@article {19699, title = {Combining preference and absolute judgements in a crowd-sourced setting}, journal = {ics.uci.edu}, year = {Submitted}, abstract = {Abstract This paper addresses the problem of obtaining gold-standard labels of objects based on subjective judgements provided by humans. Assuming each object can be associated with an underlying score, the objective of this work is to predict the underlying ...}, url = {https://www.ics.uci.edu/~qliu1/MLcrowd_ICML_workshop/Papers/ActivePaper5.pdf}, author = {Ye, P and EDU, UMD and David Doermann} } @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 {20290, title = {Spores and soil from six sides: interdisciplinarity and the environmental biology of anthrax (Bacillus anthracis)}, journal = {Biological Reviews}, year = {2018}, month = {Jan-11-2018}, pages = {1813 - 1831}, abstract = {Environmentally transmitted diseases are comparatively poorly understood and managed, and their ecology is particularly understudied. Here we identify challenges of studying environmental transmission and persistence with a six-sided interdisciplinary review of the biology of anthrax (Bacillus anthracis). Anthrax is a zoonotic disease capable of maintaining infectious spore banks in soil for decades (or even potentially centuries), and the mechanisms of its environmental persistence have been the topic of significant research and controversy. Where anthrax is endemic, it plays an important ecological role, shaping the dynamics of entire herbivore communities. The complex eco-epidemiology of anthrax, and the mysterious biology of Bacillus anthracis during its environmental stage, have necessitated an interdisciplinary approach to pathogen research. Here, we illustrate different disciplinary perspectives through key advances made by researchers working in Etosha National Park, a long-term ecological research site in Namibia that has exemplified the complexities of the enzootic process of anthrax over decades of surveillance. In Etosha, the role of scavengers and alternative routes (waterborne transmission and flies) has proved unimportant relative to the long-term persistence of anthrax spores in soil and their infection of herbivore hosts. Carcass deposition facilitates green-ups of vegetation to attract herbivores, potentially facilitated by the role of anthrax spores in the rhizosphere. The underlying seasonal pattern of vegetation, and herbivores{\textquoteright} immune and behavioural responses to anthrax risk, interact to produce regular {\textquoteleft}anthrax seasons{\textquoteright} that appear to be a stable feature of the Etosha ecosystem. Through the lens of microbiologists, geneticists, immunologists, ecologists, epidemiologists, and clinicians, we discuss how anthrax dynamics are shaped at the smallest scale by population genetics and interactions within the bacterial communities up to the broadest scales of ecosystem structure. We illustrate the benefits and challenges of this interdisciplinary approach to disease ecology, and suggest ways anthrax might offer insights into the biology of other important pathogens. Bacillus anthracis, and the more recently emerged Bacillus cereus biovar anthracis, share key features with other environmentally transmitted pathogens, including several zoonoses and panzootics of special interest for global health and conservation efforts. Understanding the dynamics of anthrax, and developing interdisciplinary research programs that explore environmental persistence, is a critical step forward for understanding these emerging threats. }, doi = {10.1111/brv.12420}, url = {https://onlinelibrary.wiley.com/doi/full/10.1111/brv.12420}, author = {Carlson, Colin J. and Getz, Wayne M. and Kausrud, Kyrre L. and Cizauskas, Carrie A. and Blackburn, Jason K. and Bustos Carrillo, Fausto A. and Rita R Colwell and Easterday, W. Ryan and Ganz, Holly H. and Kamath, Pauline L. and {\O}kstad, Ole A. and Turner, Wendy C. and Kolsto, Anne-Brit and Stenseth, Nils C.} } @article {20298, title = {Virulence-Related Genes Identified from the Genome Sequence of the Non-O1/Non-O139 Vibrio cholerae Strain VcN1, Isolated from Dhaka, Bangladesh}, journal = {Genome Announcements}, year = {2018}, month = {Aug-03-2018}, abstract = {We report here the first draft genome sequence of the non-O1/non-O139 Vibrio cholerae strain VcN1, isolated from Dhaka, Bangladesh. The data submitted to GenBank for this strain will contribute to advancing our understanding of this environmentally disseminated bacterium, including its virulence and its evolution as an important pathogen.}, doi = {10.1128/genomeA.01513-17}, url = {https://mra.asm.org/content/6/10/e01513-17}, author = {Hossain, Maqsud and Alam, Munirul and Khaleque, Abdul and Islam, Sohidul and Sadique, Abdus and Khan, Nayeim and Halim, Zahra and Sarker, Mrinmoy and El-Sayed, Najib M. and Huq, Anwar and Ahsan, Gias Uddin and Rita R Colwell} } @article {20329, title = {Climate influence on Vibrio and associated human diseases during the past half-century in the coastal North Atlantic}, journal = {Proceedings of the National Academy of Sciences}, year = {2016}, month = {Nov-08-2017}, pages = {E5062 - E5071}, abstract = {Climate change is having a dramatic impact on marine animal and plant communities but little is known of its influence on marine prokaryotes, which represent the largest living biomass in the world oceans and play a fundamental role in maintaining life on our planet. In this study, for the first time to our knowledge, experimental evidence is provided on the link between multidecadal climatic variability in the temperate North Atlantic and the presence and spread of an important group of marine prokaryotes, the vibrios, which are responsible for several infections in both humans and animals. Using archived formalin-preserved plankton samples collected by the Continuous Plankton Recorder survey over the past half-century (1958{\textendash}2011), we assessed retrospectively the relative abundance of vibrios, including human pathogens, in nine areas of the North Atlantic and North Sea and showed correlation with climate and plankton changes. Generalized additive models revealed that long-term increase in Vibrio abundance is promoted by increasing sea surface temperatures (up to \~{}1.5 {\textdegree}C over the past 54 y) and is positively correlated with the Northern Hemisphere Temperature (NHT) and Atlantic Multidecadal Oscillation (AMO) climatic indices (P < 0.001). Such increases are associated with an unprecedented occurrence of environmentally acquired Vibrio infections in the human population of Northern Europe and the Atlantic coast of the United States in recent years.}, issn = {0027-8424}, doi = {10.1073/pnas.1609157113}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1609157113}, author = {Vezzulli, Luigi and Grande, Chiara and Reid, Philip C. and {\'e}laou{\"e}t, Pierre and Edwards, Martin and {\"o}fle, Manfred G. and Brettar, Ingrid and Rita R Colwell and Pruzzo, Carla} } @article {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 {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 {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 {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 {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 {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 {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 {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 {20064, title = {Understanding the impact of image quality on segmentation accuracy}, journal = {SPIE Newsroom}, year = {2013}, month = {2013}, author = {Li-Baboud, Ya-Shian and Cardone, Antonio and Chalfoun, Joe and Bajcsy, Peter and Elliott, John} } @article {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} } @conference {19487, title = {Ask WINE: Are We Safer Today? Evaluating Operating System Security Through Big Data Analysis}, booktitle = {LEET{\textquoteright}12 Proceedings of the 5th USENIX conference on Large-Scale Exploits and Emergent Threats}, series = {LEET{\textquoteright}12}, year = {2012}, month = {2012/04/24/}, pages = {11 - 11}, publisher = {USENIX Association}, organization = {USENIX Association}, abstract = {The Internet can be a dangerous place: 800,000 new malware variants are detected each day, and this number is growing at an exponential rate--driven by the quest for economic gains. However, over the past ten years operating-system vendors have introduced a number of security technologies that aim to make exploits harder and to reduce the attack surface of the platform. Faced with these two conflicting trends, it is difficult for end-users to determine what techniques make them safer from Internet attacks. In this position paper, we argue that to answer this question conclusively we must analyze field data collected on real hosts that are targeted by attacks--e.g., the approximately 50 million records of anti-virus telemetry available through Symantec{\textquoteright}s WINE platform. Such studies can characterize the factors that drive the production of malware, can help us understand the impact of security technologies in the real world and can suggest new security metrics, derived from field observations rather than small lab experiments, indicating how susceptible to attacks a computing platform may be.}, url = {http://dl.acm.org/citation.cfm?id=2228340.2228356}, author = {Tudor Dumitras and Efstathopoulos, Petros} } @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 {19589, title = {Introspective Pushdown Analysis of Higher-Order Programs}, journal = {arXiv:1207.1813 [cs]}, year = {2012}, note = {Comment: Proceedings of the 17th ACM SIGPLAN International Conference on Functional Programming, 2012, ACM}, month = {2012/07/07/}, abstract = {In the static analysis of functional programs, pushdown flow analysis and abstract garbage collection skirt just inside the boundaries of soundness and decidability. Alone, each method reduces analysis times and boosts precision by orders of magnitude. This work illuminates and conquers the theoretical challenges that stand in the way of combining the power of these techniques. The challenge in marrying these techniques is not subtle: computing the reachable control states of a pushdown system relies on limiting access during transition to the top of the stack; abstract garbage collection, on the other hand, needs full access to the entire stack to compute a root set, just as concrete collection does. \emph{Introspective} pushdown systems resolve this conflict. Introspective pushdown systems provide enough access to the stack to allow abstract garbage collection, but they remain restricted enough to compute control-state reachability, thereby enabling the sound and precise product of pushdown analysis and abstract garbage collection. Experiments reveal synergistic interplay between the techniques, and the fusion demonstrates "better-than-both-worlds" precision.}, keywords = {Computer Science - Programming Languages, D.3.4, F.3.2}, url = {http://arxiv.org/abs/1207.1813}, author = {Earl, Christopher and Sergey, Ilya and Might, Matthew and David Van Horn} } @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} } @conference {17641, title = {Optimizing epidemic protection for socially essential workers}, booktitle = {Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium}, series = {IHI {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {31 - 40}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Public-health policy makers have many tools to mitigate an epidemic{\textquoteright}s effects. Most related research focuses on the direct effects on those infected (in terms of health, life, or productivity). Interventions including treatment, prophylaxis, quarantine, and social distancing are well studied in this context. These interventions do not address indirect effects due to the loss of critical services and infrastructures when too many of those responsible for their day-to-day operations fall ill. We examine, both analytically and through simulation, the protection of such essential subpopulations by sequestering them, effectively isolating them into groups during an epidemic. We develop a framework for studying the benefits of sequestering and heuristics for when to sequester. We also prove a key property of sequestering placement which helps partition the subpopulations optimally. Thus we provide a first step toward determining how to allocate resources between the direct protection of a population, and protection of those responsible for critical services.}, keywords = {epidemiology, OPTIMIZATION, public health informatics}, isbn = {978-1-4503-0781-9}, doi = {10.1145/2110363.2110371}, url = {http://doi.acm.org/10.1145/2110363.2110371}, author = {Barrett,Chris and Beckman,Richard and Bisset,Keith and Chen,Jiangzhuo and DuBois,Thomas and Eubank,Stephen and Kumar,V. S. Anil and Lewis,Bryan and Marathe,Madhav V. and Srinivasan, Aravind and Stretz,Paula E.} } @conference {19505, title = {The Provenance of WINE}, booktitle = {Dependable Computing Conference (EDCC), 2012 Ninth European}, year = {2012}, month = {2012///}, pages = {126 - 131}, abstract = {The results of cyber security experiments are often impossible to reproduce, owing to the lack of adequate descriptions of the data collection and experimental processes. Such provenance information is difficult to record consistently when collecting data from distributed sensors and when sharing raw data among research groups with variable standards for documenting the steps that produce the final experimental result. In the WINE benchmark, which provides field data for cyber security experiments, we aim to make the experimental process self-documenting. The data collected includes provenance information {\textendash} such as when, where and how an attack was first observed or detected {\textendash} and allows researchers to gauge information quality. Experiments are conducted on a common test bed, which provides tools for recording each procedural step. The ability to understand the provenance of research results enables rigorous cyber security experiments, conducted at scale.}, keywords = {Benchmark testing, CYBER SECURITY, cyber security experiments, data attacks, data collection, dependability benchmarking, distributed databases, distributed sensors, experimental research, field data, information quality, MALWARE, Pipelines, provenance, provenance information, raw data sharing, research groups, security of data, self-documenting experimental process, sensor fusion, software, variable standards, WINE, WINE benchmark}, author = {Tudor Dumitras and Efstathopoulos, P.} } @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 {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 {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 {12420, title = {Topic Models for Dynamic Translation Model Adaptation}, journal = {Association for Computational Linguistics}, year = {2012}, month = {2012///}, abstract = {We propose an approach that biases machine translation systems toward relevant transla- tions based on topic-specific contexts, where topics are induced in an unsupervised way using topic models; this can be thought of as inducing subcorpora for adaptation with- out any human annotation. We use these topic distributions to compute topic-dependent lex- ical weighting probabilities and directly in- corporate them into our translation model as features. Conditioning lexical probabilities on the topic biases translations toward topic- relevant output, resulting in significant im- provements of up to 1 BLEU and 3 TER on Chinese to English translation over a strong baseline.}, author = {Vladimir Eidelman and Jordan Boyd-Graber and Resnik, Philip} } @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 {18557, title = {Communicating with caps: managing usage caps in home networks}, journal = {ACM SIGCOMM Computer Communication Review}, volume = {41}, year = {2011}, month = {2011/08//}, pages = {470 - 471}, abstract = {As Internet service providers increasingly implement and impose "usage caps", consumers need better ways to help them understand and control how devices in the home use up the available network resources or available capacity. Towards this goal, we will demonstrate a system that allows users to monitor and manage their usage caps. The system uses the BISMark firmware running on network gateways to collect usage statistics and report them to a logically centralized controller, which displays usage information. The controller allows users to specify policies about how different people, devices, and applications should consume the usage cap; it implements and enforces these policies via a secure OpenFlow control channel to each gateway device. The demonstration will show various use cases, such as limiting the usage of a particular application, visualizing usage statistics, and allowing users within a single household to "trade" caps with one another.}, keywords = {home network, openflow, usage cap}, isbn = {0146-4833}, doi = {10.1145/2043164.2018526}, url = {http://doi.acm.org/10.1145/2043164.2018526}, author = {Kim,Hyojoon and Sundaresan,Srikanth and Marshini Chetty and Feamster, Nick and Edwards,W. Keith} } @article {19442, title = {Communicating with Caps: Managing Usage Caps in Home Networks}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {41}, year = {2011}, month = {2011/08//}, pages = {470 - 471}, abstract = {As Internet service providers increasingly implement and impose "usage caps", consumers need better ways to help them understand and control how devices in the home use up the available network resources or available capacity. Towards this goal, we will demonstrate a system that allows users to monitor and manage their usage caps. The system uses the BISMark firmware running on network gateways to collect usage statistics and report them to a logically centralized controller, which displays usage information. The controller allows users to specify policies about how different people, devices, and applications should consume the usage cap; it implements and enforces these policies via a secure OpenFlow control channel to each gateway device. The demonstration will show various use cases, such as limiting the usage of a particular application, visualizing usage statistics, and allowing users within a single household to "trade" caps with one another.}, keywords = {home network, openflow, usage cap}, isbn = {0146-4833}, url = {http://doi.acm.org/10.1145/2043164.2018526}, author = {Kim, Hyojoon and Sundaresan, Srikanth and Marshini Chetty and Feamster, Nick and Edwards, W. Keith} } @conference {12447, title = {Component-based restoration of speckled images}, booktitle = {2011 18th IEEE International Conference on Image Processing (ICIP)}, year = {2011}, month = {2011/09/11/14}, pages = {2797 - 2800}, publisher = {IEEE}, organization = {IEEE}, abstract = {Many coherent imaging modalities are often characterized by a multiplicative noise, known as speckle which often makes the interpretation of data difficult. In this paper, we present a speckle reduction algorithm based on separating the structure and texture components of SAR images. An iterative algorithm based on surrogate functionals is presented that solves the component optimization formulation. Experiments indicate this proposed method performs favorably compared to state-of-the-art speckle reduction methods.}, keywords = {coherent imaging modalities, component optimization formulation, component-based restoration, Dictionaries, image restoration, iterative algorithm, iterative methods, multiplicative noise, NOISE, optimisation, radar imaging, SAR images, Speckle, speckle reduction algorithm, speckled images, structure components, surrogate functionals, synthetic aperture radar, texture components, transforms, TV}, isbn = {978-1-4577-1304-0}, doi = {10.1109/ICIP.2011.6116252}, author = {Patel, Vishal M. and Easley,G. R and Chellapa, Rama} } @article {18786, title = {Design of Revolute Joints for In-Mold Assembly Using Insert Molding}, journal = {Journal of Mechanical Design}, volume = {133}, year = {2011}, month = {2011///}, pages = {121010 - 121010}, author = {Ananthanarayanan,A. and Ehrlich,L. and Desai,J. P. and Gupta,S.K.} } @article {19656, title = {Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization}, journal = {Nature Medicine}, volume = {17}, year = {2011}, month = {2011/09//}, pages = {1101 - 1108}, abstract = {Although the role of miR-200s in regulating E-cadherin expression and epithelial-to-mesenchymal transition is well established, their influence on metastatic colonization remains controversial. Here we have used clinical and experimental models of breast cancer metastasis to discover a pro-metastatic role of miR-200s that goes beyond their regulation of E-cadherin and epithelial phenotype. Overexpression of miR-200s is associated with increased risk of metastasis in breast cancer and promotes metastatic colonization in mouse models, phenotypes that cannot be recapitulated by E-cadherin expression alone. Genomic and proteomic analyses revealed global shifts in gene expression upon miR-200 overexpression toward that of highly metastatic cells. miR-200s promote metastatic colonization partly through direct targeting of Sec23a, which mediates secretion of metastasis-suppressive proteins, including Igfbp4 and Tinagl1, as validated by functional and clinical correlation studies. Overall, these findings suggest a pleiotropic role of miR-200s in promoting metastatic colonization by influencing E-cadherin{\textendash}dependent epithelial traits and Sec23a-mediated tumor cell secretome.View full text }, isbn = {1078-8956}, url = {http://www.nature.com/nm/journal/v17/n9/abs/nm.2401.html}, author = {Korpal, Manav and Ell, Brian J. and Buffa, Francesca M. and Ibrahim, Toni and Blanco, Mario A. and Celi{\`a}-Terrassa, Toni and Mercatali, Laura and Zia Khan and Goodarzi, Hani and Hua, Yuling and Wei, Yong and Hu, Guohong and Garcia, Benjamin A. and Ragoussis, Jiannis and Amadori, Dino and Harris, Adrian L. and Kang, Yibin} } @article {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 {14155, title = {Fast solvers for models of ICEO microfluidic flows}, journal = {International Journal for Numerical Methods in Fluids}, volume = {65}, year = {2011}, month = {2011///}, pages = {383 - 404}, author = {Shuttleworth, R. R and Elman, Howard and Long, K. R and Templeton, J. A} } @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.} } @conference {19452, title = {Helping Users Shop for ISPs with Internet Nutrition Labels}, booktitle = {ACM SIGCOMM Workshop on Home Networks {\textquoteright}11}, series = {HomeNets {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {13 - 18}, publisher = {ACM}, organization = {ACM}, abstract = {When purchasing home broadband access from Internet service providers (ISPs), users must decide which service plans are most appropriate for their needs. Today, ISPs advertise their available service plans using only generic upload and download speeds. Unfortunately, these metrics do not always accurately reflect the varying performance that home users will experience for a wide range of applications. In this paper, we propose that each ISP service plan carry a "nutrition label" that conveys more comprehensive information about network metrics along many dimensions, including various aspects of throughput, latency, loss rate, and jitter. We first justify why these metrics should form the basis of a network nutrition label. Then, we demonstrate that current plans that are superficially similar with respect to advertised download rates may have different performance according to the label metrics. We close with a discussion of the challenges involved in presenting a nutrition label to users in a way that is both accurate and easy to understand.}, keywords = {access networks, benchmarking, bismark, broadband networks, gateway measurements}, isbn = {978-1-4503-0798-7}, url = {http://doi.acm.org/10.1145/2018567.2018571}, author = {Sundaresan, Srikanth and Feamster, Nick and Teixeira, Renata and Tang, Anthony and Edwards, W. Keith and Grinter, Rebecca E. and Marshini Chetty and de Donato, Walter} } @book {19360, title = {Image Registration for Remote Sensing}, year = {2011}, month = {2011}, pages = {515}, publisher = {Cambridge University Press}, organization = {Cambridge University Press}, abstract = {Image registration is a digital image processing discipline that studies how to bring two or more digital images into precise alignment for analysis and comparison. Accurate registration algorithms are essential for creating mosaics of satellite images and tracking changes on the planet{\textquoteright}s surface over time. Bringing together invited contributions from 36 distinguished researchers, the book presents a detailed overview of current research and practice in the application of image registration to remote sensing imagery. Chapters cover the problem definition, theoretical issues in accuracy and efficiency, fundamental algorithms, and real-world case studies of image registration software applied to imagery from operational satellite systems. This book provides a comprehensive and practical overview for Earth and space scientists, presents image processing researchers with a summary of current research, and can be used for specialized graduate courses.}, keywords = {Science / Astronomy, Science / Earth Sciences / General, Technology \& Engineering / Environmental / General, Technology \& Engineering / Remote Sensing \& Geographic Information Systems}, isbn = {9781139494373}, author = {LeMoigne,Jacqueline and Netanyahu,Nathan S. and Eastman,Roger D.} } @article {18579, title = {Instrumenting home networks}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {41}, year = {2011}, month = {2011///}, pages = {84 - 89}, abstract = {In managing and troubleshooting home networks, one of the challenges is in knowing what is actually happening. Availability of a record of events that occurred on the home network before trouble appeared would go a long way toward addressing that challenge. In this position/work-in-progress paper, we consider requirements for a general-purpose logging facility for home networks. Such a facility, if properly designed, would potentially have other uses. We describe several such uses and discuss requirements to be considered in the design of a logging platform that would be widely supported and accepted. We also report on our initial deployment of such a facility.}, keywords = {home network management, home network troubleshooting}, isbn = {0146-4833}, doi = {10.1145/1925861.1925875}, url = {http://doi.acm.org/10.1145/1925861.1925875}, author = {Calvert,Kenneth L. and Edwards,W. Keith and Feamster, Nick and Grinter,Rebecca E. and Deng,Ye and Zhou,Xuzi} } @article {13945, title = {Linear versus Mel Frequency Cepstral Coefficients for Speaker Recognition}, journal = {IEEE Automatic Speech Recognition and Understanding Workshop}, year = {2011}, month = {2011///}, abstract = {Mel-frequency cepstral coefficients (MFCC) havebeen dominantly used in speaker recognition as well as in speech recognition. However, based on theories in speech production, some speaker characteristics associated with the structure of the vocal tract, particularly the vocal tract length, are reflected more in the high frequency range of speech. This insight suggests that a linear scale in frequency may provide some advantages in speaker recognition over the mel scale. Based on two state-of-the- art speaker recognition back-end systems (one Joint Factor Analysis system and one Probabilistic Linear Discriminant Analysis system), this study compares the performances between MFCC and LFCC (Linear frequency cepstral coefficients) in the NIST SRE (Speaker Recognition Evaluation) 2010 extended-core task. Our results in SRE10 show that, while they are complementary to each other, LFCC consistently outperforms MFCC, mainly due to its better performance in the female trials. This can be explained by the relatively shorter vocal tract in females and the resulting higher formant frequencies in speech. LFCC benefits more in female speech by better capturing the spectral characteristics in the high frequency region. In addition, our results show some advantage of LFCC over MFCC in reverberant speech. LFCC is as robust as MFCC in the babble noise, but not in the white noise. It is concluded that LFCC should be more widely used, at least for the female trials, by the mainstream of the speaker recognition community. }, author = {Zhou,X. and Garcia-Romero,D. and Duraiswami, Ramani and Espy-Wilson,C. and Shamma,S.} } @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 {19271, title = {Overview of the MPEG Reconfigurable Video Coding Framework}, journal = {Journal of Signal Processing Systems}, volume = {63}, year = {2011}, month = {2011}, pages = {251 - 263}, abstract = {Video coding technology in the last 20 years has evolved producing a variety of different and complex algorithms and coding standards. So far the specification of such standards, and of the algorithms that build them, has been done case by case providing monolithic textual and reference software specifications in different forms and programming languages. However, very little attention has been given to provide a specification formalism that explicitly presents common components between standards, and the incremental modifications of such monolithic standards. The MPEG Reconfigurable Video Coding (RVC) framework is a new ISO standard currently under its final stage of standardization, aiming at providing video codec specifications at the level of library components instead of monolithic algorithms. The new concept is to be able to specify a decoder of an existing standard or a completely new configuration that may better satisfy application-specific constraints by selecting standard components from a library of standard coding algorithms. The possibility of dynamic configuration and reconfiguration of codecs also requires new methodologies and new tools for describing the new bitstream syntaxes and the parsers of such new codecs. The RVC framework is based on the usage of a new actor/ dataflow oriented language called CAL for the specification of the standard library and instantiation of the RVC decoder model. This language has been specifically designed for modeling complex signal processing systems. CAL dataflow models expose the intrinsic concurrency of the algorithms by employing the notions of actor programming and dataflow. The paper gives an overview of the concepts and technologies building the standard RVC framework and the non standard tools supporting the RVC model from the instantiation and simulation of the CAL model to software and/or hardware code synthesis.}, keywords = {CAL actor language, Circuits and Systems, Code synthesis, Computer Imaging, Vision, Pattern Recognition and Graphics, Dataflow programming, Electrical Engineering, Image Processing and Computer Vision, pattern recognition, Reconfigurable Video Coding, Signal, Image and Speech Processing}, isbn = {1939-8018, 1939-8115}, url = {http://link.springer.com/article/10.1007/s11265-009-0399-3}, author = {Bhattacharyya, Shuvra S. and Eker, Johan and Janneck, J{\"o}rn W. and Lucarz, Christophe and Mattavelli, Marco and Raulet, Micka{\"e}l} } @article {16435, title = {Predicting author blog channels with high value future posts for monitoring}, journal = {Proceedings of the Twenty-Fifth Conference on Artificial Intelligence (AAAI)}, year = {2011}, month = {2011///}, abstract = {The phenomenal growth of social media, both in scale andimportance, has created a unique opportunity to track infor- mation diffusion and the spread of influence, but can also make efficient tracking difficult. Given data streams rep- resenting blog posts on multiple blog channels and a focal query post on some topic of interest, our objective is to pre- dict which of those channels are most likely to contain a fu- ture post that is relevant, or similar, to the focal query post. We denote this task as the future author prediction problem (FAPP). This problem has applications in information diffu- sion for brand monitoring and blog channel personalization and recommendation. We develop prediction methods in- spired by (na{\i}ve) information retrieval approaches that use historical posts in the blog channel for prediction. We also train a ranking support vector machine (SVM) to solve the problem. We evaluate our methods on an extensive social media dataset; despite the difficulty of the task, all methods perform reasonably well. Results show that ranking SVM prediction can exploit blog channel and diffusion characteris- tics to improve prediction accuracy. Moreover, it is surpris- ingly good for prediction in emerging topics and identifying inconsistent authors. }, author = {Wu,S. and Elsayed,T. and Rand, William and Raschid, Louiqa} } @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} } @conference {13467, title = {Selective transfer between learning tasks using task-based boosting}, booktitle = {Twenty-Fifth AAAI Conference on Artificial Intelligence}, year = {2011}, month = {2011///}, author = {Eaton,E. and desJardins, Marie and others} } @article {11903, title = {Threat-Aware Clustering in Wireless Sensor Networks}, journal = {IFIP Advances in Information and Communication Technology (AICT)}, volume = {264}, year = {2011}, month = {2011///}, pages = {1 - 12}, author = {Abd-Almageed, Wael and Blace,R.E. and Eltoweissy,M.} } @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} } @article {16035, title = {Visualizing Missing Data: Graph Interpretation User Study}, journal = {IFIP Lecture Notes in Computer Science (LNCS)}, volume = {3585}, year = {2011}, month = {2011/03/31/}, pages = {861 - 872}, abstract = {Visualizing Missing Data: Graph Interpretation User Study}, url = {http://dl.ifip.org/index.php/lncs/article/view/25927}, author = {Drizd,Terence and Eaton,Cyntrica and Plaisant, Catherine} } @article {15832, title = {Windowed Spectral Regularization of Inverse Problems}, journal = {SIAM Journal on Scientific Computing}, volume = {33}, year = {2011}, month = {2011///}, doi = {DOI: 10.1137/100809787}, author = {Chung,Julianne M. and Easley,Glenn R and O{\textquoteright}Leary, Dianne P.} } @conference {16682, title = {cdec: A decoder, alignment, and learning framework for finite-state and context-free translation models}, booktitle = {Proceedings of the ACL 2010 System Demonstrations}, year = {2010}, month = {2010///}, pages = {7 - 12}, author = {Dyer,C. and Weese,J. and Setiawan,H. and Lopez,A. and Ture,F. and Eidelman,V. and Ganitkevitch,J. and Blunsom,P. and Resnik, Philip} } @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} } @article {15912, title = {Compressed Synthetic Aperture Radar}, journal = {IEEE Journal of Selected Topics in Signal Processing}, volume = {4}, year = {2010}, month = {2010/04//}, pages = {244 - 254}, abstract = {In this paper, we introduce a new synthetic aperture radar (SAR) imaging modality which can provide a high-resolution map of the spatial distribution of targets and terrain using a significantly reduced number of needed transmitted and/or received electromagnetic waveforms. This new imaging scheme, requires no new hardware components and allows the aperture to be compressed. It also presents many new applications and advantages which include strong resistance to countermesasures and interception, imaging much wider swaths and reduced on-board storage requirements.}, keywords = {Compressed sensing, compressed sensing (CS), compressive sensing, electromagnetic waveforms, image resolution, radar imaging, SAR imaging modality, synthetic aperture radar, Synthetic aperture radar (SAR), targets spatial distribution}, isbn = {1932-4553}, doi = {10.1109/JSTSP.2009.2039181}, author = {Patel, Vishal M. and Easley,G. R and Healy,D. M and Chellapa, Rama} } @inbook {17598, title = {Fault-Tolerant Facility Location: A Randomized Dependent LP-Rounding Algorithm}, booktitle = {Integer Programming and Combinatorial OptimizationInteger Programming and Combinatorial Optimization}, series = {Lecture Notes in Computer Science}, volume = {6080}, year = {2010}, month = {2010///}, pages = {244 - 257}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, isbn = {978-3-642-13035-9}, url = {http://dx.doi.org/10.1007/978-3-642-13036-6_19}, author = {Byrka,Jaroslaw and Srinivasan, Aravind and Swamy,Chaitanya}, editor = {Eisenbrand,Friedrich and Shepherd,F.} } @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 {14487, title = {On the importance of sharing negative results}, journal = {SIGKDD explorations}, volume = {12}, year = {2010}, month = {2010///}, pages = {3 - 4}, author = {Giraud-Carrier,C. and Dunham,M.H. and Atreya,A. and Elkan,C. and Perlich,C. and Swirszcz,G. and Shi,X. and Philip,S.Y. and F{\"u}rnkranz,J. and Sima,J.F.} } @inbook {17635, title = {On k-Column Sparse Packing Programs}, booktitle = {Integer Programming and Combinatorial OptimizationInteger Programming and Combinatorial Optimization}, series = {Lecture Notes in Computer Science}, volume = {6080}, year = {2010}, month = {2010///}, pages = {369 - 382}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We consider the class of packing integer programs (PIPs) that are column sparse, where there is a specified upper bound k on the number of constraints that each variable appears in. We give an improved (ek + o(k))-approximation algorithm for k-column sparse PIPs. Our algorithm is based on a linear programming relaxation, and involves randomized rounding combined with alteration. We also show that the integrality gap of our LP relaxation is at least 2k - 1; it is known that even special cases of k-column sparse PIPs are (klogk)-hard to approximate.We generalize our result to the case of maximizing monotone submodular functions over k-column sparse packing constraints, and obtain an e2ke-1+o(k) -approximation algorithm. In obtaining this result, we prove a new property of submodular functions that generalizes the fractionally subadditive property, which might be of independent interest. }, isbn = {978-3-642-13035-9}, url = {http://dx.doi.org/10.1007/978-3-642-13036-6_28}, author = {Bansal,Nikhil and Korula,Nitish and Nagarajan,Viswanath and Srinivasan, Aravind}, editor = {Eisenbrand,Friedrich and Shepherd,F.} } @article {16050, title = {Making sense of archived e-mail: Exploring the Enron collection with NetLens}, journal = {Journal of the American Society for Information Science and Technology}, volume = {61}, year = {2010}, month = {2010/04/01/}, pages = {723 - 744}, abstract = {Informal communications media pose new challenges for information-systems design, but the nature of informal interaction offers new opportunities as well. This paper describes NetLens-E-mail, a system designed to support exploration of the content-actor network in large e-mail collections. Unique features of NetLens-E-mail include close coupling of orientation, specification, restriction, and expansion, and introduction and incorporation of a novel capability for iterative projection between content and actor networks within the same collection. Scenarios are presented to illustrate the intended employment of NetLens-E-mail, and design walkthroughs with two domain experts provide an initial basis for assessment of the suitability of the design by scholars and analysts.}, isbn = {1532-2890}, doi = {10.1002/asi.21275}, url = {http://onlinelibrary.wiley.com/doi/10.1002/asi.21275/full}, author = {Kang,Hyunmo and Plaisant, Catherine and Elsayed,Tamer and Oard, Douglas} } @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 {12488, title = {Multiscale directional filtering of noisy InSAR phase images}, journal = {Proceedings of SPIE}, volume = {7703}, year = {2010}, month = {2010/04/05/}, pages = {770308-770308-9 - 770308-770308-9}, abstract = {In this work, we present a new approach for the problem of interferometric phase noise reduction in synthetic aperture radar interferometry based on the shearlet representation. Shearlets provide a multidirectional and multiscale decomposition that have advantages when dealing with noisy phase fringes over standard filtering methods. Using a shearlet decomposition of a noisy phase image, we can adaptively estimate a phase representation in a multiscale and anisotropic fashion. Such denoised phase interferograms can be used to provide much better digital elevation maps (DEM). Experiments show that this method performs significantly better than many competitive methods.}, isbn = {0277786X}, doi = {doi:10.1117/12.849576}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/7703/1/770308_1?isAuthorized=no}, author = {Patel, Vishal M. and Easley,Glenn R and Chellapa, Rama} } @conference {13456, title = {Multi-view clustering with constraint propagation for learning with an incomplete mapping between views}, booktitle = {Proceedings of the 19th ACM international conference on Information and knowledge management}, series = {CIKM {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {389 - 398}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Multi-view learning algorithms typically assume a complete bipartite mapping between the different views in order to exchange information during the learning process. However, many applications provide only a partial mapping between the views, creating a challenge for current methods. To address this problem, we propose a multi-view algorithm based on constrained clustering that can operate with an incomplete mapping. Given a set of pairwise constraints in each view, our approach propagates these constraints using a local similarity measure to those instances that can be mapped to the other views, allowing the propagated constraints to be transferred across views via the partial mapping. It uses co-EM to iteratively estimate the propagation within each view based on the current clustering model, transfer the constraints across views, and update the clustering model, thereby learning a unified model for all views. We show that this approach significantly improves clustering performance over several other methods for transferring constraints and allows multi-view clustering to be reliably applied when given a limited mapping between the views.}, keywords = {constrained clustering, multi-view learning, semi-supervised learning}, isbn = {978-1-4503-0099-5}, doi = {10.1145/1871437.1871489}, url = {http://doi.acm.org/10.1145/1871437.1871489}, author = {Eaton,Eric and desJardins, Marie and Jacob,Sara} } @inbook {15597, title = {New Approaches to Robust, Point-Based Image Registration}, booktitle = {Image Registration for Remote SensingImage Registration for Remote Sensing}, year = {2010}, month = {2010///}, publisher = {Cambridge University Press}, organization = {Cambridge University Press}, abstract = {We consider various algorithmic solutions to image registration based on thealignment of a set of feature points. We present a number of enhancements to a branch-and-bound algorithm introduced by Mount, Netanyahu, and Le Moigne (Pattern Recognition, Vol. 32, 1999, pp. 17{\textendash}38), which presented a registration algorithm based on the partial Hausdorff distance. Our enhance- ments include a new distance measure, the discrete Gaussian mismatch, and a number of improvements and extensions to the above search algorithm. Both distance measures are robust to the presence of outliers, that is, data points from either set that do not match any point of the other set. We present experimental studies, which show that the new distance measure considered can provide significant improvements over the partial Hausdorff distance in instances where the number of outliers is not known in advance. These experiments also show that our other algorithmic improvements can offer tangible improvements. We demonstrate the algorithm{\textquoteright}s efficacy by considering images involving different sensors and different spectral bands, both in a traditional framework and in a multiresolution framework. }, isbn = {9780521516112}, author = {Mount, Dave and Netanyahu,N. S and Ratanasanya,S.}, editor = {LeMoigne,Jacqueline and Netanyahu,Nathan S. and Eastman,Roger D.} } @article {19591, title = {Pushdown Control-Flow Analysis of Higher-Order Programs}, journal = {arXiv:1007.4268 [cs]}, year = {2010}, note = {Comment: The 2010 Workshop on Scheme and Functional Programming}, month = {2010/07/24/}, abstract = {Context-free approaches to static analysis gain precision over classical approaches by perfectly matching returns to call sites---a property that eliminates spurious interprocedural paths. Vardoulakis and Shivers{\textquoteright}s recent formulation of CFA2 showed that it is possible (if expensive) to apply context-free methods to higher-order languages and gain the same boost in precision achieved over first-order programs. To this young body of work on context-free analysis of higher-order programs, we contribute a pushdown control-flow analysis framework, which we derive as an abstract interpretation of a CESK machine with an unbounded stack. One instantiation of this framework marks the first polyvariant pushdown analysis of higher-order programs; another marks the first polynomial-time analysis. In the end, we arrive at a framework for control-flow analysis that can efficiently compute pushdown generalizations of classical control-flow analyses.}, keywords = {Computer Science - Programming Languages, F.3.2, F.4.1}, url = {http://arxiv.org/abs/1007.4268}, author = {Earl, Christopher and Might, Matthew and David Van Horn} } @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 {17987, title = {Is teaching parallel algorithmic thinking to high school students possible?: one teacher{\textquoteright}s experience}, booktitle = {Proceedings of the 41st ACM technical symposium on Computer science education}, series = {SIGCSE {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {290 - 294}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {All students at our high school are required to take at least one course in Computer Science prior to their junior year. They are also required to complete a year-long senior project associated with a specific in-house laboratory, one of which is the Computer Systems Lab. To prepare students for this experience the lab offers elective courses at the post-AP Computer Science level. Since the early 1990s one of these electives has focused on parallel computing. The course enrolls approximately 40 students each year for two semesters of instruction. The lead programming language is C and topics include a wide array of industry-standard and experimental tools. Since the 2007-2008 school year we have included a unit on parallel algorithmic thinking (PAT) using the Explicit Multi-Threading (XMT) system. We describe our experiences using this system after self-studying the approach from a publicly available tutorial. Overall, this article provides significant evidence regarding the unique teachability of the XMT PAT approach, and advocates using it broadly in Computer Science education.}, keywords = {high school, parallel algorithmic thinking, pram algorithms, XMT}, isbn = {978-1-4503-0006-3}, doi = {10.1145/1734263.1734363}, url = {http://doi.acm.org/10.1145/1734263.1734363}, author = {Torbert,Shane and Vishkin, Uzi and Tzur,Ron and Ellison,David J.} } @conference {15496, title = {Using methods \& measures from network analysis for gui testing}, booktitle = {Software Testing, Verification, and Validation Workshops (ICSTW), 2010 Third International Conference on}, year = {2010}, month = {2010/04//}, pages = {240 - 246}, abstract = {Graphical user interfaces (GUIs) for today{\textquoteright}s applications are extremely large. Moreover, they provide many degrees of freedom to the end-user, thus allowing the user to perform a very large number of event sequences on the GUI. The large sizes and degrees of freedom create severe problems for GUI quality assurance, including GUI testing. In this paper, we leverage methods and measures from network analysis to analyze and study GUIs, with the goal of aiding GUI testing activities. We apply these methods and measures on the event-flow graph model of GUIs. Results of a case study show that "network centrality measures" are able to identify the most important events in the GUI as well as the most important sequences of events. These events and sequences are good candidates for test prioritization. In addition, the "betweenness clustering" method is able to partition the GUI into regions that can be tested separately.}, keywords = {betweenness clustering method, event sequences, event-flow graph model, Graphical user interfaces, GUI quality assurance, GUI testing, network analysis, network centrality measures, program testing, Software quality}, doi = {10.1109/ICSTW.2010.61}, author = {Elsaka,E. and Moustafa,W. E and Nguyen,Bao and Memon, Atif M.} } @inbook {15431, title = {Advances in Web Testing}, booktitle = {Computer Performance IssuesComputer Performance Issues}, volume = {Volume 75}, year = {2009}, month = {2009///}, pages = {281 - 306}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {AbstractDemand for high-quality Web applications continues to escalate as reliance on Web-based software increases and Web systems become increasingly complex. Given the importance of quality and its impact on the user experience, a significant research effort has been invested in developing tools and methodologies that facilitate effective quality assurance for Web applications. Testing, in particular, provides a critical inroad toward meeting the quality demand by enabling developers to discover failures and anomalies in applications before they are released. In this survey, we discuss advances in Web testing and begin by exploring the peculiarities of Web applications that makes evaluating their correctness a challenge and the direct translation of conventional software engineering principles impractical in some cases. We then provide an overview of research contributions in three critical aspects of Web testing: deriving adequate Web application models, defining appropriate Web testing strategies, and conducting Web portability analysis. In short, models are used to capture Web application components, their attributes, and interconnections; testing strategies use the models to generate test cases; and portability analysis enables Web developers to ensure that their applications remain correct as they are launched in highly diverse configurations. }, isbn = {0065-2458}, url = {http://www.sciencedirect.com/science/article/pii/S006524580800805X}, author = {Eaton,Cyntrica and Memon, Atif M.}, editor = {Zelkowitz, Marvin V} } @conference {15855, title = {Arabic Cross-Document Coreference Resolution}, booktitle = {Proceedings of the ACL-IJCNLP 2009 Conference Short Papers$}$}, year = {2009}, month = {2009///}, pages = {357 - 360}, author = {Sayeed,A. and Elsayed,T. and Garera,N. and Alexander,D. and Xu,T. and Oard, Douglas and Yarowsky,D. and Piatko,C.} } @conference {13108, title = {Assigning cameras to subjects in video surveillance systems}, booktitle = {Robotics and Automation, 2009. ICRA {\textquoteright}09. IEEE International Conference on}, year = {2009}, month = {2009/05//}, pages = {837 - 843}, abstract = {We consider the problem of tracking multiple agents moving amongst obstacles, using multiple cameras. Given an environment with obstacles, and many people moving through it, we construct a separate narrow field of view video for as many people as possible, by stitching together video segments from multiple cameras over time. We employ a novel approach to assign cameras to people as a function of time, with camera switches when needed. The problem is modeled as a bipartite graph and the solution corresponds to a maximum matching. As people move, the solution is efficiently updated by computing an augmenting path rather than by solving for a new matching. This reduces computation time by an order of magnitude. In addition, solving for the shortest augmenting path minimizes the number of camera switches at each update. When not all people can be covered by the available cameras, we cluster as many people as possible into small groups, then assign cameras to groups using a minimum cost matching algorithm. We test our method using numerous runs from different simulators.}, keywords = {agent, algorithm;multiple, assignment;computation, augmenting, cameras;video, cost, detection;video, graph;camera, MATCHING, matching;minimum, matching;target, path;bipartite, reduction;maximum, segment;video, Surveillance, surveillance;, system;graph, theory;image, TIME, tracking;obstacle, tracking;video, video}, doi = {10.1109/ROBOT.2009.5152753}, author = {El-Alfy,H. and Jacobs, David W. and Davis, Larry S.} } @article {14139, title = {Block-diagonal preconditioning for spectral stochastic finite-element systems}, journal = {IMA Journal of Numerical Analysis}, volume = {29}, year = {2009}, month = {2009///}, pages = {350 - 350}, author = {Powell, C. E and Elman, Howard} } @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} } @conference {19443, title = {Computer Help at Home: Methods and Motivations for Informal Technical Support}, booktitle = {SIGCHI {\textquoteright}09}, series = {CHI {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {739 - 748}, publisher = {ACM}, organization = {ACM}, abstract = {Prior research suggests that people may ask their family and friends for computer help. But what influences whether and how a "helper" will provide help? To answer this question, we conducted a qualitative investigation of people who participated in computer support activities with family and friends in the past year. We describe how factors including maintenance of one{\textquoteright}s personal identity as a computer expert and accountability to one{\textquoteright}s social network determine who receives help and the quality of help provided. We also discuss the complex, fractured relationship between the numerous stakeholders involved in the upkeep of home computing infrastructures. Based on our findings, we provide implications for the design of systems to support informal help-giving in residential settings.}, keywords = {help-giving, help-seeking, Home computing, identity management, social networks}, isbn = {978-1-60558-246-7}, url = {http://doi.acm.org/10.1145/1518701.1518816}, author = {Poole, Erika Shehan and Marshini Chetty and Morgan, Tom and Grinter, Rebecca E. and Edwards, W. Keith} } @conference {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.} } @conference {15891, title = {Cross-document coreference resolution: A key technology for learning by reading}, booktitle = {AAAI Spring Symposium on Learning by Reading and Learning to Read}, year = {2009}, month = {2009///}, author = {Mayfield,J. and Alexander,D. and Dorr, Bonnie J and Eisner,J. and Elsayed,T. and Finin,T. and Fink,C. and Freedman,M. and Garera,N. and McNamee,P. and others} } @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 {19597, title = {Dynamic Provable Data Possession}, booktitle = {CCS {\textquoteright}09 Proceedings of the 16th ACM Conference on Computer and Communications Security }, series = {CCS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {213 - 222}, publisher = {ACM}, organization = {ACM}, abstract = {We consider the problem of efficiently proving the integrity of data stored at untrusted servers. In the provable data possession (PDP) model, the client preprocesses the data and then sends it to an untrusted server for storage, while keeping a small amount of meta-data. The client later asks the server to prove that the stored data has not been tampered with or deleted (without downloading the actual data). However, the original PDP scheme applies only to static (or append-only) files. We present a definitional framework and efficient constructions for dynamic provable data possession (DPDP), which extends the PDP model to support provable updates to stored data. We use a new version of authenticated dictionaries based on rank information. The price of dynamic updates is a performance change from O(1) to O(logn) (or O(nεlog n), for a file consisting of n blocks, while maintaining the same (or better, respectively) probability of misbehavior detection. Our experiments show that this slowdown is very low in practice (e.g. 415KB proof size and 30ms computational overhead for a 1GB file). We also show how to apply our DPDP scheme to outsourced file systems and version control systems (e.g. CVS).}, keywords = {authenticated data structures, Authentication, integrity checking, outsourced storage, proof of retrievability, provable data possession, skip list}, isbn = {978-1-60558-894-0}, url = {http://doi.acm.org/10.1145/1653662.1653688}, author = {Erway, Chris and K{\"u}p\cc{\"u}, Alptekin and Charalampos Papamanthou and Tamassia, Roberto} } @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 {12997, title = {Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development}, journal = {Sci Transl Med}, volume = {1}, year = {2009}, month = {2009/10//}, pages = {2ra5 - 2ra5}, abstract = {Vaccines directed against the blood stages of Plasmodium falciparum malaria are intended to prevent the parasite from invading and replicating within host cells. No blood-stage malaria vaccine has shown clinical efficacy in humans. Most malaria vaccine antigens are parasite surface proteins that have evolved extensive genetic diversity, and this diversity could allow malaria parasites to escape vaccine-induced immunity. We examined the extent and within-host dynamics of genetic diversity in the blood-stage malaria vaccine antigen apical membrane antigen-1 in a longitudinal study in Mali. Two hundred and fourteen unique apical membrane antigen-1 haplotypes were identified among 506 human infections, and amino acid changes near a putative invasion machinery binding site were strongly associated with the development of clinical symptoms, suggesting that these residues may be important to consider in designing polyvalent apical membrane antigen-1 vaccines and in assessing vaccine efficacy in field trials. This extreme diversity may pose a serious obstacle to an effective polyvalent recombinant subunit apical membrane antigen-1 vaccine.}, doi = {10.1126/scitranslmed.3000257}, author = {Takala,S. L and Coulibaly,D. and Thera,M. A and Batchelor,A. H and Cummings, Michael P. and Escalante,A. A and Ouattara,A. and Traor{\'e},K. and Niangaly,A. and Djimd{\'e},A. A and Doumbo,OK and Plowe,CV} } @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 {19460, title = {The Ins and Outs of Home Networking: The Case for Useful and Usable Domestic Networking}, journal = {ACM Trans. Comput.-Hum. Interact.}, volume = {16}, year = {2009}, month = {2009/06//}, pages = {8:1 - 8:28}, abstract = {Householders are increasingly adopting home networking as a solution to the demands created by the presence of multiple computers, devices, and the desire to access the Internet. However, current network solutions are derived from the world of work (and initially the military) and provide poor support for the needs of the home. We present the key findings to emerge from empirical studies of home networks in the UK and US. The studies reveal two key kinds of work that effective home networking relies upon: one, the technical work of setting up and maintaining the home network, and the other, the collaborative and socially organized work of the home which the network is embedded in and supports. The two are thoroughly intertwined and rely upon one another for their realization, yet neither is adequately supported by current networking technologies and applications. Explication of the {\textquotedblleft}work to make the home network work{\textquotedblright} opens up the design space for the continued integration of the home network in domestic life and elaboration of future support. Key issues for development include the development of networking facilities that do not require advanced networking knowledge, that are flexible and support the local social order of the home and the evolution of its routines, and which ultimately make the home network visible and accountable to household members.}, keywords = {home networking, Human computer interaction}, isbn = {1073-0516}, url = {http://doi.acm.org/10.1145/1534903.1534905}, author = {Grinter, Rebecca E. and Edwards, W. Keith and Marshini Chetty and Poole, Erika S. and Sung, Ja-Young and Yang, Jeonghwa and Crabtree, Andy and Tolmie, Peter and Rodden, Tom and Greenhalgh, Chris and Benford, Steve} } @conference {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.} } @article {17753, title = {Method and system for optimal data diagnosis}, volume = {10/774,516}, year = {2009}, month = {2009/01/06/}, abstract = {In the method and system for automated data diagnosis, a relational data base is formed of attributes characterizing an entity. The framework computes optimal diagnosis for a diagnostic inference problem which separates the desirable attributes from the undesirable attributes. The user of the system is permitted to specify certain parameters based on which the system computes a set of optimal or near optimal association rules between the attributes of a specific process, product, or other entity. The system and method of the present invention considers the simplicity of conditions in addition to support and confidence when ordering them, contributes the notion of tight conditions and semi-equivalence to remove redundant rules, uses the concept of the top fringes which allows near optimal conditions to be found, in addition to optimal conditions. Numeric as well as non-numeric attributes can be analyzed.}, url = {http://www.google.com/patents?id=fHnVAAAAEBAJ}, author = {V.S. Subrahmanian and Ernst,Jason}, editor = {University of Maryland} } @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 {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 {15321, title = {Pairwise Document Similarity in Large Collections with MapReduce}, journal = {Relation}, volume = {10}, year = {2009}, month = {2009///}, pages = {8372 - 8372}, author = {Elsayed,T. and Jimmy Lin and Oard, Douglas} } @article {12972, title = {A phylogenetic mixture model for the evolution of gene expression}, journal = {Molecular biology and evolution}, volume = {26}, year = {2009}, month = {2009///}, pages = {2363 - 2363}, author = {Eng,K. H and Corrada Bravo, Hector and Kele{\c s},S.} } @article {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} } @proceedings {19206, title = {Sensing opportunities for personalized feedback technology to reduce consumption}, year = {2009}, month = {2009}, author = {Jon Froehlich and Everitt,K. and Fogarty,J. and Patel,S. and Landay,J.} } @article {12882, title = {Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, month = {2009/10/01/}, pages = {6268 - 6274}, abstract = {Forty-two strains of Vibrio parahaemolyticus were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes toxR and tlh were confirmed by PCR in all but two strains, which also lacked toxR. A total of 18 (41\%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (trh) gene, but not tdh. Ten (23\%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed tdh. Of the 18 tdh-positive strains, 17 (94\%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single trh-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., {\textquotedblleft}clonal cluster,{\textquotedblright} as did pandemic strains of diverse origin. The demonstrated prevalence of tdh-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.00266-09}, url = {http://aem.asm.org/content/75/19/6268}, author = {Alam,Munirul and Chowdhury,Wasimul B. and Bhuiyan,N. A. and Islam,Atiqul and Hasan,Nur A. and Nair,G. Balakrish and Watanabe,H. and Siddique,A. K. and Huq,Anwar and Sack,R. Bradley and Akhter,M. Z. and Grim,Christopher J. and Kam,K.-M. and Luey,C. K. Y. and Endtz,Hubert P. and Cravioto,Alejandro and Rita R Colwell} } @conference {13468, title = {Set-Based Boosting for Instance-Level Transfer}, booktitle = {Data Mining Workshops, 2009. ICDMW {\textquoteright}09. IEEE International Conference on}, year = {2009}, month = {2009/12//}, pages = {422 - 428}, publisher = {IEEE}, organization = {IEEE}, abstract = {The success of transfer to improve learning on a target task is highly dependent on the selected source data. Instance-based transfer methods reuse data from the source tasks to augment the training data for the target task. If poorly chosen, this source data may inhibit learning, resulting in negative transfer. The current best performing algorithm for instance-based transfer, TrAdaBoost, performs poorly when given irrelevant source data. We present a novel set-based boosting technique for instance-based transfer. The proposed algorithm, TransferBoost, boosts both individual instances and collective sets of instances from each source task. In effect, TransferBoost boosts each source task, assigning higher weight to those source tasks which show positive transferability to the target task, and then adjusts the weights of the instances within each source task via AdaBoost. The results demonstrate that TransferBoost significantly improves transfer performance over existing instance-based algorithms when given a mix of relevant and irrelevant source data.}, isbn = {978-1-4244-5384-9}, doi = {10.1109/ICDMW.2009.97}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5360442\&tag=1}, author = {Eaton,Eric and desJardins, Marie} } @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} } @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 {13026, title = {Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study}, journal = {BMC Evol Biol}, volume = {9}, year = {2009}, month = {2009///}, pages = {280 - 280}, abstract = {BACKGROUND: In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98\% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis. RESULTS: Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (P < 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (P < or = 0.005), and nearly so for the superfamily Drepanoidea as currently defined (P < 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data. CONCLUSION: Our results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.}, doi = {10.1186/1471-2148-9-280}, author = {Regier,J. C and Zwick,A. and Cummings, Michael P. and Kawahara,A. Y and Cho,S. and Weller,S. and Roe,A. and Baixeras,J. and Brown,J. W and Parr,C. and Davis,DR and Epstein,M and Hallwachs,W and Hausmann,A and Janzen,DH and Kitching,IJ and Solis,MA and Yen,S-H and Bazinet,A. L and Mitter,C} } @conference {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 {14375, title = {Collective Classification in Network Data}, journal = {AI Magazine}, volume = {29}, year = {2008}, month = {2008/09/06/}, pages = {93 - 93}, abstract = {Collective Classification in Network Data}, isbn = {0738-4602}, doi = {10.1609/aimag.v29i3.2157}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/2157}, author = {Sen,Prithviraj and Namata,Galileo and Bilgic,Mustafa and Getoor, Lise and Galligher,Brian and Eliassi-Rad,Tina} } @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.} } @article {14156, title = {Convergence analysis of iterative solvers in inexact Rayleigh quotient iteration}, journal = {CONVERGENCE}, volume = {31}, year = {2008}, month = {2008///}, pages = {877 - 899}, author = {Xue, F. and Elman, Howard} } @article {12127, title = {CrossTalk: The Journal of Defense Software Engineering. Volume 21, Number 10, October 2008}, year = {2008}, month = {2008///}, institution = {DTIC Document}, author = {Basili, Victor R. and Dangle,K. and Esker,L. and Marotta,F. and Rus,I. and Brosgol,B. M and Jamin,S. and Arthur,J. D and Ravichandar,R. and Wisnosky,D. E} } @article {12971, title = {Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming with an Application to Phylogenetic Analysis of Gene Expression}, volume = {1142}, year = {2008}, month = {2008///}, institution = {Department of Statistics, University of Wisconsin}, abstract = {We present a novel method for estimating tree-structured covariance matrices directly fromobserved continuous data. A representation of these classes of matrices as linear combinations of rank-one matrices indicating object partitions is used to formulate estimation as instances of well-studied numerical optimization problems. In particular, we present estimation based on projection where the covariance estimate is the nearest tree-structured covariance matrix to an observed sample covariance matrix. The problem is posed as a linear or quadratic mixed-integer program (MIP) where a setting of the integer variables in the MIP specifies a set of tree topologies of the structured covariance matrix. We solve these problems to optimality using efficient and robust existing MIP solvers. We also show that the least squares distance method of Fitch and Margoliash (1967) can be formulated as a quadratic MIP and thus solved exactly using existing, robust branch-and-bound MIP solvers. Our motivation for this method is the discovery of phylogenetic structure directly from gene expression data. Recent studies have adapted traditional phylogenetic comparative anal- ysis methods to expression data. Typically, these methods first estimate a phylogenetic tree from genomic sequence data and subsequently analyze expression data. A covariance matrix constructed from the sequence-derived tree is used to correct for the lack of independence in phy- logenetically related taxa. However, recent results have shown that the hierarchical structure of sequence-derived tree estimates are highly sensitive to the genomic region chosen to build them. To circumvent this difficulty, we propose a stable method for deriving tree-structured covariance matrices directly from gene expression as an exploratory step that can guide investigators in their modelling choices for these types of comparative analysis. We present a case study in phylogenetic analysis of expression in yeast gene families. Our method is able to corroborate the presence of phylogenetic structure in the response of expression in a subset of the gene families under particular experimental conditions. Additionally, when used in conjunction with transcription factor occupancy data, our methods show that alternative modelling choices should be considered when creating sequence-derived trees for this comparative analysis. }, author = {Corrada Bravo, Hector and Eng,K. H and Keles,S. and Wahba,G. and Wright,S.} } @article {14135, title = {H (div) preconditioning for a mixed finite element formulation of the stochastic diffusion problem}, year = {2008}, month = {2008///}, institution = {Citeseer}, author = {Elman, Howard and Furnival, D. G and Powell, C. E} } @article {12147, title = {Measures and Risk Indicators for Early Insight into Software Safety. Development of Fault-Tolerant Systems}, year = {2008}, month = {2008/10//}, institution = {ABERDEEN TEST CENTER MD}, abstract = {Software contributes an ever-increasing level of functionality and control in today{\textquoteright}s systems. This increased use of software can dramatically increase the complexity and time needed to evaluate the safety of a system. Although the actual system safety cannot be verified during its development, measures can reveal early insights into potential safety problems and risks. An approach for developing early software safety measures is presented in this article. The approach and the example software measures presented are based on experience working with the safety engineering group on a large Department of Defense program.}, keywords = {*SOFTWARE ENGINEERING, *SYSTEM SAFETY, COMPUTER PROGRAMMING AND SOFTWARE, fault tolerant computing, INDICATORS, measurement, REPRINTS, risk, SAFETY ENGINEERING}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA487120}, author = {Basili, Victor R. and Marotta,Frank and Dangle,Kathleen and Esker,Linda and Rus,Ioana} } @article {18584, title = {Method and System for Detecting and Responding to Attacking Networks}, volume = {11/538,212}, year = {2008}, month = {2008/01/31/}, abstract = {A system and method for detecting a first network of compromised computers in a second network of computers, comprising: collecting Domain Name System (DNS) data for the second network; examining the collected data relative to DNS data from known comprised and/or uncompromised computers in the second network; and determining the existence of the first network and/or the identity of compromised computers in the second network based on the examination.}, url = {http://www.google.com/patents?id=TYunAAAAEBAJ}, author = {Dagon,David and Feamster, Nick and Lee,Weake and Edmonds,Robert and Lipton,Richard and Ramachandran,Anirudh}, editor = {Damballa, Inc.} } @inbook {13455, title = {Modeling Transfer Relationships Between Learning Tasks for Improved Inductive Transfer}, booktitle = {Machine Learning and Knowledge Discovery in DatabasesMachine Learning and Knowledge Discovery in Databases}, series = {Lecture Notes in Computer Science}, volume = {5211}, year = {2008}, month = {2008///}, pages = {317 - 332}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In this paper, we propose a novel graph-based method for knowledge transfer. We model the transfer relationships between source tasks by embedding the set of learned source models in a graph using transferability as the metric. Transfer to a new problem proceeds by mapping the problem into the graph, then learning a function on this graph that automatically determines the parameters to transfer to the new learning task. This method is analogous to inductive transfer along a manifold that captures the transfer relationships between the tasks. We demonstrate improved transfer performance using this method against existing approaches in several real-world domains.}, isbn = {978-3-540-87478-2}, url = {http://dx.doi.org/10.1007/978-3-540-87479-9_39}, author = {Eaton,Eric and desJardins, Marie and Lane,Terran}, editor = {Daelemans,Walter and Goethals,Bart and Morik,Katharina} } @conference {19457, title = {More Than Meets the Eye: Transforming the User Experience of Home Network Management}, booktitle = {Proceedings of the 7th ACM conference on Designing interactive systems}, series = {DIS {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {455 - 464}, publisher = {ACM}, organization = {ACM}, abstract = {As computing migrates from the workplace to the home, householders must tackle problems of home network maintenance. Often they lack the technical knowledge or motivation to complete these tasks, making the user experience of home network maintenance frustrating. In response to these difficulties, many householders rely on handwritten reminders or interactive networking tools that are ill-suited for the home environment. In this paper, we seek to understand how to design better home network management tools through a study of sketches created by 40 people in 18 households. In our study, we obtained information about householders{\textquoteright} knowledge, practices and needs with respect to home networking. Based on our results, we present guidelines for transforming the user experience of home network management.}, keywords = {home networks, sketching, troubleshooting}, isbn = {978-1-60558-002-9}, url = {http://doi.acm.org/10.1145/1394445.1394494}, author = {Poole, Erika Shehan and Marshini Chetty and Grinter, Rebecca E. and Edwards, W. Keith} } @article {13833, title = {Multiple alternative sentence compressions and word-pair antonymy for automatic text summarization and recognizing textual entailment}, journal = {Proceedings of the Text Analysis Conference (TAC-2008), Gaithersburg, MD}, year = {2008}, month = {2008///}, abstract = {The University of Maryland participatedin three tasks organized by the Text Anal- ysis Conference 2008 (TAC 2008): (1) the update task of text summarization; (2) the opinion task of text summariza- tion; and (3) recognizing textual entail- ment (RTE). At the heart of our summa- rization system is Trimmer, which gener- ates multiple alternative compressed ver- sions of the source sentences that act as candidate sentences for inclusion in the summary. For the first time, we investi- gated the use of automatically generated antonym pairs for both text summariza- tion and recognizing textual entailment. We used an antonymy feature in both the opinion summarization task and for rec- ognizing textual entailment. More coher- ent summaries resulted when using the antonymy feature as compared to when not using it. However, performance on ROUGE dropped. The RTE system per- formed almost equally well when using antonyms from WordNet and when using automatically generated antonyms. }, author = {Mohammad,S. and Dorr, Bonnie J and Egan,M. and Jimmy Lin and Zajic, David} } @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 {18592, title = {Path splicing}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {38}, year = {2008}, month = {2008/08//}, pages = {27 - 38}, abstract = {We present path splicing, a new routing primitive that allows network paths to be constructed by combining multiple routing trees ("slices") to each destination over a single network topology. Path splicing allows traffic to switch trees at any hop en route to the destination. End systems can change the path on which traffic is forwarded by changing a small number of additional bits in the packet header. We evaluate path splicing for intradomain routing using slices generated from perturbed link weights and find that splicing achieves reliability that approaches the best possible using a small number of slices, for only a small increase in latency and no adverse effects on traffic in the network. In the case of interdomain routing, where splicing derives multiple trees from edges in alternate backup routes, path splicing achieves near-optimal reliability and can provide significant benefits even when only a fraction of ASes deploy it. We also describe several other applications of path splicing, as well as various possible deployment paths.}, keywords = {multi-path routing, path diversity, path splicing}, isbn = {0146-4833}, doi = {10.1145/1402946.1402963}, url = {http://doi.acm.org/10.1145/1402946.1402963}, author = {Motiwala,Murtaza and Elmore,Megan and Feamster, Nick and Vempala,Santosh} } @article {15463, title = {Position Paper: Improving Browsing Environment Compliance Evaluations for Websites}, journal = {Relation}, volume = {10}, year = {2008}, month = {2008///}, pages = {6113 - 6113}, abstract = {Though it would be ideal for web pages to render and function con-sistently across heterogeneous browsing environments, the browser, browser version, and operating system used to navigate and interact with web content is known to have a significant impact on the subsequent level of user accessibil- ity. While research endeavors directed toward improving web accessibility have generally focused on addressing usability issues for individuals with physical limitations, providing accessible information and services for the en- tire web population also encompasses addressing the limitations of devices and platforms used to deploy web pages. We propose that more research be in- vested in the latter issue to facilitate the development of effective tools for de- tecting browsing environment influenced usability issues before inaccessible pages are released in the field. }, author = {Eaton,C. and Memon, Atif M.} } @conference {15851, title = {Resolving personal names in email using context expansion}, booktitle = {Association for Computational Linguistics (ACL)}, year = {2008}, month = {2008///}, author = {Elsayed,T. and Oard, Douglas and Namata,G.} } @article {14077, title = {Role of transposable elements in trypanosomatids}, journal = {Microbes and Infection}, volume = {10}, year = {2008}, month = {2008/05//}, pages = {575 - 581}, abstract = {Transposable elements constitute 2-5\% of the genome content in trypanosomatid parasites. Some of them are involved in critical cellular functions, such as the regulation of gene expression in Leishmania spp. In this review, we highlight the remarkable role extinct transposable elements can play as the source of potential new functions.}, keywords = {Cellular function, Domestication, Evolution, Gene expression, Leishmania, Regulation of mRNA stability, Retroposon, Transposable element, Trypanosoma}, isbn = {1286-4579}, doi = {16/j.micinf.2008.02.009}, url = {http://www.sciencedirect.com/science/article/pii/S1286457908000464}, author = {Bringaud,Fr{\'e}d{\'e}ric and Ghedin,Elodie and El-Sayed, Najib M. and Papadopoulou,Barbara} } @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 {14103, title = {Cofactor-independent phosphoglycerate mutase is an essential gene in procyclic form Trypanosoma brucei}, journal = {Parasitology research}, volume = {100}, year = {2007}, month = {2007///}, pages = {887 - 892}, author = {Djikeng,A. and Raverdy,S. and Foster, Jeffrey S. and Bartholomeu,D. and Zhang,Y. and El-Sayed, Najib M. and Carlow,C.} } @article {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.} } @article {18697, title = {Crystal Structure and Solution NMR Studies of Lys48-linked Tetraubiquitin at Neutral pH}, journal = {Journal of Molecular Biology}, volume = {367}, year = {2007}, month = {2007/03/16/}, pages = {204 - 211}, abstract = {Ubiquitin modification of proteins is used as a signal in many cellular processes. Lysine side-chains can be modified by a single ubiquitin or by a polyubiquitin chain, which is defined by an isopeptide bond between the C terminus of one ubiquitin and a specific lysine in a neighboring ubiquitin. Polyubiquitin conformations that result from different lysine linkages presumably differentiate their roles and ability to bind specific targets and enzymes. However, conflicting results have been obtained regarding the precise conformation of Lys48-linked tetraubiquitin. We report the crystal structure of Lys48-linked tetraubiquitin at near-neutral pH. The two tetraubiquitin complexes in the asymmetric unit show the complete connectivity of the chain and the molecular details of the interactions. This tetraubiquitin conformation is consistent with our NMR data as well as with previous studies of diubiquitin and tetraubiquitin in solution at neutral pH. The structure provides a basis for understanding Lys48-linked polyubiquitin recognition under physiological conditions.}, keywords = {crystal structure, Lys48-linked, polyubiquitin chains, tetraubiquitin, ubiquitin}, isbn = {0022-2836}, doi = {10.1016/j.jmb.2006.12.065}, url = {http://www.sciencedirect.com/science/article/pii/S0022283606017554}, author = {Eddins,Michael J. and Varadan,Ranjani and Fushman, David and Pickart,Cecile M. and Wolberger,Cynthia} } @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 {15444, title = {An empirical approach to evaluating web application compliance across diverse client platform configurations}, journal = {International Journal of Web Engineering and Technology}, volume = {3}, year = {2007}, month = {2007/01/01/}, pages = {227 - 253}, abstract = {Web applications are the most widely used class of software today. Increased diversity of web-client platform configurations causes execution of web applications to vary unpredictably, creating a myriad of challenges for quality assurance during development. This paper presents a novel technique and an inductive model that leverages empirical data from fielded systems to evaluate web application correctness across multiple client configurations. The inductive model is based on HTML tags and represents how web applications are expected to execute in each client configuration based on the fielded systems observed. End-users and developers update this model by providing empirical data in the form of positive (correctly executing) and negative (incorrectly executing) instances of fielded web applications. The results of an empirical study show that the approach is useful and that popular web applications have serious client-configuration-specific flaws.}, url = {http://inderscience.metapress.com/content/7Y4ABR5FJHKRAPAA}, author = {Eaton,Cyntrica and Memon, Atif M.} } @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 {19072, title = {Evolution of genes and genomes on the Drosophila phylogeny}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007}, pages = {203 - 218}, author = {Clark, A.G. and Eisen,M. B and Smith,D. R and Bergman, C.M. and Oliver, B. and Markow, T.A. and Kaufman, T.C. and Kellis, M. and Gelbart, W. and Iyer, V.N. and others} } @article {14086, title = {The Expression of a Plant-type Ferredoxin Redox System provides Molecular Evidence for a Plastid in the Early Dinoflagellate Perkinsus marinus}, journal = {Protist}, volume = {158}, year = {2007}, month = {2007/01/22/}, pages = {119 - 130}, abstract = {Perkinsus marinus is a parasitic protozoan with a phylogenetic positioning between Apicomplexa and dinoflagellates. It is thus of interest for reconstructing the early evolution of eukaryotes, especially with regard to the acquisition of secondary plastids in these organisms. It is also an important pathogen of oysters, and the definition of parasite-specific metabolic pathways would be beneficial for the identification of efficient treatments for infected mollusks. Although these different scientific interests have resulted in the start of a genome project for this organism, it is still unknown whether P. marinus contains a plastid or plastid-like organelle like the related dinoflagellates and Apicomplexa. Here, we show that in vitro-cultivated parasites contain transcripts of the plant-type ferredoxin and its associated reductase. Both proteins are nuclear-encoded and possess N-terminal targeting sequences similar to those characterized in dinoflagellates. Since this redox pair is exclusively found in cyanobacteria and plastid-harboring organisms its presence also in P. marinus is highly indicative of a plastid. We also provide additional evidence for such an organelle by demonstrating pharmacological sensitivity to inhibitors of plastid-localized enzymes involved in fatty acid biosynthesis (e.g. acetyl-CoA carboxylase) and by detection of genes for three enzymes of plastid-localized isoprenoid biosynthesis (1-deoxy-D-xylulose 5-phosphate reductoisomerase, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, and (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate synthase).}, keywords = {Apicomplexa, ferredoxin, Perkinsozoa, plastid, transit peptide}, isbn = {1434-4610}, doi = {16/j.protis.2006.09.003}, url = {http://www.sciencedirect.com/science/article/pii/S1434461006001015}, author = {Stelter,Kathrin and El-Sayed, Najib M. and Seeber,Frank} } @article {14150, title = {IFISS: A Matlab toolbox for modelling incompressible flow}, journal = {ACM Transactions on Mathematical Software}, volume = {33}, year = {2007}, month = {2007///}, author = {Elman, Howard and Ramage, A. and Silvester, D. J} } @article {13448, title = {Learning and visualizing user preferences over sets}, journal = {American Association for Artificial Intelligence (AAAI)}, year = {2007}, month = {2007///}, abstract = {In previous work, we introduced a representation language,DD-PREF, that balances preferences for particular items with preferences about the properties of the set. Specifically, DD- PREF permits the expression of preferences for depth (i.e., preferences for specific attribute values over others) and di- versity of sets (i.e., preferences for broad vs. narrow distri- butions of attribute values). We have also shown how pref- erences represented in DD-PREF can be learned from training data. In this paper, we present a new experimental method- ology, and give results in a Mars rover image domain. We also provide new visualizations of the learned preferences in this domain. Finally, we describe a Chinese restaurant menu domain for which we are currently gathering user data. }, author = {Wagstaff,K. and desJardins, Marie and Eaton,E. and Montminy,J.} } @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.} } @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 {14088, title = {Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni}, journal = {BMC Genomics}, volume = {8}, year = {2007}, month = {2007///}, pages = {181 - 181}, abstract = {BACKGROUND:The parasitic trematode Schistosoma mansoni is one of the major causative agents of Schistosomiasis, a disease that affects approximately 200 million people, mostly in developing countries. Since much of the pathology is associated with eggs laid by the female worm, understanding the mechanisms involved in oogenesis and sexual maturation is an important step towards the discovery of new targets for effective drug therapy. It is known that the adult female worm only develops fully in the presence of a male worm and that the rates of oviposition and maturation of eggs are significantly increased by mating. In order to study gene transcripts associated with sexual maturation and oviposition, we compared the gene expression profiles of sexually mature and immature parasites using DNA microarrays.RESULTS:For each experiment, three amplified RNA microarray hybridizations and their dye swaps were analyzed. Our results show that 265 transcripts are differentially expressed in adult females and 53 in adult males when mature and immature worms are compared. Of the genes differentially expressed, 55\% are expressed at higher levels in paired females while the remaining 45\% are more expressed in unpaired ones and 56.6\% are expressed at higher levels in paired male worms while the remaining 43.4\% are more expressed in immature parasites. Real-time RT-PCR analysis validated the microarray results. Several new maturation associated transcripts were identified. Genes that were up-regulated in single-sex females were mostly related to energy generation (i.e. carbohydrate and protein metabolism, generation of precursor metabolites and energy, cellular catabolism, and organelle organization and biogenesis) while genes that were down-regulated related to RNA metabolism, reactive oxygen species metabolism, electron transport, organelle organization and biogenesis and protein biosynthesis.CONCLUSION:Our results confirm previous observations related to gene expression induced by sexual maturation in female schistosome worms. They also increase the list of S. mansoni maturation associated transcripts considerably, therefore opening new and exciting avenues for the study of the conjugal biology and development of new drugs against schistosomes.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-8-181}, url = {http://www.biomedcentral.com/1471-2164/8/181}, author = {Waisberg,Michael and Lobo,Francisco and Cerqueira,Gustavo and Passos,Liana and Carvalho,Omar and Franco,Gloria and El-Sayed, Najib M.} } @conference {13157, title = {Multi-scale video cropping}, booktitle = {Proceedings of the 15th international conference on Multimedia}, series = {MULTIMEDIA {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {97 - 106}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We consider the problem of cropping surveillance videos. This process chooses a trajectory that a small sub-window can take through the video, selecting the most important parts of the video for display on a smaller monitor. We model the information content of the video simply, by whether the image changes at each pixel. Then we show that we can find the globally optimal trajectory for a cropping window by using a shortest path algorithm. In practice, we can speed up this process without affecting the results, by stitching together trajectories computed over short intervals. This also reduces system latency. We then show that we can use a second shortest path formulation to find good cuts from one trajectory to another, improving coverage of interesting events in the video. We describe additional techniques to improve the quality and efficiency of the algorithm, and show results on surveillance videos.}, keywords = {shortest path algorithm, Surveillance, video cropping}, isbn = {978-1-59593-702-5}, doi = {10.1145/1291233.1291255}, url = {http://doi.acm.org/10.1145/1291233.1291255}, author = {El-Alfy,Hazem and Jacobs, David W. and Davis, Larry S.} } @article {14074, title = {New Trypanosoma cruzi Repeated Element That Shows Site Specificity for Insertion}, journal = {Eukaryotic Cell}, volume = {6}, year = {2007}, month = {2007/07/01/}, pages = {1228 - 1238}, abstract = {A new family of site-specific repeated elements identified in Trypanosoma cruzi, which we named TcTREZO, is described here. TcTREZO appears to be a composite repeated element, since three subregions may be defined within it on the basis of sequence similarities with other T. cruzi sequences. Analysis of the distribution of TcTREZO in the genome clearly indicates that it displays site specificity for insertion. Most TcTREZO elements are flanked by conserved sequences. There is a highly conserved 68-bp sequence at the 5{\textquoteright} end of the element and a sequence domain of [~]500 bp without a well-defined borderline at the 3{\textquoteright} end. Northern blot hybridization and reverse transcriptase PCR analyses showed that TcTREZO transcripts are expressed as oligo(A)-terminated transcripts whose length corresponds to the unit size of the element (1.6 kb). Transcripts of [~]0.2 kb derived from a small part of TcTREZO are also detected in steady-state RNA. TcTREZO transcripts are unspliced and not translated. The copy number of TcTREZO sequences was estimated to be [~]173 copies per haploid genome. TcTREZO appears to have been assembled by insertions of sequences into a progenitor element. Once associated with each other, these subunits were amplified as a new transposable element. TcTREZO shows site specificity for insertion, suggesting that a sequence-specific endonuclease could be responsible for its insertion at a unique site.}, doi = {

10.1128/EC.00036-07

}, url = {http://ec.asm.org/cgi/content/abstract/6/7/1228}, author = {Souza,Renata T. and Santos,Marcia R. M. and Lima,Fabio M. and El-Sayed, Najib M. and Myler,Peter J. and Ruiz,Jeronimo C. and da Silveira,Jose Franco} } @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.} } @article {14151, title = {Solving the stochastic steady-state diffusion problem using multigrid}, journal = {IMA journal of numerical analysis}, volume = {27}, year = {2007}, month = {2007///}, pages = {675 - 675}, author = {Elman, Howard and Furnival, D.} } @article {14143, title = {Some observations on multigrid convergence for convection{\textendash}diffusion equations}, journal = {Computing and Visualization in Science}, volume = {10}, year = {2007}, month = {2007///}, pages = {43 - 56}, author = {Ramage, A. and Elman, Howard} } @conference {13478, title = {Using multiresolution learning for transfer in image classification}, booktitle = {Proceedings of the 22nd national conference on Artificial intelligence - Volume 2}, series = {AAAI{\textquoteright}07}, year = {2007}, month = {2007///}, pages = {1852 - 1853}, publisher = {AAAI Press}, organization = {AAAI Press}, abstract = {Our work explores the transfer of knowledge at multiple levels of abstraction to improve learning. By exploiting the similarities between objects at various levels of detail, multiresolution learning can facilitate transfer between image classification tasks.We extract features from images at multiple levels of resolution, then use these features to create models at different resolutions. Upon receiving a new task, the closest-matching stored model can be generalized (adapted to the appropriate resolution) and transferred to the new task. }, isbn = {978-1-57735-323-2}, url = {http://dl.acm.org/citation.cfm?id=1619797.1619927}, author = {Eaton,Eric and desJardins, Marie and Stevenson,John} } @article {14125, title = {Analysis and comparison of geometric and algebraic multigrid for convection-diffusion equations}, journal = {ANALYSIS}, volume = {28}, year = {2006}, month = {2006///}, pages = {2208 - 2228}, author = {Wu, C. T and Elman, Howard} } @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.} } @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 {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} } @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} } @article {13160, title = {Edge affinity for pose-contour matching}, journal = {Computer Vision and Image Understanding}, volume = {104}, year = {2006}, month = {2006/10//}, pages = {36 - 47}, abstract = {We present an approach for whole-body pose-contour matching. Contour matching in natural images in the absence of foreground{\textendash}background segmentation is difficult. Usually an asymmetric approach is adopted, where a contour is said to match well if it aligns with a subset of the image{\textquoteright}s gradients. This leads to problems as the contour can match with a portion of an object{\textquoteright}s outline and ignore the remainder. We present a model for using edge continuity to address this issue. Pairs of edge elements in the image are linked with affinities if they are likely to belong to the same object. A contour that matches with a set of image gradients is constrained to also match with other gradients having high affinities with the chosen ones. Experimental results show that this improves matching performance.}, keywords = {Contour matching, Edge continuity}, isbn = {1077-3142}, doi = {10.1016/j.cviu.2006.06.008}, url = {http://www.sciencedirect.com/science/article/pii/S1077314206000737}, author = {Prasad,V. S.N and Davis, Larry S. and Tran,Son Dinh and Elgammal,Ahmed} } @article {14068, title = {Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements}, journal = {Molecular and Biochemical Parasitology}, volume = {145}, year = {2006}, month = {2006/02//}, pages = {158 - 170}, abstract = {The ingi and L1Tc non-LTR retrotransposons - which constitute the ingi clade - are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5{\textquoteright}-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.}, keywords = {Degenerate retroelement, Evolution, Ingi, L1Tc, Leishmania major, Non-LTR retrotransposon, Retroposon, Trypanosoma brucei, Trypanosoma cruzi}, isbn = {0166-6851}, doi = {16/j.molbiopara.2005.09.017}, url = {http://www.sciencedirect.com/science/article/pii/S0166685105002963}, author = {Bringaud,Fr{\'e}d{\'e}ric and Ghedin,Elodie and Blandin,Ga{\"e}lle and Bartholomeu,Daniella C. and Caler,Elisabet and Levin,Mariano J. and Baltz,Th{\'e}o and El-Sayed, Najib M.} } @article {14146, title = {Fourier analysis of multigrid for a model two-dimensional convection-diffusion equation}, journal = {BIT Numerical Mathematics}, volume = {46}, year = {2006}, month = {2006///}, pages = {283 - 306}, author = {Elman, Howard and Ramage, A.} } @conference {15543, title = {Image Registration and Fusion Studies for the Integration of Multiple Remote Sensing Data}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {5}, year = {2006}, month = {2006/05//}, pages = {V - V}, abstract = {The future of remote sensing will see the development of spacecraft formations, and with this development will come a number of complex challenges such as maintaining precise relative position and specified attitudes. At the same time, there will be increasing needs to understand planetary system processes and build accurate prediction models. One essential technology to accomplish these goals is the integration of multiple source data. For this integration, image registration and fusion represent the first steps and need to be performed with very high accuracy. In this paper, we describe studies performed in both image registration and fusion, including a modular framework that was built to describe registration algorithms, a Web-based image registration toolbox, and the comparison of several image fusion techniques using data from the EO-1/ALI and Hyperion sensors}, keywords = {ALI, EO-1, fusion studies, geophysical signal processing, Hyperion sensors, image registration, Internet, multiple remote sensing data, multiple source data, Remote sensing, Web-based image registration toolbox}, doi = {10.1109/ICASSP.2006.1661494}, author = {Le Moigne,J. and Cole-Rhodes,A. and Eastman,R. and Jain,P. and Joshua,A. and Memarsadeghi,N. and Mount, Dave and Netanyahu,N. and Morisette,J. and Uko-Ozoro,E.} } @conference {16451, title = {Implementing a bioinformatics pipeline (bip) on a mediator platform: Comparing cost and quality of alternate choices}, booktitle = {Data Engineering Workshops, 2006. Proceedings. 22nd International Conference on}, year = {2006}, month = {2006///}, pages = {67 - 67}, author = {Eckman,B. A and Gaasterland,T. and Lacroix,Z. and Raschid, Louiqa and Snyder,B. and Vidal,M. E} } @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 {13446, title = {Knowledge transfer with a multiresolution ensemble of classifiers}, journal = {ICML Workshop on Structural Knowledge Transfer for Machine Learning}, year = {2006}, month = {2006///}, author = {Eaton,E. and desJardins, Marie} } @conference {13451, title = {Learning user preferences for sets of objects}, booktitle = {Proceedings of the 23rd international conference on Machine learning}, series = {ICML {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {273 - 280}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Most work on preference learning has focused on pairwise preferences or rankings over individual items. In this paper, we present a method for learning preferences over sets of items. Our learning method takes as input a collection of positive examples---that is, one or more sets that have been identified by a user as desirable. Kernel density estimation is used to estimate the value function for individual items, and the desired set diversity is estimated from the average set diversity observed in the collection. Since this is a new learning problem, we introduce a new evaluation methodology and evaluate the learning method on two data collections: synthetic blocks-world data and a new real-world music data collection that we have gathered.}, isbn = {1-59593-383-2}, doi = {10.1145/1143844.1143879}, url = {http://doi.acm.org/10.1145/1143844.1143879}, author = {desJardins, Marie and Eaton,Eric and Wagstaff,Kiri L} } @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 {16276, title = {Metagenomic Analysis of the Human Distal Gut Microbiome}, journal = {Science}, volume = {312}, year = {2006}, month = {2006/06/02/}, pages = {1355 - 1359}, abstract = {The human intestinal microbiota is composed of 1013 to 1014 microorganisms whose collective genome ({\textquotedblleft}microbiome{\textquotedblright}) contains at least 100 times as many genes as our own genome. We analyzed \~{}78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction{\textendash}amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway{\textendash}mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1124234}, url = {http://www.sciencemag.org/content/312/5778/1355}, author = {Gill,Steven R. and Pop, Mihai and DeBoy,Robert T. and Eckburg,Paul B and Turnbaugh,Peter J and Samuel,Buck S and Gordon,Jeffrey I and Relman,David A and Fraser-Liggett,Claire M and Nelson,Karen E.} } @conference {15834, title = {Modeling identity in archival collections of email: A preliminary study}, booktitle = {Proceedings of the 2006 Conference on Email and Anti-Spam (CEAS 06)}, year = {2006}, month = {2006///}, pages = {95 - 103}, author = {Elsayed,T. and Oard, Douglas} } @article {14081, title = {Molecular Characterization of Serine-, Alanine-, and Proline-Rich Proteins of Trypanosoma cruzi and Their Possible Role in Host Cell Infection}, journal = {Infect. Immun.}, volume = {74}, year = {2006}, month = {2006/03/01/}, pages = {1537 - 1546}, abstract = {We previously reported the isolation of a novel protein gene family, termed SAP (serine-, alanine-, and proline-rich protein), from Trypanosoma cruzi. Aided by the availability of the completed genome sequence of T. cruzi, we have now identified 39 full-length sequences of SAP, six pseudogenes and four partial genes. SAPs share a central domain of about 55 amino acids and can be divided into four groups based on their amino (N)- and carboxy (C)-terminal sequences. Some SAPs have conserved N- and C-terminal domains encoding a signal peptide and a glycosylphosphatidylinositol anchor addition site, respectively. Analysis of the expression of SAPs in metacyclic trypomastigotes by two-dimensional electrophoresis and immunoblotting revealed that they are likely to be posttranslationally modified in vivo. We have also demonstrated that some SAPs are shed into the extracellular medium. The recombinant SAP exhibited an adhesive capacity toward mammalian cells, where binding was dose dependent and saturable, indicating a possible ligand-receptor interaction. SAP triggered the host cell Ca2+ response required for parasite internalization. A cell invasion assay performed in the presence of SAP showed inhibition of internalization of the metacyclic forms of the CL strain. Taken together, these results show that SAP is involved in the invasion of mammalian cells by metacyclic trypomastigotes, and they confirm the hypothesis that infective trypomastigotes exploit an arsenal of surface glycoproteins and shed proteins to induce signaling events required for their internalization.}, doi = {

10.1128/IAI.74.3.1537-1546.2006

}, url = {http://iai.asm.org/cgi/content/abstract/74/3/1537}, author = {Baida,Renata C. P. and Santos,Marcia R. M. and Carmo,Mirian S. and Yoshida,Nobuko and Ferreira,Danielle and Ferreira,Alice Teixeira and El Sayed,Najib M. and Andersson,Bjorn and da Silveira,Jose Franco} } @article {17309, title = {Nuclear Envelope Dystrophies Show a Transcriptional Fingerprint Suggesting Disruption of Rb{\textendash}MyoD Pathways in Muscle Regeneration}, journal = {BrainBrain}, volume = {129}, year = {2006}, month = {2006/04/01/}, pages = {996 - 1013}, abstract = {Mutations of lamin A/C (LMNA) cause a wide range of human disorders, including progeria, lipodystrophy, neuropathies and autosomal dominant Emery{\textendash}Dreifuss muscular dystrophy (EDMD). EDMD is also caused by X-linked recessive loss-of-function mutations of emerin, another component of the inner nuclear lamina that directly interacts with LMNA. One model for disease pathogenesis of LMNA and emerin mutations is cell-specific perturbations of the mRNA transcriptome in terminally differentiated cells. To test this model, we studied 125 human muscle biopsies from 13 diagnostic groups (125 U133A, 125 U133B microarrays), including EDMD patients with LMNA and emerin mutations. A Visual and Statistical Data Analyzer (VISDA) algorithm was used to statistically model cluster hierarchy, resulting in a tree of phenotypic classifications. Validations of the diagnostic tree included permutations of U133A and U133B arrays, and use of two probe set algorithms (MAS5.0 and MBEI). This showed that the two nuclear envelope defects (EDMD LMNA, EDMD emerin) were highly related disorders and were also related to fascioscapulohumeral muscular dystrophy (FSHD). FSHD has recently been hypothesized to involve abnormal interactions of chromatin with the nuclear envelope. To identify disease-specific transcripts for EDMD, we applied a leave-one-out (LOO) cross-validation approach using LMNA patient muscle as a test data set, with reverse transcription{\textendash}polymerase chain reaction (RT{\textendash}PCR) validations in both LMNA and emerin patient muscle. A high proportion of top-ranked and validated transcripts were components of the same transcriptional regulatory pathway involving Rb1 and MyoD during muscle regeneration (CRI-1, CREBBP, Nap1L1, ECREBBP/p300), where each was specifically upregulated in EDMD. Using a muscle regeneration time series (27 time points) we develop a transcriptional model for downstream consequences of LMNA and emerin mutations. We propose that key interactions between the nuclear envelope and Rb and MyoD fail in EDMD at the point of myoblast exit from the cell cycle, leading to poorly coordinated phosphorylation and acetylation steps. Our data is consistent with mutations of nuclear lamina components leading to destabilization of the transcriptome in differentiated cells.}, keywords = {EDMD = Emery{\textendash}Dreifuss muscular dystrophy, emerin, Emery-Dreifuss muscular dystrophy, FSHD = fascioscapulohumeral muscular dystrophy, IDG = individual discriminatory genes, JDG = jointly discriminatory genes, lamin A/C, LGMD = limb-girdle muscular dystrophy, LOO = leave-one-out, RT{\textendash}PCR = reverse transcription{\textendash}polymerase chain reaction; VISDA = Visual and Statistical Data Analyzer, Skeletal muscle, wFC = weighted Fisher criterion}, isbn = {0006-8950, 1460-2156}, doi = {10.1093/brain/awl023}, url = {http://brain.oxfordjournals.org/content/129/4/996}, author = {Bakay,Marina and Wang,Zuyi and Melcon,Gisela and Schiltz,Louis and Xuan,Jianhua and Zhao,Po and Sartorelli,Vittorio and Seo,Jinwook and Pegoraro,Elena and Angelini,Corrado and Shneiderman, Ben and Escolar,Diana and Chen,Yi-Wen and Winokur,Sara T and Pachman,Lauren M and Fan,Chenguang and Mandler,Raul and Nevo,Yoram and Gordon,Erynn and Zhu,Yitan and Dong,Yibin and Wang,Yue and Hoffman,Eric P} } @article {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 {14069, title = {Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: Sixteen new members and a novel subfamily}, journal = {Gene}, volume = {366}, year = {2006}, month = {2006/02/01/}, pages = {303 - 315}, abstract = {Nuclear receptors (NRs) are important transcriptional modulators in metazoans. Sixteen new NRs were identified in the Platyhelminth trematode, Schistosoma mansoni. Three were found to possess novel tandem DNA-binding domains that identify a new subfamily of NR. Two NRs are homologues of the thyroid hormone receptor that previously were thought to be restricted to chordates. This study brings the total number of identified NR in S. mansoni to 21. Phylogenetic and comparative genomic analyses demonstrate that S. mansoni NRs share an evolutionary lineage with that of arthropods and vertebrates. Phylogenic analysis shows that more than half of the S. mansoni nuclear receptors evolved from a second gene duplication. As the second gene duplication of NRs was thought to be specific to vertebrates, our data challenge the current theory of NR evolution.}, keywords = {Nuclear receptors, Schistosoma mansoni}, isbn = {0378-1119}, doi = {16/j.gene.2005.09.013}, url = {http://www.sciencedirect.com/science/article/pii/S0378111905005871}, author = {Wu,Wenjie and Niles,Edward G. and El-Sayed, Najib M. and Berriman,Matthew and LoVerde,Philip T.} } @article {17662, title = {Structure of social contact networks and their impact on epidemics}, journal = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science}, volume = {70}, year = {2006}, month = {2006///}, pages = {181 - 181}, abstract = {Traditional epidemiological research has focused on rate-based differential-equation models on completely mixing populations. In this paper, we outline an approach based on a combination of net- work theory and discrete-event simulations to study epidemics in large urban areas. We survey some of our results published in Nature (2004) and the Proc. ACM-SIAM Symposium on Discrete Algorithms (2004), and present some new results on: (i) mathematical properties of large social contact networks, as well as (ii) simulation-based dynamic anal- ysis of disease-spread in such networks. We identify a number of new measures that are significant for understanding epidemics and for devel- oping new strategies in policy planning. We also perform a very detailed structural analysis of the social contact networks produced by TRAN- SIMS, a simulator for detailed transportation/traffic studies, and study two random graph models to generate realistic social networks: Chung- Lu{\textquoteright}s model and the configuration model. We also develop combinatorial formulations and approximation algorithms for quarantining, vaccina- tion and sensor placement, as aids to decision-making. }, author = {Eubank,S. and Kumar,V. S.A and Marathe,M. V and Srinivasan, Aravind and Wang,N.} } @article {14585, title = {Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure}, journal = {Circulation}, volume = {114}, year = {2006}, month = {2006///}, pages = {1269 - 1276}, abstract = {Background{\textemdash} Specific transcription factors (TFs) modulate cardiac gene expression in murine models of heart failure, but their relevance in human subjects remains untested. We developed and applied a computational approach called transcriptional genomics to test the hypothesis that a discrete set of cardiac TFs is associated with human heart failure.Methods and Results{\textemdash} RNA isolates from failing (n=196) and nonfailing (n=16) human hearts were hybridized with Affymetrix HU133A arrays, and differentially expressed heart failure genes were determined. TF binding sites overrepresented in the -5-kb promoter sequences of these heart failure genes were then determined with the use of public genome sequence databases. Binding sites for TFs identified in murine heart failure models (MEF2, NKX, NF-AT, and GATA) were significantly overrepresented in promoters of human heart failure genes (P<0.002; false discovery rate 2\% to 4\%). In addition, binding sites for FOX TFs showed substantial overrepresentation in both advanced human and early murine heart failure (P<0.002 and false discovery rate <4\% for each). A role for FOX TFs was supported further by expression of FOXC1, C2, P1, P4, and O1A in failing human cardiac myocytes at levels similar to established hypertrophic TFs and by abundant FOXP1 protein in failing human cardiac myocyte nuclei.Conclusions{\textemdash} Our results provide the first evidence that specific TFs identified in murine models (MEF2, NKX, NFAT, and GATA) are associated with human heart failure. Moreover, these data implicate specific members of the FOX family of TFs (FOXC1, C2, P1, P4, and O1A) not previously suggested in heart failure pathogenesis. These findings provide a crucial link between animal models and human disease and suggest a specific role for FOX signaling in modulating the hypertrophic response of the heart to stress in humans.}, doi = {10.1161/CIRCULATIONAHA.106.632430}, url = {http://circ.ahajournals.org/content/114/12/1269.abstract}, author = {Hannenhalli, Sridhar and Putt,Mary E. and Gilmore,Joan M. and Wang,Junwen and Parmacek,Michael S. and Epstein,Jonathan A. and Morrisey,Edward E. and Margulies,Kenneth B. and Cappola,Thomas P.} } @article {14079, title = {The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion}, journal = {Molecular biology and evolution}, volume = {23}, year = {2006}, month = {2006///}, pages = {411 - 411}, author = {Bringaud,F. and Bartholomeu,D. C and Blandin,G. and Delcher,A. and Baltz,T. and El-Sayed, Najib M. and Ghedin,E.} } @article {14085, title = {Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region}, journal = {BMC Genomics}, volume = {7}, year = {2006}, month = {2006///}, pages = {60 - 60}, abstract = {BACKGROUND:The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification.RESULTS:We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5{\textquoteright}-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2.CONCLUSION:The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-7-60}, url = {http://www.biomedcentral.com/1471-2164/7/60}, author = {Westenberger,Scott and Cerqueira,Gustavo and El-Sayed, Najib M. and Zingales,Bianca and Campbell,David and Sturm,Nancy} } @article {14078, title = {Comparative Genomics of Trypanosomatid Parasitic Protozoa}, journal = {Science}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {404 - 409}, abstract = {A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that{\textemdash}along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions{\textemdash}have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.}, doi = {10.1126/science.1112181}, url = {http://www.sciencemag.org/content/309/5733/404.abstract}, author = {El-Sayed, Najib M. and Myler,Peter J. and Blandin,Ga{\"e}lle and Berriman,Matthew and Crabtree,Jonathan and Aggarwal,Gautam and Caler,Elisabet and Renauld,Hubert and Worthey,Elizabeth A. and Hertz-Fowler,Christiane and Ghedin,Elodie and Peacock,Christopher and Bartholomeu,Daniella C. and Haas,Brian J. and Tran,Anh-Nhi and Wortman,Jennifer R. and Alsmark,U. Cecilia M. and Angiuoli,Samuel and Anupama,Atashi and Badger,Jonathan and Bringaud,Frederic and Cadag,Eithon and Carlton,Jane M. and Cerqueira,Gustavo C. and Creasy,Todd and Delcher,Arthur L. and Djikeng,Appolinaire and Embley,T. Martin and Hauser,Christopher and Ivens,Alasdair C. and Kummerfeld,Sarah K. and Pereira-Leal,Jose B. and Nilsson,Daniel and Peterson,Jeremy and Salzberg,Steven L. and Shallom,Joshua and Silva,Joana C. and Sundaram,Jaideep and Westenberger,Scott and White,Owen and Melville,Sara E. and Donelson,John E. and Andersson,Bj{\"o}rn and Stuart,Kenneth D. and Hall,Neil} } @article {15745, title = {Efficient iterative algorithms for the stochastic finite element method with application to acoustic scattering}, journal = {Computer Methods in Applied Mechanics and Engineering}, volume = {194}, year = {2005}, month = {2005/03/18/}, pages = {1037 - 1055}, abstract = {In this study, we describe the algebraic computations required to implement the stochastic finite element method for solving problems in which uncertainty is restricted to right-hand side data coming from forcing functions or boundary conditions. We show that the solution can be represented in a compact outer product form which leads to efficiencies in both work and storage, and we demonstrate that block iterative methods for algebraic systems with multiple right-hand sides can be used to advantage to compute this solution. We also show how to generate a variety of statistical quantities from the computed solution. Finally, we examine the behavior of these statistical quantities in one setting derived from a model of acoustic scattering.}, keywords = {01, 28, 60, finite element, multigrid, Multiple right-hand side, Scattering, Stochastic}, isbn = {0045-7825}, doi = {10.1016/j.cma.2004.06.028}, url = {http://www.sciencedirect.com/science/article/pii/S0045782504003123}, author = {Elman, Howard and Ernst, Oliver G. and O{\textquoteright}Leary,Dianne P. and Stewart, Michael} } @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.} } @book {19347, title = {Finite Elements and Fast Iterative Solvers : with Applications in Incompressible Fluid Dynamics}, year = {2005}, month = {2005}, pages = {416}, publisher = {Oxford University Press}, organization = {Oxford University Press}, abstract = {The subject of this book is the efficient solution of partial differential equations (PDEs) that arise when modelling incompressible fluid flow. The material is organized into four groups of two chapters each, covering the Poisson equation (chapters 1 \& 2); the convection-diffucion equation (chapters 3 \& 4); the Stokes equations (chapters 5 \& 6); and the Navier-Stokes equations (chapters 7 \& 8). These equations represent important models within the domain of computational fluid dynamics, but they also arise in many other settings. For each PDE model, there is a chapter concerned with finite element discretization. For each problem and associated solvers there is a description of how to compute along with theoretical analysis which guides the choice of approaches. Illustrative numerical results occur throughout the book, which have been computed with the freely downloadable IFISS software. All numerical results should be reproducible by readers who have access to MATLAB and there is considerable scope for experimentation in the {\textquoteright}computational laboratory{\textquoteright} provided by the software. This book provides an excellent introduction to finite elements, iterative linear solvers and scientific computing aimed at graduates in engineering, numerical analysis, applied mathematics and interdisciplinary scientific computing. Including theoretical problems and practical exercises closely tied with freely downloadable MATLAB software, this book is an ideal teaching and learning resource.}, keywords = {Computers / Computer Science, Mathematics / Numerical Analysis, Science / Mechanics / Fluids, Science / Physics / General, Technology \& Engineering / Mechanical}, isbn = {9780191523786}, author = {Elman, Howard and Silvester, David J and Wathen, Andrew J} } @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 {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 {19073, title = {The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease}, journal = {Science}, volume = {309}, year = {2005}, month = {2005}, author = {El-Sayed, N.M. and Myler,P. J and Bartholomeu,D. C and Nilsson,D. and Aggarwal,G. and Tran,A. N and Ghedin,E. and Worthey,E. A and Delcher,A. L and Blandin,G. and others} } @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} } @conference {11900, title = {A learning automata based power management for ad-hoc networks}, booktitle = {2005 IEEE International Conference on Systems, Man and Cybernetics}, volume = {4}, year = {2005}, month = {2005/10//}, pages = {3569- 3573 Vol. 4 - 3569- 3573 Vol. 4}, publisher = {IEEE}, organization = {IEEE}, abstract = {Power management is a very important aspect of ad-hoc networks. It directly impacts the network throughput among other network metrics. On the other hand, transmission power management may result in disconnected networks and increased level of collisions. In this paper, we introduce a transmission power control based on stochastic learning automata (SLA) to modify the transmission power. Based on the level of successful transmissions and the level of packet retransmissions, the SLA will modify the transmission power level either by increasing it or decreasing it. The probabilistic nature of SLA makes it a useful choice for ad-hoc networks. Using the network simulator NS, we show that using SLA for transmission power will result in an increased system bandwidth and a decrease in the collision levels.}, keywords = {ad hoc networks, ad-hoc networks, Computer network management, Computer networks, Energy management, Engineering management, learning automata, network metrics, network simulator, packet retransmissions, power control, power system management, power transmission control, stochastic learning automata, stochastic learning automta, Stochastic processes, system bandwidth, Technology management, Throughput, transmission power control, transmission power level, transmission power management}, isbn = {0-7803-9298-1}, doi = {10.1109/ICSMC.2005.1571701}, author = {El-Osery,A. I and Baird,D. and Abd-Almageed, Wael} } @conference {16681, title = {The linguist{\textquoteright}s search engine: an overview}, booktitle = {Proceedings of the ACL 2005 on Interactive poster and demonstration sessions}, year = {2005}, month = {2005///}, pages = {33 - 36}, author = {Resnik, Philip and Elkiss,A.} } @article {14154, title = {Preconditioning strategies for models of incompressible flow}, journal = {Journal of Scientific Computing}, volume = {25}, year = {2005}, month = {2005///}, pages = {347 - 366}, author = {Elman, Howard} } @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} } @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 {14072, title = {Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock}, journal = {Environmental Microbiology}, volume = {7}, year = {2005}, month = {2005/06/01/}, pages = {789 - 797}, abstract = {Temperature shock of the hyperthermophilic methanarchaeon Methanococcus jannaschii from its optimal growth temperature of 85{\textdegree}C to 65{\textdegree}C and 95{\textdegree}C resulted in different transcriptional responses characteristic of both the direction of shock (heat or cold shock) and whether the shock was lethal. Specific outcomes of lethal heat shock to 95{\textdegree}C included upregulation of genes encoding chaperones, and downregulation of genes encoding subunits of the H+ transporting ATP synthase. A gene encoding an α subunit of a putative prefoldin was also upregulated, which may comprise a novel element in the protein processing pathway in M. jannaschii. Very different responses were observed upon cold shock to 65{\textdegree}C. These included upregulation of a gene encoding an RNA helicase and other genes involved in transcription and translation, and upregulation of genes coding for proteases and transport proteins. Also upregulated was a gene that codes for an 18~kDa FKBP-type PPIase, which may facilitate protein folding at low temperatures. Transcriptional profiling also revealed several hypothetical proteins that respond to temperature stress conditions.}, isbn = {1462-2920}, doi = {10.1111/j.1462-2920.2005.00751.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2005.00751.x/abstract}, author = {Boonyaratanakornkit,Boonchai B and Simpson,Anjana J. and Whitehead,Timothy A and Fraser,Claire M. and El-Sayed, Najib M. and Clark,Douglas S} } @conference {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} } @article {16109, title = {Visualizing missing data: classification and empirical study}, journal = {Proceedings of INTERACT}, year = {2005}, month = {2005///}, pages = {861 - 872}, abstract = {Most visualization tools fail to provide support for missing data. We identify sources of missing, and categorize data visualization techniques based on the impact missing data have on the display: region dependent, attribute dependent, and neighbor dependent. We then report on a user study with 30 participants that compared three design variants. A between-subject graph interpretation study provides strong evidence for the need of indicating the presence of missing information, and some direction for addressing the problem.}, author = {Eaton,C. and Plaisant, Catherine and Drizd,T.} } @inbook {16108, title = {Visualizing Missing Data: Graph Interpretation User Study}, booktitle = {Human-Computer Interaction - INTERACT 2005}, series = {Lecture Notes in Computer Science}, volume = {3585}, year = {2005}, month = {2005///}, pages = {861 - 872}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Most visualization tools fail to provide support for missing data. In this paper, we identify sources of missing data and describe three levels of impact missing data can have on the visualization: perceivable, invisible or propagating. We then report on a user study with 30 participants that compared three design variants. A between-subject graph interpretation study provides strong evidence for the need of indicating the presence of missing information, and some direction for addressing the problem.}, isbn = {978-3-540-28943-2}, url = {http://dx.doi.org/10.1007/11555261_68}, author = {Eaton,Cyntrica and Plaisant, Catherine and Drizd,Terence}, editor = {Costabile,Maria and Patern{\`o},Fabio} } @conference {16684, title = {The web in theoretical linguistics research: Two case studies using the Linguist{\textquoteright}s Search Engine}, booktitle = {31st Meeting of the Berkeley Linguistics Society}, year = {2005}, month = {2005///}, pages = {265 - 276}, author = {Resnik, Philip and Elkiss,A. and Lau,E. and Taylor,H.} } @conference {19670, title = {What Are the Ants Doing? Vision-Based Tracking and Reconstruction of Control Programs}, booktitle = {Proceedings of the 2005 IEEE International Conference on Robotics and Automation, 2005. ICRA 2005}, year = {2005}, month = {2005/04//}, pages = {4182 - 4187}, abstract = {In this paper, we study the problem of going from a real-world, multi-agent system to the generation of control programs in an automatic fashion. In particular, a computer vision system is presented, capable of simultaneously tracking multiple agents, such as social insects. Moreover, the data obtained from this system is fed into a mode-reconstruction module that generates low-complexity control programs, i.e. strings of symbolic descriptions of control-interrupt pairs, consistent with the empirical data. The result is a mechanism for going from the real system to an executable implementation that can be used for controlling multiple mobile robots.}, keywords = {Animals, Automatic generation control, Biological information theory, Computer vision, Control systems, Mobile robots, Probability distribution, Robot control, target tracking, Trajectory}, author = {Egerstedt, M. and Balch, T. and Dellaert, F. and Delmotte, F. and Zia Khan} } @article {14075, title = {Advances in schistosome genomics}, journal = {Trends in Parasitology}, volume = {20}, year = {2004}, month = {2004/04/01/}, pages = {154 - 157}, abstract = {In Spring 2004, the first draft of the 270~Mb genome of Schistosoma mansoni will be released. This sequence is based on the assembly and annotation of a >7.5-fold coverage, shotgun sequencing project. The key stages involved in the international collaborative efforts that have led to the generation of these sequencing data for the parasite S. mansoni are discussed here.}, isbn = {1471-4922}, doi = {16/j.pt.2004.02.002}, url = {http://www.sciencedirect.com/science/article/pii/S1471492204000480}, author = {El-Sayed, Najib M. and Bartholomeu,Daniella and Ivens,Alasdair and Johnston,David A. and LoVerde,Philip T.} } @article {14481, title = {Data sciences technology for homeland security information management and knowledge discovery}, journal = {Report of the DHS Workshop Data Sciences, Jointly Released by Sandia National Laboratories and Lawrence Livermore National Laboratory, Alexandria, Va}, year = {2004}, month = {2004///}, author = {Kolda,T. and Brown,D and Corones,J. and Critchlow,T. and Eliassi-Rad,T. and Getoor, Lise and Hendrickson,B. and Kumar, V. and Lambert,D. and Matarazzo,C.} } @article {15451, title = {Evaluating web page reliability across varied browsing environments}, journal = {Proceedings of the 15th IEEE International Symposium on Software Reliability Engineering (ISSRE{\textquoteright}04)}, year = {2004}, month = {2004///}, abstract = {Web page reliability is significantly influenced by thebrowser, browser version, and operating system incorpo- rated in end-user browsing environments. The tool we have developed evaluates reliability of web-bound content across various client platforms based on the relationship between two key accessibility factors: (1) the HTML tags that struc- ture a given web page and (2) the support provided for each tag in target browsing environments. To optimize evaluation accuracy, we have designed a learning mechanism that in- ductively acquires knowledge of tag support criteria based on observed samples of accessible (properly rendered) and inaccessible (faulty) web page source code. Our contribu- tion is expected to provide web developers with a basis for maximizing audience reach through improved awareness of the browsing environment profiles associated with dimin- ished accessibility to their websites. }, author = {Eaton,C. and Memon, Atif M.} } @article {15458, title = {Improving browsing environment compliance evaluations for websites}, journal = {Proceedings of the International Workshop on Web Quality (WQ{\textquoteright}04)}, year = {2004}, month = {2004///}, abstract = {Identifying accessibility issues that can threaten universal website usability is criticalfor web service and content providers who wish to accommodate the diverse web audience. Detecting page-to-environment incompliance and modifying pages to promote universal accessibility is one important step in improving the process of exploration and navigation in the web user experience. To address this issue, we have designed a system that evaluates the accessibility of a web page in a given browsing environment based on knowledge of the HyperText Markup Language (HTML) tags that comprise the page and knowledge of the tag support provided in respective browsing environments. Given this approach, one of the most important aspects of the system is the comprehensive nature of tag support knowledge. The more support rules known, the more environment-specific bugs the system can accurately identify. In order to optimize knowledge of tag support criteria, we have also incorporated a learning mechanism that can inductively determine HTML tags that are unsupported in a given environment by observing both positive and negative examples of web page appearance and behavior. }, author = {Eaton,C. and Memon, Atif M.} } @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.} } @article {17626, title = {Modelling disease outbreaks in realistic urban social networks}, journal = {Nature}, volume = {429}, year = {2004}, month = {2004/05/13/}, pages = {180 - 184}, abstract = {Most mathematical models for the spread of disease use differential equations based on uniform mixing assumptions1 or ad hoc models for the contact process2, 3, 4. Here we explore the use of dynamic bipartite graphs to model the physical contact patterns that result from movements of individuals between specific locations. The graphs are generated by large-scale individual-based urban traffic simulations built on actual census, land-use and population-mobility data. We find that the contact network among people is a strongly connected small-world-like5 graph with a well-defined scale for the degree distribution. However, the locations graph is scale-free6, which allows highly efficient outbreak detection by placing sensors in the hubs of the locations network. Within this large-scale simulation framework, we then analyse the relative merits of several proposed mitigation strategies for smallpox spread. Our results suggest that outbreaks can be contained by a strategy of targeted vaccination combined with early detection without resorting to mass vaccination of a population.}, isbn = {0028-0836}, doi = {10.1038/nature02541}, url = {http://www.nature.com/nature/journal/v429/n6988/full/nature02541.html}, author = {Eubank,Stephen and Guclu,Hasan and Kumar,V. S. Anil and Marathe,Madhav V. and Srinivasan, Aravind and Toroczkai,Zolt|[aacute]|n and Wang,Nan} } @article {13226, title = {Multi-cue exemplar-based nonparametric model for gesture recognition}, journal = {Indian Conference on Computer Vision, Graphics and Image Processing}, year = {2004}, month = {2004///}, pages = {16 - 18}, abstract = {This paper presents an approach for a multi-cue, view-based recognition of gestures. We describe an exemplar- based technique that combines two different forms of exem- plars - shape exemplars and motion exemplars - in a uni- fied probabilistic framework. Each gesture is represented as a sequence of learned body poses as well as a sequence of learned motion parameters. The shape exemplars are comprised of pose contours, and the motion exemplars are represented as affine motion parameters extracted using a robust estimation approach. The probabilistic framework learns by employing a nonparametric estimation technique to model the exemplar distributions. It imposes temporal constraints between different exemplars through a learned Hidden Markov Model (HMM) for each gesture. We use the proposed multi-cue approach to recognize a set of four- teen gestures and contrast it against a shape only, single- cue based system. }, author = {Shet,V. D and Prasad,V. S.N and Elgammal,A. and Yacoob,Yaser and Davis, Larry S.} } @article {14039, title = {On-Line Kernel-Based Tracking in Joint Feature-Spatial Spaces}, journal = {IEEE, 0-7695-2158-2164}, year = {2004}, month = {2004///}, abstract = {We will demonstrate an object tracking algorithm thatuses a novel simple symmetric similarity function between spatially-smoothed kernel-density estimates of the model and target distributions. The similarity measure is based on the expectation of the density estimates over the model or target images. The density is estimated using radial-basis kernel functions which measure the affinity between points and provide a better outlier rejection property. The mean- shift algorithm is used to track objects by iteratively max- imizing this similarity function. To alleviate the quadratic complexity of the density estimation, we employ Gaussian kernels and the fast Gauss transform to reduce the compu- tations to linear order. This leads to a very efficient and robust nonparametric tracking algorithm. More details can be found in [2]. The system processes online video stream on a P4 1.4GHz and achieves 30 frames per second using an ordinary webcam. }, author = {Yang,C. and Duraiswami, Ramani and Elgammal,A. and Davis, Larry S.} } @article {12940, title = {Polylysogeny and prophage induction by secondary infection in Vibrio cholerae}, journal = {Environmental Microbiology}, volume = {6}, year = {2004}, month = {2004/07/01/}, pages = {760 - 763}, abstract = {Strains of Vibrio cholerae O1, biotypes El Tor and classical, were infected with a known temperate phage (ΦP15) and monitored over a 15-day period for prophage induction. Over the course of the experiment two morphologically and three genomically distinct virus-like particles were observed from the phage-infected El Tor strain by transmission electron microscopy and field inversion gel electrophoresis, respectively, whereas only one phage, ΦP15, was observed from the infected classical strain. In the uninfected El Tor culture one prophage was spontaneously induced after 6~days. No induction in either strain was observed after treatment with mitomycin C. Data indicate that El Tor biotypes of V. cholerae may be polylysogenic and that secondary infection can promote multiple prophage induction. These traits may be important in the transfer of genetic material among V. cholerae by providing an environmentally relevant route for multiple prophage propagation and transmission.}, isbn = {1462-2920}, doi = {10.1111/j.1462-2920.2004.00603.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2004.00603.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Espeland,Eric M. and Lipp,Erin K. and Huq,Anwar and Rita R Colwell} } @article {13221, title = {Real-Time Kernel-Based Tracking in Joint Feature-Spatial Spaces}, year = {2004}, month = {2004/04/19/}, abstract = {An object tracking algorithm that uses a novel simple symmetric similarityfunction between spatially-smoothed kernel-density estimates of the model and target distributions is proposed and tested. The similarity measure is based on the expectation of the density estimates over the model or target images. The density is estimated using radial-basis kernel functions which measure the affinity between points and provide a better outlier rejection property. The mean-shift algorithm is used to track objects by iteratively maximizing this similarity function. To alleviate the quadratic complexity of the density estimation, we employ Gaussian kernels and the fast Gauss transform to reduce the computations to linear order. This leads to a very efficient and robust nonparametric tracking algorithm. The proposed algorithm is tested with several image sequences and shown to achieve robust and reliable real-time tracking. (UMIACS-TR-2004-12) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1341}, author = {Yang,Changjiang and Duraiswami, Ramani and Elgammal,Ahmed and Davis, Larry S.} } @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 {14080, title = {Sequencing Strategies for Parasite Genomes}, journal = {METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-}, volume = {270}, year = {2004}, month = {2004///}, pages = {1 - 16}, author = {Bartholomeu,D. and El-Sayed, Najib M. and Melville,S. E.} } @conference {17661, title = {Structural and algorithmic aspects of massive social networks}, booktitle = {Proceedings of the fifteenth annual ACM-SIAM symposium on Discrete algorithms}, series = {SODA {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {718 - 727}, publisher = {Society for Industrial and Applied Mathematics}, organization = {Society for Industrial and Applied Mathematics}, address = {Philadelphia, PA, USA}, abstract = {We study the algorithmic and structural properties of very large, realistic social contact networks. We consider the social network for the city of Portland, Oregon, USA, developed as a part of the TRANSIMS/EpiSims project at the Los Alamos National Laboratory. The most expressive social contact network is a bipartite graph, with two types of nodes: people and locations; edges represent people visiting locations on a typical day. Three types of results are presented. (i) Our empirical results show that many basic characteristics of the dataset are well-modeled by a random graph approach suggested by Fan Chung Graham and Lincoln Lu (the CL-model), with a power-law degree distribution. (ii) We obtain fast approximation algorithms for computing basic structural properties such as clustering coefficients and shortest paths distribution. We also study the dominating set problem for such networks; this problem arose in connection with optimal sensor-placement for disease-detection. We present a fast approximation algorithm for computing near-optimal dominating sets. (iii) Given the close approximations provided by the CL-model to our original dataset and the large data-volume, we investigate fast methods for generating such random graphs. We present methods that can generate such a random network in near-linear time, and show that these variants asymptotically share many key features of the CL-model, and also match the Portland social network.The structural results have been used to study the impact of policy decisions for controlling large-scale epidemics in urban environments.}, isbn = {0-89871-558-X}, url = {http://dl.acm.org/citation.cfm?id=982792.982902}, author = {Eubank,Stephen and Kumar,V. S. Anil and Marathe,Madhav V. and Srinivasan, Aravind and Wang,Nan} } @article {16480, title = {Techniques for optimization of queries on integrated biological resources}, journal = {Journal of bioinformatics and computational biology}, volume = {2}, year = {2004}, month = {2004///}, pages = {375 - 412}, author = {Lacroix,Z. and Raschid, Louiqa and Eckman,B. A} } @article {14066, title = {2003 IEEE Workshop on Applications of Signal Processing to Audio and Acoustics October 19-22, 2003, New Paltz. NY}, journal = {2003 IEEE Workshop on Applications of Signal Processing to Audio and Acoustics: October 19-22, 2003, Mohonk Mountain House, New Paltz, NY, USA}, year = {2003}, month = {2003///}, pages = {238 - 238}, author = {Adams,N. and EssI,G. and Makino,S. and Martens,A.A.C.F.W.L. and Algazi,R. and Fellers,M. and Martin,R. and Avendano,C. and Fielder,L. and Mellody,M. and others} } @article {14108, title = {An Analysis of Smoothing Effects of Upwinding Strategies for the Convection-Diffusion Equation}, journal = {SIAM Journal on Numerical Analysis}, volume = {40}, year = {2003}, month = {2003/01/01/}, pages = {254 - 281}, abstract = {Using a technique for constructing analytic expressions for discrete solutions to the convection-diffusion equation, we examine and characterize the effects of upwinding strategies on solution quality. In particular, for grid-aligned flow and discretization based on bilinear finite elements with streamline upwinding, we show precisely how the amount of upwinding included in the discrete operator affects solution oscillations and accuracy when different types of boundary layers are present. This analysis provides a basis for choosing a streamline upwinding parameter which also gives accurate solutions for problems with non-grid-aligned and variable speed flows. In addition, we show that the same analytic techniques provide insight into other discretizations, such as a finite difference method that incorporates streamline diffusion and the isotropic artificial diffusion method.}, isbn = {0036-1429}, url = {http://www.jstor.org/stable/4100953}, author = {Elman, Howard and Alison Ramage} } @conference {12076, title = {Bootstrapping security associations for routing in mobile ad-hoc networks}, booktitle = {IEEE Global Telecommunications Conference, 2003. GLOBECOM {\textquoteright}03}, volume = {3}, year = {2003}, month = {2003/12/01/5}, pages = {1511- 1515 vol.3 - 1511- 1515 vol.3}, publisher = {IEEE}, organization = {IEEE}, abstract = {To date, most solutions proposed for secure routing in mobile ad-hoc networks (MANETs), assume that secure associations between pairs of nodes can be established on-line; e.g., by a trusted third party, by distributed trust establishment. However, establishing such security associations, with or without trusted third parties, requires reliance on routing layer security. In this paper, we eliminate this apparent cyclic dependency between security services and secure routing in MANETs and show how to bootstrap security for the routing layer. We use the notion of statistically unique and cryptographically verifiable (SUCV) identifiers to implement a secure binding between IP addresses and keys that is independent of any trusted security service. We illustrate our solution with the dynamic source routing (DSR) protocol and compare it with other solutions for secure routing.}, keywords = {ad hoc networks, bootstrapping security association, Cryptographic protocols, dynamic source routing protocol, Fabrics, Intelligent networks, IP address, IP key, IP networks, Message authentication, mobile ad-hoc network, mobile radio, Protection, Public key, public key cryptography, routing layer security reliability, routing protocols, secure routing, Security, security service, statistically unique cryptographically verification, telecommunication security}, isbn = {0-7803-7974-8}, doi = {10.1109/GLOCOM.2003.1258490}, author = {Bobba,R. B and Eschenauer,L. and Gligor,V. and Arbaugh, William A.} } @conference {16144, title = {The Challenge of Missing and Uncertain Data}, booktitle = {Proceedings of the 14th IEEE Visualization 2003 (VIS{\textquoteright}03)}, series = {VIS {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {100{\textendash} - 100{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, isbn = {0-7695-2030-8}, doi = {10.1109/VIS.2003.10029}, url = {http://dx.doi.org/10.1109/VIS.2003.10029}, author = {Eaton,Cyntrica and Plaisant, Catherine and Drizd,Terence} } @article {14161, title = {A characterisation of oscillations in the discrete two-dimensional convection-diffusion equation}, journal = {Mathematics of computation}, volume = {72}, year = {2003}, month = {2003///}, pages = {263 - 288}, author = {Elman, Howard and Ramage, A.} } @article {14110, title = {Complete stagnation of}, journal = {Linear Algebra and its Applications}, volume = {367}, year = {2003}, month = {2003/07/01/}, pages = {165 - 183}, abstract = {We study problems for which the iterative method for solving linear systems of equations makes no progress in its initial iterations. Our tool for analysis is a nonlinear system of equations, the stagnation system, that characterizes this behavior. We focus on complete stagnation, for which there is no progress until the last iteration. We give necessary and sufficient conditions for complete stagnation of systems involving unitary matrices, and show that if a normal matrix completely stagnates then so does an entire family of nonnormal matrices with the same eigenvalues. Finally, we show that there are real matrices for which complete stagnation occurs for certain complex right-hand sides but not for real ones.}, keywords = {Convergence, GMRES, iterative methods, Stagnation}, isbn = {0024-3795}, doi = {16/S0024-3795(02)00612-2}, url = {http://www.sciencedirect.com/science/article/pii/S0024379502006122}, author = {Zavorin, Ilya and O{\textquoteright}Leary, Dianne P. and Elman, Howard} } @article {15730, title = {Complete stagnation of GMRES}, journal = {Linear Algebra and its Applications}, volume = {367}, year = {2003}, month = {2003/07/01/}, pages = {165 - 183}, abstract = {We study problems for which the iterative method gmres for solving linear systems of equations makes no progress in its initial iterations. Our tool for analysis is a nonlinear system of equations, the stagnation system, that characterizes this behavior. We focus on complete stagnation, for which there is no progress until the last iteration. We give necessary and sufficient conditions for complete stagnation of systems involving unitary matrices, and show that if a normal matrix completely stagnates then so does an entire family of nonnormal matrices with the same eigenvalues. Finally, we show that there are real matrices for which complete stagnation occurs for certain complex right-hand sides but not for real ones.}, keywords = {Convergence, GMRES, iterative methods, Stagnation}, isbn = {0024-3795}, doi = {10.1016/S0024-3795(02)00612-2}, url = {http://www.sciencedirect.com/science/article/pii/S0024379502006122}, author = {Zavorin, Ilya and O{\textquoteright}Leary,Dianne P. and Elman, Howard} } @book {12377, title = {Design Considerations for Optically Connected Systems on Chip}, year = {2003}, month = {2003///}, publisher = {MARYLAND UNIV COLLEGE PARK DEPT OF ELECTRICAL AND COMPUTER ENGINEERING}, organization = {MARYLAND UNIV COLLEGE PARK DEPT OF ELECTRICAL AND COMPUTER ENGINEERING}, author = {Bhattacharyya, Shuvra S. and Bambha,N. K and Euliss,G.} } @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 {14064, title = {Efficient kernel density estimation using the fast gauss transform with applications to color modeling and tracking}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {25}, year = {2003}, month = {2003///}, pages = {1499 - 1504}, author = {Elgammal,A. and Duraiswami, Ramani and Davis, Larry S.} } @article {13235, title = {Efficient kernel density estimation using the fast gauss transform with applications to color modeling and tracking}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {25}, year = {2003}, month = {2003/11//}, pages = {1499 - 1504}, abstract = {Many vision algorithms depend on the estimation of a probability density function from observations. Kernel density estimation techniques are quite general and powerful methods for this problem, but have a significant disadvantage in that they are computationally intensive. In this paper, we explore the use of kernel density estimation with the fast Gauss transform (FGT) for problems in vision. The FGT allows the summation of a mixture of ill Gaussians at N evaluation points in O(M+N) time, as opposed to O(MN) time for a naive evaluation and can be used to considerably speed up kernel density estimation. We present applications of the technique to problems from image segmentation and tracking and show that the algorithm allows application of advanced statistical techniques to solve practical vision problems in real-time with today{\textquoteright}s computers.}, keywords = {algorithms;, Color, Computer, density, estimation;, fast, function;, Gauss, image, Kernel, modeling;, segmentation;, tracking;, transform;, transforms;, VISION, vision;}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2003.1240123}, author = {Elgammal,A. and Duraiswami, Ramani and Davis, Larry S.} } @conference {13240, title = {Exemplar-based tracking and recognition of arm gestures}, booktitle = {Image and Signal Processing and Analysis, 2003. ISPA 2003. Proceedings of the 3rd International Symposium on}, volume = {2}, year = {2003}, month = {2003/09//}, pages = {656 - 661 Vol.2 - 656 - 661 Vol.2}, abstract = {This paper presents a probabilistic exemplar-based framework for recognizing gestures. The approach is based on representing each gesture as a sequence of learned body poses. The gestures are recognized through a probabilistic framework for matching these body poses and for imposing temporal constrains between different poses. Matching individual poses to image data is performed using a probabilistic formulation for edge matching to obtain a likelihood measurement for each individual pose. The paper introduces a correspondence-free weighted matching scheme for edge templates that emphasize discriminating features in the matching. The weighting does not require establishing correspondences between the different pose models. The probabilistic framework also imposes temporal constrains between different pose through a learned hidden Markov model (HMM) of each gesture.}, keywords = {arm, constrains;, correspondence-free, edge, exemplar-based, framework;, gesture, hidden, HMM;, image, logic;, Markov, MATCHING, matching;, model;, models;, probabilistic, recognition;, scheme;, segmentation;, temporal, tracking;, weighted}, doi = {10.1109/ISPA.2003.1296358}, author = {Elgammal,A. and Shet,V. and Yacoob,Yaser and Davis, Larry S.} } @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.} } @conference {13244, title = {Image-based pan-tilt camera control in a multi-camera surveillance environment}, booktitle = {Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {1}, year = {2003}, month = {2003/07//}, pages = {I - 645-8 vol.1 - I - 645-8 vol.1}, abstract = {In automated surveillance systems with multiple cameras, the system must be able to position the cameras accurately. Each camera must be able to pan-tilt such that an object detected in the scene is in a vantage position in the camera{\textquoteright}s image plane and subsequently capture images of that object. Typically, camera calibration is required. We propose an approach that uses only image-based information. Each camera is assigned a pan-tilt zero-position. Position of an object detected in one camera is related to the other cameras by homographies between the zero-positions while different pan-tilt positions of the same camera are related in the form of projective rotations. We then derive that the trajectories in the image plane corresponding to these projective rotations are approximately circular for pan and linear for tilt. The camera control technique is subsequently tested in a working prototype.}, keywords = {automated, camera, cameras;, control;, detection;, environment;, image, image-based, information;, multicamera, object, pan-tilt, position;, processing;, sensors;, Surveillance, surveillance;, systems;, vantage, zero-position;, zero-positions;}, doi = {10.1109/ICME.2003.1221000}, author = {Lim,Ser-Nam and Elgammal,A. and Davis, Larry S.} } @conference {13247, title = {Learning dynamics for exemplar-based gesture recognition}, booktitle = {Computer Vision and Pattern Recognition, 2003. Proceedings. 2003 IEEE Computer Society Conference on}, volume = {1}, year = {2003}, month = {2003/06//}, pages = {I-571 - I-578 vol.1 - I-571 - I-578 vol.1}, abstract = {This paper addresses the problem of capturing the dynamics for exemplar-based recognition systems. Traditional HMM provides a probabilistic tool to capture system dynamics and in exemplar paradigm, HMM states are typically coupled with the exemplars. Alternatively, we propose a non-parametric HMM approach that uses a discrete HMM with arbitrary states (decoupled from exemplars) to capture the dynamics over a large exemplar space where a nonparametric estimation approach is used to model the exemplar distribution. This reduces the need for lengthy and non-optimal training of the HMM observation model. We used the proposed approach for view-based recognition of gestures. The approach is based on representing each gesture as a sequence of learned body poses (exemplars). The gestures are recognized through a probabilistic framework for matching these body poses and for imposing temporal constraints between different poses using the proposed non-parametric HMM.}, keywords = {arbitrary, body, by, Computer, constraint;, detection;, discrete, distribution, dynamics;, edge, estimation;, example;, exemplar, exemplar-based, extraction;, feature, framework;, gesture, gesture;, hidden, HMM;, human, image, learning, Markov, matching;, model;, models;, motion;, nonparametric, pose, probabilistic, recognition;, sequence;, space;, state;, statistics;, system, temporal, tool;, view-based, vision;}, doi = {10.1109/CVPR.2003.1211405}, author = {Elgammal,A. and Shet,V. and Yacoob,Yaser and Davis, Larry S.} } @conference {11905, title = {Non-parametric expectation maximization: a learning automata approach}, booktitle = {IEEE International Conference on Systems, Man and Cybernetics, 2003}, volume = {3}, year = {2003}, month = {2003/10//}, pages = {2996- 3001 vol.3 - 2996- 3001 vol.3}, publisher = {IEEE}, organization = {IEEE}, abstract = {The famous expectation maximization technique suffers two major drawbacks. First, the number of components has to be specified apriori. Also, the expectation maximization is sensitive to initialization. In this paper, we present a new stochastic technique for estimating the mixture parameters. Parzen Window is used to estimate a discrete estimate of the PDF of the given data. Stochastic learning automata is then used to select the mixture parameters that minimize the distance between the discrete estimate of the PDF and the estimate of the expectation maximization. The validity of the proposed approach is verified using bivariate simulation data.}, keywords = {Automatic speech recognition, bivariate simulation data, Computational modeling, Computer vision, Density functional theory, expectation maximization technique, learning automata, mixture parameters estimation, nonparametric expectation maximization, nonparametric statistics, optimisation, parameter estimation, Parzen Window, PDF, probability, probability density function, Speech processing, Speech recognition, stochastic learning automata, Stochastic processes, stochastic technique}, isbn = {0-7803-7952-7}, doi = {10.1109/ICSMC.2003.1244347}, author = {Abd-Almageed, Wael and El-Osery,A. and Smith,C.E.} } @conference {13248, title = {Probabilistic tracking in joint feature-spatial spaces}, booktitle = {Computer Vision and Pattern Recognition, 2003. Proceedings. 2003 IEEE Computer Society Conference on}, volume = {1}, year = {2003}, month = {2003/06//}, pages = {I-781 - I-788 vol.1 - I-781 - I-788 vol.1}, abstract = {In this paper, we present a probabilistic framework for tracking regions based on their appearance. We exploit the feature-spatial distribution of a region representing an object as a probabilistic constraint to track that region over time. The tracking is achieved by maximizing a similarity-based objective function over transformation space given a nonparametric representation of the joint feature-spatial distribution. Such a representation imposes a probabilistic constraint on the region feature distribution coupled with the region structure, which yields an appearance tracker that is robust to small local deformations and partial occlusion. We present the approach for the general form of joint feature-spatial distributions and apply it to tracking with different types of image features including row intensity, color and image gradient.}, keywords = {analysis;, appearance, appearance;, color;, colour, Computer, constraint;, deformation;, detection;, distribution;, edge, estimation;, extraction;, feature, feature-spatial, feature;, function, gradient;, image, intensity;, joint, likelihood, local, maximization;, maximum, nonparametric, object, objective, occlusion;, optical, partial, probabilistic, probability;, region, representation;, row, similarity-based, small, space;, structure;, target, tracker;, tracking;, transformation, vision;}, doi = {10.1109/CVPR.2003.1211432}, author = {Elgammal,A. and Duraiswami, Ramani and Davis, Larry S.} } @article {16486, title = {A query language to support scientific discovery}, journal = {Proc. 2nd IEEE International Computer Society}, year = {2003}, month = {2003///}, author = {Eckman,B. and Deutsch,K. and Janer,M. and Lacroix,Z. and Raschid, Louiqa} } @book {12096, title = {Real 802.11 Security: Wi-Fi Protected Access and 802.11 i, 480 pages}, year = {2003}, month = {2003///}, publisher = {Addison Wesley}, organization = {Addison Wesley}, author = {Edney,J. and Arbaugh, William A.} } @conference {13245, title = {Scalable image-based multi-camera visual surveillance system}, booktitle = {Proceedings. IEEE Conference on Advanced Video and Signal Based Surveillance, 2003.}, year = {2003}, month = {2003/07//}, pages = {205 - 212}, abstract = {We describe the design of a scalable and wide coverage visual surveillance system. Scalability (the ability to add and remove cameras easily during system operation with minimal overhead and system degradation) is achieved by utilizing only image-based information for camera control. We show that when a pan-tilt-zoom camera pans and tilts, a given image point moves in a circular and a linear trajectory, respectively. We create a scene model using a plan view of the scene. The scene model makes it easy for us to handle occlusion prediction and schedule video acquisition tasks subject to visibility constraints. We describe a maximum weight matching algorithm to assign cameras to tasks that meet the visibility constraints. The system is illustrated both through simulations and real video from a 6-camera configuration.}, keywords = {ACQUISITION, algorithm;, camera;, constraints;, feature, hidden, image-based, MATCHING, maximum, multi-camera, occlusion, pan-tilt-zoom, PLAN, prediction;, processing;, removal;, scalable, scheduling;, signal, Surveillance, surveillance;, system;, task, video, view;, visibility, visual, weight}, doi = {10.1109/AVSS.2003.1217923}, author = {Lim,Ser-Nam and Davis, Larry S. and Elgammal,A.} } @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} } @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 {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} } @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.} } @article {14107, title = {Block preconditioners for the discrete incompressible Navier{\textendash}Stokes equations}, journal = {International Journal for Numerical Methods in Fluids}, volume = {40}, year = {2002}, month = {2002/09/30/}, pages = {333 - 344}, abstract = {We examine the convergence characteristics of iterative methods based on a new preconditioning operator for solving the linear systems arising from discretization and linearization of the steady-state Navier{\textendash}Stokes equations. For steady-state problems, we show that the preconditioned problem has an eigenvalue distribution consisting of a tightly clustered set together with a small number of outliers. These characteristics are directly correlated with the convergence properties of iterative solvers, with convergence rates independent of mesh size and only mildly dependent on viscosity. For evolutionary problems, we show that implicit treatment of the time derivatives leads to systems for which convergence is essentially independent of viscosity. Copyright {\textcopyright} 2002 John Wiley \& Sons, Ltd.}, keywords = {Iterative algorithms, Navier{\textendash}Stokes equations, preconditioning}, isbn = {1097-0363}, doi = {10.1002/fld.311}, url = {http://onlinelibrary.wiley.com/doi/10.1002/fld.311/abstract}, author = {Elman, Howard and Silvester, David J and Wathen, Andrew J} } @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 {17818, title = {Computational Logic: Logic Programming and Beyond, Essays in Honour of Robert A}, journal = {Kowalski, Part I}, year = {2002}, month = {2002///}, pages = {586 - 625}, author = {Eiter,T. and Mascardi,V. and V.S. Subrahmanian} } @inbook {17817, title = {Error-Tolerant Agents}, booktitle = {Computational Logic: Logic Programming and BeyondComputational Logic: Logic Programming and Beyond}, series = {Lecture Notes in Computer Science}, volume = {2407}, year = {2002}, month = {2002///}, pages = {83 - 104}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The use of agents in today{\textquoteright}s Internet world is expanding rapidly. Yet, agent developers proceed largely under the optimistic assumption that agents will be error-free. Errors may arise in agents for numerous reasons {\textemdash} agents may share a workspace with other agents or humans and updates made by these other entities may cause an agent to face a situation that it was not explicitly programmed to deal with. Likewise, errors in coding agents may lead to inconsistent situations where it is unclear how the agent should act. In this paper, we define an agent execution model that allows agents to continue acting {\textquotedblleft}reasonably{\textquotedblright} even when some errors of the above types occur. More importantly, in our framework, agents take {\textquotedblleft}repair{\textquotedblright} actions automatically when confronted with such situations, but while taking such repair actions, they can often continue to engage in work and/or interactions with other agents that are unaffected by repairs.}, keywords = {Computer, Science}, isbn = {978-3-540-43959-2}, url = {http://dx.doi.org/10.1007/3-540-45628-7_22}, author = {Eiter,Thomas and Mascardi,Viviana and Subrahmanian,V.}, editor = {Kakas,Antonis and Sadri,Fariba} } @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.} } @conference {13047, title = {GLEANS: A generator of logical extracts and abstracts for nice summaries}, booktitle = {Workshop on Automatic Summarization}, year = {2002}, month = {2002///}, pages = {9 - 14}, author = {Daum{\'e}, Hal and Echihabi,A. and Marcu,D. and Munteanu,D. and Soricut,R.} } @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 {14152, title = {A multigrid method enhanced by Krylov subspace iteration for discrete Helmholtz equations}, journal = {SIAM Journal on scientific computing}, volume = {23}, year = {2002}, month = {2002///}, pages = {1291 - 1315}, author = {Elman, Howard and Ernst, O. G and O{\textquoteright}Leary, Dianne P. and others} } @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 {14137, title = {Performance and analysis of saddle point preconditioners for the discrete steady-state Navier-Stokes equations}, journal = {Numerische Mathematik}, volume = {90}, year = {2002}, month = {2002///}, pages = {665 - 688}, author = {Elman, Howard and Silvester, D. J and Wathen, A. J} } @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 {17973, title = {System and method for entering text in a virtual environment}, volume = {:~09/364,433}, year = {2002}, month = {2002/06/18/}, abstract = {A system and method for entering text in a virtual environment by sensory gloves. The user enters a key that represents one or more letters by simulating a press of a keyboard in the gloves. The user calibrates the gloves by entering text, during which time the system establishes threshold values that represent simulated presses for each finger. After the initial calibration of the sensory gloves, the user enters text with simulated finger presses. The system distinguishes which movements are intended as simulated finger presses by examining the relative motions of fingers and maintaining dynamic thresholds. Errors are alleviated by providing feedback to the user, such as beeps and a visual display of the fingers and the current text. Because keys may represent more than one character, the system determines the intended text by probabilistic analysis and the Viterbi algorithm.}, url = {http://www.google.com/patents?id=w0QJAAAAEBAJ}, author = {Evans,Francine and Skiena,Steven and Varshney, Amitabh}, editor = {The Research Foundation of the State University of New York} } @article {15884, title = {Translation-based indexing for cross-language retrieval}, journal = {Advances in Information Retrieval}, year = {2002}, month = {2002///}, pages = {425 - 447}, author = {Oard, Douglas and Ertunc,F.} } @article {14101, title = {Trypanosoma cruzi: RNA structure and post-transcriptional control of tubulin gene expression}, journal = {Experimental Parasitology}, volume = {102}, year = {2002}, month = {2002/11//}, pages = {123 - 133}, abstract = {Changes in tubulin expression are among the biochemical and morphological adaptations that occur during the life cycle of Trypanosomatids. To investigate the mechanism responsible for the differential accumulation of tubulin mRNAs in Trypanosoma cruzi, we determine the sequences of [alpha]- and [beta]-tubulin transcripts and analyzed their expression during the life cycle of the parasite. Two [beta]-tubulin mRNAs of 1.9 and 2.3~kb were found to differ mainly by an additional 369 nucleotides at the end of the 3{\textquoteright} untranslated region (UTR). Although their transcription rates are similar in epimastigotes and amastigotes, [alpha]- and [beta]-tubulin transcripts are 3- to 6-fold more abundant in epimastigotes than in trypomastigotes and amastigotes. Accordingly, the half-lives of [alpha]- and [beta]-tubulin mRNAs are significantly higher in epimastigotes than in amastigotes. Transient transfection experiments indicated that positive regulatory elements occur in the 3{\textquoteright} UTR plus downstream intergenic region of the [alpha]-tubulin gene and that both positive and negative elements occur in the equivalent regions of the [beta]-tubulin gene.Index Descriptions and Abbreviations: Kinetoplastida; Trypanosoma cruzi; tubulin; gene regulation; PCR, polymerase chain reaction; UTR, untranslated region; IR, intergenic region; SL, spliced leader; BAC, bacterial artificial chromosome.}, isbn = {0014-4894}, doi = {16/S0014-4894(03)00034-1}, url = {http://www.sciencedirect.com/science/article/pii/S0014489403000341}, author = {Bartholomeu,Daniella C. and Silva,Rosiane A. and Galv{\~a}o,Lucia M. C. and El-Sayed, Najib M. and Donelson,John E. and Teixeira,Santuza M.R.} } @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 {14067, title = {Analysis of a donor gene region for a variant surface glycoprotein and its expression site in African trypanosomes}, journal = {Nucleic acids research}, volume = {29}, year = {2001}, month = {2001///}, pages = {2012 - 2012}, author = {LaCount,D. J and El-Sayed, Najib M. and Kaul,S. and Wanless,D. and Turner,C. M.R and Donelson,J. E} } @book {16985, title = {Becoming a Scholar in the Digital Age}, year = {2001}, month = {2001///}, publisher = {National Research Council}, organization = {National Research Council}, keywords = {bibtex-import, digital-library, dlbook}, author = {Duderstadt,James and Arms,William and Messina,Paul and Ellisman,Mark and Atkins,Daniel and Fox,Edward and Shneiderman, Ben and Nissenbaum,Helen and Lederberg,Joshua} } @conference {16466, title = {Optimized seamless integration of biomolecular data}, booktitle = {Proceedings of the IEEE 2nd International Symposium on Bioinformatics and Bioengineering Conference, 2001}, year = {2001}, month = {2001/11/04/6}, pages = {23 - 32}, publisher = {IEEE}, organization = {IEEE}, abstract = {Today, scientific data is inevitably digitized, stored in a variety of heterogeneous formats, and is accessible over the Internet. Scientists need to access an integrated view of multiple remote or local heterogeneous data sources. They then integrate the results of complex queries and apply further analysis and visualization to support the task of scientific discovery. Building a digital library for scientific discovery requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web, as well as data that is locally materialized in warehouses or is generated by software. We consider several tasks to provide optimized and seamless integration of biomolecular data. Challenges to be addressed include capturing and representing source capabilities; developing a methodology to acquire and represent metadata about source contents and access costs; and decision support to select sources and capabilities using cost based and semantic knowledge, and generating low cost query evaluation plans}, keywords = {analysis, Bioinformatics, biology computing, cost based knowledge, Costs, Data analysis, data mining, data visualisation, Data visualization, Data warehouses, decision support, digital library, Educational institutions, information resources, Internet, low cost query evaluation plans, Mediation, meta data, metadata, molecular biophysics, multiple local heterogeneous data sources, multiple remote heterogeneous data sources, optimized seamless biomolecular data integration, scientific discovery, scientific information systems, semantic knowledge, software libraries, visual databases, Visualization}, isbn = {0-7695-1423-5}, doi = {10.1109/BIBE.2001.974408}, author = {Eckman,B. A and Lacroix,Z. and Raschid, Louiqa} } @article {14164, title = {Preconditioners for Saddle Point Problems Arising in Computational Fluid Dynamics}, volume = {UMIACS-TR-2001-88}, year = {2001}, month = {2001/12/03/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Discretization and linearization of the incompressible Navier-Stokesequations leads to linear algebraic systems in which the coefficient matrix has the form of a saddle point problem ( F B^T ) (u) = (f) (1) ( B 0 ) (p) (g) In this paper, we describe the development of efficient and general iterative solution algorithms for this class of problems. We review the case where (1) arises from the steady-state Stokes equations and show that solution methods such as the Uzawa algorithm lead naturally to a focus on the Schur complement operator BF^{-1}B^T together with efficient strategies of applying the action of F^{-1} to a vector. We then discuss the advantages of explicitly working with the coupled form of the block system (1). Using this point of view, we describe some new algorithms derived by developing efficient methods for the Schur complement systems arising from the Navier-Stokes equations, and we demonstrate their effectiveness for solving both steady-state and evolutionary problems. (Also referenced as UMIACS-TR-2001-88) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/1170}, author = {Elman, Howard} } @article {17820, title = {Probabilistic object bases}, journal = {ACM Trans. Database Syst.}, volume = {26}, year = {2001}, month = {2001/09//}, pages = {264 - 312}, abstract = {Although there are many applications where an object-oriented data model is a good way of representing and querying data, current object database systems are unable to handle objects whose attributes are uncertain. In this article, we extend previous work by Kornatzky and Shimony to develop an algebra to handle object bases with uncertainty. We propose concepts of consistency for such object bases, together with an NP-completeness result, and classes of probabilistic object bases for which consistency is polynomially checkable. In addition, as certain operations involve conjunctions and disjunctions of events, and as the probability of conjunctive and disjunctive events depends both on the probabilities of the primitive events involved as well as on what is known (if anything) about the relationship between the events, we show how all our algebraic operations may be performed under arbitrary probabilistic conjunction and disjunction strategies. We also develop a host of equivalence results in our algebra, which may be used as rewrite rules for query optimization. Last but not least, we have developed a prototype probabilistic object base server on top of ObjectStore. We describe experiments to assess the efficiency of different possible rewrite rules.}, keywords = {consistency, object-oriented database, probabilistic object algebra, probabilistic object base, probability, query language, Query optimization}, isbn = {0362-5915}, doi = {10.1145/502030.502031}, url = {http://doi.acm.org/10.1145/502030.502031}, author = {Eiter,Thomas and Lu,James J. and Lukasiewicz,Thomas and V.S. Subrahmanian} } @conference {16156, title = {Therapeutic play with a storytelling robot}, booktitle = {CHI {\textquoteright}01 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {27 - 28}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We are developing a prototype storytelling robot for use with children in rehabilitation. Children can remotely control a furry robot by using a variety of body sensors adapted to their disability or rehabilitation goal. We believe this robot can motivate children and help them reach their therapy goals through therapeutic play, either by exercising muscles or joints (e.g. for physically challenged children) or by reflecting on the stories (e.g. for children with developmental disabilities). To develop this technology we use an innovative design methodology involving children as design partners.}, keywords = {children, design process, rehabilitation, robot, therapeutic play, user interface}, isbn = {1-58113-340-5}, doi = {10.1145/634067.634088}, url = {http://doi.acm.org/10.1145/634067.634088}, author = {Lathan,Corinna and Vice,Jack Maxwell and Tracey,Michael and Plaisant, Catherine and Druin, Allison and Edward,Kris and Montemayor,Jaime} } @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 {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 {12974, title = {A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity}, journal = {Molecular Biology and EvolutionMol Biol Evol}, volume = {17}, year = {2000}, month = {2000/12/01/}, pages = {1776 - 1788}, abstract = {Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling. Despite the recent development of powerful genome technologies capable of producing sequence data in large quantities (witness the recently completed first draft of the human genome), there has been relatively little change in how evolutionary studies are conducted. The application of genomic methods to evolutionary biology is a challenge, in part because gene segments from different organisms are manipulated separately, requiring individual purification, cloning, and sequencing. We suggest that a feasible approach to collecting genome-scale data sets for evolutionary biology (i.e., evolutionary genomics) may consist of combination of DNA samples prior to cloning and sequencing, followed by computational reconstruction of the original sequences. This approach will allow the full benefit of automated protocols developed by genome projects to be realized; taxon sampling levels can easily increase to thousands for targeted genomes and genomic regions. Sequence diversity at this level will dramatically improve the quality and accuracy of phylogenetic inference, as well as the accuracy and resolution of comparative evolutionary studies. In particular, it will be possible to make accurate estimates of normal evolution in the context of constant structural and functional constraints (i.e., site-specific substitution probabilities), along with accurate estimates of changes in evolutionary patterns, including pairwise coevolution between sites, adaptive bursts, and changes in selective constraints. These estimates can then be used to understand and predict the effects of protein structure and function on sequence evolution and to predict unknown details of protein structure, function, and functional divergence. In order to demonstrate the practicality of these ideas and the potential benefit for functional genomic analysis, we describe a pilot project we are conducting to simultaneously sequence large numbers of vertebrate mitochondrial genomes.}, isbn = {0737-4038, 1537-1719}, url = {http://mbe.oxfordjournals.org/content/17/12/1776}, author = {Pollock,David D and Eisen,Jonathan A. and Doggett,Norman A and Cummings, Michael P.} } @article {17958, title = {Continuously-adaptive haptic rendering}, journal = {Virtual Environments}, volume = {2000}, year = {2000}, month = {2000///}, pages = {135 - 135}, abstract = {Haptic display with force feedback is often necessary in sev-eral virtual environments. To enable haptic rendering of large datasets we introduce Continuously-Adaptive Haptic Rendering, a novel approach to reduce the complexity of the rendered dataset. We construct a continu- ous, multiresolution hierarchy of the model during the pre-processing and then at run time we use high-detail representation for regions around the probe pointer and coarser representation farther away. We achieve this by using a bell-shaped filter centered at the position of the probe pointer. Using our algorithm we are able to haptically render one to two orders of magnitude larger datasets than otherwise possible. Our approach is orthogonal to the previous work done in accelerating haptic rendering and thus can be used with them. }, author = {El-Sana,J. and Varshney, Amitabh} } @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 {17907, title = {Efficiently computing and updating triangle strips for real-time rendering}, journal = {Computer Aided Design}, volume = {32}, year = {2000}, month = {2000///}, pages = {753 - 772}, abstract = {Triangle strips are a widely used hardware-supported data-structure to compactly represent and efficiently render polygonal meshes. In thispaper we survey the efficient generation of triangle strips as well as their variants. We present efficient algorithms for partitioning polygonal meshes into triangle strips. Triangle strips have traditionally used a buffer size of two vertices. In this paper we also study the impact of larger buffer sizes and various queuing disciplines on the effectiveness of triangle strips. View-dependent simplification has emerged as a powerful tool for graphics acceleration in visualization of complex environments. However, in a view-dependent framework the triangle mesh connectivity changes at every frame making it difficult to use triangle strips. In this paper we present a novel data-structure, Skip Strip, that efficiently maintains triangle strips during such view-dependent changes. A Skip Strip stores the vertex hierarchy nodes in a skip-list-like manner with path compression. We anticipate that Skip Strips will provide a road-map to combine rendering acceleration techniques for static datasets, typical of retained-mode graphics applications, with those for dynamic datasets found in immediate-mode applications. }, author = {El-Sana,J. and Evans,F. and Kalaiah,A. and Varshney, Amitabh and Skiena,S. and Azanli,E.} } @article {18960, title = {The genome sequence of Drosophila melanogaster}, journal = {Science}, volume = {287}, year = {2000}, month = {2000///}, pages = {2185 - 2185}, abstract = {The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the \~{}120-megabase euchromatic portion of theDrosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes \~{}13,600 genes, somewhat fewer than the smaller Caenorhabditis elegansgenome, but with comparable functional diversity.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.287.5461.2185}, url = {http://www.sciencemag.org/content/287/5461/2185}, author = {Adams,M.D. and Celniker,S.E. and Holt,R.A. and Evans,C.A. and Gocayne,J.D. and Amanatides,P.G. and Scherer,S.E. and Li,P.W. and Hoskins,R.A. and Galle,R.F. and others} } @article {14128, title = {Iterative methods for stabilized discrete convection-diffusion problems}, journal = {IMA journal of numerical analysis}, volume = {20}, year = {2000}, month = {2000///}, pages = {333 - 333}, author = {Shih, Y. T and Elman, Howard} } @article {14980, title = {Kronos: A software system for the processing and retrieval of large-scale AVHRR data sets}, journal = {PE \& RS- Photogrammetric Engineering and Remote Sensing}, volume = {66}, year = {2000}, month = {2000///}, pages = {1073 - 1082}, abstract = {Raw remotely sensed satellite data have to be processed andmapped into a standard projection in order to produce a multi- temporal data set which can then be used for regional or global Earth science studies. However, traditional methods of processing remotely sensed satellite data have inherent limitations because they are based on a fixed processing chain. Different users may need the data in different forms with possibly different processing steps; hence, additional transformations may have to be applied to the processed data, resulting in potentially significant errors. In this paper, we describe a software system, Kronos, for the generation of custom-tailored products from the Advanced Very High Resolution Radiometer (AVHRR) sensor. It allows the generation of a rich set of products that can be easily specified through a simple interface by scientists wishing to carry out Earth system modeling or analysis. Kronos is based on a flexible methodology and consists of four major components: ingest and preprocessing, indexing and storage, a search and processing engine, and a Java interface. After geo-location and calibration, every pixel is indexed and stored using a combination of data structures. Following the users{\textquoteright} queries, data are selectively retrieved and secondary processing such as atmospheric correction, compositing, and projection are performed as specified. The processing is divided into two stages, the first of which involves the geo-location and calibration of the remotely sensed data and, hence, results in no loss of information. The second stage involves the retrieval of the appropriate data subsets and the application of the secondary processing specified by the user. This scheme allows the indexing and the storage of data from different sensors without any loss of information and, therefore, allows assimilation of data from multiple sensors. User specified processing can be applied later as needed. }, author = {Zhang,Z. and JaJa, Joseph F. and Bader, D.A. and Kalluri, SNV and Song,H. and El Saleous,N. and Vermote,E. and Townshend,J.R.G.} } @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} } @conference {16163, title = {A storytelling robot for pediatric rehabilitation}, booktitle = {Proceedings of the fourth international ACM conference on Assistive technologies}, series = {Assets {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {50 - 55}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {children, design process, rehabilitation, robot, therapeutic play, user interface}, isbn = {1-58113-313-8}, doi = {10.1145/354324.354338}, url = {http://doi.acm.org/10.1145/354324.354338}, author = {Plaisant, Catherine and Druin, Allison and Lathan,Corinna and Dakhane,Kapil and Edwards,Kris and Vice,Jack Maxwell and Montemayor,Jaime} } @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 {16954, title = {Agents vs. direct manipulation: what{\textquoteright}s best to disentangle the Web?}, journal = {Computer Networks: The International Journal of Computer and Telecommunications Networking}, volume = {31}, year = {1999}, month = {1999/05//}, pages = {1765 - 1767}, isbn = {1389-1286}, url = {http://dl.acm.org/citation.cfm?id=313009.313142}, author = {S{\'a}nchez,J. Alfredo and Etzioni,Oren and Kautz,Henry and Lieberman,Henry and Shneiderman, Ben} } @conference {16955, title = {Agents vs. direct manipulation: what{\textquoteright}s best to disentangle the Web?}, booktitle = {Proceedings of the eighth international conference on World Wide Web}, year = {1999}, month = {1999///}, author = {S{\'a}nchez,J.A. and Etzioni,O. and Kautz,H. and Lieberman,H. and Shneiderman, Ben} } @book {14149, title = {Efficient preconditioning of the linearized Navier-Stokes equations}, year = {1999}, month = {1999///}, publisher = {Citeseer}, organization = {Citeseer}, author = {Silvester, D. and Elman, Howard and Kay, D. and Wathen, A.} } @article {15747, title = {Eigenanalysis of Some Preconditioned Helmholtz Problems}, journal = {Numerische Mathematik}, volume = {83}, year = {1999}, month = {1999///}, pages = {231 - 257}, abstract = {In this work we calculate the eigenvalues obtained by preconditioning the discrete Helmholtz operator with Sommerfeld-like boundary conditions on a rectilinear domain, by a related operator with boundary conditions that permit the use of fast solvers. The main innovation is that the eigenvalues for two and three-dimensional domains can be calculated exactly by solving a set of one-dimensional eigenvalue problems. This permits analysis of quite large problems. For grids fine enough to resolve the solution for a given wave number, preconditioning using Neumann boundary conditions yields eigenvalues that are uniformly bounded, located in the first quadrant, and outside the unit circle. In contrast, Dirichlet boundary conditions yield eigenvalues that approach zero as the product of wave number with the mesh size is decreased. These eigenvalue properties yield the first insight into the behavior of iterative methods such as GMRES applied to these preconditioned problems.}, author = {Elman, Howard and O{\textquoteright}Leary, Dianne P.} } @conference {15923, title = {Fkpurang, darsana, traum, cfa, perlisg@ cs. umd. edu}, booktitle = {In Proceedings of the IJCAI{\textquoteright}99 Workshop on Practical Reasoning and Rationality}, year = {1999}, month = {1999///}, author = {Edu,C. U and Purang,K. and Purushothaman,D. and Traum,D. and Andersen,C. and Perlis, Don} } @article {17912, title = {Generalized View-Dependent Simplification}, journal = {Computer Graphics Forum}, volume = {18}, year = {1999}, month = {1999/09/01/}, pages = {83 - 94}, abstract = {We propose a technique for performing view-dependent geometry and topology simplifications for level-of-detail-based renderings of large models. The algorithm proceeds by preprocessing the input dataset into a binary tree, the view-dependence tree of general vertex-pair collapses. A subset of the Delaunay edges is used to limit the number of vertex pairs considered for topology simplification. Dependencies to avoid mesh foldovers in manifold regions of the input object are stored in the view-dependence tree in an implicit fashion. We have observed that this not only reduces the space requirements by a factor of two, it also highly localizes the memory accesses at run time. The view-dependence tree is used at run time to generate the triangles for display. We also propose a cubic-spline-based distance metric that can be used to unify the geometry and topology simplifications by considering the vertex positions and normals in an integrated manner.}, keywords = {Interactive Cut, Physically Based Modeling, Runge Kutta Method, Soft Tissue, Surgery Simulation, Tetrahedralization, Virtual Scalpel}, isbn = {1467-8659}, doi = {10.1111/1467-8659.00330}, url = {http://onlinelibrary.wiley.com/doi/10.1111/1467-8659.00330/abstract}, author = {El-Sana,Jihad and Varshney, Amitabh} } @conference {14927, title = {A hierarchical data archiving and processing system to generate custom tailored products from AVHRR data}, booktitle = {Geoscience and Remote Sensing Symposium, 1999. IGARSS {\textquoteright}99 Proceedings. IEEE 1999 International}, volume = {5}, year = {1999}, month = {1999///}, pages = {2374 -2376 vol.5 - 2374 -2376 vol.5}, abstract = {A novel indexing scheme is described to catalogue satellite data on a pixel basis. The objective of this research is to develop an efficient methodology to archive, retrieve and process satellite data, so that data products can be generated to meet the specific needs of individual scientists. When requesting data, users can specify the spatial and temporal resolution, geographic projection, choice of atmospheric correction, and the data selection methodology. The data processing is done in two stages. Satellite data is calibrated, navigated and quality flags are appended in the initial processing. This processed data is then indexed and stored. Secondary processing such as atmospheric correction and projection are done after a user requests the data to create custom made products. By dividing the processing in to two stages saves time, since the basic processing tasks such as navigation and calibration which are common to all requests are not repeated when different users request satellite data. The indexing scheme described can be extended to allow fusion of data sets from different sensors}, keywords = {archiving;image, AVHRR;GIS;PACS;custom, data, image;land, image;remote, mapping;, mapping;PACS;geophysical, measurement, PROCESSING, processing;geophysical, product;data, remote, scheme;infrared, sensing;optical, sensing;terrain, signal, surface;multispectral, system;indexing, tailored, technique;hierarchical, techniques;remote}, doi = {10.1109/IGARSS.1999.771514}, author = {Kalluri, SNV and Zhang,Z. and JaJa, Joseph F. and Bader, D.A. and Song,H. and El Saleous,N. and Vermote,E. and Townshend,J.R.G.} } @article {17209, title = {Human-centered computing, online communities, and virtual environments}, journal = {IEEE Computer Graphics and Applications}, volume = {19}, year = {1999}, month = {1999/12//Nov}, pages = {70 - 74}, abstract = {This report summarizes results of the first EC/NSF joint Advanced Research Workshop, which identified key research challenges and opportunities in information technology. The group agreed that the first joint research workshop should concentrate on the themes of human-centered computing and VEs. Human-centered computing is perceived as an area of strategic importance because of the move towards greater decentralization and decomposition in the location and provision of computation. The area of VEs is one where increased collaboration should speed progress in solving some of the more intractable problems in building effective applications}, keywords = {Books, Collaboration, Collaborative work, Conferences, EC/NSF joint Advanced Research Workshop, Feeds, Human computer interaction, human-centered computing, Internet, Joining materials, Laboratories, Online communities, Research initiatives, USA Councils, User interfaces, Virtual environment, virtual environments, Virtual reality}, isbn = {0272-1716}, doi = {10.1109/38.799742}, author = {Brown,J. R and van Dam,A. and Earnshaw,R. and Encarnacao,J. and Guedj,R. and Preece,J. and Shneiderman, Ben and Vince,J.} } @article {14112, title = {Modified streamline diffusion schemes for convection-diffusion problems}, journal = {Computer Methods in Applied Mechanics and Engineering}, volume = {174}, year = {1999}, month = {1999/05/04/}, pages = {137 - 151}, abstract = {We consider the design of robust and accurate finite element approximation methods for solving convection--diffusion problems. We develop some two-parameter streamline diffusion schemes with piecewise bilinear (or linear) trial functions and show that these schemes satisfy the necessary conditions for L2-uniform convergence of order greater than 1/2 introduced by Stynes and Tobiska M. Stynes and L. Tobiska, Necessary L2-uniform convergence conditions for difference schemes for two dimensional convection--diffusion problems, Comput. Math. Applic. 29 (1995) 45-53. For smooth problems, the schemes satisfy error bounds of the form O(h)u2 in an energy norm. In addition, extensive numerical experiments show that they effectively reproduce boundary layers and internal layers caused by discontinuities on relatively coarse grids, without any requirements on alignment of flow and grid.}, isbn = {0045-7825}, doi = {16/S0045-7825(98)00283-7}, url = {http://www.sciencedirect.com/science/article/pii/S0045782598002837}, author = {Shih,Yin-Tzer and Elman, Howard} } @article {14093, title = {More surprises from Kinetoplastida}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, year = {1999}, month = {1999///}, pages = {2579 - 2579}, author = {Donelson,J. E and Gardner,M. J and El-Sayed, Najib M.} } @article {14145, title = {Preconditioning for the steady-state Navier-Stokes equations with low viscosity}, journal = {SIAM Journal on Scientific Computing}, volume = {20}, year = {1999}, month = {1999///}, pages = {1299 - 1316}, author = {Elman, Howard} } @conference {17962, title = {Skip Strips: maintaining triangle strips for view-dependent rendering}, booktitle = {Visualization {\textquoteright}99. Proceedings}, year = {1999}, month = {1999/10//}, pages = {131 - 518}, abstract = {View-dependent simplification has emerged as a powerful tool for graphics acceleration in visualization of complex environments. However, view-dependent simplification techniques have not been able to take full advantage of the underlying graphics hardware. Specifically, triangle strips are a widely used hardware-supported mechanism to compactly represent and efficiently render static triangle meshes. However, in a view-dependent framework, the triangle mesh connectivity changes at every frame, making it difficult to use triangle strips. We present a novel data structure, Skip Strip, that efficiently maintains triangle strips during such view-dependent changes. A Skip Strip stores the vertex hierarchy nodes in a skip-list-like manner with path compression. We anticipate that Skip Strips will provide a road map to combine rendering acceleration techniques for static datasets, typical of retained-mode graphics applications, with those for dynamic datasets found in immediate-mode applications.}, keywords = {(computer, Acceleration, acceleration;graphics, applications;path, applications;skip-list-like, changes;view-dependent, compression;rendering, connectivity;triangle, data, datasets;graphics, datasets;static, environments;data, equipment;data, graphic, Graphics, graphics);spatial, hardware;hardware-supported, hierarchy, manner;static, mechanism;immediate-mode, mesh, meshes;triangle, nodes;view-dependent, rendering;view-dependent, simplification;visualization;computer, Skip, Strips;complex, strips;vertex, structure;dynamic, structures;, techniques;retained-mode, triangle, visualisation;rendering}, doi = {10.1109/VISUAL.1999.809877}, author = {El-Sana,J. and Azanli,E. and Varshney, Amitabh} } @article {17398, title = {TennisViewer: A Browser for Competition Trees}, journal = {Readings in information visualization: using vision to think}, year = {1999}, month = {1999///}, pages = {149 - 149}, author = {Johnson,B. and Shneiderman, Ben and Baker,MJ and Eick,SG} } @article {17957, title = {View-dependent topology simplification}, journal = {Virtual Environments}, volume = {99}, year = {1999}, month = {1999///}, pages = {11 - 22}, abstract = {We propose a technique for performing view-dependent sim-plifications for level-of-detail-based renderings of complex models. Our method is based on exploiting frame-to-frame coherence and is tolerant of various commonly found degeneracies in real-life polygonal models. The algorithm proceeds by preprocessing the input dataset into a binary tree of vertex collapses. This tree is used at run time to generate the triangles for display. Dependencies to avoid mesh foldovers in manifold regions of the input object are stored in the tree in an implicit fashion. This obviates the need for any extra storage for dependency pointers and suggests a potential for application to external memory prefetching algo- rithms. We also propose a distance metric that can be used to unify the geometry and genus simplifications with the view-dependent parameters such as viewpoint, view-frustum, and local illumination. }, author = {El-Sana,J. and Varshney, Amitabh} } @article {17005, title = {Buttons vs. menus: An exploratory study of pull-down menu selection as compared to button bars}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {Button bars are a relatively new interaction method intended to speedup application use as compared to pull-down menus. This exploratory study compares three command selection methods: pull-down menus, button bars, and user choice of pull-down menus or button bars. Effectiveness was measured in two ways: speed of selection and error rate. 15 participants performed 15 word processor related tasks. Results show that in frequently used functions, such as character attribute selection (bold, italic, u nderline, etc.), button bars are faster. There were no statistically significant differences in error rates between the three interaction methods. (Also cross-referenced as CAR-TR-764) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/428}, author = {Ellis,Jason and Tran,Chi and Ryoo,Jake and Shneiderman, Ben} } @article {15746, title = {Efficient Iterative Solution of the Three-Dimensional Helmholtz Equation}, journal = {Journal of Computational Physics}, volume = {142}, year = {1998}, month = {1998/05/01/}, pages = {163 - 181}, abstract = {We examine preconditioners for the discrete indefinite Helmholtz equation on a three-dimensional box-shaped domain with Sommerfeld-like boundary conditions. The preconditioners are of two types. The first is derived by discretization of a related continuous operator that differs from the original only in its boundary conditions. The second is derived by a block Toeplitz approximation to the descretized problem. The resulting preconditioning matrices allow the use of fast transform methods and differ from the discrete Helmholtz operator by an operator of low rank. We present experimental results demonstrating that when these methods are combined with Krylov subspace iteration, convergence rates depend only mildly on both the wave number and discretization mesh size. In addition, the methods display high efficiencies in an implementation on an IBM SP-2 parallel computer.}, isbn = {0021-9991}, doi = {10.1006/jcph.1998.5939}, url = {http://www.sciencedirect.com/science/article/pii/S0021999198959393}, author = {Elman, Howard and O{\textquoteright}Leary, Dianne P.} } @article {20053, title = {Genetic nomenclature for Trypanosoma and Leishmania.}, journal = {Mol Biochem Parasitol}, volume = {97}, year = {1998}, month = {1998 Nov 30}, pages = {221-4}, keywords = {Animals, Leishmania, Terminology as Topic, Trypanosoma}, issn = {0166-6851}, author = {Clayton, C and Adams, M and Almeida, R and Baltz, T and Barrett, M and Bastien, P and Belli, S and Beverley, S and Biteau, N and Blackwell, J and Blaineau, C and Boshart, M and Bringaud, F and Cross, G and Cruz, A and Degrave, W and Donelson, J and El-Sayed, N and Fu, G and Ersfeld, K and Gibson, W and Gull, K and Ivens, A and Kelly, J and Vanhamme, L} } @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} } @article {16180, title = {Life cycle of user interface techniques: The DJJ information system design Process}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {To take advantage of todays technology, many organizations are migrating fromtheir legacy systems. With help from the Human-Computer Interaction Laboratory (HCIL) and Cognetics Corporation, the Maryland Department of Juvenile Justice (DJJ) is currently undergoing an effort to redesign their information system to take advantage of graphical user interfaces. As a research lab, HCIL identifies interesting research problems and then prototypes solutions. As a project matures, the exploratory prototypes are adapted to suit the end product requirements. This case study describes the life cycle of three DJJ prototypes: (1) LifeLines, which uses time lines to display an overview of a youth in one screen, (2) the DJJ Navigator, which helps manage individual workloads by displaying different user views, and (3) the ProgramFinder, a tool for selecting the best program for a youth. (Also cross-referenced as CAR-TR-826) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/458}, author = {Rose,Anne and Ellis,Jason and Plaisant, Catherine and Greene,Stephan} } @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 {17963, title = {Topology simplification for polygonal virtual environments}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {4}, year = {1998}, month = {1998/06//apr}, pages = {133 - 144}, abstract = {We present a topology simplifying approach that can be used for genus reductions, removal of protuberances, and repair of cracks in polygonal models in a unified framework. Our work is complementary to the existing work on geometry simplification of polygonal datasets and we demonstrate that using topology and geometry simplifications together yields superior multiresolution hierarchies than is possible by using either of them alone. Our approach can also address the important issue of repair of cracks in polygonal models, as well as for rapid identification and removal of protuberances based on internal accessibility in polygonal models. Our approach is based on identifying holes and cracks by extending the concept of alpha;-shapes to polygonal meshes under the L infin; distance metric. We then generate valid triangulations to fill them using the intuitive notion of sweeping an L infin; cube over the identified regions}, keywords = {accessibility;intuitive, alpha;-shapes;L, approach;triangulations;unified, cube;L, datasets;polygonal, distance, environments;protuberance, framework;computational, geometry;topology;virtual, hierarchies;polygonal, infin;, meshes;polygonal, metric;genus, models;polygonal, notion;multiresolution, reality;, reductions;geometry, removal;topology, simplification;geometry, simplification;topology, simplifications;internal, simplifying, virtual}, isbn = {1077-2626}, doi = {10.1109/2945.694955}, author = {El-Sana,J. and Varshney, Amitabh} } @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 {17969, title = {Adaptive real-time level-of-detail based rendering for polygonal models}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {3}, year = {1997}, month = {1997/06//apr}, pages = {171 - 183}, abstract = {We present an algorithm for performing adaptive real-time level-of-detail-based rendering for triangulated polygonal models. The simplifications are dependent on viewing direction, lighting, and visibility and are performed by taking advantage of image-space, object-space, and frame-to-frame coherences. In contrast to the traditional approaches of precomputing a fixed number of level-of-detail representations for a given object, our approach involves statically generating a continuous level-of-detail representation for the object. This representation is then used at run time to guide the selection of appropriate triangles for display. The list of displayed triangles is updated incrementally from one frame to the next. Our approach is more effective than the current level-of-detail-based rendering approaches for most scientific visualization applications, where there are a limited number of highly complex objects that stay relatively close to the viewer. Our approach is applicable for scalar (such as distance from the viewer) as well as vector (such as normal direction) attributes}, keywords = {(computer, adaptive, attributes;scientific, attributes;view-dependent, coherence;image-space;lighting;multiresolution, direction;visibility;computational, geometry;data, graphics);, hierarchies;object-space;run, hierarchies;triangulated, level-of-detail, models;vector, polygonal, real-time, refinement;triangle, rendering;displayed, simplifications;viewing, systems;rendering, time;scalar, triangles;frame-to-frame, visualisation;real-time, visualization;selective}, isbn = {1077-2626}, doi = {10.1109/2945.597799}, author = {Xia,J. C and El-Sana,J. and Varshney, Amitabh} } @article {14096, title = {African trypanosomes have differentially expressed genes encoding homologues of the Leishmania GP63 surface protease}, journal = {Journal of Biological Chemistry}, volume = {272}, year = {1997}, month = {1997///}, pages = {26742 - 26742}, author = {El-Sayed, Najib M. and Donelson,J. E} } @conference {17961, title = {Controlled simplification of genus for polygonal models}, booktitle = {Visualization {\textquoteright}97., Proceedings}, year = {1997}, month = {1997/10//}, pages = {403 - 410}, abstract = {Genus-reducing simplifications are important in constructing multiresolution hierarchies for level-of-detail-based rendering, especially for datasets that have several relatively small holes, tunnels, and cavities. We present a genus-reducing simplification approach that is complementary to the existing work on genus-preserving simplifications. We propose a simplification framework in which genus-reducing and genus-preserving simplifications alternate to yield much better multiresolution hierarchies than would have been possible by using either one of them. In our approach we first identify the holes and the concavities by extending the concept of alpha;-hulls to polygonal meshes under the L infin; distance metric and then generate valid triangulations to fill them.}, keywords = {(computer, /spl, alpha/-hulls;L/sub, distance, framework;small, geometry;controlled, geometry;data, graphics);, hierarchies;object, holes;triangulations;tunnels;computational, infin//, meshes;polygonal, metric;cavities;computational, models;simplification, rendering;multiresolution, representations;polygonal, simplification;datasets;genus-preserving, simplifications;genus-reducing, simplifications;level-of-detail-based, visualisation;rendering}, doi = {10.1109/VISUAL.1997.663909}, author = {El-Sana,J. and Varshney, Amitabh} } @article {17901, title = {Efficient triangle strips for fast rendering}, journal = {ACM Transactions on Graphics}, year = {1997}, month = {1997///}, author = {Evans,F. and Skiena,S. and Varshney, Amitabh} } @article {17934, title = {Enabling virtual reality for large-scale mechanical CAD datasets}, journal = {Proceedings of ASME Design Engineering Technical Conferences, Sept}, volume = {14}, year = {1997}, month = {1997///}, pages = {17 - 17}, abstract = {Reconciling scene realism with interactivity has emerged asone of the most important areas in making virtual reality fea- sible for large-scale mechanical CAD datasets consisting of sev- eral millions of primitives. This paper surveys our research and related work for achieving interactivity without sacrificing real- ism in virtual reality walkthroughs and flythroughs of polygonal CAD datasets. We outline our recent work on efficient genera- tion of triangle strips from polygonal models that takes advan- tage of compression of connectivity information. This results in substantial savings in rendering, transmission, and storage. We outline our work on genus-reducing simplifications as well as real-time view-dependent simplifications that allow on-the-fly selection amongst multiple levels of detail, based upon lighting and viewing parameters. Our method allows multiple levels of detail to coexist on the same object at different regions and to merge seamlessly without any cracks or shading artifacts. We also present an overview of our work on hardware-assisted image- based rendering that allows interactive exploration of computer- generated scenes. }, author = {Varshney, Amitabh and El-Sana,J. and Evans,F. and Darsa,L. and Costa,B. and Skiena,S.} } @conference {17881, title = {Interoperability of data parallel runtime libraries}, booktitle = {IPPS}, year = {1997}, month = {1997///}, pages = {451 - 451}, author = {Edjlali,G. and Sussman, Alan and Saltz, J.} } @book {14158, title = {Iterative Methods for Linear and Nonlinear Equations.}, volume = {66}, year = {1997}, month = {1997///}, publisher = {JSTOR}, organization = {JSTOR}, author = {Elman, Howard} } @article {14148, title = {Iterative methods for problems in computational fluid dynamics}, journal = {Iterative Methods in Scientific Computing}, year = {1997}, month = {1997///}, pages = {271 - 327}, author = {Elman, Howard and Silvester, D. J and Wathen, A. J} } @article {12842, title = {Modeling and verifying active structural control systems}, journal = {Science of Computer Programming}, volume = {29}, year = {1997}, month = {1997/07//}, pages = {99 - 122}, isbn = {01676423}, doi = {10.1016/S0167-6423(96)00031-7}, url = {zotero://attachment/28808/}, author = {Elseaidy,W.} } @article {13608, title = {Multiscale Document Page Segmentation Using Soft Decision Integration}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, year = {1997}, month = {1997///}, pages = {92 - 96}, author = {Etemad,K. and David Doermann and Chellapa, Rama} } @article {14106, title = {A note on conjugate gradient convergence}, journal = {Numerische Mathematik}, volume = {76}, year = {1997}, month = {1997///}, pages = {209 - 230}, author = {Naiman, A. E and Babu{\v s}ka, I. M and Elman, Howard} } @article {14122, title = {Perturbation of eigenvalues of preconditioned Navier-Stokes operators}, journal = {SIAM Journal on Matrix Analysis and Applications}, volume = {18}, year = {1997}, month = {1997///}, pages = {733 - 751}, author = {Elman, Howard} } @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 {14095, title = {A survey of the Trypanosoma brucei rhodesiense genome using shotgun sequencing}, journal = {Molecular and Biochemical Parasitology}, volume = {84}, year = {1997}, month = {1997/02//}, pages = {167 - 178}, abstract = {A comparison of the efficiency of sequencing random genomic DNA fragments versus random cDNAs for the discovery of new genes in African trypanosomes was undertaken. Trypanosome DNA was sheared to a 1.5-2.5 kb size distribution, cloned into a plasmid and the sequences at both ends of 183 cloned fragments determined. Sequences of both kinetoplast and nuclear DNA were identified. New coding regions were discovered for a variety of proteins, including cell division proteins, an RNA-binding protein and a homologue of the Leishmania surface protease GP63. In some cases, each end of a fragment was found to contain a different gene, demonstrating the proximity of those genes and suggesting that the density of genes in the African trypanosome genome is quite high. Repetitive sequence elements found included telomeric hexamer repeats, 76 bp repeats associated with VSG gene expression sites, 177 bp satellite repeats in minichromosomes and the Ingi transposon-like elements. In contrast to cDNA sequencing, no ribosomal protein genes were detected. For the sake of comparison, the sequences of 190 expressed sequence tags (ESTs) were also determined, and a similar number of new trypanosomal homologues were found including homologues of another putative surface protein and a human leucine-rich repeat-containing protein. We conclude from this analysis and our previous work that sequencing random DNA fragments in African trypanosomes is as efficient for gene discovery as is sequencing random cDNA clones.}, keywords = {Expressed sequence tag, Genome survey sequence, Trypanosoma brucei rhodesiense}, isbn = {0166-6851}, doi = {16/S0166-6851(96)02792-2}, url = {http://www.sciencedirect.com/science/article/pii/S0166685196027922}, author = {El-Sayed, Najib M. and Donelson,John E.} } @article {14105, title = {Differential expression of the expression site-associated gene I family in African trypanosomes}, journal = {Journal of Biological Chemistry}, volume = {271}, year = {1996}, month = {1996///}, pages = {9771 - 9771}, author = {Morgan,R. W and El-Sayed, Najib M. and Kepa,J. K and Pedram,M. and Donelson,J. E} } @article {14132, title = {Fast nonsymmetric iterations and preconditioning for Navier-Stokes equations}, journal = {SIAM Journal on Scientific Computing}, volume = {17}, year = {1996}, month = {1996///}, pages = {33 - 46}, author = {Elman, Howard and Silvester, D.} } @article {16656, title = {Feature discovery and classification of Doppler umbilical artery blood flow velocity waveforms}, journal = {Computers in Biology and Medicine}, volume = {26}, year = {1996}, month = {1996/11//}, pages = {451 - 462}, abstract = {Doppler umbilical artery blood flow velocity waveform measurements are used in perinatal surveillance for the evaluation of fetal condition. There is an ongoing debate on the predictive value of Doppler measurements concerning the critical effect of the selection of parameters for the interpretation of Doppler waveforms. In this paper, we describe how neural network methods can be used both to discover relevant classification features and subsequently to classify Doppler umbilical artery blood flow velocity waveforms. Results obtained from 199 normal and high risk patients{\textquoteright} umbilical artery waveforms highlighted a classification concordance varying from 90 to 98\% accuracy.}, keywords = {Doppler umbilical artery blood flow velocity waveforms, Feature extraction, IMAGE PROCESSING, Pattern classification}, isbn = {0010-4825}, doi = {10.1016/S0010-4825(96)00018-2}, url = {http://www.sciencedirect.com/science/article/pii/S0010482596000182}, author = {Baykal,Nazife and Reogia,James A. and Yalabik,Nese and Erkmen,Aydan and Beksac,M.Sinan} } @article {14123, title = {Multigrid and Krylov subspace methods for the discrete Stokes equations}, journal = {International journal for numerical methods in fluids}, volume = {22}, year = {1996}, month = {1996///}, pages = {755 - 770}, author = {Elman, Howard} } @conference {17959, title = {Optimizing triangle strips for fast rendering}, booktitle = {Visualization {\textquoteright}96. Proceedings.}, year = {1996}, month = {1996/11/27/1}, pages = {319 - 326}, abstract = {Almost all scientific visualization involving surfaces is currently done via triangles. The speed at which such triangulated surfaces can be displayed is crucial to interactive visualization and is bounded by the rate at which triangulated data can be sent to the graphics subsystem for rendering. Partitioning polygonal models into triangle strips can significantly reduce rendering times over transmitting each triangle individually. We present new and efficient algorithms for constructing triangle strips from partially triangulated models, and experimental results showing these strips are on average 15\% better than those from previous codes. Further, we study the impact of larger buffer sizes and various queuing disciplines on the effectiveness of triangle strips.}, keywords = {buffer, data;triangulated, disciplines;rendering, model, models;polygonal, optimisation;triangulated, partitioning;queuing, rendering;graphics, sizes;fast, strip, subsystem;interactive, surfaces;data, times;scientific, triangulated, visualisation;, visualization;partially, visualization;triangle}, doi = {10.1109/VISUAL.1996.568125}, author = {Evans,F. and Skiena,S. and Varshney, Amitabh} } @conference {17872, title = {Runtime coupling of data-parallel programs}, booktitle = {Proceedings of the 10th international conference on Supercomputing}, year = {1996}, month = {1996///}, pages = {229 - 236}, author = {Ranganathan,M. and Acharya, A. and Edjlali,G. and Sussman, Alan and Saltz, J.} } @conference {17897, title = {Stripe: a software tool for efficient triangle strips}, booktitle = {ACM SIGGRAPH 96 Visual Proceedings: The art and interdisciplinary programs of SIGGRAPH {\textquoteright}96}, series = {SIGGRAPH {\textquoteright}96}, year = {1996}, month = {1996///}, pages = {153{\textendash} - 153{\textendash}}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-784-7}, doi = {10.1145/253607.253894}, url = {http://doi.acm.org/10.1145/253607.253894}, author = {Evans,Francine and Skiena,Steven and Varshney, Amitabh} } @article {12841, title = {Verification of an active control system using temporal process algebra}, journal = {Engineering with computers}, volume = {12}, year = {1996}, month = {1996///}, pages = {46 - 61}, author = {Elseaidy,W. M and Baugh,J. W. and Cleaveland, Rance} } @article {14119, title = {Algebraic Analysis of the Hierarchical Basis Preconditioner}, journal = {SIAM Journal on Matrix Analysis and ApplicationsSIAM. J. Matrix Anal. \& Appl.}, volume = {16}, year = {1995}, month = {1995///}, pages = {192 - 192}, isbn = {08954798}, doi = {10.1137/S0895479892236933}, url = {http://epubs.siam.org/sima/resource/1/sjmael/v16/i1/p192_s1}, author = {Elman, Howard and Zhang, Xuejun} } @article {14073, title = {cDNA expressed sequence tags of Trypanosoma brucei rhodesiense provide new insights into the biology of the parasite}, journal = {Molecular and Biochemical Parasitology}, volume = {73}, year = {1995}, month = {1995/07//}, pages = {75 - 90}, abstract = {A total of 518 expressed sequence tags (ESTs) have been generated from clones randomly selected from a cDNA library and a spliced leader sub-library of a Trypanosoma brucei rhodesiense bloodstream clone. 205 (39\%) of the clones were identified based on matches to 113 unique genes in the public databases. Of these, 71 cDNAs display significant similarities to genes in unrelated organisms encoding metabolic enzymes, signal transduction proteins, transcription factors, ribosomal proteins, histones, a proliferation-associated protein and thimet oligopeptidase, among others. 313 of the cDNAs are not related to any other sequences in the databases. These cDNA ESTs provide new avenues of research for exploring both the novel trypanosome-specific genes and the genome organization of this parasite, as well as a resource for identifying trypanosome homologs to genes expressed in other organisms.}, keywords = {cDNA, Expressed sequence tag, Trypanosoma brucei rhodesiense}, isbn = {0166-6851}, doi = {16/0166-6851(95)00098-L}, url = {http://www.sciencedirect.com/science/article/pii/016668519500098L}, author = {El-Sayed, Najib M. and Alarcon,Clara M. and Beck,John C. and Sheffield,Val C. and Donelson,John E.} } @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.} } @conference {17867, title = {Data parallel programming in an adaptive environment}, booktitle = {Parallel Processing Symposium, 1995. Proceedings., 9th International}, year = {1995}, month = {1995///}, pages = {827 - 832}, author = {Edjlali,G. and Agrawal,G. and Sussman, Alan and Saltz, J.} } @article {14153, title = {Use of linear algebra kernels to build an efficient finite element solver}, journal = {Parallel Computing}, volume = {21}, year = {1995}, month = {1995/01//}, pages = {161 - 173}, abstract = {For scientific codes to achieve good performance on computers with hierarchical memories, it is necessary that the ratio of memory references to arithmetic operations be low. In this paper, we show that Level 3 BLAS linear algebra kernels can be used to satisfy this requirement to produce an efficient implementation of a parallel finite element solver on a shared memory parallel computer with a fast cache memory.}, keywords = {Cache memory, finite element, hp-version, Level 3 BLAS, Parallel algorithm, shared memory multiprocessor}, isbn = {0167-8191}, doi = {16/0167-8191(94)00030-E}, url = {http://www.sciencedirect.com/science/article/pii/016781919400030E}, author = {Elman, Howard and Lee,Dennis K. -Y.} } @article {13413, title = {AAAI 1994 Spring Symposium Series Reports}, journal = {AI Magazine}, volume = {15}, year = {1994}, month = {1994/09/15/}, pages = {22 - 22}, isbn = {0738-4602}, doi = {10.1609/aimag.v15i3.1101}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/1101}, author = {Woods,William and Uckun,Sendar and Kohane,Isaac and Bates,Joseph and Hulthage,Ingemar and Gasser,Les and Hanks,Steve and Gini,Maria and Ram,Ashwin and desJardins, Marie and Johnson,Peter and Etzioni,Oren and Coombs,David and Whitehead,Steven} } @article {15992, title = {Calibrating, Counting, Grounding, Grouping}, volume = {FS-94-03}, year = {1994}, month = {1994///}, institution = {Association for the Advancement of Artificial Intelligence}, author = {Elgot-drapkin,J. and Gordon,D. and Kraus,S. and Miller,M. and Nirkhe,M. and Perlis, Don} } @article {14138, title = {On the convergence of line iterative methods for cyclically reduced non-symmetrizable linear systems}, journal = {Numerische Mathematik}, volume = {67}, year = {1994}, month = {1994///}, pages = {177 - 190}, author = {Elman, Howard and Golub, G. H and Starke, G.} } @conference {13546, title = {Document page decomposition by integration of distributed soft decisions}, booktitle = {International Conference on Neural Networks}, year = {1994}, month = {1994///}, pages = {4022 - 4027}, author = {Etemad,K. and David Doermann and Chellapa, Rama} } @article {14120, title = {Inexact and Preconditioned Uzawa Algorithms for Saddle Point Problems}, journal = {SIAM Journal on Numerical Analysis}, volume = {31}, year = {1994}, month = {1994/12/01/}, pages = {1645 - 1661}, abstract = {Variants of the Uzawa algorithm for solving symmetric indefinite linear systems are developed and analyzed. Each step of this algorithm requires the solution of a symmetric positive-definite system of linear equations. It is shown that if this computation is replaced by an approximate solution produced by an arbitrary iterative method, then with relatively modest requirements on the accuracy of the approximate solution, the resulting inexact Uzawa algorithm is convergent, with a convergence rate close to that of the exact algorithm. In addition, it is shown that preconditioning can be used to improve performance. The analysis is illustrated and supplemented using several examples derived from mixed finite element discretization of the Stokes equations.}, isbn = {0036-1429}, url = {http://www.jstor.org/stable/2158371}, author = {Elman, Howard and Golub, Gene H.} } @conference {16629, title = {Interpretation of Doppler blood flow velocity waveforms using neural networks.}, booktitle = {Proceedings of the Annual Symposium on Computer Application in Medical Care}, year = {1994}, month = {1994///}, pages = {865 - 865}, author = {Baykal,N. and Reggia, James A. and Yalabik,N. and Erkmen,A. and Beksac,M. S.} } @article {14159, title = {Iterative methods for linear systems}, journal = {Large-Scale Matrix Problems and the Numerical Solution of Partial Differential Equations}, volume = {3}, year = {1994}, month = {1994///}, pages = {69 - 177}, author = {Elman, Howard} } @conference {13621, title = {Page Segmentation Using Decision Integration and Wavelet Packet Basis}, booktitle = {ICPR}, year = {1994}, month = {1994///}, pages = {345 - 349}, author = {Etemad,K. and David Doermann and Chellapa, Rama} } @inbook {18691, title = {Software reliability analysis of three successive generations of a Switching System}, booktitle = {Dependable Computing {\textemdash} EDCC-1}, series = {Lecture Notes in Computer Science}, volume = {852}, year = {1994}, month = {1994///}, pages = {471 - 490}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Most current approaches to software reliability evaluation are based on data collected on a single generation of products. However, many applications are developed through improvements of the existing software: to the families of products are added various generations as the need for new functionalities arises. Experimental studies dealing with the analysis of data collected on families of products are seldom reported. In this paper, we analyze the data (failure and correction reports) collected on the software of three successive generations of the Brazilian Switching System {\textemdash} TROPICO-R, during validation and operation. A comparative analysis of the three products is done and the main results are outlined. Emphasis is placed on the evolution of the software and the corresponding failures and corrected faults. The analysis addresses: i) the modifications introduced on system components, ii) the distribution of failures and corrected faults in the components and the functions fulfilled by the system, and iii) the evolution of the failure intensity functions.}, keywords = {Computer science}, isbn = {978-3-540-58426-1}, url = {http://www.springerlink.com/content/f71g30v177521471/abstract/}, author = {Ka{\^a}niche,M. and Kanoun,K. and Michel Cukier and Martini,M.}, editor = {Echtle,Klaus and Hammer,Dieter and Powell,David} } @conference {12783, title = {Verifying an intelligent structural control system: a case study}, booktitle = {Real-Time Systems Symposium, 1994., Proceedings.}, year = {1994}, month = {1994/12/07/9}, pages = {271 - 275}, publisher = {IEEE}, organization = {IEEE}, abstract = {Describes the formal verification of the timing properties of the design of an intelligent structural control system using the Concurrency Workbench, an automatic verification tool for finite-state processes. The high-level design of the system is first given in Modechart, a graphical specification language for real-time systems, and then translated into a temporal process algebra supported by the Workbench. The facilities provided by this tool are then used to analyze the system and ultimately show it to be correct}, keywords = {automatic verification tool, case study, Concurrency Workbench, Distributed computing, Distributed control, distributed processing, finite automata, finite-state processes, formal verification, graphical specification language, high-level design, intelligent control, intelligent structural control system verification, Logic, Modechart, Process algebra, Real time systems, real-time systems, Specification languages, structural engineering computing, temporal logic, temporal process algebra, time-varying systems, Timing, timing properties, visual languages}, isbn = {0-8186-6600-5}, doi = {10.1109/REAL.1994.342708}, author = {Elseaidy,W. M and Cleaveland, Rance and Baugh,J. W.} } @article {16740, title = {ADMS: a testbed for incremental access methods}, journal = {IEEE Transactions on Knowledge and Data Engineering}, volume = {5}, year = {1993}, month = {1993/10//}, pages = {762 - 774}, abstract = {ADMS is an advanced database management system developed-to experiment with incremental access methods for large and distributed databases. It has been developed over the past eight years at the University of Maryland. The paper provides an overview of ADMS, and describes its capabilities and the performance attained by its incremental access methods. This paper also describes an enhanced client-server architecture that allows an incremental gateway access to multiple heterogeneous commercial database management systems}, keywords = {Add-drop multiplexers, ADMS, advanced database management system, client-server architecture, commercial database management systems, Computational modeling, Database systems, distributed databases, heterogeneous DBMS, incremental access methods, incremental gateway, Information retrieval, interoperability, join index, large databases, Navigation, network operating systems, Object oriented databases, Object oriented modeling, Query processing, System testing, very large databases, view index, Workstations}, isbn = {1041-4347}, doi = {10.1109/69.243508}, author = {Roussopoulos, Nick and Economou,N. and Stamenas,A.} } @book {14133, title = {Costs of Solving the Discrete Convection-diffusion Equation by Relaxation Methods}, year = {1993}, month = {1993///}, publisher = {University of Maryland}, organization = {University of Maryland}, author = {Chernesky, M. P and Elman, Howard} } @article {14115, title = {Ordering Effects on Relaxation Methods Applied to the Discrete One- Dimensional Convection-Diffusion Equation}, journal = {SIAM Journal on Numerical Analysis}, volume = {30}, year = {1993}, month = {1993/10/01/}, pages = {1268 - 1290}, abstract = {The authors present an analysis of relaxation methods for the one-dimensional discrete convection-diffusion equation based on norms of the iteration matrices. In contrast to standard analytic techniques that use spectral radii, these results show how the performance of iterative solvers is affected by directions of flow associated with the underlying operator, and by orderings of the discrete grid points. In particular, for problems of size n, relaxation against the flow incurs a latency of approximately n steps in which convergence is slow, and red-black relaxation incurs a latency of approximately n/2 steps. There is no latency associated with relaxation that follows that flow. These results are largely independent of the choice of discretization.}, isbn = {0036-1429}, url = {http://www.jstor.org/stable/2158237}, author = {Elman, Howard and Chernesky, Michael P.} } @article {14113, title = {Performance Enhancements and Parallel Algorithms for Two Multilevel Preconditioners}, journal = {SIAM Journal on Scientific ComputingSIAM J. Sci. Comput.}, volume = {14}, year = {1993}, month = {1993///}, pages = {890 - 890}, isbn = {10648275}, doi = {10.1137/0914055}, url = {http://link.aip.org/link/SJOCE3/v14/i4/p890/s1\&Agg=doi}, author = {Elman, Howard and Guo,Xian-Zhong} } @conference {15977, title = {Vacuum-logic}, booktitle = {Proceedings of AAAI 1993 Fall Symposium Series: Instantiating Real-World Agents}, year = {1993}, month = {1993///}, pages = {51 - 54}, author = {Elgot-drapkin,J. and Kraus,S. and Miller,M. and Nirkhe,M. and Perlis, Don} } @article {14111, title = {Parallel sparse Cholesky factorization on a shared memory multiprocessor}, journal = {Parallel Computing}, volume = {18}, year = {1992}, month = {1992/09//}, pages = {1009 - 1022}, abstract = {Parallel implementations of Cholesky factorization for sparse symmetric positive definite matrices are considered on a shared memory multiprocessor computer. Two column-oriented schemes, known as the column-Cholesky algorithm and the fan-in algorithm, along with enhancements of each, are implemented and discussed. High parallel efficiency of the column-Cholesky algorithm and its enhancement is demonstrated for test problems. A detailed investigation of the performance of the fan-in algorithm and its enhancement, the compute-ahead fan-in algorithm, is made to study the effects of overhead associated with the fan-in based schemes.}, keywords = {linear algebra, Parallel algorithms, shared memory multiprocessor, sparse Cholesky factorization}, isbn = {0167-8191}, doi = {16/0167-8191(92)90014-X}, url = {http://www.sciencedirect.com/science/article/pii/016781919290014X}, author = {Zhang, G. and Elman, Howard} } @article {14141, title = {Iterative methods for cyclically reduced non-self-adjoint linear systems II}, journal = {Math. Comp}, volume = {56}, year = {1991}, month = {1991///}, pages = {215 - 242}, author = {Elman, Howard and Golub, G. H} } @article {15971, title = {Memory, reason and time: the Step-Logic approach}, journal = {Philosophy and AI: Essays at the Interface}, year = {1991}, month = {1991///}, pages = {79 - 103}, author = {Elgot-drapkin,J. and Miller,M. and Perlis, Don} } @article {15925, title = {Nonmonotonicity and the scope of reasoning}, journal = {Artificial Intelligence}, volume = {52}, year = {1991}, month = {1991///}, pages = {221 - 261}, author = {Etherington,D. W and Kraus,S. and Perlis, Don} } @article {15980, title = {Stop the world{\textemdash}I want to think}, journal = {International Journal of Intelligent Systems}, volume = {6}, year = {1991}, month = {1991///}, pages = {443 - 456}, author = {Perlis, Don and Elgot-Drapkin,J. J and Miller,M.} } @article {17139, title = {EVALUATING HYPERMEDIA SYSTEMS}, journal = {Human factors in computing systems: CHI{\textquoteright}90 Conference proceedings, April 1-5, Seattle}, year = {1990}, month = {1990///}, pages = {387 - 387}, author = {Ehrlich,K. and Microsytems,S. and Marchionini,G. and Nielsen,J. and Shneiderman, Ben} } @article {14160, title = {Iterative methods for cyclically reduced non-self-adjoint linear systems}, journal = {Math. Comp}, volume = {54}, year = {1990}, month = {1990///}, pages = {671 - 700}, author = {Elman, Howard and Golub, G. H} } @article {15951, title = {Limited scope and circumscriptive reasoning}, journal = {International Journal of Expert Systems}, volume = {3}, year = {1990}, month = {1990///}, pages = {207 - 217}, author = {Etherington,D. W and Kraus,S. and Perlis, Don} } @book {14116, title = {Line iterative methods for cyclically reduced discrete convection-diffusion problems}, year = {1990}, month = {1990///}, publisher = {University of Maryland}, organization = {University of Maryland}, author = {Elman, Howard and Golub, G. H} } @article {16533, title = {Phase transitions in connectionist models having rapidly varying connection strengths}, journal = {Neural Computation}, volume = {2}, year = {1990}, month = {1990///}, pages = {523 - 535}, author = {Reggia, James A. and Edwards,M.} } @article {15991, title = {Reasoning situated in time I: Basic concepts}, journal = {Journal of Experimental and Theoretical Artificial Intellige}, volume = {2}, year = {1990}, month = {1990///}, pages = {75 - 98}, author = {Elgot-Drapkin,J. J and Perlis, Don} } @article {14124, title = {Approximate Schur Complement Preconditioners on Serial and Parallel Computers}, journal = {SIAM Journal on Scientific and Statistical ComputingSIAM J. Sci. and Stat. Comput.}, volume = {10}, year = {1989}, month = {1989///}, pages = {581 - 581}, isbn = {01965204}, doi = {10.1137/0910037}, url = {http://link.aip.org/link/SJOCE3/v10/i3/p581/s1\&Agg=doi}, author = {Elman, Howard} } @article {14130, title = {Fourier Analysis of Iterative Methods for Elliptic Problems}, journal = {SIAM Review}, volume = {31}, year = {1989}, month = {1989/03/01/}, pages = {20 - 49}, abstract = {This paper presents a Fourier method for analyzing stationary iterative methods and preconditioners for discretized elliptic boundary value problems. As in the von Neumann stability analysis of hyperbolic and parabolic problems, the approach is easier to apply, reveals more details about convergence properties than about standard techniques, and can be applied in a systematic way to a wide class of numerical methods. Although the analysis is applicable only to periodic problems, the results essentially reproduce those of classical convergence and condition number analysis for problems with other boundary conditions, such as the Dirichlet problem. In addition, they give suggestive new evidence of the strengths and weaknesses of methods such as incomplete factorization preconditioners in the Dirichlet case.}, isbn = {0036-1445}, url = {http://www.jstor.org/stable/2030846}, author = {Chan, Tony F. and Elman, Howard} } @article {14117, title = {Ordering techniques for the preconditioned conjugate gradient method on parallel computers}, journal = {Computer Physics Communications}, volume = {53}, year = {1989}, month = {1989/05//}, pages = {253 - 269}, abstract = {We consider the parallel implementation of the preconditioned conjugate gradient method using multicolor incomplete factorization as preconditioners. We discuss numerical experiments on sample problems arising from elliptic partial differential equations, together with an analytic study of the effects of communication and artihmetic costs on loosely coupled architectures. Our main conclusion is that multicolor orderings result in slower convergence of the preconditioned conjugate gradient method than natural orderings, but that the lower parallel costs of the multicolor techniques typically make their overall performance better.}, isbn = {0010-4655}, doi = {16/0010-4655(89)90164-1}, url = {http://www.sciencedirect.com/science/article/pii/0010465589901641}, author = {Elman, Howard and Agr{\'o}n, Elvira} } @article {14114, title = {Relaxed and stabilized incomplete factorizations for non-self-adjoint linear systems}, journal = {BIT Numerical Mathematics}, volume = {29}, year = {1989}, month = {1989///}, pages = {890 - 915}, author = {Elman, Howard} } @article {14144, title = {Some aspects of parallel implementation of the finite-element method on message passing architectures}, journal = {Journal of Computational and Applied Mathematics}, volume = {27}, year = {1989}, month = {1989/09//}, pages = {157 - 187}, abstract = {We discuss some aspects of implementing the finite-element method on parallel computers with local memory and message passing. In particular, we compare the costs of using high-order and low-order elements and of direct and iterative solvers for solving the linear systems that occur. Our model of parallel computation is a two-dimensional grid of processors chosen to be similar in shape to the underlying grid. Our main conclusions are that use of high-order methods is an effective way to achieve high accuracy for some problems, on both serial and parallel computers, and that such methods provide a natural way to achieve efficiency in parallel implementations. In addition, we show that sparse direct solvers generalize naturally to methods based on high-order elements, and that direct solvers are adequate for two-dimensional problems, especially for multiple load vectors.}, keywords = {Finite-element methods, hp-version, nested dissection, parallel computations, preconditioned conjugate gradient}, isbn = {0377-0427}, doi = {16/0377-0427(89)90365-8}, url = {http://www.sciencedirect.com/science/article/pii/0377042789903658}, author = {Babuska, I. and Elman, Howard} } @article {14118, title = {Block-Preconditioned Conjugate-Gradient-Like Methods for Numerical Reservoir Simulation}, journal = {SPE Reservoir EngineeringSPERE}, volume = {3}, year = {1988}, month = {1988/02//}, isbn = {0885-9248}, doi = {10.2118/13534-PA}, url = {http://www.onepetro.org/mslib/servlet/onepetropreview?id=00013534\&soc=SPE}, author = {Eisenstat, Stanley and Elman, Howard and Schlutz, Martin} } @article {18094, title = {Matching patterns in strings subject to multi-linear transformations}, journal = {Theoretical Computer Science}, volume = {60}, year = {1988}, month = {1988///}, pages = {231 - 254}, author = {Eilam-Tzoreff,T. and Vishkin, Uzi} } @article {16967, title = {An experimental comparison of a mouse and arrow-jump keys for an interactive encyclopedia}, journal = {International Journal of Man-Machine Studies}, volume = {24}, year = {1986}, month = {1986/01//}, pages = {29 - 45}, abstract = {This paper reports on an experiment which was conducted to examine relative merits of using a mouse or arrow-jump keys to select text in an interactive encyclopedia. Timed path traversais were performed by subjects using each device, and were followed by subjective questions. Personality and background of the subjects were recorded to see if those attributes would affect device preference and performance. The arrow-jump keys were found to have the quickest traversal times for paths with either short or long target distances. The subjective responses indicated that the arrow-jump method was overwhelmingly preferred over the mouse method. Personality type was not found to play a critical role.}, isbn = {0020-7373}, doi = {10.1016/S0020-7373(86)80038-4}, url = {http://www.sciencedirect.com/science/article/pii/S0020737386800384}, author = {Ewing,John and Mehrabanzad,Simin and Sheck,Scott and Ostroff,Dan and Shneiderman, Ben} } @article {14131, title = {A Hybrid Chebyshev Krylov Subspace Algorithm for Solving Nonsymmetric Systems of Linear Equations}, journal = {SIAM Journal on Scientific and Statistical ComputingSIAM J. Sci. and Stat. Comput.}, volume = {7}, year = {1986}, month = {1986///}, pages = {840 - 840}, isbn = {01965204}, doi = {10.1137/0907057}, url = {http://link.aip.org/link/SJOCE3/v7/i3/p840/s1\&Agg=doi}, author = {Elman, Howard and Saad, Youcef and Saylor, Paul E.} } @article {14162, title = {Polynomial iteration for nonsymmetric indefinite linear systems}, journal = {Numerical Analysis}, year = {1986}, month = {1986///}, pages = {103 - 117}, author = {Elman, Howard and Streit, R.} } @article {14157, title = {Preconditioning by Fast Direct Methods for Nonself-Adjoint Nonseparable Elliptic Equations}, journal = {SIAM Journal on Numerical Analysis}, volume = {23}, year = {1986}, month = {1986/02/01/}, pages = {44 - 57}, abstract = {We consider the use of fast direct methods as preconditioners for iterative methods for computing the numerical solution of nonself-adjoint elliptic boundary value problems. We derive bounds on convergence rates that are independent of discretization mesh size. For two-dimensional problems on rectangular domains, discretized on an n {\texttimes} n grid, these bounds lead to asymptotic operation counts of O(n2 log n log ε-1) to achieve relative error ε and O(n2(log n)2) to reach truncation error.}, isbn = {0036-1429}, url = {http://www.jstor.org/stable/2157450}, author = {Elman, Howard and Schultz, Martin H.} } @article {14127, title = {A Stability Analysis of Incomplete LU Factorizations}, journal = {Mathematics of Computation}, volume = {47}, year = {1986}, month = {1986/07/01/}, pages = {191 - 217}, abstract = {The combination of iterative methods with preconditionings based on incomplete LU factorizations constitutes an effective class of methods for solving the sparse linear systems arising from the discretization of elliptic partial differential equations. In this paper, we show that there are some settings in which the incomplete LU preconditioners are not effective, and we demonstrate that their poor performance is due to numerical instability. Our analysis consists of an analytic and numerical study of a sample two-dimensional non-self-adjoint elliptic problem discretized by several finite-difference schemes.}, isbn = {0025-5718}, doi = {10.2307/2008089}, url = {http://www.jstor.org/stable/2008089}, author = {Elman, Howard} } @conference {18439, title = {The Engineering of an Environment on Small Machines}, booktitle = {Proceedings of the IEEE 1st International Conference on Computer Workstations}, year = {1985}, month = {1985///}, pages = {61 - 69}, author = {Zelkowitz, Marvin V and Elgot,J. and Itkin,D. and Kowalchack,B. and Maggio,M.} } @article {14147, title = {The (new) Yale sparse matrix package}, journal = {Elliptic problem solvers II}, year = {1983}, month = {1983///}, pages = {45 - 52}, author = {Eisenstat, S. C and Elman, Howard and Schultz, M. H and Sherman, A. H} } @article {14142, title = {Variational Iterative Methods for Nonsymmetric Systems of Linear Equations}, journal = {SIAM Journal on Numerical Analysis}, volume = {20}, year = {1983}, month = {1983/04/01/}, pages = {345 - 357}, abstract = {We consider a class of iterative algorithms for solving systems of linear equations where the coefficient matrix is nonsymmetric with positive-definite symmetric part. The algorithms are modelled after the conjugate gradient method, and are well suited for large sparse systems. They do not make use of any associated symmetric problems. Convergence results and error bounds are presented.}, isbn = {0036-1429}, url = {http://www.jstor.org/stable/2157222}, author = {Eisenstat, Stanley C. and Elman, Howard and Schultz, Martin H.} } @article {14126, title = {Iterative methods for large, sparse, nonsymmetric systems of linear equations.}, journal = {Dissertation Abstracts International Part B: Science and Engineering[DISS. ABST. INT. PT. B- SCI. \& ENG.],}, volume = {43}, year = {1982}, month = {1982///}, pages = {1982 - 1982}, author = {Elman, Howard} } @article {14136, title = {Preconditioned Conjugate-Gradient Methods for Nonsymmetric Systems of Linear Equations.}, year = {1981}, month = {1981///}, institution = {DTIC Document}, author = {Elman, Howard} }