@article {20391, title = {Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children}, journal = {Journal of Oral Microbiology}, year = {2019}, month = {12/2018}, pages = {1557986}, abstract = {Studies of the microbiome associated with dental caries have largely relied on 16S rRNA sequence analysis, which is associated with PCR biases, low taxonomic resolution, and inability to accurately study functions. Here, we employed whole metagenome shotgun sequencing, coupled with high-resolution analysis algorithm, to analyze supragingival microbiomes from 30 children with or without dental caries. A total of 726 bacterial strains belonging to 406 species, in addition to 34 bacteriophages were identified. A core bacteriome was identified at the species and strain levels. Species of Prevotella, Veillonella, as yet unnamed Actinomyces, and Atopobium showed strongest association with caries; Streptococcus sp. AS14 and Leptotrichia sp. Oral taxon 225, among others, were overabundant in caries-free. For several species, the association was strain-specific. Furthermore, for some species, e.g. Streptococcus mitis and Streptococcus sanguinis, sister strains showed differential associations. Noteworthy, associations were also identified for phages: Streptococcus phage M102 with caries and Haemophilus phage HP1 with caries-free. Functionally, potentially relevant features were identified including urate, vitamin K2, and polyamine biosynthesis in association with caries; and three deiminases and lactate dehydrogenase with health. The results demonstrate new associations between the microbiome and dental caries at the strain and functional levels that need further investigation.}, doi = {10.1080/20002297.2018.1557986}, url = {https://www.tandfonline.com/doi/full/10.1080/20002297.2018.1557986}, author = {Al-Hebshi, Nezar Noor and Baraniya, Divyashri and Chen, Tsute and Hill, Jennifer and Puri, Sumant and Tellez, Marisol and Hassan, Nur A. and Rita R Colwell and Ismail, Amid} } @article {20295, title = {Biofilms Comprise a Component of the Annual Cycle of Vibrio cholerae in the Bay of Bengal Estuary}, journal = {mBio}, year = {2018}, month = {Feb-05-2018}, pages = {e00483-18}, abstract = {Vibrio cholerae, an estuarine bacterium, is the causative agent of cholera, a severe diarrheal disease that demonstrates seasonal incidence in Bangladesh. In an extensive study of V. cholerae occurrence in a natural aquatic environment, water and plankton samples were collected biweekly between December 2005 and November 2006 from Mathbaria, an estuarine village of Bangladesh near the mangrove forests of the Sundarbans. Toxigenic V. cholerae exhibited two seasonal growth peaks, one in spring (March to May) and another in autumn (September to November), corresponding to the two annual seasonal outbreaks of cholera in this region. The total numbers of bacteria determined by heterotrophic plate count (HPC), representing culturable bacteria, accounted for 1\% to 2.7\% of the total numbers obtained using acridine orange direct counting (AODC). The highest bacterial culture counts, including toxigenic V. cholerae, were recorded in the spring. The direct fluorescent antibody (DFA) assay was used to detect V. cholerae O1 cells throughout the year, as free-living cells, within clusters, or in association with plankton. V. cholerae O1 varied significantly in morphology, appearing as distinctly rod-shaped cells in the spring months, while small coccoid cells within thick clusters of biofilm were observed during interepidemic periods of the year, notably during the winter months. Toxigenic V. cholerae O1 was culturable in natural water during the spring when the temperature rose sharply. The results of this study confirmed biofilms to be a means of persistence for bacteria and an integral component of the annual life cycle of toxigenic V. cholerae in the estuarine environment of Bangladesh.}, doi = {10.1128/mBio.00483-18}, url = {https://mbio.asm.org/content/9/2/e00483-18}, author = {Sultana, Marzia and Nusrin, Suraia and Hasan, Nur A. and Sadique, Abdus and Ahmed, Kabir U. and Islam, Atiqul and Hossain, Anwar and Longini, Ira and Nizam, Azhar and Huq, Anwar and Siddique, Abul K. and Sack, David A. and Sack, Richard B. and Rita R Colwell and Alam, Munirul}, editor = {Vidaver, Anne K.} } @article {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 {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 {20343, title = {Downscaling river discharge to assess the effects of climate change on cholera outbreaks in the Bengal Delta}, journal = {Climate Research}, volume = {64}, year = {2015}, month = {Jul-08-2017}, pages = {257 - 274}, abstract = {Endemic cholera in the Bengal Delta region of South Asia has been associated with asymmetric and episodic variability of river discharge. Spring cholera was found to be related to intrusion of bacteria-laden coastal seawater during low flow seasons. Autumn cholera was hypothesized to result from cross-contamination of water resources when high river discharge causes massive inland inundation. The effect of climate change on diarrheal diseases has not been explored, because of the difficulties in establishing linkages between coarse-resolution global climate model outputs with localized disease outbreaks. Since rivers act as corridors for transport of cholera bacteria, the first step is to understand the discharge variability that may occur with climate change and whether it is linked to cholera. Here, we present a framework for downscaling precipitation from global climate models for river discharge in the Ganges-Brahmaputra-Meghna basin. Using a data-mining method that includes particle swarm optimization-based support vector regression, precipitation was downscaled for a statistical multiple regressive model to estimate river discharge in the basin. Key results from an ensemble of HadCM3, GFDL, and ECHAM5 models indicated 8 and 7.5\% increase in flows for the IPCC A1B and A2 scenarios, respectively. The majority of the changes are attributable to increases in flows from February through August for both scenarios, with little to no change in seasonality of high and low flows during the next century. The probability of spring and autumn cholera is likely to increase steadily in the endemic region of the Bengal Delta. }, issn = {0936-577X}, doi = {10.3354/cr01310}, url = {http://www.int-res.com/abstracts/cr/v64/n3/p257-274/}, author = {Nasr-Azadani, F and Unnikrishnan, A and Akanda, A and Islam, S and Alam, M and Huq, A and Jutla, A and Rita R Colwell} } @article {20345, title = {Molecular tools in understanding the evolution of Vibrio cholerae}, journal = {Frontiers in Microbiology}, year = {2015}, month = {Jun-10-2015}, abstract = {Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies.}, doi = {10.3389/fmicb.2015.01040}, url = {http://journal.frontiersin.org/Article/10.3389/fmicb.2015.01040/abstract}, author = {Rahaman, Md. Habibur and Islam, Tarequl and Rita R Colwell and Alam, Munirul} } @article {20361, title = {Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing}, journal = {PLoS ONE}, year = {2014}, month = {Aug-05-2015}, pages = {e97699}, abstract = {Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90\% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.}, doi = {10.1371/journal.pone.0097699}, url = {https://dx.plos.org/10.1371/journal.pone.0097699}, author = {Hasan, Nur A. and Young, Brian A. and Minard-Smith, Angela T. and Saeed, Kelly and Li, Huai and Heizer, Esley M. and McMillan, Nancy J. and Isom, Richard and Abdullah, Abdul Shakur and Bornman, Daniel M. and Faith, Seth A. and Choi, Seon Young and Dickens, Michael L. and Cebula, Thomas A. and Rita R Colwell}, editor = {Ahmed, Niyaz} } @article {20334, title = {Occurrence in Mexico, 1998{\textendash}2008, of Vibrio cholerae CTX + El Tor carrying an additional truncated CTX prophage}, journal = {Proceedings of the National Academy of Sciences}, volume = {111}, year = {2014}, month = {Aug-07-2014}, pages = {9917 - 9922}, issn = {0027-8424}, doi = {10.1073/pnas.1323408111}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1323408111}, author = {Alam, Munirul and Rashed, Shah M and Mannan, Shahnewaj Bin and Islam, Tarequl and Lizarraga-Partida, Marcial L. and Delgado, Gabriela and Morales-Espinosa, Rosario and Mendez, Jose Luis and Navarro, Armando and Watanabe, Haruo and Ohnishi, Makoto and Hasan, Nur A. and Huq, Anwar and Sack, R. Bradley and Rita R Colwell and Cravioto, Alejandro} } @article {19685, title = {Binary to Bushy: Bayesian Hierarchical Clustering with the Beta Coalescent}, year = {2013}, month = {2013/00/01}, pages = {1079 - 1087}, abstract = {Abstract Discovering hierarchical regularities in data is a key problem in interacting with large datasets, modeling cognition, and encoding knowledge. A previous Bayesian solution-- -Kingman{\textquoteright}s coalescent---provides a convenient probabilistic model for data represented ...}, url = {http://papers.nips.cc/paper/5161-binary-to-bushy-bayesian-hierarchical-clustering-with-the-beta-coalescent}, author = {Hu, Yuening and Jordan Boyd-Graber and Daume III, Hal and Ying, Z Irene} } @article {19372, title = {Parallel geometric classification of stem cells by their three-dimensional morphology}, journal = {Computational Science \& Discovery}, volume = {6}, year = {2013}, month = {01/2013}, pages = {015007}, doi = {10.1088/1749-4699/6/1/015007}, author = {Juba,Derek and Cardone, Antonio and Ip, Cheuk Yiu and Simon Jr, Carl G and K Tison, Christopher and Kumar, Girish and Brady,Mary and Varshney, Amitabh} } @article {20377, title = {A water marker monitored by satellites to predict seasonal endemic cholera}, journal = {Remote Sensing Letters}, volume = {4472741982394456}, year = {2013}, month = {Jan-08-2013}, pages = {822 - 831}, abstract = {The ability to predict an occurrence of cholera, a water-related disease, offers a significant public health advantage. Satellite-based estimates of chlorophyll, a surrogate for plankton abundance, have been linked to cholera incidence. However, cholera bacteria can survive under a variety of coastal ecological conditions, thus constraining the predictive ability of the chlorophyll, since it provides only an estimate of greenness of seawater. Here, a new remote-sensing-based index is proposed: Satellite Water Marker (SWM), which estimates the condition of coastal water, based on observed variability in the difference between blue (412 nm) and green (555 nm) wavelengths that can be related to seasonal cholera incidence. The index is bounded between physically separable wavelengths for relatively clear (blue) and turbid (green) water. Using SWM, prediction of cholera with reasonable accuracy, at least two months in advance, can potentially be achieved in the endemic coastal regions. }, issn = {2150-704X}, doi = {10.1080/2150704X.2013.802097}, url = {http://www.tandfonline.com/doi/abs/10.1080/2150704X.2013.802097}, author = {Jutla, Antarpreet and Akanda, Ali Shafqat and Huq, Anwar and Faruque, Abu Syed Golam and Rita R Colwell and Islam, Shafiqul} } @article {20374, title = {Genetic characteristics of drug-resistant Vibrio cholerae O1 causing endemic cholera in Dhaka, 2006-2011}, journal = {Journal of Medical Microbiology}, year = {2012}, month = {Jan-12-2012}, pages = {1736 - 1745}, abstract = {Vibrio cholerae O1 biotype El Tor (ET), causing the seventh cholera pandemic, was recently replaced in Bangladesh by an altered ET possessing ctxB of the Classical (CL) biotype, which caused the first six cholera pandemics. In the present study, V. cholerae O1 strains associated with endemic cholera in Dhaka between 2006 and 2011 were analysed for major phenotypic and genetic characteristics. Of 54 representative V. cholerae isolates tested, all were phenotypically ET and showed uniform resistance to trimethoprim/sulfamethoxazole (SXT) and furazolidone (FR). Resistance to tetracycline (TE) and erythromycin (E) showed temporal fluctuation, varying from year to year, while all isolates were susceptible to gentamicin (CN) and ciprofloxacin (CIP). Year-wise data revealed erythromycin resistance to be 33.3 \% in 2006 and 11 \% in 2011, while tetracycline resistance accounted for 33, 78, 0, 100 and 27 \% in 2006, 2007, 2008, 2009 and 2010, respectively; interestingly, all isolates tested were sensitive to TE in 2011, as observed in 2008. All V. cholerae isolates tested possessed genetic elements such as SXT, ctxAB, tcpA ET, rstR ET and rtxC; none had IntlI (Integron I). Double mismatch amplification mutation assay (DMAMA)-PCR followed by DNA sequencing and analysis of the ctxB gene revealed a point mutation at position 58 (C{\textrightarrow}A), which has resulted in an amino acid substitution from histidine (H) to asparagine (N) at position 20 (genotype 7) since 2008. Although the multi-resistant strains having tetracycline resistance showed minor genetic divergence, V. choleraestrains were clonal, as determined by a PFGE (NotI)-based dendrogram. This study shows 2008{\textendash}2010 to be the time of transition from ctxB genotype 1 to genotype 7 in V. cholerae ET causing endemic cholera in Dhaka, Bangladesh.}, issn = {0022-2615}, doi = {10.1099/jmm.0.049635-0}, url = {http://jmm.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.049635-0}, author = {Rashed, S. M. and Mannan, S. B. and Johura, F.-T. and Islam, M. T. and Sadique, A. and Watanabe, H. and Sack, R. B. and Huq, A. and Rita R Colwell and Cravioto, A. and Alam, M.} } @article {12854, title = {Vibrio Cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico}, journal = {Journal of Clinical Microbiology}, year = {2012}, month = {04/2012}, abstract = {Vibrio cholerae O1 Classical (CL) biotype caused the 5th and 6th, and probably the earlier cholera pandemics, before the El Tor (ET) biotype initiated the 7th pandemic in Asia in the 1970{\textquoteright}s by completely displacing the CL biotype. Although the CL biotype was thought to be extinct in Asia, and it had never been reported from Latin America, V. cholerae CL and ET biotypes, including hybrid ET were found associated with endemic cholera in Mexico between 1991 and 1997. In this study, CL biotype strains isolated from endemic cholera in Mexico, between 1983 and 1997 were characterized in terms of major phenotypic and genetic traits, and compared with CL biotype strains isolated in Bangladesh between 1962 and 1989. According to sero- and bio-typing data, all V. cholerae strains tested had the major phenotypic and genotypic characteristics specific for the CL biotype. Antibiograms revealed the majority of the Bangladeshi strains to be resistant to trimethoprim/sulfamethoxazole, furazolidone, ampicillin, and gentamycin, while the Mexican strains were sensitive to all of these drugs, as well as to ciprofloxacin, erythromycin, and tetracycline. Pulsed-field gel electrophoresis (PFGE) of NotI-digested genomic DNA revealed characteristic banding patterns for all the CL biotype strains, although the Mexican strains differed with the Bangladeshi strains in 1-2 DNA bands. The difference may be subtle, but consistent, as confirmed by the sub-clustering patterns in the PFGE-based dendrogram, and can serve as regional signature, suggesting pre-1991 existence and evolution of the CL biotype strains in the Americas, independent from that of Asia.}, isbn = {0095-1137, 1098-660X}, doi = {10.1128/JCM.00189-12}, url = {http://jcm.asm.org/content/early/2012/04/12/JCM.00189-12}, author = {Alam,Munirul and Islam,M. Tarequl and Rashed,Shah Manzur and Johura,Fatema-Tuz and Bhuiyan,Nurul A. and Delgado,Gabriela and Morales,Rosario and Mendez,Jose Luis and Navarro,Armando and Watanabe,Haruo and Hasan,Nur-A. and Rita R Colwell and Cravioto,Alejandro} } @article {20382, title = {Vibrio cholerae in a historically cholera-free country}, journal = {Environmental Microbiology Reports}, year = {2012}, month = {Jan-08-2012}, pages = {381 - 389}, abstract = {We report the autochthonous existence of Vibrio cholerae in coastal waters of Iceland, a geothermally active country where cholera is absent and has never been reported. Seawater, mussel and macroalgae samples were collected close to, and distant from, sites where geothermal activity causes a significant increase in water temperature during low tides. Vibrio cholerae was detected only at geothermal-influenced sites during low-tides. None of the V. cholerae isolates encoded cholera toxin (ctxAB) and all were non-O1/non-O139 serogroups. However, all isolates encoded other virulence factors that are associated with cholera as well as extra-intestinal V. cholerae infections. The virulence factors were functional at temperatures of coastal waters of Iceland, suggesting an ecological role. It is noteworthy that V. cholerae was isolated from samples collected at sites distant from anthropogenic influence, supporting the conclusion that V. cholerae is autochthonous to the aquatic environment of Iceland.}, doi = {10.1111/j.1758-2229.2012.00332.x}, url = {http://doi.wiley.com/10.1111/j.1758-2229.2012.00332.x}, author = {Haley, Bradd J. and Chen, Arlene and Grim, Christopher J. and Clark, Philip and Diaz, Celia M and Taviani, Elisa and Hasan, Nur A. and Sancomb, Elizabeth and Elnemr, Wessam M and Islam, Muhammad A. and Huq, Anwar and Rita R Colwell and Benediktsd{\'o}ttir, Eva} } @conference {19317, title = {Linguistic Resources for Handwriting Recognition and Translation Evaluation}, booktitle = {Eight International Conference on Language Resources and Evaluation (LREC{\textquoteright}12)}, year = {2012}, author = {Song, Zhiyi and Ismael, Safa and Grimes, Stephen and David Doermann and Strassel,Stephanie} } @article {15158, title = {On Achieving the" Best of Both Worlds" in Secure Multiparty Computation}, journal = {SIAM Journal on Computing}, volume = {40}, year = {2011}, month = {2011///}, pages = {122 - 122}, abstract = {Two settings are traditionally considered for secure multiparty computation, de-pending on whether or not a majority of the parties are assumed to be honest. Existing protocols that assume an honest majority provide {\textquotedblleft}full security{\textquotedblright} (and, in particular, guarantee output delivery and fairness) when this assumption holds, but are completely insecure if this assumption is violated. On the other hand, known protocols tolerating an arbitrary number of corruptions do not guarantee fairness or output delivery even if only a single party is dishonest. It is natural to wonder whether it is possible to achieve the {\textquotedblleft}best of both worlds{\textquotedblright}: namely, a single protocol that simultaneously achieves the best possible security in both the above settings. Here, we rule out this possibility (at least for general functionalities) and show some positive results regarding what can be achieved. }, author = {Ishai,Y. and Katz, Jonathan and Kushilevitz,E. and Lindell,Y. and Petrank,E.} } @inbook {19640, title = {On the Black-Box Complexity of Optimally-Fair Coin Tossing}, booktitle = {Theory of Cryptography}, series = {Lecture Notes in Computer Science}, year = {2011}, month = {2011/01/01/}, pages = {450 - 467}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {A fair two-party coin tossing protocol is one in which both parties output the same bit that is almost uniformly distributed (i.e., it equals 0 and 1 with probability that is at most negligibly far from one half). It is well known that it is impossible to achieve fair coin tossing even in the presence of fail-stop adversaries (Cleve, FOCS 1986). In fact, Cleve showed that for every coin tossing protocol running for r rounds, an efficient fail-stop adversary can bias the output by Ω(1/r). Since this is the best possible, a protocol that limits the bias of any adversary to O(1/r) is called optimally-fair. The only optimally-fair protocol that is known to exist relies on the existence of oblivious transfer, because it uses general secure computation (Moran, Naor and Segev, TCC 2009). However, it is possible to achieve a bias of O(1/r√)O(1/\sqrt{r}) in r rounds relying only on the assumption that there exist one-way functions. In this paper we show that it is impossible to achieve optimally-fair coin tossing via a black-box construction from one-way functions for r that is less than O(n/logn), where n is the input/output length of the one-way function used. An important corollary of this is that it is impossible to construct an optimally-fair coin tossing protocol via a black-box construction from one-way functions whose round complexity is independent of the security parameter n determining the security of the one-way function being used. Informally speaking, the main ingredient of our proof is to eliminate the random-oracle from {\textquotedblleft}secure{\textquotedblright} protocols with {\textquotedblleft}low round-complexity{\textquotedblright} and simulate the protocol securely against semi-honest adversaries in the plain model. We believe our simulation lemma to be of broader interest.}, keywords = {Algorithm Analysis and Problem Complexity, black-box separations, Coding and Information Theory, coin tossing, Computer Communication Networks, Data Encryption, lower-bound, Math Applications in Computer Science, optimally-fair coin tossing, round-complexity, Systems and Data Security}, isbn = {978-3-642-19570-9, 978-3-642-19571-6}, url = {http://link.springer.com/chapter/10.1007/978-3-642-19571-6_27}, author = {Dana Dachman-Soled and Lindell, Yehuda and Mahmoody, Mohammad and Malkin, Tal}, editor = {Ishai, Yuval} } @article {12869, title = {Clonal transmission, dual peak, and off-season cholera in Bangladesh}, journal = {Infection Ecology \& Epidemiology}, volume = {1}, year = {2011}, month = {08/2011}, abstract = {Vibrio cholerae is an estuarine bacterium associated with a single peak of cholera (March{\textendash}May) in coastal villages of Bangladesh. For an unknown reason, however, cholera occurs in a unique dual peak (March{\textendash}May and September{\textendash}November) pattern in the city of Dhaka that is bordered by a heavily polluted freshwater river system and flood embankment. In August 2007, extreme flooding was accompanied by an unusually severe diarrhea outbreak in Dhaka that resulted in a record high illness. This study was aimed to understand the unusual outbreak and if it was related to the circulation of a new V. cholerae clone. Nineteen V. cholerae isolated during the peak of the 2007 outbreak were subjected to extensive phenotypic and molecular analyses, including multi-locus genetic screening by polymerase chain reaction (PCR), sequence-typing of the ctxB gene, and pulsed-field gel electrophoresis (PFGE). Factors associated with the unusual incidence of cholera were determined and analysis of the disease severity was done. Overall, microbiological and molecular data confirmed that the hypervirulent V. cholerae was O1 biotype El Tor (ET) that possessed cholera toxin (CT) of the classical biotype. The PFGE (NotI) and dendrogram clustering confirmed that the strains were clonal and related to the pre-2007 variant ET from Dhaka and Matlab and resembled one of two distinct clones of the variant ET confirmed to be present in the estuarine ecosystem of Bangladesh. Results of the analyses of both diarrheal case data for three consecutive years (2006{\textendash}2008) and regional hydroclimatology over three decades (1980{\textendash}2009) clearly indicate that the pattern of cholera occurring in Dhaka, and not seen at other endemic sites, was associated with flood waters transmitting the infectious clone circulating via the fecal-oral route during and between the dual seasonal cholera peaks in Dhaka. Circular river systems and flood embankment likely facilitate transmission of infectious V. cholerae throughout the year that leads to both sudden and off-season outbreaks in the densely populated urban ecosystem of Dhaka. Clonal recycling of hybrid El Tor with increasing virulence in a changing climate and in a region with a growing urban population represents a serious public health concern for Bangladesh.}, doi = {10.3402/iee.v1i0.7273}, author = {Alam,M. and Islam,A. and Bhuiyan,N. A. and Rahim,N. and Hossain,A. and Khan,G. Y. and Ahmed,D. and Watanabe,H. and Izumiya,H. and Faruque,A. S. G. and Rita R Colwell} } @article {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 {16040, title = {Empirical Studies in Information Visualization: Seven Scenarios}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {PP}, year = {2011}, month = {2011///}, pages = {1 - 1}, abstract = {We take a new, scenario based look at evaluation in information visualization. Our seven scenarios, evaluating visual data analysis and reasoning, evaluating user performance, evaluating user experience, evaluating environments and work practices, evaluating communication through visualization, evaluating visualization algorithms, and evaluating collaborative data analysis were derived through an extensive literature review of over 800 visualization publications. These scenarios distinguish different study goals and types of research questions and are illustrated through example studies. Through this broad survey and the distillation of these scenarios we make two contributions. One, we encapsulate the current practices in the information visualization research community and, two, we provide a different approach to reaching decisions about what might be the most effective evaluation of a given information visualization. Scenarios can be used to choose appropriate research questions and goals and the provided examples can be consulted for guidance on how to design one{\textquoteright}s own study.}, isbn = {1077-2626}, doi = {10.1109/TVCG.2011.279}, author = {Lam,H. and Bertini,E. and Isenberg,P. and Plaisant, Catherine and Carpendale,S.} } @inbook {19034, title = {Implicit Authentication through Learning User Behavior}, booktitle = {Information Security}, series = {Lecture Notes in Computer Science}, volume = {6531}, year = {2011}, month = {2011}, pages = {99 - 113}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Users are increasingly dependent on mobile devices. However, current authentication methods like password entry are significantly more frustrating and difficult to perform on these devices, leading users to create and reuse shorter passwords and pins, or no authentication at all. We present implicit authentication - authenticating users based on behavior patterns. We describe our model for performing implicit authentication and assess our techniques using more than two weeks of collected data from over 50 subjects.}, keywords = {Computer science}, isbn = {978-3-642-18177-1}, url = {http://www.springerlink.com/content/m57u551u3133475m/abstract/}, author = {Elaine Shi and Niu, Yuan and Jakobsson, Markus and Chow, Richard}, editor = {Burmester, Mike and Tsudik, Gene and Magliveras, Spyros and Ilic, Ivana} } @conference {17904, title = {MDMap: A system for data-driven layout and exploration of molecular dynamics simulations}, booktitle = {Biological Data Visualization (BioVis), 2011 IEEE Symposium on}, year = {2011}, month = {2011/10//}, pages = {111 - 118}, abstract = {Contemporary molecular dynamics simulations result in a glut of simulation data, making analysis and discovery a difficult and burdensome task. We present MDMap, a system designed to summarize long-running molecular dynamics (MD) simulations. We represent a molecular dynamics simulation as a state transition graph over a set of intermediate (stable and semi-stable) states. The transitions amongst the states together with their frequencies represent the flow of a biomolecule through the trajectory space. MDMap automatically determines potential intermediate conformations and the transitions amongst them by analyzing the conformational space explored by the MD simulation. MDMap is an automated system to visualize MD simulations as state-transition diagrams, and can replace the current tedious manual layouts of biomolecular folding landscapes with an automated tool. The layout of the representative states and the corresponding transitions among them is presented to the user as a visual synopsis of the long-running MD simulation. We compare and contrast multiple presentations of the state transition diagrams, such as conformational embedding, and spectral, hierarchical, and force-directed graph layouts. We believe this system could provide a road-map for the visualization of other stochastic time-varying simulations in a variety of different domains.}, keywords = {computing;digital, driven, DYNAMICS, exploration;data, folding, graph;stochastic, landscapes;data, layout;molecular, MDMap;biomolecular, method;stochastic, processes;, simulation;graph, simulations;state, simulations;trajectory, space;biology, theory;molecular, time-varying, transition}, doi = {10.1109/BioVis.2011.6094055}, author = {Patro,R. and Ip, Cheuk Yiu and Bista,S. and Cho,S.S. and Thirumalai,D. and Varshney, Amitabh} } @article {16489, title = {New models and algorithms for throughput maximization in broadcast scheduling}, journal = {Approximation and Online Algorithms}, year = {2011}, month = {2011///}, pages = {71 - 82}, author = {Chekuri,C. and Gal,A. and Im,S. and Khuller, Samir and Li,J. and McCutchen,R. and Moseley,B. and Raschid, Louiqa} } @article {17965, title = {Saliency-Assisted Navigation of Very Large Landscape Images}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {17}, year = {2011}, month = {2011/12//}, pages = {1737 - 1746}, abstract = {The field of visualization has addressed navigation of very large datasets, usually meshes and volumes. Significantly less attention has been devoted to the issues surrounding navigation of very large images. In the last few years the explosive growth in the resolution of camera sensors and robotic image acquisition techniques has widened the gap between the display and image resolutions to three orders of magnitude or more. This paper presents the first steps towards navigation of very large images, particularly landscape images, from an interactive visualization perspective. The grand challenge in navigation of very large images is identifying regions of potential interest. In this paper we outline a three-step approach. In the first step we use multi-scale saliency to narrow down the potential areas of interest. In the second step we outline a method based on statistical signatures to further cull out regions of high conformity. In the final step we allow a user to interactively identify the exceptional regions of high interest that merit further attention. We show that our approach of progressive elicitation is fast and allows rapid identification of regions of interest. Unlike previous work in this area, our approach is scalable and computationally reasonable on very large images. We validate the results of our approach by comparing them to user-tagged regions of interest on several very large landscape images from the Internet.}, keywords = {acquisition;data, acquisition;saliency, analysis;, assisted, image, images;robotic, Internet;camera, navigation;statistical, processing;image, resolution;image, resolution;interactive, sensors;image, sensors;statistical, signatures;data, visualisation;geophysical, visualization;landscape}, isbn = {1077-2626}, doi = {10.1109/TVCG.2011.231}, author = {Ip, Cheuk Yiu and Varshney, Amitabh} } @article {16041, title = {Seven guiding scenarios for information visualization evaluation}, volume = {2011-992-04}, year = {2011}, month = {2011///}, institution = {Department of Computer Science, University of Calgary}, abstract = {We take a new, scenario based look at evaluation in information visualization. Our seven scenarios, evaluatingvisual data analysis and reasoning, evaluating user performance, evaluating user experience, evaluating environments and work practices, evaluating communication through visualization, automated evaluation of visualizations, and evaluating collaborative data analysis were derived through an extensive literature review of over 800 visualization publications. These scenarios are described through their goals, the types of questions they embody and illustrated through example studies. Through this broad survey and the distillation of these scenarios we make two contributions. One, we encapsulate the current practices in the information visualization research community and, two, we provide a different approach to reaching decisions about what might be the most effective evaluation of a given information visualization. For example, if the research goals or evaluative questions are known they can be used to map to specific scenarios, where practical existing examples can be considered for effective evaluation approaches. }, author = {Lam,H. and Bertini,E. and Isenberg,P. and Plaisant, Catherine and Carpendale,S.} } @conference {13329, title = {Simplifying morphological representations of 2D and 3D scalar fields}, booktitle = {Proceedings of the 19th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems}, series = {GIS {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {437 - 440}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We describe a dual graph-based representation for the ascending and descending Morse complexes of a scalar field, and a compact and dimension-independent data structure based on it, which assumes a discrete representation of the field as a simplicial mesh. We present atomic dimension-independent simplification operators on the graph-based representation. Based on such operators, we have developed a simplification algorithm, which allows generalization of the ascending and descending Morse complexes at different levels of resolution. We show here the results of our implementation, discussing the computation times and the size of the resulting simplified graphs, also in comparison with the size of the original full-resolution graph.}, keywords = {morphological representations, Morse complexes, multi-dimensional data sets, simplification}, isbn = {978-1-4503-1031-4}, doi = {10.1145/2093973.2094042}, url = {http://doi.acm.org/10.1145/2093973.2094042}, author = {{\v C}omi{\'c},Lidija and De Floriani, Leila and Iuricich,Federico} } @article {17909, title = {Social Snapshot: A System for Temporally Coupled Social Photography}, journal = {Computer Graphics and Applications, IEEE}, volume = {31}, year = {2011}, month = {2011/02//jan}, pages = {74 - 84}, abstract = {Social Snapshot actively acquires and reconstructs temporally dynamic data. The system enables spatiotemporal 3D photography using commodity devices, assisted by their auxiliary sensors and network functionality. It engages users, making them active rather than passive participants in data acquisition.}, keywords = {3D, acquisition;data, acquisition;photography;social, computing;, coupled, data, photography;data, photography;temporally, reconstruction;social, sciences, snapshot;spatiotemporal, social}, isbn = {0272-1716}, doi = {10.1109/MCG.2010.107}, author = {Patro,R. and Ip, Cheuk Yiu and Bista,S. and Varshney, Amitabh} } @inbook {12458, title = {Tracking and Identification via Object Reflectance Using a Hyperspectral Video Camera}, booktitle = {Machine Vision Beyond Visible SpectrumMachine Vision Beyond Visible Spectrum}, series = {Augmented Vision and Reality}, volume = {1}, year = {2011}, month = {2011///}, pages = {201 - 219}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Recent advances in electronics and sensor design have enabled the development of a hyperspectral video camera that can capture hyperspectral datacubes at near video rates. The sensor offers the potential for novel and robust methods for surveillance by combining methods from computer vision and hyperspectral image analysis. Here, we focus on the problem of tracking objects through challenging conditions, such as rapid illumination and pose changes, occlusions, and in the presence of confusers. A new framework that incorporates radiative transfer theory to estimate object reflectance and particle filters to simultaneously track and identify an object based on its reflectance spectra is proposed. By exploiting high-resolution spectral features in the visible and near-infrared regimes, the framework is able to track objects that appear featureless to the human eye. For example, we demonstrate that near-IR spectra of human skin can also be used to distinguish different people in a video sequence. These capabilities are illustrated using experiments conducted on real hyperspectral video data.}, isbn = {978-3-642-11568-4}, url = {http://dx.doi.org/10.1007/978-3-642-11568-4_9}, author = {Nguyen,Hien Van and Banerjee,Amit and Burlina,Philippe and Broadwater,Joshua and Chellapa, Rama}, editor = {Hammoud,Riad and Fan,Guoliang and McMillan,Robert W. W. and Ikeuchi,Katsushi and Hammoud,Riad I. and Wolff,Lawrence B.} } @article {12862, title = {Warming Oceans, Phytoplankton, and River Discharge: Implications for Cholera Outbreaks}, journal = {The American Journal of Tropical Medicine and Hygiene}, volume = {85}, year = {2011}, month = {08/2011}, pages = {303 - 308}, abstract = {Phytoplankton abundance is inversely related to sea surface temperature (SST). However, a positive relationship is observed between SST and phytoplankton abundance in coastal waters of Bay of Bengal. This has led to an assertion that in a warming climate, rise in SST may increase phytoplankton blooms and, therefore, cholera outbreaks. Here, we explain why a positive SST-phytoplankton relationship exists in the Bay of Bengal and the implications of such a relationship on cholera dynamics. We found clear evidence of two independent physical drivers for phytoplankton abundance. The first one is the widely accepted phytoplankton blooming produced by the upwelling of cold, nutrient-rich deep ocean waters. The second, which explains the Bay of Bengal findings, is coastal phytoplankton blooming during high river discharges with terrestrial nutrients. Causal mechanisms should be understood when associating SST with phytoplankton and subsequent cholera outbreaks in regions where freshwater discharge are a predominant mechanism for phytoplankton production.}, isbn = {0002-9637,}, doi = {10.4269/ajtmh.2011.11-0181}, url = {http://www.ajtmh.org/content/85/2/303}, author = {Jutla,Antarpreet S. and Akanda,Ali S. and Griffiths,Jeffrey K. and Rita R Colwell and Islam,Shafiqul} } @article {17983, title = {Computer Memory Architecture for Hybrid Serial and Parallel Computing Systems}, volume = {12/721,252}, year = {2010}, month = {2010/11/11/}, abstract = {In one embodiment, a serial processor is configured to execute software instructions in a software program in serial. A serial memory is configured to store data for use by the serial processor in executing the software instructions in serial. A plurality of parallel processors are configured to execute software instructions in the software program in parallel. A plurality of partitioned memory modules are provided and configured to store data for use by the plurality of parallel processors in executing software instructions in parallel. Accordingly, a processor/memory structure is provided that allows serial programs to use quick local serial memories and parallel programs to use partitioned parallel memories. The system may switch between a serial mode and a parallel mode. The system may incorporate pre-fetching commands of several varieties. For example, towards switching between the serial mode and the parallel mode, the serial processor is configured to send a signal to start...}, url = {http://www.google.com/patents?id=0OPbAAAAEBAJ}, author = {Vishkin, Uzi}, editor = {Xmtt Inc.} } @article {12876, title = {Diversity and distribution of cholix toxin, a novel ADP-ribosylating factor from Vibrio cholerae}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2010}, month = {2010/02/08/}, pages = {198 - 207}, abstract = {Non-toxigenic non-O1, non-O139 Vibrio cholerae strains isolated from both environmental and clinical settings carry a suite of virulence factors aside from cholera toxin. Among V. cholerae strains isolated from coastal waters of southern California, this includes cholix toxin, an ADP-ribosylating factor that is capable of halting protein synthesis in eukaryotic cells. The prevalence of the gene encoding cholix toxin, chxA, was assessed among a collection of 155 diverse V. cholerae strains originating from both clinical and environmental settings in Bangladesh and Mexico and other countries around the globe. The chxA gene was present in 47\% of 83 non-O1, non-O139 strains and 16\% of 72 O1/O139 strains screened as part of this study. A total of 86 chxA gene sequences were obtained, and phylogenetic analysis revealed that they fall into two distinct clades. These two clades were also observed in the phylogenies of several housekeeping genes, suggesting that the divergence observed in chxA extends to other regions of the V. cholerae genome, and most likely has arisen from vertical descent rather than horizontal transfer. Our results clearly indicate that ChxA is a major toxin of V. cholerae with a worldwide distribution that is preferentially associated with non-pandemic strains.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2010.00139.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2010.00139.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Purdy,Alexandra E. and Balch,Deborah and Liz{\'a}rraga-Partida,Marcial Leonardo and Islam,Mohammad Sirajul and Martinez-Urtaza,Jaime and Huq,Anwar and Rita R Colwell and Bartlett,Douglas H.} } @article {12967, title = {Intensity normalization improves color calling in SOLiD sequencing}, journal = {Nat MethNat Meth}, volume = {7}, year = {2010}, month = {2010/05//}, pages = {336 - 337}, isbn = {1548-7091}, doi = {10.1038/nmeth0510-336}, url = {http://dx.doi.org/10.1038/nmeth0510-336}, author = {Wu,Hao and Irizarry,Rafael A and Corrada Bravo, Hector} } @article {15883, title = {Investigating multi-label classification for human values}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {47}, year = {2010}, month = {2010///}, pages = {1 - 4}, author = {Ishita,E. and Oard, Douglas and Fleischmann,K.R. and Cheng,A.S. and Templeton,T.C.} } @article {17950, title = {Saliency Guided Summarization of Molecular Dynamics Simulations}, journal = {Scientific Visualization: Advanced Concepts}, volume = {1}, year = {2010}, month = {2010///}, pages = {321 - 335}, abstract = {We present a novel method to measure saliency in molecular dynamics simulation data. This saliency measure is based on a multiscale center-surround mechanism, which is fast and efficient to compute. We explore the use of the saliency function to guide the selection of representative and anomalous timesteps for summarization of simulations. To this end, we also introduce a multiscale keyframe selection procedure which automatically provides keyframes representing the simulation at varying levels of coarseness. We compare our saliency guided keyframe approach against other methods, and show that it consistently selects superior keyframes as measured by their predictive power in reconstructing the simulation.}, author = {Patro,R. and Ip,C. Y and Varshney, Amitabh and Hagen,H.} } @conference {15862, title = {Values of Stakeholders in the Net Neutrality Debate: Applying Content Analysis to Telecommunications Policy}, booktitle = {Hawaii International Conference on System Sciences}, year = {2010}, month = {2010///}, pages = {1 - 10}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Net neutrality is an important telecommunications policy debate. This debate is closely tied to technological innovation, economic development, and information access. Values help shape stakeholders{\textquoteright} positions on this debate. This paper examines the role of values in shaping the Net neutrality debate through a content analysis of public hearings on Net neutrality. The paper presents a quantitative analysis that reveals the top values implicated in the Net neutrality debate and statistically significant differences among individuals on opposite sides of the Net neutrality debate. A qualitative analysis reveals insights into the connection between specific values and positions on the Net neutrality debate. The paper concludes that values, technology, and policy are interconnected, and that it is useful to understand the values of the various stakeholders within policy debates.}, isbn = {978-0-7695-3869-3}, doi = {http://doi.ieeecomputersociety.org/10.1109/HICSS.2010.434}, author = {Cheng,An-Shou and Fleischmann,Kenneth R. and Wang,Ping and Ishita,Emi and Oard, Douglas} } @article {15876, title = {Automatic classification of human values: Applying computational thinking to information ethics}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {46}, year = {2009}, month = {2009///}, pages = {1 - 4}, author = {Fleischmann,K.R. and Oard, Douglas and Cheng,A.S. and Wang,P. and Ishita,E.} } @conference {16485, title = {Flexible and efficient querying and ranking on hyperlinked data sources}, booktitle = {Proceedings of the 12th International Conference on Extending Database Technology: Advances in Database Technology}, year = {2009}, month = {2009///}, pages = {553 - 564}, author = {Varadarajan,R. and Hristidis,V. and Raschid, Louiqa and Vidal,M. E and Ib{\'a}\ nez,L. and Rodr{\'\i}guez-Drumond,H.} } @article {12968, title = {Model-based quality assessment and base-calling for second-generation sequencing data}, journal = {Johns Hopkins University, Dept. of Biostatistics Working Papers}, year = {2009}, month = {2009///}, pages = {184 - 184}, author = {Irizarry,R. A and Corrada Bravo, Hector} } @article {13613, title = {Off-Line Loop Investigation for Handwriting Analysis}, journal = {IEEETransactions on Pattern Analysis and Machine Intelligence}, volume = {31}, year = {2009}, month = {2009/02//}, pages = {193 - 209}, author = {Steinherz,T. and David Doermann and Rivlin,E. and Intrator,N.} } @article {12884, title = {RNA Colony Blot Hybridization Method for Enumeration of Culturable Vibrio Cholerae and Vibrio Mimicus Bacteria}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, month = {2009/09/01/}, pages = {5439 - 5444}, abstract = {A species-specific RNA colony blot hybridization protocol was developed for enumeration of culturable Vibrio cholerae and Vibrio mimicus bacteria in environmental water samples. Bacterial colonies on selective or nonselective plates were lysed by sodium dodecyl sulfate, and the lysates were immobilized on nylon membranes. A fluorescently labeled oligonucleotide probe targeting a phylogenetic signature sequence of 16S rRNA of V. cholerae and V. mimicus was hybridized to rRNA molecules immobilized on the nylon colony lift blots. The protocol produced strong positive signals for all colonies of the 15 diverse V. cholerae-V. mimicus strains tested, indicating 100\% sensitivity of the probe for the targeted species. For visible colonies of 10 nontarget species, the specificity of the probe was calculated to be 90\% because of a weak positive signal produced by Grimontia (Vibrio) hollisae, a marine bacterium. When both the sensitivity and specificity of the assay were evaluated using lake water samples amended with a bioluminescent V. cholerae strain, no false-negative or false-positive results were found, indicating 100\% sensitivity and specificity for culturable bacterial populations in freshwater samples when G. hollisae was not present. When the protocol was applied to laboratory microcosms containing V. cholerae attached to live copepods, copepods were found to carry approximately 10,000 to 50,000 CFU of V. cholerae per copepod. The protocol was also used to analyze pond water samples collected in an area of cholera endemicity in Bangladesh over a 9-month period. Water samples collected from six ponds demonstrated a peak in abundance of total culturable V. cholerae bacteria 1 to 2 months prior to observed increases in pathogenic V. cholerae and in clinical cases recorded by the area health clinic. The method provides a highly specific and sensitive tool for monitoring the dynamics of V. cholerae in the environment. The RNA blot hybridization protocol can also be applied to detection of other gram-negative bacteria for taxon-specific enumeration.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.02007-08}, url = {http://aem.asm.org/content/75/17/5439}, author = {Grim,Christopher J. and Zo,Young-Gun and Hasan,Nur A. and Ali,Afsar and Chowdhury,Wasimul B. and Islam,Atiqul and Rashid,Mohammed H. and Alam,Munirul and Morris,J. Glenn and Huq,Anwar and Rita R Colwell} } @article {13856, title = {Semantically informed machine translation (SIMT)}, journal = {SCALE summer workshop final report, Human Language Technology Center Of Excellence}, year = {2009}, month = {2009///}, author = {Baker,K. and Bethard,S. and Bloodgood,M. and Brown,R. and Callison-Burch,C. and Coppersmith,G. and Dorr, Bonnie J and Filardo,W. and Giles,K. and Irvine,A. and others} } @article {12882, title = {Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, month = {2009/10/01/}, pages = {6268 - 6274}, abstract = {Forty-two strains of Vibrio parahaemolyticus were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes toxR and tlh were confirmed by PCR in all but two strains, which also lacked toxR. A total of 18 (41\%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (trh) gene, but not tdh. Ten (23\%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed tdh. Of the 18 tdh-positive strains, 17 (94\%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single trh-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., {\textquotedblleft}clonal cluster,{\textquotedblright} as did pandemic strains of diverse origin. The demonstrated prevalence of tdh-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.00266-09}, url = {http://aem.asm.org/content/75/19/6268}, author = {Alam,Munirul and Chowdhury,Wasimul B. and Bhuiyan,N. A. and Islam,Atiqul and Hasan,Nur A. and Nair,G. Balakrish and Watanabe,H. and Siddique,A. K. and Huq,Anwar and Sack,R. Bradley and Akhter,M. Z. and Grim,Christopher J. and Kam,K.-M. and Luey,C. K. Y. and Endtz,Hubert P. and Cravioto,Alejandro and Rita R Colwell} } @article {17754, title = {SPOT Databases: Efficient Consistency Checking and Optimistic Selection in Probabilistic Spatial Databases}, journal = {Knowledge and Data Engineering, IEEE Transactions on}, volume = {21}, year = {2009}, month = {2009/01//}, pages = {92 - 107}, abstract = {Spatial probabilistic temporal (SPOT) databases are a paradigm for reasoning with probabilistic statements about where a vehicle may be now or in the future. They express statements of the form "Object O is in spatial region R at some time t with some probability in the interval [L,U]." Past work on SPOT databases has developed selection operators based on selecting SPOT atoms that are entailed by the SPOT database-we call this "cautious" selection. In this paper, we study several problems. First, we note that the runtime of consistency checking and cautious selection algorithms in past work is influenced greatly by the granularity of the underlying Cartesian space. In this paper, we first introduce the notion of "optimistic" selection, where we are interested in returning all SPOT atoms in a database that are consistent with respect to a query, rather than having an entailment relationship. We then develop an approach to scaling SPOT databases that has three main contributions: 1) We develop methods to eliminate variables from the linear programs used in past work, thus greatly reducing the size of the linear programs used-the resulting advances apply to consistency checking, optimistic selection, and cautious selection. 2) We develop a host of theorems to show how we can prune the search space when we are interested in optimistic selection. 3) We use the above contributions to build an efficient index to execute optimistic selection queries over SPOT databases. Our approach is superior to past work in two major respects: First, it makes fewer assumptions than all past works on this topic except that in. Second, our experiments, which are based on real-world data about ship movements, show that our algorithms are much more efficient than those in.}, keywords = {Cartesian, checking;database, database;data, databases;, databases;visual, indexing;inference, indexing;linear, integrity;database, mechanisms;linear, probabilistic, problem;spatial, problems;temporal, processing;search, program;optimistic, programming;probability;query, query;probabilistic, reasoning;search, selection, selection;consistency, space;cautious, temporal}, isbn = {1041-4347}, doi = {10.1109/TKDE.2008.93}, author = {Parker,A. and Infantes,G. and Grant,J. and V.S. Subrahmanian} } @conference {17763, title = {An AGM-based belief revision mechanism for probabilistic spatio-temporal logics}, booktitle = {Proceedings of the 23rd national conference on Artificial intelligence}, year = {2008}, month = {2008///}, pages = {511 - 516}, author = {Parker,A. and Infantes,G. and V.S. Subrahmanian and Grant,J.} } @inbook {19030, title = {Delegating Capabilities in Predicate Encryption Systems}, booktitle = {Automata, Languages and Programming}, series = {Lecture Notes in Computer Science}, volume = {5126}, year = {2008}, month = {2008}, pages = {560 - 578}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In predicate encryption systems, given a capability, one can evaluate one or more predicates on the plaintext encrypted, while all other information about the plaintext remains hidden. We consider the role of delegation in such predicate encryption systems. Suppose Alice has a capability, and she wishes to delegate to Bob a more restrictive capability allowing the decryption of a subset of the information Alice can learn about the plaintext encrypted. We formally define delegation in predicate encryption systems, propose a new security definition for delegation, and give an efficient construction supporting conjunctive queries. The security of our construction can be reduced to the general 3-party Bilinear Diffie-Hellman assumption, and the Bilinear Decisional Diffie-Hellman assumption in composite order bilinear groups.}, keywords = {Computer science}, isbn = {978-3-540-70582-6}, url = {http://www.springerlink.com/content/w320422h15050004/abstract/}, author = {Elaine Shi and Waters,Brent}, editor = {Aceto,Luca and Damg{\r a}rd,Ivan and Goldberg,Leslie and Halld{\'o}rsson,Magn{\'u}s and Ing{\'o}lfsd{\'o}ttir,Anna and Walukiewicz,Igor} } @inbook {19642, title = {Optimal Cryptographic Hardness of Learning Monotone Functions}, booktitle = {Automata, Languages and Programming}, series = {Lecture Notes in Computer Science}, year = {2008}, month = {2008/01/01/}, pages = {36 - 47}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {A wide range of positive and negative results have been established for learning different classes of Boolean functions from uniformly distributed random examples. However, polynomial-time algorithms have thus far been obtained almost exclusively for various classes of monotone functions, while the computational hardness results obtained to date have all been for various classes of general (nonmonotone) functions. Motivated by this disparity between known positive results (for monotone functions) and negative results (for nonmonotone functions), we establish strong computational limitations on the efficient learnability of various classes of monotone functions. We give several such hardness results which are provably almost optimal since they nearly match known positive results. Some of our results show cryptographic hardness of learning polynomial-size monotone circuits to accuracy only slightly greater than 1/2+1/n--√1/2 + 1/\sqrt{n} ; this accuracy bound is close to optimal by known positive results (Blum et al., FOCS {\textquoteright}98). Other results show that under a plausible cryptographic hardness assumption, a class of constant-depth, sub-polynomial-size circuits computing monotone functions is hard to learn; this result is close to optimal in terms of the circuit size parameter by known positive results as well (Servedio, Information and Computation {\textquoteright}04). Our main tool is a complexity-theoretic approach to hardness amplification via noise sensitivity of monotone functions that was pioneered by O{\textquoteright}Donnell (JCSS {\textquoteright}04).}, keywords = {Data structures, Data Structures, Cryptology and Information Theory, Discrete Mathematics in Computer Science, Numeric Computing, Software Engineering/Programming and Operating Systems, Theory of computation}, isbn = {978-3-540-70574-1, 978-3-540-70575-8}, url = {http://link.springer.com/chapter/10.1007/978-3-540-70575-8_4}, author = {Dana Dachman-Soled and Lee, Homin K. and Malkin, Tal and Servedio, Rocco A. and Wan, Andrew and Wee, Hoeteck}, editor = {Aceto, Luca and Damg{\r a}rd, Ivan and Goldberg, Leslie Ann and Halld{\'o}rsson, Magn{\'u}s M. and Ing{\'o}lfsd{\'o}ttir, Anna and Walukiewicz, Igor} } @inbook {17668, title = {The Randomized Coloring Procedure with Symmetry-Breaking}, booktitle = {Automata, Languages and ProgrammingAutomata, Languages and Programming}, series = {Lecture Notes in Computer Science}, volume = {5125}, year = {2008}, month = {2008///}, pages = {306 - 319}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {A basic randomized coloring procedure has been used in probabilistic proofs to obtain remarkably strong results on graph coloring. These results include the asymptotic version of the List Coloring Conjecture due to Kahn, the extensions of Brooks{\textquoteright} Theorem to sparse graphs due to Kim and Johansson, and Luby{\textquoteright}s fast parallel and distributed algorithms for graph coloring. The most challenging aspect of a typical probabilistic proof is showing adequate concentration bounds for key random variables. In this paper, we present a simple symmetry-breaking augmentation to the randomized coloring procedure that works well in conjunction with Azuma{\textquoteright}s Martingale Inequality to easily yield the requisite concentration bounds. We use this approach to obtain a number of results in two areas: frugal coloring and weighted equitable coloring . A β-frugal coloring of a graph G is a proper vertex-coloring of G in which no color appears more than β times in any neighborhood. Let G = ( V , E ) be a vertex-weighted graph with weight function w : V {\textrightarrow}[0, 1] and let W = ∑ v ∈ V w ( v ). A weighted equitable coloring of G is a proper k -coloring such that the total weight of every color class is {\textquotedblleft}large{\textquotedblright}, i.e., {\textquotedblleft}not much smaller{\textquotedblright} than W / k ; this notion is useful in obtaining tail bounds for sums of dependent random variables.}, isbn = {978-3-540-70574-1}, url = {http://dx.doi.org/10.1007/978-3-540-70575-8_26}, author = {Pemmaraju,Sriram and Srinivasan, Aravind}, editor = {Aceto,Luca and Damg{\r a}rd,Ivan and Goldberg,Leslie and Halld{\'o}rsson,Magn{\'u}s and Ing{\'o}lfsd{\'o}ttir,Anna and Walukiewicz,Igor} } @article {13352, title = {Adaptive query processing}, journal = {Foundations and Trends in Databases}, volume = {1}, year = {2007}, month = {2007/01//}, pages = {1 - 140}, abstract = {As the data management field has diversified to consider settings in which queries are increasingly complex, statistics are less available, or data is stored remotely, there has been an acknowledgment that the traditional optimize-then-execute paradigm is insufficient. This has led to a plethora of new techniques, generally placed under the common banner of adaptive query processing, that focus on using runtime feed-back to modify query processing in a way that provides better response time or more efficient CPU utilization.In this survey paper, we identify many of the common issues, themes, and approaches that pervade this work, and the settings in which each piece of work is most appropriate. Our goal with this paper is to be a "value-add" over the existing papers on the material, providing not only a brief overview of each technique, but also a basic framework for understanding the field of adaptive query processing in general. We focus primarily on intra-query adaptivity of long-running, but not full-fledged streaming, queries. We conclude with a discussion of open research problems that are of high importance. }, isbn = {1931-7883}, doi = {10.1561/1900000001}, url = {http://dx.doi.org/10.1561/1900000001}, author = {Deshpande, Amol and Ives,Zachary and Vijayshankar Raman} } @conference {13354, title = {Adaptive query processing: why, how, when, what next?}, booktitle = {Proceedings of the 33rd international conference on Very large data bases}, series = {VLDB {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {1426 - 1427}, publisher = {VLDB Endowment}, organization = {VLDB Endowment}, abstract = {Adaptive query processing has been the subject of a great deal of recent work, particularly in emerging data management environments such as data integration and data streams. We provide an overview of the work in this area, identifying its common themes, laying out the space of query plans, and discussing open research problems. We discuss why adaptive query processing is needed, how it is being implemented, where it is most appropriately used, and finally, what next, i.e., open research problems.}, isbn = {978-1-59593-649-3}, url = {http://dl.acm.org/citation.cfm?id=1325851.1326033}, author = {Deshpande, Amol and Ives,Zachary and Vijayshankar Raman} } @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 {17596, title = {Fast and scalable approximation methods for finding minimum cost flows with ...}, volume = {10/053,079}, year = {2007}, month = {2007/10/09/}, abstract = {Broadly, techniques for solving network routing within a predetermined error are disclosed. These techniques may be applied to networks supporting dedicated reserve capacity, where reserved capacity on links in the network is dedicated for a particular commodity (generally, a source and sink pair of computers), and shared recovery, where reserved capacity on links is shared amongst two or more commodities. These techniques use an iterative process to determine flows on each of the links in a network. Costs are set for each commodity, and primary and secondary (i.e., backup) flows are initialized. A commodity is selected and demand for the commodity is routed through the shortest path. Costs are updated for each potential failure mode. For each commodity, the flows and costs are updated. Once all flows and costs are updated, then it is determined if a function is less than a predetermined value. If the function is less than a predetermined value, then the commodity selection, and...}, url = {http://www.google.com/patents?id=rkWpAAAAEBAJ}, author = {Fleischer,Lisa Karen and Saniee,Iraj and Shepherd,Frederick Bruce and Srinivasan, Aravind}, editor = {Lucent Technologies Inc.} } @article {14561, title = {Power optimization in fault-tolerant topology control algorithms for wireless multi-hop networks}, journal = {IEEE/ACM Transactions on Networking (TON)}, volume = {15}, year = {2007}, month = {2007///}, pages = {1345 - 1358}, author = {Hajiaghayi, Mohammad T. and Immorlica,N. and Mirrokni,V. S} } @article {18748, title = {Retrieving matching CAD models by using partial 3D point clouds}, journal = {Computer-Aided Design \& Applications}, volume = {4}, year = {2007}, month = {2007///}, pages = {629 - 638}, abstract = {The ability to search for a CAD model that represents a specific physical part is a useful capabilitythat can be used in many different applications. This paper presents an approach to use partial 3D point cloud of an artifact for retrieving the CAD model of the artifact. We assume that the information about the physical parts will be captured by a single 3D scan that produces dense point clouds. CAD models in our approach are represented as polygonal meshes. Our approach involves segmenting the point cloud and CAD mesh models into surface patches. The next step is to identify corresponding surface patches in point clouds and CAD models that could potentially match. Finally, we compute transformations to align the point cloud to the CAD model and compute distance between them. We also present experimental results to show that our approach can be used to retrieve CAD models of mechanical parts. }, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.92.8339\&rep=rep1\&type=pdf}, author = {Ip,C. Y and Gupta,S.K.} } @inbook {19622, title = {Time and Space Efficient Algorithms for Two-Party Authenticated Data Structures}, booktitle = {Information and Communications Security}, series = {Lecture Notes in Computer Science}, year = {2007}, month = {2007/01/01/}, pages = {1 - 15}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Authentication is increasingly relevant to data management. Data is being outsourced to untrusted servers and clients want to securely update and query their data. For example, in database outsourcing, a client{\textquoteright}s database is stored and maintained by an untrusted server. Also, in simple storage systems, clients can store very large amounts of data but at the same time, they want to assure their integrity when they retrieve them. In this paper, we present a model and protocol for two-party authentication of data structures. Namely, a client outsources its data structure and verifies that the answers to the queries have not been tampered with. We provide efficient algorithms to securely outsource a skip list with logarithmic time overhead at the server and client and logarithmic communication cost, thus providing an efficient authentication primitive for outsourced data, both structured (e.g., relational databases) and semi-structured (e.g., XML documents). In our technique, the client stores only a constant amount of space, which is optimal. Our two-party authentication framework can be deployed on top of existing storage applications, thus providing an efficient authentication service. Finally, we present experimental results that demonstrate the practical efficiency and scalability of our scheme.}, keywords = {Algorithm Analysis and Problem Complexity, Computer Communication Networks, computers and society, Data Encryption, Management of Computing and Information Systems, Systems and Data Security}, isbn = {978-3-540-77047-3, 978-3-540-77048-0}, url = {http://link.springer.com/chapter/10.1007/978-3-540-77048-0_1}, author = {Charalampos Papamanthou and Tamassia, Roberto}, editor = {Qing, Sihan and Imai, Hideki and Wang, Guilin} } @article {14605, title = {Differential Transcriptional Response to Nonassociative and Associative Components of Classical Fear Conditioning in the Amygdala and Hippocampus}, journal = {Learning \& MemoryLearn. Mem.}, volume = {13}, year = {2006}, month = {2006/03/01/}, pages = {135 - 142}, abstract = {Classical fear conditioning requires the recognition of conditioned stimuli (CS) and the association of the CS with an aversive stimulus. We used Affymetrix oligonucleotide microarrays to characterize changes in gene expression compared to naive mice in both the amygdala and the hippocampus 30 min after classical fear conditioning and 30 min after exposure to the CS in the absence of an aversive stimulus. We found that in the hippocampus, levels of gene regulation induced by classical fear conditioning were not significantly greater than those induced by CS alone, whereas in the amygdala, classical fear conditioning did induce significantly greater levels of gene regulation compared to the CS. Computational studies suggest that transcriptional changes in the hippocampus and amygdala are mediated by large and overlapping but distinct combinations of molecular events. Our results demonstrate that an increase in gene regulation in the amygdala was partially correlated to associative learning and partially correlated to nonassociative components of the task, while gene regulation in the hippocampus was correlated to nonassociative components of classical fear conditioning, including configural learning.}, isbn = {1072-0502, 1549-5485}, doi = {10.1101/lm.86906}, url = {http://learnmem.cshlp.org/content/13/2/135}, author = {Keeley,Michael B and Wood,Marcelo A and Isiegas,Carolina and Stein,Joel and Hellman,Kevin and Hannenhalli, Sridhar and Abel,Ted} } @article {14416, title = {A feature generation algorithm for sequences with application to splice-site prediction}, journal = {Knowledge Discovery in Databases: PKDD 2006}, year = {2006}, month = {2006///}, pages = {553 - 560}, abstract = {In this paper we present a new approach to feature selection for sequence data. We identify general feature categories and give construction algorithms for each of them. We show how they can be integrated in a system that tightly couples feature construction and feature selection. This integrated process, which we refer to as feature generation, allows us to systematically search a large space of potential features. We demonstrate the effectiveness of our approach for an important component of the gene finding problem, splice-site prediction. We show that predictive models built using our feature generation algorithm achieve a significant improvement in accuracy over existing, state-of-the-art approaches.}, doi = {10.1007/11871637_55}, author = {Islamaj,R. and Getoor, Lise and Wilbur,W.} } @article {19661, title = {How Multirobot Systems Research will Accelerate our Understanding of Social Animal Behavior}, journal = {Proceedings of the IEEE}, volume = {94}, year = {2006}, month = {2006/07//}, pages = {1445 - 1463}, abstract = {Our understanding of social insect behavior has significantly influenced artificial intelligence (AI) and multirobot systems{\textquoteright} research (e.g., ant algorithms and swarm robotics). In this work, however, we focus on the opposite question: "How can multirobot systems research contribute to the understanding of social animal behavior?" As we show, we are able to contribute at several levels. First, using algorithms that originated in the robotics community, we can track animals under observation to provide essential quantitative data for animal behavior research. Second, by developing and applying algorithms originating in speech recognition and computer vision, we can automatically label the behavior of animals under observation. In some cases the automatic labeling is more accurate and consistent than manual behavior identification. Our ultimate goal, however, is to automatically create, from observation, executable models of behavior. An executable model is a control program for an agent that can run in simulation (or on a robot). The representation for these executable models is drawn from research in multirobot systems programming. In this paper we present the algorithms we have developed for tracking, recognizing, and learning models of social animal behavior, details of their implementation, and quantitative experimental results using them to study social insects}, keywords = {Acceleration, Animal behavior, ant movement tracking, Artificial intelligence, biology computing, Computer vision, control engineering computing, Insects, Intelligent robots, Labeling, monkey movement tracking, multi-robot systems, multirobot systems, robotics algorithms, Robotics and automation, social animal behavior, social animals, social insect behavior, Speech recognition, tracking}, isbn = {0018-9219}, author = {Balch, T. and Dellaert, F. and Feldman, A. and Guillory, A. and Isbell, C.L. and Zia Khan and Pratt, S.C. and Stein, A.N. and Wilde, H.} } @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} } @conference {18877, title = {Learning to do HTN planning}, year = {2006}, month = {2006///}, pages = {390 - 393}, abstract = {We describe HDL, an algorithm that learns HTN do- main descriptions by examining plan traces produced by an expert problem-solver. Prior work on learning HTN methods requires that all the methods{\textquoteright} informa- tion except for their preconditions be given in advance so that the learner can learn the preconditions. In con- trast, HDL has no prior information about the methods. In our experiments, in most cases HDL converged fully with no more than about 200 plan traces. Furthermore, even when HDL was given only half the plan traces it required to fully converge, it usually was able to pro- duce HTN methods that were sufficient to solve more than 3/4 of the planning problems in the test set.}, url = {https://www.aaai.org/Papers/ICAPS/2006/ICAPS06-048.pdf}, author = {Ilghami,O. and Nau, Dana S. and Munoz-Avila,H.} } @article {16864, title = {Maintenance of K-nn and spatial join queries on continuously moving points}, journal = {ACM Trans. Database Syst.}, volume = {31}, year = {2006}, month = {2006/06//}, pages = {485 - 536}, abstract = {Cars, aircraft, mobile cell phones, ships, tanks, and mobile robots all have the common property that they are moving objects. A kinematic representation can be used to describe the location of these objects as a function of time. For example, a moving point can be represented by the function p(t) = \&OV0489;0 + (t - t0)\&OV0505;, where \&OV0489;0 is the start location, t0 is the start time, and \&OV0505; is its velocity vector. Instead of storing the location of the object at a given time in a database, the coefficients of the function are stored. When an object{\textquoteright}s behavior changes enough so that the function describing its location is no longer accurate, the function coefficients for the object are updated. Because the location of each object is represented as a function of time, spatial query results can change even when no transactions update the database. We present efficient algorithms to maintain k-nearest neighbor, and spatial join queries in this domain as time advances and updates occur. We assume no previous knowledge of what the updates will be before they occur. We experimentally compare these new algorithms with more straight forward adaptations of previous work to support updates. Experiments are conducted using synthetic uniformly distributed data, and real aircraft flight data. The primary metric of comparison is the number of I/O disk accesses needed to maintain the query results and the supporting data structures.}, keywords = {k-nearest neighbor, continuously moving objects, materialized view maintenance, Moving object databases, Spatial join, temporal databases}, isbn = {0362-5915}, doi = {10.1145/1138394.1138396}, url = {http://doi.acm.org/10.1145/1138394.1138396}, author = {Iwerks,Glenn S. and Samet, Hanan and Smith,Kenneth P.} } @article {17663, title = {System and method for locating a closest server in response to a client ...}, volume = {09/726,192}, year = {2006}, month = {2006/03/28/}, abstract = {A scalable system and method for locating a closest server in response to a client request via an interactive distribution network, such as the Internet, are provided. A closest content server is defined as having the least round trip time for responding to a client request. The system including a plurality of content servers; and a local server in communication with a plurality of clients, the local server acting as a proxy for communicating client requests from clients to a redirection server. Client network distance and load information is periodically collected at each content server in the network from clients communicating with each of the respective content servers. The redirection server periodically aggregates the network distance and load information from each content server to create client clusters from both current and previously aggregated network distance and load information. Each client cluster represents a division or partition of the total IP address space. Each...}, url = {http://www.google.com/patents?id=cE54AAAAEBAJ}, author = {Andrews,Matthew and Hofmann,Markus and Shepherd,Bruce and Srinivasan, Aravind and Winkler,Peter and Zane,Francis}, editor = {Lucent Technologies Inc.} } @article {18893, title = {Applications of SHOP and SHOP2}, journal = {Intelligent Systems, IEEE}, volume = {20}, year = {2005}, month = {2005/04//march}, pages = {34 - 41}, abstract = {We design the simple hierarchical ordered planner (SHOP) and its successor, SHOP2, with two goals in mind: to investigate research issues in automated planning and to provide some simple, practical planning tools. SHOP and SHOP2 are based on a planning formalism called hierarchical task network planning. SHOP and SHOP2 use a search-control strategy called ordered task decomposition, which breaks tasks into subtasks and generates the plan{\textquoteright}s actions in the same order that the plan executor executes them. So, throughout the planning process, the planner can tell what the state of the world at each step of the plan.}, keywords = {automated planning, hierarchical task network planning, ordered task decomposition, planning (artificial intelligence), problem solving, search-control strategy, simple hierarchical ordered planner, trees (mathematics), uncertainty handling}, isbn = {1541-1672}, doi = {10.1109/MIS.2005.20}, author = {Nau, Dana S. and Au,T.-C. and Ilghami,O. and Kuter,U. and Wu,D. and Yaman,F. and Munoz-Avila,H. and Murdock,J. W.} } @article {14078, title = {Comparative Genomics of Trypanosomatid Parasitic Protozoa}, journal = {Science}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {404 - 409}, abstract = {A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that{\textemdash}along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions{\textemdash}have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.}, doi = {10.1126/science.1112181}, url = {http://www.sciencemag.org/content/309/5733/404.abstract}, author = {El-Sayed, Najib M. and Myler,Peter J. and Blandin,Ga{\"e}lle and Berriman,Matthew and Crabtree,Jonathan and Aggarwal,Gautam and Caler,Elisabet and Renauld,Hubert and Worthey,Elizabeth A. and Hertz-Fowler,Christiane and Ghedin,Elodie and Peacock,Christopher and Bartholomeu,Daniella C. and Haas,Brian J. and Tran,Anh-Nhi and Wortman,Jennifer R. and Alsmark,U. Cecilia M. and Angiuoli,Samuel and Anupama,Atashi and Badger,Jonathan and Bringaud,Frederic and Cadag,Eithon and Carlton,Jane M. and Cerqueira,Gustavo C. and Creasy,Todd and Delcher,Arthur L. and Djikeng,Appolinaire and Embley,T. Martin and Hauser,Christopher and Ivens,Alasdair C. and Kummerfeld,Sarah K. and Pereira-Leal,Jose B. and Nilsson,Daniel and Peterson,Jeremy and Salzberg,Steven L. and Shallom,Joshua and Silva,Joana C. and Sundaram,Jaideep and Westenberger,Scott and White,Owen and Melville,Sara E. and Donelson,John E. and Andersson,Bj{\"o}rn and Stuart,Kenneth D. and Hall,Neil} } @conference {18911, title = {Learning approximate preconditions for methods in hierarchical plans}, series = {ICML {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {337 - 344}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {A significant challenge in developing planning systems for practical applications is the difficulty of acquiring the domain knowledge needed by such systems. One method for acquiring this knowledge is to learn it from plan traces, but this method typically requires a huge number of plan traces to converge. In this paper, we show that the problem with slow convergence can be circumvented by having the learner generate solution plans even before the planning domain is completely learned. Our empirical results show that these improvements reduce the size of the training set that is needed to find correct answers to a large percentage of planning problems in the test set.}, isbn = {1-59593-180-5}, doi = {10.1145/1102351.1102394}, url = {http://doi.acm.org/10.1145/1102351.1102394}, author = {Ilghami,Okhtay and Mu{\~n}oz-Avila,H{\'e}ctor and Nau, Dana S. and Aha,David W.} } @article {18912, title = {Learning preconditions for planning from plan traces and HTN structure}, journal = {Computational Intelligence}, volume = {21}, year = {2005}, month = {2005///}, pages = {388 - 413}, abstract = {A great challenge in developing planning systems for practical applications is the difficulty of acquiring the domain information needed to guide such systems. This paper describes a way to learn some of that knowledge. More specifically, the following points are discussed. (1) We introduce a theoretical basis for formally defining algorithms that learn preconditions for Hierarchical Task Network (HTN) methods. (2) We describe Candidate Elimination Method Learner (CaMeL), a supervised, eager, and incremental learning process for preconditions of HTN methods. We state and prove theorems about CaMeL{\textquoteright}s soundness, completeness, and convergence properties. (3) We present empirical results about CaMeL{\textquoteright}s convergence under various conditions. Among other things, CaMeL converges the fastest on the preconditions of the HTN methods that are needed the most often. Thus CaMeL{\textquoteright}s output can be useful even before it has fully converged.}, keywords = {candidate elimination, HTN planning, learning, version spaces}, isbn = {1467-8640}, doi = {10.1111/j.1467-8640.2005.00279.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-8640.2005.00279.x/abstract}, author = {Ilghami,Okhtay and Nau, Dana S. and Mu{\~n}oz-Avila,H{\'e}ctor and Aha,David W.} } @article {12769, title = {Probabilistic temporal logics via the modal mu-calculus}, journal = {Theoretical Computer Science}, volume = {342}, year = {2005}, month = {2005/09/07/}, pages = {316 - 350}, abstract = {This paper presents a mu-calculus-based modal logic for describing properties of reactive probabilistic labeled transition systems (RPLTSs) and develops a model-checking algorithm for determining whether or not states in finite-state RPLTSs satisfy formulas in the logic. The logic is based on the distinction between (probabilistic) {\^a}{\texteuro}{\oe}systems{\^a}{\texteuro} and (nonprobabilistic) {\^a}{\texteuro}{\oe}observations{\^a}{\texteuro}: using the modal mu-calculus, one may specify sets of observations, and the semantics of our logic then enable statements to be made about the measures of such sets at various system states. The logic may be used to encode a variety of probabilistic modal and temporal logics; in addition, the model-checking problem for it may be reduced to the calculation of solutions to systems of non-linear equations. Finally, the logic induces an equivalence on RPLTSs that coincides with accepted notions of probabilistic bisimulation in the literature.}, keywords = {Model-checking, Probabilistic bisimulation, Probabilistic temporal logic, Probabilistic transition systems, reactive systems}, isbn = {0304-3975}, doi = {10.1016/j.tcs.2005.03.048}, url = {http://www.sciencedirect.com/science/article/pii/S0304397505001829}, author = {Cleaveland, Rance and Iyer,S. Purushothaman and Narasimha,Murali} } @article {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 {14597, title = {CHARACTERIZATION OF Ath17, A QUANTITATIVE TRAIT LOCUS FOR ATHEROSCLEROSIS SUSCEPTIBILITY BETWEEN C57BL/6J AND 129S1/SvImJ; SINGLE-NUCLEOTIDE POLYMORPHISMS HAVE IMPORTANT IMPLICATIONS ON IDENTIFYING ATHEROSCLEROSIS MODIFIER GENES}, journal = {Cardiovascular Pathology}, volume = {13}, year = {2004}, month = {2004/06//May}, pages = {5 - 6}, abstract = {Although identifying quantitative trait loci (QTL) for atherosclerosis susceptibility in experimental murine models has helped us better understand the pathophysiology of atherosclerosis, identifying the genes underlying these QTL has been a slow and difficult process. We are currently in the process of identifying the gene that underlies Ath17, an atherosclerosis-susceptibility QTL we discovered in a (C57BL/6J{\texttimes}129S1/SvImJ)F2 intercross. Ath17 maps to a 6 cM interval region on chromosome 10 (D10Mit31, LOD score 6.6) and contains 46 annotated and 133 predicted genes. We searched the Celera Discovery System database for single nucleotide polymorphisms (SNPs) between C57BL/6J (B6) and 129S1/SvImJ in the Ath17 region and found defined blocks of high and low diversity and one polymorphic region of over 4 Mb surrounded by nonpolymorphic regions. Four of the genes, including the annotated Desrt, in the polymorphic region contained mis-sense mutations. The Desrt coding region contained four mis-sense mutations: B6 lysine to 129 glutamic acid at aa382, B6 asparagine to 129 serine at aa388, B6 threonine to 129 alanine at aa836, and B6 glycine to 129 serine at aa964. In addition, intron 5 of Desrt contained a SNP which co-localized with a putative transcription factor binding site. Desrt is a DNA binding protein, widely expressed in adult tissues, and likely plays a role in cell proliferation, differentiation, and development, making Dsert a strong candidate gene for Ath17. The murine SNP database dramatically reduced the percentage of the murine genome we had to search to find viable candidate genes for Ath17.}, isbn = {1054-8807}, doi = {10.1016/j.carpath.2004.03.010}, url = {http://www.sciencedirect.com/science/article/pii/S1054880704000377}, author = {Ishimori,Naoki and Walsh,Kenneth and Zheng,Xiangqun and Lu,Fu and Hannenhalli, Sridhar and Nusskern,Deborah and Mural,Richard and Paigen,Beverly} } @conference {14552, title = {Low-dimensional embedding with extra information}, booktitle = {Proceedings of the twentieth annual symposium on Computational geometry}, year = {2004}, month = {2004///}, pages = {320 - 329}, author = {Bǎdoiu,M. and Demaine,E. D and Hajiaghayi, Mohammad T. and Indyk,P.} } @inbook {16889, title = {Maintenance of Spatial Semijoin Queries on Moving Points}, booktitle = {Proceedings 2004 VLDB ConferenceProceedings 2004 VLDB Conference}, year = {2004}, month = {2004///}, pages = {828 - 839}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, address = {St Louis}, abstract = {In this paper, we address the maintenance of spatial semijoin queries over continuously moving points, where points are modeled as linear functions of time. This is analogous to the maintenance of a materialized view except, as time advances, the query result may change independently of updates. As in a materialized view, we assume there is no prior knowledge of updates before they occur. We present a new approach, continuous fuzzy sets (CFS), to maintain continuous spatial semijoins efficiently. CFS is compared experimentally to a simple scaling of previous work. The result is significantly better performance of CFS compared to previous work by up to an order of magnitude in some cases.}, isbn = {978-0-12-088469-8}, url = {http://www.sciencedirect.com/science/article/pii/B9780120884698500735}, author = {Iwerks,Glenn S. and Samet, Hanan and Smith,Kenneth P.} } @article {17624, title = {Method of designing signaling networks for internet telephony}, volume = {:~09/517,658}, year = {2004}, month = {2004/02/03/}, abstract = {A method is disclosed for designing a signaling network of call coordinators (CCs) for internet telephony. The new method can be used to design a CC network of arbitrary size that satisfies, with high probability, limitations on the maximum number of sockets per CC and on the maximum number of hops between an arbitrary pair of switches in the network. According to the disclosed method, the network of CCs is treated initially as a collection of isolated points, one point for each CC. Then, links are added between pairs of CCs, excluding pairs lying within the same switch. The links are added randomly, but with a particular probability p, which may be different for different pairs. Thus, whether a given link is added depends, in effect, upon the outcome of a loaded coin toss in which the probability of a positive outcome is p.}, url = {http://www.google.com/patents?id=VTsSAAAAEBAJ}, author = {Aravamudan,Murali and Kumaran,Krishnan and Ramakrishnan,Kajamalai Gopalaswamy and Srinivasan, Aravind}, editor = {Lucent Technologies Inc.} } @conference {18729, title = {New directions in design for manufacturing}, year = {2004}, month = {2004///}, pages = {1 - 9}, abstract = {This paper gives an overview of research that is expandingthe domain of design for manufacturing (DFM) into new and important areas. This paper covers DFM and concurrent engineering, DFM for conceptual design, DFM for embodiment design, DFM for detailed design, design for production, platform design for reducing time-to-market, design for system quality, design for life cycle costs, and design for environment. The paper concludes with some general guidelines that suggest how manufacturing firms can develop useful, effective DFM tools. }, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.198.8706\&rep=rep1\&type=pdf}, author = {Herrmann,J.W. and Cooper,J. and Gupta,S.K. and Hayes,C. C. and Ishii,K. and Kazmer,D. and Sandborn,P. A. and Wood,W. H.} } @article {12938, title = {Pandemic strains of O3:K6 Vibrio parahaemolyticus in the aquatic environment of Bangladesh}, journal = {Canadian Journal of Microbiology}, volume = {50}, year = {2004}, month = {2004/10//}, pages = {827 - 834}, abstract = {A total of 1500 environmental strains of Vibrio parahaemolyticus, isolated from the aquatic environment of Bangladesh, were screened for the presence of a major V. parahaemolyticus virulence factor, the thermostable direct haemolysin (tdh) gene, by the colony blot hybridization method using a digoxigenin-labeled tdh gene probe. Of 1500 strains, 5 carried the tdh sequence, which was further confirmed by PCR using primers specific for the tdh gene. Examination by PCR confirmed that the 5 strains were V. parahamolyticus and lacked the thermostable direct haemolysin-related haemolysin (trh) gene, the alternative major virulence gene known to be absent in pandemic strains. All 5 strains gave positive Kanagawa phenomenon reaction with characteristic beta-haemolysis on Wagatsuma agar medium. Southern blot analysis of the HindIII-digested chromosomal DNA demonstrated, in all 5 strains, the presence of 2 tdh genes common to strains positive for Kanagawa phenomenon. However, the 5 strains were found to belong to 3 different serotypes (O3:K29, O4:K37, and O3:K6). The 2 with pandemic serotype O3:K6 gave positive results in group-specific PCR and ORF8 PCR assays, characteristics unique to the pandemic clone. Clonal variations among the 5 isolates were analyzed by comparing RAPD and ribotyping patterns. Results showed different patterns for the 3 serotypes, but the pattern was identical among the O3:K6 strains. This is the first report on the isolation of pandemic O3:K6 strains of V. parahaemolyticus from the aquatic environment of Bangladesh.}, url = {http://umd.library.ingentaconnect.com/content/nrc/cjm/2004/00000050/00000010/art00007}, author = {Islam,M. S. and Tasmin,Rizwana and Khan,Sirajul I. s l a m and Bakht,Habibul B. M. and Mahmood,Zahid H. a y a t and Rahman,M. Z. i a u r and Bhuiyan,Nurul A. m i n and Nishibuchi,Mitsuaki and Nair,G. B. a l a k r i s h and Sack,R. B. r a d l e y and Huq,Anwar and Rita R Colwell and Sack,David A.} } @article {12942, title = {Variation of toxigenic Vibrio cholerae O1 in the aquatic environment of Bangladesh and its correlation with the clinical strains}, journal = {Microbiology and immunology}, volume = {48}, year = {2004}, month = {2004///}, pages = {773 - 777}, author = {Islam,M. S. and Talukder,K. A. and Khan,N. H. and Mahmud,Z. H. and Rahman,M. Z. and Nair,G. B. and Siddique,A. K. M. and Yunus,M. and Sack,D. A. and Sack,R. B. and Rita R Colwell} } @article {14578, title = {Whole-genome shotgun assembly and comparison of human genome assemblies}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, year = {2004}, month = {2004///}, pages = {1916 - 1916}, author = {Istrail,S. and Sutton,G. G and Florea,L. and Halpern,A. L and Mobarry,C. M and Lippert,R. and Walenz,B. and Shatkay,H. and Dew,I. and Miller,J. R and others} } @article {12955, title = {A 4-Year Study of the Epidemiology of Vibrio Cholerae in Four Rural Areas of Bangladesh}, journal = {Journal of Infectious DiseasesJ Infect Dis.}, volume = {187}, year = {2003}, month = {2003/01/01/}, pages = {96 - 101}, abstract = {How Vibrio cholerae spreads around the world and what determines its seasonal peaks in endemic areas are not known. These features of cholera have been hypothesized to be primarily the result of environmental factors associated with aquatic habitats that can now be identified. Since 1997, fortnightly surveillance in 4 widely separated geographic locations in Bangladesh has been performed to identify patients with cholera and to collect environmental data. A total of 5670 patients (53\% <5 years of age) have been studied; 14.3\% had cholera (10.4\% due to V. cholerae O1 El Tor, 3.8\% due to O139). Both serogroups were found in all locations; outbreaks were seasonal and often occurred simultaneously. Water-use patterns showed that bathing and washing clothes in tube-well water was significantly protective in two of the sites. These data will be correlated with environmental factors, to develop a model for prediction of cholera outbreaks}, isbn = {0022-1899, 1537-6613}, doi = {10.1086/345865}, url = {http://jid.oxfordjournals.org/content/187/1/96}, author = {Sack,R. Bradley and Siddique,A. Kasem and Longini,Ira M. and Nizam,Azhar and Yunus,Md and M. Sirajul Islam and Morris,Jr and Ali,Afsar and Huq,Anwar and Nair,G. Balakrish and Qadri,Firdausi and Faruque,Shah M. and Sack,David A. and Rita R Colwell} } @conference {16904, title = {Continuous k-nearest neighbor queries for continuously moving points with updates}, booktitle = {Proceedings of the 29th international conference on Very large data bases-Volume 29}, year = {2003}, month = {2003///}, pages = {512 - 523}, author = {Iwerks,G. S and Samet, Hanan and Smith,K.} } @conference {15316, title = {Extracting structural paraphrases from aligned monolingual corpora}, booktitle = {Proceedings of the second international workshop on Paraphrasing - Volume 16}, series = {PARAPHRASE {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {57 - 64}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {We present an approach for automatically learning paraphrases from aligned monolingual corpora. Our algorithm works by generalizing the syntactic paths between corresponding anchors in aligned sentence pairs. Compared to previous work, structural paraphrases generated by our algorithm tend to be much longer on average, and are capable of capturing long-distance dependencies. In addition to a standalone evaluation of our paraphrases, we also describe a question answering application currently under development that could immensely benefit from automatically-learned structural paraphrases.}, doi = {10.3115/1118984.1118992}, url = {http://dx.doi.org/10.3115/1118984.1118992}, author = {Ibrahim,Ali and Katz,Boris and Jimmy Lin} } @article {18892, title = {A General Approach to Synthesize Problem-Specific Planners}, year = {2003}, month = {2003/10/27/}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {In this paper, we describe a way to improve the performance of hand-tailorable planners by compiling each domain description into a separate domain-specific planner. We discuss why and when this approach can be useful, and we present experimental results showing that our approach produces significant increases in the speed of planning.}, keywords = {*PLANNING, *SOFTWARE ENGINEERING, Artificial intelligence, COMPUTER PROGRAMMING AND SOFTWARE, COMPUTER PROGRAMS, Logic, problem solving}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA455023}, author = {Ilghami,Okhtay and Nau, Dana S.} } @conference {16903, title = {The internet spatial spreadsheet: enabling remote visualization of dynamic spatial data and ongoing query results over a network}, booktitle = {Proceedings of the 11th ACM international symposium on Advances in geographic information systems}, series = {GIS {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {154 - 160}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Moving object databases store and process data for objects that change location frequently. Materialized views maintained over time must be updated to reflect changes due to the motion of objects in their environment. To visualize view query results, displays must be updated to reflect the change. In this paper we present the Internet Spatial Spreadsheet (ISS) as a means to organize, query, and visualize changing spatial data in a network environment such as the Internet.The goal of the ISS is to keep client visualizations of query results up to date with the server state. This is accomplished by pushing the minimal set of spatial data needed for rendering query results on the client. Incremental changes to query results are subsequently transmitted to the client as the database is updated to keep the visualization current. Additional constraints in the network environment such as firewall limitations are also considered.}, keywords = {client server, GIS, Spatial databases, Visualization}, isbn = {1-58113-730-3}, doi = {10.1145/956676.956697}, url = {http://doi.acm.org/10.1145/956676.956697}, author = {Iwerks,Glenn S. and Samet, Hanan} } @article {17264, title = {INTRODUCTION TO VOLUME 1, ISSUE 3: WEB NAVIGATION}, journal = {IT\&SOCIETY}, volume = {1}, year = {2003}, month = {2003///}, author = {Shneiderman, Ben and Lazar,J. and IVORY,M.} } @article {12953, title = {Reduction of Cholera in Bangladeshi Villages by Simple Filtration}, journal = {Proceedings of the National Academy of SciencesPNAS}, volume = {100}, year = {2003}, month = {2003/02/04/}, pages = {1051 - 1055}, abstract = {Based on results of ecological studies demonstrating that Vibrio cholerae, the etiological agent of epidemic cholera, is commensal to zooplankton, notably copepods, a simple filtration procedure was developed whereby zooplankton, most phytoplankton, and particulates >20 μm were removed from water before use. Effective deployment of this filtration procedure, from September 1999 through July 2002 in 65 villages of rural Bangladesh, of which the total population for the entire study comprised ≈133,000 individuals, yielded a 48\% reduction in cholera (P < 0.005) compared with the control.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0237386100}, url = {http://www.pnas.org/content/100/3/1051}, author = {Rita R Colwell and Huq,Anwar and M. Sirajul Islam and K. M. A. Aziz and Yunus,M. and N. Huda Khan and A. Mahmud and Sack,R. Bradley and Nair,G. B. and J. Chakraborty and Sack,David A. and E. Russek-Cohen} } @article {18870, title = {SHOP2: An HTN planning system}, journal = {J. Artif. Intell. Res. (JAIR)}, volume = {20}, year = {2003}, month = {2003///}, pages = {379 - 404}, abstract = {The SHOP2 planning system received one of the awards for distinguished performance in the 2002 International Planning Competition. This paper describes the features of SHOP2 which enabled it to excel in the competition, especially those aspects of SHOP2 that deal with temporal and metric planning domains.}, url = {https://www.aaai.org/Papers/JAIR/Vol20/JAIR-2013.pdf}, author = {Nau, Dana S. and Au,T. C and Ilghami,O. and Kuter,U. and Murdock,J. W. and Wu,D. and Yaman,F.} } @article {13414, title = {AAAI 2002 Workshops}, journal = {AI Magazine}, volume = {23}, year = {2002}, month = {2002/12/15/}, pages = {113 - 113}, isbn = {0738-4602}, doi = {10.1609/aimag.v23i4.1678}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/1678}, author = {Blake,Brian and Haigh,Karen and Hexmoor,Henry and Falcone,Rino and Soh,Leen-Kiat and Baral,Chitta and McIlraith,Sheila and Gmytrasiewicz,Piotr and Parsons,Simon and Malaka,Rainer and Krueger,Antonio and Bouquet,Paolo and Smart,Bill and Kurumantani,Koichi and Pease,Adam and Brenner,Michael and desJardins, Marie and Junker,Ulrich and Delgrande,Jim and Doyle,Jon and Rossi,Francesca and Schaub,Torsten and Gomes,Carla and Walsh,Toby and Guo,Haipeng and Horvitz,Eric J and Ide,Nancy and Welty,Chris and Anger,Frank D and Guegen,Hans W and Ligozat,Gerald} } @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} } @conference {18873, title = {CaMeL: Learning method preconditions for HTN planning}, year = {2002}, month = {2002///}, pages = {131 - 14}, abstract = {A great challenge in using any planning system to solve real-world problems is the difficulty of acquiring the do- main knowledge that the system will need. We present a way to address part of this problem, in the context of Hierarchical Task Network (HTN) planning, by having the planning system incrementally learn conditions for HTN methods under expert supervision. We present a general formal framework for learning HTN methods, and a supervised learning algorithm, named CaMeL, based on this formalism. We present theoretical results about CaMeL{\textquoteright}s soundness, completeness, and conver- gence properties. We also report experimental results about its speed of convergence under different condi- tions. The experimental results suggest that CaMeL has the potential to be useful in real-world applications.}, url = {https://www.aaai.org/Papers/AIPS/2002/AIPS02-014.pdf}, author = {Ilghami,O. and Nau, Dana S. and Munoz-Avila,H. and Aha,D. W.} } @article {12964, title = {Characterization of Pseudoalteromonas citrea and P. nigrifaciens Isolated from Different Ecological Habitats Based on REP-PCR Genomic Fingerprints}, journal = {Systematic and Applied Microbiology}, volume = {25}, year = {2002}, month = {2002///}, pages = {275 - 283}, abstract = {SummaryDNA primers corresponding to conserved repetitive interspersed genomic motifs and PCR were used to show that REP, ERIC and BOX-like DNA sequences are present in marine, oxidative, Gram-negative Pseudoalteromonas strains. REP, ERIC and BOX-PCR were used for rapid molecular characterization of both the type species of the genus and environmental strains isolated from samples collected in different geographical areas. PCR-generated genomic fingerprint patterns were found to be both complex and strain specific. Analysis of the genotypic structure of phenotypically diverse P. citrea revealed a geographic clustering of Far Eastern brown-pigmented, agar-digesting strains of this species. Marine isolates of P. nigrifaciens with 67{\textendash}70\% DNA relatedness generated genomic patterns different from those of the type strain and formed a separate cluster. It is concluded that REP, ERIC and BOX-PCR are effective in generating strain specific patterns that can be used to elucidate geographic distribution, with these genomic patterns providing a valuable biogeographic criterion. }, keywords = {biogeography, BOX-PCR, ERIC, Pseudoalteromonas, REP}, isbn = {0723-2020}, doi = {10.1078/0723-2020-00103}, url = {http://www.sciencedirect.com/science/article/pii/S0723202004701125}, author = {Ivanova,Elena P. and Matte,Glavur R. and Matte,Maria H. and Coenye,Tom and Huq,Anwarul and Rita R Colwell} } @article {12962, title = {Genomic profiles of clinical and environmental isolates of Vibrio cholerae O1 in cholera-endemic areas of Bangladesh}, journal = {Proceedings of the National Academy of Sciences}, volume = {99}, year = {2002}, month = {2002///}, pages = {12409 - 12409}, abstract = {Diversity, relatedness, and ecological interactions of toxigenic Vibrio cholerae O1 populations in two distinctive habitats, the human intestine and the aquatic environment, were analyzed. Twenty environmental isolates and 42 clinical isolates were selected for study by matching serotype, geographic location of isolation in Bangladesh, and season of isolation. Genetic profiling was done by enterobacterial repetitive intergenic consensus sequence{\textendash}PCR, optimized for profiling by using the fully sequenced V. cholerae El Tor N16961 genome. Five significant clonal clusters of haplotypes were found from 57 electrophoretic types. Isolates from different areas or habitats intermingled in two of the five significant clusters. Frequencies of haplotypes differed significantly only between the environmental populations (exact test; P < 0.05). Analysis of molecular variance yielded a population genetic structure reflecting the differentiating effects of geographic area, habitat, and sampling time. Although a parameter confounding the latter differences explained 9\% of the total molecular variance in the entire population (P < 0.01), the net effect of habitat and time could not be separated because of the small number of environmental isolates included in the study. Five subpopulations from a single area were determined, and from these we were able to estimate a relative differentiating effect of habitat, which was small compared with the effect of temporal change. In conclusion, the resulting population structure supports the hypothesis that spatial and temporal fluctuations in the composition of toxigenic V. cholerae populations in the aquatic environment can cause shifts in the dynamics of the disease.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.192426499}, url = {http://www.pnas.org/content/99/19/12409}, author = {Zo,Y. G. and Rivera,I. N. G. and E. Russek-Cohen and Islam,M. S. and Siddique,A. K. and Yunus,M. and Sack,R. B. and Huq,A. and Rita R Colwell} } @conference {13566, title = {Hidden loop recovery for handwriting recognition}, booktitle = {Frontiers in Handwriting Recognition, 2002. Proceedings. Eighth International Workshop on}, year = {2002}, month = {2002///}, pages = {375 - 380}, abstract = {One significant challenge in the recognition of off-line handwriting is in the interpretation of loop structures. Although this information is readily available in online representation, close proximity of strokes often merges their centers making them difficult to identify. In this paper a novel approach to the recovery of hidden loops in off-line scanned document images is presented. The proposed algorithm seeks blobs that resemble truncated ellipses. We use a sophisticated form analysis method based on mutual distance measurements between the two sides of a symmetric shape. The experimental results are compared with the ground truth of the online representations of each off-line word image. More than 86\% percent of the meaningful loops are handled correctly.}, keywords = {analysis;, character, contour, cursive, detection;, distance, edge, ellipses;, form, handwritten, hidden, loop, measurements;, mutual, partitioning;, recognition;, recovery;, SHAPE, shape;, sophisticated, strokes;, symmetric, truncated, word}, doi = {10.1109/IWFHR.2002.1030939}, author = {David Doermann and Intrator,N. and Rivin,E. and Steinherz,T.} } @article {15299, title = {Omnibase: Uniform access to heterogeneous data for question answering}, journal = {Natural Language Processing and Information Systems}, year = {2002}, month = {2002///}, pages = {230 - 234}, abstract = {Although the World Wide Web contains a tremendous amount of information, the lack of uniform structure makes finding the right knowledge difficult. A solution is to turn the Web into a {\textquotedblleft}virtual database{\textquotedblright} and to access it through natural language.We built Omnibase, a system that integrates heterogeneous data sources using an object- property-value model. With the help of Omnibase, our Start natural language system can now access numerous heterogeneous data sources on the Web in a uniform manner, and answers millions of user questions with high precision.}, doi = {10.1007/3-540-36271-1_23}, author = {Katz,B. and Felshin,S. and Yuret,D. and Ibrahim,A. and Jimmy Lin and Marton,G. and Jerome McFarland,A. and Temelkuran,B.} } @book {14636, title = {RECOMB {\textquoteright}02: Proceedings of the sixth annual international conference on Computational biology}, year = {2002}, month = {2002///}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The papers in this volume were presented at the Sixth Annual International Conference on Computational Biology RECOMB 2002, held in Washington, D.C. on April 18-21, 2002. The RECOMB series was started in 1997 by Sorin Istrail, Pavel Pevzner and Michael Waterman. RECOMB {\textquoteright}99 took place in Lyon, France, RECOMB 2000 was held in Tokyo, Japan, and RECOMB 2001 was held in Montreal, Quebec, Canada.This year{\textquoteright}s call for papers gave rise to 118 submissions, out of which the program committee selected 35 papers to be presented at the conference and included in the proceedings. Each submission was refereed by at least three members of the program committee. After the completion of the referees{\textquoteright} reports, an extensive web-based discussion took place.RECOMB 2002 had 8 invited speakers: Ruben Abagyan (The Scripps Research Institute), Ali H. Brivanlou (Rockefeller University), Evan Eichler (Case Western Reserve University), Harold "Skip" Garner (University of Texas Southwestern Medical Center at Dallas), David Ho (Rockefeller University), Gerry Rubin (Howard Hughes Medical Institute), J. Craig Venter (Celera) and Marc Vidal (Dana-Farber Cancer Institute). The Stanislaw Ulam Memorial Lecture was given by J. Craig Venter. The Distinguished Biology Lecture was given by David Ho. The Distinguished New Technologies Lecture was given by Harold Garner.Complete final versions of many of the papers presented in the conference will appear in a special issue of the Journal of Computational Biology, which is closely affiliated with the conference.}, isbn = {1-58113-498-3}, editor = {Myers,Gene and Hannenhalli, Sridhar and Sankoff,David and Istrail,Sorin and Pevzner,Pavel and Waterman,Michael} } @inbook {18923, title = {Theoretical and Empirical Aspects of a Planner in a Multi-agent Environment}, booktitle = {Logics in Artificial Intelligence}, series = {Lecture Notes in Computer Science}, volume = {2424}, year = {2002}, month = {2002///}, pages = {173 - 185}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We give the theoretical foundations and empirical evaluation of a planning agent, ashop, performing HTN planning in a multi-agent environment. ashop is based on ASHOP , an agentised version of the original SHOP HTN planning algorithm, and is integrated in the IMPACT multi-agent environment. We ran several experiments involving accessing various distributed, heterogeneous information sources, based on simplified versions of noncombatant evacuation operations, NEO{\textquoteright}s. As a result, we noticed that in such realistic settings the time spent on communication (including network time) is orders of magnitude higher than the actual inference process. This has important consequences for optimisations of such planners. Our main results are: (1) using NEO{\textquoteright}s as new, more realistic benchmarks for planners acting in an agent environment, and (2) a memoization mechanism implemented on top of shop, which improves the overall performance considerably.}, keywords = {Computer science}, isbn = {978-3-540-44190-8}, url = {http://www.springerlink.com/content/10lxp56u3e9k0bdd/abstract/}, author = {Dix,J{\"u}rgen and Munoz-Avila,Hector and Nau, Dana S. and Zhang,Lingling}, editor = {Flesca,Sergio and Greco,Sergio and Ianni,Giovambattista and Leone,Nicola} } @article {17670, title = {Wavelength rerouting in optical networks, or the Venetian Routing problem}, journal = {Journal of Algorithms}, volume = {45}, year = {2002}, month = {2002/11//}, pages = {93 - 125}, abstract = {Wavelength rerouting has been suggested as a viable and cost-effective method to improve the blocking performance of wavelength-routed wavelength-division multiplexing (WDM) networks. This method leads to the following combinatorial optimization problem, dubbed Venetian Routing. Given a directed multigraph G along with two vertices s and t and a collection of pairwise arc-disjoint paths, we wish to find an st-path which arc-intersects the smallest possible number of the given paths. In this paper we prove the computational hardness of this problem even in various special cases, and present several approximation algorithms for its solution. In particular we show a non-trivial connection between Venetian Routing and Label Cover.}, keywords = {Approximation algorithms, Label Cover, Optical networks, Shortest paths, Wavelength rerouting, Wavelength-division multiplexing}, isbn = {0196-6774}, doi = {10.1016/S0196-6774(02)00214-6}, url = {http://www.sciencedirect.com/science/article/pii/S0196677402002146}, author = {Caprara,Alberto and Italiano,Giuseppe F. and Mohan,G. and Panconesi,Alessandro and Srinivasan, Aravind} } @conference {12074, title = {Personal secure booting}, booktitle = {Information Security and Privacy}, year = {2001}, month = {2001///}, pages = {130 - 144}, author = {Itoi,N. and Arbaugh, William A. and Pollack,S. and Reeves,D.} } @conference {13912, title = {Designing storytelling technologies to encouraging collaboration between young children}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, year = {2000}, month = {2000///}, pages = {556 - 563}, author = {Benford,S. and Bederson, Benjamin B. and \AAkesson,K. P and Bayon,V. and Druin, Allison and Hansson,P. and Hourcade,J. P and Ingram,R. and Neale,H. and O{\textquoteright}Malley,C. and others} } @inbook {14732, title = {Scalable Resource Control in Active Networks}, booktitle = {Active NetworksActive Networks}, series = {Lecture Notes in Computer Science}, volume = {1942}, year = {2000}, month = {2000///}, pages = {343 - 357}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The increased complexity of the service model relative to store-and-forward routers has made resource management one of the paramount concerns in active networking research and engineering. In this paper,we address two major challenges in scaling resource management-to-many-node active networks. The first is the use of market mechanisms and trading amongst nodes and programs with varying degrees of competition and cooperation to provide a scalable approach to managing active network resources. The second is the use of a trust-management architecture to ensure that the participants in the resource management marketplace have a policy-driven {\textquotedblleft}rule of law{\textquotedblright} in which marketplace decisions can be made and relied upon. We have used lottery scheduling and the Keynote trust-management system for our implementation, for which we provide some initial performance indications.}, isbn = {978-3-540-41179-6}, url = {http://dx.doi.org/10.1007/3-540-40057-5_25}, author = {Anagnostakis,Kostas and Hicks, Michael W. and Ioannidis,Sotiris and Keromytis,Angelos and Smith,Jonathan}, editor = {Yasuda,Hiroshi} } @inbook {17671, title = {Wavelength Rerouting in Optical Networks, or the Venetian Routing Problem}, booktitle = {Approximation Algorithms for Combinatorial Optimization}, series = {Lecture Notes in Computer Science}, volume = {1913}, year = {2000}, month = {2000///}, pages = {71 - 84}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Wavelength rerouting has been suggested as a viable and cost-effective method to improve the blocking performance of wavelength-routed Wavelength-Division Multiplexing (WDM) networks. This method leads to the following combinatorial optimization problem, dubbed Venetian Routing. Given a directed multigraph G along with two vertices s and t and a collection of pairwise arc-disjoint paths, we wish to find an st -path which arc-intersects the smallest possible number of such paths. In this paper we prove the computational hardness oft his problem even in various special cases, and present several approximation algorithms for its solution. In particular we show a non-trivial connection between Venetian Routing and Label Cover.}, isbn = {978-3-540-67996-7}, url = {http://dx.doi.org/10.1007/3-540-44436-X_9}, author = {Caprara,Alberto and Italiano,Giuseppe and Mohan,G. and Panconesi,Alessandro and Srinivasan, Aravind}, editor = {Jansen,Klaus and Khuller, Samir} } @article {13820, title = {Machine Translation}, journal = {Multilingual Information Management: Current Levels and Future Abilities}, year = {1999}, month = {1999///}, pages = {18 - 18}, author = {Bel,N. and Dorr, Bonnie J and Hovy,E. and Knight,K. and Iida,H. and Boitet,C. and Maegaard,B. and Wilks,Y.} } @article {20053, title = {Genetic nomenclature for Trypanosoma and Leishmania.}, journal = {Mol Biochem Parasitol}, volume = {97}, year = {1998}, month = {1998 Nov 30}, pages = {221-4}, keywords = {Animals, Leishmania, Terminology as Topic, Trypanosoma}, issn = {0166-6851}, author = {Clayton, C and Adams, M and Almeida, R and Baltz, T and Barrett, M and Bastien, P and Belli, S and Beverley, S and Biteau, N and Blackwell, J and Blaineau, C and Boshart, M and Bringaud, F and Cross, G and Cruz, A and Degrave, W and Donelson, J and El-Sayed, N and Fu, G and Ersfeld, K and Gibson, W and Gull, K and Ivens, A and Kelly, J and Vanhamme, L} } @article {17951, title = {Salient Frame Detection for Molecular Dynamics Simulations}, journal = {Scientific Visualization: Interactions, Features, Metaphors}, volume = {2}, year = {1998}, month = {1998///}, pages = {160 - 175}, abstract = {Saliency-based analysis can be applied to time-varying 3D datasetsfor the purpose of summarization, abstraction, and motion analysis. As the sizes of time-varying datasets continue to grow, it becomes more and more difficult to comprehend vast amounts of data and information in a short period of time. Au- tomatically generated thumbnail images and previewing of time-varying datasets can help viewers explore and understand the datasets significantly faster as well as provide new insights. In this paper, we introduce a novel method for detect- ing salient frames for molecular dynamics simulations. Our method effectively detects crucial transitions in simulated mechanosensitive ion channel (MscS), in agreement with experimental data. }, author = {Kim,Y. and Patro,R. and Ip,C. Y and O{\textquoteright}Leary,D. P and Anishkin,A. and Sukharev,S. and Varshney, Amitabh} } @conference {17048, title = {Data models, visual representations, metaphors: how to solve the puzzle? (panel)}, booktitle = {Proceedings of the third IFIP WG2.6 working conference on Visual database systems 3 (VDB-3)}, year = {1997}, month = {1997///}, pages = {177 - 182}, publisher = {Chapman \& Hall, Ltd.}, organization = {Chapman \& Hall, Ltd.}, address = {London, UK, UK}, keywords = {data model, metaphor, visual representation}, isbn = {0-412-72170-8}, url = {http://dl.acm.org/citation.cfm?id=265394.265440}, author = {Catarci,T. and Costabile,M. F. and Cruz,I. F. and Ioannidis,Y. and Shneiderman, Ben} } @article {12768, title = {Optimality in abstractions of model checking}, journal = {Static Analysis}, year = {1995}, month = {1995///}, pages = {51 - 63}, author = {Cleaveland, Rance and Iyer,P. and Yankelevich,D.} } @article {14816, title = {The Paradyn parallel performance measurement tool}, journal = {Computer}, volume = {28}, year = {1995}, month = {1995/11//}, pages = {37 - 46}, abstract = {Paradyn is a tool for measuring the performance of large-scale parallel programs. Our goal in designing a new performance tool was to provide detailed, flexible performance information without incurring the space (and time) overhead typically associated with trace-based tools. Paradyn achieves this goal by dynamically instrumenting the application and automatically controlling this instrumentation in search of performance problems. Dynamic instrumentation lets us defer insertion until the moment it is needed (and remove it when it is no longer needed); Paradyn{\textquoteright}s Performance Consultant decides when and where to insert instrumentation}, keywords = {Aerodynamics, Automatic control, automatic instrumentation control, Debugging, dynamic instrumentation, flexible performance information, high level languages, insertion, Instruments, large-scale parallel program, Large-scale systems, measurement, Paradyn parallel performance measurement tool, Parallel machines, parallel programming, Performance Consultant, Programming profession, scalability, software performance evaluation, software tools}, isbn = {0018-9162}, doi = {10.1109/2.471178}, author = {Miller, B. P and Callaghan, M. D and Cargille, J. M and Hollingsworth, Jeffrey K and Irvin, R. B and Karavanic, K. L and Kunchithapadam, K. and Newhall, T.} } @conference {11924, title = {Integrated approaches for improving the effectiveness of Plan Reuse (A Progress Report)}, booktitle = {ARPA/Rome Laboratory knowledge-based planning and scheduling initiative: workshop proceedings: Tuscon, Arizona, February 21-24, 1994}, year = {1994}, month = {1994///}, pages = {325 - 325}, author = {Kambhampati,S. and Ihrig,L. and Katukam,S. and Chen,J. and Hendler,J. A and Agrawala, Ashok K.} } @conference {14579, title = {A SIMD solution to the sequence comparison problem on the MGAP}, booktitle = {International Conference on Application Specific Array Processors, 1994. Proceedings}, year = {1994}, month = {1994/08/22/24}, pages = {336 - 345}, publisher = {IEEE}, organization = {IEEE}, abstract = {Molecular biologists frequently compare an unknown biosequence with a set of other known biosequences to find the sequence which is maximally similar, with the hope that what is true of one sequence, either physically or functionally, could be true of its analogue. Even though efficient dynamic programming algorithms exist for the problem, when the size of the database is large, the time required is quite long, even for moderate length sequences. In this paper, we present an efficient pipelined SIMD solution to the sequence alignment problem on the Micro-Grain Array Processor (MGAP), a fine-grained massively parallel array of processors with nearest-neighbor connections. The algorithm compares K sequences of length O(M) with the actual sequence of length N, in O(M+N+K) time with O(MN) processors, which is AT-optimal. The implementation on the MGAP computes at the rate of about 0.1 million comparisons per second for sequences of length 128}, keywords = {AT-optimal algorithm, Biological information theory, biology computing, biosequence comparison problem, computational complexity, Computer science, Costs, database size, Databases, DNA computing, dynamic programming, dynamic programming algorithms, fine-grained massively parallel processor array, Genetics, Heuristic algorithms, maximally similar sequence, MGAP parallel computer, Micro-Grain Array Processor, Military computing, molecular biology, molecular biophysics, Nearest neighbor searches, nearest-neighbor connections, Parallel algorithms, pipeline processing, pipelined SIMD solution, sequence alignment problem, sequences}, isbn = {0-8186-6517-3}, doi = {10.1109/ASAP.1994.331791}, author = {Borah,M. and Bajwa,R. S and Hannenhalli, Sridhar and Irwin,M. J} } @conference {14769, title = {The integration of application and system based metrics in a parallel program performance tool}, booktitle = {ACM Sigplan Notices}, volume = {26}, year = {1991}, month = {1991///}, pages = {189 - 200}, author = {Hollingsworth, Jeffrey K and Irvin, R. B and Miller, B. P} } @article {18389, title = {Experiences building a syntax-directed editor}, journal = {Software Engineering Journal}, volume = {4}, year = {1989}, month = {1989/11//}, pages = {294 - 294}, abstract = {The paper presents a set of techniques for building robust software using the development of a microprocessor SUPPORT programming environment as an example. It discusses some of the attributes built into the system to best handle the concerns of portability, functionality, and effectiveness that had to be dealt with for the system to be reliable on a small machine, and it describes some of the choices made to obtain the best use of available hardware}, keywords = {applications;, editing;, editor;, engineering;, environment;, environments;, microcomputer, microprocessor;, portability;, Programming, robust, software, software;, Support, syntax-directed, text}, isbn = {0268-6961}, author = {Zelkowitz, Marvin V and Kowalchack,B. and Itkin,D. and Herman,L.} } @inbook {18363, title = {A support tool for teaching computer programming}, booktitle = {Issues in software engineering educationIssues in software engineering education}, year = {1989}, month = {1989///}, pages = {139 - 167}, publisher = {Springer-Verlag New York, Inc.}, organization = {Springer-Verlag New York, Inc.}, address = {New York, NY, USA}, isbn = {0-387-96840-7}, url = {http://dl.acm.org/citation.cfm?id=73064.73074}, author = {Zelkowitz, Marvin V and Kowalchack,B. and Itkin,D. and Herman,L.}, editor = {Fairley,Richard and Freeman,Peter} } @article {18098, title = {Parallel construction of a suffix tree with applications}, journal = {Algorithmica}, volume = {3}, year = {1988}, month = {1988///}, pages = {347 - 365}, author = {Apostolico,A. and Iliopoulos,C. and Landau,G. M and Schieber,B. and Vishkin, Uzi} } @conference {12024, title = {Determining three dimensional transformation parameters from images: Theory}, booktitle = {1987 IEEE International Conference on Robotics and Automation. Proceedings}, volume = {4}, year = {1987}, month = {1987/03//}, pages = {57 - 61}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present a theory for the determination of the three dimensional transformation parameters of an object, from its images. The input to this process is the image intensity function and its temporal derivative. In particular, our results are: 1) If the structure of the transforming object in view is known, then the transformation parameters are determined from the solution of a linear system. Rigid motion is a special ease of our theory. 2)If the structure of the object in view is not known, then both the structure and transformation parameters may be computed through a hill climbing or simulated annealing algorithm.}, keywords = {Automation, Computational modeling, Educational institutions, Image motion analysis, Indium tin oxide, Linear systems, Motion estimation, Optical computing, Robots, Simulated annealing}, doi = {10.1109/ROBOT.1987.1088011}, author = {Ito, E. and Aloimonos, J.} } @article {16978, title = {Applying direct manipulation concepts: direct manipulation dik operating system (DMDOS)}, journal = {SIGSOFT Softw. Eng. Notes}, volume = {11}, year = {1986}, month = {1986/04//}, pages = {22 - 26}, abstract = {Software engineers are often called upon to design user interfaces, but strategies and guidelines are only beginning to emerge. Shneiderman (1983) introduced the term "Direct Manipulation" to describe user interfaces which have:1) continuous representation of the objects of interest.2) physical actions (movement and selection by mouse, joystick, touch screen, etc.) or labeled button presses instead of complex Syntax.3) rapid, incremental, reversible operations whose impact on the object of interest is immediately visible.4) layered or spiral approach to learning that permits usage with minimal knowledge.The concepts of direct manipulation has been applied in some distinctive systems such as XEROX STAR and APPLE Macintosh, and many application software products such as spread sheets, word processors, drawing tools, desk-top managers, etc.However, the basic software of personal computers, the operating system, is still often based on command language concepts. This paper describes DMDOS (Direct Manipulation Disk Operating System), that we designed by applying the concepts of direct manipulation. to MS-DOS on the IBM PC.}, isbn = {0163-5948}, doi = {10.1145/382248.382815}, url = {http://doi.acm.org/10.1145/382248.382815}, author = {Iseki,Osamu and Shneiderman, Ben} } @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 {16966, title = {An experiment using memorization/reconstruction as a measure of programmer ability}, journal = {International Journal of Man-Machine Studies}, volume = {13}, year = {1980}, month = {1980/10//}, pages = {339 - 354}, abstract = {Measuring the abilities of programmers in a classroom or organizational setting is not a trivial task. Current approaches are not always accurate or reliable. This paper describes an experiment which provides evidence that performance on a memorization/recon- struction test can be used as a measure or predictor of programmer ability. The contribution of indentation in program comprehension is also examined.}, isbn = {0020-7373}, doi = {10.1016/S0020-7373(80)80047-2}, url = {http://www.sciencedirect.com/science/article/pii/S0020737380800472}, author = {Di Persio,Tom and Isbister,Dan and Shneiderman, Ben} }