Tree-based Label Dependency Topic Models - Nguyen, V A; Jordan Boyd-Graber; Chang, J; Resnik, P (cs.umd.edu)
Abstract Multi-labeled corpora, where each document is tagged with a set of labels, are ubiquitous. When the number of unique labels in the dataset is large, there are naturally some dependencies among the labels. In this paper, we propose TREELAD—a ...

Rapid, quantitative therapeutic screening for Alzheimer's enzymes enabled by optimal signal transduction with transistors - Le, Son T.; Morris, Michelle A.; Cardone, Antonio; Guros, Nicholas B.; Klauda, Jeffery B.; Sperling, Brent A.; Richter, Curt A.; Pant, Harish C.; Balijepalli, Arvind (The Analyst, 2020)

Quantum Capacitance-Limited MoS2 Biosensors Enable Remote Label-Free Enzyme Measurements - Le, Son T; Guros, Nicholas B; Bruce, Robert C; Cardone, Antonio; Amin, Niranjana D; Zhang, Siyuan; Klauda, Jeffery; Pant, Harish C; Richter, Curt A; Balijepalli, Arvind (Nanoscale, 2019)

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

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.

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)

Beyond cost-effectiveness: Using systems analysis for infectious disease preparedness - Phelps, Charles; Madhavan, Guruprasad; Rappuoli, Rino; Rita R Colwell; Fineberg, Harvey (Vaccine, 2017)
Until the recent outbreaks, Ebola vaccines ranked low in decision makers’ priority lists based on cost-effectiveness analysis and (or) corporate profitability. Despite a relatively small number of Ebola-related cases and deaths (compared to other causes), Ebola vaccines suddenly leapt to highest priority among international health agencies and vaccine developers. Clearly, earlier cost-effectiveness analyses badly missed some factors affecting real world decisions. Multi-criteria systems analysis can improve evaluation and prioritization of vaccine development and also of many other health policy and investment decisions. Neither cost-effectiveness nor cost-benefit analysis can capture important aspects of problems such as Ebola or the emerging threat of Zika, especially issues of inequality and disparity—issues that dominate the planning of many global health and economic organizations. Cost-benefit analysis requires assumptions about the specific value of life—an idea objectionable to many analysts and policy makers. Additionally, standard cost-effectiveness calculations cannot generally capture effects on people uninfected with Ebola for example, but nevertheless affected through such factors as contagion, herd immunity, and fear of dread disease, reduction of travel and commerce, and even the hope of disease eradication. Using SMART Vaccines, we demonstrate how systems analysis can visibly include important “other factors” and more usefully guide decision making and beneficially alter priority setting processes.

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.

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.

Are natural reservoirs important for cholera surveillance? The case of an outbreak in a Brazilian estuary - Martinelli Filho, J.E.; Lopes, R.M.; Rivera, I.N.G.; Rita R Colwell (Letters in Applied Microbiology, 2016)
Paranaguá Bay is one of the largest estuarine systems on the Southern Brazilian coast. The only recorded cholera outbreak in this region since the early 20th century occurred in 1999 and resulted in 467 cases and at least three reported deaths in a population of approx. 150 000 people. This short communication reports historical, unpublished data related to that outbreak. Water, zooplankton and bivalve samples were collected and evaluated using direct fluorescence assay to determine whether Vibrio cholerae serogroups O1 and O139 were present in the estuarine system at that time. Most of the water (83%) and zooplankton samples (75%) were positive for V. cholerae O1, while V. cholerae O139 was not detected. Shellfish (Mytella sp.) were also positive for V. cholerae O1. These results indicate that the estuary, including biological vectors such as copepods and bivalves, comprise an important reservoir of V. cholerae O1 and a probable waterborne pathway for the disease, in addition to contamination with untreated sewage.

Climate influence on Vibrio and associated human diseases during the past half-century in the coastal North Atlantic - Vezzulli, Luigi; Grande, Chiara; Reid, Philip C.; élaouët, Pierre; Edwards, Martin; öfle, Manfred G.; Brettar, Ingrid; Rita R Colwell; Pruzzo, Carla (Proceedings of the National Academy of Sciences, 2016)
Climate change is having a dramatic impact on marine animal and plant communities but little is known of its influence on marine prokaryotes, which represent the largest living biomass in the world oceans and play a fundamental role in maintaining life on our planet. In this study, for the first time to our knowledge, experimental evidence is provided on the link between multidecadal climatic variability in the temperate North Atlantic and the presence and spread of an important group of marine prokaryotes, the vibrios, which are responsible for several infections in both humans and animals. Using archived formalin-preserved plankton samples collected by the Continuous Plankton Recorder survey over the past half-century (1958–2011), we assessed retrospectively the relative abundance of vibrios, including human pathogens, in nine areas of the North Atlantic and North Sea and showed correlation with climate and plankton changes. Generalized additive models revealed that long-term increase in Vibrio abundance is promoted by increasing sea surface temperatures (up to ∼1.5 °C over the past 54 y) and is positively correlated with the Northern Hemisphere Temperature (NHT) and Atlantic Multidecadal Oscillation (AMO) climatic indices (P < 0.001). Such increases are associated with an unprecedented occurrence of environmentally acquired Vibrio infections in the human population of Northern Europe and the Atlantic coast of the United States in recent years.

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.

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)

In Plain View: A Transparent Systems Approach for Enhancing Health Policy Decisions - Guru Madhavan; Charles E. Phelps; Rita R Colwell; Rino Rappuoli; Harvey V. Fineberg (The Bridge, 2016)

IncA/C Conjugative Plasmids Mobilize a New Family of Multidrug Resistance Islands in Clinical Vibrio cholerae Non-O1/Non-O139 Isolates from Haiti - Carraro, Nicolas; Rivard, Nicolas; Ceccarelli, Daniela; Rita R Colwell; Burrus, Vincent (mBio, 2016)
Mobile genetic elements play a pivotal role in the adaptation of bacterial populations, allowing them to rapidly cope with hostile conditions, including the presence of antimicrobial compounds. IncA/C conjugative plasmids (ACPs) are efficient vehicles for dissemination of multidrug resistance genes in a broad range of pathogenic species of Enterobacteriaceae. ACPs have sporadically been reported in Vibrio cholerae, the infectious agent of the diarrheal disease cholera. The regulatory network that controls ACP mobility ultimately depends on the transcriptional activation of multiple ACP-borne operons by the master activator AcaCD. Beyond ACP conjugation, AcaCD has also recently been shown to activate the expression of genes located in the Salmonella genomic island 1 (SGI1). Here, we describe MGIVchHai6, a novel and unrelated mobilizable genomic island (MGI) integrated into the 3′ end of trmE in chromosome I of V. cholerae HC-36A1, a non-O1/non-O139 multidrug-resistant clinical isolate recovered from Haiti in 2010. MGIVchHai6 contains a mercury resistance transposon and an integron In104-like multidrug resistance element similar to the one of SGI1. We show that MGIVchHai6 excises from the chromosome in an AcaCD-dependent manner and is mobilized by ACPs. Acquisition of MGIVchHai6 confers resistance to β-lactams, sulfamethoxazole, tetracycline, chloramphenicol, trimethoprim, and streptomycin/spectinomycin. In silico analyses revealed that MGIVchHai6-like elements are carried by several environmental and clinical V. cholerae strains recovered from the Indian subcontinent, as well as from North and South America, including all non-O1/non-O139 clinical isolates from Haiti.

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.

Strategic Planning in Population Health and Public Health Practice: A Call to Action for Higher Education - Phelps, Charles; Madhavan, Guruprasad; Rappuoli, Rino; LEVIN, SCOTT; Shortlife, Edward; Rita R Colwell (The Milbank Quarterly, 2016)
POLICY POINTS: Scarce resources, especially in population health and public health practice, underlie the importance of strategic planning. Public health agencies' current planning and priority setting efforts are often narrow, at times opaque, and focused on single metrics such as cost-effectiveness. As demonstrated by SMART Vaccines, a decision support software system developed by the Institute of Medicine and the National Academy of Engineering, new approaches to strategic planning allow the formal incorporation of multiple stakeholder views and multicriteria decision making that surpass even those sophisticated cost-effectiveness analyses widely recommended and used for public health planning. Institutions of higher education can and should respond by building on modern strategic planning tools as they teach their students how to improve population health and public health practice. CONTEXT: Strategic planning in population health and public health practice often uses single indicators of success or, when using multiple indicators, provides no mechanism for coherently combining the assessments. Cost-effectiveness analysis, the most complex strategic planning tool commonly applied in public health, uses only a single metric to evaluate programmatic choices, even though other factors often influence actual decisions. METHODS: Our work employed a multicriteria systems analysis approach--specifically, multiattribute utility theory--to assist in strategic planning and priority setting in a particular area of health care (vaccines), thereby moving beyond the traditional cost-effectiveness analysis approach. FINDINGS: (1) Multicriteria systems analysis provides more flexibility, transparency, and clarity in decision support for public health issues compared with cost-effectiveness analysis. (2) More sophisticated systems-level analyses will become increasingly important to public health as disease burdens increase and the resources to deal with them become scarcer. CONCLUSIONS: The teaching of strategic planning in public health must be expanded in order to fill a void in the profession's planning capabilities. Public health training should actively incorporate model building, promote the interactive use of software tools, and explore planning approaches that transcend restrictive assumptions of cost-effectiveness analysis. The Strategic Multi-Attribute Ranking Tool for Vaccines (SMART Vaccines), which was recently developed by the Institute of Medicine and the National Academy of Engineering to help prioritize new vaccine development, is a working example of systems analysis as a basis for decision support.

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.

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.

Molecular tools in understanding the evolution of Vibrio cholerae - Rahaman, Md. Habibur; Islam, Tarequl; Rita R Colwell; Alam, Munirul (Frontiers in Microbiology, 2015)
Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies.

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.

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.

A unified initiative to harness Earth's microbiomes - Alivisatos, A. P.; Blaser, M. J.; Brodie, E. L.; Chun, M.; Dangl, J. L.; Donohue, T. J.; Dorrestein, P. C.; Gilbert, J. A.; Green, J. L.; Jansson, J. K.; Knight, R.; Maxon, M. E.; et al. (Science, 2015)

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)

Phylodynamic Analysis of Clinical and Environmental Vibrio cholerae Isolates from Haiti Reveals Diversification Driven by Positive Selection - Azarian, Taj; Ali, Afsar; Johnson, Judith A.; Mohr, David; Prosperi, Mattia; Veras, Nazle M.; Jubair, Mohammed; Strickland, Samantha L.; Rashid, Mohammad H.; Alam, Meer T.; Weppelmann, Thomas A.; Katz, Lee S.; et al. (mBio, 2014)
Phylodynamic analysis of genome-wide single-nucleotide polymorphism (SNP) data is a powerful tool to investigate underlying evolutionary processes of bacterial epidemics. The method was applied to investigate a collection of 65 clinical and environmental isolates of Vibrio cholerae from Haiti collected between 2010 and 2012. Characterization of isolates recovered from environmental samples identified a total of four toxigenic V. cholerae O1 isolates, four non-O1/O139 isolates, and a novel nontoxigenic V. cholerae O1 isolate with the classical tcpA gene. Phylogenies of strains were inferred from genome-wide SNPs using coalescent-based demographic models within a Bayesian framework. A close phylogenetic relationship between clinical and environmental toxigenic V. cholerae O1 strains was observed. As cholera spread throughout Haiti between October 2010 and August 2012, the population size initially increased and then fluctuated over time. Selection analysis along internal branches of the phylogeny showed a steady accumulation of synonymous substitutions and a progressive increase of nonsynonymous substitutions over time, suggesting diversification likely was driven by positive selection. Short-term accumulation of nonsynonymous substitutions driven by selection may have significant implications for virulence, transmission dynamics, and even vaccine efficacy.

Adaptive and Concurrent Secure Computation from New Adaptive, Non-malleable Commitments - Dana Dachman-Soled; Malkin, Tal; Raykova, Mariana; Venkitasubramaniam, Muthuramakrishnan (Advances in Cryptology - ASIACRYPT 2013, 2013)
We present a unified approach for obtaining general secure computation that achieves adaptive-Universally Composable (UC)-security. Using our approach we essentially obtain all previous results on adaptive concurrent secure computation, both in relaxed models (e.g., quasi-polynomial time simulation), as well as trusted setup models (e.g., the CRS model, the imperfect CRS model). This provides conceptual simplicity and insight into what is required for adaptive and concurrent security, as well as yielding improvements to set-up assumptions and/or computational assumptions in known models. Additionally, we provide the first constructions of concurrent secure computation protocols that are adaptively secure in the timing model, and the non-uniform simulation model. As a corollary we also obtain the first adaptively secure multiparty computation protocol in the plain model that is secure under bounded-concurrency. Conceptually, our approach can be viewed as an adaptive analogue to the recent work of Lin, Pass and Venkitasubramaniam [STOC ‘09], who considered only non-adaptive adversaries. Their main insight was that the non-malleability requirement could be decoupled from the simulation requirement to achieve UC-security. A main conceptual contribution of this work is, quite surprisingly, that it is still the case even when considering adaptive security. A key element in our construction is a commitment scheme that satisfies a strong definition of non-malleability. Our new primitive of concurrent equivocal non-malleable commitments, intuitively, guarantees that even when a man-in-the-middle adversary observes concurrent equivocal commitments and decommitments, the binding property of the commitments continues to hold for commitments made by the adversary. This definition is stronger than previous ones, and may be of independent interest. Previous constructions that satisfy our definition have been constructed in setup models, but either require existence of stronger encryption schemes such as CCA-secure encryption or require independent “trapdoors” provided by the setup for every pair of parties to ensure non-malleability. A main technical contribution of this work is to provide a construction that eliminates these requirements and requires only a single trapdoor.
Keywords: Algorithm Analysis and Problem Complexity; Applications of Mathematics; Data Encryption; Discrete Mathematics in Computer Science; Management of Computing and Information Systems; Systems and Data Security

Current Topics in Microbiology and Immunology One Health: The Human-Animal-Environment Interfaces in Emerging Infectious Diseases The Human Environment Interface: Applying Ecosystem Concepts to Health - Preston, Nicholas D.; Daszak, Peter; Rita R Colwell (Springer Berlin Heidelberg, 2013)

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)

Lexical and Hierarchical Topic Regression - Nguyen, Viet-An; Jordan Boyd-Graber; Resnik, Philip (2013)
Abstract Inspired by a two-level theory that unifies agenda setting and ideological framing, we propose supervised hierarchical latent Dirichlet allocation (SHLDA) which jointly captures documents' multi-level topic structure and their polar response variables. Our ...

Modeling topic control to detect influence in conversations using nonparametric topic models - Nguyen, Viet-An; Jordan Boyd-Graber; Resnik, Philip; Cai, Deborah A; Midberry, Jennifer E; Wang, Yuanxin (Machine Learning, 2013)
Abstract Identifying influential speakers in multi-party conversations has been the focus of research in communication, sociology, and psychology for decades. It has been long acknowledged qualitatively that controlling the topic of a conversation is a sign of ...

Personal informatics in the wild: hacking habits for health & happiness - Li, Ian; Jon Froehlich; Larsen, Jakob E; Grevet, Catherine; Ramirez, Ernesto (CHI '13 Extended Abstracts on Human Factors in Computing Systems, 2013)
Abstract Personal informatics is a class of systems that help people collect personal information to improve self-knowledge. Improving self-knowledge can foster self-insight and promote positive behaviors, such as healthy living and energy conservation. The ...

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

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

Conversion of viable but nonculturable enteric bacteria to culturable by co‐culture with eukaryotic cells - Senoh,Mitsutoshi; Ghosh‐Banerjee,Jayeeta; Ramamurthy,Thandavarayan; Rita R Colwell; Miyoshi,Shin-ichi; Nair,G. Balakrish; Takeda,Yoshifumi (Microbiology and Immunology, 2012)
Viable but nonculturable (VBNC) Vibrio cholerae non-O1/non-O139, V. parahaemolyticus, enterohemorrhagic Escherichia coli, enterotoxigenic E. coli, enteropathogenic E. coli, Shigella flexneri, and Salmonella enterica were converted to the culturable state by co-culture with selected eukaryotic cells, e.g., HT-29, Caco-2, T84, HeLa, Intestine 407, and CHO cells.
Keywords: conversion to culturability; enteric bacteria; viable but nonculturable

The design and evaluation of prototype eco-feedback displays for fixture-level water usage data - Jon Froehlich; Findlater,L.; Ostergren, M.; Ramanathan, S.; Peterson,J.; Wragg, I.; Larson,E.; Fu, F.; Bai, M.; Patel,S. (ACM, 2012)

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

Dynamic Searchable Symmetric Encryption - Kamara, Seny; Charalampos Papamanthou; Roeder, Tom (CCS '12 Proceedings of the 2012 ACM Conference on Computer and Communications Security, 2012)
Searchable symmetric encryption (SSE) allows a client to encrypt its data in such a way that this data can still be searched. The most immediate application of SSE is to cloud storage, where it enables a client to securely outsource its data to an untrusted cloud provider without sacrificing the ability to search over it. SSE has been the focus of active research and a multitude of schemes that achieve various levels of security and efficiency have been proposed. Any practical SSE scheme, however, should (at a minimum) satisfy the following properties: sublinear search time, security against adaptive chosen-keyword attacks, compact indexes and the ability to add and delete files efficiently. Unfortunately, none of the previously-known SSE constructions achieve all these properties at the same time. This severely limits the practical value of SSE and decreases its chance of deployment in real-world cloud storage systems. To address this, we propose the first SSE scheme to satisfy all the properties outlined above. Our construction extends the inverted index approach (Curtmola et al., CCS 2006) in several non-trivial ways and introduces new techniques for the design of SSE. In addition, we implement our scheme and conduct a performance evaluation, showing that our approach is highly efficient and ready for deployment.
Keywords: Cloud computing; cloud storage; searchable symmetric encryption

Encouraging consistent translation choices - Ture, Ferhan; Oard, Douglas; Resnik, Philip (Proceedings of the 2012 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, 2012)

GAGE: A Critical Evaluation of Genome Assemblies and Assembly Algorithms - Salzberg,Steven L.; Phillippy,Adam M; Zimin,Aleksey; Puiu,Daniela; Magoc,Tanja; Koren,Sergey; Treangen,Todd J; Schatz,Michael C; Delcher,Arthur L.; Roberts,Michael; Marçais,Guillaume; Pop, Mihai; et al. (Genome Research, 2012)
New sequencing technology has dramatically altered the landscape of whole-genome sequencing, allowing scientists to initiate numerous projects to decode the genomes of previously unsequenced organisms. The lowest-cost technology can generate deep coverage of most species, including mammals, in just a few days. The sequence data generated by one of these projects consist of millions or billions of short DNA sequences (reads) that range from 50 to 150 nt in length. These sequences must then be assembled de novo before most genome analyses can begin. Unfortunately, genome assembly remains a very difficult problem, made more difficult by shorter reads and unreliable long-range linking information. In this study, we evaluated several of the leading de novo assembly algorithms on four different short-read data sets, all generated by Illumina sequencers. Our results describe the relative performance of the different assemblers as well as other significant differences in assembly difficulty that appear to be inherent in the genomes themselves. Three overarching conclusions are apparent: first, that data quality, rather than the assembler itself, has a dramatic effect on the quality of an assembled genome; second, that the degree of contiguity of an assembly varies enormously among different assemblers and different genomes; and third, that the correctness of an assembly also varies widely and is not well correlated with statistics on contiguity. To enable others to replicate our results, all of our data and methods are freely available, as are all assemblers used in this study.

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 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

Grammatical structures for word-level sentiment detection - Jordan Boyd-Graber; Sayeed,Asad B.; Rusk,Bryan; Weinberg, Amy (North American Association of Computational Linguistics, 2012)
Existing work in fine-grained sentiment anal- ysis focuses on sentences and phrases but ig- nores the contribution of individual words and their grammatical connections. This is because of a lack of both (1) annotated data at the word level and (2) algorithms that can leverage syn- tactic information in a principled way. We ad- dress the first need by annotating articles from the information technology business press via crowdsourcing to provide training and testing data. To address the second need, we propose a suffix-tree data structure to represent syntac- tic relationships between opinion targets and words in a sentence that are opinion-bearing. We show that a factor graph derived from this data structure acquires these relationships with a small number of word-level features. We demonstrate that our supervised model per- forms better than baselines that ignore syntac- tic features and constraints.

A Hybrid System for Error Detection in Electronic Dictionaries - Zajic, David; David Doermann; Bloodgood,Michael; Rodrigues,Paul; Ye,Peng; Zotkina,Elena (Technical Reports of the Center for the Advanced Study of Language, 2012)
A progress report on CASL’s research on error detection in electronic dictionaries, including a hybrid system, application and evaluation on a second dictionary and a graphical user interface.

Identification of Coli Surface Antigen 23, a Novel Adhesin of Enterotoxigenic Escherichia coli - Del Canto, F.; Botkin, D.J.; Valenzuela, P.; Popov, V.; Ruiz-Perez, F.; Nataro, J.P.; Levine, M.M.; Stine, O.C.; Pop, Mihai; Torres, A.G.; others (Infection and immunity, 2012)
Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea, mainly in developing countries. Although there are 25 different ETEC adhesins described in strains affecting humans, between 15% and 50% of the clinical isolates from different geographical regions are negative for these adhesins, suggesting that additional unidentified adhesion determinants might be present. Here, we report the discovery of Coli Surface Antigen 23 (CS23), a novel adhesin expressed by an ETEC serogroup O4 strain (ETEC 1766a), which was negative for the previously known ETEC adhesins, albeit it has the ability to adhere to Caco-2 cells. CS23 is encoded by an 8.8-kb locus which contains 9 open reading frames (ORFs), 7 of them sharing significant identity with genes required for assembly of K88-related fimbriae. This gene locus, named aal (adhesion-associated locus), is required for the adhesion ability of ETEC 1766a and was able to confer this adhesive phenotype to a nonadherent E. coli HB101 strain. The CS23 major structural subunit, AalE, shares limited identity with known pilin proteins, and it is more closely related to the CS13 pilin protein CshE, carried by human ETEC strains. Our data indicate that CS23 is a new member of the diverse adhesin repertoire used by ETEC strains.

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.

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.

Making Recommendations in a Microblog to Improve the Impact of a Focal User - Wu,Shanchan; Gong, Leanna; Rand, William; Raschid, Louiqa (6th ACM Conference on Recommender Systems (RecSys), 2012)
We present a microblog recommendation system that can help monitor users, track conversations, and potentially improve diffusion impact. Given a Twitter network of active users and their followers, and historical activity of tweets, retweets and mentions, we build upon a prediction tool to predict the Top K users who will retweet or mention a focal user, in the future [10]. We develop personalized recommendations for each focal user. We identify characteristics of focal users such as the size of the follower network, or the level of sentiment averaged over all tweets; both have an impact on the quality of personalized recommendations. We use (high) betweenness centrality as a proxy of attractive users to target when making recommendations. Our recommendations successfully identify a greater fraction of users with higher betweenness centrality, in comparison to the overall distribution of betweenness centrality of the ground truth users for some focal user.

Mapping Parameterized Cyclo-static Dataflow Graphs onto Configurable Hardware - Kee, Hojin; Chung-Ching Shen; Bhattacharyya, Shuvra S.; Wong, Ian; Yong Rao; Kornerup, Jacob (Journal of Signal Processing Systems, 2012)
In recent years, parameterized dataflow has evolved as a useful framework for modeling synchronous and cyclo-static graphs in which arbitrary parameters can be changed dynamically. Parameterized dataflow has proven to have significant expressive power for managing dynamics of DSP applications in important ways. However, efficient hardware synthesis techniques for parameterized dataflow representations are lacking. This paper addresses this void; specifically, the paper investigates efficient field programmable gate array (FPGA)-based implementation of parameterized cyclo-static dataflow (PCSDF) graphs. We develop a scheduling technique for throughput-constrained minimization of dataflow buffering requirements when mapping PCSDF representations of DSP applications onto FPGAs. The proposed scheduling technique is integrated with an existing formal schedule model, called the generalized schedule tree, to reduce schedule cost. To demonstrate our new, hardware-oriented PCSDF scheduling technique, we have designed a real-time base station emulator prototype based on a subset of long-term evolution (LTE), which is a key cellular standard.
Keywords: 4G communication systems; Circuits and Systems; Computer Imaging, Vision, Pattern Recognition and Graphics; Dataflow modeling; Electrical Engineering; FPGA implementation; Image Processing and Computer Vision; Parameterized dataflow; pattern recognition; scheduling; Signal, Image and Speech Processing

Media, Aggregators and the Link Economy: Strategic Hyperlink Formation in Content Networks - Dellarocas, Chris; Katona,Zsolt; Rand, William (Management Science, 2012)
A key property of the World Wide Web is the possibility for firms to place virtually costless links to third-party content as a substitute or complement to their own content. This ability to hyperlink has enabled new types of players, such as search engines and content aggregators, to successfully enter content ecosystems, attracting traffic and revenues by hosting links to the content of others. This, in turn, has sparked a heated controversy between content producers and aggregators regarding the legitimacy and social costs/benefits of uninhibited free linking. This work is the first to model the implications of interrelated and strategic hyper-linking and content investments. Our results provide a nuanced view of the much-touted “link economy,” highlighting both the beneficial consequences and the drawbacks of free hyperlinks for content producers and consumers. We show that content sites can reduce competition and improve profits by forming links to each other; in such networks one site makes high investments in content and other sites link to it. Interestingly, competitive dynamics often preclude the formation of link networks, even in settings where they would improve everyone’s profits. Furthermore, such networks improve economic efficiency only when all members have similar abilities to produce content; otherwise the less capable nodes can free-ride on the content of the more capable nodes, reducing profits for the capable nodes as well as the average content quality available to consumers. Within these networks, aggregators have both positive and negative effects. By making it easier for consumers to access good quality content they increase the appeal of the entire content ecosystem relative to the alternatives. To the extent that this increases the total traffic flowing into the content ecosystem, aggregators can help increase the profits of the highest quality content sites. At the same time, however, the market entry of aggregators takes away some of the revenue that would otherwise go to content sites. Finally, by placing links to only a subset of available content, aggregators further increase competitive pressure on content sites. Interestingly, this can increase the likelihood that such sites will then attempt to alleviate the competitive pressure by forming link networks.

A Random Forest System Combination Approach for Error Detection in Digital Dictionaries - Bloodgood,Michael; Ye,Peng; Rodrigues,Paul; Zajic, David; David Doermann (Innovative hybrid approaches to the processing of textual data, EACL 2012 Workshop, 2012)
When digitizing a print bilingual dictionary, whether via optical character recognition or manual entry, it is inevitable that errors are introduced into the electronic version that is created. We investigate automating the process of detecting errors in an XML representation of a digitized print dictionary using a hybrid approach that combines rule-based, feature-based, and language model-based methods. We investigate combining methods and show that using random forests is a promising approach. We find that in isolation, unsupervised methods rival the performance of supervised methods. Random forests typically require training data so we investigate how we can apply random forests to combine individual base methods that are themselves unsupervised without requiring large amounts of training data. Experiments reveal empirically that a relatively small amount of data is sufficient and can potentially be further reduced through specific selection criteria.

Re-wiring Activity of Malicious Networks - Konte,Maria; Feamster, Nick (Passive and Active MeasurementPassive and Active Measurement, 2012)
This paper studies the AS-level re-wiring dynamics (changes in the connectivity) of malicious networks. Anecdotal evidence suggests that some malicious ASes that are primarily involved in nefarious activities on the Internet, were sequentially de-peered by providers before their final cut-off (as occurred in the well-publicized cases of Atrivo/Intercage). We present the first systematic study of the re-wiring dynamics of malicious ASes. We tracked the ASes that were listed by Hostexploit over the last two years and compared their AS-level re-wiring dynamics with non-reported ASes. Using a publicly available dataset of Customer-Provider (CP) relations in the Internet’s AS graph, we studied how interconnection between autonomous systems evolves, both for ASes that provide connectivity for attackers and ASes that were not reported as malicious. We find that malicious networks are more aggressive both in forming links with providers and changing their upstream connectivity than other ASes. Our results indicate that the re-wiring dynamics of the networks that host attacks are stable over time, despite the evolving nature of the attacks themselves, which suggests that existing defense mechanisms could benefit from incorporating these features.
Keywords: Computer science

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.

Rpn1 and Rpn2 coordinate ubiquitin processing factors at the proteasome - Rosenzweig,Rina; Bronner,Vered; Zhang,Daoning; Fushman, David; Glickman,Michael H. (Journal of Biological ChemistryJ. Biol. Chem., 2012)
Substrates tagged with (poly)ubiquitin for degradation can be targeted directly to the 26S proteasome where they are proteolysed. Independently, ubiquitin-conjugates may also be delivered by bivalent shuttles. The majority of shuttles attach to the proteasome through a ubiquitin-like domain (UBL) while anchoring cargo at a C-terminal polyubiquitin-binding domain(s). We found that two shuttles of this class, Rad23 and Dsk2, dock at two different receptors embedded within a single subunit of the 19S proteasome regulatory particle (RP), Rpn1. Their association/dissociation constants and affinities for Rpn1 are similar. In contrast, another UBL-containing protein, the deubiquitinase Ubp6, is also anchored by Rpn1, yet dissociates slower, thus behaving as a sometimes proteasome subunit distinct from transiently-associated shuttles. Two neighboring subunits, Rpn10 and Rpn13, show a marked preference for polyubiquitin over UBLs. Rpn10 attaches to the central solenoid portion of Rpn1 although this association is stabilized by the presence of a third subunit, Rpn2. Rpn13 binds directly to the C-terminal portion of Rpn2. These intrinsic polyubiquitin receptors may compete with substrate shuttles for their polyubiquitin-conjugates, thereby aiding release of the emptied shuttles. By binding multiple ubiquitin-processing factors simultaneously, Rpn1 is uniquely suited to coordinate substrate recruitment, deubiquitination, and movement towards the catalytic core. The broad range of affinities for ubiquitin, ubiquitin-like, and non-ubiquitin signals by adjacent yet non-overlapping sites all within the Base illustrates a hub of activity that coordinates the intricate relay of substrates within the proteasome, and consequently influences substrate residency time and commitment to degradation.
Keywords: deubiquitination; Proteasome; solenoid; Surface plasmon resonance (SPR); ubiquitin; Ubiquitin-dependent protease

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].

SITS: A Hierarchical Nonparametric Model using Speaker Identity for Topic Segmentation in Multiparty Conversations - Nguyen,Viet-An; Jordan Boyd-Graber; Resnik, Philip (Association for Computational Linguistics, 2012)
One of the key tasks for analyzing conversa- tional data is segmenting it into coherent topic segments. However, most models of topic segmentation ignore the social aspect of con- versations, focusing only on the words used. We introduce a hierarchical Bayesian nonpara- metric model, Speaker Identity for Topic Seg- mentation (SITS), that discovers (1) the top- ics used in a conversation, (2) how these top- ics are shared across conversations, (3) when these topics shift, and (4) a person-specific tendency to introduce new topics. We eval- uate against current unsupervised segmenta- tion models to show that including person- specific information improves segmentation performance on meeting corpora and on po- litical debates. Moreover, we provide evidence that SITS captures an individual’s tendency to introduce new topics in political contexts, via analysis of the 2008 US presidential debates and the television program Crossfire.

Topic Models for Dynamic Translation Model Adaptation - Vladimir Eidelman; Jordan Boyd-Graber; Resnik, Philip (Association for Computational Linguistics, 2012)
We propose an approach that biases machine translation systems toward relevant transla- tions based on topic-specific contexts, where topics are induced in an unsupervised way using topic models; this can be thought of as inducing subcorpora for adaptation with- out any human annotation. We use these topic distributions to compute topic-dependent lex- ical weighting probabilities and directly in- corporate them into our translation model as features. Conditioning lexical probabilities on the topic biases translations toward topic- relevant output, resulting in significant im- provements of up to 1 BLEU and 3 TER on Chinese to English translation over a strong baseline.

When Does Simulated Data Match Real Data? Comparing Model Calibration Functions using Genetic Algorithms - Stonedahl,Forrest; Rand, William (World Congress on Social Simulation (WCSS), Taipei, Taiwan, 2012)
Agent-based models can be manipulated to replicate real- world datasets, but choosing the best set of parameters to achieve this result can be difficult. To validate a model, the real-world dataset is often divided into a training and test set. The training set is used to calibrate the parameters and the test set is used to determine if the calibrated model represents the real-world data. The difference between the real-world data and the simulated data is determined using an error measure. When using an evolutionary computation technique to choose the parameters, this error measure becomes the fitness function, and choosing the appropriate measure becomes even more crucial for a successful calibration process. We survey the effect of five different error measures in the context of a toy problem and a real world problem (simulating on-line news consumption). We use each error measure in turn to calibrate on the training dataset, and then examine the results of all five error measures on both the training and testing datasets. For the toy problem, one measure was the Pareto-dominant choice for calibration, but no error measure dominated all the others for the real-world problem.

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

Accurate proteome-wide protein quantification from high-resolution 15N mass spectra - Zia Khan; Amini, Sasan; Bloom, Joshua S.; Ruse, Cristian; Caudy, Amy A.; Kruglyak, Leonid; Singh, Mona; Perlman, David H.; Tavazoie, Saeed (Genome Biology, 2011)
In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of 15N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach. We have addressed this challenge by introducing a new computational methodology for analyzing 15N spectra in which quantification is integrated with identification. Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods.PMID: 22182234

Action recognition using Partial Least Squares and Support Vector Machines - Ramadan,S.; Davis, Larry S. (Image Processing (ICIP), 2011 18th IEEE International Conference on, 2011)
We introduce an action recognition approach based on Partial Least Squares (PLS) and Support Vector Machines (SVM). We extract very high dimensional feature vectors representing spatio-temporal properties of actions and use multiple PLS regressors to find relevant features that distinguish amongst action classes. Finally, we use a multi-class SVM to learn and classify those relevant features. We applied our approach to INRIA's IXMAS dataset. Experimental results show that our method is superior to other methods applied to the IXMAS dataset.
Keywords: analysis; support; approach; multiclass; approximations; regression; dataset; action; dimensional; extraction; feature; extraction; image; feature; high; INRIA; IXMAS; least; machines; machines; very; partial; properties; support; recognition; recognition; least; regressors; spatiotemporal; squares; SVM; multiple; vector; vectors

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

Agent-based modeling in marketing: Guidelines for rigor - Rand, William; Rust,Roland T. (International Journal of Research in Marketing, 2011)
Agent-based modeling can illuminate how complex marketing phenomena emerge from simple decision rules. Marketing phenomena that are too complex for conventional analytical or empirical approaches can often be modeled using this approach. Agent-based modeling investigates aggregate phenomena by simulating the behavior of individual “agents,” such as consumers or organizations. Some useful examples of agent-based modeling have been published in marketing journals, but widespread acceptance of the agent-based modeling method and publication of this method in the highest-level marketing journals have been slowed by the lack of widely accepted standards of how to do agent-based modeling rigorously. We address this need by proposing guidelines for rigorous agent-based modeling. We demonstrate these guidelines, and the value of agent-based modeling for marketing research, through the use of an example. We use an agent-based modeling approach to replicate the Bass model of the diffusion of innovations, illustrating the use of the proposed guidelines to ensure the rigor of the analysis. We also show how extensions of the Bass model that would be difficult to carry out using traditional marketing research techniques are possible to implement using a rigorous agent-based approach.

Architecting for innovation - Koponen,Teemu; Shenker,Scott; Balakrishnan,Hari; Feamster, Nick; Ganichev,Igor; Ghodsi,Ali; Godfrey,P. Brighten; McKeown,Nick; Parulkar,Guru; Raghavan,Barath; Rexford,Jennifer; Arianfar,Somaya; et al. (SIGCOMM Comput. Commun. Rev., 2011)
We argue that the biggest problem with the current Internet architecture is not a particular functional deficiency, but its inability to accommodate innovation. To address this problem we propose a minimal architectural "framework" in which comprehensive architectures can reside. The proposed Framework for Internet Innovation (FII) --- which is derived from the simple observation that network interfaces should be extensible and abstract --- allows for a diversity of architectures to coexist, communicate, and evolve. We demonstrate FII's ability to accommodate diversity and evolution with a detailed examination of how information flows through the architecture and with a skeleton implementation of the relevant interfaces.
Keywords: diversity; Evolution; innovation; internet architecture

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.

Bacillus Anthracis Comparative Genome Analysis in Support of the Amerithrax Investigation - Rasko,David A; Worsham,Patricia L; Abshire,Terry G; Stanley,Scott T; Bannan,Jason D; Wilson,Mark R; Langham,Richard J; Decker,R. Scott; Jiang,Lingxia; Read,Timothy D.; Phillippy,Adam M; Salzberg,Steven L.; et al. (Proceedings of the National Academy of SciencesPNAS, 2011)
Before the anthrax letter attacks of 2001, the developing field of microbial forensics relied on microbial genotyping schemes based on a small portion of a genome sequence. Amerithrax, the investigation into the anthrax letter attacks, applied high-resolution whole-genome sequencing and comparative genomics to identify key genetic features of the letters’ Bacillus anthracis Ames strain. During systematic microbiological analysis of the spore material from the letters, we identified a number of morphological variants based on phenotypic characteristics and the ability to sporulate. The genomes of these morphological variants were sequenced and compared with that of the B. anthracis Ames ancestor, the progenitor of all B. anthracis Ames strains. Through comparative genomics, we identified four distinct loci with verifiable genetic mutations. Three of the four mutations could be directly linked to sporulation pathways in B. anthracis and more specifically to the regulation of the phosphorylation state of Spo0F, a key regulatory protein in the initiation of the sporulation cascade, thus linking phenotype to genotype. None of these variant genotypes were identified in single-colony environmental B. anthracis Ames isolates associated with the investigation. These genotypes were identified only in B. anthracis morphotypes isolated from the letters, indicating that the variants were not prevalent in the environment, not even the environments associated with the investigation. This study demonstrates the forensic value of systematic microbiological analysis combined with whole-genome sequencing and comparative genomics.

Believe Me—We Can Do This! Annotating Persuasive Acts in Blog Text - Anand,P.; King,J.; Jordan Boyd-Graber; Wagner,E.; Martell,C.; Oard, Douglas; Resnik, Philip (Workshops at the Twenty-Fifth AAAI Conference on Artificial Intelligence, 2011)

Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)? - Cho,Soowon; Zwick,Andreas; Regier,Jerome C; Mitter,Charles; Cummings, Michael P.; Yao,Jianxiu; Du,Zaile; Zhao,Hong; Kawahara,Akito Y; Weller,Susan; Davis,Donald R; Baixeras,Joaquin; et al. (Systematic BiologySyst Biol, 2011)
This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia ( > 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78–85% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A “more-genes-only” data set (41 taxa×26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.
Keywords: Ditrysia; gene sampling; Hexapoda; Lepidoptera; missing data; molecular phylogenetics; nuclear genes; taxon sampling

A Canonical Form for Testing Boolean Function Properties - Dana Dachman-Soled; Servedio, Rocco A. (Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques, 2011)
In a well-known result Goldreich and Trevisan (2003) showed that every testable graph property has a “canonical” tester in which a set of vertices is selected at random and the edges queried are the complete graph over the selected vertices. We define a similar-in-spirit canonical form for Boolean function testing algorithms, and show that under some mild conditions property testers for Boolean functions can be transformed into this canonical form. Our first main result shows, roughly speaking, that every “nice” family of Boolean functions that has low noise sensitivity and is testable by an “independent tester,” has a canonical testing algorithm. Our second main result is similar but holds instead for families of Boolean functions that are closed under ID-negative minors. Taken together, these two results cover almost all of the constant-query Boolean function testing algorithms that we know of in the literature, and show that all of these testing algorithms can be automatically converted into a canonical form.
Keywords: Algorithm Analysis and Problem Complexity; Boolean functions; Computation by Abstract Devices; Computer Communication Networks; Computer Graphics; Data structures; Discrete Mathematics in Computer Science; property testing

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.

Comparing Social Tags to Microblogs - Lai,V.; Rajashekar,C.; Rand, William (Privacy, security, risk and trust (passat), 2011 IEEE third international conference on and 2011 IEEE third international conference on social computing (socialcom), 2011)
As Internet usage and e-commerce grow, online social media serve as popular outlets for consumers to express sentiments about products. On Amazon, users can tag an album with a keyword, while tweets on Twitter represent a more natural conversation. The differing natures of these media make them difficult to compare. This project collects and analyzes social media data for newly released music albums and develops new methods of comparing a product's social tags to its microblogging data. It explores information retrieval and rank correlation measures as similarity measures, as well as term frequency-inverse document frequency (tf-idf) processing. We conclude that with sufficient Twitter activity about an album, social tags do represent the most frequent conversations occurring on Twitter. These results imply that managers can collect and analyze tags and use them as a proxy for most common consumer feedback from microblogging, which is more difficult to collect.
Keywords: (online); album; online; commerce; information; correlation; document; frequency-inverse; frequency; electronic; Internet; measure; social; measures; similarity; media; rank; networking; retrieval; microblog; music; retrieval; music; social; social; tags; term; usage; Twitter; e-commerce; information

Correcting Errors in Digital Lexicographic Resources Using a Dictionary Manipulation Language - Zajic, David; Maxwell,Michael; David Doermann; Rodrigues,Paul; Bloodgood,Michael (Electronic lexicography in the 21st century: new applications for new users (eLEX2011), 2011)
We describe a paradigm for combining manual and automatic error correction of noisy structured lexicographic data. Modifications to the structure and underlying text of the lexicographic data are expressed in a simple, interpreted programming language. Dictionary Manipulation Language (DML) commands identify nodes by unique identifiers, and manipulations are performed using simple commands such as create, move, set text, etc. Corrected lexicons are produced by applying sequences of DML commands to the source version of the lexicon. DML commands can be written manually to repair one-off errors or generated automatically to correct recurring problems. We discuss advantages of the paradigm for the task of editing digital bilingual dictionaries.

Detecting Structural Irregularity in Electronic Dictionaries Using Language Modeling - Rodrigues,Paul; Zajic, David; Bloodgood,Michael; Ye,Peng; David Doermann (Electronic lexicography in the 21st century: new applications for new users (eLEX2011), 2011)
Dictionaries are often developed using Extensible Markup Language (XML)-based standards. Very often, these standards allow many high-level repeating elements to represent lexical entries, and utilize descendants of these repeating elements to represent the structure within each lexical entry, in the form of an XML tree. In many cases, dictionaries are published that have errors and inconsistencies that would be too expensive to find manually. This paper discusses a method for dictionary writers to audit structural regularity across entries in a dictionary, quickly, by using statistical language modelling. The approach learns the patterns of XML nodes that could occur within an XML tree, and then calculates the probability of each XML tree in the dictionary against these patterns to look for entries that diverge from the norm.

Differential adaptive diffusion: Understanding diversity and learning whom to trust in viral marketing - Sharara,H.; Rand, William; Getoor, Lise (Fifth International AAAI Conference on Weblogs and Social Media, 2011)
Viral marketing mechanisms use the existing social network between customers to spread information about products and encourage product adoption. Existing viral marketing models focus on the dynamics of the diffusion process, however they typically: (a) only consider a single product campaign and (b) fail to model the evolution of the social network, as the trust between individuals changes over time, during the course of multiple campaigns. In this work, we propose an adaptive vi- ral marketing model which captures: (1) multiple different product campaigns, (2) the diversity in customer preferences among different product categories, and (3) changing con- fidence in peers’ recommendations over time. By applying our model to a real-world network extracted from the Digg social news website, we provide insights into the effects of network dynamics on the different products’ adoption. Our experiments show that our proposed model outperforms ear- lier non-adaptive diffusion models in predicting future prod- uct adoptions. We also show how this model can be used to explore new viral marketing strategies that are more success- ful than classic strategies which ignore the dynamic nature of social networks.

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

Disaggregated End-Use Energy Sensing for the Smart Grid - Jon Froehlich; Larson,E.; Gupta,S.; Cohn,G.; Reynolds,M.; Patel,S. (IEEE Pervasive Computing, 2011)
This article surveys existing and emerging disaggregation techniques for energy-consumption data and highlights signal features that might be used to sense disaggregated data in an easily installed and cost-effective manner.
Keywords: Calibration; disaggregated end-use energy sensing; Disaggregated energy sensing; disaggregation data techniques; Electricity; Energy consumption; Energy efficiency; energy-consumption data; Gas; Home appliances; Sensors; Smart grid; Smart grids; smart power grids; Sustainability; Water

Distributed Sensing and Processing for Multi-Camera Networks - Sankaranarayanan,Aswin C.; Chellapa, Rama; Baraniuk,Richard G. (Distributed Video Sensor NetworksDistributed Video Sensor Networks, 2011)
Sensor networks with large numbers of cameras are becoming increasingly prevalent in a wide range of applications, including video conferencing, motion capture, surveillance, and clinical diagnostics. In this chapter, we identify some of the fundamental challenges in designing such systems: robust statistical inference, computationally efficiency, and opportunistic and parsimonious sensing. We show that the geometric constraints induced by the imaging process are extremely useful for identifying and designing optimal estimators for object detection and tracking tasks. We also derive pipelined and parallelized implementations of popular tools used for statistical inference in non-linear systems, of which multi-camera systems are examples. Finally, we highlight the use of the emerging theory of compressive sensing in reducing the amount of data sensed and communicated by a camera network.

A Dual Framework and Algorithms for Targeted Online Data Delivery - Roitman,Haggai; Gal,Avigdor; Raschid, Louiqa (IEEE Transactions on Knowledge and Data Engineering, 2011)
A variety of emerging online data delivery applications challenge existing techniques for data delivery to human users, applications, or middleware that are accessing data from multiple autonomous servers. In this paper, we develop a framework for formalizing and comparing pull-based solutions and present dual optimization approaches. The first approach, most commonly used nowadays, maximizes user utility under the strict setting of meeting a priori constraints on the usage of system resources. We present an alternative and more flexible approach that maximizes user utility by satisfying all users. It does this while minimizing the usage of system resources. We discuss the benefits of this latter approach and develop an adaptive monitoring solution Satisfy User Profiles (SUPs). Through formal analysis, we identify sufficient optimality conditions for SUP. Using real (RSS feeds) and synthetic traces, we empirically analyze the behavior of SUP under varying conditions. Our experiments show that we can achieve a high degree of satisfaction of user utility when the estimations of SUP closely estimate the real event stream, and has the potential to save a significant amount of system resources. We further show that SUP can exploit feedback to improve user utility with only a moderate increase in resource utilization.
Keywords: client/server multitier systems; distributed databases; online data delivery.; online information services

Entropy rate superpixel segmentation - Ming-Yu Liu; Tuzel, O.; Ramalingam, S.; Chellapa, Rama (2011 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2011)
We propose a new objective function for superpixel segmentation. This objective function consists of two components: entropy rate of a random walk on a graph and a balancing term. The entropy rate favors formation of compact and homogeneous clusters, while the balancing function encourages clusters with similar sizes. We present a novel graph construction for images and show that this construction induces a matroid - a combinatorial structure that generalizes the concept of linear independence in vector spaces. The segmentation is then given by the graph topology that maximizes the objective function under the matroid constraint. By exploiting submodular and mono-tonic properties of the objective function, we develop an efficient greedy algorithm. Furthermore, we prove an approximation bound of ½ for the optimality of the solution. Extensive experiments on the Berkeley segmentation benchmark show that the proposed algorithm outperforms the state of the art in all the standard evaluation metrics.
Keywords: balancing function; Berkeley segmentation benchmark; Complexity theory; Entropy; entropy rate; graph construction; graph theory; graph topology; greedy algorithm; Greedy algorithms; homogeneous clusters; Image edge detection; Image segmentation; matrix algebra; matroid constraint; measurement; pattern clustering; Random variables; standard evaluation metrics; superpixel segmentation; vector spaces

Estimating Functional Agent-Based Models: An Application to Bid Shading in Online Markets Format - Guo,Wei; Jank,Wolfgang; Rand, William (Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2011), 2011)
Bid shading is a common strategy in online auctions to avoid the "winner’s curse". While almost all bidders shade their bids, at least to some degree, it is impossible to infer the degree and volume of shaded bids directly from observed bidding data. In fact, most bidding data only allows us to observe the resulting price process, i.e. whether prices increase fast (due to little shading) or whether they slow down (when all bidders shade their bids). In this work, we propose an agent-based model that simulates bidders with different bidding strategies and their interaction with one another. We calibrate that model (and hence estimate properties about the propensity and degree of shaded bids) by matching the emerging simulated price process with that of the observed auction data using genetic algorithms. From a statistical point of view, this is challenging because we match functional draws from simulated and real price processes. We propose several competing fitness functions and explore how the choice alters the resulting ABM calibration. We apply our model to the context of eBay auctions for digital cameras and show that a balanced fitness function yields the best results.
Keywords: Agent-based modeling; business; Calibration; Genetic algorithms; internet auctions; simulation

Exploiting Statically Schedulable Regions in Dataflow Programs - Gu, Ruirui; Janneck, Jörn W.; Raulet, Mickaël; Bhattacharyya, Shuvra S. (Journal of Signal Processing Systems, 2011)
Dataflow descriptions have been used in a wide range of Digital Signal Processing (DSP) applications, such as multi-media processing, and wireless communications. Among various forms of dataflow modeling, Synchronous Dataflow (SDF) is geared towards static scheduling of computational modules, which improves system performance and predictability. However, many DSP applications do not fully conform to the restrictions of SDF modeling. More general dataflow models, such as CAL (Eker and Janneck 2003), have been developed to describe dynamically-structured DSP applications. Such generalized models can express dynamically changing functionality, but lose the powerful static scheduling capabilities provided by SDF. This paper focuses on the detection of SDF-like regions in dynamic dataflow descriptions—in particular, in the generalized specification framework of CAL. This is an important step for applying static scheduling techniques within a dynamic dataflow framework. Our techniques combine the advantages of different dataflow languages and tools, including CAL (Eker and Janneck 2003), DIF (Hsu et al. 2005) and CAL2C (Roquier et al. 2008). In addition to detecting SDF-like regions, we apply existing SDF scheduling techniques to exploit the static properties of these regions within enclosing dynamic dataflow models. Furthermore, we propose an optimized approach for mapping SDF-like regions onto parallel processing platforms such as multi-core processors.
Keywords: Cal; Circuits and Systems; Computer Imaging, Vision, Pattern Recognition and Graphics; Dataflow; DIF; Electrical Engineering; Image Processing and Computer Vision; multicore processors; pattern recognition; Quasi-static scheduling; Signal, Image and Speech Processing

Face verification using large feature sets and one shot similarity - Guo,Huimin; Robson Schwartz,W.; Davis, Larry S. (Biometrics (IJCB), 2011 International Joint Conference on, 2011)
We present a method for face verification that combines Partial Least Squares (PLS) and the One-Shot similarity model[28]. First, a large feature set combining shape, texture and color information is used to describe a face. Then PLS is applied to reduce the dimensionality of the feature set with multi-channel feature weighting. This provides a discriminative facial descriptor. PLS regression is used to compute the similarity score of an image pair by One-Shot learning. Given two feature vector representing face images, the One-Shot algorithm learns discriminative models exclusively for the vectors being compared. A small set of unlabeled images, not containing images belonging to the people being compared, is used as a reference (negative) set. The approach is evaluated on the Labeled Face in the Wild (LFW) benchmark and shows very comparable results to the state-of-the-art methods (achieving 86.12% classification accuracy) while maintaining simplicity and good generalization ability.
Keywords: analysis; set; approximations; regression; descriptor; labeled; Face; feature; in; information; face; information; texture; least; LFW; PLS; PLS; recognition; least; regression; color; sets; one; shot; similarity; partial; squares; squares; shape; the; theory; verification; facial; wild; large

A Fast Bilinear Structure from Motion Algorithm Using a Video Sequence and Inertial Sensors - Ramachandran, M.; Veeraraghavan,A.; Chellapa, Rama (IEEE Transactions on Pattern Analysis and Machine Intelligence, 2011)
In this paper, we study the benefits of the availability of a specific form of additional information-the vertical direction (gravity) and the height of the camera, both of which can be conveniently measured using inertial sensors and a monocular video sequence for 3D urban modeling. We show that in the presence of this information, the SfM equations can be rewritten in a bilinear form. This allows us to derive a fast, robust, and scalable SfM algorithm for large scale applications. The SfM algorithm developed in this paper is experimentally demonstrated to have favorable properties compared to the sparse bundle adjustment algorithm. We provide experimental evidence indicating that the proposed algorithm converges in many cases to solutions with lower error than state-of-art implementations of bundle adjustment. We also demonstrate that for the case of large reconstruction problems, the proposed algorithm takes lesser time to reach its solution compared to bundle adjustment. We also present SfM results using our algorithm on the Google StreetView research data set.
Keywords: 3D urban modeling; algorithms; Artificial intelligence; CAMERAS; computer vision.; Convergence; fast bilinear structure; Google StreetView research data set; Image Interpretation, Computer-Assisted; Image reconstruction; Image sensors; Image sequences; Imaging, Three-Dimensional; inertial sensors; Information Storage and Retrieval; Linear systems; minimization; MOTION; motion algorithm; Motion estimation; multiple view geometry; Pattern Recognition, Automated; Sensors; SfM equations; sparse bundle adjustment algorithm; structure from motion; Three dimensional displays; vertical direction; Video Recording; video sequence; video signal processing

From slacktivism to activism: participatory culture in the age of social media - Rotman,Dana; Vieweg,Sarah; Yardi,Sarita; Chi,Ed; Preece,Jenny; Shneiderman, Ben; Pirolli,Peter; Glaisyer,Tom (Proceedings of the 2011 annual conference extended abstracts on Human factors in computing systems, 2011)
Social networking sites (e.g. Facebook), microblogging services (e.g. Twitter), and content-sharing sites (e.g. YouTube and Flickr) have introduced the opportunity for wide-scale, online social participation. Visibility of national and international priorities such as public health, political unrest, disaster relief, and climate change has increased, yet we know little about the benefits - and possible costs - of engaging in social activism via social media. These powerful social issues introduce a need for scientific research into technology mediated social participation. What are the actual, tangible benefits of "greening" Twitter profile pictures in support of the Iranian elections? Does cartooning a Facebook profile picture really raise awareness of child abuse? Are there unintended negative effects through low-risk, low-cost technology-mediated participation? And, is there a difference - in both outcome and engagement level - between different types of online social activism? This SIG will investigate technology mediated social participation through a critical lens, discussing both the potential positive and negative outcomes of such participation. Approaches to designing for increased participation, evaluating effects of participation, and next steps in scientific research directions will be discussed.
Keywords: activism; change; design; participation; slacktivism; social media

Future link prediction in the blogosphere for recommendation - Wu,S.; Raschid, Louiqa; Rand, William (Proceedings of the International Conference on Weblogs and Social Media (ICWSM), 2011)
The phenomenal growth in both scale and importance of so-cial media such as blogs, micro-blogs and user-generated content, has created a need for tools that monitor information diffusion and make recommendations within these platforms. An essential element of social media, particularly blogs, is the hyperlink graph that connects various pieces of content. There are two types of links within the blogosphere; one from blog post to blog post, and another from blog post to blog channel (an event stream of blog posts). These links can be viewed as a proxy for the flow of information between blog channels and to reflect influence. Given this assumption about links, the ability to predict future links can facilitate the monitoring of information diffusion, making recommen- dations, and word-of-mouth (WOM) marketing. We propose different methods for link predictions and we evaluate these methods on an extensive blog dataset.

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

The Importance of Chitin in the Marine Environment - Souza,C. P.; Almeida,B. C.; Rita R Colwell; Rivera,I. N. G. (Marine Biotechnology, 2011)
Chitin is the most abundant renewable polymer in the oceans and is an important source of carbon and nitrogen for marine organisms. The process of chitin degradation is a key step in the cycling of nutrients in the oceans and chitinolytic bacteria play a significant role in this process. These bacteria are autochthonous to both marine and freshwater ecosystems and produce chitinases that degrade chitin, an insoluble polysaccharide, to a biologically useful form. In this brief review, a description of the structure of chitin and diversity of chitinolytic bacteria in the oceans is provided, in the context of the significance of chitin degradation for marine life.

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)

Increased gene sampling provides stronger support for higher-level groups within gracillariid leaf mining moths and relatives (Lepidoptera: Gracillariidae) - Kawahara,A. Y; Ohshima,I; Kawakita,A; Regier,J. C; Mitter,C; Cummings, Michael P.; Davis,DR; Wagner,DL; De Prinis,J; Lopez-Vaamonde,C (BMC Evol Biol, 2011)

Increased gene sampling yields robust support for higher‐level clades within Bombycoidea (Lepidoptera) - Zwick,Andreas; Regier,Jerome C; Mitter,Charles; Cummings, Michael P. (Systematic Entomology, 2011)
This study has as its primary aim the robust resolution of higher-level relationships within the lepidopteran superfamily Bombycoidea. Our study builds on an earlier analysis of five genes (∼6.6 kbp) sequenced for 50 taxa from Bombycoidea and its sister group Lasiocampidae, plus representatives of other macrolepidoteran superfamilies. The earlier study failed to yield strong support for the monophyly of and basal splits within Bombycoidea, among others. Therefore, in an effort to increase support specifically for higher-level nodes, we generated 11.7 kbp of additional data from 20 genes for 24 of 50 bombycoid and lasiocampid taxa. The data from the genes are all derived from protein-coding nuclear genes previously used to resolve other lepidopteran relationships. With these additional data, all but a few higher-level nodes are strongly supported. Given our decision to minimize project costs by augmenting genes for only 24 of the 50 taxa, we explored whether the resulting pattern of missing data in the combined-gene matrix introduced a nonphylogenetic bias, a possibility reported by others. This was achieved by comparing node support values (i.e. nonparametric bootstrap values) based on likelihood and parsimony analyses of three datasets that differ in their number of taxa and level of missing data: 50 taxa/5 genes (dataset A), 50 taxa/25 genes (dataset B) and 24 taxa/25 genes (dataset C). Whereas datasets B and C provided similar results for common nodes, both frequently yielded higher node support relative to dataset A, arguing that: (i) more data yield increased node support and (ii) partial gene augmentation does not introduce an obvious nonphylogenetic bias. A comparison of single-gene bootstrap analyses identified four nodes for which one or two of the 25 genes provided modest to strong support for a grouping not recovered by the combined-gene result. As a summary proposal, two of these four groupings (one each within Bombycoidea and Lasiocampidae) were deemed sufficiently problematic to regard them as unresolved trichotomies. Since the alternative groupings were always highly localized on the tree, we did not judge a combined-gene analysis to present a problem outside those regions. Based on our robustly resolved results, we have revised the classification of Bombycoidea: the family Bombycidae is restricted to its nominate subfamily, and its tribe Epiini is elevated to subfamily rank (Epiinae stat.rev.), whereas the bombycid subfamily Phiditiinae is reinstated as a separate family (Phiditiidae stat.rev.). The bombycid subfamilies Oberthueriinae Kuznetzov & Stekolnikov, 1985, syn.nov. and Prismostictinae Forbes, 1955, syn.nov., and the family Mirinidae Kozlov, 1985, syn.nov. are established as subjective junior synonyms of Endromidae Boisduval, 1828. The family Anthelidae (Lasiocampoidea) is reincluded in the superfamily Bombycoidea.

Vibrio Cholerae O1 Detection in Estuarine and Coastal Zooplankton - Martinelli Filho,José E.; Lopes,Rubens M.; Rivera,Irma N. G.; Rita R Colwell (Journal of Plankton Research, 2011)
Vibrio cholerae is an autochthonous marine bacterium, and its association with diverse planktonic crustaceans has been extensively investigated; however, the presence of V. cholerae on individuals of most phyla of planktonic animals is still incompletely understood. The objective of this study was to analyze the distribution of V. cholerae serogroup O1 associated with specific zooplankton taxa in an estuary and the adjacent continental shelf of the southeastern Brazilian coast. The occurrence of the bacterium was assessed in zooplankton samples, specifically on the most abundant taxa, using direct fluorescence assay (DFA) and direct viable count–direct fluorescence assay (DVC–DFA) methods. Vibrio cholerae O1 was detected in 88% of samples collected from the Santos-Bertioga estuary and in 67% of samples from the shelf. The salinity of the estuarine water ranged from 21.8 to 34.6, significantly lower than the shelf water which was 32.1–36.1. Salinity was the only environmental variable measured that displayed a significant correlation with the presence of V. cholerae (P< 0.05). Vibrio cholerae O1 was detected in chaetognaths, pluteus larvae of echinoderms and planktonic fish eggs (Engraulidae), all new sites for this bacterium.
Keywords: DFA; estuary; plankton; Southwest Atlantic

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

Link prediction by de-anonymization: How We Won the Kaggle Social Network Challenge - Narayanan, A.; Elaine Shi; Rubinstein, B.I.P. (2011)
This paper describes the winning entry to the IJCNN 2011 Social Network Challenge run by Kaggle.com. The goal of the contest was to promote research on real-world link prediction, and the dataset was a graph obtained by crawling the popular Flickr social photo sharing website, with user identities scrubbed. By de-anonymizing much of the competition test set using our own Flickr crawl, we were able to effectively game the competition. Our attack represents a new application of de-anonymization to gaming machine learning contests, suggesting changes in how future competitions should be run. We introduce a new simulated annealing-based weighted graph matching algorithm for the seeding step of de-anonymization. We also show how to combine de-anonymization with link prediction-the latter is required to achieve good performance on the portion of the test set not de-anonymized-for example by training the predictor on the de-anonymized portion of the test set, and combining probabilistic predictions from de-anonymization and link prediction.
Keywords: deanonymization; Flickr social photo sharing Website; graph theory; IJCNN 2011 social network challenge; Kaggle social network challenge; learning (artificial intelligence); machine learning; realworld link prediction; Simulated annealing; simulated annealing-based weighted graph matching algorithm; social networking (online)

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

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.

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.

New models and algorithms for throughput maximization in broadcast scheduling - Chekuri,C.; Gal,A.; Im,S.; Khuller, Samir; Li,J.; McCutchen,R.; Moseley,B.; Raschid, Louiqa (Approximation and Online Algorithms, 2011)

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

Optimal Verification of Operations on Dynamic Sets - Charalampos Papamanthou; Tamassia, Roberto; Triandopoulos, Nikos (Advances in Cryptology – CRYPTO 2011, 2011)
We study the design of protocols for set-operation verification, namely the problem of cryptographically checking the correctness of outsourced set operations performed by an untrusted server over a dynamic collection of sets that are owned (and updated) by a trusted source. We present new authenticated data structures that allow any entity to publicly verify a proof attesting the correctness of primitive set operations such as intersection, union, subset and set difference. Based on a novel extension of the security properties of bilinear-map accumulators as well as on a primitive called accumulation tree, our protocols achieve optimal verification and proof complexity (i.e., only proportional to the size of the query parameters and the answer), as well as optimal update complexity (i.e., constant), while incurring no extra asymptotic space overhead. The proof construction is also efficient, adding a logarithmic overhead to the computation of the answer of a set-operation query. In contrast, existing schemes entail high communication and verification costs or high storage costs. Applications of interest include efficient verification of keyword search and database queries. The security of our protocols is based on the bilinear q-strong Diffie-Hellman assumption.
Keywords: Computer Communication Networks; computers and society; Data Encryption; Discrete Mathematics in Computer Science; Management of Computing and Information Systems; Systems and Data Security

Overview of the MPEG Reconfigurable Video Coding Framework - Bhattacharyya, Shuvra S.; Eker, Johan; Janneck, Jörn W.; Lucarz, Christophe; Mattavelli, Marco; Raulet, Mickaël (Journal of Signal Processing Systems, 2011)
Video coding technology in the last 20 years has evolved producing a variety of different and complex algorithms and coding standards. So far the specification of such standards, and of the algorithms that build them, has been done case by case providing monolithic textual and reference software specifications in different forms and programming languages. However, very little attention has been given to provide a specification formalism that explicitly presents common components between standards, and the incremental modifications of such monolithic standards. The MPEG Reconfigurable Video Coding (RVC) framework is a new ISO standard currently under its final stage of standardization, aiming at providing video codec specifications at the level of library components instead of monolithic algorithms. The new concept is to be able to specify a decoder of an existing standard or a completely new configuration that may better satisfy application-specific constraints by selecting standard components from a library of standard coding algorithms. The possibility of dynamic configuration and reconfiguration of codecs also requires new methodologies and new tools for describing the new bitstream syntaxes and the parsers of such new codecs. The RVC framework is based on the usage of a new actor/ dataflow oriented language called CAL for the specification of the standard library and instantiation of the RVC decoder model. This language has been specifically designed for modeling complex signal processing systems. CAL dataflow models expose the intrinsic concurrency of the algorithms by employing the notions of actor programming and dataflow. The paper gives an overview of the concepts and technologies building the standard RVC framework and the non standard tools supporting the RVC model from the instantiation and simulation of the CAL model to software and/or hardware code synthesis.
Keywords: CAL actor language; Circuits and Systems; Code synthesis; Computer Imaging, Vision, Pattern Recognition and Graphics; Dataflow programming; Electrical Engineering; Image Processing and Computer Vision; pattern recognition; Reconfigurable Video Coding; Signal, Image and Speech Processing

P2C2: Programmable pixel compressive camera for high speed imaging - Reddy, D.; Veeraraghavan,A.; Chellapa, Rama (2011 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2011)
We describe an imaging architecture for compressive video sensing termed programmable pixel compressive camera (P2C2). P2C2 allows us to capture fast phenomena at frame rates higher than the camera sensor. In P2C2, each pixel has an independent shutter that is modulated at a rate higher than the camera frame-rate. The observed intensity at a pixel is an integration of the incoming light modulated by its specific shutter. We propose a reconstruction algorithm that uses the data from P2C2 along with additional priors about videos to perform temporal super-resolution. We model the spatial redundancy of videos using sparse representations and the temporal redundancy using brightness constancy constraints inferred via optical flow. We show that by modeling such spatio-temporal redundancies in a video volume, one can faithfully recover the underlying high-speed video frames from the observed low speed coded video. The imaging architecture and the reconstruction algorithm allows us to achieve temporal super-resolution without loss in spatial resolution. We implement a prototype of P2C2 using an LCOS modulator and recover several videos at 200 fps using a 25 fps camera.
Keywords: Brightness; brightness constancy constraint; camera sensor; CAMERAS; compressive video sensing; high speed imaging; high-speed video frames; Image sequences; imaging; imaging architecture; independent shutter; Liquid crystal on silicon; low speed coded video; Modulation; optical flow; P2C2; programmable pixel compressive camera; reconstruction algorithm; sparse representation; Spatial resolution; spatio-temporal redundancies; temporal redundancy; temporal super-resolution; video coding

Practical Data-Leak Prevention for Legacy Applications in Enterprise Networks - Mundada,Y.; Ramachandran,A.; Tariq,M.B.; Feamster, Nick (Georgia Institute of Technology, 2011)
Organizations must control where private information spreads; this problem is referred to in the industry as data leak prevention. Commercial solutions for DLP are based on scanning content; these impose high overhead and are easily evaded. Research solutions for this problem, information flow control, require rewriting applications or running a custom operating system, which makes these approaches difficult to deploy. They also typically enforce information flow control on a single host, not across a network, making it difficult to implement an information flow control policy for a network of machines. This paper presents Pedigree, which enforces information flow control across a network for legacy applications. Pedigree allows enterprise administrators and users to associate a label with each file and process; a small, trusted module on the host uses these labels to determine whether two processes on the same host can communicate. When a process attempts to communicate across the network, Pedigree tracks these information flows and enforces information flow control either at end-hosts or at a network switch. Pedigree allows users and operators to specify network-wide information flow policies rather than having to specify and implement policies for each host. Enforcing information flow policies in the network allows Pedigree to operate in networks with heterogeneous devices and operating systems. We present the design and implementation of Pedigree, show that it can prevent data leaks, and investigate its feasibility and usability in common environments.

Predicting author blog channels with high value future posts for monitoring - Wu,S.; Elsayed,T.; Rand, William; Raschid, Louiqa (Proceedings of the Twenty-Fifth Conference on Artificial Intelligence (AAAI), 2011)
The phenomenal growth of social media, both in scale andimportance, has created a unique opportunity to track infor- mation diffusion and the spread of influence, but can also make efficient tracking difficult. Given data streams rep- resenting blog posts on multiple blog channels and a focal query post on some topic of interest, our objective is to pre- dict which of those channels are most likely to contain a fu- ture post that is relevant, or similar, to the focal query post. We denote this task as the future author prediction problem (FAPP). This problem has applications in information diffu- sion for brand monitoring and blog channel personalization and recommendation. We develop prediction methods in- spired by (naıve) information retrieval approaches that use historical posts in the blog channel for prediction. We also train a ranking support vector machine (SVM) to solve the problem. We evaluate our methods on an extensive social media dataset; despite the difficulty of the task, all methods perform reasonably well. Results show that ranking SVM prediction can exploit blog channel and diffusion characteris- tics to improve prediction accuracy. Moreover, it is surpris- ingly good for prediction in emerging topics and identifying inconsistent authors.

Privacy-preserving aggregation of time-series data - Elaine Shi; Chan, T.; Rieffel, E.; Chow, R.; Song,D. (2011)
We consider how an untrusted data aggregator canlearn desired statistics over multiple participants’ data, without compromising each individual’s privacy. We propose a construction that allows a group of partici- pants to periodically upload encrypted values to a data aggregator, such that the aggregator is able to compute the sum of all participants’ values in every time period, but is unable to learn anything else. We achieve strong privacy guarantees using two main techniques. First, we show how to utilize applied cryptographic techniques to allow the aggregator to decrypt the sum from multiple ciphertexts encrypted under different user keys. Second, we describe a distributed data randomization procedure that guarantees the differential privacy of the outcome statistic, even when a subset of participants might be compromised.

Recommendations in social media for brand monitoring - Wu,Shanchan; Rand, William; Raschid, Louiqa (Proceedings of the fifth ACM conference on Recommender systems, 2011)
We present a recommendation system for social media that draws upon monitoring and prediction methods. We use historical posts on some focal topic or historical links to a focal blog channel to recommend a set of authors to follow. Such a system would be useful for brand managers interested in monitoring conversations about their products. Our recommendations are based on a prediction system that trains a ranking Support Vector Machine (RSVM) using multiple features including the content of a post, similarity between posts, links between posts and/or blog channels, and links to external websites. We solve two problems, Future Author Prediction (FAP) and Future Link Prediction (FLP), and apply the prediction outcome to make recommendations. Using an extensive experimental evaluation on a blog dataset, we demonstrate the quality and value of our recommendations.
Keywords: blog; brand monitoring; recommendation; social media

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

Secure computation with sublinear amortized work - Gordon,D.; Katz, Jonathan; Kolesnikov,V.; Malkin,T.; Raykova,M.; Vahlis,Y. (Cryptology ePrint Archive, Report 2011/482, 2011)
Traditional approaches to secure computation begin by representing the function f beingcomputed as a circuit. For any function f that depends on each of its inputs, this implies a protocol with complexity at least linear in the input size. In fact, linear running time is inherent for secure computation of non-trivial functions, since each party must “touch” every bit of their input lest information about other party’s input be leaked. This seems to rule out many interesting applications of secure computation in scenarios where at least one of the inputs is huge and sublinear-time algorithms can be utilized in the insecure setting; private database search is a prime example. We present an approach to secure two-party computation that yields sublinear-time proto- cols, in an amortized sense, for functions that can be computed in sublinear time on a random access machine (RAM). Furthermore, a party whose input is “small” is required to maintain only small state. We provide a generic protocol that achieves the claimed complexity, based on any oblivious RAM and any protocol for secure two-party computation. We then present an optimized version of this protocol, where generic secure two-party computation is used only for evaluating a small number of simple operations.

Secure Efficient Multiparty Computing of Multivariate Polynomials and Applications - Dana Dachman-Soled; Malkin, Tal; Raykova, Mariana; Yung, Moti (Applied Cryptography and Network Security, 2011)
We present a robust secure methodology for computing functions that are represented as multivariate polynomials where parties hold different variables as private inputs. Our generic efficient protocols are fully black-box and employ threshold additive homomorphic encryption; they do not assume honest majority, yet are robust in detecting any misbehavior. We achieve solutions that take advantage of the algebraic structure of the polynomials, and are polynomial-time in all parameters (security parameter, polynomial size, polynomial degree, number of parties). We further exploit a “round table” communication paradigm to reduce the complexity in the number of parties. A large collection of problems are naturally and efficiently represented as multivariate polynomials over a field or a ring: problems from linear algebra, statistics, logic, as well as operations on sets represented as polynomials. In particular, we present a new efficient solution to the multi-party set intersection problem, and a solution to a multi-party variant of the polynomial reconstruction problem.
Keywords: additive homomorphic encryption; Algorithm Analysis and Problem Complexity; Computer Communication Networks; Data Encryption; Discrete Mathematics in Computer Science; Management of Computing and Information Systems; multiparty set intersection; multivariate polynomial evaluation; secret sharing; secure multiparty computation; Systems and Data Security; threshold cryptosystems

Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language - Resnik, Philip (Arxiv preprint arXiv:1105.5444, 2011)

SilverLine: Data and Network Isolation for Cloud Services - Mundada,Y.; Ramachandran,A.; Feamster, Nick (2nd USENIX Workshop on Hot Topics in Cloud Computing, 2011)
Although cloud computing service providers offer op-portunities for improving the administration, reliability, and maintenance of hosted services, they also concen- trate network resources and data in a small number of cloud service providers. The concentration of data and resources also entails various associated risks, including sharing the underlying infrastructure with unknown (and untrusted) tenants and relying on the availability and se- curity of the underlying infrastructure itself. These se- curity risks represent some of the most significant bar- riers to the adoption of cloud-based services. To begin tackling these risks, a cloud hosting infrastructure should provide strong guarantees for resource and data isolation. This paper examines data and network isolation prob- lems with today’s cloud hosting infrastructures and pro- poses SilverLine, a collection of techniques to improve data and network isolation for a cloud tenants’ service.

Spam or ham?: characterizing and detecting fraudulent "not spam" reports in web mail systems - Ramachandran,Anirudh; Dasgupta,Anirban; Feamster, Nick; Weinberger,Kilian (Proceedings of the 8th Annual Collaboration, Electronic messaging, Anti-Abuse and Spam Conference, 2011)
Web mail providers rely on users to "vote" to quickly and col-laboratively identify spam messages. Unfortunately, spammers have begun to use bots to control large collections of compromised Web mail accounts not just to send spam, but also to vote "not spam" on incoming spam emails in an attempt to thwart collaborative filtering. We call this practice a vote gaming attack. This attack confuses spam filters, since it causes spam messages to be mislabeled as legitimate; thus, spammer IP addresses can continue sending spam for longer. In this paper, we introduce the vote gaming attack and study the extent of these attacks in practice, using four months of email voting data from a large Web mail provider. We develop a model for vote gaming attacks, explain why existing detection mechanisms cannot detect them, and develop a new, scalable clustering-based detection method that identifies compromised accounts that engage in vote-gaming attacks. Our method detected 1.1 million potentially compromised accounts with only a 0.17% false positive rate, which is nearly 10 times more effective than existing clustering methods used to detect bots that send spam from compromised Web mail accounts.

Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral - Lopez, J.V.; Ledger, A.; Santiago-Vázquez, L.Z.; Pop, Mihai; Sommer, D.D.; Ranzer, L.K.; Feldman, R.A.; Russell, G.K. (Electronic Journal of Biotechnology, 2011)

A survey of virtual LAN usage in campus networks - Yu,Minlan; Rexford,J.; Sun,Xin; Rao,Sanjay; Feamster, Nick (Communications Magazine, IEEE, 2011)
VLANs are widely used in today's enterprise networks to improve Ethernet scalability and support network policies. However, manuals and textbooks offer very little information about how VLANs are actually used in practice. Through discussions with network administrators and analysis of configuration data, we describe how three university campuses and one academic department use VLANs to achieve a variety of goals. We argue that VLANs are ill-suited to some of these goals (e.g., VLANs are often used to realize access control policies, but constrain the types of policies that can be expressed). Furthermore, the use of VLANs leads to significant complexity in the configuration of network devices.
Keywords: academic department; campus network; educational computing; Educational institutions; Ethernet scalability; Local area networks; network policy support; university campus; virtual LAN usage; VLAN

TreeCovery: Coordinated dual treemap visualization for exploring the Recovery Act - Rios-Berrios,Miguel; Sharma,Puneet; Lee,Tak Yeon; Schwartz,Rachel; Shneiderman, Ben (Government Information Quarterly, 2011)
The American Recovery and Reinvestment Act dedicated $787 billion to stimulate the U.S. economy and mandated the release of the data describing the exact distribution of that money. The dataset is a large and complex one; one of its distinguishing features is its bi-hierarchical structure, arising from the distribution of money through agencies to specific projects and the natural aggregation of awards based on location. To offer a comprehensive overview of the data, a visualization must incorporate both these hierarchies. We present TreeCovery, a tool that accomplishes this through the use of two coordinated treemaps. The tool includes a number of innovative features, including coordinated zooming and filtering and a proportional highlighting technique across the two trees. TreeCovery was designed to facilitate data exploration, and initial user studies suggest that it will be helpful in insight generation. RATB (Recovery Accountability and Transparency Board) has tested TreeCovery and is considering including the concept in their visual analytics.
Keywords: Recovery Act; user interface; Visual analytic

When does simulated data match real data? - Stonedahl,Forrest; Anderson,David; Rand, William (Proceedings of the 13th annual conference companion on Genetic and evolutionary computation, 2011)
Agent-based models can replicate real-world patterns, but finding parameters that achieve the best match can be difficult. To validate a model, a real-world dataset is often divided into a training set (to calibrate the parameters) and a test set (to validate the calibrated model). The difference between the training and test data and the simulated data is determined using an error measure. In the context of evolutionary computation techniques, the error measure also serves as a fitness function, and thus affects evolutionary search dynamics. We survey the effect of five different error measures on both a toy problem and a real world problem of matching a model to empirical online news consumption behavior. We use each error measure separately for calibration on the training dataset, and then examine the results of all five error measures on both the training and testing datasets. We show that certain error measures sometimes serve as better fitness functions than others, and in fact using one error measure may result in better calibration (on a different measure) than using the different measure directly. For the toy problem, the Pearson's correlation measure dominated all other measures, but no single error measure was Pareto dominant for the real world problem.
Keywords: Agent-based modeling; business; Calibration; Genetic algorithms; information search; network analysis

Annotated RDF - Udrea,Octavian; Recupero,Diego Reforgiato; V.S. Subrahmanian (ACM Trans. Comput. Logic, 2010)
Real-world use of RDF requires the ability to transparently represent and explain metadata associated with RDF triples. For example, when RDF triples are extracted automatically by information extraction programs, there is a need to represent where the triples came from, what their temporal validity is, and how certain we are that the triple is correct. Today, there is no theoretically clean and practically scalable mechanism that spans these different needs - reification is the only solution propose to date, and its implementations have been ugly. In this paper, we present Annotated RDF (or aRDF for short) in which RDF triples are annotated by members of a partially ordered set (with bottom element) that can be selected in any way desired by the user. We present a formal declarative semantics (model theory) for annotated RDF and develop algorithms to check consistency of aRDF theories and to answer queries to aRDF theories. We show that annotated RDF supports users who need to think about the uncertainty, temporal aspects, and provenance of the RDF triples in an RDF database. We develop a prototype aRDF implementation and show that our algorithms work efficiently even on real world data sets containing over 10 million triples.
Keywords: annotated RDF; Query processing; view maintenance

Applications of a Simple Characterization of Human Gait in Surveillance - Yang Ran; Qinfen Zheng; Chellapa, Rama; Strat, T.M. (Systems, Man, and Cybernetics, Part B: Cybernetics, IEEE Transactions on, 2010)
Applications of a simple spatiotemporal characterization of human gait in the surveillance domain are presented. The approach is based on decomposing a video sequence into x-t slices, which generate periodic patterns referred to as double helical signatures (DHSs). The features of DHS are given as follows: 1) they naturally encode the appearance and kinematics of human motion and reveal geometric symmetries and 2) they are effective and efficient for recovering gait parameters and detecting simple events. We present an iterative local curve embedding algorithm to extract the DHS from video sequences. Two applications are then considered. First, the DHS is used for simultaneous segmentation and labeling of body parts in cluttered scenes. Experimental results showed that the algorithm is robust to size, viewing angles, camera motion, and severe occlusion. Then, the DHS is used to classify load-carrying conditions. By examining various symmetries in DHS, activities such as carrying, holding, and walking with objects that are attached to legs are detected. Our approach possesses several advantages: a compact representation that can be computed in real time is used; furthermore, it does not depend on silhouettes or landmark tracking, which are sensitive to errors in background subtraction stage.
Keywords: algorithms; Artificial intelligence; Automated; Photography; Reproducibility of Results; Sensitivity and Specificity; Video Recording; Biometry; Computer-Assisted; Pattern Recognition; double helical signatures; Gait; gait analysis; human gait; human motion kinematics; HUMANS; Image Enhancement; Image Interpretation; Image motion analysis; iterative local curve embedding algorithm; Object detection; simple spatiotemporal characterization; video sequence; Video surveillance

Automated generation of an efficient MPEG-4 Reconfigurable Video Coding decoder implementation - Gu, Ruirui; Piat, J.; Raulet, M.; Janneck, J.W.; Bhattacharyya, Shuvra S. (2010 Conference on Design and Architectures for Signal and Image Processing (DASIP), 2010)
This paper proposes an automatic design flow from user-friendly design to efficient implementation of video processing systems. This design flow starts with the use of coarse-grain dataflow representations based on the CAL language, which is a complete language for dataflow programming of embedded systems. Our approach integrates previously developed techniques for detecting synchronous dataflow (SDF) regions within larger CAL networks, and exploiting the static structure of such regions using analysis tools in The Dataflow interchange format Package (TDP). Using a new XML format that we have developed to exchange dataflow information between different dataflow tools, we explore systematic implementation of signal processing systems using CAL, SDF-like region detection, TDP-based static scheduling, and CAL-to-C (CAL2C) translation. Our approach, which is a novel integration of three complementary dataflow tools - the CAL parser, TDP, and CAL2C - is demonstrated on an MPEG Reconfigurable Video Coding (RVC) decoder.
Keywords: automated generation; automatic design flow; CAL language; CAL networks; CAL-to-C translation; CAL2C translation; coarse-grain dataflow representations; Computational modeling; data flow computing; dataflow information; Dataflow programming; decoding; Digital signal processing; Libraries; MPEG-4 reconfigurable video coding decoder implementation; parallel languages; SDF detection; synchronous dataflow detection; TDP; TDP-based static scheduling; The Dataflow interchange format Package; Transform coding; user-friendly design; video coding; video processing systems; XML; XML format

BioNav: An Ontology-Based Framework to Discover Semantic Links in the Cloud of Linked Data - Vidal,M. E; Raschid, Louiqa; Márquez,N.; Rivera,J.; Ruckhaus,E. (The Semantic Web: Research and Applications, 2010)

cdec: A decoder, alignment, and learning framework for finite-state and context-free translation models - Dyer,C.; Weese,J.; Setiawan,H.; Lopez,A.; Ture,F.; Eidelman,V.; Ganitkevitch,J.; Blunsom,P.; Resnik, Philip (Proceedings of the ACL 2010 System Demonstrations, 2010)

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)

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

Decoupling policy from configuration in campus and enterprise networks - Feamster, Nick; Nayak,A.; Kim,Hyojoon; Clark,R.; Mundada,Y.; Ramachandran,A.; bin Tariq,M. (Local and Metropolitan Area Networks (LANMAN), 2010 17th IEEE Workshop on, 2010)
This paper surveys our ongoing work on the use of software-defined networking to simplify two acute policy problems in campus and enterprise network operations: access control and information flow control. We describe how the current coupling of high-level policy with low-level configuration makes these problems challenging today. We describe the specific policy problems faced by campus and enterprise network operators; illustrate our approach, which leverages recent trends in separating the network's #x201C;control plane #x201D; from the data plane; and show how this approach can be applied to simplify these two enterprise network management tasks. We also describe our ongoing deployment efforts to build a campus network testbed where trial designs can be deployed and evaluated. We close with a summary of current and future research challenges for solving challenges within enterprise networks within the context of this new paradigm.
Keywords: Access control; Business communication; campus network; decoupling policy; enterprise network management tasks; enterprise network operator; information flow control; software defined network; software radio; telecommunication network management; telecommunication security

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)

Error driven paraphrase annotation using Mechanical Turk - Buzek,O.; Resnik, Philip; Bederson, Benjamin B. (Proceedings of the NAACL HLT 2010 Workshop on Creating Speech and Language Data with Amazon's Mechanical Turk, 2010)

Evolution of state-dependent risk preferences - Roos,Patrick; Carr,J. Ryan; Nau, Dana S. (ACM Transactions on Intelligent Systems and Technology (TIST), 2010)
Researchers have invested much effort in constructing models of the state-dependent (sometimes risk-averse and sometimes risk-prone) nature of human decision making. An important open question is how state-dependent risk behavior can arise and remain prominent in populations. We believe that one part of the answer is the interplay between risk-taking and sequentiality of choices in populations subject to evolutionary population dynamics. To support this hypothesis, we provide simulation and analytical results for evolutionary lottery games, including results on evolutionary stability. We consider a parameterized class of imitation dynamics in which the parameter 0 ≤ α ≤ 1 yields the replicator dynamic with α = 1 and the imitate-the-better dynamic with α = 0. Our results demonstrate that for every population dynamic in this class except for the replicator dynamic, the interplay between risk-taking and sequentiality of choices allows state-dependent risk behavior to have an evolutionary advantage over expected-value maximization.
Keywords: decision theory; Evolutionary games; Population Dynamics; risk

Evolutionary framework for Lepidoptera model systems - Roe,A.; Weller,S.; Baixeras,J.; Brown,J. W; Cummings, Michael P.; Davis,DR; Horak,M; Kawahara,A. Y; Mitter,C; Parr,C.S.; Regier,J. C; Rubinoff,D; et al. (Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera, 2010)
“Model systems” are specific organisms upon which detailed studies have been conducted examining a fundamental biological question. If the studies are robust, their results can be extrapolated among an array of organisms that possess features in common with the subject organism. The true power of model systems lies in the ability to extrapolate these details across larger groups of organisms. In order to generalize these results, comparative studies are essential and require that model systems be placed into their evolutionary or phylogenetic context. This chapter examines model systems in the insect order Lepidoptera from the perspective of several different superfamilies. Historically, many species of Lepidoptera have been essential in the development of invaluable model systems in the fields of development biology, genetics, molecular biology, physiology, co-evolution, population dynamics, and ecology.

Evolving viral marketing strategies - Stonedahl,Forrest; Rand, William; Wilensky,Uri (Proceedings of the 12th annual conference on Genetic and evolutionary computation, 2010)
One method of viral marketing involves seeding certain consumers within a population to encourage faster adoption of the product throughout the entire population. However, determining how many and which consumers within a particular social network should be seeded to maximize adoption is challenging. We define a strategy space for consumer seeding by weighting a combination of network characteristics such as average path length, clustering coefficient, and degree. We measure strategy effectiveness by simulating adoption on a Bass-like agent-based model, with five different social network structures: four classic theoretical models (random, lattice, small-world, and preferential attachment) and one empirical (extracted from Twitter friendship data). To discover good seeding strategies, we have developed a new tool, called BehaviorSearch, which uses genetic algorithms to search through the parameter-space of agent-based models. This evolutionary search also provides insight into the interaction between strategies and network structure. Our results show that one simple strategy (ranking by node degree) is near-optimal for the four theoretical networks, but that a more nuanced strategy performs significantly better on the empirical Twitter-based network. We also find a correlation between the optimal seeding budget for a network, and the inequality of the degree distribution.
Keywords: Agent-based modeling; business; diffusion; Genetic algorithms; simulation; social networks; viral marketing

Face Verification Across Age Progression Using Discriminative Methods - Ling,Haibin; Soatto,S.; Ramanathan,N.; Jacobs, David W. (Information Forensics and Security, IEEE Transactions on, 2010)
Face verification in the presence of age progression is an important problem that has not been widely addressed. In this paper, we study the problem by designing and evaluating discriminative approaches. These directly tackle verification tasks without explicit age modeling, which is a hard problem by itself. First, we find that the gradient orientation, after discarding magnitude information, provides a simple but effective representation for this problem. This representation is further improved when hierarchical information is used, which results in the use of the gradient orientation pyramid (GOP). When combined with a support vector machine GOP demonstrates excellent performance in all our experiments, in comparison with seven different approaches including two commercial systems. Our experiments are conducted on the FGnet dataset and two large passport datasets, one of them being the largest ever reported for recognition tasks. Second, taking advantage of these datasets, we empirically study how age gaps and related issues (including image quality, spectacles, and facial hair) affect recognition algorithms. We found surprisingly that the added difficulty of verification produced by age gaps becomes saturated after the gap is larger than four years, for gaps of up to ten years. In addition, we find that image quality and eyewear present more of a challenge than facial hair.
Keywords: algorithms; support; databases; dataset; age; FGnet; hair; gradient; information; image; information; recognition; machine; face; machines; visual; methods; eyewear; face; methods; support; orientation; orientation; gradient; progression; commercial; pyramid; hierarchical; quality; magnitude; recognition; gradient; systems; discriminative; vector; verification; facial

Fast Computation of Kernel Estimators - Raykar,Vikas C.; Duraiswami, Ramani; Zhao,Linda H. (Journal of Computational and Graphical Statistics, 2010)
The computational complexity of evaluating the kernel density estimate (or its derivatives) at m evaluation points given n sample points scales quadratically as O(nm)?making it prohibitively expensive for large datasets. While approximate methods like binning could speed up the computation, they lack a precise control over the accuracy of the approximation. There is no straightforward way of choosing the binning parameters a priori in order to achieve a desired approximation error. We propose a novel computationally efficient ε-exact approximation algorithm for the univariate Gaussian kernel-based density derivative estimation that reduces the computational complexity from O(nm) to linear O(n+m). The user can specify a desired accuracy ε. The algorithm guarantees that the actual error between the approximation and the original kernel estimate will always be less than ε. We also apply our proposed fast algorithm to speed up automatic bandwidth selection procedures. We compare our method to the best available binning methods in terms of the speed and the accuracy. Our experimental results show that the proposed method is almost twice as fast as the best binning methods and is around five orders of magnitude more accurate. The software for the proposed method is available online.

Finishing genomes with limited resources: lessons from an ensemble of microbial genomes - Nagarajan,Niranjan; Cook,Christopher; Di Bonaventura,Maria Pia; Ge,Hong; Richards,Allen; Bishop-Lilly,Kimberly A; DeSalle,Robert; Read,Timothy D.; Pop, Mihai (BMC Genomics, 2010)
While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores.

FPGA-based design and implementation of the 3GPP-LTE physical layer using parameterized synchronous dataflow techniques - Kee, Hojin; Bhattacharyya, Shuvra S.; Wong, I.; Yong Rao (2010 IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP), 2010)
Synchronous dataflow (SDF) is an ubiquitous dataflow model of computation that has been studied extensively for efficient simulation and software synthesis of DSP applications. In recent years, parameterized SDF (PSDF) has evolved as a useful framework for modeling SDF graphs in which arbitrary parameters can be changed dynamically. However, the potential to enable efficient hardware synthesis has been treated relatively sparsely in the literature for SDF and even more so for the newer, more general PSDF model. This paper investigates efficient FPGA-based design and implementation of the physical layer for 3GPP-Long Term Evolution (LTE), a next generation cellular standard. To capture the SDF behavior of the functional core of LTE along with higher level dynamics in the standard, we use a novel PSDF-based FPGA architecture framework. We implement our PSDF-based, LTE design framework using National Instrument's LabVIEW FPGA, a recently-introduced commercial platform for reconfigurable hardware implementation. We show that our framework can effectively model the dynamics of the LTE protocol, while also providing a synthesis framework for efficient FPGA implementation.
Keywords: 3G mobile communication; 3GPP-long term evolution; 3GPP-LTE physical layer; 4G communication systems; Computational modeling; data flow analysis; data flow graphs; Dataflow modeling; Digital signal processing; DSP applications; Field programmable gate arrays; FPGA architecture framework; FPGA implementation; FPGA-based design; Hardware; hardware synthesis; Instruments; LabVIEW FPGA; Logic Design; LTE; next generation cellular standard; parameterized synchronous data flow technique; Pervasive computing; Physical layer; Physics computing; Production; PSDF graph; reconfigurable hardware implementation; Runtime; software synthesis; Ubiquitous Computing; ubiquitous data flow model

Genetic and Physiological Activation of Osmosensitive Gene Expression Mimics Transcriptional Signatures of Pathogen Infection in C. elegans - Rohlfing,Anne-Katrin; Miteva,Yana; Hannenhalli, Sridhar; Lamitina,Todd (PLoS ONEPLoS ONE, 2010)
The soil-dwelling nematode C. elegans is a powerful system for comparative molecular analyses of environmental stress response mechanisms. Infection of worms with bacterial and fungal pathogens causes the activation of well-characterized innate immune transcriptional programs in pathogen-exposed hypodermal and intestinal tissues. However, the pathophysiological events that drive such transcriptional responses are not understood. Here, we show that infection-activated transcriptional responses are, in large part, recapitulated by either physiological or genetic activation of the osmotic stress response. Microarray profiling of wild type worms exposed to non-lethal hypertonicity identified a suite of genes that were also regulated by infection. Expression profiles of five different osmotic stress resistant (osr) mutants under isotonic conditions reiterated the wild type transcriptional response to osmotic stress and also showed substantial similarity to infection-induced gene expression under isotonic conditions. Computational, transgenic, and functional approaches revealed that two GATA transcription factors previously implicated in infection-induced transcriptional responses, elt-2 and elt-3, are also essential for coordinated tissue-specific activation of osmosensitive gene expression and promote survival under osmotically stressful conditions. Together, our data suggest infection and osmotic adaptation share previously unappreciated transcriptional similarities which might be controlled via regulation of tissue-specific GATA transcription factors.

Holistic sentiment analysis across languages: multilingual supervised latent Dirichlet allocation - Jordan Boyd-Graber; Resnik, Philip (Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing, 2010)
In this paper, we develop multilingual supervised latent Dirichlet allocation (MlSLDA), a probabilistic generative model that allows insights gleaned from one language's data to inform how the model captures properties of other languages. MlSLDA accomplishes this by jointly modeling two aspects of text: how multilingual concepts are clustered into thematically coherent topics and how topics associated with text connect to an observed regression variable (such as ratings on a sentiment scale). Concepts are represented in a general hierarchical framework that is flexible enough to express semantic ontologies, dictionaries, clustering constraints, and, as a special, degenerate case, conventional topic models. Both the topics and the regression are discovered via posterior inference from corpora. We show MlSLDA can build topics that are consistent across languages, discover sensible bilingual lexical correspondences, and leverage multilingual corpora to better predict sentiment.

Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets - Liu,Bo; Pop, Mihai (Bioinformatics Research and Applications, 2010)
Enabled by rapid advances in sequencing technology, metagenomic studies aim to characterize entire communities of microbes bypassing the need for culturing individual bacterial members. One major goal of such studies is to identify specific functional adaptations of microbial communities to their habitats. Here we describe a powerful analytical method (MetaPath) that can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge. We show that MetaPath outperforms other common approaches when evaluated on simulated datasets. We also demonstrate the power of our methods in analyzing two, publicly available, metagenomic datasets: a comparison of the gut microbiome of obese and lean twins; and a comparison of the gut microbiome of infant and adult subjects. We demonstrate that the subpathways identified by our method provide valuable insights into the biological activities of the microbiome.

Improving translation via targeted paraphrasing - Resnik, Philip; Buzek,O.; Hu,C.; Kronrod,Y.; Quinn,A.; Bederson, Benjamin B. (Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing, 2010)

Interactive information visualization for exploring and querying electronic health records: A systematic review - Rind,A.; Wang,T. D; Aigner,W.; Miksh,S.; Wongsuphasawat,K.; Plaisant, Catherine; Shneiderman, Ben (Human-Computer Interaction Lab, University of Maryland, 2010)
To overcome the complexity and scale of making medical decisions based on electronic health records (EHRs) a variety of visual methods have been proposed. This paper surveys twelve state-of-the-art information visualization systems described in the scientific literature and compares them based on a set of carefully selected criteria. It aims to systematically examine the systems’ strengths and weaknesses to inform future information visualization designs.We select twelve state-of-the-art information visualization systems from information visualization, medical information systems and human-computer interaction conferences and journals. We compare the systems using the following criteria: (1) data types covered, (2) multivariate analysis support, (3) number of patients records used (one or many), and (4) user intents addressed. The review describes the twelve systems in detail and evaluates the systems using the aforementioned criteria. We discuss how the systems differ in their features and highlight how these differences are related to their design and affect the user intent model. Examples of findings include: (1) most systems handle numerical or categorical data but not both, (2) most systems are specifically designed for looking at a single patient or multiple patients but not both, (3) most systems utilize horizontal time lines to represent time, (4) only systems that handle multiple patient records have good support for Filter, and (5) some specific user intents (e.g. the Encode and Connect intents) are rarely addressed. Based on our review results, we believe that effective information visualization can facilitate analysis of patient records, and we encourage the information visualization community to study the application of their systems and conduct more in depth evaluations. We identify potential future research topics in interactive support for data abstraction and medical tasks that involve looking at a single or multiple records. Finally, we propose to create a repository for data and tasks so benchmarks can be established for both academic and commercial patient record visualization systems.

Interlingual Annotation of Parallel Text Corpora: A New Framework for Annotation and Evaluation - Dorr, Bonnie J; Passonneau,Rebecca J.; Farwell,David; Green,Rebecca; Habash,Nizar; Helmreich,Stephen; Hovy,Eduard; Levin,Lori; Miller,Keith J.; Mitamura,Teruko; Rambow,Owen; Siddharthan,Advaith (Natural Language Engineering, 2010)
This paper focuses on an important step in the creation of a system of meaning representation and the development of semantically annotated parallel corpora, for use in applications such as machine translation, question answering, text summarization, and information retrieval. The work described below constitutes the first effort of any kind to annotate multiple translations of foreign-language texts with interlingual content. Three levels of representation are introduced: deep syntactic dependencies (IL0), intermediate semantic representations (IL1), and a normalized representation that unifies conversives, nonliteral language, and paraphrase (IL2). The resulting annotated, multilingually induced, parallel corpora will be useful as an empirical basis for a wide range of research, including the development and evaluation of interlingual NLP systems and paraphrase-extraction systems as well as a host of other research and development efforts in theoretical and applied linguistics, foreign language pedagogy, translation studies, and other related disciplines.

Linking Software Development and Business Strategy Through Measurement - Basili, Victor R.; Lindvall,M.; Regardie,M.; Seaman,C.; Heidrich,J.; Munch,J.; Rombach,D.; Trendowicz,A. (Computer, 2010)
The GQM+Strategies approach extends the goal/question/metric paradigm for measuring the success or failure of goals and strategies, adding enterprise-wide support for determining action on the basis of measurement results. An organization can thus integrate its measurement program across all levels.
Keywords: approach; business; aspects; software; development; organisational; engineering; GQM+Strategies; program; software; strategy; enterprise; support; measurement; wide

Loop transformations for interface-based hierarchies IN SDF graphs - Piat, J.; Bhattacharyya, Shuvra S.; Raulet, M. (2010 21st IEEE International Conference on Application-specific Systems Architectures and Processors (ASAP), 2010)
Data-flow has proven to be an attractive computation model for programming digital signal processing (DSP) applications. A restricted version of data-flow, termed synchronous data-flow (SDF), offers strong compile-time predictability properties, but has limited expressive power. A new type of hierarchy (Interface-based SDF) has been proposed allowing more expressivity while maintaining its predictability. One of the main problems with this hierarchical SDF model is the lack of trade-off between parallelism and network clustering. This paper presents a systematic method for applying an important class of loop transformation techniques in the context of interface-based SDF semantics. The resulting approach provides novel capabilities for integrating parallelism extraction properties of the targeted loop transformations with the useful modeling, analysis, and code reuse properties provided by SDF.
Keywords: Application software; code generation; Computer architecture; Computer interfaces; Data-Flow programming; Digital signal processing; Loop parallelization; PARALLEL PROCESSING; Power engineering computing; Power system modeling; Processor scheduling; Programming profession; scheduling; SDF graph; system recovery

Measuring transitivity using untrained annotators - Madnani,Nitin; Jordan Boyd-Graber; Resnik, Philip (Proceedings of the NAACL HLT 2010 Workshop on Creating Speech and Language Data with Amazon's Mechanical Turk, 2010)
Hopper and Thompson (1980) defined a multi-axis theory of transitivity that goes beyond simple syntactic transitivity and captures how much "action" takes place in a sentence. Detecting these features requires a deep understanding of lexical semantics and real-world pragmatics. We propose two general approaches for creating a corpus of sentences labeled with respect to the Hopper-Thompson transitivity schema using Amazon Mechanical Turk. Both approaches assume no existing resources and incorporate all necessary annotation into a single system; this is done to allow for future generalization to other languages. The first task attempts to use language-neutral videos to elicit human-composed sentences with specified transitivity attributes. The second task uses an iterative process to first label the actors and objects in sentences and then annotate the sentences' transitivity. We examine the success of these techniques and perform a preliminary classification of the transitivity of held-out data.

Modeling perspective using adaptor grammars - Hardisty,Eric A.; Jordan Boyd-Graber; Resnik, Philip (Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing, 2010)
Strong indications of perspective can often come from collocations of arbitrary length; for example, someone writing get the government out of my X is typically expressing a conservative rather than progressive viewpoint. However, going beyond unigram or bigram features in perspective classification gives rise to problems of data sparsity. We address this problem using nonparametric Bayesian modeling, specifically adaptor grammars (Johnson et al., 2006). We demonstrate that an adaptive naïve Bayes model captures multiword lexical usages associated with perspective, and establishes a new state-of-the-art for perspective classification results using the Bitter Lemons corpus, a collection of essays about mid-east issues from Israeli and Palestinian points of view.

Modelling Type 1a Supernova Light Curves - Rust,Bert W.; O'Leary, Dianne P.; Mullen,Katharine M. (Exponential Data Fitting and Its ApplicationsExponential Data Fitting and Its Applications, 2010)

New Approaches to Robust, Point-Based Image Registration - Mount, Dave; Netanyahu,N. S; Ratanasanya,S. (Image Registration for Remote SensingImage Registration for Remote Sensing, 2010)
We consider various algorithmic solutions to image registration based on thealignment of a set of feature points. We present a number of enhancements to a branch-and-bound algorithm introduced by Mount, Netanyahu, and Le Moigne (Pattern Recognition, Vol. 32, 1999, pp. 17–38), which presented a registration algorithm based on the partial Hausdorff distance. Our enhance- ments include a new distance measure, the discrete Gaussian mismatch, and a number of improvements and extensions to the above search algorithm. Both distance measures are robust to the presence of outliers, that is, data points from either set that do not match any point of the other set. We present experimental studies, which show that the new distance measure considered can provide significant improvements over the partial Hausdorff distance in instances where the number of outliers is not known in advance. These experiments also show that our other algorithmic improvements can offer tangible improvements. We demonstrate the algorithm’s efficacy by considering images involving different sensors and different spectral bands, both in a traditional framework and in a multiresolution framework.

New forms of Human-Computer Interaction for Visualizing Information - Reiterer,H.; Kerren,A.; Plaisant, Catherine; Stasko,J.T. (Information Visualization, 2010)
The Graphical User Interface (GUI) – although developed in research laboratories in the late 1970s – is still the dominant interaction paradigm in Information Visualization. We propose a new interaction paradigm called Blended Interaction. It combines ideas of Embodied Cognition, Multimodal Interaction, Reality-Based Interaction & Ubiquitous Computing. This is intended to stress that a single increase in the reality aspect of the interaction cannot go far enough. The particular challenge – and from the user's standpoint, the key advantage – lies in a meaningful marriage between the tested real-world options and the digital world. As a minimum this marriage must exist on the levels of the interaction, communication, of the way we solve problems with conventional tools (workflows), and of the design of the space or the architecture of buildings and places. The digital world often offers entirely new possibilities and takes the form of interactive devices of various shapes but also of intelligent everyday objects (e.g. the 'Internet of things'). In our view, interaction concepts can indeed offer a new quality of interaction, but only when the design of the interaction includes all these domains at the same time and with equal weighting. We test the suitability of our ideas of Blended Interaction concepts by using specific application examples that are being worked on as part of current research projects. Our experiences show that this new interaction paradigm has also great potential for interacting with visualization. For example, we have developed multi-touch scatter plots & facet maps for tangible user interfaces supporting the searching & browsing in Digital Libraries. We have embedded different visualizations into a Zoomable Object-oriented Information Landscape (ZOIL), which supports our vision of using visualizations on different displays of different size at the same time. We have developed specific kind of search tokens that supports collaborative search activities. For example, we try to address the following research questions: * How can future interactive InfoVis tools look like, especially in the light of the idea Blended Interaction? * How can future interactive InfoVis tools benefit from Multi-Displays & Multimodal environments used by Multiple Users? * What are the specific design requirements for multi-touch visualizations? * How can we support the collaborative use visualization tools?

Overlay Networking and Resiliency - Bhattacharjee, Bobby; Rabinovich,M. (Guide to Reliable Internet Services and Applications, 2010)

Parsimonious rule generation for a nature-inspired approach to self-assembly - Grushin,A.; Reggia, James A. (ACM Transactions on Autonomous and Adaptive Systems (TAAS), 2010)

The problem with zoning: nonlinear effects of interactions between location preferences and externalities on land use and utility - Zellner,M.L.; Riolo,R.L.; Rand, William; Brown,D.G.; Page,S.E.; Fernandez,L.E. (Environment and Planning B: Planning and Design, 2010)

Sectored Random Projections for Cancelable Iris Biometrics - Pillai,J.K.; Patel, Vishal M.; Chellapa, Rama; Ratha,N. K (2010 IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP), 2010)
Privacy and security are essential requirements in practical biometric systems. In order to prevent the theft of biometric patterns, it is desired to modify them through revocable and non invertible transformations called Cancelable Biometrics. In this paper, we propose an efficient algorithm for generating a Cancelable Iris Biometric based on Sectored Random Projections. Our algorithm can generate a new pattern if the existing one is stolen, retain the original recognition performance and prevent extraction of useful information from the transformed patterns. Our method also addresses some of the drawbacks of existing techniques and is robust to degradations due to eyelids and eyelashes.
Keywords: biometric pattern; Biometrics; Cancelable Biometrics; cancelable iris biometrics; data mining; data privacy; Degradation; Eyelashes; Eyelids; Iris; iris recognition; pattern recognition; privacy; random processes; Random Projections; Robustness; sectored random projection; Secure Biometrics; Security; security of data

Secure and robust iris recognition using random projections and sparse representations - Pillai, J.; Patel, Vishal M.; Chellapa, Rama; Ratha, N. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2010)

Secure network coding over the integers - Gennaro,R.; Katz, Jonathan; Krawczyk,H.; Rabin,T. (Public Key Cryptography–PKC 2010, 2010)
Network coding offers the potential to increase throughput and improve robustness without any centralized control. Unfortunately, network coding is highly susceptible to “pollution attacks” in which malicious nodes modify packets improperly so as to prevent message recovery at the recipient(s); such attacks cannot be prevented using standard end-to-end cryptographic authentication because network coding mandates that intermediate nodes modify data packets in transit.Specialized “network coding signatures” addressing this problem have been developed in recent years using homomorphic hashing and homomorphic signatures. We contribute to this area in several ways: • We show the first homomorphic signature scheme based on the RSA assumption (in the random oracle model). • We give a homomorphic hashing scheme that is more efficient than existing schemes, and which leads to network coding signatures based on the hardness of factoring (in the standard model). • We describe variants of existing schemes that reduce the communication overhead for moderate-size networks, and improve computational efficiency (in some cases quite dramatically – e.g., we achieve a 20-fold speedup in signature generation at intermediate nodes). Underlying our techniques is a modified approach to random linear network coding where instead of working in a vector space over a field, we work in a module over the integers (with small coefficients).

Self-assembly of neural networks viewed as swarm intelligence - Martin,C. E; Reggia, James A. (Swarm Intelligence, 2010)

THE SHAKY LADDER HYPERPLANE-DEFINED FUNCTIONS AND CLASSIC DYNAMIC PROBLEMS - Alharbi,Abir; Rand, William (International Journal of Computational Intelligence and Applications, 2010)
To improve the understanding of the GA in dynamic environments we explore a set of test problems, the shaky ladder hyper-defined functions (sl-hdf), and extend these functions to create versions that are equivalent to many classical dynamic problems. We do this by constraining the space of all sl-hdfs to create representations of these classical functions. We have examined three classical problems, and compared sl-hdf versions of these problems with their standard representations. These results show that the sl-hdfs are representative of a larger class of problems, and can represent a larger class of test suite. Previous results on sl-hdf showed that GA performance is best in the Defined Cliffs variant of the sl-hdf. We build upon these results to improve GA performance in several classes of real world dynamic problems by modifying the problem representation. These results lend insight into dynamic problems where the GA will perform well.

Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. - Jeremy D Selengut; Rusch, Douglas B; Haft, Daniel H (BMC Bioinformatics, 2010)
BACKGROUND: Comparative genomics methods such as phylogenetic profiling can mine powerful inferences from inherently noisy biological data sets. We introduce Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL), a method that applies the Partial Phylogenetic Profiling (PPP) approach locally within a protein sequence to discover short sequence signatures associated with functional sites. The approach is based on the basic scoring mechanism employed by PPP, namely the use of binomial distribution statistics to optimize sequence similarity cutoffs during searches of partitioned training sets. RESULTS: Here we illustrate and validate the ability of the SIMBAL method to find functionally relevant short sequence signatures by application to two well-characterized protein families. In the first example, we partitioned a family of ABC permeases using a metabolic background property (urea utilization). Thus, the TRUE set for this family comprised members whose genome of origin encoded a urea utilization system. By moving a sliding window across the sequence of a permease, and searching each subsequence in turn against the full set of partitioned proteins, the method found which local sequence signatures best correlated with the urea utilization trait. Mapping of SIMBAL "hot spots" onto crystal structures of homologous permeases reveals that the significant sites are gating determinants on the cytosolic face rather than, say, docking sites for the substrate-binding protein on the extracellular face. In the second example, we partitioned a protein methyltransferase family using gene proximity as a criterion. In this case, the TRUE set comprised those methyltransferases encoded near the gene for the substrate RF-1. SIMBAL identifies sequence regions that map onto the substrate-binding interface while ignoring regions involved in the methyltransferase reaction mechanism in general. Neither method for training set construction requires any prior experimental characterization. CONCLUSIONS: SIMBAL shows that, in functionally divergent protein families, selected short sequences often significantly outperform their full-length parent sequence for making functional predictions by sequence similarity, suggesting avenues for improved functional classifiers. When combined with structural data, SIMBAL affords the ability to localize and model functional sites.
Keywords: algorithms; Amino Acid Sequence; Gene Expression Profiling; Molecular Sequence Data; Phylogeny; Proteins; Sequence Analysis, Protein; Structure-Activity Relationship

Strategy generation in multi-agent imperfect-information pursuit games - Raboin,Eric; Nau, Dana S.; Kuter,Ugur; Gupta, Satyandra K.; Svec,Petr (International Foundation for Autonomous Agents and Multiagent Systems, 2010)
We describe a formalism and algorithms for game-tree search in partially-observable Euclidean space, and implementation and tests in a scenario where a multi-agent team, called tracking agents, pursues a target agent that wants to evade the tracking agents. Our contributions include--- • A formalism that combines geometric elements (agents' locations and trajectories and observable regions, and obstacles that restrict mobility and observability) with game-theoretic elements (information sets, utility functions, and strategies). • A recursive formula for information-set minimax values based on our formalism, and a implementation of the formula in a game-tree search algorithm. • A heuristic evaluation function for use at the leaf nodes of the game-tree search. It works by doing a quick lookahead search of its own, in a relaxed version of the problem. • Experimental results in 500 randomly generated trials. With the strategies generated by our heuristic, the tracking agents were more than twice as likely to know the target agent's location at the end of the game than with the strategies generated by heuristics that compute estimates of the target's possible locations.
Keywords: game tree search; multi-agent planning; visibility-based pursuit-evasion games

System and method for analysis of an opinion expressed in documents with regard to a particular topic - V.S. Subrahmanian; Picariello,Antonio; Dorr, Bonnie J; Reforgiato,Diego Recupero; Cesarano,Carmine; Sagoff,Amelia (2010)
System and method for analysis of an opinion expressed in documents on a particular topic computes opinion strength on a continuous numeric scale, or qualitatively. A variety of opinion scoring techniques are plugged in to score opinion expressing words and sentences in documents. These scores are aggregated to measure the opinion intensity of documents. Multilingual opinion analysis is supported by capability to concurrently identify and visualize the opinion intensity expressed in documents in multiple languages. A multi-dimensional representation of the measured opinion intensity is generated which is agreeable with multi-lingual domain.

On trade-offs in event delivery systems - Roitman,H.; Gal,A.; Raschid, Louiqa (Proceedings of the Fourth ACM International Conference on Distributed Event-Based Systems, 2010)

Understanding Interactive Legends: a Comparative Evaluation with Standard Widgets - Riche,Nathalie Henry; Lee,Bongshin; Plaisant, Catherine (Computer Graphics Forum, 2010)
Interactive information visualization systems rely on widgets to allow users to interact with the data and modify the representation. We define interactive legends as a class of controls combining the visual representation of static legends and interaction mechanisms of widgets. As interactive legends start to appear in popular websites, we categorize their designs for common data types and evaluate their effectiveness compare to standard widgets. Results suggest that 1) interactive legends can lead to faster perception of the mapping between data values and visual encodings and 2) interaction time is affected differently depending on the data type. Additionally, our study indicates superiority both in terms of perception and interaction of ordinal controls over numerical ones. Numerical techniques are mostly used in today's systems. By providing solutions to allowing users to modify ranges interactively, we believe that interactive legends make it possible to increase the use of ordinal techniques for visual exploration.
Keywords: H.5 [Information Interfaces and Presentation]: Miscellaneous—

Using symbolic evaluation to understand behavior in configurable software systems - Reisner,E.; Song,C.; Ma,K.K.; Foster, Jeffrey S.; Porter, Adam (Software Engineering, 2010 ACM/IEEE 32nd International Conference on, 2010)

Validating the systematic position of ıt Plationus Segers, Murugan & Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase - Reyna-Fabian,ME; Laclette,J. P; Cummings, Michael P.; García-Varela,M (Hydrobiologia, 2010)
Members of the family Brachionidae are free-living organisms that range in size from 170 to 250 microns. They comprise part of the zooplankton in freshwater and marine systems worldwide. Morphologically, members of the family are characterized by a single piece loricated body without furrows, grooves, sulci or dorsal head shields, and a malleate trophi. Differences in these structures have been traditionally used to recognize 217 species that are classified into seven genera. However, the validity of the species, Plationus patulus, P. patulus macracanthus P. polyacanthus, and P. felicitas have been confused because they were alternatively assigned in Brachionus or Platyias, when considering only morphological and ecological characters. Based on scanning electron microscope (SEM) images of the trophi, these taxa were assigned in a new genus, Plationus. In this study, we examined the systematic position of P. patulus and P. patulus macracanthus using DNA sequences of two genes: the cytochrome oxidase subunit 1 (cox1) and domains D2 and D3 of the large subunit of the nuclear ribosomal RNA (LSU). In addition, the cox1 and LSU sequences representing five genera of Brachionidae (Anuraeopsis, Brachionus, Keratella, Plationus, and Platyias) plus four species of three families from the order Ploima were used as the outgroup. The maximum likelihood (ML) analyses were conducted for each individual gene as well as for the combined (cox1 + LSU) data set. The ML tree from the combined data set yielded the family Brachionidae as a monophyletic group with weak bootstrap support (< 50%). Five main clades in this tree had high (> 85%) bootstrap support. The first clade was composed of three populations of P. patulus + P. patulus macracanthus. The second clade was composed of a single species of Platyias. The third clade was composed of six species of Brachionus. The fourth clade included a single species of the genus Anuraeopsis, and the fifth clade was composed of three species of the genus Keratella. The genetic divergence between Plationus and Platyias ranged from 18.4 to 19.2% for cox1, and from 4.5 to 4.9% for LSU, and between Brachionus and Plationus, it ranged from 16.9 to 23.1% (cox1), and from 7.3 to 9.1% (LSU). Morphological evidence, the amount of genetic divergence, the systematic position of Plationus within the family Brachionidae, and the position of Plationus as a sister group of Brachionus and Platyias support the validity of Plationus patulus and P. patulus macracanthus into the genus Plationus.
Keywords: Cox1; likelihood; LSU; maximum; Phylogeny; Plationus

Who's Hogging the Bandwidth: The Consequences of Revealing the Invisible in the Home - Marshini Chetty; Banks, Richard; Harper, Richard; Regan, Tim; Sellen, Abigail; Gkantsidis, Christos; Karagiannis, Thomas; Key, Peter (SIGCHI '10, 2010)
As more technologies enter the home, householders are burdened with the task of digital housekeeping-managing and sharing digital resources like bandwidth. In response to this, we created and evaluated a domestic tool for bandwidth management called Home Watcher. Our field trial showed that when resource contention amongst different household members is made visible, people's understanding of bandwidth changes and household politics are revealed. In this paper, we describe the consequences of showing real time resource usage in a home, and how this varies depending on the social make up of the household.
Keywords: bandwidth monitoring; home broadband; home networks

Wide-area route control for distributed services - Valancius,Vytautas; Feamster, Nick; Rexford,Jennifer; Nakao,Akihiro (Proceedings of the 2010 USENIX conference on USENIX annual technical conference, 2010)
Many distributed services would benefit from control over the flow of traffic to and from their users, to offer better performance and higher reliability at a reasonable cost. Unfortunately, although today's cloud-computing platforms offer elastic computing and bandwidth resources, they do not give services control over wide-area routing. We propose replacing the data center's border router with a Transit Portal (TP) that gives each service the illusion of direct connectivity to upstream ISPs, without requiring each service to deploy hardware, acquire IP address space, or negotiate contracts with ISPs. Our TP prototype supports many layer-two connectivity mechanisms, amortizes memory and message overhead over multiple services, and protects the rest of the Internet from misconfigured and malicious applications. Our implementation extends and synthesizes open-source software components such as the Linux kernel and the Quagga routing daemon. We also implement a management plane based on the GENI control framework and couple this with our four-site TP deployment and Amazon EC2 facilities. Experiments with an anycast DNS application demonstrate the benefits the TP offers to distributed services.

Age progression in human faces: A survey - Ramanathan,N.; Chellapa, Rama; Biswas,S. (Journal of Visual Languages and Computing, 2009)
Facial aging, a new dimension that has recently beenadded to the problem of face recognition, poses interesting theo- retical and practical challenges to the research community. The problem which originally generated interest in the psychophysics and human perception community, has recently found enhanced interest in the computer vision community. How do humans perceive age ? What constitutes an age-invariant signature that can be derived from faces ? How compactly can the facial growth event be described ? How does facial aging impact recognition performance ? In this paper, we give a thorough analysis on the problem of facial aging and further provide a complete account of the many interesting studies that have been performed on this topic from different fields. We offer a comparative analysis of various approaches that have been proposed for problems such as age estimation, appearance prediction, face verification etc. and offer insights into future research on this topic.

ApproxRank: Estimating Rank for a Subgraph - Yao Wu; Raschid, Louiqa (IEEE 25th International Conference on Data Engineering, 2009. ICDE '09, 2009)
Customized semantic query answering, personalized search, focused crawlers and localized search engines frequently focus on ranking the pages contained within a subgraph of the global Web graph. The challenge for these applications is to compute PageRank-style scores efficiently on the subgraph, i.e., the ranking must reflect the global link structure of the Web graph but it must do so without paying the high overhead associated with a global computation. We propose a framework of an exact solution and an approximate solution for computing ranking on a subgraph. The IdealRank algorithm is an exact solution with the assumption that the scores of external pages are known. We prove that the IdealRank scores for pages in the subgraph converge. Since the PageRank-style scores of external pages may not typically be available, we propose the ApproxRank algorithm to estimate scores for the subgraph. Both IdealRank and ApproxRank represent the set of external pages with an external node L1 and extend the subgraph with links to L1. They also modify the PageRank-style transition matrix with respect to L1. We analyze the L1 distance between IdealRank scores and ApproxRank scores of the subgraph and show that it is within a constant factor of the L1 distance of the external pages (e.g., the true PageRank scores and uniform scores assumed by ApproxRank). We compare ApproxRank and a stochastic complementation approach (SC), a current best solution for this problem, on different types of subgraphs. ApproxRank has similar or superior performance to SC and typically improves on the runtime performance of SC by an order of magnitude or better. We demonstrate that ApproxRank provides a good approximation to PageRank for a variety of subgraphs.
Keywords: Application software; ApproxRank; Computer applications; Crawlers; customized semantic query answering; Data engineering; Educational institutions; Explosions; focused crawlers; global Web graph; graph theory; IdealRank algorithm; Internet; localized search engines; PageRank-style; personalized search; Query processing; Runtime; Search engines; Stochastic processes; Web pages

Computational methods for modeling facial aging: A survey - Ramanathan,Narayanan; Chellapa, Rama; Biswas,Soma (Journal of Visual Languages & Computing, 2009)
Facial aging, a new dimension that has recently been added to the problem of face recognition, poses interesting theoretical and practical challenges to the research community. The problem which originally generated interest in the psychophysics and human perception community has recently found enhanced interest in the computer vision community. How do humans perceive age? What constitutes an age-invariant signature that can be derived from faces? How compactly can the facial growth event be described? How does facial aging impact recognition performance? In this paper, we give a thorough analysis on the problem of facial aging and further provide a complete account of the many interesting studies that have been performed on this topic from different fields. We offer a comparative analysis of various approaches that have been proposed for problems such as age estimation, appearance prediction, face verification, etc. and offer insights into future research on this topic.
Keywords: age estimation; Age progression; Craniofacial growth; face recognition

Conceptual modeling: past, present and the continuum of the future - Roussopoulos, Nick; Karagiannis,D. (Conceptual Modeling: Foundations and Applications, 2009)

Concurrent transition and shot detection in football videos using Fuzzy Logic - Refaey,M.A.; Elsayed,K.M.; Hanafy,S.M.; Davis, Larry S. (Image Processing (ICIP), 2009 16th IEEE International Conference on, 2009)
Shot detection is a fundamental step in video processing and analysis that should be achieved with high degree of accuracy. In this paper, we introduce a unified algorithm for shot detection in sports video using fuzzy logic as a powerful inference mechanism. Fuzzy logic overcomes the problems of hard cut thresholds and the need to large training data used in previous work. The proposed algorithm integrates many features like color histogram, edgeness, intensity variance, etc. Membership functions to represent different features and transitions between shots have been developed to detect different shot boundary and transition types. We address the detection of cut, fade, dissolve, and wipe shot transitions. The results show that our algorithm achieves high degree of accuracy.
Keywords: analysis; inference; boundary; shot; Color; colour; detection; sports; functions; shot; histogram; concurrent; logic; image; logic; inference; mechanism; intensity; mechanisms; sport; video; processing; processing; videonanalysis; fuzzy; signal; transition; edgeness; football; variance; membership; video; video; videos; fuzzy

A cooperative combinatorial Particle Swarm Optimization algorithm for side-chain packing - Lapizco-Encinas,G.; Kingsford, Carl; Reggia, James A. (IEEE Swarm Intelligence Symposium, 2009. SIS '09, 2009)
Particle Swarm Optimization (PSO) is a well-known, competitive technique for numerical optimization with real-parameter representation. This paper introduces CCPSO, a new Cooperative Particle Swarm Optimization algorithm for combinatorial problems. The cooperative strategy is achieved by splitting the candidate solution vector into components, where each component is optimized by a particle. Particles move throughout a continuous space, their movements based on the influences exerted by static particles that then get feedback based on the fitness of the candidate solution. Here, the application of this technique to side-chain packing (a proteomics optimization problem) is investigated. To verify the efficiency of the proposed CCPSO algorithm, we test our algorithm on three side-chain packing problems and compare our results with the provably optimal result. Computational results show that the proposed algorithm is very competitive, obtaining a conformation with an energy value within 1% of the provably optimal solution in many proteins.
Keywords: Algorithm design and analysis; Amino acids; combinatorial mathematics; cooperative combinatorial particle swarm optimization algorithm; Design optimization; Encoding; Feedback; numerical optimization; Optimization methods; particle swarm optimisation; Particle swarm optimization; Partitioning algorithms; Proteins; proteomics; proteomics optimization; Robustness; side-chain packing

CPM: Adaptive Video-on-Demand with Cooperative Peer Assists and Multicast - Gopalakrishnan,V.; Bhattacharjee, Bobby; Ramakrishnan,K.K.; Jana,R.; Srivastava,D. (INFOCOM 2009, IEEE, 2009)
We present CPM, a unified approach that exploits server multicast, assisted by peer downloads, to provide efficient video-on-demand (VoD) in a service provider environment. We describe our architecture and show how CPM is designed to dynamically adapt to a wide range of situations including highly different peer-upload bandwidths, content popularity, user request arrival patterns, video library size, and subscriber population. We demonstrate the effectiveness of CPM using simulations (based on an actual implementation codebase) across the range of situations described above and show that CPM does significantly better than traditional unicast, different forms of multicast, as well as peer-to-peer schemes. Along with synthetic parameters, we augment our experiments using data from a deployed VoD service to evaluate the performance of CPM.
Keywords: assists; multicast; peer-to-peer; communication; peer-to-peer; computing; video; CPM; cooperative; demand; on; parameters; video-on-demand; multicast; peer; schemes; synthetic

Creativity challenges and opportunities in social computing - Fischer,Gerhard; Jennings,Pamela; Maher,Mary Lou; Resnick,Mitchel; Shneiderman, Ben (Proceedings of the 27th international conference extended abstracts on Human factors in computing systems, 2009)
There is a convergence in recent theories of creativity that go beyond characteristics and cognitive processes of individuals to recognize the importance of the social construction of creativity. In parallel, there has been a rise in social computing supporting the collaborative construction of knowledge. The panel will discuss the challenges and opportunities from the confluence of these two developments by bringing together the contrasting and controversial perspective of the individual panel members. It will synthesize from different perspectives an analytic framework to understand these new developments, and how to promote rigorous research methods and how to identify the unique challenges in developing evaluation and assessment methods for creativity research.
Keywords: creativity; social computing

Design guidelines for agent based model visualization - Kornhauser,D.; Wilensky,U.; Rand, William (Journal of Artificial Societies and Social Simulation, 2009)
In the field of agent-based modeling (ABM), visualizations play an important role in identifying, communicating and understanding important behavior of the modeled phenomenon. However, many modelers tend to create ineffective visualizations of Agent Based Models (ABM) due to lack of experience with visual design. This paper provides ABM visualization design guidelines in order to improve visual design with ABM toolkits. These guidelines will assist the modeler in creating clear and understandable ABM visualizations. We begin by introducing a non-hierarchical categorization of ABM visualizations. This categorization serves as a starting point in the creation of an ABM visualization. We go on to present well-known design techniques in the context of ABM visualization. These techniques are based on Gestalt psychology, semiology of graphics, and scientific visualization. They improve the visualization design by facilitating specific tasks, and providing a common language to critique visualizations through the use of visual variables. Subsequently, we discuss the application of these design techniques to simplify, emphasize and explain an ABM visualization. Finally, we illustrate these guidelines using a simple redesign of a NetLogo ABM visualization. These guidelines can be used to inform the development of design tools that assist users in the creation of ABM visualizations.

Detecting humans carrying objects - Yang Ran; Qinfen Zheng; Chellapa, Rama (SPIE Newsroom, 2009)
Decomposing an image sequence into slices that generate twisted patterns sufficiently characterizes human gait and a particular class of activities.

Determination of relationships among non-toxigenic Vibrio cholerae O1 biotype El Tor strains from housekeeping gene sequences and ribotype patterns - Mohapatra,Saswat S.; Ramachandran,Dhanya; Mantri,Chinmay K.; Rita R Colwell; Singh,Durg V. (Research in Microbiology, 2009)
Sequencing of three housekeeping genes, mdh, dnaE and recA, and ribotyping for seven non-toxigenic Vibrio cholerae O1 strains isolated from different geographic sources indicate a phylogenetic relationship among the strains. Results of MLST and ribotyping indicate a clear difference between three toxigenic strains (N16961, O395, and 569B) and three non-toxigenic strains from India (GS1, GS2, and GW87) and one Guam strain (X392), the latter of which were similar in both MLST and ribotyping, while two other non-toxigenic strains from the USA and India (2740-80 and OR69) appeared to be more closely related to toxigenic strains than to non-toxigenic strains, although this was not supported by ribotyping. These results provide clues to the emergence of toxigenic strains from a non-toxigenic progenitor by acquisition of virulence gene clusters. Results of split decomposition analysis suggest that widespread recombination occurs among the three housekeeping genes and that recombination plays an important role in the emergence of toxigenic strains of V. cholerae O1.
Keywords: Housekeeping genes; Ribotyping; sequencing; Vibrio cholerae

A distributed learning algorithm for particle systems - Rodríguez,A.; Reggia, James A. (Integrated Computer-Aided Engineering, 2009)

Do you know the way to SNA?: A process model for analyzing and visualizing social media data - Hansen,D. L; Rotman,D.; Bonsignore,E.; Milic-Frayling,N.; Rodrigues,E.M.; Smith,M.; Shneiderman, Ben (University of Maryland Tech Report: HCIL-2009-17, 2009)
Traces of activity left by social media users can shed lighton individual behavior, social relationships, and community efficacy. Tools and processes to analyze social traces are essential for enabling practitioners to study and nurture meaningful and sustainable social interaction. Yet such tools and processes remain in their infancy. We conducted a study of 15 graduate students who were learning to apply Social Network Analysis (SNA) to data from online communities. Based on close observations of their emergent practices, we derived the Network Analysis and Visualization (NAV) process model and identified stages where intervention from peers, experts, and an SNA tool were most useful. We show how the NAV model informs the design of SNA tools and services, education practices, and support for social media practitioners.

Efficient Robust Private Set Intersection - Dana Dachman-Soled; Malkin, Tal; Raykova, Mariana; Yung, Moti (Applied Cryptography and Network Security, 2009)
Computing Set Intersection privately and efficiently between two mutually mistrusting parties is an important basic procedure in the area of private data mining. Assuring robustness, namely, coping with potentially arbitrarily misbehaving (i.e., malicious) parties, while retaining protocol efficiency (rather than employing costly generic techniques) is an open problem. In this work the first solution to this problem is presented.
Keywords: Coding and Information Theory; Computer Communication Networks; Cryptographic protocols; Data Encryption; Data Structures, Cryptology and Information Theory; Information Systems Applications (incl.Internet); Privacy Preserving Data Mining; Secure Two-party Computation; Set Intersection; Systems and Data Security

The emergence of zoning policy games in exurban jurisdictions: Informing collective action theory - Zellner,Moira L.; Page,Scott E.; Rand, William; Brown,Daniel G.; Robinson,Derek T.; Nassauer,Joan; Low,Bobbi (Land Use Policy, 2009)
Theoretical urban policy literature predicts the likelihood of free riding in the management of common goods such as forested open space; such outcome is often characterized as a Prisoner's Dilemma game. Numerous cases exist in which neighboring jurisdictions cooperate to maintain public goods, challenging the expected results, yet theoretical explanations of these cases have not been fully developed. In this paper, we use an agent-based model to explore how underlying micro-behaviors affect the payoffs obtained by two neighboring municipalities in a hypothetical exurban area. Payoffs are measured in terms of regional forested space and of local tax revenue at the end of the agent-based simulations; the municipalities affect these payoffs through their choice of residential zoning policies and the spillover effect between the neighboring jurisdictions. Zoning restrictions influence the conversion of farmland into residential subdivisions of different types, and consequently the location of heterogeneous residential households in the region. Developers and residents respond to the changing landscape characteristics, thus establishing a feedback between early and future land-use patterns. The structure of the simulated payoffs is analyzed using standard game theory. Our analysis shows that a variety of games, in addition to Prisoner's Dilemma, can emerge between the neighboring jurisdictions. Other games encourage coordination or subsidization, offering some explanations for the unexpected observations. The game realized in any given context depends on the initial characteristics of the landscape, the value given to the objectives each township seeks to maximize, and the income distribution of the population.
Keywords: Agent-based modeling; game theory; Land-use policy; Local government cooperation; Scale interaction

Enforcing integrability by error correction using ℓ1-minimization - Reddy, D.; Agrawal,A.; Chellapa, Rama (Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on, 2009)
Surface reconstruction from gradient fields is an important final step in several applications involving gradient manipulations and estimation. Typically, the resulting gradient field is non-integrable due to linear/non-linear gradient manipulations, or due to presence of noise/outliers in gradient estimation. In this paper, we analyze integrability as error correction, inspired from recent work in compressed sensing, particulary lscr0 - lscr1 equivalence. We propose to obtain the surface by finding the gradient field which best fits the corrupted gradient field in lscr1 sense. We present an exhaustive analysis of the properties of lscr1 solution for gradient field integration using linear algebra and graph analogy. We consider three cases: (a) noise, but no outliers (b) no-noise but outliers and (c) presence of both noise and outliers in the given gradient field. We show that lscr1 solution performs as well as least squares in the absence of outliers. While previous lscr0 - lscr1 equivalence work has focused on the number of errors (outliers), we show that the location of errors is equally important for gradient field integration. We characterize the lscr1 solution both in terms of location and number of outliers, and outline scenarios where lscr1 solution is equivalent to lscr0 solution. We also show that when lscr1 solution is not able to remove outliers, the property of local error confinement holds: i.e., the errors do not propagate to the entire surface as in least squares. We compare with previous techniques and show that lscr1 solution performs well across all scenarios without the need for any tunable parameter adjustments.
Keywords: -; algebra; lscr0; algebra; minimisation; analogy; integrability; least; compressed; correction; gradient; equivalence; lscr1-minimization; noise-outlier; surface; estimation; gradient; field; integration; gradient; lscr1; manipulation; graph; methods; graph; reconstruction; error; reconstruction; linear; sensing; error; squares; linear; theory; image

Estimating semantic distance using soft semantic constraints in knowledge-source-corpus hybrid models - Marton,Y.; Mohammad,S.; Resnik, Philip (Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 2-Volume 2, 2009)

First Steps to Netviz Nirvana: Evaluating Social Network Analysis with NodeXL - Bonsignore,E. M; Dunne,C.; Rotman,D.; Smith,M.; Capone,T.; Hansen,D. L; Shneiderman, Ben (International Conference on Computational Science and Engineering, 2009. CSE '09, 2009)
Social Network Analysis (SNA) has evolved as a popular, standard method for modeling meaningful, often hidden structural relationships in communities. Existing SNA tools often involve extensive pre-processing or intensive programming skills that can challenge practitioners and students alike. NodeXL, an open-source template for Microsoft Excel, integrates a library of common network metrics and graph layout algorithms within the familiar spreadsheet format, offering a potentially low-barrier-to-entry framework for teaching and learning SNA. We present the preliminary findings of 2 user studies of 21 graduate students who engaged in SNA using NodeXL. The majority of students, while information professionals, had little technical background or experience with SNA techniques. Six of the participants had more technical backgrounds and were chosen specifically for their experience with graph drawing and information visualization. Our primary objectives were (1) to evaluate NodeXL as an SNA tool for a broad base of users and (2) to explore methods for teaching SNA. Our complementary dual case-study format demonstrates the usability of NodeXL for a diverse set of users, and significantly, the power of a tightly integrated metrics/visualization tool to spark insight and facilitate sense-making for students of SNA.
Keywords: Computer science; computer science education; data visualisation; Data visualization; Educational institutions; graph drawing; graph layout algorithm; Information services; Information Visualization; Internet; Libraries; Microsoft Excel open-source template; MILC; multi-dimensional in-depth long-term case studies; Netviz Nirvana; NodeXL; Open source software; Programming profession; SNA; social network analysis; Social network services; social networking (online); spreadsheet programs; structural relationship; teaching; visual analytics; visualization tool; Web sites

Flexible and efficient querying and ranking on hyperlinked data sources - Varadarajan,R.; Hristidis,V.; Raschid, Louiqa; Vidal,M. E; Ibá\ nez,L.; Rodríguez-Drumond,H. (Proceedings of the 12th International Conference on Extending Database Technology: Advances in Database Technology, 2009)

From New Zealand to Mongolia: Co-designing and deploying a digital library for the world's children - Druin, Allison; Bederson, Benjamin B.; Rose,A.; Weeks,A. (Special issue of Children, Youth and Environments: Children in Technological Environments: Interaction, Development, and Design, 2009)

Gene Profiling of Human Adipose Tissue During Evoked Inflammation In Vivo - Shah,Rachana; Lu,Yun; Hinkle,Christine C; McGillicuddy,Fiona C; Kim,Roy; Hannenhalli, Sridhar; Cappola,Thomas P.; Heffron,Sean; Wang,XingMei; Mehta,Nehal N; Putt,Mary; Reilly,Muredach P (DiabetesDiabetes, 2009)
OBJECTIVE Adipose inflammation plays a central role in obesity-related metabolic and cardiovascular complications. However, few human adipose-secreted proteins are known to mediate these processes. We hypothesized that microarray mRNA profiling of human adipose during evoked inflammation could identify novel adipocytokines.RESEARCH DESIGN AND METHODS Healthy human volunteers (n = 14) were treated with intravenous endotoxin (3 ng/kg lipopolysaccharide [LPS]) and underwent subcutaneous adipose biopsies before and after LPS. On Affymetrix U133Plus 2.0 arrays, adipose mRNAs modulated >1.5-fold (with P < 0.00001) were selected. SignalP 3.0 and SecretomeP 2.0 identified genes predicted to encode secreted proteins. Of these, 86 candidates were chosen for validation in adipose from an independent human endotoxemia protocol (N = 7, with 0.6 ng/kg LPS) and for exploration of cellular origin in primary human adipocytes and macrophages in vitro. RESULTS Microarray identified 776 adipose genes modulated by LPS; 298 were predicted to be secreted. Of detectable prioritized genes, 82 of 85 (96% [95% CI 90–99]) were upregulated (fold changes >1.0) during the lower-dose (LPS 0.6 ng/kg) validation study and 51 of 85 (59% [49–70]) were induced greater than 1.5-fold. Treatment of primary adipocytes with LPS and macrophage polarization to M1 proinflammatory phenotype increased expression by 1.5-fold for 58 and 73% of detectable genes, respectively. CONCLUSIONS We demonstrate that evoked inflammation of human adipose in vivo modulated expression of multiple genes likely secreted by adipocytes and monocytes. These included established adipocytokines and chemokines implicated in recruitment and activation of lymphocytes, adhesion molecules, antioxidants, and several novel genes with unknown function. Such candidates may represent biomarkers and therapeutic targets for obesity-related complications.

Generating surveys of scientific paradigms - Mohammad,S.; Dorr, Bonnie J; Egan,M.; Hassan,A.; Muthukrishan,P.; Qazvinian,V.; Radev,D.; Zajic, David (Proceedings of HLT-NAACL, 2009)
The number of research publications in var-ious disciplines is growing exponentially. Researchers and scientists are increasingly finding themselves in the position of having to quickly understand large amounts of tech- nical material. In this paper we present the first steps in producing an automatically gen- erated, readily consumable, technical survey. Specifically we explore the combination of citation information and summarization tech- niques. Even though prior work (Teufel et al., 2006) argues that citation text is unsuitable for summarization, we show that in the frame- work of multi-document survey creation, cita- tion texts can play a crucial role.

GrouPeer: Dynamic clustering of P2P databases - Kantere,Verena; Tsoumakos,Dimitrios; Sellis,Timos; Roussopoulos, Nick (Information Systems, 2009)
Sharing structured data in a P2P network is a challenging problem, especially in the absence of a mediated schema. The standard practice of answering a consecutively rewritten query along the propagation path often results in significant loss of information. On the opposite, the use of mediated schemas requires human interaction and global agreement, both during creation and maintenance. In this paper we present GrouPeer, an adaptive, automated approach to both issues in the context of unstructured P2P database overlays. By allowing peers to individually choose which rewritten version of a query to answer and evaluate the received answers, information-rich sources left hidden otherwise are discovered. Gradually, the overlay is restructured as semantically similar peers are clustered together. Experimental results show that our technique produces very accurate answers and builds clusters that are very close to the optimal ones by contacting a very small number of nodes in the overlay.
Keywords: Peer-to-Peer databases; Query reformulation in P2P databases; Semantics in P2P query answering; Structured data in unstructured P2P overlays

How would you look as you age ? - Ramanathan,N.; Chellapa, Rama (Image Processing (ICIP), 2009 16th IEEE International Conference on, 2009)
Facial appearances change with increase in age. While generic growth patterns that are characteristic of different age groups can be identified, facial growth is also observed to be influenced by individual-specific attributes such as one's gender, ethnicity, life-style etc. In this paper, we propose a facial growth model that comprises of transformation models for facial shape and texture. We collected empirical data pertaining to facial growth from a database of age-separated face images of adults and used the same in developing the aforementioned transformation models. The proposed model finds applications in predicting one's appearance across ages and in performing face verification across ages.
Keywords: age-separated; appearances; facial; database; face; Face; growth; image; model; face; model; facial; models; facial; recognition; image; SHAPE; TEXTURE; texture; transformation; verification; facial

Improved statistical machine translation using monolingually-derived paraphrases - Marton,Y.; Callison-Burch,C.; Resnik, Philip (Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 1-Volume 1, 2009)

Improving rule extraction from neural networks by modifying hidden layer representations - Huynh,T. Q; Reggia, James A. (Neural Networks, 2009. IJCNN 2009. International Joint Conference on, 2009)

The infinite hierarchical factor regression model - Rai,P.; Daumé, Hal (Arxiv preprint arXiv:0908.0570, 2009)