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 ...

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)

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

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.

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

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

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

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

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

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.

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

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

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.

Recognition of achievement – priorities and process - Madsen, Lynnette D.; Rita R Colwell (Materials Today, 2016)

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

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.

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

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

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

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

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

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)

Can Optimally-Fair Coin Tossing Be Based on One-Way Functions? - Dana Dachman-Soled; Mahmoody, Mohammad; Malkin, Tal (Theory of Cryptography, 2014)
Coin tossing is a basic cryptographic task that allows two distrustful parties to obtain an unbiased random bit in a way that neither party can bias the output by deviating from the protocol or halting the execution. Cleve [STOC’86] showed that in any r round coin tossing protocol one of the parties can bias the output by Ω(1/r) through a “fail-stop” attack; namely, they simply execute the protocol honestly and halt at some chosen point. In addition, relying on an earlier work of Blum [COMPCON’82], Cleve presented an r-round protocol based on one-way functions that was resilient to bias at most O(1/r√)O(1/\sqrt r) . Cleve’s work left open whether ”‘optimally-fair’” coin tossing (i.e. achieving bias O(1/r) in r rounds) is possible. Recently Moran, Naor, and Segev [TCC’09] showed how to construct optimally-fair coin tossing based on oblivious transfer, however, it was left open to find the minimal assumptions necessary for optimally-fair coin tossing. The work of Dachman-Soled et al. [TCC’11] took a step toward answering this question by showing that any black-box construction of optimally-fair coin tossing based on a one-way functions with n-bit input and output needs Ω(n/logn) rounds. In this work we take another step towards understanding the complexity of optimally-fair coin-tossing by showing that this task (with an arbitrary number of rounds) cannot be based on one-way functions in a black-box way, as long as the protocol is ”‘oblivious’” to the implementation of the one-way function. Namely, we consider a natural class of black-box constructions based on one-way functions, called function oblivious, in which the output of the protocol does not depend on the specific implementation of the one-way function and only depends on the randomness of the parties. Other than being a natural notion on its own, the known coin tossing protocols of Blum and Cleve (both based on one-way functions) are indeed function oblivious. Thus, we believe our lower bound for function-oblivious constructions is a meaningful step towards resolving the fundamental open question of the complexity of optimally-fair coin tossing.
Keywords: Algorithm Analysis and Problem Complexity; black-box separations; Coin-Tossing; Computation by Abstract Devices; Data Encryption; Discrete Mathematics in Computer Science; One-Way Functions; Systems and Data Security

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

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

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

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

Stable isotope labeling of phosphoproteins for large-scale phosphorylation rate determination - Molden, Rosalynn C.; Goya, Jonathan; Zia Khan; Garcia, Benjamin A. (Molecular & Cellular Proteomics, 2014)
Signals that control response to stimuli and cellular function are transmitted through dynamic phosphorylation of thousands of proteins by protein kinases. Many techniques have been developed to study phosphorylation dynamics, including several mass spectrometry (MS)-based methods. Over the last few decades, substantial developments have been made in MS techniques for the large-scale identification of proteins and their post-translational modifications. Nevertheless, all of the current MS-based techniques for quantifying protein phosphorylation dynamics rely on the measurement of changes in peptide abundance levels and many methods suffer from low confidence in phosphopeptide identification due to poor fragmentation. Here we have optimized an approach for the Stable Isotope Labeling of Amino acids by Phosphate (SILAP) using [gamma-18O4]ATP in nucleo to determine global site-specific phosphorylation rates. The advantages of this metabolic labeling technique are: increased confidence in phosphorylated peptide identification, direct labeling of phosphorylation sites, measurement phosphorylation rates, and the identification of actively phosphorylated sites in a cell-like environment. In this study we calculated approximate rate constants for over 500 phosphorylation sites based on labeling progress curves. We measured a wide range of phosphorylation rate constants from 0.34 min-1 to 0.001 min-1. Finally, we applied SILAP to determine sites that have different phosphorylation kinetics during G1/S and M phase. We found that most sites have very similar phosphorylation rates under both conditions; however a small subset of sites on proteins involved in the mitotic spindle were more actively phosphorylated during M phase, while proteins involved in DNA replication and transcription were more actively phosphorylated during G1/S phase.
Keywords: DYNAMICS; Phosphoproteins*; Phosphoproteome; Phosphorylation; Post-translational modifications*; Signal Transduction*; turnover

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.

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

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

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

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 ...

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 ...

Optimizing Abstract Abstract Machines - Johnson, J. Ian; Labich, Nicholas; Might, Matthew; David Van Horn (arXiv:1211.3722 [cs], 2013)
The technique of abstracting abstract machines (AAM) provides a systematic approach for deriving computable approximations of evaluators that are easily proved sound. This article contributes a complementary step-by-step process for subsequently going from a naive analyzer derived under the AAM approach, to an efficient and correct implementation. The end result of the process is a two to three order-of-magnitude improvement over the systematically derived analyzer, making it competitive with hand-optimized implementations that compute fundamentally less precise results.
Comment: Proceedings of the International Conference on Functional Programming 2013 (ICFP 2013). Boston, Massachusetts. September, 2013
Keywords: Computer Science - Programming Languages; F.3.2

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures - Zia Khan; Ford, Michael J.; Cusanovich, Darren A.; Mitrano, Amy; Pritchard, Jonathan K.; Gilad, Yoav (Science, 2013)
Changes in gene regulation have likely played an important role in the evolution of primates. Differences in messenger RNA (mRNA) expression levels across primates have often been documented; however, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are probably more important in determining phenotypic differences. We used high-resolution, quantitative mass spectrometry to collect protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines and compared them to transcript expression data from the same samples. We found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest that protein expression levels evolve under stronger evolutionary constraint than mRNA levels.Don't Ape Protein Variation Changes in DNA and messenger RNA (mRNA) expression levels have been used to estimate evolutionary changes between species. However protein expression levels may better reflect selection on divergent and constrained phenotypes. Khan et al. (p. 1100, published online 17 October; see the Perspective by Vogel) measured the differences among and within species between mRNA expression and protein levels in humans, chimpanzees, and rhesus macaques, identifying protein transcripts that seem to be under lineage-specific constraint between humans and chimpanzees.

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

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

Advances in Computers - Memon, Atif M. (Academic Press, 2012)
Since its first volume in 1960, Advances in Computers has presented detailed coverage of innovations in computer hardware, software, theory, design, and applications. It has also provided contributors with a medium in which they can explore their subjects in greater depth and breadth than journal articles usually allow. As a result, many articles have become standard references that continue to be of sugnificant, lasting value in this rapidly expanding field. In-depth surveys and tutorials on new computer technologyWell-known authors and researchers in the fieldExtensive bibliographies with most chaptersMany of the volumes are devoted to single themes or subfields of computer science
Keywords: Computers / Programming / General; Computers / Software Development & Engineering / General; Mathematics / General

AGORA: Assembly Guided by Optical Restriction Alignment - Lin, H.C.; Goldstein, S.; Mendelowitz, L.; Zhou, S.; Wetzel, J.; Schwartz, D.C.; Pop, Mihai (BMC bioinformatics, 2012)
Genome assembly is difficult due to repeated sequences within the genome, which create ambiguities and cause the final assembly to be broken up into many separate sequences (contigs). Long range linking information, such as mate-pairs or mapping data, is necessary to help assembly software resolve repeats, thereby leading to a more complete reconstruction of genomes. Prior work has used optical maps for validating assemblies and scaffolding contigs, after an initial assembly has been produced. However, optical maps have not previously been used within the genome assembly process. Here, we use optical map information within the popular de Bruijn graph assembly paradigm to eliminate paths in the de Bruijn graph which are not consistent with the optical map and help determine the correct reconstruction of the genome.We developed a new algorithm called AGORA: Assembly Guided by Optical Restriction Alignment. AGORA is the first algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. Our simulations on bacterial genomes show that AGORA is effective at producing assemblies closely matching the reference sequences. Additionally, we show that noise in the optical map can have a strong impact on the final assembly quality for some complex genomes, and we also measure how various characteristics of the starting de Bruijn graph may impact the quality of the final assembly. Lastly, we show that a proper choice of restriction enzyme for the optical map may substantially improve the quality of the final assembly. Our work shows that optical maps can be used effectively to assemble genomes within the de Bruijn graph assembly framework. Our experiments also provide insights into the characteristics of the mapping data that most affect the performance of our algorithm, indicating the potential benefit of more accurate optical mapping technologies, such as nano-coding.

BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection - Lee, Song Hee; Kalejta, Robert F.; Kerry, Julie; Semmes, Oliver John; O’Connor, Christine M.; Zia Khan; Garcia, Benjamin A.; Shenk, Thomas; Murphy, Eain (Proceedings of the National Academy of Sciences, 2012)
Cell proteins can restrict the replication of viruses. Here, we identify the cellular BclAF1 protein as a human cytomegalovirus restriction factor and describe two independent mechanisms the virus uses to decrease its steady-state levels. Immediately following infection, the viral pp71 and UL35 proteins, which are delivered to cells within virions, direct the proteasomal degradation of BclAF1. Although BclAF1 reaccumulates through the middle stages of infection, it is subsequently down-regulated at late times by miR-UL112-1, a virus-encoded microRNA. In the absence of BclAF1 neutralization, viral gene expression and replication are inhibited. These data identify two temporally and mechanistically distinct functions used by human cytomegalovirus to down-regulate a cellular antiviral protein.
Keywords: innate immunity; intrinsic immunity; miRNA; Proteasome; UL82

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.

Computational Analysis of Terrorist Groups: Lashkar-e-Taiba - V.S. Subrahmanian; Mannes, Aaron; Sliva,Amy; Shakarian, Jana; Dickerson, John P. (Springer Publishing Company, Incorporated, 2012)
Computational Analysis of Terrorist Groups: Lashkar-e-Taiba provides an in-depth look at Web intelligence, and how advanced mathematics and modern computing technology can influence the insights we have on terrorist groups. This book primarily focuses on one famous terrorist group known as Lashkar-e-Taiba (or LeT), and how it operates. After 10 years of counter Al Qaeda operations, LeT is considered by many in the counter-terrorism community to be an even greater threat to the US and world peace than Al Qaeda. Computational Analysis of Terrorist Groups: Lashkar-e-Taiba is the first book that demonstrates how to use modern computational analysis techniques including methods for big data analysis. This book presents how to quantify both the environment in which LeT operate, and the actions it took over a 20-year period, and represent it as a relational database table. This table is then mined using sophisticated data mining algorithms in order to gain detailed, mathematical, computational and statistical insights into LeT and its operations. This book also provides a detailed history of Lashkar-e-Taiba based on extensive analysis conducted by using open source information and public statements. Each chapter includes a case study, as well as a slide describing the key results which are available on the authors web sites. Computational Analysis of Terrorist Groups: Lashkar-e-Taiba is designed for a professional market composed of government or military workers, researchers and computer scientists working in the web intelligence field. Advanced-level students in computer science will also find this valuable as a reference book.

Computational Extractors and Pseudorandomness - Dana Dachman-Soled; Gennaro, Rosario; Krawczyk, Hugo; Malkin, Tal (Theory of Cryptography, 2012)
Computational extractors are efficient procedures that map a source of sufficiently high min-entropy to an output that is computationally indistinguishable from uniform. By relaxing the statistical closeness property of traditional randomness extractors one hopes to improve the efficiency and entropy parameters of these extractors, while keeping their utility for cryptographic applications. In this work we investigate computational extractors and consider questions of existence and inherent complexity from the theoretical and practical angles, with particular focus on the relationship to pseudorandomness. An obvious way to build a computational extractor is via the “extract-then-prg” method: apply a statistical extractor and use its output to seed a PRG. This approach carries with it the entropy cost inherent to implementing statistical extractors, namely, the source entropy needs to be substantially higher than the PRG’s seed length. It also requires a PRG and thus relies on one-way functions. We study the necessity of one-way functions in the construction of computational extractors and determine matching lower and upper bounds on the “black-box efficiency” of generic constructions of computational extractors that use a one-way permutation as an oracle. Under this efficiency measure we prove a direct correspondence between the complexity of computational extractors and that of pseudorandom generators, showing the optimality of the extract-then-prg approach for generic constructions of computational extractors and confirming the intuition that to build a computational extractor via a PRG one needs to make up for the entropy gap intrinsic to statistical extractors. On the other hand, we show that with stronger cryptographic primitives one can have more entropy- and computationally-efficient constructions. In particular, we show a construction of a very practical computational extractor from any weak PRF without resorting to statistical extractors.
Keywords: Algorithm Analysis and Problem Complexity; Coding and Information Theory; Computer Communication Networks; Data Encryption; Math Applications in Computer Science; Systems and Data Security

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

Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease - Liu,B.; Faller, L.L.; Klitgord, N.; Mazumdar, V.; Ghodsi,M.; Sommer, D.D.; Gibbons, T.R.; Treangen, T.J.; Chang, Y.C.; Li,S. (PloS one, 2012)
The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (~2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ~90%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.

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

Exploiting sparseness in de novo genome assembly - Ye, C.; Ma, Z.S.; Cannon, C.H.; Pop, Mihai; Yu, D.W. (BMC bioinformatics, 2012)
The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments.In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k-mers as nodes and the links between these nodes allows the de novo assembly of even moderately-sized genomes (~500 M) on a typical laptop computer. We implement this sparse graph concept in a proof-of-principle software package, SparseAssembler, utilizing a new sparse k-mer graph structure evolved from the de Bruijn graph. We test our SparseAssembler with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers.

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.

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

Genetic characteristics of drug-resistant Vibrio cholerae O1 causing endemic cholera in Dhaka, 2006-2011 - Rashed, S. M.; Mannan, S. B.; Johura, F.-T.; Islam, M. T.; Sadique, A.; Watanabe, H.; Sack, R. B.; Huq, A.; Rita R Colwell; Cravioto, A.; Alam, M. (Journal of Medical Microbiology, 2012)
Vibrio cholerae O1 biotype El Tor (ET), causing the seventh cholera pandemic, was recently replaced in Bangladesh by an altered ET possessing ctxB of the Classical (CL) biotype, which caused the first six cholera pandemics. In the present study, V. cholerae O1 strains associated with endemic cholera in Dhaka between 2006 and 2011 were analysed for major phenotypic and genetic characteristics. Of 54 representative V. cholerae isolates tested, all were phenotypically ET and showed uniform resistance to trimethoprim/sulfamethoxazole (SXT) and furazolidone (FR). Resistance to tetracycline (TE) and erythromycin (E) showed temporal fluctuation, varying from year to year, while all isolates were susceptible to gentamicin (CN) and ciprofloxacin (CIP). Year-wise data revealed erythromycin resistance to be 33.3 % in 2006 and 11 % in 2011, while tetracycline resistance accounted for 33, 78, 0, 100 and 27 % in 2006, 2007, 2008, 2009 and 2010, respectively; interestingly, all isolates tested were sensitive to TE in 2011, as observed in 2008. All V. cholerae isolates tested possessed genetic elements such as SXT, ctxAB, tcpA ET, rstR ET and rtxC; none had IntlI (Integron I). Double mismatch amplification mutation assay (DMAMA)-PCR followed by DNA sequencing and analysis of the ctxB gene revealed a point mutation at position 58 (C→A), which has resulted in an amino acid substitution from histidine (H) to asparagine (N) at position 20 (genotype 7) since 2008. Although the multi-resistant strains having tetracycline resistance showed minor genetic divergence, V. choleraestrains were clonal, as determined by a PFGE (NotI)-based dendrogram. This study shows 2008–2010 to be the time of transition from ctxB genotype 1 to genotype 7 in V. cholerae ET causing endemic cholera in Dhaka, Bangladesh.

Gradient-based Image Recovery Methods from Incomplete Fourier Measurements - Patel, Vishal M.; Maleh,R.; Gilbert,A. C; Chellapa, Rama (IEEE Transactions on Image Processing, 2012)
A major problem in imaging applications such as Magnetic Resonance Imaging (MRI) and Synthetic Aperture Radar (SAR) is the task of trying to reconstruct an image with the smallest possible set of Fourier samples, every single one of which has a potential time and/or power cost. The theory of Compressive Sensing (CS) points to ways of exploiting inherent sparsity in such images in order to achieve accurate recovery using sub- Nyquist sampling schemes. Traditional CS approaches to this problem consist of solving total-variation minimization programs with Fourier measurement constraints or other variations thereof. This paper takes a different approach: Since the horizontal and vertical differences of a medical image are each more sparse or compressible than the corresponding total-variational image, CS methods will be more successful in recovering these differences individually. We develop an algorithm called GradientRec that uses a CS algorithm to recover the horizontal and vertical gradients and then estimates the original image from these gradients. We present two methods of solving the latter inverse problem: one based on least squares optimization and the other based on a generalized Poisson solver. After a thorough derivation of our complete algorithm, we present the results of various experiments that compare the effectiveness of the proposed method against other leading methods.
Keywords: Compressed sensing; Fourier transforms; Image coding; Image edge detection; Image reconstruction; L1–minimization; minimization; Noise measurement; OPTIMIZATION; Poisson solver; Sparse recovery; Total variation; TV

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

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

Introspective Pushdown Analysis of Higher-Order Programs - Earl, Christopher; Sergey, Ilya; Might, Matthew; David Van Horn (arXiv:1207.1813 [cs], 2012)
In the static analysis of functional programs, pushdown flow analysis and abstract garbage collection skirt just inside the boundaries of soundness and decidability. Alone, each method reduces analysis times and boosts precision by orders of magnitude. This work illuminates and conquers the theoretical challenges that stand in the way of combining the power of these techniques. The challenge in marrying these techniques is not subtle: computing the reachable control states of a pushdown system relies on limiting access during transition to the top of the stack; abstract garbage collection, on the other hand, needs full access to the entire stack to compute a root set, just as concrete collection does. Introspective pushdown systems resolve this conflict. Introspective pushdown systems provide enough access to the stack to allow abstract garbage collection, but they remain restricted enough to compute control-state reachability, thereby enabling the sound and precise product of pushdown analysis and abstract garbage collection. Experiments reveal synergistic interplay between the techniques, and the fusion demonstrates "better-than-both-worlds" precision.
Comment: Proceedings of the 17th ACM SIGPLAN International Conference on Functional Programming, 2012, ACM
Keywords: Computer Science - Programming Languages; D.3.4; F.3.2

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.

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

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.

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

Personal informatics in practice: improving quality of life through data - Li, I.; Medynskiy, Y.; Jon Froehlich; Larsen, J. (ACM, 2012)

Polytope approximation and the Mahler volume - Arya,Sunil; da Fonseca,Guilherme D.; Mount, Dave (Proceedings of the Twenty-Third Annual ACM-SIAM Symposium on Discrete Algorithms, 2012)
The problem of approximating convex bodies by polytopes is an important and well studied problem. Given a convex body K in Rd, the objective is to minimize the number of vertices (alternatively, the number of facets) of an approximating polytope for a given Hausdorff error ε. Results to date have been of two types. The first type assumes that K is smooth, and bounds hold in the limit as ε tends to zero. The second type requires no such assumptions. The latter type includes the well known results of Dudley (1974) and Bronshteyn and Ivanov (1976), which show that in spaces of fixed dimension, O((diam(K)/ε)(d−1)/2) vertices (alt., facets) suffice. Our results are of this latter type. In our first result, under the assumption that the width of the body in any direction is at least ε, we strengthen the above bound to [EQUATION]. This is never worse than the previous bound (by more than logarithmic factors) and may be significantly better for skinny bodies. Our analysis exploits an interesting analogy with a classical concept from the theory of convexity, called the Mahler volume. This is a dimensionless quantity that involves the product of the volumes of a convex body and its polar dual. In our second result, we apply the same machinery to improve upon the best known bounds for answering ε-approximate polytope membership queries. Given a convex polytope P defined as the intersection of halfspaces, such a query determines whether a query point q lies inside or outside P, but may return either answer if q's distance from P's boundary is at most ε. We show that, without increasing storage, it is possible to reduce the best known search times for ε-approximate polytope membership significantly. This further implies improvements to the best known search times for approximate nearest neighbor searching in spaces of fixed dimension.

Preserving Link Privacy in Social Network Based Systems - Mittal, Prateek; Charalampos Papamanthou; Song, Dawn (arXiv:1208.6189 [cs], 2012)
A growing body of research leverages social network based trust relationships to improve the functionality of the system. However, these systems expose users' trust relationships, which is considered sensitive information in today's society, to an adversary. In this work, we make the following contributions. First, we propose an algorithm that perturbs the structure of a social graph in order to provide link privacy, at the cost of slight reduction in the utility of the social graph. Second we define general metrics for characterizing the utility and privacy of perturbed graphs. Third, we evaluate the utility and privacy of our proposed algorithm using real world social graphs. Finally, we demonstrate the applicability of our perturbation algorithm on a broad range of secure systems, including Sybil defenses and secure routing.
Comment: 16 pages, 15 figures
Keywords: Computer Science - Cryptography and Security; Computer Science - Social and Information Networks

Scientific Freedom and Human Rights - Minker, Jack (IEEE Computer Society Press, 2012)
There is a great deal of difference between feeling empathy for those whose human rights are being violated around the world and actually doing something about it. This memoir, written by the Vice-Chair Computer Science (CS) of the Committee of Concerned Scientists (CCS), 1962-present, and Vice-Chair of the Committee on Scientific Freedom and Human Rights (CSFHR) of the ACM, 1980-1989, is a first-hand account of computer scientists working with numerous other constituencies to safeguard or advance the human rights of scientists throughout the world. Drawing from the author's considerable archives from the period, "Scientific Freedom and Human Rights" is a treasure trove of historical information about a critical -- and relatively unsung -- human rights campaign, its successes and heartbreaking challenges, and possible lessons to be applied to future human rights campaigns. "The solidarity of the global scientific community was especially important in giving moral support to the intellectual leaders of the struggle for Soviet Jewry, helping them to continue their scientific activity even in a time of persecution. Their activism also helped to link scientific cooperation with the Soviet Union with freedom within the Soviet Union.... You will read these stories and see the support given many scientists throughout the world in this book." -- Natan Sharansky, Jewish Agency Chairman of the Executive "It is not very often that solidarity among scientists is brought to the public eye, and it is certainly not common for people outside science to associate scientists with heroic struggles for human rights, freedom, and dignity. Jack Minker's new book will change this perception." -- Professor Judea Pearl, University of California at Los Angeles
Keywords: Biography & Autobiography / Science & Technology

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

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.

Towards a cost model for network traffic - Motiwala,Murtaza; Dhamdhere,Amogh; Feamster, Nick; Lakhina,Anukool (SIGCOMM Comput. Commun. Rev., 2012)
We develop a holistic cost model that operators can use to help evaluate the costs of various routing and peering decisions. Using real traffic data from a large carrier network, we show how network operators can use this cost model to significantly reduce the cost of carrying traffic in their networks. We find that adjusting the routing for a small fraction of total flows (and total traffic volume) significantly reduces cost in many cases. We also show how operators can use the cost model both to evaluate potential peering arrangements and for other network operations problems.
Keywords: cost optimization; traffic cost model

Two-server password-only authenticated key exchange - Katz, Jonathan; MacKenzie,Philip; Taban,Gelareh; Gligor,Virgil (Journal of Computer and System Sciences, 2012)
Typical protocols for password-based authentication assume a single server that stores all the information (e.g., the password) necessary to authenticate a user. An inherent limitation of this approach, assuming low-entropy passwords are used, is that the userʼs password is exposed if this server is ever compromised. To address this issue, it has been suggested to share a userʼs password information among multiple servers, and to have these servers cooperate (possibly in a threshold manner) when the user wants to authenticate. We show here a two-server version of the password-only key-exchange protocol of Katz, Ostrovsky, and Yung (the KOY protocol). Our work gives the first secure two-server protocol for the password-only setting (in which the user need remember only a password, and not the serversʼ public keys), and is the first two-server protocol (in any setting) with a proof of security in the standard model. Our work thus fills a gap left by the work of MacKenzie et al. (2006) [31] and Di Raimondo and Gennaro (2006) [16]. As an additional benefit of our work, we show modifications that improve the efficiency of the original KOY protocol.
Keywords: Key-exchange protocols; passwords

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

Abduction in Annotated Probabilistic Temporal Logic - Molinaro,Cristian; Sliva,Amy; V.S. Subrahmanian (Technical Communications of the 27th International Conference on Logic Programming (ICLP'11), 2011)
Annotated Probabilistic Temporal (APT) logic programs are a form of logic programs that allow users to state (or systems to automatically learn)rules of the form ``formula G becomes true K time units after formula F became true with L to U% probability.'' In this paper, we develop a theory of abduction for APT logic programs. Specifically, given an APT logic program Pi, a set of formulas H that can be ``added'' to Pi, and a goal G, is there a subset S of H such that Pi \cup S is consistent and entails the goal G? In this paper, we study the complexity of the Basic APT Abduction Problem (BAAP). We then leverage a geometric characterization of BAAP to suggest a set of pruning strategies when solving BAAP and use these intuitions to develop a sound and complete algorithm.

Abstracting Abstract Machines: A Systematic Approach to Higher-Order Program Analysis - David Van Horn; Might, Matthew (arXiv:1105.1743 [cs], 2011)
Predictive models are fundamental to engineering reliable software systems. However, designing conservative, computable approximations for the behavior of programs (static analyses) remains a difficult and error-prone process for modern high-level programming languages. What analysis designers need is a principled method for navigating the gap between semantics and analytic models: analysis designers need a method that tames the interaction of complex languages features such as higher-order functions, recursion, exceptions, continuations, objects and dynamic allocation. We contribute a systematic approach to program analysis that yields novel and transparently sound static analyses. Our approach relies on existing derivational techniques to transform high-level language semantics into low-level deterministic state-transition systems (with potentially infinite state spaces). We then perform a series of simple machine refactorings to obtain a sound, computable approximation, which takes the form of a non-deterministic state-transition systems with finite state spaces. The approach scales up uniformly to enable program analysis of realistic language features, including higher-order functions, tail calls, conditionals, side effects, exceptions, first-class continuations, and even garbage collection.
Comment: Communications of the ACM, Research Highlight
Keywords: Computer Science - Programming Languages; F.3.2; F.4.1

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

Approximate polytope membership queries - Arya,S.; da Fonseca,G. D; Mount, Dave (Proceedings of 43rd Annual ACM Symposium on Theory of Computing, 2011)
We consider an approximate version of a fundamental geo-metric search problem, polytope membership queries. Given a convex polytope P in Rd, presented as the intersection of halfspaces, the objective is to preprocess P so that, given a query point q, it is possible to determine efficiently whether q lies inside P subject to an error bound ε. Previous solutions to this problem were based on straight- forward applications of classic polytope approximation tech- niques by Dudley (1974) and Bentley et al. (1982). The former yields minimum storage, and the latter yields con- stant query time. A space-time tradeoff can be obtained by interpolating between the two. We present the first sig- nificant improvements to this tradeoff. For example, using the same storage as Dudley, we reduce the query time from O(1/ε (d−1)/2 ) to O(1/ε (d−1)/4 ). Our approach is based on a very simple algorithm. Both lower bounds and upper bounds on the performance of the algorithm are presented. To establish the relevance of our results, we introduce a reduction from approximate nearest neighbor searching to approximate polytope membership queries. We show that our tradeoff provides significant improvements to the best known space-time tradeoffs for approximate nearest neigh- bor searching. Furthermore, this is achieved with construc- tions that are much simpler than existing methods

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

Associating the visual representation of user interfaces with their internal structures and metadata - Chang,Tsung-Hsiang; Tom Yeh; Miller,Rob (Proceedings of the 24th annual ACM symposium on User interface software and technology, 2011)
Pixel-based methods are emerging as a new and promising way to develop new interaction techniques on top of existing user interfaces. However, in order to maintain platform independence, other available low-level information about GUI widgets, such as accessibility metadata, was neglected intentionally. In this paper, we present a hybrid framework, PAX, which associates the visual representation of user interfaces (i.e. the pixels) and their internal hierarchical metadata (i.e. the content, role, and value). We identify challenges to building such a framework. We also develop and evaluate two new algorithms for detecting text at arbitrary places on the screen, and for segmenting a text image into individual word blobs. Finally, we validate our framework in implementations of three applications. We enhance an existing pixel-based system, Sikuli Script, and preserve the readability of its script code at the same time. Further, we create two novel applications, Screen Search and Screen Copy, to demonstrate how PAX can be applied to development of desktop-level interactive systems.
Keywords: accessibility api; Graphical user interfaces; Pixel; text detection; text segmentation

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

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

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)

Birdlets: Subordinate categorization using volumetric primitives and pose-normalized appearance - Farrell,R.; Oza,O.; Zhang,Ning; Morariu,V.I.; Darrell,T.; Davis, Larry S. (Computer Vision (ICCV), 2011 IEEE International Conference on, 2011)
Subordinate-level categorization typically rests on establishing salient distinctions between part-level characteristics of objects, in contrast to basic-level categorization, where the presence or absence of parts is determinative. We develop an approach for subordinate categorization in vision, focusing on an avian domain due to the fine-grained structure of the category taxonomy for this domain. We explore a pose-normalized appearance model based on a volumetric poselet scheme. The variation in shape and appearance properties of these parts across a taxonomy provides the cues needed for subordinate categorization. Training pose detectors requires a relatively large amount of training data per category when done from scratch; using a subordinate-level approach, we exploit a pose classifier trained at the basic-level, and extract part appearance and shape information to build subordinate-level models. Our model associates the underlying image pattern parameters used for detection with corresponding volumetric part location, scale and orientation parameters. These parameters implicitly define a mapping from the image pixels into a pose-normalized appearance space, removing view and pose dependencies, facilitating fine-grained categorization from relatively few training examples.
Keywords: appearance; Birdlets; category; categorization; subordinate-level; detection; pose; detectors; pose-normalized; distinctions; shape; estimation; extraction; pose; extraction; subordinate-level; information; model; salient; models; volumetric; pixels; part; poselet; primitives; computer; resolution; information; retrieval; object; scheme; volumetric; taxonomy; computer; vision; image

On the Black-Box Complexity of Optimally-Fair Coin Tossing - Dana Dachman-Soled; Lindell, Yehuda; Mahmoody, Mohammad; Malkin, Tal (Theory of Cryptography, 2011)
A fair two-party coin tossing protocol is one in which both parties output the same bit that is almost uniformly distributed (i.e., it equals 0 and 1 with probability that is at most negligibly far from one half). It is well known that it is impossible to achieve fair coin tossing even in the presence of fail-stop adversaries (Cleve, FOCS 1986). In fact, Cleve showed that for every coin tossing protocol running for r rounds, an efficient fail-stop adversary can bias the output by Ω(1/r). Since this is the best possible, a protocol that limits the bias of any adversary to O(1/r) is called optimally-fair. The only optimally-fair protocol that is known to exist relies on the existence of oblivious transfer, because it uses general secure computation (Moran, Naor and Segev, TCC 2009). However, it is possible to achieve a bias of O(1/r√)O(1/\sqrt{r}) in r rounds relying only on the assumption that there exist one-way functions. In this paper we show that it is impossible to achieve optimally-fair coin tossing via a black-box construction from one-way functions for r that is less than O(n/logn), where n is the input/output length of the one-way function used. An important corollary of this is that it is impossible to construct an optimally-fair coin tossing protocol via a black-box construction from one-way functions whose round complexity is independent of the security parameter n determining the security of the one-way function being used. Informally speaking, the main ingredient of our proof is to eliminate the random-oracle from “secure” protocols with “low round-complexity” and simulate the protocol securely against semi-honest adversaries in the plain model. We believe our simulation lemma to be of broader interest.
Keywords: Algorithm Analysis and Problem Complexity; black-box separations; Coding and Information Theory; coin tossing; Computer Communication Networks; Data Encryption; lower-bound; Math Applications in Computer Science; optimally-fair coin tossing; round-complexity; Systems and Data Security

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

Capacity of wireless networks under SINR interference constraints - Chafekar,Deepti; Anil Kumar,V.; Marathe,Madhav; Parthasarathy,Srinivasan; Srinivasan, Aravind (Wireless Networks, 2011)
A fundamental problem in wireless networks is to estimate their throughput capacity—given a set of wireless nodes and a set of connections, what is the maximum rate at which data can be sent on these connections. Most of the research in this direction has focused either on random distributions of points, or has assumed simple graph-based models for wireless interference. In this paper, we study the capacity estimation problem using a realistic Signal to Interference Plus Noise Ratio (SINR) model for interference, on arbitrary wireless networks without any assumptions on node distributions. The problem becomes much more challenging for this setting, because of the non-locality of the SINR model. Recent work by Moscibroda et al. (IEEE INFOCOM 2006, ACM MobiHoc 2006) has shown that the throughput achieved by using SINR models can differ significantly from that obtained by using graph-based models. In this work, we develop polynomial time algorithms to provably approximate the throughput capacity of wireless network under the SINR model.

Computing morse decompositions for triangulated terrains: an analysis and an experimental evaluation - Vitali,M.; De Floriani, Leila; Magillo,P. (Image Analysis and Processing–ICIAP 2011, 2011)
We consider the problem of extracting the morphology of a terrain discretized as a triangle mesh. We discuss first how to transpose Morse theory to the discrete case in order to describe the morphology of triangulated terrains. We review algorithms for computing Morse decompositions, that we have adapted and implemented for triangulated terrains. We compare the the Morse decompositions produced by them, by considering two different metrics.

Constant-Round Private Function Evaluation with Linear Complexity - Katz, Jonathan; Malka,L. (Advances in Cryptology–ASIACRYPT 2011, 2011)
We consider the problem of private function evaluation (PFE) in the two-party setting. Here, informally, one party holds an input x while the other holds a (circuit describing a) function f; the goal is for one (or both) of the parties to learn f(x) while revealing nothing more to either party. In contrast to the usual setting of secure computation, where the function being computed is known to both parties, PFE is useful in settings where the function (i.e., algorithm) itself must remain secret, e.g., because it is proprietary or classified.It is known that PFE can be reduced to standard secure computation by having the parties evaluate a universal circuit, and this is the approach taken in most prior work. Using a universal circuit, however, introduces additional overhead and results in a more complex implementation. We show here a completely new technique for PFE that avoids universal circuits, and results in constant-round protocols with communication/computational complexity linear in the size of the circuit computing f. This gives the first constant-round protocol for PFE with linear complexity (without using fully homomorphic encryption), even restricted to semi-honest adversaries.

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.

Cross Language Entity Linking - McNamee,Paul; Mayfield,James; Lawrie,Dawn; Oard, Douglas; David Doermann (IJCNLP: International Joint Conference on Natural Language Processing, 2011)
There has been substantial recent interest in aligning mentions of named entities in unstructured texts to knowledge base descriptors, a task commonly called entity linking. This technology is crucial for applications in knowledge discovery and text data mining. This paper presents experiments in the new problem of cross language entity linking, where documents and named entities are in a different language than that used for the content of the reference knowledge base. We have created a new test collection to evaluate cross-language entity linking performance in twenty-one languages. We present experiments that examine issues such as: the importance of transliteration; the utility of cross-language information retrieval; and, the potential benefit of multilingual named entity recognition. Our best model achieves performance which is 94% of a strong monolingual baseline.

Cross-Language Entity Linking in Maryland during a Hurricane - McNamee,Paul; Mayfield,James; Oard, Douglas; David Doermann; Xu,Tan; Wu,Ke (TAC, 2011)
Our team from the JHUHLTCOE and the University of Maryland submitted runs for all three variants of the TACKBP entity linking task. For the monolingual tasks, we essentially mirrored our HLTCOETAC-KBP 2010 submission, making only modest changes to accommodate differences in 2011, namely the requirement to cluster NIL responses, and the change in evaluation measure. However, our work on the cross-lingual task was significantly more involved, requiring development of robust, multiphased transliteration software, use of techniques in cross-language information retrieval, and reliance on a Chinese-to- English statistical machine translation system. In this paper we describe our work for the 2011 evaluation and the results we obtained.

Declarative analysis of noisy information networks - Moustafa,W. E; Namata,G.; Deshpande, Amol; Getoor, Lise (2011 IEEE 27th International Conference on Data Engineering Workshops (ICDEW), 2011)
There is a growing interest in methods for analyzing data describing networks of all types, including information, biological, physical, and social networks. Typically the data describing these networks is observational, and thus noisy and incomplete; it is often at the wrong level of fidelity and abstraction for meaningful data analysis. This has resulted in a growing body of work on extracting, cleaning, and annotating network data. Unfortunately, much of this work is ad hoc and domain-specific. In this paper, we present the architecture of a data management system that enables efficient, declarative analysis of large-scale information networks. We identify a set of primitives to support the extraction and inference of a network from observational data, and describe a framework that enables a network analyst to easily implement and combine new extraction and analysis techniques, and efficiently apply them to large observation networks. The key insight behind our approach is to decouple, to the extent possible, (a) the operations that require traversing the graph structure (typically the computationally expensive step), from (b) the operations that do the modification and update of the extracted network. We present an analysis language based on Datalog, and show how to use it to cleanly achieve such decoupling. We briefly describe our prototype system that supports these abstractions. We include a preliminary performance evaluation of the system and show that our approach scales well and can efficiently handle a wide spectrum of data cleaning operations on network data.
Keywords: Cleaning; Data analysis; data cleaning operations; data management system; data mining; Databases; Datalog; declarative analysis; graph structure; information networks; Noise measurement; noisy information networks; Prediction algorithms; semantics; Syntactics

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

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

Discrete Curvature Estimators: an Experimental Evaluation - Mesmoudi,M. M.; De Floriani, Leila; Magillo,P. (Department of Computer Science and Information Science, University of Genoa, 2011)
In this paper, we consider a surface, embedded in 3D space, which is discretely approximatedas triangle mesh. We define a method for estimating mean and Gaussian curvatures of such a discrete surface, based on simulating the analytic definition of mean and Gaussian curvatures in the continuum. Such method leads to what we call mean and Gaussian Ccurvatures. We present experiments evaluating such curvatures.

A Dive into Online Community Properties - Wagstrom, Patrick; Martino, Jacquelyn; von Kaenel, Juerg; Marshini Chetty; Thomas, John; Jones, Lauretta (CSCW '11, 2011)
As digital communities grow in size their feature sets also grow with them. Different users have different experiences with the same tools and communities. Enterprises and other organizations seeking to leverage these communities need a straightforward way to analyze and compare a variety of salient attributes of these communities. We describe a taxonomy and tool for crowd-sourcing user based evaluations of enterprise relevant attributes of digital communities and present the results of a small scale study on its usefulness and stability across multiple raters.
Keywords: enterprise; Online communities; Taxonomy; Visualization

Do You Know Where Your Data Are? Secure Data Capsules for Deployable Data Protection - Maniatis, P.; Akhawe, D.; Fall,K.; Elaine Shi; McCamant, S.; Song,D. (2011)

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

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

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

Energy efficient monitoring in sensor networks - Deshpande, Amol; Khuller, Samir; Malekian,A.; Toossi,M. (Algorithmica, 2011)
We study a set of problems related to efficient battery energy utilization for monitoring applications in a wireless sensor network with the goal to increase the sensor network lifetime. We study several generalizations of a basic problem called Set k-Cover. The problem can be described as follows: we are given a set of sensors, and a set of targets to be monitored. Each target can be monitored by a subset of the sensors. To increase the lifetime of the sensor network, we would like to partition the sensors into k sets (or time-slots), and activate each set of sensors in a different time-slot, thus extending the battery life of the sensors by a factor of k. The goal is to find a partitioning that maximizes the total coverage of the targets for a given k. This problem is known to be NP-hard. We develop an improved approximation algorithm for this problem using a reduction to Max k-Cut. Moreover, we are able to demonstrate that this algorithm is efficient, and yields almost optimal solutions in practice.We also consider generalizations of this problem in several different directions. First, we allow each sensor to be active in α different sets (time-slots). This means that the battery life is extended by a factor of k, and allows for a richer space of solutions. We also consider different coverage requirements, such as requiring that all targets, or at least a certain number of targets, be covered in each time slot. In the Set k-Cover formulation, there is no requirement that a target be monitored at all, or in any number of time slots. We develop a randomized rounding algorithm for this problem. We also consider extensions where each sensor can monitor only a bounded number of targets in any time-slot, and not all the targets adjacent to it. This kind of problem may arise when a sensor has a directional camera, or some other physical constraint might prevent it from monitoring all adjacent targets even when it is active. We develop the first approximation algorithms for this problem.

Exploiting statistical and relational information on the web and in social media - Getoor, Lise; Mihalkova,Lilyana (Proceedings of the fourth ACM international conference on Web search and data mining, 2011)
The popularity of Web 2.0, characterized by a proliferation of social media sites, and Web 3.0, with more richly semantically annotated objects and relationships, brings to light a variety of important prediction, ranking, and extraction tasks. The input to these tasks is often best seen as a (noisy) multi-relational graph, such as the click graph, defined by user interactions with Web sites; and the social graph, defined by friendships and affiliations on social media sites. This tutorial will provide an overview of statistical relational learning and inference techniques, motivating and illustrating them using web and social media applications. We will start by briefly surveying some of the sources of statistical and relational information on the web and in social media and will then dedicate most of the tutorial time to an introduction to representations and techniques for learning and reasoning with multi-relational information, viewing them through the lens of web and social media domains. We will end with a discussion of current trends and related fields, such as privacy in social networks.
Keywords: graph analysis; probabilistic inference; query log data; social media; statistical relational learning

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

A family of abstract interpretations for static analysis of concurrent higher-order programs - Might, Matthew; David Van Horn (arXiv:1103.5167 [cs], 2011)
We develop a framework for computing two foundational analyses for concurrent higher-order programs: (control-)flow analysis (CFA) and may-happen-in-parallel analysis (MHP). We pay special attention to the unique challenges posed by the unrestricted mixture of first-class continuations and dynamically spawned threads. To set the stage, we formulate a concrete model of concurrent higher-order programs: the P(CEK*)S machine. We find that the systematic abstract interpretation of this machine is capable of computing both flow and MHP analyses. Yet, a closer examination finds that the precision for MHP is poor. As a remedy, we adapt a shape analytic technique-singleton abstraction-to dynamically spawned threads (as opposed to objects in the heap). We then show that if MHP analysis is not of interest, we can substantially accelerate the computation of flow analysis alone by collapsing thread interleavings with a second layer of abstraction.
Comment: The 18th International Static Analysis Symposium (SAS 2011)
Keywords: Computer Science - Programming Languages

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

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

GUI Interaction Testing: Incorporating Event Context - Xun Yuan; Cohen,M. B; Memon, Atif M. (Software Engineering, IEEE Transactions on, 2011)
Graphical user interfaces (GUIs), due to their event-driven nature, present an enormous and potentially unbounded way for users to interact with software. During testing, it is important to #x201C;adequately cover #x201D; this interaction space. In this paper, we develop a new family of coverage criteria for GUI testing grounded in combinatorial interaction testing. The key motivation of using combinatorial techniques is that they enable us to incorporate #x201C;context #x201D; into the criteria in terms of event combinations, sequence length, and by including all possible positions for each event. Our new criteria range in both efficiency (measured by the size of the test suite) and effectiveness (the ability of the test suites to detect faults). In a case study on eight applications, we automatically generate test cases and systematically explore the impact of context, as captured by our new criteria. Our study shows that by increasing the event combinations tested and by controlling the relative positions of events defined by the new criteria, we can detect a large number of faults that were undetectable by earlier techniques.
Keywords: automatic test case generation; automatic test pattern generation; combinatorial interaction testing; event driven nature; graphical user interface; Graphical user interfaces; GUI interaction testing; program testing

Homage to Michael Gelfond on His 65 th Birthday - Minker, Jack (Logic programming, knowledge representation, and nonmonotonic reasoning, 2011)
Michael Gelfond is one of the world leading scientists in the field of logic programming and nonmonotonic reasoning. This essay covers several aspects of Michael’s personal life, starting from his birth in the USSR, through his experiences in the USSR up to the time he emigrated to the United States (U.S.). This is followed by his first experiences in the U.S.: how he became involved in logic programming and nonmonotonic reasoning and some of his major scientific achievements. Michael is a warm, generous person, and I discuss his impact on some colleagues and students. In the concluding section, I observe that starting his career with impediments in the FSU, he overcame them to become one of the top computer scientists in logic programming and nonmonotonic reasoning.

Illumination Recovery From Image With Cast Shadows Via Sparse Representation - Mei,Xue; Ling,Haibin; Jacobs, David W. (Image Processing, IEEE Transactions on, 2011)
In this paper, we propose using sparse representation for recovering the illumination of a scene from a single image with cast shadows, given the geometry of the scene. The images with cast shadows can be quite complex and, therefore, cannot be well approximated by low-dimensional linear subspaces. However, it can be shown that the set of images produced by a Lambertian scene with cast shadows can be efficiently represented by a sparse set of images generated by directional light sources. We first model an image with cast shadows composed of a diffusive part (without cast shadows) and a residual part that captures cast shadows. Then, we express the problem in an #x2113;1-regularized least-squares formulation, with nonnegativity constraints (as light has to be non-negative at any point in space). This sparse representation enjoys an effective and fast solution thanks to recent advances in compressive sensing. In experiments on synthetic and real data, our approach performs favorably in comparison with several previously proposed methods.
Keywords: #x2113; 1-regularized; approximations; coding; image; compression; image; constraints; sparse; formulation; Lambertian; illumination; image; least-square; light; linear; reconstruction; image; recovery; low-dimensional; representation; data; representation; least; scene; cast; sensing; directional; shadows; compressive; sources; image; squares; subspaces; nonnegativity

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

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

Improving Classifier Performance by Autonomously Collecting Background Knowledge from the Web - Minton,S.N.; Michelson,M.; See,K.; Macskassy,S.; Gazen,B.C.; Getoor, Lise (2011 10th International Conference on Machine Learning and Applications Workshops, 2011)
Many websites allow users to tag data items to makethem easier to find. In this paper we consider the problem of classifying tagged data according to user-specified interests. We present an approach for aggregating background knowledge from the Web to improve the performance of a classier. In previous work, researchers have developed technology for extracting knowledge, in the form of relational tables, from semi- structured websites. In this paper we integrate this extraction technology with generic machine learning algorithms, showing that knowledge extracted from the Web can significantly benefit the learning process. Specifically, the knowledge can lead to better generalizations, reduce the number of samples required for supervised learning, and eliminate the need to retrain the system when the environment changes. We validate the approach with an application that classifies tagged Fickr data.

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

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

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

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

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

Learning statistical models from relational data - Getoor, Lise; Mihalkova,Lilyana (Proceedings of the 2011 international conference on Management of data, 2011)
Statistical Relational Learning (SRL) is a subarea of machine learning which combines elements from statistical and probabilistic modeling with languages which support structured data representations. In this survey, we will: 1) provide an introduction to SRL, 2) describe some of the distinguishing characteristics of SRL systems, including relational feature construction and collective classification, 3) describe three SRL systems in detail, 4) discuss applications of SRL techniques to important data management problems such as entity resolution, selectivity estimation, and information integration, and 5) discuss connections between SRL methods and existing database research such as probabilistic databases.
Keywords: machine learning; probabilistic graphical models; statistical relational learning

Learning to predict web collaborations - Mihalkova,L.; Moustafa,W.; Getoor, Lise (Workshop on User Modeling for Web Applications (UMWA-11), 2011)
Much of the knowledge available on the web today comes asa result of fruitful collaborations among large groups of peo- ple. One of the most striking examples of successful web col- laboration is the online encyclopedia Wikipedia. The web is used as a collaboration platform by highly specialized blog- ging communities and by the scientific community. An im- portant reason for the richness of content generated through web collaborations is that the participants in such collabo- rations are not constrained by geographic location. Thus, like-minded individuals from across the world can join their efforts. This also means, however, that web collaborators of- ten do not know each other, and, thus, finding collaborators on the web is more difficult than it is with more traditional forms of collaboration that are initiated based on acquain- tance. This difficulty is further exacerbated by the fact that web collaborations tend to be more dynamic as participants join and abandon communities. We consider the task of rec- ommending project-specific potential collaborators to web users and propose an approach that is based on statistical relational learning. Our proposed model thus has the ad- vantages that it can include complex features composed of multiple properties and relationships of the entities, it can handle the high levels of noise and uncertainty inherent in user actions, and it allows for joint decision-making, which leads to more accurate predictions. To ensure scalability, our model is trained in an online fashion. We demonstrate the effectiveness of our approach on a data set collected from Wikipedia.

Machine Translation Evaluation and Optimization - Dorr, Bonnie J; Olive,Joseph; McCary,John; Christianson,Caitlin (Handbook of Natural Language Processing and Machine TranslationHandbook of Natural Language Processing and Machine Translation, 2011)
The evaluation of machine translation (MT) systems is a vital field of research, both for determining the effectiveness of existing MT systems and for optimizing the performance of MT systems. This part describes a range of different evaluation approaches used in the GALE community and introduces evaluation protocols and methodologies used in the program. We discuss the development and use of automatic, human, task-based and semi-automatic (human-in-the-loop) methods of evaluating machine translation, focusing on the use of a human-mediated translation error rate HTER as the evaluation standard used in GALE. We discuss the workflow associated with the use of this measure, including post editing, quality control, and scoring. We document the evaluation tasks, data, protocols, and results of recent GALE MT Evaluations. In addition, we present a range of different approaches for optimizing MT systems on the basis of different measures. We outline the requirements and specific problems when using different optimization approaches and describe how the characteristics of different MT metrics affect the optimization. Finally, we describe novel recent and ongoing work on the development of fully automatic MT evaluation metrics that have the potential to substantially improve the effectiveness of evaluation and optimization of MT systems.

Materializing multi-relational databases from the web using taxonomic queries - Michelson,Matthew; Macskassy,Sofus A.; Minton,Steven N.; Getoor, Lise (Proceedings of the fourth ACM international conference on Web search and data mining, 2011)
Recently, much attention has been given to extracting tables from Web data. In this problem, the column definitions and tuples (such as what "company" is headquartered in what "city,") are extracted from Web text, structured Web data such as lists, or results of querying the deep Web, creating the table of interest. In this paper, we examine the problem of extracting and discovering multiple tables in a given domain, generating a truly multi-relational database as output. Beyond discovering the relations that define single tables, our approach discovers and leverages "within column" set membership relations, and discovers relations across the extracted tables (e.g., joins). By leveraging within-column relations our method can extract table instances that are ambiguous or rare, and by discovering joins, our method generates truly multi-relational output. Further, our approach uses taxonomic queries to bootstrap the extraction, rather than the more traditional "seed instances." Creating seeds often requires more domain knowledge than taxonomic queries, and previous work has shown that extraction methods may be sensitive to which input seeds they are given. We test our approach on two real world domains: NBA basketball and cancer information. Our results demonstrate that our approach generates databases of relevant tables from disparate Web information, and discovers the relations between them. Further, we show that by leveraging the "within column" relation our approach can identify a significant number of relevant tuples that would be difficult to do so otherwise.
Keywords: discovering multi-relational data; multirelational data

Maximum bipartite flow in networks with adaptive channel width - Azar,Yossi; Mądry,Aleksander; Moscibroda,Thomas; Panigrahi,Debmalya; Srinivasan, Aravind (Theoretical Computer Science, 2011)
Traditionally, network optimization problems assume that each link in the network has a fixed capacity. Recent research in wireless networking has shown that it is possible to design networks where the capacity of the links can be changed adaptively to suit the needs of specific applications. In particular, one gets a choice of having a few high capacity outgoing links or many low capacity ones at any node of the network. This motivates us to have a re-look at classical network optimization problems and design algorithms to solve them in this new framework. In particular, we consider the problem of maximum bipartite flow, which has been studied extensively in the fixed-capacity network model. One of the motivations for studying this problem arises from the need to maximize the throughput of an infrastructure wireless network comprising base-stations (one set of vertices in the bipartition) and clients (the other set of vertices in the bipartition). We show that this problem has a significantly different combinatorial structure in this new network model from the fixed-capacity one. While there are several polynomial time algorithms for the maximum bipartite flow problem in traditional networks, we show that the problem is NP-hard in the new model. In fact, our proof extends to showing that the problem is APX-hard. We complement our lower bound by giving two algorithms for solving the problem approximately. The first algorithm is deterministic and achieves an approximation factor of O ( log N ) , where N is the number of nodes in the network, while the second algorithm is randomized and achieves an approximation factor of e e − 1 .
Keywords: Adaptive channel width; graph algorithm; Linear program rounding; Maximum flow; Wireless networks

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

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

Method and System for Dereverberation of Signals Propagating in ... - O'donovan,Adam; Duraiswami, Ramani; Zotkin,Dmitry N (2011)
The dereverberation of signals in reverberating environments is carried out via acquiring the representation (image) of spatial distribution of the signals in space of interest and automatic identification of reflections of the source signal in the reverberative space. The technique relies on identification of prominent features at the image, as well as corresponding directions of propagation of signals manifested by the prominent features at the image, and computation of similarity metric between signals corresponding to the prominent features in the image. The time delays between the correlated signals (i.e., source signal and related reflections) are found and the signals are added coherently. Multiple beamformers operate on the source signal and corresponding reflections, enabling one to improve the signal-to-noise ratio in multi-path environments.

Method and system for markerless motion capture using multiple cameras - Sundaresan,Aravind; Chellapa, Rama (2011)
Completely automated end-to-end method and system for markerless motion capture performs segmentation of articulating objects in Laplacian Eigenspace and is applicable to handling of the poses of some complexity. 3D voxel representation of acquired images are mapped to a higher dimensional space (k), where k depends on the number of articulated chains of the subject body, so as to extract the 1-D representations of the articulating chains. A bottom-up approach is suggested in order to build a parametric (spline-based) representation of a general articulated body in the high dimensional space followed by a top-down probabilistic approach that registers the segments to an average human body model. The parameters of the model are further optimized using the segmented and registered voxels.

MOMMIE Knows Best: Systematic Optimizations for Verifiable Distributed Algorithms - Maniatis, Petros; Dietz, Michael; Charalampos Papamanthou (HotOS'13 Proceedings of the 13th USENIX Conference on Hot Topics in Operating Systems, 2011)

Multi-agent event recognition in structured scenarios - Morariu,V.I.; Davis, Larry S. (Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on, 2011)
We present a framework for the automatic recognition of complex multi-agent events in settings where structure is imposed by rules that agents must follow while performing activities. Given semantic spatio-temporal descriptions of what generally happens (i.e., rules, event descriptions, physical constraints), and based on video analysis, we determine the events that occurred. Knowledge about spatio-temporal structure is encoded using first-order logic using an approach based on Allen's Interval Logic, and robustness to low-level observation uncertainty is provided by Markov Logic Networks (MLN). Our main contribution is that we integrate interval-based temporal reasoning with probabilistic logical inference, relying on an efficient bottom-up grounding scheme to avoid combinatorial explosion. Applied to one-on-one basketball, our framework detects and tracks players, their hands and feet, and the ball, generates event observations from the resulting trajectories, and performs probabilistic logical inference to determine the most consistent sequence of events. We demonstrate our approach on 1hr (100,000 frames) of outdoor videos.
Keywords: Allen; analysis; Markov; descriptions; video; event; grounding; inference; semantic; interval; Logic; logic; interval-based; logic; Markov; logic; multi-agent; logical; networks; bottom-up; processes; formal; processing; reasoning; multiagent; reasoning; video; recognition; probabilistic; recognition; temporal; scheme; first-order; signal; spatio-temporal; systems; object; temporal

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

Overview of the FIRE 2011 RISOTTask - Garain,Utpal; Paik,Jiaul; Pal,Tamaltaru; Majumder,Prasenjit; David Doermann; Oard, Douglas (FIRE, 2011)
RISOT was a pilot task in FIRE 2011 which focused on the retrieval of automatically recognized text from machine printed sources. The collection used for search was a subset of the FIRE 2008 and 2010 Bengali test collections that contained 92 topics and 62,825 documents. Two teams participated, submitting a total of 11 monolingual runs.

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

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

Privacy settings from contextual attributes: A case study using Google Buzz - Mashima, D.; Elaine Shi; Chow, R.; Sarkar, P.; Li,C.; Song,D. (2011)
Social networks provide users with privacy settings to control what information is shared with connections and other users. In this paper, we analyze factors influencing changes in privacy-related settings in the Google Buzz social network. Specifically, we show statistics on contextual data related to privacy settings that are derived from crawled datasets and analyze the characteristics of users who changed their privacy settings. We also investigate potential neighboring effects among such users.
Keywords: contextual attributes; data privacy; Google Buzz; privacy settings; social networking (online); social networks; Statistics

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

A robust and rotationally invariant local surface descriptor with applications to non-local mesh processing - Maximo, A.; Patro,R.; Varshney, Amitabh; Farias, R. (Graphical Models, 2011)
In recent years, we have witnessed a striking increase in research concerning how to describe a meshed surface. These descriptors are commonly used to encode mesh properties or guide mesh processing, not to augment existing computations by replication. In this work, we first define a robust surface descriptor based on a local height field representation, and present a transformation via the extraction of Zernike moments. Unlike previous work, our local surface descriptor is innately rotationally invariant. Second, equipped with this novel descriptor, we present SAMPLE – similarity augmented mesh processing using local exemplars – a method which uses feature neighbourhoods to propagate mesh processing done in one part of the mesh, the local exemplar, to many others. Finally, we show that SAMPLE can be used in a number of applications, such as detail transfer and parameterization.
Keywords: Local descriptors; Non-local mesh processing; shape analysis; Similarity processing

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

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

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

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

Smale-like decomposition and forman theory for discrete scalar fields - Čomić,L.; Mesmoudi,M.; De Floriani, Leila (Discrete Geometry for Computer Imagery, 2011)
Forman theory, which is a discrete alternative for cell complexes to the well-known Morse theory, is currently finding several applications in areas where the data to be handled are discrete, such as image processing and computer graphics. Here, we show that a discrete scalar field f, defined on the vertices of a triangulated multidimensional domain Σ, and its gradient vector field Grad f through the Smale-like decomposition of f [6], are both the restriction of a Forman function F and its gradient field Grad F that extends f over all the simplexes of Σ. We present an algorithm that gives an explicit construction of such an extension. Hence, the scalar field f inherits the properties of Forman gradient vector fields and functions from field Grad F and function F.

Smart task-driven video collection - Lim,Ser-Nam; Mittal,Anurag; Davis, Larry S. (2011)
A multi-camera system that collects images and videos of moving objects in dynamic and crowded scenes, subject to task constraints is disclosed. The system constructs “task visibility intervals” comprising information about what can be sensed in future time intervals. Methods for constructing these intervals applying prediction of future object motion and including consideration of factors such as object occlusion and camera control parameters are also disclosed. Using a plane-sweep algorithm, these atomic intervals can be combined in a method to form multi-task intervals, during which a single camera can collect videos suitable for multiple tasks simultaneously. Methods for fast camera scheduling that yield solutions within a small constant factor of an optimal solution are also disclosed.

Systematic Abstraction of Abstract Machines - David Van Horn; Might, Matthew (arXiv:1107.3539 [cs], 2011)
We describe a derivational approach to abstract interpretation that yields novel and transparently sound static analyses when applied to well-established abstract machines for higher-order and imperative programming languages. To demonstrate the technique and support our claim, we transform the CEK machine of Felleisen and Friedman, a lazy variant of Krivine's machine, and the stack-inspecting CM machine of Clements and Felleisen into abstract interpretations of themselves. The resulting analyses bound temporal ordering of program events; predict return-flow and stack-inspection behavior; and approximate the flow and evaluation of by-need parameters. For all of these machines, we find that a series of well-known concrete machine refactorings, plus a technique of store-allocated continuations, leads to machines that abstract into static analyses simply by bounding their stores. We demonstrate that the technique scales up uniformly to allow static analysis of realistic language features, including tail calls, conditionals, side effects, exceptions, first-class continuations, and even garbage collection. In order to close the gap between formalism and implementation, we provide translations of the mathematics as running Haskell code for the initial development of our method.
Keywords: Computer Science - Programming Languages

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

Towards incremental component compatibility testing - Yoon,I.; Sussman, Alan; Memon, Atif M.; Porter, Adam (Proceedings of the 14th international ACM Sigsoft symposium on Component based software engineering, CBSE, 2011)
Software components are increasingly assembled from othercomponents. Each component may further depend on oth- ers, and each may have multiple active versions. The to- tal number of configurations—combinations of components and their versions—deployed by end users can be very large. Component developers, therefore, spend considerable time and effort doing compatibility testing – determining whether their components can be built correctly for all deployed con- figurations. In previous work we developed Rachet to sup- port large-scale compatibility testing of components. In this paper, we describe and evaluate methods to enable Rachet to perform incremental compatibility testing. We de- scribe algorithms to compute differences in component com- patibilities between current and previous component builds, a formal test adequacy criterion based on covering the differ- ences, and cache-aware configuration sampling and testing methods that attempt to reuse effort from previous testing sessions. We evaluate our approach using the 5-year evo- lution history of a scientific middleware component. Our results show significant performance improvements over Ra- chet’s previous retest-all approach, making the process of compatibility testing practical for evolving components.

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.

Understanding actor loyalty to event-based groups in affiliation networks - Sharara,H.; Singh,L.; Getoor, Lise; Mann,J. (Social Network Analysis and Mining, 2011)
In this paper, we introduce a method for analyzing the temporal dynamics of affiliation networks. We define affiliation groups which describe temporally related subsets of actors and describe an approach for exploring changing memberships in these affiliation groups over time. To model the dynamic behavior in these networks, we consider the concept of loyalty and introduce a measure that captures an actor’s loyalty to an affiliation group as the degree of ‘commitment’ an actor shows to the group over time. We evaluate our measure using three real world affiliation networks: a publication network, a senate bill cosponsorship network, and a dolphin network. The results show the utility of our measure for analyzing the dynamic behavior of actors and quantifying their loyalty to different time-varying affiliation groups.

Universally composable synchronous computation - Katz, Jonathan; Maurer,U.; Tackmann,B.; Zikas,V. (Cryptology ePrint Archive, Report 2011/310, 2011. http://eprint. iacr. org, 2011)
In synchronous networks, protocols can achieve security guarantees that are not possible in an asynchronousworld: i.e., they can simultaneously achieve input completeness (all honest parties’ inputs are included in the computation) and guaranteed termination (honest parties do not “hang” indefinitely). In practice truly syn- chronous networks rarely exist, but synchrony can be emulated if channels have (known) latency and parties have loosely synchronized clocks. The framework of universal composability (UC) is inherently asynchronous, but several approaches for adding synchrony to the framework have been proposed. However, we show that the existing proposals do not provide the expected guarantees. Given this, we propose a “clean slate” approach to defining synchrony in the UC framework by introducing functionalities exactly meant to model, respectively, bounded-delay networks and loosely synchronized clocks. We show that the expected guarantees of synchronous computation can be realized given these functionalities, and that previous models can all be expressed within our new framework.

Usability and Accessibility in Consumer Health Informatics: Current Trends and Future Challenges - Goldberg,Larry; Lide,Bettijoyce; Lowry,Svetlana; Massett,Holly A.; O'Connell,Trisha; Preece,Jennifer; Quesenbery,Whitney; Shneiderman, Ben (American Journal of Preventive Medicine, 2011)
It is a truism that, for innovative eHealth systems to have true value and impact, they must first and foremost be usable and accessible by clinicians, consumers, and other stakeholders. In this paper, current trends and future challenges in the usability and accessibility of consumer health informatics will be described. Consumer expectations of their healthcare providers and healthcare records in this new era of consumer-directed care will be explored, and innovative visualizations, assistive technologies, and other ways that healthcare information is currently being provided and/or shared will be described. Challenges for ensuring the usability of current and future systems will also be discussed. An innovative model for conducting systematic, timely, user-centered research on consumer-facing websites at the National Cancer Institute (NCI) and the ongoing efforts at the National Institute of Standards and Technology (NIST) to promote health information technology (HIT) usability standards and evaluation criteria will also be presented.

Variable remapping of images from very different sources - Wei Zhang; Yanlin Guo; Meth, R.; Sokoloff, H.; Pope, A.; Strat, T.; Chellapa, Rama (2011 18th IEEE International Conference on Image Processing (ICIP), 2011)
We present a system which registers image sequences acquired by very different sources, so that multiple views could be transformed to the same coordinates system. This enables the functionality of automatic object identification and confirmation across views and platforms. The capability of the system comes from three ingredients: 1) image context enlargement through temporal integration; 2) robust motion estimation using the G-RANSAC framework with a relaxed correspondence criteria; 3) constrained motion estimation within the G-RANSAC framework. The proposed system has worked successfully on thousands of frames from multiple collections with significant variations in scale and resolution.
Keywords: automatic object identification; Buildings; CAMERAS; Conferences; constrained motion estimation; coordinates system; Estimation; G-RANSAC framework; image context enlargement; Image Enhancement; image registration; image sequence registration; Image sequences; Motion estimation; Robustness; temporal integration; variable image remapping

Visual Exploration across Biomedical Databases - Lieberman,M.D.; Taheri, S.; Guo,Huimin; Mirrashed,F.; Yahav,I.; Aris,A.; Shneiderman, Ben (IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011)
Though biomedical research often draws on knowledge from a wide variety of fields, few visualization methods for biomedical data incorporate meaningful cross-database exploration. A new approach is offered for visualizing and exploring a query-based subset of multiple heterogeneous biomedical databases. Databases are modeled as an entity-relation graph containing nodes (database records) and links (relationships between records). Users specify a keyword search string to retrieve an initial set of nodes, and then explore intra- and interdatabase links. Results are visualized with user-defined semantic substrates to take advantage of the rich set of attributes usually present in biomedical data. Comments from domain experts indicate that this visualization method is potentially advantageous for biomedical knowledge exploration.
Keywords: Bioinformatics; Biomedical computing; biomedical databases; cross-database exploration; Data exploration and discovery; Data visualization; database management systems; Databases, Factual; DNA; graph theory; Information Storage and Retrieval; information visualization.; Keyword search; medical computing; natural language processing; Proteins; semantic networks; semantics; sequences; text mining; User-Computer Interface; user-defined semantics; visual databases

Abstracting Abstract Machines - David Van Horn; Might, Matthew (arXiv:1007.4446 [cs], 2010)
We describe a derivational approach to abstract interpretation that yields novel and transparently sound static analyses when applied to well-established abstract machines. To demonstrate the technique and support our claim, we transform the CEK machine of Felleisen and Friedman, a lazy variant of Krivine's machine, and the stack-inspecting CM machine of Clements and Felleisen into abstract interpretations of themselves. The resulting analyses bound temporal ordering of program events; predict return-flow and stack-inspection behavior; and approximate the flow and evaluation of by-need parameters. For all of these machines, we find that a series of well-known concrete machine refactorings, plus a technique we call store-allocated continuations, leads to machines that abstract into static analyses simply by bounding their stores. We demonstrate that the technique scales up uniformly to allow static analysis of realistic language features, including tail calls, conditionals, side effects, exceptions, first-class continuations, and even garbage collection.
Comment: The 15th ACM SIGPLAN International Conference on Functional Programming (ICFP'10), Baltimore, Maryland, September, 2010
Keywords: Computer Science - Programming Languages; F.3.2; F.4.1

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.

Advances in Automated Model-Based System Testing of Software Applications with a GUI Front-End - Memon, Atif M.; Nguyen,Bao N. (Advances in ComputersAdvances in Computers, 2010)
Despite the ubiquity of software applications that employ a graphical-user interface (GUI) front-end, functional system testing of these applications has remained, until recently, an understudied research area. During “GUI testing,” test cases, modeled as sequences of user input events, are created and executed on the software by exercising the GUI's widgets. Because each possible sequence of user events may potentially be a test case and today's GUIs offer enormous flexibility to end-users, in principle, GUI testing requires a prohibitively large number of test cases. Any practical test-case generation technique must sample the vast GUI input space. Existing techniques are largely manual, and hence extremely resource intensive. Several new automated model-based techniques have been developed in the past decade. All these techniques develop, either manually or automatically, a model of the GUI and employ it to generate test cases. This chapter presents the first detailed taxonomy of these techniques. A small GUI application is used as a running example to demonstrate each technique and illustrate its relative strengths and weaknesses.

Aligning Spatio-Temporal Signals on a Special Manifold - Ruonan Li; Chellapa, Rama (Computer Vision – ECCV 2010Computer Vision – ECCV 2010, 2010)
We investigate the spatio-temporal alignment of videos or features/signals extracted from them. Specifically, we formally define an alignment manifold and formulate the alignment problem as an optimization procedure on this non-linear space by exploiting its intrinsic geometry. We focus our attention on semantically meaningful videos or signals, e.g., those describing or capturing human motion or activities, and propose a new formalism for temporal alignment accounting for executing rate variations among realizations of the same video event. By construction, we address this static and deterministic alignment task in a dynamic and stochastic manner: we regard the search for optimal alignment parameters as a recursive state estimation problem for a particular dynamic system evolving on the alignment manifold. Consequently, a Sequential Importance Sampling iteration on the alignment manifold is designed for effective and efficient alignment. We demonstrate the performance on several types of input data that arise in vision problems.

Approximate range searching: The absolute model - da Fonseca,Guilherme D.; Mount, Dave (Computational Geometry, 2010)
Range searching is a well known problem in the area of geometric data structures. We consider this problem in the context of approximation, where an approximation parameter ε > 0 is provided. Most prior work on this problem has focused on the case of relative errors, where each range shape R is bounded, and points within distance ε ⋅ diam ( R ) of the range's boundary may or may not be included. We consider a different approximation model, called the absolute model, in which points within distance ε of the range's boundary may or may not be included, regardless of the diameter of the range. We consider range spaces consisting of halfspaces, Euclidean balls, simplices, axis-aligned rectangles, and general convex bodies. We consider a variety of problem formulations, including range searching under general commutative semigroups, idempotent semigroups, groups, and range emptiness. We show how idempotence can be used to improve not only approximate, but also exact halfspace range searching. Our data structures are much simpler than both their exact and relative model counterparts, and so are amenable to efficient implementation.
Keywords: Absolute model; approximation; Halfbox quadtree; Idempotence; Range searching

Approximation algorithm for the kinetic robust K-center problem - Friedler,Sorelle A.; Mount, Dave (Computational Geometry, 2010)
Two complications frequently arise in real-world applications, motion and the contamination of data by outliers. We consider a fundamental clustering problem, the k-center problem, within the context of these two issues. We are given a finite point set S of size n and an integer k. In the standard k-center problem, the objective is to compute a set of k center points to minimize the maximum distance from any point of S to its closest center, or equivalently, the smallest radius such that S can be covered by k disks of this radius. In the discrete k-center problem the disk centers are drawn from the points of S, and in the absolute k-center problem the disk centers are unrestricted.We generalize this problem in two ways. First, we assume that points are in continuous motion, and the objective is to maintain a solution over time. Second, we assume that some given robustness parameter 0 < t ⩽ 1 is given, and the objective is to compute the smallest radius such that there exist k disks of this radius that cover at least ⌈ t n ⌉ points of S. We present a kinetic data structure (in the KDS framework) that maintains a ( 3 + ε ) -approximation for the robust discrete k-center problem and a ( 4 + ε ) -approximation for the robust absolute k-center problem, both under the assumption that k is a constant. We also improve on a previous 8-approximation for the non-robust discrete kinetic k-center problem, for arbitrary k, and show that our data structure achieves a ( 4 + ε ) -approximation. All these results hold in any metric space of constant doubling dimension, which includes Euclidean space of constant dimension.
Keywords: Approximation algorithms; clustering; kinetic data structures; robust statistics

Articulation-Invariant Representation of Non-planar Shapes - Gopalan,Raghuraman; Turaga,Pavan; Chellapa, Rama (Computer Vision – ECCV 2010Computer Vision – ECCV 2010, 2010)
Given a set of points corresponding to a 2D projection of a non-planar shape, we would like to obtain a representation invariant to articulations (under no self-occlusions). It is a challenging problem since we need to account for the changes in 2D shape due to 3D articulations, viewpoint variations, as well as the varying effects of imaging process on different regions of the shape due to its non-planarity. By modeling an articulating shape as a combination of approximate convex parts connected by non-convex junctions, we propose to preserve distances between a pair of points by (i) estimating the parts of the shape through approximate convex decomposition, by introducing a robust measure of convexity and (ii) performing part-wise affine normalization by assuming a weak perspective camera model, and then relating the points using the inner distance which is insensitive to planar articulations. We demonstrate the effectiveness of our representation on a dataset with non-planar articulations, and on standard shape retrieval datasets like MPEG-7.

Authentication in the clouds: a framework and its application to mobile users - Chow, Richard; Jakobsson, Markus; Masuoka, Ryusuke; Molina,Jesus; Niu, Yuan; Elaine Shi; Song,Zhexuan (ACM, 2010)
Cloud computing is a natural fit for mobile security. Typical handsets have input constraints and practical computational and power limitations, which must be respected by mobile security technologies in order to be effective. We describe how cloud computing can address these issues. Our approach is based on a flexible framework for supporting authentication decisions we call TrustCube (to manage the authentication infrastructure) and on a behavioral authentication approach referred to as implicit authentication (to translate user behavior into authentication scores). The combination results in a new authentication paradigm for users of mobile technologies, one where an appropriate balance between usability and trust can be managed through flexible policies and dynamic tuning.
Keywords: Authentication; Cloud computing; Mobile computing

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

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

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.

Community-based, collaborative testing and analysis - Memon, Atif M.; Porter, Adam; Sussman, Alan (Proceedings of the FSE/SDP workshop on Future of software engineering research, 2010)
This article proposes a research agenda aimed at enabling optimized testing and analysis processes and tools to support component-based software development communities. We hypothesize that de facto communities---sets of projects that provide, maintain and integrate many shared infrastructure components---are commonplace. Currently, community members, often unknown to each other, tend to work in isolation, duplicating work, failing to learn from each other's effort, and missing opportunities to efficiently improve the common infrastructure. We further hypothesize that as software integration continues to become the predominant mode of software development, there will be increasing value in tools and techniques that empower these communities to coordinate and optimize their development efforts, and to generate and broadly share information. Such tools and techniques will greatly improve the robustness, quality and usability of the common infrastructure which, in turn, will greatly reduce the time and effort needed to produce and use the end systems that are the true goal of the entire community.
Keywords: component-based software development communities; testing and analysis

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

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 SENSING SYSTEM AND METHOD FOR BEARING ESTIMATION OF SPARSE SOURCES IN THE ANGLE DOMAIN - Cevher,Volkan; Gurbuz,Ali Cafer; McClellan,James H.; Chellapa, Rama (2010)
Compressive Sensing (CS) is an emerging area which uses a relatively small number of non-traditional samples in the form of randomized projections to reconstruct sparse or com-pressible signals. Direction-of-arrival (DOA) estimation is performed with an array of sensors using CS. Using random projections of the sensor data, along with a full waveform recording on one reference sensor, a sparse angle space scenario can be reconstructed, giving the number of sources and their DOA's. Signal processing algorithms are also developed and described herein for randomly deployable wireless sensor arrays that are severely constrained in communication bandwidth. There is a focus on the acoustic bearing estimation problem and it is shown that when the target bearings are modeled as a sparse vector in the angle space, functions of the low dimensional random projections of the microphone signals can be used to determine multiple source bearings as a solution of an 1]-norm minimization problem.

Confidence-based feature acquisition to minimize training and test costs - desJardins, Marie; MacGlashan,James; Wagstaff,Kiri L (Proceedings of the SIAM Conference on Data Mining, 2010)
We present Confidence-based Feature Acquisition (CFA), a novel supervised learning method for acquiring missing feature values when there is missing data at both training and test time. Previous work has considered the cases of missing data at training time (e.g., Active Feature Acquisition, AFA 8), or at test time (e.g., Cost-Sensitive Naive Bayes, CSNB 2), but not both. At training time, CFA constructs a cascaded ensemble of classifiers, starting with the zero-cost features and adding a single feature for each successive model. For each model, CFA selects a subset of training instances for which the added feature should be acquired. At test time, the set of models is applied sequentially (as a cascade), stopping when a user-supplied confidence threshold is met. We compare CFA to AFA, CSNB, and several other baselines, and find that CFAs accuracy is at least as high as the other methods, while incurring significantly lower feature acquisition costs.

Connecting generations: developing co-design methods for older adults and children - Xie,B.; Druin, Allison; Fails,J.; Massey,S.; Golub,E.; Franckel,S.; Schneider,K. (Behaviour & Information Technology, 2010)

Crowdsourcing the evaluation of a domain-adapted named entity recognition system - Sayeed,Asad B.; Meyer,Timothy J.; Nguyen,Hieu C.; Buzek,Olivia; Weinberg, Amy (Association for Computational Linguistics, 2010)
Named entity recognition systems sometimes have difficulty when applied to data from domains that do not closely match the training data. We first use a simple rule-based technique for domain adaptation. Data for robust validation of the technique is then generated, and we use crowdsourcing techniques to show that this strategy produces reliable results even on data not seen by the rule designers. We show that it is possible to extract large improvements on the target data rapidly at low cost using these techniques.

Data hiding in compiled program binaries for supplementing computer functionality - M. Wu; Swaminathan,Ashwin; Mao,Yinian (2010)
Bit reductions in program instructions are achieved by determining the set of bit patterns in bit locations of the instructions. If only a subset of bit patterns is present in the instructions, they may be represented by an index value having a smaller number of bits. The index value may be substituted into the instruction and later used in decoding by referencing a corresponding bit pattern in a lookup table. The bit-reduction in the instruction makes way for supplemental data bits which may then be embedded.

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

Design, Analysis and Comparison of Spatial Indexes for Tetrahedral Meshes - De Floriani, Leila; Fellegara,R.; Magillo,P. (Department of Computer Science and Information Science, University of Genoa, 2010)
We address the problem of performing spatial queries on tetrahedral meshes. These latterarise in several application domains including 3D GIS, scientific visualization, finite element analysis. We have defined and implemented a family of spatial indexes, that we call tetrahedral trees. Tetrahedral trees are based on a subdivision of a cubic domain containing the mesh defined either by an octree or a 3D kd-tree. For each of them, we have four variants of the spatial index, depending on four different subdivision criteria. Here, we present such indexes, we discuss how to construct them and perform classical spatial queries such as point location and window queries. We compare the various tetrahedral trees based in memory usage, performances in spatial queries and computation times for constructing them.

Distributed Implementation of Coordinated, Network-Wide Policies and Protocols with FlowFlex - Mundada,Y.; Sherwood,R.; Feamster, Nick (Georgia Institute of Technology, 2010)
The increasing programmability of network devices gives protocol designers and network operators considerably more flexibility in defining custom protocols and traffic processing functions. Today, network operators and protocol designers have the option of either operating at flow-level granularity, which offers coordinated control; or packet-level granularity, which offers flexibility, but not coordinated control. Today’s network programming paradigms force operators to choose between the fine-grained control and expressiveness of packet processing and the coordination of flow processing, which makes it difficult to quickly realize a distributed implementation of a global, network-wide policy. Designers must also choose between the flexibility of hardware-based solutions and the fast development cycles offered by software. This paper proposes a system called FlowFlex that offers network designers the best of both worlds: with FlowFlex, operators can quickly design, implement, and deploy network systems and protocols that offer fast, distributed, implementations that require coordinated control and fine-grained operations on packets. We present the design and implementation of the FlowFlex framework and show how it can improve both expressiveness and efficiency for three real-world networking applications.

Diversity and distribution of cholix toxin, a novel ADP‐ribosylating factor from Vibrio cholerae - Purdy,Alexandra E.; Balch,Deborah; Lizárraga‐Partida,Marcial Leonardo; Islam,Mohammad Sirajul; Martinez‐Urtaza,Jaime; Huq,Anwar; Rita R Colwell; Bartlett,Douglas H. (Environmental Microbiology Reports, 2010)
Non-toxigenic non-O1, non-O139 Vibrio cholerae strains isolated from both environmental and clinical settings carry a suite of virulence factors aside from cholera toxin. Among V. cholerae strains isolated from coastal waters of southern California, this includes cholix toxin, an ADP-ribosylating factor that is capable of halting protein synthesis in eukaryotic cells. The prevalence of the gene encoding cholix toxin, chxA, was assessed among a collection of 155 diverse V. cholerae strains originating from both clinical and environmental settings in Bangladesh and Mexico and other countries around the globe. The chxA gene was present in 47% of 83 non-O1, non-O139 strains and 16% of 72 O1/O139 strains screened as part of this study. A total of 86 chxA gene sequences were obtained, and phylogenetic analysis revealed that they fall into two distinct clades. These two clades were also observed in the phylogenies of several housekeeping genes, suggesting that the divergence observed in chxA extends to other regions of the V. cholerae genome, and most likely has arisen from vertical descent rather than horizontal transfer. Our results clearly indicate that ChxA is a major toxin of V. cholerae with a worldwide distribution that is preferentially associated with non-pandemic strains.

A dynamic data structure for approximate range searching - Mount, Dave; Park,Eunhui (Proceedings of the 2010 annual symposium on Computational geometry, 2010)
In this paper, we introduce a simple, randomized dynamic data structure for storing multidimensional point sets, called a quadtreap. This data structure is a randomized, balanced variant of a quadtree data structure. In particular, it defines a hierarchical decomposition of space into cells, which are based on hyperrectangles of bounded aspect ratio, each of constant combinatorial complexity. It can be viewed as a multidimensional generalization of the treap data structure of Seidel and Aragon. When inserted, points are assigned random priorities, and the tree is restructured through rotations as if the points had been inserted in priority order. In any fixed dimension d, we show it is possible to store a set of n points in a quadtreap of space O(n). The height h of the tree is O(log n) with high probability. It supports point insertion in time O(h). It supports point deletion in worst-case time O(h2) and expected-case time O(h), averaged over the points of the tree. It can answer ε-approximate spherical range counting queries over groups and approximate nearest neighbor queries in time O(h + (1/ε)d-1).
Keywords: Approximation algorithms; dynamic data structures; geometric data structures; quadtrees; Range searching

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

Efficient kriging for real-time spatio-temporal interpolation - Srinivasan,B.V.; Duraiswami, Ramani; Murtugudde,R. (Proceedings of the 20 th Conference on Probability and Statistics in the Atmospheric Sciences, 2010)
Atmospheric data is often recorded at scattered stationlocations. While the data is generally available over a long period of time it cannot be used directly for extract- ing coherent patterns and mechanistic correlations. The only recourse is to spatially and temporally interpolate the data both to organize the station recording to a reg- ular grid and to query the data for predictions at a par- ticular location or time of interest. Spatio-temporal in- terpolation approaches require the evaluation of weights at each point of interest. A widely used interpolation ap- proach is kriging. However, kriging has a computational cost that scales as the cube of the number of data points N, resulting in cubic time complexity for each point of interest, which leads to a time complexity of O(N4) for interpolation at O(N) points. In this work, we formulate the kriging problem, to first reduce the computational cost to O(N3). We use an iterative solver (Saad, 2003), and further accelerate the solver using fast summation algo- rithms like GPUML (Srinivasan and Duraiswami, 2009) or FIGTREE (Morariu et al., 2008). We illustrate the speedup on synthetic data and compare the performance with other standard kriging approaches to demonstrate substantial improvement in the performance of our ap- proach. We then apply the developed approach on ocean color data from the Chesapeake Bay and present some quantitative analysis of the kriged results.

Efficient Policy-Based Inconsistency Management in Relational Knowledge Bases - Martinez,M. V; Parisi,F.; Pugliese, A.; Simari,G. I; V.S. Subrahmanian (Scalable Uncertainty Management: 4th International Conference, 2010)
Real-world databases are frequently inconsistent. Even though the users who work with a body of data are far more familiar not only with that data, but also their own job and the risks they are willing to take and the inferences they are willing to make from inconsistent data, most DBMSs force them to use the policy embedded in the DBMS. Inconsistency management policies (IMPs) were introduced so that users can apply policies that they deem are appropriate for data they know and understand better than anyone else. In this paper, we develop an efficient “cluster table” method to implement IMPs and show that using cluster tables instead of a standard DBMS index is far more efficient when less than about 3% of a table is involved in an inconsistency (which is hopefully the case in most real world DBs), while standard DBMS indexes perform better when the amount of inconsistency in a database is over 3%.

Electromagnetic Modeling of Ethernet Transformers - Bowen,D.; Mayergoyz, Issak D; Krafft,C. (Magnetics, IEEE Transactions on, 2010)
The unique features of Ethernet transformers are reviewed, and novel testing techniques for identification of lumped parameters of equivalent circuits are presented. To account for the distributed nature of the cross-winding and intrawinding capacitances, novel distributed models for electromagnetic analysis of Ethernet transformers are presented.
Keywords: analysis; electromagnetic; area; capacitances; lumped; circuits; ethernet; circuits; local; cross-winding; distributed; modeling; equivalent; models; electromagnetic; networks; lumped; networks; transformer; parameter; parameters; novel; techniques; capacitance; equivalent; Testing; transformers; intrawinding; windings; transformers

Evolutionary dynamics of U12-type spliceosomal introns - Lin,Chiao-Feng; Mount, Stephen M.; Jarmołowski,Artur; Makałowski,Wojciech (BMC Evolutionary Biology, 2010)
Many multicellular eukaryotes have two types of spliceosomes for the removal of introns from messenger RNA precursors. The major (U2) spliceosome processes the vast majority of introns, referred to as U2-type introns, while the minor (U12) spliceosome removes a small fraction (less than 0.5%) of introns, referred to as U12-type introns. U12-type introns have distinct sequence elements and usually occur together in genes with U2-type introns. A phylogenetic distribution of U12-type introns shows that the minor splicing pathway appeared very early in eukaryotic evolution and has been lost repeatedly.

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

An Experimental Study of Color-Based Segmentation Algorithms Based on the Mean-Shift Concept - Bitsakos,K.; Fermüller, Cornelia; Aloimonos, J. (Computer Vision – ECCV 2010Computer Vision – ECCV 2010, 2010)
We point out a difference between the original mean-shift formulation of Fukunaga and Hostetler and the common variant in the computer vision community, namely whether the pairwise comparison is performed with the original or with the filtered image of the previous iteration. This leads to a new hybrid algorithm, called Color Mean Shift, that roughly speaking, treats color as Fukunaga’s algorithm and spatial coordinates as Comaniciu’s algorithm. We perform experiments to evaluate how different kernel functions and color spaces affect the final filtering and segmentation results, and the computational speed, using the Berkeley and Weizmann segmentation databases. We conclude that the new method gives better results than existing mean shift ones on four standard comparison measures ( improvement on RAND and BDE measures respectively for color images), with slightly higher running times ( ). Overall, the new method produces segmentations comparable in quality to the ones obtained with current state of the art segmentation algorithms.

Expresses-an-opinion-about: using corpus statistics in an information extraction approach to opinion mining - Sayeed,Asad B.; Nguyen,Hieu C.; Meyer,Timothy J.; Weinberg, Amy (Association for Computational Linguistics, 2010)
We present a technique for identifying the sources and targets of opinions without actually identifying the opinions themselves. We are able to use an information extraction approach that treats opinion mining as relation mining; we identify instances of a binary "expresses-an-opinion-about" relation. We find that we can classify source-target pairs as belonging to the relation at a performance level significantly higher than two relevant baselines. This technique is particularly suited to emerging approaches in corpus-based social science which focus on aggregating interactions between sources to determine their effects on socio-economically significant targets. Our application is the analysis of information technology (IT) innovations. This is an example of a more general problem where opinion is expressed using either sub- or supersets of expressive words found in newswire. We present an annotation scheme and an SVM-based technique that uses the local context as well as the corpus-wide frequency of a source-target pair as data to determine membership in "expresses-an-opinion-about". While the presence of conventional subjectivity keywords appears significant in the success of this technique, we are able to find the most domain-relevant keywords without sacrificing recall.

Generating Event Sequence-Based Test Cases Using GUI Runtime State Feedback - Xun Yuan; Memon, Atif M. (Software Engineering, IEEE Transactions on, 2010)
This paper presents a fully automatic model-driven technique to generate test cases for graphical user interfaces (GUIs)-based applications. The technique uses feedback from the execution of a ??seed test suite,?? which is generated automatically using an existing structural event interaction graph model of the GUI. During its execution, the runtime effect of each GUI event on all other events pinpoints event semantic interaction (ESI) relationships, which are used to automatically generate new test cases. Two studies on eight applications demonstrate that the feedback-based technique 1) is able to significantly improve existing techniques and helps identify serious problems in the software and 2) the ESI relationships captured via GUI state yield test suites that most often detect more faults than their code, event, and event-interaction-coverage equivalent counterparts.
Keywords: automatic model driven technique; event interaction coverage equivalent counterparts; event semantic interaction relationships; event sequence based test cases; Graphical user interfaces; GUI runtime state feedback; program testing; Software quality

Generating Phrasal and Sentential Paraphrases: A Survey of Data-Driven Methods - Madnani,Nitin; Dorr, Bonnie J (Computational Linguistics, 2010)
The task of paraphrasing is inherently familiar to speakers of all languages. Moreover, the task of automatically generating or extracting semantic equivalences for the various units of language—words, phrases, and sentences—is an important part of natural language processing (NLP) and is being increasingly employed to improve the performance of several NLP applications. In this article, we attempt to conduct a comprehensive and application-independent survey of data-driven phrasal and sentential paraphrase generation methods, while also conveying an appreciation for the importance and potential use of paraphrases in the field of NLP research. Recent work done in manual and automatic construction of paraphrase corpora is also examined. We also discuss the strategies used for evaluating paraphrase generation techniques and briefly explore some future trends in paraphrase generation.

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

A geometric approach to curvature estimation on triangulated 3D shapes - Mesmoudi,M. M.; De Floriani, Leila; Magillo,P. (Int. Conf. on Computer Graphics Theory and Applications (GRAPP), 2010)
We present a geometric approach to define discrete normal, principal, Gaussian and mean curvatures, thatwe call Ccurvature. Our approach is based on the notion of concentrated curvature of a polygonal line and a simulation of rotation of the normal plane of the surface at a point. The advantages of our approach is its simplicity and its natural meaning. A comparison with widely-used discrete methods is presented.

GUI testing using computer vision - Chang,Tsung-Hsiang; Tom Yeh; Miller,Robert C. (Proceedings of the 28th international conference on Human factors in computing systems, 2010)
Testing a GUI's visual behavior typically requires human testers to interact with the GUI and to observe whether the expected results of interaction are presented. This paper presents a new approach to GUI testing using computer vision for testers to automate their tasks. Testers can write a visual test script that uses images to specify which GUI components to interact with and what visual feedback to be observed. Testers can also generate visual test scripts by demonstration. By recording both input events and screen images, it is possible to extract the images of components interacted with and the visual feedback seen by the demonstrator, and generate a visual test script automatically. We show that a variety of GUI behavior can be tested using this approach. Also, we show how this approach can facilitate good testing practices such as unit testing, regression testing, and test-driven development.
Keywords: gui automation; GUI testing; test by demonstration

Identification of Pathogenic Vibrio Species by Multilocus PCR-Electrospray Ionization Mass Spectrometry and Its Application to Aquatic Environments of the Former Soviet Republic of Georgia - Whitehouse,Chris A.; Baldwin,Carson; Sampath,Rangarajan; Blyn,Lawrence B.; Melton,Rachael; Li,Feng; Hall,Thomas A.; Harpin,Vanessa; Matthews,Heather; Tediashvili,Marina; Jaiani,Ekaterina; Kokashvili,Tamar; et al. (Applied and Environmental MicrobiologyAppl. Environ. Microbiol., 2010)
The Ibis T5000 is a novel diagnostic platform that couples PCR and mass spectrometry. In this study, we developed an assay that can identify all known pathogenic Vibrio species and field-tested it using natural water samples from both freshwater lakes and the Georgian coastal zone of the Black Sea. Of the 278 total water samples screened, 9 different Vibrio species were detected, 114 (41%) samples were positive for V. cholerae, and 5 (0.8%) samples were positive for the cholera toxin A gene (ctxA). All ctxA-positive samples were from two freshwater lakes, and no ctxA-positive samples from any of the Black Sea sites were detected.

Image classification of vascular smooth muscle cells - Grasso,Michael A.; Mokashi,Ronil; Dalvi,Darshana; Cardone, Antonio; Dima,Alden A.; Bhadriraju,Kiran; Plant,Anne L.; Brady,Mary; Yesha,Yaacov; Yesha,Yelena (Proceedings of the 1st ACM International Health Informatics Symposium, 2010)
Keywords: cell biology; digital image processing; machine learning

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

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

Iterative execution-feedback model-directed GUI testing - Xun Yuan; Memon, Atif M. (Information and Software Technology, 2010)
Current fully automatic model-based test-case generation techniques for GUIs employ a static model. Therefore they are unable to leverage certain state-based relationships between GUI events (e.g., one enables the other, one alters the other’s execution) that are revealed at run-time and non-trivial to infer statically. We present ALT – a new technique to generate GUI test cases in batches. Because of its “alternating” nature, ALT enhances the next batch by using GUI run-time information from the current batch. An empirical study on four fielded GUI-based applications demonstrated that ALT was able to detect new 4- and 5-way GUI interaction faults; in contrast, previous techniques, due to their requirement of too many test cases, were unable to even test 4- and 5-way GUI interactions.
Keywords: event-driven software; event-flow graphs; GUI testing; model-based testing; test-case generation

Joint analysis of network incidents and intradomain routing changes - Medem,A.; Teixeira,R.; Feamster, Nick; Meulle,M. (Network and Service Management (CNSM), 2010 International Conference on, 2010)
This paper studies how intradomain routing instability relates to events in network trouble tickets for two networks: a VPN provider and the Internet2 backbone network. Our goal in performing this joint analysis of routing and trouble tickets is to better understand the likely underlying causes of intradomain routing instability. We develop a method to correlate trouble tickets with instability events and find that, although unplanned events last longer than scheduled maintenance, there is no single underlying cause for most instability, and that these causes differ across networks. In comparison to a similar study from Labovitz et al. from ten years ago, we find that, while certain causes of instability such as maintenance and circuit problems remain significant, power issues have become much less prevalent, and software-related problems have become more common.
Keywords: correlation method; Internet; Internet2 backbone network; intradomain routing instability; network maintenance; network routing joint analysis; telecommunication network routing; Virtual private networks; VPN provider

Large-scale matrix factorization with missing data under additional constraints - Mitra, K.; Sheorey,S.; Chellapa, Rama (Advances in Neural Information Processing Systems, 2010)
Matrix factorization in the presence of missing data is at the core of many com-puter vision problems such as structure from motion (SfM), non-rigid SfM and photometric stereo. We formulate the problem of matrix factorization with miss- ing data as a low-rank semidefinite program (LRSDP) with the advantage that: 1) an efficient quasi-Newton implementation of the LRSDP enables us to solve large-scale factorization problems, and 2) additional constraints such as ortho- normality, required in orthographic SfM, can be directly incorporated in the new formulation. Our empirical evaluations suggest that, under the conditions of ma- trix completion theory, the proposed algorithm finds the optimal solution, and also requires fewer observations compared to the current state-of-the-art algorithms. We further demonstrate the effectiveness of the proposed algorithm in solving the affine SfM problem, non-rigid SfM and photometric stereo problems.

Learning to efficiently rank - Wang,Lidan; Jimmy Lin; Metzler,Donald (Proceedings of the 33rd international ACM SIGIR conference on Research and development in information retrieval, 2010)
It has been shown that learning to rank approaches are capable of learning highly effective ranking functions. However, these approaches have mostly ignored the important issue of efficiency. Given that both efficiency and effectiveness are important for real search engines, models that are optimized for effectiveness may not meet the strict efficiency requirements necessary to deploy in a production environment. In this work, we present a unified framework for jointly optimizing effectiveness and efficiency. We propose new metrics that capture the tradeoff between these two competing forces and devise a strategy for automatically learning models that directly optimize the tradeoff metrics. Experiments indicate that models learned in this way provide a good balance between retrieval effectiveness and efficiency. With specific loss functions, learned models converge to familiar existing ones, which demonstrates the generality of our framework. Finally, we show that our approach naturally leads to a reduction in the variance of query execution times, which is important for query load balancing and user satisfaction.
Keywords: effectiveness and efficiency tradeoff; Learning to rank; Linear Models

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