Discovering Pronoun Categories using Discourse Information - McKeown, R; Feldman, N H; Lidz, J; Jordan Boyd-Graber (Proceedings of the 35th Annual Conference of the Cognitive Science Society)
Abstract Interpretation of a pronoun is driven by properties of syntactic distribution. Consequently, acquiring the meaning and the distribution are intertwined. In order to learn that a pronoun is reflexive, learners need to know which entity the pronoun refers to in a ...

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

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

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)

Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children - Al-Hebshi, Nezar Noor; Baraniya, Divyashri; Chen, Tsute; Hill, Jennifer; Puri, Sumant; Tellez, Marisol; Hassan, Nur A.; Rita R Colwell; Ismail, Amid (Journal of Oral Microbiology, 2019)
Studies of the microbiome associated with dental caries have largely relied on 16S rRNA sequence analysis, which is associated with PCR biases, low taxonomic resolution, and inability to accurately study functions. Here, we employed whole metagenome shotgun sequencing, coupled with high-resolution analysis algorithm, to analyze supragingival microbiomes from 30 children with or without dental caries. A total of 726 bacterial strains belonging to 406 species, in addition to 34 bacteriophages were identified. A core bacteriome was identified at the species and strain levels. Species of Prevotella, Veillonella, as yet unnamed Actinomyces, and Atopobium showed strongest association with caries; Streptococcus sp. AS14 and Leptotrichia sp. Oral taxon 225, among others, were overabundant in caries-free. For several species, the association was strain-specific. Furthermore, for some species, e.g. Streptococcus mitis and Streptococcus sanguinis, sister strains showed differential associations. Noteworthy, associations were also identified for phages: Streptococcus phage M102 with caries and Haemophilus phage HP1 with caries-free. Functionally, potentially relevant features were identified including urate, vitamin K2, and polyamine biosynthesis in association with caries; and three deiminases and lactate dehydrogenase with health. The results demonstrate new associations between the microbiome and dental caries at the strain and functional levels that need further investigation.

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)

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

Interpolation-Based Gray-Level Co-Occurrence Matrix Computation for Texture Directionality Estimation - Marcin Kociolek; Mary Brady; Peter Bajcsy; Cardone, Antonio (IEEE 22nd Signal Processing Algorithms, Architectures, Arrangements, and Applications Conference, 2018)
A novel interpolation-based model for the computation of the Gray Level Co-occurrence Matrix (GLCM) is presented. The model enables GLCM computation for any real valued angles and offsets, as opposed to the traditional, lattice-based model. A texture directionality estimation algorithm is defined using the GLCM-derived correlation feature. The robustness of the algorithm with respect to image blur and additive Gaussian noise is evaluated. It is concluded that directionality estimation is robust to image blur and low noise levels. For high noise levels, the mean error increases but remains bounded. The performance of the directionality estimation algorithm is illustrated on fluorescence microscopy images of fibroblast cells. The algorithm was implemented in C++ and the source code is available in an openly accessible repository.

Occurrence of Vibrio cholerae in water reservoirs of Burkina Faso - Kaboré, Saidou; Cecchi, Philippe; Mosser, Thomas; Toubiana, Mylène; Traoré, Oumar; Ouattara, Aboubakar S.; Traoré, Alfred S.; Barro, Nicolas; Rita R Colwell; Monfort, Patrick (Research in Microbiology, 2018)
Africa is currently an important region in which cholera epidemics occur. Little is known about the presence of Vibrio cholerae in freshwater bodies in Africa. There are ca. 1700 lakes and reservoirs in Burkina Faso, most of which have been built within recent decades to secure water resources. The purpose of this study was to investigate the presence of V. cholerae in the water of reservoirs, using the most-probable-number polymerase chain reaction. Results showed that V. cholerae could be detected in water samples collected from 14 of 39 sampled reservoirs. The concentrations varied from 0 MPN/l to more than 1100 MPN/l. Fifty strains of V. cholerae isolated on CHROMagar™ vibrio were identified as V. cholerae non-O1/non-O139, none of which carried the ctxA gene. A significant positive correlation was found between the presence of V. cholerae in the reservoirs and both alkaline pH and phytoplankton biomass. V. cholerae was present in significantly higher numbers in reservoirs of urban areas than in rural areas. Since V. cholerae non-O1/non-O139 has been shown to be a causative agent of endemic diarrheal outbreaks, their presence in Burkina Faso reservoirs suggests they may play a role in gastroenteritis in that country.

Spores and soil from six sides: interdisciplinarity and the environmental biology of anthrax (Bacillus anthracis) - Carlson, Colin J.; Getz, Wayne M.; Kausrud, Kyrre L.; Cizauskas, Carrie A.; Blackburn, Jason K.; Bustos Carrillo, Fausto A.; Rita R Colwell; Easterday, W. Ryan; Ganz, Holly H.; Kamath, Pauline L.; Økstad, Ole A.; Turner, Wendy C.; et al. (Biological Reviews, 2018)
Environmentally transmitted diseases are comparatively poorly understood and managed, and their ecology is particularly understudied. Here we identify challenges of studying environmental transmission and persistence with a six‐sided interdisciplinary review of the biology of anthrax (Bacillus anthracis). Anthrax is a zoonotic disease capable of maintaining infectious spore banks in soil for decades (or even potentially centuries), and the mechanisms of its environmental persistence have been the topic of significant research and controversy. Where anthrax is endemic, it plays an important ecological role, shaping the dynamics of entire herbivore communities. The complex eco‐epidemiology of anthrax, and the mysterious biology of Bacillus anthracis during its environmental stage, have necessitated an interdisciplinary approach to pathogen research. Here, we illustrate different disciplinary perspectives through key advances made by researchers working in Etosha National Park, a long‐term ecological research site in Namibia that has exemplified the complexities of the enzootic process of anthrax over decades of surveillance. In Etosha, the role of scavengers and alternative routes (waterborne transmission and flies) has proved unimportant relative to the long‐term persistence of anthrax spores in soil and their infection of herbivore hosts. Carcass deposition facilitates green‐ups of vegetation to attract herbivores, potentially facilitated by the role of anthrax spores in the rhizosphere. The underlying seasonal pattern of vegetation, and herbivores' immune and behavioural responses to anthrax risk, interact to produce regular ‘anthrax seasons’ that appear to be a stable feature of the Etosha ecosystem. Through the lens of microbiologists, geneticists, immunologists, ecologists, epidemiologists, and clinicians, we discuss how anthrax dynamics are shaped at the smallest scale by population genetics and interactions within the bacterial communities up to the broadest scales of ecosystem structure. We illustrate the benefits and challenges of this interdisciplinary approach to disease ecology, and suggest ways anthrax might offer insights into the biology of other important pathogens. Bacillus anthracis, and the more recently emerged Bacillus cereus biovar anthracis, share key features with other environmentally transmitted pathogens, including several zoonoses and panzootics of special interest for global health and conservation efforts. Understanding the dynamics of anthrax, and developing interdisciplinary research programs that explore environmental persistence, is a critical step forward for understanding these emerging threats.

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)

A Bioinformatics 3D Cellular Morphotyping Strategy for Assessing Biomaterial Scaffold Niches - Florczyk, Stephen J.; Simon, Mylene; Juba, Derek; Pine, P. Scott; Sarkar, Sumona; Chen, Desu; Baker, Paula J.; Bodhak, Subhadip; Cardone, Antonio; Brady, Mary C.; Bajcsy, Peter; Simon, Carl G. (ACS Biomaterials Science & Engineering, 2017)

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

CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules - Carpenter, Megan R.; Kalburge, Sai S.; Borowski, Joseph D.; Peters, Molly C.; Rita R Colwell; Boyd, E. Fidelma (Journal of Bacteriology, 2017)
Pathogenicity islands (PAIs) are mobile integrated genetic elements that contain a diverse range of virulence factors. PAIs integrate into the host chromosome at a tRNA locus that contains their specific bacterial attachment site, attB, via integrase-mediated site-specific recombination generating attL and attR sites. We identified conserved recombination modules (integrases and att sites) previously described in choleragenic Vibrio cholerae PAIs but with novel cargo genes. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins) and a type VI secretion system (T6SS) gene cluster were identified at the Vibrio pathogenicity island 1 (VPI-1) insertion site in 19 V. cholerae strains and contained the same recombination module. Two divergent type I-F CRISPR-Cas systems were identified, which differed in Cas protein homology and content. The CRISPR repeat sequence was identical among all V. cholerae strains, but the CRISPR spacer sequences and the number of spacers varied. In silico analysis suggests that the CRISPR-Cas systems were active against phages and plasmids. A type III secretion system (T3SS) was present in 12 V. cholerae strains on a 68-kb island inserted at the same tRNA-serine insertion site as VPI-2 and contained the same recombination module. Bioinformatics analysis showed that two divergent T3SSs exist among the strains examined. Both the CRISPR and T3SS islands excised site specifically from the bacterial chromosome as complete units, and the cognate integrases were essential for this excision. These data demonstrated that identical recombination modules that catalyze integration and excision from the chromosome can acquire diverse cargo genes, signifying a novel method of acquisition for both CRISPR-Cas systems and T3SSs.

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.

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

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

3D Cellular Morphotyping of Scaffold Niches - Florczyk, Stephen J; Simon, Mylene; Juba, Derek; Pine, P Scott; Sarkar, Sumona; Chen, Desu; Baker, Paula J; Bodhak, Subhadip; Cardone, Antonio; Brady, Mary; others (2016 32nd Southern Biomedical Engineering Conference (SBEC), 2016)

Chitin promotes Mycobacterium ulcerans growth - Sanhueza, Daniel; Chevillon, Christine; Rita R Colwell; Babonneau, Jérémie; Marion, Estelle; Marsollier, Laurent; égan, çois (FEMS Microbiology Ecology, 2016)
Mycobacterium ulcerans (MU) is the causative agent of Buruli ulcer, an emerging human infectious disease. However, both the ecology and life cycle of MU are poorly understood. The occurrence of MU has been linked to the aquatic environment, notably water bodies affected by human activities. It has been hypothesized that one or a combination of environmental factor(s) connected to human activities could favour growth of MU in aquatic systems. Here, we tested in vitro the growth effect of two ubiquitous polysaccharides and five chemical components on MU at concentration ranges shown to occur in endemic regions. Real-time PCR showed that chitin increased MU growth significantly providing a nutrient source or environmental support for the bacillus, thereby, providing a focus on the association between MU and aquatic arthropods. Aquatic environments with elevated population of arthropods provide increased chitin availability and, thereby, enhanced multiplication of MU. If calcium very slightly enhanced MU growth, iron, zinc, sulphate and phosphate did not stimulate MU growth, and at the concentration ranges of this study would limit MU population in natural ecosystems.

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.

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

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)

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.

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

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

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

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

Estimating Actin Fiber Orientation using Interpolation-Based Grey-Level Co-Occurrence Matrix Computation - Cardone, Antonio; Brady, Mary; Kociolek, Marcin; Bajcsy, Peter (BioImage Informatics Conference, 2015)

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.

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

Segmentation and sub-cellular feature-based analysis of microscopy images - Cardone, Antonio; Chalfoun, Joe; Peskin, Adele; Bajcsy, Peter; Kociolek, Marcin; Bhadriraju, Kiran; Brady, Mary (BioImage Informatics Conference, 2015)

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

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)

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

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

Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing - Hasan, Nur A.; Young, Brian A.; Minard-Smith, Angela T.; Saeed, Kelly; Li, Huai; Heizer, Esley M.; McMillan, Nancy J.; Isom, Richard; Abdullah, Abdul Shakur; Bornman, Daniel M.; Faith, Seth A.; Choi, Seon Young; et al. (PLoS ONE, 2014)
Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.

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)

Validation of high throughput sequencing and microbial forensics applications - Budowle, Bruce; Connell, Nancy D; Bielecka-Oder, Anna; Rita R Colwell; Corbett, Cindi R; Fletcher, Jacqueline; Forsman, Mats; Kadavy, Dana R; Markotic, Alemka; Morse, Stephen A; Murch, Randall S; Sajantila, Antti; et al. (Investigative Genetics, 2014)
High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security.

Viewing Marine Bacteria, Their Activity and Response to Environmental Drivers from Orbit - Grimes, D. Jay; Ford, Tim E.; Rita R Colwell; Baker-Austin, Craig; Martinez-Urtaza, Jaime; Subramaniam, Ajit; Capone, Douglas G. (Microbial Ecology, 2014)
Satellite-based remote sensing of marine microorganisms has become a useful tool in predicting human health risks associated with these microscopic targets. Early applications were focused on harmful algal blooms, but more recently methods have been developed to interrogate the ocean for bacteria. As satellite-based sensors have become more sophisticated and our ability to interpret information derived from these sensors has advanced, we have progressed from merely making fascinating pictures from space to developing process models with predictive capability. Our understanding of the role of marine microorganisms in primary production and global elemental cycles has been vastly improved as has our ability to use the combination of remote sensing data and models to provide early warning systems for disease outbreaks. This manuscript will discuss current approaches to monitoring cyanobacteria and vibrios, their activity and response to environmental drivers, and will also suggest future directions.

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

Binary to Bushy: Bayesian Hierarchical Clustering with the Beta Coalescent - Hu, Yuening; Jordan Boyd-Graber; Daume III, Hal; Ying, Z Irene (2013)
Abstract Discovering hierarchical regularities in data is a key problem in interacting with large datasets, modeling cognition, and encoding knowledge. A previous Bayesian solution-- -Kingman's coalescent---provides a convenient probabilistic model for data represented ...

Dirichlet Mixtures, the Dirichlet Process, and the Structure of Protein Space - Nguyen,Viet-An; Jordan Boyd-Graber; Altschul, Stephen F. (Journal of Computational Biology, 2013)
The Dirichlet process is used to model probability distributions that are mixtures of an unknown number of components. Amino acid frequencies at homologous positions within related proteins have been fruitfully modeled by Dirichlet mixtures, and we use the Dirichlet process to derive such mixtures with an unbounded number of components. This application of the method requires several technical innovations to sample an unbounded number of Dirichlet-mixture components. The resulting Dirichlet mixtures model multiple-alignment data substantially better than do previously derived ones. They consist of over 500 components, in contrast to fewer than 40 previously, and provide a novel perspective on the structure of proteins. Individual protein positions should be seen not as falling into one of several categories, but rather as arrayed near probability ridges winding through amino acid multinomial space.
Keywords: ALIGNMENT; computational molecular biology; dynamic programming; multiple alignment; sequence analysis

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

Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments - Bozo-Hurtado, Lorelei; García-Amado, M; Chistoserdov, Andrei; Varela, Ramon; Narvaez, J; Rita R Colwell; Suárez, Paula (Aquatic Biosystems, 2013)
Background The Cariaco Basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. Marine water samples were collected in May, 2005 and 2006, at the sampling stations A (10°30′ N, 64°40′ W), B (10°40′ N, 64°45′ W) and D (10°43’N, 64°32’W) from different depths, including surface, redox interface, and anoxic zones. In order to enrich for sulfate reducing bacteria (SRB), water samples were inoculated into anaerobic media amended with lactate or acetate as carbon source. To analyze the composition of enrichment cultures, we performed DNA extraction, PCR-DGGE, and sequencing of selected bands. Results DGGE results indicate that many bacterial genera were present that are associated with the sulfur cycle, including Desulfovibrio spp., as well as heterotrophs belonging to Vibrio, Enterobacter, Shewanella, Fusobacterium, Marinifilum, Mariniliabilia, and Spirochaeta. These bacterial populations are related to sulfur coupling and carbon cycles in an environment of variable redox conditions and oxygen availability. Conclusions In our studies, we found an association of SRB-like Desulfovibrio with Vibrio species and other genera that have a previously defined relevant role in sulfur transformation and coupling of carbon and sulfur cycles in an environment where there are variable redox conditions and oxygen availability. This study provides new information about microbial species that were culturable on media for SRB at anaerobic conditions at several locations and water depths in the Cariaco Basin.

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

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 ...

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

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 ...

Online Latent Dirichlet Allocation with Infinite Vocabulary - Zhai,Ke; Jordan Boyd-Graber (International Conference on Machine Learning, 2013)
Topic models based on latent Dirichlet allocation (LDA) assume a predefined vocabulary. This is reasonable in batch settings but not reasonable for streaming and online settings. To address this lacuna, we extend LDA by drawing topics from a Dirichlet process whose base distribution is a distribution over all strings rather than from a finite Dirichlet. We develop inference using online variational inference and—to only consider a finite number of words for each topic—propose heuristics to dynamically order, expand, and contract the set of words we consider in our vocabulary. We show our model can successfully incorporate new words and that it performs better than topic models with finite vocabularies in evaluations of topic quality and classification performance.

Parallel geometric classification of stem cells by their three-dimensional morphology - Juba,Derek; Cardone, Antonio; Ip, Cheuk Yiu; Simon Jr, Carl G; K Tison, Christopher; Kumar, Girish; Brady,Mary; Varshney, Amitabh (Computational Science & Discovery, 2013)

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

Spoiler Alert: Machine Learning Approaches to Detect Social Media Posts with Revelatory Information - Jordan Boyd-Graber; Glasgow, K; Zajac, J S (2013)
ABSTRACT Spoilers—critical plot information about works of fiction that “spoil” a viewer's enjoyment—have prompted elaborate conventions on social media to allow readers to insulate themselves from spoilers. However, these solutions depend on 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

Understanding the impact of image quality on segmentation accuracy - Li-Baboud, Ya-Shian; Cardone, Antonio; Chalfoun, Joe; Bajcsy, Peter; Elliott, John (SPIE Newsroom, 2013)

Why “Fiat-Shamir for Proofs” Lacks a Proof - Bitansky, Nir; Dana Dachman-Soled; Garg, Sanjam; Jain, Abhishek; Kalai, Yael Tauman; López-Alt, Adriana; Wichs, Daniel (Theory of Cryptography, 2013)
The Fiat-Shamir heuristic [CRYPTO ’86] is used to convert any 3-message public-coin proof or argument system into a non-interactive argument, by hashing the prover’s first message to select the verifier’s challenge. It is known that this heuristic is sound when the hash function is modeled as a random oracle. On the other hand, the surprising result of Goldwasser and Kalai [FOCS ’03] shows that there exists a computationally sound argument on which the Fiat-Shamir heuristic is never sound, when instantiated with any actual efficient hash function. This leaves us with the following interesting possibility: perhaps we can securely instantiates the Fiat-Shamir heuristic for all 3-message public-coin statistically sound proofs, even if we must fail for some computationally sound arguments. Indeed, this has been conjectured to be the case by Barak, Lindell and Vadhan [FOCS ’03], but we do not have any provably secure instantiation under any “standard assumption”. In this work, we give a broad black-box separation result showing that the security of the Fiat-Shamir heuristic for statistically sound proofs cannot be proved under virtually any standard assumption via a black-box reduction. More precisely: –If we want to have a “universal” instantiation of the Fiat-Shamir heuristic that works for all 3-message public-coin proofs, then we cannot prove its security via a black-box reduction from any assumption that has the format of a “cryptographic game”. –For many concrete proof systems, if we want to have a “specific” instantiation of the Fiat-Shamir heuristic for that proof system, then we cannot prove its security via a black box reduction from any “falsifiable assumption” that has the format of a cryptographic game with an efficient challenger.
Keywords: Algorithm Analysis and Problem Complexity; Computation by Abstract Devices; Data Encryption; Systems and Data Security

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

Before We Knew It: An Empirical Study of Zero-day Attacks in the Real World - Bilge, Leyla; Tudor Dumitras (CCS '12 Proceedings of the 2012 ACM conference on Computer and Communications Security, 2012)
Little is known about the duration and prevalence of zero-day attacks, which exploit vulnerabilities that have not been disclosed publicly. Knowledge of new vulnerabilities gives cyber criminals a free pass to attack any target of their choosing, while remaining undetected. Unfortunately, these serious threats are difficult to analyze, because, in general, data is not available until after an attack is discovered. Moreover, zero-day attacks are rare events that are unlikely to be observed in honeypots or in lab experiments. In this paper, we describe a method for automatically identifying zero-day attacks from field-gathered data that records when benign and malicious binaries are downloaded on 11 million real hosts around the world. Searching this data set for malicious files that exploit known vulnerabilities indicates which files appeared on the Internet before the corresponding vulnerabilities were disclosed. We identify 18 vulnerabilities exploited before disclosure, of which 11 were not previously known to have been employed in zero-day attacks. We also find that a typical zero-day attack lasts 312 days on average and that, after vulnerabilities are disclosed publicly, the volume of attacks exploiting them increases by up to 5 orders of magnitude.
Keywords: full disclosure; vulnerabilities; zero-day attacks

Besting the Quiz Master: Crowdsourcing Incremental Classification Games - Satinoff,Brianna; Jordan Boyd-Graber (Empirical Methods in Natural Language Processing, 2012)
Cost-sensitive classification, where the features used in machine learning tasks have a cost, has been explored as a means of balancing knowl- edge against the expense of obtaining new fea- tures. We introduce a setting where humans engage in classification with incrementally re- vealed features: the collegiate trivia circuit. By providing the community with a web-based system to practice, we collected tens of thou- sands of implicit word-by-word ratings of how useful features are for eliciting correct answers. Observing humans’ classification process, we improve the performance of a state-of-the art classifier. We also use the dataset to evaluate a system to compete in the incremental classifica- tion task through a reduction of reinforcement learning to classification. Our system learns when to answer a question, performing better than baselines and most human players.

Biases from model assumptions in texture sub-cellular image segmentation - Cardone, Antonio; Amelot, Julien; Li-Baboud, Ya-Shian; Brady, Mary; Bajcsy, Peter (SPIE Newsroom, 2012)

Collecting Semantic Similarity Ratings to Connect Concepts in Assistive Communication Tools - Nikolova,Sonya; Jordan Boyd-Graber; Fellbaum,Christiane (Modeling, Learning, and Processing of Text Technological Data StructuresModeling, Learning, and Processing of Text Technological Data Structures, 2012)
To compensate for the common inability of people with lexical production impairments to access and express intended concepts, we make use of models of human semantic memory that build on the notion of semantic similarity and relatedness. Such models, constructed on evidence gained from psycholinguistic experiments, form the basis of a large lexical database, WordNet . We augment WordNet with many additional links among words and concepts that are semantically related. Making this densely connected semantic network available to people with anomic aphasia through assistive technologies should enable them to navigate among related words and concepts and retrieve the words that they intend to express.

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)

Design and Synthesis for Multimedia Systems Using the Targeted Dataflow Interchange Format - Chung-Ching Shen; Wu, Shenpei; Sane, N.; Wu, Hsiang-Huang; Plishker,W.; Bhattacharyya, Shuvra S. (IEEE Transactions on Multimedia, 2012)
Development of multimedia systems that can be targeted to different platforms is challenging due to the need for rigorous integration between high-level abstract modeling, and low-level synthesis and optimization. In this paper, a new dataflow-based design tool called the targeted dataflow interchange format is introduced for retargetable design, analysis, and implementation of embedded software for multimedia systems. Our approach provides novel capabilities, based on principles of task-level dataflow analysis, for exploring and optimizing interactions across design components; object-oriented data structures for encapsulating contextual information for components; a novel model for representing parameterized schedules that are derived from repetitive graph structures; and automated code generation for programming interfaces and low-level customizations that are geared toward high-performance embedded-processing architectures. We demonstrate our design tool for cross-platform application design, parameterized schedule representation, and associated dataflow graph-code generation using a case study centered around an image registration application.
Keywords: associated dataflow graph-code generation; Computational modeling; contextual information encapsulation; cross-platform application design; data flow graphs; Data models; Data structures; Dataflow graphs; design components; design tools; Digital signal processing; electronic data interchange; embedded signal processing; Embedded software; high-level abstract modeling; high-performance embedded-processing architectures; Image coding; image registration application; image representation; low-level customizations; low-level optimization; low-level synthesis; Multimedia communication; multimedia systems; multimedia systems development; object-oriented data structures; object-oriented methods; parameterized schedule representation; programming interfaces; repetitive graph structures; retargetable design; Schedules; scheduling; software synthesis; Streaming media; targeted dataflow interchange format; task-level dataflow analysis

Determining Protein Dynamics from 15N Relaxation Data by Using DYNAMICS - Fushman, David (Protein NMR Techniques, 2012)
Motions are essential for protein function, and knowledge of protein dynamics is a key to our understanding the mechanisms underlying protein folding and stability, ligand recognition, allostery, and catalysis. In the last two decades, NMR relaxation measurements have become a powerful tool for characterizing backbone and side chain dynamics in complex biological macromolecules such as proteins and nucleic acids. Accurate analysis of the experimental data in terms of motional parameters is an essential prerequisite for developing physical models of motions to paint an adequate picture of protein dynamics. Here, I describe in detail how to use the software package DYNAMICS that was developed for accurate characterization of the overall tumbling and local dynamics in a protein from nuclear spin-relaxation rates measured by NMR. Step-by-step instructions are provided and illustrated through an analysis of 15 N relaxation data for protein G.
Keywords: Biomedical and Life Sciences

Dictionary-based Face Recognition Under Variable Lighting and Pose - Patel, Vishal M.; Wu,T.; Biswas,S.; Phillips,P.; Chellapa, Rama (IEEE Transactions on Information Forensics and Security, 2012)
We present a face recognition algorithm based on simultaneous sparse approximations under varying illumination and pose. A dictionary is learned for each class based on given training examples which minimizes the representation error with a sparseness constraint. A novel test image is projected onto the span of the atoms in each learned dictionary. The resulting residual vectors are then used for classification. To handle variations in lighting conditions and pose, an image relighting technique based on pose-robust albedo estimation is used to generate multiple frontal images of the same person with variable lighting. As a result, the proposed algorithm has the ability to recognize human faces with high accuracy even when only a single or a very few images per person are provided for training. The efficiency of the proposed method is demonstrated using publicly available databases and it is shown that this method is efficient and can perform significantly better than many competitive face recognition algorithms.
Keywords: Biometrics; dictionary learning; face recognition; illumination variation,; outlier rejection

Drosophila Src regulates anisotropic apical surface growth to control epithelial tube size - Nelson, Kevin S.; Zia Khan; Molnár, Imre; Mihály, József; Kaschube, Matthias; Beitel, Greg J. (Nature Cell Biology, 2012)
Networks of epithelial and endothelial tubes are essential for the function of organs such as the lung, kidney and vascular system. The sizes and shapes of these tubes are highly regulated to match their individual functions. Defects in tube size can cause debilitating diseases such as polycystic kidney disease and ischaemia. It is therefore critical to understand how tube dimensions are regulated. Here we identify the tyrosine kinase Src as an instructive regulator of epithelial-tube length in the Drosophila tracheal system. Loss-of-function Src42 mutations shorten tracheal tubes, whereas Src42 overexpression elongates them. Surprisingly, Src42 acts distinctly from known tube-size pathways and regulates both the amount of apical surface growth and, with the conserved formin dDaam, the direction of growth. Quantitative three-dimensional image analysis reveals that Src42- and dDaam-mutant tracheal cells expand more in the circumferential than the axial dimension, resulting in tubes that are shorter in length—but larger in diameter—than wild-type tubes. Thus, Src42 and dDaam control tube dimensions by regulating the direction of anisotropic growth, a mechanism that has not previously been described.

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

Efficient Password Authenticated Key Exchange via Oblivious Transfer - Canetti, Ran; Dana Dachman-Soled; Vaikuntanathan, Vinod; Wee, Hoeteck (Public Key Cryptography – PKC 2012, 2012)
We present a new framework for constructing efficient password authenticated key exchange (PAKE) protocols based on oblivious transfer (OT). Using this framework, we obtain: an efficient and simple UC-secure PAKE protocol that is secure against adaptive corruptions without erasures. efficient and simple PAKE protocols under the Computational Diffie-Hellman (CDH) assumption and the hardness of factoring. (Previous efficient constructions rely on hash proof systems, which appears to be inherently limited to decisional assumptions.) All of our constructions assume a common reference string (CRS) but do not rely on random oracles.
Keywords: adaptive security; Algorithm Analysis and Problem Complexity; Computer Communication Networks; Data Encryption; Discrete Mathematics in Computer Science; Management of Computing and Information Systems; oblivious transfer; Password Authenticated Key Exchange; search assumptions; Systems and Data Security; UC security

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

The first international workshop on entity-oriented search (EOS) - Balog,Krisztian; de Vries,Arjen P.; Serdyukov,Pavel; Wen,Ji-Rong (SIGIR Forum, 2012)
The First International Workshop on Entity-Oriented Search (EOS) workshop was held on July 28, 2011 in Beijing, China, in conjunction with the 34th Annual International ACM SIGIR Conference (SIGIR 2011). The objective for the workshop was to bring together academic researchers and industry practitioners working on entity-oriented search to discuss tasks and challenges, and to uncover the next frontiers for academic research on the topic. The workshop program accommodated two invited talks, eleven refereed papers divided into three technical paper sessions, and a group discussion.

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

Global secretome analysis identifies novel mediators of bone metastasis - Blanco, Mario Andres; LeRoy, Gary; Zia Khan; Alečković, Maša; Zee, Barry M.; Garcia, Benjamin A.; Kang, Yibin (Cell Research, 2012)
Bone is the one of the most common sites of distant metastasis of solid tumors. Secreted proteins are known to influence pathological interactions between metastatic cancer cells and the bone stroma. To comprehensively profile secreted proteins associated with bone metastasis, we used quantitative and non-quantitative mass spectrometry to globally analyze the secretomes of nine cell lines of varying bone metastatic ability from multiple species and cancer types. By comparing the secretomes of parental cells and their bone metastatic derivatives, we identified the secreted proteins that were uniquely associated with bone metastasis in these cell lines. We then incorporated bioinformatic analyses of large clinical metastasis datasets to obtain a list of candidate novel bone metastasis proteins of several functional classes that were strongly associated with both clinical and experimental bone metastasis. Functional validation of selected proteins indicated that in vivo bone metastasis can be promoted by high expression of (1) the salivary cystatins CST1, CST2, and CST4; (2) the plasminogen activators PLAT and PLAU; or (3) the collagen functionality proteins PLOD2 and COL6A1. Overall, our study has uncovered several new secreted mediators of bone metastasis and therefore demonstrated that secretome analysis is a powerful method for identification of novel biomarkers and candidate therapeutic targets.
Keywords: bone; cancer; metastasis; proteomics; secretome

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.

Grey-box GUI Testing: Efficient Generation of Event Sequences - Arlt,Stephan; Banerjee,Ishan; Bertolini,Cristiano; Memon, Atif M.; Schäf,Martin (arXiv:1205.4928, 2012)
Graphical user interfaces (GUIs), due to their event driven nature, present a potentially unbounded space of all possible ways to interact with software. During testing it becomes necessary to effectively sample this space. In this paper we develop algorithms that sample the GUI's input space by only generating sequences that (1) are allowed by the GUI's structure, and (2) chain together only those events that have data dependencies between their event handlers. We create a new abstraction, called an event-dependency graph (EDG) of the GUI, that captures data dependencies between event handler code. We develop a mapping between EDGs and an existing black-box user-level model of the GUI's workflow, called an event-flow graph (EFG). We have implemented automated EDG construction in a tool that analyzes the bytecode of each event handler. We evaluate our "grey-box" approach using four open-source applications and compare it with the current state-of-the-art EFG approach. Our results show that using the EDG reduces the number of test cases while still achieving at least the same coverage. Furthermore, we were able to detect 2 new bugs in the subject applications.
Keywords: 68N30; Computer Science - Software Engineering

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.

Vibrio cholerae in a historically cholera-free country - Haley, Bradd J.; Chen, Arlene; Grim, Christopher J.; Clark, Philip; Diaz, Celia M; Taviani, Elisa; Hasan, Nur A.; Sancomb, Elizabeth; Elnemr, Wessam M; Islam, Muhammad A.; Huq, Anwar; Rita R Colwell; et al. (Environmental Microbiology Reports, 2012)
We report the autochthonous existence of Vibrio cholerae in coastal waters of Iceland, a geothermally active country where cholera is absent and has never been reported. Seawater, mussel and macroalgae samples were collected close to, and distant from, sites where geothermal activity causes a significant increase in water temperature during low tides. Vibrio cholerae was detected only at geothermal‐influenced sites during low‐tides. None of the V. cholerae isolates encoded cholera toxin (ctxAB) and all were non‐O1/non‐O139 serogroups. However, all isolates encoded other virulence factors that are associated with cholera as well as extra‐intestinal V. cholerae infections. The virulence factors were functional at temperatures of coastal waters of Iceland, suggesting an ecological role. It is noteworthy that V. cholerae was isolated from samples collected at sites distant from anthropogenic influence, supporting the conclusion that V. cholerae is autochthonous to the aquatic environment of Iceland.

Lithium: Event-Driven Network Control - Kim,H.; Voellmy,A.; Burnett,S.; Feamster, Nick; Clark,R. (Georgia Institute of Technology, 2012)
This paper introduces event-driven network control, a network control framework that makes networks easier to manage by automating many tasks that must currently be performed by manually modifying low-level, distributed, and complex device configuration. We identify four policy domains that inherently capture many events: time, user, history, and traffic flow. We then present Lithium, an event-driven network control framework that can implement policies expressed using these domains. Lithium can support policies that automatically react to a wide range of events, from fluctuations in traffic volumes to changes in the time of day. Lithium allows network operators to specify networkwide policies in terms of a high-level, event-driven policy model, as opposed to configuring individual network devices with low-level commands. To show that Lithium is practical, general, and applicable in different types of network scenarios, we have deployed Lithium in both a campus network and a home network and used it to implement more flexible and dynamic network policies. We also perform evaluations to show that Lithium introduces negligible overhead beyond a conventional OpenFlow-based control framework.

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.

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

Modality and Negation in SIMT Use of Modality and Negation in Semantically-Informed Syntactic MT - Baker,Kathryn; Bloodgood,Michael; Dorr, Bonnie J; Callison-Burch,Chris; Filardo,Nathaniel W.; Piatko,Christine; Levin,Lori; Miller,Scott (Computational Linguistics, 2012)
This paper describes the resource- and system-building efforts of an eight-week Johns Hopkins University Human Language Technology Center of Excellence Summer Camp for Applied Language Exploration (SCALE-2009) on Semantically-Informed Machine Translation (SIMT). We describe a new modality/negation (MN) annotation scheme, the creation of a (publicly available) MN lexicon, and two automated MN taggers that we built using the annotation scheme and lexicon. Our annotation scheme isolates three components of modality and negation: a trigger (a word that conveys modality or negation), a target (an action associated with modality or negation) and a holder (an experiencer of modality). We describe how our MN lexicon was semi-automatically produced and we demonstrate that a structure-based MN tagger results in precision around 86% (depending on genre) for tagging of a standard LDC data set.

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

Mr. LDA: A Flexible Large Scale Topic Modeling Package using Variational Inference in MapReduce - Zhai,Ke; Jordan Boyd-Graber; Asadi,Nima; Alkhouja,Mohamad (Proceedings of ACM International Conference on World Wide Web, 2012, 2012)
Latent Dirichlet Allocation (LDA) is a popular topic modeling tech- nique for exploring document collections. Because of the increasing prevalence of large datasets, there is a need to improve the scal- ability of inference for LDA. In this paper, we introduce a novel and flexible large scale topic modeling package in MapReduce (Mr. LDA). As opposed to other techniques which use Gibbs sampling, our proposed framework uses variational inference, which easily fits into a distributed environment. More importantly, this variational implementation, unlike highly tuned and specialized implementa- tions based on Gibbs sampling, is easily extensible. We demonstrate two extensions of the models possible with this scalable framework: informed priors to guide topic discovery and extracting topics from a multilingual corpus. We compare the scalability of Mr. LDA against Mahout, an existing large scale topic modeling package. Mr. LDA out-performs Mahout both in execution speed and held-out likelihood.

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

Optimizing epidemic protection for socially essential workers - Barrett,Chris; Beckman,Richard; Bisset,Keith; Chen,Jiangzhuo; DuBois,Thomas; Eubank,Stephen; Kumar,V. S. Anil; Lewis,Bryan; Marathe,Madhav V.; Srinivasan, Aravind; Stretz,Paula E. (Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, 2012)
Public-health policy makers have many tools to mitigate an epidemic's effects. Most related research focuses on the direct effects on those infected (in terms of health, life, or productivity). Interventions including treatment, prophylaxis, quarantine, and social distancing are well studied in this context. These interventions do not address indirect effects due to the loss of critical services and infrastructures when too many of those responsible for their day-to-day operations fall ill. We examine, both analytically and through simulation, the protection of such essential subpopulations by sequestering them, effectively isolating them into groups during an epidemic. We develop a framework for studying the benefits of sequestering and heuristics for when to sequester. We also prove a key property of sequestering placement which helps partition the subpopulations optimally. Thus we provide a first step toward determining how to allocate resources between the direct protection of a population, and protection of those responsible for critical services.
Keywords: epidemiology; OPTIMIZATION; public health informatics

Preparation and probing of coherent vibrational wave packets in the ground electronic state of HD^{+} - Bhattacharya, Rangana; Chatterjee, Souvik; Bhattacharyya, Shuvra S. (Physical Review A, 2012)
We have investigated the formation of coherent vibrational wave packets in the ground electronic state of HD+ on exposure to intense ultrashort laser pulses of wavelength 1060 nm. The effects of the duration and field strength of the pulse on the final composition of the residual bound nuclear wave packet generated by such impulsive excitations have been studied. The resulting wave packet is allowed to evolve freely on the potential surface for some time, after which a weak pulse of sufficiently large duration is used for probing its composition. This pulse can cause only single-photon dissociation. The simulations have been performed with different probe wavelengths for accessing information about different portions of the wave packet in the vibrational quantum number space. Our aim was to investigate the extent to which information obtained from the kinetic-energy spectra of the photofragments induced by the probe pulse can be correlated to the structure of the wave packet. Simple time-dependent perturbation calculations have also been performed for obtaining the relative strengths of photofragment signals arising from different vibrational levels due to wave-packet dissociation. A comparison with our numerical results indicates that though the general features of the photofragment kinetic-energy spectra from a wave packet are consistent with the perturbation theory results in the intensity regime studied, dynamical evolution during a long pulse can modify the relative heights of the kinetic-energy peaks through nonperturbative interactions in some cases.

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

Quantitative measurement of allele‐specific protein expression in a diploid yeast hybrid by LC‐MS - Zia Khan; Bloom, Joshua S.; Amini, Sasan; Singh, Mona; Perlman, David H.; Caudy, Amy A.; Kruglyak, Leonid (Molecular Systems Biology, 2012)
Understanding the genetic basis of gene regulatory variation is a key goal of evolutionary and medical genetics. Regulatory variation can act in an allele‐specific manner (cis‐acting) or it can affect both alleles of a gene (trans‐acting). Differential allele‐specific expression (ASE), in which the expression of one allele differs from another in a diploid, implies the presence of cis‐acting regulatory variation. While microarrays and high‐throughput sequencing have enabled genome‐wide measurements of transcriptional ASE, methods for measurement of protein ASE (pASE) have lagged far behind. We describe a flexible, accurate, and scalable strategy for measurement of pASE by liquid chromatography‐coupled mass spectrometry (LC‐MS). We apply this approach to a hybrid between the yeast species Saccharomyces cerevisiae and Saccharomyces bayanus. Our results provide the first analysis of the relative contribution of cis‐acting and trans‐acting regulatory differences to protein expression divergence between yeast species.Synopsis A novel strategy for the quantitative measurement of allele‐specific protein expression is used to infer the contributions of cis‐ and trans‐acting factors influencing the divergence of protein levels between yeast species. Rigorous experimental controls and analyses confirm the accuracy of the new strategy for the quantitative measurement of allele‐specific protein expression by high‐throughput mass spectrometry.Analysis of allele‐specific protein expression in an interspecies yeast hybrid and protein expression differences between species reveals that both cis‐effects and trans‐effects contribute to protein expression divergence between two yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus.
Keywords: allele specific; divergence; mass spectrometry; protein expression; proteomics

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.

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

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.

Speeding Up Particle Trajectory Simulations under Moving Force Fields using GPUs - Patro,R.; Dickerson,J. P.; Bista,S.; Gupta,S.K.; Varshney, Amitabh (Journal of Computing and Information Science in Engineering, 2012)
In this paper, we introduce a GPU-based framework forsimulating particle trajectories under both static and dynamic force fields. By exploiting the highly parallel nature of the problem and making efficient use of the available hardware, our simulator exhibits a significant speedup over its CPU- based analog. We apply our framework to a specific experi- mental simulation: the computation of trapping probabilities associated with micron-sized silica beads in optical trapping workbenches. When evaluating large numbers of trajectories (4096), we see approximately a 356 times speedup of the GPU-based simulator over its CPU-based counterpart.

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

Sub-cellular feature detection and automated extraction of collocalized actin and myosin regions - Martineau, Justin; Mokashi,Ronil; Chapman, David; Grasso, Michael; Brady,Mary; Yesha,Yelena; Yesha,Yaacov; Cardone, Antonio; Dima, Alden (the 2nd ACM SIGHIT symposiumProceedings of the 2nd ACM SIGHIT symposium on International health informatics - IHI '12, 2012)

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

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.

You'Re Capped: Understanding the Effects of Bandwidth Caps on Broadband Use in the Home - Marshini Chetty; Banks, Richard; Brush, A.J.; Donner, Jonathan; Grinter, Rebecca (SIGCHI '12, 2012)
Bandwidth caps, a limit on the amount of data users can upload and download in a month, are common globally for both home and mobile Internet access. With caps, each bit of data consumed comes at a cost against a monthly quota or a running tab. Yet, relatively little work has considered the implications of this usage-based pricing model on the user experience. In this paper, we present results from a qualitative study of households living with bandwidth caps. Our findings suggest home users grapple with three uncertainties regarding their bandwidth usage: invisible balances, mysterious processes, and multiple users. We discuss how these uncertainties impact their usage and describe the potential for better tools to help monitor and manage data caps. We conclude that as a community we need to cater for users under Internet cost constraints.
Keywords: Bandwidth; bandwidth cap; data cap; Internet; metered use; pricing; usage-based billing; usage-based pricing

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

Active inference for retrieval in camera networks - Daozheng Chen; Bilgic,Mustafa; Getoor, Lise; Jacobs, David W.; Mihalkova,Lilyana; Tom Yeh (Person-Oriented Vision (POV), 2011 IEEE Workshop on, 2011)
We address the problem of searching camera network videos to retrieve frames containing specified individuals. We show the benefit of utilizing a learned probabilistic model that captures dependencies among the cameras. In addition, we develop an active inference framework that can request human input at inference time, directing human attention to the portions of the videos whose correct annotation would provide the biggest performance improvements. Our primary contribution is to show that by mapping video frames in a camera network onto a graphical model, we can apply collective classification and active inference algorithms to significantly increase the performance of the retrieval system, while minimizing the number of human annotations required.

Active inference for retrieval in camera networks - Daozheng Chen; Bilgic,M.; Getoor, Lise; Jacobs, David W.; Mihalkova,L.; Tom Yeh (Person-Oriented Vision (POV), 2011 IEEE Workshop on, 2011)
We address the problem of searching camera network videos to retrieve frames containing specified individuals. We show the benefit of utilizing a learned probabilistic model that captures dependencies among the cameras. In addition, we develop an active inference framework that can request human input at inference time, directing human attention to the portions of the videos whose correct annotation would provide the biggest performance improvements. Our primary contribution is to show that by mapping video frames in a camera network onto a graphical model, we can apply collective classification and active inference algorithms to significantly increase the performance of the retrieval system, while minimizing the number of human annotations required.
Keywords: active; annotation; probabilistic; frame; cameras; inference; inference; camera; mechanisms; probability; search; model; human; model; retrieval; network; graphical; problem; video; problems; video; processing; retrieval; video; signal; system; searching

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

Applying graphics processor acceleration in a software defined radio prototyping environment - Plishker,W.; Zaki, G.F.; Bhattacharyya, Shuvra S.; Clancy, C.; Kuykendall, J. (2011 22nd IEEE International Symposium on Rapid System Prototyping (RSP), 2011)
With higher bandwidth requirements and more complex protocols, software defined radio (SDR) has ever growing computational demands. SDR applications have different levels of parallelism that can be exploited on multicore platforms, but design and programming difficulties have inhibited the adoption of specialized multicore platforms like graphics processors (GPUs). In this work we propose a new design flow that augments a popular existing SDR development environment (GNU Radio), with a dataflow foundation and a stand-alone GPU accelerated library. The approach gives an SDR developer the ability to prototype a GPU accelerated application and explore its design space fast and effectively. We demonstrate this design flow on a standard SDR benchmark and show that deciding how to utilize a GPU can be non-trivial for even relatively simple applications.
Keywords: Acceleration; coprocessors; dataflow foundation; GNU radio; Graphics processing unit; graphics processor acceleration; Kernel; Libraries; multicore platforms; Multicore processing; PARALLEL PROCESSING; Pipelines; Protocols; software defined radio prototyping environment; software radio; stand-alone GPU accelerated library

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

An assessment of systems and software engineering scholars and institutions (2003–2007 and 2004–2008) - Wong,W. Eric; Tse,T.H.; Glass,Robert L.; Basili, Victor R.; Chen,T.Y. (Journal of Systems and Software, 2011)
An ongoing, annual survey of publications in systems and software engineering identifies the top 15 scholars and institutions in the field over a 5-year period. Each ranking is based on the weighted scores of the number of papers published in TSE, TOSEM, JSS, SPE, EMSE, IST, and Software of the corresponding period. This report summarizes the results for 2003–2007 and 2004–2008. The top-ranked institution is Korea Advanced Institute of Science and Technology, Korea for 2003–2007, and Simula Research Laboratory, Norway for 2004–2008, while Magne Jørgensen is the top-ranked scholar for both periods.
Keywords: Research publications; Systems and software engineering; Top institutions; Top scholars

Automated Planning Logic Synthesis for Autonomous Unmanned Vehicles in Competitive Environments with Deceptive Adversaries - Svec,Petr; Gupta, Satyandra K. (New Horizons in Evolutionary Robotics, 2011)
We developed a new approach for automated synthesis of a planning logic for autonomous unmanned vehicles. This new approach can be viewed as an automated iterative process during which an initial version of a logic is synthesized and then gradually improved by detecting and fixing its shortcomings. This is achieved by combining data mining for extraction of vehicle’s states of failure and Genetic Programming (GP) technique for synthesis of corresponding navigation code. We verified the feasibility of the approach using unmanned surface vehicles (USVs) simulation. Our focus was specifically on the generation of a planning logic used for blocking the advancement of an intruder boat towards a valuable target. Developing autonomy logic for this behavior is challenging as the intruder’s attacking logic is human-competitive with deceptive behavior so the USV is required to learn specific maneuvers for specific situations to do successful blocking. We compared the performance of the generated blocking logic to the performance of logic that was manually implemented. Our results show that the new approach was able to synthesize a blocking logic with performance closely approaching the performance of the logic coded by hand.
Keywords: engineering

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 case study of measuring process risk for early insights into software safety - Layman,L.; Basili, Victor R.; Zelkowitz, Marvin V; Fisher,K.L. (Software Engineering (ICSE), 2011 33rd International Conference on, 2011)
In this case study, we examine software safety risk in three flight hardware systems in NASA's Constellation spaceflight program. We applied our Technical and Process Risk Measurement (TPRM) methodology to the Constellation hazard analysis process to quantify the technical and process risks involving software safety in the early design phase of these projects. We analyzed 154 hazard reports and collected metrics to measure the prevalence of software in hazards and the specificity of descriptions of software causes of hazardous conditions. We found that 49-70% of 154 hazardous conditions could be caused by software or software was involved in the prevention of the hazardous condition. We also found that 12-17% of the 2013 hazard causes involved software, and that 23-29% of all causes had a software control. The application of the TRPM methodology identified process risks in the application of the hazard analysis process itself that may lead to software safety risk.
Keywords: analysis; software; and; computing; risk; constellation; control; software; Hardware; maintenance; measurement; aerospace; measurement; software; NASA; process; program; TPRM; flight; risk; safety; technical; spaceflight; systems; process

Characterizing Attackers and Attacks: An Empirical Study - Salles-Loustau,G.; Berthier,R.; Collange,E.; Sobesto,B.; Michel Cukier (2011)
This paper describes an empirical research study to characterize attackers and attacks against targets of opportunity. A honey net infrastructure was built and deployed over 167 days that leveraged three different honey pot configurations and a SSH-based authentication proxy to attract and follow attackers over several weeks. A total of 211 attack sessions were recorded and evidence was collected at each stage of the attack sequence: from discovery to intrusion and exploitation of rogue software. This study makes two important contributions: 1) we introduce a new approach to measure attacker skills, and 2) we leverage keystroke profile analysis to differentiate attackers beyond their IP address of origin.
Keywords: attack sessions; attacker characterization; attacker skill measurement; honey net infrastructure; honey pot configurations; IP address; keystroke profile analysis; opportunity target; rogue software exploitation; security of data; SSH-based authentication proxy

CHI 2011 sustainability community invited panel: challenges ahead - Khan,Azam; Bartram,Lyn; Blevis,Eli; DiSalvo,Carl; Jon Froehlich; Kurtenbach,Gordon (2011 annual conference extended abstracts on Human factors in computing systems, 2011)
As part of a new CHI Sustainability Community, focused on environmental sustainability, this panel will discuss specific ways in which HCI research will be critical in finding solutions to this global challenge. While research to date has primarily focused on the end consumer, the panel will be challenged with enlarging the discussion to include the designer as a target user and to consider interfaces and interactions that support sustainable design and sustainable manufacturing, as well as sustainable consumption. Specifically, to make real progress, we seek to enumerate ways that HCI needs to grow, as well as to find ways that can help more HCI researchers to become involved.
Keywords: design; Environment; sustainability; community; user behavior

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 values and sentiment using Mechanical Turk - Templeton,Thomas Clay; Fleischmann,Kenneth R.; Jordan Boyd-Graber (Proceedings of the 2011 iConference, 2011)
Human values can help to explain people's sentiment toward current events. In this experiment, we compare people's values with their agreement or disagreement with paragraphs that were classified as either supporting or opposing a specific topic. We found that five value types have statistically significant agreement (p<0.001) for both the supporting and opposing paragraphs, in opposite directions. We hope to use these paragraph ratings to train an automatic text classifier to agree or disagree with paragraphs based on a specific value profile.
Keywords: human values; sentiment analysis; text classification

Computing the Tree of Life: Leveraging the Power of Desktop and Service Grids - Bazinet,A. L; Cummings, Michael P. (Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on, 2011)
The trend in life sciences research, particularly in molecular evolutionary systematics, is toward larger data sets and ever-more detailed evolutionary models, which can generate substantial computational loads. Over the past several years we have developed a grid computing system aimed at providing researchers the computational power needed to complete such analyses in a timely manner. Our grid system, known as The Lattice Project, was the first to combine two models of grid computing - the service model, which mainly federates large institutional HPC resources, and the desktop model, which harnesses the power of PCs volunteered by the general public. Recently we have developed a "science portal" style web interface that makes it easier than ever for phylogenetic analyses to be completed using GARLI, a popular program that uses a maximum likelihood method to infer the evolutionary history of organisms on the basis of genetic sequence data. This paper describes our approach to scheduling thousands of GARLI jobs with diverse requirements to heterogeneous grid resources, which include volunteer computers running BOINC software. A key component of this system provides a priori GARLI runtime estimates using machine learning with random forests.
Keywords: (artificial; (mathematics); user; analysis; science; BOINC; computation; grid; computational; computing; computing; information; computing; machine; data; grid; estimation; portals; trees; evolutionary; Grid; grids; service; handling; evolutionary; history; evolutionary; intelligence); maximum; interface; computational; interfaces; jobs; HPC; learning; maximum; likelihood; load; Internet; data; method; molecular; model; genetic; model; substantial; portal; service; power; data; project; life; resource; lattice; resource; Web; sequence; services; learning; sets; evolutionary; software; GARLI; system; heterogeneous; systematics; phylogenetic; tree

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.

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

Dataflow-based Design and Implementation of Image Processing Applications - Chung-Ching Shen; Plishker,William; Bhattacharyya, Shuvra S. (Technical Reports from UMIACS, 2011)
Dataflow is a well known computational model and is widely used forexpressing the functionality of digital signal processing (DSP) applications, such as audio and video data stream processing, digital communications, and image processing. These applications usually require real-time processing capabilities and have critical performance constraints. Dataflow provides a formal mechanism for describing specifications of DSP applications, imposes minimal data-dependency constraints in specifications, and is effective in exposing and exploiting task or data level parallelism for achieving high performance implementations. To demonstrate dataflow-based design methods in a manner that is concrete and easily adapted to different platforms and back-end design tools, we present in this report a number of case studies based on the lightweight dataflow (LWDF) programming methodology. LWDF is designed as a "minimalistic" approach for integrating coarse grain dataflow programming structures into arbitrary simulation- or platform-oriented languages, such as C, C++, CUDA, MATLAB, SystemC, Verilog, and VHDL. In particular, LWDF requires minimal dependence on specialized tools or libraries. This feature --- together with the rigorous adherence to dataflow principles throughout the LWDF design framework --- allows designers to integrate and experiment with dataflow modeling approaches relatively quickly and flexibly into existing design methodologies and processes.
Keywords: Technical Report

Dataflow-Based Implementation of Layered Sensing Applications - Bhattacharyya, Shuvra S.; Chung-Ching Shen; Plishker,William; Sane, Nimish; Wu, Hsiang-Huang; Gu, Ruirui (2011)
This report describes a new dataflow-based technology and associated design tools for high-productivity design, analysis, and optimization of layered sensing software for signal processing systems. Our approach provides novel capabilities, based on the principles of task-level dataflow analysis, for exploring and optimizing interactions across application behavior; operational context; high performance embedded processing platforms, and implementation constraints. Particularly, we introduce and deliver novel software tools, called the targeted dataflow interchange format (TDIF) and Dataflow Interchange Format Markup Language (DIFML), for design and implementation of layered sensing and signal processing systems. The TDIF-CUDA (Compute Unified Device Architecture) environment is a graphics processing unit targeted software synthesis tool that provides a unique integration of dynamic dataflow modeling; retargetable actor construction; software synthesis; and instrumentation-based schedule evaluation and tuning. The DIFML package is a software package for the DIFML format, which is an Extensible Markup Language (XML)-based format for exchanging information between DIF and other tools.
Keywords: *COMPUTER AIDED DESIGN; *DATA FUSION; *DATAFLOW; *LAYERS; *SOFTWARE TOOLS; COMPUTER PROGRAMMING AND SOFTWARE; DETECTION; High performance computing; LAYERED SENSING; OPTIMIZATION; Signal processing; synthesis; T2KA

Decentralized, accurate, and low-cost network bandwidth prediction - Sukhyun Song; Keleher,P.; Bhattacharjee, Bobby; Sussman, Alan (2011 Proceedings IEEE INFOCOM, 2011)
The distributed nature of modern computing makes end-to-end prediction of network bandwidth increasingly important. Our work is inspired by prior work that treats the Internet and bandwidth as an approximate tree metric space. This paper presents a decentralized, accurate, and low cost system that predicts pairwise bandwidth between hosts. We describe an algorithm to construct a distributed tree that embeds bandwidth measurements. The correctness of the algorithm is provable when driven by precise measurements. We then describe three novel heuristics that achieve high accuracy for predicting bandwidth even with imprecise input data. Simulation experiments with a real-world dataset confirm that our approach shows high accuracy with low cost.
Keywords: accuracy; approximate tree metric space; Bandwidth; bandwidth allocation; bandwidth measurement; decentralized low cost system; distributed tree; end-to-end prediction; Extraterrestrial measurements; Internet; low-cost network bandwidth prediction; Measurement uncertainty; pairwise bandwidth; Peer to peer computing; Prediction algorithms; trees (mathematics)

Decision and Game Theory for Security: Second International Conference, GameSec 2011, College Park, MD, Maryland, USA, November 14-15, 2011, Proceedings - Baras,John S; Katz, Jonathan; Altman,Eitan (Springer, 2011)
This book constitutes the refereed proceedings of the Second International Conference on Decision and Game Theory for Security, GameSec 2011, held in College Park, Maryland, USA, in November 2011. The 16 revised full papers and 2 plenary keynotes presented were carefully reviewed and selected from numerous submissions. The papers are organized in topical sections on attacks, adversaries, and game theory, wireless adhoc and sensor networks, network games, security insurance, security and trust in social networks and security investments.
Keywords: Business & Economics / Information Management; Computers / Hardware / Network Hardware; Computers / Information Technology; Computers / Programming / Algorithms; Computers / Security / General; Mathematics / Applied; Mathematics / Game Theory; Mathematics / General

Design and fabrication of miniature compliant hinges for multi-material compliant mechanisms - Bejgerowski,Wojciech; Gerdes,John; Gupta, Satyandra K.; Bruck,Hugh (The International Journal of Advanced Manufacturing Technology, 2011)
Multi-material molding (MMM) enables the creation of multi-material mechanisms that combine compliant hinges, serving as revolute joints, and rigid links in a single part. There are three important challenges in creating these structures: (1) bonding between the materials used, (2) the ability of the hinge to transfer the required loads in the mechanism while allowing for the prescribed degree(s) of freedom, and (3) incorporating the process-specific requirements in the design stage. This paper presents the approach for design and fabrication of miniature compliant hinges in multi-material compliant mechanisms. The methodology described in this paper allows for the concurrent design of the part and the manufacturing process. For the first challenge, mechanical interlocking strategies are presented. For the second challenge, the development of a simulation-based optimization model of the hinge is presented, involving functional and manufacturing constrains. For the third challenge, the development of hinge positioning features and gate positioning constraints is presented. The developed MMM process is described, along with the main constraints and performance measures. This includes the process sequence, the mold cavity design, gate selection, and runner system development. A case study is presented to demonstrate the feasibility of creating multi-material mechanisms with miniature hinges serving as joints through MMM process. The approach described in this paper was utilized to design a drive mechanism for a flapping wing micro air vehicle. The methods described in this paper are applicable to any lightweight, load-bearing compliant mechanism manufactured using multi-material injection molding.
Keywords: engineering

Design methods for Wireless Sensor Network Building Energy Monitoring Systems - Cho, Inkeun; Chung-Ching Shen; Potbhare, S.; Bhattacharyya, Shuvra S.; Goldsman,N. (2011 IEEE 36th Conference on Local Computer Networks (LCN), 2011)
In this paper, we present a new energy analysis method for evaluating energy consumption of embedded sensor nodes at the application level and the network level. Then we apply the proposed energy analysis method to develop new energy management schemes in order to maximize lifetime for Wireless Sensor Network Building Energy Monitoring Systems (WSNBEMS). At the application level, we develop a new design approach that uses dataflow techniques to model the application-level interfacing behavior between the processor and sensors on an embedded sensor node. At the network level, we analyze the energy consumption of the IEEE 802.15.4 MAC functionality. Based on our techniques for modeling and energy analysis, we have implemented an optimized WSNBEMS for a real building, and validated our energy analysis techniques through measurements on this implementation. The performance of our implementation is also evaluated in terms of monitoring accuracy and energy consumption savings. We have demonstrated that by applying the proposed scheme, system lifetime can be improved significantly without affecting monitoring accuracy.
Keywords: Analytical models; application-level interfacing behavior; building energy monitoring system; Buildings; dataflow technique; embedded sensor node; energy analysis method; Energy consumption; energy management systems; Energy resolution; IEEE 802.15.4 MAC functionality; Monitoring; OPTIMIZATION; wireless sensor network; Wireless sensor networks; WSNBEMS; Zigbee

A design tool for efficient mapping of multimedia applications onto heterogeneous platforms - Chung-Ching Shen; Wu, Hsiang-Huang; Sane, N.; Plishker,W.; Bhattacharyya, Shuvra S. (2011 IEEE International Conference on Multimedia and Expo (ICME), 2011)
Development of multimedia systems on heterogeneous platforms is a challenging task with existing design tools due to a lack of rigorous integration between high level abstract modeling, and low level synthesis and analysis. In this paper, we present a new dataflow-based design tool, called the targeted dataflow interchange format (TDIF), for design, analysis, and implementation of embedded software for multimedia systems. Our approach provides novel capabilities, based on the principles of task-level dataflow analysis, for exploring and optimizing interactions across application behavior; operational context; heterogeneous platforms, including high performance embedded processing architectures; and implementation constraints.
Keywords: Dataflow graphs; design tools; embedded signal processing; software synthesis

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.

Developing a Single Model and Test Prioritization Strategies for Event-Driven Software - Bryce,R.C.; Sampath,S.; Memon, Atif M. (Software Engineering, IEEE Transactions on, 2011)
Event-Driven Software (EDS) can change state based on incoming events; common examples are GUI and Web applications. These EDSs pose a challenge to testing because there are a large number of possible event sequences that users can invoke through a user interface. While valuable contributions have been made for testing these two subclasses of EDS, such efforts have been disjoint. This work provides the first single model that is generic enough to study GUI and Web applications together. In this paper, we use the model to define generic prioritization criteria that are applicable to both GUI and Web applications. Our ultimate goal is to evolve the model and use it to develop a unified theory of how all EDS should be tested. An empirical study reveals that the GUI and Web-based applications, when recast using the new model, show similar behavior. For example, a criterion that gives priority to all pairs of event interactions did well for GUI and Web applications; another criterion that gives priority to the smallest number of parameter value settings did poorly for both. These results reinforce our belief that these two subclasses of applications should be modeled and studied together.
Keywords: EDS; event-driven software; graphical user interface; Graphical user interfaces; GUI testing; Internet; program testing; service-oriented architecture; test prioritization strategy; Web application testing

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

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.

The DSPCAD Integrative Command Line Environment: Introduction to DICE Version 1.1 - Bhattacharyya, Shuvra S.; Plishker,William; Chung-Ching Shen; Sane, Nimish; Zaki, George (2011)
DICE (the DSPCAD Integrative Command Line Environment) is a package of utilities that facilitates efficient management of software projects. Key areas of emphasis in DICE are cross-platform operation, support for projects that integrate heterogeneous programming languages, and support for applying and integrating different kinds of design and testing methodologies. The package is being developed at the University of Maryland to facilitate the research and teaching of methods for implementation, testing, evolution, and revision of engineering software. The package is also being developed as a foundation for developing experimental research software for techniques and tools in the area of computer-aided design (CAD) of digital signal processing (DSP) systems. The package is intended for cross-platform operation, and is currently being developed and used actively on the Linux, Mac OS, Solaris, and Windows (equipped with Cygwin) platforms. This report provides an introduction to DICE, and provides background on some of the key features in DICE Version 1.1. This report also gives a brief introduction to dicelang, which is a plug-in package for DICE that provides additional utilities, libraries, and tools for managing software projects in specific programming languages.
Keywords: *SOFTWARE ENGINEERING; COMPUTER PROGRAMMING; COMPUTER PROGRAMMING AND SOFTWARE; COMPUTER PROGRAMS; DICE(COMPUTER PROGRAM); programming languages; Project management

The DSPCAD Lightweight Dataflow Environment: Introduction to LIDE Version 0.1 - Chung-Ching Shen; Wang, Lai-Huei; Cho, Inkeun; Kim, Scott; Won, Stephen; Plishker,William; Bhattacharyya, Shuvra S. (Technical Reports from UMIACS, 2011)
LIDE (the DSPCAD Lightweight Dataflow Environment) is a flexible,lightweight design environment that allows designers to experiment with dataflow-based approaches for design and implementation of digital signal processing (DSP) systems. LIDE contains libraries of dataflow graph elements (primitive actors, hierarchical actors, and edges) and utilities that assist designers in modeling, simulating, and implementing DSP systems using formal dataflow techniques. The libraries of dataflow graph elements (mainly actors) contained in LIDE provide useful building blocks that can be used to construct signal processing applications, and that can be used as examples that designers can adapt to create their own, customized LIDE actors. Furthermore, by using LIDE along with the DSPCAD Integrative Command Line Environment (DICE), designers can efficiently create and execute unit tests for user-designed actors. This report provides an introduction to LIDE. The report includes details on the process for setting up the LIDE environment, and covers methods for using pre-designed libraries of graph elements, as well as creating user-designed libraries and associated utilities using the C language. The report also gives an introduction to the C language plug-in for dicelang. This plug-in, called dicelang-C, provides features for efficient C-based project development and maintenance that are useful to apply when working with LIDE.
Keywords: Technical Report

Dynamic Processing Allocation in Video - Daozheng Chen; Bilgic,M.; Getoor, Lise; Jacobs, David W. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2011)
Large stores of digital video pose severe computational challenges to existing video analysis algorithms. In applying these algorithms, users must often trade off processing speed for accuracy, as many sophisticated and effective algorithms require large computational resources that make it impractical to apply them throughout long videos. One can save considerable effort by applying these expensive algorithms sparingly, directing their application using the results of more limited processing. We show how to do this for retrospective video analysis by modeling a video using a chain graphical model and performing inference both to analyze the video and to direct processing. We apply our method to problems in background subtraction and face detection, and show in experiments that this leads to significant improvements over baseline algorithms.
Keywords: algorithms; digital; allocation; video; analysis; computer; background; detection; graphical; detection; resource; graphics; face; model; resource; processing; processing; face; recognition; object; signal; subtraction; baseline; video

Eighth workshop on mining and learning with graphs - Brefeld,Ulf; Getoor, Lise; Macskassy,Sofus A. (SIGKDD Explor. Newsl., 2011)
The Eighth Workshop on Mining and Learning with Graphs (MLG)1was held at KDD 2010 in Washington DC. It brought together a variete of researchers interested in analyzing data that is best represented as a graph. Examples include the WWW, social networks, biological networks, communication networks, and many others. The importance of being able to effectively mine and learn from such data is growing, as more and more structured and semi-structured data is becoming available. This is a problem across widely different fields such as economics, statistics, social science, physics and computer science, and is studied within a variety of sub-disciplines of machine learning and data mining including graph mining, graphical models, kernel theory, statistical relational learning, etc. The objective of this workshop was to bring together practitioners from these various fields and areas to foster a rich discussion of which problems we work on, how we frame them in the context of graphs, which tools and algorithms we apply and our general findings and lessons learned. This year's workshop was very successful with well over 100 attendees, excellent keynote speakers and papers. This is a rapidly growing area and we believe that this community is only in its infancy. We hope that the readers will join us next year for MLG 2011.
Keywords: data mining; dynamic network analysis; graph mining; kernel methods; link mining; machine learning; network analysis; pattern recognition; relational learning; scalable graph mining; statistical relational learning

Empirical Studies in Information Visualization: Seven Scenarios - Lam,H.; Bertini,E.; Isenberg,P.; Plaisant, Catherine; Carpendale,S. (Visualization and Computer Graphics, IEEE Transactions on, 2011)
We take a new, scenario based look at evaluation in information visualization. Our seven scenarios, evaluating visual data analysis and reasoning, evaluating user performance, evaluating user experience, evaluating environments and work practices, evaluating communication through visualization, evaluating visualization algorithms, and evaluating collaborative data analysis were derived through an extensive literature review of over 800 visualization publications. These scenarios distinguish different study goals and types of research questions and are illustrated through example studies. Through this broad survey and the distillation of these scenarios we make two contributions. One, we encapsulate the current practices in the information visualization research community and, two, we provide a different approach to reaching decisions about what might be the most effective evaluation of a given information visualization. Scenarios can be used to choose appropriate research questions and goals and the provided examples can be consulted for guidance on how to design one's own study.

The Evolution of Network Configuration: A Tale of Two Campuses - Kim,H.; Benson,T.; Akella,A.; Feamster, Nick (Networks, 2011)
Studying network configuration evolution can improve our under- standing of the evolving complexity of networks and can be helpful in making network configuration less error-prone. Unfortunately, the nature of changes that operators make to network configuration is poorly understood. Towards improving our understanding, we examine and analyze five years of router, switch, and firewall con- figurations from two large campus networks using the logs from version control systems used to store the configurations. We study how network configuration is distributed across different network operations tasks and how the configuration for each task evolves over time, for different types of devices and for different loca- tions in the network. To understand the trends of how configura- tion evolves over time, we study the extent to which configuration for various tasks are added, modified, or deleted. We also study whether certain devices experience configuration changes more fre- quently than others, as well as whether configuration changes tend to focus on specific portions of the configuration (or on specific tasks). We also investigate when network operators make configu- ration changes of various types. Our results concerning configura- tion changes can help the designers of configuration languages un- derstand which aspects of configuration might be more automated or tested more rigorously and may ultimately help improve config- uration languages.

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 Tracking and Recognition in a Camera Network - Bhanu,Bir; Govindaraju,Venu (Multibiometrics for Human IdentificationMultibiometrics for Human Identification, 2011)

Fast approximations of the rotational diffusion tensor and their application to structural assembly of molecular complexes - Berlin,Konstantin; O'Leary, Dianne P.; Fushman, David (Proteins: Structure, Function, and Bioinformatics, 2011)
We present and evaluate a rigid-body, deterministic, molecular docking method, called ELMDOCK, that relies solely on the three-dimensional structure of the individual components and the overall rotational diffusion tensor of the complex, obtained from nuclear spin-relaxation measurements. We also introduce a docking method, called ELMPATIDOCK, derived from ELMDOCK and based on the new concept of combining the shape-related restraints from rotational diffusion with those from residual dipolar couplings, along with ambiguous contact/interface-related restraints obtained from chemical shift perturbations. ELMDOCK and ELMPATIDOCK use two novel approximations of the molecular rotational diffusion tensor that allow computationally efficient docking. We show that these approximations are accurate enough to properly dock the two components of a complex without the need to recompute the diffusion tensor at each iteration step. We analyze the accuracy, robustness, and efficiency of these methods using synthetic relaxation data for a large variety of protein-protein complexes. We also test our method on three protein systems for which the structure of the complex and experimental relaxation data are available, and analyze the effect of flexible unstructured tails on the outcome of docking. Additionally, we describe a method for integrating the new approximation methods into the existing docking approaches that use the rotational diffusion tensor as a restraint. The results show that the proposed docking method is robust against experimental errors in the relaxation data or structural rearrangements upon complex formation and is computationally more efficient than current methods. The developed approximations are accurate enough to be used in structure refinement protocols. Proteins 2011; © 2011 Wiley-Liss, Inc.
Keywords: diffusion‐guided molecular assembly; ellipsoid model; ELM; PATI; protein complexes; residual dipolar couplings; rigid‐body docking

GameSec'11: Proceedings of the Second international conference on Decision and Game Theory for Security - Baras,John S; Katz, Jonathan; Altman,Eitan (Springer-Verlag, 2011)

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

Heterogeneous Design in Functional DIF - Plishker,William; Sane, Nimish; Kiemb, Mary; Bhattacharyya, Shuvra S. (Transactions on High-Performance Embedded Architectures and Compilers IV, 2011)
Dataflow formalisms have provided designers of digital signal processing (DSP) systems with analysis and optimizations for many years. As system complexity increases, designers are relying on more types of dataflow models to describe applications while retaining these implementation benefits. The semantic range of DSP-oriented dataflow models has expanded to cover heterogeneous models and dynamic applications, but efficient design, simulation, and scheduling of such applications has not. To facilitate implementing heterogeneous applications, we utilize a new dataflow model of computation and show how actors designed in other dataflow models are directly supported by this framework, allowing system designers to immediately compose and simulate actors from different models. Using examples, we show how this approach can be applied to quickly describe and functionally simulate a heterogeneous dataflow-based application such that a designer may analyze and tune trade-offs among different models and schedules for simulation time, memory consumption, and schedule size.
Keywords: Arithmetic and Logic Structures; Computer Communication Networks; Dataflow; heterogeneous; Input/Output and Data Communications; Logic Design; Processor Architectures; Programming Languages, Compilers, Interpreters; Signal processing

A Hierarchical Algorithm for Fast Debye Summation with Applications to Small Angle Scattering - Gumerov, Nail A.; Berlin,Konstantin; Fushman, David; Duraiswami, Ramani (Technical Reports from UMIACS, 2011)
Debye summation, which involves the summation of sinc functions of distances between all pair of atoms in three dimensional space, arises in computations performed in crystallography, small/wide angle X-ray scattering (SAXS/WAXS) and small angle neutron scattering (SANS). Direct evaluation of Debye summation has quadratic complexity, which results in computational bottleneck when determining crystal properties, or running structure refinement protocols that involve SAXS or SANS, even for moderately sized molecules. We present a fast approximation algorithm that efficiently computes the summation to any prescribed accuracy epsilon in linear time. The algorithm is similar to the fast multipole method (FMM), and is based on a hierarchical spatial decomposition of the molecule coupled with local harmonic expansions and translation of these expansions. An even more efficient implementation is possible when the scattering profile is all that is required, as in small angle scattering reconstruction (SAS) of macromolecules. We examine the relationship of the proposed algorithm to existing approximate methods for profile computations, and provide detailed description of the algorithm, including error bounds and algorithms for stable computation of the translation operators. Our theoretical and computational results show orders of magnitude improvement in computation complexity over existing methods, while maintaining prescribed accuracy.
Keywords: Technical Report

Illumination modeling for face recognition - Basri,R.; Jacobs, David W. (Handbook of face recognition, 2011)
In this chapter, we show that effective systems can account for the effects of lighting using fewer than 10 degrees of freedom. This can have considerable impact on the speed and accuracy of recognition systems. We will describe theoretical results that, with some simplifying assumptions, prove the validity of low-dimensional, linear approximations to the set of images produced by a face.

Illumination robust dictionary-based face recognition - Patel, Vishal M.; Tao Wu; Biswas,S.; Phillips,P.J.; Chellapa, Rama (2011 18th IEEE International Conference on Image Processing (ICIP), 2011)
In this paper, we present a face recognition method based on simultaneous sparse approximations under varying illumination. Our method consists of two main stages. In the first stage, a dictionary is learned for each face class based on given training examples which minimizes the representation error with a sparseness constraint. In the second stage, a test image is projected onto the span of the atoms in each learned dictionary. The resulting residual vectors are then used for classification. Furthermore, to handle changes in lighting conditions, we use a relighting approach based on a non-stationary stochastic filter to generate multiple images of the same person with different lighting. As a result, our algorithm has the ability to recognize human faces with good accuracy even when only a single or a very few images are provided for training. The effectiveness of the proposed method is demonstrated on publicly available databases and it is shown that this method is efficient and can perform significantly better than many competitive face recognition algorithms.
Keywords: albedo; approximation theory; classification; competitive face recognition algorithms; Databases; Dictionaries; Face; face recognition; face recognition method; filtering theory; human face recognition; illumination robust dictionary-based face recognition; illumination variation; image representation; learned dictionary; learning (artificial intelligence); lighting; lighting conditions; multiple images; nonstationary stochastic filter; publicly available databases; relighting; relighting approach; representation error; residual vectors; Robustness; simultaneous sparse approximations; simultaneous sparse signal representation; sparseness constraint; Training; varying illumination; vectors

Implicit Authentication through Learning User Behavior - Elaine Shi; Niu, Yuan; Jakobsson, Markus; Chow, Richard (Information Security, 2011)
Users are increasingly dependent on mobile devices. However, current authentication methods like password entry are significantly more frustrating and difficult to perform on these devices, leading users to create and reuse shorter passwords and pins, or no authentication at all. We present implicit authentication - authenticating users based on behavior patterns. We describe our model for performing implicit authentication and assess our techniques using more than two weeks of collected data from over 50 subjects.
Keywords: Computer science

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

IP geolocation in metropolitan areas - Singh,Satinder Pal; Baden,Randolph; Lee,Choon; Bhattacharjee, Bobby; La,Richard; Shayman,Mark (Proceedings of the ACM SIGMETRICS joint international conference on Measurement and modeling of computer systems, 2011)
Current IP geoloation techniques can geolocate an IP address to a region approximately 700 square miles, roughly the size of a metropolitan area. We model geolocation as a pattern-recognition problem, and introduce techniques that geolocate addresses to within 5 miles inside a metropolitan area. We propose two complementary algorithms: The first algorithm, Pattern Based Geolocation (PBG), models the distribution of latencies to the target and compares it to those of the reference landmarks to resolve an address to within 5 miles in a metropolitan area. The second approach, Perturbation Augmented PBG (PAPBG), provides higher resolution by sending extra traffic in the network. While sending an aggregate of 600 Kbps extra traffic to 20 nodes for approximately 2 minutes, PAPBG geolocates addresses to within 3 miles.
Keywords: geolocation; pattern recognition; perturbation

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

Limits on the power of zero-knowledge proofs in cryptographic constructions - Brakerski,Z.; Katz, Jonathan; Segev,G.; Yerukhimovich,A. (Theory of Cryptography, 2011)
For over 20 years, black-box impossibility results have been used to argue the infeasibility of constructing certain cryptographic primitives (e.g., key agreement) from others (e.g., one-way functions). A widely recognized limitation of such impossibility results, however, is that they say nothing about the usefulness of (known) nonblack-box techniques. This is unsatisfying, as we would at least like to rule out constructions using the set of techniques we have at our disposal.With this motivation in mind, we suggest a new framework for black-box constructions that encompasses constructions with a nonblack-box flavor: specifically, those that rely on zero-knowledge proofs relative to some oracle. We show that our framework is powerful enough to capture the Naor-Yung/Sahai paradigm for building a (shielding) CCA-secure public-key encryption scheme from a CPA-secure one, something ruled out by prior black-box separation results. On the other hand, we show that several black-box impossibility results still hold even in a setting that allows for zero-knowledge proofs.

Localizing parts of faces using a consensus of exemplars - Belhumeur,P. N.; Jacobs, David W.; Kriegman, D.J.; Kumar,N. (Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on, 2011)
We present a novel approach to localizing parts in images of human faces. The approach combines the output of local detectors with a non-parametric set of global models for the part locations based on over one thousand hand-labeled exemplar images. By assuming that the global models generate the part locations as hidden variables, we derive a Bayesian objective function. This function is optimized using a consensus of models for these hidden variables. The resulting localizer handles a much wider range of expression, pose, lighting and occlusion than prior ones. We show excellent performance on a new dataset gathered from the internet and show that our localizer achieves state-of-the-art performance on the less challenging BioID dataset.
Keywords: Bayesian; faces; lighting; occlusion; pose; Bayes; function; exemplar; images; expression; face; localization; human; methods; face; objective; part; recognition

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

MDMap: A system for data-driven layout and exploration of molecular dynamics simulations - Patro,R.; Ip, Cheuk Yiu; Bista,S.; Cho,S.S.; Thirumalai,D.; Varshney, Amitabh (Biological Data Visualization (BioVis), 2011 IEEE Symposium on, 2011)
Contemporary molecular dynamics simulations result in a glut of simulation data, making analysis and discovery a difficult and burdensome task. We present MDMap, a system designed to summarize long-running molecular dynamics (MD) simulations. We represent a molecular dynamics simulation as a state transition graph over a set of intermediate (stable and semi-stable) states. The transitions amongst the states together with their frequencies represent the flow of a biomolecule through the trajectory space. MDMap automatically determines potential intermediate conformations and the transitions amongst them by analyzing the conformational space explored by the MD simulation. MDMap is an automated system to visualize MD simulations as state-transition diagrams, and can replace the current tedious manual layouts of biomolecular folding landscapes with an automated tool. The layout of the representative states and the corresponding transitions among them is presented to the user as a visual synopsis of the long-running MD simulation. We compare and contrast multiple presentations of the state transition diagrams, such as conformational embedding, and spectral, hierarchical, and force-directed graph layouts. We believe this system could provide a road-map for the visualization of other stochastic time-varying simulations in a variety of different domains.
Keywords: computing; digital; driven; DYNAMICS; exploration; data; folding; graph; stochastic; landscapes; data; layout; molecular; MDMap; biomolecular; method; stochastic; processes; simulation; graph; simulations; state; simulations; trajectory; space; biology; theory; molecular; time-varying; transition

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

Methods for design and implementation of dynamic signal processing systems - Bhattacharyya, Shuvra S. (2011 International Conference on Embedded Computer Systems (SAMOS), 2011)
Summary form only given. Dynamic signal processing systems, where significant changes in functionality and computational structure must be achieved while applications are running, are becoming increasingly important as computational platforms become more powerful, and feature-sets of DSP-powered products become more sophisticated. This talk covers two new, complementary dataflow models of computation that are being developed in the Maryland DSPCAD Research Group to help address the challenges of structured design, simulation, and synthesis of dynamic signal processing systems. The first of these models, called enable-invoke dataflow (EIDF), is aimed improving the predictability of actor invocation and the efficiency with which dynamic scheduling techniques can be realized. The second model, called the dataflow schedule graph (DSG), provides a formal framework for representing and analyzing dataflow graph schedules that is rooted in formal dataflow semantics, and accommodates a wide range of schedule classes, including static, quasi-static, and dynamic schedules, as well as both sequential and parallel schedule formats. In this talk, I will present the EIDF and DSG models and discuss their potential to improve the processes by which dynamic signal processing systems are developed.
Keywords: actor invocation predictability; complementary dataflow models; Computational modeling; computational structure; COMPUTERS; data flow graphs; dataflow schedule graph; DSG models; DSP-powered products; Dynamic scheduling; dynamic scheduling techniques; dynamic signal processing systems; Educational institutions; EIDF models; enable-invoke dataflow; formal dataflow semantics; functionality structure; Laboratories; Maryland DSPCAD Research Group; quasi-static schedules; Schedules; scheduling; Signal processing; static schedules

Model-based precision analysis and optimization for digital signal processors - Kedilaya, Soujanya; Plishker,William; Purkovic, Aleksandar; Johnson, Brian; Bhattacharyya, Shuvra S. (Proceedings of the European Signal Processing Conference, 2011)
Embedded signal processing has witnessed explosive growth in re-cent years in both scientific and consumer applications, driving the need for complex, high-performance signal processing systems that are largely application driven. In order to efficiently implement these systems on programmable platforms such as digital signal processors (DSPs), it is important to analyze and optimize the ap- plication design from early stages of the design process. A key per- formance concern for designers is choosing the data format. In this work, we propose a systematic and efficient design flow involving model-based design to analyze application data sets and precision requirements. We demonstrate this design flow with an exploration study into the required precision for eigenvalue decomposition (EVD) using the Jacobi algorithm. We demonstrate that with a high degree of structured analysis and automation, we are able to analyze the data set to derive an efficient data format, and optimize important parts of the algorithm with respect to precision.

A Model-Based Schedule Representation for Heterogeneous Mapping of Dataflow Graphs - Wu, Hsiang-Huang; Chung-Ching Shen; Sane, N.; Plishker,W.; Bhattacharyya, Shuvra S. (2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011)
Dataflow-based application specifications are widely used in model-based design methodologies for signal processing systems. In this paper, we develop a new model called the dataflow schedule graph (DSG) for representing a broad class of dataflow graph schedules. The DSG provides a graphical representation of schedules based on dataflow semantics. In conventional approaches, applications are represented using dataflow graphs, whereas schedules for the graphs are represented using specialized notations, such as various kinds of sequences or looping constructs. In contrast, the DSG approach employs dataflow graphs for representing both application models and schedules that are derived from them. Our DSG approach provides a precise, formal framework for unambiguously representing, analyzing, manipulating, and interchanging schedules. We develop detailed formulations of the DSG representation, and present examples and experimental results that demonstrate the utility of DSGs in the context of heterogeneous signal processing system design.
Keywords: Computational modeling; data flow graphs; dataflow schedule graph; dataflow semantics; dataflow-based application specifications; Dynamic scheduling; heterogeneous mapping; heterogeneous signal processing system design; model-based design methodologies; model-based schedule representation; Processor scheduling; Program processors; Schedules; semantics; Signal processing; synchronization

Modeling and optimization of dynamic signal processing in resource-aware sensor networks - Bhattacharyya, Shuvra S.; Plishker,W.; Sane, N.; Chung-Ching Shen; Wu, Hsiang-Huang (2011 8th IEEE International Conference on Advanced Video and Signal-Based Surveillance (AVSS), 2011)
Sensor node processing in resource-aware sensor networks is often critically dependent on dynamic signal processing functionality - i.e., signal processing functionality in which computational structure must be dynamically assessed and adapted based on time-varying environmental conditions, operating constraints or application requirements. In dynamic signal processing systems, it is important to provide flexibility for run-time adaptation of application behavior and execution characteristics, but in the domain of resource-aware sensor networks, such flexibility cannot come with significant costs in terms of power consumption overhead or reduced predictability. In this paper, we review a variety of complementary models of computation that are being developed as part of the dataflow interchange format (DIF) project to facilitate efficient and reliable implementation of dynamic signal processing systems. We demonstrate these methods in the context of resource-aware sensor networks.
Keywords: Adaptation models; Aerodynamics; Computational modeling; data flow graphs; dataflow interchange format; Dynamic scheduling; dynamic signal processing; power consumption overhead; Program processors; resource-aware sensor networks; run-time adaptation; Schedules; sensor node processing; Signal processing; Wireless sensor networks

Modeling diverse standpoints in text classification: learning to be human by modeling human values - Fleischmann,Kenneth R.; Templeton,Thomas Clay; Jordan Boyd-Graber (Proceedings of the 2011 iConference, 2011)
An annotator's classification of a text not only tells us something about the intent of the text's author, it also tells us something about the annotator's standpoint. To understand authorial intent, we can consider all of these diverse standpoints, as well as the extent to which the annotators' standpoints affect their perceptions of authorial intent. To model human behavior, it is important to model humans' unique standpoints. Human values play an especially important role in determining human behavior and how people perceive the world around them, so any effort to model human behavior and perception can benefit from an effort to understand and model human values. Instead of training humans to obscure their standpoints and act like computers, we should teach computers to have standpoints of their own.
Keywords: diversity; framing theory; machine learning; standpoint epistemology; value sensitive computing

Multi-material compliant mechanisms for mobile millirobots - Vogtmann,Dana E.; Gupta, Satyandra K.; Bergbreiter,Sarah (2011)
This paper describes a new process for fabricating planar, multi-material, compliant mechanisms, intended for use in small scale robotics. The process involves laser cutting the mechanism geometry from a rigid material, and refilling the joint areas with a second, elastomeric material. This method allows for a large set of potential materials, with a wide range of material properties, to be used in combination to create mechanisms with highly tailored mechanical properties. These multi-material compliant mechanisms have minimum feature sizes of approximately 100 #x00B5;m and have demonstrated long lifetimes, easily surviving 100,000 bending cycles. We also present the first use of these compliant mechanisms in a 2.5cm #x00D7; 2.5cm #x00D7; 7.5cm, 6g hexapod. This hexapod has been demonstrated moving at speeds up to 6 cm/s, with a predicted maximum speed of up to 17 cm/s.

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

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

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

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

Recent advances and future challenges in automated manufacturing planning - Bourne,D.; Corney,J.; Gupta,S.K. (Journal of Computing and Information Science in Engineering, 2011)

Re-engineering health care with information technology: the role of computer-human interaction - Butler,Keith; Payne,Thomas; Shneiderman, Ben; Brennan,Patricia; Zhang,Jiajie (PART 2 ———– Proceedings of the 2011 annual conference extended abstracts on Human factors in computing systems, 2011)
There is critical, nation-wide need to improve health care and its cost. Health information technology has great promise that is yet to be realized. In this panel four noted experts will discuss key issues that should drive health IT, and the challenges for the CHI community to play a leading role.
Keywords: clinical workflow; electronic medical records; health information technology visualization; healthcare informatics; participatory design; usability standards & evaluation

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

Seven guiding scenarios for information visualization evaluation - Lam,H.; Bertini,E.; Isenberg,P.; Plaisant, Catherine; Carpendale,S. (Department of Computer Science, University of Calgary, 2011)
We take a new, scenario based look at evaluation in information visualization. Our seven scenarios, evaluatingvisual data analysis and reasoning, evaluating user performance, evaluating user experience, evaluating environments and work practices, evaluating communication through visualization, automated evaluation of visualizations, and evaluating collaborative data analysis were derived through an extensive literature review of over 800 visualization publications. These scenarios are described through their goals, the types of questions they embody and illustrated through example studies. Through this broad survey and the distillation of these scenarios we make two contributions. One, we encapsulate the current practices in the information visualization research community and, two, we provide a different approach to reaching decisions about what might be the most effective evaluation of a given information visualization. For example, if the research goals or evaluative questions are known they can be used to map to specific scenarios, where practical existing examples can be considered for effective evaluation approaches.

Simulating Audiences: Automating Analysis of Values, Attitudes, and Sentiment - Templeton,T.C.; Fleischmann,K.R.; Jordan Boyd-Graber (Privacy, Security, Risk and Trust (PASSAT), 2011 IEEE Third International Conference on and 2011 IEEE Third International Confernece on Social Computing (SocialCom), 2011)
Current events such as the Park51 Project in downtown Manhattan create "critical discourse moments," explosions of discourse around a topic that can be exploited for data gathering. Policymakers have a need to understand the dynamics of public discussion in real time. Human values, which are cognitively related to attitudes and serve as reference points in moral argument, are important indicators of what's at stake in a public controversy. This work shows that it is possible to link values data with reader behavior to infer values implicit in a topical corpus, and that it is possible to automate this process using machine learning.
Keywords: audience simulation; behavioural sciences computing; crowdsourcing; Educational institutions; human values; HUMANS; learning (artificial intelligence); machine learning; moral argument; natural language processing; Park51 project; Presses; public controversy; public discussion; Security; social sciences computing; support vector machines; Weaving

Social Snapshot: A System for Temporally Coupled Social Photography - Patro,R.; Ip, Cheuk Yiu; Bista,S.; Varshney, Amitabh (Computer Graphics and Applications, IEEE, 2011)
Social Snapshot actively acquires and reconstructs temporally dynamic data. The system enables spatiotemporal 3D photography using commodity devices, assisted by their auxiliary sensors and network functionality. It engages users, making them active rather than passive participants in data acquisition.
Keywords: 3D; acquisition; data; acquisition; photography; social; computing; coupled; data; photography; data; photography; temporally; reconstruction; social; sciences; snapshot; spatiotemporal; social

SYSTEM AND METHOD FOR DATA MANAGEMENT IN LARGE DATA NETWORKS - BROECHELER,M.; V.S. Subrahmanian; Pugliese, A. (2011)
A system and method for storing an input data network, in the form of graph is provided. The system includes a master node and a plurality of slave nodes. The master node is operable to receive the data network in the form of a graph, the graph including a plurality of vertices connected by edges; calculate a probability of co-retrieval for each of the plurality of vertices; and assign each of the plurality of vertices to one of the plurality of compute nodes based on the calculated probability of co-retrieval. Another method and system are provided for converting a dataset into a graph based index and storing the index on disk. Respective systems and methods of querying such data networks are also provided.

Teaching cross-platform design and testing methods for embedded systems using DICE - Bhattacharyya, Shuvra S.; Plishker,William; Gupta, Ayush; Chung-Ching Shen (ACM, 2011)
DICE (the DSPCAD Integrative Command Line Environment) is a package of utilities that facilitates efficient management of software projects. Key areas of emphasis in DICE are cross-platform operation, support for projects that integrate heterogeneous programming languages, and support for applying and integrating different kinds of design and testing methodologies. The package is being developed at the University of Maryland to facilitate the research and teaching of methods for implementation, testing, evolution, and revision of engineering software. The platform- and language-independent focus of DICE makes it an effective vehicle for teaching high-productivity, high-reliability methods for design and implementation of embedded systems for a variety of courses. In this paper, we provide an overview of features of DICE --- particularly as they relate to testing driven design practices --- that are useful in embedded systems education, and discuss examples and experiences of applying the tool in courses at the University of Maryland aimed at diverse groups of students --- undergraduate programming concepts for engineers, graduate VLSI architectures (aimed at research-oriented students), and graduate FPGA system design (aimed at professional Master's students).

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

Threat-Aware Clustering in Wireless Sensor Networks - Abd-Almageed, Wael; Blace,R.E.; Eltoweissy,M. (IFIP Advances in Information and Communication Technology (AICT), 2011)

Toolchain for Programming, Simulating and Studying the XMT Many-Core Architecture - Keceli,F.; Tzannes,A.; Caragea,G.C.; Barua,R.; Vishkin, Uzi (Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on, 2011)
The Explicit Multi-Threading (XMT) is a general-purpose many-core computing platform, with the vision of a 1000-core chip that is easy to program but does not compromise on performance. This paper presents a publicly available tool chain for XMT, complete with a highly configurable cycle-accurate simulator and an optimizing compiler. The XMT tool chain has matured and has been validated to a point where its description merits publication. In particular, research and experimentation enabled by the tool chain played a central role in supporting the ease-of-programming and performance aspects of the XMT architecture. The compiler and the simulator are also important milestones for an efficient programmer's workflow from PRAM algorithms to programs that run on the shared memory XMT hardware. This workflow is a key component in accomplishing the dual goal of ease-of-programming and performance. The applicability of our tool chain extends beyond specific XMT choices. It can be used to explore the much greater design space of shared memory many-cores by system researchers or by programmers. As the tool chain can practically run on any computer, it provides a supportive environment for teaching parallel algorithmic thinking with a programming component. Unobstructed by techniques such as decomposition-first and programming for locality, this environment may be useful in deferring the teaching of these techniques, when desired, to more advanced or platform-specific courses.
Keywords: algorithm; XMT; architecture; XMT; architectures; shared; chain; cycle-accurate; compiler; programmer; compilers; parallel; component; shared; computing; optimizing; hardware; shared; many-core; many-core; concurrency; memory; multithreading; general-purpose; PRAM; simulator; ease-of-programming; explicit; systems; theory; multi-threading; optimising; tool; workflow; programming; XMT

Topological Patterns for Scalable Representation and Analysis of Dataflow Graphs - Sane, Nimish; Kee, Hojin; Seetharaman, Gunasekaran; Bhattacharyya, Shuvra S. (Journal of Signal Processing Systems, 2011)
Tools for designing signal processing systems with their semantic foundation in dataflow modeling often use high-level graphical user interfaces (GUIs) or text based languages that allow specifying applications as directed graphs. Such graphical representations serve as an initial reference point for further analysis and optimizations that lead to platform-specific implementations. For large-scale applications, the underlying graphs often consist of smaller substructures that repeat multiple times. To enable more concise representation and direct analysis of such substructures in the context of high level DSP specification languages and design tools, we develop the modeling concept of topological patterns, and propose ways for supporting this concept in a high-level language. We augment the dataflow interchange format (DIF) language—a language for specifying DSP-oriented dataflow graphs—with constructs for supporting topological patterns, and we show how topological patterns can be effective in various aspects of embedded signal processing design flows using specific application examples.
Keywords: Circuits and Systems; Computer Imaging, Vision, Pattern Recognition and Graphics; Dataflow graphs; Electrical Engineering; High-level languages; Image Processing and Computer Vision; model-based design; pattern recognition; Signal processing systems; Signal, Image and Speech Processing; Topological patterns

Tracking and Identification via Object Reflectance Using a Hyperspectral Video Camera - Nguyen,Hien Van; Banerjee,Amit; Burlina,Philippe; Broadwater,Joshua; Chellapa, Rama (Machine Vision Beyond Visible SpectrumMachine Vision Beyond Visible Spectrum, 2011)
Recent advances in electronics and sensor design have enabled the development of a hyperspectral video camera that can capture hyperspectral datacubes at near video rates. The sensor offers the potential for novel and robust methods for surveillance by combining methods from computer vision and hyperspectral image analysis. Here, we focus on the problem of tracking objects through challenging conditions, such as rapid illumination and pose changes, occlusions, and in the presence of confusers. A new framework that incorporates radiative transfer theory to estimate object reflectance and particle filters to simultaneously track and identify an object based on its reflectance spectra is proposed. By exploiting high-resolution spectral features in the visible and near-infrared regimes, the framework is able to track objects that appear featureless to the human eye. For example, we demonstrate that near-IR spectra of human skin can also be used to distinguish different people in a video sequence. These capabilities are illustrated using experiments conducted on real hyperspectral video data.

TreeVersity: Comparing tree structures by topology and node's attributes differences - Gomez,J.A.G.; Buck-Coleman,A.; Plaisant, Catherine; Shneiderman, Ben (2011 IEEE Conference on Visual Analytics Science and Technology (VAST), 2011)
It is common to classify data in hierarchies, they provide a comprehensible way of understanding big amounts of data. From budgets to organizational charts or even the stock market, trees are everywhere and people find them easy to use. However when analysts need to compare two versions of the same tree structure, or two related taxonomies, the task is not so easy. Much work has been done on this topic, but almost all of it has been restricted to either compare the trees by topology, or by the node attribute values. With this project we are proposing TreeVersity, a framework for comparing tree structures, both by structural changes and by differences in the node attributes. This paper is based on our previous work on comparing traffic agencies using LifeFlow [1, 2] and on a first prototype of TreeVersity.
Keywords: Computer science; data classification; Data visualization; Educational institutions; hierarchy; Image color analysis; LifeFlow; node attributes differences; Pattern classification; structural changes; Topology; topology attributes differences; traffic agencies; tree structures comparison; trees (mathematics); TreeVersity; Vegetation; Visualization

TreeVersity: Comparing tree structures by topology and node's attributes differences - Gomez,J.A.G.; Buck-Coleman,A.; Plaisant, Catherine; Shneiderman, Ben (Visual Analytics Science and Technology (VAST), 2011 IEEE Conference on, 2011)
It is common to classify data in hierarchies, they provide a comprehensible way of understanding big amounts of data. From budgets to organizational charts or even the stock market, trees are everywhere and people find them easy to use. However when analysts need to compare two versions of the same tree structure, or two related taxonomies, the task is not so easy. Much work has been done on this topic, but almost all of it has been restricted to either compare the trees by topology, or by the node attribute values. With this project we are proposing TreeVersity, a framework for comparing tree structures, both by structural changes and by differences in the node attributes. This paper is based on our previous work on comparing traffic agencies using LifeFlow [1, 2] and on a first prototype of TreeVersity.
Keywords: (mathematics); agencies; tree; attributes; changes; topology; classification; hierarchy; node; classification; trees; comparison; pattern; differences; structural; differences; traffic; LifeFlow; TreeVersity; data; STRUCTURES

Using the DSPCAD Integrative Command-Line Environment: User's Guide for DICE Version 1.1 - Bhattacharyya, Shuvra S.; Chung-Ching Shen; Plishker,William; Sane, Nimish; Zaki, George (Technical Reports from UMIACS, 2011)
This document provides instructions on setting up, starting up, andbuilding DICE and its key companion packages, dicemin and dicelang. This installation process is based on a general set of conventions, which we refer to as the DICE organizational conventions, for software packages. The DICE organizational conventions are specified in this report. These conventions are applied in DICE, dicemin, and dicelang, and also to other software packages that are developed in the Maryland DSPCAD Research Group.
Keywords: Technical Report

Using Variational Inference and MapReduce to Scale Topic Modeling - Zhai,Ke; Jordan Boyd-Graber; Asadi,Nima (arXiv:1107.3765, 2011)
Latent Dirichlet Allocation (LDA) is a popular topic modeling technique for exploring document collections. Because of the increasing prevalence of large datasets, there is a need to improve the scalability of inference of LDA. In this paper, we propose a technique called ~MapReduce LDA (Mr. LDA) to accommodate very large corpus collections in the MapReduce framework. In contrast to other techniques to scale inference for LDA, which use Gibbs sampling, we use variational inference. Our solution efficiently distributes computation and is relatively simple to implement. More importantly, this variational implementation, unlike highly tuned and specialized implementations, is easily extensible. We demonstrate two extensions of the model possible with this scalable framework: informed priors to guide topic discovery and modeling topics from a multilingual corpus.
Keywords: Computer Science - Artificial Intelligence; Computer Science - Distributed, Parallel, and Cluster Computing

Value of information lattice: exploiting probabilistic independence for effective feature subset acquisition - Bilgic,Mustafa; Getoor, Lise (Journal of Artificial Intelligence Research, 2011)
We address the cost-sensitive feature acquisition problem, where misclassifying an instance is costly but the expected misclassification cost can be reduced by acquiring the values of the missing features. Because acquiring the features is costly as well, the objective is to acquire the right set of features so that the sum of the feature acquisition cost and misclassification cost is minimized. We describe the Value of Information Lattice (VOILA), an optimal and eficient feature subset acquisition framework. Unlike the common practice, which is to acquire features greedily, VOILA can reason with subsets of features. VOILA eficiently searches the space of possible feature subsets by discovering and exploiting conditional independence properties between the features and it reuses probabilistic inference computations to further speed up the process. Through empirical evaluation on five medical datasets, we show that the greedy strategy is often reluctant to acquire features, as it cannot forecast the benefit of acquiring multiple features in combination.

Vectorization and mapping of software defined radio applications on heterogeneous multi-processor platforms - Zaki, G.F.; Plishker,W.; Bhattacharyya, Shuvra S.; Clancy, C.; Kuykendall, J. (2011 IEEE Workshop on Signal Processing Systems (SiPS), 2011)
A variety of multiprocessor architectures have proliferated even for off-the-shelf computing platforms. To improve performance and productivity for common heterogeneous systems, we have developed a workflow to generate efficient solutions. By starting with a formal description of an application and the mapping problem we are able to generate a range of designs that efficiently trade-of latency and throughput. In this approach, efficient utilization of SIMD cores is achieved by applying extensive block processing in conjunction with efficient mapping and scheduling. We demonstrate our approach through an integration into the GNU Radio environment for software defined radio system design.
Keywords: Benchmark testing; block processing; Design methodology; formal description; GNU radio environment; Graphic Processor Unit; Graphics processing unit; heterogeneous multiprocessor platform; mapping problem; Multicore processing; Multiprocessing systems; multiprocessor architecture; multiprocessor scheduling; operating systems (computers); PARALLEL PROCESSING; Processor scheduling; Schedules; SIMD core; Software Defined Radio; software defined radio system design; software radio; telecommunication computing; Throughput; vectorization; workflow

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

Active inference for collective classification - Bilgic,M.; Getoor, Lise (AAAI’10, 2010)
Labeling nodes in a network is an important problem that has seen a growing interest. A number of methods that exploit both local and relational information have been developed for this task. Acquiring the labels for a few nodes at inference time can greatly improve the ac- curacy, however the question of figuring out which node labels to acquire is challenging. Previous approaches have been based on simple structural properties. Here, we present a novel technique, which we refer to as re- flect and correct, that can learn and predict when the un- derlying classification system is likely to make mistakes and it suggests acquisitions to correct those mistakes.

Active learning for networked data - Bilgic,M.; Mihalkova,L.; Getoor, Lise (ICML’10, 2010)
We introduce a novel active learning algo-rithm for classification of network data. In this setting, training instances are connected by a set of links to form a network, the labels of linked nodes are correlated, and the goal is to exploit these dependencies and accu- rately label the nodes. This problem arises in many domains, including social and biologi- cal network analysis and document classifica- tion, and there has been much recent interest in methods that collectively classify the nodes in the network. While in many cases labeled examples are expensive, often network infor- mation is available. We show how an active learning algorithm can take advantage of net- work structure. Our algorithm effectively ex- ploits the links between instances and the in- teraction between the local and collective as- pects of a classifier to improve the accuracy of learning from fewer labeled examples. We ex- periment with two real-world benchmark col- lective classification domains, and show that we are able to achieve extremely accurate re- sults even when only a small fraction of the data is labeled.

Adaptive Threshold Estimation via Extreme Value Theory - Broadwater, J.B.; Chellapa, Rama (Signal Processing, IEEE Transactions on, 2010)
Determining a detection threshold to automatically maintain a low false alarm rate is a challenging problem. In a number of different applications, the underlying parametric assumptions of most automatic target detection algorithms are invalid. Therefore, thresholds derived using these incorrect distribution assumptions do not produce desirable results when applied to real sensor data. Monte Carlo methods for threshold determination work well but tend to perform poorly when targets are present. In order to mitigate these effects, we propose an algorithm using extreme value theory through the use of the generalized Pareto distribution (GPD) and a Kolmogorov-Smirnov statistical test. Unlike previous work based on GPD estimates, this algorithm incorporates a way to adaptively maintain low false alarm rates in the presence of targets. Both synthetic and real-world detection results demonstrate the usefulness of this algorithm.
Keywords: detection; detection; Pareto; distribution; adaptive; distribution; signal; estimation; extreme; estimation; signal; Kolmogorov-Smirnov; Pareto; statistical; test; adaptive; theory; generalized; threshold; value

Are developers complying with the process: an XP study - Zazworka, Nico; Stapel,Kai; Knauss,Eric; Shull, Forrest; Basili, Victor R.; Schneider,Kurt (Proceedings of the 2010 ACM-IEEE International Symposium on Empirical Software Engineering and Measurement, 2010)
Adapting new software processes and practices in organizational and academic environments requires training the developers and validating the applicability of the newly introduced activities. Investigating process conformance during training and understanding if programmers are able and willing to follow the specific steps are crucial to evaluating whether the process improves various software product quality factors. In this paper we present a process model independent approach to detect process non-conformance. Our approach is based on non-intrusively collected data captured by a version control system and provides the project manager with timely updates. Further, we provide evidence of the applicability of our approach by investigating process conformance in a five day training class on eXtreme Programming (XP) practices at the Leibniz Universität Hannover. Our results show that the approach enabled researchers to formulate minimal intrusive methods to check for conformance and that for the majority of the investigated XP practices violations could be detected.
Keywords: process conformance; process improvement; XP programming

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

Brief announcement: decentralized network bandwidth prediction - Song,S.; Keleher,P.; Bhattacharjee, Bobby; Sussman, Alan (Distributed Computing, 2010)
Distributed applications can often benefit from knowledge of the bandwidth between hosts, without performing measurements between all host pairs. For example, if a peer-to-peer (P2P) computational grid system predicts pairwise bandwidth between all nodes in the system, that information could increase overall system performance by finding high-bandwidth nodes to store large scientific input or output datasets. Another possible beneficiary is a P2P online game, which can provide users a seamless gaming experience by selecting a coordinator node that has high-bandwidth connections to the players in a game region.

Buffer management for multi-application image processing on multi-core platforms: Analysis and case study - Ko,Dong-Ik; Won, N.; Bhattacharyya, Shuvra S. (2010 IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP), 2010)
Due to the limited amounts of on-chip memory, large volumes of data, and performance and power consumption overhead associated with interprocessor communication, efficient management of buffer memory is critical to multi-core image processing. To address this problem, this paper develops new modeling and analysis techniques based on dataflow representations, and demonstrates these techniques on a multi-core implementation case study involving multiple, concurrently-executing image processing applications. Our techniques are based on careful representation and exploitation of frame- or block-based operations, which involve repeated invocations of the same computations across regularly- arranged subsets of data. Using these new approaches to manage block-based image data, this paper demonstrates methods to analyze synchronization overhead and FIFO buffer sizes when mapping image processing applications onto heterogeneous, multi core architectures.
Keywords: block-based image data; buffer memory management; buffer storage; concurrently-executing image processing application; data flow computing; data flow representation; data subset; Dataflow; Digital signal processing; Energy consumption; Energy management; Engineering management; FIFO buffer sizes; Hardware; Image analysis; IMAGE PROCESSING; image processing application; image representation; interprocessor communication; memory architecture; Memory management; multiapplication image processing; multicore image processing; multiprocessing; on-chip memory; power consumption; power consumption overhead; Runtime; scheduling; set theory; shared memory; storage management chips; synchronization overhead

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)

Chipping away at censorship firewalls with user-generated content - Burnett,S.; Feamster, Nick; Vempala,S. (Proc. 19th USENIX Security Symposium, Washington, DC, 2010)
Oppressive regimes and even democratic governmentsrestrict Internet access. Existing anti-censorship systems often require users to connect through proxies, but these systems are relatively easy for a censor to discover and block. This paper offers a possible next step in the cen- sorship arms race: rather than relying on a single system or set of proxies to circumvent censorship firewalls, we explore whether the vast deployment of sites that host user-generated content can breach these firewalls. To ex- plore this possibility, we have developed Collage, which allows users to exchange messages through hidden chan- nels in sites that host user-generated content. Collage has two components: a message vector layer for embedding content in cover traffic; and a rendezvous mechanism to allow parties to publish and retrieve messages in the cover traffic. Collage uses user-generated content (e.g., photo-sharing sites) as “drop sites” for hidden messages. To send a message, a user embeds it into cover traffic and posts the content on some site, where receivers retrieve this content using a sequence of tasks. Collage makes it difficult for a censor to monitor or block these messages by exploiting the sheer number of sites where users can exchange messages and the variety of ways that a mes- sage can be hidden. Our evaluation of Collage shows that the performance overhead is acceptable for sending small messages (e.g., Web articles, email). We show how Collage can be used to build two applications: a direct messaging application, and a Web content delivery system.

Circumventing censorship with collage - Burnett,Sam; Feamster, Nick; Vempala,Santosh (Proceedings of the ACM SIGCOMM 2010 conference, 2010)
Oppressive regimes and even democratic governments restrict Internet access. Existing anti-censorship systems often require users to connect through proxies, but these systems are relatively easy for a censor to discover and block. We explore a possible next step in the censorship arms race: rather than relying on a single system or set of proxies to circumvent censorship firewalls, we use the vast deployment of sites that host user-generated content to breach these firewalls. We have developed Collage, which allows users to exchange messages through hidden channels in sites that host user-generated content. To send a message, a user embeds it into cover traffic and posts the content on some site, where receivers retrieve this content. Collage makes it difficult for a censor to monitor or block these messages by exploiting the sheer number of sites where users can exchange messages and the variety of ways that a message can be hidden. We have built a censorship-resistant news reader using Collage that can retrieve from behind a censorship firewall and show Collage's effectiveness with a live demonstration of its complete infrastructure.
Keywords: Availability; censorship

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

Coherent turbulent motions in a Mach 3 boundary layer - Beekman,I.; Kan,Y. C; Priebe,S.; Martin, M.P (Bulletin of the American Physical Society, 2010)

Common Mode Analysis of Ethernet Transformers - Bowen,D.; Mayergoyz, Issak D; Krafft,C.; Kroop,D. (Magnetics Letters, IEEE, 2010)
In this letter, a distributed model for Ethernet transformers subject to common mode signals is developed.Explicit formulas for transfer functions are derived and illustrated by numerical examples.

Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae - Bradd,H.; Christopher,G.; Nur,H.; Seon-Young,C.; Jongsik,C.; Thomas,B.; David,B.; Jean,C.; Chris,D. J.; Cliff,H.; Rita R Colwell (BMC Microbiology, 2010)
In recent years genome sequencing has been used to characterize new bacterial species, a method of analysis available as a result of improved methodology and reduced cost. Included in a constantly expanding list of Vibrio species are several that have been reclassified as novel members of the Vibrionaceae. The description of two putative new Vibrio species, Vibrio sp. RC341 and Vibrio sp. RC586 for which we propose the names V. metecus and V. parilis, respectively, previously characterized as non-toxigenic environmental variants of V. cholerae is presented in this study. Results Based on results of whole-genome average nucleotide identity (ANI), average amino acid identity (AAI), rpoB similarity, MLSA, and phylogenetic analysis, the new species are concluded to be phylogenetically closely related to V. cholerae and V. mimicus. Vibrio sp. RC341 and Vibrio sp. RC586 demonstrate features characteristic of V. cholerae and V. mimicus, respectively, on differential and selective media, but their genomes show a 12 to 15% divergence (88 to 85% ANI and 92 to 91% AAI) compared to the sequences of V. cholerae and V. mimicus genomes (ANI <95% and AAI <96% indicative of separate species). Vibrio sp. RC341 and Vibrio sp. RC586 share 2104 ORFs (59%) and 2058 ORFs (56%) with the published core genome of V. cholerae and 2956 (82%) and 3048 ORFs (84%) with V. mimicus MB-451, respectively. The novel species share 2926 ORFs with each other (81% Vibrio sp. RC341 and 81% Vibrio sp. RC586). Virulence-associated factors and genomic islands of V. cholerae and V. mimicus, including VSP-I and II, were found in these environmental Vibrio spp. Conclusions Results of this analysis demonstrate these two environmental vibrios, previously characterized as variant V. cholerae strains, are new species which have evolved from ancestral lineages of the V. cholerae and V. mimicus clade. The presence of conserved integration loci for genomic islands as well as evidence of horizontal gene transfer between these two new species, V. cholerae, and V. mimicus suggests genomic islands and virulence factors are transferred between these species.

Compressive Acquisition of Dynamic Scenes - Sankaranarayanan,Aswin; Turaga,Pavan; Baraniuk,Richard; Chellapa, Rama (Computer Vision – ECCV 2010Computer Vision – ECCV 2010, 2010)
Compressive sensing (CS) is a new approach for the acquisition and recovery of sparse signals and images that enables sampling rates significantly below the classical Nyquist rate. Despite significant progress in the theory and methods of CS, little headway has been made in compressive video acquisition and recovery. Video CS is complicated by the ephemeral nature of dynamic events, which makes direct extensions of standard CS imaging architectures and signal models infeasible. In this paper, we develop a new framework for video CS for dynamic textured scenes that models the evolution of the scene as a linear dynamical system (LDS). This reduces the video recovery problem to first estimating the model parameters of the LDS from compressive measurements, from which the image frames are then reconstructed. We exploit the low-dimensional dynamic parameters (the state sequence) and high-dimensional static parameters (the observation matrix) of the LDS to devise a novel compressive measurement strategy that measures only the dynamic part of the scene at each instant and accumulates measurements over time to estimate the static parameters. This enables us to considerably lower the compressive measurement rate considerably. We validate our approach with a range of experiments including classification experiments that highlight the effectiveness of the proposed approach.

Compressive Video Acquisition, Fusion and Processing - Baraniuk,Richard G.; Chellapa, Rama; Wakin,Michael (2010)
Modern developments in sensor technology, signal processing, and wireless communications have enabled the conception and deployment of large-scale networked sensing systems spanning numerous collection platforms and varied modalities. These systems have the potential to make intelligent decisions by integrating information from massive amounts of sensor data. Before such benefits can be achieved, significant advances must be made in methods for communicating, fusing, and processing this evergrowing volume of diverse data. In this one-year research project, we aimed to expose the fundamental issues and pave the way for further careful study of compressive approaches to video acquisition, fusion, and processing. In doing so, we developed a theoretical definition of video temporal bandwidth and applied the theory to compressive sampling and reconstruction. We created a new framework for compressive video sensing based on linear dynamical systems, lowering the compressive measurement rate. Finally, we applied our own joint manifold model to a variety of relevant image processing problems, demonstrating the model's effectiveness and ability to overcome noise and occlusion obstacles. We also showed how joint manifold models can discover an object's trajectory, an important step towards video fusion.
Keywords: *DATA FUSION; *DETECTORS; *SIGNAL PROCESSING; *VIDEO SIGNALS; ACQUISITION; COLLECTION; COMMUNICATION AND RADIO SYSTEMS; COMPRESSIVE PROPERTIES; COMPRESSIVE SAMPLING; compressive sensing; COMPRESSIVE VIDEO; decision making; DEPLOYMENT; DETECTION; DYNAMICS; IMAGE PROCESSING; Linear systems; Linearity; MANIFOLDS(ENGINES); measurement; MISCELLANEOUS DETECTION AND DETECTORS; MODELS; sampling; THEORY; TRAJECTORIES