodal Technologies for Perception of Humans}, year = {2008}, month = {2008///}, pages = {179 - 190}, abstract = {This paper presents a cooperative body part labeling and tracking algorithm for locating body parts in a videoimage sequence. The body part labeling procedure is used to initialize the tracking procedure and to prevent tracking from getting lost; and the tracking procedure is used to analyze frames that cannot be handled reliably by the labeling procedure. This results in an automatic and robust body part tracking system. Unlike previous work that always start tracking from the first frame which may be difficult to analyze, our tracking procedure starts with some key frames in which body parts can be located reliably. Key frames are selected based on a labeling confidence measure which evaluates the similarity between the human model and the image features. The labeled body parts are tracked in-between frames based on such cues as shape, color, and location interpolated between key frames iteratively. The proposed algorithm has been applied to analyze NASA videotapes in which crew members present challenging postures of bending, twisting, and rotating in a space station. The experimental results demonstrate the effectiveness of the proposed algorithm. }, author = {Tran,S. and Lin,Z. and Harwood,D. and Davis, Larry S.} } @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} } @article {15888, title = {User-assisted query translation for interactive cross-language information retrieval}, journal = {Information Processing \& Management}, volume = {44}, year = {2008}, month = {2008/01//}, pages = {181 - 211}, abstract = {Interactive Cross-Language Information Retrieval (CLIR), a process in which searcher and system collaborate to find documents that satisfy an information need regardless of the language in which those documents are written, calls for designs in which synergies between searcher and system can be leveraged so that the strengths of one can cover weaknesses of the other. This paper describes an approach that employs user-assisted query translation to help searchers better understand the system{\^a}{\texteuro}{\texttrademark}s operation. Supporting interaction and interface designs are introduced, and results from three user studies are presented. The results indicate that experienced searchers presented with this new system evolve new search strategies that make effective use of the new capabilities, that they achieve retrieval effectiveness comparable to results obtained using fully automatic techniques, and that reported satisfaction with support for cross-language searching increased. The paper concludes with a description of a freely available interactive CLIR system that incorporates lessons learned from this research.}, keywords = {Cross-language information retrieval, Machine translation, User studies}, isbn = {0306-4573}, doi = {10.1016/j.ipm.2006.12.009}, url = {http://www.sciencedirect.com/science/article/pii/S0306457307000337}, author = {Oard, Douglas and He,Daqing and Wang,Jianqiang} } @conference {14348, title = {Using wearable sensors and real time inference to understand human recall of routine activities}, booktitle = {Proceedings of the 10th international conference on Ubiquitous computing}, series = {UbiComp {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {154 - 163}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {empirical evaluation, ESM, experience sampling method, recall accuracy, self-reports, survey frequency, user study}, isbn = {978-1-60558-136-1}, doi = {10.1145/1409635.1409656}, url = {http://doi.acm.org/10.1145/1409635.1409656}, author = {Klasnja,Predrag and Harrison,Beverly L. and LeGrand,Louis and LaMarca,Anthony and Jon Froehlich and Hudson,Scott E.} } @article {14754, title = {Verified enforcement of automaton-based information release policies}, journal = {Proceedings of the 2008 Workshop on Programming Languages and Analysis for Security. ACM Press}, year = {2008}, month = {2008///}, abstract = {Many organizations specify information release policies to describe the terms under which sensitive information may bereleased to other organizations. This paper presents a new approach for ensuring that security-critical software correctly enforces its information release policy. Our approach has two parts. First, an information release policy is specified as a security automaton written in a new language called AIR. Second, we enforce an AIR policy by translating it into an API for programs written in λAIR, a core formalism for a functional programming language. λAIR uses a novel combination of dependent, affine, and singleton types to ensure that the API is used correctly. As a consequence we can certify that programs written in λAIR meet the requirements of the original AIR policy specification. }, author = {Swamy,N. and Hicks, Michael W.} } @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 {18161, title = {Adaptive Detection for Group-Based Multimedia Fingerprinting}, journal = {Signal Processing Letters, IEEE}, volume = {14}, year = {2007}, month = {2007/12//}, pages = {964 - 967}, abstract = {Grouping strategy has been proposed recently to leverage the prior knowledge on collusion pattern to improve collusion resistance in multimedia fingerprinting. However, the improvement is not consistent, as reduced performance of the existing group-based fingerprinting schemes than the non-grouped ones is observed when the grouping does not match the true collusion pattern well. In this letter, we propose a new adaptive detection method, where the threshold for the group detection can be adjusted automatically according to the detection statistics that reflect the underlying collusion pattern. Experimental results show that the proposed adaptive detection outperforms nonadaptive detection and provides consistent performance improvement over non-grouped orthogonal fingerprinting schemes under various collusion scenarios.}, keywords = {adaptive, computing;security, data;, detection;collusion, detection;group-based, fingerprinting;copy, fingerprinting;grouping, multimedia, of, orthogonal, pattern;detection, protection;multimedia, statistics;group, strategy;nongrouped}, isbn = {1070-9908}, doi = {10.1109/LSP.2007.907992}, author = {He,Shan and M. Wu} } @conference {18165, title = {Analysis of Nonlinear Collusion Attacks on Fingerprinting Systems for Compressed Multimedia}, booktitle = {Image Processing, 2007. ICIP 2007. IEEE International Conference on}, volume = {2}, year = {2007}, month = {2007/10/16/19}, pages = {II -133 -II -136 - II -133 -II -136}, abstract = {In this paper, we analyze the effect of various collusion attacks on fingerprinting systems for compressed multimedia. We evaluate the effectiveness of the collusion attacks in terms of the probability of detection and accuracy in estimating the host signal. Our analysis shows that applying averaging collusion on copies of moderately compressed content gives a highly accurate estimation of the host, and can effectively remove the embedded fingerprints. Averaging is thus the best choice for an attacker as the probability of detection and the distortion introduced are the lowest.}, keywords = {attacks;data, coding;multimedia, coding;security, collusion, compressed, compression;image, data;watermarking;, fingerprinting, multimedia;data, of, systems;nonlinear}, doi = {10.1109/ICIP.2007.4379110}, author = {Varna,A.L. and He,Shan and Swaminathan,A. and M. Wu} } @article {14662, title = {Analyzing information flow}, journal = {Conference on Programming Language Design and Implementation: Proceedings of the 2007 workshop on Programming languages and analysis for security}, year = {2007}, month = {2007///}, author = {Hicks, Michael W.} } @article {14663, title = {Appendix to CMod: Modular Information Hiding and Type-Safe Linking for C}, journal = {Technical Reports of the Computer Science Department}, year = {2007}, month = {2007/06/30/undef}, abstract = {This brief note is an appendix to the paper "CMod: Modular Information Hiding and Type-Safe Linking for C." It consists of the proof of soundness for the formal language presented in that paper.}, author = {Srivastava,S. and Hicks, Michael W. and Foster, Jeffrey S.} } @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} } @conference {14664, title = {Automated detection of persistent kernel control-flow attacks}, booktitle = {Proceedings of the 14th ACM conference on Computer and communications security}, series = {CCS {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {103 - 115}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper presents a new approach to dynamically monitoring operating system kernel integrity, based on a property called state-based control-flow integrity (SBCFI). Violations of SBCFI signal a persistent, unexpected modification of the kernel{\textquoteright}s control-flow graph. We performed a thorough analysis of 25 Linux rootkits and found that 24 (96\%) employ persistent control-flow modifications; an informal study of Windows rootkits yielded similar results. We have implemented SBCFI enforcement as part of the Xen and VMware virtual machine monitors. Our implementation detected all the control-flow modifying rootkits we could install, while imposing unnoticeable overhead for both a typical web server workload and CPU-intensive workloads when operating at 10 second intervals.}, keywords = {CFI, integrity, Kernel, rootkit, virtualization}, isbn = {978-1-59593-703-2}, doi = {10.1145/1315245.1315260}, url = {http://doi.acm.org/10.1145/1315245.1315260}, author = {Petroni,Jr.,Nick L. and Hicks, Michael W.} } @conference {14808, title = {Automatic software interference detection in parallel applications}, booktitle = {Proceedings of the 2007 ACM/IEEE conference on Supercomputing}, series = {SC {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {14:1{\textendash}14:12 - 14:1{\textendash}14:12}, publisher = {ACM}, organization = {ACM}, address = {Reno, Nevada}, abstract = {We present an automated software interference detection methodology for Single Program, Multiple Data (SPMD) parallel applications. Interference comes from the system and unexpected processes. If not detected and corrected such interference may result in performance degradation. Our goal is to provide a reliable metric for software interference that can be used in soft-failure protection and recovery systems. A unique feature of our algorithm is that we measure the relative timing of application events (i.e. time between MPI calls) rather than system level events such as CPU utilization. This approach lets our system automatically accommodate natural variations in an application{\textquoteright}s utilization of resources. We use performance irregularities and degradation as signs of software interference. However, instead of relying on temporal changes in performance, our system detects spatial performance degradation across multiple processors. We also include a case study that demonstrates our technique{\textquoteright}s effectiveness, resilience and robustness.}, isbn = {978-1-59593-764-3}, doi = {10.1145/1362622.1362642}, author = {Tabatabaee, Vahid and Hollingsworth, Jeffrey K} } @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.} } @article {14556, title = {Cell breathing in wireless LANs: Algorithms and evaluation}, journal = {IEEE Transactions on Mobile Computing}, volume = {6}, year = {2007}, month = {2007///}, pages = {164 - 178}, author = {Hajiaghayi, Mohammad T. and Mirrokni,S. V. and Saberi,A. and Bahl,P. and Jain,K. and Qiu,L.} } @article {16238, title = {Characterization of Ehp, a Secreted Complement Inhibitory Protein from Staphylococcus aureus}, journal = {Journal of Biological Chemistry}, volume = {282}, year = {2007}, month = {2007/10/12/}, pages = {30051 - 30061}, abstract = {We report here the discovery and characterization of Ehp, a new secreted Staphylococcus aureus protein that potently inhibits the alternative complement activation pathway. Ehp was identified through a genomic scan as an uncharacterized secreted protein from S. aureus, and immunoblotting of conditioned S. aureus culture medium revealed that the Ehp protein was secreted at the highest levels during log-phase bacterial growth. The mature Ehp polypeptide is composed of 80 residues and is 44\% identical to the complement inhibitory domain of S. aureus Efb (extracellular fibrinogen-binding protein). We observed preferential binding by Ehp to native and hydrolyzed C3 relative to fully active C3b and found that Ehp formed a subnanomolar affinity complex with these various forms of C3 by binding to its thioester-containing C3d domain. Site-directed mutagenesis demonstrated that Arg75 and Asn82 are important in forming the Ehp{\textperiodcentered}C3d complex, but loss of these side chains did not completely disrupt Ehp/C3d binding. This suggested the presence of a second C3d-binding site in Ehp, which was mapped to the proximity of Ehp Asn63. Further molecular level details of the Ehp/C3d interaction were revealed by solving the 2.7-{\r A} crystal structure of an Ehp{\textperiodcentered}C3d complex in which the low affinity site had been mutationally inactivated. Ehp potently inhibited C3b deposition onto sensitized surfaces by the alternative complement activation pathway. This inhibition was directly related to Ehp/C3d binding and was more potent than that seen for Efb-C. An altered conformation in Ehp-bound C3 was detected by monoclonal antibody C3-9, which is specific for a neoantigen exposed in activated forms of C3. Our results suggest that increased inhibitory potency of Ehp relative to Efb-C is derived from the second C3-binding site in this new protein.}, doi = {10.1074/jbc.M704247200}, url = {http://www.jbc.org/content/282/41/30051.abstract}, author = {Hammel,Michal and Sfyroera,Georgia and Pyrpassopoulos,Serapion and Ricklin,Daniel and Ramyar,Kasra X. and Pop, Mihai and Jin,Zhongmin and Lambris,John D. and Geisbrecht,Brian V.} } @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 {18174, title = {Colluding Fingerprinted Video using the Gradient Attack}, booktitle = {Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on}, volume = {2}, year = {2007}, month = {2007/04//}, pages = {II-161 -II-164 - II-161 -II-164}, abstract = {Digital fingerprinting is an emerging tool to protect multimedia content from unauthorized distribution by embedding a unique fingerprint into each user{\textquoteright}s copy. Although several fingerprinting schemes have been proposed in related work, disproportional effort has been targeted towards identifying effective collusion attacks on fingerprinting schemes. Recent introduction of the gradient attack has refined the definition of an optimal attack and demonstrated strong effect on direct-sequence, uniformly distributed, and Gaussian spread spectrum fingerprints when applied to synthetic signals. In this paper, we apply the gradient attack on an existing well-engineered video fingerprinting scheme, refine the attack procedure, and demonstrate that the gradient attack is effective on Laplace fingerprints. Finally, we explore an improvement on fingerprint design to thwart the gradient attack. Results suggest that Laplace fingerprint should be avoided. However, we show that a signal mixed of Laplace and Gaussian fingerprints may serve as a design strategy to disable the gradient attack and force pirates into averaging as a form of adversary collusion.}, keywords = {attack;multimedia, attacks;digital, content, data;video, distribution;fingerprint, effort;gradient, fingerprinted, fingerprinting;disproportional, fingerprints;colluding, fingerprints;Laplace, Gaussian, identification;multimedia, of, processing;, protection;unauthorized, signal, spectrum, spread, systems;security, video;collusion}, doi = {10.1109/ICASSP.2007.366197}, author = {He,Shan and Kirovski,D. and M. Wu} } @conference {18177, title = {Collusion-Resistant Dynamic Fingerprinting for Multimedia}, booktitle = {Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on}, volume = {2}, year = {2007}, month = {2007/04//}, pages = {II-289 -II-292 - II-289 -II-292}, abstract = {This paper considers protecting multimedia content from unauthorized redistribution in subscription based services, where adversaries work together to pirate multiple multimedia programs during a subscription period. Collusion-resistant fingerprinting is an emerging tool for traitor tracing. However, most of the existing fingerprinting works did not consider multiple rounds of interaction between collusion and detection. In this paper, we exploit the temporal dimension and propose a dynamic fingerprinting scheme that adjusts the fingerprint design based on the detection result of previously pirated signal. We also examine colluders{\textquoteright} strategies to combat the tracing by dynamic fingerprinting. Both analytical and simulation results show that the proposed dynamic fingerprinting provides better collusion resistance than conventional static fingerprinting}, keywords = {based, collusion-resistant, communication;security, data;, dimension;traitor, dynamic, fingerprinting;multiple, multimedia, of, piracy;subscription, program, redistribution;multimedia, services;temporal, tracing;unauthorized}, doi = {10.1109/ICASSP.2007.366229}, author = {He,Shan and M. Wu} } @conference {18178, title = {Collusion-Resistant Fingerprinting for Compressed Multimedia Signals}, booktitle = {Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on}, volume = {2}, year = {2007}, month = {2007/04//}, pages = {II-165 -II-168 - II-165 -II-168}, abstract = {Most existing collusion-resistant fingerprinting techniques are for fingerprinting uncompressed signals. In this paper, we first study the performance of the traditional Gaussian based spread spectrum sequences for fingerprinting compressed signals and show that the system can be easily defeated by averaging or taking the median of a few copies. To overcome the collusion problem for compressed multimedia host signals, we propose a technique called anti-collusion dithering to mimic an uncompressed signal. Results show higher probability of catching a colluder using the proposed scheme compared to using Gaussian based fingerprints.}, keywords = {based, compression;Gaussian, compression;multimedia, dithering;collusion-resistant, fingerprinting;multimedia, Gaussian, processes;data, sequences;anticollusion, signals, spectrum, spread, systems;}, doi = {10.1109/ICASSP.2007.366198}, author = {Varna,A.L. and He,Shan and Swaminathan,A. and M. Wu and Lu,Haiming and Lu,Zengxiang} } @article {18181, title = {Collusion-Resistant Video Fingerprinting for Large User Group}, journal = {Information Forensics and Security, IEEE Transactions on}, volume = {2}, year = {2007}, month = {2007/12//}, pages = {697 - 709}, abstract = {Digital fingerprinting protects multimedia content from illegal redistribution by uniquely marking copies of the content distributed to users. Most existing multimedia fingerprinting schemes consider a user set on the scale of thousands. However, in such real-world applications as video-on-demand distribution, the number of potential users can be as many as 10-100 million. This large user size demands not only strong collusion resistance but also high efficiency in fingerprint construction, and detection, which makes most existing schemes incapable of being applied to these applications. A recently proposed joint coding and embedding fingerprinting framework provides a promising balance between collusion resistance, efficient construction, and detection, but several issues remain unsolved for applications involving a large group of users. In this paper, we explore how to employ the joint coding and embedding framework and develop practical algorithms to fingerprint video in such challenging settings as to accommodate more than ten million users and resist hundreds of users{\textquoteright} collusion. We investigate the proper code structure for large-scale fingerprinting and propose a trimming detection technique that can reduce the decoding computational complexity by more than three orders of magnitude at the cost of less than 0.5\% loss in detection probability under moderate to high watermark-to-noise ratios. Both analytic and experimental results show a high potential of joint coding and embedding to meet the needs of real-world large-scale fingerprinting applications.}, keywords = {code, coding-embedding, coding;video, communication;video, complexity;decoding;digital, complexity;digital, computational, content;trimming, demand;watermarking;, DETECTION, distribution;computational, fingerprinting, fingerprinting;decoding, fingerprinting;joint, framework;large, group;multimedia, identification;multimedia, on, signatures;fingerprint, structure;collusion-resistant, technique;video-on-demand, user, video}, isbn = {1556-6013}, doi = {10.1109/TIFS.2007.908179}, author = {He,Shan and M. Wu} } @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.} } @article {14600, title = {COMPUTATIONAL BIOLOGY}, journal = {Nucleic acids research}, volume = {35}, year = {2007}, month = {2007///}, pages = {3163 - 3163}, author = {Leparc,GG and Mitra,RD and Vardhanabhuti,S. and Wang,J. and Hannenhalli, Sridhar and Smit,S. and Widmann,J. and Knight,R. and Wu,S. and Zhang,Y. and others} } @article {15175, title = {Concurrently-secure blind signatures without random oracles or setup assumptions}, journal = {Theory of Cryptography}, year = {2007}, month = {2007///}, pages = {323 - 341}, abstract = {We show a new protocol for blind signatures in which security is preserved even under arbitrarily-many concurrent executions. The protocol can be based on standard cryptographic assumptions and is the first to be proven secure in a concurrent setting (under any assumptions) without random oracles or a trusted setup assumption such as a common reference string. Along the way, we also introduce new definitions of security for blind signature schemes.This research was supported by US-Israel Binational Science Foundation grant $\#$2004240. Work of the first author was also supported by an Eshkol fellowship from the Israel Ministry of Science and Technology. Work of the second author was also supported by NSF CAREER award $\#$0447075. }, doi = {10.1007/978-3-540-70936-7_18}, author = {Hazay,C. and Katz, Jonathan and Koo,C. Y and Lindell,Y.} } @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 {15904, title = {Confidentiality-preserving rank-ordered search}, booktitle = {Proceedings of the 2007 ACM workshop on Storage security and survivability}, series = {StorageSS {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {7 - 12}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper introduces a new framework for confidentiality preserving rank-ordered search and retrieval over large document collections. The proposed framework not only protects document/query confidentiality against an outside intruder, but also prevents an untrusted data center from learning information about the query and the document collection. We present practical techniques for proper integration of relevance scoring methods and cryptographic techniques, such as order preserving encryption, to protect data collections and indices and provide efficient and accurate search capabilities to securely rank-order documents in response to a query. Experimental results on the W3C collection show that these techniques have comparable performance to conventional search systems designed for non-encrypted data in terms of search accuracy. The proposed methods thus form the first steps to bring together advanced information retrieval and secure search capabilities for a wide range of applications including managing data in government and business operations, enabling scholarly study of sensitive data, and facilitating the document discovery process in litigation.}, keywords = {encrypted domain search, Ranked retrieval, secure index}, isbn = {978-1-59593-891-6}, doi = {10.1145/1314313.1314316}, url = {http://doi.acm.org/10.1145/1314313.1314316}, author = {Swaminathan,Ashwin and Mao,Yinian and Su,Guan-Ming and Gou,Hongmei and Varna,Avinash L. and He,Shan and M. Wu and Oard, Douglas} } @article {13361, title = {Data Management in the Worldwide Sensor Web}, journal = {IEEE Pervasive Computing}, volume = {6}, year = {2007}, month = {2007///}, pages = {30 - 40}, abstract = {Advances in hardware and miniaturization technologies have led to a rapid increase in the number of large-scale sensor network deployments around the world, bringing us closer to the vision of a worldwide sensor web. Exploiting the sensor web to its full potential, however, raises several hard data management challenges. Addressing these challenges requires a concerted multidisciplinary effort encompassing many computer science fields. This article outlines some of the key data management challenges of a worldwide sensor web. It also presents recent advances in data management research that aim to address these challenges. Hopefully, the scientific, ubiquitous computing, and sensor network communities will adopt some of these solutions for managing their data. The article also attempts to bring many of the remaining open issues to the attention of the database community. This article is part of a special issue on Building a Sensor-Rich World.}, keywords = {data modeling, data streams, data uncertainty, distributed systems, interoperability, sensor networks}, isbn = {1536-1268}, author = {Balazinska,Magdalena and Deshpande, Amol and Franklin,Michael J. and Gibbons,Phillip B. and Gray,Jim and Hansen,Mark and Liebhold,Michael and Nath,Suman and Szalay,Alexander and Tao,Vincent} } @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.} } @conference {14675, title = {Defeating script injection attacks with browser-enforced embedded policies}, booktitle = {Proceedings of the 16th international conference on World Wide Web}, series = {WWW {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {601 - 610}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Web sites that accept and display content such as wiki articles or comments typically filter the content to prevent injected script code from running in browsers that view the site. The diversity of browser rendering algorithms and the desire to allow rich content make filtering quite difficult, however, and attacks such as the Samy and Yamanner worms have exploited filtering weaknesses. This paper proposes a simple alternative mechanism for preventing script injection called Browser-Enforced Embedded Policies (BEEP). The idea is that a web site can embed a policy in its pages that specifies which scripts are allowed to run. The browser, which knows exactly when it will run a script, can enforce this policy perfectly. We have added BEEP support to several browsers, and built tools to simplify adding policies to web applications. We found that supporting BEEP in browsers requires only small and localized modifications, modifying web applications requires minimal effort, and enforcing policies is generally lightweight.}, keywords = {cross-site scripting, script injection, web application security}, isbn = {978-1-59593-654-7}, doi = {10.1145/1242572.1242654}, url = {http://doi.acm.org/10.1145/1242572.1242654}, author = {Jim,Trevor and Swamy,Nikhil and Hicks, Michael W.} } @article {18564, title = {Diagnosing network disruptions with network-wide analysis}, journal = {SIGMETRICS Perform. Eval. Rev.}, volume = {35}, year = {2007}, month = {2007/06//}, pages = {61 - 72}, abstract = {To maintain high availability in the face of changing network conditions, network operators must quickly detect, identify, and react to events that cause network disruptions. One way to accomplish this goal is to monitor routing dynamics, by analyzing routing update streams collected from routers. Existing monitoring approaches typically treat streams of routing updates from different routers as independent signals, and report only the "loud" events (i.e., events that involve large volume of routing messages). In this paper, we examine BGP routing data from all routers in the Abilene backbone for six months and correlate them with a catalog of all known disruptions to its nodes and links. We find that many important events are not loud enough to be detected from a single stream. Instead, they become detectable only when multiple BGP update streams are simultaneously examined. This is because routing updates exhibit network-wide dependencies. This paper proposes using network-wide analysis of routing information to diagnose (i.e., detect and identify) network disruptions. To detect network disruptions, we apply a multivariate analysis technique on dynamic routing information, (i.e., update traffic from all the Abilene routers) and find that this technique can detect every reported disruption to nodes and links within the network with a low rate of false alarms. To identify the type of disruption, we jointly analyze both the network-wide static configuration and details in the dynamic routing updates; we find that our method can correctly explain the scenario that caused the disruption. Although much work remains to make network-wide analysis of routing data operationally practical, our results illustrate the importance and potential of such an approach.}, keywords = {anomaly detection, network management, statistical inference}, isbn = {0163-5999}, doi = {10.1145/1269899.1254890}, url = {http://doi.acm.org/10.1145/1269899.1254890}, author = {Huang,Yiyi and Feamster, Nick and Lakhina,Anukool and Xu,Jim (Jun)} } @conference {13543, title = {Document Image Mosaicing with Mobile Phones}, booktitle = {International Conference on Image Analysis and Processing (ICIAP{\textquoteright}07)}, year = {2007}, month = {2007/09//}, pages = {1 - 8}, abstract = {This paper presents a novel user interaction oncept for document image scanning with mobile phones. A high resolution mosaic image is constructed in two main stages. Firstly, online camera motion estimation is applied on the phone to assist the user to capture small image batches of the document page. Automatic image stitching process with a help of estimated device motion is carried out to reconstruct the full view of the document. Experiments on document images captured and processed with the mosaicing software clearly show the feasibility of the approach.}, author = {Hannuksela,J. and Sangi,P. and Heikkila,J. and Liu,X. and David Doermann} } @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} } @article {12357, title = {Efficient simulation of critical synchronous dataflow graphs}, journal = {ACM Transactions on Design Automation of Electronic Systems (TODAES)}, volume = {12}, year = {2007}, month = {2007///}, pages = {1 - 28}, author = {Hsu,C. J and Ko,M. Y and Bhattacharyya, Shuvra S. and Ramasubbu,S. and Pino,J. L} } @article {17123, title = {eHealth Research from the User{\textquoteright}s Perspective}, journal = {American Journal of Preventive Medicine}, volume = {32}, year = {2007}, month = {2007/05//}, pages = {S97-S103 - S97-S103}, abstract = {The application of information technology (IT) to issues of healthcare delivery has had a long and tortuous history in the United States. Within the field of eHealth, vanguard applications of advanced computing techniques, such as applications in artificial intelligence or expert systems, have languished in spite of a track record of scholarly publication and decisional accuracy. The problem is one of purpose, of asking the right questions for the science to solve. Historically, many computer science pioneers have been tempted to ask {\textquotedblleft}what can the computer do?{\textquotedblright} New advances in eHealth are prompting developers to ask {\textquotedblleft}what can people do?{\textquotedblright} How can eHealth take part in national goals for healthcare reform to empower relationships between healthcare professionals and patients, healthcare teams and families, and hospitals and communities to improve health equitably throughout the population? To do this, eHealth researchers must combine best evidence from the user sciences (human factors engineering, human{\textendash}computer interaction, psychology, and usability) with best evidence in medicine to create transformational improvements in the quality of care that medicine offers. These improvements should follow recommendations from the Institute of Medicine to create a healthcare system that is (1) safe, (2) effective (evidence based), (3) patient centered, and (4) timely. Relying on the eHealth researcher{\textquoteright}s intuitive grasp of systems issues, improvements should be made with considerations of users and beneficiaries at the individual (patient{\textendash}physician), group (family{\textendash}staff), community, and broad environmental levels.}, isbn = {0749-3797}, doi = {10.1016/j.amepre.2007.01.019}, url = {http://www.sciencedirect.com/science/article/pii/S0749379707000487}, author = {Hesse,Bradford W. and Shneiderman, Ben} } @article {12118, title = {An Environment of Conducting Families of Software Engineering Experiments}, year = {2007}, month = {2007/05//}, institution = {University of Maryland, College Park}, abstract = {The classroom is a valuable resource for conducting software engineering experiments. However, coordinating a family of experiments in classroom environments presents a number of challenges to researchers. This paper describes an environment that simplifies the process of collecting, managing and sanitizing data from classroom experiments, while minimizing disruption to natural subject behavior. We have successfully used this environment to study the impact of parallel programming languages on programmer productivity at multiple universities across the United States.}, keywords = {collecting data, managing data, parallel programming languages, sanitizing data, software engineering experiments, universities}, url = {http://drum.lib.umd.edu/handle/1903/7545}, author = {Hochstein, Lorin and Nakamura,Taiga and Shull, Forrest and Zazworka, Nico and Voelp,Martin and Zelkowitz, Marvin V and Basili, Victor R.} } @article {14570, title = {Eukaryotic Transcriptional Regulation: Signals, Interactions, and Modules}, journal = {Computational genomics: current methods}, year = {2007}, month = {2007///}, pages = {21 - 21}, author = {Hannenhalli, Sridhar} } @article {16670, title = {Evaluating a cross-cultural children{\textquoteright}s online book community: Lessons learned for sociability, usability, and cultural exchange}, journal = {Interacting with Computers}, volume = {19}, year = {2007}, month = {2007/07//}, pages = {494 - 511}, abstract = {The use of computers for human-to-human communication among adults has been studied for many years, but using computer technology to enable children from all over the world to talk to each other has rarely been discussed by researchers. The goal of our research is to fill this gap and explore the design and evaluation of children{\textquoteright}s cross-language online communities via a case study of the International Children{\textquoteright}s Digital Library Communities (ICDLCommunities). This project supports the development of communities for children (ages 7{\textendash}11) that form around the International Digital Children{\textquoteright}s Library (ICDL) book collection. In this community the children can learn about each others{\textquoteright} cultures and make friends even if they do not speak the same language. They can also read and create stories and ask and answer questions about these. From this evaluation study we learned that: (i) children are very interested in their counterparts in other countries and a remarkable amount of communication takes place even when they do not share a common language; (ii) representing their identity online in many different forms is particularly important to children when communicating in an online community; (iii) children enjoy drawing but representing stories in a sequence of diagrams is challenging and needs support; and (iv) asking and answering questions without language is possible using graphical templates. In this paper we present our findings and make recommendations for designing children{\textquoteright}s cross-cultural online communities.}, keywords = {children, Cross-cultural, Evaluation and design, International Children{\textquoteright}s Digital Library, Online communities}, isbn = {0953-5438}, doi = {10.1016/j.intcom.2007.03.001}, url = {http://www.sciencedirect.com/science/article/pii/S0953543807000240}, author = {Komlodi,Anita and Hou,Weimin and Preece,Jenny and Druin, Allison and Golub,Evan and Alburo,Jade and Liao,Sabrina and Elkiss,Aaron and Resnik, Philip} } @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 {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} } @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.} } @article {14618, title = {Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex}, journal = {Genome Biology}, volume = {8}, year = {2007}, month = {2007/11/20/}, pages = {R247 - R247}, abstract = {The prefrontal cortex is important in regulating sleep and mood. Diurnally regulated genes in the prefrontal cortex may be controlled by the circadian system, by sleep:wake states, or by cellular metabolism or environmental responses. Bioinformatics analysis of these genes will provide insights into a wide-range of pathways that are involved in the pathophysiology of sleep disorders and psychiatric disorders with sleep disturbances.}, isbn = {1465-6906}, doi = {10.1186/gb-2007-8-11-r247}, url = {http://genomebiology.com/2007/8/11/R247}, author = {Yang,Shuzhang and Wang,Kai and Valladares,Otto and Hannenhalli, Sridhar and Bucan,Maja} } @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.} } @conference {15986, title = {Hood College, Master of Business Administration, 2005 Hood College, Master of Science (Computer Science), 2001 Hood College, Bachelor of Science (Computer Science), 1998 Frederick Community College, Associate in Arts (Business Administration), 1993}, booktitle = {Proceedings of the Workshop on Metareasoning in Agent-Based Systems}, year = {2007}, month = {2007///}, author = {Anderson,M. L and Schmill,M. and Oates,T. and Perlis, Don and Josyula,D. and Wright,D. and Human,S. W.T.D.N and Metacognition,L. and Fults,S. and Josyula,D. P} } @article {13149, title = {Human appearance modeling for matching across video sequences}, journal = {Machine Vision and Applications}, volume = {18}, year = {2007}, month = {2007///}, pages = {139 - 149}, abstract = {We present an appearance model for establishing correspondence between tracks of people which may be taken at different places, at different times or across different cameras. The appearance model is constructed by kernel density estimation. To incorporate structural information and to achieve invariance to motion and pose, besides color features, an additional feature of path-length is used. To achieve illumination invariance, two types of illumination insensitive color features are discussed: brightness color feature and RGB rank feature. The similarity between a test image and an appearance model is measured by the information gain or Kullback{\textendash}Leibler distance. To thoroughly represent the information contained in a video sequence with as little data as possible, a key frame selection and matching scheme is proposed. Experimental results demonstrate the important role of the path-length feature in the appearance model and the effectiveness of the proposed appearance model and matching method.}, author = {Yu,Y. and Harwood,D. and Yoon,K. and Davis, Larry S.} } @article {13156, title = {On implementing graph cuts on cuda}, journal = {First Workshop on General Purpose Processing on Graphics Processing Units}, year = {2007}, month = {2007///}, abstract = {The Compute Unified Device Architecture (CUDA)has enabled graphics processors to be explicitly programmed as general-purpose shared-memory multi-core processors with a high level of parallelism. In this paper, we present our preliminary results of implementing the Graph Cuts algorithm on CUDA. Our primary focus is on implementing Graph Cuts on grid graphs, which are extensively used in imaging applications. We first explain our implementation of breadth first search (BFS) graph traversal on CUDA, which is extensively used in our Graph Cuts implementation. We then present a basic implementation of Graph Cuts that succeeds to achieve absolute and relative speedups when used for foreground-background segmentation on synthesized images. Finally, we introduce two optimizations that utilize the special structure of grid graphs. The first one is lockstep BFS, which is used to reduce the overhead of BFS traversals. The second is cache emulation, which is a general technique to regularize memory access patterns and hence enhance memory access throughput. We experimentally show how each of the two optimizations can enhance the performance of the basic implementation on the image segmentation application. }, author = {Hussein,M. and Varshney, Amitabh and Davis, Larry S.} } @conference {14701, title = {Improving software quality with static analysis}, booktitle = {Proceedings of the 7th ACM SIGPLAN-SIGSOFT workshop on Program analysis for software tools and engineering}, series = {PASTE {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {83 - 84}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {At the University of Maryland, we have been working to improve the reliability and security of software by developing new, effective static analysis tools. These tools scan software for bug patterns or show that the software is free from a particular class of defects. There are two themes common to our different projects: 1. Our ultimate focus is on utility: can a programmer actually improve the quality of his or her software using an analysis tool? The important first step toward answering this question is to engineer tools so that they can analyze existing, nontrivial programs, and to carefully report the results of such analyses experimentally. The desire to better understand a more human-centered notion of utility underlies much of our future work. 2. We release all of our tools open source. This allows other researchers to verify our results, and to reuse some or all of our implementations, which often required significant effort to engineer. We believe that releasing source code is important for accelerating the pace of research results software quality, and just as importantly allows feedback from the wider community. In this research group presentation, we summarize some recent work and sketch future directions.}, keywords = {bug patterns, bugs, C, Data races, FFIs, java, modularity, network protocols, Software quality}, isbn = {978-1-59593-595-3}, doi = {10.1145/1251535.1251549}, url = {http://doi.acm.org/10.1145/1251535.1251549}, author = {Foster, Jeffrey S. and Hicks, Michael W. and Pugh, William} } @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.} } @article {18236, title = {Joint Uplink and Downlink Optimization for Real-Time Multiuser Video Streaming Over WLANs}, journal = {Selected Topics in Signal Processing, IEEE Journal of}, volume = {1}, year = {2007}, month = {2007/08//}, pages = {280 - 294}, abstract = {In this paper, a network-aware and source-aware video streaming system is proposed to support interactive multiuser communications within single-cell and multicell IEEE 802.11 networks. Unlike the traditional streaming video services, the strict delay constraints of an interactive video streaming system pose more challenges. These challenges include the heterogeneity of uplink and downlink channel conditions experienced by different users, the multiuser resource allocation of limited radio resources, the incorporation of the cross-layer design, and the diversity of content complexities exhibited by different video sequences. With the awareness of video content and network resources, the proposed system integrates cross-layer error protection mechanism and performs dynamic resource allocation across multiple users. We formulate the proposed system as to minimize the maximal end-to-end expected distortion received by all users, subject to maximal transmission power and delay constraints. To reduce the high dimensionality of the search space, fast multiuser algorithms are proposed to find the near-optimal solutions. Compared to the strategy without dynamically and jointly allocating bandwidth resource for uplinks and downlinks, the proposed framework outperforms by 2.18 7.95 dB in terms of the average received PSNR of all users and by 3.82 11.50 dB in terms of the lowest received PSNR among all users. Furthermore, the proposed scheme can provide more uniform video quality for all users and lower quality fluctuation for each received video sequence.}, keywords = {802.11, allocation;image, allocation;real-time, communications;maximal, distortion;multiuser, end-to-end, error, expected, IEEE, LAN;, mechanism;downlink, multiuser, networks;WLAN;cross-layer, optimization;interactive, optimization;video, Protection, quality;video, resource, sequences;video, streaming, streaming;uplink, streaming;wireless, system;bandwidth, video}, isbn = {1932-4553}, doi = {10.1109/JSTSP.2007.901518}, author = {Su,Guan-Ming and Han,Zhu and M. Wu and Liu,K. J.R} } @conference {18000, title = {Layout-Accurate Design and Implementation of a High-Throughput Interconnection Network for Single-Chip Parallel Processing}, booktitle = {High-Performance Interconnects, 2007. HOTI 2007. 15th Annual IEEE Symposium on}, year = {2007}, month = {2007/08//}, pages = {21 - 28}, abstract = {A mesh of trees (MoT) on-chip interconnection network has been proposed recently to provide high throughput between memory units and processors for single-chip parallel processing (Balkan et al., 2006). In this paper, we report our findings in bringing this concept to silicon. Specifically, we conduct cycle-accurate Verilog simulations to verify the analytical results claimed in (Balkan et al., 2006). We synthesize and obtain the layout of the MoT interconnection networks of various sizes. To further improve throughput, we investigate different arbitration primitives to handle load and store, the two most common memory operations. We also study the use of pipeline registers in large networks when there are long wires. Simulation based on full network layout demonstrates that significant throughput improvement can be achieved over the original proposed MoT interconnection network. The importance of this work lies in its validation of performance features of the MoT interconnection network, as they were previously shown to be competitive with traditional network solutions. The MoT network is currently used in an eXplicit multi-threading (XMT) on-chip parallel processor, which is engineered to support parallel programming. In that context, a 32-terminal MoT network could support up to 512 on-chip XMT processors. Our 8-terminal network that could serve 8 processor clusters (or 128 total processors), was also accepted recently for fabrication.}, keywords = {description, design;mesh, interconnection, languages;multi-threading;multiprocessor, MoT, multi-threading;layout-accurate, network;on-chip, network;Verilog, networks;parallel, of, on-chip, Parallel, processing;, processing;hardware, processor;parallel, processors;on-chip, programming;pipeline, registers;single-chip, simulations;eXplicit, TREES, XMT}, doi = {10.1109/HOTI.2007.11}, author = {Balkan,A.O. and Horak,M.N. and Gang Qu and Vishkin, Uzi} } @article {14129, title = {Least squares preconditioners for stabilized discretizations of the Navier-Stokes equations}, journal = {SIAM J. Sci. Comput}, volume = {30}, year = {2007}, month = {2007///}, pages = {290 - 311}, author = {Elman, Howard and Howle, V. E and Shadid, J. and Silvester, D. and Tuminaro, R.} } @article {18706, title = {Mapping the Interactions between Lys48 and Lys63-Linked Di-ubiquitins and a Ubiquitin-Interacting Motif of S5a}, journal = {Journal of Molecular Biology}, volume = {368}, year = {2007}, month = {2007/05/04/}, pages = {753 - 766}, abstract = {Numerous cellular processes are regulated by (poly)ubiquitin-mediated signaling events, which involve a covalent modification of the substrate protein by a single ubiquitin or a chain of ubiquitin molecules linked via a specific lysine. Remarkably, the outcome of polyubiquitination is linkage-dependent. For example, Lys48-linked chains are the principal signal for proteasomal degradation, while Lys63-linked chains act as nonproteolytic signals. Despite significant progress in characterization of various cellular pathways involving ubiquitin, understanding of the structural details of polyubiquitin chain recognition by downstream cellular effectors is missing. Here we use NMR to study the interaction of a ubiquitin-interacting motif (UIM) of the proteasomal subunit S5a with di-ubiquitin, the simplest model for polyubiquitin chain, to gain insights into the mechanism of polyubiquitin recognition by the proteasome. We have mapped the binding interface and characterized the stoichiometry and the process of UIM binding to Lys48- and Lys63-linked di-ubiquitin chains. Our data provide the first direct evidence that UIM binding involves a conformational transition in Lys48-linked di-ubiquitin, which opens the hydrophobic interdomain interface. This allows UIM to enter the interface and bind directly to the same ubiquitin hydrophobic-patch surface as utilized in UIM:monoubiquitin complexes. The results indicate that up to two UIM molecules can bind di-ubiquitin, and the binding interface between UIM and ubiquitin units in di-ubiquitin is essentially the same for both Lys48- and Lys63-linked chains. Our data suggest possible structural models for the binding of UIM and of full-length S5a to di-ubiquitin.}, keywords = {chemical shift perturbation mapping, polyubiquitin, S5a, ubiquitin, ubiquitin-interacting motif}, isbn = {0022-2836}, doi = {10.1016/j.jmb.2007.02.037}, url = {http://www.sciencedirect.com/science/article/pii/S0022283607002185}, author = {Haririnia,Aydin and D{\textquoteright}Onofrio,Mariapina and Fushman, David} } @conference {15910, title = {An M-channel directional filter bank compatible with the contourlet and shearlet frequency tiling}, booktitle = {Proceedings of SPIE}, volume = {6701}, year = {2007}, month = {2007///}, pages = {67010C - 67010C}, author = {Easley,G. R and Patel, Vishal M. and Healy Jr,D.M.} } @article {14586, title = {MetaProm: a neural network based meta-predictor for alternative human promoter prediction}, journal = {BMC Genomics}, volume = {8}, year = {2007}, month = {2007///}, pages = {374 - 374}, abstract = {BACKGROUND:De novo eukaryotic promoter prediction is important for discovering novel genes and understanding gene regulation. In spite of the great advances made in the past decade, recent studies revealed that the overall performances of the current promoter prediction programs (PPPs) are still poor, and predictions made by individual PPPs do not overlap each other. Furthermore, most PPPs are trained and tested on the most-upstream promoters; their performances on alternative promoters have not been assessed.RESULTS:In this paper, we evaluate the performances of current major promoter prediction programs (i.e., PSPA, FirstEF, McPromoter, DragonGSF, DragonPF, and FProm) using 42,536 distinct human gene promoters on a genome-wide scale, and with emphasis on alternative promoters. We describe an artificial neural network (ANN) based meta-predictor program that integrates predictions from the current PPPs and the predicted promoters{\textquoteright} relation to CpG islands. Our specific analysis of recently discovered alternative promoters reveals that although only 41\% of the 3{\textquoteright} most promoters overlap a CpG island, 74\% of 5{\textquoteright} most promoters overlap a CpG island.CONCLUSION:Our assessment of six PPPs on 1.06 x 109 bps of human genome sequence reveals the specific strengths and weaknesses of individual PPPs. Our meta-predictor outperforms any individual PPP in sensitivity and specificity. Furthermore, we discovered that the 5{\textquoteright} alternative promoters are more likely to be associated with a CpG island.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-8-374}, url = {http://www.biomedcentral.com/1471-2164/8/374}, author = {Wang,Junwen and Ungar,Lyle and Tseng,Hung and Hannenhalli, Sridhar} } @article {14711, title = {Mutatis Mutandis: Safe and predictable dynamic software updating}, journal = {ACM Trans. Program. Lang. Syst.}, volume = {29}, year = {2007}, month = {2007/08//}, abstract = {This article presents Proteus, a core calculus that models dynamic software updating, a service for fixing bugs and adding features to a running program. Proteus permits a program{\textquoteright}s type structure to change dynamically but guarantees the updated program remains type-correct by ensuring a property we call con-freeness. We show how con-freeness can be enforced dynamically, and how it can be approximated via a novel static analysis. This analysis can be used to assess the implications of a program{\textquoteright}s structure on future updates in order to make update success more predictable. We have implemented Proteus for C, and briefly discuss our implementation which we have tested on several well-known programs.}, keywords = {capability, dynamic software updating, proteus, Type inference, updateability analysis}, isbn = {0164-0925}, doi = {10.1145/1255450.1255455}, url = {http://doi.acm.org/10.1145/1255450.1255455}, author = {Stoyle,Gareth and Hicks, Michael W. and Bierman,Gavin and Sewell,Peter and Neamtiu,Iulian} } @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.} } @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} } @article {14555, title = {Oblivious routing on node-capacitated and directed graphs}, journal = {ACM Transactions on Algorithms (TALG)}, volume = {3}, year = {2007}, month = {2007///}, pages = {51{\textendash}es - 51{\textendash}es}, author = {Hajiaghayi, Mohammad T. and Kleinberg,R. D and R\{\"a}cke,H. and Leighton,T.} } @conference {14803, title = {Performance Measurement of Novice HPC Programmers Code}, booktitle = {Proceedings of the 3rd International Workshop on Software Engineering for High Performance Computing Applications}, series = {SE-HPC {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {3{\textendash} - 3{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, abstract = {Performance is one of the key factors of improving productivity in High Performance Computing (HPC). In this paper we discuss current studies in the field of performance measurement of codes captured in classroom experiments for the High Productivity Computing Project (HPCS). We give two examples of measurements introducing two new hypotheses: spending more effort doesn{\textquoteright}t always result in improvement of performance for novices; the use of higher level MPI functions promises better performance for novices. We also present a tool - the Automated Performance Measurement System (APMS). APMS helps to partially automate the measurement of the performance of a set of parallel programs with several inputs. The design and implementation of the tool is flexible enough to allow other researchers to conduct similar studies.}, keywords = {measurement, performance, performance measures, product metrics, program analysis}, isbn = {0-7695-2969-0}, doi = {http://dx.doi.org/10.1109/SE-HPC.2007.4}, url = {http://dx.doi.org/10.1109/SE-HPC.2007.4}, author = {Alameh, Rola and Zazworka, Nico and Hollingsworth, Jeffrey K} } @conference {19040, title = {Portcullis: protecting connection setup from denial-of-capability attacks}, series = {SIGCOMM {\textquoteright}07}, year = {2007}, month = {2007}, pages = {289 - 300}, publisher = {ACM}, organization = {ACM}, abstract = {Systems using capabilities to provide preferential service to selected flows have been proposed as a defense against large-scale network denial-of-service attacks. While these systems offer strong protection for established network flows, the Denial-of-Capability (DoC) attack, which prevents new capability-setup packets from reaching the destination, limits the value of these systems. Portcullis mitigates DoC attacks by allocating scarce link bandwidth for connection establishment packets based on per-computation fairness. We prove that a legitimate sender can establish a capability with high probability regardless of an attacker{\textquoteright}s resources or strategy and that no system can improve on our guarantee. We simulate full and partial deployments of Portcullis on an Internet-scale topology to confirm our theoretical results and demonstrate the substantial benefits of using per-computation fairness.}, keywords = {network capability, per-computation fairness}, isbn = {978-1-59593-713-1}, url = {http://doi.acm.org/10.1145/1282380.1282413}, author = {Parno, Bryan and Wendlandt, Dan and Elaine Shi and Perrig, Adrian and Maggs, Bruce and Hu, Yih-Chun} } @article {14582, title = {Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation}, journal = {Nucleic Acids Research}, volume = {35}, year = {2007}, month = {2007/05/01/}, pages = {3203 - 3213}, abstract = {Computational discovery of cis-regulatory elements remains challenging. To cope with the high false positives, evolutionary conservation is routinely used. However, conservation is only one of the attributes of cis-regulatory elements and is neither necessary nor sufficient. Here, we assess two additional attributes{\textemdash}positional and inter-motif distance specificity{\textemdash}that are critical for interactions between transcription factors. We first show that for a greater than expected fraction of known motifs, the genes that contain the motifs in their promoters in a position-specific or distance-specific manner are related, both in function and/or in expression pattern. We then use the position and distance specificity to discover novel motifs. Our work highlights the importance of distance and position specificity, in addition to the evolutionary conservation, in discovering cis-regulatory motifs.}, doi = {10.1093/nar/gkm201}, url = {http://nar.oxfordjournals.org/content/35/10/3203.abstract}, author = {Vardhanabhuti,Saran and Wang,Junwen and Hannenhalli, Sridhar} } @article {14561, title = {Power optimization in fault-tolerant topology control algorithms for wireless multi-hop networks}, journal = {IEEE/ACM Transactions on Networking (TON)}, volume = {15}, year = {2007}, month = {2007///}, pages = {1345 - 1358}, author = {Hajiaghayi, Mohammad T. and Immorlica,N. and Mirrokni,V. S} } @article {12362, title = {Probabilistic design of multimedia embedded systems}, journal = {ACM Transactions on Embedded Computing Systems (TECS)}, volume = {6}, year = {2007}, month = {2007///}, pages = {15{\textendash}es - 15{\textendash}es}, author = {Hua,S. and Qu,G. and Bhattacharyya, Shuvra S.} } @conference {13140, title = {Probabilistic Fusion Tracking Using Mixture Kernel-Based Bayesian Filtering}, booktitle = {Computer Vision, 2007. ICCV 2007. IEEE 11th International Conference on}, year = {2007}, month = {2007/10//}, pages = {1 - 8}, abstract = {Even though sensor fusion techniques based on particle filters have been applied to object tracking, their implementations have been limited to combining measurements from multiple sensors by the simple product of individual likelihoods. Therefore, the number of observations is increased as many times as the number of sensors, and the combined observation may become unreliable through blind integration of sensor observations - especially if some sensors are too noisy and non-discriminative. We describe a methodology to model interactions between multiple sensors and to estimate the current state by using a mixture of Bayesian filters - one filter for each sensor, where each filter makes a different level of contribution to estimate the combined posterior in a reliable manner. In this framework, an adaptive particle arrangement system is constructed in which each particle is allocated to only one of the sensors for observation and a different number of samples is assigned to each sensor using prior distribution and partial observations. We apply this technique to visual tracking in logical and physical sensor fusion frameworks, and demonstrate its effectiveness through tracking results.}, keywords = {(numerical, adaptive, arrangement, Bayesian, Filtering, filtering;multiple, filters;probabilistic, fusion, fusion;tracking;, integration;mixture, kernel-based, methods);sensor, methods;array, particle, processing;particle, sensors;object, signal, system;blind, techniques;visual, tracking;Bayes, tracking;particle, tracking;sensor}, doi = {10.1109/ICCV.2007.4408938}, author = {Han,Bohyung and Joo,Seong-Wook and Davis, Larry S.} } @article {14366, title = {Probabilistic interval XML}, journal = {ACM Transactions on Computational Logic (TOCL)}, volume = {8}, year = {2007}, month = {2007/08//}, abstract = {Interest in XML databases has been expanding rapidly over the last few years. In this paper, we study the problem of incorporating probabilistic information into XML databases. We propose the Probabilistic Interval XML (PIXML for short) data model in this paper. Using this data model, users can express probabilistic information within XML markups. In addition, we provide two alternative formal model-theoretic semantics for PIXML data. The first semantics is a {\textquotedblleft}global{\textquotedblright} semantics which is relatively intuitive, but is not directly amenable to computation. The second semantics is a {\textquotedblleft}local{\textquotedblright} semantics which supports efficient computation. We prove several correspondence results between the two semantics. To our knowledge, this is the first formal model theoretic semantics for probabilistic interval XML. We then provide an operational semantics that may be used to compute answers to queries and that is correct for a large class of probabilistic instances.}, keywords = {Semistructured Databases, XML}, isbn = {1529-3785}, doi = {10.1145/1276920.1276926}, url = {http://doi.acm.org/10.1145/1276920.1276926}, author = {Hung,Edward and Getoor, Lise and V.S. Subrahmanian} } @inbook {17646, title = {Randomized Algorithms and Probabilistic Analysis in Wireless Networking}, booktitle = {Stochastic Algorithms: Foundations and ApplicationsStochastic Algorithms: Foundations and Applications}, series = {Lecture Notes in Computer Science}, volume = {4665}, year = {2007}, month = {2007///}, pages = {54 - 57}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Devices connected wirelessly, in various forms including computers, hand-held devices, ad hoc networks, and embedded systems, are expected to become ubiquitous all around us. Wireless networks pose interesting new challenges, some of which do not arise in standard (wired) networks. This survey discusses some key probabilistic notions {\textendash} both randomized algorithms and probabilistic analysis {\textendash} in wireless networking.}, isbn = {978-3-540-74870-0}, url = {http://dx.doi.org/10.1007/978-3-540-74871-7_5}, author = {Srinivasan, Aravind}, editor = {Hromkovic,Juraj and Kr{\'a}lovic,Richard and Nunkesser,Marc and Widmayer,Peter} } @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 {14544, title = {Scheduling to minimize gaps and power consumption}, booktitle = {Proceedings of the nineteenth annual ACM symposium on Parallel algorithms and architectures}, year = {2007}, month = {2007///}, pages = {46 - 54}, author = {Demaine,E. D and Ghodsi,M. and Hajiaghayi, Mohammad T. and Sayedi-Roshkhar,A. S and Zadimoghaddam,M.} } @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 {13270, title = {A semantic web environment for digital shapes understanding}, booktitle = {Proceedings of the semantic and digital media technologies 2nd international conference on Semantic Multimedia}, series = {SAMT{\textquoteright}07}, year = {2007}, month = {2007///}, pages = {226 - 239}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {Berlin, Heidelberg}, abstract = {In the last few years, the volume of multimedia content available on the Web significantly increased. This led to the need for techniques to handle such data. In this context, we see a growing interest in considering the Semantic Web in action and in the definition of tools capable of analyzing and organizing digital shape models. In this paper, we present a Semantic Web environment, be-SMART, for inspecting 3D shapes and for structuring and annotating such shapes according to ontology-driven metadata. Specifically, we describe in details the first module of be-SMART, the Geometry and Topology Analyzer, and the algorithms we have developed for extracting geometrical and topological information from 3D shapes. We also describe the second module, the Topological Decomposer, which produces a graph-based representation of the decomposition of the shape into manifold components. This is successively modified by the third and the fourth modules, which perform the automatic and manual segmentation of the manifold parts.}, keywords = {digital shapes, semantic annotation, semantic web, shape analysis, shape understanding}, isbn = {3-540-77033-X, 978-3-540-77033-6}, url = {http://dl.acm.org/citation.cfm?id=1780533.1780565}, author = {De Floriani, Leila and Hui,Annie and Papaleo,Laura and Huang,May and Hendler,James} } @conference {16299, title = {Software configuration management using ontologies}, booktitle = {3rd International Workshop on Semantic Web Enabled Software Engineering (SWESE 2007), Innsubruk, Austria}, year = {2007}, month = {2007///}, author = {Shahri,H. H and Hendler,J. A and Porter, Adam} } @article {18998, title = {Spliceosomal small nuclear RNA genes in 11 insect genomes}, journal = {RNARNA}, volume = {13}, year = {2007}, month = {2007/01/01/}, pages = {5 - 14}, abstract = {A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms}, keywords = {honeybee, Insecta, secondary structure, snRNA, spliceosomal snRNA, U12 introns}, isbn = {1355-8382, 1469-9001}, doi = {10.1261/rna.259207}, url = {http://rnajournal.cshlp.org/content/13/1/5}, author = {Mount, Stephen M. and Gotea,Valer and Lin,Chiao-Feng and Hernandez,Kristina and Maka{\l}owski,Wojciech} } @article {13922, title = {Supporting elementary-age children{\textquoteright}s searching and browsing: Design and evaluation using the international children{\textquoteright}s digital library}, journal = {Journal of the American Society for Information Science and Technology}, volume = {58}, year = {2007}, month = {2007///}, pages = {1618 - 1630}, author = {Hutchinson,H.B. and Druin, Allison and Bederson, Benjamin B.} } @article {16523, title = {Swarm Intelligence Systems Using Guided Self-Organization for Collective Problem Solving}, journal = {Advances in Complex Systems}, volume = {10}, year = {2007}, month = {2007///}, pages = {5 - 34}, author = {RodrIGuez,A. and Grushin,A. and Reggia, James A. and HAUPTMAN,AMI and SIPPER,M. and PAN,Z. and Reggia, James A. and GAO,D. and DARABOS,C. and GIACOBINI,M. and others} } @article {13870, title = {Task-based evaluation of text summarization using Relevance Prediction}, journal = {Information Processing \& Management}, volume = {43}, year = {2007}, month = {2007/11//}, pages = {1482 - 1499}, abstract = {This article introduces a new task-based evaluation measure called Relevance Prediction that is a more intuitive measure of an individual{\textquoteright}s performance on a real-world task than interannotator agreement. Relevance Prediction parallels what a user does in the real world task of browsing a set of documents using standard search tools, i.e., the user judges relevance based on a short summary and then that same user{\textemdash}not an independent user{\textemdash}decides whether to open (and judge) the corresponding document. This measure is shown to be a more reliable measure of task performance than LDC Agreement, a current gold-standard based measure used in the summarization evaluation community. Our goal is to provide a stable framework within which developers of new automatic measures may make stronger statistical statements about the effectiveness of their measures in predicting summary usefulness. We demonstrate{\textemdash}as a proof-of-concept methodology for automatic metric developers{\textemdash}that a current automatic evaluation measure has a better correlation with Relevance Prediction than with LDC Agreement and that the significance level for detected differences is higher for the former than for the latter.}, keywords = {Relevance prediction, Summarization evaluation, Summary usefulness}, isbn = {0306-4573}, doi = {10.1016/j.ipm.2007.01.002}, url = {http://www.sciencedirect.com/science/article/pii/S0306457307000234}, author = {Hobson,Stacy President and Dorr, Bonnie J and Monz,Christof and Schwartz,Richard} } @article {16322, title = {Techniques for Classifying Executions of Deployed Software to Support Software Engineering Tasks}, journal = {IEEE Transactions on Software Engineering}, volume = {33}, year = {2007}, month = {2007///}, pages = {287 - 304}, abstract = {There is an increasing interest in techniques that support analysis and measurement of fielded software systems. These techniques typically deploy numerous instrumented instances of a software system, collect execution data when the instances run in the field, and analyze the remotely collected data to better understand the system{\textquoteright}s in-the-field behavior. One common need for these techniques is the ability to distinguish execution outcomes (e.g., to collect only data corresponding to some behavior or to determine how often and under which condition a specific behavior occurs). Most current approaches, however, do not perform any kind of classification of remote executions and either focus on easily observable behaviors (e.g., crashes) or assume that outcomes{\textquoteright} classifications are externally provided (e.g., by the users). To address the limitations of existing approaches, we have developed three techniques for automatically classifying execution data as belonging to one of several classes. In this paper, we introduce our techniques and apply them to the binary classification of passing and failing behaviors. Our three techniques impose different overheads on program instances and, thus, each is appropriate for different application scenarios. We performed several empirical studies to evaluate and refine our techniques and to investigate the trade-offs among them. Our results show that 1) the first technique can build very accurate models, but requires a complete set of execution data; 2) the second technique produces slightly less accurate models, but needs only a small fraction of the total execution data; and 3) the third technique allows for even further cost reductions by building the models incrementally, but requires some sequential ordering of the software instances{\textquoteright} instrumentation.}, keywords = {execution classification, remote analysis/measurement.}, isbn = {0098-5589}, doi = {http://doi.ieeecomputersociety.org/10.1109/TSE.2007.1004}, author = {Haran,Murali and Karr,Alan and Last,Michael and Orso,Alessandro and Porter, Adam and Sanil,Ashish and Fouch?,Sandro} } @article {13338, title = {Topological Decompositions for 3D Non-manifold Simplicial Shapes}, volume = {CS-TR-4855}, year = {2007}, month = {2007/02/06/}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {Modeling and understanding complex non-manifold shapes is a key issue in several applications including form-feature identification in CAD/CAE, and shape recognition for Web searching. Geometric shapes are commonly discretized as simplicial 2- or 3-complexes embedded in the 3D Euclidean space. The topological structure of a non-manifold simplicial shape can be analyzed through its decomposition into a collection of components with simpler topology. The granularity of the decomposition depends on the combinatorial complexity of the components. In this paper, we present topological tools for structural analysis of three-dimensional non-manifold shapes. This analysis is based on a topological decomposition at two different levels. We discuss the topological properties of the components at each level, and we present algorithms for computing such decompositions. We investigate the relations among the components, and propose a graph-based representation for such relations.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/7429}, author = {Hui,Annie and De Floriani, Leila} } @article {14746, title = {Toward Specifying and Validating Cross-Domain Policies}, journal = {Technical Reports from UMIACS}, year = {2007}, month = {2007/04/17/undef}, abstract = {Formal security policies are extremely useful for two related reasons. First, they allow a policy to be considered in isolation, separate from programs under the purview of the policy and separate from the implementation of the policy{\textquoteright}s enforcement. Second, policies can be checked for compliance against higher-level security goals by using automated analyses. By contrast, ad hoc enforcement mechanisms (for which no separate policies are specified) enjoy neither benefit, and non-formal policies enjoy the first but not the second. We would like to understand how best to define (and enforce) multi-level security policies when information must be shared across domains that have varying levels of trust (the so-called "cross domain" problem). Because we wish to show such policies meet higher-level security goals with high assurance, we are interested in specifying cross domain policies formally, and then reasoning about them using automated tools. In this report, we briefly survey work that presents formal security policies with cross-domain concerns, in particular with respect to the problem of downgrading. We also describe correctness properties for such policies, all based on noninterference. Finally, we briefly discuss recently-developed tools for analyzing formal security policies; though no existing tools focus on the analysis of downgrading-oriented policies, existing research points the way to providing such support.}, author = {Hicks, Michael W. and Swamy,N. and Tsang,S.} } @conference {13340, title = {Towards a semantic web system for understanding real world representations}, booktitle = {Proceedings of the Tenth International Conference on Computer Graphics and Artificial Intelligence}, year = {2007}, month = {2007///}, abstract = {As the volume of multimedia content available on the Web continues to increase, there is a clearneed for more advanced techniques for effective retrieval and management of such data. In this context, we see a growing interest in exploiting the potential of the Semantic Web in different research fields. But, on the other hand, there is a general lack of tools able to analyse, organize and understand digital shape models (especially 3D models) for easily populating repositories with complete and well-detailed metadata. Several steps are necessary to create and associate semantics with a shape and some of them are clearly context-dependent. In this paper, we present the design details of our new system, that we call be-SMART, for inspecting digital 3D shapes by extracting geometrical and topological information from them and for structuring and annotating these shapes using ontology-driven metadata. In particular, we describe the general structure of the system, the different modules and their mutual relations. We then concentrate on the first two modules of the system showing how the 3D models are annotated following ontology-driven metadata. We also provide motivations for further work in developing new techniques for both annotating and managing 3D models on the Web. }, author = {Papaleo,L. and De Floriani, Leila and Hendler,J. and Hui,A.} } @article {14567, title = {TREMOR{\textemdash}a tool for retrieving transcriptional modules by incorporating motif covariance}, journal = {Nucleic Acids Research}, volume = {35}, year = {2007}, month = {2007/12/01/}, pages = {7360 - 7371}, abstract = {A transcriptional module (TM) is a collection of transcription factors (TF) that as a group, co-regulate multiple, functionally related genes. The task of identifying TMs poses an important biological challenge. Since TFs belong to evolutionarily and structurally related families, TF family members often bind to similar DNA motifs and can confound sequence-based approaches to TM identification. A previous approach to TM detection addresses this issue by pre-selecting a single representative from each TF family. One problem with this approach is that closely related transcription factors can still target sufficiently distinct genes in a biologically meaningful way, and thus, pre-selecting a single family representative may in principle miss certain TMs. Here we report a method{\textemdash}TREMOR (Transcriptional Regulatory Module Retriever). This method uses the Mahalanobis distance to assess the validity of a TM and automatically incorporates the inter-TF binding similarity without resorting to pre-selecting family representatives. The application of TREMOR on human muscle-specific, liver-specific and cell-cycle-related genes reveals TFs and TMs that were validated from literature and also reveals additional related genes.}, doi = {10.1093/nar/gkm885}, url = {http://nar.oxfordjournals.org/content/35/21/7360.abstract}, author = {Singh,Larry N. and Wang,Li-San and Hannenhalli, Sridhar} } @conference {13273, title = {A two-level topological decomposition for non-manifold simplicial shapes}, booktitle = {Proceedings of the 2007 ACM symposium on Solid and physical modeling}, series = {SPM {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {355 - 360}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Modeling and understanding complex non-manifold shapes is a key issue in shape analysis. Geometric shapes are commonly discretized as two- or three-dimensional simplicial complexes embedded in the 3D Euclidean space. The topological structure of a nonmanifold simplicial shape can be analyzed through its decomposition into a collection of components with a simpler topology. Here, we present a topological decomposition of a shape at two different levels, with different degrees of granularity. We discuss the topological properties of the components at each level, and we present algorithms for computing such decompositions. We investigate the relations among the components, and propose a graph-based representation for such relations.}, keywords = {Non-manifold modeling, shape decomposition, shape modeling, simplicial complexes}, isbn = {978-1-59593-666-0}, doi = {10.1145/1236246.1236297}, url = {http://doi.acm.org/10.1145/1236246.1236297}, author = {Hui,Annie and De Floriani, Leila} } @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 {15141, title = {Universally-composable two-party computation in two rounds}, booktitle = {Proceedings of the 27th annual international cryptology conference on Advances in cryptology}, series = {CRYPTO{\textquoteright}07}, year = {2007}, month = {2007///}, pages = {111 - 129}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {Berlin, Heidelberg}, abstract = {Round complexity is a central measure of efficiency, and characterizing the round complexity of various cryptographic tasks is of both theoretical and practical importance. We show here a universally-composable (UC) protocol (in the common reference string model) for two-party computation of any functionality, where both parties receive output, using only two rounds. (This assumes honest parties are allowed to transmit messages simultaneously in any given round; we obtain a three-round protocol when parties are required to alternate messages.) Our results match the obvious lower bounds for the round complexity of secure two-party computation under any reasonable definition of security, regardless of what setup is used. Thus, our results establish that secure two-party computation can be obtained under a commonly-used setup assumption with maximal security (i.e., security under general composition) in a minimal number of rounds. To give but one example of the power of our general result, we observe that as an almost immediate corollary we obtain a two-round UC blind signature scheme, matching a result by Fischlin at Crypto 2006 (though, in contrast to Fischlin, we use specific number-theoretic assumptions).}, isbn = {3-540-74142-9, 978-3-540-74142-8}, url = {http://dl.acm.org/citation.cfm?id=1777777.1777788}, author = {Horvitz,Omer and Katz, Jonathan} } @article {16846, title = {Using a distributed quadtree index in peer-to-peer networks}, journal = {The VLDB Journal}, volume = {16}, year = {2007}, month = {2007/04//}, pages = {165 - 178}, abstract = {Peer-to-peer (P2P) networks have become a powerful means for online data exchange. Currently, users are primarily utilizing these networks to perform exact-match queries and retrieve complete files. However, future more data intensive applications, such as P2P auction networks, P2P job-search networks, P2P multiplayer games, will require the capability to respond to more complex queries such as range queries involving numerous data types including those that have a spatial component. In this paper, a distributed quadtree index that adapts the MX-CIF quadtree is described that enables more powerful accesses to data in P2P networks. This index has been implemented for various prototype P2P applications and results of experiments are presented. Our index is easy to use, scalable, and exhibits good load-balancing properties. Similar indices can be constructed for various multidimensional data types with both spatial and non-spatial components.}, keywords = {Distributed data structures, peer-to-peer networks, quadtrees, spatial data structures}, isbn = {1066-8888}, doi = {10.1007/s00778-005-0001-y}, url = {http://dx.doi.org/10.1007/s00778-005-0001-y}, author = {Tanin,Egemen and Harwood,Aaron and Samet, Hanan} } @article {14572, title = {Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes}, journal = {Virology}, volume = {365}, year = {2007}, month = {2007/08/15/}, pages = {60 - 69}, abstract = {Topoisomerase enzymes regulate superhelical tension in DNA resulting from transcription, replication, repair, and other molecular transactions. Poxviruses encode an unusual type IB topoisomerase that acts only at conserved DNA sequences containing the core pentanucleotide 5{\textquoteright}-(T/C)CCTT-3{\textquoteright}. In X-ray structures of the variola virus topoisomerase bound to DNA, protein-DNA contacts were found to extend beyond the core pentanucleotide, indicating that the full recognition site has not yet been fully defined in functional studies. Here we report quantitation of DNA cleavage rates for an optimized 13~bp site and for all possible single base substitutions (40 total sites), with the goals of understanding the molecular mechanism of recognition and mapping topoisomerase sites in poxvirus genome sequences. The data allow a precise definition of enzyme-DNA interactions and the energetic contributions of each. We then used the resulting "action matrix" to show that favorable topoisomerase sites are distributed all along the length of poxvirus DNA sequences, consistent with a requirement for local release of superhelical tension in constrained topological domains. In orthopox genomes, an additional central cluster of sites was also evident. A negative correlation of predicted topoisomerase sites was seen relative to early terminators, but no correlation was seen with early or late promoters. These data define the full variola virus topoisomerase recognition site and provide a new window on topoisomerase function in vivo.}, keywords = {Annotation of topoisomerase sites, Sequence specific recognition, Topoisomerase IB, Variola virus}, isbn = {0042-6822}, doi = {16/j.virol.2007.02.037}, url = {http://www.sciencedirect.com/science/article/pii/S0042682207001225}, author = {Minkah,Nana and Hwang,Young and Perry,Kay and Van Duyne,Gregory D. and Hendrickson,Robert and Lefkowitz,Elliot J. and Hannenhalli, Sridhar and Bushman,Frederic D.} } @conference {14755, title = {Verified Enforcement of Security Policies for Cross-Domain Information Flows}, booktitle = {IEEE Military Communications Conference, 2007. MILCOM 2007}, year = {2007}, month = {2007/10/29/31}, pages = {1 - 7}, publisher = {IEEE}, organization = {IEEE}, abstract = {We describe work in progress that uses program analysis to show that security-critical programs, such as cross-domain guards, correctly enforce cross-domain security policies. We are enhancing existing techniques from the field of Security-oriented Programming Languages to construct a new language for the construction of secure networked applications, SELINKS. In order to specify and enforce expressive and fine-grained policies, we advocate dynamically associating security labels with sensitive entities. Programs written in SELINKS are statically guaranteed to correctly manipulate an entity{\textquoteright}s security labels and to ensure that the appropriate policy checks mediate all operations that are performed on the entity. We discuss the design of our main case study : a web-based Collaborative Planning Application that will permit a collection of users, with varying security requirements and clearances, to access sensitive data sources and collaboratively create documents based on these sources.}, keywords = {Collaboration, Computer languages, Data security, Educational institutions, Government, Information analysis, Information filtering, Information filters, Information security, Vehicles}, isbn = {978-1-4244-1513-7}, doi = {10.1109/MILCOM.2007.4455189}, author = {Swamy,Nikhil and Hicks, Michael W. and Tsang,Simon} } @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 {13723, title = {Annotation compatibility working group report}, booktitle = {Proceedings of the Workshop on Frontiers in Linguistically Annotated Corpora 2006}, series = {LAC {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {38 - 53}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This report explores the question of compatibility between annotation projects including translating annotation formalisms to each other or to common forms. Compatibility issues are crucial for systems that use the results of multiple annotation projects. We hope that this report will begin a concerted effort in the field to track the compatibility of annotation schemes for part of speech tagging, time annotation, treebanking, role labeling and other phenomena.}, isbn = {1-932432-78-7}, url = {http://dl.acm.org/citation.cfm?id=1641991.1641997}, author = {Meyers,A. and Fang,A. C. and Ferro,L. and K{\"u}bler,S. and Jia-Lin,T. and Palmer,M. and Poesio,M. and Dolbey,A. and Schuler,K. K. and Loper,E. and Zinsmeister,H. and Penn,G. and Xue,N. and Hinrichs,E. and Wiebe,J. and Pustejovsky,J. and Farwell,D. and Hajicova,E. and Dorr, Bonnie J and Hovy,E. and Onyshkevych,B. A. and Levin,L.} } @article {13170, title = {Appearance-based person recognition using color/path-length profile}, journal = {Journal of Visual Communication and Image Representation}, volume = {17}, year = {2006}, month = {2006///}, pages = {605 - 622}, author = {Yoon,K. and Harwood,D. and Davis, Larry S.} } @inbook {19624, title = {Applications of Parameterized st-Orientations in Graph Drawing Algorithms}, booktitle = {Graph Drawing}, series = {Lecture Notes in Computer Science}, year = {2006}, month = {2006/01/01/}, pages = {355 - 367}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Many graph drawing algorithms use st-numberings (st-orien-tations or bipolar orientations) as a first step. An st-numbering of a biconnected undirected graph defines a directed graph with no cycles, one single source s and one single sink t. As there exist exponentially many st-numberings that correspond to a certain undirected graph G, using different st-numberings in various graph drawing algorithms can result in aesthetically different drawings with different area bounds. In this paper, we present results concerning new algorithms for parameterized st-orientations, their impact on graph drawing algorithms and especially in visibility representations.}, keywords = {Algorithm Analysis and Problem Complexity, Computer Graphics, Data structures, Discrete Mathematics in Computer Science}, isbn = {978-3-540-31425-7, 978-3-540-31667-1}, url = {http://link.springer.com/chapter/10.1007/11618058_32}, author = {Charalampos Papamanthou and Tollis, Ioannis G.}, editor = {Healy, Patrick and Nikolov, Nikola S.} } @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 {16352, title = {Atomic instructions in java}, journal = {ECOOP 2002{\textemdash}Object-Oriented Programming}, year = {2006}, month = {2006///}, pages = {5 - 16}, author = {Hovemeyer,D. and Pugh, William and Spacco,J.} } @article {18874, title = {Automatic web services composition using Shop2}, year = {2006}, month = {2006///}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {Semantic markup of Web services will enable the automation of various kinds of tasks, including discovery, composition, and execution of Web services. We describe how an AI planning system (SHOP2) can be used with DAML-S Web service descriptions to automatically compose Web services.}, url = {http://www.stormingmedia.us/96/9697/A969744.html}, author = {Hendler,J. and Nau, Dana S. and Parsia,B. and Sirin,E. and Wu,D.} } @article {14140, title = {Block preconditioners based on approximate commutators}, journal = {SIAM Journal on Scientific Computing}, volume = {27}, year = {2006}, month = {2006///}, pages = {1651 - 1668}, author = {Elman, Howard and Howle, V. E and Shadid, J. and Shuttleworth, R. and Tuminaro, R.} } @article {16866, title = {Building and querying a P2P virtual world}, journal = {Geoinformatica}, volume = {10}, year = {2006}, month = {2006///}, pages = {91 - 116}, abstract = {Peer-to-Peer (P2P) systems are known to provide excellent scalability in a networked environment. One peer is introduced to the system by each participant. However current P2P applications can only provide file sharing and other forms of relatively simple data communications, and, in this paper, we demonstrate how this limitation can be bridged by indexing and querying a 3D virtual-world on a dynamic distributed network. We present an algorithm for 3D range queries as well as an algorithm for nearest neighbor queries. We also show how to build such a complex application from the ground level of a P2P routing algorithm.}, doi = {10.1007/s10707-005-4887-8}, author = {Tanin,E. and Harwood,A. and Samet, Hanan and Nayar,D. and Nutanong,S.} } @article {13736, title = {Challenges in building an Arabic-English GHMT system with SMT components}, journal = {Proceedings of the 11th Annual Conference of the European Association for Machine Translation (EAMT-2006)}, year = {2006}, month = {2006///}, pages = {56 - 65}, abstract = {The research context of this paper is de-veloping hybrid machine translation (MT) systems that exploit the advantages of linguistic rule-based and statistical MT systems. Arabic, as a morphologically rich language, is especially challenging even without addressing the hybridiza- tion question. In this paper, we describe the challenges in building an Arabic- English generation-heavy machine trans- lation (GHMT) system and boosting it with statistical machine translation (SMT) components. We present an extensive evaluation of multiple system variants and report positive results on the advantages of hybridization. }, author = {Habash,N. and Dorr, Bonnie J and Monz,C.} } @conference {14549, title = {Combination can be hard: Approximability of the unique coverage problem}, booktitle = {Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm}, year = {2006}, month = {2006///}, pages = {162 - 171}, author = {Demaine,E. D and Hajiaghayi, Mohammad T. and Feige,U. and Salavatipour,M. R} } @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} } @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.} } @inbook {14601, title = {Conservation Patterns in cis-Elements Reveal Compensatory Mutations}, booktitle = {Comparative GenomicsComparative Genomics}, series = {Lecture Notes in Computer Science}, volume = {4205}, year = {2006}, month = {2006///}, pages = {186 - 199}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Transcriptional regulation critically depends on proper interactions between transcription factors (TF) and their cognate DNA binding sites or cis elements. A better understanding and modelling of the TF-DNA interaction is an important area of research. The Positional Weight Matrix (PWM) is the most common model of TF-DNA binding and it presumes that the nucleotide preferences at individual positions within the binding site are independent. However, studies have shown that this independence assumption does not always hold. If the nucleotide preference at one position depends on the nucleotide at another position, a chance mutation at one position should exert selection pressures at the other position. By comparing the patterns of evolutionary conservation at individual positions within cis elements, here we show that positional dependence within binding sites is highly prevalent. We also show that dependent positions are more likely to be functional, as evidenced by a higher information content and higher conservation. We discuss two examples{\textemdash}Elk-1 and SAP-1 where the inferred compensatory mutation is consistent with known TF-DNA crystal structure.}, isbn = {978-3-540-44529-6}, url = {http://dx.doi.org/10.1007/11864127_15}, author = {Evans,Perry and Donahue,Greg and Hannenhalli, Sridhar}, editor = {Bourque,Guillaume and El-Mabrouk,Nadia} } @article {14668, title = {Context-sensitive correlation analysis for detecting races}, journal = {Proceedings of the ACM Conference on Programming Language Design and Implementation (PLDI)}, year = {2006}, month = {2006///}, pages = {320 - 331}, author = {Pratikakis,P. and Foster, Jeffrey S. and Hicks, Michael W.} } @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} } @inbook {13751, title = {Cross-Language Access to Recorded Speech in the MALACH Project}, booktitle = {Text, Speech and DialogueText, Speech and Dialogue}, series = {Lecture Notes in Computer Science}, volume = {2448}, year = {2006}, month = {2006///}, pages = {197 - 212}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The MALACH project seeks to help users find information in a vast multilingual collections of untranscribed oral history interviews. This paper introduces the goals of the project and focuses on supporting access by users who are unfamiliar with the interview language. It begins with a review of the state of the art in crosslanguage speech retrieval; approaches that will be investigated in the project are then described. Czech was selected as the first non-English language to be supported, so results of an initial experiment with Czech/English cross-language retrieval are reported.}, isbn = {978-3-540-44129-8}, url = {http://dx.doi.org/10.1007/3-540-46154-X_8}, author = {Oard, Douglas and Demner-Fushman,Dina and Haji{\v c},Jan and Ramabhadran,Bhuvana and Gustman,Samuel and Byrne,William and Soergel,Dagobert and Dorr, Bonnie J and Resnik, Philip and Picheny,Michael}, editor = {Sojka,Petr and Kopecek,Ivan and Pala,Karel} } @book {15740, title = {Deblurring Images: Matrices, Spectra, and Filtering}, year = {2006}, month = {2006///}, publisher = {SIAM Press}, organization = {SIAM Press}, address = {Philadelphia}, author = {Hansen,Per Christian and Nagy,James G. and O{\textquoteright}Leary, Dianne P.} } @conference {13258, title = {A decomposition-based representation for 3D simplicial complexes}, booktitle = {Proceedings of the fourth Eurographics symposium on Geometry processing}, series = {SGP {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {101 - 110}, publisher = {Eurographics Association}, organization = {Eurographics Association}, address = {Aire-la-Ville, Switzerland, Switzerland}, abstract = {We define a new representation for non-manifold 3D shapes described by three-dimensional simplicial complexes, that we call the Double-Level Decomposition (DLD) data structure. The DLD data structure is based on a unique decomposition of the simplicial complex into nearly manifold parts, and encodes the decomposition in an efficient and powerful two-level representation. It is compact, and it supports efficient topological navigation through adjacencies. It also provides a suitable basis for geometric reasoning on non-manifold shapes. We describe an algorithm to decompose a 3D simplicial complex into nearly manifold parts. We discuss how to build the DLD data structure from a description of a 3D complex as a collection of tetrahedra, dangling triangles and wire edges, and we present algorithms for topological navigation. We present a thorough comparison with existing representations for 3D simplicial complexes.}, isbn = {3-905673-36-3}, url = {http://dl.acm.org/citation.cfm?id=1281957.1281970}, author = {Hui,Annie and Vaczlavik,Lucas and De Floriani, Leila} } @article {14604, title = {Dense Subgraph Computation Via Stochastic Search: Application to Detect Transcriptional Modules}, journal = {BioinformaticsBioinformatics}, volume = {22}, year = {2006}, month = {2006/07/15/}, pages = {e117-e123 - e117-e123}, abstract = {Motivation: In a tri-partite biological network of transcription factors, their putative target genes, and the tissues in which the target genes are differentially expressed, a tightly inter-connected (dense) subgraph may reveal knowledge about tissue specific transcription regulation mediated by a specific set of transcription factors{\textemdash}a tissue-specific transcriptional module. This is just one context in which an efficient computation of dense subgraphs in a multi-partite graph is needed.Result: Here we report a generic stochastic search based method to compute dense subgraphs in a graph with an arbitrary number of partitions and an arbitrary connectivity among the partitions. We then use the tool to explore tissue-specific transcriptional regulation in the human genome. We validate our findings in Skeletal muscle based on literature. We could accurately deduce biological processes for transcription factors via the tri-partite clusters of transcription factors, genes, and the functional annotation of genes. Additionally, we propose a few previously unknown TF-pathway associations and tissue-specific roles for certain pathways. Finally, our combined analysis of Cardiac, Skeletal, and Smooth muscle data recapitulates the evolutionary relationship among the three tissues. Contact:sridharh@pcbi.upenn.edu }, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/btl260}, url = {http://bioinformatics.oxfordjournals.org/content/22/14/e117}, author = {Everett,Logan and Wang,Li-San and Hannenhalli, Sridhar} } @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 {14605, title = {Differential Transcriptional Response to Nonassociative and Associative Components of Classical Fear Conditioning in the Amygdala and Hippocampus}, journal = {Learning \& MemoryLearn. Mem.}, volume = {13}, year = {2006}, month = {2006/03/01/}, pages = {135 - 142}, abstract = {Classical fear conditioning requires the recognition of conditioned stimuli (CS) and the association of the CS with an aversive stimulus. We used Affymetrix oligonucleotide microarrays to characterize changes in gene expression compared to naive mice in both the amygdala and the hippocampus 30 min after classical fear conditioning and 30 min after exposure to the CS in the absence of an aversive stimulus. We found that in the hippocampus, levels of gene regulation induced by classical fear conditioning were not significantly greater than those induced by CS alone, whereas in the amygdala, classical fear conditioning did induce significantly greater levels of gene regulation compared to the CS. Computational studies suggest that transcriptional changes in the hippocampus and amygdala are mediated by large and overlapping but distinct combinations of molecular events. Our results demonstrate that an increase in gene regulation in the amygdala was partially correlated to associative learning and partially correlated to nonassociative components of the task, while gene regulation in the hippocampus was correlated to nonassociative components of classical fear conditioning, including configural learning.}, isbn = {1072-0502, 1549-5485}, doi = {10.1101/lm.86906}, url = {http://learnmem.cshlp.org/content/13/2/135}, author = {Keeley,Michael B and Wood,Marcelo A and Isiegas,Carolina and Stein,Joel and Hellman,Kevin and Hannenhalli, Sridhar and Abel,Ted} } @article {13260, title = {A Dimension-Independent Representation for Multiresolution Nonmanifold Meshes}, journal = {Journal of Computing and Information Science in Engineering}, volume = {6}, year = {2006}, month = {2006///}, pages = {397 - 404}, abstract = {We consider the problem of representing and manipulating nonmanifold objects of any dimension and at multiple resolutions. We present a modeling scheme based on (1) a multiresolution representation, called the vertex-based nonmanifold multitessellation, (2) a compact and dimension-independent data structure, called the Simplified Incidence Graph (SIG), and (3) an atomic mesh update operator, called vertex-pair contraction/vertex expansion. We propose efficient algorithms for performing the vertex-pair contraction on a simplicial mesh encoded as a SIG, and an effective representation for encoding this multiresolution model based on a compact encoding of vertex-pair contractions and vertex expansions.}, keywords = {computational geometry, graph theory, mesh generation}, doi = {10.1115/1.2364207}, url = {http://link.aip.org/link/?CIS/6/397/1}, author = {De Floriani, Leila and Hui,Annie} } @article {13261, title = {A dimension-independent simplicial data structure for non-manifold shapes}, volume = {CS-TR-4794}, year = {2006}, month = {2006/04/07/}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {We consider the problem of representing and manipulating non-manifoldmulti-dimensional shapes, discretized as $d$-dimensional simplicial Euclidean complexes, for modeling finite element meshes derived from CAD models. We propose a dimension-independent data structure for simplicial complexes, that we call the {\em Incidence Simplicial (IS)} data structure. The IS data structure is scalable to manifold complexes, and supports efficient traversal and update algorithms for performing topological modifications, such as hole removal or dimension reduction. It has the same expressive power and performances as the incidence graph, commonly used for dimension-independent representation of simplicial and cell complexes, but it is much more compact. We present efficient algorithms for traversing, generating and updating a simplicial complex described as an IS data structure. We compare the IS data structure with dimension-independent and dimension-specific representations for simplicial complexes. Finally, we briefly discuss two applications that the IS data structure supports, namely decomposition of non-manifold objects for effective geometric reasoning, and multi-resolution modeling of non-manifold multi-dimensional shapes. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/7427}, author = {Hui,Annie and De Floriani, Leila} } @conference {16423, title = {The effect of crossover on the behavior of the GA in dynamic environments: a case study using the shaky ladder hyperplane-defined functions}, booktitle = {Proceedings of the 8th annual conference on Genetic and evolutionary computation}, series = {GECCO {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {1289 - 1296}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {One argument as to why the hyperplane-defined functions (hdf{\textquoteright}s) are a good testbed for the genetic algorithm (GA) is that the hdf{\textquoteright}s are built in the same way that the GA works. In this paper we test that hypothesis in a new setting by exploring the GA on a subset of the hdf{\textquoteright}s which are dynamic---the shaky ladder hyperplane-defined functions (sl-hdf{\textquoteright}s). In doing so we gain insight into how the GA makes use of crossover during its traversal of the sl-hdf search space. We begin this paper by explaining the sl-hdf{\textquoteright}s. We then conduct a series of experiments with various crossover rates and various rates of environmental change. Our results show that the GA performs better with than without crossover in dynamic environments. Though these results have been shown on some static functions in the past, they are re-confirmed and expanded here for a new type of function (the hdf) and a new type of environment (dynamic environments). Moreover we show that crossover is even more beneficial in dynamic environments than it is in static environments. We discuss how these results can be used to develop a richer knowledge about the use of building blocks by the GA.}, keywords = {crossover, dynamic environments, Genetic algorithms, hyperplane-defined functions, search}, isbn = {1-59593-186-4}, doi = {10.1145/1143997.1144198}, url = {http://doi.acm.org/10.1145/1143997.1144198}, author = {Rand, William and Riolo,Rick and Holland,John H.} } @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 {12348, title = {Efficient simulation of critical synchronous dataflow graphs}, booktitle = {Proceedings of the 43rd annual Design Automation Conference}, year = {2006}, month = {2006///}, pages = {893 - 898}, author = {Hsu,C. J and Ramasubbu,S. and Ko,M. Y and Pino,J. L and Bhattacharyya, Shuvra S.} } @conference {12115, title = {An empirical study to compare two parallel programming models}, booktitle = {Proceedings of the eighteenth annual ACM symposium on Parallelism in algorithms and architectures}, series = {SPAA {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {114 - 114}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {While there are strong beliefs within the community about whether one particular parallel programming model is easier to use than another, there has been little research to analyze these claims empirically. Currently, the most popular paradigm is message-passing, as implemented by the MPI library [1]. However, MPI is considered to be difficult for developing programs, because it forces the programmer to work at a very low level of abstraction. One alternative parallel programming model is the PRAM model, which supports fine-grained parallelism and has a substantial history of algorithmic theory [2]. It is not possible to program current parallel machines using the PRAM model because modern architectures are not designed to support such a model efficiently. However, current trends towards multicore chips suggest that large-scale, fine-grained uniform-memory access parallel machines may soon be feasible. XMT-C is an extension of the C language that supports parallel directives to provide a PRAM-like model to the programmer. A prototype compiler exists that generates code which runs on a simulator for an XMT architecture [3].To better understand how much benefit a PRAM-like model could provide over a message-passing model, we conducted a feasibility study in an academic setting to compare the effort required to solve a particular problem. The questions under study were: can we measure the effort in developing a program using these two programming models and can we differentiate the amount of effort for each model?.The subjects participating in the study were divided up into two groups. One group solved a problem using the MPI library in either C,C++, or Fortran, and the other group solved the problem using XMT-C. The task was to write a function to multiply a sparse matrix with a dense vector. To obtain subjects, we leveraged existing graduate-level parallel programming courses at two different universities: University of California, Santa Barbara (UCSB), and University of Maryland (UMD). At UCSB, the students solved the problem in MPI, and at UMD, the students solved the same problem in XMT-C. The focus of the UCSB class was on developing parallel programs to run on the current generation of architectures, and the students were taught MPI, as well as other models. The focus of the UMD class was parallel algorithms in the PRAM model, and the students were taught XMT-C. The students were assigned to treatment groups by class. The study was integrated into each class, as the problem was a required assignment in each class.Subjects kept track of their effort with a self-reported effort log. We also collected automatic effort data by instrumenting the compilers, which recorded data at each compile. We computed three effort measures: self-reported, instrumented, and combined. Self-reported effort measures are based entirely on effort logs, instrumented effort measures are based entirely on timestamps from the instrumented compilers, and combined effort measures are based on compiler timestamps when the subject is working on the instrumented machine, and self-reported effort when the subject is working off the instrumented machine.The results of this preliminary study answer both of our questions in the positive. In this case, on average, students required less effort to solve the problem using XMT-C compared to MPI. The reduction in mean effort was approximately 50\% for all three measures, which was statistically significant at the level of p < .05 using a t-test.This study demonstrates that the effect of programming model on effort can be directly measured through empirical studies with human subjects. While no single study can conclusively demonstrate the advantage of one programming model over another, a series of studies examining different models and different problems can provide insights into the relative strengths of parallel programming models in different contexts. The study described above is one of a series of such studies that we are currently conducting.}, keywords = {effort, empirical study, HPC, Message-passing, MPI, parallel programming, PRAM, Productivity, XMT}, isbn = {1-59593-452-9}, doi = {10.1145/1148109.1148127}, url = {http://doi.acm.org/10.1145/1148109.1148127}, author = {Hochstein, Lorin and Basili, Victor R.} } @article {12355, title = {Energy-efficient embedded software implementation on multiprocessor system-on-chip with multiple voltages}, journal = {ACM Transactions on Embedded Computing Systems (TECS)}, volume = {5}, year = {2006}, month = {2006///}, pages = {321 - 341}, author = {Hua,S. and Qu,G. and Bhattacharyya, Shuvra S.} } @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 {12182, title = {The evolution of the international children{\textquoteright}s digital library searching and browsing interface}, booktitle = {Proceedings of the 2006 conference on Interaction design and children}, year = {2006}, month = {2006///}, pages = {105 - 112}, author = {Hutchinson,H.B. and Bederson, Benjamin B. and Druin, Allison} } @inbook {14693, title = {Existential Label Flow Inference Via CFL Reachability}, booktitle = {Static AnalysisStatic Analysis}, series = {Lecture Notes in Computer Science}, volume = {4134}, year = {2006}, month = {2006///}, pages = {88 - 106}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In programming languages, existential quantification is useful for describing relationships among members of a structured type. For example, we may have a list in which there exists some mutual exclusion lock l in each list element such that l protects the data stored in that element. With this information, a static analysis can reason about the relationship between locks and locations in the list even when the precise identity of the lock and/or location is unknown. To facilitate the construction of such static analyses, this paper presents a context-sensitive label flow analysis algorithm with support for existential quantification. Label flow analysis is a core part of many static analysis systems. Following Rehof et al, we use context-free language (CFL) reachability to develop an efficient O(n 3) label flow inference algorithm. We prove the algorithm sound by reducing its derivations to those in a system based on polymorphically-constrained types, in the style of Mossin. We have implemented a variant of our analysis as part of a data race detection tool for C programs.}, isbn = {978-3-540-37756-6}, url = {http://dx.doi.org/10.1007/11823230_7}, author = {Pratikakis,Polyvios and Foster, Jeffrey S. and Hicks, Michael W.}, editor = {Yi,Kwangkeun} } @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 {18211, title = {Exploring QIM-based anti-collusion fingerprinting for multimedia}, journal = {Proceedings of SPIE}, volume = {6072}, year = {2006}, month = {2006///}, pages = {698 - 709}, abstract = {Digital fingerprinting is an emerging technology to protect multimedia from unauthorizeduse by embedding a unique fingerprint signal into each user{\textquoteright}s copy. A robust embedding algorithm is an important building block in order to make the fingerprint resilient to vari- ous distortions and collusion attacks. Spread spectrum embedding has been widely used for multimedia fingerprinting. In this paper, we explore another class of embedding methods {\textendash} Quantization Index Modulation (QIM) for fingerprinting applications. We first employ Dither Modulation (DM) technique and extend it for embedding multiple symbols through a basic dither sequence design. We then develop a theoretical model and propose a new algorithm to improve the collusion resistance of the basic scheme. Simulation results show that the improvement algorithm enhances the collusion resistance, while there is still a performance gap with the existing spread spectrum based fingerprinting. We then explore coded fingerprinting based on spread transform dither modulation (STDM) embedding. Simulation results show that this coded STDM based fingerprinting has significant advantages over spread spectrum based fingerprinting under blind detection. }, author = {Swaminathan,A. and He,S. and Wu,M.} } @article {14909, title = {First Steps Toward an Electronic Field Guide for Plants}, journal = {Taxon}, volume = {55}, year = {2006}, month = {2006///}, pages = {597 - 610}, abstract = {this paper, we will describe our progress towards building a digital collection of the Smithsonian{\textquoteright}s type specimens, developing recognition algorithms that can match an image of a leaf to the species of plant from which it comes, and designing user interfaces for interacting with an electronic field guide. To start, we are developing a prototype electronic field guide for the flora of Plummers Island, a small, well-studied island in the Potomac River. This prototype system contains multiple images for each of about 130 species of plants on the island, and should soon grow to cover all 200+ species currently recorded (Shetler et al., 2005). Images of full specimens are available, as well as images of isolated leaves of each species. A zoomable user interface allows a user to browse these images, zooming in on ones of interest. Visual recognition algorithms assist a botanist in locating the specimens that are most relevant to identify the species of a plant. The system currently runs on a small hand-held computer. We will describe the components of this prototype, and also describe some of the future challenges we anticipate if we are to provide botanists in the field with all the resources that are now currently available in the world{\textquoteright}s museums and herbaria. Type Specimen Digital Collection The first challenge in producing our electronic field guide is to create a digital collection covering all of the Smithsonian{\textquoteright}s 85,000 vascular plant type specimens. For each type specimen, the database should eventually include systematically acquired high-resolution digital images of the specimen, textual descriptions, links to decision trees, images of live plants, and 3D models. Figure 1: On the left, our set-up at the Smithsonian for digitally photographing type specimens. On the...}, author = {Haibin,Gaurav Agarwal and Agarwal,Gaurav and Ling,Haibin and Jacobs, David W. and Shirdhonkar,Sameer and Kress,W. John and Russell,Rusty and Belhumeur,Peter and Dixit,An and Feiner,Steve and Mahajan,Dhruv and Sunkavalli,Kalyan and Ramamoorthi,Ravi and White,Sean} } @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 {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} } @article {17968, title = {Geometry-dependent lighting}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {12}, year = {2006}, month = {2006/04//march}, pages = {197 - 207}, abstract = {In this paper, we introduce geometry-dependent lighting that allows lighting parameters to be defined independently and possibly discrepantly over an object or scene based on the local geometry. We present and discuss light collages, a lighting design system with geometry-dependent lights for effective feature-enhanced visualization. Our algorithm segments the objects into local surface patches and places lights that are locally consistent but globally discrepant to enhance the perception of shape. We use spherical harmonics for efficiently storing and computing light placement and assignment. We also outline a method to find the minimal number of light sources sufficient to illuminate an object well with our globally discrepant lighting approach.}, keywords = {Computer-Assisted;Imaging, feature-enhanced visualization;geometry-dependent light;light collage;light placement;lighting design system;computational geometry;data visualisation;lighting;Algorithms;Computer Graphics;Image Enhancement;Image Interpretation, Three-Dimensional;Information Storage and Retrieval;Lighting;User-Computer Interface;}, isbn = {1077-2626}, doi = {10.1109/TVCG.2006.30}, author = {Lee,C. H and Hao,X. and Varshney, Amitabh} } @article {17908, title = {Geometry-guided computation of 3D electrostatics for large biomolecules}, journal = {Computer Aided Geometric Design}, volume = {23}, year = {2006}, month = {2006/08//}, pages = {545 - 557}, abstract = {Electrostatic interactions play a central role in biological processes. Development of fast computational methods to solve the underlying Poisson{\textendash}Boltzmann equation (PBE) is vital for biomolecular modeling and simulation package. In this paper, we propose new methods for efficiently computing the electrostatic potentials for large molecules by using the geometry of the molecular shapes to guide the computation. The accuracy and stability of the solution to the PBE is quite sensitive to the boundary layer between the solvent and the solute which defines the molecular surface. In this paper, we present a new interface-layer-focused PBE solver. First, we analytically construct the molecular surface of the molecule and compute a distance field from the surface. We then construct nested iso-surface layers outwards and inwards from the surface using the distance field. We have developed a volume simplification algorithm to adaptively adjust the density of the irregular grid based on the importance to the PBE solution. We have generalized the finite difference methods using Taylor series expansion on the irregular grids. Our algorithm achieves about three times speedup in the iterative solution process of PBE, with more accurate results on an analytical solvable testing case, compared with the popular optimized DelPhi program.}, keywords = {Finite difference methods, Iso-surface generation, Level-of-detail of hierarchy, Poisson{\textendash}Boltzmann equation, Scalar field, Tetrahedron decomposition}, isbn = {0167-8396}, doi = {10.1016/j.cagd.2006.04.003}, url = {http://www.sciencedirect.com/science/article/pii/S0167839606000434}, author = {Hao,Xuejun and Varshney, Amitabh} } @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.} } @article {14623, title = {Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements}, journal = {Osteoarthritis and Cartilage}, volume = {14}, year = {2006}, month = {2006/08//}, pages = {830 - 838}, abstract = {SummaryObjectiveTo better understand transcription regulation of osteoarthritis (OA) by examining common promoter motifs in canine osteoarthritic genes, to identify other genes containing these motifs and to assess the conservation of these motifs between canine, human, mouse and rat. Design Differentially expressed transcripts in canine OA were mapped to the human genome. We thus identified 20 orthologous human transcripts representing 19 up-regulated genes and 62 orthologous transcripts representing 60 down-regulated genes. The 5\&$\#$xa0;kbp upstream regions of these transcripts were used to identify binding sites and build promoter models based on those sites. The human genome was subsequently searched for other transcripts likely to be regulated by the same promoter models. Orthologous transcripts were then identified in canine, rat and mouse for determination of potential cross-species conservation of binding sites comprising the promoter model. Results Four promoter models containing 5{\textendash}6 transcripts and 5{\textendash}8 common transcription factor binding sites were developed. They include binding sites for AP-4, AP-2α and γ, and E2F. Several hundred other human genes were found to contain these promoter motifs. Furthermore these motifs were significantly over represented in the orthologous genes in canine, rat and mouse genomes. Conclusions We have developed and applied a computational methodology to identify common promoter elements implicated in OA and shared amongst four higher vertebrates. The transcription factors associated with these binding sites and other genes driven by these promoter motifs have been implicated in OA, chondrocyte development and with other biological factors involved in the disease. }, keywords = {Chondrocyte, Gene expression, Osteoarthritis, Promoter}, isbn = {1063-4584}, doi = {10.1016/j.joca.2006.02.007}, url = {http://www.sciencedirect.com/science/article/pii/S1063458406000379}, author = {Hannenhalli, Sridhar and Middleton,R.P. and Levy,S. and Perroud,B. and Holzwarth,J.A. and McDonald,K. and Hannah,S.S.} } @conference {12137, title = {Identifying domain-specific defect classes using inspections and change history}, booktitle = {Proceedings of the 2006 ACM/IEEE international symposium on Empirical software engineering}, series = {ISESE {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {346 - 355}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present an iterative, reading-based methodology for analyzing defects in source code when change history is available. Our bottom-up approach can be applied to build knowledge of recurring defects in a specific domain, even if other sources of defect data such as defect reports and change requests are unavailable, incomplete or at the wrong level of abstraction for the purposes of the defect analysis. After defining the methodology, we present the results of an empirical study where our method was applied to analyze defects in parallel programs which use the MPI (Message Passing Interface) library to express parallelism. This library is often used in the domain of high performance computing, where there is much discussion but little empirical data about the frequency and severity of defect types. Preliminary results indicate the methodology is feasible and can provide insights into the nature of real defects. We present the results, derived hypothesis, and lessons learned.}, keywords = {change history, code reading, domain specific defects, Inspection}, isbn = {1-59593-218-6}, doi = {10.1145/1159733.1159785}, url = {http://doi.acm.org/10.1145/1159733.1159785}, author = {Nakamura,Taiga and Hochstein, Lorin and Basili, Victor R.} } @article {15249, title = {An improved approximation algorithm for vertex cover with hard capacities}, journal = {Journal of Computer and System Sciences}, volume = {72}, year = {2006}, month = {2006/02//}, pages = {16 - 33}, abstract = {We study the capacitated vertex cover problem, a generalization of the well-known vertex-cover problem. Given a graph G = ( V , E ) , the goal is to cover all the edges by picking a minimum cover using the vertices. When we pick a vertex, we can cover up to a pre-specified number of edges incident on this vertex (its capacity). The problem is clearly NP-hard as it generalizes the well-known vertex-cover problem. Previously, approximation algorithms with an approximation factor of 2 were developed with the assumption that an arbitrary number of copies of a vertex may be chosen in the cover. If we are allowed to pick at most a fixed number of copies of each vertex, the approximation algorithm becomes much more complex. Chuzhoy and Naor (FOCS, 2002) have shown that the weighted version of this problem is at least as hard as set cover; in addition, they developed a 3-approximation algorithm for the unweighted version. We give a 2-approximation algorithm for the unweighted version, improving the Chuzhoy{\textendash}Naor bound of three and matching (up to lower-order terms) the best approximation ratio known for the vertex-cover problem.}, keywords = {Approximation algorithms, Capacitated covering, Linear programming, Randomized rounding, Set cover, Vertex cover}, isbn = {0022-0000}, doi = {10.1016/j.jcss.2005.06.004}, url = {http://www.sciencedirect.com/science/article/pii/S0022000005000747}, author = {Gandhi,Rajiv and Halperin,Eran and Khuller, Samir and Kortsarz,Guy and Srinivasan, Aravind} } @conference {14547, title = {Improved lower and upper bounds for universal TSP in planar metrics}, booktitle = {Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm}, year = {2006}, month = {2006///}, pages = {649 - 658}, author = {Hajiaghayi, Mohammad T. and Kleinberg,R. and Leighton,T.} } @article {18577, title = {In VINI veritas: realistic and controlled network experimentation}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {36}, year = {2006}, month = {2006/08//}, pages = {3 - 14}, abstract = {This paper describes VINI, a virtual network infrastructure that allows network researchers to evaluate their protocols and services in a realistic environment that also provides a high degree of control over network conditions. VINI allows researchers to deploy and evaluate their ideas with real routing software, traffic loads, and network events. To provide researchers flexibility in designing their experiments, VINI supports simultaneous experiments with arbitrary network topologies on a shared physical infrastructure. This paper tackles the following important design question: What set of concepts and techniques facilitate flexible, realistic, and controlled experimentation (e.g., multiple topologies and the ability to tweak routing algorithms) on a fixed physical infrastructure? We first present VINI{\textquoteright}s high-level design and the challenges of virtualizing a single network. We then present PL-VINI, an implementation of VINI on PlanetLab, running the "Internet In a Slice". Our evaluation of PL-VINI shows that it provides a realistic and controlled environment for evaluating new protocols and services.}, keywords = {architecture, experimentation, Internet, Routing, virtualization}, isbn = {0146-4833}, doi = {10.1145/1151659.1159916}, url = {http://doi.acm.org/10.1145/1151659.1159916}, author = {Bavier,Andy and Feamster, Nick and Huang,Mark and Peterson,Larry and Rexford,Jennifer} } @article {16088, title = {Integrating data and interfaces to enhance understanding of government statistics: toward the national statistical knowledge network project briefing}, journal = {Proceedings of 7th Annual International Conference on Digital Libraries (DG06)}, year = {2006}, month = {2006///}, pages = {21 - 24}, abstract = {This paper reports the results of work in the final no-costextension year of a digital government project that developed user interface models and prototypes to help people find and understand government statistics; proposed a Statistical Knowledge Network architecture that supports cross agency information access; and demonstrated models for government- academic collaboration. }, author = {Marchionini,G. and Haas,S. and Plaisant, Catherine and Shneiderman, Ben} } @inbook {14593, title = {An Interaction-Dependent Model for Transcription Factor Binding}, booktitle = {Systems Biology and Regulatory GenomicsSystems Biology and Regulatory Genomics}, series = {Lecture Notes in Computer Science}, volume = {4023}, year = {2006}, month = {2006///}, pages = {225 - 234}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Transcriptional regulation is accomplished by several transcription factor proteins that bind to specific DNA elements in the relative vicinity of the gene, and interact with each other and with Polymerase enzyme. Thus the determination of transcription factor-DNA binding is an important step toward understanding transcriptional regulation. An effective way to experimentally determine the genomic regions bound by a transcription factor is by a ChIP-on-chip assay. Then, given the putative genomic regions, computational motif finding algorithms are applied to estimate the DNA binding motif or positional weight matrix for the TF. The a priori expectation is that the presence or absence of the estimated motif in a promoter should be a good indicator of the binding of the TF to that promoter. This association between the presence of the transcription factor motif and its binding is however weak in a majority of cases where the whole genome ChIP experiments have been performed. One possible reason for this is that the DNA binding of a particular transcription factor depends not only on its own motif, but also on synergistic or antagonistic action of neighboring motifs for other transcription factors. We believe that modeling this interaction-dependent binding with linear regression can better explain the observed binding data. We assess this hypothesis based on the whole genome ChIP-on-chip data for Yeast. The derived interactions are largely consistent with previous results that combine ChIP-on-chip data with expression data. We additionally apply our method to determine interacting partners for CREB and validate our findings based on published experimental results.}, isbn = {978-3-540-48293-2}, url = {http://dx.doi.org/10.1007/978-3-540-48540-7_19}, author = {Wang,Li-San and Jensen,Shane and Hannenhalli, Sridhar}, editor = {Eskin,Eleazar and Ideker,Trey and Raphael,Ben and Workman,Christopher} } @article {14625, title = {Invited Talk: Deciphering Gene Regulatory Networks by in silico approaches}, journal = {6th International Workshop on Data Mining in Bioinformatics (BIOKDD06)}, year = {2006}, month = {2006///}, pages = {31 - 31}, abstract = {Biological processes are controlled at various levels in the celland while these mechanisms are poorly understood, tran- scriptional control is widely recognized as an important com- ponent and a better understanding of which will provide an efficient means for the therapeutic intervention in disease processes. We have been focusing on various computational problems pertaining to transcriptional regulation, namely, (1) representation and identification of transcription factor binding sites,(2) PolII promoter prediction,(3) Predicting interaction among transcription factors,(4) Transcriptional modeling, ie identifying arrangements of TFs that co- regulate a set of transcripts. I will present a brief overview of the computational approaches and challenges as well as a number of applications including transcriptional regulation in memory storage, heart failure, and osteoarthritis. }, author = {Hannenhalli, Sridhar} } @article {18233, title = {Joint coding and embedding techniques for MultimediaFingerprinting}, journal = {Information Forensics and Security, IEEE Transactions on}, volume = {1}, year = {2006}, month = {2006/06//}, pages = {231 - 247}, abstract = {Digital fingerprinting protects multimedia content from illegal redistribution by uniquely marking every copy of the content distributed to each user. The collusion attack is a powerful attack where several different fingerprinted copies of the same content are combined together to attenuate or even remove the fingerprints. One major category of collusion-resistant fingerprinting employs an explicit step of coding. Most existing works on coded fingerprinting mainly focus on the code-level issues and treat the embedding issues through abstract assumptions without examining the overall performance. In this paper, we jointly consider the coding and embedding issues for coded fingerprinting systems and examine their performance in terms of collusion resistance, detection computational complexity, and distribution efficiency. Our studies show that coded fingerprinting has efficient detection but rather low collusion resistance. Taking advantage of joint coding and embedding, we propose a permuted subsegment embedding technique and a group-based joint coding and embedding technique to improve the collusion resistance of coded fingerprinting while maintaining its efficient detection. Experimental results show that the number of colluders that the proposed methods can resist is more than three times as many as that of the conventional coded fingerprinting approaches.}, keywords = {coding-embedding, coding;, collusion-resistant, complexity;, computational, data;, DETECTION, embedded, EMBEDDING, fingerprinting;, group-based, image, joint, multimedia, of, Security, subsegment, systems;, technique;, techniques;}, isbn = {1556-6013}, doi = {10.1109/TIFS.2006.873597}, author = {He,Shan and M. Wu} } @article {15581, title = {On the Least Median Square Problem}, journal = {Discrete \& Computational Geometry}, volume = {36}, year = {2006}, month = {2006///}, pages = {593 - 607}, abstract = {We consider the exact and approximate computational complexity of the multivariate least median-of-squares (LMS) linear regression estimator. The LMS estimator is among the most widely used robust linear statistical estimators. Given a set of n points in and a parameter k, the problem is equivalent to computing the narrowest slab bounded by two parallel hyperplanes that contains k of the points. We present algorithms for the exact and approximate versions of the multivariate LMS problem. We also provide nearly matching lower bounds for these problems. These lower bounds hold under the assumptions that k is Ω(n) and that deciding whether n given points in are affinely non-degenerate requires Ω(n d ) time.}, keywords = {Mathematics and Statistics}, isbn = {0179-5376}, doi = {10.1007/s00454-006-1267-6}, url = {http://www.springerlink.com/content/j44818j11173017k/abstract/}, author = {Erickson,Jeff and Har-Peled,Sariel and Mount, Dave} } @article {13812, title = {Leveraging recurrent phrase structure in large-scale ontology translation}, journal = {Proceedings of the 11th Annual Conference of the European Association for Machine Translation}, year = {2006}, month = {2006///}, abstract = {This paper presents a process for leveraging structural relationships and reusablephrases when translating large-scale ontologies. Digital libraries are becoming more and more prevalent. An important step in providing universal access to such material is to pro- vide multi-lingual access to the underlying principles of organization via ontologies, thesauri, and controlled vocabularies. Machine translation of these resources requires high accuracy and a deep vocabulary. Human input is often required, but full manual translation can be slow and expensive. We report on a cost-effective approach to ontology translation. We describe our technique of prioritization, our process of collecting aligned translations and generating a new lexicon, and the resulting improvement to translation system output. Our preliminary evaluation indicates that this technique provides significant cost savings for human-assisted translation. The process we developed can be applied to ontologies in other domains and is easily incorporated into other translation systems. }, author = {Murray,G. C and Dorr, Bonnie J and Jimmy Lin and Haji{\v c},J. and Pecina,P.} } @conference {13813, title = {Leveraging reusability: cost-effective lexical acquisition for large-scale ontology translation}, booktitle = {Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the Association for Computational Linguistics}, series = {ACL-44}, year = {2006}, month = {2006///}, pages = {945 - 952}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Thesauri and ontologies provide important value in facilitating access to digital archives by representing underlying principles of organization. Translation of such resources into multiple languages is an important component for providing multilingual access. However, the specificity of vocabulary terms in most ontologies precludes fully-automated machine translation using general-domain lexical resources. In this paper, we present an efficient process for leveraging human translations when constructing domain-specific lexical resources. We evaluate the effectiveness of this process by producing a probabilistic phrase dictionary and translating a thesaurus of 56,000 concepts used to catalogue a large archive of oral histories. Our experiments demonstrate a cost-effective technique for accurate machine translation of large ontologies.}, doi = {10.3115/1220175.1220294}, url = {http://dx.doi.org/10.3115/1220175.1220294}, author = {Murray,G. Craig and Dorr, Bonnie J and Jimmy Lin and Haji{\v c},Jan and Pecina,Pavel} } @conference {14703, title = {Lock inference for atomic sections}, booktitle = {Proceedings of the First ACM SIGPLAN Workshop on Languages, Compilers, and Hardware Support for Transactional Computing}, year = {2006}, month = {2006///}, abstract = {To prevent unwanted interactions in multithreaded programs, pro-grammers have traditionally employed pessimistic, blocking con- currency primitives. Using such primitives correctly and efficiently is notoriously difficult. To simplify the problem, recent research proposes that programmers specify atomic sections of code whose executions should be atomic with respect to one another, without dictating exactly how atomicity enforced. Much work has explored using optimistic concurrency, or software transactions, as a means to implement atomic sections. This paper proposes to implement atomic sections using a static whole-program analysis to insert necessary uses of pessimistic con- currency primitives. Given a program that contains programmer- specified atomic sections and thread creations, our mutex infer- ence algorithm efficiently infers a set of locks for each atomic section that should be acquired (released) upon entering (exiting) the atomic section. The key part of this algorithm is determining which memory locations in the program could be shared between threads, and using this information to generate the necessary locks. To determine sharing, our analysis uses the notion of continuation effects to track the locations accessed after each program point. As continuation effects are flow sensitive, a memory location may be thread-local before a thread creation and thread-shared afterward. We prove that our algorithm is correct, and provides parallelism according to the precision of the points-to analysis. While our al- gorithm also attempts to reduce the number locks while preserving parallelism, we show that minimizing the number of locks is NP- hard. }, author = {Hicks, Michael W. and Foster, Jeffrey S. and Pratikakis,P.} } @article {14704, title = {LOCKSMITH: context-sensitive correlation analysis for race detection}, journal = {SIGPLAN Not.}, volume = {41}, year = {2006}, month = {2006/06//}, pages = {320 - 331}, abstract = {One common technique for preventing data races in multi-threaded programs is to ensure that all accesses to shared locations are consistently protected by a lock. We present a tool called LOCKSMITH for detecting data races in C programs by looking for violations of this pattern. We call the relationship between locks and the locations they protect consistent correlation, and the core of our technique is a novel constraint-based analysis that infers consistent correlation context-sensitively, using the results to check that locations are properly guarded by locks. We present the core of our algorithm for a simple formal language λ> which we have proven sound, and discuss how we scale it up to an algorithm that aims to be sound for all of C. We develop several techniques to improve the precision and performance of the analysis, including a sharing analysis for inferring thread locality; existential quantification for modeling locks in data structures; and heuristics for modeling unsafe features of C such as type casts. When applied to several benchmarks, including multi-threaded servers and Linux device drivers, LOCKSMITH found several races while producing a modest number of false alarm.}, keywords = {context-sensitivity, correlation, locksmith, multi-threaded programming, race detection, Type inference}, isbn = {0362-1340}, doi = {10.1145/1133255.1134019}, url = {http://doi.acm.org/10.1145/1133255.1134019}, author = {Pratikakis,Polyvios and Foster, Jeffrey S. and Hicks, Michael W.} } @inbook {13825, title = {Machine Translation: Interlingual Methods}, booktitle = {Encyclopedia of Language \& Linguistics (Second Edition)Encyclopedia of Language \& Linguistics (Second Edition)}, year = {2006}, month = {2006///}, pages = {383 - 394}, publisher = {Elsevier}, organization = {Elsevier}, address = {Oxford}, abstract = {An interlingua is a notation for representing the content of a text that abstracts away from the characteristics of the language itself and focuses on the meaning (semantics) alone. Interlinguas are typically used as pivot representations in machine translation, allowing the contents of a source text to be generated in many different target languages. Because of the complexities involved, few interlinguas are more than demonstration prototypes, and only one has been used in a commercial MT system. In this article, we define the components of an interlingua and the principal issues faced by designers and builders of interlinguas and interlingua MT systems, illustrating with examples from operational systems and research prototypes. We discuss current efforts to annotate texts with interlingua-based information.}, keywords = {approximate interlingua, compositionality, conceptual knowledge, cross-language divergences, interlingua, interlingual speech translation, language-independent representation, lexical-conceptual structure, Machine translation, ontology, predicate-argument structure, semantic annotation, semantic frames, semantic zones, text-meaning representations, THEMATIC ROLES}, isbn = {978-0-08-044854-1}, url = {http://www.sciencedirect.com/science/article/pii/B0080448542009391}, author = {Dorr, Bonnie J and Hovy,E. and Levin,L.}, editor = {Editor-in-Chief:~~ Keith Brown} } @article {14583, title = {A mammalian promoter model links cis elements to genetic networks}, journal = {Biochemical and Biophysical Research Communications}, volume = {347}, year = {2006}, month = {2006/08/18/}, pages = {166 - 177}, abstract = {An accurate identification of gene promoters remains an important challenge. Computational approaches for this problem rely on promoter sequence attributes that are believed to be critical for transcription initiation. Here we report a probabilistic model that captures two important properties of promoters, not used by previous methods, viz., the location preference and co-occurrence of promoter elements. Additionally, we found that many of the position-specific DNA elements are strongly linked with the function of the gene product. For instance, a highly conserved motif CCTTT at -1 position is strongly associated with protein synthesis, cellular and tissue development. Our comparative analysis of promoter classes reveals that the promoters devoid of CpG islands are more conserved and have fewer alternative transcription start sites. The discovered links between promoter elements and gene function allows us to infer genetic networks from promoter elements. The web server for the PSPA promoter predictor is available at http://cagr.pcbi.upenn.edu/PSPA.}, keywords = {conservation, Core promoter prediction, CpG island, Genetic networks, Position-specific motif, Propensity, Transcription factor binding site (TFBS)}, isbn = {0006-291X}, doi = {16/j.bbrc.2006.06.062}, url = {http://www.sciencedirect.com/science/article/pii/S0006291X06013635}, author = {Wang,Junwen and Hannenhalli, Sridhar} } @conference {14706, title = {Managing policy updates in security-typed languages}, booktitle = {19th IEEE Computer Security Foundations Workshop, 2006}, year = {2006}, month = {2006///}, pages = {13 pp.-216 - 13 pp.-216}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper presents Rx, a new security-typed programming language with features intended to make the management of information-flow policies more practical. Security labels in Rx, in contrast to prior approaches, are defined in terms of owned roles, as found in the RT role-based trust-management framework. Role-based security policies allow flexible delegation, and our language Rx provides constructs through which programs can robustly update policies and react to policy updates dynamically. Our dynamic semantics use statically verified transactions to eliminate illegal information flows across updates, which we call transitive flows. Because policy updates can be observed through dynamic queries, policy updates can potentially reveal sensitive information. As such, Rx considers policy statements themselves to be potentially confidential information and subject to information-flow metapolicies}, keywords = {Access control, Computer languages, Data security, Database systems, dynamic queries, dynamic semantics, Educational institutions, high level languages, Information security, information-flow policy management, Lattices, Network servers, Operating systems, policy update management, Robustness, role-based security policies, RT role-based trust-management framework, Rx security-typed programming language, security of data, statically verified transactions, transitive flows}, isbn = {0-7695-2615-2}, doi = {10.1109/CSFW.2006.17}, author = {Swamy,N. and Hicks, Michael W. and Tse,S. and Zdancewic,S.} } @article {18860, title = {Manufacturing of multi-material compliant mechanisms using multi-material molding}, journal = {The International Journal of Advanced Manufacturing Technology}, volume = {30}, year = {2006}, month = {2006///}, pages = {1049 - 1075}, abstract = {Multi-material compliant mechanisms enable many new design possibilities. Significant progress has been made in the area of design and analysis of multi-material compliant mechanisms. What is now needed is a method to mass-produce such mechanisms economically. A feasible and practical way of producing such mechanisms is through multi-material molding. Devices based on compliant mechanisms usually consist of compliant joints. Compliant joints in turn are created by carefully engineering interfaces between a compliant and a rigid material. This paper presents an overview of multi-material molding technology and describes feasible mold designs for creating different types of compliant joints found in multi-material compliant mechanisms. It also describes guidelines essential to successfully utilizing the multi-material molding process for creating compliant mechanisms. Finally, practical applications for the use of multi-material molding to create compliant mechanisms are demonstrated.}, keywords = {engineering}, isbn = {0268-3768}, doi = {10.1007/s00170-005-0152-4}, url = {http://www.springerlink.com/content/djk6wq2213447pqn/abstract/}, author = {Gouker,Regina and Gupta, Satyandra K. and Bruck,Hugh and Holzschuh,Tobias} } @conference {12391, title = {Mapping Multimedia Applications Onto Configurable Hardware With Parameterized Cyclo-Static Dataflow Graphs}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {3}, year = {2006}, month = {2006/05//}, pages = {III - III}, abstract = {This paper develops methods for model-based design and implementation of image processing applications. We apply our previously developed meta-modeling technique of homogeneous parameterized dataflow (HPDF) (M. Sen et al., 2005) to the framework of cyclostatic dataflow (CSDF) (G. Bilsen et al., 1996), and demonstrate this integrated modeling methodology through hardware mapping of a gesture recognition application. We also provide a comparative study between HPDF/CSDF-based representation of the gesture recognition application, and a previously developed version based on applying HPDF in conjunction with conventional synchronous dataflow (SDF) semantics (M. Sen et al., 2005)}, keywords = {configurable hardware, Data communication, Gesture recognition, gesture recognition application, graph theory, hardware mapping, image processing applications, mapping multimedia applications, meta-modeling technique, model-based design, Multimedia communication, parameterized cyclo-static dataflow graphs}, doi = {10.1109/ICASSP.2006.1660838}, author = {Haim,F. and Sen,M. and Ko,Dong-Ik and Bhattacharyya, Shuvra S. and Wolf,W.} } @conference {12333, title = {Model-based mapping of image registration applications onto configurable hardware}, booktitle = {Signals, Systems and Computers, 2006. ACSSC{\textquoteright}06. Fortieth Asilomar Conference on}, year = {2006}, month = {2006///}, pages = {1453 - 1457}, author = {Hemaraj,Y. and Sen,M. and Shekhar,R. and Bhattacharyya, Shuvra S.} } @conference {17854, title = {Model-based OpenMP implementation of a 3D facial pose tracking system}, booktitle = {2006 International Conference on Parallel Processing Workshops, 2006. ICPP 2006 Workshops}, year = {2006}, month = {2006///}, pages = {8 pp.-73 - 8 pp.-73}, publisher = {IEEE}, organization = {IEEE}, abstract = {Most image processing applications are characterized by computation-intensive operations, and high memory and performance requirements. Parallelized implementation on shared-memory systems offer an attractive solution to this class of applications. However, we cannot thoroughly exploit the advantages of such architectures without proper modeling and analysis of the application. In this paper, we describe our implementation of a 3D facial pose tracking system using the OpenMP platform. Our implementation is based on a design methodology that uses coarse-grain dataflow graphs to model and schedule the application. We present our modeling approach, details of the implementation that we derived based on this modeling approach, and associated performance results. The parallelized implementation achieves significant speedup, and meets or exceeds the target frame rate under various configurations}, keywords = {3D facial pose tracking system, application modeling, application program interfaces, application scheduling, coarse-grain dataflow graphs, Concurrent computing, data flow graphs, Educational institutions, face recognition, IMAGE PROCESSING, image processing applications, Inference algorithms, Message passing, OpenMP platform, parallel implementation, PARALLEL PROCESSING, parallel programming, Particle tracking, Processor scheduling, SHAPE, shared memory systems, shared-memory systems, Solid modeling, tracking}, isbn = {0-7695-2637-3}, doi = {10.1109/ICPPW.2006.55}, author = {Saha,S. and Chung-Ching Shen and Chia-Jui Hsu and Aggarwal,G. and Veeraraghavan,A. and Sussman, Alan and Bhattacharyya, Shuvra S.} } @article {18254, title = {Multiuser distortion management of layered video over resource limited downlink multicode-CDMA}, journal = {Wireless Communications, IEEE Transactions on}, volume = {5}, year = {2006}, month = {2006/11//}, pages = {3056 - 3067}, abstract = {Transmitting multiple real-time encoded videos to multiple users over wireless cellular networks is a key driving force for developing broadband technology. We propose a new framework to transmit multiple users{\textquoteright} video programs encoded by MPEG-4 FGS codec over downlink multicode CDMA networks in real time. The proposed framework jointly manages the rate adaptation of source and channel coding, CDMA code allocation, and power control. Subject to the limited system resources, such as the number of pseudo-random codes and the maximal power for CDMA transmission, we develop an adaptive scheme of distortion management to ensure baseline video quality for each user and further reduce the overall distortion received by all users. To efficiently utilize system resources, the proposed scheme maintains a balanced ratio between the power and code usages. We also investigate three special scenarios where demand, power, or code is limited, respectively. Compared with existing methods in the literature, the proposed algorithm can reduce the overall system{\textquoteright}s distortion by 14\% to 26\%. In the demand-limited case and the code-limited but power-unlimited case, the proposed scheme achieves the optimal solutions. In the power-limited but code-unlimited case, the proposed scheme has a performance very close to a performance upper bound}, keywords = {(mobile, access;combined, allocation;broadband, case;layered, CDMA, cellular, code, codes;radio, codes;real-time, codes;telecommunication, coding;mobility, coding;video, coding;wireless, communication;, control;pseudo-random, control;pseudonoise, control;video, distortion, division, downlink, encoded, limited, links;random, management, management;power, multicode-CDMA;source-channel, multiple, networks;broadband, networks;cellular, radio);power, radio;code, source-channel, technology;code-unlimited, video;multiuser, videos;resource}, isbn = {1536-1276}, doi = {10.1109/TWC.2006.258231}, author = {Han,Z. and Su,Guan-Ming and Kwasinski,A. and M. Wu and Liu,K. J.R} } @article {13174, title = {Multivalued default logic for identity maintenance in visual surveillance}, journal = {Computer Vision{\textendash}ECCV 2006}, year = {2006}, month = {2006///}, pages = {119 - 132}, abstract = {Recognition of complex activities from surveillance video requires detection and temporal ordering of its constituent {\textquotedblleft}atomic{\textquotedblright} events. It also requires the capacity to robustly track individuals and maintain their identities across single as well as multiple camera views. Identity maintenance is a primary source of uncertainty for activity recognition and has been traditionally addressed via different appearance matching approaches. However these approaches, by themselves, are inadequate. In this paper, we propose a prioritized, multivalued, default logic based framework that allows reasoning about the identities of individuals. This is achieved by augmenting traditional appearance matching with contextual information about the environment and self identifying traits of certain actions. This framework also encodes qualitative confidence measures for the identity decisions it takes and finally, uses this information to reason about the occurrence of certain predefined activities in video.}, author = {Shet,V. and Harwood,D. and Davis, Larry S.} } @article {14799, title = {A New Hardware Monitor Design to Measure Data Structure-Specific Cache Eviction Information}, journal = {International Journal of High Performance Computing Applications}, volume = {20}, year = {2006}, month = {2006///}, pages = {353 - 363}, abstract = {In this paper, we propose a hardware performance monitor that provides support not only for measuring cache misses and the addresses associated with them, but also for determining what data is being evicted from the cache when a miss occurs. We describe how to use this hardware support to efficiently determine the cache behavior of application data structures at the source code level. We also present the results of a simulation-based study of this technique, in which we examined the overhead, perturbation of results, and usefulness of collecting this information.}, doi = {10.1177/1094342006067470}, url = {http://hpc.sagepub.com/content/20/3/353.abstract}, author = {Buck, B. R and Hollingsworth, Jeffrey K} } @conference {14557, title = {New lower bounds for oblivious routing in undirected graphs}, booktitle = {Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm}, year = {2006}, month = {2006///}, pages = {918 - 927}, author = {Hajiaghayi, Mohammad T. and Kleinberg,R. D and Leighton,T. and R\{\"a}cke,H.} } @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} } @conference {14554, title = {Oblivious network design}, booktitle = {Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm}, year = {2006}, month = {2006///}, pages = {970 - 979}, author = {Gupta,A. and Hajiaghayi, Mohammad T. and R\{\"a}cke,H.} } @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} } @article {13839, title = {Parallel syntactic annotation of multiple languages}, journal = {Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC2006). Genoa, Italy}, year = {2006}, month = {2006///}, abstract = {This paper describes an effort to investigate the incrementally deepening development of an interlingua notation, validated by humanannotation of texts in English plus six languages. We begin with deep syntactic annotation, and in this paper present a series of annotation manuals for six different languages at the deep-syntactic level of representation. Many syntactic differences between languages are removed in the proposed syntactic annotation, making them useful resources for multilingual NLP projects with semantic components. }, author = {Rambow,O. and Dorr, Bonnie J and Farwell,D. and Green,R. and Habash,N. and Helmreich,S. and Hovy,E. and Levin,L. and Miller,K.J. and Mitamura,T. and others} } @article {14631, title = {Patterns of sequence conservation in presynaptic neural genes}, journal = {Genome Biology}, volume = {7}, year = {2006}, month = {2006/11/10/}, pages = {R105 - R105}, abstract = {The neuronal synapse is a fundamental functional unit in the central nervous system of animals. Because synaptic function is evolutionarily conserved, we reasoned that functional sequences of genes and related genomic elements known to play important roles in neurotransmitter release would also be conserved.}, isbn = {1465-6906}, doi = {10.1186/gb-2006-7-11-r105}, url = {http://genomebiology.com/2006/7/11/R105}, author = {Hadley,Dexter and Murphy,Tara and Valladares,Otto and Hannenhalli, Sridhar and Ungar,Lyle and Kim,Junhyong and Bu{\'c}an,Maja} } @conference {13841, title = {PCFGs with syntactic and prosodic indicators of speech repairs}, booktitle = {Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the Association for Computational Linguistics}, series = {ACL-44}, year = {2006}, month = {2006///}, pages = {161 - 168}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {A grammatical method of combining two kinds of speech repair cues is presented. One cue, prosodic disjuncture, is detected by a decision tree-based ensemble classifier that uses acoustic cues to identify where normal prosody seems to be interrupted (Lickley, 1996). The other cue, syntactic parallelism, codifies the expectation that repairs continue a syntactic category that was left unfinished in the reparandum (Levelt, 1983). The two cues are combined in a Treebank PCFG whose states are split using a few simple tree transformations. Parsing performance on the Switchboard and Fisher corpora suggests that these two cues help to locate speech repairs in a synergistic way.}, doi = {10.3115/1220175.1220196}, url = {http://dx.doi.org/10.3115/1220175.1220196}, author = {Hale,John and Shafran,Izhak and Yung,Lisa and Dorr, Bonnie J and Harper,Mary and Krasnyanskaya,Anna and Lease,Matthew and Liu,Yang and Roark,Brian and Snover,Matthew and Stewart,Robin} } @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 {14724, title = {Practical dynamic software updating for C}, journal = {SIGPLAN Not.}, volume = {41}, year = {2006}, month = {2006/06//}, pages = {72 - 83}, abstract = {Software updates typically require stopping and restarting an application, but many systems cannot afford to halt service, or would prefer not to. Dynamic software updating (DSU) addresses this difficulty by permitting programs to be updated while they run. DSU is appealing compared to other approaches for on-line upgrades because it is quite general and requires no redundant hardware. The challenge is in making DSU practical: it should be flexible, and yet safe, efficient, and easy to use.In this paper, we present Ginseng, a DSU implementation for C that aims to meet this challenge. We compile programs specially so that they can be dynamically patched, and generate most of a dynamic patch automatically. Ginseng performs a series of analyses that when combined with some simple runtime support ensure that an update will not violate type-safety while guaranteeing that data is kept up-to-date. We have used Ginseng to construct and dynamically apply patches to three substantial open-source server programs---Very Secure FTP daemon, OpenSSH sshd daemon, and GNU Zebra. In total, we dynamically patched each program with three years{\textquoteright} worth of releases. Though the programs changed substantially, the majority of updates were easy to generate. Performance experiments show that all patches could be applied in less than 5 ms, and that the overhead on application throughput due to updating support ranged from 0 to at most 32\%.}, keywords = {dynamic software updating, function indirection, loop extraction, type wrapping}, isbn = {0362-1340}, doi = {10.1145/1133255.1133991}, url = {http://doi.acm.org/10.1145/1133255.1133991}, author = {Neamtiu,Iulian and Hicks, Michael W. and Stoyle,Gareth and Oriol,Manuel} } @conference {14558, title = {The prize-collecting generalized Steiner tree problem via a new approach of primal-dual schema}, booktitle = {Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm}, year = {2006}, month = {2006///}, pages = {631 - 640}, author = {Hajiaghayi, Mohammad T. and Jain,K.} } @article {16875, title = {A probabilistic analysis of trie-based sorting of large collections of line segments in spatial databases}, journal = {SIAM Journal on Computing}, volume = {35}, year = {2006}, month = {2006///}, pages = {22 - 58}, author = {Lindenbaum,M. and Samet, Hanan and Hjaltason,G. R} } @conference {13169, title = {Real-Time Human Detection, Tracking, and Verification in Uncontrolled Camera Motion Environments}, booktitle = {Computer Vision Systems, 2006 ICVS {\textquoteright}06. IEEE International Conference on}, year = {2006}, month = {2006/01//}, pages = {41 - 41}, abstract = {In environments where a camera is installed on a freely moving platform, e.g. a vehicle or a robot, object detection and tracking becomes much more difficult. In this paper, we presents a real time system for human detection, tracking, and verification in such challenging environments. To deliver a robust performance, the system integrates several computer vision algorithms to perform its function: a human detection algorithm, an object tracking algorithm, and a motion analysis algorithm. To utilize the available computing resources to the maximum possible extent, each of the system components is designed to work in a separate thread that communicates with the other threads through shared data structures. The focus of this paper is more on the implementation issues than on the algorithmic issues of the system. Object oriented design was adopted to abstract algorithmic details away from the system structure.}, doi = {10.1109/ICVS.2006.52}, author = {Hussein,M. and Abd-Almageed, Wael and Yang Ran and Davis, Larry S.} } @conference {12374, title = {Reconfigurable image registration on FPGA platforms}, booktitle = {Biomedical Circuits and Systems Conference, 2006. BioCAS 2006. IEEE}, year = {2006}, month = {2006///}, pages = {154 - 157}, author = {Sen,M. and Hemaraj,Y. and Bhattacharyya, Shuvra S. and Shekhar,R.} } @article {14637, title = {Recurring genomic breaks in independent lineages support genomic fragility}, journal = {BMC Evolutionary Biology}, volume = {6}, year = {2006}, month = {2006/11/07/}, pages = {90 - 90}, abstract = {Recent findings indicate that evolutionary breaks in the genome are not randomly distributed, and that certain regions, so-called fragile regions, are predisposed to breakages. Previous approaches to the study of genomic fragility have examined the distribution of breaks, as well as the coincidence of breaks with segmental duplications and repeats, within a single species. In contrast, we investigate whether this regional fragility is an inherent genomic characteristic and is thus conserved over multiple independent lineages.}, isbn = {1471-2148}, doi = {10.1186/1471-2148-6-90}, url = {http://www.biomedcentral.com/1471-2148/6/90}, author = {Hinsch,Hanno and Hannenhalli, Sridhar} } @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} } @conference {13849, title = {Reranking for Sentence Boundary Detection in Conversational Speech}, booktitle = {2006 IEEE International Conference on Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings}, volume = {1}, year = {2006}, month = {2006/05/14/19}, pages = {I-I - I-I}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present a reranking approach to sentence-like unit (SU) boundary detection, one of the EARS metadata extraction tasks. Techniques for generating relatively small n-best lists with high oracle accuracy are presented. For each candidate, features are derived from a range of information sources, including the output of a number of parsers. Our approach yields significant improvements over the best performing system from the NIST RT-04F community evaluation}, keywords = {Automatic speech recognition, conversational speech, data mining, Ear, EARS metadata extraction tasks, Feature extraction, hidden Markov models, meta data, Model driven engineering, NIST, NIST RT-04F community evaluation, oracle accuracy, performance evaluation, reranking, sentence-like unit boundary detection, Speech processing, Speech recognition, Telephony}, isbn = {1-4244-0469-X}, doi = {10.1109/ICASSP.2006.1660078}, author = {Roark,B. and Liu,Yang and Harper,M. and Stewart,R. and Lease,M. and Snover,M. and Shafran,I. and Dorr, Bonnie J and Hale,J. and Krasnyanskaya,A. and Yung,L.} } @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 {14731, title = {Safe manual memory management in Cyclone}, journal = {Science of Computer Programming}, volume = {62}, year = {2006}, month = {2006/10/01/}, pages = {122 - 144}, abstract = {The goal of the Cyclone project is to investigate how to make a low-level C-like language safe. Our most difficult challenge has been providing programmers with control over memory management while retaining safety. This paper describes our experience trying to integrate and use effectively two previously-proposed, safe memory-management mechanisms: statically-scoped regions and tracked pointers. We found that these typing mechanisms can be combined to build alternative memory-management abstractions, such as reference counted objects and arenas with dynamic lifetimes, and thus provide a flexible basis. Our experience {\textemdash} porting C programs and device drivers, and building new applications for resource-constrained systems {\textemdash} confirms that experts can use these features to improve memory footprint and sometimes to improve throughput when used instead of, or in combination with, conservative garbage collection.}, keywords = {cyclone, Memory management, memory safety, Reaps, Reference counting, regions, unique pointers}, isbn = {0167-6423}, doi = {10.1016/j.scico.2006.02.003}, url = {http://www.sciencedirect.com/science/article/pii/S0167642306000785}, author = {Swamy,Nikhil and Hicks, Michael W. and Morrisett,Greg and Grossman,Dan and Jim,Trevor} } @article {18159, title = {A Scalable Multiuser Framework for Video Over OFDM Networks: Fairness and Efficiency}, journal = {Circuits and Systems for Video Technology, IEEE Transactions on}, volume = {16}, year = {2006}, month = {2006/10//}, pages = {1217 - 1231}, abstract = {In this paper, we propose a framework to transmit multiple scalable video programs over downlink multiuser orthogonal frequency division multiplex (OFDM) networks in real time. The framework explores the scalability of the video codec and multidimensional diversity of multiuser OFDM systems to achieve the optimal service objectives subject to constraints on delay and limited system resources. We consider two essential service objectives, namely, the fairness and efficiency. Fairness concerns the video quality deviation among users who subscribe the same quality of service, and efficiency relates to how to attain the highest overall video quality using the available system resources. We formulate the fairness problem as minimizing the maximal end-to-end distortion received among all users and the efficiency problem as minimizing total end-to-end distortion of all users. Fast suboptimal algorithms are proposed to solve the above two optimization problems. The simulation results demonstrated that the proposed fairness algorithm outperforms a time division multiple (TDM) algorithm by 0.5 3 dB in terms of the worst received video quality among all users. In addition, the proposed framework can achieve a desired tradeoff between fairness and efficiency. For achieving the same average video quality among all users, the proposed framework can provide fairer video quality with 1 1.8 dB lower PSNR deviation than a TDM algorithm}, keywords = {algorithm;video, codec;video, coding;video, communication;, deviation;downlink, deviation;OFDM, distortion;multidimensional, diversity;multiple, division, end-to-end, framework;time, Frequency, modulation;diversity, multiple, multiplex, multiuser, network;efficiency, networks;video, objectives;optimization, of, OFDM, orthogonal, over, problem;fairness, problem;maximal, problems;quality, programs;multiuser, PSNR, QUALITY, reception;image, resolution;optimisation;quality, scalable, service, service;scalable, service;video, systems;optimal, video}, isbn = {1051-8215}, doi = {10.1109/TCSVT.2006.883513}, author = {Su,Guan-Ming and Han,Zhu and M. Wu and Liu,K. J.R} } @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} } @article {14642, title = {Selection of Target Sites for Mobile DNA Integration in the Human Genome}, journal = {PLoS Comput BiolPLoS Comput Biol}, volume = {2}, year = {2006}, month = {2006/11/24/}, pages = {e157 - e157}, abstract = {DNA sequences from retroviruses, retrotransposons, DNA transposons, and parvoviruses can all become integrated into the human genome. Accumulation of such sequences accounts for at least 40\% of our genome today. These integrating elements are also of interest as gene-delivery vectors for human gene therapy. Here we present a comprehensive bioinformatic analysis of integration targeting by HIV, MLV, ASLV, SFV, L1, SB, and AAV. We used a mathematical method which allowed annotation of each base pair in the human genome for its likelihood of hosting an integration event by each type of element, taking advantage of more than 200 types of genomic annotation. This bioinformatic resource documents a wealth of new associations between genomic features and integration targeting. The study also revealed that the length of genomic intervals analyzed strongly affected the conclusions drawn{\textemdash}thus, answering the question {\textquotedblleft}What genomic features affect integration?{\textquotedblright} requires carefully specifying the length scale of interest.}, doi = {10.1371/journal.pcbi.0020157}, url = {UR - http://dx.plos.org/10.1371/journal.pcbi.0020157,http://dx.plos.org/10.1371/journal.pcbi.0020157}, author = {Berry,Charles and Hannenhalli, Sridhar and Leipzig,Jeremy and Bushman,Frederic D.} } @conference {13179, title = {Semi-Parametric Model-Based Clustering for DNA Microarray Data}, booktitle = {Pattern Recognition, 2006. ICPR 2006. 18th International Conference on}, volume = {3}, year = {2006}, month = {2006//00/0}, pages = {324 - 327}, abstract = {Various clustering methods have been proposed for the analysis of gene expression data, but conventional clustering algorithms have several critical limitations; how to set parameters such as number of clusters, initial cluster centers, and so on. In this paper, we propose a semi-parametric model-based clustering algorithm in which the underlying model is a mixture of Gaussian. Each gene expression data builds a Gaussian kernel, and the uncertainty of microarray data is naturally integrated in the data representation. Our algorithm provides a principled method to automatically determine parameters - number of components in the mixture, mean, covariance, and weight of each Gaussian - by mean-shift procedure (Comaniciu and Meer, 1999) and curvature fitting. After the initialization, expectation maximization (EM) algorithm is employed for clustering to achieve maximum likelihood (ML). The performance of our algorithm is compared with standard EM algorithm using real data as well as synthetic data}, keywords = {clustering;, clustering;DNA;Gaussian, computing;genetics;pattern, data;Gaussian, data;maximum, DNA, Expression, fitting;data, kernel;Gaussian, likelihood;mean-shift, maximization;gene, Microarray, mixtures;curvature, model-based, procedure;semiparametric, processes;biology, representation;expectation}, doi = {10.1109/ICPR.2006.1044}, author = {Han,Bohyung and Davis, Larry S.} } @article {17356, title = {Severity and impact of computer user frustration: A comparison of student and workplace users}, journal = {Interacting with Computers}, volume = {18}, year = {2006}, month = {2006/03//}, pages = {187 - 207}, abstract = {User frustration with information and computing technology is a pervasive 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. Our exploratory study of 107 student computer users and 50 workplace computer users shows high levels of frustration and loss of 1/3{\textendash}1/2 of time spent. This paper reports on the incident and individual factors that cause of frustration, and how they raise frustration severity. It examines the frustration impacts on the daily interactions of the users. The time lost and time to fix problem, and importance of task, strongly correlate with frustration levels for both student and workplace users. Differences between students and workplace users are discussed in the paper, as are implications for researchers.}, keywords = {Computer anxiety, Computer experience, Helpdesk, Training, User frustration, user interface design}, isbn = {0953-5438}, doi = {10.1016/j.intcom.2005.06.001}, url = {http://www.sciencedirect.com/science/article/pii/S0953543805000561}, author = {Lazar,Jonathan and Jones,Adam and Hackley,Mary and Shneiderman, Ben} } @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} } @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 {17663, title = {System and method for locating a closest server in response to a client ...}, volume = {09/726,192}, year = {2006}, month = {2006/03/28/}, abstract = {A scalable system and method for locating a closest server in response to a client request via an interactive distribution network, such as the Internet, are provided. A closest content server is defined as having the least round trip time for responding to a client request. The system including a plurality of content servers; and a local server in communication with a plurality of clients, the local server acting as a proxy for communicating client requests from clients to a redirection server. Client network distance and load information is periodically collected at each content server in the network from clients communicating with each of the respective content servers. The redirection server periodically aggregates the network distance and load information from each content server to create client clusters from both current and previously aggregated network distance and load information. Each client cluster represents a division or partition of the total IP address space. Each...}, url = {http://www.google.com/patents?id=cE54AAAAEBAJ}, author = {Andrews,Matthew and Hofmann,Markus and Shepherd,Bruce and Srinivasan, Aravind and Winkler,Peter and Zane,Francis}, editor = {Lucent Technologies Inc.} } @conference {16089, title = {Task taxonomy for graph visualization}, booktitle = {Proceedings of the 2006 AVI workshop on BEyond time and errors: novel evaluation methods for information visualization}, series = {BELIV {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {1 - 5}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Our goal is to define a list of tasks for graph visualization that has enough detail and specificity to be useful to: 1) designers who want to improve their system and 2) to evaluators who want to compare graph visualization systems. In this paper, we suggest a list of tasks we believe are commonly encountered while analyzing graph data. We define graph specific objects and demonstrate how all complex tasks could be seen as a series of low-level tasks performed on those objects. We believe that our taxonomy, associated with benchmark datasets and specific tasks, would help evaluators generalize results collected through a series of controlled experiments.}, keywords = {Evaluation, graph visualization, task taxonomy}, isbn = {1-59593-562-2}, doi = {10.1145/1168149.1168168}, url = {http://doi.acm.org/10.1145/1168149.1168168}, author = {Lee,Bongshin and Plaisant, Catherine and Parr,Cynthia Sims and Fekete,Jean-Daniel and Henry,Nathalie} } @conference {13173, title = {Top-down, bottom-up multivalued default reasoning for identity maintenance}, booktitle = {Proceedings of the 4th ACM international workshop on Video surveillance and sensor networks}, series = {VSSN {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {79 - 86}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Persistent tracking systems require the capacity to track individuals by maintaining identity across visibility gaps caused by occlusion events. In traditional computer vision systems, the flow of information is typically bottom-up. The low level image processing modules take video input, perform early vision tasks such as background subtraction and object detection,and pass this information to the high level reasoning module. This paper describes the architecture of a system that uses top-down information flow to perform identity maintenance across occlusion events. This system uses the high level reasoning module to provide control feedback to the low level image processing module to perform forensic analysis of archival video and actively acquire information required to arrive at identity decisions. This functionality is in addition to traditional bottom-up reasoning about identity, employing contextual cues and appearance matching, within the multivalued default logic framework proposed in [18]. This framework, in addition to bestowing upon the system the property of nonmonotonicity, also allows for it to qualitatively encode its confidence in the identity decisions it takes.}, keywords = {default logic, identity maintenance, nonmonotonic reasoning, tracking, visual surveillance}, isbn = {1-59593-496-0}, doi = {10.1145/1178782.1178795}, url = {http://doi.acm.org/10.1145/1178782.1178795}, author = {Shet,Vinay D. and Harwood,David and Davis, Larry S.} } @conference {13339, title = {Topology-based reasoning on non-manifold shapes}, booktitle = {Proceedings of the 1st International Symposium on Shapes and Semantics, Matsushima, Japan}, year = {2006}, month = {2006///}, abstract = {Topological information is a promising resource to research in shape-understanding as it provides a high-level description of the characteristics of a shape, and such high-level description often has strong association with the semantics of an object. The Shape Acquisition and Processing (SAP) ontology has been designed to maintain useful information of a model. We propose here an extension to the SAP ontology, that addresses the non-manifold properties of a model. Useful information about the connectivity of an object can be obtained based on an analysis of its non- manifold properties, because the structure of a non-manifold object can be considered as a graph of manifold parts connected together at non-manifold joints. The manifold parts are often pieces that have strong semantic associations. In this work, we describe the type of non-manifold properties, the various types of connected components in a non-manifold object and their semantical significance. We address how the Euler{\textquoteright} characteristics of a non-manifold object can be found based on such information. All such information are extractable from a model using TopMesh, a tool that we have developed. In this work, we also describe the features of TopMesh, namely, all the topological properties it extracts. }, author = {De Floriani, Leila and Hui,A. and Papaleo,L.} } @article {17434, title = {Toward an enriched (and revitalized) sense of help: Summary of an ASIS\&T 2005 panel session}, journal = {Bulletin of the American Society for Information Science and Technology}, volume = {32}, year = {2006}, month = {2006/06/01/}, pages = {23 - 26}, isbn = {1550-8366}, doi = {10.1002/bult.2006.1720320509}, url = {http://onlinelibrary.wiley.com/doi/10.1002/bult.2006.1720320509/abstract}, author = {Haas,Stephanie W and Denn,Sheila and Locke,David and Shneiderman, Ben and Brown,Laurie} } @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} } @conference {13161, title = {Tracking Articulating Objects from Ground Vehicles using Mixtures of Mixtures}, booktitle = {Intelligent Robots and Systems, 2006 IEEE/RSJ International Conference on}, year = {2006}, month = {2006/10//}, pages = {1230 - 1236}, abstract = {An algorithm for tracking articulating objects from moving camera platforms is presented. Mixtures of mixtures are used to model the appearance of the object and the background. The state of the object is tracked using a particle filter. Egomotion information are estimated and used to set the state variance of the particle filter. Results of tracking human objects from an unmanned ground vehicle are used to evaluate the tracking algorithm}, keywords = {articulating, filter;unmanned, ground, information;mixtures, mixtures;particle, objects, of, operated, tracking;egomotion, vehicle;remotely, vehicles;robot, vision;}, doi = {10.1109/IROS.2006.281881}, author = {Abd-Almageed, Wael and Hussein,M. and Davis, Larry S.} } @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.} } @conference {14750, title = {Trusted declassification:: high-level policy for a security-typed language}, booktitle = {Proceedings of the 2006 workshop on Programming languages and analysis for security}, series = {PLAS {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {65 - 74}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Security-typed languages promise to be a powerful tool with which provably secure software applications may be developed. Programs written in these languages enforce a strong, global policy of noninterferencewhich ensures that high-security data will not be observable on low-security channels. Because noninterference is typically too strong a property, most programs use some form of declassification to selectively leak high security information, e.g. when performing a password check or data encryption. Unfortunately, such a declassification is often expressed as an operation within a given program, rather than as part of a global policy, making reasoning about the security implications of a policy more difficult.In this paper, we propose a simple idea we call trusted declassification in which special declassifier functions are specified as part of the global policy. In particular, individual principals declaratively specify which declassifiers they trust so that all information flows implied by the policy can be reasoned about in absence of a particular program. We formalize our approach for a Java-like language and prove a modified form of noninterference which we call noninterference modulo trusted methods. We have implemented our approach as an extension to Jif and provide some of our experience using it to build a secure e-mail client.}, keywords = {noninterference modolo trusted methods, declassification, FJifP, information-flow control, Jif, security policy, security-typed languages, trusted declassification}, isbn = {1-59593-374-3}, doi = {10.1145/1134744.1134757}, url = {http://doi.acm.org/10.1145/1134744.1134757}, author = {Hicks,Boniface and King,Dave and McDaniel,Patrick and Hicks, Michael W.} } @inbook {16090, title = {Visualizing Graphs as Trees: Plant a Seed and Watch it Grow}, booktitle = {Graph DrawingGraph Drawing}, series = {Lecture Notes in Computer Science}, volume = {3843}, year = {2006}, month = {2006///}, pages = {516 - 518}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {TreePlus is a graph browsing technique based on a tree-style layout. It shows the missing graph structure using interaction techniques and enables users to start with a specific node and incrementally explore the local structure of graphs. We believe that it supports particularly well tasks that require rapid reading of labels.}, isbn = {978-3-540-31425-7}, url = {http://dx.doi.org/10.1007/11618058_50}, author = {Lee,Bongshin and Parr,Cynthia and Plaisant, Catherine and Bederson, Benjamin B.}, editor = {Healy,Patrick and Nikolov,Nikola} } @inbook {13416, title = {Active Constrained Clustering by Examining Spectral Eigenvectors}, booktitle = {Discovery ScienceDiscovery Science}, series = {Lecture Notes in Computer Science}, volume = {3735}, year = {2005}, month = {2005///}, pages = {294 - 307}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This work focuses on the active selection of pairwise constraints for spectral clustering. We develop and analyze a technique for Active Constrained Clustering by Examining Spectral eigenvectorS (ACCESS) derived from a similarity matrix. The ACCESS method uses an analysis based on the theoretical properties of spectral decomposition to identify data items that are likely to be located on the boundaries of clusters, and for which providing constraints can resolve ambiguity in the cluster descriptions. Empirical results on three synthetic and five real data sets show that ACCESS significantly outperforms constrained spectral clustering using randomly selected constraints.}, isbn = {978-3-540-29230-2}, url = {http://dx.doi.org/10.1007/11563983_25}, author = {Xu,Qianjun and desJardins, Marie and Wagstaff,Kiri}, editor = {Hoffmann,Achim and Motoda,Hiroshi and Scheffer,Tobias} } @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 {14563, title = {Algorithmic graph minor theory: Decomposition, approximation, and coloring}, booktitle = {Foundations of Computer Science, 2005. FOCS 2005. 46th Annual IEEE Symposium on}, year = {2005}, month = {2005///}, pages = {637 - 646}, abstract = {At the core of the seminal graph minor theory of Robertson and Seymour is a powerful structural theorem capturing the structure of graphs excluding a fixed minor. This result is used throughout graph theory and graph algorithms, but is existential. We develop a polynomial-time algorithm using topological graph theory to decompose a graph into the structure guaranteed by the theorem: a clique-sum of pieces almost-embeddable into bounded-genus surfaces. This result has many applications. In particular we show applications to developing many approximation algorithms, including a 2-approximation to graph coloring, constant-factor approximations to treewidth and the largest grid minor, combinatorial polylogarithmic approximation to half-integral multicommodity flow, subexponential fixed-parameter algorithms, and PTASs for many minimization and maximization problems, on graphs excluding a fixed minor.}, keywords = {algorithmic graph minor theory, approximation algorithm, combinatorial polylogarithmic approximation, computational complexity, constant-factor approximation, graph algorithm, graph coloring, graph colouring, half-integral multicommodity flow, largest grid minor, maximization problem, minimization problem, polynomial-time algorithm, subexponential fixed-parameter algorithm, topological graph theory, treewidth}, doi = {10.1109/SFCS.2005.14}, author = {Demaine,E. D and Hajiaghayi, Mohammad T. and Kawarabayashi,K.} } @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} } @article {16961, title = {An Augmented Visual Query Mechanism for Finding Patterns in Time Series Data (2002)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, 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.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6495}, author = {Keogh,Eamonn and Hochheiser,Harry and Shneiderman, Ben} } @article {14798, title = {Automatic Mining of Source Code Repositories to Improve Bug Finding Techniques}, journal = {IEEE Transactions on Software Engineering}, volume = {31}, year = {2005}, month = {2005///}, pages = {466 - 480}, abstract = {We describe a method to use the source code change history of a software project to drive and help to refine the search for bugs. Based on the data retrieved from the source code repository, we implement a static source code checker that searches for a commonly fixed bug and uses information automatically mined from the source code repository to refine its results. By applying our tool, we have identified a total of 178 warnings that are likely bugs in the Apache Web server source code and a total of 546 warnings that are likely bugs in Wine, an open-source implementation of the Windows API. We show that our technique is more effective than the same static analysis that does not use historical data from the source code repository.}, keywords = {configuration control, debugging aids., index terms- testing tools, version control}, isbn = {0098-5589}, doi = {http://doi.ieeecomputersociety.org/10.1109/TSE.2005.63}, author = {Williams, Chadd C and Hollingsworth, Jeffrey K} } @article {13205, title = {Background updating for visual surveillance}, journal = {Advances in Visual Computing}, year = {2005}, month = {2005///}, pages = {337 - 346}, abstract = {Scene changes such as moved objects, parked vehicles, or opened/closed doors need to be carefully handled so that interesting foreground targets can be detected along with the short-term background layers created by those changes. A simple layered modeling technique is embedded into a codebook-based background subtraction algorithm to update a background model. In addition, important issues related to background updating for visual surveillance are discussed. Experimental results on surveillance examples, such as unloaded packages and unattended objects, are presented by showing those objects as short-term background layers.}, author = {Kim,K. and Harwood,D. and Davis, Larry S.} } @article {14029, title = {Bayesian filtering and integral image for visual tracking}, journal = {Proceedings of the Worshop on Image Analysis for Multimedia Interactive Services (WIAMIS{\textquoteright}05)}, year = {2005}, month = {2005///}, abstract = {This paper describes contributions to two problems related tovisual tracking: control model design and observation process design. We describe the use of kernel-based Bayesian filtering for the tracking control procedure, and feature-based tracking to improve the observation process of tracking. In the kernel- based Bayesian filtering framework, the analytical represen- tation of density functions by density interpolation and density approximation for the likelihood and the posterior contributes to efficient sampling. Feature-based tracking combines rec- tangular features with edge oriented histogram so that the combined features are robust to illumination changes, partial occlusion, and clutter while capturing the spatial information of the target. The use of integral image allows the features to be efficiently evaluated. The effectiveness of both algorithms are demonstrated by object tracking results on real videos. }, author = {Han,B. and Yang,C. and Duraiswami, Ramani and Davis, Larry S.} } @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 {15099, title = {Bounds on the efficiency of black-box commitment schemes}, journal = {Automata, Languages and Programming}, year = {2005}, month = {2005///}, pages = {62 - 62}, abstract = {Constructions of cryptographic primitives based on general assumptions (e.g., the existence of one-way functions) tend to be less efficient than constructions based on specific (e.g., number-theoretic) assumptions. This has prompted a recent line of research aimed at investigating the best possible efficiency of (black-box) constructions based on general assumptions. Here, we present bounds on the efficiency of statistically-binding commitment schemes constructed using black-box access to one-way permutations; our bounds are tight for the case of perfectly-binding schemes. We present the bounds in an extension of the Impagliazzo-Rudich model; that is, we show that any construction beating our bounds would imply the unconditional existence of a one-way function (from which a commitment scheme could be constructed {\textquotedblleft}from scratch{\textquotedblright}). Our analysis is the first in the area to pertain directly to an information-theoretic component of the security notion.}, doi = {10.1007/11523468_11}, author = {Horvitz,O. and Katz, Jonathan} } @article {18928, title = {Breaking the resource bottleneck for multilingual parsing}, year = {2005}, month = {2005///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {We propose a framework that enables the acquisition of annotation-heavy resources such as syntacfic dependency tree corpora for low-resource languages by importing linguistic annotations from high-quality English resources. We present a large-scale experiment showing that Chinese dependency trees can be induced by using an English parser, a word alignment package, and a large corpus of sentence-aligned bilingual text. As a part of the experiment, we evaluate the quality of a Chinese parser trained on the induced dependency treebank. We find that a parser trained in this manner out-performs some simple baselines inspite of the noise in the induced treebank. The results suggest that projecting syntactic structures from English is a viable option for acquiring annotated syntactic structures quickly and cheaply. We expect the quality of the induced treebank to improve when more sophisticated filtering and error-correction techniques are applied.}, url = {http://oai.dtic.mil/oai/oai?verb=getRecord\&metadataPrefix=html\&identifier=ADA440432}, author = {Hwa,R. and Resnik, Philip and Weinberg, Amy} } @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} } @conference {18171, title = {Building efficient and effective multimedia fingerprints via joint coding and embedding}, booktitle = {Proceedings of the 7th workshop on Multimedia and security}, series = {MM\&$\#$38;Sec {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {127 - 136}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Digital fingerprinting protects multimedia content from illegal redistribution by uniquely marking every copy of the content distributed to each user. One major category of collusion-resistant fingerprinting employs an explicit step of coding. Most existing works on coded fingerprinting mainly focus on the code-level issues and treat the embedding issues through abstract assumptions without examining the overall performance. In this paper, we jointly consider the coding and embedding issues for coded fingerprinting systems and examine their performance in terms of collusion resistance, detection computational complexity, and distribution efficiency. Our studies show that coded fingerprinting has efficient detection but rather low collusion resistance. Taking advantage of joint coding and embedding, we propose two new techniques, namely, a Permuted Subsegment Embedding technique and a Group-based Joint Coding and Embedding (GRACE) technique, to improve the collusion resistance of coded fingerprinting while maintaining its efficient detection. Experimental results show that the number of colluders that the proposed methods can resist is more than three times as many as that of the conventional coded fingerprinting approaches.}, keywords = {collusion resistance, error correcting code, multimedia fingerprinting}, isbn = {1-59593-032-9}, doi = {10.1145/1073170.1073194}, url = {http://doi.acm.org/10.1145/1073170.1073194}, author = {He,Shan and M. Wu} } @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} } @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 {17033, title = {Coordinating Overviews and Detail Views of WWW Log Data (2000)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {Web server log analysis tools provide site operators with useful information regarding the visitors to their sites. Unfortunately, the utility of these tools is often limited by the use of aggregate summaries that hide the information associated with individual requests, and by the absence of contextual data that might help users interpret those summaries. Building upon earlier work in the use of starfield visualizations to display web site requests as individual data points [8], this paper describes the use of multiple-coordinated visualizations of web log data at varying granularities, and alongside additional related displays of appropriate contextual information.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6476}, author = {Hochheiser,Harry and Shneiderman, Ben} } @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 {14673, title = {Cyclone: A type-safe dialect of C}, journal = {C/C++ Users Journal}, volume = {23}, year = {2005}, month = {2005///}, pages = {112 - 139}, abstract = {If any bug has achieved celebrity status, it is thebuffer overflow. It made front-page news as early as 1987, as the enabler of the Morris worm, the first worm to spread through the Internet. In recent years, attacks exploiting buffer overflows have become more frequent, and more virulent. This year, for exam- ple, the Witty worm was released to the wild less than 48 hours after a buffer overflow vulnerability was publicly announced; in 45 minutes, it infected the entire world-wide population of 12,000 machines running the vulnerable programs. Notably, buffer overflows are a problem only for the C and C++ languages{\textemdash}Java and other {\textquotedblleft}safe{\textquotedblright} lan- guages have built-in protection against them. More- over, buffer overflows appear in C programs written by expert programmers who are security concious{\textemdash} programs such as OpenSSH, Kerberos, and the com- mercial intrusion detection programs that were the target of Witty. This is bad news for C. If security experts have trouble producing overflow-free C programs, then there is not much hope for ordinary C program- mers. On the other hand, programming in Java is no panacea; for certain applications, C has no com- petition. From a programmer{\textquoteright}s point of view, all the safe languages are about the same, while C is a very different beast. }, author = {Grossman,D. and Hicks, Michael W. and Jim,T. and Morrisett,G.} } @conference {13284, title = {Data structures for simplicial complexes: an analysis and a comparison}, booktitle = {Proceedings of the third Eurographics symposium on Geometry processing}, series = {SGP {\textquoteright}05}, year = {2005}, month = {2005///}, publisher = {Eurographics Association}, organization = {Eurographics Association}, address = {Aire-la-Ville, Switzerland, Switzerland}, abstract = {In this paper, we review, analyze and compare representations for simplicial complexes. We classify such representations, based on the dimension of the complexes they can encode, into dimension-independent structures, and data structures for three- and for two-dimensional simplicial complexes. We further classify the data structures in each group according to the basic kinds of the topological entities they represent. We present a description of each data structure in terms of the entities and topological relations encoded, and we evaluate it based on its expressive power, on its storage cost and on the efficiency in supporting navigation inside the complex, i.e., in retrieving topological relations not explicitly encoded. We compare the various data structures inside each category based on the above features.}, isbn = {3-905673-24-X}, url = {http://dl.acm.org/citation.cfm?id=1281920.1281940}, author = {De Floriani, Leila and Hui,Annie} } @conference {16878, title = {A distributed quadtree index for peer-to-peer settings}, booktitle = {PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON DATA ENGINEERING}, volume = {21}, year = {2005}, month = {2005///}, pages = {254 - 254}, author = {Tanin,E. and Harwood,A. and Samet, Hanan} } @conference {13547, title = {Document Ranking by Layout Relevance}, booktitle = {ICDAR}, year = {2005}, month = {2005/08//}, pages = {362 - 366}, abstract = {This paper describes the development of a new document ranking system based on layout similarity. The user has a need represented by a set of {\textquotedblright}wanted{\textquotedblright} documents, and the system ranks documents in the collection according to this need. Rather than performing complete document analysis, the system extracts text lines, and models layouts as relationships between pairs of these lines. This paper explores three novel feature sets to support scoring in large document collections. First, pairs of lines are used to form quadrilaterals, which are represented by their turning functions. A non- Euclidean distance is used to measure similarity. Second, the quadrilaterals are represented by 5DEuclidean vectors, and third, each line is represented by a 5DEuclidean vector. We compare the classification performance and computation speed of these three feature sets using a large database of diverse documents including forms, academic papers and handwritten pages in English and Arabic. The approach using quadrilaterals and turning functions produces slightly better results, but the approach using vectors to represent text lines is much faster for large document databases.}, author = {Huang,Mei and DeMenthon,Daniel and David Doermann and Golebiowski,Lynn} } @article {14680, title = {Dynamic inference of polymorphic lock types}, journal = {Science of Computer Programming}, volume = {58}, year = {2005}, month = {2005/12//}, pages = {366 - 383}, abstract = {We present FindLocks, an approach for automatically proving the absence of data races in multi-threaded Java programs, using a combination of dynamic and static analysis. The program in question is instrumented so that when executed it will gather information about locking relationships. This information is then used to automatically generate annotations needed to type check the program using the Race-Free Java type system. Programs that type check are sure to be free from races. We call this technique dynamic annotation inference. We describe the design and implementation of our approach, and our experience applying the tool to a variety of Java programs. We have found that when using a reasonably comprehensive test suite, which is easy for small programs but harder for larger ones, the approach generates useful annotations.}, keywords = {Data races, Dynamic analysis, java, Multithreading, Type inference}, isbn = {0167-6423}, doi = {10.1016/j.scico.2005.03.003}, url = {http://www.sciencedirect.com/science/article/pii/S0167642305000705}, author = {Rose,James and Swamy,Nikhil and Hicks, Michael W.} } @article {17110, title = {Dynamic query tools for time series data sets: Timebox widgets for interactive exploration (2004)}, year = {2005}, month = {2005///}, abstract = {Timeboxes are rectangular widgets that can be used in direct-manipulation graphical user interfaces (GUIs) to specify query constraints on time series data sets. Timeboxes are used to specify simultaneously two sets of constraints: given a set of N time series profiles, a timebox covering time periods x1...x2 (x1rx2) and values y1...y2 (y1ry2) will retrieve only those nAN that have values y1ryry2 during all times x1rxrx2. TimeSearcher is an information visualization tool that combines timebox queries with overview displays, query-byexample facilities, and support for queries over multiple time-varying attributes. Query manipulation tools including pattern inversion and eaders \& laggards graphical bookmarks provide additional support for interactive exploration of data sets. Extensions to the basic timebox model that provide additional expressivity include variable time timeboxes, which can be used to express queries with variability in the time interval, and angular queries, which search for ranges of differentials, rather than absolute values. Analysis of the algorithmic requirements for providing dynamic query performance for timebox queries showed that a sequential search outperformed searches based on geometric indices. Design studies helped identify the strengths and weaknesses of the query tools. Extended case studies involving the analysis of two different types of data from molecular biology experiments provided valuable feedback and validated the utility of both the timebox model and the TimeSearcher tool.

Timesearcher is available [url=http://www.cs.umd.edu/hcil/ timesearcher]online.[/url]}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6521}, author = {Hochheiser,Harry and Shneiderman, Ben} } @article {17114, title = {Dynamic Querying for Pattern Identification in Microarray and Genomic Data (2003)}, year = {2005}, month = {2005///}, abstract = {Data sets involving linear ordered sequences are a recurring theme in bioinformatics. Dynamic query tools that support exploration of these data sets can be useful for identifying patterns of interest. This paper describes the use of one such tool TimeSearcher - to interactively explore linear sequence data sets taken from two bioinformatics problems. Microarray time course data sets involve expression levels for large numbers of genes over multiple time points. TimeSearcher can be used to interactively search these data sets for genes with expression profiles of interest. The occurrence frequencies of short sequences of DNA in aligned exons can be used to identify sequences that play a role in the pre-mRNA splicing. TimeSearcher can be used to search these data sets for candidate splicing signals.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6503}, author = {Hochheiser,Harry and Baehrecke,Eric H and Mount, Stephen M. and Shneiderman, Ben} } @article {14686, title = {Dynamic software updating}, journal = {ACM Trans. Program. Lang. Syst.}, volume = {27}, year = {2005}, month = {2005/11//}, pages = {1049 - 1096}, abstract = {Many important applications must run continuously and without interruption, and yet also must be changed to fix bugs or upgrade functionality. No prior general-purpose methodology for dynamic updating achieves a practical balance between flexibility, robustness, low overhead, ease of use, and low cost.We present an approach for C-like languages that provides type-safe dynamic updating of native code in an extremely flexible manner---code, data, and types may be updated, at programmer-determined times---and permits the use of automated tools to aid the programmer in the updating process. Our system is based on dynamic patches that contain both the updated code and the code needed to transition from the old version to the new. A novel aspect of our patches is that they consist of verifiable native code (e.g. Proof-Carrying Code or Typed Assembly Language), which is native code accompanied by annotations that allow online verification of the code{\textquoteright}s safety. We discuss how patches are generated mostly automatically, how they are applied using dynamic-linking technology, and how code is compiled to make it updateable.To concretely illustrate our system, we have implemented a dynamically updateable web server, FlashEd. We discuss our experience building and maintaining FlashEd, and generalize to present observations about updateable software development. Performance experiments show that for FlashEd, the overhead due to updating is low: typically less than 1 percent.}, keywords = {dynamic software updating, typed assembly language}, isbn = {0164-0925}, doi = {10.1145/1108970.1108971}, url = {http://doi.acm.org/10.1145/1108970.1108971}, author = {Hicks, Michael W. and Nettles,Scott} } @article {14687, title = {Dynamic updating of information-flow policies}, journal = {Proceedings of the International Workshop on Foundations of Computer Security (FCS)}, year = {2005}, month = {2005///}, author = {Hicks, Michael W. and Tse,S. and Hicks,B. and Zdancewic,S.} } @article {14763, title = {Efficient online computation of statement coverage}, journal = {Journal of Systems and Software}, volume = {78}, year = {2005}, month = {2005/11//}, pages = {146 - 165}, abstract = {Evaluation of statement coverage is the problem of identifying the statements of a program that execute in one or more runs of a program. The traditional approach for statement coverage tools is to use static code instrumentation. In this paper we present a new approach to dynamically insert and remove instrumentation code to reduce the runtime overhead of statement coverage measurement. We also explore the use of dominator tree information to reduce the number of instrumentation points needed. Our experiments show that our approach reduces runtime overhead by 38-90\% compared with purecov, a commercial statement coverage tool. Our tool is fully automated and available for download from the Internet.}, isbn = {0164-1212}, doi = {16/j.jss.2004.12.021}, url = {http://www.sciencedirect.com/science/article/pii/S0164121205000051}, author = {Tikir, Mustafa M. and Hollingsworth, Jeffrey K} } @conference {14793, title = {EMPS: an environment for memory performance studies}, booktitle = {Parallel and Distributed Processing Symposium, 2005. Proceedings. 19th IEEE International}, year = {2005}, month = {2005/04//}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper describes an overview of environment for memory performance studies (EMPS). EMPS is a framework to allow different data gathering and simulation tools to be composed together to predict the performance of parallel programs on a variety of current and future high end computing (HEC) systems. The framework seeks to combine the automated nature of direct execution simulation with the predictive capabilities of performance modeling.}, keywords = {Application software, cache storage, Computational modeling, Concurrent computing, data gathering, Delay, digital simulation, Economic forecasting, EMP radiation effects, high end computing system, High performance computing, memory architecture, memory performance, Moore{\textquoteright}s Law, PARALLEL PROCESSING, parallel program, Predictive models, simulation tool, Writing}, isbn = {0-7695-2312-9}, doi = {10.1109/IPDPS.2005.196}, author = {Hollingsworth, Jeffrey K and Snavely, A. and Sbaraglia, S. and Ekanadham, K.} } @article {14606, title = {Enhanced position weight matrices using mixture models}, journal = {Bioinformatics}, volume = {21}, year = {2005}, month = {2005/06/16/}, pages = {i204-i212 - i204-i212}, abstract = {Motivation: Positional weight matrix (PWM) is derived from a set of experimentally determined binding sites. Here we explore whether there exist subclasses of binding sites and if the mixture of these subclass-PWMs can improve the binding site prediction. Intuitively, the subclasses correspond to either distinct binding preference of the same transcription factor in different contexts or distinct subtypes of the transcription factor.Result: We report an Expectation Maximization algorithm adapting the mixture model of Baily and Elkan. We assessed the relative merit of using two subclass-PWMs. The resulting PWMs were evaluated with respect to preferred conservation (relative to mouse) of potential sites in human promoters and expression coherence of the potential target genes. Based on 64 JASPAR vertebrate PWMs, 61{\textendash}81\% of the cases resulted in a higher conservation using the mixture model. Also in 98\% of the cases the expression coherence was higher for the target genes of one of the subclass-PWMs. Our analysis of Reb1 sites is consistent with previously discovered subtypes using independent methods. Additionally application of our method to mutated sites for transcription factor LEU3 reveals subclasses that segregate into strongly binding and weakly binding sites with P-value of 0.008. This is the first study which attempts to quantify the subtly different binding specificities of a transcription factor on a large scale and suggests the use of a mixture of PWMs, instead of the current practice of using a single PWM, for a transcription factor. }, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/bti1001}, url = {http://bioinformatics.oxfordjournals.org/content/21/suppl_1/i204}, author = {Hannenhalli, Sridhar and Wang,L.-S.} } @article {17135, title = {Envisioning help resources for the future information ecology: Toward an enriched sense of help}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {42}, year = {2005}, month = {2005/01/01/}, pages = {n/a-n/a - n/a-n/a}, isbn = {1550-8390}, doi = {10.1002/meet.14504201123}, url = {http://onlinelibrary.wiley.com/doi/10.1002/meet.14504201123/abstract}, author = {Haas,Stephanie W and Brown,Laurie and Denn,Sheila and Locke,David and Shneiderman, Ben} } @conference {16372, title = {Evaluating and tuning a static analysis to find null pointer bugs}, booktitle = {Proceedings of the 6th ACM SIGPLAN-SIGSOFT workshop on Program analysis for software tools and engineering}, year = {2005}, month = {2005///}, pages = {13 - 19}, author = {Hovemeyer,D. and Spacco,J. and Pugh, William} } @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.} } @conference {13367, title = {Exploiting Correlated Attributes in Acquisitional Query Processing}, booktitle = {21st International Conference on Data Engineering, 2005. ICDE 2005. Proceedings}, year = {2005}, month = {2005/04/05/08}, pages = {143 - 154}, publisher = {IEEE}, organization = {IEEE}, abstract = {Sensor networks and other distributed information systems (such as the Web) must frequently access data that has a high per-attribute acquisition cost, in terms of energy, latency, or computational resources. When executing queries that contain several predicates over such expensive attributes, we observe that it can be beneficial to use correlations to automatically introduce low-cost attributes whose observation will allow the query processor to better estimate the selectivity of these expensive predicates. In particular, we show how to build conditional plans that branch into one or more sub-plans, each with a different ordering for the expensive query predicates, based on the runtime observation of low-cost attributes. We frame the problem of constructing the optimal conditional plan for a given user query and set of candidate low-cost attributes as an optimization problem. We describe an exponential time algorithm for finding such optimal plans, and describe a polynomial-time heuristic for identifying conditional plans that perform well in practice. We also show how to compactly model conditional probability distributions needed to identify correlations and build these plans. We evaluate our algorithms against several real-world sensor-network data sets, showing several-times performance increases for a variety of queries versus traditional optimization techniques.}, keywords = {acquisitional query processing, Computer networks, Costs, data acquisition, Delay, Distributed computing, distributed information system, Distributed information systems, distributed processing, exponential time algorithm, optimization techniques, polynomial-time heuristic, Polynomials, probability, Query processing, real-time systems, real-world sensor-network, Runtime, Sensor phenomena and characterization, Sensor systems}, isbn = {0-7695-2285-8}, doi = {10.1109/ICDE.2005.63}, author = {Deshpande, Amol and Guestrin,C. and Wei Hong and Madden,S.} } @article {17157, title = {Extending User Understanding of Federal Statistics in Tables (2000)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {This paper describes progress toward improving user interfaces for US Federal government statistics that are presented in tables. Based on studies of user behaviors and needs related to statistical tables, we describe interfaces to assist diverse users with a range of statistical literacy to explore, find, understand, and use US Federal government statistics.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6473}, author = {Marchionini,Gary and Hert,Carol and Liddy,Liz and Shneiderman, Ben} } @article {13772, title = {Finite-State Language resources and Language Processing}, journal = {Machine Translation}, volume = {18}, year = {2005}, month = {2005///}, pages = {381 - 382}, author = {Hale,K. and Keyser,S.J. and Hutchins,W.J. and Habash,N. and Dorr, Bonnie J and Traum,D.} } @article {14580, title = {Generalizations of Markov model to characterize biological sequences}, journal = {BMC Bioinformatics}, volume = {6}, year = {2005}, month = {2005///}, pages = {219 - 219}, abstract = {BACKGROUND:The currently used kth order Markov models estimate the probability of generating a single nucleotide conditional upon the immediately preceding (gap = 0) k units. However, this neither takes into account the joint dependency of multiple neighboring nucleotides, nor does it consider the long range dependency with gap>0.RESULT:We describe a configurable tool to explore generalizations of the standard Markov model. We evaluated whether the sequence classification accuracy can be improved by using an alternative set of model parameters. The evaluation was done on four classes of biological sequences - CpG-poor promoters, all promoters, exons and nucleosome positioning sequences. Using di- and tri-nucleotide as the model unit significantly improved the sequence classification accuracy relative to the standard single nucleotide model. In the case of nucleosome positioning sequences, optimal accuracy was achieved at a gap length of 4. Furthermore in the plot of classification accuracy versus the gap, a periodicity of 10-11 bps was observed which might indicate structural preferences in the nucleosome positioning sequence. The tool is implemented in Java and is available for download at ftp://ftp.pcbi.upenn.edu/GMM/.CONCLUSION:Markov modeling is an important component of many sequence analysis tools. We have extended the standard Markov model to incorporate joint and long range dependencies between the sequence elements. The proposed generalizations of the Markov model are likely to improve the overall accuracy of sequence analysis tools.}, isbn = {1471-2105}, doi = {10.1186/1471-2105-6-219}, url = {http://www.biomedcentral.com/1471-2105/6/219}, author = {Wang,Junwen and Hannenhalli, Sridhar} } @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 {14076, title = {The genetic map and comparative analysis with the physical map of Trypanosoma brucei}, journal = {Nucleic acids research}, volume = {33}, year = {2005}, month = {2005///}, pages = {6688 - 6688}, author = {MacLeod,A. and Tweedie,A. and McLellan,S. and Taylor,S. and Hall,N. and Berriman,M. and El-Sayed, Najib M. and Hope,M. and Turner,C. M.R and Tait,A.} } @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 {19077, title = {The genome of the protist parasite Entamoeba histolytica}, journal = {Nature}, volume = {433}, year = {2005}, month = {2005}, pages = {865 - 868}, author = {Loftus,B. and Anderson,I. and Davies,R. and Alsmark,U. C.M and Samuelson,J. and Amedeo,P. and Roncaglia,P. and Berriman,M. and Hirt,R. P and Mann,B. J and others} } @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 {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 {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 {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 {18219, title = {Group-based joint coding and embedding technique for multimedia fingerprinting}, journal = {Proc. SPIE}, volume = {5681}, year = {2005}, month = {2005///}, pages = {96 - 105}, abstract = {This paper proposes a group-based fingerprinting scheme employing a joint coding and embedding strategy totrace multimedia distribution and proactively prevent the leak of multimedia information. Taking advantage of the prior knowledge on the collusion pattern, we construct compact fingerprints that consist of user sub-codeword and group sub-codeword and are embedded in host signal via spread spectrum technique. The detection is done in two levels, which identifies guilty groups through correlation and then narrows down to specific colluders through minimum distance decoding. Experimental results show that the proposed method provides higher collusion resistance than the existing non-grouped fingerprint codes. }, author = {He,S. and Wu,M.} } @article {13927, title = {How do I find blue books about dogs? The errors and frustrations of young digital library users}, journal = {Proceedings of HCII 2005}, year = {2005}, month = {2005///}, author = {Hutchinson,H. and Druin, Allison and Bederson, Benjamin B. and Reuter,K. and Rose,A. and Weeks,A. C} } @conference {18227, title = {Improving collusion resistance of error correcting code based multimedia fingerprinting}, booktitle = {Acoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP {\textquoteright}05). IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/03//}, pages = {ii/1029 - ii/1032 Vol. 2 - ii/1029 - ii/1032 Vol. 2}, abstract = {Digital fingerprinting protects multimedia content from illegal redistribution by uniquely marking copies of the content distributed to each user. Collusion is a powerful attack whereby several differently fingerprinted copies of the same content are combined together to attenuate or remove the fingerprints. Focusing on the error correction code (ECC) based fingerprinting, we explore in this paper new avenues that can substantially improve its collusion resistance, and in the mean time retain its advantages in detection complexity and fast distribution. Our analysis suggests a great need of jointly considering the coding, embedding, and detection issues, and inspires the proposed technique of permuted subsegment embedding that is able to substantially improve the collusion resistance of ECC based fingerprinting.}, keywords = {based, code, codes;, coding;, collusion, correcting, correction, data;, detection;, digital, ECC;, embedding;, error, fingerprint, fingerprinting, fingerprinting;, multimedia, of, permuted, resistance;, Security, signatures;, subsegment, systems;}, doi = {10.1109/ICASSP.2005.1415583}, author = {He,Shan and M. Wu} } @article {18910, title = {Information gathering during planning for Web Service composition}, journal = {Web Semantics: Science, Services and Agents on the World Wide Web}, volume = {3}, year = {2005}, month = {2005/10//}, pages = {183 - 205}, abstract = {Hierarchical task network (HTN) based planning techniques have been applied to the problem of composing Web Services, especially when described using the OWL-S service ontologies. Many of the existing Web Services are either exclusively information providing or crucially depend on information-providing services. Thus, many interesting service compositions involve collecting information either during execution or during the composition process itself. In this paper, we focus on the latter issue. In particular, we present ENQUIRER , an HTN-planning algorithm designed for planning domains in which the information about the initial state of the world may not be complete, but it is discoverable through plan-time information-gathering queries. We have shown that ENQUIRER is sound and complete, and derived several mathematical relationships among the amount of available information, the likelihood of the planner finding a plan, and the quality of the plan found. We have performed experimental tests that confirmed our theoretical results and that demonstrated how ENQUIRER can be used for Web Service composition.}, keywords = {HTN planning, Information gathering, Web Service composition}, isbn = {1570-8268}, doi = {10.1016/j.websem.2005.07.001}, url = {http://www.sciencedirect.com/science/article/pii/S1570826805000168}, author = {Kuter,Ugur and Sirin,Evren and Parsia,Bijan and Nau, Dana S. and Hendler,James} } @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} } @conference {13920, title = {The International Children{\textquoteright}s Digital Library: A Case Study in Designing for a MultiLingual}, booktitle = {Multi-Cultural, Multi-Generational Audience. Information Technology and Libraries}, year = {2005}, month = {2005///}, author = {Hutchinson,H.B. and Rose,A. and Bederson, Benjamin B. and Weeks,A. C and Druin, Allison} } @article {13806, title = {Johns Hopkins summer workshop final report on parsing and spoken structural event detection}, journal = {Johns Hopkins University, Tech. Rep}, year = {2005}, month = {2005///}, abstract = {This report describes research conducted by the Parsing and Spoken Structural Event Detection(PaSSED) team as part of the 2005 Johns Hopkins Summer Workshop on Language Engineering. This project investigated the interaction between parsing and the detection of structural metadata in conversational speech, including sentence boundaries, edits (the reparandum portion of speech repairs), and fillers. In terms of parsing, we explored alternative methods of exploiting metadata information in parsing models and measured how varying accuracy in transcription and metadata information affects parsing accuracy. In the other direction, we similarly considered how syntactic and prosodic knowledge could be leveraged in metadata detection, measuring how this knowledge impacts metadata detection accuracy. As part of this work, we investigated metrics for evaluating parse accuracy in the presence of tran- scription and metadata detection errors, and we report on our experience using these metrics with several parsers and across varying experimental conditions. A range of methods for handling edits during pars- ing were evaluated in this research (excision, addition of markups to the input string, and grammar modification). We also developed a ToBI (a prosodic structure annotation scheme [SBP+92]) prosodic event classifier and describe its evaluation. Finally, we present methods for effective n-best sentence boundary candidate generation and reranking using syntactic, prosodic, and other features. These stud- ies are complemented by a second set of reranking investigations wherein we optimize sentence boundary detection explicitly to improve parse accuracy. The PaSSED project has: {\textbullet} investigated various techniques to enhance parsing of speech given metadata detection on conver- sational speech; {\textbullet} defined metrics for evaluating speech parsing accuracy, implemented them in the publically avail- able SParseval software package, and evaluated them under a wide variety of conditions; {\textbullet} recast SU detection as an n-best reranking problem with a relatively small n. Using this approach, we demonstrated significant improvements over a very strong baseline SU detection system. {\textbullet} reported on the interaction between parsing and metadata detection and their synergy; {\textbullet} fostered new collaborations and identified a number of interesting avenues for future work. }, author = {Harper,MP and Dorr, Bonnie J and Hale,J. and Roark,B. and Shafran,I. and Lease,M. and Liu,Y. and Snover,M. and Yung,L. and Krasnyanskaya,A.} } @conference {18237, title = {Joint uplink and downlink optimization for video conferencing over wireless LAN}, booktitle = {Acoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP {\textquoteright}05). IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/03//}, pages = {ii/1101 - ii/1104 Vol. 2 - ii/1101 - ii/1104 Vol. 2}, abstract = {A real-time video conferencing framework is proposed for multiple conferencing pairs by jointly considering the uplink and downlink conditions within IEEE 802.11 networks. We formulate this system so as to minimize the maximal end-to-end expected distortion received by all users by selecting the PHY modes and transmission time. Compared with the strategy of individually optimizing uplink and downlink, the proposed framework outperforms by 3.67-8.65 dB for the average received PSNR among all users.}, keywords = {802.11, conferencing, conferencing;, distortion;, end-to-end, expected, IEEE, joint, LAN;, maximal, minimisation;, modes;, multiple, networks;, optimization;, pairs;, PHY, PSNR;, real-time, teleconferencing;, time;, transmission, uplink-downlink, video, wireless}, doi = {10.1109/ICASSP.2005.1415601}, author = {Su,Guan-Ming and Han,Zhu and M. Wu and Liu,K. J.R} } @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.} } @inbook {16931, title = {A Knowledge Integration Framework for Information Visualization}, booktitle = {From Integrated Publication and Information Systems to Information and Knowledge EnvironmentsFrom Integrated Publication and Information Systems to Information and Knowledge Environments}, series = {Lecture Notes in Computer Science}, volume = {3379}, year = {2005}, month = {2005///}, pages = {207 - 220}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Users can better understand complex data sets by combining insights from multiple coordinated visual displays that include relevant domain knowledge. When dealing with multidimensional data and clustering results, the most familiar displays and comprehensible are 1- and 2-dimensional projections (histograms, and scatterplots). Other easily understood displays of domain knowledge are tabular and hierarchical information for the same or related data sets. The novel parallel coordinates view [6] powered by a direct-manipulation search, offers strong advantages, but requires some training for most users. We provide a review of related work in the area of information visualization, and introduce new tools and interaction examples on how to incorporate users{\textquoteright} domain knowledge for understanding clustering results. Our examples present hierarchical clustering of gene expression data, coordinated with a parallel coordinates view and with the gene annotation and gene ontology.}, isbn = {978-3-540-24551-3}, url = {http://dx.doi.org/10.1007/978-3-540-31842-2_21}, author = {Seo,Jinwook and Shneiderman, Ben}, editor = {Hemmje,Matthias and Nieder{\'e}e,Claudia and Risse,Thomas} } @conference {18402, title = {Measuring productivity on high performance computers}, booktitle = {11th IEEE International Symposium on Software Metric}, year = {2005}, month = {2005///}, abstract = {In the high performance computing domain, the speed ofexecution of a program has typically been the primary performance metric. But productivity is also of concern to high performance computing developers. In this paper we will discuss the problems of defining and measuring productivity for these machines and we develop a model of productivity that includes both a performance component and a component that measures the development time of the program. We ran several experiments using students in high performance courses at several universities, and we report on those results with respect to our model of productivity. }, author = {Zelkowitz, Marvin V and Basili, Victor R. and Asgari, S. and Hochstein, L. and Hollingsworth, Jeffrey K and Nakamura, T.} } @inbook {14707, title = {Merging Network Measurement with Data Transport}, booktitle = {Passive and Active Network MeasurementPassive and Active Network Measurement}, series = {Lecture Notes in Computer Science}, volume = {3431}, year = {2005}, month = {2005///}, pages = {368 - 371}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The tasks of measurement and data transport are often treated independently, but we believe there are benefits to bringing them together. This paper proposes the simple idea of a transport agent to encapsulate useful data within probe packets in place of useless padding.}, isbn = {978-3-540-25520-8}, url = {http://dx.doi.org/10.1007/978-3-540-31966-5_36}, author = {Papageorgiou,Pavlos and Hicks, Michael W.}, editor = {Dovrolis,Constantinos} } @conference {12108, title = {A metric space for productivity measurement in software development}, 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 = {13 - 16}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We define a metric space to measure the contributions of individual programmers to a software development project. It allows us to measure the distance between the contributions of two different programmers as well as the absolute contribution of each individual programmer. Our metric is based on an action function that provides a picture of how one programmer{\textquoteright}s approach differs from another at each instance of time during the project. We apply our metric to data we collected from students taking a course in parallel programming. We display the pictures for two students who showed approximately equal contributions but who followed very different paths through the course.}, isbn = {1-59593-117-1}, doi = {10.1145/1145319.1145324}, url = {http://doi.acm.org/10.1145/1145319.1145324}, author = {Numrich,Robert W. and Hochstein, Lorin and Basili, Victor R.} } @article {13387, title = {Model-based approximate querying in sensor networks}, journal = {The VLDB Journal}, volume = {14}, year = {2005}, month = {2005///}, pages = {417 - 443}, abstract = {Declarative queries are proving to be an attractive paradigm for interacting with networks of wireless sensors. The metaphor that {\textquotedblleft}the sensornet is a database{\textquotedblright} is problematic, however, because sensors do not exhaustively represent the data in the real world. In order to map the raw sensor readings onto physical reality, a model of that reality is required to complement the readings. In this article, we enrich interactive sensor querying with statistical modeling techniques. We demonstrate that such models can help provide answers that are both more meaningful, and, by introducing approximations with probabilistic confidences, significantly more efficient to compute in both time and energy. Utilizing the combination of a model and live data acquisition raises the challenging optimization problem of selecting the best sensor readings to acquire, balancing the increase in the confidence of our answer against the communication and data acquisition costs in the network. We describe an exponential time algorithm for finding the optimal solution to this optimization problem, and a polynomial-time heuristic for identifying solutions that perform well in practice. We evaluate our approach on several real-world sensor-network datasets, taking into account the real measured data and communication quality, demonstrating that our model-based approach provides a high-fidelity representation of the real phenomena and leads to significant performance gains versus traditional data acquisition techniques.}, isbn = {1066-8888}, url = {http://dx.doi.org/10.1007/s00778-005-0159-3}, author = {Deshpande, Amol and Guestrin,Carlos and Madden,Samuel and Hellerstein,Joseph and Wei Hong} } @conference {14710, title = {Mutatis mutandis: safe and predictable dynamic software updating}, booktitle = {Proceedings of the 32nd ACM SIGPLAN-SIGACT symposium on Principles of programming languages}, series = {POPL {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {183 - 194}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Dynamic software updates can be used to fix bugs or add features to a running program without downtime. Essential for some applications and convenient for others, low-level dynamic updating has been used for many years. Perhaps surprisingly, there is little high-level understanding or language support to help programmers write dynamic updates effectively.To bridge this gap, we present Proteus, a core calculus for dynamic software updating in C-like languages that is flexible, safe, and predictable. Proteus supports dynamic updates to functions (even active ones), to named types and to data, allowing on-line evolution to match source-code evolution as we have observed it in practice. We ensure updates are type-safe by checking for a property we call "con-freeness" for updated types t at the point of update. This means that non-updated code will not use t concretely beyond that point (concrete usages are via explicit coercions) and thus t{\textquoteright}s representation can safely change. We show how con-freeness can be enforced dynamically for a particular program state. We additionally define a novel and efficient static updateability analysis to establish con-freeness statically, and can thus automatically infer program points at which all future (well-formed) updates will be type-safe. We have implemented our analysis for C and tested it on several well-known programs.}, keywords = {capability, dynamic software updating, proteus, Type inference, updateability analysis}, isbn = {1-58113-830-X}, doi = {10.1145/1040305.1040321}, url = {http://doi.acm.org/10.1145/1040305.1040321}, author = {Stoyle,Gareth and Hicks, Michael W. and Bierman,Gavin and Sewell,Peter and Neamtiu,Iulian} } @conference {14546, title = {Online auctions with re-usable goods}, booktitle = {Proceedings of the 6th ACM conference on Electronic commerce}, year = {2005}, month = {2005///}, pages = {165 - 174}, author = {Hajiaghayi, Mohammad T.} } @conference {13189, title = {On-line density-based appearance modeling for object tracking}, booktitle = {Computer Vision, 2005. ICCV 2005. Tenth IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/10//}, pages = {1492 -1499 Vol. 2 - 1492 -1499 Vol. 2}, abstract = {Object tracking is a challenging problem in real-time computer vision due to variations of lighting condition, pose, scale, and view-point over time. However, it is exceptionally difficult to model appearance with respect to all of those variations in advance; instead, on-line update algorithms are employed to adapt to these changes. We present a new on-line appearance modeling technique which is based on sequential density approximation. This technique provides accurate and compact representations using Gaussian mixtures, in which the number of Gaussians is automatically determined. This procedure is performed in linear time at each time step, which we prove by amortized analysis. Features for each pixel and rectangular region are modeled together by the proposed sequential density approximation algorithm, and the target model is updated in scale robustly. We show the performance of our method by simulations and tracking in natural videos}, keywords = {appearance, approximation;Gaussian, Computer, density, density-based, detection;target, Gaussian, mixtures;object, modeling, modeling;real-time, processes;computer, sequences;object, technique;online, tracking;, tracking;online, vision;image, vision;sequential}, doi = {10.1109/ICCV.2005.181}, author = {Han,B. and Davis, Larry S.} } @article {19652, title = {An outdoor 3-D visual tracking system for the study of spatial navigation and memory in rhesus monkeys}, journal = {Behavior Research Methods}, volume = {37}, year = {2005}, month = {2005/08/01/}, pages = {453 - 463}, abstract = {Previous studies of the navigational abilities of nonhuman primates have largely been limited to what could be described by a human observer with a pen and paper. Consequently, we have developed a system that uses a pair of cameras to automatically obtain the three-dimensional trajectory of rhesus monkeys performing an outdoor spatial navigation and memory task. The system provides trajectories, path length, speed, and other variables that would be impossible for an unaided observer to note. From trajectory data, we computed and validated a path-length measurement. We use this measurement to compare the navigation abilities of several animals. In addition, we provide quantitative data on the accuracy of a method for automatic behavior detection. Currently, the system is being used to examine the sex differences in spatial navigation of rhesus monkeys. We expect that measures derived from the trajectory data will reveal strategies used by animals to solve spatial problems.}, keywords = {cognitive psychology}, isbn = {1554-351X, 1554-3528}, url = {http://link.springer.com/article/10.3758/BF03192714}, author = {Zia Khan and Herman, Rebecca A. and Wallen, Kim and Balch, Tucker} } @article {15071, title = {A pairwise key predistribution scheme for wireless sensor networks}, journal = {ACM Trans. Inf. Syst. Secur.}, volume = {8}, year = {2005}, month = {2005/05//}, pages = {228 - 258}, abstract = {To achieve security in wireless sensor networks, it is important to be able to encrypt and authenticate messages sent between sensor nodes. Before doing so, keys for performing encryption and authentication must be agreed upon by the communicating parties. Due to resource constraints, however, achieving key agreement in wireless sensor networks is nontrivial. Many key agreement schemes used in general networks, such as Diffie-Hellman and other public-key based schemes, are not suitable for wireless sensor networks due to the limited computational abilities of the sensor nodes. Predistribution of secret keys for all pairs of nodes is not viable due to the large amount of memory this requires when the network size is large.In this paper, we provide a framework in which to study the security of key predistribution schemes, propose a new key predistribution scheme which substantially improves the resilience of the network compared to previous schemes, and give an in-depth analysis of our scheme in terms of network resilience and associated overhead. Our scheme exhibits a nice threshold property: when the number of compromised nodes is less than the threshold, the probability that communications between any additional nodes are compromised is close to zero. This desirable property lowers the initial payoff of smaller-scale network breaches to an adversary, and makes it necessary for the adversary to attack a large fraction of the network before it can achieve any significant gain.}, keywords = {key predistribution, Security, Wireless sensor networks}, isbn = {1094-9224}, doi = {10.1145/1065545.1065548}, url = {http://doi.acm.org/10.1145/1065545.1065548}, author = {Du,Wenliang and Deng,Jing and Han,Yunghsiang S. and Varshney,Pramod K. and Katz, Jonathan and Khalili,Aram} } @conference {14814, title = {Parallel Parameter Tuning for Applications with Performance Variability}, booktitle = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing}, series = {SC {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {57{\textendash} - 57{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, abstract = {In this paper, we present parallel on-line optimization algorithms for parameter tuning of parallel programs. We employ direct search algorithms that update parameters based on real-time performance measurements. We discuss the impact of performance variability on the accuracy and efficiency of the optimization algorithms and proposed modified versions of the direct search algorithms to cope with it. The modified version uses multiple samples instead of single sample to estimate the performance more accurately.We present preliminary results that the performance variability of applications on clusters is heavy tailed. Finally, we studay and demonstrate the performance ofthe proposed algorithms for real scientific application.}, keywords = {algorithms, compilers, design}, isbn = {1-59593-061-2}, doi = {http://dx.doi.org/10.1109/SC.2005.52}, url = {http://dx.doi.org/10.1109/SC.2005.52}, author = {Tabatabaee, Vahid and Tiwari, Ananta and Hollingsworth, Jeffrey K} } @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.} } @article {18263, title = {Performance study on multimedia fingerprinting employing traceability codes}, journal = {Digital Watermarking}, year = {2005}, month = {2005///}, pages = {84 - 96}, abstract = {Digital fingerprinting is a tool to protect multimedia content from illegal redistribution by uniquely marking copies of the content distributed to each user. Collusion attack is a powerful attack whereby several differently-fingerprinted copies of the same content are combined together to attenuate or even remove the fingerprint. Coded fingerprinting is one major category of fingerprinting techniques against collusion. Many fingerprinting codes are proposed with tracing capability and collusion resistance, such as Traceability (TA) codes and Identifiable Parent Property (IPP) codes. Most of these works treat the important embedding issue in terms of a set of simplified and abstract assumptions, and they do not examine the end-to-end performance of the coded multimedia fingerprinting. In this paper we jointly consider the coding and embedding issues and examine the collusion resistance of coded fingerprinting systems with various code parameters. Our results show that TA codes generally offer better collusion resistance than IPP codes, and a TA code with a larger alphabet size and a longer code length is preferred.}, doi = {10.1007/11551492_7}, author = {He,S. and Wu,M.} } @conference {12387, title = {Porting DSP applications across design tools using the dataflow interchange format}, booktitle = {Rapid System Prototyping, 2005. (RSP 2005). The 16th IEEE International Workshop on}, year = {2005}, month = {2005/06//}, pages = {40 - 46}, abstract = {Modeling DSP applications through coarse-grain dataflow graphs is popular in the DSP design community, and a growing set of rapid prototyping tools support such dataflow semantics. Since different tools may be suitable for different phases or generations of a design, it is often desirable to migrate a dataflow-based application model from one prototyping tool to another. Two critical problems in transferring dataflow-based designs across different prototyping tools are the lack of a vendor-independent language for DSP-oriented dataflow graphs, and the lack of an efficient porting methodology. In our previous work, the dataflow interchange format (DIF) (C. Hsu et al., 2004) has been developed as a standard language to specify mixed-grain dataflow models for DSP systems. This paper presents the augmentation of the DIF infrastructure with a systematic porting approach that integrates DIF tightly with the specific exporting and importing mechanisms that interface DIF to specific DSP design tools. In conjunction with this porting mechanism, this paper also introduces a novel language, called the actor interchange format (AIF), for transferring relevant information pertaining to DSP library components across different tools. Through a case study of a synthetic aperture radar application, we demonstrate the high degree of automation offered by our DIF-based porting approach.}, keywords = {actor interchange format, coarse-grain dataflow graph, data flow analysis, data flow graphs, dataflow interchange format, dataflow model, dataflow semantic, DSP application, DSP design tool, DSP library component, electronic data interchange, formal specification, rapid prototyping tool, Signal processing, software prototyping, Specification languages, vendor-independent language}, doi = {10.1109/RSP.2005.39}, author = {Hsu,C.-J. and Bhattacharyya, Shuvra S.} } @inbook {17793, title = {Probabilistic Ontologies and Relational Databases}, booktitle = {On the Move to Meaningful Internet Systems 2005: CoopIS, DOA, and ODBASEOn the Move to Meaningful Internet Systems 2005: CoopIS, DOA, and ODBASE}, series = {Lecture Notes in Computer Science}, volume = {3760}, year = {2005}, month = {2005///}, pages = {1 - 17}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The relational algebra and calculus do not take the semantics of terms into account when answering queries. As a consequence, not all tuples that should be returned in response to a query are always returned, leading to low recall. In this paper, we propose the novel notion of a constrained probabilistic ontology (CPO). We developed the concept of a CPO-enhanced relation in which each attribute of a relation has an associated CPO. These CPOs describe relationships between terms occurring in the domain of that attribute. We show that the relational algebra can be extended to handle CPO-enhanced relations. This allows queries to yield sets of tuples, each of which has a probability of being correct.}, keywords = {Computer, Science}, isbn = {978-3-540-29736-9}, url = {http://dx.doi.org/10.1007/11575771_1}, author = {Udrea,Octavian and Yu,Deng and Hung,Edward and Subrahmanian,V.}, editor = {Meersman,Robert and Tari,Zahir} } @article {14100, title = {Promoter architecture and response to a positive regulator of archaeal transcription}, journal = {Molecular Microbiology}, volume = {56}, year = {2005}, month = {2005/05/01/}, pages = {625 - 637}, abstract = {The archaeal transcription apparatus is chimeric: its core components (RNA polymerase and basal factors) closely resemble those of eukaryotic RNA polymerase II, but the putative archaeal transcriptional regulators are overwhelmingly of bacterial type. Particular interest attaches to how these bacterial-type effectors, especially activators, regulate a eukaryote-like transcription system. The hyperthermophilic archaeon Methanocaldococcus jannaschii encodes a potent transcriptional activator, Ptr2, related to the Lrp/AsnC family of bacterial regulators. Ptr2 activates rubredoxin 2 (rb2) transcription through a bipartite upstream activating site (UAS), and conveys its stimulatory effects on its cognate transcription machinery through direct recruitment of the TATA binding protein (TBP). A functional dissection of the highly constrained architecture of the rb2 promoter shows that a {\textquoteleft}one-site{\textquoteright} minimal UAS suffices for activation by Ptr2, and specifies the required placement of this site. The presence of such a simplified UAS upstream of the natural rubrerythrin (rbr) promoter also suffices for positive regulation by Ptr2 in vitro, and TBP recruitment remains the primary means of transcriptional activation at this promoter.}, isbn = {1365-2958}, doi = {10.1111/j.1365-2958.2005.04563.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2005.04563.x/abstract}, author = {Ouhammouch,Mohamed and Langham,Geoffrey E and Hausner,Winfried and Simpson,Anjana J. and El-Sayed, Najib M. and Geiduschek,E. Peter} } @conference {17790, title = {RDF aggregate queries and views}, booktitle = {Data Engineering, 2005. ICDE 2005. Proceedings. 21st International Conference on}, year = {2005}, month = {2005/04//}, pages = {717 - 728}, abstract = {Resource description framework (RDF) is a rapidly expanding Web standard. RDF databases attempt to track the massive amounts of Web data and services available. In this paper, we study the problem of aggregate queries. We develop an algorithm to compute answers to aggregate queries over RDF databases and algorithms to maintain views involving those aggregates. Though RDF data can be stored in a standard relational DBMS (and hence we can execute standard relational aggregate queries and view maintenance methods on them), we show experimentally that our algorithms that operate directly on the RDF representation exhibit significantly superior performance.}, keywords = {aggregate, databases;, DBMS;, description, framework;, languages;, Maintenance, methods;, processing;, queries;, query, RDF, relational, resource, standard;, standards;, view, Web}, doi = {10.1109/ICDE.2005.121}, author = {Hung,E. and Deng,Yu and V.S. Subrahmanian} } @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 {14758, title = {Recovering system specific rules from software repositories}, journal = {SIGSOFT Softw. Eng. Notes}, volume = {30}, year = {2005}, month = {2005/05//}, pages = {1 - 5}, abstract = {One of the most successful applications of static analysis based bug finding tools is to search the source code for violations of system-specific rules. These rules may describe how functions interact in the code, how data is to be validated or how an API is to be used. To apply these tools, the developer must encode a rule that must be followed in the source code. The difficulty is that many of these system-specific rules are undocumented and "grow" over time as the source code changes. Most research in this area relies on expert programmers to document these little-known rules. In this paper we discuss a method to automatically recover a subset of these rules, function usage patterns, by mining the software repository. We present a preliminary study that applies our work to a large open source software project.}, keywords = {data warehouse and repository, debugging aids, design, experimentation, measurement, performance}, isbn = {0163-5948}, doi = {10.1145/1082983.1083144}, author = {Williams, Chadd C and Hollingsworth, Jeffrey K} } @article {15089, title = {Reducing complexity assumptions for statistically-hiding commitment}, journal = {Advances in Cryptology{\textendash}EUROCRYPT 2005}, year = {2005}, month = {2005///}, pages = {614 - 614}, abstract = {Determining the minimal assumptions needed to construct various cryptographic building blocks has been a focal point of research in theoretical cryptography. Here, we revisit the following question: what are the minimal assumptions needed to construct statistically-hiding commitment schemes? Previously, it was known how to construct such schemes based on one-way permutations. We improve upon this by constructing statistically-hiding commitment schemes based on approximable-preimage-size one-way functions. These are one-way functions for which there is an efficient way to approximate the number of preimages of a given output. A special case (for which we show a somewhat simpler construction) is that of regular one-way functions where all outputs have the same number of preimages.We utilize two different approaches in constructing statistically-hiding commitment schemes. Our first approach proceeds by showing that the scheme of Naor et al. can be implemented using any one-way function having an output distribution which is {\textquotedblleft}sufficiently similar{\textquotedblright} to uniform. We then construct one-way functions with this property from approximable-preimage-size one-way functions. Our second approach begins by constructing a commitment scheme which is statistically hiding against an honest-but-curious receiver. We then demonstrate a compiler which transforms any such commitment scheme into one which is statistically hiding even against a malicious receiver. This compiler and its analysis may be of independent interest. }, doi = {10.1007/11426639_4}, author = {Haitner,I. and Horvitz,O. and Katz, Jonathan and Koo,C. Y and Morselli,R. and Shaltiel,R.} } @conference {13193, title = {Robust observations for object tracking}, booktitle = {Image Processing, 2005. ICIP 2005. IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/09//}, pages = {II - 442-5 - II - 442-5}, abstract = {It is a difficult task to find an observation model that will perform well for long-term visual tracking. In this paper, we propose an adaptive observation enhancement technique based on likelihood images, which are derived from multiple visual features. The most discriminative likelihood image is extracted by principal component analysis (PCA) and incrementally updated frame by frame to reduce temporal tracking error. In the particle filter framework, the feasibility of each sample is computed using this most discriminative likelihood image before the observation process. Integral image is employed for efficient computation of the feasibility of each sample. We illustrate how our enhancement technique contributes to more robust observations through demonstrations.}, keywords = {(numerical, adaptive, analysis;, component, enhancement;, filter, Filtering, framework;, image, images;, likelihood, methods);, object, observation, particle, PCA;, principal, tracking;}, doi = {10.1109/ICIP.2005.1530087}, author = {Han,Bohyung and Davis, Larry S.} } @article {16285, title = {Serendipitous discovery of Wolbachia genomes in multiple Drosophila species}, journal = {Genome Biology}, volume = {6}, year = {2005}, month = {2005/02/22/}, pages = {R23 - R23}, abstract = {The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism.}, isbn = {1465-6906}, doi = {10.1186/gb-2005-6-3-r23}, url = {http://genomebiology.com/2005/6/3/R23}, author = {Salzberg,Steven L. and Hotopp,Julie CD and Delcher,Arthur L. and Pop, Mihai and Smith,Douglas R. and Eisen,Michael B. and Nelson,William C.} } @article {17357, title = {Severity and Impact of Computer User Frustration: A Comparison of Student and Workplace Users (2002)}, year = {2005}, month = {2005///}, abstract = {User frustration with information and computing technology is a pervasive 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. Our study of 107 student computer users and 50 workplace computer users shows high levels of frustration and loss of 1/3 to 1/2 of time spent. This paper reports on the incident-specific and user-specific causes of frustration, and they raise frustration severity. It examines the frustration impacts on the daily interactions of the users. The time lost and time to fix problem, and importance of task, strongly correlate with frustration levels for both student and workplace users. Differences between students and workplace users are discussed in the paper.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6496}, author = {Lazar,Jonathan and Jones,Adam and Hackley,Mary and Shneiderman, Ben} } @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 {16357, title = {Software repository mining with Marmoset: an automated programming project snapshot and testing system}, journal = {ACM SIGSOFT Software Engineering Notes}, volume = {30}, year = {2005}, month = {2005///}, pages = {1 - 5}, author = {Spacco,J. and Strecker,J. and Hovemeyer,D. and Pugh, William} } @conference {12375, title = {Software synthesis from the dataflow interchange format}, booktitle = {Proceedings of the 2005 workshop on Software and compilers for embedded systems}, year = {2005}, month = {2005///}, pages = {37 - 49}, author = {Hsu,C. J and Ko,M. Y and Bhattacharyya, Shuvra S.} } @article {13865, title = {Structural metadata and parsing speech}, year = {2005}, month = {2005///}, institution = {JHU Language Engineering Workshop}, author = {Harper,M. and Dorr, Bonnie J and Hale,J. and Roark,B. and Shafran,I. and Lease,M. and Liu,Y. and Snover,M. and Yung,L. and Krasnyanskaya,A. and others} } @inbook {14739, title = {Tagged Sets: A Secure and Transparent Coordination Medium}, booktitle = {Coordination Models and LanguagesCoordination Models and Languages}, series = {Lecture Notes in Computer Science}, volume = {3454}, year = {2005}, month = {2005///}, pages = {193 - 205}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {A simple and effective way of coordinating distributed, mobile, and parallel applications is to use a virtual shared memory (VSM), such as a Linda tuple-space. In this paper, we propose a new kind of VSM, called a tagged set . Each element in the VSM is a value with an associated tag, and values are read or removed from the VSM by matching the tag. Tagged sets exhibit three properties useful for VSMs: 1 Ease of use . A tagged value naturally corresponds to the notion that data has certain attributes, expressed by the tag, which can be used for later retrieval. 2 Flexibility . Tags are implemented as propositional logic formulae, and selection as logical implication, so the resulting system is quite powerful. Tagged sets naturally support a variety of applications, such as shared data repositories (e.g., for media or e-mail), message passing, and publish/subscribe algorithms; they are powerful enough to encode existing VSMs, such as Linda spaces. 3 Security . Our notion of tags naturally corresponds to keys, or capabilities: a user may not select data in the set unless she presents a legal key or keys. Normal tags correspond to symmetric keys, and we introduce asymmetric tags that correspond to public and private key pairs. Treating tags as keys permits users to easily specify protection criteria for data at a fine granularity. This paper motivates our approach, sketches its basic theory, and places it in the context of other data management strategies.}, isbn = {978-3-540-25630-4}, url = {http://dx.doi.org/10.1007/11417019_17}, author = {Oriol,Manuel and Hicks, Michael W.}, editor = {Jacquet,Jean-Marie and Picco,Gian} } @article {16104, title = {Toward a Statistical Knowledge Network (2004)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {Statistics support planning and decision making and enormous efforts are made to collect data and produce statistics at all levels of governance. An important principle of democratic societies is that government statistics should be accessible to the broadest possible constituencies to empower better plans and decisions in all aspects of life. Given the potential of near-ubiquitous Internet access in homes and workplaces and efforts by government agencies to mount websites, physical access to large volumes of government is close to a fait accompli. What remains a significant challenge is enabling access to the right statistical information at the right time and in the right form.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6522}, author = {Marchionini,Gary and Haas,Stephanie and Plaisant, Catherine and Shneiderman, Ben and Hert,Carol} } @article {13406, title = {Toward on-line schema evolution for non-stop systems}, journal = {11th High Performance Transaction Systems Workshop}, year = {2005}, month = {2005///}, author = {Deshpande, Amol and Hicks, Michael W.} } @conference {14752, title = {Understanding source code evolution using abstract syntax tree matching}, booktitle = {Proceedings of the 2005 international workshop on Mining software repositories}, series = {MSR {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {1 - 5}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Mining software repositories at the source code level can provide a greater understanding of how software evolves. We present a tool for quickly comparing the source code of different versions of a C program. The approach is based on partial abstract syntax tree matching, and can track simple changes to global variables, types and functions. These changes can characterize aspects of software evolution useful for answering higher level questions. In particular, we consider how they could be used to inform the design of a dynamic software updating system. We report results based on measurements of various versions of popular open source programs. including BIND, OpenSSH, Apache, Vsftpd and the Linux kernel.}, keywords = {abstract syntax trees, software evolution, source code analysis}, isbn = {1-59593-123-6}, doi = {10.1145/1082983.1083143}, url = {http://doi.acm.org/10.1145/1082983.1083143}, author = {Neamtiu,Iulian and Foster, Jeffrey S. and Hicks, Michael W.} } @article {17456, title = {Universal Usability as a Stimulus to Advanced Interface Design (2001)}, year = {2005}, month = {2005///}, abstract = {The desire to make computing available to broader populations has historically been a motivation for research and innovation that led to new breakthroughs in usability. Menus, graphical user interfaces, and the World-Wide Web, are examples of innovative technological solutions that have arisen out of the challenge of bringing larger and more diverse groups of users into the world of computing. Universal usability is the latest such challenge: In order to build systems that are universally usable, designers must account for technology variety, user diversity, and gaps in user knowledge. These issues are particularly challenging and important in the context of increasing the usability of the World-Wide-Web. To raise awareness, we urge web designers to provide universal usability statements, to provide users with useful information about the usability of their sites. These statements can inform users and thereby reduce frustration and confusion. Further steps toward universal usability might be achieved through research aimed at developing tools that would encourage or promote usability. We close with five proposals for future research.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6485}, author = {Shneiderman, Ben and Hochheiser,Harry} } @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.} } @conference {14785, title = {Using Dynamic Tracing Sampling to Measure Long Running Programs}, booktitle = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing}, series = {SC {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {59{\textendash} - 59{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, abstract = {Detailed cache simulation can be useful to both system developers and application writers to understand an application{\textquoteright}s performance. However, measuring long running programs can be extremely slow. In this paper we present a technique to use dynamic sampling of trace snippets throughout an application{\textquoteright}s execution. We demonstrate that our approach improves accuracy compared to sampling a few timesteps at the beginning of execution by judiciously choosing the frequency, as well as the points in the control flow, at which samples are collected. Our approach is validated using the SIGMA tracing and simulation framework for the IBM Power family of processors.}, keywords = {data communications, design, experimentation, measurement, performance, tracing}, isbn = {1-59593-061-2}, doi = {http://dx.doi.org/10.1109/SC.2005.77}, url = {http://dx.doi.org/10.1109/SC.2005.77}, author = {Odom, Jeffrey and Hollingsworth, Jeffrey K and DeRose,Luiz and Ekanadham, Kattamuri and Sbaraglia, Simone} } @conference {13191, title = {VidMAP: video monitoring of activity with Prolog}, booktitle = {Advanced Video and Signal Based Surveillance, 2005. AVSS 2005. IEEE Conference on}, year = {2005}, month = {2005/09//}, pages = {224 - 229}, abstract = {This paper describes the architecture of a visual surveillance system that combines real time computer vision algorithms with logic programming to represent and recognize activities involving interactions amongst people, packages and the environments through which they move. The low level computer vision algorithms log primitive events of interest as observed facts, while the higher level Prolog based reasoning engine uses these facts in conjunction with predefined rules to recognize various activities in the input video streams. The system is illustrated in action on a multi-camera surveillance scenario that includes both security and safety violations.}, keywords = {activities, algorithms;, based, Computer, computerised, engine;, higher, image, level, Logic, monitoring;, multicamera, processing;, programming;, Prolog, PROLOG;, reasoning, recognition;, scenario;, signal, streaming;, streams;, Surveillance, surveillance;, system;, video, VISION, vision;, visual}, doi = {10.1109/AVSS.2005.1577271}, author = {Shet,V. D and Harwood,D. and Davis, Larry S.} } @article {17494, title = {Visual Specification of Queries for Finding Patterns in Time-Series Data (2001)}, year = {2005}, month = {2005///}, abstract = {Widespread interest in discovering features and trends in time- series has generated a need for tools that support interactive exploration.This paper introduces timeboxes: a powerful graphical, directmanipulation metaphor for the specification of queries over time-series datasets. Our TimeFinder implementation of timeboxes supports interactive formulation and modification of queries, thus speeding the process of exploring time-series data sets and guiding data mining. TimeFinder includes windows for timebox queries, individual time-series, and details-on-demand. Other features include drag-and-drop support for query-by-example and graphical envelopes for displaying the extent of the entire data set and result set from a given query. Extensions involving increased expressive power and general temporal data sets are discussed.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6479}, author = {Hochheiser,Harry and Shneiderman, Ben} } @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.} } @conference {14559, title = {Adaptive limited-supply online auctions}, booktitle = {Proceedings of the 5th ACM Conference on Electronic Commerce}, year = {2004}, month = {2004///}, pages = {71 - 80}, author = {Hajiaghayi, Mohammad T. and Kleinberg,R. and Parkes,D. C} } @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} } @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} } @article {13508, title = {Automatic recognition of spontaneous speech for access to multilingual oral history archives}, journal = {IEEE Transactions on Speech and Audio Processing, Special Issue on Spontaneous Speech Processing}, volume = {12}, year = {2004}, month = {2004/07//}, pages = {420 - 435}, abstract = {The MALACH project has the goal of developing the technologies needed to facilitate access to large collections of spontaneous speech. Its aim is to dramatically improve the state of the art in key Automatic Speech Recognition (ASR), Natural Language Processing (NLP) technologies for use in large-scale retrieval systems. The project leverages a unique collection of oral history interviews with survivors of the Holocaust that has been assembled and extensively annotated by the Survivors of the Shoah Visual History Foundation. This paper describes the collection, 116,000 hours of interviews in 32 languages, and the way in which system requirements have been discerned through user studies. It discusses ASR methods for very difficult speech (heavily accented, emotional, and elderly spontaneous speech), including transcription to create training data and methods for language modeling and speaker adaptation. Results are presented for for English and Czech. NLP results are presented for named entity tagging, topic segmentation, and supervised topic classification, and the architecture of an integrated search system that uses these results is described.}, author = {Byrne,W. and David Doermann and Franz,M. and Gustman,S. and Hajic,J. and Oard, Douglas and Picheny,M. and Psutka,J. and Ramabhadran,B.} } @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.} } @conference {14550, title = {Bidimensional Parameters and Local Treewidth}, booktitle = {Latin 2004: Theoretical Informatics: 6th Latin American Symposium, Buenos Aires, Argentina, April 5-8, 2004: Proceedings}, year = {2004}, month = {2004///}, pages = {109 - 109}, author = {Fomin,E. D.D.F.V and Hajiaghayi, Mohammad T. and Thilikos,D. M} } @conference {14782, title = {Bug driven bug finders}, booktitle = {Proceedings of the International Workshop on Mining Software Repositories}, year = {2004}, month = {2004///}, pages = {70 - 74}, author = {Williams, C. C and Hollingsworth, Jeffrey K} } @conference {15901, title = {Building an information retrieval test collection for spontaneous conversational speech}, booktitle = {Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {41 - 48}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Test collections model use cases in ways that facilitate evaluation of information retrieval systems. This paper describes the use of search-guided relevance assessment to create a test collection for retrieval of spontaneous conversational speech. Approximately 10,000 thematically coherent segments were manually identified in 625 hours of oral history interviews with 246 individuals. Automatic speech recognition results, manually prepared summaries, controlled vocabulary indexing, and name authority control are available for every segment. Those features were leveraged by a team of four relevance assessors to identify topically relevant segments for 28 topics developed from actual user requests. Search-guided assessment yielded sufficient inter-annotator agreement to support formative evaluation during system development. Baseline results for ranked retrieval are presented to illustrate use of the collection.}, keywords = {assessment, Automatic speech recognition, oral history, search-guided relevance}, isbn = {1-58113-881-4}, doi = {10.1145/1008992.1009002}, url = {http://doi.acm.org/10.1145/1008992.1009002}, author = {Oard, Douglas and Soergel,Dagobert and David Doermann and Huang,Xiaoli and Murray,G. Craig and Wang,Jianqiang and Ramabhadran,Bhuvana and Franz,Martin and Gustman,Samuel and Mayfield,James and Kharevych,Liliya and Strassel,Stephanie} } @article {13933, title = {Building KidPad: an application for children{\textquoteright}s collaborative storytelling}, journal = {Software: Practice and Experience}, volume = {34}, year = {2004}, month = {2004///}, pages = {895 - 914}, author = {Hourcade,J. P and Bederson, Benjamin B. and Druin, Allison} } @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 {14597, title = {CHARACTERIZATION OF Ath17, A QUANTITATIVE TRAIT LOCUS FOR ATHEROSCLEROSIS SUSCEPTIBILITY BETWEEN C57BL/6J AND 129S1/SvImJ; SINGLE-NUCLEOTIDE POLYMORPHISMS HAVE IMPORTANT IMPLICATIONS ON IDENTIFYING ATHEROSCLEROSIS MODIFIER GENES}, journal = {Cardiovascular Pathology}, volume = {13}, year = {2004}, month = {2004/06//May}, pages = {5 - 6}, abstract = {Although identifying quantitative trait loci (QTL) for atherosclerosis susceptibility in experimental murine models has helped us better understand the pathophysiology of atherosclerosis, identifying the genes underlying these QTL has been a slow and difficult process. We are currently in the process of identifying the gene that underlies Ath17, an atherosclerosis-susceptibility QTL we discovered in a (C57BL/6J{\texttimes}129S1/SvImJ)F2 intercross. Ath17 maps to a 6 cM interval region on chromosome 10 (D10Mit31, LOD score 6.6) and contains 46 annotated and 133 predicted genes. We searched the Celera Discovery System database for single nucleotide polymorphisms (SNPs) between C57BL/6J (B6) and 129S1/SvImJ in the Ath17 region and found defined blocks of high and low diversity and one polymorphic region of over 4 Mb surrounded by nonpolymorphic regions. Four of the genes, including the annotated Desrt, in the polymorphic region contained mis-sense mutations. The Desrt coding region contained four mis-sense mutations: B6 lysine to 129 glutamic acid at aa382, B6 asparagine to 129 serine at aa388, B6 threonine to 129 alanine at aa836, and B6 glycine to 129 serine at aa964. In addition, intron 5 of Desrt contained a SNP which co-localized with a putative transcription factor binding site. Desrt is a DNA binding protein, widely expressed in adult tissues, and likely plays a role in cell proliferation, differentiation, and development, making Dsert a strong candidate gene for Ath17. The murine SNP database dramatically reduced the percentage of the murine genome we had to search to find viable candidate genes for Ath17.}, isbn = {1054-8807}, doi = {10.1016/j.carpath.2004.03.010}, url = {http://www.sciencedirect.com/science/article/pii/S1054880704000377}, author = {Ishimori,Naoki and Walsh,Kenneth and Zheng,Xiangqun and Lu,Fu and Hannenhalli, Sridhar and Nusskern,Deborah and Mural,Richard and Paigen,Beverly} } @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 {14807, title = {Data Centric Cache Measurement on the Intel ltanium 2 Processor}, booktitle = {Proceedings of the 2004 ACM/IEEE conference on Supercomputing}, series = {SC {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {58{\textendash} - 58{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, abstract = {Processor speed continues to increase faster than the speed of access to main memory, making effective use of memory caches more important. Information about an application{\'y}s interaction with the cache is therefore critical to performance tuning. To be most useful, tools that measure this information should relate it to the source code level data structures in an application. We describe how to gather such information by using hardware performance counters to sample cache miss addresses, and present a new tool named Cache Scope that does this using the Intel Itanium 2 performance monitors. We present experimental results concerning Cache Scope{\'y}s accuracy and perturbation of cache behavior. We also describe a case study of using Cache Scope to tune two applications, achieving 24\% and 19\% reductions in running time.}, isbn = {0-7695-2153-3}, doi = {http://dx.doi.org/10.1109/SC.2004.21}, url = {http://dx.doi.org/10.1109/SC.2004.21}, author = {Buck, Bryan R and Hollingsworth, Jeffrey K} } @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.} } @conference {13256, title = {A data structure for non-manifold simplicial d-complexes}, booktitle = {Proceedings of the 2004 Eurographics/ACM SIGGRAPH symposium on Geometry processing}, series = {SGP {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {83 - 92}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We propose a data structure for d-dimensional simplicial complexes, that we call the Simplified Incidence Graph (SIG). The simplified incidence graph encodes all simplices of a simplicial complex together with a set of boundary and partial co-boundary topological relations. It is a dimension-independent data structure in the sense that it can represent objects of arbitrary dimensions. It scales well to the manifold case, i.e. it exhibits a small overhead when applied to simplicial complexes with a manifold domain, Here, we present efficient navigation algorithms for retrieving all topological relations from a SIG, and an algorithm for generating a SIG from a representation of the complex as an incidence graph. Finally, we compare the simplified incidence graph with the incidence graph, with a widely-used data structure for d-dimensional pseudo-manifold simplicial complexes, and with two data structures specific for two-and three-dimensional simplicial complexes.}, isbn = {3-905673-13-4}, doi = {10.1145/1057432.1057444}, url = {http://doi.acm.org/10.1145/1057432.1057444}, author = {De Floriani, Leila and Greenfieldboyce,David and Hui,Annie} } @article {12340, title = {DIF: An interchange format for dataflow-based design tools}, journal = {Computer Systems: Architectures, Modeling, and Simulation}, year = {2004}, month = {2004///}, pages = {3 - 32}, author = {Hsu,C. J and Keceli,F. and Ko,M. Y and Shahparnia,S. and Bhattacharyya, Shuvra S.} } @conference {18200, title = {Distortion management of real-time MPEG-4 video over downlink multicode CDMA networks}, booktitle = {Communications, 2004 IEEE International Conference on}, volume = {5}, year = {2004}, month = {2004/06//}, pages = {3071 - 3075 Vol.5 - 3071 - 3075 Vol.5}, abstract = {In this paper, a protocol is designed to manage source rate/channel coding rate adaptation, code allocation, and power control to transmit real-time MPEG-4 FGS video over downlink multicode CDMA networks. We develop a fast adaptive scheme of distortion management to reduce the overall distortion received by all users subject, to the limited number of codes and maximal transmitted power. Compared with a modified greedy method in literature, our proposed algorithm can reduce the overall system{\textquoteright}s distortion by at least 45\%.}, keywords = {access;, adaptation;, allocation;, CDMA, channel, code, coding, coding;, combined, communication;, compression;, control;, data, distortion, division, downlink, links;, management;, MPEG-4, multicode, multiple, networks;, power, radio, rate, real-time, resource, source, source-channel, video, video;, visual}, doi = {10.1109/ICC.2004.1313096}, author = {Su,Guan-Ming and Han,Zhu and Kwasinski,A. and M. Wu and Liu,K. J.R and Farvardin,N.} } @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.} } @conference {13757, title = {Divergence Unraveling for Word Alignment...}, booktitle = {Natural Language Engineering}, year = {2004}, month = {2004///}, abstract = {We describe the use of parallel text for divergence unraveling in word-level alignment. DUSTer (Divergence Unraveling for Statistical Translation) is a system that combines linguistic and statistical knowledge to resolve structural di$\#$erences between languages, i.e., translation divergences, during the process of alignment. Our immediate goal is to induce word-level alignments that are more accurate than those produced by an existing state-ofthe -art statistical system. The long-term goal is to improve the output quality of statistical machine translation and lexical acquisition systems by using DUSTer as one possible input to a framework that accommodates multiple alignments. We show that a systematic characterization of alignment errors made by a statistical system validates the use of linguistically-motivated universal rules for identifying and handling divergences. These rules relate one or more linguistically-motivated categories associated with the (English) input words to those of another language (foreign language); the resulting match sets are used to infer corrected alignments. Using a human-aligned corpus as our gold standard, we demonstrate an improvement in alignments over an existing state-of-the-art alignment algorithm.}, author = {Dorr, Bonnie J and Ayan,N.F. and Habash,N.} } @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} } @conference {18201, title = {Dynamic distortion control for 3-D embedded wavelet video over multiuser OFDM networks}, booktitle = {Global Telecommunications Conference, 2004. GLOBECOM {\textquoteright}04. IEEE}, volume = {2}, year = {2004}, month = {2004/12/03/nov}, pages = {650 - 654 Vol.2 - 650 - 654 Vol.2}, abstract = {In this paper, we propose a system to transmit multiple 3D embedded wavelet video programs over downlink multiuser OFDM. We consider the fairness among users and formulate the problem as minimizing the users{\textquoteright} maximal distortion subject to power, rate, and subcarrier constraints. By exploring frequency, time, and multiuser diversity in OFDM and flexibility of the 3D embedded wavelet video codec, the proposed algorithm can achieve fair video qualities among all users. Compared to a scheme similar to the current multiuser OFDM standard (IEEE 802.11a), the proposed scheme outperforms it by 1-5 dB on the worst received PSNR among all users and has much smaller PSNR deviation.}, keywords = {3D, 802.11a;, channels;, codec;, codecs;, communication;, control;, deviation;, distortion, diversity, diversity;, downlink, dynamic, embedded, fairness;, Frequency, IEEE, LAN;, maximal, minimax, minimization;, modulation;, multimedia, multiuser, OFDM, OFDM;, PSNR, rate, reception;, streaming;, systems;, techniques;, theory;, TIME, transforms;, video, video;, wavelet, wireless}, doi = {10.1109/GLOCOM.2004.1378042}, author = {Su,Guan-Ming and Han,Zhu and M. Wu and Liu,K. J.R} } @article {17109, title = {Dynamic Query Tools for Time Series Data Sets: Timebox Widgets for Interactive Exploration}, journal = {Information VisualizationInformation Visualization}, volume = {3}, year = {2004}, month = {2004/03/20/}, pages = {1 - 18}, abstract = {Timeboxes are rectangular widgets that can be used in direct-manipulation graphical user interfaces (GUIs) to specify query constraints on time series data sets. Timeboxes are used to specify simultaneously two sets of constraints: given a set of N time series profiles, a timebox covering time periods x1{\textellipsis}x2 (x1 <= x2) and values y1{\textellipsis}y2 (y1 <= y2) will retrieve only those n√N that have values y1 <= y2 during all times x1 <= x <= x2. TimeSearcher is an information visualization tool that combines timebox queries with overview displays, query-by-example facilities, and support for queries over multiple time-varying attributes. Query manipulation tools including pattern inversion and {\textquoteleft}leaders \& laggards{\textquoteright} graphical bookmarks provide additional support for interactive exploration of data sets. Extensions to the basic timebox model that provide additional expressivity include variable time timeboxes, which can be used to express queries with variability in the time interval, and angular queries, which search for ranges of differentials, rather than absolute values. Analysis of the algorithmic requirements for providing dynamic query performance for timebox queries showed that a sequential search outperformed searches based on geometric indices. Design studies helped identify the strengths and weaknesses of the query tools. Extended case studies involving the analysis of two different types of data from molecular biology experiments provided valuable feedback and validated the utility of both the timebox model and the TimeSearcher tool. Timesearcher is available at http://www.cs.umd.edu/hcil/timesearcher}, keywords = {angular queries, Bioinformatics, dynamic query, Graphical user interfaces, temporal data, time series, timeboxes, TimeSearcher, visual query}, isbn = {1473-8716, 1473-8724}, doi = {10.1057/palgrave.ivs.9500061}, url = {http://ivi.sagepub.com/content/3/1/1}, author = {Hochheiser,Harry and Shneiderman, Ben} } @article {17922, title = {Efficient solution of poisson-boltzmann equation for electrostatics of large molecules}, journal = {High-Performance Computing Symposium (April 2004)}, year = {2004}, month = {2004///}, pages = {71 - 76}, abstract = {Development of fast computational methods to solve thePoisson-Boltzmann equation (PBE) for molecular elec- trostatics is important because of the central role played by electrostatic interactions in many biological processes. The accuracy and stability of the solution to the PBE is quite sensitive to the boundary layer between the sol- vent and the solute which defines the solvent-accessible surface. In this paper, we propose a new interface- layer-focused PBE solver for efficiently computing the electrostatic potential for large molecules. Our method analytically constructs the solvent-accessible surface of molecules and then builds nested iso-surface layers out- wards and inwards from the surface using the distance field around the surface. We then develop a volume sim- plification algorithm to adaptively adjust the density of the irregular grid based on the importance to the PBE solution. We also generalize finite difference methods on our irregular grids using Taylor series expansions. Our algorithm achieves about three times speedup in the iter- ative solution process of PBE, with more accurate results on an analytical solvable testing case, compared with the popular optimized DelPhi program. Our approach can also be applied directly to solve partial differential equa- tions arising in other application domains. }, author = {Hao,X. and Varshney, Amitabh} } @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 {14694, title = {Experience with safe manual memory-management in cyclone}, booktitle = {Proceedings of the 4th international symposium on Memory management}, series = {ISMM {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {73 - 84}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The goal of the Cyclone project is to investigate type safety for low-level languages such as C. Our most difficult challenge has been providing programmers control over memory management while retaining type safety. This paper reports on our experience trying to integrate and effectively use two previously proposed, type-safe memory management mechanisms: statically-scoped regions and unique pointers. We found that these typing mechanisms can be combined to build alternative memory-management abstractions, such as reference counted objects and arenas with dynamic lifetimes, and thus provide a flexible basis. Our experience---porting C programs and building new applications for resource-constrained systems---confirms that experts can use these features to improve memory footprint and sometimes to improve throughput when used instead of, or in combination with, conservative garbage collection.}, keywords = {cyclone, Memory management, memory safety, regions, unique pointers}, isbn = {1-58113-945-4}, doi = {10.1145/1029873.1029883}, url = {http://doi.acm.org/10.1145/1029873.1029883}, author = {Hicks, Michael W. and Morrisett,Greg and Grossman,Dan and Jim,Trevor} } @article {16344, title = {Finding bugs is easy}, journal = {ACM SIGPLAN NoticesSIGPLAN Not.}, volume = {39}, year = {2004}, month = {2004/12//}, pages = {92 - 92}, isbn = {03621340}, doi = {10.1145/1052883.1052895}, url = {http://dl.acm.org/citation.cfm?id=1052895}, author = {Hovemeyer, David and Pugh, William} } @conference {16361, title = {Finding concurrency bugs in java}, booktitle = {Proceedings of the PODC Workshop on Concurrency and Synchronization in Java Programs, St. John{\textquoteright}s, Newfoundland, Canada}, year = {2004}, month = {2004///}, author = {Hovemeyer,D. and Pugh, William} } @article {18905, title = {HTN planning for Web Service composition using SHOP2}, journal = {Web Semantics: Science, Services and Agents on the World Wide Web}, volume = {1}, year = {2004}, month = {2004/10//}, pages = {377 - 396}, abstract = {Automated composition of Web Services can be achieved by using AI planning techniques. Hierarchical Task Network (HTN) planning is especially well-suited for this task. In this paper, we describe how HTN planning system SHOP2 can be used with OWL-S Web Service descriptions. We provide a sound and complete algorithm to translate OWL-S service descriptions to a SHOP2 domain. We prove the correctness of the algorithm by showing the correspondence to the situation calculus semantics of OWL-S. We implemented a system that plans over sets of OWL-S descriptions using SHOP2 and then executes the resulting plans over the Web. The system is also capable of executing information-providing Web Services during the planning process. We discuss the challenges and difficulties of using planning in the information-rich and human-oriented context of Web Services.}, keywords = {HTN planning, OWL-S, SHOP2, Web Service composition, Web services}, isbn = {1570-8268}, doi = {10.1016/j.websem.2004.06.005}, url = {http://www.sciencedirect.com/science/article/pii/S1570826804000113}, author = {Sirin,Evren and Parsia,Bijan and Wu,Dan and Hendler,James and Nau, Dana S.} } @article {15875, title = {iCLEF 2003 at Maryland: Translation selection and document selection}, journal = {Comparative Evaluation of Multilingual Information Access Systems}, year = {2004}, month = {2004///}, pages = {231 - 265}, author = {Dorr, Bonnie J and He,D. and Luo,J. and Oard, Douglas and Schwartz,R. and Wang,J. and Zajic, David} } @inbook {13787, title = {iCLEF 2003 at Maryland: Translation Selection and Document Selection}, booktitle = {Comparative Evaluation of Multilingual Information Access SystemsComparative Evaluation of Multilingual Information Access Systems}, series = {Lecture Notes in Computer Science}, volume = {3237}, year = {2004}, month = {2004///}, pages = {231 - 265}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Maryland performed two sets of experiments for the 2003 Cross-Language Evaluation Forum{\textquoteright}s interactive track, one focused on interactive selection of appropriate translations for query terms, the second focused on interactive selection of relevant documents. Translation selection was supported using possible synonyms discovered through back translation and two techniques for generating KeyWord In Context (KWIC) examples of usage. The results indicate that searchers typically achieved a similar search effectiveness using fewer query iterations when interactive translation selection was available. For document selection, a complete extract of the first 40 words of each news story was compared to a compressed extract generated using an automated parse-and-trim approach that approximates one way in which people can produce headlines. The results indicate that compressed {\textquotedblleft}headlines{\textquotedblright} result in faster assessment, but with a 20\% relative reduction in the F α = 0.8 search effectiveness measure.}, isbn = {978-3-540-24017-4}, url = {http://dx.doi.org/10.1007/978-3-540-30222-3_42}, author = {Dorr, Bonnie J and He,Daqing and Luo,Jun and Oard, Douglas and Schwartz,Richard and Wang,Jianqiang and Zajic, David}, editor = {Peters,Carol and Gonzalo,Julio and Braschler,Martin and Kluck,Michael} } @conference {15842, title = {iCLEF 2004 at Maryland: Summarization design for interactive cross-language question answering}, booktitle = {Proceeding of Cross Language Evaluation Forum (CLEF2004)}, year = {2004}, month = {2004///}, author = {He,D. and Wang,J. and Luo,J. and Oard, Douglas} } @article {15760, title = {Implementation of the regularized structured total least squares algorithms for blind image deblurring}, journal = {Linear Algebra and its Applications}, volume = {391}, year = {2004}, month = {2004/11/01/}, pages = {203 - 221}, abstract = {The structured total least squares (STLS) problem has been introduced to handle problems involving structured matrices corrupted by noise. Often the problem is ill-posed. Recently, regularization has been proposed in the STLS framework to solve ill-posed blind deconvolution problems encountered in image deblurring when both the image and the blurring function have uncertainty. The kernel of the regularized STLS (RSTLS) problem is a least squares problem involving Block{\textendash}Toeplitz{\textendash}Toeplitz{\textendash}Block matrices.In this paper an algorithm is described to solve this problem, based on a particular implementation of the generalized Schur Algorithm (GSA). It is shown that this new implementation improves the computational efficiency of the straightforward implementation of GSA from O(N2.5) to O(N2), where N is the number of pixels in the image. }, keywords = {Block Toeplitz matrix, Displacement rank, Generalized Schur algorithm, Image deblurring, Structured total least squares, Tikhonov regularization}, isbn = {0024-3795}, doi = {10.1016/j.laa.2004.07.006}, url = {http://www.sciencedirect.com/science/article/pii/S0024379504003362}, author = {Mastronardi,N. and Lemmerling,P. and Kalsi,A. and O{\textquoteright}Leary,D. P and Huffel,S. Van} } @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.} } @conference {16886, title = {Indexing distributed complex data for complex queries}, booktitle = {Proceedings of the 2004 annual national conference on Digital government research}, series = {dg.o {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {63:1{\textendash}63:10 - 63:1{\textendash}63:10}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {Peer-to-peer networks are becoming a common form of online data exchange. Querying data, mostly files, using keywords on peer-to-peer networks is well-known. But users cannot perform many types of queries on complex data and on many of the attributes of the data on such networks other than mostly exact-match queries. We introduce a distributed hashing-based index for enabling more powerful accesses on complex data over peer-to-peer networks that we expect to be commonly deployed for digital government applications. Preliminary experiments show that our index scales well and we believe that it can be extended to obtain similar indices for many other data types for performing various complex queries, such as range queries.}, url = {http://dl.acm.org/citation.cfm?id=1124191.1124254}, author = {Tanin,Egemen and Harwood,Aaron and Samet, Hanan} } @inbook {18909, title = {Information Gathering During Planning for Web Service Composition}, booktitle = {The Semantic Web {\textendash} ISWC 2004}, series = {Lecture Notes in Computer Science}, volume = {3298}, year = {2004}, month = {2004///}, pages = {335 - 349}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Hierarchical Task-Network (HTN) based planning techniques have been applied to the problem of composing Web Services, especially when described using the OWL - S service ontologies. Many of the existing Web Services are either exclusively information providing or crucially depend on information-providing services. Thus, many interesting service compositions involve collecting information either during execution or during the composition process itself. In this paper, we focus on the latter issue. In particular, we present ENQUIRER , an HTN-planning algorithm designed for planning domains in which the information about the initial state of the world may not be complete, but it is discoverable through plan-time information-gathering queries. We have shown that ENQUIRER is sound and complete, and derived several mathematical relationships among the amount of available information, the likelihood of the planner finding a plan, and the quality of the plan found. We have performed experimental tests that confirmed our theoretical results and that demonstrated how ENQUIRER can be used in Web Service composition.}, keywords = {Computer science}, isbn = {978-3-540-23798-3}, url = {http://www.springerlink.com/content/v829m5080fc0bpng/abstract/}, author = {Kuter,Ugur and Sirin,Evren and Nau, Dana S. and Parsia,Bijan and Hendler,James}, editor = {McIlraith,Sheila and Plexousakis,Dimitris and van Harmelen,Frank} } @article {14087, title = {The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei}, journal = {Molecular biology and evolution}, volume = {21}, year = {2004}, month = {2004///}, pages = {520 - 520}, author = {Bringaud,F. and Biteau,N. and Zuiderwijk,E. and Berriman,M. and El-Sayed, Najib M. and Ghedin,E. and Melville,S. E. and Hall,N. and Baltz,T.} } @conference {14771, title = {Interactive binary instrumentation}, booktitle = {Second International Workshop on Remote Analysis and Measurement of Software Systems (RAMSS)}, year = {2004}, month = {2004///}, author = {Williams, C. C and Hollingsworth, Jeffrey K} } @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} } @inbook {13795, title = {Interlingual Annotation for MT Development}, booktitle = {Machine Translation: From Real Users to ResearchMachine Translation: From Real Users to Research}, series = {Lecture Notes in Computer Science}, volume = {3265}, year = {2004}, month = {2004///}, pages = {236 - 245}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {MT systems that use only superficial representations, including the current generation of statistical MT systems, have been successful and useful. However, they will experience a plateau in quality, much like other {\textquotedblleft}silver bullet{\textquotedblright} approaches to MT. We pursue work on the development of interlingual representations for use in symbolic or hybrid MT systems. In this paper, we describe the creation of an interlingua and the development of a corpus of semantically annotated text, to be validated in six languages and evaluated in several ways. We have established a distributed, well-functioning research methodology, designed a preliminary interlingua notation, created annotation manuals and tools, developed a test collection in six languages with associated English translations, annotated some 150 translations, and designed and applied various annotation metrics. We describe the data sets being annotated and the interlingual (IL) representation language which uses two ontologies and a systematic theta-role list. We present the annotation tools built and outline the annotation process. Following this, we describe our evaluation methodology and conclude with a summary of issues that have arisen.}, isbn = {978-3-540-23300-8}, url = {http://dx.doi.org/10.1007/978-3-540-30194-3_26}, author = {Reeder,Florence and Dorr, Bonnie J and Farwell,David and Habash,Nizar and Helmreich,Stephen and Hovy,Eduard and Levin,Lori and Mitamura,Teruko and Miller,Keith and Rambow,Owen and Siddharthan,Advaith}, editor = {Frederking,Robert and Taylor,Kathryn} } @article {13796, title = {Interlingual annotation of multilingual text corpora}, journal = {Proceedings of the North American Chapter of the Association for Computational Linguistics Workshop on Frontiers in Corpus Annotation}, year = {2004}, month = {2004///}, pages = {55 - 62}, abstract = {This paper describes a multi-site project toannotate six sizable bilingual parallel corpora for interlingual content. After presenting the background and objectives of the effort, we describe the data set that is being annotated, the interlingua representation language used, an interface environment that supports the an- notation task and the annotation process itself. We will then present a preliminary version of our evaluation methodology and conclude with a summary of the current status of the project along with a number of issues which have arisen. }, author = {Farwell,D. and Helmreich,S. and Dorr, Bonnie J and Habash,N. and Reeder,F. and Miller,K. and Levin,L. and Mitamura,T. and Hovy,E. and Rambow,O. and others} } @conference {13379, title = {Lifting the burden of history from adaptive query processing}, booktitle = {Proceedings of the Thirtieth international conference on Very large data bases - Volume 30}, series = {VLDB {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {948 - 959}, publisher = {VLDB Endowment}, organization = {VLDB Endowment}, abstract = {Adaptive query processing schemes attempt to re-optimize query plans during the course of query execution. A variety of techniques for adaptive query processing have been proposed, varying in the granularity at which they can make decisions [8]. The eddy [1] is the most aggressive of these techniques, with the flexibility to choose tuple-by-tuple how to order the application of operators. In this paper we identify and address a fundamental limitation of the original eddies proposal: the burden of history in routing. We observe that routing decisions have long-term effects on the state of operators in the query, and can severely constrain the ability of the eddy to adapt over time. We then propose a mechanism we call STAIRs that allows the query engine to manipulate the state stored inside the operators and undo the effects of past routing decisions. We demonstrate that eddies with STAIRs achieve both high adaptivity and good performance in the face of uncertainty, outperforming prior eddy proposals by orders of magnitude.}, isbn = {0-12-088469-0}, url = {http://dl.acm.org/citation.cfm?id=1316689.1316771}, author = {Deshpande, Amol and Hellerstein,Joseph M.} } @conference {17947, title = {Light Collages: Lighting Design for Effective Visualization}, booktitle = {Proceedings of the conference on Visualization {\textquoteright}04}, series = {VIS {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {281 - 288}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {We introduce Light Collages {\textquestiondown} a lighting design system for effective visualization based on principles of human perception. Artists and illustrators enhance perception of features with lighting that is locally consistent and globally inconsistent. Inspired by these techniques, we design the placement of light sources to convey a greater sense of realism and better perception of shape with globally inconsistent lighting. Our algorithm segments the objects into local surface patches and uses a number of perceptual heuristics, such as highlights, shadows, and silhouettes, to enhance the perception of shape. We show our results on scientific and sculptured datasets.}, keywords = {inconsistent lighting, light placement, lighting design, proximity shadows, scientific illustration, silhouette enhancement}, isbn = {0-7803-8788-0}, doi = {10.1109/VISUAL.2004.62}, url = {http://dx.doi.org/10.1109/VISUAL.2004.62}, author = {Lee,Chang Ha and Hao,Xuejun and Varshney, Amitabh} } @conference {14552, title = {Low-dimensional embedding with extra information}, booktitle = {Proceedings of the twentieth annual symposium on Computational geometry}, year = {2004}, month = {2004///}, pages = {320 - 329}, author = {Bǎdoiu,M. and Demaine,E. D and Hajiaghayi, Mohammad T. and Indyk,P.} } @article {17804, title = {Maintaining RDF views}, year = {2004}, month = {2004///}, institution = {Tech. Rep. CS-TR-4612 (UMIACS-TR-2004-54)}, abstract = {Resource Description Framework (RDF) has been recommended bythe World Wide Web Consortium for integrating web data. RDF specifications are increasingly being stored in RDF databases. Many applications will maintain views over RDF databases {\textendash} these views may describe resources of interest to the owner of the views. As data about the resources available on the web is subject to frequent change, there is a need to incrementally maintain such views. We present algorithms to maintain materialized RDF views when data is inserted into, deleted from, or modified in RDF database instances. We have developed a prototype of our algorithms. For each of these three cases, we compare the performance of our algorithm against the naive approach of storing RDF data in a relational database and using the standard view maintenance algorithm }, author = {Deng,Y. and Hung,E. and V.S. Subrahmanian} } @conference {13388, title = {Model-driven data acquisition in sensor networks}, booktitle = {Proceedings of the Thirtieth international conference on Very large data bases - Volume 30}, series = {VLDB {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {588 - 599}, publisher = {VLDB Endowment}, organization = {VLDB Endowment}, abstract = {Declarative queries are proving to be an attractive paradigm for ineracting with networks of wireless sensors. The metaphor that "the sensornet is a database" is problematic, however, because sensors do not exhaustively represent the data in the real world. In order to map the raw sensor readings onto physical reality, a model of that reality is required to complement the readings. In this paper, we enrich interactive sensor querying with statistical modeling techniques. We demonstrate that such models can help provide answers that are both more meaningful, and, by introducing approximations with probabilistic confidences, significantly more efficient to compute in both time and energy. Utilizing the combination of a model and live data acquisition raises the challenging optimization problem of selecting the best sensor readings to acquire, balancing the increase in the confidence of our answer against the communication and data acquisition costs in the network. We describe an exponential time algorithm for finding the optimal solution to this optimization problem, and a polynomial-time heuristic for identifying solutions that perform well in practice. We evaluate our approach on several real-world sensor-network data sets, taking into account the real measured data and communication quality, demonstrating that our model-based approach provides a high-fidelity representation of the real phenomena and leads to significant performance gains versus traditional data acquisition techniques.}, isbn = {0-12-088469-0}, url = {http://dl.acm.org/citation.cfm?id=1316689.1316741}, author = {Deshpande, Amol and Guestrin,Carlos and Madden,Samuel R. and Hellerstein,Joseph M. and Wei Hong} } @inbook {13830, title = {Multi-align: Combining Linguistic and Statistical Techniques to Improve Alignments for Adaptable MT}, booktitle = {Machine Translation: From Real Users to ResearchMachine Translation: From Real Users to Research}, series = {Lecture Notes in Computer Science}, volume = {3265}, year = {2004}, month = {2004///}, pages = {17 - 26}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {An adaptable statistical or hybrid MT system relies heavily on the quality of word-level alignments of real-world data. Statistical alignment approaches provide a reasonable initial estimate for word alignment. However, they cannot handle certain types of linguistic phenomena such as long-distance dependencies and structural differences between languages. We address this issue in Multi-Align, a new framework for incremental testing of different alignment algorithms and their combinations. Our design allows users to tune their systems to the properties of a particular genre/domain while still benefiting from general linguistic knowledge associated with a language pair. We demonstrate that a combination of statistical and linguistically-informed alignments can resolve translation divergences during the alignment process.}, isbn = {978-3-540-23300-8}, url = {http://dx.doi.org/10.1007/978-3-540-30194-3_3}, author = {Ayan,Necip and Dorr, Bonnie J and Habash,Nizar}, editor = {Frederking,Robert and Taylor,Kathryn} } @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.} } @article {12149, title = {New year{\textquoteright}s resolutions for software quality}, journal = {IEEE Software}, volume = {21}, year = {2004}, month = {2004///}, pages = {12 - 13}, abstract = {In the spirit of making resolutions for betterment in the New Year, ten distinguished individuals in the software quality field offer their recommendations on how organizations can improve software quality In the spirit of making resolutions for betterment in the New Year, ten distinguished individuals in the software quality field offer their recommendations on how organizations can improve software quality.}, author = {Basili, Victor R. and Boehm,B. and Davis,A. and Humphrey,W. S and Leveson,N. and Mead,N. R and Musa,J. D and Parnas,D. L and Pfleeger,S. L and Weyuker,E.} } @article {14590, title = {A Note on Efficient Computation of Haplotypes via Perfect Phylogeny}, journal = {Journal of Computational Biology}, volume = {11}, year = {2004}, month = {2004/10//}, pages = {858 - 866}, abstract = {The problem of inferring haplotype phase from a population of genotypes has received a lot of attention recently. This is partly due to the observation that there are many regions on human genomic DNA where genetic recombination is rare (Helmuth, 2001; Daly et al., 2001; Stephens et al., 2001; Friss et al., 2001). A Haplotype Map project has been announced by NIH to identify and characterize populations in terms of these haplotypes. Recently, Gusfield introduced the perfect phylogeny haplotyping problem, as an algorithmic implication of the no-recombination in long blocks observation, together with the standard population-genetic assumption of infinite sites. Gusfield{\textquoteright}s solution based on matroid theory was followed by direct θ(nm2 ) solutions that use simpler techniques (Bafna et al., 2003; Eskin et al., 2003), and also bound the number of solutions to the PPH problem. In this short note, we address two questions that were left open. First, can the algorithms of Bafna et al. (2003) and Eskin et al. (2003) be sped-up to O(nm + m2 ) time, which would imply an O(nm) time-bound for the PPH problem? Second, if there are multiple solutions, can we find one that is most parsimonious in terms of the number of distinct haplotypes.We give reductions that suggests that the answer to both questions is "no." For the first problem, we show that computing the output of the first step (in either method) is equivalent to Boolean matrix multiplication. Therefore, the best bound we can presently achieve is O(nmω{\textendash}1), where ω <= 2.52 is the exponent of matrix multiplication. Thus, any linear time solution to the PPH problem likely requires a different approach. For the second problem of computing a PPH solution that minimizes the number of distinct haplotypes, we show that the problem is NP-hard using a reduction from Vertex Cover (Garey and Johnson, 1979).}, isbn = {1066-5277, 1557-8666}, doi = {10.1089/cmb.2004.11.858}, url = {http://www.liebertonline.com/doi/abs/10.1089/cmb.2004.11.858}, author = {Bafna,Vineet and Gusfield,Dan and Hannenhalli, Sridhar and Yooseph,Shibu} } @conference {13214, title = {Object tracking by adaptive feature extraction}, booktitle = {Image Processing, 2004. ICIP {\textquoteright}04. 2004 International Conference on}, volume = {3}, year = {2004}, month = {2004/10//}, pages = {1501 - 1504 Vol. 3 - 1501 - 1504 Vol. 3}, abstract = {Tracking objects in the high-dimensional feature space is not only computationally expensive but also functionally inefficient. Selecting a low-dimensional discriminative feature set is a critical step to improve tracker performance. A good feature set for tracking can differ from frame to frame due to the changes in the background against the tracked object, and due to an on-line algorithm that adaptively determines a advantageous distinctive feature set. In this paper, multiple heterogeneous features are assembled, and likelihood images are constructed for various subspaces of the combined feature space. Then, the most discriminative feature is extracted by principal component analysis (PCA) based on those likelihood images. This idea is applied to the mean-shift tracking algorithm [D. Comaniciu et al., June 2000], and we demonstrate its effectiveness through various experiments.}, keywords = {adaptive, algorithm;, analysis;, colour, component, extraction;, feature, feature;, heterogeneous, image, image;, likelihood, Mean-shift, object, online, principal, tracking, tracking;}, doi = {10.1109/ICIP.2004.1421349}, author = {Han,Bohyung and Davis, Larry S.} } @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 {18262, title = {Performance study of ECC-based collusion-resistant multimedia fingerprinting}, journal = {Proceedings of the 38th CISS}, year = {2004}, month = {2004///}, pages = {827 - 832}, abstract = {Digital fingerprinting is a tool to protect multimediacontent from illegal redistribution by uniquely marking copies of the content distributed to each user. Fingerprinting based on error correction coding (ECC) handle the important issue of how to embed the fingerprint into host data in an abstract way known as the marking assumptions, which often do not fully account for multimedia specific issues. In this paper, we examine the performance of ECC based fingerprinting by considering both coding and embedding issues. We provide performance comparison of ECC-based scheme and a major alternative of orthogonal fingerprinting. As averaging is a feasible and cost-effective collusion attack against multimedia fingerprints yet is generally not considered in the ECC-based system, we also investigate the resistance against averaging collusion and identify avenues for improving collusion resistance. }, author = {He,S. and Wu,M.} } @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} } @conference {13919, title = {Preschool children{\textquoteright}s use of mouse buttons}, booktitle = {CHI{\textquoteright}04 extended abstracts on Human factors in computing systems}, year = {2004}, month = {2004///}, pages = {1411 - 1412}, author = {Hourcade,J. P and Bederson, Benjamin B. and Druin, Allison} } @conference {16120, title = {Project highlight: toward the statistical knowledge network}, booktitle = {Proceedings of the 2004 annual national conference on Digital government research}, series = {dg.o {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {125:1{\textendash}125:2 - 125:1{\textendash}125:2}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {This project aims to help people find and understand government statistical information. To achieve this goal, we envision a statistical knowledge network that brings stakeholders from government at all levels together with citizens who provide or seek statistical information. The linchpin of this network is a series of human-computer interfaces that facilitate information seeking, understanding, and use. In turn, these interfaces depend on high-quality metadata and intra-agency cooperation. In this briefing, we summarize our accomplishments in the second year of the project.}, url = {http://dl.acm.org/citation.cfm?id=1124191.1124316}, author = {Marchionini,Gary and Haas,Stephanie and Shneiderman, Ben and Plaisant, Catherine and Hert,Carol A.} } @article {17899, title = {Real-time rendering of translucent meshes}, journal = {ACM Trans. Graph.}, volume = {23}, year = {2004}, month = {2004/04//}, pages = {120 - 142}, abstract = {Subsurface scattering is important for photo-realistic rendering of translucent materials. We make approximations to the BSSRDF model and propose a simple lighting model to simulate the effects on translucent meshes. Our approximations are based on the observation that subsurface scattering is relatively local due to its exponential falloff.In the preprocessing stage we build subsurface scattering neighborhood information, which includes all the vertices within effective scattering range from each vertex. We then modify the traditional local illumination model into a run-time two-stage process. The first stage involves computation of reflection and transmission of light on surface vertices. The second stage bleeds in scattering effects from a vertex{\textquoteright}s neighborhood to generate the final result. We then merge the run-time two-stage process into a run-time single-stage process using precomputed integrals, and reduce the complexity of our run-time algorithm to O(N), where N is the number of vertices. The selection of the optimum set size for precomputed integrals is guided by a standard imagespace error-metric. Furthermore, we show how to compress the precomputed integrals using spherical harmonics. We compensate for the inadequacy of spherical harmonics for storing high frequency components by a reference points scheme to store high frequency components of the precomputed integrals explicitly. With this approach, we greatly reduce memory usage without loss of visual quality under a high-frequency lighting environment and achieve interactive frame rates for medium-sized scenes. Our model is able to capture the most important features of subsurface scattering: reflection and transmission due to multiple scattering.}, keywords = {BSSRDF, local illumination, reflection models, subsurface scattering}, isbn = {0730-0301}, doi = {10.1145/990002.990004}, url = {http://doi.acm.org/10.1145/990002.990004}, author = {Hao,Xuejun and Varshney, Amitabh} } @conference {15109, title = {Reducing complexity assumptions for statistically-hiding commitment}, booktitle = {In EUROCRYPT}, year = {2004}, month = {2004///}, abstract = {Determining the minimal assumptions needed to construct various cryptographic buildingblocks has been a focal point of research in theoretical cryptography. For most {\textemdash} but not all! {\textemdash} cryptographic primitives, complexity assumptions both necessary and sufficient for their existence are known. Here, we revisit the following, decade-old question: what are the minimal assumptions needed to construct a statistically-hiding bit commitment scheme? Previously, it was known how to construct such schemes based on any one-way permutation. In this work, we show that regular one-way functions suffice. We show two constructions of statistically-hiding commitment schemes from regular one-way functions. Our first construction is more direct, and serves as a {\textquotedblleft}stepping-stone{\textquotedblright} for our second construction which has improved round complexity. Of independent interest, as part of our work we show a compiler transforming any commitment scheme which is statistically-hiding against an honest-but-curious receiver to one which is statistically-hiding against a malicious receiver. This demonstrates the equivalence of these two formulations of the problem. }, author = {Horvitz,O. and Katz, Jonathan and Koo,C. Y and Morselli,R.} } @article {18989, title = {Reducing storage requirements for biological sequence comparison}, journal = {BioinformaticsBioinformatics}, volume = {20}, year = {2004}, month = {2004/12/12/}, pages = {3363 - 3369}, abstract = {Motivation: Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the {\textquoteleft}seed-and-extend{\textquoteright} approach, in which occurrences of short subsequences called {\textquoteleft}seeds{\textquoteright} are used to search for potentially longer matches in a large database of sequences. Each such potential match is then checked to see if it extends beyond the seed. To be effective, the seed-and-extend approach needs to catalogue seeds from virtually every substring in the database of search strings. Projects such as mammalian genome assemblies and large-scale protein matching, however, have such large sequence databases that the resulting list of seeds cannot be stored in RAM on a single computer. This significantly slows the matching process.Results: We present a simple and elegant method in which only a small fraction of seeds, called {\textquoteleft}minimizers{\textquoteright}, needs to be stored. Using minimizers can speed up string-matching computations by a large factor while missing only a small fraction of the matches found using all seeds. }, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/bth408}, url = {http://bioinformatics.oxfordjournals.org/content/20/18/3363}, author = {Roberts,Michael and Hayes,Wayne and Hunt,Brian R. and Mount, Stephen M. and Yorke,James A.} } @article {14768, title = {Resource policing to support fine-grain cycle stealing in networks of workstations}, journal = {IEEE Transactions on Parallel and Distributed Systems}, volume = {15}, year = {2004}, month = {2004/10//}, pages = {878 - 892}, abstract = {We present the design, implementation, and performance evaluation of a suite of resource policing mechanisms that allow guest processes to efficiently and unobtrusively exploit otherwise idle workstation resources. Unlike traditional policies that harvest cycles only from unused machines, we employ fine-grained cycle stealing to exploit resources even from machines that have active users. We developed a suite of kernel extensions that enable these policies to operate without significantly impacting host processes: 1) a new starvation-level CPU priority for guest jobs, 2) a new page replacement policy that imposes hard bounds on physical memory usage by guest processes, and 3) a new I/O scheduling mechanism called rate windows that throttle guest processes{\textquoteright} usage of I/O and network bandwidth. We evaluate both the individual impacts of each mechanism, and their utility for our fine-grain cycle stealing.}, keywords = {65, Application software, Bandwidth, cluster computing, Computer networks, Computer Society, Concurrent computing, cycle stealing, cycle stealing., grid computing, I/O scheduling, Intelligent networks, Kernel, network bandwidth, networks of workstations, page replacement policy, parallel computing, performance evaluation, Processor scheduling, resource allocation, resource scheduling, starvation-level CPU priority, workstation clusters, workstation resources, Workstations}, isbn = {1045-9219}, doi = {10.1109/TPDS.2004.58}, author = {Ryu, K. D and Hollingsworth, Jeffrey K} } @conference {12295, title = {Running on the bare metal with GeekOS}, booktitle = {Proceedings of the 35th SIGCSE technical symposium on Computer science education}, series = {SIGCSE {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {315 - 319}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Undergraduate operating systems courses are generally taught using one of two approaches: abstract or concrete. In the abstract approach, students learn the concepts underlying operating systems theory, and perhaps apply them using user-level threads in a host operating system. In the concrete approach, students apply concepts by working on a real operating system kernel. In the purest manifestation of the concrete approach, students implement operating system projects that run on real hardware.GeekOS is an instructional operating system kernel which runs on real hardware. It provides the minimum functionality needed to schedule threads and control essential devices on an x86 PC. On this foundation, we have developed projects in which students build processes, semaphores, a multilevel feedback scheduler, paged virtual memory, a filesystem, and inter-process communication. We use the Bochs emulator for ease of development and debugging. While this approach (tiny kernel run on an emulator) is not new, we believe GeekOS goes further towards the goal of combining realism and simplicity than previous systems have.}, keywords = {education, emulation, Hardware, Operating systems}, isbn = {1-58113-798-2}, doi = {10.1145/971300.971411}, url = {http://doi.acm.org/10.1145/971300.971411}, author = {Hovemeyer, David and Hollingsworth, Jeffrey K and Bhattacharjee, Bobby} } @article {14070, title = {Schistosoma mansoni genome project: an update}, journal = {Parasitology International}, volume = {53}, year = {2004}, month = {2004/06//}, pages = {183 - 192}, abstract = {A schistosome genome project was initiated by the World Health Organization in 1994 with the notion that the best prospects for identifying new targets for drugs, vaccines, and diagnostic development lie in schistosome gene discovery, development of chromosome maps, whole genome sequencing and genome analysis. Schistosoma mansoni has a haploid genome of 270 Mb contained on 8 pairs of chromosomes. It is estimated that the S. mansoni genome contains between 15~000 and 25~000 genes. There are approximately 16~689 ESTs obtained from diverse libraries representing different developmental stages of S. mansoni, deposited in the NCBI EST database. More than half of the deposited sequences correspond to genes of unknown function. Approximately 40-50\% of the sequences form unique clusters, suggesting that approximately 20-25\% of the total schistosome genes have been discovered. Efforts to develop low resolution chromosome maps are in progress. There is a genome sequencing program underway that will provide 3X sequence coverage of the S. mansoni genome that will result in approximately 95\% gene discovery. The genomics era has provided the resources to usher in the era of functional genomics that will involve microarrays to focus on specific metabolic pathways, proteomics to identify relevant proteins and protein-protein interactions to understand critical parasite pathways. Functional genomics is expected to accelerate the development of control and treatment strategies for schistosomiasis.}, keywords = {Chromosome mapping, Gene discovery, Genomics, Schistosoma mansoni}, isbn = {1383-5769}, doi = {16/j.parint.2004.01.009}, url = {http://www.sciencedirect.com/science/article/pii/S1383576904000108}, author = {LoVerde,Philip T. and Hirai,Hirohisa and Merrick,Joseph M and Lee,Norman H and El-Sayed, Najib M.} } @article {13854, title = {Semantic annotation and lexico-syntactic paraphrase}, journal = {Proceedings of the 4th International Conference on Language Resources and Evaluation (LREC) Workshop on Building Lexical Resources from Semantically Annotated Corpora}, year = {2004}, month = {2004///}, pages = {47 - 52}, abstract = {The IAMTC project (Interlingual Annotation of Multilingual Translation Corpora) is developing an interlingual representation frameworkfor annotation of parallel corpora (English paired with Arabic, French, Hindi, Japanese, Korean, and Spanish) with deep-semantic representations. In particular, we are investigating meaning equivalent paraphrases involving conversives and non-literal language use, as well as extended paraphrases involving syntax, lexicon, and grammatical features. The interlingua representation has three levels of depth. Each level is characterized by the types of meaning equivalent paraphrases that receive identical representations at that level. }, author = {Dorr, Bonnie J and Green,R. and Levin,L. and Rambow,O. and Farwell,D. and Habash,N. and Helmreich,S. and Hovy,E. and Miller,K.J. and Mitamura,T. and others} } @article {13855, title = {Semantic Annotation for Interlingual Representation of Multilingual Texts}, journal = {Workshop Programme}, year = {2004}, month = {2004///}, pages = {19 - 19}, abstract = {This paper describes the annotation process being used in a multi-site project to create six sizable bilingual parallel corpora annotated with a consistent interlingua representation. After presenting the background and objectives of the effort, we describe the multilingual corpora and the three stages of interlingual representation being developed. We then focus on the annotation process itself, including an interface environment that supports the annotation task, and the methodology for evaluating the interlingua representation. Finally, we discuss some issues encountered during the annotation tasks. The resulting annotated multilingual corpora will be useful for a wide range of natural language processing research tasks, including machine translation, question answering, text summarization, and information extraction.}, author = {Mitamura,T. and Miller,K. and Dorr, Bonnie J and Farwell,D. and Habash,N. and Helmreich,S. and Hovy,E. and Levin,L. and Rambow,O. and Reeder,F. and others} } @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.} } @conference {16885, title = {A serverless 3D world}, booktitle = {Proceedings of the 12th annual ACM international workshop on Geographic information systems}, series = {GIS {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {157 - 165}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Online multi-participant virtual-world systems have attracted significant interest from the Internet community but are hindered by their inability to efficiently support interactivity for a large number of participants. Current solutions divide a large virtual-world into a few mutually exclusive zones, with each zone controlled by a different server, and/or limit the number of participants per server or per virtual-world. Peer-to-Peer (P2P) systems are known to provide excellent scalability in a networked environment (one peer is introduced to the system by each participant), however current P2P applications can only provide file sharing and other forms of relatively simple data communications. In this paper, we present a generic 3D virtual-world application that runs on a P2P network with no central administration or server. Two issues are addressed by this paper to enable such a spatial application on a P2P network. First, we demonstrate how to index and query a 3D space on a dynamic distributed network. Second, we show how to build such a complex application from the ground level of a P2P routing algorithm. Our work leads to new directions for the development of online virtual-worlds that we believe can be used for many government, industry, and public domain applications.}, keywords = {distributed hash tables, peer-to-peer systems, spatial data, virtual-worlds}, isbn = {1-58113-979-9}, doi = {10.1145/1032222.1032246}, url = {http://doi.acm.org/10.1145/1032222.1032246}, author = {Tanin,Egemen and Harwood,Aaron and Samet, Hanan and Nutanong,Sarana and Truong,Minh Tri} } @article {18713, title = {Solution Conformation of Lys63-linked Di-ubiquitin Chain Provides Clues to Functional Diversity of Polyubiquitin Signaling}, journal = {Journal of Biological ChemistryJ. Biol. Chem.}, volume = {279}, year = {2004}, month = {2004/02/20/}, pages = {7055 - 7063}, abstract = {Diverse cellular events are regulated by post-translational modification of substrate proteins via covalent attachment of one or a chain of ubiquitin molecules. The outcome of (poly)ubiquitination depends upon the specific lysine residues involved in the formation of polyubiquitin chains. Lys48-linked chains act as a universal signal for proteasomal degradation, whereas Lys63-linked chains act as a specific signal in several non-degradative processes. Although it has been anticipated that functional diversity between alternatively linked polyubiquitin chains relies on linkage-dependent differences in chain conformation/topology, direct structural evidence in support of this model has been lacking. Here we use NMR methods to determine the structure of a Lys63-linked di-ubiquitin chain. The structure is characterized by an extended conformation, with no direct contact between the hydrophobic residues Leu8, Ile44, and Val70 on the ubiquitin units. This structure contrasts with the closed conformation observed for Lys48-linked di-ubiquitin wherein these residues form the interdomain interface (Cook, W. J., Jeffrey, L. C., Carson, M., Zhijian, C., and Pickart, C. M. (1992) J. Biol. Chem. 267, 16467-16471; Varadan, R., Walker, O., Pickart, C., and Fushman, D. (2002) J. Mol. Biol. 324, 637-647). Consistent with the open conformation of the Lys63-linked di-ubiquitin, our binding studies show that both ubiquitin domains in this chain can bind a ubiquitin-associated domain from HHR23A independently and in a mode similar to that for mono-ubiquitin. In contrast, Lys48-linked di-ubiquitin binds in a different, higher affinity mode that has yet to be determined. This is the first experimental evidence that alternatively linked polyubiquitin chains adopt distinct conformations.}, isbn = {0021-9258, 1083-351X}, doi = {10.1074/jbc.M309184200}, url = {http://www.jbc.org/content/279/8/7055}, author = {Varadan,Ranjani and Assfalg,Michael and Haririnia,Aydin and Raasi,Shahri and Pickart,Cecile and Fushman, David} } @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} } @article {13867, title = {Symbolic MT With Statistical NLP Components}, year = {2004}, month = {2004/06//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This reports provides an overview of the findings and software that have evolved from the "Symbolic MT with Statistical NLP Components" project over the last year. We present the major goals that have been achieved and discuss some of the open issues that we intend to address in the near future. This report also contains some details on the usage of some software that has been implemented during the project.}, keywords = {*MACHINE TRANSLATION, computational linguistics, COMPUTER PROGRAMS, CYBERNETICS, DIVERGENCE UNRAVELING, GHMT(GENERATION-HEAVY MACHINE TRANSLATION), INFORMATION SCIENCE, linguistics, natural language, RESOURCE PROJECTION}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458796}, author = {Dorr, Bonnie J and Habash,Nizar Y and Monz,Christof} } @conference {17801, title = {TOSS: an extension of TAX with ontologies and similarity queries}, booktitle = {Proceedings of the 2004 ACM SIGMOD international conference on Management of data}, series = {SIGMOD {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {719 - 730}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {TAX is perhaps the best known extension of the relational algebra to handle queries to XML databases. One problem with TAX (as with many existing relational DBMSs) is that the semantics of terms in a TAX DB are not taken into account when answering queries. Thus, even though TAX answers queries with 100\% precision, the recall of TAX is relatively low. Our TOSS system improves the recall of TAX via the concept of a similarity enhanced ontology (SEO). Intuitively, an ontology is a set of graphs describing relationships (such as isa, partof, etc.) between terms in a DB. An SEO also evaluates how similarities between terms (e.g. "J. Ullman", "Jeff Ullman", and "Jeffrey Ullman") affect ontologies. Finally, we show how the algebra proposed in TAX can be extended to take SEOs into account. The result is a system that provides a much higher answer quality than TAX does alone (quality is defined as the square root of the product of precision and recall). We experimentally evaluate the TOSS system on the DBLP and SIGMOD bibliographic databases and show that TOSS has acceptable performance.}, keywords = {ontologies, semantic integration of heterogeneous data, similarity enhancement, XML databases}, isbn = {1-58113-859-8}, doi = {10.1145/1007568.1007649}, url = {http://doi.acm.org/10.1145/1007568.1007649}, author = {Hung,Edward and Deng,Yu and V.S. Subrahmanian} } @conference {14749, title = {Transparent proxies for java futures}, booktitle = {Proceedings of the 19th annual ACM SIGPLAN conference on Object-oriented programming, systems, languages, and applications}, series = {OOPSLA {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {206 - 223}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {A proxy object is a surrogate or placeholder that controls access to another target object. Proxies can be used to support distributed programming, lazy or parallel evaluation, access control, and other simple forms of behavioral reflection. However, wrapper proxies (like futures or suspensions> for yet-to-be-computed results) can require significant code changes to be used in statically-typed languages, while proxies more generally can inadvertently violate assumptions of transparency, resulting in subtle bugs. To solve these problems, we have designed and implemented a simple framework for proxy programming that employs a static analysis based on qualifier inference, but with additional novelties. Code for using wrapper proxies is automatically introduced via a classfile-to-classfile transformation, and potential violations of transparency are signaled to the programmer. We have formalized our analysis and proven it sound. Our framework has a variety of applications, including support for asynchronous method calls returning futures. Experimental results demonstrate the benefits of our framework: programmers are relieved of managing and/or checking proxy usage, analysis times are reasonably fast, overheads introduced by added dynamic checks are negligible, and performance improvements can be significant. For example, changing two lines in a simple RMI-based peer-to-peer application and then using our framework resulted in a large performance gain.}, keywords = {future, java, proxy, Type inference, type qualifier}, isbn = {1-58113-831-8}, doi = {10.1145/1028976.1028994}, url = {http://doi.acm.org/10.1145/1028976.1028994}, author = {Pratikakis,Polyvios and Spacco,Jaime and Hicks, Michael W.} } @conference {14817, title = {Unobtrusiveness and efficiency in idle cycle stealing for PC grids}, booktitle = {Parallel and Distributed Processing Symposium, 2004. Proceedings. 18th International}, year = {2004}, month = {2004/04/26/30}, publisher = {IEEE}, organization = {IEEE}, abstract = {Summary form only given. Studies have shown that for a significant fraction of the time desktop PCs and workstations are under-utilized. To exploit these idle resources, various desktop/workstation grid systems have been developed. The ultimate goal of such systems is to maximize efficiency of resource usage while maintaining low obtrusiveness to machine owners. To this end, we created a new fine-grain cycle stealing approach and conducted a performance comparison study against the traditional coarse-grain cycle stealing. We developed a prototype of fine-grain cycle stealing, the Linger-Longer system, on a Linux cluster. The experiments on a cluster of desktop Linux PCs with benchmark applications show that, overall, fine-grain cycle stealing can improve efficiency of idle cycle usage by increasing the guest job throughput by 50\% to 70\%, while limiting obtrusiveness with no more than 3\% of host job slowdown.}, keywords = {Biological system modeling, Computational modeling, Computer science, Computer simulation, Contracts, desktop grid system, fine-grain cycle stealing approach, grid computing, idle cycle stealing, Linger-Longer system, Linux, Linux cluster, microcomputers, PC grids, Personal communication networks, Prototypes, resource allocation, Throughput, workstation clusters, workstation grid systems, Workstations}, isbn = {0-7695-2132-0}, doi = {10.1109/IPDPS.2004.1302987}, author = {Ryu, K. D and Hollingsworth, Jeffrey K} } @conference {13342, title = {Update operations on 3D simplicial decompositions of non-manifold objects}, booktitle = {Proceedings of the ninth ACM symposium on Solid modeling and applications}, series = {SM {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {169 - 180}, publisher = {Eurographics Association}, organization = {Eurographics Association}, address = {Aire-la-Ville, Switzerland, Switzerland}, abstract = {We address the problem of updating non-manifold mixed-dimensional objects, described by three-dimensional simplicial complexes embedded in 3D Euclidean space. We consider two local update operations, edge collapse and vertex split, which are the most common operations performed for simplifying a simplicial complex. We examine the effect of such operations on a 3D simplicial complex, and we describe algorithms for edge collapse and vertex split on a compact representation of a 3D simplicial complex, that we call the Non-Manifold Indexed data structure with Adjacencies (NMIA). We also discuss how to encode the information needed for performing a vertex split and an edge collapse on a 3D simplicial complex. The encoding of such information together with the algorithms for updating the NMIA data structure form the basis for defining progressive as well as multi-resolution representations for objects described by 3D simplicial complexes and for extracting variable-resolution object descriptions.}, isbn = {3-905673-55-X}, url = {http://dl.acm.org/citation.cfm?id=1217875.1217900}, author = {De Floriani, Leila and Hui,Annie} } @article {13886, title = {Use of Minimal Lexical Conceptual Structures for Single-Document Summarization}, year = {2004}, month = {2004/06//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This reports provides an overview of the findings and software that have evolved from the Use of Minimal Lexical Conceptual Structures for Single-Document Summarization project over the last six months. We present the major goals that have been achieved and discuss some of the open issues that we intend to address in the near future. This report also contains some details on the usage of some software that has been implemented during the project.}, keywords = {*COMPUTATIONAL LINGUISTICS, AUTOMATIC HEADLINE GENERATION, CYBERNETICS, DOCUMENT SUMMARIZATION, Information retrieval, INFORMATION SCIENCE, linguistics, Machine translation}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458797}, author = {Dorr, Bonnie J and Habash,Nizar Y and Monz,Christof and Schwartz,Richard} } @conference {14789, title = {Using Hardware Counters to Automatically Improve Memory Performance}, booktitle = {Proceedings of the 2004 ACM/IEEE conference on Supercomputing}, series = {SC {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {46{\textendash} - 46{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, abstract = {In this paper, we introduce a profile-driven online page migration scheme and investigate its impact on the performance of multithreaded applications. We use lightweight, inexpensive plug-in hardware counters to profile the memory access behavior of an application, and then migrate pages to memory local to the most frequently accessing processor. Using the Dyninst runtime instrumentation combined with hardware counters, we were able to add page migration capabilities to the system without having to modify the operating system kernel, or to re-compile application programs. This approach reduced the total number of non-local memory accesses of applications by up to 90\%. Even on a system with small remote to local memory access latency rations, this resulted in up to 16\% improvement in execution time.}, isbn = {0-7695-2153-3}, doi = {http://dx.doi.org/10.1109/SC.2004.64}, url = {http://dx.doi.org/10.1109/SC.2004.64}, author = {Tikir, Mustafa M. and Hollingsworth, Jeffrey K} } @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 {14578, title = {Whole-genome shotgun assembly and comparison of human genome assemblies}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, year = {2004}, month = {2004///}, pages = {1916 - 1916}, author = {Istrail,S. and Sutton,G. G and Florea,L. and Halpern,A. L and Mobarry,C. M and Lippert,R. and Walenz,B. and Shatkay,H. and Dew,I. and Miller,J. R and others} } @article {14486, title = {A workshop report: mining for and from the Semantic Web at KDD 2004}, journal = {SIGKDD Explor. Newsl.}, volume = {6}, year = {2004}, month = {2004/12//}, pages = {142 - 143}, abstract = {The international workshop on Mining for and from the Semantic Web (MSW) at the KDD 2004 successfully brought together people from the communities Semantic Web and Knowledge Discovery. The goal of the workshop was to strengthen the communication and interaction between these communities as there is currently an agreement that both can benefit largely from each other. Overall the contributions and discussions showed that today mining for the semantic web is the primarily targeted research area. However, with a growing amount of available semantic web data also mining from the semantic web will be more prominent.}, isbn = {1931-0145}, doi = {10.1145/1046456.1046482}, url = {http://doi.acm.org/10.1145/1046456.1046482}, author = {Hotho,Andreas and Sure,York and Getoor, Lise} } @book {18790, title = {19th Biennial Conference on Mechanical Vibration and Noise}, year = {2003}, month = {2003///}, publisher = {American Society of Mechanical Engineers}, organization = {American Society of Mechanical Engineers}, author = {Gupta,A. K. and Fadel,G. M. and Lewicki,D. G. and Shabana,A. A. and Royston,T. J. and Gupta,S.K. and Hayes,C. and Herrmann,J.W. and Dym,C. L. and Schmidt,L. C.} } @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 {13923, title = {Accuracy, Target Reentry and Fitts{\textquoteright} Law Performance of Preschool Children Using Mice}, journal = {University of Maryland Technical Report, HCIL-2003}, volume = {16}, year = {2003}, month = {2003///}, author = {Hourcade,J. P and Bederson, Benjamin B. and Druin, Allison and Guimbretiere,F.} } @article {18730, title = {Algorithms for computing global accessibility cones}, journal = {Journal of Computing and Information Science in Engineering}, volume = {3}, year = {2003}, month = {2003///}, pages = {200 - 200}, author = {Dhaliwal,S. and Gupta,S.K. and Huang,J. and Priyadarshini,A.} } @article {17556, title = {Approximating the domatic number}, journal = {SIAM Journal on Computing}, volume = {32}, year = {2003}, month = {2003///}, pages = {172 - 195}, abstract = {A set of vertices in a graph is a dominating set if every vertex outside the set hasa neighbor in the set. The domatic number problem is that of partitioning the vertices of a graph into the maximum number of disjoint dominating sets. Let n denote the number of vertices, δ the minimum degree, and ∆ the maximum degree. We show that every graph has a domatic partition with (1 - o(1))(δ + 1)/ ln n dominating sets and, moreover, that such a domatic partition can be found in polynomial-time. This implies a (1 + o(1)) ln n-approximation algorithm for domatic number, since the domatic number is always at most δ+1. We also show this to be essentially best possible. Namely, extending the approximation hardness of set cover by combining multiprover protocols with zero-knowledge techniques, we show that for every ϵ > 0, a (1 - ϵ) ln n-approximation implies that NP ⊆ DTIME(nO(log log n)). This makes domatic number the first natural maximization problem (known to the authors) that is provably approximable to within polylogarithmic factors but no better. We also show that every graph has a domatic partition with (1 - o(1))(δ + 1)/ ln ∆ dominating sets, where the {\textquotedblleft}o(1){\textquotedblright} term goes to zero as ∆ increases. This can be turned into an efficient algorithm that produces a domatic partition of {\textohm}(δ/ ln ∆) sets. }, author = {Feige,U. and Halld{\'o}rsson,M.M. and Kortsarz,G. and Srinivasan, Aravind} } @inbook {18896, title = {Automating DAML-S Web Services Composition Using SHOP2}, booktitle = {The Semantic Web - ISWC 2003}, series = {Lecture Notes in Computer Science}, volume = {2870}, year = {2003}, month = {2003///}, pages = {195 - 210}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The DAML-S Process Model is designed to support the application of AI planning techniques to the automated composition of Web services. SHOP2 is an Hierarchical Task Network (HTN) planner well-suited for working with the Process Model. We have proven the correspondence between the semantics of SHOP2 and the situation calculus semantics of the Process Model. We have also implemented a system which soundly and completely plans over sets of DAML-S descriptions using a SHOP2 planner, and then executes the resulting plans over the Web. We discuss the challenges and difficulties of using SHOP2 in the information-rich and human-oriented context of Web services.}, keywords = {Computer science}, isbn = {978-3-540-20362-9}, url = {http://www.springerlink.com/content/rm5ejwlmbw0mdv97/abstract/}, author = {Wu,Dan and Parsia,Bijan and Sirin,Evren and Hendler,James and Nau, Dana S.}, editor = {Fensel,Dieter and Sycara,Katia and Mylopoulos,John} } @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} } @conference {13699, title = {A categorial variation database for English}, booktitle = {Proceedings of the 2003 Conference of the North American Chapter of the Association for Computational Linguistics on Human Language Technology - Volume 1}, series = {NAACL {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {17 - 23}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {We describe our approach to the construction and evaluation of a large-scale database called "CatVar" which contains categorial variations of English lexemes. Due to the prevalence of cross-language categorial variation in multilingual applications, our categorial-variation resource may serve as an integral part of a diverse range of natural language applications. Thus, the research reported herein overlaps heavily with that of the machine-translation, lexicon-construction, and information-retrieval communities.We apply the information-retrieval metrics of precision and recall to evaluate the accuracy and coverage of our database with respect to a human-produced gold standard. This evaluation reveals that the categorial database achieves a high degree of precision and recall. Additionally, we demonstrate that the database improves on the linkability of Porter stemmer by over 30\%.}, doi = {10.3115/1073445.1073458}, url = {http://dx.doi.org/10.3115/1073445.1073458}, author = {Habash,Nizar and Dorr, Bonnie J} } @article {13735, title = {CATVAR: A database of categorial variations for English}, journal = {Proceedings of the MT Summit}, year = {2003}, month = {2003///}, pages = {471 - 474}, abstract = {We present a new large-scale database called {\textquotedblleft}CatVar{\textquotedblright} (Habash and Dorr, 2003) which contains categorial variationsof English lexemes. Due to the prevalence of cross-language categorial variation in multilingual applications, our categorial-variation resource may serve as an integral part of a diverse range of natural language applications. Thus, the research reported herein overlaps heavily with that of the machine-translation, lexicon-construction, and information- retrieval communities. We demonstrate this database, embedded in a graphical interface; we also show a GUI for user input of corrections to the database. }, author = {Habash,N. and Dorr, Bonnie J} } @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} } @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.} } @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 {15854, title = {Comparing user-assisted and automatic query translation}, journal = {Advances in cross-language information retrieval}, year = {2003}, month = {2003///}, pages = {400 - 415}, author = {He,D. and Wang,J. and Oard, Douglas and Nossal,M.} } @conference {15479, title = {DART: a framework for regression testing "nightly/daily builds" of GUI applications}, booktitle = {Software Maintenance, 2003. ICSM 2003. Proceedings. International Conference on}, year = {2003}, month = {2003/09//}, pages = {410 - 419}, abstract = {"Nightly/daily building and smoke testing" have become widespread since they often reveal bugs early in the software development process. During these builds, software is compiled, linked, and (re)tested with the goal of validating its basic functionality. Although successful for conventional software, smoke tests are difficult to develop and automatically rerun for software that has a graphical user interface (GUI). In this paper, we describe a framework called DART (daily automated regression tester) that addresses the needs of frequent and automated re-testing of GUI software. The key to our success is automation: DART automates everything from structural GUI analysis; test case generation; test oracle creation; to code instrumentation; test execution; coverage evaluation; regeneration of test cases; and their re-execution. Together with the operating system{\textquoteright}s task scheduler, DART can execute frequently with little input from the developer/tester to retest the GUI software. We provide results of experiments showing the time taken and memory required for GUI analysis, test case and test oracle generation, and test execution. We also empirically compare the relative costs of employing different levels of detail in the GUI test cases.}, keywords = {automated retesting, automatic test software, coverage evaluation, daily automated regression tester, DART, frequent retesting, graphical user interface, Graphical user interfaces, GUI software, instrumentation coding, program testing, regression testing, Software development management, Software development process, Software maintenance, Software quality, structural GUI analysis, Test Case Generation, test cases regeneration, Test execution, test oracle creation}, doi = {10.1109/ICSM.2003.1235451}, author = {Memon, Atif M. and Banerjee,I. and Hashmi,N. and Nagarajan,A.} } @article {16893, title = {Data-parallel polygonization}, journal = {Parallel Computing}, volume = {29}, year = {2003}, month = {2003/10//}, pages = {1381 - 1401}, abstract = {Data-parallel algorithms are presented for polygonizing a collection of line segments represented by a data-parallel bucket PMR quadtree, a data-parallel R-tree, and a data-parallel R+-tree. Such an operation is useful in a geographic information system (GIS). A sample performance comparison of the three data-parallel structures for this operation is also given.}, keywords = {Data-parallel algorithms, Hierarchical spatial data structures, Lines, Polygonization}, isbn = {0167-8191}, doi = {10.1016/j.parco.2003.05.001}, url = {http://www.sciencedirect.com/science/article/pii/S0167819103001091}, author = {Hoel,Erik G. and Samet, Hanan} } @article {12194, title = {Designing a digital library for young children: An intergenerational partnership}, journal = {The craft of information visualization: readings and reflections}, volume = {178}, year = {2003}, month = {2003///}, author = {Druin, Allison and Bederson, Benjamin B. and Hourcade,J. P and Sherman,L. and Revelle,G. and Platner,M. and Weng,S.} } @article {13754, title = {Desparately seeking cebuano}, journal = {Third Conference on Human Language Technologies}, year = {2003}, month = {2003///}, abstract = {This paper describes an effort to rapidly de-velop language resources and component tech- nology to support searching Cebuano news sto- ries using English queries. Results from the first 60 hours of the exercise are presented. }, author = {Oard, Douglas and David Doermann and Dorr, Bonnie J and He,D. and Resnik, Philip and Weinberg, Amy and Byrne,W. and Khudanpur,S. and Yarowsky,D. and Leuski,A. and others} } @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 {16289, title = {The Dog Genome: Survey Sequencing and Comparative Analysis}, journal = {ScienceScience}, volume = {301}, year = {2003}, month = {2003/09/26/}, pages = {1898 - 1903}, abstract = {A survey of the dog genome sequence (6.22 million sequence reads; 1.5{\texttimes} coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of species-specific resources. More than 650 million base pairs (>25\%) of dog sequence align uniquely to the human genome, including fragments of putative orthologs for 18,473 of 24,567 annotated human genes. Mutation rates, conserved synteny, repeat content, and phylogeny can be compared among human, mouse, and dog. A variety of polymorphic elements are identified that will be valuable for mapping the genetic basis of diseases and traits in the dog.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1086432}, url = {http://www.sciencemag.org/content/301/5641/1898}, author = {Kirkness,Ewen F. and Bafna,Vineet and Halpern,Aaron L. and Levy,Samuel and Remington,Karin and Rusch,Douglas B and Delcher,Arthur L. and Pop, Mihai and Wang,Wei and Fraser,Claire M. and Venter,J. Craig} } @article {19078, title = {The dog genome: survey sequencing and comparative analysis}, journal = {Science}, volume = {301}, year = {2003}, month = {2003}, author = {Kirkness,E. F and Bafna,V. and Halpern,A. L and Levy,S. and Remington,K. and Rusch,D. B and Delcher,A. L and Pop, Mihai and Wang,W. and Fraser,C. M and others} } @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} } @conference {17113, title = {Dynamic querying for pattern identification in microarray and genomic data}, booktitle = {2003 International Conference on Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings}, volume = {3}, year = {2003}, month = {2003/07/06/9}, pages = {III- 453-6 vol.3 - III- 453-6 vol.3}, publisher = {IEEE}, organization = {IEEE}, abstract = {Data sets involving linear ordered sequences are a recurring theme in bioinformatics. Dynamic query tools that support exploration of these data sets can be useful for identifying patterns of interest. This paper describes the use of one such tool - timesearcher - to interactively explore linear sequence data sets taken from two bioinformatics problems. Microarray time course data sets involve expression levels for large numbers of genes over multiple time points. Timesearcher can be used to interactively search these data sets for genes with expression profiles of interest. The occurrence frequencies of short sequences of DNA in aligned exons can be used to identify sequences that play a role in the pre-mRNA splicing. Timesearcher can be used to search these data sets for candidate splicing signals.}, keywords = {Bioinformatics, data sets, Displays, dynamic querying, expression profiles, Frequency, Gene expression, genes, Genetics, genomic data, Genomics, linear ordered sequences, macromolecules, medical signal processing, Mice, Microarray, pattern identification, pattern recognition, premRNA splicing, Query processing, sequences, Signal processing, splicing, TimeSearcher}, isbn = {0-7803-7965-9}, doi = {10.1109/ICME.2003.1221346}, author = {Hochheiser,H. and Baehrecke,E. H and Mount, Stephen M. and Shneiderman, Ben} } @conference {14682, title = {Dynamic rebinding for marshalling and update, with destruct-time ?}, booktitle = {Proceedings of the eighth ACM SIGPLAN international conference on Functional programming}, series = {ICFP {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {99 - 110}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Most programming languages adopt static binding, but for distributed programming an exclusive reliance on static binding is too restrictive: dynamic binding is required in various guises, for example when a marshalled value is received from the network, containing identifiers that must be rebound to local resources. Typically it is provided only by ad-hoc mechanisms that lack clean semantics.In this paper we adopt a foundational approach, developing core dynamic rebinding mechanisms as extensions to simply-typed call-by-value ? -calculus. To do so we must first explore refinements of the call-by-value reduction strategy that delay instantiation, to ensure computations make use of the most recent versions of rebound definitions. We introduce redex-time and destruct-time strategies. The latter forms the basis for a ?marsh calculus that supports dynamic rebinding of marshalled values, while remaining as far as possible statically-typed. We sketch an extension of ? marsh with concurrency and communication, giving examples showing how wrappers for encapsulating untrusted code can be expressed. Finally, we show that a high-level semantics for dynamic updating can also be based on the destruct-time strategy, defining a ?marsh calculus with simple primitives to provide type-safe updating of running code. We thereby establish primitives and a common semantic foundation for a variety of real-world dynamic rebinding requirements.}, keywords = {distributed programming, dynamic binding, dynamic update, lambda calculus, marshalling, programming languages, serialisation}, isbn = {1-58113-756-7}, doi = {10.1145/944705.944715}, url = {http://doi.acm.org/10.1145/944705.944715}, author = {Bierman,Gavin and Hicks, Michael W. and Sewell,Peter and Stoyle,Gareth and Wansbrough,Keith} } @conference {12200, title = {Electronic voting system usability issues}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, year = {2003}, month = {2003///}, pages = {145 - 152}, author = {Bederson, Benjamin B. and Lee,B. and Sherman,R.M. and Herrnson,P.S. and Niemi,R.G.} } @conference {12322, title = {Energy reduction techniques for multimedia applications with tolerance to deadline misses}, booktitle = {Proceedings of the 40th annual Design Automation Conference}, year = {2003}, month = {2003///}, pages = {131 - 136}, author = {Hua,S. and Qu,G. and Bhattacharyya, Shuvra S.} } @article {18938, title = {Evaluating Translational Correspondence using Annotation Projection}, volume = {UMIACS-TR-2003-25}, year = {2003}, month = {2003///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Recently, statistical machine translation models have begun to take advantage of higherlevel linguistic structures such as syntactic dependencies. Underlying these models is an assumption about the directness of translational correspondence between sentences in the two languages; however, the extent to which this assumption is valid and useful is not well understood. In this paper, we present an empirical study that quantifies the degree to which syntactic dependencies are preserved when parses are projected directly from En- glish to Chinese. Our results show that although the direct correspondence assumption is often too restrictive, a small set of principled, elementary linguistic transformations can boost the quality of the projected Chinese parses by 76\% relative to the unimproved baseline. }, url = {http://lampsrv02.umiacs.umd.edu/pubs/TechReports/LAMP_100/LAMP_100.pdf}, author = {Hwa,R. and Resnik, Philip and Weinberg, Amy and Kolak,O.} } @conference {12381, title = {Exploring the probabilistic design space of multimedia systems}, booktitle = {14th IEEE International Workshop on Rapid Systems Prototyping, 2003. Proceedings}, year = {2003}, month = {2003/06/09/11}, pages = {233 - 240}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we propose the novel concept of probabilistic design for multimedia systems and a methodology to quickly explore such design space at an early design stage. The probabilistic design is motivated by the challenge of how to design, but not over-design, multimedia embedded systems while systematically incorporating such application{\textquoteright}s performance requirements, uncertainties in execution time, and tolerance for reasonable execution failures. Our goal is to bridge the gap between real-time analysis and embedded software implementation for rapid and economic (multimedia) system prototyping. Our method takes advantage of multimedia system{\textquoteright}s unique features mentioned above to relax the rigid hardware requirements for software implementation and eventually avoid over-designing the system.}, keywords = {economic system prototyping, embedded software implementation, Embedded system, Energy consumption, execution time uncertainties, Hardware, multimedia embedded systems, multimedia system prototyping, multimedia systems, performance requirements, probabilistic design space, rapid system prototyping, Real time systems, real-time analysis, reasonable execution failure tolerance, Resource management, software prototyping, Space exploration, Streaming media, systems analysis, Timing, Uncertainty}, isbn = {0-7695-1943-1}, doi = {10.1109/IWRSP.2003.1207053}, author = {Shaoxiong Hua and Gang Qu and Bhattacharyya, Shuvra S.} } @article {16126, title = {Family Calendar Survey}, journal = {Technical Reports from UMIACS}, year = {2003}, month = {2003/01/21/}, abstract = {Beginning in late July 2002, we conducted a survey about people{\textquoteright}s personal andfamily calendaring habits. By the end of September, we had over 400 responses, which are summarized below. The survey was conducted to help inform our work in designing new technologies for families, motivated in part by our work on the interLiving project. InterLiving is a 3 year, European Union-funded project where we work with distributed, multi-generational families as design partners to create new technologies (see http://www.cs.umd.edu/hcil/interliving for details). The survey was administered from a web page (https://www.cs.umd.edu/users/hilary/survey/survey.htm), and participants were solicited via a "chain-mail" email approach. We began by sending a request to fill out a survey to our friends, families, and colleagues. We asked that they forward the request on to their friends, family and colleagues as well. While we realize that this was an imperfect approach, we believed that the respondents would be representative of the users we are initially targeting in our research on family calendaring and coordination - individuals who are already making relatively heavy use of computers at home and/or work. The results seem to validate this assumption. Many of our respondents likely come from the HCI community as the mailing went to our large lab mailing list. We may have some pollution in the data as a result of people in the same household (e.g. husband and wife) both filling out the survey. Despite these issues, the results we got were helpful in eliciting a number of important findings, namely that people rely on multiple calendars, many of which are still paper. (UMIACS-TR-2002-92) (HCIL-TR-2002-21) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1236}, author = {Hutchinson,Hilary and Bederson, Benjamin B. and Plaisant, Catherine and Druin, Allison} } @article {14697, title = {Formalizing dynamic software updating}, journal = {Proceedings of the Second International Workshop on Unanticipated Software Evolution (USE)}, year = {2003}, month = {2003///}, abstract = {Dynamic software updating (DSU) enables running programs to beupdated with new code and data without interrupting their execution. A number of DSU systems have been designed, but there is still little rig- orous understanding of how to use DSU technology so that updates are safe. As a first step in this direction, we introduce a small update calculus with a precise mathematical semantics. The calculus is formulated as an extension of a typed lambda calculus, and supports updating technology similar to that of the programming language Erlang [2]. Our goal is to provide a simple yet expressive foundation for reasoning about dynam- ically updateable software. In this paper, we present the details of the calculus, give some examples of its expressive power, and discuss how it might be used or extended to guarantee safety properties. }, author = {Bierman,G. and Hicks, Michael W. and Sewell,P. and Stoyle,G.} } @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 {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 {13234, title = {Guest editors{\textquoteright} Introduction to the special section on energy minimization methods in computer vision and pattern recognition}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {25}, year = {2003}, month = {2003/11//}, pages = {1361 - 1363}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2003.1240110}, author = {Figueiredo,M.A.T. and Hancock,E.R. and Pelillo,M. and Zerubia, J.} } @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} } @conference {13236, title = {HRTF personalization using anthropometric measurements}, booktitle = {Applications of Signal Processing to Audio and Acoustics, 2003 IEEE Workshop on.}, year = {2003}, month = {2003/10//}, pages = {157 - 160}, abstract = {Individualized head related transfer functions (HRTFs) are needed for accurate rendering of spatial audio, which is important in many applications. Since these are relatively tedious to acquire, they may not be acceptable for some applications. A number of studies have sought to perform simple customization of the HRTF. We propose and test a strategy for HRTF personalization, based on matching certain anthropometric ear parameters with the HRTF database, and the incorporation of a low-frequency "head-and-torso" model. We present preliminary tests aimed at evaluation of this customization. Results show that the approach improves both the accuracy of the localization and subjective perception of the virtual auditory scene.}, keywords = {acoustic, anthropometric, audio, audio;, auditory, Ear, functions;, Head, head-and-torso, HRTF, individualized, localization;, measurements;, model;, models;, parameters;, perception;, personalization;, physiological, processing;, related, scattering;, scene;, signal, sound, spatial, subjective, transfer, virtual, wave}, doi = {10.1109/ASPAA.2003.1285855}, author = {Zotkin,Dmitry N and Hwang,J. and Duraiswami, Ramani and Davis, Larry S.} } @article {13786, title = {Hybrid Natural Language Generation from Lexical Conceptual Structures}, journal = {Machine Translation}, volume = {18}, year = {2003}, month = {2003///}, pages = {81 - 128}, abstract = {This paper describes Lexogen, a system for generating natural-languagesentences from Lexical Conceptual Structure, an interlingualrepresentation. The system has been developed as part of aChinese{\textendash}English Machine Translation (MT) system; however, it isdesigned to be used for many other MT language pairs and naturallanguage applications. The contributions of this work include: (1)development of a large-scale Hybrid Natural Language Generation system withlanguage-independent components; (2) enhancements to an interlingualrepresentation and associated algorithm forgeneration from ambiguous input; (3) development of an efficientreusable language-independent linearization module with a grammardescription language that can be used with other systems; (4)improvements to an earlier algorithm forhierarchically mapping thematic roles to surface positions; and (5)development of a diagnostic tool for lexicon coverage and correctnessand use of the tool for verification of English, Spanish, and Chineselexicons. An evaluation of Chinese{\textendash}English translation quality showscomparable performance with a commercial translation system. Thegeneration system can also be extended to other languages and this isdemonstrated and evaluated for Spanish.}, isbn = {0922-6567}, url = {http://dx.doi.org/10.1023/B:COAT.0000020960.27186.18}, author = {Habash,Nizar and Dorr, Bonnie J and Traum,David} } @mastersthesis {14699, title = {Implementing On-line Software Upgrades in Java}, year = {2003}, month = {2003/05//}, school = {University of Maryland, College Park}, abstract = {There are many systems that have to be available without interruption and so cannot bebrought down for modifications. Examples of such applications include financial transaction processors, telephone switches and air traffic control systems. On the other hand, hardly any software is deployed error-free or fully functional, thus requiring fixes and changes. Therefore, there is a need for runtime software upgrading capability for such systems. This paper discusses existing approaches of {\textquotedblleft}hotswapping{\textquotedblright} {\textendash} runtime updating of classes {\textendash} for the Java language. The different implementations of hotswapping are compared with respect to functionality, efficiency, ease of use and limitations. In addition, an improvement for one hotswapping mechanism is suggested and implemented. }, author = {Gebremichael,M. and Hicks, Michael W.} } @article {16892, title = {Improved search heuristics for the sa-tree}, journal = {Pattern Recognition Letters}, volume = {24}, year = {2003}, month = {2003/11//}, pages = {2785 - 2795}, abstract = {The sa-tree is an interesting metric space indexing structure that is inspired by the Voronoi diagram. In essence, the sa-tree records a portion of the Delaunay graph of the data set, a graph whose vertices are the Voronoi cells, with edges between adjacent cells. An improvement is presented on the original search strategy for the sa-tree. This consists of details on the intuition behind the improvement as well as the original search strategy and a proof of their correctness. Furthermore, it is shown how to adapt an incremental nearest neighbor algorithm to the sa-tree, which allows computing nearest neighbor in a progressive manner. Unlike other adaptations, the resulting algorithm does not take the unnecessary steps to ensure that keys of {\textquotedblleft}node{\textquotedblright} elements are monotonically non-decreasing.}, keywords = {distance-based indexing, Metric spaces, Nearest neighbor algorithms}, isbn = {0167-8655}, doi = {10.1016/S0167-8655(03)00122-3}, url = {http://www.sciencedirect.com/science/article/pii/S0167865503001223}, author = {Hjaltason,G{\i}́sli R. and Samet, Hanan} } @article {18980, title = {Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {31}, year = {2003}, month = {2003/10/01/}, pages = {5654 - 5666}, abstract = {The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble clusters of overlapping transcript alignments (ESTs and full-length cDNAs) into maximal alignment assemblies, thereby comprehensively incorporating all available transcript data and capturing subtle splicing variations. Complete and partial gene structures identified by this method were used to improve The Institute for Genomic Research Arabidopsis genome annotation (TIGR release v.4.0). The alignment assemblies permitted the automated modeling of several novel genes and >1000 alternative splicing variations as well as updates (including UTR annotations) to nearly half of the \~{}27 000 annotated protein coding genes. The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/gkg770}, url = {http://nar.oxfordjournals.org/content/31/19/5654}, author = {Haas,Brian J. and Delcher,Arthur L. and Mount, Stephen M. and Wortman,Jennifer R. and Jr,Roger K. Smith and Hannick,Linda I. and Maiti,Rama and Ronning,Catherine M. and Rusch,Douglas B and Town,Christopher D. and Salzberg,Steven L. and White,Owen} } @article {17229, title = {In vivo filtering of in vitro expression data reveals MyoD targets}, journal = {Comptes Rendus Biologies}, volume = {326}, year = {2003}, month = {2003/10//}, pages = {1049 - 1065}, abstract = {A published set of downstream targets of MyoD defined in a well-controlled in vitro experiment was filtered for relevance to muscle regeneration using a 27-time-point in vivo murine regeneration series. Using interactive hierarchical and Bayes soft clustering, only a minority of the targets defined in vitro can be confirmed in vivo (\~{}50\% of induced transcripts, and none of repressed transcripts). This approach provided strong support that 18 targets including of MyoD are biologically relevant during myoblast differentiation. To cite this article: P.~Zhao et al., C.~R. Biologies 326 (2003).}, keywords = {clustering, expression profiling, Microarray, micror{\'e}seaux, muscle regeneration, MyoD, profil d{\textquoteright}expression, r{\'e}g{\'e}n{\'e}ration musculaire, regroupement}, isbn = {1631-0691}, doi = {10.1016/j.crvi.2003.09.035}, url = {http://www.sciencedirect.com/science/article/pii/S1631069103002324}, author = {Zhao,Po and Seo,Jinwook and Wang,Zuyi and Wang,Yue and Shneiderman, Ben and Hoffman,Eric P} } @article {16891, title = {Index-driven similarity search in metric spaces (Survey Article)}, journal = {ACM Trans. Database Syst.}, volume = {28}, year = {2003}, month = {2003/12//}, pages = {517 - 580}, abstract = {Similarity search is a very important operation in multimedia databases and other database applications involving complex objects, and involves finding objects in a data set S similar to a query object q, based on some similarity measure. In this article, we focus on methods for similarity search that make the general assumption that similarity is represented with a distance metric d. Existing methods for handling similarity search in this setting typically fall into one of two classes. The first directly indexes the objects based on distances (distance-based indexing), while the second is based on mapping to a vector space (mapping-based approach). The main part of this article is dedicated to a survey of distance-based indexing methods, but we also briefly outline how search occurs in mapping-based methods. We also present a general framework for performing search based on distances, and present algorithms for common types of queries that operate on an arbitrary "search hierarchy." These algorithms can be applied on each of the methods presented, provided a suitable search hierarchy is defined.}, keywords = {distance-based indexing, Hiearchical metric data structures, nearest neighbor queries, range queries, Ranking, similarity searching}, isbn = {0362-5915}, doi = {10.1145/958942.958948}, url = {http://doi.acm.org/10.1145/958942.958948}, author = {Hjaltason,Gisli R. and Samet, Hanan} } @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 {17615, title = {Integrality ratio for group Steiner trees and directed steiner trees}, booktitle = {Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms}, series = {SODA {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {275 - 284}, publisher = {Society for Industrial and Applied Mathematics}, organization = {Society for Industrial and Applied Mathematics}, address = {Philadelphia, PA, USA}, abstract = {We present an Ω(log2k) lower bound on the integrality ratio of the flow-based relaxation for the Group Steiner Tree problem, where k denotes the number of groups; this holds even for input graphs that are Hierarchically Well-Separated Trees, introduced by Bartal [Symp. Foundations of Computer Science, pp. 184--193, 1996], in which case this lower bound is tight. This relaxation appears to be the only one that have been studied for the problem, as well as for its generalization, the Directed Steiner Tree problem. For the latter problem, our results imply an Ω(log2n/(log logn)2) integrality ratio, where n is the number of vertices in the graph. For both problems, this is the first known lower bound on the integrality ratio that is superlogarithmic in the input size. We also show algorithmically that the integrality ratio for Group Steiner Tree is much better for certain families of instances, which helps pinpoint the types of instances that appear to be most difficult to approximate.}, isbn = {0-89871-538-5}, url = {http://dl.acm.org/citation.cfm?id=644108.644155}, author = {Halperin,Eran and Kortsarz,Guy and Krauthgamer,Robert and Srinivasan, Aravind and Wang,Nan} } @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.} } @conference {17939, title = {Interactive subsurface scattering for translucent meshes}, booktitle = {Proceedings of the 2003 symposium on Interactive 3D graphics}, series = {I3D {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {75 - 82}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We propose a simple lighting model to incorporate subsurface scattering effects within the local illumination framework. Subsurface scattering is relatively local due to its exponential falloff and has little effect on the appearance of neighboring objects. These observations have motivated us to approximate the BSSRDF model and to model subsurface scattering effects by using only local illumination. Our model is able to capture the most important features of subsurface scattering: reflection and transmission due to multiple scattering.In our approach we build the neighborhood information as a preprocess and modify the traditional local illumination model into a run-time two-stage process. In the first stage we compute the reflection and transmission of light on the surface. The second stage involves bleeding the scattering effects from a vertex{\textquoteright}s neighborhood to produce the final result. We then show how to merge the run-time two-stage process into a run-time single-stage process using precomputed integral. The complexity of our run-time algorithm is O(N), where N is the number of vertices. Using this approach, we achieve interactive frame rates with about one to two orders of magnitude speedup compared with the state-of-the-art methods.}, keywords = {BSSRDF, local illumination, reflection models, subsurface scattering}, isbn = {1-58113-645-5}, doi = {10.1145/641480.641497}, url = {http://doi.acm.org/10.1145/641480.641497}, author = {Hao,Xuejun and Baby,Thomas and Varshney, Amitabh} } @article {12190, title = {The International Children{\textquoteright}s Digital Library}, journal = {First Monday}, volume = {8}, year = {2003}, month = {2003///}, author = {Druin, Allison and Bederson, Benjamin B. and Weeks,A. and Farber,A. and Grosjean,J. and Guha,M.L. and Hourcade,J. P and Lee,J. and Liao,S. and Reuter,K. and others} } @article {13928, title = {The International Children{\textquoteright}s Digital Library: Description and analysis of first use}, journal = {First Monday}, volume = {8}, year = {2003}, month = {2003///}, pages = {315 - 315}, author = {Druin, Allison and Bederson, Benjamin B. and Weeks,A. and Farber,A. and Grosjean,J. and Guha,M.L. and Hourcade,J. P and Lee,J. and Liao,S. and Reuter,K. and others} } @article {13904, title = {The International Children{\textquoteright}s Digital Library: viewing digital books online}, journal = {Interacting with Computers}, volume = {15}, year = {2003}, month = {2003///}, pages = {151 - 167}, author = {Hourcade,J. P and Bederson, Benjamin B. and Druin, Allison and Rose,A. and Farber,A. and Takayama,Y.} } @inbook {16129, title = {LifeLines: Using Visualization to Enhance Navigation and Analysis of Patient Records}, booktitle = {The Craft of Information VisualizationThe Craft of Information Visualization}, year = {2003}, month = {2003///}, pages = {308 - 312}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, address = {San Francisco}, isbn = {978-1-55860-915-0}, url = {http://www.sciencedirect.com/science/article/pii/B978155860915050038X}, author = {Plaisant, Catherine and Mushlin,Richard and Snyder,Aaron and Li,Jia and Heller,Dan and Shneiderman, Ben}, editor = {Bederson, Benjamin B. and Shneiderman, Ben} } @article {15847, title = {Making miracles: Interactive translingual search for cebuano and hindi}, journal = {ACM Transactions on Asian Language Information Processing (TALIP)}, volume = {2}, year = {2003}, month = {2003///}, pages = {219 - 244}, author = {He,D. and Oard, Douglas and Wang,J. and Luo,J. and Demner-Fushman,D. and Darwish,K. and Resnik, Philip and Khudanpur,S. and Nossal,M. and Subotin,M. and others} } @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 {16127, title = {Navigation patterns \& usability of zoomable user interfaces: with and without an overview}, journal = {interactions}, volume = {10}, year = {2003}, month = {2003/01//}, pages = {11 - 12}, abstract = {The following abstracts are from recent issues and the forthcoming issue of ACM{\textquoteright}s Transactions of Computer Human Interaction (ToCHI). They are included here to alert interactions{\textquoteright} readers to what research is being done in the field of Computer Human Interaction. The complete papers, when published, can be found in ACM{\textquoteright}s Digital Library at www.acm.org/pubs/contents/journals/tochi/}, isbn = {1072-5520}, doi = {10.1145/604575.604582}, url = {http://doi.acm.org/10.1145/604575.604582}, author = {Hornbaek,Kasper and Bederson, Benjamin B. and Plaisant, Catherine} } @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 {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 {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} } @inbook {16140, title = {Preserving Context with Zoomable User Interfaces}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {83 - 83}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, isbn = {978-1-55860-915-0}, author = {Hombsek,K. and Bederson, Benjamin B. and Plaisant, Catherine} } @article {16897, title = {Properties of embedding methods for similarity searching in metric spaces}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {25}, year = {2003}, month = {2003/05//}, pages = {530 - 549}, abstract = {Complex data types-such as images, documents, DNA sequences, etc.-are becoming increasingly important in modern database applications. A typical query in many of these applications seeks to find objects that are similar to some target object, where (dis)similarity is defined by some distance function. Often, the cost of evaluating the distance between two objects is very high. Thus, the number of distance evaluations should be kept at a minimum, while (ideally) maintaining the quality of the result. One way to approach this goal is to embed the data objects in a vector space so that the distances of the embedded objects approximates the actual distances. Thus, queries can be performed (for the most part) on the embedded objects. We are especially interested in examining the issue of whether or not the embedding methods will ensure that no relevant objects are left out. Particular attention is paid to the SparseMap, FastMap, and MetricMap embedding methods. SparseMap is a variant of Lipschitz embeddings, while FastMap and MetricMap are inspired by dimension reduction methods for Euclidean spaces. We show that, in general, none of these embedding methods guarantee that queries on the embedded objects have no false dismissals, while also demonstrating the limited cases in which the guarantee does hold. Moreover, we describe a variant of SparseMap that allows queries with no false dismissals. In addition, we show that with FastMap and MetricMap, the distances of the embedded objects can be much greater than the actual distances. This makes it impossible (or at least impractical) to modify FastMap and MetricMap to guarantee no false dismissals.}, keywords = {complex, contractiveness;, data, databases;, decomposition;, dimension, distance, distortion;, DNA, documents;, EMBEDDING, embeddings;, Euclidean, evaluations;, FastMap;, images;, Lipschitz, methods;, metric, MetricMap;, multimedia, processing;, query, reduction, search;, searching;, sequences;, similarity, singular, spaces;, SparseMap;, types;, value}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2003.1195989}, author = {Hjaltason,G. R and Samet, Hanan} } @conference {14387, title = {PXML: a probabilistic semistructured data model and algebra}, booktitle = {Data Engineering, 2003. Proceedings. 19th International Conference on}, year = {2003}, month = {2003/03//}, pages = {467 - 478}, abstract = {Despite the recent proliferation of work on semistructured data models, there has been little work to date on supporting uncertainty in these models. We propose a model for probabilistic semistructured data (PSD). The advantage of our approach is that it supports a flexible representation that allows the specification of a wide class of distributions over semistructured instances. We provide two semantics for the model and show that the semantics are probabilistically coherent. Next, we develop an extension of the relational algebra to handle probabilistic semistructured data and describe efficient algorithms for answering queries that use this algebra. Finally, we present experimental results showing the efficiency of our algorithms.}, keywords = {algebra;, data, databases;, instances;, model;, models;, probabilistic, processing;, PXML;, query, relational, semistructured, structures;, tree, XML;}, doi = {10.1109/ICDE.2003.1260814}, author = {Hung,E. and Getoor, Lise and V.S. Subrahmanian} } @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} } @article {13846, title = {Rapid porting of DUSTer to Hindi}, journal = {ACM Transactions on Asian Language Information Processing (TALIP)}, volume = {2}, year = {2003}, month = {2003/06//}, pages = {118 - 123}, abstract = {The frequent occurrence of divergences{\textemdash}structural differences between languages---presents a great challenge for statistical word-level alignment and machine translation. This paper describes the adaptation of DUSTer, a divergence unraveling package, to Hindi during the DARPA TIDES-2003 Surprise Language Exercise. We show that it is possible to port DUSTer to Hindi in under 3 days.}, keywords = {Divergences, Machine translation}, isbn = {1530-0226}, doi = {10.1145/974740.974744}, url = {http://doi.acm.org/10.1145/974740.974744}, author = {Dorr, Bonnie J and Ayan,Necip Fazil and Habash,Nizar and Madnani,Nitin and Hwa,Rebecca} } @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} } @conference {15963, title = {RGL study in a hybrid real-time system}, booktitle = {Proceedings of the IASTED NCI}, year = {2003}, month = {2003///}, author = {Hennacy,K. and Swamy,N. and Perlis, Don} } @article {14729, title = {Safe and flexible memory management in Cyclone}, journal = {Technical Reports from UMIACS}, year = {2003}, month = {2003/08/01/undef}, abstract = {Cyclone is a type-safe programming language intended for applications requiring control over memory management. Our previous work on Cyclone included support for stack allocation, lexical region allocation, and a garbage-collected heap. We achieved safety (i.e., prevented dangling pointers) through a region-based type-and-effects system. This paper describes some new memory-management mechanisms that we have integrated into Cyclone: dynamic regions, unique pointers, and reference-counted objects. Our experience shows that these new mechanisms are well suited for the timely recovery of objects in situations where it is awkward to use lexical regions. Crucially, programmers can write reusable functions without unnecessarily restricting callers{\textquoteright} choices among the variety of memory-management options. To achieve this goal, Cyclone employs a combination of polymorphism and scoped constructs that temporarily let us treat objects as if they were allocated in a lexical region.}, author = {Hicks, Michael W. and Morrisett,G. and Grossman,D. and Jim,T.} } @conference {13269, title = {A scalable data structure for three-dimensional non-manifold objects}, booktitle = {Proceedings of the 2003 Eurographics/ACM SIGGRAPH symposium on Geometry processing}, series = {SGP {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {72 - 82}, publisher = {Eurographics Association}, organization = {Eurographics Association}, address = {Aire-la-Ville, Switzerland, Switzerland}, abstract = {In this paper, we address the problem of representing and manipulating non-manifold, mixed-dimensional objects described by three-dimensional simplicial complexes embedded in the 3D Euclidean space. We describe the design and the implementation of a new data structure, that we call the non-manifold indexed data structure with adjacencies (NMIA), which can represent any three-dimensional Euclidean simplicial complex compactly, since it encodes only the vertices and the top simplexes of the complex plus a restricted subset of topological relations among simplexes. The NMIA structure supports efficient traversal algorithms which retrieve topological relations in optimal time, and it scales very well to the manifold case. Here, we sketch traversal algorithms, and we compare the NMIA structure with data structures for manifold and regular 3D simplicial complexes.}, isbn = {1-58113-687-0}, url = {http://dl.acm.org/citation.cfm?id=882370.882380}, author = {De Floriani, Leila and Hui,Annie} } @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 {14653, title = {A secure PLAN}, journal = {IEEE Transactions on Systems, Man, and Cybernetics, Part C: Applications and Reviews}, volume = {33}, year = {2003}, month = {2003/08//}, pages = {413 - 426}, abstract = {Active networks, being programmable, promise greater flexibility than current networks. Programmability, however, may introduce safety and security risks. This correspondence describes the design and implementation of a security architecture for the active network PLANet. Security is obtained with a two-level architecture that combines a functionally restricted packet language, PLAN, with an environment of general-purpose service routines governed by trust management. In particular, a technique is used which expands or contracts a packet{\textquoteright}s service environment based on its level of privilege, termed namespace-based security. The design and implementation of an active-network firewall and virtual private network is used as an application of the security architecture. Measurements of the system show that the addition of the firewall imposes an approximately 34\% latency overhead and as little as a 6.7\% space overhead to incoming packets.}, keywords = {active networks, active-network firewall, Authentication, Authorization, Contracts, cryptography, Environmental management, Extraterrestrial measurements, functionally restricted packet language, general-purpose service routines, Internet, latency overhead, namespace-based security, packet switching, PLANet, Planets, privilege level, programmable networks, Safety, safety risks, secure PLAN, security of data, security risks, trust management, two-level architecture, virtual private network, Virtual private networks, Web and internet services}, isbn = {1094-6977}, doi = {10.1109/TSMCC.2003.817347}, author = {Hicks, Michael W. and Keromytis,A. D and Smith,J. M} } @article {14104, title = {The sequence and analysis of Trypanosoma brucei chromosome II}, journal = {Nucleic acids research}, volume = {31}, year = {2003}, month = {2003///}, pages = {4856 - 4856}, author = {El-Sayed, Najib M. and Ghedin,E. and Song,J. and MacLeod,A. and Bringaud,F. and Larkin,C. and Wanless,D. and Peterson,J. and Hou,L. and Taylor,S. and others} } @article {13253, title = {Special Issue on Visual Analysis of Human Movement}, journal = {The International Journal of Robotics Research}, volume = {22}, year = {2003}, month = {2003///}, pages = {357 - 357}, author = {Davis, Larry S. and Horaud,R.} } @article {17387, title = {Supporting statistical electronic table usage by citizens}, journal = {Commun. ACM}, volume = {46}, year = {2003}, month = {2003/01//}, pages = {52 - 54}, abstract = {Over 70 agencies at the federal level are charged with collecting data and producing and disseminating statistics. These statistics are used to inform government policy, shape health care initiatives, provide information on the state of the economy, and others. They also have significant impact on the lives of citizens who use the statistics, for example, to determine job opportunities, changes in social security benefits, and quality of life in particular areas. Our digital government project developed several specific technologies to support the location, manipulation, and understanding of a quintessential format for statistical information---the table.}, isbn = {0001-0782}, doi = {10.1145/602421.602449}, url = {http://doi.acm.org/10.1145/602421.602449}, author = {Hert,Carol A. and Liddy,Elizabeth D. and Shneiderman, Ben and Marchionini,Gary} } @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 {16133, title = {Toward a statistical knowledge network}, booktitle = {Proceedings of the 2003 annual national conference on Digital government research}, series = {dg.o {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {1 - 6}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {This paper describes an architecture for a statistical knowledge network that depends on user interfaces as the glue among the components. These interfaces aim to serve non-expert users with diverse needs and statistical and computing experiences. Such interfaces are crucially dependent on different indexing schemes and good metadata.}, url = {http://dl.acm.org/citation.cfm?id=1123196.1123312}, author = {Marchionini,Gary and Haas,Stephanie and Plaisant, Catherine and Shneiderman, Ben and Hert,Carol} } @article {14645, title = {Transcriptional regulation of protein complexes and biological pathways}, journal = {Mammalian Genome}, volume = {14}, year = {2003}, month = {2003///}, pages = {611 - 619}, abstract = {The cis-element profile (or cis-profile) of a gene refers to the collection of transcription factor binding sites (TFBS) regulating the transcription of the gene. Underlying the various published studies that attempt to discover cis-elements in the vicinity of co-expressed genes via pattern detection algorithms, there is an implicit assumption that a correlation exists between co-expressed genes and their cis-profiles. In this study, we show that the cis-similarity, defined as the proportion of shared TFBS between two cis-element profiles, is higher for functionally linked interacting proteins as well as for members of a signal transduction pathway. A similar analysis of the enzymes catalyzing the conversion of adjacent substrates to products in a collection of metabolic pathways, did not reveal higher cis-similarity. The analysis is based on three distinct sources of publicly available data, namely, 1) the BIND database of interacting proteins, 2) known interactions in NMDAR protein complex, 3) the apoptosis pathway and nine pathways related to metabolism of cofactors and vitamins all from KEGG. Additionally, we analyze the cis-element profiles of all the genes in the glutamate receptor (GR) sub-complex of NMDAR complex to detect a set of cis-elements that occur adjacent to a majority of the genes. We show that most of the corresponding transcription factors are known to be involved in GR regulation by comparing our findings with the published biomedical literature. In addition, we were able to detect transcripts whose gene products associate with GR by searching for transcripts that share the same regulatory signals as those detected for GR. This suggests a novel computational methodology for constructing high-order gene regulatory models and detecting co-regulated gene products.}, isbn = {0938-8990}, url = {http://dx.doi.org/10.1007/s00335-002-2260-x}, author = {Hannenhalli, Sridhar and Levy,Samuel} } @article {16898, title = {Use of the SAND spatial browser for digital government applications}, journal = {Commun. ACM}, volume = {46}, year = {2003}, month = {2003/01//}, pages = {61 - 64}, abstract = {Numerous federal agencies produce official statistics made accessible to ordinary citizens for searching and data retrieval. This is frequently done via the Internet through a Web browser interface. If this data is presented in textual format, it can often be searched and retrieved by such attributes as topic, responsible agency, keywords, or press release. However, if the data is of spatial nature, for example, in the form of a map, then using text-based queries is often too cumbersome for the intended audience. We describe the use of the SAND Spatial Browser to provide more power to users of these databases by enabling them to define and explore the specific spatial region of interest graphically. The SAND Spatial Browser allows users to form either purely spatial or mixed spatial/nonspatial queries intuitively, which can present information to users that might have been missed if only a textual interface was available.}, keywords = {GIS}, isbn = {0001-0782}, doi = {10.1145/602421.602453}, url = {http://doi.acm.org/10.1145/602421.602453}, author = {Samet, Hanan and Alborzi,Houman and Brabec,Franti{\v s}ek and Esperan{\c c}a,Claudio and Hjaltason,G{\'\i}sli R. and Morgan,Frank and Tanin,Egemen} } @conference {14753, title = {User-specified adaptive scheduling in a streaming media network}, booktitle = {2003 IEEE Conference on Open Architectures and Network Programming}, year = {2003}, month = {2003/04/04/5}, pages = {87 - 96}, publisher = {IEEE}, organization = {IEEE}, abstract = {In disaster and combat situations, mobile cameras and other sensors transmit real-time data, used by many operators or analysis tools. Unfortunately, in the face of limited, unreliable resources, and varying demands, not all users may be able to get the fidelity they require. This paper describes MediaNet, a distributed stream processing system designed with the above scenarios in mind. Unlike past approaches, MediaNet{\textquoteright}s users can intuitively specify how the system should adapt based on their individual needs. MediaNet uses both local and online global resource scheduling to improve user performance and network utilization, and adapts without requiring underlying support for resource reservations. Performance experiments show that our scheduling algorithm is reasonably fast, and that user performance and network utilization are both significantly improved.}, keywords = {Adaptive scheduling, CAMERAS, Computer networks, Computer science, distributed stream processing system, Educational institutions, global resource scheduling, Intelligent networks, MediaNet, Mobile computing, network utilization, Process design, Processor scheduling, quality of service, Streaming media, streaming media network, user performance, user-specified adaptive scheduling}, isbn = {0-7803-7764-8}, doi = {10.1109/OPNARC.2003.1196376}, author = {Hicks, Michael W. and Nagarajan,A. and van Renesse,R.} } @conference {13343, title = {Using state modules for adaptive query processing}, booktitle = {19th International Conference on Data Engineering, 2003. Proceedings}, year = {2003}, month = {2003/03/05/8}, pages = {353 - 364}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present a query architecture in which join operators are decomposed into their constituent data structures (State Modules, or SteMs), and dataflow among these SteMs is managed adaptively by an eddy routing operator [R. Avnur et al., (2000)]. Breaking the encapsulation of joins serves two purposes. First, it allows the eddy to observe multiple physical operations embedded in a join algorithm, allowing for better calibration and control of these operations. Second, the SteM on a relation serves as a shared materialization point, enabling multiple competing access methods to share results, which can be leveraged by multiple competing join algorithms. Our architecture extends prior work significantly, allowing continuously adaptive decisions for most major aspects of traditional query optimization: choice of access methods and join algorithms, ordering of operators, and choice of a query spanning tree. SteMs introduce significant routing flexibility to the eddy, enabling more opportunities for adaptation, but also introducing the possibility of incorrect query results. We present constraints on eddy routing through SteMs that ensure correctness while preserving a great deal of flexibility. We also demonstrate the benefits of our architecture via experiments in the Telegraph dataflow system. We show that even a simple routing policy allows significant flexibility in adaptation, including novel effects like automatic "hybridization " of multiple algorithms for a single join.}, keywords = {adaptive query processing, Bandwidth, Calibration, data encapsulation, data structure, Data structures, Databases, Dictionaries, eddy routing, eddy routing operator, Encapsulation, join operator, multiple algorithm automatic hybridization, multiple competing join algorithm, query architecture, Query processing, query spanning tree, Routing, routing policy, Runtime, shared materialization point, State Module, SteMs, Telegraph dataflow system, Telegraphy, Tree data structures}, isbn = {0-7803-7665-X}, doi = {10.1109/ICDE.2003.1260805}, author = {Vijayshankar Raman and Deshpande, Amol and Hellerstein,J. M} } @conference {15285, title = {What makes a good answer? The role of context in question answering}, booktitle = {Human-Computer Interaction, Interact {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {25 - 25}, author = {Jimmy Lin and Quan,D. and Sinha,V. and Bakshi,K. and Huynh,D. and Katz,B. and Karger,D. R} } @article {12084, title = {WLAN problems and solutions}, journal = {Communications of the ACM}, volume = {46}, year = {2003}, month = {2003///}, pages = {31 - 34}, author = {Housley,R. and Arbaugh, William A.} } @inbook {14589, title = {1.375-Approximation Algorithm for Sorting by Reversals}, booktitle = {Algorithms {\textemdash} ESA 2002Algorithms {\textemdash} ESA 2002}, series = {Lecture Notes in Computer Science}, volume = {2461}, year = {2002}, month = {2002///}, pages = {401 - 408}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Analysis of genomes evolving by inversions leads to a general combinatorial problem of Sorting by Reversals , MIN-SBR, the problem of sorting a permutation by a minimum number of reversals. Following a series of preliminary results, Hannenhalli and Pevzner developed the first exact polynomial time algorithm for the problem of sorting signed permutations by reversals, and a polynomial time algorithm for a special case of unsigned permutations. The best known approximation algorithm for MIN-SBR, due to Christie, gives a performance ratio of 1.5. In this paper, by exploiting the polynomial time algorithm for sorting signed permutations and by developing a new approximation algorithm for maximum cycle decomposition of breakpoint graphs, we design a new 1.375-algorithm for the MIN-SBR problem.}, isbn = {978-3-540-44180-9}, url = {http://dx.doi.org/10.1007/3-540-45749-6_21}, author = {Berman,Piotr and Hannenhalli, Sridhar and Karpinski,Marek}, editor = {M{\"o}hring,Rolf and Raman,Rajeev} } @article {13414, title = {AAAI 2002 Workshops}, journal = {AI Magazine}, volume = {23}, year = {2002}, month = {2002/12/15/}, pages = {113 - 113}, isbn = {0738-4602}, doi = {10.1609/aimag.v23i4.1678}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/1678}, author = {Blake,Brian and Haigh,Karen and Hexmoor,Henry and Falcone,Rino and Soh,Leen-Kiat and Baral,Chitta and McIlraith,Sheila and Gmytrasiewicz,Piotr and Parsons,Simon and Malaka,Rainer and Krueger,Antonio and Bouquet,Paolo and Smart,Bill and Kurumantani,Koichi and Pease,Adam and Brenner,Michael and desJardins, Marie and Junker,Ulrich and Delgrande,Jim and Doyle,Jon and Rossi,Francesca and Schaub,Torsten and Gomes,Carla and Walsh,Toby and Guo,Haipeng and Horvitz,Eric J and Ide,Nancy and Welty,Chris and Anger,Frank D and Guegen,Hans W and Ligozat,Gerald} } @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} } @article {15541, title = {Algorithmic issues in modeling motion}, journal = {ACM Comput. Surv.}, volume = {34}, year = {2002}, month = {2002/12//}, pages = {550 - 572}, abstract = {This article is a survey of research areas in which motion plays a pivotal role. The aim of the article is to review current approaches to modeling motion together with related data structures and algorithms, and to summarize the challenges that lie ahead in producing a more unified theory of motion representation that would be useful across several disciplines.}, keywords = {computational geometry, Computer vision, mobile networks, modeling, molecular biology, motion modeling, physical simulation, robotoics, spatio-temporal databases}, isbn = {0360-0300}, doi = {10.1145/592642.592647}, url = {http://doi.acm.org/10.1145/592642.592647}, author = {Agarwal,Pankaj K. and Guibas,Leonidas J. and Edelsbrunner,Herbert and Erickson,Jeff and Isard,Michael and Har-Peled,Sariel and Hershberger,John and Jensen,Christian and Kavraki,Lydia and Koehl,Patrice and Lin,Ming and Manocha,Dinesh and Metaxas,Dimitris and Mirtich,Brian and Mount, Dave and Muthukrishnan,S. and Pai,Dinesh and Sacks,Elisha and Snoeyink,Jack and Suri,Subhash and Wolefson,Ouri} } @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} } @conference {13729, title = {Automatic transcription of Czech language oral history in the MALACH project: resources and initial experiments}, booktitle = {Proceedings of the The 5th International Conference on Text, Speech and Dialogue}, year = {2002}, month = {2002///}, pages = {57 - 64}, author = {Oard, Douglas and Demner-Fushman,D. and Hajic,J. and Ramabhadran,B. and Gustman,S. and Byrne,WJ and Soergel,D. and Dorr, Bonnie J and Resnik, Philip and Picheny,M.} } @conference {18930, title = {Breaking the resource bottleneck for multilingual applications}, year = {2002}, month = {2002///}, author = {Hwa,R. and Resnik, Philip and Weinberg, Amy} } @article {16151, title = {Case study: a message board as a technology probe for family communication and coordination}, journal = {Proceedings of the 2002 Conference on Human Factors in Computing Systems}, year = {2002}, month = {2002///}, abstract = {In this paper, we describe the design of an electronic family message board and the initial results of its deployment in three households. The message board was used as a {\textquotedblleft}technology probe{\textquotedblright} to help understand the communication and coordination needs of a distributed, multigenerational family. Using this information, we are working with the family as design partners to design new technologies.}, author = {Hutchinson,H. and Plaisant, Catherine and Druin, Allison} } @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} } @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.} } @article {16250, title = {Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus Anthracis}, journal = {Science}, volume = {296}, year = {2002}, month = {2002/06/14/}, pages = {2028 - 2033}, abstract = {Comparison of the whole-genome sequence ofBacillus anthracis isolated from a victim of a recent bioterrorist anthrax attack with a reference reveals 60 new markers that include single nucleotide polymorphisms (SNPs), inserted or deleted sequences, and tandem repeats. Genome comparison detected four high-quality SNPs between the two sequenced B. anthracischromosomes and seven differences among different preparations of the reference genome. These markers have been tested on a collection of anthrax isolates and were found to divide these samples into distinct families. These results demonstrate that genome-based analysis of microbial pathogens will provide a powerful new tool for investigation of infectious disease outbreaks.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1071837}, url = {http://www.sciencemag.org/content/296/5575/2028}, author = {Read,Timothy D. and Salzberg,Steven L. and Pop, Mihai and Shumway,Martin and Umayam,Lowell and Jiang,Lingxia and Holtzapple,Erik and Busch,Joseph D and Smith,Kimothy L and Schupp,James M and Solomon,Daniel and Keim,Paul and Fraser,Claire M.} } @article {19075, title = {Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440}, journal = {Environmental microbiology}, volume = {4}, year = {2002}, month = {2002}, pages = {799 - 808}, abstract = {Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85\% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.}, author = {Nelson,K. E and Weinel,C. and Paulsen,IT and Dodson,RJ and Hilbert,H. and Martins dos Santos,VAP and Fouts,DE and Gill,S. R and Pop, Mihai and Holmes,M. and others} } @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.} } @conference {13363, title = {Decoupled query optimization for federated database systems}, booktitle = {18th International Conference on Data Engineering, 2002. Proceedings}, year = {2002}, month = {2002///}, pages = {716 - 727}, publisher = {IEEE}, organization = {IEEE}, abstract = {We study the problem of query optimization in federated relational database systems. The nature of federated databases explicitly decouples many aspects of the optimization process, often making it imperative for the optimizer to consult underlying data sources while doing cost-based optimization. This not only increases the cost of optimization, but also changes the trade-offs involved in the optimization process significantly. The dominant cost in the decoupled optimization process is the "cost of costing" that traditionally has been considered insignificant. The optimizer can only afford a few rounds of messages to the underlying data sources and hence the optimization techniques in this environment must be geared toward gathering all the required cost information with minimal communication. In this paper, we explore the design space for a query optimizer in this environment and demonstrate the need for decoupling various aspects of the optimization process. We present minimum-communication decoupled variants of various query optimization techniques, and discuss tradeoffs in their performance in this scenario. We have implemented these techniques in the Cohera federated database system and our experimental results, somewhat surprisingly, indicate that a simple two-phase optimization scheme performs fairly well as long as the physical database design is known to the optimizer, though more aggressive algorithms are required otherwise}, keywords = {Algorithm design and analysis, Cohera federated database, Computer science, Corporate acquisitions, Cost function, Database systems, decoupled optimization, Design optimization, distributed databases, federated databases, federated relational database systems, Internet, Query optimization, query optimizer, Query processing, Relational databases, Space exploration}, isbn = {0-7695-1531-2}, doi = {10.1109/ICDE.2002.994788}, author = {Deshpande, Amol and Hellerstein,J. M} } @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} } @inbook {13760, title = {DUSTer: A Method for Unraveling Cross-Language Divergences for Statistical Word-Level Alignment}, booktitle = {Machine Translation: From Research to Real UsersMachine Translation: From Research to Real Users}, series = {Lecture Notes in Computer Science}, volume = {2499}, year = {2002}, month = {2002///}, pages = {31 - 43}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The frequent occurrence of divergenceS {\textemdash}structural differences between languages{\textemdash}presents a great challenge for statistical word-level alignment. In this paper, we introduce DUSTer, a method for systematically identifying common divergence types and transforming an English sentence structure to bear a closer resemblance to that of another language. Our ultimate goal is to enable more accurate alignment and projection of dependency trees in another language without requiring any training on dependency-tree data in that language. We present an empirical analysis comparing the complexities of performing word-level alignments with and without divergence handling. Our results suggest that our approach facilitates word-level alignment, particularly for sentence pairs containing divergences.}, isbn = {978-3-540-44282-0}, url = {http://dx.doi.org/10.1007/3-540-45820-4_4}, author = {Dorr, Bonnie J and Pearl,Lisa and Hwa,Rebecca and Habash,Nizar}, editor = {Richardson,Stephen} } @conference {16921, title = {A dynamic query interface for finding patterns in time series data}, booktitle = {CHI {\textquoteright}02 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {522 - 523}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Identification of patterns in time series data sets is a task that arises in a wide variety of application domains. This demonstration presents the timebox model of rectangular regions that specify constraints for dynamic queries over time series data sets, and the TimeSearcher application, which uses timeboxes as the basis of an interactive query tool.}, keywords = {dynamic queries, Information Visualization, time series}, isbn = {1-58113-454-1}, doi = {10.1145/506443.506460}, url = {http://doi.acm.org/10.1145/506443.506460}, author = {Hochheiser,Harry and Shneiderman, Ben} } @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 {14800, title = {Efficient instrumentation for code coverage testing}, booktitle = {ACM SIGSOFT Software Engineering Notes}, volume = {27}, year = {2002}, month = {2002///}, pages = {86 - 96}, author = {Tikir, M. M and Hollingsworth, Jeffrey K} } @conference {18942, title = {Evaluating translational correspondence using annotation projection}, series = {ACL {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {392 - 399}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Recently, statistical machine translation models have begun to take advantage of higher level linguistic structures such as syntactic dependencies. Underlying these models is an assumption about the directness of translational correspondence between sentences in the two languages; however, the extent to which this assumption is valid and useful is not well understood. In this paper, we present an empirical study that quantifies the degree to which syntactic dependencies are preserved when parses are projected directly from English to Chinese. Our results show that although the direct correspondence assumption is often too restrictive, a small set of principled, elementary linguistic transformations can boost the quality of the projected Chinese parses by 76\% relative to the unimproved baseline.}, doi = {10.3115/1073083.1073149}, url = {http://dx.doi.org/10.3115/1073083.1073149}, author = {Hwa,Rebecca and Resnik, Philip and Weinberg, Amy and Kolak,Okan} } @conference {16669, title = {Evaluating translational correspondence using annotation projection}, booktitle = {Proceedings of the 40th Annual Meeting on Association for Computational Linguistics}, year = {2002}, month = {2002///}, pages = {392 - 399}, author = {Hwa,R. and Resnik, Philip and Weinberg, Amy and Kolak,O.} } @inbook {14692, title = {Evolution in Action: Using Active Networking to Evolve Network Support for Mobility}, booktitle = {Active NetworksActive Networks}, series = {Lecture Notes in Computer Science}, volume = {2546}, year = {2002}, month = {2002///}, pages = {146 - 161}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {A key early objective of Active Networking (AN) was to support on-the-fly network evolution. Although AN has been used relatively extensively to build application-customized protocols and even whole networking systems, demonstrations of evolution have been limited. This paper examines three AN mechanisms and how they enable evolution: active packets and plug-in extensions, well-known to the AN community, and update extensions, which are novel to AN. We devote our presentation to a series of demonstrations of how each type of evolution can be applied to the problem of adding support for mobility to a network. This represents the most large-scale demonstration of AN evolution to date. These demonstrations show what previous AN research has not: that AN technology can, in fact, support very significant changes to the network, even while the network is operational.}, isbn = {978-3-540-00223-9}, url = {http://dx.doi.org/10.1007/3-540-36199-5_12}, author = {Seong-Kyu,Song and Shannon,Stephen and Hicks, Michael W. and Nettles,Scott}, editor = {Sterbenz,James and Takada,Osamu and Tschudin,Christian and Plattner,Bernhard} } @article {12133, title = {Experience in implementing a learning software organization}, journal = {Software, IEEE}, volume = {19}, year = {2002}, month = {2002/06//may}, pages = {46 - 49}, abstract = {In an effort to improve software development and acquisition processes and explicitly reuse knowledge from previous software projects, DaimlerChrysler created a software experience center (SEC). The authors report on challenges the company faced in creating the SEC}, keywords = {ACQUISITION, center;software, centres;project, DaimlerChrysler;explicit, development, experience, improvement;, improvement;automobile, industry;computer, knowledge, management;software, organization;previous, process, processes;software, projects;software, reuse;learning, software}, isbn = {0740-7459}, doi = {10.1109/MS.2002.1003453}, author = {Schneider,K. and von Hunnius,J.-P. and Basili, Victor R.} } @conference {14695, title = {Experiences with capsule-based active networking}, booktitle = {DARPA Active NEtworks Conference and Exposition, 2002. Proceedings}, year = {2002}, month = {2002///}, pages = {16 - 24}, publisher = {IEEE}, organization = {IEEE}, abstract = {Active networking adds programmability to the elements of the network, most aggressively by using programmable packets, or capsules. ANTS [22, 21] and PLANet [10, 8] are the most mature examples of capsule-based systems, both having been publicly available for several years. This paper presents our experience with these systems and the lessons they hold for the future of capsule-based active networking. The paper focuses on four key issues: flexibility, performance, security, and usability. We consider how ANTS and PLANet address these issues, noting that despite substantial surface differences, both systems identify similar key problems and use closely related solutions. Based on our experience with these systems we conclude that capsule-based systems can achieve useful levels of flexibility, performance, and usability. Many aspects of security can also be adequately addressed, but some important problems related to denial of service remain as open problems}, keywords = {active networking, ANTS, application-specific routing, capsule architecture, capsule-based systems, computer crime, Computer network management, Computer networks, Computer science, Contracts, Electronic switching systems, INFORMATION SCIENCE, Internet, internetworking, network management, PLANet, Planets, programmability, programmable packets, Programming, Security, Standards development, telecommunication network routing, usability}, isbn = {0-7695-1564-9}, doi = {10.1109/DANCE.2002.1003481}, author = {Hicks, Michael W. and Moore,J. T and Wetherall,D. and Nettles,S.} } @article {14551, title = {Exponential speedup of fixed-parameter algorithms on K 3, 3-minor-free or K 5-minor-free graphs}, journal = {Algorithms and Computation}, year = {2002}, month = {2002///}, pages = {277 - 287}, author = {Demaine,E. and Hajiaghayi, Mohammad T. and Thilikos,D.} } @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} } @inbook {13782, title = {Handling Translation Divergences: Combining Statistical and Symbolic Techniques in Generation-Heavy Machine Translation}, booktitle = {Machine Translation: From Research to Real UsersMachine Translation: From Research to Real Users}, series = {Lecture Notes in Computer Science}, volume = {2499}, year = {2002}, month = {2002///}, pages = {84 - 93}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper describes a novel approach to handling translation divergences in a Generation-Heavy Hybrid Machine Translation (GHMT) system. The translation divergence problem is usually reserved for Transfer and Interlingual MT because it requires a large combination of complex lexical and structural mappings. A major requirement of these approaches is the accessibility of large amounts of explicit symmetric knowledge for both source and target languages. This limitation renders Transfer and Interlingual approaches ineffective in the face of structurally-divergent language pairs with asymmetric resources. GHMT addresses the more common form of this problem, source-poor/targetrich, by fully exploiting symbolic and statistical target-language resources. This non-interlingual non-transfer approach is accomplished by using target-language lexical semantics, categorial variations and subcategorization frames to overgenerate multiple lexico-structural variations from a target-glossed syntactic dependency of the source-language sentence. The symbolic overgeneration, which accounts for different possible translation divergences, is constrained by a statistical target-language model.}, isbn = {978-3-540-44282-0}, url = {http://dx.doi.org/10.1007/3-540-45820-4_9}, author = {Habash,Nizar and Dorr, Bonnie J}, editor = {Richardson,Stephen} } @article {14091, title = {Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi}, journal = {Molecular and Biochemical Parasitology}, volume = {124}, year = {2002}, month = {2002/09/10/}, pages = {73 - 78}, abstract = {As observed for most eukaryotic cells, trypanosomatids contains non-LTR retrotransposons randomly inserted in the nuclear genome. Autonomous retroelements which, code for their own transposition, have been characterized in Trypanosoma brucei (ingi) and Trypanosoma cruzi (L1Tc), whereas non-autonomous retroelements have only been characterized in T. brucei (RIME). Here, we have characterized in the genome of Trypanosoma cruzi four complete copies of a non-autonomous non-LTR retrotransposon, called NARTc. This 0.26 kb NARTc element has the characteristics of non-LTR retrotransposons: the presence a poly(dA) tail and of a short flanking duplicated motif. Analysis of the Genome Survey Sequence databases indicated that the Trypanosoma cruzi haploid genome contains about 140 NARTc copies and about twice as many L1Tc copies. Interestingly, the NARTc and L1Tc retroelements share, with the Trypanosoma brucei ingi and RIME retrotransposons, a common sequence (the first 45 bp with 91\% identity), whereas the remaining sequences are very divergent. This suggests that these four trypanosome non-LTR retrotransposons were derived from the same common ancester and the sequence of their 5{\textquoteright}-extremity may have a functional role. In addition, the genome of Leishmania major contains the same conserved motif present in the trypanosome retroelements, whicle no transposable elements have been detected so far in Leishmania sp.}, keywords = {Ingi, L1Tc, Non-LTR retrotransposon, RIME, Trypanosoma brucei, Trypanosoma cruzi}, isbn = {0166-6851}, doi = {16/S0166-6851(02)00167-6}, url = {http://www.sciencedirect.com/science/article/pii/S0166685102001676}, author = {Bringaud,Fr{\'e}d{\'e}ric and Garc{\'\i}a-P{\'e}rez,Jos{\'e} Luis and Heras,Sara R. and Ghedin,Elodie and El-Sayed, Najib M. and Andersson,Bj{\"o}rn and Baltz,Th{\'e}o and Lopez,Manuel C.} } @article {14624, title = {Identification of transcription factor binding sites in the human genome sequence}, journal = {Mammalian Genome}, volume = {13}, year = {2002}, month = {2002///}, pages = {510 - 514}, abstract = {The identification of transcription factor binding sites (TFBS) is an important initial step in determining the DNA signals that regulate transcription of the genome. We tested the performance of three distinct computational methods for the identification of TFBS applied to the human genome sequence, as judged by their ability to recover the location of experimentally determined, and uniquely mapped, TFBS taken from the TRANSFAC database. These identification methods all attempt to filter the quantity of TFBS identified by aligning positional weight matrices that describe the binding site and employ either (i) a P-value threshold for accepting a site, (ii) an over-representation measure of neighboring sites, or (iii) conservation with the mouse genome and application of P-value thresholds. The results show that the best recognition of TFBS is achieved by combining the identification of TFBS in regions of human{\textendash}mouse conservation and also by applying a high stringency P-value to the TFBS identified in non-coding regions that are not conserved. Additionally, we find that only half of the 481 experimentally mapped sites can be found in sequence regions conserved with mouse, but the predictive power of the binding site identification method is up to threefold higher in the conserved regions.}, isbn = {0938-8990}, url = {http://dx.doi.org/10.1007/s00335-002-2175-6}, author = {Levy,Samuel and Hannenhalli, Sridhar} } @inbook {17604, title = {Improved Approximation Algorithms for the Partial Vertex Cover Problem}, booktitle = {Approximation Algorithms for Combinatorial OptimizationApproximation Algorithms for Combinatorial Optimization}, series = {Lecture Notes in Computer Science}, volume = {2462}, year = {2002}, month = {2002///}, pages = {161 - 174}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The partial vertex cover problem is a generalization of the vertex cover problem:given an undirected graph G = ( V,E ) and an integer k , we wish to choose a minimum number of vertices such that at least k edges are covered. Just as for vertex cover, 2-approximation algorithms are known for this problem, and it is of interest to see if we can do better than this.The current-best approximation ratio for partial vertex cover, when parameterized by the maximum degree d of G , is (2 - Θ (1/ d )).We improve on this by presenting a $$ {\l}eft( 2 - \Theta {\l}eft( \tfrac{\l}n {\l}n d {\l}n d \right) \right) $$ -approximation algorithm for partial vertex cover using semidefinite programming, matching the current-best bound for vertex cover. Our algorithmuses a new rounding technique, which involves a delicate probabilistic analysis.}, isbn = {978-3-540-44186-1}, url = {http://dx.doi.org/10.1007/3-540-45753-4_15}, author = {Halperin,Eran and Srinivasan, Aravind}, editor = {Jansen,Klaus and Leonardi,Stefano and Vazirani,Vijay} } @article {13790, title = {Improved Word-Level Alignment: Injecting Knowledge about MT Divergences}, year = {2002}, month = {2002/02/14/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Word-level alignments of bilingual text (bitexts) are not an integral part of statistical machine translation models, but also useful for lexical acquisition, treebank construction. and part-of-speech tagging. The frequent occurrence of divergences, structural differences between languages, presents a great challenge to the alignment task. We resolve some of the most prevalent divergence cases by using syntactic parse information to transform the sentence structure of one language to bear a closer resemblance to that of the other language. In this paper, we show that common divergence types can be found in multiple language pairs (in particular, we focus on English-Spanish and English-Arabic) and systematically identified. We describe our techniques for modifying English parse trees to form resulting sentences that share more similarity with the sentences in the other languages; finally, we present an empirical analysis comparing the complexities of performing word-level alignments with an without divergence handling. Our results suggest that divergence-handling can improve word-level alignment.}, keywords = {*LEXICOGRAPHY, *MACHINE TRANSLATION, *STATISTICAL ANALYSIS, *WORDS(LANGUAGE), ACQUISITION, ALIGNMENT, EXPERIMENTAL DATA, LANGUAGE, linguistics, MATHEMATICAL MODELS, STATISTICS AND PROBABILITY, TREES}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458774}, author = {Dorr, Bonnie J and Pearl,Lisa and Hwa,Rebecca and Habash,Nizar} } @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} } @article {18489, title = {Infranet: Circumventing web censorship and surveillance}, journal = {Proceedings of the 11th USENIX Security Symposium}, year = {2002}, month = {2002///}, pages = {247 - 262}, abstract = {An increasing number of countries and companies routinely block or monitor access to parts of the Internet. To counteract these measures, we propose Infranet, a system that enables clients to surreptitiously retrieve sensitive content via cooperating Web servers distributed across the global Internet. These Infranet servers provide clients access to censored sites while continuing to host normal uncensored content. Infranet uses a tunnel protocol that provides a covert communication channel between its clients and servers, modulated over standard HTTP transactions that resemble innocuous Web browsing. In the upstream direction, Infranet clients send covert messages to Infranet servers by associating meaning to the sequence of HTTP requests being made. In the downstream direction, Infranet servers return content by hiding censored data in uncensored images using steganographic techniques. We describe the design, a prototype implementation, security properties, and performance of Infranet. Our security analysis shows that Infranet can successfully circumvent several sophisticated censoring techniques.}, author = {Feamster, Nick and Balazinska,M. and Harfst,G. and Balakrishnan,H. and Karger,D.} } @conference {17243, title = {Interacting with identification technology: can it make us more secure?}, booktitle = {CHI {\textquoteright}02 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {564 - 565}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {Biometrics, civil liberties, face recognition, national id card, privacy, Security}, isbn = {1-58113-454-1}, doi = {10.1145/506443.506484}, url = {http://doi.acm.org/10.1145/506443.506484}, author = {Scholtz,Jean and Johnson,Jeff and Shneiderman, Ben and Hope-Tindall,Peter and Gosling,Marcus and Phillips,Jonathon and Wexelblat,Alan} } @article {13794, title = {Interlingua approximation: A generation-heavy approach}, journal = {Proceedings of AMTA-2002}, year = {2002}, month = {2002///}, author = {Dorr, Bonnie J and Habash,N.} } @article {16152, title = {Navigation patterns and usability of zoomable user interfaces with and without an overview}, journal = {ACM Transactions on Computer-Human Interaction (TOCHI)}, volume = {9}, year = {2002}, month = {2002///}, pages = {362 - 389}, author = {Hornbaek,K. and Bederson, Benjamin B. and Plaisant, Catherine} } @article {14090, title = {A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei}, journal = {Eukaryotic cell}, volume = {1}, year = {2002}, month = {2002///}, pages = {137 - 137}, author = {Bringaud,F. and Biteau,N. and Melville,S. E. and Hez,S. and El-Sayed, Najib M. and Leech,V. and Berriman,M. and Hall,N. and Donelson,J. E and Baltz,T.} } @article {14163, title = {A Parallel Block Multi-level Preconditioner for the 3D Incompressible Navier--Stokes Equations}, volume = {UMIACS-TR-2002-95}, year = {2002}, month = {2002/10/25/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {The development of robust and efficient algorithms for both steady-statesimulations and fully-implicit time integration of the Navier--Stokes equations is an active research topic. To be effective, the linear subproblems generated by these methods require solution techniques that exhibit robust and rapid convergence. In particular, they should be insensitive to parameters in the problem such as mesh size, time step, and Reynolds number. In this context, we explore a parallel preconditioner based on a block factorization of the coefficient matrix generated in an Oseen nonlinear iteration for the primitive variable formulation of the system. The key to this preconditioner is the approximation of a certain Schur complement operator by a technique first proposed by Kay, Loghin, and Wathen [25] and Silvester, Elman, Kay, and Wathen [45]. The resulting operator entails subsidiary computations (solutions of pressure Poisson and convection--diffusion subproblems) that are similar to those required for decoupled solution methods; however, in this case these solutions are applied as preconditioners to the coupled Oseen system. One important aspect of this approach is that the convection--diffusion and Poisson subproblems are significantly easier to solve than the entire coupled system, and a solver can be built using tools developed for the subproblems. In this paper, we apply smoothed aggregation algebraic multigrid to both subproblems. Previous work has focused on demonstrating the optimality of these preconditioners with respect to mesh size on serial, two-dimensional, steady-state computations employing geometric multi-grid methods; we focus on extending these methods to large-scale, parallel, three-dimensional, transient and steady-state simulations employing algebraic multigrid (AMG) methods. Our results display nearly optimal convergence rates for steady-state solutions as well as for transient solutions over a wide range of CFL numbers on the two-dimensional and three-dimensional lid-driven cavity problem. Also UMIACS-TR-2002-95 }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/1239}, author = {Elman, Howard and Howle, V. E and Shadid,John and Tuminaro,Ray} } @article {14634, title = {Predicting Transcription Factor Synergism}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {30}, year = {2002}, month = {2002/10/01/}, pages = {4278 - 4284}, abstract = {Transcriptional regulation is mediated by a battery of transcription factor (TF) proteins, that form complexes involving protein{\textendash}protein and protein{\textendash}DNA interactions. Individual TFs bind to their cognate cis-elements or transcription factor-binding sites (TFBS). TFBS are organized on the DNA proximal to the gene in groups confined to a few hundred base pair regions. These groups are referred to as modules. Various modules work together to provide the combinatorial regulation of gene transcription in response to various developmental and environmental conditions. The sets of modules constitute a promoter model. Determining the TFs that preferentially work in concert as part of a module is an essential component of understanding transcriptional regulation. The TFs that act synergistically in such a fashion are likely to have their cis-elements co-localized on the genome at specific distances apart. We exploit this notion to predict TF pairs that are likely to be part of a transcriptional module on the human genome sequence. The computational method is validated statistically, using known interacting pairs extracted from the literature. There are 251 TFBS pairs up to 50 bp apart and 70 TFBS pairs up to 200 bp apart that score higher than any of the known synergistic pairs. Further investigation of 50 pairs randomly selected from each of these two sets using PubMed queries provided additional supporting evidence from the existing biological literature suggesting TF synergism for these novel pairs.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/gkf535}, url = {http://nar.oxfordjournals.org/content/30/19/4278}, author = {Hannenhalli, Sridhar and Levy,Samuel} } @article {17815, title = {Presentation planning for distributed VoD systems}, journal = {Knowledge and Data Engineering, IEEE Transactions on}, volume = {14}, year = {2002}, month = {2002/10//sep}, pages = {1059 - 1077}, abstract = {A distributed video-on-demand (VoD) system is one where a collection of video data is located at dispersed sites across a computer network. In a single site environment, a local video server retrieves video data from its local storage device. However, in distributed VoD systems, when a customer requests a movie from the local server, the server may need to interact with other servers located across the network. In this paper, we present different types of presentation plans that a local server can construct in order to satisfy a customer request. Informally speaking, a presentation plan is a temporally synchronized sequence of steps that the local server must perform in order to present the requested movie to the customer. This involves obtaining commitments from other video servers, obtaining commitments from the network service provider, as well as making commitments of local resources, while keeping within the limitations of available bandwidth, available buffer, and customer data consumption rates. Furthermore, in order to evaluate the quality of a presentation plan, we introduce two measures of optimality for presentation plans: minimizing wait time for a customer and minimizing access bandwidth which, informally speaking, specifies how much network/disk bandwidth is used. We develop algorithms to compute three different optimal presentation plans that work at a block level, or at a segment level, or with a hybrid mix of the two, and compare their performance through simulation experiments. We have also mathematically proven effects of increased buffer or bandwidth and data replications for presentation plans which had previously been verified experimentally in the literature.}, keywords = {Computer, computing;, databases;, demand;, distributed, local, multimedia, network;, on, optimal, plan;, plans;, presentation, presentation;, server;, servers;, video, video-on-demand;, VoD;}, isbn = {1041-4347}, doi = {10.1109/TKDE.2002.1033774}, author = {Hwang,Eenjun and Prabhakaran,B. and V.S. Subrahmanian} } @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} } @book {14636, title = {RECOMB {\textquoteright}02: Proceedings of the sixth annual international conference on Computational biology}, year = {2002}, month = {2002///}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The papers in this volume were presented at the Sixth Annual International Conference on Computational Biology RECOMB 2002, held in Washington, D.C. on April 18-21, 2002. The RECOMB series was started in 1997 by Sorin Istrail, Pavel Pevzner and Michael Waterman. RECOMB {\textquoteright}99 took place in Lyon, France, RECOMB 2000 was held in Tokyo, Japan, and RECOMB 2001 was held in Montreal, Quebec, Canada.This year{\textquoteright}s call for papers gave rise to 118 submissions, out of which the program committee selected 35 papers to be presented at the conference and included in the proceedings. Each submission was refereed by at least three members of the program committee. After the completion of the referees{\textquoteright} reports, an extensive web-based discussion took place.RECOMB 2002 had 8 invited speakers: Ruben Abagyan (The Scripps Research Institute), Ali H. Brivanlou (Rockefeller University), Evan Eichler (Case Western Reserve University), Harold "Skip" Garner (University of Texas Southwestern Medical Center at Dallas), David Ho (Rockefeller University), Gerry Rubin (Howard Hughes Medical Institute), J. Craig Venter (Celera) and Marc Vidal (Dana-Farber Cancer Institute). The Stanislaw Ulam Memorial Lecture was given by J. Craig Venter. The Distinguished Biology Lecture was given by David Ho. The Distinguished New Technologies Lecture was given by Harold Garner.Complete final versions of many of the papers presented in the conference will appear in a special issue of the Journal of Computational Biology, which is closely affiliated with the conference.}, isbn = {1-58113-498-3}, editor = {Myers,Gene and Hannenhalli, Sridhar and Sankoff,David and Istrail,Sorin and Pevzner,Pavel and Waterman,Michael} } @conference {14772, title = {Recompilation for debugging support in a JIT-compiler}, booktitle = {Proceedings of the 2002 ACM SIGPLAN-SIGSOFT workshop on Program analysis for software tools and engineering}, series = {PASTE {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {10 - 17}, publisher = {ACM}, organization = {ACM}, address = {Charleston, South Carolina, USA}, abstract = {A static Java compiler converts Java source code into a verifiably secure and compact architecture-neutral intermediate format, called Java byte codes. The Java byte codes can be either interpreted by a Java Virtual Machine or translated into native code by Java Just-In-Time compilers. Static Java compilers embed debug information in the Java class files to be used by the source level debuggers. However, the debug information is generated for architecture independent byte codes and most of the debug information is valid only when the byte codes are interpreted. Translating byte codes into native instructions puts a limitation on the amount of usable debug information that can be used by source level debuggers. In this paper, we present a new technique to generate valid debug information when Just-In-Time compilers are used. Our approach is based on the dynamic recompilation of Java methods by a fast code generator and lazily generates debug information when it is required. We also present three implementations for field watch support in the Java Virtual Machine Debugger Interface to investigate the runtime overhead and code size growth by our approach.}, keywords = {algorithms, debug information, debugging aids, dynamic recompilation, field access watch, java, java virtual machine debugger interface, just-in-time compilation, measurement, performance}, isbn = {1-58113-479-7}, doi = {10.1145/586094.586100}, author = {Tikir, Mustafa M. and Hollingsworth, Jeffrey K and Lueh,Guei-Yuan} } @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 {14654, title = {A secure PLAN (extended version)}, booktitle = {DARPA Active NEtworks Conference and Exposition, 2002. Proceedings}, year = {2002}, month = {2002///}, pages = {224 - 237}, publisher = {IEEE}, organization = {IEEE}, abstract = {Active networks promise greater flexibility than current networks, but threaten safety and security by virtue of their programmability. We describe the design and implementation of a security architecture for the active network PLANet (Hicks et al., 1999). Security is obtained with a two-level architecture that combines a functionally restricted packet language, PLAN (Hicks et al., 1998), with an environment of general-purpose service routines governed by trust management (Blaze et al., 1996). In particular, we employ a technique which expands or contracts a packet{\textquoteright}s service environment based on its level of privilege, termed namespace-based security. As an application of our security architecture, we present the design and implementation of an active-network firewall. We find that the addition of the firewall imposes an approximately 34\% latency overhead and as little as a 6.7\% space overhead to incoming packets}, keywords = {active internetwork, active networks, active-network firewall, Authentication, authorisation, Authorization, Cities and towns, Computer networks, Computer science, cryptography, functionally restricted packet language, general-purpose service routines, Information security, internetworking, IP networks, latency overhead, namespace-based security, PLAN, PLANet, Planets, programmability, Safety, security architecture, telecommunication security, trust management, two-level architecture, Web and internet services}, isbn = {0-7695-1564-9}, doi = {10.1109/DANCE.2002.1003496}, author = {Hicks, Michael W. and Keromytis,A. D and Smith,J. M} } @conference {14779, title = {SIGMA: A Simulator Infrastructure to Guide Memory Analysis}, booktitle = {SC Conference}, year = {2002}, month = {2002///}, pages = {1 - 1}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {In this paper we present SIGMA (Simulation Infrastructure to Guide Memory Analysis), a new data collection framework and family of cache analysis tools. The SIGMA environment provides detailed cache information by gathering memory reference data using software-based instrumentation. This infrastructure can facilitate quick probing into the factors that influence the performance of an application by highlighting bottleneck scenarios including: excessive cache/TLB misses and inefficient data layouts. The tool can also assist in perturbation analysis to determine performance variations caused by changes to architecture or program. Our validation tests using the SPEC Swim benchmark show that most of the performance metrics obtained with SIGMA are within 1\% of the metrics obtained with hardware performance counters, with the advantage that SIGMA provides performance data on a data structure level, as specified by the programmer.}, doi = {http://doi.ieeecomputersociety.org/10.1109/SC.2002.10055}, author = {DeRose,Luiz and Ekanadham, K. and Hollingsworth, Jeffrey K and Sbaraglia, Simone} } @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 {16908, title = {Speeding up construction of PMR quadtree-based spatial indexes}, journal = {The VLDB Journal}, volume = {11}, year = {2002}, month = {2002/10//}, pages = {109 - 137}, abstract = {Spatial indexes, such as those based on the quadtree, are important in spatial databases for efficient execution of queries involving spatial constraints, especially when the queries involve spatial joins. In this paper we present a number of techniques for speeding up the construction of quadtree-based spatial indexes, specifically the PMR quadtree, which can index arbitrary spatial data. We assume a quadtree implementation using the {\textquotedblleft}linear quadtree{\textquotedblright}, a disk-resident representation that stores objects contained in the leaf nodes of the quadtree in a linear index (e.g., a B-tree) ordered based on a space-filling curve. We present two complementary techniques: an improved insertion algorithm and a bulk-loading method. The bulk-loading method can be extended to handle bulk-insertions into an existing PMR quadtree. We make some analytical observations about the I/O cost and CPU cost of our PMR quadtree bulk-loading algorithm, and conduct an extensive empirical study of the techniques presented in the paper. Our techniques are found to yield significant speedup compared to traditional quadtree building methods, even when the size of a main memory buffer is very small compared to the size of the resulting quadtrees.}, keywords = {Bulk-loading, I/O, spatial indexing}, isbn = {1066-8888}, doi = {10.1007/s00778-002-0067-8}, url = {http://dx.doi.org/10.1007/s00778-002-0067-8}, author = {Hjaltason,Gisli R. and Samet, Hanan} } @conference {18804, title = {A Step Towards Automated Design of Multi-Piece Sacrificial Molds}, volume = {3}, year = {2002}, month = {2002///}, pages = {337 - 347}, publisher = {ASME}, organization = {ASME}, address = {Montreal, Quebec, Canada}, abstract = {This paper describes a feature-based approach for design of multi-piece sacrificial molds. Our mold design algorithm consists of the following three steps. First, the desired gross mold shape is formed based on the feature-based description of the part geometry. Second, if the desired gross mold shape is not machinable as a single piece, the gross mold shape is decomposed into simpler geometric components to make sure that each component is manufacturable using 3-axis CNC machining. The decomposition is performed to ensure that each component is accessible to end-milling tools, and decomposed components can be assembled together to form the gross mold shape. Finally, assembly features are added to mold components to facilitate assembly of mold components and eliminate unnecessary degree of freedoms from the final mold assembly. We expect that our decomposition algorithm will provide a step towards the necessary foundations for automating the design of multi-piece mold and therefore will help in significantly reducing the mold design and manufacturing lead-time.}, isbn = {0-7918-3623-1}, doi = {10.1115/DETC2002/DFM-34188}, url = {http://link.aip.org/link/ASMECP/v2002/i36231/p337/s1\&Agg=doi}, author = {Dhaliwal,Savinder and Gupta, Satyandra K. and Huang,Jun and Kumar,Malay} } @conference {16149, title = {Technologies for families}, booktitle = {CHI {\textquoteright}02 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {938 - 939}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this workshop, we propose to bring together researchers from industry and academia to discuss the design of new technologies for families. We will focus on both design techniques and the technologies themselves. Through discussions and brainstorming we hope to discover new ideas, which can be disseminated more broadly.}, keywords = {cooperative design, disappearing computer, family, Home, participatory design, probe, user interface}, isbn = {1-58113-454-1}, doi = {10.1145/506443.506669}, url = {http://doi.acm.org/10.1145/506443.506669}, author = {Plaisant, Catherine and Druin, Allison and Hutchinson,Hilary} } @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 {13392, title = {On using correlation-based synopses during query optimization}, journal = {Computer Science Division (EECS), University of California Berkeley}, year = {2002}, month = {2002/02//}, abstract = {In recent years, a variety of complex synopsis structures have been proposed to capturestatistical correlations present in database relations. The goal of that work has been to improve cardinality estimation during query optimization by improving statistics on base tables. In order to use the correlation information for multi-table estimations as well, synopses must also be constructed on intermediate result tables during query optimization. We address that problem here, and show how to efficiently integrate multi-dimensional histograms and other complex synopsis structures into the search algorithm of a traditional query optimizer such as that of System R. A main challenge in this work is minimizing the computational expense of dynamically computing synopses on intermediate tables during query optimization. We show that one only needs to construct a very small subset of all possible synopses to get the full estimation bene- fits of multi-dimensional modeling. We also show that choosing this subset unwisely can have unacceptable performance overheads. This leads to an {\textquotedblleft}estimation planning{\textquotedblright} problem that has been ignored to date in literature: how to choose the most efficiently-computable collection of intermediate synopses to construct, so that all the required cardinality estimates can be com- puted as accurately as possible from the base-table synopses? In this paper, we identify and formalize the estimation planning problem in the context of a System R-style optimizer extended with complex synopsis techniques such as multi-dimensional histograms. We propose algorithms that find very good estimation plans efficiently, and discuss properties of synopsis structures that make them amenable to efficient use in an optimizer. }, author = {Deshpande, Amol and Hellerstein,J.} } @article {13479, title = {Virtual Telescopes in Education}, journal = {Journal of Digital Information}, volume = {2}, year = {2002}, month = {2002///}, abstract = {Virtual Telescopes in Education is providing the services required to operate a virtual observatory comprising distributed telescopes, including an interactive, constraint-based scheduling service, data and resource archive, proposal preparation and review environment, and a VTIE Journal. A major goal of VTIE is to elicit from learners questions about the nature of celestial objects and the physical processes that give rise to the spectacular imagery that catches their imaginations. Generation of constrained science questions will assist learners in the science process. To achieve interoperability with other NSDL resources, our approach follows the Open Archives Initiative and the W3C Semantic Web activity.}, author = {Hoban,S. and desJardins, Marie and Farrell,N. and Rathod,P. and Sachs,J. and Sansare,S. and Yesha,Y. and Keating,J. and Busschots,B. and Means,J. and others} } @article {17492, title = {Visual queries for finding patterns in time series data}, journal = {University of Maryland, Computer Science Dept. Tech Report, CS-TR-4365}, year = {2002}, month = {2002///}, abstract = {Few tools exist for data exploration and pattern iden-tification in time series data sets. Timeboxes are rectan- gular, direct-manipulation queries for studying time-series datasets. Timeboxes are the primary query tool in our Time- Searcher application, which supports interactive explo- ration via dynamic queries, along with overviews of query results and drag-and-drop support for query-by-example. This paper describes the TimeSearcher application and pos- sible extensions to the timebox query model, along with a discussion of the use of TimeSearcher for exploring a time series data set involving gene expression profiles. }, author = {Hochheiser,H. and Shneiderman, Ben} } @article {12175, title = {A visual search tool for early elementary science students}, journal = {Journal of Science Education and Technology}, volume = {11}, year = {2002}, month = {2002///}, pages = {49 - 57}, author = {Revelle,G. and Druin, Allison and Platner,M. and Bederson, Benjamin B. and Hourcade,J. P and Sherman,L.} } @article {16720, title = {Word-level Alignment for Multilingual Resource Acquisition}, year = {2002}, month = {2002/04//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {We present a simple, one-pass word alignment algorithm for parallel text. Our algorithm utilizes synchronous parsing and takes advantage of existing syntactic annotations. In our experiments the performance of this model is comparable to more complicated iterative methods. We discuss the challenges and potential benefits of using the model to train syntactic parsers for new languages.}, keywords = {*LEARNING MACHINES, *MULTILINGUAL RESOURCES, *WORDS(LANGUAGE), ACQUISITION, algorithms, ALIGNMENT, BENEFITS, ITERATIONS, LANGUAGE, linguistics}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458782}, author = {Lopez,Adam and Nossal,Michael and Hwa,Rebecca and Resnik, Philip} } @article {14783, title = {Achieving Efficiency and Accuracy in Simulation for I/O-Intensive Applications}, journal = {Journal of Parallel and Distributed Computing}, volume = {61}, year = {2001}, month = {2001/12//}, pages = {1732 - 1750}, abstract = {This paper presents a family of simulators for data-intensive applications, and a methodology to select the most efficient simulator based on a user-supplied requirement for accuracy. The methodology consists of a series of tests that select an appropriate simulation based on the attributes of the application. In addition, each simulator provides two estimates of application execution time: one for the minimum expected time and the other for the maximum. We present the results of applying the strategy to existing applications and show that we can accurately simulate applications tens to hundreds of times faster than application execution time.}, keywords = {simulation; I/O-intensive applications; parallel or distributed applications; performance prediction; discrete-event simulation}, isbn = {0743-7315}, doi = {06/jpdc.2001.1769}, url = {http://www.sciencedirect.com/science/article/pii/S0743731501917691}, author = {Eom, Hyeonsang and Hollingsworth, Jeffrey K} } @article {14595, title = {Analysis and prediction of protein functional sub-types from protein sequence alignments}, volume = {EP20000203764}, year = {2001}, month = {2001/05/02/}, abstract = {Here we present a method for analysis and prediction of functional sub-types from multiple protein sequence alignments. Given an alignment and set of proteins grouped into sub-types according to some definition of function, such as enzymatic specificity, the method identifies positions that are indicative of functional differences by subtraction of sequence profiles, and analysis of positional entropy in the alignment.}, url = {http://www.freepatentsonline.com/EP1096411.html}, author = {Hannenhalli, Sridhar and Russell,Robert B.}, editor = {SMITHKLINE BEECHAM CORP (US) SMITHKLINE BEECHAM PLC (GB)} } @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} } @article {14651, title = {A Calculus for Dynamic Loading}, journal = {Technical Reports (CIS)}, year = {2001}, month = {2001/02/06/}, abstract = {We present the load-calculus, used to model dynamic loading, and prove it sound. The calculus extends the polymorphic λ-calculus with a load primitive that dynamically loads terms that are closed, with respect to values. The calculus is meant to approximate the process of dynamic loading in TAL/Load [4], a version of Typed Assembly Language [7] extending with dynamic linking. To model the key aspects of TAL, the calculus contains references and facilities for named types. Loadable programs may refer to named types defined by the running program, and may export new types to code loaded later. Our approach follows the framework initially outlined by Glew et. al [3]. This calculus has been implemented in the TALx86 [6] version of Typed Assembly Language, and is used to implement a full-featured dynamic linking library, DLpop [4].}, url = {http://repository.upenn.edu/cis_reports/169}, author = {Hicks, Michael W. and Weirich,Stephanie} } @inbook {14667, title = {Compiling PLAN to SNAP}, booktitle = {Active NetworksActive Networks}, series = {Lecture Notes in Computer Science}, volume = {2207}, year = {2001}, month = {2001///}, pages = {134 - 151}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {PLAN (Packet Language for Active Networks) [ 3 ] is a highly flexible and usable active packet language, whereas SNAP (Safe and Nimble Active Packets) [ 12 ] offers significant resource usage safety and achieves much higher performance compared to PLAN, but at the cost of flexibility and usability. Ideally, we would like to combine the good properties of PLAN with those of SNAP. We have achieved this end by developing a compiler that translates PLANi nto SNAP. The compiler allows us to achieve the flexibility and usability of PLAN, but with the safety and efficiency of SNAP. In this paper, we describe both languages, highlighting the features that require special compilation techniques. We then present the details of our compiler and experimental results to evaluate our compiler with respect to code size.}, isbn = {978-3-540-42678-3}, url = {http://dx.doi.org/10.1007/3-540-45451-9_9}, author = {Hicks, Michael W. and Moore,Jonathan and Nettles,Scott}, editor = {Marshall,Ian and Nettles,Scott and Wakamiya,Naoki} } @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.} } @conference {14685, title = {Dynamic software updating}, booktitle = {Proceedings of the ACM SIGPLAN 2001 conference on Programming language design and implementation}, series = {PLDI {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {13 - 23}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Many important applications must run continuously and without interruption, yet must be changed to fix bugs or upgrade functionality. No prior general-purpose methodology for dynamic updating achieves a practical balance between flexibility, robustness, low overhead, and ease of use.We present a new approach for C-like languages that provides type-safe dynamic updating of native code in an extremely flexible manner (code, data, and types may be updated, at programmer-determined times) and permits the use of automated tools to aid the programmer in the updating process. Our system is based on dynamic patches that both contain the updated code and the code needed to transition from the old version to the new. A novel aspect of our patches is that they consist of verifiable native code (e.g. Proof-Carrying Code [17] or Typed Assembly Language [16]), which is native code accompanied by annotations that allow on-line verification of the code{\textquoteright}s safety. We discuss how patches are generated mostly automatically, how they are applied using dynamic-linking technology, and how code is compiled to make it updateable. To concretely illustrate our system, we have implemented a dynamically-updateable web server, FlashEd. We discuss our experience building and maintaining FlashEd. Performance experiments show that for FlashEd, the overhead due to updating is typically less than 1\%. }, isbn = {1-58113-414-2}, doi = {10.1145/378795.378798}, url = {http://doi.acm.org/10.1145/378795.378798}, author = {Hicks, Michael W. and Moore,Jonathan T. and Nettles,Scott} } @article {13761, title = {Efficient Language Independent Generation from Lexical Conceptual Structure}, year = {2001}, month = {2001/09//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This paper describes a system for generating natural-language sentences from an interlingual representation, Lexical Conceptual Structure (LCS). The system has been developed as part of a Chinese-English Machine Translation system; however, it is designed to be used for many other MT language pairs and Natural Language applications. The contributions of this work include: (1) Development of a language-independent generation system that maximizes efficiency through the use of a hybrid rule-based/statistical module; (2) Enhancements to an interlingual representation and associated algorithms for interpretation of multiply ambiguous input sentences; (3) Development of an efficient reusable language-independent linearization module with a grammar description language that can be used with other systems; (4) Improvements to an earlier algorithm for hierarchically mapping thematic roles to surface positions; (5) Development of a diagnostic tool for lexicon coverage and correctness and use of the tool for verification of English, Spanish, and Chinese lexicons. An evaluation of translation quality shows comparable performance with commercial translation system. The generation system can also be straightforwardly extended to their languages and this is demonstrated and evaluated for Spanish.}, keywords = {*LEXICAL CONCEPTUAL STRUCTURE, *LEXICOGRAPHY, *MACHINE TRANSLATION, *VOCABULARY, *WORDS(LANGUAGE), algorithms, CHINA, COMMERCE, DIAGNOSTIC EQUIPMENT, efficiency, English language, grammars, INPUT, INTERLINGUAL, LANGUAGE, LANGUAGE-INDEPENDENT NLP., linguistics, MAPPING, natural language, QUALITY, SPANISH LANGUAGE, verification}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458756}, author = {Habash,Nizar and Dorr, Bonnie J and Traum,David} } @conference {14766, title = {Efficient network and I/O throttling for fine-grain cycle stealing}, booktitle = {Proceedings of the 2001 ACM/IEEE conference on Supercomputing (CDROM) - Supercomputing {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {3 - 3}, address = {Denver, Colorado}, doi = {10.1145/582034.582037}, url = {http://dl.acm.org/citation.cfm?id=582037}, author = {Ryu, Kyung D. and Hollingsworth, Jeffrey K and Keleher, Peter J.} } @conference {16260, title = {Efficient perspective-accurate silhouette computation and applications}, booktitle = {Proceedings of the seventeenth annual symposium on Computational geometry}, series = {SCG {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {60 - 68}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Silhouettes are perceptually and geometrically salient features of geo metric models. Hence a number of graphics and visualization applications need to find them to aid further processing. The efficient computation of silhouettes, especially in the context of perspective projection, is known to be difficult. This paper presents a novel efficient and practical algorithm to compute silhouettes from a sequence of viewpoints under perspective projection. Parallel projection is a special case of this algorithm. Our approach is based on a point-plane duality in three dimensions, which allows an efficient computation of the \emph{changes} in the silhouette of a polygonal model between consecutive frames. In addition, we present several applications of our technique to problems from computer graphics and medical visualization. We also provide experimental data that show the efficiency of our approach. million vertices on an SGI Onyx workstation.}, keywords = {rendering, silhouette, simplification}, isbn = {1-58113-357-X}, doi = {10.1145/378583.378618}, url = {http://doi.acm.org/10.1145/378583.378618}, author = {Pop, Mihai and Duncan,Christian and Barequet,Gill and Goodrich,Michael and Huang,Wenjing and Kumar,Subodh} } @article {16324, title = {An empirical study of regression test selection techniques}, journal = {ACM Transactions on Software Engineering and MethodologyACM Trans. Softw. Eng. Methodol.}, volume = {10}, year = {2001}, month = {2001/04//}, pages = {184 - 208}, isbn = {1049331X}, doi = {10.1145/367008.367020}, url = {http://dl.acm.org/citation.cfm?id=367020}, author = {Graves,Todd L. and Harrold,Mary Jean and Kim,Jung-Min and Porter, Adam and Rothermel,Gregg} } @article {14607, title = {Enrichment of Regulatory Signals in Conserved Non-Coding Genomic Sequence}, journal = {BioinformaticsBioinformatics}, volume = {17}, year = {2001}, month = {2001/10/01/}, pages = {871 - 877}, abstract = {Motivation: Whole genome shotgun sequencing strategies generate sequence data prior to the application of assembly methodologies that result in contiguous sequence. Sequence reads can be employed to indicate regions of conservation between closely related species for which only one genome has been assembled. Consequently, by using pairwise sequence alignments methods it is possible to identify novel, non-repetitive, conserved segments in non-coding sequence that exist between the assembled human genome and mouse whole genome shotgun sequencing fragments. Conserved non-coding regions identify potentially functional DNA that could be involved in transcriptional regulation.Results: Local sequence alignment methods were applied employing mouse fragments and the assembled human genome. In addition, transcription factor binding sites were detected by aligning their corresponding positional weight matrices to the sequence regions. These methods were applied to a set of transcripts corresponding to 502 genes associated with a variety of different human diseases taken from the Online Mendelian Inheritance in Man database. Using statistical arguments we have shown that conserved non-coding segments contain an enrichment of transcription factor binding sites when compared to the sequence background in which the conserved segments are located. This enrichment of binding sites was not observed in coding sequence. Conserved non-coding segments are not extensively repeated in the genome and therefore their identification provides a rapid means of finding genes with related conserved regions, and consequently potentially related regulatory mechanism. Conserved segments in upstream regions are found to contain binding sites that are co-localized in a manner consistent with experimentally known transcription factor pairwise co-occurrences and afford the identification of novel co-occurring Transcription Factor (TF) pairs. This study provides a methodology and more evidence to suggest that conserved non-coding regions are biologically significant since they contain a statistical enrichment of regulatory signals and pairs of signals that enable the construction of regulatory models for human genes. Contact: samuel.levy@celera.com }, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/17.10.871}, url = {http://bioinformatics.oxfordjournals.org/content/17/10/871}, author = {Levy,Samuel and Hannenhalli, Sridhar and Workman,Christopher} } @article {17116, title = {E-tables: Non-specialist use and understanding of statistical data}, journal = {SURFACE, the Syracuse University Research Facility And Collaborative Environment}, year = {2001}, month = {2001///}, pages = {33 - 33}, abstract = {This paper provides a progress report on a project that aims to understand how people think about and understand statistical data presented in tables. The focus is on people who are not statistical specialists. To this end, studies of various user populations were conducted, underlying data enrichment and explanation was investigated, and interactive user interface prototypes were developed and tested.}, author = {Marchionini,G. and Hert,C. and Shneiderman, Ben and Liddy,L.} } @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} } @article {18732, title = {A feature-based approach to automated design of multi-piece sacrificial molds}, journal = {Journal of Computing and Information Science in Engineering}, volume = {1}, year = {2001}, month = {2001///}, pages = {225 - 225}, author = {Dhaliwal,S. and Gupta,S.K. and Huang,J. and Kumar,M.} } @inbook {14221, title = {Geometry of Eye Design: Biology and Technology}, booktitle = {Multi-Image Analysis}, series = {Lecture Notes in Computer Science}, volume = {2032}, year = {2001}, month = {2001///}, pages = {22 - 38}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Natural or artificial vision systems process the images that they collect with their eyes or cameras in order to derive information for performing tasks related to navigation and recognition. Since the way images are acquired determines how dificult it is to perform a visual task, and since systems have to cope with limited resources, the eyes used by a specific system should be designed to optimize subsequent image processing as it relates to particular tasks. Different ways of sampling light, i.e., different eyes, may be less or more powerful with respect to particular competences. This seems intuitively evident in view of the variety of eye designs in the biological world. It is shown here that a spherical eye (an eye or system of eyes providing panoramic vision) is superior to a camera-type eye (an eye with restricted field of view) as regards the competence of three-dimensional motion estimation. This result is derived from a statistical analysis of all the possible computational models that can be used for estimating 3D motion from an image sequence. The findings explain biological design in a mathematical manner, by showing that systems that fly and thus need good estimates of 3D motion gain advantages from panoramic vision. Also, insights obtained from this study point to new ways of constructing powerful imaging devices that suit particular tasks in robotics, visualization and virtual reality better than conventional cameras, thus leading to a new camera technology.}, isbn = {978-3-540-42122-1}, url = {http://dx.doi.org/10.1007/3-540-45134-X_2}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Klette,Reinhard and Gimel{\textquoteright}farb,Georgy and Huang,Thomas} } @inbook {17252, title = {Interactive Exploration of Time Series Data}, booktitle = {Discovery ScienceDiscovery Science}, series = {Lecture Notes in Computer Science}, volume = {2226}, year = {2001}, month = {2001///}, pages = {441 - 446}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Widespread interest in discovering features and trends in time- series has generated a need for tools that support interactive exploration.This paper introduces timeboxes: a powerful direct-manipulation metaphor for the specification of queries over time series datasets. Our TimeSearcher implementation of timeboxes supports interactive formulation and modification of queries, thus speeding the process of exploring time series data sets and guiding data mining.}, isbn = {978-3-540-42956-2}, url = {http://dx.doi.org/10.1007/3-540-45650-3_38}, author = {Hochheiser,Harry and Shneiderman, Ben}, editor = {Jantke,Klaus and Shinohara,Ayumi} } @conference {16347, title = {More efficient network class loading through bundling}, booktitle = {Proceedings of the 2001 Symposium on Java TM Virtual Machine Research and Technology Symposium-Volume 1}, year = {2001}, month = {2001///}, pages = {17 - 17}, author = {Hovemeyer,D. and Pugh, William} } @conference {14725, title = {Practical programmable packets}, booktitle = {IEEE INFOCOM 2001. Twentieth Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings}, volume = {1}, year = {2001}, month = {2001///}, pages = {41-50 vol.1 - 41-50 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present SNAP (safe and nimble active packets), a new scheme for programmable (or active) packets centered around a new low-level packet language. Unlike previous active packet approaches, SNAP is practical: namely, adding significant flexibility over IP without compromising safety and security or efficiency. In this paper we show how to compile from the well-known active picket language PLAN to SNAP, showing that SNAP retains PLAN{\textquoteright}s flexibility; give proof sketches of its novel approach to resource control; and present experimental data showing SNAP attains performance very close to that of a software IP router}, keywords = {active picket language, Application software, complier, Contracts, Data security, efficiency, Explosives, INFORMATION SCIENCE, Internet, IP, IP networks, low-level packet language, packet switching, performance, PLAN, practical programmable packets, program compilers, Protection, resource control, Resource management, safe and nimble active packets, Safety, Security, SNAP, software IP router, Software performance, telecommunication security, Transport protocols}, isbn = {0-7803-7016-3}, doi = {10.1109/INFCOM.2001.916685}, author = {Moore,J. T and Hicks, Michael W. and Nettles,S.} } @article {14635, title = {Promoter prediction in the human genome}, journal = {Bioinformatics}, volume = {17}, year = {2001}, month = {2001/06/01/}, pages = {S90-S96 - S90-S96}, abstract = {Computational prediction of eukaryotic polII promoters has been one of the most elusive problems despite considerable effort devoted to the study. Researchers have looked for various types of signals around the transcriptional start site (TSS), viz. oligo-nucleotide statistics, potential binding sites for core factors, clusters of binding sites, proximity to CpG islands etc.. The proximity of CpG islands to gene starts is now a well established fact, although until recently, it was based on very little genomic data. In this work we explore the possibility of enhancing the promoter prediction accuracy by combining CpG island information with a few other, biologically motivated, seemingly independent signals, that cover most of the known knowledge. We benchmarked the method on a much larger genomic datasets compared to previous studies. We were able to improve slightly upon current prediction accuracy. Furthermore, we observe that CpG islands are the most dominant signals and the other signals do not improve the prediction. This suggests that the computational prediction of promoters for genes with no associated CpG-island (typically having tissue-specific expression) looking only at the immediate neighborhood of the TSS may not even be possible. We suggest some biological experiments and studies to better understand the biology of transcription.}, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/17.suppl_1.S90}, url = {http://bioinformatics.oxfordjournals.org/content/17/suppl_1/S90.short}, author = {Hannenhalli, Sridhar and Levy,S.} } @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 {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.} } @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 {14805, title = {A tool to help tune where computation is performed}, journal = {IEEE Transactions on Software Engineering}, volume = {27}, year = {2001}, month = {2001/07//}, pages = {618 - 629}, abstract = {We introduce a new performance metric, called load balancing factor (LBF), to assist programmers when evaluating different tuning alternatives. The LBF metric differs from traditional performance metrics since it is intended to measure the performance implications of a specific tuning alternative rather than quantifying where time is spent in the current version of the program. A second unique aspect of the metric is that it provides guidance about moving work within a distributed or parallel program rather than reducing it. A variation of the LBF metric can also be used to predict the performance impact of changing the underlying network. The LBF metric is computed incrementally and online during the execution of the program to be tuned. We also present a case study that shows that our metric can accurately predict the actual performance gains for a test suite of six programs}, keywords = {Computational modeling, Current measurement, Distributed computing, distributed program, distributed programming, load balancing factor, Load management, parallel program, parallel programming, Performance analysis, performance evaluation, Performance gain, performance metric, Programming profession, software metrics, software performance evaluation, Testing, Time measurement, tuning}, isbn = {0098-5589}, doi = {10.1109/32.935854}, author = {Eom, Hyeonsang and Hollingsworth, Jeffrey K} } @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 {17455, title = {Universal usability as a stimulus to advanced interface design}, journal = {Behaviour \& Information Technology}, volume = {20}, year = {2001}, month = {2001///}, pages = {367 - 376}, abstract = {The desire to make computing available to broader populations has historically been a motivation for research and innovation that led to new breakthroughs in usability. Menus, graphical user interfaces and the World Wide Web are examples of innovative technological solutions that have arisen out of the challenge of bringing larger and more diverse groups of users into the world of computing. Universal usability is the latest such challenge: In order to build systems that are universally usable, designers must account for technology variety, user diversity and gaps in user knowledge. These issues are particularly challenging and important in the context of increasing the usability of the World Wide Web. To raise awareness, web designers are urged to provide universal usability statements that offer users information about the usability of their sites. These statements can inform users and thereby reduce frustration and confusion. Further steps toward universal usability might be achieved through research aimed at developing tools that would encourage or promote usability. The paper closes with five proposals for future research.The desire to make computing available to broader populations has historically been a motivation for research and innovation that led to new breakthroughs in usability. Menus, graphical user interfaces and the World Wide Web are examples of innovative technological solutions that have arisen out of the challenge of bringing larger and more diverse groups of users into the world of computing. Universal usability is the latest such challenge: In order to build systems that are universally usable, designers must account for technology variety, user diversity and gaps in user knowledge. These issues are particularly challenging and important in the context of increasing the usability of the World Wide Web. To raise awareness, web designers are urged to provide universal usability statements that offer users information about the usability of their sites. These statements can inform users and thereby reduce frustration and confusion. Further steps toward universal usability might be achieved through research aimed at developing tools that would encourage or promote usability. The paper closes with five proposals for future research. }, isbn = {0144-929X}, doi = {10.1080/01449290110083602}, url = {http://www.tandfonline.com/doi/abs/10.1080/01449290110083602}, author = {Shneiderman, Ben and Hochheiser,Harry} } @article {17457, title = {Universal usability statements: Marking the trail for all users}, journal = {interactions}, volume = {8}, year = {2001}, month = {2001/03//}, pages = {16 - 18}, isbn = {1072-5520}, doi = {10.1145/361897.361913}, url = {http://doi.acm.org/10.1145/361897.361913}, author = {Hochheiser,Harry and Shneiderman, Ben} } @article {17478, title = {Using interactive visualizations of WWW log data to characterize access patterns and inform site design}, journal = {Journal of the American Society for Information Science and Technology}, volume = {52}, year = {2001}, month = {2001/01/01/}, pages = {331 - 343}, abstract = {HTTP server log files provide Web site operators with substantial detail regarding the visitors to their sites. Interest in interpreting this data has spawned an active market for software packages that summarize and analyze this data, providing histograms, pie graphs, and other charts summarizing usage patterns. Although useful, these summaries obscure useful information and restrict users to passive interpretation of static displays. Interactive visualizations can be used to provide users with greater abilities to interpret and explore Web log data. By combining two-dimensional displays of thousands of individual access requests, color, and size coding for additional attributes, and facilities for zooming and filtering, these visualizations provide capabilities for examining data that exceed those of traditional Web log analysis tools. We introduce a series of interactive visualizations that can be used to explore server data across various dimensions. Possible uses of these visualizations are discussed, and difficulties of data collection, presentation, and interpretation are explored.}, isbn = {1532-2890}, doi = {10.1002/1532-2890(2000)9999:9999<::AID-ASI1066>3.0.CO;2-Y}, url = {http://onlinelibrary.wiley.com/doi/10.1002/1532-2890(2000)9999:9999\%3C::AID-ASI1066\%3E3.0.CO;2-Y/abstract}, author = {Hochheiser,Harry and Shneiderman, Ben} } @conference {17937, title = {Variable-precision rendering}, booktitle = {Proceedings of the 2001 symposium on Interactive 3D graphics}, series = {I3D {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {149 - 158}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {hierarchical rendering, levels of detail, variable-precision rendering, view-dependent rendering}, isbn = {1-58113-292-1}, doi = {10.1145/364338.364384}, url = {http://doi.acm.org/10.1145/364338.364384}, author = {Hao,Xuejun and Varshney, Amitabh} } @article {17493, title = {Visual specification of queries for finding patterns in time-series data}, journal = {Proceedings of discovery science}, year = {2001}, month = {2001///}, pages = {441 - 446}, abstract = {Widespread interest in discovering features and trends in time- series has generated a need for tools that support interactive exploration.This paper introduces timeboxes: a powerful graphical, direct-manipulation metaphor for the specification of queries over time-series datasets. Our TimeFinder implementation of timeboxes supports interactive formulation and modification of queries, thus speeding the process of exploring time-series data sets and guiding data mining. TimeFinder includes windows for timebox queries, individual time-series, and details-on-demand. Other features include drag-and-drop support for� query-by-example and graphical envelopes for displaying the extent of the entire data set and result set from a given query. Extensions involving increased expressive power and general temporal data sets are discussed.}, author = {Hochheiser,H. and Shneiderman, Ben} } @article {15238, title = {z-Approximations}, journal = {Journal of Algorithms}, volume = {41}, year = {2001}, month = {2001/11//}, pages = {429 - 442}, abstract = {Approximation algorithms for NP-hard optimization problems have been widely studied for over three decades. Most of these measure the quality of the solution produced by taking the ratio of the cost of the solution produced by the algorithm to the cost of an optimal solution. In certain cases, this ratio may not be very meaningful{\textemdash}for example, if the ratio of the worst solution to the best solution is at most some constant α, then an approximation algorithm with factor α may in fact yield the worst solution! To overcome this hurdle (among others), several authors have independently suggested the use of a different measure which we call z-approximation. An algorithm is an α z-approximation if it runs in polynomial time and produces a solution whose distance from the optimal one is at most α times the distance between the optimal solution and the worst possible solution. The results known so far about z-approximations are either of the inapproximability type or rather straightforward observations. We design polynomial time algorithms for several fundamental discrete optimization problems; in particular we obtain a z-approximation factor of 12 for the directed traveling salesman problem (TSP) (with no triangle inequality assumption). For the undirected TSP this improves to 13. We also show that if there is a polynomial time algorithm that for any fixed ϵ\&$\#$xa0;\>\&$\#$xa0;0 yields an ϵ z-approximation then P\&$\#$xa0;=\&$\#$xa0;NP. We also present z-approximations for severa1 other problems such as max cut, stacker crane, maximum acyclic subgraph, and minimum disjoint cycle cover.}, isbn = {0196-6774}, doi = {10.1006/jagm.2001.1187}, url = {http://www.sciencedirect.com/science/article/pii/S0196677401911873}, author = {Hassin,Refael and Khuller, Samir} } @inbook {14659, title = {Active Networking Means Evolution (or Enhanced Extensibility Required)}, booktitle = {Active NetworksActive Networks}, series = {Lecture Notes in Computer Science}, volume = {1942}, year = {2000}, month = {2000///}, pages = {16 - 32}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {A primary goal of active networking is to increase the pace of network evolution. Evolution is typically achieved via extensibility; that is, typical active network implementations provide an interface to extend network nodes withdyna mically loaded code. Most implementations employ plug-in extensibility , a technique for loading code characterized by a concrete, pre-defined abstraction of future change. While flexible and convenient, we argue that plug-in extensibility alone is not sufficient for true network evolution. Instead, we propose dynamic software updating , a technique that reduces the a priori assumptions of plug-in extensibility, improving flexibility and eliminating the need to pre-plan extensions. However, this additional flexibility creates issues involving validity and security. We discuss these issues, and describe the state-of-the-art in systems that support dynamic software updating, thus framing the problem for researchers developing next-generation active networks.}, isbn = {978-3-540-41179-6}, url = {http://dx.doi.org/10.1007/3-540-40057-5_2}, author = {Hicks, Michael W. and Nettles,Scott}, editor = {Yasuda,Hiroshi} } @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} } @article {14089, title = {The African trypanosome genome}, journal = {International Journal for Parasitology}, volume = {30}, year = {2000}, month = {2000/04//}, pages = {329 - 345}, abstract = {The haploid nuclear genome of the African trypanosome, Trypanosoma brucei, is about 35 Mb and varies in size among different trypanosome isolates by as much as 25\%. The nuclear DNA of this diploid organism is distributed among three size classes of chromosomes: the megabase chromosomes of which there are at least 11 pairs ranging from 1 Mb to more than 6 Mb (numbered I-XI from smallest to largest); several intermediate chromosomes of 200-900 kb and uncertain ploidy; and about 100 linear minichromosomes of 50-150 kb. Size differences of as much as four-fold can occur, both between the two homologues of a megabase chromosome pair in a specific trypanosome isolate and among chromosome pairs in different isolates. The genomic DNA sequences determined to date indicated that about 50\% of the genome is coding sequence. The chromosomal telomeres possess TTAGGG repeats and many, if not all, of the telomeres of the megabase and intermediate chromosomes are linked to expression sites for genes encoding variant surface glycoproteins (VSGs). The minichromosomes serve as repositories for VSG genes since some but not all of their telomeres are linked to unexpressed VSG genes. A gene discovery program, based on sequencing the ends of cloned genomic DNA fragments, has generated more than 20 Mb of discontinuous single-pass genomic sequence data during the past year, and the complete sequences of chromosomes I and II (about 1 Mb each) in T. brucei GUTat 10.1 are currently being determined. It is anticipated that the entire genomic sequence of this organism will be known in a few years. Analysis of a test microarray of 400 cDNAs and small random genomic DNA fragments probed with RNAs from two developmental stages of T. brucei demonstrates that the microarray technology can be used to identify batteries of genes differentially expressed during the various life cycle stages of this parasite.}, isbn = {0020-7519}, doi = {16/S0020-7519(00)00015-1}, url = {http://www.sciencedirect.com/science/article/pii/S0020751900000151}, author = {El-Sayed, Najib M. and Hegde,Priti and Quackenbush,John and Melville,Sara E. and Donelson,John E.} } @article {14661, title = {Agents in Network Management}, journal = {Technical Reports (CIS)}, year = {2000}, month = {2000/02/26/}, abstract = {The ubiquity and complexity of modern networks require automated management and control. With increases in scale, automated solutions based on simple data access models such as SNMP will give way to more distributed and algorithmic techniques. This article outlines present and near-term solutions based on the ideas of active networks and mobile agents, which permit sophisticated programmable control and management of ultra large scale networks.}, url = {http://repository.upenn.edu/cis_reports/138}, author = {Ertugay,Osman and Hicks, Michael W. and Smith,Jonathan and Kornblum,Jessica} } @article {14594, title = {Analysis and prediction of functional sub-types from protein sequence alignments}, journal = {Journal of Molecular Biology}, volume = {303}, year = {2000}, month = {2000/10/13/}, pages = {61 - 76}, abstract = {The increasing number and diversity of protein sequence families requires new methods to define and predict details regarding function. Here, we present a method for analysis and prediction of functional sub-types from multiple protein sequence alignments. Given an alignment and set of proteins grouped into sub-types according to some definition of function, such as enzymatic specificity, the method identifies positions that are indicative of functional differences by comparison of sub-type specific sequence profiles, and analysis of positional entropy in the alignment. Alignment positions with significantly high positional relative entropy correlate with those known to be involved in defining sub-types for nucleotidyl cyclases, protein kinases, lactate/malate dehydrogenases and trypsin-like serine proteases. We highlight new positions for these proteins that suggest additional experiments to elucidate the basis of specificity. The method is also able to predict sub-type for unclassified sequences. We assess several variations on a prediction method, and compare them to simple sequence comparisons. For assessment, we remove close homologues to the sequence for which a prediction is to be made (by a sequence identity above a threshold). This simulates situations where a protein is known to belong to a protein family, but is not a close relative of another protein of known sub-type. Considering the four families above, and a sequence identity threshold of 30 \%, our best method gives an accuracy of 96 \% compared to 80 \% obtained for sequence similarity and 74 \% for BLAST. We describe the derivation of a set of sub-type groupings derived from an automated parsing of alignments from PFAM and the SWISSPROT database, and use this to perform a large-scale assessment. The best method gives an average accuracy of 94 \% compared to 68 \% for sequence similarity and 79 \% for BLAST. We discuss implications for experimental design, genome annotation and the prediction of protein function and protein intra-residue distances.}, keywords = {prediction, protein function, protein structure, sequence alignment}, isbn = {0022-2836}, doi = {10.1006/jmbi.2000.4036}, url = {http://www.sciencedirect.com/science/article/pii/S0022283600940361}, author = {Hannenhalli, Sridhar and Russell,Robert B.} } @article {14802, title = {An API for Runtime Code Patching}, journal = {International Journal of High Performance Computing Applications}, volume = {14}, year = {2000}, month = {2000///}, pages = {317 - 329}, abstract = {The authors present a postcompiler program manipulation tool called Dyninst, which provides a C++ class library for program instrumentation. Using this library, it is possible to instrument and modify application programs during execution. A unique feature of this library is that it permits machine-independent binary instrumentation programs to be written. The authors describe the interface that a tool sees when using this library. They also discuss three simple tools built using this interface: a utility to count the number of times a function is called, a program to capture the output of an already running program to a file, and an implementation of conditional breakpoints. For the conditional breakpoint example, the authors show that by using their interface compared with gdb, they are able to execute a program with conditional breakpoints up to 900 times faster.}, doi = {10.1177/109434200001400404}, url = {http://hpc.sagepub.com/content/14/4/317.abstract}, author = {Buck, Bryan and Hollingsworth, Jeffrey K} } @article {15230, title = {Approximation algorithms with bounded performance guarantees for the clustered traveling salesman problem}, journal = {Algorithmica}, volume = {28}, year = {2000}, month = {2000///}, pages = {422 - 437}, abstract = {Let G=(V,E) be a complete undirected graph with vertex set V , edge set E , and edge weights l(e) satisfying triangle inequality. The vertex set V is partitioned into clusters V 1 , . . ., V k . The clustered traveling salesman problem is to compute a shortest Hamiltonian cycle (tour) that visits all the vertices, and in which the vertices of each cluster are visited consecutively. Since this problem is a generalization of the traveling salesman problem, it is NP-hard. In this paper we consider several variants of this basic problem and provide polynomial time approximation algorithms for them.}, doi = {10.1007/s004530010045}, author = {Guttmann-Beck,N. and Hassin,R. and Khuller, Samir and Raghavachari,B.} } @conference {18463, title = {An audio-video front-end for multimedia applications}, booktitle = {2000 IEEE International Conference on Systems, Man, and Cybernetics}, volume = {2}, year = {2000}, month = {2000///}, pages = {786-791 vol.2 - 786-791 vol.2}, publisher = {IEEE}, organization = {IEEE}, abstract = {Applications such as video gaming, virtual reality, multimodal user interfaces and videoconferencing, require systems that can locate and track persons in a room through a combination of visual and audio cues, enhance the sound that they produce, and perform identification. We describe the development of a particular multimodal sensor fusion system that is portable, runs in real time and achieves these objectives. The system employs novel algorithms for acoustical source location, video-based person tracking and overall system control, which are also described}, keywords = {Acoustic noise, acoustical source location, Application software, audio cues, audio-video front-end, CAMERAS, Computer vision, Microphones, multimedia applications, multimedia systems, multimodal sensor fusion system, multimodal user interfaces, Position measurement, REAL TIME, Real time systems, real-time systems, sensor fusion, sound, Speech recognition, User interfaces, video cameras, video gaming, video-based person tracking, Videoconference, videoconferencing, Virtual reality, visual cues, Working environment noise}, isbn = {0-7803-6583-6}, doi = {10.1109/ICSMC.2000.885945}, author = {Zotkin,Dmitry N and Duraiswami, Ramani and Davis, Larry S. and Haritaoglu,I.} } @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 {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.} } @article {17032, title = {Coordinating overviews and detail views of WWW log data}, journal = {Workshop on New Paradigms in Information Visualization and Manipulation (NPIVM 2000), ACM Press}, year = {2000}, month = {2000///}, abstract = {Web server log analysis tools provide site operators with useful information regarding the visitors to their sites.� Unfortunately, the utility of these tools is often limited by the use of aggregate summaries that hide the information associated with individual requests, and by the absence of contextual data that might help users interpret those summaries. Building upon earlier work in the use of starfield visualizations to display web site requests as individual data points [8], this paper describes the use of multiple-coordinated visualizations of web log data at varying granularities, and alongside additional related displays of appropriate contextual information.}, author = {Hochheiser,H. and Shneiderman, Ben} } @conference {13893, title = {Designing StoryRooms: interactive storytelling spaces for children}, booktitle = {Proceedings of the 3rd conference on Designing interactive systems: processes, practices, methods, and techniques}, year = {2000}, month = {2000///}, pages = {95 - 104}, author = {Alborzi,H. and Druin, Allison and Montemayor,J. and Platner,M. and Porteous,J. and Sherman,L. and Boltman,A. and Tax{\'e}n,G. and Best,J. and Hammer,J. and others} } @conference {13912, title = {Designing storytelling technologies to encouraging collaboration between young children}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, year = {2000}, month = {2000///}, pages = {556 - 563}, author = {Benford,S. and Bederson, Benjamin B. and \AAkesson,K. P and Bayon,V. and Druin, Allison and Hansson,P. and Hourcade,J. P and Ingram,R. and Neale,H. and O{\textquoteright}Malley,C. and others} } @article {14764, title = {Efficient performance prediction for large-scale, data-intensive applications}, journal = {International Journal of High Performance Computing Applications}, volume = {14}, year = {2000}, month = {2000///}, pages = {216 - 216}, author = {Kurc, T. and Uysal, M. and Eom, H. and Hollingsworth, Jeffrey K and Saltz, J. and Sussman, Alan} } @article {14775, title = {Exploiting fine-grained idle periods in networks of workstations}, journal = {IEEE Transactions on Parallel and Distributed Systems}, volume = {11}, year = {2000}, month = {2000/07//}, pages = {683 - 698}, abstract = {Studies have shown that for a significant fraction of the time, workstations are idle. In this paper, we present a new scheduling policy called Linger-Longer that exploits the fine-grained availability of workstations to run sequential and parallel jobs. We present a two-level workload characterization study and use it to simulate a cluster of workstations running our new policy. We compare two variations of our policy to two previous policies: Immediate-Eviction and Pause-and-Migrate. Our study shows that the Linger-Longer policy can improve the throughput of foreign jobs on a cluster by 60 percent with only a 0.5 percent slowdown of local jobs. For parallel computing, we show that the Linger-Longer policy outperforms reconfiguration strategies when the processor utilization by the local process is 20 percent or less in both synthetic bulk synchronous and real data-parallel applications}, keywords = {cluster of workstations, Computer networks, Concurrent computing, Contracts, Delay, fine-grained availability, Intelligent networks, Linger-Longer, networks of workstations, PARALLEL PROCESSING, Predictive models, Processor scheduling, Resumes, scheduling policy, Throughput, workload characterization, workstation clusters, Workstations}, isbn = {1045-9219}, doi = {10.1109/71.877793}, author = {Kyung Dong Ryu and Hollingsworth, Jeffrey K} } @conference {17156, title = {Extending understanding of federal statistics in tables}, booktitle = {Proceedings of the 2000 annual national conference on Digital government research}, series = {dg.o {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {1 - 7}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {This paper describes progress toward improving user interfaces for US Federal government statistics that are presented in tables. Based on studies of user behaviors and needs related to statistical tables, we describe interfaces to assist diverse users with a range of statistical literacy to explore, find, understand, and use US Federal government statistics.}, keywords = {data exploration, dynamic queries, Statistics, tablular data, User interfaces}, url = {http://dl.acm.org/citation.cfm?id=1123075.1123079}, author = {Marchionini,Gary and Hert,Carol and Liddy,Liz and Shneiderman, Ben} } @article {16161, title = {Facilitating data exploration with query previews: A study of user performance and preference}, journal = {Behaviour \& Information Technology}, volume = {19}, year = {2000}, month = {2000///}, pages = {393 - 403}, abstract = {Networked and local data exploration systems that use command languages, menus, or form fill-in interfaces rarely give users an indication of the distribution of data. This often leads users to waste time, posing queries that have zero-hit or mega-hit results. Query previews are a novel visual approach for browsing databases. Query previews supply users with data distribution information for selected attributes of the database, and give continuous feedback about the size of the result set as the query is being formed. Subsequent refinements might be necessary to narrow the search. As there is a risk that query previews are an additional step, leading to a more complex and slow search process, a within-subjects empirical study was ran with 12 subjects who used interfaces with and without query previews and with minimized network delays. Even with 12 subjects and minimized network delays statistically significant differences were found, showing that query previews could speed up performance 1.6 to 2.1 times and lead to higher user satisfaction.Networked and local data exploration systems that use command languages, menus, or form fill-in interfaces rarely give users an indication of the distribution of data. This often leads users to waste time, posing queries that have zero-hit or mega-hit results. Query previews are a novel visual approach for browsing databases. Query previews supply users with data distribution information for selected attributes of the database, and give continuous feedback about the size of the result set as the query is being formed. Subsequent refinements might be necessary to narrow the search. As there is a risk that query previews are an additional step, leading to a more complex and slow search process, a within-subjects empirical study was ran with 12 subjects who used interfaces with and without query previews and with minimized network delays. Even with 12 subjects and minimized network delays statistically significant differences were found, showing that query previews could speed up performance 1.6 to 2.1 times and lead to higher user satisfaction. }, isbn = {0144-929X}, doi = {10.1080/014492900750052651}, url = {http://www.tandfonline.com/doi/abs/10.1080/014492900750052651}, author = {Tanin,Egemen and Lotem,Amnon and Haddadin,Ihab and Shneiderman, Ben and Plaisant, Catherine and Slaughter,Laura} } @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} } @conference {15591, title = {Geo-registration of Landsat data by robust matching of wavelet features}, booktitle = {Geoscience and Remote Sensing Symposium, 2000. Proceedings. IGARSS 2000. IEEE 2000 International}, volume = {4}, year = {2000}, month = {2000///}, pages = {1610 -1612 vol.4 - 1610 -1612 vol.4}, abstract = {The goal of our project is to build an operational system, which will provide a sub-pixel accuracy registration of Landsat-5 and Landsat-7 data. Integrated within an automated mass processing/analysis system for Landsat data (REALM), the input to our registration method consists of scenes that have been geometrically and radiometrically corrected, as well as pre-processed for the detection of clouds and cloud shadows. Such pre-processed scenes are then geo-registered relative to a database of Landsat chips. This paper describes our registration process, including the use of a database of landmark chips, a feature extraction performed by an overcomplete wavelet representation, and feature matching using statistically robust techniques. Knowing the approximate longitudes and latitudes of the four corners of the scene, a subset of chips which represent landmarks included in the scene are extracted from the database. For each of these selected landmark chips, a corresponding window is extracted from the scene, and each chip-window pair is registered using our robust wavelet feature matching. First results and future directions are presented in the paper}, keywords = {atmospheric techniques, automated mass processing/analysis system, chip-window pair, cloud shadows, Clouds, Feature extraction, feature matching, geo-registration, geometrically corrected scene, geophysical signal processing, Image matching, image registration, landmark chips, Landsat chips, Landsat data, Landsat-5 data, Landsat-7 data, overcomplete wavelet representation, pre-processed scenes, radiometrically corrected scene, REALM, Remote sensing, robust matching, robust wavelet feature matching, scenes, statistically robust techniques, sub-pixel accuracy registration, wavelet features, Wavelet transforms, window}, doi = {10.1109/IGARSS.2000.857287}, author = {Le Moigne,J. and Netanyahu,N. S and Masek,J. G and Mount, Dave and Goward,S. and Honzak,M.} } @article {14626, title = {Ligand-Receptor Pairing Via Tree Comparison}, journal = {Journal of Computational Biology}, volume = {7}, year = {2000}, month = {2000/02//}, pages = {59 - 70}, abstract = {This paper introduces a novel class of tree comparison problems strongly motivated by an important and cost intensive step in drug discovery pipeline viz., mapping cell bound receptors to the ligands they bind to and vice versa. Tree comparison studies motivated by problems such as virus-host tree comparison, gene-species tree comparison and consensus tree problem have been reported. None of these studies are applicable in our context because in all these problems, there is a well-defined mapping of the nodes the trees are built on across the set of trees being compared. A new class of tree comparison problems arises in cases where finding the correspondence among the nodes of the trees being compared is itself the problem. The problem arises while trying to find the interclass correspondence between the members of a pair of coevolving classes, e.g., cell bound receptors and their ligands. Given the evolution of the two classes, the combinatorial problem is to find a mapping among the leaves of the two trees that optimizes a given cost function. In this work we formulate various combinatorial optimization problems motivated by the aforementioned biological problem for the first time. We present hardness results, give an efficient algorithm for a restriction of the problem and demonstrate its applicability.}, isbn = {1066-5277, 1557-8666}, doi = {10.1089/10665270050081388}, url = {http://www.liebertonline.com/doi/abs/10.1089/10665270050081388}, author = {Bafna,Vineet and Hannenhalli, Sridhar and Rice,Ken and Vawter,Lisa} } @article {15396, title = {Numerical simulation of small-signal microwave performance of 4H{\textendash}SiC MESFET}, journal = {Solid-State Electronics}, volume = {44}, year = {2000}, month = {2000/07/01/}, pages = {1281 - 1287}, abstract = {Small-signal high frequency characteristics of 4H{\textendash}SiC MESFET has been studied by using two-dimensional numerical drift-diffusion model in frequency domain. Non-ideal Schottky boundary conditions have been introduced that take into account a thin interfacial layer and interface energy states. It has been demonstrated that the 10 dB/dec small-signal current gain roll-off can be attributed to the existence of high density interface states at the metal{\textendash}semiconductor interface. It has been found that as the gate length is reduced to 0.1 μm, fT and fmax may reach as high as 30 and 62 GHz, respectively.}, isbn = {0038-1101}, doi = {10.1016/S0038-1101(00)00025-3}, url = {http://www.sciencedirect.com/science/article/pii/S0038110100000253}, author = {Huang,Mingwei and Mayergoyz, Issak D and Goldsman,Neil} } @article {17319, title = {Performance Benefits of Simultaneous Over Sequential Menus as Task Complexity Increases}, journal = {International Journal of Human-Computer Interaction}, volume = {12}, year = {2000}, month = {2000///}, pages = {173 - 192}, abstract = {To date, experimental comparisons of menu layouts have concentrated on variants of hierarchical structures of sequentially presented menus. Simultaneous menus-layouts that present multiple active menus on a screen at the same time-are an alternative arrangement that may be useful in many Web design situations. This article describes an experiment involving a between-subject comparison of simultaneous menus and their traditional sequential counterparts. A total of 20 experienced Web users used either simultaneous or sequential menus in a standard Web browser to answer questions based on U.S. Census data. Our results suggest that appropriate use of simultaneous menus can lead to improved task performance speeds without harming subjective satisfaction measures. For novice users performing simple tasks, the simplicity of sequential menus appears to be helpful, but experienced users performing complex tasks may benefit from simultaneous menus. Design improvements can amplify the benefits of simultaneous menu layouts.To date, experimental comparisons of menu layouts have concentrated on variants of hierarchical structures of sequentially presented menus. Simultaneous menus-layouts that present multiple active menus on a screen at the same time-are an alternative arrangement that may be useful in many Web design situations. This article describes an experiment involving a between-subject comparison of simultaneous menus and their traditional sequential counterparts. A total of 20 experienced Web users used either simultaneous or sequential menus in a standard Web browser to answer questions based on U.S. Census data. Our results suggest that appropriate use of simultaneous menus can lead to improved task performance speeds without harming subjective satisfaction measures. For novice users performing simple tasks, the simplicity of sequential menus appears to be helpful, but experienced users performing complex tasks may benefit from simultaneous menus. Design improvements can amplify the benefits of simultaneous menu layouts. }, isbn = {1044-7318}, doi = {10.1207/S15327590IJHC1202_2}, url = {http://www.tandfonline.com/doi/abs/10.1207/S15327590IJHC1202_2}, author = {Hochheiser,Harry and Shneiderman, Ben} } @inbook {14801, title = {Resource-aware meta-computing}, booktitle = {Emphasizing Distributed SystemsEmphasizing Distributed Systems}, volume = {Volume 53}, year = {2000}, month = {2000///}, pages = {109 - 169}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {Meta-computing, is an increasingly popular and useful method of obtaining resources to solve large computational problems. However, meta-computer environments pose a number of unique challenges, many of which have yet to be addressed effectively. Among these are dynamicism in both applications and environments, and heterogeneity at several different levels. This chapter discusses current approaches to these problems, and uses them in the Active Harmony system as a running example. Harmony supports an interface that allows applications to export tuning alternatives to the higher-level system. By exposing different parameters that can be changed at runtime, applications can be automatically adapted to changes in their execution environment caused by other programs, the addition or deletion of nodes, or changes in the availability of resources like communication links. Applications expose not only options, but also expected resource utilization with each option and the effect that the option will have on the application{\textquoteright}s performance. We discuss how this flexibility can be used to tune the overall performance of a collection of applications in a system.}, isbn = {0065-2458}, url = {http://www.sciencedirect.com/science/article/pii/S0065245800800054}, author = {Hollingsworth, Jeffrey K and Keleher, Peter J. and Ryu, Kyung D.}, editor = {Marvin V. Zelkowits} } @article {14652, title = {A Review of Current Routing Protocols for Ad Hoc}, journal = {IEEE Personal Communications}, volume = {29}, year = {2000}, month = {2000///}, pages = {156 - 71}, author = {Royer,E.M. and Toh,C.K. and Hicks, Michael W. and Kakkar,P. and Moore,J. T and Hicks, Michael W. and Moore,J. T and Alexander,D. S and Gunter,C. A and Nettles,S. and others} } @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} } @inbook {14732, title = {Scalable Resource Control in Active Networks}, booktitle = {Active NetworksActive Networks}, series = {Lecture Notes in Computer Science}, volume = {1942}, year = {2000}, month = {2000///}, pages = {343 - 357}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The increased complexity of the service model relative to store-and-forward routers has made resource management one of the paramount concerns in active networking research and engineering. In this paper,we address two major challenges in scaling resource management-to-many-node active networks. The first is the use of market mechanisms and trading amongst nodes and programs with varying degrees of competition and cooperation to provide a scalable approach to managing active network resources. The second is the use of a trust-management architecture to ensure that the participants in the resource management marketplace have a policy-driven {\textquotedblleft}rule of law{\textquotedblright} in which marketplace decisions can be made and relied upon. We have used lottery scheduling and the Keynote trust-management system for our implementation, for which we provide some initial performance indications.}, isbn = {978-3-540-41179-6}, url = {http://dx.doi.org/10.1007/3-540-40057-5_25}, author = {Anagnostakis,Kostas and Hicks, Michael W. and Ioannidis,Sotiris and Keromytis,Angelos and Smith,Jonathan}, editor = {Yasuda,Hiroshi} } @conference {14818, title = {Speed vs. Accuracy in Simulation for I/O-Intensive Applications}, booktitle = {Parallel and Distributed Processing Symposium, International}, year = {2000}, month = {2000///}, pages = {315 - 315}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper presents a family of simulators that have been developed for data-intensive applications, and a methodology to select the most efficient one based on a user-supplied requirement for accuracy. The methodology consists of a series of tests that select an appropriate simulation based on the attributes of the application. In addition, each simulator provides two estimates of application execution time: one for the minimum expected time and the other for the maximum. We present the results of applying the strategy to existing applications and show that we can accurately simulate applications tens to hundreds of times faster than application execution time.}, keywords = {discrete-event simulation, i/o-intensive applications, parallel or distributed applications, performance prediction, simulation}, doi = {http://doi.ieeecomputersociety.org/10.1109/IPDPS.2000.846001}, author = {Eom, Hyeonsang and Hollingsworth, Jeffrey K} } @article {16950, title = {A Trip Report on Creativity and Cognition 1999: An Insider{\textquoteright}s Report on a Far Out Conference}, journal = {SIGCHI BULLETIN}, volume = {32}, year = {2000}, month = {2000///}, pages = {43 - 46}, author = {Shneiderman, Ben and Hewett,T.} } @conference {14765, title = {Using hardware performance monitors to isolate memory bottlenecks}, booktitle = {Proceedings of the 2000 ACM/IEEE conference on Supercomputing (CDROM)}, year = {2000}, month = {2000///}, pages = {40 - 40}, author = {Buck, B. R and Hollingsworth, Jeffrey K} } @book {17972, title = {Visualization 2000}, year = {2000}, month = {2000///}, publisher = {IEEE Computer Society Press}, organization = {IEEE Computer Society Press}, author = {Ertl,T. and Hamann,B. and Varshney, Amitabh} } @article {14596, title = {Bacterial Start Site Prediction}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {27}, year = {1999}, month = {1999/09/01/}, pages = {3577 - 3582}, abstract = {With the growing number of completely sequenced bacterial genes, accurate gene prediction in bacterial genomes remains an important problem. Although the existing tools predict genes in bacterial genomes with high overall accuracy, their ability to pinpoint the translation start site remains unsatisfactory. In this paper, we present a novel approach to bacterial start site prediction that takes into account multiple features of a potential start site, viz., ribosome binding site (RBS) binding energy, distance of the RBS from the start codon, distance from the beginning of the maximal ORF to the start codon, the start codon itself and the coding/non-coding potential around the start site. Mixed integer programing was used to optimize the discriminatory system. The accuracy of this approach is up to 90\%, compared to 70\%, using the most common tools in fully automated mode (that is, without expert human post-processing of results). The approach is evaluated using Bacillus subtilis, Escherichia coli and Pyrococcus furiosus. These three genomes cover a broad spectrum of bacterial genomes, since B.subtilis is a Gram-positive bacterium, E.coli is a Gram-negative bacterium and P.furiosus is an archaebacterium. A significant problem is generating a set of {\textquoteleft}true{\textquoteright} start sites for algorithm training, in the absence of experimental work. We found that sequence conservation between P.furiosus and the related Pyrococcus horikoshii clearly delimited the gene start in many cases, providing a sufficient training set.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/27.17.3577}, url = {http://nar.oxfordjournals.org/content/27/17/3577}, author = {Hannenhalli, Sridhar and Hayes,William S and Hatzigeorgiou,Artemis G and Fickett,James W} } @article {14781, title = {Binary version management for computational grids}, journal = {Parallel processing letters}, volume = {9}, year = {1999}, month = {1999///}, pages = {215 - 225}, author = {Hollingsworth, Jeffrey K and Miller, E. L and Akala, K.} } @article {14665, title = {Chunks in PLAN: Language support for programs as packets}, journal = {PROCEEDINGS OF THE ANNUAL ALLERTON CONFERENCE ON COMMUNICATION CONTROL AND COMPUTING}, volume = {37}, year = {1999}, month = {1999///}, pages = {PROCEEDINGS OF THE ANNUAL ALLERTON CONFERENCE ON COMMUNICATION CONTROL AND COMPUTING - PROCEEDINGS OF THE ANNUAL ALLERTON CONFER}, author = {Moore,J. T and Hicks, Michael W. and Nettles,S.} } @article {18693, title = {A comparative study of the backbone dynamics of two closely related lipid binding proteins: Bovine heart fatty acid binding protein and porcine ileal lipid binding protein}, journal = {Molecular and Cellular Biochemistry}, volume = {192}, year = {1999}, month = {1999///}, pages = {109 - 121}, abstract = {The backbone dynamics of bovine heart fatty acid binding protein (H-FABP) and porcine ileal lipid binding protein (ILBP) were studied by 15N NMR relaxation (T1 and T2) and steady state heteronuclear 15N1H NOE measurements. The microdynamic parameters characterizing the backbone mobility were determined using the {\textquoteleft}model-free{\textquoteright} approach. For H-FABP, the non-terminal backbone amide groups display a rather compact protein structure of low flexibility. In contrast, for ILBP an increased number of backbone amide groups display unusually high internal mobility. Furthermore, the data indicate a higher degree of conformational exchange processes in the {\textmu}sec-msec time range for ILBP compared to H-FABP. These results suggest significant differences in the conformational stability for these two structurally highly homologous members of the fatty acid binding protein family.}, keywords = {Biomedical and Life Sciences}, isbn = {0300-8177}, doi = {10.1023/A:1006834708786}, url = {http://www.springerlink.com/content/w2j255781546j880/abstract/}, author = {L{\"u}cke,Christian and Fushman, David and Ludwig,Christian and Hamilton,James A. and Sacchettini,James C. and R{\"u}terjans,Heinz} } @conference {13938, title = {Designing PETS: a personal electronic teller of stories}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems: the CHI is the limit}, series = {CHI {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {326 - 329}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We have begun the development of a new robotic pet that cansupport children in the storytelling process. Children can build their own pet by snapping together the modular animal parts of the PETS robot. After their pet is built, children can tell stories using the My Pets software. These stories can then be acted out by their robotic pet. This video paper describes the motivation for this research and the design process of our intergenerational design team in building the first PETS prototypes. We will discuss our progress to date and our focus for the future. }, keywords = {children, cooperative inquiry, design techniques, educational applications, intergenerational design team, PETS, ROBOTICS}, isbn = {0-201-48559-1}, doi = {10.1145/302979.303103}, url = {http://doi.acm.org/10.1145/302979.303103}, author = {Druin, Allison and Montemayor,Jamie and Hendler,Jim and McAlister,Britt and Boltman,Angela and Fiterman,Eric and Plaisant,Aurelie and Kruskal,Alex and Olsen,Hanne and Revett,Isabella and Schwenn,Thomas Plaisant and Sumida,Lauren and Wagner,Rebecca} } @article {14954, title = {Designing practical efficient algorithms for symmetric multiprocessors}, journal = {Algorithm Engineering and Experimentation}, year = {1999}, month = {1999///}, pages = {663 - 663}, abstract = {Symmetric multiprocessors (SMPs) dominate the high-end server market and are currently the primary candidate for constructing large scale multiprocessor systems. Yet, the design of efficient parallel algorithms for this platform currently poses several challenges. In this paper, we present a computational model for designing efficient algorithms for symmetric multiprocessors. We then use this model to create efficient solutions to two widely different types of problems - linked list prefix computations and generalized sorting. Our novel algorithm for prefix computations builds upon the sparse ruling set approach of Reid-Miller and Blelloch. Besides being somewhat simpler and requiring nearly half the number of memory accesses, we can bound our complexity with high probability instead of merely on average. Our algorithm for generalized sorting is a modification of our algorithm for sorting by regular sampling on distributed memory architectures. The algorithm is a stable sort which appears to be asymptotically faster than any of the published algorithms for SMPs. Both of our algorithms were implemented in C using POSIX threads and run on four symmetric multiprocessors - the IBM SP-2 (High Node), the HP-Convex Exemplar (S-Class), the DEC AlphaServer, and the Silicon Graphics Power Challenge. We ran our code for each algorithm using a variety of benchmarks which we identified to examine the dependence of our algorithm on memory access patterns. In spite of the fact that the processors must compete for access to main memory, both algorithms still yielded scalable performance up to 16 processors, which was the largest platform available to us. For some problems, our prefix computation algorithm actually matched or exceeded the performance of the standard sequential solution using only a single thread. Similarly, our generalized sorting algorithm always beat the performance of sequential merge sort by at least an order of magnitude, even with a single thread.}, doi = {10.1007/3-540-48518-X_3}, author = {Helman,D. and JaJa, Joseph F.} } @conference {17080, title = {Developing the next generation of Earth science data systems: the Global Land Cover Facility}, booktitle = {Geoscience and Remote Sensing Symposium, 1999. IGARSS {\textquoteright}99 Proceedings. IEEE 1999 International}, volume = {1}, year = {1999}, month = {1999///}, pages = {616-618 vol.1 - 616-618 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {A recent initiative by NASA has resulted in the formation of a federation of Earth science data partners. These Earth Science Information Partners (ESIPs) have been tasked with creating novel Earth science data products and services as well as distributing new and existing data sets to the Earth science community and the general public. The University of Maryland established its ESIP activities with the creation of the Global Land Cover Facility (GLCF). This joint effort of the Institute for Advanced Computer Studies (UMIACS) and the Department of Geography has developed an operational data archiving and distribution system aimed at advancing current land cover research efforts. The success of the GLCF is tied closely to assessing user needs as well. As the timely delivery of data products to the research community. This paper discusses the development and implementation of a web-based interface that allows users to query the authors{\textquoteright} data holdings and perform user requested processing tasks on demand. The GLCF takes advantage of a scaleable, high performance computing architecture for the manipulation of very large remote sensing data sets and the rapid spatial indexing of multiple format data types. The user interface has been developed with the cooperation of the Human-Computer Interaction Laboratory (HCIL) and demonstrates advances in spatial and temporal querying tools as well as the ability to overlay multiple raster and vector data sets. Their work provides one perspective concerning how critical earth science data may be handled in the near future by a coalition of distributed data centers}, keywords = {Computer architecture, data archiving, data distribution system, Data systems, Distributed computing, Earth science data products, Earth science data system, ESIP, geographic information system, geographic information systems, Geography, geophysical measurement technique, geophysical signal processing, geophysical techniques, Geoscience, GIS, GLCF, Global Land Cover Facility, High performance computing, Indexing, information service, Information services, Institute for Advanced Computer Studies, land cover, NASA, next generation, PACS, Remote sensing, terrain mapping, UMIACS, University of Maryland, User interfaces, web-based interface}, isbn = {0-7803-5207-6}, doi = {10.1109/IGARSS.1999.773583}, author = {Lindsay,F.E. and Townshend,J.R.G. and JaJa, Joseph F. and Humphries,J. and Plaisant, Catherine and Shneiderman, Ben} } @conference {14778, title = {Exposing Application Alternatives}, booktitle = {Distributed Computing Systems, International Conference on}, year = {1999}, month = {1999///}, pages = {0384 - 0384}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {We present the design of an interface to allow applications to export tuning alternatives to a higher-level system. By exposing different parameters that can be changed at runtime, applications can be made to adapt to changes in their execution environment due to other programs, or the addition or deletion of nodes, communication links etc. An integral part of this interface is that an application not only expose its options, but also the resource utilization of each option and the effect that the option will have on the application{\textquoteright}s performance. We discuss how these options can be evaluated to tune the overall performance of a collection of applications in the system. Finally, we show preliminary results from a database application that is automatically reconfigured by the system from query shipping to data shipping based on the number of active clients.}, keywords = {computational grids, metacomputing, scheduling}, isbn = {0-7695-0222-9}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICDCS.1999.776540}, author = {Keleher, Peter J. and Hollingsworth, Jeffrey K and Perkovic, Dejan} } @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.} } @conference {15386, title = {Gate leakage current simulation by Boltzmann transport equation and its dependence on the gate oxide thickness}, booktitle = {Simulation of Semiconductor Processes and Devices, 1999. SISPAD {\textquoteright}99. 1999 International Conference on}, year = {1999}, month = {1999///}, pages = {247 - 250}, abstract = {As device dimensions shrink toward 0.1 mu;m, gate oxides are becoming so thin that MOSFET gate leakage current and oxide degradation are becoming limiting issues. We provide a more rigorous way to calculate gate leakage current. To achieve this we build upon the Spherical Harmonic Method of modeling, which deterministically solves the Boltzmann equation for an entire device. The method gives the distribution function and is 1000 times faster than MC. Once the distribution function is calculated, the tunneling probability is derived from the first principle WKB method. The barrier lowering effect is accounted for by the method of image charges. We calculate gate leakage current as a function of DC bias. The thermionic and tunneling components are compared at different DC bias points. The dependence of gate leakage current on gate oxide thickness is simulated}, keywords = {30, angstrom;60, angstrom;Boltzmann, Bias, calculations;leakage, charges;spherical, component;tunneling, current, currents;semiconductor, dependence;method, dependence;MOSFET;barrier, device, effect;distribution, equation;DC, equation;MOSFET;WKB, function;first, harmonic, image, leakage, lowering, method, method;gate, model;thermionic, models;tunnelling;, of, oxide, principle, probability;Boltzmann, simulation;gate, thickness, transport, WKB}, doi = {10.1109/SISPAD.1999.799307}, author = {Han,Zhiyi and Lin,Chung-Kai and Goldsman,N. and Mayergoyz, Issak D and Yu,S. and Stettler,M.} } @conference {14790, title = {Imprecise Calendars: an Approach to Scheduling Computational Grids}, booktitle = {Distributed Computing Systems, International Conference on}, year = {1999}, month = {1999///}, pages = {0352 - 0352}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {We describe imprecise calendars, a way to organize and schedule clusters of nodes in a computation grid. Imprecise calendars permit the easy and efficient sharing of resources between different clusters of computers that are part of a computational grid. In addition, they can be used to provide specific time reservations for applications. We describe the algorithms and policies for manipulation of imprecise calendars. We also include a series of simulation studies that compare our approach to previous batch scheduling systems for both a single cluster and collection of clusters up to over 3,000 nodes.}, keywords = {parallel computing distributed scheduling computational grid batch scheduler meta computing}, isbn = {0-7695-0222-9}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICDCS.1999.776537}, author = {Hollingsworth, Jeffrey K and Maneewongvatana, Songrit} } @article {13820, title = {Machine Translation}, journal = {Multilingual Information Management: Current Levels and Future Abilities}, year = {1999}, month = {1999///}, pages = {18 - 18}, author = {Bel,N. and Dorr, Bonnie J and Hovy,E. and Knight,K. and Iida,H. and Boitet,C. and Maegaard,B. and Wilks,Y.} } @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} } @book {14913, title = {Perceptual Organization in Computer Vision}, year = {1999}, month = {1999///}, publisher = {Academic Press}, organization = {Academic Press}, author = {Boyer,K.L. and Sarkar,S. and Feldman,J. and Granlund,G. and Horaud,R. and Hutchinson,S. and Jacobs, David W. and Kak,A. and Lowe,D. and Malik,J.} } @article {14722, title = {PLAN: A programming language for active networks}, journal = {ACM SIGPLAN NOTICES}, volume = {34}, year = {1999}, month = {1999///}, pages = {86 - 93}, abstract = {PLAN (Programming Language for Active Networks) is anew language for programs that are carried in the packets of a programmable network. PLAN programs replace the packet headers (which can be viewed as {\textquoteleft}dumb{\textquoteright} programs) used in current networks. As a header replacement, PLAN programs must be lightweight and of limited functionality. These limitations are mitigated by allowing PLAN code to call service routines written in other, more powerful lan- guages. These service routines may also be loaded into the routers dynamically. This two-level architecture, in which PLAN serves as a scripting or {\textquoteleft}glue{\textquoteright} language for more gen- eral services, is the primary contribution of the paper. PLAN is a strict functional language providing a limited set of primitives and datatypes. PLAN de nes primitives for remotely executing PLAN programs on other nodes, and these primitives are used to provide basic data transport in the network. Because remote execution makes debugging di cult, PLAN provides strong static guarantees to the pro- grammer, such as type safety. A more novel property aimed at protecting network availability is a guarantee that PLAN programs use a bounded amount of space and time on active routers and bandwidth in the network. }, author = {Hicks, Michael W. and Kakkar,P. and Moore,J. T and Gunter,C. A and Nettles,S.} } @article {14720, title = {PLAN Service Programmer{\textquoteright}s Guide for PLAN version 3.2}, journal = {University of Pennsylvania}, year = {1999}, month = {1999/08/12/}, author = {Hicks, Michael W.} } @conference {14723, title = {PLANet: an active internetwork}, booktitle = {IEEE INFOCOM {\textquoteright}99. Eighteenth Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings}, volume = {3}, year = {1999}, month = {1999/03/21/25}, pages = {1124-1133 vol.3 - 1124-1133 vol.3}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present PLANet: an active network architecture and implementation. In addition to a standard suite of Internet-like services, PLANet has two key programmability features: (1) all packets contain programs; and (2) router functionality may be extended dynamically. Packet programs are written in our special purpose programming language PLAN, the Packet Language for Active Networks, while dynamic router extensions are written in OCaml, a dialect of ML. Currently, PLANet routers run as byte-code-interpreted Linux user-space applications, and support Ethernet and IP as link layers. PLANet achieves respectable performance on standard networking operations: on 300 MHz Pentium-II{\textquoteright}s attached to 100 Mbps Ethernet, PLANet can route 48 Mbps and switch over 5000 packets per second. We demonstrate the utility of PLANet{\textquoteright}s activeness by showing experimentally how it can nontrivially improve application and aggregate network performance in congested conditions}, keywords = {100 Mbit/s, 300 MHz, 48 Mbit/s, active internetwork, active network architecture, active network implementation, byte-code-interpreted applications, Computer architecture, Computer languages, Computer networks, congested conditions, dynamic programming, dynamic router extensions, Ethernet, Ethernet networks, INFORMATION SCIENCE, Internet, Internet-like services, internetworking, IP, IP networks, link layers, Linux user-space applications, Local area networks, ML dialect, Network performance, networking operations, OCaml, Packet Language for Active Networks, packet programs, packet switching, Pentium-II, performance, performance evaluation, PLAN, PLANet, Planets, programmability features, programming languages, router functionality, special purpose programming language, Switches, telecommunication network routing, Transport protocols, Web and internet services}, isbn = {0-7803-5417-6}, doi = {10.1109/INFCOM.1999.751668}, author = {Hicks, Michael W. and Moore,J. T and Alexander,D. S and Gunter,C. A and Nettles,S. M} } @conference {17535, title = {Predicting the CPU availability of time-shared Unix systems on the computational grid}, booktitle = {The Eighth International Symposium on High Performance Distributed Computing, 1999. Proceedings}, year = {1999}, month = {1999///}, pages = {105 - 112}, publisher = {IEEE}, organization = {IEEE}, abstract = {Focuses on the problem of making short- and medium-term forecasts of CPU availability on time-shared Unix systems. We evaluate the accuracy with which availability can be measured using the Unix load average, the Unix utility {\textquotedblleft}vmstat{\textquotedblright} and the Network Weather Service (NWS) CPU sensor that uses both. We also examine the autocorrelation between successive CPU measurements to determine their degree of self-similarity. While our observations show a long-range autocorrelation dependence, we demonstrate how this dependence manifests itself in the short- and medium-term predictability of the CPU resources in our study}, keywords = {accuracy, Application software, Autocorrelation, Availability, Central Processing Unit, computational grid, correlation methods, CPU availability prediction, CPU resources predictability, CPU sensor, Dynamic scheduling, grid computing, Load forecasting, long-range autocorrelation dependence, medium-term forecasts, network operating systems, Network Weather Service, NWS, performance evaluation, self-similarity degree, short-term forecasts, successive CPU measurements, Time measurement, Time sharing computer systems, time-shared Unix systems, time-sharing systems, Unix, Unix load average, vmstat utility, Weather forecasting}, isbn = {0-7803-5681-0}, doi = {10.1109/HPDC.1999.805288}, author = {Wolski,R. and Spring, Neil and Hayes,J.} } @conference {15018, title = {Prefix computations on symmetric multiprocessors}, booktitle = {Parallel and Distributed Processing, 1999. 13th International and 10th Symposium on Parallel and Distributed Processing, 1999. 1999 IPPS/SPDP. Proceedings}, year = {1999}, month = {1999/04//}, pages = {7 - 13}, abstract = {We introduce a new optimal prefix computation algorithm on linked lists which builds upon the sparse ruling set approach of Reid-Miller and Blelloch. Besides being somewhat simpler and requiring nearly half the number of memory accesses, we can bound our complexity with high probability instead of merely on average. Moreover, whereas Reid-Miller and Blelloch (1996) targeted their algorithm for implementation on a vector multiprocessor architecture, we develop our algorithm for implementation on the symmetric multiprocessor architecture (SMP). These symmetric multiprocessors dominate the high-end server market and are currently the primary candidate for constructing large scale multiprocessor systems. Our prefix computation algorithm was implemented in C using POSIX threads and run on four symmetric multiprocessors-the IBM SP-2 (High Node), the HP-Convex Exemplar (S-Class), the DEC AlphaServer; and the Silicon Graphics Power Challenge. We ran our code using a variety of benchmarks which we identified to examine the dependence of our algorithm on memory access patterns. For some problems, our algorithm actually matched or exceeded the performance of the standard sequential solution using only a single thread. Moreover, in spite of the fact that the processors must compete for access to main memory, our algorithm still achieved scalable performance with up to 16 processors, which was the largest platform available to us}, keywords = {access, algorithms;, AlphaServer;HP-Convex, approach;symmetric, architecture;symmetric, Challenge;high-end, computations;scalable, DEC, Exemplar;IBM, Graphics, market;large, multiprocessor, multiprocessors;Unix;distributed, patterns;prefix, performance;sparse, power, ruling, scale, server, set, SP-2;POSIX, systems;memory, threads;Silicon}, doi = {10.1109/IPPS.1999.760427}, author = {Helman,D.R. and JaJa, Joseph F.} } @article {18455, title = {A real-time audio{\textendash}video front-end for multimedia applications}, journal = {The Journal of the Acoustical Society of America}, volume = {106}, year = {1999}, month = {1999///}, pages = {2271 - 2271}, author = {Zotkin,Dmitry N and Duraiswami, Ramani and Hariatoglu,I. and Davis, Larry S. and Otsuka,T.} } @conference {16167, title = {Refining query previews techniques for data with multivalued attributes: the case of NASA EOSDIS}, booktitle = {Research and Technology Advances in Digital Libraries, 1999. ADL {\textquoteright}99. Proceedings. IEEE Forum on}, year = {1999}, month = {1999///}, pages = {50 - 59}, abstract = {Query Previews allow users to rapidly gain an understanding of the content and scope of a digital data collection. These previews present overviews of abstracted metadata, enabling users to rapidly and dynamically avoid undesired data. We present our recent work on developing query previews for a variety of NASA EOSDIS situations. We focus on approaches that successfully address the challenge of multi-valued attribute data. Memory requirements and processing time associated with running these new solutions remain independent of the number of records in the dataset. We describe two techniques and their respective prototypes used to preview NASA Earth science data}, keywords = {attribute, attributes;processing, collection;memory, computing;meta, data, data;abstracted, data;digital, data;multivalued, data;query, Earth, EOSDIS;NASA, libraries;geophysics, metadata;dataset;digital, NASA, previews, processing;, requirements;multi-valued, Science, techniques;undesired, time;query}, doi = {10.1109/ADL.1999.777690}, author = {Plaisant, Catherine and Venkatraman,M. and Ngamkajorwiwat,K. and Barth,R. and Harberts,B. and Feng,Wenlan} } @article {14735, title = {Specifying the PLAN Network Programming Langauge}, journal = {Electronic Notes in Theoretical Computer Science}, volume = {26}, year = {1999}, month = {1999///}, pages = {87 - 104}, abstract = {We discuss how the specification of the PLAN programming language supports the design objectives of the language. The specification aims to provide a mathematically precise operational semantics that can serve as a standard for implementing interpreters and portable programs. The semantics should also support proofs of key properties of PLAN that would hold of all conformant implementations. This paper discusses two such properties. (1) Type checking is required, but interpreters are given significant flexibility about when types are checked; the specification must support a clear description of the possible behaviors of a network of conformant implementations. (2) It is essential to have guarantees about how PLAN programs use global resources, but the specification must be flexible about extensions in the network service layer. We illustrate on of kind of issue that will arise in using to specification to prove properties of the network based on the choice of services.}, isbn = {1571-0661}, doi = {10.1016/S1571-0661(05)80285-3}, url = {http://www.sciencedirect.com/science/article/pii/S1571066105802853}, author = {Kakkar,Pankaj and Hicks, Michael W. and Moore,Jon and Gunter,Carl A.} } @article {13349, title = {A Study of the Structure of the Web}, journal = {University of California, Berkeley}, year = {1999}, month = {1999///}, abstract = {The World Wide Web is a huge, growing repository of information on a wide range of topics. It is alsobecoming important, commercially and sociologically, as a place of human interaction within different communities. In this paper we present an experimental study of the structure of the Web. We analyze link topologies of various communities, and patterns of mirroring of content, on 1997 and 1999 snapshots of the Web. Our results give insight into patterns of interaction within communities and how they evolve, as well as patterns of data replication. We also describe the techniques we have developed for performing complex processing on this large data set, and our experiences in doing so. We present new algorithms for finding partial and complete mirrors in URL hierarchies; these are also of independent interest for search and redirection. In order to study and visualize link topologies of different communities, we have developed techniques to compact these large link graphs without much information loss. }, author = {Deshpande, Amol and Huang,R. and Raman,V. and Riggs,T. and Song,D. and Subramanian,L.} } @article {16171, title = {Temporal visualization for legal case histories}, journal = {PROCEEDINGS OF THE ANNUAL MEETING-AMERICAN SOCIETY FOR INFORMATION SCIENCE}, volume = {36}, year = {1999}, month = {1999///}, pages = {271 - 279}, abstract = {This paper discusses visualization of legal information using a tool for temporal information called LifeLines. The direct and indirect histories of cases can become very complex. We explored ways that LifeLines could aid in viewing the links between the original case and the direct and indirect histories. The Apple Computer, Inc. v. Microsoft Corporation and Hewlett Packard Company case is used to illustrate the prototype. For example, if users want to find out how the rulings or statutes changed throughout this case, they could retrieve this information within a single display. Using the timeline, users could also choose at which point in time they would like to begin viewing the case. LifeLines support various views of a case{\textquoteright}s history. For instance, users can view the trial history of a case, the references involved in a case, and citations made to a case. The paper describes improvements to LifeLines that could help in providing a more useful visualization of case history.}, author = {Harris,C. and Allen,R.B. and Plaisant, Catherine and Shneiderman, Ben} } @article {15823, title = {Tikhonov Regularization and Total Least Squares}, journal = {SIAM Journal on Matrix Analysis and Applications}, volume = {21}, year = {1999}, month = {1999///}, pages = {185 - 194}, abstract = {Discretizations of inverse problems lead to systems of linear equations with a highly ill-conditioned coefficient matrix, and in order to computestable solutions to these systems it is necessary to apply regularization methods. We show how Tikhonov{\textquoteright}s regularization method, which in its original formulation involves a least squares problem, can be recast in a total least squares formulation suited for problems in which both the coefficient matrix and the right-hand side are known only approximately. We analyze the regularizing properties of this method and demonstrate by a numerical example that, in certain cases with large perturbations, the new method is superior to standard regularization methods.}, keywords = {bidiagonalization, discrete ill-posed problems, regularization, total least squares}, doi = {10.1137/S0895479897326432}, url = {http://link.aip.org/link/?SML/21/185/1}, author = {Golub, Gene H. and Hansen,Per Christian and O{\textquoteright}Leary, Dianne P.} } @article {14648, title = {Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals}, journal = {J. ACM}, volume = {46}, year = {1999}, month = {1999/01//}, pages = {1 - 27}, abstract = {Genomes frequently evolve by reversals \&rgr;(i,j) that transform a gene order \&pgr;1 {\textellipsis} \&pgr;i\&pgr;i+1 {\textellipsis} \&pgr;j-1\&pgr;j {\textellipsis} \&pgr;n into \&pgr;1 {\textellipsis} \&pgr;i\&pgr;j-1 {\textellipsis} \&pgr;i+1\&pgr;j {\textellipsis} \&pgr;n. Reversal distance between permutations \&pgr; and \&sgr;is the minimum number of reversals to transform \&pgr; into \&Agr;. Analysis of genome rearrangements in molecular biology started in the late 1930{\textquoteright}s, when Dobzhansky and Sturtevant published a milestone paper presenting a rearrangement scenario with 17 inversions between the species of Drosophilia. Analysis of genomes evolving by inversions leads to a combinatorial problem of sorting by reversals studied in detail recently. We study sorting of signed permutations by reversals, a problem that adequately models rearrangements in a small genomes like chloroplast or mitochondrial DNA. The previously suggested approximation algorithms for sorting signed permutations by reversals compute the reversal distance between permutations with an astonishing accuracy for both simulated and biological data. We prove a duality theorem explaining this intriguing performance and show that there exists a {\textquotedblleft}hidden{\textquotedblright} parameter that allows one to compute the reversal distance between signed permutations in polynomial time.}, keywords = {Computational Biology, Genetics}, isbn = {0004-5411}, doi = {10.1145/300515.300516}, url = {http://doi.acm.org/10.1145/300515.300516}, author = {Hannenhalli, Sridhar and Pevzner,Pavel A.} } @conference {14747, title = {Transparent communication for distributed objects in Java}, booktitle = {Proceedings of the ACM 1999 conference on Java Grande}, series = {JAVA {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {160 - 170}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {1-58113-161-5}, doi = {10.1145/304065.304119}, url = {http://doi.acm.org/10.1145/304065.304119}, author = {Hicks, Michael W. and Jagannathan,Suresh and Kelsey,Richard and Moore,Jonathan T. and Ungureanu,Cristian} } @article {17452, title = {Understanding Patterns of User Visits to Web Sites: Interactive Starfield Visualization of WWW Log Data-Short Version}, journal = {Tech Report HCIL-99-06}, year = {1999}, month = {1999///}, abstract = {HTTP server log files provide Web site operators with substantial detail regarding the visitors to their sites. Interest in interpreting this data has spawned an active market for software packages that summarize and analyze this data, providing histograms, pie graphs, and other charts summarizing usage patterns. While useful, these summaries obscure useful information and restrict users to passive interpretation of static displays.Interactive starfield visualizations can be used to provide users with greater abilities to interpret and explore web log data. By combining two-dimensional displays of thousands of individual access requests, color and size coding for additional attributes, and facilities for zooming and filtering, these visualizations provide capabilities for examining data that exceed those of traditional web log analysis tools. We introduce a series of interactive starfield visualizations, which can be used to explore server data across various dimensions. Possible uses of these visualizations are discussed, and difficulties of data collection, presentation, and interpretation are explored. }, author = {Hochheiser,H. and Shneiderman, Ben} } @article {17479, title = {Using Interactive Visualizations of WWW Log Data to Characterize Access Patterns and Inform Site Design}, year = {1999}, month = {1999///}, abstract = {HTTP server log files provide Web site operators with substantial detail regarding the visitors to their sites. Interest ininterpreting this data has spawned an active market for software packages that summarize and analyze this data, providing histograms, pie graphs, and other charts summarizing usage patterns. While useful, these summaries obscureuseful information and restrict users to passive interpretation of static displays. Interactive visualizations can be used to provide users with greater abilities to interpret and explore web log data. Bycombining two-dimensional displays of thousands of individual access requests, color and size coding for additional attributes, and facilities for zooming and filtering, these visualizations provide capabilities for examining data that exceed those of traditional web log analysis tools.

We introduce a series of interactive visualizations that can be used to explore server data across various dimensions. Sample visualizations of server data from two web sites are presented. Coordinated, snap-together visualizations (STVs) of log data are introduced as a means of gaining additional expressive power. Possible uses of these visualizations are discussed, and difficulties of data collection, presentation, and interpretation are explored.}, keywords = {Information Visualization, log file analysis, World Wide Web}, url = {http://drum.lib.umd.edu/handle/1903/6034}, author = {Hochheiser,Harry and Shneiderman, Ben} } @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.} } @conference {14762, title = {Benchmarking a network of PCs running parallel applications}, booktitle = {Performance, Computing and Communications, 1998. IPCCC {\textquoteright}98., IEEE International}, year = {1998}, month = {1998/02/16/18}, pages = {1 - 7}, publisher = {IEEE}, organization = {IEEE}, abstract = {Presents a benchmarking study that compares the performance of a network of four PCs connected by a 100 Mbit/s fast Ethernet running three different system software configurations: TCP/IP on Windows NT, TCP/IP on Linux and a lightweight message-passing protocol (U-Net active messages) on Linux. For each configuration, we report results for communication micro-benchmarks and the NAS (Numerical Aerodynamics Simulation) parallel benchmarks. For the NAS benchmarks, the overall running time using Linux TCP/IP was 12-500\% less than the Windows NT TCP/IP configuration. Likewise, the Linux U-Net based message-passing protocol outperformed the Linux TCP/IP version by 5-200\%+. We also show that, by using Linux U-Net, we are able to achieve 125 μs latency between two processes using PVM. Finally, we report that the default mathematical libraries supplied with NT (for both gcc and Visual C++) are substantially slower than the one supplied with Linux}, keywords = {100 Mbit/s, 125 mus, Aerodynamics, Application software, communication micro-benchmarks, default mathematical libraries, Delay, Ethernet, Ethernet networks, gcc, latency, lightweight message-passing protocol, Linux, Local area networks, mathematics computing, Message passing, microcomputer applications, Microsoft Windows NT, NAS parallel benchmarks, network operating systems, Numerical simulation, parallel applications, PARALLEL PROCESSING, PC network benchmarking, performance comparison, performance evaluation, Personal communication networks, Protocols, PVM, running time, software libraries, System software, system software configurations, TCP/IP, TCPIP, Transport protocols, U-Net active messages, Visual C++}, isbn = {0-7803-4468-5}, doi = {10.1109/PCCC.1998.659876}, author = {Hollingsworth, Jeffrey K and Guven, E. and Akinlar, C.} } @article {13700, title = {A Comparative Study of Knowledge-Based Approaches for Cross-Language}, year = {1998}, month = {1998///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Cross-language retrieval systems seek to use queries in one natural language to guide theretrieval of documents that might be written in another. Acquisition and representation of translation knowledge plays a central role in this process. This paper explores the util- ity of two sources of manually encoded translation knowledge, bilingual dictionaries and translation lexicons, for cross-language retrieval. We have implemented six query trans- lation techniques that use bilingual dictionaries, one based on lexical-semantic analysis, and one based on direct use of the translation output from an existing machine transla- tion system; these are compared with a document translation technique that uses output from the same existing translation system. Average precision measures on portions of the TREC collection suggest that arbitrarily selecting a single translation from a bilingual dictionary is typically no less effective than using every translation in the dictionary, that query translation using an existing machine translation system can achieve some- what better effectiveness than simple dictionary-based techniques, and that performing document translation rather than query translation may result in further improvements in retrieval effectiveness under some conditions. }, author = {Oard, Douglas and Dorr, Bonnie J and Hackett,P. and Katsova,M.} } @article {14770, title = {Critical path profiling of message passing and shared-memory programs}, journal = {IEEE Transactions on Parallel and Distributed Systems}, volume = {9}, year = {1998}, month = {1998/10//}, pages = {1029 - 1040}, abstract = {We introduce a runtime, nontrace-based algorithm to compute the critical path profile of the execution of message passing and shared-memory parallel programs. Our algorithm permits starting or stopping the critical path computation during program execution and reporting intermediate values. We also present an online algorithm to compute a variant of critical path, called critical path zeroing, that measures the reduction in application execution time that improving a selected procedure will have. Finally, we present a brief case study to quantify the runtime overhead of our algorithm and to show that online critical path profiling can be used to find program bottlenecks}, keywords = {Computer Society, Concurrent computing, critical path computation, critical path profile, critical path zeroing, distributed processing, distributed shared memory systems, Instruments, Message passing, Monitoring, online algorithm, online critical path profiling, Parallel algorithms, program bottlenecks, Runtime, runtime nontrace-based algorithm, runtime overhead, shared-memory programs, system monitoring, Time measurement, Yarn}, isbn = {1045-9219}, doi = {10.1109/71.730530}, author = {Hollingsworth, Jeffrey K} } @inbook {16255, title = {De-amortization of Algorithms}, booktitle = {Computing and CombinatoricsComputing and Combinatorics}, series = {Lecture Notes in Computer Science}, volume = {1449}, year = {1998}, month = {1998///}, pages = {4 - 14}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {De-amortization aims to convert algorithms with excellent overall speed, f ( n ) for performing n operations, into algorithms that take no more than O ( f ( n )/ n ) steps for each operation. The paper reviews several existing techniques for de-amortization of algorithms.}, isbn = {978-3-540-64824-6}, url = {http://dx.doi.org/10.1007/3-540-68535-9_4}, author = {Rao Kosaraju,S. and Pop, Mihai}, editor = {Hsu,Wen-Lian and Kao,Ming-Yang} } @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 {17076, title = {Designing to facilitate browsing: A look back at the Hyperties workstation browser}, year = {1998}, month = {1998/10/15/}, abstract = {Since browsing hypertext can present a formidable cognitivechallenge, user interface design plays a major role in determining acceptability. In the Unix workstation version of Hyperties, a research-oriented prototype, we focussed on design features that facilitate browsing. We first give a general overview of Hyperties and its markup language. Customizable documents can be generated by the conditional text feature that enables dynamic and selective display of text and graphics. In addition we present: - an innovative solution to link identification: pop-out graphical buttons of arbitrary shape. - application of pie menus to permit low cognitive load actions that reduce the distraction of common actions, such as page turning or window selection. - multiple window selection strategies that reduce clutter and housekeeping effort. We preferred piles-of-tiles, in which standard-sized windows were arranged in a consistent pattern on the display and actions could be done rapidly, allowing users to concentrate on the contents. (Also cross-referenced as CAR-TR-494) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/362}, author = {Shneiderman, Ben and Plaisant, Catherine and Botafogo,Rodrigo and Hopkins,Don and Weiland,William} } @inbook {13763, title = {Enhancing Automatic Acquisition of Thematic Structure in a Large-Scale Lexicon for Mandarin Chinese}, booktitle = {Machine Translation and the Information SoupMachine Translation and the Information Soup}, series = {Lecture Notes in Computer Science}, volume = {1529}, year = {1998}, month = {1998///}, pages = {41 - 50}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper describes a refinement to our procedure for porting lexical conceptual structure (LCS) into new languages. Specifically we describe a two-step process for creating candidate thematic grids for Mandarin Chinese verbs, using the English verb heading the VP in the subde_nitions to separate senses, and roughly parsing the verb complement structure to match thematic structure templates. We accomplished a substantial reduction in manual effort, without substantive loss. The procedure is part of a larger process of creating a usable lexicon for interlingual machine translation from a large on-line resource with both too much and too little information.}, isbn = {978-3-540-65259-5}, url = {http://dx.doi.org/10.1007/3-540-49478-2_4}, author = {Olsen,Mari and Dorr, Bonnie J and Thomas,Scott}, editor = {Farwell,David and Gerber,Laurie and Hovy,Eduard} } @article {16178, title = {Facilitating Network Data Exploration with Query Previews: A Study of User Performance and Preference}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {Current network data exploration systems which use command languages (e.g.SQL) or form fill-in interfaces fail to give users an indication of the distribution of data items. This leads many users to waste time posing queries which have zero-hit or mega-hit result sets. Query previewing is a novel visual approach for browsing huge networked information warehouses. Query previews supply data distribution information about the database that is being searched and give continuous feedback about the size of the result set for the query as it is being formed. Our within-subjects empirical comparison studied 12 subjects using a form fill-in interface with and without query previews. We found statistically significant differences showing that query previews sped up performance 1.6 to 2.1 times and led to higher subjective satisfaction. (Also cross-referenced as UMIACS-98-14) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/488}, author = {Tanin,Egemen and Lotem,Amnon and Haddadin,Ihab and Shneiderman, Ben and Plaisant, Catherine and Slaughter,Laura} } @conference {14806, title = {Instrumentation and measurement}, booktitle = {The grid}, year = {1998}, month = {1998///}, pages = {339 - 365}, author = {Hollingsworth, Jeffrey K and Miller, B.} } @conference {14784, title = {LBF: a performance metric for program reorganization}, booktitle = {18th International Conference on Distributed Computing Systems, 1998. Proceedings}, year = {1998}, month = {1998/05/26/29}, pages = {222 - 229}, publisher = {IEEE}, organization = {IEEE}, abstract = {We introduce a new performance metric, called Load Balancing Factor (LBF), to assist programmers with evaluating different tuning alternatives. The LBF metric differs from traditional performance metrics since it is intended to measure the performance implications of a specific tuning alternative rather than quantifying where time is spent in the current version of the program. A second unique aspect of the metric is that it provides guidance about moving work within a distributed or parallel program rather than reducing it. A variation of the LBF metric can also be used to predict the performance impact of changing the underlying network. The LBF metric can be computed incrementally and online during the execution of the program to be tuned. We also present a case study that shows that our metric can predict the actual performance gains accurately for a test suite of six programs}, keywords = {case study, Computational modeling, computer network, Computer science, Debugging, distributed processing, distributed program, Educational institutions, Integrated circuit testing, LBF metric, load balancing factor, Load management, measurement, NIST, parallel program, parallel programming, performance metric, program reorganization, program tuning, Programming profession, resource allocation, software metrics, software performance evaluation, US Department of Energy}, isbn = {0-8186-8292-2}, doi = {10.1109/ICDCS.1998.679505}, author = {Eom, H. and Hollingsworth, Jeffrey K} } @inbook {13817, title = {Lexical Selection for Cross-Language Applications: Combining LCS with WordNet}, booktitle = {Machine Translation and the Information SoupMachine Translation and the Information Soup}, series = {Lecture Notes in Computer Science}, volume = {1529}, year = {1998}, month = {1998///}, pages = {438 - 447}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper describes experiments for testing the power of large-scale resources for lexical selection in machine translation (MT) and cross-language information retrieval (CLIR). We adopt the view that verbs with similar argument structure share certain meaning components, but that those meaning components are more relevant to argument realization than to idiosyncratic verb meaning. We verify this by demonstrating that verbs with similar argument structure as encoded in Lexical Conceptual Structure (LCS) are rarely synonymous in WordNet. We then use the results of this work to guide our implementation of an algorithm for cross-language selection of lexical items, exploiting the strengths of each resource: LCS for semantic structure and WordNet for semantic content. We use the Parka Knowledge-Based System to encode LCS representations and WordNet synonym sets and we implement our lexical-selection algorithm as Parka-based queries into a knowledge base containing both information types.}, isbn = {978-3-540-65259-5}, url = {http://dx.doi.org/10.1007/3-540-49478-2_39}, author = {Dorr, Bonnie J and Katsova,Maria}, editor = {Farwell,David and Gerber,Laurie and Hovy,Eduard} } @article {16190, title = {LifeLines: using visualization to enhance navigation and analysis of patient records}, journal = {In Proceedings of the 1998 American Medical Informatic Association Annual Fall SymposiumProc AMIA Symp}, year = {1998}, month = {1998///}, pages = {76 - 80}, abstract = {LifeLines provide a general visualization environment for personal histories. We explore its use for clinical patient records. A Java user interface is described, which presents a one-screen overview of a computerized patient record using timelines. Problems, diagnoses, test results or medications can be represented as dots or horizontal lines. Zooming provides more details; line color and thickness illustrate relationships or significance. The visual display acts as a giant menu, giving direct access to the data.}, isbn = {1531-605X}, author = {Plaisant, Catherine and Mushlin,R. and Snyder,A. and Li,J. and Heller,D. and Shneiderman, Ben} } @article {17281, title = {LifeLines: using visualization to enhance navigation and analysis of patient records.}, journal = {Proceedings of the AMIA Symposium}, year = {1998}, month = {1998///}, pages = {76 - 80}, abstract = {LifeLines provide a general visualization environment for personal histories. We explore its use for clinical patient records. A Java user interface is described, which presents a one-screen overview of a computerized patient record using timelines. Problems, diagnoses, test results or medications can be represented as dots or horizontal lines. Zooming provides more details; line color and thickness illustrate relationships or significance. The visual display acts as a giant menu, giving direct access to the data.}, isbn = {1531-605X}, author = {Plaisant, Catherine and Mushlin,R. and Snyder,A. and Li,J. and Heller,D. and Shneiderman, Ben} } @conference {14815, title = {Linger longer: Fine-grain cycle stealing for networks of workstations}, booktitle = {Proceedings of the 1998 ACM/IEEE Conference on Supercomputing (CDROM)}, year = {1998}, month = {1998///}, pages = {1 - 12}, author = {Ryu, K. D and Hollingsworth, Jeffrey K} } @article {14804, title = {Modeling and evaluating design alternatives for an on-line instrumentation system: a case study}, journal = {IEEE Transactions on Software Engineering}, volume = {24}, year = {1998}, month = {1998/06//}, pages = {451 - 470}, abstract = {This paper demonstrates the use of a model-based evaluation approach for instrumentation systems (ISs). The overall objective of this study is to provide early feedback to tool developers regarding IS overhead and performance; such feedback helps developers make appropriate design decisions about alternative system configurations and task scheduling policies. We consider three types of system architectures: network of workstations (NOW), symmetric multiprocessors (SMP), and massively parallel processing (MPP) systems. We develop a Resource OCCupancy (ROCC) model for an on-line IS for an existing tool and parameterize it for an IBM SP-2 platform. This model is simulated to answer several {\textquotedblleft}what if{\textquotedblright} questions regarding two policies to schedule instrumentation data forwarding: collect-and-forward (CF) and batch-and-forward (BF). In addition, this study investigates two alternatives for forwarding the instrumentation data: direct and binary tree forwarding for an MPP system. Simulation results indicate that the BF policy can significantly reduce the overhead and that the tree forwarding configuration exhibits desirable scalability characteristics for MPP systems. Initial measurement-based testing results indicate more than 60 percent reduction in the direct IS overhead when the BF policy was added to Paradyn parallel performance measurement tool}, keywords = {alternative system configurations, Application software, batch-and-forward, collect-and-forward, Computer aided software engineering, design alternatives, design decisions, Feedback, IBM SP-2 platform, Instruments, massively parallel processing, model-based evaluation approach, Monitoring, multiprocessing programs, on-line instrumentation system, Paradyn parallel performance measurement tool, PARALLEL PROCESSING, Real time systems, scalability characteristics, software metrics, software tools, Space technology, symmetric multiprocessors, system architectures, system monitoring, System testing, task scheduling policies, tool developers, tree forwarding configuration, Workstations}, isbn = {0098-5589}, doi = {10.1109/32.689402}, author = {Waheed, A. and Rover, D. T and Hollingsworth, Jeffrey K} } @article {14084, title = {Multiple mechanisms of immune evasion by African trypanosomes}, journal = {Molecular and Biochemical Parasitology}, volume = {91}, year = {1998}, month = {1998/03/01/}, pages = {51 - 66}, abstract = {During infection of a mammalian host, African trypanosomes are in constant contact with the host{\textquoteright}s immune system. These protozoan parasites are infamous for their ability to evade the immune responses by periodically switching their major variant surface glycoprotein (VSG), a phenomenon called antigenic variation. Antigenic variation, however, is likely to be only one of several mechanisms enabling these organisms to thrive in the face of the immune defenses. The ability to grow in high levels of interferon-gamma (IFN-[gamma]) and to avoid complement-mediated destruction may also facilitate the parasite{\textquoteright}s survival. In this review we summarize (i) the activation of trypanosome genes for three different VSGs during antigenic variation, (ii) the secretion of a trypanosome protein that induces host CD8+ T cells to produce IFN-[gamma], and (iii) the evidence for trypansome protein similar to a surface protease of Leishmania that plays a role in resistance to complement-mediated lysis.}, keywords = {Leishmania, Recombinant cloning, T cell, Trypanosomes, VSG genes}, isbn = {0166-6851}, doi = {16/S0166-6851(97)00209-0}, url = {http://www.sciencedirect.com/science/article/pii/S0166685197002090}, author = {Donelson,John E. and Hill,Kent L. and El-Sayed, Najib M.} } @article {14931, title = {A new deterministic parallel sorting algorithm with an experimental evaluation}, journal = {Journal of Experimental Algorithmics (JEA)}, volume = {3}, year = {1998}, month = {1998/09//}, abstract = {We introduce a new deterministic parallel sorting algorithm for distributed memory machines based on the regular sampling approach. The algorithm uses only two rounds of regular all-to-all personalized communication in a scheme that yields very good load balancing with virtually no overhead. Moreover, unlike previous variations, our algorithm efficiently handles the presence of duplicate values without the overhead of tagging each element with a unique identifier. This algorithm was implemented in SPLIT-C and run on a variety of platforms, including the Thinking Machines CM-5, the IBM SP-2-WN, and the Cray Research T3D. We ran our code using widely different benchmarks to examine the dependence of our algorithm on the input distribution. Our experimental results illustrate the efficiency and scalability of our algorithm across different platforms. In fact, the performance compares closely to that of our random sample sort algorithm, which seems to outperform all similar algorithms known to the authors on these platforms. Together, their performance is nearly invariant over the set of input distributions, unlike previous efficient algorithms. However, unlike our randomized sorting algorithm, the performance and memory requirements of our regular sorting algorithm can be deterministically guaranteed.}, keywords = {generalized sorting, integer sorting, Parallel algorithms, parallel performance, sorting by regular sampling}, isbn = {1084-6654}, doi = {10.1145/297096.297128}, url = {http://doi.acm.org/10.1145/297096.297128}, author = {Helman,David R. and JaJa, Joseph F. and Bader,David A.} } @article {15781, title = {Overcoming Instability In Computing The Fundamental Matrix For A Markov Chain}, journal = {SIAM Journal on Matrix Analysis and Applications}, volume = {19}, year = {1998}, month = {1998///}, pages = {534 - 540}, abstract = {We present an algorithm for solving linear systems involving the probability or rate matrix for a Markov chain. It is based on a UL factorization but works only with a submatrix of the factor U. We demonstrate its utility on Erlang-B models as well as more complicated models of a telephone multiplexing system.}, keywords = {decision process, fundamental matrix, Markov chains}, doi = {10.1137/S0895479896301753}, url = {http://link.aip.org/link/?SML/19/534/1}, author = {Heyman,Daniel P. and O{\textquoteright}Leary, Dianne P.} } @article {14934, title = {A Parallel Sorting Algorithm With an Experimental Study}, volume = {UMIACS-TR-95-102}, year = {1998}, month = {1998/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Previous schemes for sorting on general-purpose parallel machineshave had to choose between poor load balancing and irregular communication or multiple rounds of all-to-all personalized communication. In this paper, we introduce a novel variation on sample sort which uses only two rounds of regular all-to-all personalized communication in a scheme that yields very good load balancing with virtually no overhead. This algorithm was implemented in Split-C and run on a variety of platforms, including the Thinking Machines CM-5, the IBM SP-2, and the Cray Research T3D. We ran our code using widely different benchmarks to examine the dependence of our algorithm on the input distribution. Our experimental results are consistent with the theoretical analysis and illustrate the efficiency and scalability of our algorithm across different platforms. In fact, it seems to outperform all similar algorithms known to the authors on these platforms, and its performance is invariant over the set of input distributions unlike previous efficient algorithms. Our results also compare favorably with those reported for the simpler ranking problem posed by the NAS Integer Sorting (IS) Benchmark. (Also cross-referenced as UMIACS-TR-95-102) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/768}, author = {Helman,David R. and Bader,David A. and JaJa, Joseph F.} } @conference {14809, title = {Performance measurement using low perturbation and high precision hardware assists}, booktitle = {, The 19th IEEE Real-Time Systems Symposium, 1998. Proceedings}, year = {1998}, month = {1998/12/02/4}, pages = {379 - 388}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present the design and implementation of MultiKron PCI, a hardware performance monitor that can be plugged into any computer with a free PCI bus slot. The monitor provides a series of high-resolution timers, and the ability to monitor the utilization of the PCI bus. We also demonstrate how the monitor can be integrated with online performance monitoring tools such as the Paradyn parallel performance measurement tools to improve the overhead of key timer operations by a factor of 25. In addition, we present a series of case studies using the MultiKron hardware performance monitor to measure and tune high-performance parallel completing applications. By using the monitor, we were able to find and correct a performance bug in a popular implementation of the MPI message passing library that caused some communication primitives to run at one half their potential speed}, keywords = {Clocks, Computerized monitoring, Counting circuits, Debugging, Hardware, hardware performance monitor, high precision hardware assists, low perturbation, measurement, MPI message passing library, MultiKron hardware performance monitor, MultiKron PCI, NIST, online performance monitoring tools, Paradyn parallel performance measurement tools, PCI bus slot, performance bug, performance evaluation, performance measurement, program debugging, program testing, real-time systems, Runtime, Timing}, isbn = {0-8186-9212-X}, doi = {10.1109/REAL.1998.739771}, author = {Mink, A. and Salamon, W. and Hollingsworth, Jeffrey K and Arunachalam, R.} } @article {14721, title = {PLAN: a packet language for active networks}, journal = {SIGPLAN Not.}, volume = {34}, year = {1998}, month = {1998/09//}, pages = {86 - 93}, abstract = {PLAN (Packet Language for Active Networks) is a new language for programs that form the packets of a programmable network. These programs replace the packet headers (which can be viewed as very rudimentary programs) used in current networks. As such, PLAN programs are lightweight and of restricted functionality. These limitations are mitigated by allowing PLAN code to call node-resident service routines written in other, more powerful languages. This two-level architecture, in which PLAN serves as a scripting or {\textquoteright}glue{\textquoteright} language for more general services, is the primary contribution of this paper. We have successfully applied the PLAN programming environment to implement an IP-free internetwork.PLAN is based on the simply typed lambda calculus and provides a restricted set of primitives and datatypes. PLAN defines a special construct called a chunk used to describe the remote execution of PLAN programs on other nodes. Primitive operations on chunks are used to provide basic data transport in the network and to support layering of protocols. Remote execution can make debugging difficult, so PLAN provides strong static guarantees to the programmer, such as type safety. A more novel property aimed at protecting network availability is a guarantee that PLAN programs use a bounded amount of network resources.}, isbn = {0362-1340}, doi = {10.1145/291251.289431}, url = {http://doi.acm.org/10.1145/291251.289431}, author = {Hicks, Michael W. and Kakkar,Pankaj and Moore,Jonathan T. and Gunter,Carl A. and Nettles,Scott} } @article {14718, title = {PLAN Security System}, year = {1998}, month = {1998/07/14/}, abstract = {Active Networks offer the ability to program the network on a per-router, per-user, or even per-packet basis. Unfortunately, this added programmability compromises the security of the system by allowing a wider range of potential attacks. Any feasible Active Network architecture therefore requires strong security guarantees. Of course, we should like these guarantees to come at the lowest possible price to the flexibility, performance, and usability of the system.The PLAN system is a distributed programming framework we have used to build an Active Network, PLANet [4]. In the PLAN system, code implementing distributed programs is broken into two parts: the PLAN level, and the Service Level. All programs in the PLAN level reside in the messages, or packets, that are sent between the nodes of the system. These programs are written in the Programming Language for Active Networks [6] (or simply, PLAN). PLAN programs serve to "glue" together Service level programs; PLAN may be thought of as a network scripting language. In contrast, Service level programs (or simply, services), reside at each node and are invoked by executing PLAN programs. Services are written in general-purpose languages (in particular, the language that the PLAN interpreter is written in) and may be dynamically loaded. The current Internet (IP and its supporting protocols) allows any user with a network connection to have some basic services. In addition to basic packet delivery provided by IP, basic information services like DNS, finger, and whois, and protocols like HTTP, FTP, TCP, SMTP, and so forth are provided. Similarly, a goal of PLANet is to allow any user of the network to have access to basic services; these services should naturally include some "activeness." This goal implies that some functionality, like packet delivery in the current Internet, should not require authentication; in PLANet, we allow "pure" PLAN programs to run unauthenticated. A PLAN program is considered "pure" if it only makes calls to services considered safe; for example, determining the name of the current host is a safe operation, while updating the host{\textquoteright}s router table is not. Successfully calling unsafe services would require proper authorization. This security policy is stated more formally in the following subsection. }, url = {http://repository.upenn.edu/cis_reports/108}, author = {Hicks, Michael W.} } @article {14719, title = {PLAN Service Programmer{\textquoteright}s Guide}, journal = {University of Pennsylvania}, year = {1998}, month = {1998///}, author = {Hicks, Michael W.} } @article {14742, title = {The PLAN system for building Active Networks}, journal = {University of Pennsylvania (February 27, 1998)}, year = {1998}, month = {1998///}, author = {Hicks, Michael W. and Kakkar,P. and Moore,J. T and Gunter,C. A and Alexander,D. S and Nettles,S.} } @conference {14767, title = {Prediction and Adaptation in Active Harmony}, booktitle = {High-Performance Distributed Computing, International Symposium on}, year = {1998}, month = {1998///}, pages = {180 - 180}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {We describe the design and early functionality of the Active Harmony global resource management system. Harmony is an infrastructure designed to efficiently execute parallel applications in large-scale, dynamic environments.Harmony differs from other projects with similar goals in that the system automatically adapts ongoing computations to changing conditions through online reconfiguration. This reconfiguration can consist of system-directed migration of work at several different levels, or automatic application adaptation through the use of tuning options exported by Harmony-aware applications.We describe early experience with work migration at the level of procedures, processes and lightweight threads.}, keywords = {adaptation, resource management., scheduling}, doi = {http://doi.ieeecomputersociety.org/10.1109/HPDC.1998.709971}, author = {Hollingsworth, Jeffrey K and Keleher, Peter J.} } @article {14936, title = {A Randomized Parallel Sorting Algorithm with an Experimental Study}, journal = {Journal of Parallel and Distributed Computing}, volume = {52}, year = {1998}, month = {1998/07/10/}, pages = {1 - 23}, abstract = {Previous schemes for sorting on general-purpose parallel machines have had to choose between poor load balancing and irregular communication or multiple rounds of all-to-all personalized communication. In this paper, we introduce a novel variation on sample sort which uses only two rounds of regular all-to-all personalized communication in a scheme that yields very good load balancing with virtually no overhead. Moreover, unlike previous variations, our algorithm efficiently handles the presence of duplicate values without the overhead of tagging each element with a unique identifier. This algorithm was implemented in Split-C and run on a variety of platforms, including the Thinking Machines CM-5, the IBM SP-2, and the Cray Research T3D. We ran our code using widely different benchmarks to examine the dependence of our algorithm on the input distribution. Our experimental results illustrate the efficiency and scalability of our algorithm across different platforms. In fact, it seems to outperform all similar algorithms known to the authors on these platforms, and its performance is invariant over the set of input distributions unlike previous efficient algorithms. Our results also compare favorably with those reported for the simpler ranking problem posed by the NAS Integer Sorting (IS) Benchmark.}, keywords = {generalized sorting, integer sorting, sample sort, parallel performance, Parallel algorithms}, isbn = {0743-7315}, doi = {10.1006/jpdc.1998.1462}, url = {http://www.sciencedirect.com/science/article/pii/S0743731598914629}, author = {Helman,David R. and Bader,David A. and JaJa, Joseph F.} } @conference {14656, title = {A study of large object spaces}, booktitle = {Proceedings of the 1st international symposium on Memory management}, series = {ISMM {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {138 - 145}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper examines the design space for copying garbage collectors (GCs) in which "large objects" are managed in a separate, non-copy-collected space. We focus on two main issues:1. how to set the policy for classifying objects as "large"2. how to manage the large object spaceWe explore these issues experimentally using the Oscar GC testbed. In particular, we vary the threshold size of large objects and also whether the objects may contain pointers. Furthermore, we compare the performance of treadmill collection to that of mark-and-sweep collection for managing the large object space.We find that for some heaps there is a minimum cutoff size below which adding objects to the large object space does not result in a performance improvement, while for others no such cutoff exists. In general, including pointer-containing objects in the large object space seems beneficial. Finally, the exact method used to collect the large object space does not significantly influence overall performance.}, isbn = {1-58113-114-3}, doi = {10.1145/286860.286875}, url = {http://doi.acm.org/10.1145/286860.286875}, author = {Hicks, Michael W. and Hornof,Luke and Moore,Jonathan T. and Nettles,Scott M.} } @article {12079, title = {The SwitchWare active network architecture}, journal = {IEEE Network}, volume = {12}, year = {1998}, month = {1998/06//May}, pages = {29 - 36}, abstract = {Active networks must balance the flexibility of a programmable network infrastructure against the safety and security requirements inherent in sharing that infrastructure. Furthermore, this balance must be achieved while maintaining the usability of the network. The SwitchWare active network architecture is a novel approach to achieving this balance using three layers: active packets, which contain mobile programs that replace traditional packets; active extensions, which provide services on the network elements and can be dynamically loaded; and a secure active router infrastructure, which forms a high-integrity base on which the security of the other layers depends. In addition to integrity checking and cryptography-based authentication, security in our architecture depends heavily on verification techniques from programming languages, such as strong type checking}, keywords = {active extensions, active packets, Authentication, Computer languages, Computer networks, cryptography, cryptography-based authentication, high-integrity base, integrity checking, IP networks, LAN interconnection, mobile programs, network operating systems, packet switching, programmable network infrastructure, programming languages, Protocols, Safety, safety requirements, scalability, secure active router infrastructure, Security, security requirements, services, strong type checking, Switches, SwitchWare active network architecture, telecommunication network routing, Tin, usability, verification techniques}, isbn = {0890-8044}, doi = {10.1109/65.690959}, author = {Alexander,D. S and Arbaugh, William A. and Hicks, Michael W. and Kakkar,P. and Keromytis,A. D and Moore,J. T and Gunter,C. A and Nettles,S. M and Smith,J. M} } @article {14745, title = {The switchware active network implementation}, journal = {The ML Workshop, International Conference on Functional Programming (ICFP)}, year = {1998}, month = {1998///}, author = {Alexander,D. S and Hicks, Michael W. and Kakkar,P. and Keromytis,A. D and Shaw,M. and Moore,J. T and Gunter,C. A and Jim,T. and Nettles,S. M and Smith,J. M} } @inbook {13718, title = {A Thematic Hierarchy for Efficient Generation from Lexical-Conceptual Structure}, booktitle = {Machine Translation and the Information SoupMachine Translation and the Information Soup}, series = {Lecture Notes in Computer Science}, volume = {1529}, year = {1998}, month = {1998///}, pages = {333 - 343}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper describes an implemented algorithm for syntactic realization of a target-language sentence from an interlingual representation called Lexical Conceptual Structure (LCS). We provide a mapping between LCS thematic roles and Abstract Meaning Representation (AMR) relations; these relations serve as input to an off-the-shelf generator (Nitrogen). There are two contributions of this work: (1) the development of a thematic hierarchy that provides ordering information for realization of arguments in their surface positions; (2) the provision of a diagnostic tool for detecting inconsistencies in an existing online LCS-based lexicon that allows us to enhance principles for thematic-role assignment.}, isbn = {978-3-540-65259-5}, url = {http://dx.doi.org/10.1007/3-540-49478-2_30}, author = {Dorr, Bonnie J and Habash,Nizar and Traum,David}, editor = {Farwell,David and Gerber,Laurie and Hovy,Eduard} } @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} } @article {14751, title = {Types and intermediate representations}, journal = {Technical Reports (CIS)}, year = {1998}, month = {1998///}, pages = {796 - 796}, author = {Hicks, Michael W.} } @conference {16189, title = {Visualizing medical records with LifeLines}, booktitle = {CHI 98 conference summary on Human factors in computing systems}, series = {CHI {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {28 - 29}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {healthcare, History, medical record, overview, timeline, Visualization}, isbn = {1-58113-028-7}, doi = {10.1145/286498.286513}, url = {http://doi.acm.org/10.1145/286498.286513}, author = {Plaisant, Catherine and Heller,Daniel and Li,Jia and Shneiderman, Ben and Mushlin,Rich and Karat,John} } @article {17679, title = {Accuracy and Stability of Numerical Algorithms}, journal = {SIAM Review}, volume = {39}, year = {1997}, month = {1997///}, pages = {164 - 165}, author = {Higham,N. J and Stewart, G.W.} } @conference {13492, title = {ADistributed Management System for Testing Document Image Database Analysis Algorithms}, booktitle = {ICDAR}, year = {1997}, month = {1997///}, pages = {989 - 995}, author = {David Doermann and Sauvola,J. and Haapakoski,S. and Kauniskangas,H. and Seppanen,T. and Pietikainen,M.} } @conference {17070, title = {Designing interactive multimedia (panel)}, booktitle = {Proceedings of the fifth ACM international conference on Multimedia}, series = {MULTIMEDIA {\textquoteright}97}, year = {1997}, month = {1997///}, pages = {215 - 218}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-991-2}, doi = {10.1145/266180.266370}, url = {http://doi.acm.org/10.1145/266180.266370}, author = {Scarlatos,Lori L. and Darken,Rudolph P. and Harada,Komei and Heeter,Carrie and Muller,Richard and Shneiderman, Ben} } @article {14571, title = {Hardness of flip-cut problems from optical mapping}, journal = {Journal of Computational Biology}, volume = {4}, year = {1997}, month = {1997///}, pages = {119 - 125}, author = {DAN{\v C}{\'I}K,V. and Hannenhalli, Sridhar and Muthukrishnan,S.} } @conference {14621, title = {Hardness of flip-cut problems from optical mapping [DNA molecules application]}, booktitle = {Compression and Complexity of Sequences 1997. Proceedings}, year = {1997}, month = {1997/06/11/13}, pages = {275 - 284}, publisher = {IEEE}, organization = {IEEE}, abstract = {Optical mapping is a new technology for constructing restriction maps. Associated computational problems include aligning multiple partial restriction maps into a single {\textquotedblleft}consensus{\textquotedblright} restriction map, and determining the correct orientation of each molecule, which was formalized as the exclusive binary flip cut (EBFC) problem by Muthukrishnan and Parida (see Proc. of the First ACM Conference on Computational Molecular Biology (RECOMB), Santa Fe, p.209-19, 1997). Here, the authors prove that the EBFC problem, as well as a number of its variants, are NP-complete. They also identify another problem formalized as binary shift cut (BSC) problem motivated by the fact that there might be missing fragments at the beginnings and/or the ends of the molecules, and prove it to be NP-complete. Therefore, they do not have efficient, that is, polynomial time solutions unless P=NP}, keywords = {binary shift cut, Biochemistry, Bioinformatics, biological techniques, Biology, biomedical optical imaging, combinatorial mathematics, combinatorial problem, computational complexity, computational problems, DNA, DNA molecule, exclusive binary flip cut, flip-cut problem hardness, Genetic engineering, Genomics, MATHEMATICS, molecular biology, molecular biophysics, molecule orientation, multiple partial restriction maps, NP-complete problem, optical mapping, polynomial time solutions, Polynomials, sequences}, isbn = {0-8186-8132-2}, doi = {10.1109/SEQUEN.1997.666922}, author = {Dancik,V. and Hannenhalli, Sridhar and Muthukrishnan,S.} } @conference {12217, title = {KidPad: a design collaboration between children, technologists, and educators}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, year = {1997}, month = {1997///}, pages = {463 - 470}, author = {Druin, Allison and Stewart,J. and Proft,D. and Bederson, Benjamin B. and Hollan,J.} } @article {14627, title = {Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model}, journal = {Journal of Computational Biology}, volume = {4}, year = {1997}, month = {1997/01//}, pages = {275 - 296}, abstract = {We consider the problem of determining the three-dimensional folding of a protein given its one-dimensional amino acid sequence. We use the HP model for protein folding proposed by Dill (1985), which models protein as a chain of amino acid residues that are either hydrophobic or polar, and hydrophobic interactions are the dominant initial driving force for the protein folding. Hart and Istrail (1996a) gave approximation algorithms for folding proteins on the cubic lattice under the HP model. In this paper, we examine the choice of a lattice by considering its algorithmic and geometric implications and argue that the triangular lattice is a more reasonable choice. We present a set of folding rules for a triangular lattice and analyze the approximation ratio they achieve. In addition, we introduce a generalization of the HP model to account for residues having different levels of hydrophobicity. After describing the biological foundation for this generalization, we show that in the new model we are able to achieve similar constant factor approximation guarantees on the triangular lattice as were achieved in the standard HP model. While the structures derived from our folding rules are probably still far from biological reality, we hope that having a set of folding rules with different properties will yield more interesting folds when combined.}, isbn = {1066-5277, 1557-8666}, doi = {10.1089/cmb.1997.4.275}, url = {http://www.liebertonline.com/doi/abs/10.1089/cmb.1997.4.275}, author = {Agarwala,Richa and Batzoglou,Serafim and Dan{\v c}{\'\i}K,Vlado and Decatur,Scott E. and Hannenhalli, Sridhar and Farach,Martin and Muthukrishnan,S. and Skiena,Steven} } @conference {14813, title = {MDL: a language and compiler for dynamic program instrumentation}, booktitle = {, 1997 International Conference on Parallel Architectures and Compilation Techniques., 1997. Proceedings}, year = {1997}, month = {1997/11/10/14}, pages = {201 - 212}, publisher = {IEEE}, organization = {IEEE}, abstract = {We use a form of dynamic code generation, called dynamic instrumentation, to collect data about the execution of an application program. Dynamic instrumentation allows us to instrument running programs to collect performance and other types of information. The instrumentation code is generated incrementally and can be inserted and removed at any time. Our instrumentation currently runs on the SPARC, PA-RISC, Power 2, Alpha, and x86 architectures. Specification of what data to collect are written in a specialized language called the Metric Description Language, that is part of the Paradyn Parallel Performance Tools. This language allows platform independent descriptions of how to collect performance data. It also provides a concise way to specify, how to constrain performance data to particular resources such as modules, procedures, nodes, files, or message channels (or combinations of these resources). We also describe the details of how we weave instrumentation into a running program}, keywords = {Alpha architecture, application program, application program interfaces, Application software, compiler generators, Computer science, dynamic code generation, Dynamic compiler, dynamic program instrumentation, Educational institutions, files, instrumentation code, Instruments, MDL, measurement, message channels, Message passing, Metric Description Language, modules, nodes, Operating systems, optimising compilers, PA-RISC, Paradyn Parallel Performance Tools, Parallel architectures, parallel programming, performance data, platform independent descriptions, Power 2 architecture, Power generation, procedures, program debugging, Program processors, running programs, Runtime, software metrics, SPARC, Specification languages, x86 architecture}, isbn = {0-8186-8090-3}, doi = {10.1109/PACT.1997.644016}, author = {Hollingsworth, Jeffrey K and Niam, O. and Miller, B. P and Zhichen Xu and Goncalves,M. J.R and Ling Zheng} } @article {14741, title = {The measured cost of copying garbage collection mechanisms}, journal = {SIGPLAN Not.}, volume = {32}, year = {1997}, month = {1997/08//}, pages = {292 - 305}, abstract = {We examine the costs and benefits of a variety of copying garbage collection (GC) mechanisms across multiple architectures and programming languages. Our study covers both low-level object representation and copying issues as well as the mechanisms needed to support more advanced techniques such as generational collection, large object spaces, and type segregated areas.Our experiments are made possible by a novel performance analysis tool, Oscar. Oscar allows us to capture snapshots of programming language heaps that may then be used to replay garbage collections. The replay program is self-contained and written in C, which makes it easy to port to other architectures and to analyze with standard performance analysis tools. Furthermore, it is possible to study additional programming languages simply by instrumenting existing implementations to capture heap snapshots.In general, we found that careful implementation of GC mechanisms can have a significant benefit. For a simple collector, we measured improvements of as much as 95\%. We then found that while the addition of advanced features can have a sizeable overhead (up to 15\%), the net benefit is quite positive, resulting in additional gains of up to 42\%. We also found that results varied depending upon the platform and language. Machine characteristics such as cache arrangements, instruction set (RISC/CISC), and register pool were important. For different languages, average object size seemed to be most important.The results of our experiments demonstrate the usefulness of a tool like Oscar for studying GC performance. Without much overhead, we can easily identify areas where programming language implementors could collaborate with GC implementors to improve GC performance.}, isbn = {0362-1340}, doi = {10.1145/258949.258976}, url = {http://doi.acm.org/10.1145/258949.258976}, author = {Hicks, Michael W. and Moore,Jonathan T. and Nettles,Scott M.} } @article {17954, title = {Multiresolution surface modeling}, journal = {SIGGRAPH 1997 Course Notes}, year = {1997}, month = {1997///}, author = {Heckbert,P. and Rossignac,J. and Hoppe,H. and Schroeder,W. and Soucy,M. and Varshney, Amitabh} } @inbook {15795, title = {Regularization algorithms based on total least squares}, booktitle = {Recent advances in total least squares techniques and errors-in-variables modeling (Leuven, 1996)Recent advances in total least squares techniques and errors-in-variables modeling (Leuven, 1996)}, year = {1997}, month = {1997///}, pages = {127 - 137}, publisher = {SIAM}, organization = {SIAM}, address = {Philadelphia, PA}, author = {Hansen,Per Christian and O{\textquoteright}Leary, Dianne P.} } @article {15796, title = {Regularization by Truncated Total Least Squares}, journal = {SIAM Journal on Scientific Computing}, volume = {18}, year = {1997}, month = {1997///}, pages = {1223 - 1241}, abstract = {The total least squares (TLS) method is a successful method for noise reduction in linear least squares problems in a number of applications. The TLS method is suited to problems in which both the coefficient matrix and the right-hand side are not precisely known. This paper focuses on the use of TLS for solving problems with very ill-conditioned coefficient matrices whose singular values decay gradually (so-called discrete ill-posed problems), where some regularization is necessary to stabilize the computed solution. We filter the solution by truncating the small singular values of the TLS matrix. We express our results in terms of the singular value decomposition (SVD) of the coefficient matrix rather than the augmented matrix. This leads to insight into the filtering properties of the truncated TLS method as compared to regularized least squares solutions. In addition, we propose and test an iterative algorithm based on Lanczos bidiagonalization for computing truncated TLS solutions.}, keywords = {bidiagonalization, discrete ill-posed problems, regularization, total least squares}, doi = {10.1137/S1064827594263837}, url = {http://link.aip.org/link/?SCE/18/1223/1}, author = {Fierro,R. D. and Golub, G. H and Hansen,P. C. and O{\textquoteright}Leary, Dianne P.} } @article {17879, title = {Run-time and compiler support for programming in adaptive parallel environments}, journal = {Scientific Programming}, volume = {6}, year = {1997}, month = {1997///}, pages = {215 - 227}, author = {Edjlali,G. and Agrawal,G. and Sussman, Alan and Humphries,J. and Saltz, J.} } @article {14655, title = {A Service Layer Routing Protocol for PLAN}, journal = {PLAN documentation, September}, year = {1997}, month = {1997///}, author = {Moore,J. T and Hicks, Michael W.} } @article {14794, title = {Using content-derived names for configuration management}, journal = {ACM SIGSOFT Software Engineering Notes}, volume = {22}, year = {1997}, month = {1997///}, pages = {104 - 109}, author = {Hollingsworth, Jeffrey K and Miller, E. L} } @conference {17846, title = {The virtual microscope.}, booktitle = {Proceedings of the AMIA Annual Fall Symposium}, year = {1997}, month = {1997///}, pages = {449 - 449}, author = {Ferreira,R. and Moon,B. and Humphries,J. and Sussman, Alan and Saltz, J. and Miller,R. and Demarzo,A.} } @article {18305, title = {Visual surveillance of human activity}, journal = {Computer Vision{\textemdash}ACCV{\textquoteright}98}, year = {1997}, month = {1997///}, pages = {267 - 274}, author = {Davis, Larry S. and Fejes,S. and Harwood,D. and Yacoob,Yaser and Hariatoglu,I. and Black,M.} } @article {12177, title = {A zooming web browser}, journal = {Human Factors in Web Development}, year = {1997}, month = {1997///}, author = {Bederson, Benjamin B. and Hollan,J.D. and Stewart,J. and Rogers,D. and Druin, Allison and Vick,D. and Ring,L. and Grose,E. and Forsythe,C.} } @conference {14797, title = {An adaptive cost system for parallel program instrumentation}, booktitle = {Euro-Par{\textquoteright}96 Parallel Processing}, year = {1996}, month = {1996///}, pages = {88 - 97}, author = {Hollingsworth, Jeffrey K and Miller, B.} } @article {16615, title = {Computational studies of synaptic alterations in Alzheimer{\textquoteright}s disease}, journal = {Neural modeling of brain and cognitive disorders}, year = {1996}, month = {1996///}, pages = {63 - 87}, author = {Ruppin,E. and Horn,D. and Levy,N. and Reggia, James A.} } @conference {18322, title = {Computing 3-D head orientation from a monocular image sequence}, booktitle = {Automatic Face and Gesture Recognition, 1996., Proceedings of the Second International Conference on}, year = {1996}, month = {1996/10//}, pages = {242 - 247}, abstract = {An approach for estimating 3D head orientation in a monocular image sequence is proposed. The approach employs recently developed image-based parameterized tracking for face and face features to locate the area in which a sub-pixel parameterized shape estimation of the eye{\textquoteright}s boundary is performed. This involves tracking of five points (four at the eye corners and the fifth is the lip of the nose). The authors describe an approach that relies on the coarse structure of the face to compute orientation relative to the camera plane. Our approach employs projective invariance of the cross-ratios of the eye corners and anthropometric statistics to estimate the head yaw, roll and pitch. Analytical and experimental results are reported}, keywords = {3D head orientation computation, anthropometric statistics, camera plane, coarse structure, eye, eye boundary, eye corners, face features, face recognition, Feature extraction, head pitch, head roll, head yaw, Image sequences, image-based parameterized tracking, monocular image sequence, projective cross-ratio invariance, sub-pixel parameterized shape estimation, tracking}, doi = {10.1109/AFGR.1996.557271}, author = {Horprasert,T. and Yacoob,Yaser and Davis, Larry S.} } @article {17964, title = {Controlled topology simplification}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {2}, year = {1996}, month = {1996/06//}, pages = {171 - 184}, abstract = {We present a simple, robust, and practical method for object simplification for applications where gradual elimination of high frequency details is desired. This is accomplished by converting an object into multi resolution volume rasters using a controlled filtering and sampling technique. A multiresolution triangle mesh hierarchy can then be generated by applying the Marching Cubes algorithm. We further propose an adaptive surface generation algorithm to reduce the number of triangles generated by the standard Marching Cubes. Our method simplifies the topology of objects in a controlled fashion. In addition, at each level of detail, multilayered meshes can be used for an efficient antialiased rendering}, keywords = {(computer, algorithm;adaptive, algorithm;controlled, antialiased, Cubes, Cubes;antialiasing;computational, details;multi, filtering;controlled, Frequency, generation, geometry;rendering, graphics);topology;, hierarchy;object, Marching, mesh, meshes;multiresolution, rasters;multilayered, rendering;high, resolution, simplification;efficient, simplification;sampling, surface, technique;standard, Topology, triangle, volume}, isbn = {1077-2626}, doi = {10.1109/2945.506228}, author = {He,Taosong and Hong,Lichan and Varshney, Amitabh and Wang,S.W.} } @inbook {14610, title = {Fast sorting by reversal}, booktitle = {Combinatorial Pattern MatchingCombinatorial Pattern Matching}, series = {Lecture Notes in Computer Science}, volume = {1075}, year = {1996}, month = {1996///}, pages = {168 - 185}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Analysis of genomes evolving by inversions leads to a combinatorial problem of sorting by reversals studied in detail recently. Following a series of work recently, Hannenhalli and Pevzner developed the first polynomial algorithm for the problem of sorting signed permutations by reversals and proposed an O(n 4 ) implementation of the algorithm. In this paper we exploit a few combinatorial properties of the cycle graph of a permutation and propose an O(n 2 (n)) implementation of the algorithm where is the inverse Ackerman function. Besides making this algorithm practical, our technique improves implementations of the other rearrangement distance problems.}, isbn = {978-3-540-61258-2}, url = {http://dx.doi.org/10.1007/3-540-61258-0_14}, author = {Berman,Piotr and Hannenhalli, Sridhar}, editor = {Hirschberg,Dan and Myers,Gene} } @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} } @conference {13924, title = {Local tools: an alternative to tool palettes}, booktitle = {Proceedings of the 9th annual ACM symposium on User interface software and technology}, year = {1996}, month = {1996///}, pages = {169 - 170}, author = {Bederson, Benjamin B. and Hollan,J.D. and Druin, Allison and Stewart,J. and Rogers,D. and Proft,D.} } @conference {14787, title = {Modeling, Evaluation, and Testing of Paradyn Instrumentation System}, booktitle = {Proceedings of the 1996 ACM/IEEE Conference on Supercomputing, 1996}, year = {1996}, month = {1996///}, pages = {18 - 18}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper presents a case study of modeling, evaluating, and testing the data collection services (called an instrumentation system) of the Paradyn parallel performance measurement tool using well-known performance evaluation and experiment design techniques. The overall objective of the study is to use modeling- and simulation-based evaluation to provide feedback to the tool developers to help them choose system configurations and task scheduling policies that can significantly reduce the data collection overheads. We develop and parameterize a resource occupancy model for the Paradyn instrumentation system (IS) for an IBM SP-2 platform. This model is parameterized with a measurement-based workload characterization and subsequently used to answer several "what if" questions regarding configuration options and two policies to schedule instrumentation system tasks: collect-and-forward (CF) and batch-and-forward (BF) policies. Simulation results indicate that the BF policy can significantly reduce the overheads. Based on this feedback, the BF policy was implemented in the Paradyn IS as an option to manage the data collection. Measurement-based testing results obtained from this enhanced version of the Paradyn IS are reported in this paper and indicate more than 60\% reduction in the direct IS overheads when the BF policy is used.}, keywords = {Distributed control, Feedback, High performance computing, Instruments, Monitoring, Real time systems, Software measurement, Software systems, Software testing, System testing}, isbn = {0-89791-854-1}, doi = {10.1109/SUPERC.1996.183524}, author = {Waheed, A. and Rover, D. T and Hollingsworth, Jeffrey K} } @article {16548, title = {A neural model of positive schizophrenic symptoms}, journal = {Schizophrenia Bulletin}, volume = {22}, year = {1996}, month = {1996///}, pages = {105 - 123}, author = {Ruppin,E. and Reggia, James A. and Horn,D.} } @conference {14776, title = {An online computation of critical path profiling}, booktitle = {Proceedings of the SIGMETRICS symposium on Parallel and distributed tools}, year = {1996}, month = {1996///}, pages = {11 - 20}, author = {Hollingsworth, Jeffrey K} } @article {15007, title = {Parallel algorithms for image enhancement and segmentation by region growing, with an experimental study}, journal = {The Journal of Supercomputing}, volume = {10}, year = {1996}, month = {1996///}, pages = {141 - 168}, abstract = {This paper presents efficient and portable implementations of a powerful image enhancement process, the Symmetric Neighborhood Filter (SNF), and an image segmentation technique that makes use of the SNF and a variant of the conventional connected components algorithm which we call delta-Connected Components. We use efficient techniques for distributing and coalescing data as well as efficient combinations of task and data parallelism. The image segmentation algorithm makes use of an efficient connected components algorithm based on a novel approach for parallel merging. The algorithms have been coded in Split-C and run on a variety of platforms, including the Thinking Machines CM-5, IBM SP-1 and SP-2, Cray Research T3D, Meiko Scientific CS-2, Intel Paragon, and workstation clusters. Our experimental results are consistent with the theoretical analysis (and provide the best known execution times for segmentation, even when compared with machine-specific implementations). Our test data include difficult images from the Landsat Thematic Mapper (TM) satellite data.}, doi = {10.1007/BF00130707}, author = {Bader, D.A. and JaJa, Joseph F. and Harwood,D. and Davis, Larry S.} } @conference {15010, title = {Parallel algorithms for personalized communication and sorting with an experimental study (extended abstract)}, booktitle = {Proceedings of the eighth annual ACM symposium on Parallel algorithms and architectures}, series = {SPAA {\textquoteright}96}, year = {1996}, month = {1996///}, pages = {211 - 222}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-809-6}, doi = {10.1145/237502.237558}, url = {http://doi.acm.org/10.1145/237502.237558}, author = {Helman,David R. and Bader,David A. and JaJa, Joseph F.} } @article {16564, title = {Pathogenesis of schizophrenic delusions and hallucinations: a neural model}, journal = {Schizophrenia bulletin}, volume = {22}, year = {1996}, month = {1996///}, pages = {105 - 105}, author = {Ruppin,E. and Reggia, James A. and Horn,D.} } @article {14633, title = {Polynomial-time algorithm for computing translocation distance between genomes}, journal = {Discrete Applied Mathematics}, volume = {71}, year = {1996}, month = {1996/12/05/}, pages = {137 - 151}, abstract = {With the advent of large-scale DNA physical mapping and sequencing, studies of genome rearrangements are becoming increasingly important in evolutionary molecular biology. From a computational perspective, the study of evolution based on rearrangements leads to a rearrangement distance problem, i.e., computing the minimum number of rearrangement events required to transform one genome into another. Different types of rearrangement events give rise to a spectrum of interesting combinatorial problems. The complexity of most of these problems is unknown. Multichromosomal genomes frequently evolve by a rearrangement event called translocation which exchanges genetic material between different chromosomes. In this paper we study the translocation distance problem, modeling the evolution of genomes evolving by translocations. The translocation distance problem was recently studied for the first time by Kececioglu and Ravi, who gave a 2-approximation algorithm for computing translocation distance. In this paper we prove a duality theorem leading to a polynomial time algorithm for computing translocation distance for the case when the orientations of the genes are known. This leads to an algorithm generating a most parsimonious (shortest) scenario, transforming one genome into another by translocations.}, isbn = {0166-218X}, doi = {10.1016/S0166-218X(96)00061-3}, url = {http://www.sciencedirect.com/science/article/pii/S0166218X96000613}, author = {Hannenhalli, Sridhar} } @article {14568, title = {Positional sequencing by hybridization}, journal = {Computer applications in the biosciences : CABIOS}, volume = {12}, year = {1996}, month = {1996/02/01/}, pages = {19 - 24}, abstract = {Sequencing by hybridization (SBH) is a promising alternative to the classical DNA sequencing approaches. However, the resolving power of SBH is rather low: with 64kb sequencing chips, unknown DNA fragments only as long as 200 bp can be reconstructed in a single SBH experiment. To improve the resolving power of SBH, positional SBH (PSBH) has recently been suggested; this allows (with additional experimental work) approximate positions of every l-tuple in a target DNA fragment to be measured. We study the positional Eulerian path problem motivated by PSBH. The input to the positional eulerian path problem is an Eulerian graph G( V, E) in which every edge has an associated range of integers and the problem is to find an Eulerian path el, {\textellipsis}, e|E| in G such that the range of ei, contains i. We show that the positional Eulerian path problem is NP-complete even when the maximum out-degree (in-degree) of any vertex in the graph is 2. On a positive note we present polynomial algorithms to solve a special case of PSBH (bounded PSBH), where the range of the allowed positions for any edge is bounded by a constant (it corresponds to accurate experimental measurements of positions in PSBH). Moreover, if the positions of every l-tuple in an unknown DNA fragment of length n are measured with O(log n) error, then our algorithm runs in polynomial time. We also present an estimate of the resolving power of PSBH for a more realistic case when positions are measured with Θ(n) error.}, doi = {10.1093/bioinformatics/12.1.19}, url = {http://bioinformatics.oxfordjournals.org/content/12/1/19.abstract}, author = {Hannenhalli, Sridhar and Feldman,William and Lewis,Herbert F. and Skiena,Steven S. and Pevzner,Pavel A.} } @article {15017, title = {Practical parallel algorithms for personalized communication and integer sorting}, journal = {Journal of Experimental Algorithmics (JEA)}, volume = {1}, year = {1996}, month = {1996/01//}, abstract = {A fundamental challenge for parallel computing is to obtain high-level, architecture independent, algorithms which efficiently execute on general-purpose parallel machines. With the emergence of message passing standards such as MPI, it has become easier to design efficient and portable parallel algorithms by making use of these communication primitives. While existing primitives allow an assortment of collective communication routines, they do not handle an important communication event when most or all processors have non-uniformly sized personalized messages to exchange with each other. We focus in this paper on the h-relation personalized communication whose efficient implementation will allow high performance implementations of a large class of algorithms. While most previous h-relation algorithms use randomization, this paper presents a new deterministic approach for h-relation personalized communication with asymptotically optimal complexity for h>p2. As an application, we present an efficient algorithm for stable integer sorting. The algorithms presented in this paper have been coded in Split-C and run on a variety of platforms, including the Thinking Machines CM-5, IBM SP-1 and SP-2, Cray Research T3D, Meiko Scientific CS-2, and the Intel Paragon. Our experimental results are consistent with the theoretical analysis and illustrate the scalability and efficiency of our algorithms across different platforms. In fact, they seem to outperform all similar algorithms known to the authors on these platforms.}, isbn = {1084-6654}, doi = {10.1145/235141.235148}, url = {http://doi.acm.org/10.1145/235141.235148}, author = {Bader,David A. and Helman,David R. and JaJa, Joseph F.} } @inbook {13627, title = {Quantitative Measurement of the Performance of Raster-to-vector Conversion Algorithms}, booktitle = {Graphics Recognition: Methods and ApplicationsGraphics Recognition: Methods and Applications}, year = {1996}, month = {1996///}, pages = {57 - 68}, publisher = {Springer}, organization = {Springer}, author = {Hori,O. and David Doermann} } @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 {13656, title = {Table-Form Structure Analysis Based on Box-Driven Reasoning}, journal = {IEICE TRANSACTIONS on Information and Systems}, volume = {E79-D}, year = {1996}, month = {1996/05/20/}, pages = {542 - 547}, abstract = {Table-form document structure analysis is an important problem in the document processing domain. This paper presents a new method called Box-Driven Reasoning (BDR) to robustly analyze the structure of table-form documents that include touching characters and broken lines. Real documents are copied repeatedly and overlaid with printed data, resulting in characters that touch cells and lines that are broken. Most previous methods employ a line-oriented approach, but touching characters and broken lines make the procedure fail at an early stage. BDR deals with regions directly in contrast with other previous methods and a reduced resolution image is introduced to supplement information deteriorated by noise. Experimental tests show that BDR reliably recognizes cells and strings in document images with touching characters and broken lines.}, isbn = {, 0916-8532}, url = {http://search.ieice.org/bin/summary.php?id=e79-d_5_542}, author = {Hori,Osamu and David Doermann} } @conference {14643, title = {To cut{\textellipsis} or not to cut (applications of comparative physical maps in molecular evolution)}, booktitle = {Proceedings of the seventh annual ACM-SIAM symposium on Discrete algorithms}, series = {SODA {\textquoteright}96}, year = {1996}, month = {1996///}, pages = {304 - 313}, publisher = {Society for Industrial and Applied Mathematics}, organization = {Society for Industrial and Applied Mathematics}, address = {Philadelphia, PA, USA}, isbn = {0-89871-366-8}, url = {http://dl.acm.org/citation.cfm?id=313852.314077}, author = {Hannenhalli, Sridhar and Pevzner,Pavel} } @conference {14796, title = {Tuning the performance of I/O-intensive parallel applications}, booktitle = {Proceedings of the fourth workshop on I/O in parallel and distributed systems: part of the federated computing research conference}, year = {1996}, month = {1996///}, pages = {15 - 27}, author = {Acharya, A. and Uysal, M. and Bennett, R. and Mendelson, A. and Beynon, M. and Hollingsworth, Jeffrey K and Saltz, J. and Sussman, Alan} } @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} } @article {14094, title = {Crystallization and preliminary X-ray investigation of the recombinant Trypanosoma brucei rhodesiense calmodulin}, journal = {Proteins: Structure, Function, and Bioinformatics}, volume = {21}, year = {1995}, month = {1995///}, pages = {354 - 357}, author = {El-Sayed, Najib M. and Patton,C. L and Harkins,P. C and Fox,R. O and Anderson,K.} } @article {17091, title = {Dissertations}, journal = {ACM SIGCHI Bulletin}, volume = {27}, year = {1995}, month = {1995/01//}, pages = {73 - 75}, abstract = {The following are citations selected by title and abstract as being related to Computer-Human Interaction, resulting from a computer search, using Dialog Information Services, of the Dissertation Abstracts Online database produced by University Microfilms International (UMI). Included are UMI order number, title, author, degree, year, institution; number of pages, Dissertation Abstracts International (DAI) subject category chosen by the author, and abstract. Unless otherwise specified, paper or microform copies of dissertations may be ordered from University Microfilms International, Dissertation Copies, Post Office Box 1764, Ann Arbor, MI 48106; telephone for U.S. (except Michigan, Hawaii, Alaska): 1-800-521-3042, for Canada: 1-800-343-5299. Price lists and other ordering and shipping information are in the introduction to the published DAI. An alternate source for copies is sometimes provided. Dissertation titles and abstracts contained here are published with permission of University Microfilms International, publishers of Dissertation Abstracts International (copyright by University Microfilms International), and may not be reproduced without their prior permission.}, isbn = {0736-6906}, doi = {10.1145/202642.570129}, url = {http://doi.acm.org/10.1145/202642.570129}, editor = {Humphrey,Susanne M. and Shneiderman, Ben} } @article {14958, title = {Efficient image processing algorithms on the scan line array processor}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {17}, year = {1995}, month = {1995/01//}, pages = {47 - 56}, abstract = {Develops efficient algorithms for low and intermediate level image processing on the scan line array processor, a SIMD machine consisting of a linear array of cells that processes images in a scan line fashion. For low level processing, the authors present algorithms for block DFT, block DCT, convolution, template matching, shrinking, and expanding which run in real-time. By real-time, the authors mean that, if the required processing is based on neighborhoods of size m times;m, then the output lines are generated at a rate of O(m) operations per line and a latency of O(m) scan lines, which is the best that can be achieved on this model. The authors also develop an algorithm for median filtering which runs in almost real-time at a cost of O(m log m) time per scan line and a latency of [m/2] scan lines. For intermediate level processing, the authors present optimal algorithms for translation, histogram computation, scaling, and rotation. The authors also develop efficient algorithms for labelling the connected components and determining the convex hulls of multiple figures which run in O(n log n) and O(n log2n) time, respectively. The latter algorithms are significantly simpler and easier to implement than those already reported in the literature for linear arrays}, keywords = {algorithms;, algorithms;intermediate, algorithms;rotation;scaling;scan, array, computation;image, DCT;block, DFT;convex, filtering;optimal, hulls;convolution;expanding;histogram, level, line, machine;block, matching;translation;convolution;image, PROCESSING, processing;labelling;low, processing;median, processing;parallel, processor;shrinking;template, SIMD}, isbn = {0162-8828}, doi = {10.1109/34.368153}, author = {Helman,D. and JaJa, Joseph F.} } @article {12384, title = {Generating compact code from dataflow specifications of multirate signal processing algorithms}, journal = {Circuits and Systems I: Fundamental Theory and Applications, IEEE Transactions on}, volume = {42}, year = {1995}, month = {1995///}, pages = {138 - 150}, author = {Bhattacharyya, Shuvra S. and Buck,J. T and Ha,S. and Lee,E. A} } @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.} } @conference {16620, title = {A large-scale neural model linking local neuronal dynamics to positron emission tomography (PET) regional cerebral blood ffow (rCBF) data}, booktitle = {Soc Neurosci Abstr}, volume = {21}, year = {1995}, month = {1995///}, pages = {1988 - 1988}, author = {Tagamets,M. A and Horwitz,B. and Reggia, James A.} } @article {16607, title = {A modified cellular automata model of nucleotide interactions and non-enzymatic transcription of DNA}, journal = {inbs}, year = {1995}, month = {1995///}, pages = {136 - 136}, author = {Hilke,J. and Reggia, James A. and Navarro-Gonzalez,R. and Lohn,J.} } @article {16524, title = {A neural model of delusions and hallucinations in schizophrenia}, journal = {Advances in Neural Information Processing Systems}, year = {1995}, month = {1995///}, pages = {149 - 156}, author = {Ruppin,E. and Reggia, James A. and Horn,D.} } @conference {14946, title = {An Optimal Ear Decomposition Algorithm with Applications on Fixed-Size Linear Arrays}, booktitle = {PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING}, year = {1995}, month = {1995///}, author = {Huang,Y. M. and JaJa, Joseph F.} } @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.} } @inbook {14632, title = {Polynomial-time algorithm for computing translocation distance between genomes}, booktitle = {Combinatorial Pattern MatchingCombinatorial Pattern Matching}, series = {Lecture Notes in Computer Science}, volume = {937}, year = {1995}, month = {1995///}, pages = {162 - 176}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {With the advent of large-scale DNA physical mapping and sequencing, studies of genome rearrangements are becoming increasingly important in evolutionary molecular biology. From a computational perspective, study of evolution based on rearrangements leads to rearrangement distance problem, i.e., computing the minimum number of rearrangement events required to transform one genome into another. Different types of rearrangement events give rise to a spectrum of interesting combinatorial problems. The complexity of most of these problems is unknown. Multichromosomal genomes frequently evolve by a rearrangement event called translocation which exchanges genetic material between different chromosomes. In this paper we study the translocation distance problem, modeling evolution of genomes evolving by translocations. Translocation distance problem was recently studied for the first time by Kececioglu and Ravi, who gave a 2-approximation algorithm for computing translocation distance. In this paper we prove a duality theorem leading to a polynomial algorithm for computing translocation distance for the case when the orientation of the genes are known. This leads to an algorithm generating a most parsimonious (shortest) scenario, transforming one genome into another by translocations.}, isbn = {978-3-540-60044-2}, url = {http://dx.doi.org/10.1007/3-540-60044-2_41}, author = {Hannenhalli, Sridhar}, editor = {Galil,Zvi and Ukkonen,Esko} } @article {13679, title = {The representation of document structure: A generic object-process approach}, volume = {CAR-TR-785}, year = {1995}, month = {1995///}, institution = {University of Maryland, College Park}, author = {Dori,D. and David Doermann and Shin,C. and Haralick,R. and Phillips,I. and Buchman,M. and Ross,D.} } @conference {13638, title = {Robust table-form structure analysis based on box-driven reasoning}, booktitle = {Document Analysis and Recognition, 1995., Proceedings of the Third International Conference on}, volume = {1}, year = {1995}, month = {1995/08//}, pages = {218 -221 vol.1 - 218 -221 vol.1}, abstract = {Table form document structure analysis is an important problem in the document processing domain. The paper presents a method called Box Driven Reasoning (BDR) to robustly analyze the structure of table form documents which include touching characters and broken lines. Most previous methods employ a line oriented approach. Real documents are copied repeatedly and overlaid with printed data, resulting in characters which touch cells and lines which are broken. BDR deals with regions directly, in contrast with other previous methods. Experimental tests show that BDR reliably recognizes cells and strings in document images with touching characters and broken lines}, keywords = {analysis;table, analysis;touching, BDR;box, characters;character, document, domain;robust, driven, form, image, images;document, lines;document, mechanisms;, PROCESSING, processing;inference, reasoning;broken, recognition;data, structure, structures;document, table}, doi = {10.1109/ICDAR.1995.598980}, author = {Hori,O. and David Doermann} } @article {14786, title = {Techniques for performance measurement of parallel programs}, journal = {Parallel computers: theory and practice}, year = {1995}, month = {1995///}, pages = {225 - 240}, author = {Hollingsworth, Jeffrey K and Lumpp, J. E and Miller, B. P} } @inbook {14644, title = {Towards a computational theory of genome rearrangements}, booktitle = {Computer Science TodayComputer Science Today}, series = {Lecture Notes in Computer Science}, volume = {1000}, year = {1995}, month = {1995///}, pages = {184 - 202}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Analysis of genome rearrangements in molecular biology started in the late 1930{\textquoteright}s, when Dobzhansky and Sturtevant published a milestone paper presenting a rearrangement scenario with 17 inversions for the species of Drosophila. However, until recently there were no computer science results allowing a biologist to analyze genome rearrangements. The paper describes combinatorial problems motivated by genome rearrangements, surveys recently developed algorithms for genomic sequence comparison and presents applications of these algorithms to analyze rearrangements in herpes viruses, plant organelles, and mammalian chromosomes.}, isbn = {978-3-540-60105-0}, url = {http://dx.doi.org/10.1007/BFb0015244}, author = {Hannenhalli, Sridhar and Pevzner,Pavel}, editor = {van Leeuwen,Jan} } @conference {14647, title = {Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals}, booktitle = {Proceedings of the twenty-seventh annual ACM symposium on Theory of computing}, series = {STOC {\textquoteright}95}, year = {1995}, month = {1995///}, pages = {178 - 189}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-718-9}, doi = {10.1145/225058.225112}, url = {http://doi.acm.org/10.1145/225058.225112}, author = {Hannenhalli, Sridhar and Pevzner,Pavel} } @mastersthesis {14649, title = {Transforming men into mice (a computational theory of genome rearrangements)}, year = {1995}, month = {1995///}, school = {The Pennsylvania State University}, author = {Hannenhalli, Sridhar} } @conference {14565, title = {Transforming men into mice (polynomial algorithm for genomic distance problem)}, booktitle = {Foundations of Computer Science, Annual IEEE Symposium on}, year = {1995}, month = {1995///}, pages = {581 - 581}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Many people believe that transformations of humans into mice happen only in fairy tales. However, despite some differences in appearance and habits, men and mice are genetically very similar. In the pioneering paper, J.H. Nadeau and B.A. Taylor (1984) estimated that surprisingly few genomic rearrangements (178/spl plusmn/39) happened since the divergence of human and mouse 80 million years ago. However, their analysis is nonconstructive and no rearrangement scenario for human-mouse evolution has been suggested yet. The problem is complicated by the fact that rearrangements in multi chromosomal genomes include inversions, translocations, fusions and fissions of chromosomes, a rather complex set of operations. As a result, at first glance, a polynomial algorithm for the genomic distance problem with all these operations looks almost as improbable as the transformation of a (real) man into a (real) mouse. We prove a duality theorem which expresses the genomic distance in terms of easily computable parameters reflecting different combinatorial properties of sets of strings. This theorem leads to a polynomial time algorithm for computing most parsimonious rearrangement scenarios. Based on this result and the latest comparative physical mapping data we have constructed a scenario of human-mouse evolution with 131 reversals/translocaitons/fusions/fissions. A combination of the genome rearrangement algorithm with the recently proposed experimental technique called ZOO FISH suggests a new constructive approach to the 100 year old problem of reconstructing mammalian evolution.}, keywords = {biology computing, combinatorial properties, comparative physical mapping data, computable parameters, duality (mathematics), duality theorem, evolution (biological), Genetics, genome rearrangement algorithm, genomic distance problem, genomic rearrangements, human-mouse evolution, mammalian evolution, multi chromosomal genomes, parsimonious rearrangement scenarios, pattern matching, polynomial algorithm, polynomial time algorithm, set theory, sorting, string matching, strings, zoo fish}, doi = {http://doi.ieeecomputersociety.org/10.1109/SFCS.1995.492588}, author = {Hannenhalli, Sridhar and Pevzner,P.A.} } @conference {17943, title = {Voxel based object simplification}, booktitle = {Proceedings of the 6th conference on Visualization {\textquoteright}95}, series = {VIS {\textquoteright}95}, year = {1995}, month = {1995///}, pages = {296{\textendash} - 296{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {Presents a simple, robust and practical method for object simplification for applications where gradual elimination of high-frequency details is desired. This is accomplished by sampling and low-pass filtering the object into multi-resolution volume buffers and applying the marching cubes algorithm to generate a multi-resolution triangle-mesh hierarchy. Our method simplifies the genus of objects and can also help existing object simplification algorithms achieve better results. At each level of detail, a multi-layered mesh can be used for an optional and efficient antialiased rendering.}, keywords = {antialiased rendering, antialiasing, buffer storage, data visualisation, high-frequency detail elimination, low-pass filtering, low-pass filters, marching cubes algorithm, mesh generation, multi-layered mesh, multi-resolution triangle-mesh hierarchy, multi-resolution volume buffers, object genus, Rendering (computer graphics), sampling, Smoothing methods, voxel based object simplification}, isbn = {0-8186-7187-4}, url = {http://dl.acm.org/citation.cfm?id=832271.833850}, author = {He,Taosong and Hong,Lichan and Kaufman,A. and Varshney, Amitabh and Wang,S.} } @inbook {15829, title = {What is Fundamental for Markov Chains: First Passage Times, Fundamental Matrices, and Group Generalized Inverses}, booktitle = {Proceedings of the Second International Workshop on Markov ChainsProceedings of the Second International Workshop on Markov Chains}, year = {1995}, month = {1995///}, pages = {151 - 161}, publisher = {Kluwer Academic Publishers}, organization = {Kluwer Academic Publishers}, author = {Heyman,D. P. and O{\textquoteright}Leary, Dianne P.}, editor = {Stewart,W.} } @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} } @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 {12019, title = {How normal flow constrains relative depth for an active observer}, journal = {Image and vision computing}, volume = {12}, year = {1994}, month = {1994///}, pages = {435 - 445}, author = {Huang, L. and Aloimonos, J.} } @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 {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.} } @article {16649, title = {A modified cellular automata model of nucleotide interactions and DNA replication}, year = {1994}, month = {1994///}, institution = {University of Maryland at College Park}, address = {College Park, MD, USA}, author = {Hilke,James and Lohn,Jason and Reggia, James A. and Navarro,Rafael} } @article {17337, title = {QUEST{\textemdash}Query Environment for Science Teaching}, journal = {Digital Libraries{\textquoteright} 94}, year = {1994}, month = {1994///}, abstract = {QUery Environment for Science Teaching (QUEST) is a proposed digital library implementation consisting of a set of research projects dealing with data capture and organization, content analysis, information seeking and visual interfaces.The QUEST team includes a large number of renown technical collaborators and prominent source collaborators, as well as a significant number of contributors in the University of Maryland, the central, co-ordinating agency.A large collection of multidisciplinary materials in visual and textual formats, made accessible to us by our source collaborators, will be organized to allow integrated access by users from the science education community, that is elementary school through college level teachers. QUEST will be structured so as to provide seamless access to widespread resources on disparate subjects. We intend to provide first-rate subject analysis and representation in order to provide ready access. QUEST will be accessible nationally by means of Mosaic. We propose to provide highly sophisticated querying, browsing and information investigation facilities which will handle integrated textual and visual materials without difficulty. They will be augmented by online reference and referral services, immediately accessible by the user. QUEST will provide a comprehensive information resource for science education accessible through a dynamic, visual user interface. }, author = {Shneiderman, Ben and Rosenfeld, A. and Marchioni,G. and Holliday,W. and Ricart, G. and Faloutsos,С. and Dick,J.} } @proceedings {15797, title = {Regularization by Truncated Total Least Squares}, year = {1994}, month = {1994///}, pages = {250 - 254}, publisher = {SIAM Press}, address = {Philadelphia}, author = {Fierro,Richardo and Golub, Gene H. and Hansen,Per Christian and O{\textquoteright}Leary, Dianne P.}, editor = {Lewis,J.G.} } @conference {14579, title = {A SIMD solution to the sequence comparison problem on the MGAP}, booktitle = {International Conference on Application Specific Array Processors, 1994. Proceedings}, year = {1994}, month = {1994/08/22/24}, pages = {336 - 345}, publisher = {IEEE}, organization = {IEEE}, abstract = {Molecular biologists frequently compare an unknown biosequence with a set of other known biosequences to find the sequence which is maximally similar, with the hope that what is true of one sequence, either physically or functionally, could be true of its analogue. Even though efficient dynamic programming algorithms exist for the problem, when the size of the database is large, the time required is quite long, even for moderate length sequences. In this paper, we present an efficient pipelined SIMD solution to the sequence alignment problem on the Micro-Grain Array Processor (MGAP), a fine-grained massively parallel array of processors with nearest-neighbor connections. The algorithm compares K sequences of length O(M) with the actual sequence of length N, in O(M+N+K) time with O(MN) processors, which is AT-optimal. The implementation on the MGAP computes at the rate of about 0.1 million comparisons per second for sequences of length 128}, keywords = {AT-optimal algorithm, Biological information theory, biology computing, biosequence comparison problem, computational complexity, Computer science, Costs, database size, Databases, DNA computing, dynamic programming, dynamic programming algorithms, fine-grained massively parallel processor array, Genetics, Heuristic algorithms, maximally similar sequence, MGAP parallel computer, Micro-Grain Array Processor, Military computing, molecular biology, molecular biophysics, Nearest neighbor searches, nearest-neighbor connections, Parallel algorithms, pipeline processing, pipelined SIMD solution, sequence alignment problem, sequences}, isbn = {0-8186-6517-3}, doi = {10.1109/ASAP.1994.331791}, author = {Borah,M. and Bajwa,R. S and Hannenhalli, Sridhar and Irwin,M. J} } @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} } @article {14873, title = {A study of affine matching with bounded sensor error}, journal = {International Journal of Computer Vision}, volume = {13}, year = {1994}, month = {1994///}, pages = {7 - 32}, abstract = {Affine transformations of the plane have been used in a number of model-based recognition systems. Because the underlying mathematics are based on exact data, in practice various heuristics are used to adapt the methods to real data where there is positional uncertainty. This paper provides a precise analysis of affine point matching under uncertainty. We obtain an expression for the range of affine-invariant values that are consistent with a given set of four points, where each image point lies in an isin-disc of uncertainty. This range is shown to depend on the actualx-y-positions of the data points. In other words, given uncertainty in the data there are no representations that are invariant with respect to the Cartesian coordinate system of the data. This is problematic for methods, such as geometric hashing, that are based on affine-invariant representations. We also analyze the effect that uncertainty has on the probability that recognition methods using affine transformations will find false positive matches. We find that there is a significant probability of false positives with even moderate levels of sensor error, suggesting the importance of good verification techniques and good grouping techniques.}, doi = {10.1007/BF01420793}, author = {Grimson,W. E.L and Huttenlocher,D. P and Jacobs, David W.} } @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 {17884, title = {Applying the CHAOS/PARTI library to irregular problems in computational chemistry and computational aerodynamics}, booktitle = {Scalable Parallel Libraries Conference, 1993., Proceedings of the}, year = {1993}, month = {1993///}, pages = {45 - 56}, author = {Das,R. and Hwang,Y. S and Uysal, M. and Saltz, J. and Sussman, Alan} } @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 {14780, title = {Dynamic control of performance monitoring on large scale parallel systems}, booktitle = {Proceedings of the 7th international conference on Supercomputing - ICS {\textquoteright}93}, year = {1993}, month = {1993///}, pages = {185 - 194}, address = {Tokyo, Japan}, doi = {10.1145/165939.165969}, url = {http://dl.acm.org/citation.cfm?id=165969}, author = {Hollingsworth, Jeffrey K and Miller, Barton P.} } @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 {15702, title = {A Krylov multisplitting algorithm for solving linear systems of equations}, journal = {Linear Algebra and its Applications}, volume = {194}, year = {1993}, month = {1993/11/15/}, pages = {9 - 29}, abstract = {We consider the practical implementation of Krylov subspace methods (conjugate gradients, Gmres, etc.) for parallel computers in the case where the preconditioning matrix arises from a multisplitting. We show that the algorithm can be efficiently implemented by dividing the work into tasks that generate search directions and a single task that minimizes over the resulting subspace. Each task is assigned to a subset of processors. It is not necessary for the minimization task to send frequent information to the direction generating tasks, and this leads to high utilization with a minimum of synchronization. We study the convergence properties of various forms of the algorithm and present results of numerical examples on a sequential computer.}, isbn = {0024-3795}, doi = {10.1016/0024-3795(93)90110-A}, url = {http://www.sciencedirect.com/science/article/pii/002437959390110A}, author = {Huang,Chiou-Ming and O{\textquoteright}Leary, Dianne P.} } @article {16735, title = {MANDATE: managing networks using database technology}, journal = {IEEE Journal on Selected Areas in Communications}, volume = {11}, year = {1993}, month = {1993/12//}, pages = {1360 - 1372}, abstract = {There has been a growing demand for the development of tools to manage enterprise communication networks. A management information database is the heart of a network management system-it provides the interface between all functions of the network management system and, therefore, has to provide sophisticated functionality allied with high performance. The authors introduce the design of MANDATE (MAnaging Networks using DAtabase TEchnology), a proposed database system for effectively supporting the management of large enterprise networks. The MANDATE design makes a conscious attempt to take advantage of the special characteristics of network data and transactions, and of advances in database technology, to efficiently derive some of the required management functionality}, keywords = {Communication networks, database management systems, enterprise communication networks, Heart, Information management, interface, internetworking, Local area networks, management functionality, management information database, managing networks using database technology, MANDATE, Manufacturing, network operating systems, open systems, Optical fiber cables, Research and development management, Technology management, telecommunication network management, Transaction databases, wide area networks}, isbn = {0733-8716}, doi = {10.1109/49.257929}, author = {Haritsa,J. R and Ball,M. O and Roussopoulos, Nick and Datta,A. and Baras,J. S} } @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} } @conference {16710, title = {Structural ambiguity and conceptual relations}, booktitle = {Proceedings of the Workshop on Very Large Corpora: Academic and Industrial Perspectives}, year = {1993}, month = {1993///}, pages = {58 - 64}, author = {Resnik, Philip and Hearst,M.} } @book {13885, title = {Use of lexical conceptual structure for intelligent tutoring}, year = {1993}, month = {1993///}, publisher = {University of Maryland}, organization = {University of Maryland}, abstract = {We describe the use of an LCS-based semantics for question-answeringexercises in foreign language training. We start by reviewing the LCS model and show how this representation can be used to support a question answering lesson as well as a limited domain discourse. An authoring tool for entering the relevant semantic knowledge is also described. }, author = {Dorr, Bonnie J and Hendler,J. and Blanksteen,S. and Migdalof,B.} } @article {15822, title = {The Use of the L-Curve in the Regularization of Discrete Ill-Posed Problems}, journal = {SIAM Journal on Scientific Computing}, volume = {14}, year = {1993}, month = {1993///}, pages = {1487 - 1503}, abstract = {Regularization algorithms are often used to produce reasonable solutions to ill-posed problems. The L-curve is a plot{\textemdash}for all valid regularization parameters{\textemdash}of the size of the regularized solution versus the size of the corresponding residual. Two main results are established. First a unifying characterization of various regularization methods is given and it is shown that the measurement of {\textquotedblleft}size{\textquotedblright} is dependent on the particular regularization method chosen. For example, the 2-norm is appropriate for Tikhonov regularization, but a 1-norm in the coordinate system of the singular value decomposition (SVD) is relevant to truncated SVD regularization. Second, a new method is proposed for choosing the regularization parameter based on the L-curve, and it is shown how this method can be implemented efficiently. The method is compared to generalized cross validation and this new method is shown to be more robust in the presence of correlated errors.}, keywords = {discrepancy principle, generalized cross validation, ill-posed problems, L-curve, parameter choice, regularization}, doi = {10.1137/0914086}, url = {http://link.aip.org/link/?SCE/14/1487/1}, author = {Hansen,Per Christian and O{\textquoteright}Leary, Dianne P.} } @article {14199, title = {Behavioral Visual Motion Analysis,"}, journal = {Proceedings, DARPA Image Understanding Workshop}, year = {1992}, month = {1992///}, pages = {521 - 541}, author = {Aloimonos, J. and Duri{\c c},Z. and Ferm{\"u}ller, Cornelia and Huang, L. and Rivlin,E. and Sharma, R.} } @article {17092, title = {DISSERTATIONS: ABSTRACTS OF INTEREST}, journal = {ACM SIGCHI Bulletin}, volume = {24}, year = {1992}, month = {1992/04//}, pages = {58 - 75}, abstract = {The following abstracts were selected from a computer search using the BRS Information Technologies retrieval services of the Dissertation Abstracts International (DAI) database produced by University Microfilms International.Unless otherwise specified, paper or microform copies of dissertations may be ordered, using the UM order number, from University Microfilms International, Dissertation Copies, Post Office Box 1794, Ann Arbor, MI 488106; telephone for U.S. (except Michigan, Hawaii, or Alaska): 800/521-3042, for Canada: 800/268-6090. Price lists, ordering, and shipping information are in the introduction to the published DAI. An alternative source for copies is sometimes provided at the end of the abstract.The dissertation titles and abstracts contained here are published with permission of University Microfilms International, publishers of Dissertation Abstracts International (copyright 1985) by University Microfilms International), and may not be reproduced without their prior permission.}, isbn = {0736-6906}, doi = {10.1145/142386.1055546}, url = {http://doi.acm.org/10.1145/142386.1055546}, author = {Humphrey,Susanne M. and Shneiderman, Ben} } @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 {12020, title = {Exploratory active vision: theory}, booktitle = {Proceedings of 1992 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 1992}, year = {1992}, month = {1992/06/15/18}, pages = {10 - 15}, publisher = {IEEE}, organization = {IEEE}, abstract = {An active approach to the integration of shape from x modules-here shape from shading and shape from texture-is proposed. The question of what constitutes a good motion for the active observer is addressed. Generally, the role of the visual system is to provide depth information to an autonomous robot; a trajectory module will then interpret it to determine a motion for the robot, which in turn will affect the visual information received. It is suggested that the motion can also be chosen so as to improve the performance of the visual system}, keywords = {active observer, Active shape model, active vision, Automation, autonomous robot, CAMERAS, Computer science, Computer vision, depth information, Laboratories, Layout, Mobile robots, Motion analysis, optical flow, Robots, shape from shading, shape from texture, shape from x modules, trajectory module, Visual system}, isbn = {0-8186-2855-3}, doi = {10.1109/CVPR.1992.223234}, author = {Herve,J. -Y and Aloimonos, J.} } @conference {14792, title = {Parallel program performance metrics: a comprison and validation}, booktitle = {Proceedings of the 1992 ACM/IEEE conference on Supercomputing}, year = {1992}, month = {1992///}, pages = {4 - 13}, author = {Hollingsworth, Jeffrey K and Miller, B. P} } @conference {15789, title = {Preconditioning parallel multisplittings for solving linear systems of equations}, booktitle = {Proceedings of the 6th international conference on Supercomputing}, series = {ICS {\textquoteright}92}, year = {1992}, month = {1992///}, pages = {478 - 484}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We consider the practical implementation of Krylov subspace methods (conjugate gradients, GMRES, etc.) for parallel computers in the case where the preconditioning matrix is a multisplitting. The algorithm can be efficiently implemented by dividing the work into tasks that generate search directions and a single task that minimizes over the resulting subspace. Each task is assigned to a subset of processors. It is not necessary for the minimization task to send information to the direction generating tasks, and this leads to high utilization with a minimum of synchronization. We study the convergence properties of various forms of the algorithm.}, isbn = {0-89791-485-6}, doi = {10.1145/143369.143454}, url = {http://doi.acm.org/10.1145/143369.143454}, author = {Huang,Chiou-Ming and O{\textquoteright}Leary, Dianne P.} } @article {17971, title = {Six Generations of Building Walkthrough: Final Technical Report to the National Science Foundation}, year = {1992}, month = {1992///}, institution = {University of North Carolina at Chapel Hill}, address = {Chapel Hill, NC, USA}, author = {Brooks,Frederick P. and Airey,John and Alspaugh,John and Bell,Andrew and Brown,Randolph and Hill,Curtis and Nimscheck,Uwe and Rheingans,Penny and Rohlf,John and Smith,Dana and Turner,Douglass and Varshney, Amitabh and Wang,Yulan and Weber,Hans and Yuan,Xialin} } @article {19000, title = {Splicing signals in Drosophila: intron size, information content, and consensus sequences}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {20}, year = {1992}, month = {1992/08/25/}, pages = {4255 - 4262}, abstract = {A database of 209 Drosophila Introns was extracted from Genbank (release number 64.0) and examined by a number of methods in order to characterize features that might serve as signals for messenger RNA splicing. A tight distribution of sizes was observed: while the smallest introns in the database are 51 nucleotides, more than half are less than 80 nucleotides in length, and most of these have lengths in the range of 59 {\textendash} 67 nucleotides. Drosophila splice sites found in large and small introns differ in only minor ways from each other and from those found in vertebrate Introns. However, larger introns have greater pyrimidlne-richness in the region between 11 and 21 nucleotides upstream of 3' splice sites. The Drosophila branchpoint consensus matrix resembles C T A A T (in which branch formation occurs at the underlined A), and differs from the corresponding mammalian signal in the absence of G at the position immediately preceding the branchpoint. The distribution of occurrences of this sequence suggests a minimum distance between 5' splice shies and branchpoints of about 38 nucleotides, and a minimum distance between 3' splice sites and branchpoints of 15 nucleotides. The methods we have used detect no information in exon sequences other than in the few nucleotides immediately adjacent to the splice sites. However, Drosophila resembles many other species in that there is a discontinuity in A + T content between exons and introns, which are A + T rich.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/20.16.4255}, url = {http://nar.oxfordjournals.org/content/20/16/4255}, author = {Mount, Stephen M. and Burks,Christian and Herts,Gerald and Stormo,Gary D. and White,Owen and Fields,Chris} } @article {14854, title = {A study of affine matching with bounded sensor error}, journal = {Computer Vision{\textemdash}ECCV{\textquoteright}92}, year = {1992}, month = {1992///}, pages = {291 - 306}, abstract = {Affine transformations of the plane have been used by modelbased recognition systems to approximate the effects of perspective projection. Because the underlying mathematics are based on exact data, in practice various heuristics are used to adapt the methods to real data where there is positional uncertainty. This paper provides a precise analysis of affine point matching under uncertainty. We obtain an expression for the range of affine-invariant values consistent with a given set of four points, where each data point lies in an exist-disc. This range is shown to depend on the actual x- y-positions of the data points. Thus given uncertainty in the data, the representation is no longer invariant with respect to the Cartesian coordinate system. This is problematic for methods, such as geometric hashing, that depend on the invariant properties of the representation. We also analyze the effect that uncertainty has on the probability that recognition methods using affine transformations will find false positive matches. We find that such methods will produce false positives with even moderate levels of sensor error.}, doi = {10.1007/3-540-55426-2_34}, author = {Grimson,W. and Huttenlocher,D. and Jacobs, David W.} } @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} } @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.} } @conference {14769, title = {The integration of application and system based metrics in a parallel program performance tool}, booktitle = {ACM Sigplan Notices}, volume = {26}, year = {1991}, month = {1991///}, pages = {189 - 200}, author = {Hollingsworth, Jeffrey K and Irvin, R. B and Miller, B. P} } @conference {14575, title = {Parallel transitive closure computations using topological sort}, booktitle = {, Proceedings of the First International Conference on Parallel and Distributed Information Systems, 1991}, year = {1991}, month = {1991/12/04/6}, pages = {122 - 129}, publisher = {IEEE}, organization = {IEEE}, abstract = {Deals with parallel transitive closure computations. The sort-based approaches introduced sorts the tuples of the relation into topological order, and the sorted relation is then horizontally partitioned and distributed across several processing nodes of a message passing multiprocessor system. This data partitioning strategy allows the transitive closure computation of the local data fragments to be computed in parallel with no interprocessor communication. The construction of the final result then requires only a small number of joins. Extensive analytical results are included in the paper as well. They show that the proposed techniques leads to a speedup that is essentially linear with the number of processors. Its performance is significantly better than the recently published hashless parallel algorithm}, keywords = {Computer science, Concurrent computing, data partitioning, Database systems, database theory, deductive databases, File systems, horizontal partitioning, joins, local data fragments, message passing multiprocessor system, Multiprocessing systems, Parallel algorithms, PARALLEL PROCESSING, parallel programming, parallel transitive closure, processing nodes, relation tuples, Relational databases, sorting, topological sort}, isbn = {0-8186-2295-4}, doi = {10.1109/PDIS.1991.183079}, author = {Hua,K. A and Hannenhalli, Sridhar} } @article {15944, title = {Reasoning about ignorance: A note on the Bush-Gorbachev problem}, journal = {Fundam. Inform.}, volume = {15}, year = {1991}, month = {1991///}, pages = {325 - 332}, author = {Kraus,S. and Perlis, Don and Horty,J. F} } @conference {11990, title = {Relative depth from motion using normal flow: an active and purposive solution}, booktitle = {Proceedings of the IEEE Workshop on Visual Motion, 1991}, year = {1991}, month = {1991/10/07/9}, pages = {196 - 204}, publisher = {IEEE}, organization = {IEEE}, abstract = {The authors show how an active observer can compute the relative depth of (stationary or moving) objects in the field of view using only the spatiotemporal derivatives of the time varying image intensity function. The solution they propose is purposive in the sense that it solves only the relative depth from motion problem and cannot be used for other problems related to motion; active in the sense that the activity of the observer is essential for the solution of the problem. Results indicate that exact computation of retinal motion does not appear to be a necessary first step for some problems related to visual motion. In addition, optic flow, whose computation is an ill-posed problem, is related to the motion of the scene only under very restrictive assumptions. As a result, the use of optic flow in some quantitative motion analysis studies is questionable}, keywords = {3D information, Automation, Computer vision, Educational institutions, Image motion analysis, image recognition, Image sequences, Laboratories, Layout, Motion analysis, Motion estimation, Nonlinear optics, normal flow, optic flow, Optical computing, Optical sensors, relative depth, retinal motion, spatiotemporal derivatives, time varying image intensity function, visual motion}, isbn = {0-8186-2153-2}, doi = {10.1109/WVM.1991.212807}, author = {Huang, Liuqing and Aloimonos, J.} } @article {16743, title = {Trie hashing with controlled load}, journal = {IEEE Transactions on Software Engineering}, volume = {17}, year = {1991}, month = {1991/07//}, pages = {678 - 691}, abstract = {Trie hashing (TH), a primary key access method for storing and accessing records of dynamic files, is discussed. The key address is computed through a trie. A key search usually requires only one disk access when the trie is in core and two disk accesses for very large files when the trie must be on disk. A refinement to trie hashing, trie hashing with controlled load (THCL), is presented. It is designed to control the load factor of a TH file as tightly as that of a B-tree file, allows high load factor of up to 100\% for ordered insertions, and increases the load factor for random insertions from 70\% to over 85\%. It is shown that these properties make trie hashing preferable to a B-tree}, keywords = {B-tree file, Computer science, controlled load, Databases, disk access, dynamic files, file organisation, high load factor, information retrieval systems, key search, load factor, Military computing, ordered insertions, Predictive models, primary key access method, Protocols, random insertions, TH file, THCL, Tree data structures, trees (mathematics), trie hashing}, isbn = {0098-5589}, doi = {10.1109/32.83904}, author = {Litwin,W. A and Roussopoulos, Nick and Levy,G. and Hong,W.} } @conference {12062, title = {Catastrophe theory and computational vision}, booktitle = {Proc. AAAI-90 Workshop on Qualitative Vision}, year = {1990}, month = {1990///}, pages = {96 - 100}, author = {Herve, J. and Aloimonos, J.} } @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.} } @article {11971, title = {Motion--Boundary Illusions and their Regularization}, journal = {Proceedings of the Royal Society of London. Series B: Biological Sciences}, volume = {242}, year = {1990}, month = {1990/11/22/}, pages = {75 - 81}, abstract = {Humans use various cues to understand the structure of the world from images. One such cue is the contours of an object formed by occlusion or from surface discontinuities. It is known that contours in the image of an object provide various amounts of information about the shape of the object in view, depending on assumptions that the observer makes. Another powerful cue is motion. The ability of the human visual system to discern structure from a motion stimulus is well known and has a solid theoretical and experimental foundation. However, when humans interpret a visual scene they use various cues to understand what they observe, and the interpretation comes from combining the information acquired from the various modules devoted to specific cues. In such an integration of modules it seems that each cue carries a different weight and importance. We performed several experiments where we made sure that the only cues available to the observer were contour and motion. It turns out that when humans combine information from contour and motion to reconstruct the shape of an object in view, if the results of the two modules - shape from contour and structure from motion - are inconsistent, they experience a perceptual result which is due to the combination of the two modules, with the influence of the contour dominating, thus giving rise to the illusion. We describe here examples of such illusions and identify the conditions under which they happen. Finally, we introduce a computational theory for combining contour and motion using the theory of regularization. The theory explains such illusions and predicts many more. The same computational theory, when applied to retinal motion estimation, explains the effect of boundaries on the perception of motion that gives rise to a set of well-known illusions described by Wallach (1976).}, doi = {10.1098/rspb.1990.0106}, url = {http://rspb.royalsocietypublishing.org/content/242/1304/75.abstract}, author = {Aloimonos, J. and Huang, Liuqing} } @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} } @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.} } @article {18389, title = {Experiences building a syntax-directed editor}, journal = {Software Engineering Journal}, volume = {4}, year = {1989}, month = {1989/11//}, pages = {294 - 294}, abstract = {The paper presents a set of techniques for building robust software using the development of a microprocessor SUPPORT programming environment as an example. It discusses some of the attributes built into the system to best handle the concerns of portability, functionality, and effectiveness that had to be dealt with for the system to be reliable on a small machine, and it describes some of the choices made to obtain the best use of available hardware}, keywords = {applications;, editing;, editor;, engineering;, environment;, environments;, microcomputer, microprocessor;, portability;, Programming, robust, software, software;, Support, syntax-directed, text}, isbn = {0268-6961}, author = {Zelkowitz, Marvin V and Kowalchack,B. and Itkin,D. and Herman,L.} } @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 {12344, title = {Gabriel: A design environment for DSP}, journal = {Acoustics, Speech and Signal Processing, IEEE Transactions on}, volume = {37}, year = {1989}, month = {1989///}, pages = {1751 - 1762}, author = {Lee,E. A and Ho,W. H and Goei,E. E and Bier,J. C and Bhattacharyya, Shuvra S.} } @inbook {18363, title = {A support tool for teaching computer programming}, booktitle = {Issues in software engineering educationIssues in software engineering education}, year = {1989}, month = {1989///}, pages = {139 - 167}, publisher = {Springer-Verlag New York, Inc.}, organization = {Springer-Verlag New York, Inc.}, address = {New York, NY, USA}, isbn = {0-387-96840-7}, url = {http://dl.acm.org/citation.cfm?id=73064.73074}, author = {Zelkowitz, Marvin V and Kowalchack,B. and Itkin,D. and Herman,L.}, editor = {Fairley,Richard and Freeman,Peter} } @book {11943, title = {Correspondenceless detection of depth and motion for a planar surface}, year = {1988}, month = {1988///}, publisher = {University of Maryland}, organization = {University of Maryland}, author = {Aloimonos, J. and Herv{\'e}, J. Y} } @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 {15961, title = {Intentionality as internality}, journal = {Behavioral and Brain Sciences}, volume = {9}, year = {1986}, month = {1986///}, pages = {151 - 152}, author = {Perlis, Don and Hall,R.} } @article {17273, title = {Learning a menu selection tree: training methods compared}, journal = {Behaviour \& Information Technology}, volume = {4}, year = {1985}, month = {1985///}, pages = {81 - 91}, abstract = {Abstract Abstract. Menu selection systems sometimes present learning problems for novice users. This comparison of four training methods for novice users found that the global tree diagram of the menu system was superior to command sequence and frame presentation methods, and somewhat better than trial and error. Methods were evaluated on the basis of (1) number of target nodes found, (2) mean number of selections to a target node, (3) recall of the menu structure, and (4) subjective rating of ease of learning.Abstract Abstract. Menu selection systems sometimes present learning problems for novice users. This comparison of four training methods for novice users found that the global tree diagram of the menu system was superior to command sequence and frame presentation methods, and somewhat better than trial and error. Methods were evaluated on the basis of (1) number of target nodes found, (2) mean number of selections to a target node, (3) recall of the menu structure, and (4) subjective rating of ease of learning. }, isbn = {0144-929X}, doi = {10.1080/01449298508901790}, url = {http://www.tandfonline.com/doi/abs/10.1080/01449298508901790}, author = {Parton,Diana and Huffman,Keith and Pridgen,Patty and Norman,Kent and Shneiderman, Ben} } @article {16610, title = {Computer-aided assessment of transient ischemic attacks. A clinical evaluation.}, journal = {Archives of neurology}, volume = {41}, year = {1984}, month = {1984///}, pages = {1248 - 1248}, author = {Reggia, James A. and Tabb,D. R. and Price,T. R. and Banko,M. and Hebel,R.} } @article {16582, title = {SLIPS}, journal = {Journal of Medical Systems}, volume = {8}, year = {1984}, month = {1984///}, pages = {197 - 204}, author = {Morris,M. S and Reggia, James A. and Ahuja,S. B and Hart,J. and Watson,V.} } @article {18429, title = {Software Engineering Practices in the US and Japan}, journal = {Computer}, volume = {17}, year = {1984}, month = {1984/06//}, pages = {57 - 66}, isbn = {0018-9162}, doi = {10.1109/MC.1984.1659162}, author = {Zelkowitz, Marvin V and Yeh,R. T and Hamlet,R.G. and Gannon,J. D and Basili, Victor R.} } @article {16963, title = {An empirical comparison of two PLATO text editors.}, journal = {Journal of Computer-Based Instruction}, volume = {10}, year = {1983}, month = {1983///}, pages = {43 - 50}, abstract = {Two PLATO system text editors were evaluated with 14 nonprogrammers and 14 programmers who were either university staff or college students. Half of each group learned the "plain" editor, which had 8 commands and 3 screens of HELP material; while the other half of each group learned the "fancy" editor, which had 15 commands and 1 screen of HELP material. The fancy editor is a subset of the widely used TUTOR editor, but nonprogrammers preferred the plain editor. Faster learning, faster performance, fewer invocations of HELP material, and fewer requests for human assistance were characteristic of the plain editor.}, author = {Shneiderman, Ben and Hill,R. and Jacob,R. and Mah,W.} } @article {18996, title = {Small Ribonucleoproteins from Eukaryotes: Structures and Roles in RNA Biogenesis}, journal = {Cold Spring Harbor Symposia on Quantitative BiologyCold Spring Harb Symp Quant Biol}, volume = {47}, year = {1983}, month = {1983/01/01/}, pages = {893 - 900}, abstract = {Detailed reviews describing work presented at the annual Cold Spring Harbor Symposia on Quantitative Biology}, isbn = {0091-7451, 1943-4456}, doi = {10.1101/SQB.1983.047.01.103}, url = {http://symposium.cshlp.org/content/47/893}, author = {Steitz,J. A. and Wolin,S. L. and Rinke,J. and Pettersson,I. and Mount, Stephen M. and Lerner,E. A. and Hinterberger,M. and Gottlieb,E.} } @article {18444, title = {The Software Industry: A State of the Art Survey}, journal = {Foundations of Empirical Software Engineering: The Legacy of Victor R. Basili}, volume = {1}, year = {1983}, month = {1983///}, pages = {383 - 383}, author = {Zelkowitz, Marvin V and Yeh,R. and Hamlet,R.G. and Gannon,J. D and Basili, Victor R.} } @article {19006, title = {The U1 small nuclear RNA-protein complex selectively binds a 5' splice site in vitro}, journal = {Cell}, volume = {33}, year = {1983}, month = {1983/06//}, pages = {509 - 518}, abstract = {The ability of purified U1 small nuclear RNA-protein complexes (U1 snRNPs) to bind in vitro to two RNAs transcribed from recombinant DNA clones by bacteriophage T7 RNA polymerase has been studied. A transcript which contains sequences corresponding to the small intron and flanking exons of the major mouse beta-globin gene is bound in marked preference to an RNA devoid of splice site sequences. The site of U1 snRNP binding to the globin RNA has been defined by T1 ribonuclease digestion of the RNA-U1 snRNP complex. A 15-17-nucleotide region, including the 5{\textquoteright} splice site, remains undigested and complexed with the snRNP such that it can be co-precipitated by antibodies directed against the U1 snRNP. Partial proteinase K digestion of the U1 snRNP abolishes interaction with the globin RNA, indicating that the snRNP proteins contribute significantly to RNA binding. No RNA cleavage, splicing, or recognition of the 3{\textquoteright} splice site by U1 snRNPs has been detected. Our results are discussed in terms of the probable role of U1 snRNPs in the messenger RNA splicing of eucaryotic cell nuclei.}, isbn = {00928674}, doi = {10.1016/0092-8674(83)90432-4}, url = {http://ukpmc.ac.uk/abstract/MED/6190573}, author = {Mount, Stephen M. and Pettersson,Ingvar and Hinterberger,Monique and Karmas,Aavo and Steitz,Joan A.} } @article {19002, title = {Structure and function of small ribonucleoproteins from eukaryotic cells}, journal = {Princess Takamatsu symposiaInt. Symp. Princess Takamatsu Cancer Res. Fund}, volume = {12}, year = {1982}, month = {1982///}, pages = {101 - 107}, abstract = {Autoantibodies from patients with systemic lupus erythematosus and other related diseases have been used to identify and study small RNA-protein complexes from mammalian cells. Properties of three previously described and several new classes of small ribonucleoproteins (RNPs) are reviewed. The sequence of Drosophila U1 RNA reveals that the region proposed to pair with 5{\textquoteright} splice junctions is conserved, while that proposed to interact with 3{\textquoteright} junctions diverges; this forces some revision of the model for U1 small nuclear (sn)RNP participation in hnRNA splicing. Further characterization of the Ro and La small RNPs has shown that the Ro small cytoplasmic (sc)RNPs are a subclass of La RNPs. Both tRNA and 5S rRNA precursors are at least transiently associated with the La protein. This raises the possibility that the La protein may be an RNA polymerase III transcription factor.}, keywords = {Antigen-Antibody Complex, Autoantibodies, HUMANS, Lupus Erythematosus, Systemic, Nucleoproteins, Ribonucleoproteins, RNA Polymerase III, Transcription, Genetic}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7166547}, author = {Steitz,J. A. and Berg,C and Gottlieb,E. and Hardin,J A and Hashimoto,C and Hendrick,J P and Hinterberger,M. and Krikeles,M and Lerner,M R and Mount, Stephen M.} } @article {15725, title = {Classification of Gynecologic Flow Cytometry Data: A Comparison of Methods}, journal = {Journal of Analytical and Quantitative Cytology}, volume = {3}, year = {1981}, month = {1981///}, pages = {135 - 142}, author = {O{\textquoteright}Leary,Timothy J and O{\textquoteright}Leary, Dianne P. and Habbersett,Mary C. and Herman,Chester J.} } @article {19007, title = {Transcription of cloned tRNA and 5S RNA genes in a Drosophila cell free extract}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {9}, year = {1981}, month = {1981/08/25/}, pages = {3907 - 3918}, abstract = {We describe the preparation of a cell-free extract from Drosophila Kc cells which allows transcription of a variety of cloned eukaryotic RNA polymerase III genes. The extract has low RNA-processing nuclease activity and thus the major products obtained are primary transcripts.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/9.16.3907}, url = {http://nar.oxfordjournals.org/content/9/16/3907}, author = {Dingermann,Theodor and Sharp,Stephen and Appel,Bernd and DeFranco,Donald and Mount, Stephen M. and Heiermann,Reinhard and Pongs,Olaf and S{\"o}ll,Dieter} } @article {17147, title = {Experimental investigations of the utility of detailed flowcharts in programming}, journal = {Communications of the ACM}, volume = {20}, year = {1977}, month = {1977/06//}, pages = {373 - 381}, abstract = {This paper describes previous research on flowcharts and a series of controlled experiments to test the utility of detailed flowcharts as an aid to program composition, comprehension, debugging, and modification. No statistically significant difference between flowchart and nonflowchart groups has been shown, thereby calling into question the utility of detailed flowcharting. A program of further research is suggested.}, keywords = {Debugging, experimental testing, flowcharts, human factors, modification, program composition, program comprehension}, isbn = {0001-0782}, doi = {10.1145/359605.359610}, url = {http://doi.acm.org/10.1145/359605.359610}, author = {Shneiderman, Ben and Mayer,Richard and McKay,Don and Heller,Peter} } @book {17447, title = {Two Exploratory Experiments in Program Comprehension}, year = {1975}, month = {1975///}, publisher = {Indiana University, Computer Science Department}, organization = {Indiana University, Computer Science Department}, author = {Shneiderman, Ben and Ho,M.H.} } @article {16927, title = {A graph theoretic model of data structures}, journal = {SIGIR Forum}, volume = {7}, year = {1972}, month = {1972/12//}, pages = {36 - 44}, abstract = {The widespread development of large shared data bases has proceeded mainly on empirical notions. Only in the past few years have there been attempts at formalizing the underlying concepts into a theory of data structures. The present models have been founded on the well-established mathematical theories of sets, relations and graphs, but few descriptions have been sufficiently developed to meet the needs of a complete theory of data structures. The set theoretic formalism offered by Childs(1) or Schwartz(2) or the relational model by Codd(3) are useful but fail to give a complete description of the complex structures found in modern data bases. The graph theoretic concepts found in papers by Harary and Hsiao(4) and Earley(5) are more appealing but need further elaboration. This paper is an attempt to develop a graph theoretic model into a useful formalism for describing and manipulating data structures.}, isbn = {0163-5840}, doi = {10.1145/1095495.1095499}, url = {http://doi.acm.org/10.1145/1095495.1095499}, author = {Heller,J. and Shneiderman, Ben} }