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)

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

Biofilms Comprise a Component of the Annual Cycle of Vibrio cholerae in the Bay of Bengal Estuary - Sultana, Marzia; Nusrin, Suraia; Hasan, Nur A.; Sadique, Abdus; Ahmed, Kabir U.; Islam, Atiqul; Hossain, Anwar; Longini, Ira; Nizam, Azhar; Huq, Anwar; Siddique, Abul K.; Sack, David A.; et al. (mBio, 2018)
Vibrio cholerae, an estuarine bacterium, is the causative agent of cholera, a severe diarrheal disease that demonstrates seasonal incidence in Bangladesh. In an extensive study of V. cholerae occurrence in a natural aquatic environment, water and plankton samples were collected biweekly between December 2005 and November 2006 from Mathbaria, an estuarine village of Bangladesh near the mangrove forests of the Sundarbans. Toxigenic V. cholerae exhibited two seasonal growth peaks, one in spring (March to May) and another in autumn (September to November), corresponding to the two annual seasonal outbreaks of cholera in this region. The total numbers of bacteria determined by heterotrophic plate count (HPC), representing culturable bacteria, accounted for 1% to 2.7% of the total numbers obtained using acridine orange direct counting (AODC). The highest bacterial culture counts, including toxigenic V. cholerae, were recorded in the spring. The direct fluorescent antibody (DFA) assay was used to detect V. cholerae O1 cells throughout the year, as free-living cells, within clusters, or in association with plankton. V. cholerae O1 varied significantly in morphology, appearing as distinctly rod-shaped cells in the spring months, while small coccoid cells within thick clusters of biofilm were observed during interepidemic periods of the year, notably during the winter months. Toxigenic V. cholerae O1 was culturable in natural water during the spring when the temperature rose sharply. The results of this study confirmed biofilms to be a means of persistence for bacteria and an integral component of the annual life cycle of toxigenic V. cholerae in the estuarine environment of Bangladesh.

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

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

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)

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

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.

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

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

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

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

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.

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

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

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.

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)

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.

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)

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

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

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

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

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

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

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

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.

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

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

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

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

#bias: Measuring the Tweeting Behavior of Propagandists - Lumezanu,Cristian; Feamster, Nick; Klein,Hans (Sixth International AAAI Conference on Weblogs and Social Media, 2012)
#bias: Measuring the Tweeting Behavior of Propagandists

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

Class consistent k-means: Application to face and action recognition - Zhuolin Jiang; Zhe Lin; Davis, Larry S. (Computer Vision and Image Understanding, 2012)
A class-consistent k-means clustering algorithm (CCKM) and its hierarchical extension (Hierarchical CCKM) are presented for generating discriminative visual words for recognition problems. In addition to using the labels of training data themselves, we associate a class label with each cluster center to enforce discriminability in the resulting visual words. Our algorithms encourage data points from the same class to be assigned to the same visual word, and those from different classes to be assigned to different visual words. More specifically, we introduce a class consistency term in the clustering process which penalizes assignment of data points from different classes to the same cluster. The optimization process is efficient and bounded by the complexity of k-means clustering. A very efficient and discriminative tree classifier can be learned for various recognition tasks via the Hierarchical CCKM. The effectiveness of the proposed algorithms is validated on two public face datasets and four benchmark action datasets.
Keywords: Action recognition; Class consistent k-means; Discriminative tree classifier; face recognition; Supervised clustering

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.

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.

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

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

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

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

Efficient Verification of Web-content Searching Through Authenticated Web Crawlers - Goodrich, Michael T.; Charalampos Papamanthou; Nguyen, Duy; Tamassia, Roberto; Lopes, Cristina Videira; Ohrimenko, Olga; Triandopoulos, Nikos (Proc. VLDB Endow., 2012)
We consider the problem of verifying the correctness and completeness of the result of a keyword search. We introduce the concept of an authenticated web crawler and present its design and prototype implementation. An authenticated web crawler is a trusted program that computes a specially-crafted signature over the web contents it visits. This signature enables (i) the verification of common Internet queries on web pages, such as conjunctive keyword searches---this guarantees that the output of a conjunctive keyword search is correct and complete; (ii) the verification of the content returned by such Internet queries---this guarantees that web data is authentic and has not been maliciously altered since the computation of the signature by the crawler. In our solution, the search engine returns a cryptographic proof of the query result. Both the proof size and the verification time are proportional only to the sizes of the query description and the query result, but do not depend on the number or sizes of the web pages over which the search is performed. As we experimentally demonstrate, the prototype implementation of our system provides a low communication overhead between the search engine and the user, and fast verification of the returned results by the user.

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

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

Gene Prediction with Glimmer for Metagenomic Sequences Augmented by Classification and Clustering - Kelley,David R; Liu,Bo; Delcher,Arthur L.; Pop, Mihai; Salzberg,Steven L. (Nucleic Acids ResearchNucl. Acids Res., 2012)
Environmental shotgun sequencing (or metagenomics) is widely used to survey the communities of microbial organisms that live in many diverse ecosystems, such as the human body. Finding the protein-coding genes within the sequences is an important step for assessing the functional capacity of a metagenome. In this work, we developed a metagenomics gene prediction system Glimmer-MG that achieves significantly greater accuracy than previous systems via novel approaches to a number of important prediction subtasks. First, we introduce the use of phylogenetic classifications of the sequences to model parameterization. We also cluster the sequences, grouping together those that likely originated from the same organism. Analogous to iterative schemes that are useful for whole genomes, we retrain our models within each cluster on the initial gene predictions before making final predictions. Finally, we model both insertion/deletion and substitution sequencing errors using a different approach than previous software, allowing Glimmer-MG to change coding frame or pass through stop codons by predicting an error. In a comparison among multiple gene finding methods, Glimmer-MG makes the most sensitive and precise predictions on simulated and real metagenomes for all read lengths and error rates tested.

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

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

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

Gripper synthesis for indirect manipulation of cells using Holographic Optical Tweezers - Chowdhury,Sagar; Svec,Petr; Wang,Chenlu; Losert,Wolfgang; Gupta, Satyandra K. (2012)
Optical Tweezers (OT) are used for highly accurate manipulations of biological cells. However, the direct exposure of cells to focused laser beam may negatively influence their biological functions. In order to overcome this problem, we generate multiple optical traps to grab and move a 3D ensemble of inert particles such as silica microspheres to act as a reconfigurable gripper for a manipulated cell. The relative positions of the microspheres are important in order for the gripper to be robust against external environmental forces and the exposure of high intensity laser on the cell to be minimized. In this paper, we present results of different gripper configurations, experimentally tested using our OT setup, that provide robust gripping as well as minimize laser intensity experienced by the cell. We developed a computational approach that allowed us to perform preliminary modeling and synthesis of the gripper configurations. The gripper synthesis is cast as a multi-objective optimization problem.

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

Individuals among commuters: Building personalised transport information services from fare collection systems - Lathia,N.; Smith,C.; Jon Froehlich; Capra,L. (Pervasive and Mobile Computing, 2012)

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

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.

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

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

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

Recognizing Human Actions by Learning and Matching Shape-Motion Prototype Trees - Zhuolin Jiang; Zhe Lin; Davis, Larry S. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2012)
A shape-motion prototype-based approach is introduced for action recognition. The approach represents an action as a sequence of prototypes for efficient and flexible action matching in long video sequences. During training, an action prototype tree is learned in a joint shape and motion space via hierarchical K-means clustering and each training sequence is represented as a labeled prototype sequence; then a look-up table of prototype-to-prototype distances is generated. During testing, based on a joint probability model of the actor location and action prototype, the actor is tracked while a frame-to-prototype correspondence is established by maximizing the joint probability, which is efficiently performed by searching the learned prototype tree; then actions are recognized using dynamic prototype sequence matching. Distance measures used for sequence matching are rapidly obtained by look-up table indexing, which is an order of magnitude faster than brute-force computation of frame-to-frame distances. Our approach enables robust action matching in challenging situations (such as moving cameras, dynamic backgrounds) and allows automatic alignment of action sequences. Experimental results demonstrate that our approach achieves recognition rates of 92.86 percent on a large gesture data set (with dynamic backgrounds), 100 percent on the Weizmann action data set, 95.77 percent on the KTH action data set, 88 percent on the UCF sports data set, and 87.27 percent on the CMU action data set.
Keywords: action prototype; actor location; brute-force computation; CMU action data set; distance measures; dynamic backgrounds; dynamic prototype sequence matching; flexible action matching; frame-to-frame distances; frame-to-prototype correspondence; hierarchical k-means clustering; human action recognition; Image matching; image recognition; Image sequences; joint probability model; joint shape; KTH action data set; large gesture data set; learning; learning (artificial intelligence); look-up table indexing; motion space; moving cameras; pattern clustering; prototype-to-prototype distances; shape-motion prototype-based approach; table lookup; training sequence; UCF sports data set; Video sequences; video signal processing; Weizmann action data set

Structural and biochemical studies of the open state of Lys48-linked diubiquitin - Lai,Ming-Yih; Zhang,Daoning; LaRonde-LeBlanc,Nicole; Fushman, David (Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 2012)
Ubiquitin (Ub) is a small protein highly conserved among eukaryotes and involved in practically all aspects of eukaryotic cell biology. Polymeric chains assembled from covalently-linked Ub monomers function as molecular signals in the regulation of a host of cellular processes. Our previous studies have shown that the predominant state of Lys48-linked di- and tetra-Ub chains at near-physiological conditions is a closed conformation, in which the Ub–Ub interface is formed by the hydrophobic surface residues of the adjacent Ub units. Because these very residues are involved in (poly)Ub interactions with the majority of Ub-binding proteins, their sequestration at the Ub–Ub interface renders the closed conformation of polyUb binding incompetent. Thus the existence of open conformation(s) and the interdomain motions opening and closing the Ub–Ub interface is critical for the recognition of Lys48-linked polyUb by its receptors. Knowledge of the conformational properties of a polyUb signal is essential for our understanding of its specific recognition by various Ub-receptors. Despite their functional importance, open states of Lys48-linked chains are poorly characterized. Here we report a crystal structure of the open state of Lys48-linked di-Ub. Moreover, using NMR, we examined interactions of the open state of this chain (at pH4.5) with a Lys48-linkage-selective receptor, the UBA2 domain of a shuttle protein hHR23a. Our results show that di-Ub binds UBA2 in the same mode and with comparable affinity as the closed state. Our data suggest a mechanism for polyUb signal recognition, whereby Ub-binding proteins select specific conformations out of the available ensemble of polyUb chain conformations. This article is part of a Special Issue entitled: Ubiquitin Drug Discovery and Diagnostics.
Keywords: Lys48-linked diubiquitin; Lysine-48 linkage selectivity; polyubiquitin; ubiquitin; Ubiquitin-associated domain

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)

Systems and Methods for Energy Harvesting in a Contained Fluid Circuit - Campbell,Tim; Larson,Eric; Cohn, Gabriel; Alcaide,Ramses; Jon Froehlich; Patel,Shwetak (UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION, CAMPBELL, Tim, LARSON, Eric, COHN, Gabriel, ALCAIDE, Ramses, FROEHLICH, Jon, PATEL, Shwetak, 2012)
Systems and methods for harvesting energy from a closed fluid circuit, such as a water pipe system in a building. An energy harvester can be installed at a point in a water circuit and can generate energy from pressure differentials caused when a valve is opened or closed at any other point in the water circuit that is in fluid communication with the energy harvester. The energy can be used to power, for example, a sensor and/or a transmitter., L'invention concerne des systèmes et des procédés de collecte de l'énergie qui provient d'un circuit de fluide fermé, comme un système de conduites d'eau dans un immeuble. Un collecteur d'énergie peut être installé à un certain point au sein d'un circuit d'eau et peut générer de l'énergie à partir des différentiels de pression provoqués lorsqu'une soupape est ouverte ou fermée à n'importe quel autre point au sein du circuit d'eau qui est en communication fluidique avec le collecteur d'énergie. L'énergie peut être utilisée pour alimenter, par exemple, un capteur et/ou un émetteur.
Keywords: Systems and Methods for Energy Harvesting in a Contained Fluid Circuit

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

Verifying Search Results Over Web Collections - Goodrich, Michael T.; Nguyen, Duy; Ohrimenko, Olga; Charalampos Papamanthou; Tamassia, Roberto; Triandopoulos, Nikos; Lopes, Cristina Videira (arXiv:1204.5446 [cs], 2012)
Searching accounts for one of the most frequently performed computations over the Internet as well as one of the most important applications of outsourced computing, producing results that critically affect users' decision-making behaviors. As such, verifying the integrity of Internet-based searches over vast amounts of web contents is essential. We provide the first solution to this general security problem. We introduce the concept of an authenticated web crawler and present the design and prototype implementation of this new concept. An authenticated web crawler is a trusted program that computes a special "signature" $s$ of a collection of web contents it visits. Subject to this signature, web searches can be verified to be correct with respect to the integrity of their produced results. This signature also allows the verification of complicated queries on web pages, such as conjunctive keyword searches. In our solution, along with the web pages that satisfy any given search query, the search engine also returns a cryptographic proof. This proof, together with the signature $s$, enables any user to efficiently verify that no legitimate web pages are omitted from the result computed by the search engine, and that no pages that are non-conforming with the query are included in the result. An important property of our solution is that the proof size and the verification time both depend solely on the sizes of the query description and the query result, but not on the number or sizes of the web pages over which the search is performed. Our authentication protocols are based on standard Merkle trees and the more involved bilinear-map accumulators. As we experimentally demonstrate, the prototype implementation of our system gives a low communication overhead between the search engine and the user, and allows for fast verification of the returned results on the user side.
Keywords: Computer Science - Cryptography and Security

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

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences - Liu,Bo; Gibbons,Theodore; Ghodsi,Mohammad; Treangen,Todd; Pop, Mihai (BMC Genomics, 2011)
A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences in the copy number of the gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from metagenomic shotgun sequencing data by matching individual reads against a database of reference sequences. One major limitation of prior computational methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels.

On Achieving the" Best of Both Worlds" in Secure Multiparty Computation - Ishai,Y.; Katz, Jonathan; Kushilevitz,E.; Lindell,Y.; Petrank,E. (SIAM Journal on Computing, 2011)
Two settings are traditionally considered for secure multiparty computation, de-pending on whether or not a majority of the parties are assumed to be honest. Existing protocols that assume an honest majority provide “full security” (and, in particular, guarantee output delivery and fairness) when this assumption holds, but are completely insecure if this assumption is violated. On the other hand, known protocols tolerating an arbitrary number of corruptions do not guarantee fairness or output delivery even if only a single party is dishonest. It is natural to wonder whether it is possible to achieve the “best of both worlds”: namely, a single protocol that simultaneously achieves the best possible security in both the above settings. Here, we rule out this possibility (at least for general functionalities) and show some positive results regarding what can be achieved.

Adapting a map query interface for a gesturing touch screen interface - Samet, Hanan; Teitler,Benjamin E.; Adelfio,Marco D.; Lieberman,Michael D. (Proceedings of the 20th international conference companion on World wide web, 2011)
NewsStand is an example application of a general framework that we are developing to enable searching for information using a map query interface, where the information results from monitoring the output of over 8,000 RSS news sources and is available for retrieval within minutes of publication. The user interface of NewsStand was recently adapted so that NewsStand can execute on mobile and tablet devices with a gesturing touch screen interface such as the iPhone, iPod Touch, and iPad. This action led to a discovery of some shortcomings of current mapping APIs as well as devising some interesting new widgets. These issues are discussed, and the realization can be seen by a demo at http://newsstand.umiacs.umd.edu on any of the above Apple devices as well as other devices that support gestures such as an Android phone.
Keywords: map query interface; newsstand; touch screen gesturing interface

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

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

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

Boosting the scalability of botnet detection using adaptive traffic sampling - Zhang,Junjie; Luo,Xiapu; Perdisci,Roberto; Gu,Guofei; Lee,Wenke; Feamster, Nick (Proceedings of the 6th ACM Symposium on Information, Computer and Communications Security, 2011)
Botnets pose a serious threat to the health of the Internet. Most current network-based botnet detection systems require deep packet inspection (DPI) to detect bots. Because DPI is a computational costly process, such detection systems cannot handle large volumes of traffic typical of large enterprise and ISP networks. In this paper we propose a system that aims to efficiently and effectively identify a small number of suspicious hosts that are likely bots. Their traffic can then be forwarded to DPI-based botnet detection systems for fine-grained inspection and accurate botnet detection. By using a novel adaptive packet sampling algorithm and a scalable spatial-temporal flow correlation approach, our system is able to substantially reduce the volume of network traffic that goes through DPI, thereby boosting the scalability of existing botnet detection systems. We implemented a proof-of-concept version of our system, and evaluated it using real-world legitimate and botnet-related network traces. Our experimental results are very promising and suggest that our approach can enable the deployment of botnet-detection systems in large, high-speed networks.
Keywords: adaptive sampling; botnet; intrusion detection; NETWORK SECURITY

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

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

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

A computational statistics approach for estimating the spatial range of morphogen gradients - Kanodia, Jitendra S.; Kim, Yoosik; Tomer, Raju; Zia Khan; Chung, Kwanghun; Storey, John D.; Lu, Hang; Keller, Philipp J.; Shvartsman, Stanislav Y. (Development, 2011)
A crucial issue in studies of morphogen gradients relates to their range: the distance over which they can act as direct regulators of cell signaling, gene expression and cell differentiation. To address this, we present a straightforward statistical framework that can be used in multiple developmental systems. We illustrate the developed approach by providing a point estimate and confidence interval for the spatial range of the graded distribution of nuclear Dorsal, a transcription factor that controls the dorsoventral pattern of the Drosophila embryo.
Keywords: Computational Biology; Confidence interval; Dorsal gradient; Drosophila embryo; Morphogen gradient; Statistics

Countering Botnets: Anomaly-Based Detection, Comprehensive Analysis, and Efficient Mitigation - Lee,Wenke; Dagon,David; Giffin,Jon; Feamster, Nick; Ollman,Gunter; Westby,Jody; Wesson,Rick; Vixie,Paul (GEORGIA TECH RESEARCH CORP ATLANTA, 2011)
We cover five general areas: (1) botnet detection, (2) botnet analysis, (3) botnet mitigation, (4) add-on tasks to the original contract, including the Conficker Working Group Lessons Learned, Layer-8 Exploration of Botnet Organization, and DREN research, and (5) commercialization in this paper. We have successfully developed new botnet detection and analysis capabilities in this project. These algorithms have been evaluated using real-world data, and have been put into actual, deployed systems. The most significant technical developments include a new dynamic reputation systems for DNS domains, a scalable anomaly detection system for botnet detection in very large network, and a transparent malware analysis system. In addition, on several occasions we have used our botnet data and analysis to help law enforcement agencies arrest botmasters. We also have had great success transitioning technologies to commercial products that are now used by government agencies, ISPs, and major corporations.
Keywords: *ELECTRONIC SECURITY; *INFORMATION SECURITY; *INTERNET; *INTRUSION DETECTION(COMPUTERS); algorithms; BGP ROUTE INJECTION; BGP(BORDER GATEWAY PROTOCOLS); BOTNET DETECTION; BOTNET TRACEBACK AND ATTRIBUTION; BOTNETS(MALWARE); CLIENT SERVER SYSTEMS; COMMUNICATIONS PROTOCOLS; COMPUTER PROGRAMMING AND SOFTWARE; COMPUTER SYSTEMS MANAGEMENT AND STANDARDS; CYBER ATTACKS; CYBER SECURITY; CYBERNETICS; CYBERTERRORISM; CYBERWARFARE; DATA PROCESSING SECURITY; DNS BASED MONITORING; DNS BASED REDIRECTION; DNS(DOMAIN NAME SYSTEMS); INFORMATION SCIENCE; INTERNET BROWSERS; ISP(INTERNET SERVICE PROVIDERS); MALWARE; MALWARE ANALYSIS; Online Systems; WUAFRLDHS1BOTN

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.

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

DNACLUST: accurate and efficient clustering of phylogenetic marker genes - Ghodsi,Mohammadreza; Liu,Bo; Pop, Mihai (BMC Bioinformatics, 2011)
Clustering is a fundamental operation in the analysis of biological sequence data. New DNA sequencing technologies have dramatically increased the rate at which we can generate data, resulting in datasets that cannot be efficiently analyzed by traditional clustering methods.

Domain adaptation for object recognition: An unsupervised approach - Gopalan,R.; Ruonan Li; Chellapa, Rama (2011 IEEE International Conference on Computer Vision (ICCV), 2011)
Adapting the classifier trained on a source domain to recognize instances from a new target domain is an important problem that is receiving recent attention. In this paper, we present one of the first studies on unsupervised domain adaptation in the context of object recognition, where we have labeled data only from the source domain (and therefore do not have correspondences between object categories across domains). Motivated by incremental learning, we create intermediate representations of data between the two domains by viewing the generative subspaces (of same dimension) created from these domains as points on the Grassmann manifold, and sampling points along the geodesic between them to obtain subspaces that provide a meaningful description of the underlying domain shift. We then obtain the projections of labeled source domain data onto these subspaces, from which a discriminative classifier is learnt to classify projected data from the target domain. We discuss extensions of our approach for semi-supervised adaptation, and for cases with multiple source and target domains, and report competitive results on standard datasets.
Keywords: Data models; data representations; discriminative classifier; Feature extraction; Grassmann manifold; image sampling; incremental learning; labeled source domain; Manifolds; measurement; object category; Object recognition; Principal component analysis; sampling points; semisupervised adaptation; target domain; underlying domain shift; unsupervised approach; unsupervised domain adaptation; Unsupervised learning; vectors

EFFICIENT PARALLEL NON-NEGATIVE LEAST SQUARES ON MULTI-CORE ARCHITECTURES - Luo,Y.; Duraiswami, Ramani (SIAM Journal on Scientific Computing, 2011)
We parallelize a version of the active-set iterative algorithm derived from the originalworks of Lawson and Hanson [Solving Least Squares Problems, Prentice-Hall, 1974] on multicore architectures. This algorithm requires the solution of an unconstrained least squares problem in every step of the iteration for a matrix composed of the passive columns of the original system matrix. To achieve improved performance, we use parallelizable procedures to efficiently update and downdate the QR factorization of the matrix at each iteration, to account for inserted and removed columns. We use a reordering strategy of the columns in the decomposition to reduce computation and memory access costs. We consider graphics processing units (GPUs) as a new mode for efficient parallel computations and compare our implementations to that of multicore CPUs. Both synthetic and nonsynthetic data are used in the experiments.

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

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

Face Tracking and Recognition in Video - Chellapa, Rama; Du,Ming; Turaga,Pavan; Zhou,Shaohua Kevin (Handbook of Face RecognitionHandbook of Face Recognition, 2011)
In this chapter, we describe the utility of videos in enhancing performance of image-based recognition tasks. We discuss a joint tracking-recognition framework that allows for using the motion information in a video to better localize and identify the person in the video using still galleries. We discuss how to jointly capture facial appearance and dynamics to obtain a parametric representation for video-to-video recognition. We discuss recognition in multi-camera networks where the probe and gallery both consist of multi-camera videos. Concluding remarks and directions for future research are provided.

Fast solvers for models of ICEO microfluidic flows - Shuttleworth, R. R; Elman, Howard; Long, K. R; Templeton, J. A (International Journal for Numerical Methods in Fluids, 2011)

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

How Many Tiers? Pricing in the Internet Transit Market - Valancius,V.; Lumezanu,C.; Feamster, Nick; Johari,R.; Vazirani,V. V (SIGCOMM-Computer Communication Review, 2011)
ISPs are increasingly selling “tiered” contracts, which offer Inter-net connectivity to wholesale customers in bundles, at rates based on the cost of the links that the traffic in the bundle is traversing. Although providers have already begun to implement and deploy tiered pricing contracts, little is known about how to structure them. Although contracts that sell connectivity on finer granularities im- prove market efficiency, they are also more costly for ISPs to im- plement and more difficult for customers to understand. Our goal is to analyze whether current tiered pricing practices in the whole- sale transit market yield optimal profits for ISPs and whether better bundling strategies might exist. In the process, we offer two contri- butions: (1) we develop a novel way of mapping traffic and topol- ogy data to a demand and cost model; and (2) we fit this model on three large real-world networks: an European transit ISP, a content distribution network, and an academic research network, and run counterfactuals to evaluate the effects of different bundling strate- gies. Our results show that the common ISP practice of structuring tiered contracts according to the cost of carrying the traffic flows (e.g., offering a discount for traffic that is local) can be suboptimal and that dividing contracts based on both traffic demand and the cost of carrying it into only three or four tiers yields near-optimal profit for the ISP.

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 Registration for Remote Sensing - LeMoigne,Jacqueline; Netanyahu,Nathan S.; Eastman,Roger D. (Cambridge University Press, 2011)
Image registration is a digital image processing discipline that studies how to bring two or more digital images into precise alignment for analysis and comparison. Accurate registration algorithms are essential for creating mosaics of satellite images and tracking changes on the planet's surface over time. Bringing together invited contributions from 36 distinguished researchers, the book presents a detailed overview of current research and practice in the application of image registration to remote sensing imagery. Chapters cover the problem definition, theoretical issues in accuracy and efficiency, fundamental algorithms, and real-world case studies of image registration software applied to imagery from operational satellite systems. This book provides a comprehensive and practical overview for Earth and space scientists, presents image processing researchers with a summary of current research, and can be used for specialized graduate courses.
Keywords: Science / Astronomy; Science / Earth Sciences / General; Technology & Engineering / Environmental / General; Technology & Engineering / Remote Sensing & Geographic Information Systems

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)

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

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

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 a discriminative dictionary for sparse coding via label consistent K-SVD - Zhuolin Jiang; Zhe Lin; Davis, Larry S. (Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on, 2011)
A label consistent K-SVD (LC-KSVD) algorithm to learn a discriminative dictionary for sparse coding is presented. In addition to using class labels of training data, we also associate label information with each dictionary item (columns of the dictionary matrix) to enforce discriminability in sparse codes during the dictionary learning process. More specifically, we introduce a new label consistent constraint called `discriminative sparse-code error' and combine it with the reconstruction error and the classification error to form a unified objective function. The optimal solution is efficiently obtained using the K-SVD algorithm. Our algorithm learns a single over-complete dictionary and an optimal linear classifier jointly. It yields dictionaries so that feature points with the same class labels have similar sparse codes. Experimental results demonstrate that our algorithm outperforms many recently proposed sparse coding techniques for face and object category recognition under the same learning conditions.
Keywords: classification error; Dictionaries; dictionary learning process; discriminative sparse code error; face recognition; image classification; Image coding; K-SVD; label consistent; learning (artificial intelligence); object category recognition; Object recognition; optimal linear classifier; reconstruction error; singular value decomposition; Training data

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

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

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

Maximizing Expected Utility for Stochastic Combinatorial Optimization Problems - Li,Jian; Deshpande, Amol (2011 IEEE 52nd Annual Symposium on Foundations of Computer Science (FOCS), 2011)
We study the stochastic versions of a broad class of combinatorial problems where the weights of the elements in the input dataset are uncertain. The class of problems that we study includes shortest paths, minimum weight spanning trees, and minimum weight matchings over probabilistic graphs, and other combinatorial problems like knapsack. We observe that the expected value is inadequate in capturing different types of risk averse or risk-prone behaviors, and instead we consider a more general objective which is to maximize the expected utility of the solution for some given utility function, rather than the expected weight (expected weight becomes a special case). We show that we can obtain a polynomial time approximation algorithm with additive error ϵ for any ϵ >; 0, if there is a pseudopolynomial time algorithm for the exact version of the problem (This is true for the problems mentioned above) and the maximum value of the utility function is bounded by a constant. Our result generalizes several prior results on stochastic shortest path, stochastic spanning tree, and stochastic knapsack. Our algorithm for utility maximization makes use of the separability of exponential utility and a technique to decompose a general utility function into exponential utility functions, which may be useful in other stochastic optimization problems.
Keywords: Approximation algorithms; Approximation methods; combinatorial problems; Fourier series; knapsack problems; optimisation; OPTIMIZATION; polynomial approximation; polynomial time approximation algorithm; Polynomials; Random variables; stochastic combinatorial optimization; stochastic knapsack; stochastic shortest path; stochastic spanning tree; vectors

MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets - Liu,B.; Pop, Mihai (BMC proceedings, 2011)

A method for the detection of meaningful and reproducible group signatures from gene expression profiles - Licamele,L.; Getoor, Lise (Journal of Bioinformatics and Computational Biology, 2011)
Gene expression microarrays are commonly used to detect the biological signature of a disease or to gain a better understanding of the underlying mechanism of how a group of drugs treat a specific disease. The outcome of such experiments, e.g. the signature, is a list of differentially expressed genes. Reproducibility across independent experiments remains a challenge. We are interested in creating a method that can detect the shared signature of a group of expression profiles, e.g. a group of samples from individuals with the same disease or a group of drugs that treat the same therapeutic indication. We have developed a novel Weighted Influence — Rank of Ranks (WIMRR) method, and we demonstrate its ability to produce both meaningful and reproducible group signatures.

Modeling Tiered Pricing in the Internet Transit Market - Valancius,Vytautas; Lumezanu,Cristian; Feamster, Nick; Johari,Ramesh; Vazirani,Vijay V. (Arxiv preprint arXiv:1112.3740, 2011)
ISPs are increasingly selling "tiered" contracts, which offer Internet connectivity to wholesale customers in bundles, at rates based on the cost of the links that the traffic in the bundle is traversing. Although providers have already begun to implement and deploy tiered pricing contracts, little is known about how such pricing affects ISPs and their customers. While contracts that sell connectivity on finer granularities improve market efficiency, they are also more costly for ISPs to implement and more difficult for customers to understand. In this work we present two contributions: (1) we develop a novel way of mapping traffic and topology data to a demand and cost model; and (2) we fit this model on three large real-world networks: an European transit ISP, a content distribution network, and an academic research network, and run counterfactuals to evaluate the effects of different pricing strategies on both the ISP profit and the consumer surplus. We highlight three core findings. First, ISPs gain most of the profits with only three or four pricing tiers and likely have little incentive to increase granularity of pricing even further. Second, we show that consumer surplus follows closely, if not precisely, the increases in ISP profit with more pricing tiers. Finally, the common ISP practice of structuring tiered contracts according to the cost of carrying the traffic flows (e.g., offering a discount for traffic that is local) can be suboptimal and that dividing contracts based on both traffic demand and the cost of carrying it into only three or four tiers yields near-optimal profit for the ISP.
Keywords: Computer Science - Networking and Internet Architecture

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)

NSF/IEEE-TCPP curriculum initiative on parallel and distributed computing: core topics for undergraduates - Prasad,S. K.; Chtchelkanova,A.; Das,S.; Dehne,F.; Gouda,M.; Gupta,A.; JaJa, Joseph F.; Kant,K.; La Salle,A.; LeBlanc,R.; others (Proceedings of the 42nd ACM technical symposium on Computer science education, 2011)

Oblivious RAM with O((logN)^3) Worst-Case Cost - Elaine Shi; Chan, T.; Stefanov, Emil; Li, Mingfei (Advances in Cryptology – ASIACRYPT 2011, 2011)
Oblivious RAM is a useful primitive that allows a client to hide its data access patterns from an untrusted server in storage outsourcing applications. Until recently, most prior works on Oblivious RAM aim to optimize its amortized cost, while suffering from linear or even higher worst-case cost. Such poor worst-case behavior renders these schemes impractical in realistic settings, since a data access request can occasionally be blocked waiting for an unreasonably large number of operations to complete. This paper proposes novel Oblivious RAM constructions that achieves poly-logarithmic worst-case cost, while consuming constant client-side storage. To achieve the desired worst-case asymptotic performance, we propose a novel technique in which we organize the O-RAM storage into a binary tree over data buckets, while moving data blocks obliviously along tree edges.
Keywords: Computer science

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

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

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

A probabilistic approach for learning folksonomies from structured data - Plangprasopchok,Anon; Lerman,Kristina; Getoor, Lise (Proceedings of the fourth ACM international conference on Web search and data mining, 2011)
Learning structured representations has emerged as an important problem in many domains, including document and Web data mining, bioinformatics, and image analysis. One approach to learning complex structures is to integrate many smaller, incomplete and noisy structure fragments. In this work, we present an unsupervised probabilistic approach that extends affinity propagation [7] to combine the small ontological fragments into a collection of integrated, consistent, and larger folksonomies. This is a challenging task because the method must aggregate similar structures while avoiding structural inconsistencies and handling noise. We validate the approach on a real-world social media dataset, comprised of shallow personal hierarchies specified by many individual users, collected from the photosharing website Flickr. Our empirical results show that our proposed approach is able to construct deeper and denser structures, compared to an approach using only the standard affinity propagation algorithm. Additionally, the approach yields better overall integration quality than a state-of-the-art approach based on incremental relational clustering.
Keywords: collective knowledge; data mining; folksonomies; social information processing; social metadata; taxonomies

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

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

Seam carving estimation using forensic hash - Lu,Wenjun; M. Wu (Proceedings of the thirteenth ACM multimedia workshop on Multimedia and security, 2011)
Seam carving is an adaptive multimedia retargeting technique to resize multimedia data for different display sizes. This technique has found promising applications in media consumption on mobile devices such as tablets and smartphones. However, seam carving can also be used to maliciously alter image content and when combined with other tampering operations, makes tampering detection very difficult by traditional multimedia forensic techniques. In this paper, we study the problem of seam carving estimation and tampering localization using very compact side information called forensic hash. The forensic hash technique bridges two related areas, namely robust image hashing and blind multimedia forensics, to answer a broader scope of forensic questions in a more efficient and accurate manner. We show that our recently proposed forensic hash construction can be extended to accurately estimate seam carving and detect local tampering.
Keywords: forensic hash; seam carving; sift; visual words

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

Secure video processing: Problems and challenges - Lu,Wenjun; Varna,A.; M. Wu (Acoustics, Speech and Signal Processing (ICASSP), 2011 IEEE International Conference on, 2011)
Secure signal processing is an emerging technology to enable signal processing tasks in a secure and privacy-preserving fashion. It has attracted a great amount of research attention due to the increasing demand to enable rich functionalities for private data stored online. Desirable functionalities may include search, analysis, clustering, etc. In this paper, we discuss the research issues and challenges in secure video processing with focus on the application of secure online video management. Video is different from text due to its large data volume and rich content diversity. To be practical, secure video processing requires efficient solutions that may involve a trade-off between security and complexity. We look at three representative video processing tasks and review existing techniques that can be applied. Many of the tasks do not have efficient solutions yet, and we discuss the challenges and research questions that need to be addressed.
Keywords: data; video; fashion; secure; management; secure; of; online; privacy-preserving; processing; processing; security; signal; video

Sensitivity analysis and explanations for robust query evaluation in probabilistic databases - Kanagal,B.; Li,J.; Deshpande, Amol (Proceedings of the 2011 international conference on Management of data, 2011)
Probabilistic database systems have successfully established them-selves as a tool for managing uncertain data. However, much of the research in this area has focused on efficient query evaluation and has largely ignored two key issues that commonly arise in uncer- tain data management: First, how to provide explanations for query results, e.g., “Why is this tuple in my result?” or “Why does this output tuple have such high probability?”. Second, the problem of determining the sensitive input tuples for the given query, e.g., users are interested to know the input tuples that can substantially alter the output, when their probabilities are modified (since they may be unsure about the input probability values). Existing systems pro- vide the lineage/provenance of each of the output tuples in addition to the output probabilities, which is a boolean formula indicating the dependence of the output tuple on the input tuples. However, lineage does not immediately provide a quantitative relationship and it is not informative when we have multiple output tuples. In this paper, we propose a unified framework that can handle both the issues mentioned above to facilitate robust query processing. We formally define the notions of influence and explanations and provide algorithms to determine the top-l influential set of variables and the top-l set of explanations for a variety of queries, including conjunctive queries, probabilistic threshold queries, top-k queries and aggregation queries. Further, our framework naturally enables highly efficient incremental evaluation when input probabilities are modified (e.g., if uncertainty is resolved). Our preliminary exper- imental results demonstrate the benefits of our framework for per- forming robust query processing over probabilistic databases.

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

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.

Speeding Up Network Layout and Centrality Measures for Social Computing Goals - Sharma,Puneet; Khurana,Udayan; Shneiderman, Ben; Scharrenbroich,Max; Locke,John (Social Computing, Behavioral-Cultural Modeling and PredictionSocial Computing, Behavioral-Cultural Modeling and Prediction, 2011)
This paper presents strategies for speeding up calculation of graph metrics and layout by exploiting the parallel architecture of modern day Graphics Processing Units (GPU), specifically Compute Unified Device Architecture ( CUDA ) by Nvidia . Graph centrality metrics like Eigenvector , Betweenness , Page Rank and layout algorithms like Fruchterman − Rheingold are essential components of Social Network Analysis ( SNA ). With the growth in adoption of SNA in different domains and increasing availability of huge networked datasets for analysis, social network analysts require faster tools that are also scalable. Our results, using NodeXL, show up to 802 times speedup for a Fruchterman-Rheingold graph layout and up to 17,972 times speedup for Eigenvector centrality metric calculations on a 240 core CUDA-capable GPU.

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

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

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

A unified approach to ranking in probabilistic databases - Li,Jian; Saha,Barna; Deshpande, Amol (The VLDB Journal, 2011)
Ranking is a fundamental operation in data analysis and decision support and plays an even more crucial role if the dataset being explored exhibits uncertainty. This has led to much work in understanding how to rank the tuples in a probabilistic dataset in recent years. In this article, we present a unified approach to ranking and top-k query processing in probabilistic databases by viewing it as a multi-criterion optimization problem and by deriving a set of features that capture the key properties of a probabilistic dataset that dictate the ranked result. We contend that a single, specific ranking function may not suffice for probabilistic databases, and we instead propose two parameterized ranking functions, called PRF ¿ and PRF e, that generalize or can approximate many of the previously proposed ranking functions. We present novel generating functions-based algorithms for efficiently ranking large datasets according to these ranking functions, even if the datasets exhibit complex correlations modeled using probabilistic and/xor trees or Markov networks. We further propose that the parameters of the ranking function be learned from user preferences, and we develop an approach to learn those parameters. Finally, we present a comprehensive experimental study that illustrates the effectiveness of our parameterized ranking functions, especially PRF e, at approximating other ranking functions and the scalability of our proposed algorithms for exact or approximate ranking.
Keywords: Approximation techniques; Graphical models; Learning to rank; Probabilistic databases; Ranking

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.

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

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.

An animated multivariate visualization for physiological and clinical data in the ICU - Ordóñez,Patricia; desJardins, Marie; Lombardi,Michael; Lehmann,Christoph U.; Fackler,Jim (Proceedings of the 1st ACM International Health Informatics Symposium, 2010)
Current visualizations of electronic medical data in the Intensive Care Unit (ICU) consist of stacked univariate plots of variables over time and a tabular display of the current numeric values for the corresponding variables and occasionally an alarm limit. The value of information is dependent upon knowledge of historic values to determine a change in state. With the ability to acquire more historic information, providers need more sophisticated visualization tools to assist them in analyzing the data in a multivariate fashion over time. We present a multivariate time series visualization that is interactive and animated, and has proven to be as effective as current methods in the ICU for predicting an episode of acute hypotension in terms of accuracy, confidence, and efficiency with only 30-60 minutes of training.
Keywords: computational physiology; Information Visualization; multivariate; time series

Autonomous Traffic Engineering using Self-Configuring Link Weights - Sundaresan,S.; Lumezanu,C.; Feamster, Nick; François,P. (School of Computer Science, Georgia Tech, 2010)
Network operators use traffic engineering to control the flow of traffic across their networks. Existing TE methods establish static topologies offline, either by setting link weights or by configuring paths a priori. These methods require manual configuration and may not be robust in the face of failures. Some methods also require knowledge about traffic demands and may not be able to handle traffic fluctuations. Even when changes in demand are expected, operators must manually tune network configurations to prepare for them. Because adjusting configurations is difficult to get right, we start from an extreme design point, asking instead whether it is possible to perform traffic engineering online without having to perform any a priori configuration. Our traffic engineering technique, SculpTE, adapts to changing traffic demands by automatically configuring link weights in a stable manner. SculpTE balances load across the network by continually adjusting link weights to expose lightly-loaded paths. We evaluate SculpTE using a simple analytical model and simulations on realistic ISP network topologies. Our results show that SculpTE achieves excellent load balancing, responsiveness, and stability compared to state-of-the-art TE schemes, without requiring network operators to perform any offline configuration.

Autonomous traffic engineering with self-configuring topologies - Sundaresan,Srikanth; Lumezanu,Cristian; Feamster, Nick; Francois,Pierre (SIGCOMM Comput. Commun. Rev., 2010)
Network operators use traffic engineering (TE) to control the flow of traffic across their networks. Existing TE methods require manual configuration of link weights or tunnels, which is difficult to get right, or prior knowledge of traffic demands and hence may not be robust to link failures or traffic fluctuations. We present a self-configuring TE scheme, SculpTE, which automatically adapts the network-layer topology to changing traffic demands. SculpTE is responsive, stable, and achieves excellent load balancing.
Keywords: multi-path routing; online; sculpte; self-configuring; traffic engineering

Behavioral clustering of HTTP-based malware and signature generation using malicious network traces - Perdisci,Roberto; Lee,Wenke; Feamster, Nick (Proceedings of the 7th USENIX conference on Networked systems design and implementation, 2010)
We present a novel network-level behavioral malware clustering system. We focus on analyzing the structural similarities among malicious HTTP traffic traces generated by executing HTTP-based malware. Our work is motivated by the need to provide quality input to algorithms that automatically generate network signatures. Accordingly, we define similarity metrics among HTTP traces and develop our system so that the resulting clusters can yield high-quality malware signatures. We implemented a proof-of-concept version of our network-level malware clustering system and performed experiments with more than 25,000 distinct malware samples. Results from our evaluation, which includes real-world deployment, confirm the effectiveness of the proposed clustering system and show that our approach can aid the process of automatically extracting network signatures for detecting HTTP traffic generated by malware-compromised machines.

Broadening student enthusiasm for computer science with a great insights course - desJardins, Marie; Littman,Michael (Proceedings of the 41st ACM technical symposium on Computer science education, 2010)
We describe the "Great Insights in Computer Science" courses that are taught at Rutgers and UMBC. These courses were designed independently, but have in common a broad, engaging introduction to computing for non-majors. Both courses include a programming component to help the students gain an intuition for computational concepts, but neither is primarily programming focused. We present data to show that these courses attract a diverse group of students; are rated positively; and increase students' understanding of, and attitudes towards, computing and computational issues.
Keywords: attitudes towards computing; introductory courses

Building a dynamic reputation system for DNS - Antonakakis,M.; Perdisci,R.; Dagon,D.; Lee,W.; Feamster, Nick (19th Usenix Security Symposium, 2010)
The Domain Name System (DNS) is an essential protocolused by both legitimate Internet applications and cyber at- tacks. For example, botnets rely on DNS to support agile com- mand and control infrastructures. An effective way to disrupt these attacks is to place malicious domains on a “blocklist” (or “blacklist”) or to add a filtering rule in a firewall or net- work intrusion detection system. To evade such security coun- termeasures, attackers have used DNS agility, e.g., by using new domains daily to evade static blacklists and firewalls. In this paper we propose Notos, a dynamic reputation system for DNS. The premise of this system is that malicious, agile use of DNS has unique characteristics and can be distinguished from legitimate, professionally provisioned DNS services. No- tos uses passive DNS query data and analyzes the network and zone features of domains. It builds models of known legit- imate domains and malicious domains, and uses these models to compute a reputation score for a new domain indicative of whether the domain is malicious or legitimate. We have eval- uated Notos in a large ISP’s network with DNS traffic from 1.4 million users. Our results show that Notos can identify malicious domains with high accuracy (true positive rate of 96.8%) and low false positive rate (0.38%), and can identify these domains weeks or even months before they appear in public blacklists.

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

On Computing Compression Trees for Data Collection in Wireless Sensor Networks - Li,Jian; Deshpande, Amol; Khuller, Samir (2010 Proceedings IEEE INFOCOM, 2010)
We address the problem of efficiently gathering correlated data from a wireless sensor network, with the aim of designing algorithms with provable optimality guarantees, and understanding how close we can get to the known theoretical lower bounds. Our proposed approach is based on finding an optimal or a near-optimal compression tree for a given sensor network: a compression tree is a directed tree over the sensor network nodes such that the value of a node is compressed using the value of its parent. We focus on broadcast communication model in this paper, but our results are more generally applicable to a unicast communication model as well. We draw connections between the data collection problem and a previously studied graph concept called weakly connected dominating sets, and we use this to develop novel approximation algorithms for the problem. We present comparative results on several synthetic and real-world datasets showing that our algorithms construct near-optimal compression trees that yield a significant reduction in the data collection cost.
Keywords: Approximation algorithms; Base stations; Communications Society; Computer networks; Computer science; computing compression trees; Costs; data collection; Data communication; data compression; designing algorithms; Educational institutions; Entropy; graph concept; Monitoring; Protocols; trees (mathematics); weakly connected dominating sets; Wireless sensor networks

Constructing folksonomies by integrating structured metadata - Plangprasopchok,Anon; Lerman,Kristina; Getoor, Lise (Proceedings of the 19th international conference on World wide web, 2010)
Aggregating many personal hierarchies into a common taxonomy, also known as a folksonomy, presents several challenges due to its sparseness, ambiguity, noise, and inconsistency. We describe an approach to folksonomy learning based on relational clustering that addresses these challenges by exploiting structured metadata contained in personal hierarchies. Our approach clusters similar hierarchies using their structure and tag statistics, then incrementally weaves them into a deeper, bushier tree. We study folksonomy learning using social metadata extracted from the photo-sharing site Flickr. We evaluate the learned folksonomy quantitatively by automatically comparing it to a reference taxonomy created by the Open Directory Project. Our empirical results suggest that the proposed approach improves upon the state-of-the-art folksonomy learning method.
Keywords: collective knowledge; data mining; folksonomies

Constructing Folksonomies by Integrating Structured Metadata with Relational Clustering - Plangprasopchok,A.; Lerman,K.; Getoor, Lise (Workshops at the Twenty-Fourth AAAI Conference on Artificial Intelligence, 2010)
Many social Web sites allow users to annotate the content with descriptive metadata, such as tags, and more recently also to organize content hierarchically. These types of struc- tured metadata provide valuable evidence for learning how a community organizes knowledge. For instance, we can ag- gregate many personal hierarchies into a common taxonomy, also known as a folksonomy, that will aid users in visual- izing and browsing social content, and also to help them in organizing their own content. However, learning from so- cial metadata presents several challenges: sparseness, ambi- guity, noise, and inconsistency. We describe an approach to folksonomy learning based on relational clustering that ad- dresses these challenges by exploiting structured metadata contained in personal hierarchies. Our approach clusters sim- ilar hierarchies using their structure and tag statistics, then incrementally weaves them into a deeper, bushier tree. We study folksonomy learning using social metadata extracted from the photo-sharing site Flickr. We evaluate the learned folksonomy quantitatively by automatically comparing it to a reference taxonomy. Our empirical results suggest that the proposed framework, which addresses the challenges listed above, improves on existing folksonomy learning methods.

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

Decentralized dynamic scheduling across heterogeneous multi-core desktop grids - Jaehwan Lee; Keleher,P.; Sussman, Alan (2010 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW), 2010)
The recent advent of multi-core computing environments increases both the heterogeneity and complexity of managing desktop grid resources, making efficient load balancing challenging even for a centralized manager. Even with good initial job assignments, dynamic scheduling is still needed to adapt to dynamic environments, as well as for applications whose running times are not known a priori. In this paper, we propose new decentralized scheduling schemes that backfill jobs locally and dynamically migrate waiting jobs across nodes to leverage residual resources, while guaranteeing bounded waiting times for all jobs. The methods attempt to maximize total throughput while balancing load across available grid resources. Experimental results via simulation show that our scheduling scheme has performance competitive with an online centralized scheduler.
Keywords: backfill jobs; bounded waiting time; Computer science; decentralized dynamic scheduling; desktop grid resource management; Dynamic scheduling; Educational institutions; Environmental management; grid computing; heterogeneous multicore desktop grid; job assignment; job migration; load balancing; Load management; multicore computing environment; Peer to peer computing; Processor scheduling; residual resources; resource allocation; Resource management; scheduling; Scheduling algorithm; Throughput

The design of eco-feedback technology - Jon Froehlich; Findlater,Leah; Landay,James (Proceedings of the 28th international conference on Human factors in computing systems, 2010)
Keywords: eco-feedback; environmental hci; reflective hci; survey

Determining the spatial reader scopes of news sources using local lexicons - Quercini,Gianluca; Samet, Hanan; Sankaranarayanan,Jagan; Lieberman,Michael D. (Proceedings of the 18th SIGSPATIAL International Conference on Advances in Geographic Information Systems, 2010)
Information sources on the Internet (e.g., Web versions of newspapers) usually have an implicit spatial reader scope, which is the geographical location for which the content has been primarily produced. Knowledge of the spatial reader scope facilitates the construction of a news search engine that provides readers a set of news sources relevant to the location in which they are interested. In particular, it plays an important role in disambiguating toponyms (e.g., textual specifications of geographical locations) in news articles, as the process of selecting an interpretation for the toponym often reduces to one of selecting an interpretation that seems natural in the context of the spatial reader scope. The key to determining the spatial reader scope of news sources is the notion of local lexicon, which for a location s is a set of concepts such as, but not limited to, names of people, landmarks, and historical events, that are spatially related to s. Techniques to automatically generate the local lexicon of a location by using the link structure of Wikipedia are described and evaluated. A key contribution is the improvement of existing methods used in the semantic relatedness domain to extract concepts spatially related to a given location from the Wikipedia. Results of experiments are presented that indicate that the knowledge of the spatial reader scope significantly improves the disambiguation of textually specified locations in news articles and that using local lexicons is an effective method to determine the spatial reader scopes of news sources.
Keywords: geotagging; local lexicon; news search engine; spatial reader scope; spatial relatedness

Developing a Stochastic Dynamic Programming Framework for Optical Tweezer-Based Automated Particle Transport Operations - Banerjee,A. G.; Pomerance,A.; Losert,W.; Gupta,S.K. (Automation Science and Engineering, IEEE Transactions on, 2010)
Automated particle transport using optical tweezers requires the use of motion planning to move the particle while avoiding collisions with randomly moving obstacles. This paper describes a stochastic dynamic programming based motion planning framework developed by modifying the discrete version of an infinite-horizon partially observable Markov decision process algorithm. Sample trajectories generated by this algorithm are presented to highlight effectiveness in crowded scenes and flexibility. The algorithm is tested using silica beads in a holographic tweezer set-up and data obtained from the physical experiments are reported to validate various aspects of the planning simulation framework. This framework is then used to evaluate the performance of the algorithm under a variety of operating conditions.
Keywords: holographic tweezer set-up; holography; infinite-horizon partially observable Markov decision process algorithm; Markov processes; motion planning framework; optical tweezer-based automated particle transport operations; optical tweezers; radiation pressure; silica beads; stochastic dynamic programming framework; stochastic programming

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

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

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

Dynamic and Multidimensional Dataflow Graphs - Bhattacharyya, Shuvra S.; Deprettere, Ed F.; Keinert, Joachim (Handbook of Signal Processing Systems, 2010)
Much of the work to date on dataflow models for signal processing system design has focused decidable dataflow models that are best suited for onedimensional signal processing. In this chapter, we review more general dataflow modeling techniques that are targeted to applications that include multidimensional signal processing and dynamic dataflow behavior. As dataflow techniques are applied to signal processing systems that are more complex, and demand increasing degrees of agility and flexibility, these classes of more general dataflow models are of correspondingly increasing interest. We begin with a discussion of two dataflow modeling techniques - multi-dimensional synchronous dataflow and windowed dataflow - that are targeted towards multidimensional signal processing applications. We then provide a motivation for dynamic dataflow models of computation, and review a number of specific methods that have emerged in this class of models. Our coverage of dynamic dataflowmodels in this chapter includes Boolean dataflow, the stream-based function model, CAL, parameterized dataflow, and enable-invoke dataflow.
Keywords: Communications Engineering, Networks; Computer Systems Organization and Communication Networks; Processor Architectures; Signal, Image and Speech Processing

The effect of packet loss on redundancy elimination in cellular wireless networks - Lumezanu,Cristian; Guo,Katherine; Spring, Neil; Bhattacharjee, Bobby (Proceedings of the 10th annual conference on Internet measurement, 2010)
Network-level redundancy elimination (RE) algorithms reduce traffic volume on bandwidth-constrained network paths by avoiding the transmission of repeated byte sequences. Previous work shows that RE can suppress the transmission of 20-50% bytes when deployed at ISP access links or between routers. In this paper, we focus on the challenges of deploying RE in cellular networks. The potential benefifit is substantial, since cellular networks have a growing subscriber base and network links, including wired backhaul, are often oversubscribed. Using three large traces captured at two North American and one European wireless network providers, we show that RE can reduce the bandwidth consumption of the majority of mobile users by at least 10%. However, cellular links have much higher packet loss rates than their wired counterparts, which makes applying RE much more difficult. Our experiments also show that the loss of only a few packets can disrupt RE and eliminate the bandwidth savings. We propose informed marking, a lightweight scheme that detects lost packets and prevents RE algorithms from using them for future encodings. We implement RE with informed marking and deploy it in a real-world cellular network. Our results show that with informed marking, more than 60% of the bandwidth savings of RE are preserved, even when packet loss rates are high.
Keywords: cellular networks; loss; redundancy elimination

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

Energy efficient scheduling via partial shutdown - Khuller, Samir; Li,Jian; Saha,Barna (Proceedings of the Twenty-First Annual ACM-SIAM Symposium on Discrete Algorithms, 2010)
Motivated by issues of saving energy in data centers we define a collection of new problems referred to as "machine activation" problems. The central framework we introduce considers a collection of m machines (unrelated or related) with each machine i having an activation cost of ai. There is also a collection of n jobs that need to be performed, and pi, j is the processing time of job j on machine i. Standard scheduling models assume that the set of machines is fixed and all machines are available. However, in our setting, we assume that there is an activation cost budget of A - we would like to select a subset S of the machines to activate with total cost a(S) ≤ A and find a schedule for the n jobs on the machines in S minimizing the makespan (or any other metric). We consider both the unrelated machines setting, as well as the setting of scheduling uniformly related parallel machines, where machine i has activation cost ai and speed si, and the processing time of job j on machine i is pi, j = pjsi, where pj is the processing requirement of job j. For the general unrelated machine activation problem, our main results are that if there is a schedule with makespan T and activation cost A then we can obtain a schedule with makespan (2 + ε)T and activation cost 2(1 + 1/ε)(ln n/OPT + 1)A, for any ε > 0. We also consider assignment costs for jobs as in the generalized assignment problem, and using our framework, provide algorithms that minimize the machine activation and the assignment cost simultaneously. In addition, we present a greedy algorithm which only works for the basic version and yields a makespan of 2T and an activation cost A(1 + ln n). For the uniformly related parallel machine sceduling problem, we develop a polynomial time approximation scheme that outputs a schedule with the property that the activation cost of the subset of machines is at most A and the makespan is at most (1 + ε)T for any ε > 0. For the special case of m identical speed machines, the machine activation problem is trivial, since the cheapest subset of k machines is always the best choice if the optimal solution activates k machines. In addition, we consider the case whem some jobs can be dropped (and are treated as outliers).

Evaluation of information retrieval for E-discovery - Oard, Douglas; Baron,Jason R.; Hedin,Bruce; Lewis,David D.; Tomlinson,Stephen (Artificial Intelligence and Law, 2010)

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.

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

Fast directional chamfer matching - Ming-Yu Liu; Tuzel, O.; Veeraraghavan,A.; Chellapa, Rama (Computer Vision and Pattern Recognition (CVPR), 2010 IEEE Conference on, 2010)
We study the object localization problem in images given a single hand-drawn example or a gallery of shapes as the object model. Although many shape matching algorithms have been proposed for the problem over the decades, chamfer matching remains to be the preferred method when speed and robustness are considered. In this paper, we significantly improve the accuracy of chamfer matching while reducing the computational time from linear to sublinear (shown empirically). Specifically, we incorporate edge orientation information in the matching algorithm such that the resulting cost function is piecewise smooth and the cost variation is tightly bounded. Moreover, we present a sublinear time algorithm for exact computation of the directional chamfer matching score using techniques from 3D distance transforms and directional integral images. In addition, the smooth cost function allows to bound the cost distribution of large neighborhoods and skip the bad hypotheses within. Experiments show that the proposed approach improves the speed of the original chamfer matching upto an order of 45 #x00D7;, and it is much faster than many state of art techniques while the accuracy is comparable.
Keywords: 3D; algorithm; edge; algorithms; single; chamfer; cost; detection; image; directional; distance; distribution; cost; example; smooth; function; sublinear; hand-drawn; images; edge; information; fast; integral; localization; MATCHING; matching; gallery; matching; transforms; model; piecewise; of; orientation; problem; object; score; directional; shapes; object; smooth; shape; TIME; time; cost; transforms; computational; variation; directional

Forensic hash for multimedia information - Lu,W.; Varna,A.L.; Wu,M. (SPIE Media Forensics and Security, 2010)
Digital multimedia such as images and videos are prevalent on today’s internet and cause significantsocial impact, which can be evidenced by the proliferation of social networking sites with user generated contents. Due to the ease of generating and modifying images and videos, it is critical to establish trustworthiness for online multimedia information. In this paper, we propose a new framework to perform multimedia forensics by using compact side information to reconstruct the processing history of a multimedia document. We refer to this framework as FASHION, standing for Forensic hASH for informatION assurance. As a first step in the modular design for FASHION, we propose new algorithms based on Radon transform and scale space theory to effectively estimate the parameters of geometric transforms and detect local tampering that an image may have undergone. The FASHION framework is designed to answer a much broader range of questions regarding the processing history of multimedia data than simple binary decision from robust image hashing, and also offers more efficient and accurate forensic analysis than multimedia forensic techniques that do not use any side information.

GasSense: Appliance-Level, Single-Point Sensing of Gas Activity in the Home - Cohn,Gabe; Gupta,Sidhant; Jon Froehlich; Larson,Eric; Patel,Shwetak (Pervasive Computing, 2010)
This paper presents GasSense, a low-cost, single-point sensing solution for automatically identifying gas use down to its source (e.g., water heater, furnace, fireplace). This work adds a complementary sensing solution to the growing body of work in infrastructure-mediated sensing. GasSense analyzes the acoustic response of a home’s government mandated gas regulator, which provides the unique capability of sensing both the individual appliance at which gas is currently being consumed as well as an estimate of the amount of gas flow. Our approach provides a number of appealing features including the ability to be easily and safely installed without the need of a professional. We deployed our solution in nine different homes and initial results show that GasSense has an average accuracy of 95.2% in identifying individual appliance usage.

GEDI - AGroundtruthing Environment for Document Images - David Doermann; Zotkina,Elena; Huiping Li (Ninth IAPRInternational Workshop on Document Analysis Systems (DAS 2010), 2010)
In this paper, we describe a freely available highly configurable document image annotation tool called GEDI – Groundtruthing Environment for Document Images. Its basic structure involves two types of files, an Image file, and a corresponding .xml file in GEDI format. When users begin ground truthing an image, they can configure the interface to allow the creation of different types of zones, each of which may have a custom set of “attributes”. The output is compatible with the UMDDocLib architecture [2] and has been used in numerous funded and unfunded programs to create datasets in multiple languages. GEDI has been developed and released to the community as a comprehensive tool that we hope will ease the burden of document annotation and encourage additional sharing of data.

A general framework for efficient geographic routing in wireless networks - Lee,Seungjoon; Bhattacharjee, Bobby; Banerjee,Suman; Han,Bo (Computer Networks, 2010)
We propose a new link metric called normalized advance (NADV) for geographic routing in multihop wireless networks. NADV selects neighbors with the optimal trade-off between proximity and link cost. Coupled with the local next hop decision in geographic routing, NADV enables an adaptive and efficient cost-aware routing strategy. Depending on the objective or message priority, applications can use the NADV framework to minimize various types of link cost.We present efficient methods for link cost estimation and perform detailed experiments in simulated environments. Our results show that NADV outperforms current schemes in many aspects: for example, in high noise environments with frequent packet losses, the use of NADV leads to 81% higher delivery ratio. When compared to centralized routing under certain settings, geographic routing using NADV finds paths whose cost is close to the optimum. We also conducted experiments in Emulab testbed and the results demonstrate that our proposed approach performs well in practice.
Keywords: Geographic routing; Link cost estimation; Routing metric; Wireless multihop networks

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.

Genomic characterization of the Yersinia genus - Chen, P.E.; Cook, C.; Stewart, A.C.; Nagarajan,N.; Sommer, D.D.; Pop, Mihai; Thomason, B.; Thomason, M.P.K.; Lentz, S.; Nolan, N.; others (Genome biology, 2010)

Geotagging: using proximity, sibling, and prominence clues to understand comma groups - Lieberman,Michael D.; Samet, Hanan; Sankaranayananan,Jagan (Proceedings of the 6th Workshop on Geographic Information Retrieval, 2010)
Geotagging is the process of recognizing textual references to geographic locations, known as toponyms, and resolving these references by assigning each lat/long values. Typical geotagging algorithms use a variety of heuristic evidence to select the correct interpretation for each toponym. A study is presented of one such heuristic which aids in recognizing and resolving lists of toponyms, referred to as comma groups. Comma groups of toponyms are recognized and resolved by inferring the common threads that bind them together, based on the toponyms' shared geographic attributes. Three such common threads are proposed and studied --- population-based prominence, distance-based proximity, and sibling relationships in a geographic hierarchy --- and examples of each are noted. In addition, measurements are made of these comma groups' usage and variety in a large dataset of news articles, indicating that the proposed heuristics, and in particular the proximity and sibling heuristics, are useful for resolving comma group toponyms.
Keywords: comma groups; geotagging; toponyms

Geotagging with local lexicons to build indexes for textually-specified spatial data - Lieberman,M.D.; Samet, Hanan; Sankaranarayanan,J. (Data Engineering (ICDE), 2010 IEEE 26th International Conference on, 2010)
The successful execution of location-based and feature-based queries on spatial databases requires the construction of spatial indexes on the spatial attributes. This is not simple when the data is unstructured as is the case when the data is a collection of documents such as news articles, which is the domain of discourse, where the spatial attribute consists of text that can be (but is not required to be) interpreted as the names of locations. In other words, spatial data is specified using text (known as a toponym) instead of geometry, which means that there is some ambiguity involved. The process of identifying and disambiguating references to geographic locations is known as geotagging and involves using a combination of internal document structure and external knowledge, including a document-independent model of the audience's vocabulary of geographic locations, termed its spatial lexicon. In contrast to previous work, a new spatial lexicon model is presented that distinguishes between a global lexicon of locations known to all audiences, and an audience-specific local lexicon. Generic methods for inferring audiences' local lexicons are described. Evaluations of this inference method and the overall geotagging procedure indicate that establishing local lexicons cannot be overlooked, especially given the increasing prevalence of highly local data sources on the Internet, and will enable the construction of more accurate spatial indexes.
Keywords: data; Internet; data; databases; databases; spatial; document; indexes; spatial; information; Internet; document-independent; knowledge; feature-based; lexicon; lexicons; location-based; locations; geotagging; inference; method; internal; methods; geographic; mining; geographic; model; external; model; textually-specified; queries; generic; queries; spatial; spatial; structure; local; systems; visual

Group motion segmentation using a Spatio-Temporal Driving Force Model - Ruonan Li; Chellapa, Rama (Computer Vision and Pattern Recognition (CVPR), 2010 IEEE Conference on, 2010)
We consider the `group motion segmentation' problem and provide a solution for it. The group motion segmentation problem aims at analyzing motion trajectories of multiple objects in video and finding among them the ones involved in a `group motion pattern'. This problem is motivated by and serves as the basis for the `multi-object activity recognition' problem, which is currently an active research topic in event analysis and activity recognition. Specifically, we learn a Spatio-Temporal Driving Force Model to characterize a group motion pattern and design an approach for segmenting the group motion. We illustrate the approach using videos of American football plays, where we identify the offensive players, who follow an offensive motion pattern, from motions of all players in the field. Experiments using GaTech Football Play Dataset validate the effectiveness of the segmentation algorithm.
Keywords: activity; American; analysis; image; dataset; group; driving; football; force; model; image; MOTION; pattern; group; play; plays; GaTech; problem; spatiotemporal; recognition; recognition; image; segmentation; segmentation; motion; trajectories; multiobject

Growing a tree in the forest: constructing folksonomies by integrating structured metadata - Plangprasopchok,Anon; Lerman,Kristina; Getoor, Lise (Proceedings of the 16th ACM SIGKDD international conference on Knowledge discovery and data mining, 2010)
Many social Web sites allow users to annotate the content with descriptive metadata, such as tags, and more recently to organize content hierarchically. These types of structured metadata provide valuable evidence for learning how a community organizes knowledge. For instance, we can aggregate many personal hierarchies into a common taxonomy, also known as a folksonomy, that will aid users in visualizing and browsing social content, and also to help them in organizing their own content. However, learning from social metadata presents several challenges, since it is sparse, shallow, ambiguous, noisy, and inconsistent. We describe an approach to folksonomy learning based on relational clustering, which exploits structured metadata contained in personal hierarchies. Our approach clusters similar hierarchies using their structure and tag statistics, then incrementally weaves them into a deeper, bushier tree. We study folksonomy learning using social metadata extracted from the photo-sharing site Flickr, and demonstrate that the proposed approach addresses the challenges. Moreover, comparing to previous work, the approach produces larger, more accurate folksonomies, and in addition, scales better.
Keywords: collective knowledge; data mining; folksonomies; relational clustering; social information processing; social metadata; taxonomies

Hopx and Hdac2 Interact to Modulate Gata4 Acetylation and Embryonic Cardiac Myocyte Proliferation - Trivedi,Chinmay M.; Zhu,Wenting; Wang,Qiaohong; Jia,Cheng; Kee,Hae Jin; Li,Li; Hannenhalli, Sridhar; Epstein,Jonathan A. (Developmental Cell, 2010)
SummaryRegulation of chromatin structure via histone modification has recently received intense attention. Here, we demonstrate that the chromatin-modifying enzyme histone deacetylase 2 (Hdac2) functions with a small homeodomain factor, Hopx, to mediate deacetylation of Gata4, which is expressed by cardiac progenitor cells and plays critical roles in the regulation of cardiogenesis. In the absence of Hopx and Hdac2 in mouse embryos, Gata4 hyperacetylation is associated with a marked increase in cardiac myocyte proliferation, upregulation of Gata4 target genes, and perinatal lethality. Hdac2 physically interacts with Gata4, and this interaction is stabilized by Hopx. The ability of Gata4 to transactivate cell cycle genes is impaired by Hopx/Hdac2-mediated deacetylation, and this effect is abrogated by loss of Hdac2-Gata4 interaction. These results suggest that Gata4 is a nonhistone target of Hdac2-mediated deacetylation and that Hdac2, Hopx, and Gata4 coordinately regulate cardiac myocyte proliferation during embryonic development.

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.

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

Illusory Lightness Perception Due to Signal Compression and Reconstruction - Fermüller, Cornelia; Li,Yi (Journal of VisionJ Vis, 2010)
We propose a computational model that can account for a large number of lightness illusions, including the seemingly opposing effects of brightness contrast and assimilation. The underlying mathematics is based on the new theory of compressive sensing, which provides an efficient method for sampling and reconstructing a signal that is sparse or compressible. The model states that at the retina the intensity signal is compressed. This process amounts to a random sampling of locally averaged values. In the cortex the intensity values are reconstructed using as input the compressed signal, and combined with the edges. Reconstruction amounts to solving an underdetermined linear equation system using L1 norm minimization. Assuming that the intensity signal is sparse in the Fourier domain, the reconstructed signal, which is a linear combination of a small number of Fourier components, deviates from the original signal. The reconstruction error is consistent with the perception of many well known lightness illusions, including the contrast and the assimilation effect, the articulated enhanced brightness contrast, the checker shadow illusion, and the grating induction. Considering in addition, the space-variant resolution of the human eye, the model also explains illusory patterns with changes in perceived lightness over large ranges, such as the Cornsweet and related illusions. We conducted experiments with new variations of the White and the Dungeon illusion, whose perception changes with the resolution at which the different parts of the patterns appear on the eye, and found that the model predicted well the perception in these stimuli.

Indirect two-sided relative ranking: a robust similarity measure for gene expression data - Licamele,L.; Getoor, Lise (BMC bioinformatics, 2010)
There is a large amount of gene expression data that exists in the public domain. This data has been generated under a variety of experimental conditions. Unfortunately, these experimental variations have generally prevented researchers from accurately comparing and combining this wealth of data, which still hides many novel insights. Results In this paper we present a new method, which we refer to as indirect two-sided relative ranking, for comparing gene expression profiles that is robust to variations in experimental conditions. This method extends the current best approach, which is based on comparing the correlations of the up and down regulated genes, by introducing a comparison based on the correlations in rankings across the entire database. Because our method is robust to experimental variations, it allows a greater variety of gene expression data to be combined, which, as we show, leads to richer scientific discoveries. Conclusions We demonstrate the benefit of our proposed indirect method on several datasets. We first evaluate the ability of the indirect method to retrieve compounds with similar therapeutic effects across known experimental barriers, namely vehicle and batch effects, on two independent datasets (one private and one public). We show that our indirect method is able to significantly improve upon the previous state-of-the-art method with a substantial improvement in recall at rank 10 of 97.03% and 49.44%, on each dataset, respectively. Next, we demonstrate that our indirect method results in improved accuracy for classification in several additional datasets. These datasets demonstrate the use of our indirect method for classifying cancer subtypes, predicting drug sensitivity/resistance, and classifying (related) cell types. Even in the absence of a known (i.e., labeled) experimental barrier, the improvement of the indirect method in each of these datasets is statistically significant.

Integrating structured metadata with relational affinity propagation - Plangprasopchok,A.; Lerman,K.; Getoor, Lise (In proceedings of AAAI Workshop on Statistical Relational AI, 2010)
Structured and semi-structured data describing entities, tax- onomies and ontologies appears in many domains. There is a huge interest in integrating structured information from multiple sources; however integrating structured data to in- fer complex common structures is a difficult task because the integration must aggregate similar structures while avoiding structural inconsistencies that may appear when the data is combined. In this work, we study the integration of struc- tured social metadata: shallow personal hierarchies specified by many individual users on the Social Web, and focus on in- ferring a collection of integrated, consistent taxonomies. We frame this task as an optimization problem with structural constraints. We propose a new inference algorithm, which we refer to as Relational Affinity Propagation (RAP) that ex- tends affinity propagation (Frey and Dueck 2007) by intro- ducing structural constraints. We validate the approach on a real-world social media dataset, collected from the photoshar- ing website Flickr. Our empirical results show that our pro- posed approach is able to construct deeper and denser struc- tures compared to an approach using only the standard affin- ity propagation algorithm.

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.

Learning shift-invariant sparse representation of actions - Li,Yi; Fermüller, Cornelia; Aloimonos, J.; Hui Ji (2010 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2010)
A central problem in the analysis of motion capture (MoCap) data is how to decompose motion sequences into primitives. Ideally, a description in terms of primitives should facilitate the recognition, synthesis, and characterization of actions. We propose an unsupervised learning algorithm for automatically decomposing joint movements in human motion capture (MoCap) sequences into shift-invariant basis functions. Our formulation models the time series data of joint movements in actions as a sparse linear combination of short basis functions (snippets), which are executed (or “activated”) at different positions in time. Given a set of MoCap sequences of different actions, our algorithm finds the decomposition of MoCap sequences in terms of basis functions and their activations in time. Using the tools of L1 minimization, the procedure alternately solves two large convex minimizations: Given the basis functions, a variant of Orthogonal Matching Pursuit solves for the activations, and given the activations, the Split Bregman Algorithm solves for the basis functions. Experiments demonstrate the power of the decomposition in a number of applications, including action recognition, retrieval, MoCap data compression, and as a tool for classification in the diagnosis of Parkinson (a motion disorder disease).
Keywords: action characterization; Action recognition; action retrieval; action synthesis; Character recognition; data compression; human motion capture; HUMANS; Image matching; Image motion analysis; image representation; Image sequences; Information retrieval; joint movements; large convex minimizations; learning (artificial intelligence); learning shift-invariant sparse representation; Matching pursuit algorithms; minimisation; Minimization methods; MoCap data compression; Motion analysis; motion capture analysis; motion disorder disease; motion sequences; orthogonal matching pursuit; Parkinson diagnosis; Parkinson's disease; Pursuit algorithms; shift-invariant basis functions; short basis functions; snippets; sparse linear combination; split Bregman algorithm; time series; time series data; Unsupervised learning; unsupervised learning algorithm

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

Maranello: practical partial packet recovery for 802.11 - Han,Bo; Schulman,Aaron; Gringoli,Francesco; Spring, Neil; Bhattacharjee, Bobby; Nava,Lorenzo; Ji,Lusheng; Lee,Seungjoon; Miller,Robert (Proceedings of the 7th USENIX conference on Networked systems design and implementation, 2010)
Partial packet recovery protocols attempt to repair corrupted packets instead of retransmitting them in their entirety. Recent approaches have used physical layer confidence estimates or additional error detection codes embedded in each transmission to identify corrupt bits, or have applied forward error correction to repair without such explicit knowledge. In contrast to these approaches, our goal is a practical design that simultaneously: (a) requires no extra bits in correct packets, (b) reduces recovery latency, except in rare instances, (c) remains compatible with existing 802.11 devices by obeying timing and backoff standards, and (d) can be incrementally deployed on widely available access points and wireless cards. In this paper, we design, implement, and evaluate Maranello, a novel partial packet recovery mechanism for 802.11. In Maranello, the receiver computes checksums over blocks in corrupt packets and bundles these checksums into a negative acknowledgment sent when the sender expects to receive an acknowledgment. The sender then retransmits only those blocks for which the checksum is incorrect, and repeats this partial retransmission until it receives an acknowledgment. Successful transmissions are not burdened by additional bits and the receiver needs not infer which bits were corrupted. We implemented Maranello using OpenFWWF (open source firmware for Broadcom wireless cards) and deployed it in a small testbed. We compare Maranello to alternative recovery protocols using a trace-driven simulation and to 802.11 using a live implementation under various channel conditions. To our knowledge, Maranello is the first partial packet recovery design to be implemented in commonly available firmware.

MetaPhyler: Taxonomic profiling for metagenomic sequences - Liu,Bo; Gibbons,T.; Ghodsi,M.; Pop, Mihai (2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2010)
A major goal of metagenomics is to characterize the microbial diversity of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences in the copy number of the 16S rRNA gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from whole-metagenome sequencing data by matching individual sequences against a database of reference genes. One major limitation of prior methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels. We propose that better classification results can be obtained by tuning the taxonomic classifier to each matching length, reference gene, and taxonomic level. We present a novel taxonomic profiler MetaPhyler, which uses marker genes as a taxonomic reference. Results on simulated datasets demonstrate that MetaPhyler outperforms other tools commonly used in this context (CARMA, Megan and PhymmBL). We also present interesting results obtained by applying MetaPhyler to a real metagenomic dataset.
Keywords: Bioinformatics; CARMA comparison; Databases; Genomics; Linear regression; marker genes; matching length; Megan comparison; metagenomic sequences; metagenomics; MetaPhyler; microbial diversity; microorganisms; molecular biophysics; molecular configurations; Pattern classification; pattern matching; phylogenetic classification; Phylogeny; PhymmBL comparison; reference gene database; Sensitivity; sequence matching; taxonomic classifier; taxonomic level; taxonomic profiling; whole metagenome sequencing data

Methods for efficient implementation of Model Predictive Control on multiprocessor systems - Gu, Ruirui; Bhattacharyya, Shuvra S.; Levine,W. S (2010 IEEE International Conference on Control Applications (CCA), 2010)
Model Predictive Control (MPC) has been used in a wide range of application areas including chemical engineering, food processing, automotive engineering, aerospace, and metallurgy. An important limitation on the application of MPC is the difficulty in completing the necessary computations within the sampling interval. Recent trends in computing hardware towards greatly increased parallelism offer a solution to this problem. This paper describes modeling and analysis tools to facilitate implementing the MPC algorithms on parallel computers, thereby greatly reducing the time needed to complete the calculations. The use of these tools is illustrated by an application to a class of MPC problems.
Keywords: Computational modeling; COMPUTERS; Equations; Hardware; Linear systems; Mathematical model; model predictive control; MPC algorithms; Multiprocessing systems; Multiprocessor systems; parallel computers; predictive control; Program processors

Mining Public Transport Usage for Personalised Intelligent Transport Systems - Lathia,N.; Jon Froehlich; Capra,L. (2010 IEEE 10th International Conference on Data Mining (ICDM), 2010)
Traveller information, route planning, and service updates have become essential components of public transport systems: they help people navigate built environments by providing access to information regarding delays and service disruptions. However, one aspect that these systems lack is a way of tailoring the information they offer in order to provide personalised trip time estimates and relevant notifications to each traveller. Mining each user's travel history, collected by automated ticketing systems, has the potential to address this gap. In this work, we analyse one such dataset of travel history on the London underground. We then propose and evaluate methods to (a) predict personalised trip times for the system users and (b) rank stations based on future mobility patterns, in order to identify the subset of stations that are of greatest interest to the user and thus provide useful travel updates.
Keywords: automated ticketing systems; data mining; Intelligent Transport Systems; London underground; mobility patterns; personalised intelligent transport systems; personalised trip times; Personalization; public administration; public information systems; public transport systems; rapid transit systems; route planning; service disruptions; service updates; traffic information systems; travel history; traveller information

Mobile Visual Aid Tools for Users with Visual Impairments - Liu,Xu; David Doermann; Huiping Li (Mobile Multimedia ProcessingMobile Multimedia Processing, 2010)
In this chapter we describe “MobileEye”, a software suite which converts a camera enabled mobile device into a multi-function vision tool that can assist the visually impaired in their daily activities. MobileEye consists of four subsystems, each customized for a specific type of visual disabilities: A color channel mapper which can tell the visually impaired different colors; a software based magnifier which provides image magnification as well as enhancement; a pattern recognizer which can read currencies; and a document retriever which allows access to printed materials. We developed cutting edge computer vision and image processing technologies, and tackled the challenges of implementing them on mobile devices with limited computational resources and low image quality. The system minimizes keyboard operation for the usability of users with visual impairments. Currently the software suite runs on Symbian and Windows Mobile handsets. In this chapter we provides a high level overview of the system, and then discuss the pattern recognizer in detail. The challenge is how to build a real-time recognition system on mobile devices and we present our detailed solutions.

A modality lexicon and its use in automatic tagging - Baker,K.; Bloodgood,M.; Dorr, Bonnie J; Filardo,N.W.; Levin,L.; Piatko,C. (Proceedings of the Seventh conference on International Language Resources and Evaluation (LREC’10), 2010)
This paper describes our resource-building results for an eight-week JHU Human Language Technology Center of Excellence SummerCamp for Applied Language Exploration (SCALE-2009) on Semantically-Informed Machine Translation. Specifically, we describe the construction of a modality annotation scheme, a modality lexicon, and two automated modality taggers that were built using the lexicon and annotation scheme. Our annotation scheme is based on identifying three components of modality: a trigger, a target and a holder. We describe how our modality lexicon was produced semi-automatically, expanding from an initial hand-selected list of modality trigger words and phrases. The resulting expanded modality lexicon is being made publicly available. We demonstrate that one tagger—a structure-based tagger—results in precision around 86% (depending on genre) for tagging of a standard LDC data set. In a machine translation application, using the structure-based tagger to annotate English modalities on an English-Urdu training corpus improved the translation quality score for Urdu by 0.3 Bleu points in the face of sparse training data.

Multimedia forensic hash based on visual words - Lu,W.; Wu,M. (IEEE Computer Society International Conference on Image Processing, 2010)
In recent years, digital images and videos have become in-creasingly popular over the internet and bring great social im- pact to a wide audience. In the meanwhile, technology ad- vancement allows people to easily alter the content of dig- ital multimedia and brings serious concern on the trustwor- thiness of online multimedia information. Forensic hash is a short signature attached to an image before transmission and acts as side information for analyzing the processing history and trustworthiness of the received image. In this paper, we propose a new construction of forensic hash based on visual words representation. We encode SIFT features into a com- pact visual words representation for robust estimation of geo- metric transformations and propose a hybrid construction us- ing both SIFT and block-based features to detect and localize image tampering. The proposed hash construction achieves more robust and accurate forensic analysis than prior work.

Natural language annotations for the Semantic Web - Katz,B.; Jimmy Lin; Quan,D. (On the Move to Meaningful Internet Systems 2002: CoopIS, DOA, and ODBASE, 2010)

Network I/O fairness in virtual machines - Anwer,Muhammad Bilal; Nayak,Ankur; Feamster, Nick; Liu,Ling (Proceedings of the second ACM SIGCOMM workshop on Virtualized infrastructure systems and architectures, 2010)
We present a mechanism for achieving network I/O fairness in virtual machines, by applying flexible rate limiting mechanisms directly to virtual network interfaces. Conventional approaches achieve this fairness by implementing rate limiting either in the virtual machine monitor or hypervisor, which generates considerable CPU interrupt and instruction overhead for forwarding packets. In contrast, our design pushes per-VM rate limiting as close as possible to the physical hardware themselves, effectively implementing per-virtual interface rate limiting in hardware. We show that this design reduces CPU overhead (both interrupts and instructions) by an order of magnitude. Our design can be applied either to virtual servers for cloud-based services, or to virtual routers
Keywords: netfpga; network virtualization; xen

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

Obtaining valid safety data for software safety measurement and process improvement - Basili, Victor R.; Zelkowitz, Marvin V; Layman,Lucas; Dangle,Kathleen; Diep,Madeline (Proceedings of the 2010 ACM-IEEE International Symposium on Empirical Software Engineering and Measurement, 2010)
We report on a preliminary case study to examine software safety risk in the early design phase of the NASA Constellation spaceflight program. Our goal is to provide NASA quality assurance managers with information regarding the ongoing state of software safety across the program. We examined 154 hazard reports created during the preliminary design phase of three major flight hardware systems within the Constellation program. Our purpose was two-fold: 1) to quantify the relative importance of software with respect to system safety; and 2) to identify potential risks due to incorrect application of the safety process, deficiencies in the safety process, or the lack of a defined process. One early outcome of this work was to show that there are structural deficiencies in collecting valid safety data that make software safety different from hardware safety. In our conclusions we present some of these deficiencies.
Keywords: case study; NASA; risk analysis; safety metrics

Ontuition: intuitive data exploration via ontology navigation - Adelfio,Marco D.; Lieberman,Michael D.; Samet, Hanan; Firozvi,Kashif A. (Proceedings of the 18th SIGSPATIAL International Conference on Advances in Geographic Information Systems, 2010)
Ontuition, a system for mapping ontologies, is presented. Transforming data to a usable format for Ontuition involves recognizing and resolving data values corresponding to concepts in multiple ontological domains. In particular, for datasets with a geographic component an attempt is made to identify and extract enough spatio-textual data that specific lat/long values to dataset entries can be assigned. Next, a gazetteer is used to transform the textually-specified locations into lat/long values that can be displayed on a map. Non-spatial ontological concepts are also discovered. This methodology is applied to the National Library of Medicine's very popular clinical trials website (http://clinicaltrials.gov/) whose users are generally interested in locating trials near where they live. The trials are specified using XML files. The location data is extracted and coupled with a disease ontology to enable general queries on the data with the result being of use to a very large group of people. The goal is to do this automatically for such ontology datasets with a locational component.
Keywords: MAPPING; ontology; ontuition; spatio-textual

Perturbing the Ubiquitin Pathway Reveals How Mitosis Is Hijacked to Denucleate and Regulate Cell Proliferation and Differentiation In Vivo - Caceres,Andrea; Shang,Fu; Wawrousek,Eric; Liu,Qing; Avidan,Orna; Cvekl,Ales; Yang,Ying; Haririnia,Aydin; Storaska,Andrew; Fushman, David; Kuszak,Jer; Dudek,Edward; et al. (PLoS ONEPLoS ONE, 2010)
BackgroundThe eye lens presents a unique opportunity to explore roles for specific molecules in cell proliferation, differentiation and development because cells remain in place throughout life and, like red blood cells and keratinocytes, they go through the most extreme differentiation, including removal of nuclei and cessation of protein synthesis. Ubiquitination controls many critical cellular processes, most of which require specific lysines on ubiquitin (Ub). Of the 7 lysines (K) least is known about effects of modification of K6. Methodology and Principal Findings We replaced K6 with tryptophan (W) because K6 is the most readily modified K and W is the most structurally similar residue to biotin. The backbone of K6W-Ub is indistinguishable from that of Wt-Ub. K6W-Ub is effectively conjugated and deconjugated but the conjugates are not degraded via the ubiquitin proteasome pathways (UPP). Expression of K6W-ubiquitin in the lens and lens cells results in accumulation of intracellular aggregates and also slows cell proliferation and the differentiation program, including expression of lens specific proteins, differentiation of epithelial cells into fibers, achieving proper fiber cell morphology, and removal of nuclei. The latter is critical for transparency, but the mechanism by which cell nuclei are removed has remained an age old enigma. This was also solved by expressing K6W-Ub. p27kip, a UPP substrate accumulates in lenses which express K6W-Ub. This precludes phosphorylation of nuclear lamin by the mitotic kinase, a prerequisite for disassembly of the nuclear membrane. Thus the nucleus remains intact and DNAseIIβ neither gains entry to the nucleus nor degrades the DNA. These results could not be obtained using chemical proteasome inhibitors that cannot be directed to specific tissues. Conclusions and Significance K6W-Ub provides a novel, genetic means to study functions of the UPP because it can be targeted to specific cells and tissues. A fully functional UPP is required to execute most stages of lens differentiation, specifically removal of cell nuclei. In the absence of a functional UPP, small aggregate prone, cataractous lenses are formed.

Pose estimation in heavy clutter using a multi-flash camera - Ming-Yu Liu; Tuzel, O.; Veeraraghavan,A.; Chellapa, Rama; Agrawal,A.; Okuda, H. (Robotics and Automation (ICRA), 2010 IEEE International Conference on, 2010)
We propose a novel solution to object detection, localization and pose estimation with applications in robot vision. The proposed method is especially applicable when the objects of interest may not be richly textured and are immersed in heavy clutter. We show that a multi-flash camera (MFC) provides accurate separation of depth edges and texture edges in such scenes. Then, we reformulate the problem, as one of finding matches between the depth edges obtained in one or more MFC images to the rendered depth edges that are computed offline using 3D CAD model of the objects. In order to facilitate accurate matching of these binary depth edge maps, we introduce a novel cost function that respects both the position and the local orientation of each edge pixel. This cost function is significantly superior to traditional Chamfer cost and leads to accurate matching even in heavily cluttered scenes where traditional methods are unreliable. We present a sub-linear time algorithm to compute the cost function using techniques from 3D distance transforms and integral images. Finally, we also propose a multi-view based pose-refinement algorithm to improve the estimated pose. We implemented the algorithm on an industrial robot arm and obtained location and angular estimation accuracy of the order of 1 mm and 2 #x00B0; respectively for a variety of parts with minimal texture.
Keywords: 3D; algorithm; object; based; camera; multiview; depth; detection; object; detection; pose; distance; edge; edges; cameras; image; edges; integral; estimation; binary; estimation; multiflash; estimation; robot; function; depth; images; location; localization; pose; maps; matching; cost; matching; image; pose-refinement; texture; object; transforms; angular; vision; texture; vision; transforms

Putting the user in the loop: interactive Maximal Marginal Relevance for query-focused summarization - Jimmy Lin; Madnani,Nitin; Dorr, Bonnie J (Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics, 2010)
This work represents an initial attempt to move beyond "single-shot" summarization to interactive summarization. We present an extension to the classic Maximal Marginal Relevance (MMR) algorithm that places a user "in the loop" to assist in candidate selection. Experiments in the complex interactive Question Answering (ciQA) task at TREC 2007 show that interactively-constructed responses are significantly higher in quality than automatically-generated ones. This novel algorithm provides a starting point for future work on interactive summarization.

Ranking continuous probabilistic datasets - Li,Jian; Deshpande, Amol (Proc. VLDB Endow., 2010)
Ranking is a fundamental operation in data analysis and decision support, and plays an even more crucial role if the dataset being explored exhibits uncertainty. This has led to much work in understanding how to rank uncertain datasets in recent years. In this paper, we address the problem of ranking when the tuple scores are uncertain, and the uncertainty is captured using continuous probability distributions (e.g. Gaussian distributions). We present a comprehensive solution to compute the values of a parameterized ranking function (PRF) [18] for arbitrary continuous probability distributions (and thus rank the uncertain dataset); PRF can be used to simulate or approximate many other ranking functions proposed in prior work. We develop exact polynomial time algorithms for some continuous probability distribution classes, and efficient approximation schemes with provable guarantees for arbitrary probability distributions. Our algorithms can also be used for exact or approximate evaluation of k-nearest neighbor queries over uncertain objects, whose positions are modeled using continuous probability distributions. Our experimental evaluation over several datasets illustrates the effectiveness of our approach at efficiently ranking uncertain datasets with continuous attribute uncertainty.

Ranking under temporal constraints - Wang,Lidan; Metzler,Donald; Jimmy Lin (Proceedings of the 19th ACM international conference on Information and knowledge management, 2010)
This paper introduces the notion of temporally constrained ranked retrieval, which, given a query and a time constraint, produces the best possible ranked list within the specified time limit. Naturally, more time should translate into better results, but the ranking algorithm should always produce some results. This property is desirable from a number of perspectives: to cope with diverse users and information needs, as well as to better manage system load and variance in query execution times. We propose two temporally constrained ranking algorithms based on a class of probabilistic prediction models that can naturally incorporate efficiency constraints: one that makes independent feature selection decisions, and the other that makes joint feature selection decisions. Experiments on three different test collections show that both ranking algorithms are able to satisfy imposed time constraints, although the joint model outperforms the independent model in being able to deliver more effective results, especially under tight time constraints, due to its ability to capture feature dependencies.
Keywords: efficiency; Learning to rank; Linear Models

Recognizing offensive strategies from football videos - Ruonan Li; Chellapa, Rama (Image Processing (ICIP), 2010 17th IEEE International Conference on, 2010)
We address the problem of recognizing offensive play strategies from American football play videos. Specifically, we propose a probabilistic model which describes the generative process of an observed football play and takes into account practical issues in real football videos, such as difficulty in identifying offensive players, view changes, and tracking errors. In particular, we exploit the geometric properties of nonlinear spaces of involved variables and design statistical models on these manifolds. Then recognition is performed via 'analysis-by-synthesis' technique. Experiments on a newly established dataset of American football videos demonstrate the effectiveness of the approach.
Keywords: American; analysis; video; changes; image; errors; variables; football; identification; tracking; models; geometric; models; view; play; players; processing; properties; nonlinear; recognition; offensive; recognition; statistical; signal; spaces; offensive; statistical; strategies; technique; design; videos; analysis-by-synthesis

Regulating the Regulators: Modulators of Transcription Factor Activity - Everett,Logan; Hansen,Matthew; Hannenhalli, Sridhar (Computational Biology of Transcription Factor BindingComputational Biology of Transcription Factor Binding, 2010)
Gene transcription is largely regulated by DNA-binding transcription factors ( TFs ). However, the TF activity itself is modulated via, among other things, post-translational modifications ( PTMs ) by specific modification enzymes in response to cellular stimuli. TF-PTMs thus serve as “molecular switchboards” that map upstream signaling events to the downstream transcriptional events. An important long-term goal is to obtain a genome-wide map of “regulatory triplets” consisting of a TF, target gene, and a modulator gene that specifically modulates the regulation of the target gene by the TF. A variety of genome-wide data sets can be exploited by computational methods to obtain a rough map of regulatory triplets, which can guide directed experiments. However, a prerequisite to developing such computational tools is a systematic catalog of known instances of regulatory triplets. We first describe PTM-Switchboard, a recent database that stores triplets of genes such that the ability of one gene (the TF) to regulate a target gene is dependent on one or more PTMs catalyzed by a third gene, the modifying enzyme. We also review current computational approaches to infer regulatory triplets from genome-wide data sets and conclude with a discussion of potential future research. PTM-Switchboard is accessible at http://cagr.pcbi.upenn.edu/PTMswitchboard /

Reversible Post-Translational Carboxylation Modulates the Enzymatic Activity of N-Acetyl-l-ornithine Transcarbamylase - Li,Yongdong; Yu,Xiaolin; Ho,Jeremy; Fushman, David; Allewell,Norma M.; Tuchman,Mendel; Shi,Dashuang (Biochemistry, 2010)
N-Acetyl-l-ornithine transcarbamylase (AOTCase), rather than ornithine transcarbamylase (OTCase), is the essential carbamylase enzyme in the arginine biosynthesis of several plant and human pathogens. The specificity of this unique enzyme provides a potential target for controlling the spread of these pathogens. Recently, several crystal structures of AOTCase from Xanthomonas campestris (xc) have been determined. In these structures, an unexplained electron density at the tip of the Lys302 side chain was observed. Using 13C NMR spectroscopy, we show herein that Lys302 is post-translationally carboxylated. The structure of wild-type AOTCase in a complex with the bisubstrate analogue Nδ-(phosphonoacetyl)-Nα-acetyl-l-ornithine (PALAO) indicates that the carboxyl group on Lys302 forms a strong hydrogen bonding network with surrounding active site residues, Lys252, Ser253, His293, and Glu92 from the adjacent subunit either directly or via a water molecule. Furthermore, the carboxyl group is involved in binding N-acetyl-l-ornithine via a water molecule. Activity assays with the wild-type enzyme and several mutants demonstrate that the post-translational modification of lysine 302 has an important role in catalysis.N-Acetyl-l-ornithine transcarbamylase (AOTCase), rather than ornithine transcarbamylase (OTCase), is the essential carbamylase enzyme in the arginine biosynthesis of several plant and human pathogens. The specificity of this unique enzyme provides a potential target for controlling the spread of these pathogens. Recently, several crystal structures of AOTCase from Xanthomonas campestris (xc) have been determined. In these structures, an unexplained electron density at the tip of the Lys302 side chain was observed. Using 13C NMR spectroscopy, we show herein that Lys302 is post-translationally carboxylated. The structure of wild-type AOTCase in a complex with the bisubstrate analogue Nδ-(phosphonoacetyl)-Nα-acetyl-l-ornithine (PALAO) indicates that the carboxyl group on Lys302 forms a strong hydrogen bonding network with surrounding active site residues, Lys252, Ser253, His293, and Glu92 from the adjacent subunit either directly or via a water molecule. Furthermore, the carboxyl group is involved in binding N-acetyl-l-ornithine via a water molecule. Activity assays with the wild-type enzyme and several mutants demonstrate that the post-translational modification of lysine 302 has an important role in catalysis.

Scaling Populations of a Genetic Algorithm for Job Shop Scheduling Problems Using MapReduce - Di-Wei Huang; Jimmy Lin (Cloud Computing Technology and Science (CloudCom), 2010 IEEE Second International Conference on, 2010)
Inspired by Darwinian evolution, a genetic algorithm (GA) approach is one popular heuristic method for solving hard problems such as the Job Shop Scheduling Problem (JSSP), which is one of the hardest problems lacking efficient exact solutions today. It is intuitive that the population size of a GA may greatly affect the quality of the solution, but it is unclear what are the effects of having population sizes that are significantly greater than typical experiments. The emergence of MapReduce, a framework running on a cluster of computers that aims to provide large-scale data processing, offers great opportunities to investigate this issue. In this paper, a GA is implemented to scale the population using MapReduce. Experiments are conducted on a large cluster, and population sizes up to 107 are inspected. It is shown that larger population sizes not only tend to yield better solutions, but also require fewer generations. Therefore, it is clear that when dealing with a hard problem such as JSSP, an existing GA can be improved by massively scaling up populations with MapReduce, so that the solution can be parallelized and completed in reasonable time.
Keywords: algorithm; job; algorithms; job; computing; genetic; data; large-scale; MapReduce; cloud; problems; parallel; processing; processing; cloud; scheduling; scheduling; parallel; shop

Security analysis for privacy preserving search of multimedia - Lu,W.; Varna,A.L.; Wu,M. (Image Processing (ICIP), 2010)
With the increasing popularity of digital multimedia such asimages and videos and the advent of the cloud computing paradigm, a fast growing amount of private and sensitive mul- timedia data are being stored and managed over the network cloud. To provide enhanced security and privacy protection beyond traditional access control techniques, privacy preserv- ing multimedia retrieval techniques have been proposed re- cently to allow content-based multimedia retrieval directly over encrypted databases and achieve accurate retrieval com- parable to conventional retrieval schemes. In this paper, we introduce a security definition for the privacy preserving re- trieval scenario and show that the recently proposed schemes are secure under the proposed security definition.

Sensing Events Affecting Liquid Flow in a Liquid Distribution System - Patel,Shwetak N.; Fogarty,James A.; Jon Froehlich; Larson,Eric C. (University of Washington, 2010)
By monitoring pressure transients in a liquid within a liquid distribution system using only a single sensor, events such as the opening and closing of valves at specific fixtures are readily detected. The sensor, which can readily be coupled to a faucet bib, transmits an output signal to a computing device. Each such event can be identified by the device based by comparing characteristic features of the pressure transient waveform with previously observed characteristic features for events in the system. These characteristic features, which can include the varying pressure, derivative, and real Cepstrum of the pressure transient waveform, can be used to select a specific fixture where a valve open or close event has occurred. Flow to each fixture and leaks in the system can also be determined from the pressure transient signal. A second sensor disposed at a point disparate from the first sensor provides further event information.

Serodiversity and ecological distribution of Vibrio parahaemolyticus in the Venetian Lagoon, Northeast Italy - Caburlotto,Greta; Haley,Bradd J.; Lleò,Maria M.; Huq,Anwar; Rita R Colwell (Environmental Microbiology Reports, 2010)
Vibrio parahaemolyticus is a natural inhabitant of estuarine and marine environments constituting part of the autochthonous microflora. This species is associated with human gastroenteritis caused by ingestion of contaminated water and undercooked seafood. During the past several years, the number of V. parahaemolyticus gastroenteritis cases have increased worldwide, causing over half of all food-poisoning outbreaks of bacterial origin. Vibrio populations in water are known to be influenced by environmental factors. Notably, it has been shown that in different parts of the world the distribution of V. parahaemolyticus in the marine environment is related to the water temperature. In this study, we identified environmental determinants affecting distribution of V. parahaemolyticus in the Venetian Lagoon, in the Italian North Adriatic Sea. Data obtained revealed that sea surface temperature constitutes the key factor influencing occurrence of V. parahaemolyticus, but salinity and chlorophyll concentration are also important. Serotyping of a collection of V. parahaemolyticus environmental isolates revealed high serodiversity, with serotypes O3:KUT and O1:KUT, belonging to the ‘pandemic group’, occurring with higher frequency. From our results, we conclude that there is no correlation between serotype and specific geographic site or season of the year. However, certain serotypes were isolated in the Lagoon during the entire 18 months of the study, strongly suggesting persistence in this environment.

Shape analysis and its applications in image understanding - Zhe Lin; Davis, Larry S. (IEEE transactions on pattern analysis and machine intelligence, 2010)
We propose a shape-based, hierarchical part-template matching approach to simultaneous human detection and segmentation combining local part-based and global shape-template-based schemes. The approach relies on the key idea of matching a part-template tree to images hierarchically to detect humans and estimate their poses. For learning a generic human detector, a pose-adaptive feature computation scheme is developed based on a tree matching approach. Instead of traditional concatenation-style image location-based feature encoding, we extract features adaptively in the context of human poses and train a kernel-SVM classifier to separate human/nonhuman patterns. Specifically, the features are collected in the local context of poses by tracing around the estimated shape boundaries. We also introduce an approach to multiple occluded human detection and segmentation based on an iterative occlusion compensation scheme. The output of our learned generic human detector can be used as an initial set of human hypotheses for the iterative optimization. We evaluate our approaches on three public pedestrian data sets (INRIA, MIT-CBCL, and USC-B) and two crowded sequences from Caviar Benchmark and Munich Airport data sets.

Shape-based human detection and segmentation via hierarchical part-template matching - Lin,Z.; Davis, Larry S. (Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2010)
We propose a shape-based, hierarchical part-template matching approach to simultaneous human detection and segmentation combining local part-based and global shape-template-based schemes. The approach relies on the key idea of matching a part-template tree to images hierarchically to detect humans and estimate their poses. For learning a generic human detector, a pose-adaptive feature computation scheme is developed based on a tree matching approach. Instead of traditional concatenation-style image location-based feature encoding, we extract features adaptively in the context of human poses and train a kernel-SVM classifier to separate human/nonhuman patterns. Specifically, the features are collected in the local context of poses by tracing around the estimated shape boundaries. We also introduce an approach to multiple occluded human detection and segmentation based on an iterative occlusion compensation scheme. The output of our learned generic human detector can be used as an initial set of human hypotheses for the iterative optimization. We evaluate our approaches on three public pedestrian data sets (INRIA, MIT-CBCL, and USC-B) and two crowded sequences from Caviar Benchmark and Munich Airport data sets.

SPECIAL SECTION ON SHAPE ANALYSIS AND ITS APPLICATIONS IN IMAGE UNDERSTANDING - Srivastava, A.; Damon,J.N.; Dryden,I.L.; Jermyn,I.H.; Das,S.; Vaswani, N.; Huckemann,S.; Hotz,T.; Munk,A.; Lin,Z.; others (IEEE Transactions on Pattern Analysis and Machine Intelligence, 2010)