Evaluating Regularized Anchor Words - Nguyen, T; Hu, Y; Jordan Boyd-Graber (mimno.infosci.cornell.edu)
Abstract We perform a comprehensive examination of the recently proposed anchor method for topic model inference using topic interpretability and held-out likelihood measures. After measuring the sensitivity to the anchor selection process, we incorporate L2 and Beta ...

Topic Models for Translation Domain Adaptation - Hu, Y; Zhai, K; Edelman, V; Jordan Boyd-Graber (mimno.infosci.cornell.edu)
Abstract Topic models have been successfully applied in domain adaptation for translation models. However, previous works applied topic models only on source side and ignored the relations between source and target languages in machine translation. This paper ...

Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children - Al-Hebshi, Nezar Noor; Baraniya, Divyashri; Chen, Tsute; Hill, Jennifer; Puri, Sumant; Tellez, Marisol; Hassan, Nur A.; Rita R Colwell; Ismail, Amid (Journal of Oral Microbiology, 2019)
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.

Biofilms Comprise a Component of the Annual Cycle of Vibrio cholerae in the Bay of Bengal Estuary - Sultana, Marzia; Nusrin, Suraia; Hasan, Nur A.; Sadique, Abdus; Ahmed, Kabir U.; Islam, Atiqul; Hossain, Anwar; Longini, Ira; Nizam, Azhar; Huq, Anwar; Siddique, Abul K.; Sack, David A.; et al. (mBio, 2018)
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.

Characterization of the Microbiome at the World’s Largest Potable Water Reuse Facility - Stamps, Blake W.; Leddy, Menu B.; Plumlee, Megan H.; Hasan, Nur A.; Rita R Colwell; Spear, John R. (Frontiers in Microbiology, 2018)
Conventional water resources are not sufficient in many regions to meet the needs of growing populations. Due to cyclical weather cycles, drought, and climate change, water stress has increased worldwide including in Southern California, which serves as a model for regions that integrate reuse of wastewater for both potable and non-potable use. The Orange County Water District (OCWD) Advanced Water Purification Facility (AWPF) is a highly engineered system designed to treat and produce up to 100 million gallons per day (MGD) of purified water from a municipal wastewater source for potable reuse. Routine facility microbial water quality analysis is limited to standard indicators at this and similar facilities. Given recent advances in high throughput DNA sequencing techniques, complete microbial profiling of communities in water samples is now possible. By using 16S/18S rRNA gene sequencing, metagenomic and metatranscriptomic sequencing coupled to a highly accurate identification method along with 16S rRNA gene qPCR, we describe a detailed view of the total microbial community throughout the facility. The total bacterial load of the water at stages of the treatment train ranged from 3.02 × 106 copies in source, unchlorinated wastewater feed to 5.49 × 101 copies of 16S rRNA gene/mL after treatment (consisting of microfiltration, reverse osmosis, and ultraviolet/advanced oxidation). Microbial diversity and load decreased by several orders of magnitude after microfiltration and reverse osmosis treatment, falling to almost non-detectable levels that more closely resembled controls of molecular grade laboratory water than the biomass detected in the source water. The presence of antibiotic resistance genes and viruses was also greatly reduced. Overall, system design performance was achieved, and comprehensive microbial community analysis was found to enable a more complete characterization of the water/wastewater microbial signature. Keywords: water reuse, pathogens, water purification, metatranscriptomics, metagenomics

Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome Between Neonatal Intensive Care Unit (NICU) Environments - Hourigan, Suchitra K.; Subramanian, Poorani; Hasan, Nur A.; Ta, Allison; Klein, Elisabeth; Chettout, Nassim; Huddleston, Kathi; Deopujari, Varsha; Levy, Shira; Baveja, R; Clemency, Nicole C.; Baker, Robin L.; et al. (Frontiers in Microbiology, 2018)

Distinct consequences of amoxicillin and ertapenem exposure in the porcine gut microbiome - Connelly, Sheila; Subramanian, Poorani; Hasan, Nur A.; Rita R Colwell; Kaleko, Michael (Anaerobe, 2018)

Environmental and hydroclimatic factors influencing Vibrio populations in the estuarine zone of the Bengal delta - Neogi, Sucharit; Rubin, Lara; Alam, Munirul; Harder, Jens; Yamasaki, Shinji; Rita R Colwell (Environmental Monitoring and Assessment, 2018)
The objective of this study was to determine environmental parameters driving Vibrio populations in the estuarine zone of the Bengal delta. Spatio-temporal data were collected at river estuary, mangrove, beach, pond, and canal sites. Effects of salinity, tidal amplitude, and a cyclone and tsunami were included in the study. Vibrio population shifts were found to be correlated with tide-driven salinity and suspended particulate matter (SPM). Increased abundance of Vibrio spp. in surface water was observed after a cyclone, attributed to re-suspension of benthic particulate organic carbon (POC), and increased availability of chitin and dissolved organic carbon (DOC). Approximately a two log10 increase in the (p < 0.05) number of Vibrio spp. was observed in < 20 μm particulates, compared with microphytoplankton (20–60 μm) and zooplankton > 60 μm fractions. Benthic and suspended sediment comprised a major reservoir of Vibrio spp. Results of microcosm experiments showed enhanced growth of vibrios was related to concentration of organic matter in SPM. It is concluded that SPM, POC, chitin, and salinity significantly influence abundance and distribution of vibrios in the Bengal delta estuarine zone. Keywords Vibrio Salinity Cyclone Tide Chitin Sediment dynamics

High-Throughput DNA Sequencing To Profile Microbial Water Quality Of Potable Reuse - Menu B. Leddy; Megan H. Plumlee; Rose S. Kantor; Kara L. Nelson; Scott E. Miller; Lauren C. Kennedy; Blake W. Stamps; John R. Spear; Nur A. Hasan; Rita R Colwell (2018)

A Metagenomic Approach to Evaluating Surface Water Quality in Haiti - Roy, Monika; Arnaud, Jean; Jasmin, Paul; Hamner, Steve; Hasan, Nur; Rita R Colwell; Ford, Timothy (International Journal of Environmental Research and Public Health, 2018)
The cholera epidemic that occurred in Haiti post-earthquake in 2010 has resulted in over 9000 deaths during the past eight years. Currently, morbidity and mortality rates for cholera have declined, but cholera cases still occur on a daily basis. One continuing issue is an inability to accurately predict and identify when cholera outbreaks might occur. To explore this surveillance gap, a metagenomic approach employing environmental samples was taken. In this study, surface water samples were collected at two time points from several sites near the original epicenter of the cholera outbreak in the Central Plateau of Haiti. These samples underwent whole genome sequencing and subsequent metagenomic analysis to characterize the microbial community of bacteria, fungi, protists, and viruses, and to identify antibiotic resistance and virulence associated genes. Replicates from sites were analyzed by principle components analysis, and distinct genomic profiles were obtained for each site. Cholera toxin converting phage was detected at one site, and Shiga toxin converting phages at several sites. Members of the Acinetobacter family were frequently detected in samples, including members implicated in waterborne diseases. These results indicate a metagenomic approach to evaluating water samples can be useful for source tracking and the surveillance of pathogens such as Vibrio cholerae over time, as well as for monitoring virulence factors such as cholera toxin.

Satellites and Cell Phones Form a Cholera Early-Warning System - Akanda, Ali; Aziz, Sonia; Jutla, Antarpreet; Huq, Anwar; Alam, Munirul; Ahsan, Gias; Rita R Colwell (Eos, 2018)

Virulence-Related Genes Identified from the Genome Sequence of the Non-O1/Non-O139 Vibrio cholerae Strain VcN1, Isolated from Dhaka, Bangladesh - Hossain, Maqsud; Alam, Munirul; Khaleque, Abdul; Islam, Sohidul; Sadique, Abdus; Khan, Nayeim; Halim, Zahra; Sarker, Mrinmoy; El-Sayed, Najib M.; Huq, Anwar; Ahsan, Gias Uddin; Rita R Colwell (Genome Announcements, 2018)
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.

Application of a paper based device containing a new culture medium to detect Vibrio cholerae in water samples collected in Haiti - Briquaire, Romain; Rita R Colwell; Boncy, Jacques; Rossignol, Emmanuel; Dardy, Aline; Pandini, Isabelle; Villeval, François; Machuron, Jean-Louis; Huq, Anwar; Rashed, Shah; Vandevelde, Thierry; Rozand, Christine (Journal of Microbiological Methods, 2017)

Assessment of Risk of Cholera in Haiti following Hurricane Matthew - Huq, Anwar; Anwar, Rifat; Rita R Colwell; McDonald, Michael D.; Khan, Rakib; Jutla, Antarpreet; Akanda, Shafqat (The American Journal of Tropical Medicine and Hygiene, 2017)
Damage to the inferior and fragile water and sanitation infrastructure of Haiti after Hurricane Matthew has created an urgent public health emergency in terms of likelihood of cholera occurring in the human population. Using satellite-derived data on precipitation, gridded air temperature, and hurricane path and with information on water and sanitation (WASH) infrastructure, we tracked changing environmental conditions conducive for growth of pathogenic vibrios. Based on these data, we predicted and validated the likelihood of cholera cases occurring past hurricane. The risk of cholera in the southwestern part of Haiti remained relatively high since November 2016 to the present. Findings of this study provide a contemporary process for monitoring ground conditions that can guide public health intervention to control cholera in human population by providing access to vaccines, safe WASH facilities. Assuming current social and behavioral patterns remain constant, it is recommended that WASH infrastructure should be improved and considered a priority especially before 2017 rainy season.

Characterization of Microbial Signatures From Advanced Treated Wastewater Biofilms - Leddy, Menu B.; Hasan, Nur A.; Subramanian, Poorani; Heberling, Colin; Cotruvo, Joseph; Rita R Colwell (Journal - American Water Works Association, 2017)
Next‐generation sequencing (NGS) and metagenomics were used to identify microbial communities in biofilms of microfiltration (MF) and reverse osmosis (RO) membranes in an advanced water purification facility (AWPF) that treats municipal wastewater to produce potable quality water. Secondary treated wastewater effluent is the source of influent to the AWPF treatment train and was also characterized by NGS. Results show low bacterial diversity in biofilms obtained from the feed‐side surfaces of MF and RO membranes. Microbial communities and antibiotic resistance genes (ARGs) in the RO biofilm were compared with those of the MF and influent, revealing lower abundance of bacterial species and ARGs in the RO biofilm than in the other samples. Opportunistic pathogens were detected in all samples; however, indicator bacteria, viruses, and bacteriophages were not detected in the RO biofilm. It is concluded that NGS has great potential for improved detection and characterization of microbial communities in biofilms that form on AWPF MF and RO membranes.

Characterization of Pathogenic Vibrio parahaemolyticus from the Chesapeake Bay, Maryland - Chen, Arlene J.; Hasan, Nur A.; Haley, Bradd J.; Taviani, Elisa; Tarnowski, Mitch; Brohawn, Kathy; Johnson, Crystal N.; Rita R Colwell; Huq, Anwar (Frontiers in Microbiology, 2017)

Characterization of Two Cryptic Plasmids Isolated in Haiti from Clinical Vibrio cholerae Non-O1/Non-O139 - Ceccarelli, Daniela; Garriss, Genevieve; Choi, Seon Y.; Hasan, Nur A.; Stepanauskas, Ramunas; Pop, Mihai; Huq, Anwar; Rita R Colwell (Frontiers in Microbiology, 2017)

Comparative genomic analysis and characterization of incompatibility group FIB plasmid encoded virulence factors of Salmonella enterica isolated from food sources - Khajanchi, Bijay K.; Hasan, Nur A.; Choi, Seon Young; Han, Jing; Zhao, Shaohua; Rita R Colwell; Cerniglia, Carl E.; Foley, Steven L. (BMC Genomics, 2017)
BACKGROUND: The degree to which the chromosomal mediated iron acquisition system contributes to virulence of many bacterial pathogens is well defined. However, the functional roles of plasmid encoded iron acquisition systems, specifically Sit and aerobactin, have yet to be determined for Salmonella spp. In a recent study, Salmonella enterica strains isolated from different food sources were sequenced on the Illumina MiSeq platform and found to harbor the incompatibility group (Inc) FIB plasmid. In this study, we examined sequence diversity and the contribution of factors encoded on the IncFIB plasmid to the virulence of S. enterica. RESULTS: Whole genome sequences of seven S. enterica isolates were compared to genomes of serovars of S. enterica isolated from food, animal, and human sources. SeqSero analysis predicted that six strains were serovar Typhimurium and one was Heidelberg. Among the S. Typhimurium strains, single nucleotide polymorphism (SNP)-based phylogenetic analyses revealed that five of the isolates clustered as a single monophyletic S. Typhimurium subclade, while one of the other strains branched with S. Typhimurium from a bovine source. DNA sequence based phylogenetic diversity analyses showed that the IncFIB plasmid-encoded Sit and aerobactin iron acquisition systems are conserved among bacterial species including S. enterica. The IncFIB plasmid was transferred to an IncFIB plasmid deficient strain of S. enterica by conjugation. The transconjugant SE819::IncFIB persisted in human intestinal epithelial (Caco-2) cells at a higher rate than the recipient SE819. Genes of the Sit and aerobactin operons in the IncFIB plasmid were differentially expressed in iron-rich and iron-depleted growth media. CONCLUSIONS: Minimal sequence diversity was detected in the Sit and aerobactin operons in the IncFIB plasmids present among different bacterial species, including foodborne Salmonella strains. IncFIB plasmid encoded factors play a role during infection under low-iron conditions in host cells.

Comparative Genomics of Escherichia coli Isolated from Skin and Soft Tissue and Other Extraintestinal Infections - Ranjan, Amit; Shaik, Sabiha; Nandanwar, Nishant; Hussain, Arif; Tiwari, Sumeet K.; Semmler, Torsten; Jadhav, Savita; Wieler, Lothar H.; Alam, Munirul; Rita R Colwell; Ahmed, Niyaz (mBio, 2017)
Escherichia coli, an intestinal Gram-negative bacterium, has been shown to be associated with a variety of diseases in addition to intestinal infections, such as urinary tract infections (UTIs), meningitis in neonates, septicemia, skin and soft tissue infections (SSTIs), and colisepticemia. Thus, for nonintestinal infections, it is categorized as extraintestinal pathogenic E. coli (ExPEC). It is also an opportunistic pathogen, causing cross infections, notably as an agent of zoonotic diseases. However, comparative genomic data providing functional and genetic coordinates for ExPEC strains associated with these different types of infections have not proven conclusive. In the study reported here, ExPEC E. coli isolated from SSTIs was characterized, including virulence and drug resistance profiles, and compared with isolates from patients suffering either pyelonephritis or septicemia. Results revealed that the majority of the isolates belonged to two pathogenic phylogroups, B2 and D. Approximately 67% of the isolates were multidrug resistant (MDR), with 85% producing extended-spectrum beta-lactamase (ESBL) and 6% producing metallo-beta-lactamase (MBL). The blaCTX-M-15 genotype was observed in at least 70% of the E. coli isolates in each category, conferring resistance to an extended range of beta-lactam antibiotics. Whole-genome sequencing and comparative genomics of the ExPEC isolates revealed that two of the four isolates from SSTIs, NA633 and NA643, belong to pandemic sequence type ST131, whereas functional characteristics of three of the ExPEC pathotypes revealed that they had equal capabilities to form biofilm and were resistant to human serum. Overall, the isolates from a variety of ExPEC infections demonstrated similar resistomes and virulomes and did not display any disease-specific functional or genetic coordinates. IMPORTANCE Infections caused by extraintestinal pathogenic E. coli (ExPEC) are of global concern as they result in significant costs to health care facilities management. The recent emergence of a multidrug-resistant pandemic clone, Escherichia coli ST131, is of primary concern as a global threat. In developing countries, such as India, skin and soft tissue infections (SSTIs) associated with E. coli are marginally addressed. In this study, we employed both genomic analysis and phenotypic assays to determine relationships, if any, among the ExPEC pathotypes. Similarity between antibiotic resistance and virulence profiles was observed, ST131 isolates from SSTIs were reported, and genomic similarities among strains isolated from different disease conditions were detected. This study provides functional molecular infection epidemiology insight into SSTI-associated E. coli compared with ExPEC pathotypes.

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers - McIntyre, Alexa B. R.; Ounit, Rachid; Afshinnekoo, Ebrahim; Prill, Robert J.; Hénaff, Elizabeth; Alexander, Noah; Minot, Samuel S.; Danko, David; Foox, Jonathan; Ahsanuddin, Sofia; Tighe, Scott; Hasan, Nur A.; et al. (Genome Biology, 2017)

Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP) - Tighe, Scott; Afshinnekoo, Ebrahim; Rock, Tara M.; McGrath, Ken; Alexander, Noah; McIntyre, Alexa; Ahsanuddin, Sofia; Bezdan, Daniela; Green, Stefan J.; Joye, Samantha; Stewart Johnson, Sarah; Baldwin, Don A.; et al. (Journal of Biomolecular Techniques : JBT, 2017)
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the “Door to Hell” crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.

Hydroclimatic sustainability assessment of changing climate on cholera in the Ganges-Brahmaputra basin - Nasr-Azadani, Fariborz; Khan, Rakibul; Rahimikollu, Javad; Unnikrishnan, Avinash; Akanda, Ali; Alam, Munirul; Huq, Anwar; Jutla, Antarpreet; Rita R Colwell (Advances in Water Resources, 2017)
The association of cholera and climate has been extensively documented. However, determining the effects of changing climate on the occurrence of disease remains a challenge. Bimodal peaks of cholera in Bengal Delta are hypothesized to be linked to asymmetric flow of the Ganges and Brahmaputra rivers. Spring cholera is related to intrusion of bacteria-laden coastal seawater during low flow seasons, while autumn cholera results from cross-contamination of water resources when high flows in the rivers cause massive inundation. Coarse resolution of General Circulation Model (GCM) output (usually at 100 – 300 km)cannot be used to evaluate variability at the local scale(10–20 km),hence the goal of this study was to develop a framework that could be used to understand impacts of climate change on occurrence of cholera. Instead of a traditional approach of downscaling precipitation, streamflow of the two rivers was directly linked to GCM outputs, achieving reasonable accuracy (R2 = 0.89 for the Ganges and R2 = 0.91 for the Brahmaputra)using machine learning algorithms (Support Vector Regression-Particle Swarm Optimization). Copula methods were used to determine probabilistic risks of cholera under several discharge conditions. Key results, using model outputs from ECHAM5, GFDL, andHadCM3for A1B and A2 scenarios, suggest that the combined low flow of the two rivers may increase in the future, with high flows increasing for first half of this century, decreasing thereafter. Spring and autumn cholera, assuming societal conditions remain constant e.g., at the current rate, may decrease. However significant shifts were noted in the magnitude of river discharge suggesting that cholera dynamics of the delta may well demonstrate an uncertain predictable pattern of occurrence over the next century.

Vibrio cholerae O1 with Reduced Susceptibility to Ciprofloxacin and Azithromycin Isolated from a Rural Coastal Area of Bangladesh - Rashed, Shah M.; Hasan, Nur A.; Alam, Munirul; Sadique, Abdus; Sultana, Marzia; Hoq, Md. Mozammel; Sack, R. Bradley; Rita R Colwell; Huq, Anwar (Frontiers in Microbiology, 2017)
Cholera outbreaks occur each year in the remote coastal areas of Bangladesh and epidemiological surveillance and routine monitoring of cholera in these areas is challenging. In this study, a total of 97 Vibrio cholerae O1 isolates from Mathbaria, Bangladesh, collected during 2010 and 2014 were analyzed for phenotypic and genotypic traits, including antimicrobial susceptibility. Of the 97 isolates, 95 possessed CTX-phage mediated genes, ctxA, ace, and zot, and two lacked the cholera toxin gene, ctxA. Also both CTX+ and CTX− V. cholerae O1 isolated in this study carried rtxC, tcpAET, and hlyA. The classical cholera toxin gene, ctxB1, was detected in 87 isolates, while eight had ctxB7. Of 95 CTX+ V. cholerae O1, 90 contained rstRET and 5 had rstRCL. All isolates, except two, contained SXT related integrase intSXT. Resistance to penicillin, streptomycin, nalidixic acid, sulfamethoxazole-trimethoprim, erythromycin, and tetracycline varied between the years of study period. Most importantly, 93% of the V. cholerae O1 were multidrug resistant. Six different resistance profiles were observed, with resistance to streptomycin, nalidixic acid, tetracycline, and sulfamethoxazole-trimethoprim predominant every year. Ciprofloxacin and azithromycin MIC were 0.003–0.75 and 0.19–2.00 μg/ml, respectively, indicating reduced susceptibility to these antibiotics. Sixteen of the V. cholerae O1 isolates showed higher MIC for azithromycin (≥0.5 μg/ml) and were further examined for 10 macrolide resistance genes, erm(A), erm(B), erm(C), ere(A), ere(B), mph(A), mph(B), mph(D), mef(A), and msr(A) with none testing positive for the macrolide resistance genes.

Membrane Bioreactor-Based Wastewater Treatment Plant in Saudi Arabia: Reduction of Viral Diversity, Load, and Infectious Capacity - Jumat, Muhammad; Hasan, Nur; Subramanian, Poorani; Heberling, Colin; Rita R Colwell; Hong, Pei-Ying (Water, 2017)

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs - Junqueira, AC; Ratan, Aakrosh; Acerbi, Enzo; Drautz-Moses, Daniela I.; Premkrishnan, BNV; Costea, PI; Linz, Bodo; Purbojati, Rikky W.; Paulo, Daniel F.; Gaultier, Nicolas E.; Subramanian, Poorani; Hasan, Nur A.; et al. (Scientific Reports, 2017)
Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome. Legs and wings displayed the largest microbial diversity and were shown to be an important route for microbial dispersion. The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.

SYN-004 (ribaxamase), an oral beta-lactamase, mitigates antibiotic-mediated dysbiosis in a porcine gut microbiome model - Connelly, S.; Bristol, J.A.; Hubert, S.; Subramanian, P.; Hasan, N.A.; Rita R Colwell; Kaleko, M. (Journal of Applied Microbiology, 2017)
Aim To evaluate an antibiotic inactivation strategy to protect the gut microbiome from antibiotic‐mediated damage. Methods and Results SYN‐004 (ribaxamase) is an orally delivered beta‐lactamase intended to degrade penicillins and cephalosporins within the gastrointestinal tract to protect the microbiome. Pigs (20 kg, n = 10) were treated with ceftriaxone (CRO) (IV, 50 mg kg−1, SID) for 7 days and a cohort (n = 5) received ribaxamase (PO, 75 mg, QID) for 9 days beginning the day before antibiotic administration. Ceftriaxone serum levels were not statistically different in the antibiotic‐alone and antibiotic + ribaxamase groups, indicating ribaxamase did not alter systemic antibiotic levels. Whole‐genome metagenomic analyses of pig faecal DNA revealed that CRO caused significant changes to the gut microbiome and an increased frequency of antibiotic resistance genes. With ribaxamase, the gut microbiomes were not significantly different from pretreatment and antibiotic resistance gene frequency was not increased. Conclusion Ribaxamase mitigated CRO‐mediated gut microbiome dysbiosis and attenuated propagation of the antibiotic resistance genes in pigs. Significance and Impact of the Study Damage of the microbiome can lead to overgrowth of pathogenic organisms and antibiotic exposure can promote selection for antibiotic‐resistant micro‐organisms. Ribaxamase has the potential to become the first therapy designed to protect the gut microbiome from antibiotic‐mediated dysbiosis and reduce emergence of antibiotic resistance.

Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1 - Rashid, Mahamud-ur; Almeida, Mathieu; Azman, Andrew S.; Lindsay, Brianna R.; Sack, David A.; Rita R Colwell; Huq, Anwar; Morris, J. Glenn; Alam, Munirul; Stine, O. Colin (FEMS Microbiology Letters, 2016)
Vibrio cholerae causes cholera, a severe diarrheal disease. Understanding the local genetic diversity and transmission of V. cholerae will improve our ability to control cholera. Vibrio cholerae isolates clustered in genetically related groups (clonal complexes, CC) by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (WGS). Isolates in CC1 had been isolated from two geographical locations. Isolates in a second genetically distinct group, CC2, were isolated only at one location. Using WGS, CC1 isolates from both locations revealed, on average, 43.8 nucleotide differences, while those strains comprising CC2 averaged 19.7 differences. Strains from both MLVA-CCs had an average difference of 106.6. Thus, isolates comprising CC1 were more closely related (P < 10−6) to each other than to isolates in CC2. Within a MLVA-CC, after removing all paralogs, alternative alleles were found in all possible combinations on separate chromosomes indicative of recombination within the core genome. Including recombination did not affect the distinctiveness of the MLVA-CCs when measured by WGS. We found that WGS generally reflected the same genetic relatedness of isolates as MLVA, indicating that isolates from the same MLVA-CC shared a more recent common ancestor than isolates from the same location that clustered in a distinct MLVA-CC.

Computational study of the inhibitory mechanism of the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore - Cardone, Antonio; Brady, M.; Sriram, R.; Pant, H. C.; Hassan, S. A. (Journal of Computer-Aided Molecular Design, 2016)

Cross-talk among flesh-eating Aeromonas hydrophila strains in mixed infection leading to necrotizing fasciitis - Ponnusamy, Duraisamy; Kozlova, Elena V.; Sha, Jian; Erova, Tatiana E.; Azar, Sasha R.; Fitts, Eric C.; Kirtley, Michelle L.; Tiner, Bethany L.; Andersson, Jourdan A.; Grim, Christopher J.; Isom, Richard P.; Hasan, Nur A.; et al. (Proceedings of the National Academy of Sciences, 2016)
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–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.

Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak - Ottesen, Andrea; Ramachandran, Padmini; Reed, Elizabeth; White, James R.; Hasan, Nur; Subramanian, Poorani; Ryan, Gina; Jarvis, Karen; Grim, Christopher; Daquiqan, Ninalynn; Hanes, Darcy; Allard, Marc; et al. (BMC Microbiology, 2016)

Modeling Sustainability: Population, Inequality, Consumption, and Bidirectional Coupling of the Earth and Human Systems - Motesharrei, Safa; Rivas, Jorge; Kalnay, Eugenia; Asrar, Ghassem R.; Busalacchi, Antonio J.; Cahalan, Robert F.; Cane, Mark A.; Rita R Colwell; Feng, Kuishuang; Franklin, Rachel S.; Hubacek, Klaus; Miralles-Wilhelm, Fernando; et al. (National Science Review, 2016)
Over the last two centuries, the impact of the Human System has grown dramatically, becoming strongly dominant within the Earth System in many different ways. Consumption, inequality, and population have increased extremely fast, especially since about 1950, threatening to overwhelm the many critical functions and ecosystems of the Earth System. Changes in the Earth System, in turn, have important feedback effects on the Human System, with costly and potentially serious consequences. However, current models do not incorporate these critical feedbacks. We argue that in order to understand the dynamics of either system, Earth System Models must be coupled with Human System Models through bidirectional couplings representing the positive, negative, and delayed feedbacks that exist in the real systems. In particular, key Human System variables, such as demographics, inequality, economic growth, and migration, are not coupled with the Earth System but are instead driven by exogenous estimates, such as United Nations population projections. This makes current models likely to miss important feedbacks in the real Earth–Human system, especially those that may result in unexpected or counterintuitive outcomes, and thus requiring different policy interventions from current models. The importance and imminence of sustainability challenges, the dominant role of the Human System in the Earth System, and the essential roles the Earth System plays for the Human System, all call for collaboration of natural scientists, social scientists, and engineers in multidisciplinary research and modeling to develop coupled Earth–Human system models for devising effective science-based policies and measures to benefit current and future generations.

Phylogenetic Diversity of Vibrio cholerae Associated with Endemic Cholera in Mexico from 1991 to 2008 - Choi, Seon Y; Rashed, Shah M.; Hasan, Nur A.; Alam, Munirul; Islam, Tarequl; Sadique, Abdus; Johura, Fatema-Tuz; Eppinger, Mark; Ravel, Jacques; Huq, Anwar; Cravioto, Alejandro; Rita R Colwell (mBio, 2016)
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.

Reduced Susceptibility to Extended-Spectrum β-Lactams in Vibrio cholerae Isolated in Bangladesh - Ceccarelli, Daniela; Alam, Munirul; Huq, Anwar; Rita R Colwell (Frontiers in Public Health, 2016)

Building Infectious Disease Research Programs to Promote Security and Enhance Collaborations with Countries of the Former Soviet Union - Bartholomew, James C.; Pearson, Andrew D.; Stenseth, Nils C.; LeDuc, James W.; Hirschberg, David L.; Rita R Colwell (Frontiers in Public Health, 2015)

Concordance and discordance of sequence survey methods for molecular epidemiology - Castro-Nallar, Eduardo; Hasan, Nur A.; Cebula, Thomas A.; Rita R Colwell; Robison, Richard A.; Johnson, W. Evan; Crandall, Keith A. (PeerJ, 2015)
The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes), and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST) impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly associated with geography, irrespective of the molecular survey approach used, while Brucella spp. phylogeny appears to be strongly associated with geography and host origin. We contrast inferences made among monomorphic (clonal) and non-monomorphic bacteria, and between intra- and inter-specific datasets. We also discuss our results in light of underlying assumptions of different approaches.

Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species - Hasan, Nur A.; Grim, Christopher J.; Lipp, Erin K.; Rivera, Irma N. G.; Chun, Jongsik; Haley, Bradd J.; Taviani, Elisa; Choi, Seon Young; Hoq, Mozammel; Munk, A. Christine; Brettin, Thomas S.; Bruce, David; et al. (Proceedings of the National Academy of Sciences, 2015)
Vibrio species are both ubiquitous and abundant in marine coastal waters, estuaries, ocean sediment, and aquaculture settings worldwide. We report here the isolation, characterization, and genome sequence of a novel Vibrio species, Vibrio antiquarius, isolated from a mesophilic bacterial community associated with hydrothermal vents located along the East Pacific Rise, near the southwest coast of Mexico. Genomic and phenotypic analysis revealed V. antiquarius is closely related to pathogenic Vibrio species, namely Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio harveyi, and Vibrio vulnificus, but sufficiently divergent to warrant a separate species status. The V. antiquarius genome encodes genes and operons with ecological functions relevant to the environment conditions of the deep sea and also harbors factors known to be involved in human disease caused by freshwater, coastal, and brackish water vibrios. The presence of virulence factors in this deep-sea Vibrio species suggests a far more fundamental role of these factors for their bacterial host. Comparative genomics revealed a variety of genomic events that may have provided an important driving force in V. antiquarius evolution, facilitating response to environmental conditions of the deep sea.

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

Diagnostic Approach for Monitoring Hydroclimatic Conditions Related to Emergence of West Nile Virus in West Virginia - Jutla, Antarpreet; Huq, Anwar; Rita R Colwell (Frontiers in Public Health, 2015)
West Nile virus (WNV), mosquito-borne and water-based disease, is increasingly a global threat to public health. Since its appearance in the northeastern United States in 1999, WNV has since been reported in several states in the continental United States. The objective of this study is to highlight role of hydroclimatic processes estimated through satellite sensors in capturing conditions for emergence of the vectors in historically disease free regions. We tested the hypothesis that an increase in surface temperature, in combination with intensification of vegetation, and enhanced precipitation, lead to conditions favorable for vector (mosquito) growth. Analysis of land surface temperature (LST) pattern shows that temperature values >16°C, with heavy precipitation, may lead to abundance of the mosquito population. This hypothesis was tested in West Virginia where a sudden epidemic of WNV infection was reported in 2012. Our results emphasize the value of hydroclimatic processes estimated by satellite remote sensing, as well as continued environmental surveillance of mosquitoes, because when a vector-borne infection like WNV is discovered in contiguous regions, the risk of spread of WNV mosquitoes increase at points where appropriate hydroclimatic processes intersect with the vector niche.

Downscaling river discharge to assess the effects of climate change on cholera outbreaks in the Bengal Delta - Nasr-Azadani, F; Unnikrishnan, A; Akanda, A; Islam, S; Alam, M; Huq, A; Jutla, A; Rita R Colwell (Climate Research, 2015)
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.

Environmental Surveillance for Toxigenic Vibrio cholerae in Surface Waters of Haiti - Hill, Vincent R.; Humphrys, Michael S.; Kahler, Amy M.; Boncy, Jacques; Tarr, Cheryl L.; Huq, Anwar; Chen, Arlene; Katz, Lee S.; Mull, Bonnie J.; Derado, Gordana; Haley, Bradd J.; Freeman, Nicole; et al. (The American Journal of Tropical Medicine and Hygiene, 2015)
Epidemic cholera was reported in Haiti in 2010, with no information available on the occurrence or geographic distribution of toxigenic Vibrio cholerae in Haitian waters. In a series of field visits conducted in Haiti between 2011 and 2013, water and plankton samples were collected at 19 sites. Vibrio cholerae was detected using culture, polymerase chain reaction, and direct viable count methods (DFA-DVC). Cholera toxin genes were detected by polymerase chain reaction in broth enrichments of samples collected in all visits except March 2012. Toxigenic V. cholerae was isolated from river water in 2011 and 2013. Whole genome sequencing revealed that these isolates were a match to the outbreak strain. The DFA-DVC tests were positive for V. cholerae O1 in plankton samples collected from multiple sites. Results of this survey show that toxigenic V. cholerae could be recovered from surface waters in Haiti more than 2 years after the onset of the epidemic.

Hybrid Vibrio cholerae El Tor Lacking SXT Identified as the Cause of a Cholera Outbreak in the Philippines - Klinzing, David C.; Choi, Seon Young; Hasan, Nur A.; Matias, Ronald R.; Tayag, Enrique; Geronimo, Josefina; Skowronski, Evan; Rashed, Shah M.; Kawashima, Kent; Rosenzweig, C. Nicole; Gibbons, Henry S.; Torres, Brian C.; et al. (mBio, 2015)
Cholera continues to be a global threat, with high rates of morbidity and mortality. In 2011, a cholera outbreak occurred in Palawan, Philippines, affecting more than 500 people, and 20 individuals died. Vibrio cholerae O1 was confirmed as the etiological agent. Source attribution is critical in cholera outbreaks for proper management of the disease, as well as to control spread. In this study, three V. cholerae O1 isolates from a Philippines cholera outbreak were sequenced and their genomes analyzed to determine phylogenetic relatedness to V. cholerae O1 isolates from recent outbreaks of cholera elsewhere. The Philippines V. cholerae O1 isolates were determined to be V. cholerae O1 hybrid El Tor belonging to the seventh-pandemic clade. They clustered tightly, forming a monophyletic clade closely related to V. cholerae O1 hybrid El Tor from Asia and Africa. The isolates possess a unique multilocus variable-number tandem repeat analysis (MLVA) genotype (12-7-9-18-25 and 12-7-10-14-21) and lack SXT. In addition, they possess a novel 15-kb genomic island (GI-119) containing a predicted type I restriction-modification system. The CTXΦ-RS1 array of the Philippines isolates was similar to that of V. cholerae O1 MG116926, a hybrid El Tor strain isolated in Bangladesh in 1991. Overall, the data indicate that the Philippines V. cholerae O1 isolates are unique, differing from recent V. cholerae O1 isolates from Asia, Africa, and Haiti. Furthermore, the results of this study support the hypothesis that the Philippines isolates of V. cholerae O1 are indigenous and exist locally in the aquatic ecosystem of the Philippines.

Non-O1/Non-O139 Vibrio cholerae Carrying Multiple Virulence Factors and V. cholerae O1 in the Chesapeake Bay, Maryland - Ceccarelli, Daniela; Chen, Arlene; Hasan, Nur A.; Rashed, Shah M.; Huq, Anwar; Rita R Colwell (Applied and Environmental Microbiology, 2015)
Non-O1/non-O139 Vibrio cholerae inhabits estuarine and coastal waters globally, but its clinical significance has not been sufficiently investigated, despite the fact that it has been associated with septicemia and gastroenteritis. The emergence of virulent non-O1/non-O139 V. cholerae is consistent with the recognition of new pathogenic variants worldwide. Oyster, sediment, and water samples were collected during a vibrio surveillance program carried out from 2009 to 2012 in the Chesapeake Bay, Maryland. V. cholerae O1 was detected by a direct fluorescent-antibody (DFA) assay but was not successfully cultured, whereas 395 isolates of non-O1/non-O139 V. cholerae were confirmed by multiplex PCR and serology. Only a few of the non-O1/non-O139 V. cholerae isolates were resistant to ampicillin and/or penicillin. Most of the isolates were sensitive to all antibiotics tested, and 77 to 90% carried the El Tor variant hemolysin gene hlyA ET, the actin cross-linking repeats in toxin gene rtxA, the hemagglutinin protease gene hap, and the type 6 secretion system. About 19 to 21% of the isolates carried the neuraminidase-encoding gene nanH and/or the heat-stable toxin (NAG-ST), and only 5% contained a type 3 secretion system. None of the non-O1/non-O139 V. cholerae isolates contained Vibrio pathogenicity island-associated genes. However, ctxA, ace, or zot was present in nine isolates. Fifty-five different genotypes showed up to 12 virulence factors, independent of the source of isolation, and represent the first report of both antibiotic susceptibility and virulence associated with non-O1/non-O139 V. cholerae from the Chesapeake Bay. Since these results confirm the presence of potentially pathogenic non-O1/non-O139 V. cholerae, monitoring for total V. cholerae, regardless of serotype, should be done within the context of public health.

Nontoxigenic Vibrio cholerae Non-O1/O139 Isolate from a Case of Human Gastroenteritis in the U.S. Gulf Coast - Hasan, Nur A.; Rezayat, Talayeh; Blatz, Peter J.; Choi, Seon Young; Griffitt, Kimberly J.; Rashed, Shah M.; Huq, Anwar; Conger, Nicholas G.; Rita R Colwell; Grimes, D. Jay (Journal of Clinical Microbiology, 2015)
An occurrence of Vibrio cholerae non-O1/O139 gastroenteritis in the U.S. Gulf Coast is reported here. Genomic analysis revealed that the isolate lacked known virulence factors associated with the clinical outcome of a V. cholerae infection but did contain putative genomic islands and other accessory virulence factors. Many of these factors are widespread among environmental strains of V. cholerae, suggesting that there might be additional virulence factors in non-O1/O139 V. cholerae yet to be determined. Phylogenetic analysis revealed that the isolate belonged to a phyletic lineage of environmental V. cholerae isolates associated with sporadic cases of gastroenteritis in the Western Hemisphere, suggesting a need to monitor non-O1/O139 V. cholerae in the interest of public health.

Occurrence and Diversity of Clinically Important Vibrio Species in the Aquatic Environment of Georgia - Kokashvili, Tamar; Whitehouse, Chris A.; Tskhvediani, Ana; Grim, Christopher J.; Elbakidze, Tinatin; Mitaishvili, Nino; Janelidze, Nino; Jaiani, Ekaterine; Haley, Bradd J.; Lashkhi, Nino; Huq, Anwar; Rita R Colwell; et al. (Frontiers in Public Health, 2015)

Predictive Time Series Analysis Linking Bengal Cholera with Terrestrial Water Storage Measured from Gravity Recovery and Climate Experiment Sensors - Rita R Colwell; Unnikrishnan, Avinash; Jutla, Antarpreet; Huq, Anwar; Akanda, Ali (The American Journal of Tropical Medicine and Hygiene, 2015)
Outbreaks of diarrheal diseases, including cholera, are related to floods and droughts in regions where water and sanitation infrastructure are inadequate or insufficient. However, availability of data on water scarcity and abundance in transnational basins, are a prerequisite for developing cholera forecasting systems. With more than a decade of terrestrial water storage (TWS) data from the Gravity Recovery and Climate Experiment, conditions favorable for predicting cholera occurrence may now be determined. We explored lead–lag relationships between TWS in the Ganges–Brahmaputra–Meghna basin and endemic cholera in Bangladesh. Since bimodal seasonal peaks in cholera in Bangladesh occur during spring and autumn seasons, two separate logistical models between TWS and disease time series (2002–2010) were developed. TWS representing water availability showed an asymmetrical, strong association with cholera prevalence in the spring (τ = −0.53; P < 0.001) and autumn (τ = 0.45; P < 0.001) up to 6 months in advance. One unit (centimeter of water) decrease in water availability in the basin increased odds of above normal cholera by 24% (confidence interval [CI] = 20–31%; P < 0.05) in the spring, while an increase in regional water by 1 unit, through floods, increased odds of above average cholera in the autumn by 29% (CI = 22–33%; P < 0.05).

Rapid Proliferation of Vibrio parahaemolyticus, Vibrio vulnificus, and Vibrio cholerae during Freshwater Flash Floods in French Mediterranean Coastal Lagoons - Esteves, Kevin; Hervio-Heath, Dominique; Mosser, Thomas; Rodier, Claire; Tournoud, Marie-George; Jumas-Bilak, Estelle; Rita R Colwell; Monfort, Patrick (Applied and Environmental Microbiology, 2015)
Vibrio parahaemolyticus, Vibrio vulnificus, and Vibrio cholerae of the non-O1/non-O139 serotype are present in coastal lagoons of southern France. In these Mediterranean regions, the rivers have long low-flow periods followed by short-duration or flash floods during and after heavy intense rainstorms, particularly at the end of the summer and in autumn. These floods bring large volumes of freshwater into the lagoons, reducing their salinity. Water temperatures recorded during sampling (15 to 24°C) were favorable for the presence and multiplication of vibrios. In autumn 2011, before heavy rainfalls and flash floods, salinities ranged from 31.4 to 36.1‰ and concentrations of V. parahaemolyticus, V. vulnificus, and V. cholerae varied from 0 to 1.5 × 103 most probable number (MPN)/liter, 0.7 to 2.1 × 103 MPN/liter, and 0 to 93 MPN/liter, respectively. Following heavy rainstorms that generated severe flash flooding and heavy discharge of freshwater, salinity decreased, reaching 2.2 to 16.4‰ within 15 days, depending on the site, with a concomitant increase in Vibrio concentration to ca. 104 MPN/liter. The highest concentrations were reached with salinities between 10 and 20‰ for V. parahaemolyticus, 10 and 15‰ for V. vulnificus, and 5 and 12‰ for V. cholerae. Thus, an abrupt decrease in salinity caused by heavy rainfall and major flooding favored growth of human-pathogenic Vibrio spp. and their proliferation in the Languedocian lagoons. Based on these results, it is recommended that temperature and salinity monitoring be done to predict the presence of these Vibrio spp. in shellfish-harvesting areas of the lagoons.

Satellite Based Assessment of Hydroclimatic Conditions Related to Cholera in Zimbabwe - Jutla, Antarpreet; Aldaach, Haidar; Billian, Hannah; Akanda, Ali; Huq, Anwar; Rita R Colwell (PLOS ONE, 2015)
Introduction Cholera, an infectious diarrheal disease, has been shown to be associated with large scale hydroclimatic processes. The sudden and sporadic occurrence of epidemic cholera is linked with high mortality rates, in part, due to uncertainty in timing and location of outbreaks. Improved understanding of the relationship between pathogenic abundance and climatic processes allows prediction of disease outbreak to be an achievable goal. In this study, we show association of large scale hydroclimatic processes with the cholera epidemic in Zimbabwe reported to have begun in Chitungwiza, a city in Mashonaland East province, in August, 2008. Principal Findings Climatic factors in the region were found to be associated with triggering cholera outbreak and are shown to be related to anomalies of temperature and precipitation, validating the hypothesis that poor conditions of sanitation, coupled with elevated temperatures, and followed by heavy rainfall can initiate outbreaks of cholera. Spatial estimation by satellite of precipitation and global gridded air temperature captured sensitivities in hydroclimatic conditions that permitted identification of the location in the region where the disease outbreak began. Discussion Satellite derived hydroclimatic processes can be used to capture environmental conditions related to epidemic cholera, as occurred in Zimbabwe, thereby providing an early warning system. Since cholera cannot be eradicated because the causative agent, Vibrio cholerae, is autochthonous to the aquatic environment, prediction of conditions favorable for its growth and estimation of risks of triggering the disease in a given population can be used to alert responders, potentially decreasing infection and saving lives.

Survey statistics of automated segmentations applied to optical imaging of mammalian cells - Bajcsy, Peter; Cardone, Antonio; Chalfoun, Joe; Halter, Michael; Juba, Derek; Kociolek, Marcin; Majurski, Michael; Peskin, Adele; Simon, Carl; Simon, Mylene; others (BMC bioinformatics, 2015)

Use of Environmental Parameters to Model Pathogenic Vibrios in Chesapeake Bay - Zaitchik, B. F.; Guikema, S. D.; Haley, B. J.; Taviani, E.; Chen, A.; Brown, M.E.; Huq, A.; Rita R Colwell (Journal of Environmental Informatics, 2015)
Although the transportation sector is a major contributor to urban air pollution and global climate change due to its substantial energy consumptions, previous studies for evacuation practices in this sector seldom took environmental consequences into account. As an attempt in event-related evacuation planning under uncertainty, this study proposed an emission-mitigation-oriented fuzzy evacuation management (emoFEM) model. Comprehensive considerations over system efficiency, environmental protection, economic cost and resource availability were incorporated within a general modeling formulation to facilitate evacuation management in a systematic and compromise manner. Vague and ambiguous information embedded within evacuation problems could be quantified and directly communicated into the optimization process, greatly improving conventional tools for evacuation management under uncertainty. The proposed emoFEM model was then applied to a hypothetic but representative case. Useful solutions were generated, which could help identify timely, safe and cost-effective evacuation schemes without significant disturbances over normal municipal traffic and environmental quality. The advantages of emoFEM were further revealed through comparing its solutions with those from its deterministic counterpart.

Vibrio metoecus sp. nov., a close relative of Vibrio cholerae isolated from coastal brackish ponds and clinical specimens - Kirchberger, P. C.; Turnsek, M.; Hunt, D. E.; Haley, B. J.; Rita R Colwell; Polz, M. F.; Tarr, C. L.; Boucher, Y. (INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2014)

Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing - Hasan, Nur A.; Young, Brian A.; Minard-Smith, Angela T.; Saeed, Kelly; Li, Huai; Heizer, Esley M.; McMillan, Nancy J.; Isom, Richard; Abdullah, Abdul Shakur; Bornman, Daniel M.; Faith, Seth A.; Choi, Seon Young; et al. (PLoS ONE, 2014)
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.

Molecular diversity and predictability of Vibrio parahaemolyticus along the Georgian coastal zone of the Black Sea - Haley, Bradd J.; Kokashvili, Tamar; Tskshvediani, Ana; Janelidze, Nino; Mitaishvili, Nino; Grim, Christopher J.; Constantin_de_Magny, Guillaume; Chen, Arlene J.; Taviani, Elisa; Eliashvili, Tamar; Tediashvili, Marina; Whitehouse, Chris A.; et al. (Frontiers in Microbiology, 2014)
Vibrio parahaemolyticus is a leading cause of seafood-related gastroenteritis and is also an autochthonous member of marine and estuarine environments worldwide. One-hundred seventy strains of V. parahaemolyticus were isolated from water and plankton samples collected along the Georgian coast of the Black Sea during 28 months of sample collection. All isolated strains were tested for presence of tlh, trh, and tdh. A subset of strains were serotyped and tested for additional factors and markers of pandemicity. Twenty-six serotypes, five of which are clinically relevant, were identified. Although all 170 isolates were negative for tdh, trh, and the Kanagawa Phenomenon, 7 possessed the GS-PCR sequence and 27 the 850 bp sequence of V. parahaemolyticus pandemic strains. The V. parahaemolyticus population in the Black Sea was estimated to be genomically heterogeneous by rep-PCR and the serodiversity observed did not correlate with rep-PCR genomic diversity. Statistical modeling was used to predict presence of V. parahaemolyticus as a function of water temperature, with strongest concordance observed for Green Cape site samples (Percent of total variance = 70, P < 0.001). Results demonstrate a diverse population of V. parahaemolyticus in the Black Sea, some of which carry pandemic markers, with increased water temperature correlated to an increase in abundance of V. parahaemolyticus.

Occurrence in Mexico, 1998–2008, of Vibrio cholerae CTX + El Tor carrying an additional truncated CTX prophage - Alam, Munirul; Rashed, Shah M; Mannan, Shahnewaj Bin; Islam, Tarequl; Lizarraga-Partida, Marcial L.; Delgado, Gabriela; Morales-Espinosa, Rosario; Mendez, Jose Luis; Navarro, Armando; Watanabe, Haruo; Ohnishi, Makoto; Hasan, Nur A.; et al. (Proceedings of the National Academy of Sciences, 2014)

Argviz: Interactive Visualization of Topic Dynamics in Multi-party Conversations - Nguyen, V A; Hu, Y; Jordan Boyd-Graber (Human Language Technologies: The 2013 Annual Conference of the North American Chapter of the Association for Computational Linguistics, 2013)
Abstract We introduce an efficient, interactive framework—Argviz—for experts to analyze the dynamic topical structure of multi-party conversations. Users inject their needs, expertise, and insights into models via iterative topic refinement. The refined topics feed into a ...

Binary to Bushy: Bayesian Hierarchical Clustering with the Beta Coalescent - Hu, Yuening; Jordan Boyd-Graber; Daume III, Hal; Ying, Z Irene (2013)
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's coalescent---provides a convenient probabilistic model for data represented ...

Combining Crowdsourcing and Google Street View to Identify Street-level Accessibility Problems - Hara, K.; Le, V.; Jon Froehlich (CHI 2013 To Appear, 2013)
Poorly maintained sidewalks, missing curb ramps, and other obstacles pose considerable accessibility challenges; however, there are currently few if any, mechanisms to determine accessible areas of a city a priori. In this paper, we investigate the feasibility of using untrained crowd workers from Amazon Mechanical Turk (turkers) to find, label, and assess sidewalk accessibility problems in Google Street View imagery. We report on two studies: Study 1 examines the feasibility of this labeling task with six dedicated labelers including three wheelchair users; Study 2 investigates the comparative performance of turkers. In all, we collected 13,379 labels and 19,189 verification labels from a total of 402 turkers We show that turkers are capable of determining the presence of an accessibility problem with 81% accuracy. With simple quality control methods, this number increases to 93%. Our work demonstrates a promising new, highly scalable method for acquiring knowledge about sidewalk accessibility.

Detection of Vibrio cholerae in environmental waters including drinking water reservoirs of Azerbaijan - Rashid, Ahmadov; Haley, Bradd J.; Rajabov, Mukhtar; Ahmadova, Sevinj; Gurbanov, Shair; Rita R Colwell; Huq, Anwar (Environmental Microbiology Reports, 2013)

Distribution of Virulence Genes in Clinical and Environmental Vibrio cholerae Strains in Bangladesh - Hasan, Nur A.; Ceccarelli, Daniela; Grim, Christopher J.; Taviani, Elisa; Choi, Jinna; Sadique, Abdus; Alam, Munirul; Siddique, Abul K.; Sack, R. Bradley; Huq, Anwar; Rita R Colwell (Applied and Environmental Microbiology, 2013)
Vibrio cholerae, an environmental organism, is a facultative human pathogen. Here, we report the virulence profiles, comprising 18 genetic markers, of 102 clinical and 692 environmental V. cholerae strains isolated in Bangladesh between March 2004 and January 2006, showing the variability of virulence determinants within the context of public health.

Drug response and genetic properties of Vibrio cholerae associated with endemic cholera in north-eastern Thailand, 2003-2011 - Chomvarin, C.; Johura, F.-T.; Mannan, S. B.; Jumroenjit, W.; Kanoktippornchai, B.; Tangkanakul, W.; Tantisuwichwong, N.; Huttayananont, S.; Watanabe, H.; Hasan, N. A.; Huq, A.; Cravioto, A.; et al. (Journal of Medical Microbiology, 2013)
Cholera, caused by Vibrio cholerae, results in significant morbidity and mortality worldwide, including Thailand. Representative V. cholerae strains associated with endemic cholera (n = 32), including strains (n = 3) from surface water sources, in Khon Kaen, Thailand (2003–2011), were subjected to microbiological, molecular and phylogenetic analyses. According to phenotypic and related genetic data, all tested V. cholerae strains belonged to serogroup O1, biotype El Tor (ET), Inaba (IN) or Ogawa (OG). All of the strains were sensitive to gentamicin and ciprofloxacin, while multidrug-resistant (MDR) strains showing resistance to erythromycin, tetracycline, trimethoprim/sulfamethoxazole and ampicillin were predominant in 2007. V. cholerae strains isolated before and after 2007 were non-MDR. All except six diarrhoeal strains possessed ctxA and ctxB genes and were toxigenic altered ET, confirmed by MAMA-PCR and DNA sequencing. Year-wise data revealed that V. cholerae INET strains isolated between 2003 and 2004, plus one strain isolated in 2007, lacked the RS1 sequence (rstC) and toxin-linked cryptic plasmid (TLC)-specific genetic marker, but possessed CTXCL prophage genes ctxB CL and rstR CL. A sharp genetic transition was noted, namely the majority of V. cholerae strains in 2007 and all in 2010 and 2011 were not repressor genotype rstR CL but instead were rstR ET, and all ctx + strains possessed RS1 and TLC-specific genetic markers. DNA sequencing data revealed that strains isolated since 2007 had a mutation in the tcpA gene at amino acid position 64 (N→S). Four clonal types, mostly of environmental origin, including subtypes, reflected genetic diversity, while distinct signatures were observed for clonally related, altered ET from Thailand, Vietnam and Bangladesh, confirmed by distinct subclustering patterns observed in the PFGE (NotI)-based dendrogram, suggesting that endemic cholera is caused by V. cholerae indigenous to Khon Kaen.

Engaging Actively with Issues in the Responsible Conduct of Science: Lessons from International Efforts Are Relevant for Undergraduate Education in the United States - Clements, John D.; Connell, Nancy D.; Dirks, Clarissa; El-Faham, Mohamed; Hay, Alastair; Heitman, Elizabeth; Stith, James H.; Bond, Enriqueta C.; Rita R Colwell; Anestidou, Lida; Husbands, Jo L.; Labov, Jay B. (CBE—Life Sciences Education, 2013)
Numerous studies are demonstrating that engaging undergraduate students in original research can improve their achievement in the science, technology, engineering, and mathematics (STEM) fields and increase the likelihood that some of them will decide to pursue careers in these disciplines. Associated with this increased prominence of research in the undergraduate curriculum are greater expectations from funders, colleges, and universities that faculty mentors will help those students, along with their graduate students and postdoctoral fellows, develop an understanding and sense of personal and collective obligation for responsible conduct of science (RCS). This Feature describes an ongoing National Research Council (NRC) project and a recent report about educating faculty members in culturally diverse settings (Middle East/North Africa and Asia) to employ active-learning strategies to engage their students and colleagues deeply in issues related to RCS. The NRC report describes the first phase of this project, which took place in Aqaba and Amman, Jordan, in September 2012 and April 2013, respectively. Here we highlight the findings from that report and our subsequent experience with a similar interactive institute in Kuala Lumpur, Malaysia. Our work provides insights and perspectives for faculty members in the United States as they engage undergraduate and graduate students, as well as postdoctoral fellows, to help them better understand the intricacies of and connections among various components of RCS. Further, our experiences can provide insights for those who may wish to establish “train-the-trainer” programs at their home institutions.

Environmental Factors Influencing Epidemic Cholera - Huq, Anwar; Hasan, Nur; Akanda, Ali; Whitcombe, Elizabeth; Rita R Colwell; Haley, Bradd; Alam, Munir; Jutla, Antarpreet; Sack, R. Bradley (The American Journal of Tropical Medicine and Hygiene, 2013)
Cholera outbreak following the earthquake of 2010 in Haiti has reaffirmed that the disease is a major public health threat. Vibrio cholerae is autochthonous to aquatic environment, hence, it cannot be eradicated but hydroclimatology-based prediction and prevention is an achievable goal. Using data from the 1800s, we describe uniqueness in seasonality and mechanism of occurrence of cholera in the epidemic regions of Asia and Latin America. Epidemic regions are located near regional rivers and are characterized by sporadic outbreaks, which are likely to be initiated during episodes of prevailing warm air temperature with low river flows, creating favorable environmental conditions for growth of cholera bacteria. Heavy rainfall, through inundation or breakdown of sanitary infrastructure, accelerates interaction between contaminated water and human activities, resulting in an epidemic. This causal mechanism is markedly different from endemic cholera where tidal intrusion of seawater carrying bacteria from estuary to inland regions, results in outbreaks.

Exploring Early Solutions for Automatically Identifying Inaccessible Sidewalks in the Physical World Using Google Street View - Hara, K; Le, V; Sun, J; Jacobs, D; Jon Froehlich (HCIC 2013, 2013)
Abstract Poorly maintained sidewalks , missing curb ramps, and other obstacles pose considerable accessibility challenges. Although pedestrian-and bicycle-oriented maps and associated routing algorithms continue to improve, there has been a lack of work focusing ...

Improving public transit accessibility for blind riders by crowdsourcing bus stop landmark locations with Google street view - Hara, Kotaro; Azenkot, Shiri; Campbell, Megan; Bennett, Cynthia L; Le, Vicki; Pannella, Sean; Moore, Robert; Minckler, Kelly; Ng, Rochelle H; Jon Froehlich (The 15th International ACM SIGACCESS Conference, 2013)
Abstract Low-vision and blind bus riders often rely on known physical landmarks to help locate and verify bus stop locations (eg., by searching for a shelter, bench, newspaper bin). However, there are currently few, if any, methods to determine this information a priori via ...

An Initial Study of Automatic Curb Ramp Detection with Crowdsourced Verification Using Google Street View Images - Hara, Kotaro; Sun, Jin; Chazan, Jonah; Jacobs, David; Jon Froehlich (First AAAI Conference on Human Computation and Crowdsourcing, 2013)
In our previous research, we examined whether minimally trained crowd workers could find, categorize, and assess sidewalk accessibility problems using Google Street View (GSV) images. This poster paper presents a first step towards combining automated methods ( e.g., machine vision-based curb ramp detectors) in concert with human computation to improve the overall scalability of our approach.

Mind the Theoretical Gap: Interpreting, Using, and Developing Behavioral Theory in HCI Research - Hekler, E. B.; Klasnja,P.; Jon Froehlich; Buman, M. P. (CHI 2013 To Appear, 2013)

A new integrative conjugative element detected in Haitian isolates of Vibrio cholerae non-O1/non-O139 - Ceccarelli, Daniela; Spagnoletti, Matteo; Hasan, Nur A.; Lansing, Stephanie; Huq, Anwar; Rita R Colwell (Research in Microbiology, 2013)
The presence of SXT/R391-related integrating conjugative elements (ICEs) in Vibrio cholerae O1 and non-O1/non-O139 isolated from clinical and environmental samples in Haiti in 2010 was studied. The main finding of this work was the identification of the novel ICEVchHai2 among closely related V. cholerae non-O1/non-O139 clinical strains. The mosaic structure of this element confirms the role of ICEs as efficient recombination systems whereby new genetic material can be acquired and exchanged, according V. cholerae strains new accessory functions.

Quantification of Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae in French Mediterranean coastal lagoons - Cantet, Franck; Hervio-Heath, Dominique; Caro, Audrey; Le Mennec, Cécile; Monteil, Caroline; Quéméré, Catherine; Jolivet-Gougeon, Anne; Rita R Colwell; Monfort, Patrick (Research in Microbiology, 2013)
Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae are human pathogens. Little is known about these Vibrio spp. in the coastal lagoons of France. The purpose of this study was to investigate their incidence in water, shellfish and sediment of three French Mediterranean coastal lagoons using the most probable number-polymerase chain reaction (MPN-PCR). In summer, the total number of V. parahaemolyticus in water, sediment, mussels and clams collected from the three lagoons varied from 1 to >1.1 × 103 MPN/l, 0.09 to 1.1 × 103 MPN/ml, 9 to 210 MPN/g and 1.5 to 2.1 MPN/g, respectively. In winter, all samples except mussels contained V. parahaemolyticus, but at very low concentrations. Pathogenic (tdh- or trh2-positive) V. parahaemolyticus were present in water, sediment and shellfish samples collected from these lagoons. The number of V. vulnificus in water, sediment and shellfish samples ranged from 1 to 1.1 × 103 MPN/l, 0.07 to 110 MPN/ml and 0.04 to 15 MPN/g, respectively, during summer. V. vulnificus was not detected during winter. V. cholerae was rarely detected in water and sediment during summer. In summary, results of this study highlight the finding that the three human pathogenic Vibrio spp. are present in the lagoons and constitute a potential public health hazard.

Segmenting time-lapse phase contrast images of adjacent NIH 3T3 cells. - Chalfoun, J; Kociolek, M; Dima, A; Halter, M; Cardone, Antonio; Peskin, A; Bajcsy, P; Brady, M. (Journal of microscopy, 2013)
We present a new method for segmenting phase contrast images of NIH 3T3 fibroblast cells that is accurate even when cells are physically in contact with each other. The problem of segmentation, when cells are in contact, poses a challenge to the accurate automation of cell counting, tracking and lineage modelling in cell biology. The segmentation method presented in this paper consists of (1) background reconstruction to obtain noise-free foreground pixels and (2) incorporation of biological insight about dividing and nondividing cells into the segmentation process to achieve reliable separation of foreground pixels defined as pixels associated with individual cells. The segmentation results for a time-lapse image stack were compared against 238 manually segmented images (8219 cells) provided by experts, which we consider as reference data. We chose two metrics to measure the accuracy of segmentation: the 'Adjusted Rand Index' which compares similarities at a pixel level between masks resulting from manual and automated segmentation, and the 'Number of Cells per Field' (NCF) which compares the number of cells identified in the field by manual versus automated analysis. Our results show that the automated segmentation compared to manual segmentation has an average adjusted rand index of 0.96 (1 being a perfect match), with a standard deviation of 0.03, and an average difference of the two numbers of cells per field equal to 5.39% with a standard deviation of 4.6%.
Keywords: Animals; Cell Adhesion; Cell Count; Cell Division; Cell Shape; Computational Biology; Fibroblasts; Image Processing, Computer-Assisted; Mice; Microscopy, Phase-Contrast; NIH 3T3 Cells; Reproducibility of results; Sensitivity and Specificity; Time-Lapse Imaging

Species composition of limnetic zooplankton from the southern coastal areas (Mathbaria and Bakerganj) in Bangladesh - Mozumder, Pronob K; Nahar, Samsun; Naser, M Niamul; Alam, Munirul; Huq, Anwar; Sack, R Bradley; Rita R Colwell (Journal of the Asiatic Society of Bangladesh, Science, 2013)
We studied the coastal zooplankton community structure of six waterbodies of Mathbaria and Bakerganj from January 2008 to June 2009. In total 35 zooplankton species were identified under 26 genera under 20 families under 8 orders from Mathbaria. Among them 6 were protozoans, 24 were rotifers, 3 were copepods, 1 was cladocerans and 1 was ostracods. From Bakergonj a total of 42 zooplankton species were identified under 23 genera under 17 Families under 7 orders. Among them 3 were protozoans, 25 were rotifers, 7 were copepods, 6 were cladocerans and 1 was ostracods. Results showed that abundance of rotifera group from both area was higher in Mathbaria (64.86%) and Bakerganj (60.98%) than other groups while abundance of ostracoda of Bakerganj area was lowest.

Specific and Non-Specific Protein Association in Solution: Computation of Solvent Effects and Prediction of First-Encounter Modes for Efficient Configurational Bias Monte Carlo Simulations - Cardone, Antonio; Pant, Harish; Hassan, Sergio A. (The Journal of Physical Chemistry B, 2013)

TIGRFAMs and Genome Properties in 2013. - Haft, Daniel H; Jeremy D Selengut; Richter, Roland A; Harkins, Derek; Basu, Malay K; Beck, Erin (Nucleic Acids Res, 2013)
TIGRFAMs, available online at http://www.jcvi.org/tigrfams is a database of protein family definitions. Each entry features a seed alignment of trusted representative sequences, a hidden Markov model (HMM) built from that alignment, cutoff scores that let automated annotation pipelines decide which proteins are members, and annotations for transfer onto member proteins. Most TIGRFAMs models are designated equivalog, meaning they assign a specific name to proteins conserved in function from a common ancestral sequence. Models describing more functionally heterogeneous families are designated subfamily or domain, and assign less specific but more widely applicable annotations. The Genome Properties database, available at http://www.jcvi.org/genome-properties, specifies how computed evidence, including TIGRFAMs HMM results, should be used to judge whether an enzymatic pathway, a protein complex or another type of molecular subsystem is encoded in a genome. TIGRFAMs and Genome Properties content are developed in concert because subsystems reconstruction for large numbers of genomes guides selection of seed alignment sequences and cutoff values during protein family construction. Both databases specialize heavily in bacterial and archaeal subsystems. At present, 4284 models appear in TIGRFAMs, while 628 systems are described by Genome Properties. Content derives both from subsystem discovery work and from biocuration of the scientific literature.
Keywords: Databases, Protein; Genome, Archaeal; Genome, Bacterial; Genomics; Internet; Markov chains; Molecular Sequence Annotation; Proteins; sequence alignment

A water marker monitored by satellites to predict seasonal endemic cholera - Jutla, Antarpreet; Akanda, Ali Shafqat; Huq, Anwar; Faruque, Abu Syed Golam; Rita R Colwell; Islam, Shafiqul (Remote Sensing Letters, 2013)
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.

An additional step in the transmission of Yersinia pestis? - Easterday, W Ryan; Kausrud, Kyrre L; Star, Bastiaan; Heier, Lise; Haley, Bradd J; Ageyev, Vladimir; Rita R Colwell; Stenseth, Nils Chr (The ISME Journal, 2012)
Plague, caused by the bacterium Yersinia pestis, is a mammalian vector-borne disease, transmitted by fleas that serve as the vector between rodent hosts. For many pathogens, including Y. pestis, there are strong evolutionary pressures that lead to a reduction in ‘useless genes’, with only those retained that reflect function in the specific environment inhabited by the pathogen. Genetic traits critical for survival and transmission between two environments, the rodent and the flea, are conserved in epizootic/epidemic plague strains. However, there are genes that remain conserved for which no function in the flea–rodent cycle has yet been observed, indicating an additional environment may exist in the transmission cycle of plague. Here, we present evidence for highly conserved genes that suggests a role in the persistence of Y. pestis after death of its host. Furthermore, maintenance of these genes points to Y. pestis traversing a post-mortem path between, and possibly within, epizootic periods and offering insight into mechanisms that may allow Y. pestis an alternative route of transmission in the natural environment.

Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. - Haft, Daniel H; Payne, Samuel H; Jeremy D Selengut (J Bacteriol, 2012)
Multiple new prokaryotic C-terminal protein-sorting signals were found that reprise the tripartite architecture shared by LPXTG and PEP-CTERM: motif, TM helix, basic cluster. Defining hidden Markov models were constructed for all. PGF-CTERM occurs in 29 archaeal species, some of which have more than 50 proteins that share the domain. PGF-CTERM proteins include the major cell surface protein in Halobacterium, a glycoprotein with a partially characterized diphytanylglyceryl phosphate linkage near its C terminus. Comparative genomics identifies a distant exosortase homolog, designated archaeosortase A (ArtA), as the likely protein-processing enzyme for PGF-CTERM. Proteomics suggests that the PGF-CTERM region is removed. Additional systems include VPXXXP-CTERM/archeaosortase B in two of the same archaea and PEF-CTERM/archaeosortase C in four others. Bacterial exosortases often fall into subfamilies that partner with very different cohorts of extracellular polymeric substance biosynthesis proteins; several species have multiple systems. Variant systems include the VPDSG-CTERM/exosortase C system unique to certain members of the phylum Verrucomicrobia, VPLPA-CTERM/exosortase D in several alpha- and deltaproteobacterial species, and a dedicated (single-target) VPEID-CTERM/exosortase E system in alphaproteobacteria. Exosortase-related families XrtF in the class Flavobacteria and XrtG in Gram-positive bacteria mark distinctive conserved gene neighborhoods. A picture emerges of an ancient and now well-differentiated superfamily of deeply membrane-embedded protein-processing enzymes. Their target proteins are destined to transit cellular membranes during their biosynthesis, during which most undergo additional posttranslational modifications such as glycosylation.
Keywords: Amino Acid Sequence; Aminoacyltransferases; Archaeal Proteins; Bacterial Proteins; Cell Membrane; Cysteine Endopeptidases; Gene Expression Regulation, Archaeal; Gene Expression Regulation, Bacterial; Gene Expression Regulation, Enzymologic; Molecular Sequence Data; Protein Processing, Post-Translational

Automatic Authentication of Banknotes - Roy,Ankush; Halder,Biswaiit; Garain,Utpal; David Doermann (IEEE Transactions on Information Forensics & Security, 2012)
In this paper, we address the problem of the automatic authentication of paper currency. Indian banknotes are used to show how a system can be developed for discriminating counterfeit notes from genuine notes. Image processing and pattern recognition techniques are designed to carefully analyze embedded security features. Experiments conducted on forensic samples show that a high precision low cost machine can be developed to address this problem. The analysis of current security features’ ability to protect against counterfeiting also suggest topics that should be considered in designing future currency notes.

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics - Ayres,Daniel L; Darling,Aaron; Zwickl,Derrick J; Beerli,Peter; Holder,Mark T; Lewis,Paul O; Huelsenbeck,John P; Ronquist,Fredrik; Swofford,David L; Cummings, Michael P.; Rambaut,Andrew; Suchard,Marc A (Systematic BiologySyst Biol, 2012)
Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.
Keywords: Bayesian phylogenetics; gpu; maximum likelihood; parallel computing

Bioinformatics for the Human Microbiome Project - Gevers, Dirk; Pop, Mihai; Schloss, Patrick D.; Huttenhower, Curtis (PLoS Computational Biology, 2012)

Co-designing an e-health tutorial for older adults - Xie,Bo; Tom Yeh; Walsh,Greg; Watkins,Ivan; Huang,Man (Proceedings of the 2012 iConference, 2012)
Older adults' ability to access and use electronic health information is generally low, requiring innovative approaches for improvement. An integrated e-tutorial overlays instructions onto Websites. The literature suggests integrated e-tutorials are more effective than paper or video-based tutorials for younger people, but little is known about their effectiveness for older adults. This study explores the applicability of an integrated e-health tutorial for older adults. An integrated e-tutorial, the Online Tutorial Overlay Presenter (OnTOP), added an instructional overlay to the NIHSeniorHealth.gov Website. Overlay features were examined in seven participatory design sessions with seven older adults. Participatory design techniques were used to elicit participants' preferences for tutorial features. Three themes emerged: 1) using contextual cues; 2) tailoring to the learner's literacy level; and 3) enhancing interfaces with multimedia cues. These findings improved the design features of OnTOP. They also generated empirical evidence about the effects of multimedia learning among older adults.
Keywords: e-health literacy; health information seeking; integrated e-tutorial; participatory design

Density-Based Multifeature Background Subtraction with Support Vector Machine - Han,Bohyung; Davis, Larry S. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2012)
Background modeling and subtraction is a natural technique for object detection in videos captured by a static camera, and also a critical preprocessing step in various high-level computer vision applications. However, there have not been many studies concerning useful features and binary segmentation algorithms for this problem. We propose a pixelwise background modeling and subtraction technique using multiple features, where generative and discriminative techniques are combined for classification. In our algorithm, color, gradient, and Haar-like features are integrated to handle spatio-temporal variations for each pixel. A pixelwise generative background model is obtained for each feature efficiently and effectively by Kernel Density Approximation (KDA). Background subtraction is performed in a discriminative manner using a Support Vector Machine (SVM) over background likelihood vectors for a set of features. The proposed algorithm is robust to shadow, illumination changes, spatial variations of background. We compare the performance of the algorithm with other density-based methods using several different feature combinations and modeling techniques, both quantitatively and qualitatively.
Keywords: algorithm; density-based; application; illumination; approximation; object; background; camera; support; change; kernel; Computer; density; detection; pixelwise; detection; support; extraction; image; feature; background; generative; Haar-like; likelihood; machine; Haar; machines; vectors; modeling; multifeature; segmentation; segmentation; object; subtraction; technique; discriminative; technique; high-level; techniques; spatial; transforms; cameras; computer; variation; spatio-temporal; variation; static; vector; vector; binary; VISION; vision; feature

Detection, Isolation, and Identification of Vibrio cholerae from the Environment - Huq, Anwar; Haley, Bradd J.; Taviani, Elisa; Chen, Arlene; Hasan, Nur A.; Rita R Colwell (Current Protocols in Microbiology, 2012)
Recent molecular advances in microbiology have greatly improved the detection of bacterial pathogens in the environment. These improvements and a downward trend in the cost of molecular detection methods have contributed to increased frequency of detection of pathogenic microorganisms where traditional culture‐based detection methods have failed. Culture methods also have been greatly improved, and the confluence of the two suites of methods provides a powerful tool for detection, isolation, and characterization of pathogens. While molecular detection provides data on the presence and type of pathogens, culturing methods allow a researcher to preserve the organism of interest for “‐omics” studies, such as genomic, metabolomic, secretomic, and transcriptomic analysis, which are rapidly becoming more affordable. This has yielded a clearer understanding of the ecology and epidemiology of microorganisms that cause disease. In this unit, we present commonly accepted methods for isolation, detection, and characterization of V. cholerae, providing more extensive knowledge of the ecology and epidemiology of this organism. This unit has been fully revised and updated from the earlier version with the latest knowledge and additional information not previously included. Curr. Protoc. Microbiol. 26:6A.5.1‐6A.5.51. © 2012 by John Wiley & Sons, Inc.

Disaggregated water sensing from a single, pressure-based sensor: An extended analysis of HydroSense using staged experiments - Larson,Eric; Jon Froehlich; Campbell,Tim; Haggerty,Conor; Atlas,Les; Fogarty,James; Patel,Shwetak N. (Pervasive and Mobile Computing, 2012)
We present an extended analysis of our previous work on the HydroSense technology, which is a low-cost and easily installed single-point sensor of pressure for automatically disaggregating water usage activities in the home (Froehlich et al., 2009 [53]). We expand upon this work by providing a survey of existing and emerging water disaggregation techniques, a more comprehensive description of the theory of operation behind our approach, and an expanded analysis section that includes hot versus cold water valve usage classification and a comparison between two classification approaches: the template-based matching scheme used in Froehlich et al. (2009) [53] and a new stochastic approach using a Hidden Markov Model. We show that both are successful in identifying valve- and fixture-level water events with greater than 90% accuracies. We conclude with a discussion of the limitations in our experimental methodology and open problems going forward.
Keywords: Activity sensing; H1.2; H5.2; Infrastructure-mediated sensing; Sensors; Water usage

Dynamic changes in motivation in collaborative citizen-science projects - Rotman,Dana; Preece,Jenny; Hammock,Jen; Procita,Kezee; Hansen,Derek; Parr,Cynthia; Lewis,Darcy; Jacobs, David W. (Proceedings of the ACM 2012 conference on Computer Supported Cooperative Work, 2012)
Online citizen science projects engage volunteers in collecting, analyzing, and curating scientific data. Existing projects have demonstrated the value of using volunteers to collect data, but few projects have reached the full collaborative potential of scientists and volunteers. Understanding the shared and unique motivations of these two groups can help designers establish the technical and social infrastructures needed to promote effective partnerships. We present findings from a study of the motivational factors affecting participation in ecological citizen science projects. We show that volunteers are motivated by a complex framework of factors that dynamically change throughout their cycle of work on scientific projects; this motivational framework is strongly affected by personal interests as well as external factors such as attribution and acknowledgment. Identifying the pivotal points of motivational shift and addressing them in the design of citizen-science systems will facilitate improved collaboration between scientists and volunteers.
Keywords: citizen science; Collaboration; crowdsourcing; ecology; motivation; scientists; volunteers

Ecology of Vibrio parahaemolyticus and Vibrio vulnificus in the Coastal and Estuarine Waters of Louisiana, Maryland, Mississippi, and Washington (United States) - Johnson, Crystal N.; Bowers, John C.; Griffitt, Kimberly J.; Molina, Vanessa; Clostio, Rachel W.; Pei, Shaofeng; Laws, Edward; Paranjpye, Rohinee N.; Strom, Mark S.; Chen, Arlene; Hasan, Nur A.; Huq, Anwar; et al. (Applied and Environmental Microbiology, 2012)
Vibrio parahaemolyticus and Vibrio vulnificus, which are native to estuaries globally, are agents of seafood-borne or wound infections, both potentially fatal. Like all vibrios autochthonous to coastal regions, their abundance varies with changes in environmental parameters. Sea surface temperature (SST), sea surface height (SSH), and chlorophyll have been shown to be predictors of zooplankton and thus factors linked to vibrio populations. The contribution of salinity, conductivity, turbidity, and dissolved organic carbon to the incidence and distribution of Vibrio spp. has also been reported. Here, a multicoastal, 21-month study was conducted to determine relationships between environmental parameters and V. parahaemolyticus and V. vulnificus populations in water, oysters, and sediment in three coastal areas of the United States. Because ecologically unique sites were included in the study, it was possible to analyze individual parameters over wide ranges. Molecular methods were used to detect genes for thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) as indicators of V. parahaemolyticus and the hemolysin gene vvhA for V. vulnificus. SST and suspended particulate matter were found to be strong predictors of total and potentially pathogenic V. parahaemolyticus and V. vulnificus. Other predictors included chlorophyll a, salinity, and dissolved organic carbon. For the ecologically unique sites included in the study, SST was confirmed as an effective predictor of annual variation in vibrio abundance, with other parameters explaining a portion of the variation not attributable to SST.

Efficient Tree-Based Topic Modeling - Hu,Yuening; Jordan Boyd-Graber (Association for Computational Linguistics, 2012)
Topic modeling with a tree-based prior has been used for a variety of applications be- cause it can encode correlations between words that traditional topic modeling cannot. How- ever, its expressive power comes at the cost of more complicated inference. We extend the SPARSELDA (Yao et al., 2009) inference scheme for latent Dirichlet allocation (LDA) to tree-based topic models. This sampling scheme computes the exact conditional distri- bution for Gibbs sampling much more quickly than enumerating all possible latent variable assignments. We further improve performance by iteratively refining the sampling distribution only when needed. Experiments show that the proposed techniques dramatically improve the computation time.

Fast track article: Disaggregated water sensing from a single, pressure-based sensor: An extended analysis of HydroSense using staged experiments - Larson,Eric; Jon Froehlich; Campbell,Tim; Haggerty,Conor; Atlas,Les; Fogarty,James; Patel,Shwetak N. (Pervasive Mob. Comput., 2012)
We present an extended analysis of our previous work on the HydroSense technology, which is a low-cost and easily installed single-point sensor of pressure for automatically disaggregating water usage activities in the home (Froehlich et al., 2009 [53]). We expand upon this work by providing a survey of existing and emerging water disaggregation techniques, a more comprehensive description of the theory of operation behind our approach, and an expanded analysis section that includes hot versus cold water valve usage classification and a comparison between two classification approaches: the template-based matching scheme used in Froehlich et al. (2009) [53] and a new stochastic approach using a Hidden Markov Model. We show that both are successful in identifying valve- and fixture-level water events with greater than 90% accuracies. We conclude with a discussion of the limitations in our experimental methodology and open problems going forward.
Keywords: Activity sensing; H1.2; H5.2; Infrastructure-mediated sensing; Sensors; Water usage

A feasibility study of crowdsourcing and google street view to determine sidewalk accessibility - Hara, K.; Le, V.; Jon Froehlich (ACM, 2012)

A framework for human microbiome research - Methé, B.A.; Nelson,K. E; Pop, Mihai; Creasy, H.H.; Giglio, M.G.; Huttenhower, C.; Gevers, D.; Petrosino, J.F.; Abubucker, S.; Badger, J.H. (Nature, 2012)
A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.

Genetic characteristics of drug-resistant Vibrio cholerae O1 causing endemic cholera in Dhaka, 2006-2011 - Rashed, S. M.; Mannan, S. B.; Johura, F.-T.; Islam, M. T.; Sadique, A.; Watanabe, H.; Sack, R. B.; Huq, A.; Rita R Colwell; Cravioto, A.; Alam, M. (Journal of Medical Microbiology, 2012)
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→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 2008–2010 to be the time of transition from ctxB genotype 1 to genotype 7 in V. cholerae ET causing endemic cholera in Dhaka, Bangladesh.

Genomic analysis of ICE Vch Ban8: An atypical genetic element in Vibrio cholerae - Taviani, Elisa; Spagnoletti, Matteo; Ceccarelli, Daniela; Haley, Bradd J.; Hasan, Nur A.; Chen, Arlene; Colombo, Mauro M.; Huq, Anwar; Rita R Colwell (FEBS Letters, 2012)
Genomic islands (GIs) and integrative conjugative elements (ICEs) are major players in bacterial evolution since they encode genes involved in adaptive functions of medical or environmental importance. Here we performed the genomic analysis of ICEVchBan8, an unusual ICE found in the genome of a clinical non‐toxigenic Vibrio cholerae O37 isolate. ICEVchBan8 shares most of its genetic structure with SXT/R391 ICEs. However, this ICE codes for a different integration/excision module is located at a different insertion site, and part of its genetic cargo shows homology to other pathogenicity islands of V. cholerae.

Genomic diversity of 2010 Haitian cholera outbreak strains - Hasan, N. A.; Choi, S. Y.; Eppinger, M.; Clark, P. W.; Chen, A.; Alam, M.; Haley, B. J.; Taviani, E.; Hine, E.; Su, Q.; Tallon, L. J.; Prosper, J. B.; et al. (Proceedings of the National Academy of Sciences, 2012)

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. - Dupont, Chris L; Rusch, Douglas B; Yooseph, Shibu; Lombardo, Mary-Jane; Richter, R Alexander; Valas, Ruben; Novotny, Mark; Yee-Greenbaum, Joyclyn; Jeremy D Selengut; Haft, Dan H; Halpern, Aaron L; Lasken, Roger S; et al. (ISME J, 2012)
Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition.
Keywords: Computational Biology; Gammaproteobacteria; Genome, Bacterial; Genomic Library; metagenomics; Oceans and Seas; Phylogeny; plankton; Rhodopsin; RNA, Ribosomal, 16S; Seawater

Interactive Dynamics for Visual Analysis - Heer,Jeffrey; Shneiderman, Ben (Queue - Micoprocessors, 2012)
A taxonomy of tools that support the fluent and flexible use of visualizations

InterPro in 2011: new developments in the family and domain prediction database. - Hunter, Sarah; Jones, Philip; Mitchell, Alex; Apweiler, Rolf; Attwood, Teresa K; Bateman, Alex; Bernard, Thomas; Binns, David; Bork, Peer; Burge, Sarah; de Castro, Edouard; Coggill, Penny; et al. (Nucleic Acids Res, 2012)
InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces.
Keywords: Databases, Protein; Protein Structure, Tertiary; Proteins; Sequence Analysis, Protein; software; Terminology as Topic; User-Computer Interface

Vibrio Cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico - Alam,Munirul; Islam,M. Tarequl; Rashed,Shah Manzur; Johura,Fatema-Tuz; Bhuiyan,Nurul A.; Delgado,Gabriela; Morales,Rosario; Mendez,Jose Luis; Navarro,Armando; Watanabe,Haruo; Hasan,Nur-A.; Rita R Colwell; et al. (Journal of Clinical Microbiology, 2012)
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'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.

Vibrio cholerae in a historically cholera-free country - Haley, Bradd J.; Chen, Arlene; Grim, Christopher J.; Clark, Philip; Diaz, Celia M; Taviani, Elisa; Hasan, Nur A.; Sancomb, Elizabeth; Elnemr, Wessam M; Islam, Muhammad A.; Huq, Anwar; Rita R Colwell; et al. (Environmental Microbiology Reports, 2012)
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.

Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios - Vezzulli, Luigi; Brettar, Ingrid; Pezzati, Elisabetta; Reid, Philip C; Rita R Colwell; Höfle, Manfred G; Pruzzo, Carla (The ISME Journal, 2012)
The long-term effects of ocean warming on prokaryotic communities are unknown because of lack of historical data. We overcame this gap by applying a retrospective molecular analysis to the bacterial community on formalin-fixed samples from the historical Continuous Plankton Recorder archive, which is one of the longest and most geographically extensive collections of marine biological samples in the world. We showed that during the last half century, ubiquitous marine bacteria of the Vibrio genus, including Vibrio cholerae, increased in dominance within the plankton-associated bacterial community of the North Sea, where an unprecedented increase in bathing infections related to these bacteria was recently reported. Among environmental variables, increased sea surface temperature explained 45% of the variance in Vibrio data, supporting the view that ocean warming is favouring the spread of vibrios and may be the cause of the globally increasing trend in their associated diseases.

Mobile Data Offloading through Opportunistic Communications and Social Participation - Han,Bo; Hui,Pan; Kumar,V. S.A; Marathe,M. V; Shao,Jianhua; Srinivasan, Aravind (Mobile Computing, IEEE Transactions on, 2012)
3G networks are currently overloaded, due to the increasing popularity of various applications for smartphones. Offloading mobile data traffic through opportunistic communications is a promising solution to partially solve this problem, because there is almost no monetary cost for it. We propose to exploit opportunistic communications to facilitate information dissemination in the emerging Mobile Social Networks (MoSoNets) and thus reduce the amount of mobile data traffic. As a case study, we investigate the target-set selection problem for information delivery. In particular, we study how to select the target set with only k users, such that we can minimize the mobile data traffic over cellular networks. We propose three algorithms, called Greedy, Heuristic, and Random, for this problem and evaluate their performance through an extensive trace-driven simulation study. Our simulation results verify the efficiency of these algorithms for both synthetic and real-world mobility traces. For example, the Heuristic algorithm can offload mobile data traffic by up to 73.66 percent for a real-world mobility trace. Moreover, to investigate the feasibility of opportunistic communications for mobile phones, we implement a proof-of-concept prototype, called Opp-off, on Nokia N900 smartphones, which utilizes their Bluetooth interface for device/service discovery and content transfer.
Keywords: 3G mobile communication; 3G networks; Bluetooth interface; cellular networks; cellular radio; content transfer; device/service discovery; graph theory; greedy algorithm; heuristic algorithm; information delivery; information dissemination; mobile data offloading; mobile data traffic; mobile phones; mobile social networks; MoSoNets; Nokia N900 smartphones; Opp-off; opportunistic communications; random algorithm; real-world mobility traces; smart phones; social networking (online); social participation; target-set selection problem; telecommunication network routing; Telecommunication traffic; trace-driven simulation study

Modeling Images using Transformed Indian Buffet Processes - Zhai,Ke; Hu,Yuening; Williamson,Sinead; Jordan Boyd-Graber (International Conference of Machine Learning, 2012)
Latent feature models are attractive for image modeling, since images generally contain mul- tiple objects. However, many latent feature models ignore that objects can appear at dif- ferent locations or require pre-segmentation of images. While the transformed Indian buffet process (tIBP) provides a method for modeling transformation-invariant features in unsegmented binary images, its current form is inappropriate for real images because of its computational cost and modeling assumptions. We combine the tIBP with likelihoods appropriate for real images and develop an efficient inference, using the cross- correlation between images and features, that is theoretically and empirically faster than existing inference techniques. Our method discovers rea- sonable components and achieve effective image reconstruction in natural images.

Occurrence of protozoans & their limnological relationships in some ponds of Mathbaria, Bangladesh - Mozumder,P. K.; Banu,M. A.; Naser,M. N.; Ali,M. S.; Alam,M.; Sack,R. B.; Rita R Colwell; Huq,A. (University Journal of Zoology, Rajshahi University, 2012)

Organizing User Search Histories - Hwang,Heasoo; Lauw,H. W; Getoor, Lise; Ntoulas,A. (Knowledge and Data Engineering, IEEE Transactions on, 2012)
Users are increasingly pursuing complex task-oriented goals on the web, such as making travel arrangements, managing finances, or planning purchases. To this end, they usually break down the tasks into a few codependent steps and issue multiple queries around these steps repeatedly over long periods of time. To better support users in their long-term information quests on the web, search engines keep track of their queries and clicks while searching online. In this paper, we study the problem of organizing a user's historical queries into groups in a dynamic and automated fashion. Automatically identifying query groups is helpful for a number of different search engine components and applications, such as query suggestions, result ranking, query alterations, sessionization, and collaborative search. In our approach, we go beyond approaches that rely on textual similarity or time thresholds, and we propose a more robust approach that leverages search query logs. We experimentally study the performance of different techniques, and showcase their potential, especially when combined together.
Keywords: alteration; query; analysis; user; engines; search; engines; text; goal; textual; group; historical; History; identification; query; information; interfaces; log; sessionization; task-oriented; organization; query; processing; search; query; query; user; quest; query; ranking; search; search; search; long-term; similarity; time; suggestion; result; threshold; user; Web; collaborative

Prototyping scalable digital signal processing systems for radio astronomy using dataflow models - Sane, N.; Ford, J.; Harris, A. I.; Bhattacharyya, Shuvra S. (Radio Science, 2012)
There is a growing trend toward using high-level tools for design and implementation of radio astronomy digital signal processing (DSP) systems. Such tools, for example, those from the Collaboration for Astronomy Signal Processing and Electronics Research (CASPER), are usually platform-specific, and lack high-level, platform-independent, portable, scalable application specifications. This limits the designer's ability to experiment with designs at a high-level of abstraction and early in the development cycle. We address some of these issues using a model-based design approach employing dataflow models. We demonstrate this approach by applying it to the design of a tunable digital downconverter (TDD) used for narrow-bandwidth spectroscopy. Our design is targeted toward an FPGA platform, called theInterconnect Break-out Board (IBOB), that is available from the CASPER. We use the term TDD to refer to a digital downconverter for which the decimation factor and center frequency can be reconfigured without the need for regenerating the hardware code. Such a design is currently not available in the CASPER DSP library. The work presented in this paper focuses on two aspects. First, we introduce and demonstrate a dataflow-based design approach using thedataflow interchange format (DIF) tool for high-level application specification, and we integrate this approach with the CASPER tool flow. Secondly, we explore the trade-off between the flexibility of TDD designs and the low hardware cost of fixed-configuration digital downconverter (FDD) designs that use the available CASPER DSP library. We further explore this trade-off in the context of a two-stage downconversion scheme employing a combination of TDD or FDD designs.
Keywords: dataflow models; digital downconverter; Digital signal processing; model-based design; radio astronomy; rapid prototyping

Quid Pro Quo-tocols: Strengthening Semi-Honest Protocols with Dual Execution - Huang,Y.; Katz, Jonathan; Evans,D. (IEEE Symposium on Security and Privacy, 2012)
Known protocols for secure two-party computa-tion that are designed to provide full security against malicious behavior are significantly less efficient than protocols intended only to thwart semi-honest adversaries. We present a concrete design and implementation of protocols achieving security guarantees that are much stronger than are possible with semi-honest protocols, at minimal extra cost. Specifically, we consider protocols in which a malicious adversary may learn a single (arbitrary) bit of additional information about the honest party’s input. Correctness of the honest party’s output is still guaranteed. Adapting prior work of Mohassel and Franklin, the basic idea in our protocols is to conduct two separate runs of a (specific) semi-honest, garbled-circuit protocol, with the parties swapping roles, followed by an inexpensive secure equality test. We provide a rigorous definition and prove that this protocol leaks no more than one additional bit against a malicious adversary. In addition, we propose some heuristic enhancements to reduce the overall information a cheating adversary learns. Our experiments show that protocols meeting this security level can be implemented at cost very close to that of protocols that only achieve semi-honest security. Our results indicate that this model enables the large-scale, practical applications possible within the semi-honest security model, while providing stronger security guarantees.

Role of GbpA protein, an important virulence-related colonization factor, for Vibrio cholerae's survival in the aquatic environment - Stauder, Monica; Huq, Anwar; Pezzati, Elisabetta; Grim, Christopher J.; Ramoino, Paola; Pane, Luigi; Rita R Colwell; Pruzzo, Carla; Vezzulli, Luigi (Environmental Microbiology Reports, 2012)
Vibrio cholerae N‐acetyl glucosamine‐binding protein A (GbpA) is a chitin binding protein and a virulence factor involved in the colonization of human intestine. We investigated the distribution and genetic variations of gbpA in 488 V. cholerae strains of environmental and clinical origin, belonging to different serogroups and biotypes. We found that the gene is consistently present and highly conserved including an environmental V. cholerae‐related strain of ancestral origin. The gene was also consistently expressed in a number of representative V. cholerae strains cultured in laboratory aquatic microcosms under conditions simulating those found in temperate marine environments. Functional analysis carried out on V. cholerae O1 El Tor N16961 showed that GbpA is not involved in adhesion to inorganic surfaces but promotes interaction with environmental biotic substrates (plankton and bivalve hepatopancreas cells) representing known marine reservoir or host for the bacterium. It is suggested that the ability of GbpA to colonize human intestinal cells most probably originated from its primary function in the aquatic environment.

Role of Shrimp Chitin in the Ecology of Toxigenic Vibrio cholerae and Cholera Transmission - Nahar,Shamsun; Sultana,Marzia; Naser,M. Niamul; Nair,Gopinath B.; Watanabe,Haruo; Ohnishi,Makoto; Yamamoto,Shouji; Endtz,Hubert; Cravioto,Alejandro; Sack,R. Bradley; Hasan,Nur A.; Sadique,Abdus; et al. (Frontiers in Microbiology, 2012)
Seasonal plankton blooms correlate with occurrence of cholera in Bangladesh, although the mechanism of how dormant Vibrio cholerae, enduring interepidemic period in biofilms and plankton, initiates seasonal cholera is not fully understood. In this study, laboratory microcosms prepared with estuarine Mathbaria water (MW) samples supported active growth of toxigenic V. cholerae O1 up to 7 weeks as opposed to 6 months when microcosms were supplemented with dehydrated shrimp chitin chips (CC) as the single source of nutrient. Bacterial counting and detection of wbe and ctxA genes were done employing culture, direct fluorescent antibody (DFA) assay, and multiplex-polymerase chain reaction methods. In MW microcosm, the aqueous phase became clear as the non-culturable cells settled, whereas the aqueous phase of the MW–CC microcosm became turbid from bacterial growth stimulated by chitin. Bacterial chitin degradation and biofilm formation proceeded from an initial steady state to a gradually declining bacterial culturable count. V. cholerae within the microenvironments of chitin and chitin-associated biofilms remained metabolically active even in a high acidic environment without losing either viability or virulence. It is concluded that the abundance of chitin that occurs during blooms plays an important role in the aquatic life cycle of V. cholerae and, ultimately, in the seasonal transmission of cholera.

Secure multi-party computation of boolean circuits with applications to privacy in on-line marketplaces - Choi,S.; Hwang,K.W.; Katz, Jonathan; Malkin,T.; Rubenstein,D. (Topics in Cryptology–CT-RSA 2012, 2012)
Protocols for generic secure multi-party computation (MPC) generally come in two forms: they either represent the function being computed as a boolean circuit, or as an arithmetic circuit over a large field. Either type of protocol can be used for any function, but the choice of which protocol to use can have a significant impact on efficiency. The magnitude of the effect, however, has never been quantified.With this in mind, we implement the MPC protocol of Goldreich, Micali, and Wigderson [13], which uses a boolean representation and is secure against a semi-honest adversary corrupting any number of parties. We then consider applications of secure MPC in on-line marketplaces, where customers select resources advertised by providers and it is desired to ensure privacy to the extent possible. Problems here are more naturally formulated in terms of boolean circuits, and we study the performance of our MPC implementation relative to existing ones that use an arithmetic-circuit representation. Our protocol easily handles tens of customers/providers and thousands of resources, and outperforms existing implementations including FairplayMP [3], VIFF [11], and SEPIA [7].

Structure, function and diversity of the healthy human microbiome - Huttenhower, C.; Gevers, D.; Knight,R.; Abubucker, S.; Badger, J.H.; Chinwalla, A.T.; Creasy, H.H.; Earl, A.M.; Fitzgerald, M.G.; Fulton, R.S.; others (Nature, 2012)
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

Temporal and Spatial Variability in the Distribution of Vibrio vulnificus in the Chesapeake Bay: A Hindcast Study - Banakar,V.; Constantin de Magny,G.; Jacobs,J.; Murtugudde,R.; Huq,A.; J. Wood,R.; Rita R Colwell (EcoHealth, 2012)
Vibrio vulnificus, an estuarine bacterium, is the causative agent of seafood-related gastroenteritis, primary septicemia, and wound infections worldwide. It occurs as part of the normal microflora of coastal marine environments and can be isolated from water, sediment, and oysters. Hindcast prediction was undertaken to determine spatial and temporal variability in the likelihood of occurrence of V. vulnificus in surface waters of the Chesapeake Bay. Hindcast predictions were achieved by forcing a multivariate habitat suitability model with simulated sea surface temperature and salinity in the Bay for the period between 1991 and 2005 and the potential hotspots of occurrence of V. vulnificus in the Chesapeake Bay were identified. The likelihood of occurrence of V. vulnificus during high and low rainfall years was analyzed. From results of the study, it is concluded that hindcast prediction yields an improved understanding of environmental conditions associated with occurrence of V. vulnificus in the Chesapeake Bay.

Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. - Ricaldi, Jessica N; Fouts, Derrick E; Jeremy D Selengut; Harkins, Derek M; Patra, Kailash P; Moreno, Angelo; Lehmann, Jason S; Purushe, Janaki; Sanka, Ravi; Torres, Michael; Webster, Nicholas J; Vinetz, Joseph M; et al. (PLoS Negl Trop Dis, 2012)
The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010(T) and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics.
Keywords: DNA, Bacterial; Evolution, Molecular; Gene Transfer, Horizontal; Genome, Bacterial; Genomic islands; HUMANS; Leptospira; Molecular Sequence Data; Multigene Family; Prophages; Sequence Analysis, DNA; Virulence factors

Ability-based design: Concept, principles and examples - Wobbrock,J.O.; Kane,S.K.; Gajos,K.Z.; Harada,S.; Jon Froehlich (ACM Transactions on Accessible Computing (TACCESS), 2011)

Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1 - Yaklichkin,Sergey Yu; Darnell,Diana K; Pier,Maricela V; Antin,Parker B; Hannenhalli, Sridhar (BMC Evolutionary Biology, 2011)
The forkhead transcription factor gene E1 (FOXE1) plays an important role in regulation of thyroid development, palate formation and hair morphogenesis in mammals. However, avian FOXE1 genes have not been characterized and as such, codon evolution of FOXE1 orthologs in a broader evolutionary context of mammals and birds is not known.

Active progress bars: facilitating the switch to temporary activities - Hurter,Christophe; Girouard,Audrey; Riche,Nathalie; Plaisant, Catherine (Proceedings of the 2011 annual conference extended abstracts on Human factors in computing systems, 2011)
In this paper, we seek to find a better way of effective task management when a progress bar interrupts user's primary activity. We propose to augment progress bars with user controlled functionalities facilitating the switch to temporary activities. We detail a taxonomy of waiting period contexts and possible temporary tasks, then report on 5 participatory design, and a follow-up survey of 96 respondents. Finally we describe an early prototype of active progress bars, and report on initial use.
Keywords: Frustration; participatory design; progress bars; task switching

Analysis of SystemC actor networks for efficient synthesis - Falk, Joachim; Zebelein, Christian; Keinert, Joachim; Haubelt, Christian; Teich, Juergen; Bhattacharyya, Shuvra S. (ACM Trans. Embed. Comput. Syst., 2011)
Applications in the signal processing domain are often modeled by dataflow graphs. Due to heterogeneous complexity requirements, these graphs contain both dynamic and static dataflow actors. In previous work, we presented a generalized clustering approach for these heterogeneous dataflow graphs in the presence of unbounded buffers. This clustering approach allows the application of static scheduling methodologies for static parts of an application during embedded software generation for multiprocessor systems. It systematically exploits the predictability and efficiency of the static dataflow model to obtain latency and throughput improvements. In this article, we present a generalization of this clustering technique to dataflow graphs with bounded buffers, therefore enabling synthesis for embedded systems without dynamic memory allocation. Furthermore, a case study is given to demonstrate the performance benefits of the approach.
Keywords: actor-oriented design; clustering; Dataflow analysis; scheduling

Aquatic Realm and Cholera - Huq,A.; Grim,C. J.; Rita R Colwell (Epidemiological and Molecular Aspects on Cholera, 2011)
Cholera is an ancient disease that can be severe and life threatening. It occurs predominantly in areas of the world where populations lack safe drinking water. Epidemics of cholera are linked with malnutrition, poor sanitation, and conditions resulting from natural disasters such as severe flooding. According to a report published by WHO in 2000 [1], cholera remains a major public health problem and is becoming increasingly important since the number of countries in which cholera is endemic continues to increase. Unfortunately, outbreaks of the disease continue into the twenty-first century with ominous portent in the wake of global climate change [1]. Yet cholera is a preventable disease if people have access to safe drinking water and are properly educated how to protect themselves from the risk of infection with vibrios. Cholera also is an easily treatable disease. Oral rehydration therapy, a solution containing glucose and appropriate salts, has proven to be effective for treatment of most cholera victims [2]. Nevertheless, each year, tens of thousands of people are victims of the disease, bringing this “curse of humankind” to modern civilization. Present understanding of cholera is based on studies conducted over the past three decades and significant new information has been gained concerning environmental factors associated with this disease, especially how to detect the bacterium and where it lives in the natural environment, outside the human gut, and what triggers the annual outbreaks that occur with remarkable regularity. Environmental research on Vibrio cholerae and cholera has provided insights for prediction and prevention of the disease it causes, while the race for effective vaccines against cholera continues.

Article 28 (28 pages)-New Constructive Aspects of the Lovász Local Lemma - Haeupler,B.; Saha,B.; Srinivasan, Aravind (Journal of the ACM-Association for ComputingMachinery, 2011)

AVSS 2011 demo session: A large-scale benchmark dataset for event recognition in surveillance video - Oh,Sangmin; Hoogs,Anthony; Perera,Amitha; Cuntoor,Naresh; Chen,Chia-Chih; Lee,Jong Taek; Mukherjee,Saurajit; Aggarwal, JK; Lee,Hyungtae; Davis, Larry S.; Swears,Eran; Wang,Xiaoyang; et al. (Advanced Video and Signal-Based Surveillance (AVSS), 2011 8th IEEE International Conference on, 2011)
We introduce to the surveillance community the VIRAT Video Dataset[1], which is a new large-scale surveillance video dataset designed to assess the performance of event recognition algorithms in realistic scenes1.

A Case Study in Optimization of Gait and Physical Parameters for a Snake-Inspired Robot Based on a Rectilinear Gait - Hopkins,James K.; Spranklin,Brent W.; Gupta, Satyandra K. (Journal of mechanisms and robotics, 2011)
Physical parameters of the constituent modules and gait parameters affect the overall performance of snake-inspired robots. Hence, a system-level optimization model needs to concurrently optimize the module parameters and the gait. Incorporating a physics-based model of rectilinear gaits in the system-level optimization model is a computationally challenging problem. This paper presents a case study to illustrate how metamodels of the precomputed optimal rectilinear gaits can be utilized to reduce the complexity of the system-level optimization model. An example is presented to illustrate the importance of concurrently optimizing the module parameters and the gait to obtain the optimal performance for a given mission.

Cell cycle dependent TN-C promoter activity determined by live cell imaging. - Halter, Michael; Sisan, Daniel R; Chalfoun, Joe; Stottrup, Benjamin L; Cardone, Antonio; Dima,Alden A.; Tona, Alessandro; Plant,Anne L.; Elliott, John T (Cytometry. Part A : the journal of the International Society for Analytical Cytology, 2011)
The extracellular matrix protein tenascin-C plays a critical role in development, wound healing, and cancer progression, but how it is controlled and how it exerts its physiological responses remain unclear. By quantifying the behavior of live cells with phase contrast and fluorescence microscopy, the dynamic regulation of TN-C promoter activity is examined. We employ an NIH 3T3 cell line stably transfected with the TN-C promoter ligated to the gene sequence for destabilized green fluorescent protein (GFP). Fully automated image analysis routines, validated by comparison with data derived from manual segmentation and tracking of single cells, are used to quantify changes in the cellular GFP in hundreds of individual cells throughout their cell cycle during live cell imaging experiments lasting 62 h. We find that individual cells vary substantially in their expression patterns over the cell cycle, but that on average TN-C promoter activity increases during the last 40% of the cell cycle. We also find that the increase in promoter activity is proportional to the activity earlier in the cell cycle. This work illustrates the application of live cell microscopy and automated image analysis of a promoter-driven GFP reporter cell line to identify subtle gene regulatory mechanisms that are difficult to uncover using population averaged measurements.
Keywords: Animals; cell cycle; Gene Expression Regulation; Green Fluorescent Proteins; Image Processing, Computer-Assisted; Mice; Microscopy, Fluorescence; Microscopy, Phase-Contrast; NIH 3T3 Cells; Promoter Regions, Genetic; Tenascin

Clonal transmission, dual peak, and off-season cholera in Bangladesh - Alam,M.; Islam,A.; Bhuiyan,N. A.; Rahim,N.; Hossain,A.; Khan,G. Y.; Ahmed,D.; Watanabe,H.; Izumiya,H.; Faruque,A. S. G.; Rita R Colwell (Infection Ecology & Epidemiology, 2011)
Vibrio cholerae is an estuarine bacterium associated with a single peak of cholera (March–May) in coastal villages of Bangladesh. For an unknown reason, however, cholera occurs in a unique dual peak (March–May and September–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 (2006–2008) and regional hydroclimatology over three decades (1980–2009) 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.

Complete Fairness in Secure Two-Party Computation - Gordon,S. Dov; Hazay,Carmit; Katz, Jonathan; Lindell,Yehuda (Journal of the ACM, 2011)
In the setting of secure two-party computation, two mutually distrusting parties wish to compute some function of their inputs while preserving, to the extent possible, various security properties such as privacy, correctness, and more. One desirable property is fairness which guarantees, informally, that if one party receives its output, then the other party does too. Cleve [1986] showed that complete fairness cannot be achieved in general without an honest majority. Since then, the accepted folklore has been that nothing non-trivial can be computed with complete fairness in the two-party setting. We demonstrate that this folklore belief is false by showing completely fair protocols for various nontrivial functions in the two-party setting based on standard cryptographic assumptions. We first show feasibility of obtaining complete fairness when computing any function over polynomial-size domains that does not contain an “embedded XOR”; this class of functions includes boolean AND/OR as well as Yao’s “millionaires’ problem”. We also demonstrate feasibility for certain functions that do contain an embedded XOR, though we prove a lower bound showing that any completely fair protocol for such functions must have round complexity super-logarithmic in the security parameter. Our results demonstrate that the question of completely fair secure computation without an honest majority is far from closed.
Keywords: cryptography; fairness; secure computation

Co‐designing contextual tutorials for older adults on searching health information on the internet - Xie,Bo; Tom Yeh; Walsh,Greg; Watkins,Ivan; Huang,Man (Proceedings of the American Society for Information Science and Technology, 2011)
Evidence in the literature suggests an integrated e-tutorial is more effective than a paper- or video-based tutorial among younger people. Yet, relatively little is known about the effectiveness of an integrated e-tutorial on the older population. This study explored the applicability of an integrated e-tutorial to an older population, focusing on the content area of e-health literacy. A specific integrated e- tutorial, the Online Tutorial Overlay Presenter (OnTOP), was used to add an overlay to the NIHSeniorHealth.gov Website. Features of the overlay were examined thoroughly in seven 2-hour-long participatory design sessions with ten older adults. Several participatory design techniques were used to elicit participants' preferences for design features of the OnTOP tutorial. These techniques included drawing on the board, voice recording and integration, and peer instruction. Three major themes emerged: 1) using contextual cues to facilitate learning; 2) tailoring to accommodate the learner's literacy level; and 3) enhancing existing interfaces with multimedia cues. These findings improved the design of OnTOP. They also contribute to the multimedia learning literature, generating empirical evidence about the effects of multimedia learning among the understudied older adult population.

Creating contextual help for GUIs using screenshots - Tom Yeh; Chang,Tsung-Hsiang; Xie,Bo; Walsh,Greg; Watkins,Ivan; Wongsuphasawat,Krist; Huang,Man; Davis, Larry S.; Bederson, Benjamin B. (Proceedings of the 24th annual ACM symposium on User interface software and technology, 2011)
Contextual help is effective for learning how to use GUIs by showing instructions and highlights on the actual interface rather than in a separate viewer. However, end-users and third-party tech support typically cannot create contextual help to assist other users because it requires programming skill and source code access. We present a creation tool for contextual help that allows users to apply common computer skills-taking screenshots and writing simple scripts. We perform pixel analysis on screenshots to make this tool applicable to a wide range of applications and platforms without source code access. We evaluated the tool's usability with three groups of participants: developers, in-structors, and tech support. We further validated the applicability of our tool with 60 real tasks supported by the tech support of a university campus.
Keywords: contextual help; help; pixel analysis

Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization - Korpal, Manav; Ell, Brian J.; Buffa, Francesca M.; Ibrahim, Toni; Blanco, Mario A.; Celià-Terrassa, Toni; Mercatali, Laura; Zia Khan; Goodarzi, Hani; Hua, Yuling; Wei, Yong; Hu, Guohong; et al. (Nature Medicine, 2011)
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–dependent epithelial traits and Sec23a-mediated tumor cell secretome.View full text

Directed Symbolic Execution - Ma,Kin-Keung; Yit Phang,Khoo; Foster, Jeffrey S.; Hicks, Michael W. (Static AnalysisStatic Analysis, 2011)
In this paper, we study the problem of automatically finding program executions that reach a particular target line. This problem arises in many debugging scenarios; for example, a developer may want to confirm that a bug reported by a static analysis tool on a particular line is a true positive. We propose two new directed symbolic execution strategies that aim to solve this problem: shortest-distance symbolic execution (SDSE) uses a distance metric in an interprocedural control flow graph to guide symbolic execution toward a particular target; and call-chain-backward symbolic execution (CCBSE) iteratively runs forward symbolic execution, starting in the function containing the target line, and then jumping backward up the call chain until it finds a feasible path from the start of the program. We also propose a hybrid strategy, Mix-CCBSE, which alternates CCBSE with another (forward) search strategy. We compare these three with several existing strategies from the literature on a suite of six GNU Coreutils programs. We find that SDSE performs extremely well in many cases but may fail badly. CCBSE also performs quite well, but imposes additional overhead that sometimes makes it slower than SDSE. Considering all our benchmarks together, Mix-CCBSE performed best on average, combining to good effect the features of its constituent components.

Dynamic Enforcement of Knowledge-Based Security Policies - Mardziel,P.; Magill,S.; Hicks, Michael W.; Srivatsa,M. (Computer Security Foundations Symposium (CSF), 2011 IEEE 24th, 2011)
This paper explores the idea of knowledge-based security policies, which are used to decide whether to answer queries over secret data based on an estimation of the querier's (possibly increased) knowledge given the results. Limiting knowledge is the goal of existing information release policies that employ mechanisms such as noising, anonymization, and redaction. Knowledge-based policies are more general: they increase flexibility by not fixing the means to restrict information flow. We enforce a knowledge-based policy by explicitly tracking a model of a querier's belief about secret data, represented as a probability distribution, and denying any query that could increase knowledge above a given threshold. We implement query analysis and belief tracking via abstract interpretation using a novel probabilistic polyhedral domain, whose design permits trading off precision with performance while ensuring estimates of a querier's knowledge are sound. Experiments with our implementation show that several useful queries can be handled efficiently, and performance scales far better than would more standard implementations of probabilistic computation based on sampling.
Keywords: abstract interpretation; belief networks; belief tracking; Data models; dynamic enforcement; Facebook; information flow; knowledge based systems; knowledge-based security; knowledge-based security policy; privacy; probabilistic computation; probabilistic logic; probabilistic polyhedral domain; probabilistic polyhedron; probability; query analysis; Security; security of data; semantics; Waste materials

Dynamic inference of static types for ruby - An,Jong-hoon (David); Chaudhuri,Avik; Foster, Jeffrey S.; Hicks, Michael W. (Proceedings of the 38th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages, 2011)
There have been several efforts to bring static type inference to object-oriented dynamic languages such as Ruby, Python, and Perl. In our experience, however, such type inference systems are extremely difficult to develop, because dynamic languages are typically complex, poorly specified, and include features, such as eval and reflection, that are hard to analyze. In this paper, we introduce constraint-based dynamic type inference, a technique that infers static types based on dynamic program executions. In our approach, we wrap each run-time value to associate it with a type variable, and the wrapper generates constraints on this type variable when the wrapped value is used. This technique avoids many of the often overly conservative approximations of static tools, as constraints are generated based on how values are used during actual program runs. Using wrappers is also easy to implement, since we need only write a constraint resolution algorithm and a transformation to introduce the wrappers. The best part is that we can eat our cake, too: our algorithm will infer sound types as long as it observes every path through each method body---note that the number of such paths may be dramatically smaller than the number of paths through the program as a whole. We have developed Rubydust, an implementation of our algorithm for Ruby. Rubydust takes advantage of Ruby's dynamic features to implement wrappers as a language library. We applied Rubydust to a number of small programs and found it to be both easy to use and useful: Rubydust discovered 1 real type error, and all other inferred types were correct and readable.
Keywords: dynamic languages; dynamic type inference; ruby; static types

Efficient and secure threshold-based event validation for vanets - Hsiao, H. C.; Studer, A.; Dubey, R.; Elaine Shi; Perrig, A. (2011)
Determining whether the number of vehicles reporting anevent is above a threshold is an important mechanism for VANETs, because many applications rely on a threshold number of notifications to reach agreement among vehicles, to determine the validity of an event, or to prevent the abuse of emergency alarms. We present the first efficient and se- cure threshold-based event validation protocol for VANETs. Quite counter-intuitively, we found that the z-smallest ap- proach offers the best tradeoff between security and effi- ciency since other approaches perform better for probabilis- tic counting. Analysis and simulation shows that our pro- tocol provides > 99% accuracy despite the presence of at- tackers, collection and distribution of alerts in less than 1 second, and negligible impact on network performance.

Efficient privacy-preserving biometric identification - Huang,Y.; Malka,L.; Evans,D.; Katz, Jonathan (Network and Distributed System Security Symposium, 2011)
We present an efficient matching protocol that can be usedin many privacy-preserving biometric identification systems in the semi-honest setting. Our most general technical con- tribution is a new backtracking protocol that uses the by- product of evaluating a garbled circuit to enable efficient oblivious information retrieval. We also present a more ef- ficient protocol for computing the Euclidean distances of vectors, and optimized circuits for finding the closest match between a point held by one party and a set of points held by another. We evaluate our protocols by implementing a practical privacy-preserving fingerprint matching system.

Efficient Secure Computation with Garbled Circuits - Huang,Y.; Shen,C.; Evans,D.; Katz, Jonathan; Shelat,A. (Information Systems Security, 2011)
Secure two-party computation enables applications in which participants compute the output of a function that depends on their private inputs, without revealing those inputs or relying on any trusted third party. In this paper, we show the potential of building privacy-preserving applications using garbled circuits, a generic technique that until recently was believed to be too inefficient to scale to realistic problems. We present a Java-based framework that uses pipelining and circuit-level optimizations to build efficient and scalable privacy-preserving applications. Although the standard garbled circuit protocol assumes a very week, honest-but-curious adversary, techniques are available for converting such protocols to resist stronger adversaries, including fully malicious adversaries. We summarize approaches to producing malicious-resistant secure computations that reduce the costs of transforming a protocol to be secure against stronger adversaries. In addition, we summarize results on ensuring fairness, the property that either both parties receive the result or neither party does. Several open problems remain, but as theory and pragmatism advance, secure computation is approaching the point where it offers practical solutions for a wide variety of important problems.

Electronic medical records: usability challenges and opportunities - Hochheiser,H.; Shneiderman, Ben (Interactions, 2011)

Epigenomic and RNA structural correlates of polyadenylation - Khaladkar,Mugdha; Smyda,Mark; Hannenhalli, Sridhar (RNA Biology, 2011)
Polyadenylation (poly(A)) of mRNA plays a critical role in regulating gene expression. Identifying the sequence, structural, and epigenomic determinants of poly(A) site usage is an important long term goal. Several cis elements that mediate poly(A) regulation have been identified. Highly used poly(A) sites are also known to have a greater nucleosome occupancy in the immediate downstream. However, a detailed exploration of additional epigenomic and mRNA structural correlates of poly(A) site usage has not been reported. Importantly, functional interaction between sequence, structure, and the epigenome in determining the poly(A) site usage is not known. We show that highly used poly(A) sites are positively associated with an mRNA structure that is energetically more favorable and one that better exposes a critical polyadenylation cis element. In exploring potential interplay between RNA and chromatin structure, we found that a stronger nucleosome occupancy downstream of poly(A) site strongly correlated with (1) a more favorable mRNA structure, and (2) a greater accumulation of RNA Polymerase II (PolII) at the poly(A) site. Further analysis suggested a causal relationship pointing from PolII accumulation to a stable RNA structure. Additionally, we found that distinct patterns of histone modifications characterize poly(A) sites and these epigenetic patterns alone can distinguish true poly(A) sites with ~76% accuracy and also discriminate between high and low usage poly(A) sites with ~74% accuracy. Our results suggest a causative link between chromatin structure and mRNA structure whereby a compacted chromatin downstream of the poly(A) site slows down the elongating transcript, thus facilitating the folding of nascent mRNA in a favorable structure at poly(A) site during transcription. Additionally we report hitherto unknown epigenomic correlates for poly(A) site usage.

Evaluating Dynamic Software Update Safety Using Systematic Testing - Hayden,C.; Smith,E.; Hardisty,E.; Hicks, Michael W.; Foster, Jeffrey S. (IEEE Transactions on Software Engineering, 2011)
Dynamic software updating (DSU) systems patch programs on the fly without incurring downtime. To avoid failures due to the updating process itself, many DSU systems employ timing restrictions. However, timing restrictions are theoretically imperfect, and their practical effectiveness is an open question. This paper presents the first significant empirical evaluation of three popular timing restrictions: activeness safety (AS), which prevents updates to active functions; con-freeness safety (CFS), which only allows modifications to active functions when doing so is provably type-safe; and manual identification of the event-handling loops during which an update may occur. We evaluated these timing restrictions using a series of DSU patches to three programs: OpenSSH, vsftpd, and ngIRCd. We systematically applied updates at each distinct update point reached during execution of a suite of system tests for these programs to determine which updates pass and which fail. We found that all three timing restrictions prevented most failures, but only manual identification allowed none. Further, although CFS and AS allowed many more update points, manual identification still supported updates with minimal delay. Finally, we found that manual identification required the least developer effort. Overall, we conclude that manual identification is most effective.
Keywords: and serviceability; Availability; Computer Systems Organization; Delay; Manuals; Performance of Systems; reliability; Safety; servers; software; software engineering; Test execution; Testing and Debugging

EventGraphs: Charting Collections of Conference Connections - Hansen,D.; Smith,M. A; Shneiderman, Ben (2011 44th Hawaii International Conference on System Sciences (HICSS), 2011)
EventGraphs are social media network diagrams of conversations related to events, such as conferences. Many conferences now communicate a common "hashtag" or keyword to identify messages related to the event. EventGraphs help make sense of the collections of connections that form when people follow, reply or mention one another and a keyword. This paper defines EventGraphs, characterizes different types, and shows how the social media network analysis add-in NodeXL supports their creation and analysis. The structural patterns to look for in EventGraphs are highlighted and design ideas for their improvement are discussed.
Keywords: conference connections; Conferences; Data visualization; EventGraphs; hashtag; measurement; Media; message identification; multimedia computing; NodeXL; Real time systems; social media network diagrams; social networking (online); Twitter

Evolution in Action: Using Active Networking to Evolve Network Support for Mobility - Hicks, Michael W.; Nettles,S.; Seong-Kyu,S.; Shannon,S. (IFIP Lecture Notes in Computer Science (LNCS), 2011)
key early objective of Active Networking (AN) was to support on-the-fly network evolution. Although AN has been used relatively extensively to build application-customized protocols and even whole networking systems, demonstrations of evolution have been limited.

Face Detection - Gopalan,Raghuraman; Schwartz,William R.; Chellapa, Rama; Srivastava,Ankur (Visual Analysis of HumansVisual Analysis of Humans, 2011)
Face detection in still images and videos has been extensively studied over the last two decades. Attributed to the recent proliferation of cameras in consumer applications, research in face detection has gradually transformed into more unconstrained settings, with the goal of achieving performance close to humans. This presents two main challenges: (i) in addition to modeling the facial characteristics, understanding the information portrayed by the surrounding scene is important in resolving visual ambiguities, and (ii) the computational time needed for decision making should be compatible for real-time applications, since detection is primarily a front-end process on which additional knowledge extraction is built upon. This chapter begins with a review of recent work in modeling face-specific information, including appearance-based methods used by sliding window classifiers, concepts from learning and local interest-point descriptors, and then focuses on representing the contextual information shared by faces with the surrounding scene. To provide better understanding of working concepts, we discuss a method for learning the semantic context shared by the face with other human body parts that facilitates reasoning under occlusion, and then present an image representation which efficiently encodes contour information to enable fast detection of faces. We conclude the chapter by discussing some existing challenges.

Faster secure two-party computation using garbled circuits - Huang,Y.; Evans,D.; Katz, Jonathan; Malka,L. (USENIX Security Symposium, 2011)
Secure two-party computation enables two parties toevaluate a function cooperatively without revealing to ei- ther party anything beyond the function’s output. The garbled-circuit technique, a generic approach to secure two-party computation for semi-honest participants, was developed by Yao in the 1980s, but has been viewed as being of limited practical significance due to its in- efficiency. We demonstrate several techniques for im- proving the running time and memory requirements of the garbled-circuit technique, resulting in an implemen- tation of generic secure two-party computation that is significantly faster than any previously reported while also scaling to arbitrarily large circuits. We validate our approach by demonstrating secure computation of cir- cuits with over 109 gates at a rate of roughly 10 µs per garbled gate, and showing order-of-magnitude improve- ments over the best previous privacy-preserving proto- cols for computing Hamming distance, Levenshtein dis- tance, Smith-Waterman genome alignment, and AES.

Gene Coexpression Network Topology of Cardiac Development, Hypertrophy, and FailureClinical Perspective - Dewey,Frederick E; Perez,Marco V; Wheeler,Matthew T; Watt,Clifton; Spin,Joshua; Langfelder,Peter; Horvath,Steve; Hannenhalli, Sridhar; Cappola,Thomas P.; Ashley,Euan A (Circulation: Cardiovascular GeneticsCirc Cardiovasc Genet, 2011)
Background— Network analysis techniques allow a more accurate reflection of underlying systems biology to be realized than traditional unidimensional molecular biology approaches. Using gene coexpression network analysis, we define the gene expression network topology of cardiac hypertrophy and failure and the extent of recapitulation of fetal gene expression programs in failing and hypertrophied adult myocardium.Methods and Results— We assembled all myocardial transcript data in the Gene Expression Omnibus (n=1617). Because hierarchical analysis revealed species had primacy over disease clustering, we focused this analysis on the most complete (murine) dataset (n=478). Using gene coexpression network analysis, we derived functional modules, regulatory mediators, and higher-order topological relationships between genes and identified 50 gene coexpression modules in developing myocardium that were not present in normal adult tissue. We found that known gene expression markers of myocardial adaptation were members of upregulated modules but not hub genes. We identified ZIC2 as a novel transcription factor associated with coexpression modules common to developing and failing myocardium. Of 50 fetal gene coexpression modules, 3 (6%) were reproduced in hypertrophied myocardium and 7 (14%) were reproduced in failing myocardium. One fetal module was common to both failing and hypertrophied myocardium. Conclusions— Network modeling allows systems analysis of cardiovascular development and disease. Although we did not find evidence for a global coordinated program of fetal gene expression in adult myocardial adaptation, our analysis revealed specific gene expression modules active during both development and disease and specific candidates for their regulation.
Keywords: fetal; Gene expression; heart failure; hypertrophy; myocardium

Genome-Wide Survey of Natural Selection on Functional, Structural, and Network Properties of Polymorphic Sites in Saccharomyces Paradoxus - Vishnoi,Anchal; Sethupathy,Praveen; Simola,Daniel; Plotkin,Joshua B.; Hannenhalli, Sridhar (Molecular Biology and EvolutionMol Biol Evol, 2011)
Background. To characterize the genetic basis of phenotypic evolution, numerous studies have identified individual genes that have likely evolved under natural selection. However, phenotypic changes may represent the cumulative effect of similar evolutionary forces acting on functionally related groups of genes. Phylogenetic analyses of divergent yeast species have identified functional groups of genes that have evolved at significantly different rates, suggestive of differential selection on the functional properties. However, due to environmental heterogeneity over long evolutionary timescales, selection operating within a single lineage may be dramatically different, and it is not detectable via interspecific comparisons alone. Moreover, interspecific studies typically quantify selection on protein-coding regions using the Dn/Ds ratio, which cannot be extended easily to study selection on noncoding regions or synonymous sites. The population genetic-based analysis of selection operating within a single lineage ameliorates these limitations. Findings. We investigated selection on several properties associated with genes, promoters, or polymorphic sites, by analyzing the derived allele frequency spectrum of single nucleotide polymorphisms (SNPs) in 28 strains of Saccharomyces paradoxus. We found evidence for significant differential selection between many functionally relevant categories of SNPs, underscoring the utility of function-centric approaches for discovering signatures of natural selection. When comparable, our findings are largely consistent with previous studies based on interspecific comparisons, with one notable exception: our study finds that mutations from an ancient amino acid to a relatively new amino acid are selectively disfavored, whereas interspecific comparisons have found selection against ancient amino acids. Several of our findings have not been addressed through prior interspecific studies: we find that synonymous mutations from preferred to unpreferred codons are selected against and that synonymous SNPs in the linker regions of proteins are relatively less constrained than those within protein domains. Conclusions. We present the first global survey of selection acting on various functional properties in S. paradoxus. We found that selection pressures previously detected over long evolutionary timescales have also shaped the evolution of S. paradoxus. Importantly, we also make novel discoveries untenable via conventional interspecific analyses.
Keywords: derived allele frequency; Evolution; natural selection; yeast

Group-in-a-Box Layout for Multi-faceted Analysis of Communities - Rodrigues,E.M.; Milic-Frayling,N.; Smith,M.; Shneiderman, Ben; Hansen,D. (Privacy, Security, Risk and Trust (PASSAT), 2011 IEEE Third International Conference on and 2011 IEEE Third International Confernece on Social Computing (SocialCom), 2011)
Communities in social networks emerge from interactions among individuals and can be analyzed through a combination of clustering and graph layout algorithms. These approaches result in 2D or 3D visualizations of clustered graphs, with groups of vertices representing individuals that form a community. However, in many instances the vertices have attributes that divide individuals into distinct categories such as gender, profession, geographic location, and similar. It is often important to investigate what categories of individuals comprise each community and vice-versa, how the community structures associate the individuals from the same category. Currently, there are no effective methods for analyzing both the community structure and the category-based partitions of social graphs. We propose Group-In-a-Box (GIB), a meta-layout for clustered graphs that enables multi-faceted analysis of networks. It uses the tree map space filling technique to display each graph cluster or category group within its own box, sized according to the number of vertices therein. GIB optimizes visualization of the network sub-graphs, providing a semantic substrate for category-based and cluster-based partitions of social graphs. We illustrate the application of GIB to multi-faceted analysis of real social networks and discuss desirable properties of GIB using synthetic datasets.
Keywords: Algorithm design and analysis; category based social graph partitions; clustered graphs; clustering; Clustering algorithms; Communities; data visualisation; force-directed; gender; geographic location; graph layout algorithms; graph theory; group-in-a-box; group-in-a-box layout; Image edge detection; Layout; meta-layout; multifaceted community analysis; network subgraph visualization; network visualization; pattern clustering; profession; semantic substrates; Social network services; social networking (online); social networks; treemap space filling technique; Visualization

HCI for peace: from idealism to concrete steps - Hourcade,Juan Pablo; Bullock-Rest,Natasha E.; Friedman,Batya; Nelson,Mark; Shneiderman, Ben; Zaphiris,Panayiotis (PART 2 ———– Proceedings of the 2011 annual conference extended abstracts on Human factors in computing systems, 2011)
This panel will contribute diverse perspectives on the use of computer technology to promote peace and prevent armed conflict. These perspectives include: the use of social media to promote democracy and citizen participation, the role of computers in helping people communicate across division lines in zones of conflict, how persuasive technology can promote peace, and how interaction design can play a role in post-conflict reconciliation.
Keywords: cyprus; peace; persuasive technology; post-conflict reconciliation; social media; value sensitive design; war

Image and Video-Based Biometrics - Patel, Vishal M.; Pillai,Jaishanker K.; Chellapa, Rama (Visual Analysis of HumansVisual Analysis of Humans, 2011)
Biometrics deals with the problem of identifying individuals based on physiological or behavioral characteristics. Since many physical characteristics, such as face, iris, etc., and behavioral characteristics, such as voice, expression, etc., are unique to an individual, biometric analysis offers a reliable and natural solution to the problem of identity verification. In this chapter, we discuss image and video-based biometrics involving face, iris and gait. In particular, we discuss several recent approaches to physiological biometrics based on Sparse Representations and Compressed Sensing. Some of the most compelling challenges and issues that confront research in biometrics are also addressed.

Improved Identification and Visualization of Emergency Department Patient Visits - Hettinger,AZ; Rackoff,A.; Wongsuphasawat,K.; Cheng,H.; Fairbanks,RJ; Plaisant, Catherine; Smith,M. S (Annals of Emergency Medicine, 2011)

Interaction of Vibrio cholerae non-O1/non-O139 with Copepods, Cladocerans and Competing Bacteria in the Large Alkaline Lake Neusiedler See, Austria - Kirschner,A. K. T.; Schauer,S.; Steinberger,B.; Wilhartitz,I.; Grim,C. J.; Huq,A.; Rita R Colwell; Herzig,A.; Sommer,R. (Microbial ecology, 2011)
Vibrio cholerae is a human pathogen and natural inhabitant of aquatic environments. Serogroups O1/O139 have been associated with epidemic cholera, while non-O1/non-O139 serogroups usually cause human disease other than classical cholera. V. cholerae non-O1/non-O139 from the Neusiedler See, a large Central European lake, have caused ear and wound infections, including one case of fatal septicaemia. Recent investigations demonstrated rapid planktonic growth of V. cholerae non-O1/non-O139 and correlation with zooplankton biomass. The aim of this study was to elucidate the interaction of autochthonous V. cholerae with two dominant crustacean zooplankton species in the lake and investigate the influence of the natural bacterial community on this interaction. An existing data set was evaluated for statistical relationships between zooplankton species and V. cholerae and co-culture experiments were performed in the laboratory. A new fluorescence in situ hybridisation protocol was applied for quantification of V. cholerae non-O1/non-O139 cells, which significantly reduced analysis time. The experiments clearly demonstrated a significant relationship of autochthonous V. cholerae non-O1/non-O139 with cladocerans by promoting growth of V. cholerae non-O1/non-O139 in the water and on the surfaces of the cladocerans. In contrast, copepods had a negative effect on the growth of V. cholerae non-O1/non-O139 via competing bacteria from their surfaces. Thus, beside other known factors, biofilm formation by V. cholerae on crustacean zooplankton appears to be zooplankton taxon specific and may be controlled by the natural bacterial community.

Interactive topic modeling - Hu, Yuening; Jordan Boyd-Graber; Satinoff, Brianna (Association for Computational Linguistics, 2011)
Abstract Topic models have been used extensively as a tool for corpus exploration, and a cottage industry has developed to tweak topic models to better encode human intuitions or to better model data. However, creating such extensions requires expertise in machine ...

An iterative algorithm for homology computation on simplicial shapes - Boltcheva,Dobrina; Canino,David; Merino Aceituno,Sara; Léon,Jean-Claude; De Floriani, Leila; Hétroy,Franck (Computer-Aided Design, 2011)
We propose a new iterative algorithm for computing the homology of arbitrary shapes discretized through simplicial complexes. We demonstrate how the simplicial homology of a shape can be effectively expressed in terms of the homology of its sub-components. The proposed algorithm retrieves the complete homological information of an input shape including the Betti numbers, the torsion coefficients and the representative homology generators.To the best of our knowledge, this is the first algorithm based on the constructive Mayer–Vietoris sequence, which relates the homology of a topological space to the homologies of its sub-spaces, i.e. the sub-components of the input shape and their intersections. We demonstrate the validity of our approach through a specific shape decomposition, based only on topological properties, which minimizes the size of the intersections between the sub-components and increases the efficiency of the algorithm.
Keywords: Computational topology; Generators; Mayer–Vietoris sequence; shape decomposition; simplicial complexes; Z -homology

A large-scale benchmark dataset for event recognition in surveillance video - Oh,Sangmin; Hoogs, A.; Perera,A.; Cuntoor, N.; Chen,Chia-Chih; Lee,Jong Taek; Mukherjee,S.; Aggarwal, JK; Lee,Hyungtae; Davis, Larry S.; Swears,E.; Wang,Xioyang; et al. (Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on, 2011)
We introduce a new large-scale video dataset designed to assess the performance of diverse visual event recognition algorithms with a focus on continuous visual event recognition (CVER) in outdoor areas with wide coverage. Previous datasets for action recognition are unrealistic for real-world surveillance because they consist of short clips showing one action by one individual [15, 8]. Datasets have been developed for movies [11] and sports [12], but, these actions and scene conditions do not apply effectively to surveillance videos. Our dataset consists of many outdoor scenes with actions occurring naturally by non-actors in continuously captured videos of the real world. The dataset includes large numbers of instances for 23 event types distributed throughout 29 hours of video. This data is accompanied by detailed annotations which include both moving object tracks and event examples, which will provide solid basis for large-scale evaluation. Additionally, we propose different types of evaluation modes for visual recognition tasks and evaluation metrics along with our preliminary experimental results. We believe that this dataset will stimulate diverse aspects of computer vision research and help us to advance the CVER tasks in the years ahead.
Keywords: algorithm; evaluation; CVER; databases; databases; video; dataset; moving; event; metrics; large-scale; object; recognition; recognition; diverse; recognition; video; scenes; surveillance; surveillance; visual; tasks; computer; tracks; outdoor; video; video; computer; vision; continuous; vision; image; visual

Lightweight monadic programming in ML - Swamy,Nikhil; Guts,Nataliya; Leijen,Daan; Hicks, Michael W. (Proceedings of the 16th ACM SIGPLAN international conference on Functional programming, 2011)
Many useful programming constructions can be expressed as monads. Examples include probabilistic modeling, functional reactive programming, parsing, and information flow tracking, not to mention effectful functionality like state and I/O. In this paper, we present a type-based rewriting algorithm to make programming with arbitrary monads as easy as using ML's built-in support for state and I/O. Developers write programs using monadic values of type m τ as if they were of type τ, and our algorithm inserts the necessary binds, units, and monad-to-monad morphisms so that the program type checks. Our algorithm, based on Jones' qualified types, produces principal types. But principal types are sometimes problematic: the program's semantics could depend on the choice of instantiation when more than one instantiation is valid. In such situations we are able to simplify the types to remove any ambiguity but without adversely affecting typability; thus we can accept strictly more programs. Moreover, we have proved that this simplification is efficient (linear in the number of constraints) and coherent: while our algorithm induces a particular rewriting, all related rewritings will have the same semantics. We have implemented our approach for a core functional language and applied it successfully to simple examples from the domains listed above, which are used as illustrations throughout the paper.
Keywords: coercion; coherence; monad; rewriting; type

LOCKSMITH: Practical static race detection for C - Pratikakis,Polyvios; Foster, Jeffrey S.; Hicks, Michael W. (ACM Trans. Program. Lang. Syst., 2011)
Locksmith is a static analysis tool for automatically detecting data races in C programs. In this article, we describe each of Locksmith's component analyses precisely, and present systematic measurements that isolate interesting trade-offs between precision and efficiency in each analysis. Using a benchmark suite comprising stand-alone applications and Linux device drivers totaling more than 200,000 lines of code, we found that a simple no-worklist strategy yielded the most efficient interprocedural dataflow analysis; that our sharing analysis was able to determine that most locations are thread-local, and therefore need not be protected by locks; that modeling C structs and void pointers precisely is key to both precision and efficiency; and that context sensitivity yields a much more precise analysis, though with decreased scalability. Put together, our results illuminate some of the key engineering challenges in building Locksmith and data race detection analyses in particular, and constraint-based program analyses in general.
Keywords: context sensitivity; contextual effects; correlation inference; Data race; locksmith; race detection; sharing analysis; static analysis

A Longitudinal Study of Pressure Sensing to Infer Real-World Water Usage Events in the Home - Jon Froehlich; Larson,Eric; Saba,Elliot; Campbell,Tim; Atlas,Les; Fogarty,James; Patel,Shwetak (Pervasive ComputingPervasive Computing, 2011)
We present the first longitudinal study of pressure sensing to infer real-world water usage events in the home (e.g., dishwasher, upstairs bathroom sink, downstairs toilet). In order to study the pressure-based approach out in the wild , we deployed a ground truth sensor network for five weeks in three homes and two apartments that directly monitored valve-level water usage by fixtures and appliances . We use this data to, first, demonstrate the practical challenges in constructing water usage activity inference algorithms and, second, to inform the design of a new probabilistic-based classification approach. Inspired by algorithms in speech recognition, our novel Bayesian approach incorporates template matching, a language model, grammar, and prior probabilities. We show that with a single pressure sensor, our probabilistic algorithm can classify real-world water usage at the fixture level with 90% accuracy and at the fixturecategory level with 96% accuracy. With two pressure sensors, these accuracies increase to 94% and 98%. Finally, we show how our new approach can be trained with fewer examples than a strict template-matching approach alone.

A Longitudinal Study of Pressure Sensing to Infer Real-World Water Usage Events in the Home - Jon Froehlich; Larson,Eric; Saba,Elliot; Campbell,Tim; Atlas,Les; Fogarty,James; Patel,Shwetak (Pervasive Computing, 2011)
We present the first longitudinal study of pressure sensing to infer real-world water usage events in the home (e.g., dishwasher, upstairs bathroom sink, downstairs toilet). In order to study the pressure-based approach out in the wild , we deployed a ground truth sensor network for five weeks in three homes and two apartments that directly monitored valve-level water usage by fixtures and appliances . We use this data to, first, demonstrate the practical challenges in constructing water usage activity inference algorithms and, second, to inform the design of a new probabilistic-based classification approach. Inspired by algorithms in speech recognition, our novel Bayesian approach incorporates template matching, a language model, grammar, and prior probabilities. We show that with a single pressure sensor, our probabilistic algorithm can classify real-world water usage at the fixture level with 90% accuracy and at the fixturecategory level with 96% accuracy. With two pressure sensors, these accuracies increase to 94% and 98%. Finally, we show how our new approach can be trained with fewer examples than a strict template-matching approach alone.

Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios - Vezzulli,Luigi; Brettar,Ingrid; Pezzati,Elisabetta; Reid,Philip C.; Rita R Colwell; Höfle,Manfred G.; Pruzzo,Carla (The ISME Journal, 2011)
The long-term effects of ocean warming on prokaryotic communities are unknown because of lack of historical data. We overcame this gap by applying a retrospective molecular analysis to the bacterial community on formalin-fixed samples from the historical Continuous Plankton Recorder archive, which is one of the longest and most geographically extensive collections of marine biological samples in the world. We showed that during the last half century, ubiquitous marine bacteria of the Vibrio genus, including Vibrio cholerae, increased in dominance within the plankton-associated bacterial community of the North Sea, where an unprecedented increase in bathing infections related to these bacteria was recently reported. Among environmental variables, increased sea surface temperature explained 45% of the variance in Vibrio data, supporting the view that ocean warming is favouring the spread of vibrios and may be the cause of the globally increasing trend in their associated diseases.
Keywords: ecophysiology; ecosystems; environmental biotechnology; geomicrobiology; ISME J; microbe interactions; microbial communities; microbial ecology; microbial engineering; microbial epidemiology; microbial genomics; microorganisms

A Low-Overhead Asynchronous Interconnection Network for GALS Chip Multiprocessors - Horak,M.N.; Nowick,S.M.; Carlberg,M.; Vishkin, Uzi (Computer-Aided Design of Integrated Circuits and Systems, IEEE Transactions on, 2011)
A new asynchronous interconnection network is introduced for globally-asynchronous locally-synchronous (GALS) chip multiprocessors. The network eliminates the need for global clock distribution, and can interface multiple synchronous timing domains operating at unrelated clock rates. In particular, two new highly-concurrent asynchronous components are introduced which provide simple routing and arbitration/merge functions. Post-layout simulations in identical commercial 90 nm technology indicate that comparable recent synchronous router nodes have 5.6-10.7 more energy per packet and 2.8-6.4 greater area than the new asynchronous nodes. Under random traffic, the network provides significantly lower latency and identical throughput over the entire operating range of the 800 MHz network and through mid-range traffic rates for the 1.36 GHz network, but with degradation at higher traffic rates. Preliminary evaluations are also presented for a mixed-timing (GALS) network in a shared-memory parallel architecture, running both random traffic and parallel benchmark kernels, as well as directions for further improvement.
Keywords: 1.36; 800; 90; architecture; size; architectures; shared; asynchronous; benchmark; chip; chips; multiprocessor; distribution; distribution; frequency; GALS; GHz; frequency; interconnection; kernel; post-layout; layout; clock; locally-synchronous; memory; MHz; globally-asynchronous; multiple; multiprocessor; clock; multiprocessor; interface; network; mixed-timing; network; network; networks; microprocessor; networks; network; nm; circuit; Parallel; routing; network-on-chip; parallel; routing; parallel; simulation; random; synchronous; systems; timing; low-overhead; traffic; shared-memory

Medication Reconciliation: Work Domain Ontology, Prototype Development, and a Predictive Model - Markowitz,Eliz; Bernstam,Elmer V.; Herskovic,Jorge; Zhang,Jiajie; Shneiderman, Ben; Plaisant, Catherine; Johnson,Todd R. (AMIA Annual Symposium ProceedingsAMIA Annu Symp Proc, 2011)
Medication errors can result from administration inaccuracies at any point of care and are a major cause for concern. To develop a successful Medication Reconciliation (MR) tool, we believe it necessary to build a Work Domain Ontology (WDO) for the MR process. A WDO defines the explicit, abstract, implementation-independent description of the task by separating the task from work context, application technology, and cognitive architecture. We developed a prototype based upon the WDO and designed to adhere to standard principles of interface design. The prototype was compared to Legacy Health System’s and Pre-Admission Medication List Builder MR tools via a Keystroke-Level Model analysis for three MR tasks. The analysis found the prototype requires the fewest mental operations, completes tasks in the fewest steps, and completes tasks in the least amount of time. Accordingly, we believe that developing a MR tool, based upon the WDO and user interface guidelines, improves user efficiency and reduces cognitive load.

Metagenomic 16S rDNA Targeted PCR-DGGE in Determining Bacterial Diversity in Aquatic Ecosystem - Hasan,Nur A.; Chowdhury,W Bari; Rahim,Niaz; Sultana,Marzia; Shabnam,S Antara; Mai,Volker; Ali,Afsar; Morris,Glen J; Sack,R. Bradley; Huq,Anwar; Rita R Colwell; Endtz,Hubert Ph; et al. (Bangladesh Journal of Microbiology, 2011)
Bacterial numbers in surface water samples, collected randomly from six different water bodies, were estimated by acridine orange direct counting (AODC) and conventional culture-based heterotrophic plate counting (HPC). Bacterial genomic DNA was prepared from water samples by employing methods used for stool samples, including the population dynamics, were determined by primer extension of the 16S rDNA (V6/V8 region) using polymerase chain reaction (PCR), followed by denaturing gradient gel electrophoresis (DGGE), a metagenomic tool that is capable of separating unrelated DNAs based on the differences in their sequences and GC contents. The bacterial numbers in water samples ranged from 103 – 106 CFU/ mL for HPC and 104 – 107 cells/ mL for AODC, showing that a great majority of bacteria prevail as uncultivable which do not respond to culture methods that are used widely for tracking bacterial pathogens. The acridine orange-stained bacteria varied in sizes and shapes, and appeared either as planktonic (solitary) cells or as clusters of biofilms, showing the presence of diverse community under the epifluorescence microscope. The DGGE of the ca. 457 bp amplicons, as confirmed by agarose gel electrophoresis, produced bands that ranged in intensities and numbers from 18 to 31, with each band possibly indicating the presence of one or more closely related bacterial species. The enrichment of pathogenic bacteria in the aquatic ecosystem is known to precede the seasonal diarrhoeal outbreaks; therefore, bacterial community dynamics determined by Metagenomic 16S PCR-DGGE during pre-epidemic enrichment appears promising in predicting the upcoming diarrheal outbreaks.

Modeling Multiresolution 3D Scalar Fields through Regular Simplex Bisection - Weiss,K.; De Floriani, Leila; Hagen,H. (Scientific Visualization: Interactions, Features, Metaphors, 2011)
We review modeling techniques for multiresolution three-dimensional scalar fields based on a dis-cretization of the field domain into nested tetrahedral meshes generated through regular simplex bisection. Such meshes are described through hierarchical data structures and their representa- tion is characterized by the modeling primitive used. The primary conceptual distinction among the different approaches proposed in the literature is whether they treat tetrahedra or clusters of tetrahedra, called diamonds, as the modeling primitive. We first focus on representations for the modeling primitive and for nested meshes. Next, we survey the applications of these meshes to modeling multiresolution 3D scalar fields, with an emphasis on interactive visualization. We also consider the relationship of such meshes to octrees. Finally, we discuss directions for further research

Motivation for Participation in Online Neighborhood Watch Communities: An Empirical Study Involving Invitation Letters - Violi,N.; Shneiderman, Ben; Hanson,A.; Rey,P. J (Privacy, Security, Risk and Trust (PASSAT), 2011 IEEE Third International Conference on and 2011 IEEE Third International Confernece on Social Computing (SocialCom), 2011)
This paper presents a three-part experiment designed to investigate the motivations of users of a community safety and neighborhood watch social networking website. The experiment centers around an intervention into the invitation system that current users employ to invite nonmembers to join the site, and involves several versions of an invitation email which differ by expressing one of four possible motivations for using such a site. The research presented investigates how potential users' choice of whether or not to join the site is affected by the use case presented by the invitation. It also includes an investigation of the motivations of current users of the site, as reported in an online survey. The experiment yielded no significant difference in responses to the emails. Overall, invitations that included a specific motivation slightly outperformed those which did not, but not to a statistically significant degree. We conclude that although users have specific motivations for using the site, as reported in the survey, attempting to increase response rates to invitation emails by suggesting use cases of the site is surprisingly unlikely to be successful.
Keywords: Art; Communities; community safety; Electronic mail; Interviews; invitation email; invitations; motivation; neighborhood watch; Online communities; online neighborhood watch communities; online survey; participation; Safety; Security; social media; Social network services; social networking (online); social networking Website

MultiOtter: Multiprocess Symbolic Execution - Turpie,J.; Reisner,E.; Foster, Jeffrey S.; Hicks, Michael W. (Technical Reports of the Computer Science Department, 2011)
Symbolic execution can be an effective technique for exploring large numbers of program paths, but it has generally been applied to programs running in isolation, whose inputs are files or command-line arguments. Programs that take inputs from other programs---servers, for example---have been beyond the reach of symbolic execution. To address this, we developed a multiprocess symbolic executor called MultiOtter, along with an implementation of many of the POSIX functions, such as socket and select, that interactive programs usually rely on. However, that is just a first step. Next, we must determine what symbolic inputs to feed to an interactive program to make multiprocess symbolic execution effective. Providing completely unconstrained symbolic values causes symbolic execution to spend too much time exploring uninteresting paths, such as paths to handle invalid inputs. MultiOtter allows us to generate inputs that conform to a context-free grammar, similar to previous work, but it also enables new input generation capabilities because we can now run arbitrary programs concurrently with the program being studied. As examples, we symbolically executed a key-value store server, redis, and an FTP server, vsftpd, each with a variety of inputs, including symbolic versions of tests from redis's test suite and wget as a client for vsftpd. We report the coverage provided by symbolic execution with various forms of symbolic input, showing that different testing goals require different degrees of symbolic inputs.

Multithreaded Simulation for Synchronous Dataflow Graphs - Chia-Jui Hsu; Pino, José Luis; Bhattacharyya, Shuvra S. (ACM Trans. Des. Autom. Electron. Syst., 2011)
For system simulation, Synchronous DataFlow (SDF) has been widely used as a core model of computation in design tools for digital communication and signal processing systems. The traditional approach for simulating SDF graphs is to compute and execute static schedules in single-processor desktop environments. Nowadays, however, multicore processors are increasingly popular desktop platforms for their potential performance improvements through thread-level parallelism. Without novel scheduling and simulation techniques that explicitly explore thread-level parallelism for executing SDF graphs, current design tools gain only minimal performance improvements on multicore platforms. In this article, we present a new multithreaded simulation scheduler, called MSS, to provide simulation runtime speedup for executing SDF graphs on multicore processors. MSS strategically integrates graph clustering, intracluster scheduling, actor vectorization, and intercluster buffering techniques to construct InterThread Communication (ITC) graphs at compile-time. MSS then applies efficient synchronization and dynamic scheduling techniques at runtime for executing ITC graphs in multithreaded environments. We have implemented MSS in the Advanced Design System (ADS) from Agilent Technologies. On an Intel dual-core, hyper-threading (4 processing units) processor, our results from this implementation demonstrate up to 3.5 times speedup in simulating modern wireless communication systems (e.g., WCDMA3G, CDMA 2000, WiMax, EDGE, and Digital TV).
Keywords: multithreaded simulation; scheduling; Synchronous dataflow

Occurrence of Vibrio cholerae in Municipal and Natural Waters and Incidence of Cholera in Azerbaijan - Gurbanov, Shair; Akhmadov, Rashid; Shamkhalova, Gulnara; Akhmadova, Sevinj; Haley, Bradd J.; Rita R Colwell; Huq, Anwar (EcoHealth, 2011)
Cholera, a waterborne disease caused by Vibrio cholerae, is an autochthonous member of the aquatic environment and predominantly reported from developing countries. Technical reports and proceedings were reviewed to determine the relationship between occurrence of V. cholerae in natural waters, including sources of municipal water, and cases of cholera in Azerbaijan. Water samples collected from different environmental sources from 1970 to 1998 were tested for V. cholerae and 0.73% (864/117,893) were positive. The results showed that in April of each year, when the air temperature rose by approximately 5°C, V. cholerae could be isolated. With each increase in air temperature, 6–8 weeks after, impact on cases of cholera was recorded. The incidence of cholera peaked when the air temperature reached >25°C during the month of September. It is concluded that a distinct seasonality in cholera incidence exists in Azerbaijan, with increased occurrence during warmer months.

Odd Leaf Out: Improving Visual Recognition with Games - Hansen,D. L; Jacobs, David W.; Lewis,D.; Biswas,A.; Preece,J.; Rotman,D.; Stevens,E. (Privacy, security, risk and trust (passat), 2011 ieee third international conference on and 2011 ieee third international conference on social computing (socialcom), 2011)
A growing number of projects are solving complex computational and scientific tasks by soliciting human feedback through games. Many games with a purpose focus on generating textual tags for images. In contrast, we introduce a new game, Odd Leaf Out, which provides players with an enjoyable and educational game that serves the purpose of identifying misclassification errors in a large database of labeled leaf images. The game uses a novel mechanism to solicit useful information from players' incorrect answers. A study of 165 players showed that game data can be used to identify mislabeled leaves much more quickly than would have been possible using a computer vision algorithm alone. Domain novices and experts were equally good at identifying mislabeled images, although domain experts enjoyed the game more. We discuss the successes and challenges of this new game, which can be applied to other domains with labeled image datasets.
Keywords: algorithm; educational; classification; object; computational; computing; botany; computer; datasets; misclassification; errors; scientific; feedback; labeled; game; human; games; computer; games; image; image; leaf; Odd; Out; complex; recognition; recognition; biology; tags; visual; tasks; computer; tasks; textual; VISION

Private Set Intersection: Are Garbled Circuits Better than Custom Protocols? - Huang,Y.; Evans,D.; Katz, Jonathan (19th Network and Distributed Security Symposium, 2011)
Cryptographic protocols for Private Set Intersection (PSI)are the basis for many important privacy-preserving ap- plications. Over the past few years, intensive research has been devoted to designing custom protocols for PSI based on homomorphic encryption and other public-key tech- niques, apparently due to the belief that solutions using generic approaches would be impractical. This paper ex- plores the validity of that belief. We develop three classes of protocols targeted to different set sizes and domains, all based on Yao’s generic garbled-circuit method. We then compare the performance of our protocols to the fastest custom PSI protocols in the literature. Our results show that a careful application of garbled circuits leads to solu- tions that can run on million-element sets on typical desk- tops, and that can be competitive with the fastest custom protocols. Moreover, generic protocols like ours can be used directly for performing more complex secure com- putations, something we demonstrate by adding a simple information-auditing mechanism to our PSI protocols.

ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. - Basu, Malay K; Jeremy D Selengut; Haft, Daniel H (BMC Bioinformatics, 2011)
BACKGROUND: Phylogenetic profiling is a technique of scoring co-occurrence between a protein family and some other trait, usually another protein family, across a set of taxonomic groups. In spite of several refinements in recent years, the technique still invites significant improvement. To be its most effective, a phylogenetic profiling algorithm must be able to examine co-occurrences among protein families whose boundaries are uncertain within large homologous protein superfamilies. RESULTS: Partial Phylogenetic Profiling (PPP) is an iterative algorithm that scores a given taxonomic profile against the taxonomic distribution of families for all proteins in a genome. The method works through optimizing the boundary of each protein family, rather than by relying on prebuilt protein families or fixed sequence similarity thresholds. Double Partial Phylogenetic Profiling (DPPP) is a related procedure that begins with a single sequence and searches for optimal granularities for its surrounding protein family in order to generate the best query profiles for PPP. We present ProPhylo, a high-performance software package for phylogenetic profiling studies through creating individually optimized protein family boundaries. ProPhylo provides precomputed databases for immediate use and tools for manipulating the taxonomic profiles used as queries. CONCLUSION: ProPhylo results show universal markers of methanogenesis, a new DNA phosphorothioation-dependent restriction enzyme, and efficacy in guiding protein family construction. The software and the associated databases are freely available under the open source Perl Artistic License from ftp://ftp.jcvi.org/pub/data/ppp/.
Keywords: algorithms; Archaea; Archaeal Proteins; DNA; Methane; Phylogeny; software

Reducing Missed Laboratory Results: Defining Temporal Responsibility, Generating User Interfaces for Test Process Tracking, and Retrospective Analyses to Identify Problems - Tarkan,Sureyya; Plaisant, Catherine; Shneiderman, Ben; Hettinger,A. Zachary (AMIA Annual Symposium ProceedingsAMIA Annu Symp Proc, 2011)
Researchers have conducted numerous case studies reporting the details on how laboratory test results of patients were missed by the ordering medical providers. Given the importance of timely test results in an outpatient setting, there is limited discussion of electronic versions of test result management tools to help clinicians and medical staff with this complex process. This paper presents three ideas to reduce missed results with a system that facilitates tracking laboratory tests from order to completion as well as during follow-up: (1) define a workflow management model that clarifies responsible agents and associated time frame, (2) generate a user interface for tracking that could eventually be integrated into current electronic health record (EHR) systems, (3) help identify common problems in past orders through retrospective analyses.

Regulation of Lung Endoderm Progenitor Cell Behavior by miR302/367 - Tian,Ying; Zhang,Yuzhen; Hurd,Laura; Hannenhalli, Sridhar; Liu,Feiyan; Lu,Min Min; Morrisey,Edward E. (DevelopmentDevelopment, 2011)
The temporal and spatial control of organ-specific endoderm progenitor development is poorly understood. miRNAs affect cell function by regulating programmatic changes in protein expression levels. We show that the miR302/367 cluster is a target of the transcription factor Gata6 in mouse lung endoderm and regulates multiple aspects of early lung endoderm progenitor development. miR302/367 is expressed at early stages of lung development, but its levels decline rapidly as development proceeds. Gain- and loss-of-function studies show that altering miR302/367 expression disrupts the balance of lung endoderm progenitor proliferation and differentiation, as well as apical-basal polarity. Increased miR302/367 expression results in the formation of an undifferentiated multi-layered lung endoderm, whereas loss of miR302/367 activity results in decreased proliferation and enhanced lung endoderm differentiation. miR302/367 coordinates the balance between proliferation and differentiation, in part, through direct regulation of Rbl2 and Cdkn1a, whereas apical-basal polarity is controlled by regulation of Tiam1 and Lis1. Thus, miR302/367 directs lung endoderm development by coordinating multiple aspects of progenitor cell behavior, including proliferation, differentiation and apical-basal polarity.
Keywords: Lung; MicroRNA; mouse; Progenitor

Research Directions in Data Wrangling: Visualizations and Transformations for Usable and Credible Data - Kandel,Sean; Heer,Jeffrey; Plaisant, Catherine; Kennedy,Jessie; Van Ham,Frank; Riche,Nathalie Henry; Weaver,Chris; Lee,Bongshin; Brodbeck,Dominique; Buono,Paolo (Information VisualizationInformation Visualization, 2011)
In spite of advances in technologies for working with data, analysts still spend an inordinate amount of time diagnosing data quality issues and manipulating data into a usable form. This process of ‘data wrangling’ often constitutes the most tedious and time-consuming aspect of analysis. Though data cleaning and integration arelongstanding issues in the database community, relatively little research has explored how interactive visualization can advance the state of the art. In this article, we review the challenges and opportunities associated with addressing data quality issues. We argue that analysts might more effectively wrangle data through new interactive systems that integrate data verification, transformation, and visualization. We identify a number of outstanding research questions, including how appropriate visual encodings can facilitate apprehension of missing data, discrepant values, and uncertainty; how interactive visualizations might facilitate data transform specification; and how recorded provenance and social interaction might enable wider reuse, verification, and modification of data transformations.
Keywords: data cleaning; data quality; data transformation; Uncertainty; Visualization

Role of Zooplankton Diversity in Vibrio Cholerae Population Dynamics and in the Incidence of Cholera in the Bangladesh Sundarbans - De Magny,Guillaume Constantin; Mozumder,Pronob K.; Grim,Christopher J.; Hasan,Nur A.; Naser,M. Niamul; Alam,Munirul; Sack,R. Bradley; Huq,Anwar; Rita R Colwell (Applied and Environmental Microbiology, 2011)
Vibrio cholerae, a bacterium autochthonous to the aquatic environment, is the causative agent of cholera, a severe watery, life-threatening diarrheal disease occurring predominantly in developing countries. V. cholerae, including both serogroups O1 and O139, is found in association with crustacean zooplankton, mainly copepods, and notably in ponds, rivers, and estuarine systems globally. The incidence of cholera and occurrence of pathogenic V. cholerae strains with zooplankton were studied in two areas of Bangladesh: Bakerganj and Mathbaria. Chitinous zooplankton communities of several bodies of water were analyzed in order to understand the interaction of the zooplankton population composition with the population dynamics of pathogenic V. cholerae and incidence of cholera. Two dominant zooplankton groups were found to be consistently associated with detection of V. cholerae and/or occurrence of cholera cases, namely, rotifers and cladocerans, in addition to copepods. Local differences indicate there are subtle ecological factors that can influence interactions between V. cholerae, its plankton hosts, and the incidence of cholera.

Scalable fast multipole methods on distributed heterogeneous architectures - Hu,Qi; Gumerov, Nail A.; Duraiswami, Ramani (High Performance Computing, Networking, Storage and Analysis (SC), 2011 International Conference for, 2011)
We fundamentally reconsider implementation of the Fast Multipole Method (FMM) on a computing node with a heterogeneous CPU-GPU architecture with multicore CPU(s) and one or more GPU accelerators, as well as on an interconnected cluster of such nodes. The FMM is a divide- and-conquer algorithm that performs a fast N-body sum using a spatial decomposition and is often used in a time- stepping or iterative loop. Using the observation that the local summation and the analysis-based translation parts of the FMM are independent, we map these respectively to the GPUs and CPUs. Careful analysis of the FMM is performed to distribute work optimally between the multicore CPUs and the GPU accelerators. We first develop a single node version where the CPU part is parallelized using OpenMP and the GPU version via CUDA. New parallel algorithms for creating FMM data structures are presented together with load balancing strategies for the single node and distributed multiple-node versions. Our implementation can perform the N-body sum for 128M particles on 16 nodes in 4.23 seconds, a performance not achieved by others in the literature on such clusters.
Keywords: accelerators; OpenMP; analysis; algorithm; iterative; and; architecture; CUDA; FMM; architectures; architectures; divide-and-conquer; based; conquer; CPU-GPU; CPU; scalable; data; fast; heterogeneous; loop; data; loop; multicore; methods; graphics; methods; multiprocessing; methods; time; multipole; parts; distributed; PROCESSING; stepping; structures; divide; structures; GPU; systems; parallel; translation; units; iterative

State transfer for clear and efficient runtime updates - Hayden,C.M.; Smith,E. K; Hicks, Michael W.; Foster, Jeffrey S. (2011 IEEE 27th International Conference on Data Engineering Workshops (ICDEW), 2011)
Dynamic software updating (DSU), the practice of updating software while it executes, is a lively area of research. The DSU approach most prominent in both commercial and research systems is in-place updating, in which patches containing program modifications are loaded into a running process. However, in-place updating suffers from several problems: it requires complex tool support, it may adversely affect the performance of normal execution, it requires challenging reasoning to understand the behavior of an updated program, and it requires extra effort to modify program state to be compatible with an update. This paper presents preliminary work investigating the potential for state transfer updating to address these problems. State transfer updates work by launching a new process running the updated program version and transferring program state from the running process to the updated version. In this paper, we describe the use and implementation of Ekiden, a new state transfer updating library for C/C++ programs. Ekiden seeks to redress the difficulties of in-place updating, and we report on our experience updating VSFTPD using Ekiden. This initial experience suggests that state transfer provides the availability benefits of in-place DSU approaches while addressing many of their shortcomings.
Keywords: C++ language; C++ program; Cognition; complex tool support; dynamic software updating; efficient runtime update; in-place DSU approach; Libraries; Operating systems; program modification; Program processors; program transfer; program version; Runtime; servers; software libraries; Software maintenance; state transfer update; Steady-state; updating library; VSFTPD

Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus - Kimes,Nikole E.; Grim,Christopher J.; Johnson,Wesley R.; Hasan,Nur A.; Tall,Ben D.; Kothary,Mahendra H.; Kiss,Hajnalka; Munk,A. Christine; Tapia,Roxanne; Green,Lance; Detter,Chris; Bruce,David C.; et al. (The ISME Journal, 2011)
Sea surface temperatures (SST) are rising because of global climate change. As a result, pathogenic Vibrio species that infect humans and marine organisms during warmer summer months are of growing concern. Coral reefs, in particular, are already experiencing unprecedented degradation worldwide due in part to infectious disease outbreaks and bleaching episodes that are exacerbated by increasing SST. For example, Vibrio coralliilyticus, a globally distributed bacterium associated with multiple coral diseases, infects corals at temperatures above 27 °C. The mechanisms underlying this temperature-dependent pathogenicity, however, are unknown. In this study, we identify potential virulence mechanisms using whole genome sequencing of V. coralliilyticus ATCC (American Type Culture Collection) BAA-450. Furthermore, we demonstrate direct temperature regulation of numerous virulence factors using proteomic analysis and bioassays. Virulence factors involved in motility, host degradation, secretion, antimicrobial resistance and transcriptional regulation are upregulated at the higher virulent temperature of 27 °C, concurrent with phenotypic changes in motility, antibiotic resistance, hemolysis, cytotoxicity and bioluminescence. These results provide evidence that temperature regulates multiple virulence mechanisms in V. coralliilyticus, independent of abundance. The ecological and biological significance of this temperature-dependent virulence response is reinforced by climate change models that predict tropical SST to consistently exceed 27 °C during the spring, summer and fall seasons. We propose V. coralliilyticus as a model Gram-negative bacterium to study temperature-dependent pathogenicity in Vibrio-related diseases.
Keywords: ecophysiology; ecosystems; environmental biotechnology; geomicrobiology; ISME J; microbe interactions; microbial communities; microbial ecology; microbial engineering; microbial epidemiology; microbial genomics; microorganisms

Toward improved aeromechanics simulations using recent advancements in scientific computing - Hu,Q.; Syal,M.; Gumerov, Nail A.; Duraiswami, Ramani; Leishman,J.G. (Proceedings 67th Annual Forum of the American Helicopter Society, 2011)

Tracking and Identification via Object Reflectance Using a Hyperspectral Video Camera - Nguyen,Hien Van; Banerjee,Amit; Burlina,Philippe; Broadwater,Joshua; Chellapa, Rama (Machine Vision Beyond Visible SpectrumMachine Vision Beyond Visible Spectrum, 2011)
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.

Transcriptional Regulation Via TF-Modifying Enzymes: An Integrative Model-Based Analysis - Everett,Logan J; Jensen,Shane T; Hannenhalli, Sridhar (Nucleic Acids ResearchNucl. Acids Res., 2011)
Transcription factor activity is largely regulated through post-translational modification. Here, we report the first integrative model of transcription that includes both interactions between transcription factors and promoters, and between transcription factors and modifying enzymes. Simulations indicate that our method is robust against noise. We validated our tool on a well-studied stress response network in yeast and on a STAT1-mediated regulatory network in human B cells. Our work represents a significant step toward a comprehensive model of gene transcription.

A trust model for supply chain management - Haghpanah,Y.; desJardins, Marie; others (The 10th International Conference on Autonomous Agents and Multiagent Systems-Volume 3, 2011)

Vehicle Detection Using Partial Least Squares - Kembhavi,A.; Harwood,D.; Davis, Larry S. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2011)
Detecting vehicles in aerial images has a wide range of applications, from urban planning to visual surveillance. We describe a vehicle detector that improves upon previous approaches by incorporating a very large and rich set of image descriptors. A new feature set called Color Probability Maps is used to capture the color statistics of vehicles and their surroundings, along with the Histograms of Oriented Gradients feature and a simple yet powerful image descriptor that captures the structural characteristics of objects named Pairs of Pixels. The combination of these features leads to an extremely high-dimensional feature set (approximately 70,000 elements). Partial Least Squares is first used to project the data onto a much lower dimensional subspace. Then, a powerful feature selection analysis is employed to improve the performance while vastly reducing the number of features that must be calculated. We compare our system to previous approaches on two challenging data sets and show superior performance.
Keywords: aerial images; color probability maps; oriented gradients feature; partial least squares; powerful feature selection analysis; urban planning; vehicle detection; visual surveillance; gradient methods; image colour analysis; least squares approximations; road vehicle; Automated

Why is My Internet Slow?: Making Network Speeds Visible - Marshini Chetty; Haslem, David; Baird, Andrew; Ofoha, Ugochi; Sumner, Bethany; Grinter, Rebecca (SIGCHI '11, 2011)
With widespread broadband adoption, more households report experiencing sub-optimal speeds. Not only are slow speeds frustrating, they may indicate consumers are not receiving the services they are paying for from their internet service providers. Yet, determining the speed and source of slow-downs is difficult because few tools exist for broadband management. We report on results of a field trial with 10 households using a visual network probe designed to address these problems. We describe the results of the study and provide design implications for future tools. More importantly, we argue that tools like this can educate and empower consumers by making broadband speeds and sources of slow-downs more visible.
Keywords: broadband speed; broadband tools; home networks

Adapting Scrum to Managing a Research Group - Hicks, Michael W.; Foster, Jeffrey S. (Technical Reports of the Computer Science Department, 2010)
Score is an adaptation of the Scrum agile software development methodology to the task of managing Ph.D. students in an academic research group. This paper describes Score, conceived in October 2006, and our experience using it. We have found that Score enables us---faculty and students---to be more efficient and thereby more productive, and enhances the cohesion of our research group.

Advanced tracking systems: computational approaches to be introduced to new series - HAMMOUD,R.; Porikli, F.; Davis, Larry S. (Augmented vision & reality, 2010)
Modern visual tracking systems implement a computational process that is often divided into several modules such as localization, tracking, recognition, behavior analysis and classification of events. This book will focus on recent advances in computational approaches for detection and tracking of human body, road boundaries and lane markers as well as on recognition of human activities, drowsiness and distraction state. This book is composed of seven distinct parts. Part I covers people localization algorithms in video sequences. Part II describes successful approaches for tracking people and bodyparts. The third part focuses on tracking of pedestrian and vehicles in outdoor images. Part IV describes recent methods to track lane markers and road boundaries. In part V, methods to track head, hand and facial features are reviewed. The last two parts cover the topics of automatic recognition and classification of activity, gesture, behavior, drowsiness and visual distraction state of humans.

AI Theory and Practice: A Discussion on Hard Challenges and Opportunities Ahead - Horvitz,Eric; Getoor, Lise; Guestrin,Carlos; Hendler,James; Konstan,Joseph; Subramanian,Devika; Wellman,Michael; Kautz,Henry (AI Magazine, 2010)
AI Theory and Practice: A Discussion on Hard Challenges and Opportunities Ahead

Analyzing Social Media Networks with NodeXL - Hansen,Derek; Shneiderman, Ben; Smith,Marc A. (Morgan Kaufmann, 2010)
"Analyzing Social Media Networks with NodeXL provides a much needed resource for the social media research community, as it describes network theory, provides compelling examples using data sources like Twitter and Flickr, and highlights how to use a free sophisticated tool for analysis. This is the perfect book for anyone trying to analyze the behavior of online social networks and beyond." ---Adam Perer, Research Scientist, IBM Research "This book provides a basic introduction to social network analysis, followed by practical instruction and examples on gathering data from online sources, importing into Excel, and then analyzing the data through Excel. The book will be important for promoting research in the area for those in information science, sociology, cultural studies, virtual community, and e-commerce."---Caroline Haythornthwaite, PhD, Professor, Graduate School of Library and Information Science, University of Illinois at Urbana-Champaign Businesses, entrepreneurs, individuals, and government agencies alike are looking to social network analysis (SNA) tools for insight into trends, connections, and fluctuations in social media. Microsoft's NodeXL is a free, open-source SNA plug-in for use with Excel. It provides instant graphical representation of relationships of complex networked data. But it goes further than other SNA tools - NodeXL was developed by a multidisciplinary team of experts that bring together information studies, computer science, sociology, human-computer interaction, and over 20 years of visual analytic theory and information visualization into a simple tool anyone can use. This makes NodeXL of interest not only to end-users but also to researchers and students studying visual and network analytics and their application in the real world.
Keywords: Business & Economics / Marketing / Research; Computers / Computer Science; Computers / Data Processing; Computers / Database Management / Data Mining; Computers / General; Computers / Information Theory; Computers / Interactive & Multimedia; Computers / Social Aspects / General; Computers / Social Aspects / Human-Computer Interaction; Computers / User Interfaces; data mining; Data mining - Computer programs; Data mining/ Computer programs; Information Visualization; Information visualization - Computer programs; Information visualization/ Computer programs; NodeXL; online social networks; Social Science / General; Social Science / Reference; Social Science / Sociology / General; Technology & Engineering / General; Technology & Engineering / Social Aspects; Webometrics; Webometrics - Computer programs; Webometrics/ Computer programs

Analyzing Social Media Networks with NodeXL: Insights from a Connected World - Hansen,Derek; Shneiderman, Ben; Smith,Marc A. (Morgan Kaufmann, 2010)
Businesses, entrepreneurs, individuals, and government agencies alike are looking to social network analysis (SNA) tools for insight into trends, connections, and fluctuations in social media. Microsoft’s NodeXL is a free, open-source SNA plug-in for use with Excel. It provides instant graphical representation of relationships of complex networked data. But it goes further than other SNA tools -- NodeXL was developed by a multidisciplinary team of experts that bring together information studies, computer science, sociology, human-computer interaction, and over 20 years of visual analytic theory and information visualization into a simple tool anyone can use. This makes NodeXL of interest not only to end-users but also to researchers and students studying visual and network analytics and their application in the real world. In Analyzing Social Media Networks with NodeXL, members of the NodeXL development team up to provide readers with a thorough and practical guide for using the tool while also explaining the development behind each feature. Blending the theoretical with the practical, this book applies specific SNA instructions directly to NodeXL, but the theory behind the implementation can be applied to any SNA. To learn more about Analyzing Social Media Networks and NodeXL, visit the companion site at www.mkp.com/nodexl*Walks you through NodeXL, while explaining the theory and development behind each step, providing takeaways that can apply to any SNA *Demonstrates how visual analytics research can be applied to SNA tools for the mass market *Includes case studies from researchers who use NodeXL on popular networks like email, Facebook, Twitter, and wikis
Keywords: Computers / Computer Science; Computers / General; Computers / Social Aspects / General; Computers / Social Aspects / Human-Computer Interaction; Computers / User Interfaces

Approximation Algorithms for Non-Uniform Buy-at-Bulk Network Design - Chekuri,C.; Hajiaghayi, Mohammad T.; Kortsarz,G.; Salavatipour,M. R (SIAM Journal on Computing, 2010)

Assessor error in stratified evaluation - Webber,W.; Oard, Douglas; Scholer,F.; Hedin,B. (Proceedings of the 19th ACM international conference on Information and knowledge management, 2010)

Bounds on the efficiency of black-box commitment schemes - Horvitz,Omer; Katz, Jonathan (Theoretical Computer Science, 2010)
Constructions of cryptographic primitives based on general assumptions (e.g., one-way functions) tend to be less efficient than constructions based on specific (e.g., number-theoretic) assumptions. This has prompted a recent line of research aimed at investigating the best possible efficiency of (black-box) cryptographic constructions based on general assumptions. Here, we present bounds on the efficiency of statistically-binding commitment schemes constructed using black-box access to one-way permutations; our bounds are tight for the case of perfectly-binding schemes. Our bounds hold in an extension of the Impagliazzo–Rudich model: we show that any construction beating our bounds would imply the unconditional existence of a one-way function (from which a statistically-binding commitment scheme could be constructed “from scratch”).
Keywords: Commitment schemes; cryptography

Cellular traffic offloading through opportunistic communications: a case study - Han,Bo; Hui,Pan; Kumar,V. S. Anil; Marathe,Madhav V.; Guanhong Pei; Srinivasan, Aravind (Proceedings of the 5th ACM workshop on Challenged networks, 2010)
Due to the increasing popularity of various applications for smartphones, 3G networks are currently overloaded by mobile data traffic. Offloading cellular traffic through opportunistic communications is a promising solution to partially solve this problem, because there is no monetary cost for it. As a case study, we investigate the target-set selection problem for information delivery in the emerging Mobile Social Networks (MoSoNets). We propose to exploit opportunistic communications to facilitate the information dissemination and thus reduce the amount of cellular traffic. In particular, we study how to select the target set with only k users, such that we can minimize the cellular data traffic. In this scenario, initially the content service providers deliver information over cellular networks to only users in the target set. Then through opportunistic communications, target-users will further propagate the information among all the subscribed users. Finally, service providers will send the information to users who fail to receive it before the delivery deadline (i.e., delay-tolerance threshold). We propose three algorithms, called Greedy, Heuristic, and Random, for this problem and evaluate their performance through an extensive trace-driven simulation study. The simulation results verify the efficiency of these algorithms for both synthetic and real-world mobility traces. For example, the Heuristic algorithm can offload cellular traffic by up to 73.66% for a real-world mobility trace.
Keywords: cellular traffic offloading; mobile social networks; opportunistic communications; target-set selection

Challenges in personalized authority flow based ranking of social media - Sayyadi,H.; Edmonds,J.; Hristidis,V.; Raschid, Louiqa (Proceedings of the 19th ACM international conference on Information and knowledge management, 2010)

Children's roles using keyword search interfaces at home - Druin, Allison; Foss,E.; Hutchinson,H.; Golub,E.; Hatley,L. (Proceedings of the 28th international conference on Human factors in computing systems, 2010)

Clear Panels: a technique to design mobile application interactivity - Brown,Q.; Bonsignore,E.; Hatley,L.; Druin, Allison; Walsh,G.; Foss,E.; Brewer,R.; Hammer,J.; Golub,E. (Proceedings of the 8th ACM Conference on Designing Interactive Systems, 2010)

Comparative Genomics of Clinical and Environmental Vibrio Mimicus - Hasan,Nur A.; Grim,Christopher J.; Haley,Bradd J.; Jongsik Chun; Alam,Munirul; Taviani,Elisa; Mozammel Hoq; Munk,A. Christine; Rita R Colwell (Proceedings of the National Academy of SciencesPNAS, 2010)
Whether Vibrio mimicus is a variant of Vibrio cholerae or a separate species has been the subject of taxonomic controversy. A genomic analysis was undertaken to resolve the issue. The genomes of V. mimicus MB451, a clinical isolate, and VM223, an environmental isolate, comprise ca. 4,347,971 and 4,313,453 bp and encode 3,802 and 3,290 ORFs, respectively. As in other vibrios, chromosome I (C-I) predominantly contains genes necessary for growth and viability, whereas chromosome II (C-II) bears genes for adaptation to environmental change. C-I harbors many virulence genes, including some not previously reported in V. mimicus, such as mannose-sensitive hemagglutinin (MSHA), and enterotoxigenic hemolysin (HlyA); C-II encodes a variant of Vibrio pathogenicity island 2 (VPI-2), and Vibrio seventh pandemic island II (VSP-II) cluster of genes. Extensive genomic rearrangement in C-II indicates it is a hot spot for evolution and genesis of speciation for the genus Vibrio. The number of virulence regions discovered in this study (VSP-II, MSHA, HlyA, type IV pilin, PilE, and integron integrase, IntI4) with no notable difference in potential virulence genes between clinical and environmental strains suggests these genes also may play a role in the environment and that pathogenic strains may arise in the environment. Significant genome synteny with prototypic pre-seventh pandemic strains of V. cholerae was observed, and the results of phylogenetic analysis support the hypothesis that, in the course of evolution, V. mimicus and V. cholerae diverged from a common ancestor with a prototypic sixth pandemic genomic backbone.

Compressed Synthetic Aperture Radar - Patel, Vishal M.; Easley,G. R; Healy,D. M; Chellapa, Rama (IEEE Journal of Selected Topics in Signal Processing, 2010)
In this paper, we introduce a new synthetic aperture radar (SAR) imaging modality which can provide a high-resolution map of the spatial distribution of targets and terrain using a significantly reduced number of needed transmitted and/or received electromagnetic waveforms. This new imaging scheme, requires no new hardware components and allows the aperture to be compressed. It also presents many new applications and advantages which include strong resistance to countermesasures and interception, imaging much wider swaths and reduced on-board storage requirements.
Keywords: Compressed sensing; compressed sensing (CS); compressive sensing; electromagnetic waveforms; image resolution; radar imaging; SAR imaging modality; synthetic aperture radar; Synthetic aperture radar (SAR); targets spatial distribution

Context-Aware Query Recommendations - Ntoulas,Alexandros; Hwang,Heasoo; Getoor, Lise; Paparizos,Stelios; Lauw,Hady Wirawan (2010)
Described is a search-related technology in which context information regarding a user's prior search actions is used in making query recommendations for a current user action, such as a query or click. To determine whether each set or subset of context information is relevant to the user action, data obtained from a query log is evaluated. More particularly, a query transition (query-query) graph and a query click (query-URL) graph are extracted from the query log; vectors are computed for the current action and each context/sub-context and evaluated against vectors in the graphs to determine current action-to-context similarity. Also described is using similar context to provide the query recommendations, using parameters to control the similarity strictness, and/or whether more recent context information is more relevant than less recent context information, and using context information to distinguish between user sessions.

Conversion of viable but nonculturable Vibrio cholerae to the culturable state by co‐culture with eukaryotic cells - Senoh,Mitsutoshi; Ghosh‐Banerjee,Jayeeta; Ramamurthy,Thandavarayan; Hamabata,Takashi; Kurakawa,Takashi; Takeda,Makoto; Rita R Colwell; Nair,G. Balakrish; Takeda,Yoshifumi (Microbiology and Immunology, 2010)
VBNC Vibrio cholerae O139 VC-280 obtained by incubation in 1% solution of artificial sea water IO at 4°C for 74 days converted to the culturable state when co-cultured with CHO cells. Other eukaryotic cell lines, including HT-29, Caco-2, T84, HeLa, and Intestine 407, also supported conversion of VBNC cells to the culturable state. Conversion of VBNC V. cholerae O1 N16961 and V. cholerae O139 VC-280/pG13 to the culturable state, under the same conditions, was also confirmed. When VBNC V. cholerae O139 VC-280 was incubated in 1% IO at 4°C for up to 91 days, the number of cells converted by co-culture with CHO cells declined with each additional day of incubation and after 91 days conversion was not observed.
Keywords: conversion to culturability; co‐culture; eukaryotic cell; viable but nonculturable (VBNC) Vibrio cholerae

Correlated Changes Between Regulatory Cis Elements and Condition-Specific Expression in Paralogous Gene Families - Singh,Larry N.; Hannenhalli, Sridhar (Nucleic Acids ResearchNucl. Acids Res., 2010)
Gene duplication is integral to evolution, providing novel opportunities for organisms to diversify in function. One fundamental pathway of functional diversification among initially redundant gene copies, or paralogs, is via alterations in their expression patterns. Although the mechanisms underlying expression divergence are not completely understood, transcription factor binding sites and nucleosome occupancy are known to play a significant role in the process. Previous attempts to detect genomic variations mediating expression divergence in orthologs have had limited success for two primary reasons. First, it is inherently challenging to compare expressions among orthologs due to variable trans-acting effects and second, previous studies have quantified expression divergence in terms of an overall similarity of expression profiles across multiple samples, thereby obscuring condition-specific expression changes. Moreover, the inherently inter-correlated expressions among homologs present statistical challenges, not adequately addressed in many previous studies. Using rigorous statistical tests, here we characterize the relationship between cis element divergence and condition-specific expression divergence among paralogous genes in Saccharomyces cerevisiae. In particular, among all combinations of gene family and TFs analyzed, we found a significant correlation between TF binding and the condition-specific expression patterns in over 20% of the cases. In addition, incorporating nucleosome occupancy reveals several additional correlations. For instance, our results suggest that GAL4 binding plays a major role in the expression divergence of the genes in the sugar transporter family. Our work presents a novel means of investigating the cis regulatory changes potentially mediating expression divergence in paralogous gene families under specific conditions.

Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs - Saha,B.; Hoch,A.; Khuller, Samir; Raschid, Louiqa; Zhang,X. N (Research in Computational Molecular Biology, 2010)
In this paper, we focus on finding complex annotation patterns representing novel and interesting hypotheses from gene annotation data. We define a generalization of the densest subgraph problem by adding an additional distance restriction (defined by a separate metric) to the nodes of the subgraph. We show that while this generalization makes the problem NP-hard for arbitrary metrics, when the metric comes from the distance metric of a tree, or an interval graph, the problem can be solved optimally in polynomial time. We also show that the densest subgraph problem with a specified subset of vertices that have to be included in the solution can be solved optimally in polynomial time. In addition, we consider other extensions when not just one solution needs to be found, but we wish to list all subgraphs of almost maximum density as well. We apply this method to a dataset of genes and their annotations obtained from The Arabidopsis Information Resource (TAIR). A user evaluation confirms that the patterns found in the distance restricted densest subgraph for a dataset of photomorphogenesis genes are indeed validated in the literature; a control dataset validates that these are not random patterns. Interestingly, the complex annotation patterns potentially lead to new and as yet unknown hypotheses. We perform experiments to determine the properties of the dense subgraphs, as we vary parameters, including the number of genes and the distance.

Deploying sensor networks with guaranteed fault tolerance - Bredin,J. L; Demaine,E. D; Hajiaghayi, Mohammad T.; Rus,D. (IEEE/ACM Transactions on Networking (TON), 2010)

Discovery of novel Vibrio cholerae VSP‐II genomic islands using comparative genomic analysis - Taviani,Elisa; Grim,Christopher J.; Choi,Jinna; Jongsik Chun; Haley,Bradd; Hasan,Nur A.; Huq,Anwar; Rita R Colwell (FEMS Microbiology Letters, 2010)
This report describes Vibrio seventh pandemic island II (VSP-II) and three novel variants revealed by comparative genomics of 23 Vibrio cholerae strains and their presence among a large and diverse collection of V. cholerae isolates. Three VSP-II variants were reported previously and our results demonstrate the presence of three novel VSP-II in clinical and environmental V. cholerae marked by major deletions and genetic rearrangements. A new VSP-II cluster was found in the seventh pandemic V. cholerae O1 El Tor strain CIRS101, which is dominant (95%) among the recent (2004–2007) seven pandemic V. cholerae O1 El Tor isolates from two endemic sites, but was not found in older strains from the same region. Two other variants were found in V. cholerae TMA21 and RC385, two environmental strains from coastal Brazil and the Chesapeake Bay, respectively, the latter being prevalent among environmental V. cholerae non-O1/non-O139 and Vibrio mimicus. The results of this study indicate that the VSP-II island has undergone significant rearrangement through a complex evolutionary pathway in V. cholerae. Interestingly, one of the new VSP-II revealed the presence of ‘old’ and ‘new’V. cholerae O1 El Tor pandemic clones circulating in some of the areas where cholera is endemic.
Keywords: Vibrio cholerae; Vibrio mimicus; VPS‐II

Diversity and distribution of cholix toxin, a novel ADP‐ribosylating factor from Vibrio cholerae - Purdy,Alexandra E.; Balch,Deborah; Lizárraga‐Partida,Marcial Leonardo; Islam,Mohammad Sirajul; Martinez‐Urtaza,Jaime; Huq,Anwar; Rita R Colwell; Bartlett,Douglas H. (Environmental Microbiology Reports, 2010)
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.

Don't Configure the Network, Program It! Domain-Specific Programming Languages for Network Systems - Feamster, Nick; Voellmy,A.; Agarwal,A.; Hudak,P.; Burnett,S.; Launchbury,J. (Yale University, 2010)
Network operators must configure networks to accomplish critical, complex, and often conflicting requirements: they must ensure good performance while maintaining security, and satisfy contractual obligations while ensuring profitable use of interdomain connections. Unfortunately, today they have no choice but to implement these high-level goals by configuring hundreds of individual network devices. These interact in complex and unexpected ways, often resulting in misconfigurations or downtime. We propose a new approach: rather than configure individual network devices, operators should program the network holistically, according to high-level policies. Towards this goal, we present Nettle, a system for clearly and concisely expressing network requirements together with mechanisms to control the network accordingly. At the lowest level, we rely on OpenFlow switches for programmable network hardware. On top of this layer, we build an extensible family of embedded domain-specific languages (EDSLs), each aimed at different operational concerns and provide convenient ways to sensibly combine expressions in these languages. We present a case study demonstrating a DSL for networks that provides fine-grained, dynamic access control policies.

Don't love thy nearest neighbor - Lumezanu,Cristian; Levin,Dave; Han,Bo; Spring, Neil; Bhattacharjee, Bobby (Proceedings of the 9th international conference on Peer-to-peer systems, 2010)

Dynamically checking ownership policies in concurrent c/c++ programs - Martin,Jean-Phillipe; Hicks, Michael W.; Costa,Manuel; Akritidis,Periklis; Castro,Miguel (Proceedings of the 37th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages, 2010)
Concurrent programming errors arise when threads share data incorrectly. Programmers often avoid these errors by using synchronization to enforce a simple ownership policy: data is either owned exclusively by a thread that can read or write the data, or it is read owned by a set of threads that can read but not write the data. Unfortunately, incorrect synchronization often fails to enforce these policies and memory errors in languages like C and C++ can violate these policies even when synchronization is correct. In this paper, we present a dynamic analysis for checking ownership policies in concurrent C and C++ programs despite memory errors. The analysis can be used to find errors in commodity multi-threaded programs and to prevent attacks that exploit these errors. We require programmers to write ownership assertions that describe the sharing policies used by different parts of the program. These policies may change over time, as may the policies' means of enforcement, whether it be locks, barriers, thread joins, etc. Our compiler inserts checks in the program that signal an error if these policies are violated at runtime. We evaluated our tool on several benchmark programs. The run-time overhead was reasonable: between 0 and 49% with an average of 26%. We also found the tool easy to use: the total number of ownership assertions is small, and the asserted specification and implementation can be debugged together by running the instrumented program and addressing the errors that arise. Our approach enjoys a pleasing modular soundness property: if a thread executes a sequence of statements on variables it owns, the statements are serializable within a valid execution, and thus their effects can be reasoned about in isolation from other threads in the program.
Keywords: concurrency; Debugging; Dynamic analysis; Security; Testing; tools

Effect on Human Cells of Environmental Vibrio Parahaemolyticus Strains Carrying Type III Secretion System 2 - Caburlotto,Greta; Lleò,Maria M.; Hilton,Tamara; Huq,Anwar; Rita R Colwell; Kaper,James B. (Infection and ImmunityInfect. Immun., 2010)
Vibrio parahaemolyticus is an inhabitant of estuarine and marine environments that causes seafood-borne gastroenteritis worldwide. Recently, a type 3 secretion system (T3SS2) able to secrete and translocate virulence factors into the eukaryotic cell has been identified in a pathogenicity island (VP-PAI) located on the smaller chromosome. These virulence-related genes have previously been detected only in clinical strains. Classical virulence genes for this species (tdh, trh) are rarely detected in environmental strains, which are usually considered to lack virulence potential. However, during screening of a collection of environmental V. parahaemolyticus isolates obtained in the North Adriatic Sea in Italy, a number of marine strains carrying virulence-related genes, including genes involved in the T3SS2, were detected. In this study, we investigated the pathogenic potential of these marine V. parahaemolyticus strains by studying their adherence ability, their cytotoxicity, their effect on zonula occludin protein 1 (ZO-1) of the tight junctions, and their effect on transepithelial resistance (TER) in infected Caco-2 cells. By performing a reverse transcription-PCR, we also tested the expression of the T3SS2 genes vopT and vopB2, encoding an effector and a translocon protein, respectively. Our results indicate that, similarly to clinical strains, marine V. parahaemolyticus strains carrying vopT and vopB2 and that other genes included in the VP-PAI are capable of adhering to human cells and of causing cytoskeletal disruption and loss of membrane integrity in infected cells. On the basis of data presented here, environmental V. parahaemolyticus strains should be included in coastal water surveillance plans, as they may represent a risk for human health.

Environmental reservoirs of Vibrio cholerae and their role in cholera - Vezzulli,Luigi; Pruzzo,Carla; Huq,Anwar; Rita R Colwell (Environmental Microbiology Reports, 2010)
In the aquatic environment, Vibrio cholerae has been reported to be associated with a variety of living organisms, including animals with an exoskeleton of chitin, aquatic plants, protozoa, bivalves, waterbirds, as well as abiotic substrates (e.g. sediments). Most of these are well-known or putative environmental reservoirs for the bacterium, defined as places where the pathogen lives over time, with the potential to be released and to cause human infection. Environmental reservoirs also serve as V. cholerae disseminators and vectors. They can be responsible for the start of an epidemic, may be critical to cholera endemicity, and affect the evolution of pathogen virulence. To date, in addition to the generally recognized role of zooplankton as the largest environmental reservoir for V. cholerae, other environmental reservoirs play some role in cholera epidemiology by favouring persistence of the pathogen during inter-epidemic periods. Little is known about the ecological factors affecting V. cholerae survival in association with aquatic substrates. Studies aimed at these aspects, i.e. understanding how environmental reservoirs interact, are affected by climate, and contribute to disease epidemiology, will be useful for understanding global implications of V. cholerae and the disease cholera.