System and Method for Optimal Verification of Operations on Dynamic Sets - Charalampos Papamanthou; Tamassia, Roberto; Triandopoulos, Nikolaos
A system and method for cryptographically checking the correctness of outsourced set operations performed by an untrusted server over a dynamic collection of sets that are owned (and updated) by a trusted source is disclosed. The system and method provides new authentication mechanisms that allow any entity to publicly verify a proof attesting the correctness of primitive set operations such as intersection, union, subset and set difference. Based on a novel extension of the security properties of bilinear-map accumulators as well as on a primitive called accumulation tree, the system and method achieves optimal verification and proof complexity, as well as optimal update complexity, while incurring no extra asymptotic space overhead. The method provides an efficient proof construction, adding a logarithmic overhead to the computation of the answer of a set-operation query. Applications of interest include efficient verification of keyword search and database queries.

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

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

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

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

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)

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

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

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

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

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)

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

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

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

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

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

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

Cross-talk among flesh-eating Aeromonas hydrophila strains in mixed infection leading to necrotizing fasciitis - Ponnusamy, Duraisamy; Kozlova, Elena V.; Sha, Jian; Erova, Tatiana E.; Azar, Sasha R.; Fitts, Eric C.; Kirtley, Michelle L.; Tiner, Bethany L.; Andersson, Jourdan A.; Grim, Christopher J.; Isom, Richard P.; Hasan, Nur A.; et al. (Proceedings of the National Academy of Sciences, 2016)
Necrotizing fasciitis (NF) caused by flesh-eating bacteria is associated with high case fatality. In an earlier study, we reported infection of an immunocompetent individual with multiple strains of Aeromonas hydrophila (NF1–NF4), the latter three constituted a clonal group whereas NF1 was phylogenetically distinct. To understand the complex interactions of these strains in NF pathophysiology, a mouse model was used, whereby either single or mixed A. hydrophila strains were injected intramuscularly. NF2, which harbors exotoxin A (exoA) gene, was highly virulent when injected alone, but its virulence was attenuated in the presence of NF1 (exoA-minus). NF1 alone, although not lethal to animals, became highly virulent when combined with NF2, its virulence augmented by cis-exoA expression when injected alone in mice. Based on metagenomics and microbiological analyses, it was found that, in mixed infection, NF1 selectively disseminated to mouse peripheral organs, whereas the other strains (NF2, NF3, and NF4) were confined to the injection site and eventually cleared. In vitro studies showed NF2 to be more effectively phagocytized and killed by macrophages than NF1. NF1 inhibited growth of NF2 on solid media, but ExoA of NF2 augmented virulence of NF1 and the presence of NF1 facilitated clearance of NF2 from animals either by enhanced priming of host immune system or direct killing via a contact-dependent mechanism.

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

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)

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

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

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

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

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

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

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

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 ...

Ocean Warming and Spread of Pathogenic Vibrios in the Aquatic Environment - Vezzulli, Luigi; Rita R Colwell; Pruzzo, Carla (Microbial Ecology, 2013)
Vibrios are among the most common bacteria that inhabit surface waters throughout the world and are responsible for a number of severe infections both in humans and animals. Several reports recently showed that human Vibrio illnesses are increasing worldwide including fatal acute diarrheal diseases, such as cholera, gastroenteritis, wound infections, and septicemia. Many scientists believe this increase may be associated with global warming and rise in sea surface temperature (SST), although not enough evidence is available to support a causal link between emergence of Vibrio infections and climate warming. The effect of increased SST in promoting spread of vibrios in coastal and brackish waters is considered a causal factor explaining this trend. Field and laboratory studies carried out over the past 40 years supported this hypothesis, clearly showing temperature promotes Vibrio growth and persistence in the aquatic environment. Most recently, a long-term retrospective microbiological study carried out in the coastal waters of the southern North Sea provided the first experimental evidence for a positive and significant relationship between SST and Vibrio occurrence over a multidecadal time scale. As a future challenge, macroecological studies of the effects of ocean warming on Vibrio persistence and spread in the aquatic environment over large spatial and temporal scales would conclusively support evidence acquired to date combined with studies of the impact of global warming on epidemiologically relevant variables, such as host susceptibility and exposure. Assessing a causal link between ongoing climate change and enhanced growth and spread of vibrios and related illness is expected to improve forecast and mitigate future outbreaks associated with these pathogens.

Parallel and Dynamic Searchable Symmetric Encryption - Kamara, Seny; Charalampos Papamanthou (Financial Cryptography and Data Security, 2013)
Searchable symmetric encryption (SSE) enables a client to outsource a collection of encrypted documents in the cloud and retain the ability to perform keyword searches without revealing information about the contents of the documents and queries. Although efficient SSE constructions are known, previous solutions are highly sequential. This is mainly due to the fact that, currently, the only method for achieving sub-linear time search is the inverted index approach (Curtmola, Garay, Kamara and Ostrovsky, CCS ’06) which requires the search algorithm to access a sequence of memory locations, each of which is unpredictable and stored at the previous location in the sequence. Motivated by advances in multi-core architectures, we present a new method for constructing sub-linear SSE schemes. Our approach is highly parallelizable and dynamic. With roughly a logarithmic number of cores in place, searches for a keyword w in our scheme execute in o(r) parallel time, where r is the number of documents containing keyword w (with more cores, this bound can go down to O(logn), i.e., independent of the result size r). Such time complexity outperforms the optimal Θ(r) sequential search time—a similar bound holds for the updates. Our scheme also achieves the following important properties: (a) it enjoys a strong notion of security, namely security against adaptive chosen-keyword attacks; (b) compared to existing sub-linear dynamic SSE schemes (e.g., Kamara, Papamanthou, Roeder, CCS ’12), updates in our scheme do not leak any information, apart from information that can be inferred from previous search tokens; (c) it can be implemented efficiently in external memory (with logarithmic I/O overhead). Our technique is simple and uses a red-black tree data structure; its security is proven in the random oracle model.
Keywords: cloud storage; Computer Appl. in Administrative Data Processing; Data Encryption; e-Commerce/e-business; parallel search; Searchable encryption; Systems and Data Security

Practical Dynamic Proofs of Retrievability - Shi, Elaine; Stefanov, Emil; Charalampos Papamanthou (CCS '13 Proceedings of the 2013 ACM SIGSAC Conference on Computer & Communications Security, 2013)
Proofs of Retrievability (PoR), proposed by Juels and Kaliski in 2007, enable a client to store n file blocks with a cloud server so that later the server can prove possession of all the data in a very efficient manner (i.e., with constant computation and bandwidth). Although many efficient PoR schemes for static data have been constructed, only two dynamic PoR schemes exist. The scheme by Stefanov et. al. (ACSAC 2012) uses a large of amount of client storage and has a large audit cost. The scheme by Cash (EUROCRYPT 2013) is mostly of theoretical interest, as it employs Oblivious RAM (ORAM) as a black box, leading to increased practical overhead (e.g., it requires about 300 times more bandwidth than our construction). We propose a dynamic PoR scheme with constant client storage whose bandwidth cost is comparable to a Merkle hash tree, thus being very practical. Our construction outperforms the constructions of Stefanov et. al. and Cash et. al., both in theory and in practice. Specifically, for n outsourced blocks of beta bits each, writing a block requires beta+O(lambdalog n) bandwidth and O(betalog n) server computation (lambda is the security parameter). Audits are also very efficient, requiring beta+O(lambda^2log n) bandwidth. We also show how to make our scheme publicly verifiable, providing the first dynamic PoR scheme with such a property. We finally provide a very efficient implementation of our scheme.
Keywords: dynamic proofs of retrievability; erasure code; por

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

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

Signatures of Correct Computation - Charalampos Papamanthou; Shi, Elaine; Tamassia, Roberto (Theory of Cryptography, 2013)
We introduce Signatures of Correct Computation (SCC), a new model for verifying dynamic computations in cloud settings. In the SCC model, a trusted source outsources a function f to an untrusted server, along with a public key for that function (to be used during verification). The server can then produce a succinct signature σ vouching for the correctness of the computation of f, i.e., that some result v is indeed the correct outcome of the function f evaluated on some point a. There are two crucial performance properties that we want to guarantee in an SCC construction: (1) verifying the signature should take asymptotically less time than evaluating the function f; and (2) the public key should be efficiently updated whenever the function changes. We construct SCC schemes (satisfying the above two properties) supporting expressive manipulations over multivariate polynomials, such as polynomial evaluation and differentiation. Our constructions are adaptively secure in the random oracle model and achieve optimal updates, i.e., the function’s public key can be updated in time proportional to the number of updated coefficients, without performing a linear-time computation (in the size of the polynomial). We also show that signatures of correct computation imply Publicly Verifiable Computation (PVC), a model recently introduced in several concurrent and independent works. Roughly speaking, in the SCC model, any client can verify the signature σ and be convinced of some computation result, whereas in the PVC model only the client that issued a query (or anyone who trusts this client) can verify that the server returned a valid signature (proof) for the answer to the query. Our techniques can be readily adapted to construct PVC schemes with adaptive security, efficient updates and without the random oracle model.
Keywords: Algorithm Analysis and Problem Complexity; Computation by Abstract Devices; Data Encryption; Systems and Data Security

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

Streaming Authenticated Data Structures - Charalampos Papamanthou; Shi, Elaine; Tamassia, Roberto; Yi, Ke (Advances in Cryptology – EUROCRYPT 2013, 2013)
We consider the problem of streaming verifiable computation, where both a verifier and a prover observe a stream of n elements x 1,x 2,…,x n and the verifier can later delegate some computation over the stream to the prover. The prover must return the output of the computation, along with a cryptographic proof to be used for verifying the correctness of the output. Due to the nature of the streaming setting, the verifier can only keep small local state (e.g., logarithmic) which must be updatable in a streaming manner and with no interaction with the prover. Such constraints make the problem particularly challenging and rule out applying existing verifiable computation schemes. We propose streaming authenticated data structures, a model that enables efficient verification of data structure queries on a stream. Compared to previous work, we achieve an exponential improvement in the prover’s running time: While previous solutions have linear prover complexity (in the size of the stream), even for queries executing in sublinear time (e.g., set membership), we propose a scheme with O(logM logn)O(\log M\ log n) prover complexity, where n is the size of the stream and M is the size of the universe of elements. Our schemes support a series of expressive queries, such as (non-)membership, successor, range search and frequency queries, over an ordered universe and even in higher dimensions. The central idea of our construction is a new authentication tree, called generalized hash tree. We instantiate our generalized hash tree with a hash function based on lattices assumptions, showing that it enjoys suitable algebraic properties that traditional Merkle trees lack. We exploit such properties to achieve our results.
Keywords: Algorithm Analysis and Problem Complexity; Data Encryption; Discrete Mathematics in Computer Science; 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.

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

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

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

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

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

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

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

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.

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

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

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

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)

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

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

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

Local Segmentation of Touching Characters using Contour based Shape Decomposition - Kang,Le; David Doermann; Cao,Huiagu; Prasad,Rohit; Natarajan,Prem (Document Analysis Systems, 2012)
We propose a contour based shape decomposition approach that provides local segmentation of touching characters. The shape contour is linearized into edgelets and edgelets are merged into boundary fragments. Connection cost between boundary fragments is obtained by considering local smoothness, connection length and a stroke-level property Similar Stroke Rate. Samples of connections among boundary fragments are randomly generated and the one with the minimum global cost is selected to produce optimal segmentation of the shape. To obtain a binary segmentation using this approach, we make an iterative search for the parameters that yields two components on a shape. Experimental results on a number of synthetic shape images and the LTP dataset showed that this contour based shape decomposition technique is promising and it is effective on providing local segmentation of touching characters.

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

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.

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

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

Querying event sequences by exact match or similarity search: Design and empirical evaluation - Wongsuphasawat,Krist; Plaisant, Catherine; Taieb-Maimon,Meirav; Shneiderman, Ben (Interacting with Computers, 2012)
Specifying event sequence queries is challenging even for skilled computer professionals familiar with SQL. Most graphical user interfaces for database search use an exact match approach, which is often effective, but near misses may also be of interest. We describe a new similarity search interface, in which users specify a query by simply placing events on a blank timeline and retrieve a similarity-ranked list of results. Behind this user interface is a new similarity measure for event sequences which the users can customize by four decision criteria, enabling them to adjust the impact of missing, extra, or swapped events or the impact of time shifts. We describe a use case with Electronic Health Records based on our ongoing collaboration with hospital physicians. A controlled experiment with 18 participants compared exact match and similarity search interfaces. We report on the advantages and disadvantages of each interface and suggest a hybrid interface combining the best of both.
Keywords: Event sequence; Similan; similarity measure; Similarity Search; temporal categorical data; Temporal query interface

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

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

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

TACI: Taxonomy-Aware Catalog Integration - Papadimitriou,P.; Tsaparas,P.; Fuxman,A.; Getoor, Lise (IEEE Transactions on Knowledge and Data Engineering (TKDE), 2012)
A fundamental data integration task faced by online commercial portals and commerce search engines is the integration of products coming from multiple providers to their product catalogs. In this scenario, the commercial portal has its own taxonomy (the “master taxonomy”), while each data provider organizes its products into a different taxonomy (the “provider taxonomy”). In this paper, we consider the problem of categorizing products from the data providers into the master taxonomy, while making use of the provider taxonomy information. Our approach is based on a taxonomy-aware processing step that adjusts the results of a text-based classifier to ensure that products that are close together in the provider taxonomy remain close in the master taxonomy. We formulate this intuition as a structured prediction optimization problem. To the best of our knowledge, this is the first approach that leverages the structure of taxonomies in order to enhance catalog integration. We propose algorithms that are scalable and thus applicable to the large datasets that are typical on the Web. We evaluate our algorithms on real-world data and we show that taxonomy-aware classification provides a significant improvement over existing approaches.

Towards event sequence representation, reasoning and visualization for EHR data - Tao,Cui; Wongsuphasawat,Krist; Clark,Kimberly; Plaisant, Catherine; Shneiderman, Ben; Chute,Christopher G. (Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, 2012)
Efficient analysis of event sequences and the ability to answer time-related, clinically important questions can accelerate clinical research in several areas such as causality assessments, decision support systems, and retrospective studies. The Clinical Narrative Temporal Reasoning Ontology (CNTRO)-based system is designed for semantically representing, annotating, and inferring temporal relations and constraints for clinical events in Electronic Health Records (EHR) represented in both structured and unstructured ways. The LifeFlow system is designed to support an interactive exploration of event sequences using visualization techniques. The combination of the two systems will provide a comprehensive environment for users to visualize inferred temporal relationships from EHR data. This paper discusses our preliminary efforts on connecting the two systems and the benefits we envision from such an environment.
Keywords: ehr; semantic web; temporal relation reasoning; time trend visualization

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

We are what we eat: how the diet of infants affects their gut microbiome - Pop, Mihai (Genome Biology, 2012)
Simultaneous analysis of the gut microbiome and host gene expression in infants reveals the impact of diet (breastfeeding versus formula) on host-microbiome interactions.

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

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

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.

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

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.

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

Analyzing Incident Management Event Sequences with Interactive Visualization - Guerra Gómez,J.; Wongsuphasawat,K.; Wang,T. D; Pack,M.; Plaisant, Catherine (Transportation Research Board 90th Annual Meeting Compendium of Papers, 2011)
While traditional safety and incident analysis has mostly focused on incident attributesdata, such as the location and time of the incident, there are other aspects in incident response that are temporal in nature and are more difficult to analyze. We describe a visual analytics tool for temporal data exploration, called LifeFlow, used for the analysis of incident response data. LifeFlow provides user-controlled overviews of event sequences (e.g. notification, arrival, clearance etc). It allows analysts to interactively explore temporal patterns, find anomalies in sequences and compare management practices. This type of analysis can potentially lead to process improvements and save human lives. We used NCHRP traffic incident data with more than 200,000 incidents are reported by 8 different agencies in a period of about 28 months. Our experience suggest that even non expert analysts can spot many anomalies in the data using the LifeFlow overviews, and are able to rapidly ask many questions and find differences between agencies.

Annotated probabilistic temporal logic - Shakarian,Paulo; Parker,Austin; Simari,Gerardo; V.S. Subrahmanian (ACM Trans. Comput. Logic, 2011)
The semantics of most logics of time and probability is given via a probability distribution over threads, where a thread is a structure specifying what will be true at different points in time (in the future). When assessing the probabilities of statements such as “Event a will occur within 5 units of time of event b,” there are many different semantics possible, even when assessing the truth of this statement within a single thread. We introduce the syntax of annotated probabilistic temporal (APT) logic programs and axiomatically introduce the key notion of a frequency function (for the first time) to capture different types of intrathread reasoning, and then provide a semantics for intrathread and interthread reasoning in APT logic programs parameterized by such frequency functions. We develop a comprehensive set of complexity results for consistency checking and entailment in APT logic programs, together with sound and complete algorithms to check consistency and entailment. The basic algorithms use linear programming, but we then show how to substantially and correctly reduce the sizes of these linear programs to yield better computational properties. We describe a real world application we are developing using APT logic programs.
Keywords: frequency functions; imprecise probabilities; Probabilistic and temporal reasoning; threads

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

Approximation algorithms for throughput maximization in wireless networks with delay constraints - Guanhong Pei; Anil Kumar,V. S; Parthasarathy,S.; Srinivasan, Aravind (2011 Proceedings IEEE INFOCOM, 2011)
We study the problem of throughput maximization in multi-hop wireless networks with end-to-end delay constraints for each session. This problem has received much attention starting with the work of Grossglauser and Tse (2002), and it has been shown that there is a significant tradeoff between the end-to-end delays and the total achievable rate. We develop algorithms to compute such tradeoffs with provable performance guarantees for arbitrary instances, with general interference models. Given a target delay-bound Δ(c) for each session c, our algorithm gives a stable flow vector with a total throughput within a factor of O (logΔm/log log Δm) of the maximum, so that the per-session (end-to-end) delay is O ((logΔm/log log Δm Δ(c))2), where Δm = maxc{Δ(c)}; note that these bounds depend only on the delays, and not on the network size, and this is the first such result, to our knowledge.
Keywords: Approximation algorithms; Approximation methods; approximation theory; Delay; delay constraints; delays; general interference model; Interference; multihop wireless networks; optimisation; Optimized production technology; radio networks; radiofrequency interference; target delay bound; Throughput; throughput maximization; Wireless networks

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

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies - Wetzel,Joshua; Kingsford, Carl; Pop, Mihai (BMC Bioinformatics, 2011)
Next-generation sequencing technologies allow genomes to be sequenced more quickly and less expensively than ever before. However, as sequencing technology has improved, the difficulty of de novo genome assembly has increased, due in large part to the shorter reads generated by the new technologies. The use of mated sequences (referred to as mate-pairs) is a standard means of disambiguating assemblies to obtain a more complete picture of the genome without resorting to manual finishing. Here, we examine the effectiveness of mate-pair information in resolving repeated sequences in the DNA (a paramount issue to overcome). While it has been empirically accepted that mate-pairs improve assemblies, and a variety of assemblers use mate-pairs in the context of repeat resolution, the effectiveness of mate-pairs in this context has not been systematically evaluated in previous literature.

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.

Bambus 2: scaffolding metagenomes - Koren, S.; Treangen, T.J.; Pop, Mihai (Bioinformatics, 2011)

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

Broadband internet performance: A view from the gateway - Sundaresan,S.; de Donato,W.; Feamster, Nick; Teixeira,R.; Crawford,S.; Pescapè,A. (SIGCOMM-Computer Communication Review, 2011)
We present the first study of network access link performance mea-sured directly from home gateway devices. Policymakers, ISPs, and users are increasingly interested in studying the performance of Internet access links. Because of many confounding factors in a home network or on end hosts, however, thoroughly understanding access network performance requires deploying measurement in- frastructure in users’ homes as gateway devices. In conjunction with the Federal Communication Commission’s study of broad- band Internet access in the United States, we study the throughput and latency of network access links using longitudinal measure- ments from nearly 4,000 gateway devices across 8 ISPs from a de- ployment of over 4,200 devices. We study the performance users achieve and how various factors ranging from the user’s choice of modem to the ISP’s traffic shaping policies can affect performance. Our study yields many important findings about the characteristics of existing access networks. Our findings also provide insights into the ways that access network performance should be measured and presented to users, which can help inform ongoing broader efforts to benchmark the performance of access networks.

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

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

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

Component-based restoration of speckled images - Patel, Vishal M.; Easley,G. R; Chellapa, Rama (2011 18th IEEE International Conference on Image Processing (ICIP), 2011)
Many coherent imaging modalities are often characterized by a multiplicative noise, known as speckle which often makes the interpretation of data difficult. In this paper, we present a speckle reduction algorithm based on separating the structure and texture components of SAR images. An iterative algorithm based on surrogate functionals is presented that solves the component optimization formulation. Experiments indicate this proposed method performs favorably compared to state-of-the-art speckle reduction methods.
Keywords: coherent imaging modalities; component optimization formulation; component-based restoration; Dictionaries; image restoration; iterative algorithm; iterative methods; multiplicative noise; NOISE; optimisation; radar imaging; SAR images; Speckle; speckle reduction algorithm; speckled images; structure components; surrogate functionals; synthetic aperture radar; texture components; transforms; TV

A computational framework for authoring and searching product design specifications - Weissman,Alexander; Petrov,Martin; Gupta, Satyandra K. (Advanced Engineering Informatics, 2011)
The development of product design specifications (PDS) is an important part of the product development process. Incompleteness, ambiguity, or inconsistency in the PDS can lead to problems during the design process and may require unnecessary design iterations. This generally results in increased design time and cost. Currently, in many organizations, PDS are written using word processors. Since documents written by different authors can be inconsistent in style and word choice, it is difficult to automatically search for specific requirements. Moreover, this approach does not allow the possibility of automated design verification and validation against the design requirements and specifications.In this paper, we present a computational framework and a software tool based on this framework for writing, annotating, and searching computer-interpretable PDS. Our approach allows authors to write requirement statements in natural language to be consistent with the existing authoring practice. However, using mathematical expressions, keywords from predefined taxonomies, and other metadata the author of PDS can then annotate different parts of the requirement statements. This approach provides unambiguous meaning to the information contained in PDS, and helps to eliminate mistakes later in the process when designers must interpret requirements. Our approach also enables users to construct a new PDS document from the results of the search for requirements of similar devices and in similar contexts. This capability speeds up the process of creating PDS and helps authors write more detailed documents by utilizing previous, well written PDS documents. Our approach also enables checking for internal inconsistencies in the requirement statements.
Keywords: Engineering design; Product design specifications; Requirements engineering

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

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

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

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

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.

Document Image Classification and Labeling using Multiple Instance Learning - Kumar,Jayant; Pillai,Jaishanker; David Doermann (Intl. Conf. on Document Analysis and Recognition (ICDAR 11), 2011)
The labeling of large sets of images for training or testing analysis systems can be a very costly and time-consuming process. Multiple instance learning (MIL) is a generalization of traditional supervised learning which relaxes the need for exact labels on training instances. Instead, the labels are required only for a set of instances known as bags. In this paper, we apply MIL to the retrieval and localization of signatures and the retrieval of images containing machine-printed text, and show that a gain of 15-20% in performance can be achieved over the supervised learning with weak-labeling. We also compare our approach to supervised learning with fully annotated training data and report a competitive accuracy for MIL. Using our experiments on real-world datasets, we show that MIL is a good alternative when the training data has only document-level annotation.

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

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

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

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.

Example-Driven Manifold Priors for Image Deconvolution - Ni,Jie; Turaga,P.; Patel, Vishal M.; Chellapa, Rama (Image Processing, IEEE Transactions on, 2011)
Image restoration methods that exploit prior information about images to be estimated have been extensively studied, typically using the Bayesian framework. In this paper, we consider the role of prior knowledge of the object class in the form of a patch manifold to address the deconvolution problem. Specifically, we incorporate unlabeled image data of the object class, say natural images, in the form of a patch-manifold prior for the object class. The manifold prior is implicitly estimated from the given unlabeled data. We show how the patch-manifold prior effectively exploits the available sample class data for regularizing the deblurring problem. Furthermore, we derive a generalized cross-validation (GCV) function to automatically determine the regularization parameter at each iteration without explicitly knowing the noise variance. Extensive experiments show that this method performs better than many competitive image deconvolution methods.
Keywords: Bayesian; cross-validation; data; Bayes; deconvolution; image; determination; deblurring; estimation; framework; GCV; function; automatic; function; image; image; image; patch-manifold; manifold; method; iteration; method; natural; methods; deconvolution; image; methods; natural; parameter; prior; generalized; prior; unlabeled; problem; regularization; regularization; example-driven; restoration; restoration; iterative; scenes; parameter

Extracting Insights from Electronic Health Records: Case Studies, a Visual Analytics Process Model, and Design Recommendations - Wang,Taowei; Wongsuphasawat,Krist; Plaisant, Catherine; Shneiderman, Ben (Journal of Medical Systems, 2011)
Current electronic health record (EHR) systems facilitate the storage, retrieval, persistence, and sharing of patient data. However, the way physicians interact with EHRs has not changed much. More specifically, support for temporal analysis of a large number of EHRs has been lacking. A number of information visualization techniques have been proposed to alleviate this problem. Unfortunately, due to their limited application to a single case study, the results are often difficult to generalize across medical scenarios. We present the usage data of Lifelines2 (Wang et al. 2008 ), our information visualization system, and user comments, both collected over eight different medical case studies. We generalize our experience into a visual analytics process model for multiple EHRs. Based on our analysis, we make seven design recommendations to information visualization tools to explore EHR systems.

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

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

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

Hawkeye and AMOS: Visualizing and Assessing the Quality of Genome Assemblies - Schatz,Michael C; Phillippy,Adam M; Sommer,Daniel D; Delcher,Arthur L.; Puiu,Daniela; Narzisi,Giuseppe; Salzberg,Steven L.; Pop, Mihai (Briefings in Bioinformatics, 2011)
Since its launch in 2004, the open-source AMOS project has released several innovative DNA sequence analysis applications including: Hawkeye, a visual analytics tool for inspecting the structure of genome assemblies; the Assembly Forensics and FRCurve pipelines for systematically evaluating the quality of a genome assembly; and AMOScmp, the first comparative genome assembler. These applications have been used to assemble and analyze dozens of genomes ranging in complexity from simple microbial species through mammalian genomes. Recent efforts have been focused on enhancing support for new data characteristics brought on by second- and now third-generation sequencing. This review describes the major components of AMOS in light of these challenges, with an emphasis on methods for assessing assembly quality and the visual analytics capabilities of Hawkeye. These interactive graphical aspects are essential for navigating and understanding the complexities of a genome assembly, from the overall genome structure down to individual bases. Hawkeye and AMOS are available open source at http://amos.sourceforge.net.
Keywords: assembly forensics; DNA Sequencing; genome assembly; visual analytics

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

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

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

Implicitly-weighted total least squares - Park,Sungwoo; O’Leary,Dianne P. (Linear Algebra and its Applications, 2011)
In a total least squares (TLS) problem, we estimate an optimal set of model parameters X , so that ( A - Δ A ) X = B - Δ B , where A is the model matrix, B is the observed data, and Δ A and Δ B are corresponding corrections. When B is a single vector, Rao (1997) and Paige and Strakoš (2002) suggested formulating standard least squares problems, for which Δ A = 0 , and data least squares problems, for which Δ B = 0 , as weighted and scaled TLS problems. In this work we define an implicitly-weighted TLS formulation (ITLS) that reparameterizes these formulations to make computation easier. We derive asymptotic properties of the estimates as the number of rows in the problem approaches infinity, handling the rank-deficient case as well. We discuss the role of the ratio between the variances of errors in A and B in choosing an appropriate parameter in ITLS. We also propose methods for computing the family of solutions efficiently and for choosing the appropriate solution if the ratio of variances is unknown. We provide experimental results on the usefulness of the ITLS family of solutions.
Keywords: Data least squares; Errors in variables; least squares; Linear regression; total least squares; Variance estimation

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

Information Visualization: State of the Field and New Research Directions - Kerren,Andreas; Plaisant, Catherine; Stasko,John T (Information VisualizationInformation Visualization, 2011)

Language Models for Semantic Extraction and Filtering in Video Action Recognition - Tzoukermann,Evelyne; Neumann, Jan; Kosecka,Jana; Fermüller, Cornelia; Perera,Ian; Ferraro,Frank; Sapp,Ben; Chaudhry,Rizwan; Singh,Gautam (Workshops at the Twenty-Fifth AAAI Conference on Artificial Intelligence, 2011)
The paper addresses the following issues: (a) how to represent semantic information from natural language so that a vision model can utilize it? (b) how to extract the salient textual information relevant to vision? For a given domain, we present a new model of semantic extraction that takes into account word relatedness as well as word disambiguation in order to apply to a vision model. We automatically process the text transcripts and perform syntactic analysis to extract dependency relations. We then perform semantic extraction on the output to filter semantic entities related to actions. The resulting data are used to populate a matrix of co-occurrences utilized by the vision processing modules. Results show that explicitly modeling the co-occurrence of actions and tools significantly improved performance.

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

LifeFlow: visualizing an overview of event sequences - Wongsuphasawat,Krist; Guerra Gómez,John Alexis; Plaisant, Catherine; Wang,Taowei David; Taieb-Maimon,Meirav; Shneiderman, Ben (Proceedings of the 2011 annual conference on Human factors in computing systems, 2011)
Event sequence analysis is an important task in many domains: medical researchers may study the patterns of transfers within the hospital for quality control; transportation experts may study accident response logs to identify best practices. In many cases they deal with thousands of records. While previous research has focused on searching and browsing, overview tasks are often overlooked. We introduce a novel interactive visual overview of event sequences called LifeFlow. LifeFlow is scalable, can summarize all possible sequences, and represents the temporal spacing of the events within sequences. Two case studies with healthcare and transportation domain experts are presented to illustrate the usefulness of LifeFlow. A user study with ten participants confirmed that after 15 minutes of training novice users were able to rapidly answer questions about the prevalence and temporal characteristics of sequences, find anomalies, and gain significant insight from the data.
Keywords: Information Visualization; overview visualization; temporal categorical data; timestamped event sequences

LifeFlow: visualizing an overview of event sequences (video preview) - Wongsuphasawat,Krist; Guerra Gómez,John Alexis; Plaisant, Catherine; Wang,Taowei; Taieb-Maimon,Meirav; Shneiderman, Ben (Proceedings of the 2011 annual conference extended abstracts on Human factors in computing systems, 2011)
Event sequence analysis is an important task in many domains: medical researchers may study the patterns of transfers within the hospital for quality control; transportation experts may study accident response logs to identify best practices. In many cases they deal with thousands of records. While previous research has focused on searching and browsing, overview tasks are often overlooked. We introduce a novel interactive visual overview of event sequences called LifeFlow. LifeFlow is scalable, can summarize all possible sequences, and represents the temporal spacing of the events within sequences. In this video, we show an example of patient transfer data and briefly demonstrate how to analyze them with LifeFlow. Please see [11] or visit http:www.cs.umd.eduhcillifeflow for more detail.
Keywords: emergency room; healthcare; Information Visualization; overview visualization; temporal categorical data; timestamped event sequences

Local Response Context Applied to Pedestrian Detection - Schwartz,W.; Davis, Larry S.; Pedrini,H. (Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications, 2011)
Appearing as an important task in computer vision, pedestrian detection has been widely investigated in the recent years. To design a robust detector, we propose a feature descriptor called Local Response Context (LRC). This descriptor captures discriminative information regarding the surrounding of the person’s location by sampling the response map obtained by a generic sliding window detector. A partial least squares regression model using LRC descriptors is learned and employed as a second classification stage (after the execution of the generic detector to obtain the response map). Experiments based on the ETHZ pedestrian dataset show that the proposed approach improves significantly the results achieved by the generic detector alone and is comparable to the state-of-the-art methods.

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

A Longitudinal Study of Pressure Sensing to Infer Real-World Water Usage Events in the Home - Jon Froehlich; Larson,Eric; Saba,Elliot; Campbell,Tim; Atlas,Les; Fogarty,James; Patel,Shwetak (Pervasive 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.

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

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

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

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

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

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

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

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

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

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

Next Generation Sequence Assembly with AMOS - Treangen, T.J.; Sommer, D.D.; Angly, F.E.; Koren, S.; Pop, Mihai (Current Protocols in Bioinformatics, 2011)

A novel feature descriptor based on the shearlet transform - Schwartz, W.R.; da Silva,R.D.; Davis, Larry S.; Pedrini,H. (Image Processing (ICIP), 2011 18th IEEE International Conference on, 2011)
Problems such as image classification, object detection and recognition rely on low-level feature descriptors to represent visual information. Several feature extraction methods have been proposed, including the Histograms of Oriented Gradients (HOG), which captures edge information by analyzing the distribution of intensity gradients and their directions. In addition to directions, the analysis of edge at different scales provides valuable information. Shearlet transforms provide a general framework for analyzing and representing data with anisotropic information at multiple scales. As a consequence, signal singularities, such as edges, can be precisely detected and located in images. Based on the idea of employing histograms to estimate the distribution of edge orientations and on the accurate multi-scale analysis provided by shearlet transforms, we propose a feature descriptor called Histograms of Shearlet Coefficients (HSC). Experimental results comparing HOG with HSC show that HSC provides significantly better results for the problems of texture classification and face identification.
Keywords: analysis; multiscale; analysis; object; classification; face; classification; image; classification; intensity; coefficients; image; descriptor; feature; detection; object; distribution; edge; EXTRACTION; extraction; image; gradient; gradients; histograms; identification; feature; methods; histograms; of; orientations; face; oriented; recognition; feature; recognition; shearlet; recognition; transforms; shearlet; singularities; texture; texture; object; transform; signal

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)

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

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

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

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

Realizing the value of social media requires innovative computing research - Shneiderman, Ben; Preece,Jennifer; Pirolli,Peter (Communications of the ACM, 2011)
How social media are expanding traditional research and development topics for computer and information scientists.

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

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

Remote identification of faces: Problems, prospects, and progress - Chellapa, Rama; Ni,Jie; Patel, Vishal M. (Pattern Recognition Letters, 2011)
Face recognition in unconstrained acquisition conditions is one of the most challenging problems that has been actively researched in recent years. It is well known that many state-of-the-art still face recognition algorithms perform well, when constrained (frontal, well illuminated, high-resolution, sharp, and full) face images are acquired. However, their performance degrades significantly when the test images contain variations that are not present in the training images. In this paper, we highlight some of the key issues in remote face recognition. We define the remote face recognition as one where faces are several tens of meters (10–250 m) from the cameras. We then describe a remote face database which has been acquired in an unconstrained outdoor maritime environment. Recognition performance of a subset of existing still image-based face recognition algorithms is evaluated on the remote face data set. Further, we define the remote re-identification problem as matching a subject at one location with candidate sets acquired at a different location and over time in remote conditions. We provide preliminary experimental results on remote re-identification. It is demonstrated that in addition to applying a good classification algorithm, finding features that are robust to variations mentioned above and developing statistical models which can account for these variations are very important for remote face recognition.
Keywords: Blur; illumination; low-resolution; pose variation; Re-identification; Remote face recognition

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

Robotson Crusoe–or–What Is Common Sense? - Perlis, Don (Logical Formalizations of Commonsense Reasoning — Papers from the AAAI 2011 Spring Symposium, 2011)
I will present a perspective on human-level commonsense behavior (HLCSB) that differs from commonsense reasoning (CSR) as the latter is often characterized in AI. I will argue that HLCSB is not far beyond the reach of current technology, and that it also provides solutions to some of the problems that plague CSR, most notably the brittleness problem. A key is the judicious use of metacognitive monitoring and control, especially in the area of automated learning.

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

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.

Shape Codebook based Handwritten and Machine Printed Text Zone Extraction - Kumar,Jayant; Prasad,Rohit; Cao,Huiagu; Abd-Almageed, Wael; David Doermann; Natarajan,Prem (Document Recognition and Retrieval, 2011)
We present a novel method for extracting handwritten and printed text zones from noisy document images with mixed content. We use Triple-Adjacent-Segment (TAS) based features which encode local shape characteristics of text in a consistent manner. We first construct two different codebooks of the shape features extracted from a set of handwritten and printed text documents. In the next step, we compute the normalized histogram of codewords for each segmented zone and use it to train Support Vector Machine (SVM) classifier. Due to a codebook based approach, our method is robust to the background noise present in the image. The TAS features used are invariant to translation, scale and rotation of text. In our experimental results, we show that a pixel-weighted zone classification accuracy of 98% can be achieved for noisy Arabic documents. Further, we demonstrate the effectiveness of our method for document page classification and show that a high precision can be achieved for machine printed documents. The proposed method is robust to the size of zones, which may contain text content at word, line or paragraph level.

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

Sparsity-motivated automatic target recognition - Patel, Vishal M.; Nasrabadi,Nasser M.; Chellapa, Rama (Applied OpticsAppl. Opt., 2011)
We present an automatic target recognition algorithm using the recently developed theory of sparse representations and compressive sensing. We show how sparsity can be helpful for efficient utilization of data for target recognition. We verify the efficacy of the proposed algorithm in terms of the recognition rate and confusion matrices on the well known Comanche (Boeing–Sikorsky, USA) forward-looking IR data set consisting of ten different military targets at different orientations.
Keywords: IMAGE PROCESSING; Image recognition, algorithms and filters; pattern recognition; Vision - patterns and recognition

Special Issue on Video Analysis on Resource-Limited Systems - Chellapa, Rama; Cavallaro, A.; Wu,Y.; Shan, C.; Fu, Y.; Pulli, K. (IEEE Transactions on Circuits and Systems for Video Technology, 2011)
The 17 papers in this special issue focus on resource-limited systems.
Keywords: computational complexity; Image Enhancement; Special issues and sections; Video compression

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)

Synthesis-based recognition of low resolution faces - Shekhar, S.; Patel, Vishal M.; Chellapa, Rama (2011 International Joint Conference on Biometrics (IJCB), 2011)
Recognition of low resolution face images is a challenging problem in many practical face recognition systems. Methods have been proposed in the face recognition literature for the problem when the probe is of low resolution, and a high resolution gallery is available for recognition. These methods modify the probe image such that the resultant image provides better discrimination. We formulate the problem differently by leveraging the information available in the high resolution gallery image and propose a generative approach for classifying the probe image. An important feature of our algorithm is that it can handle resolution changes along with illumination variations. The effective- ness of the proposed method is demonstrated using standard datasets and a challenging outdoor face dataset. It is shown that our method is efficient and can perform significantly better than many competitive low resolution face recognition algorithms.
Keywords: Dictionaries; Face; face images; face recognition; face recognition literature; face recognition systems; illumination variations; image resolution; low resolution faces; Organizations; PROBES; support vector machines; synthesis based recognition

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

A task taxonomy of network evolution analysis - Ahn,JW; Plaisant, Catherine; Shneiderman, Ben (University of Maryland, Human-Computer Interaction Lab Tech Report HCIL-2011-09, 2011)
Visualization is a useful tool for understanding the nature of networks. The recent growth of social media requires morepowerful visualization techniques beyond static network diagrams. One of the most important challenges is the visualization of temporal network evolution. In order to provide strong temporal visualization methods, we need to understand what tasks users accomplish. This study provides a taxonomy of the temporal network visualization tasks. We identify (1) the entities, (2) the properties to be visualized, and (3) the hierarchy of temporal features, which were extracted by surveying existing temporal network visualization systems. By building and examining the task taxonomy, we report which tasks have been covered so far and suggest additions for designing the future visualizations. We also present example visualizations constructed using the task taxonomy for a social networking site in order to validate the quality of the taxonomy.

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

Temporal Visualization of Social Network Dynamics: Prototypes for Nation of Neighbors - Ahn,Jae-wook; Taieb-Maimon,Meirav; Sopan,Awalin; Plaisant, Catherine; Shneiderman, Ben (Social Computing, Behavioral-Cultural Modeling and PredictionSocial Computing, Behavioral-Cultural Modeling and Prediction, 2011)
Information visualization is a powerful tool for analyzing the dynamic nature of social communities. Using Nation of Neighbors community network as a testbed, we propose five principles of implementing temporal visualizations for social networks and present two research prototypes: NodeXL and TempoVis. Three different states are defined in order to visualize the temporal changes of social networks. We designed the prototypes to show the benefits of the proposed ideas by letting users interactively explore temporal changes of social networks.

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

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

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

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.

Using classifier cascades for scalable e-mail classification - Pujara,J.; Daumé, Hal; Getoor, Lise (Collaboration, Electronic Messaging, Anti-Abuse and Spam Conference, ACM International Conference Proceedings Series, 2011)
In many real-world scenarios, we must make judgments in the presence of computational constraints. One common computational constraint arises when the features used to make a judgment each have differing acquisition costs, but there is a fixed total budget for a set of judgments. Par- ticularly when there are a large number of classifications that must be made in a real-time, an intelligent strategy for optimizing accuracy versus computational costs is essential. E-mail classification is an area where accurate and timely results require such a trade-off. We identify two scenarios where intelligent feature acquisition can improve classifier performance. In granular classification we seek to clas- sify e-mails with increasingly specific labels structured in a hierarchy, where each level of the hierarchy requires a differ- ent trade-off between cost and accuracy. In load-sensitive classification, we classify a set of instances within an ar- bitrary total budget for acquiring features. Our method, Adaptive Classifier Cascades (ACC), designs a policy to combine a series of base classifiers with increasing compu- tational costs given a desired trade-off between cost and ac- curacy. Using this method, we learn a relationship between feature costs and label hierarchies, for granular classification and cost budgets, for load-sensitive classification. We eval- uate our method on real-world e-mail datasets with realistic estimates of feature acquisition cost, and we demonstrate su- perior results when compared to baseline classifiers that do not have a granular, cost-sensitive feature acquisition policy.

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

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

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

Visualizing Missing Data: Graph Interpretation User Study - Drizd,Terence; Eaton,Cyntrica; Plaisant, Catherine (IFIP Lecture Notes in Computer Science (LNCS), 2011)
Visualizing Missing Data: Graph Interpretation User Study

Achieving anonymity via clustering - Aggarwal,Gagan; Panigrahy,Rina; Feder,Tomás; Thomas,Dilys; Kenthapadi,Krishnaram; Khuller, Samir; Zhu,An (ACM Trans. Algorithms, 2010)
Publishing data for analysis from a table containing personal records, while maintaining individual privacy, is a problem of increasing importance today. The traditional approach of deidentifying records is to remove identifying fields such as social security number, name, etc. However, recent research has shown that a large fraction of the U.S. population can be identified using nonkey attributes (called quasi-identifiers) such as date of birth, gender, and zip code. The k-anonymity model protects privacy via requiring that nonkey attributes that leak information are suppressed or generalized so that, for every record in the modified table, there are at least k−1 other records having exactly the same values for quasi-identifiers. We propose a new method for anonymizing data records, where quasi-identifiers of data records are first clustered and then cluster centers are published. To ensure privacy of the data records, we impose the constraint that each cluster must contain no fewer than a prespecified number of data records. This technique is more general since we have a much larger choice for cluster centers than k-anonymity. In many cases, it lets us release a lot more information without compromising privacy. We also provide constant factor approximation algorithms to come up with such a clustering. This is the first set of algorithms for the anonymization problem where the performance is independent of the anonymity parameter k. We further observe that a few outlier points can significantly increase the cost of anonymization. Hence, we extend our algorithms to allow an ε fraction of points to remain unclustered, that is, deleted from the anonymized publication. Thus, by not releasing a small fraction of the database records, we can ensure that the data published for analysis has less distortion and hence is more useful. Our approximation algorithms for new clustering objectives are of independent interest and could be applicable in other clustering scenarios as well.
Keywords: anonymity; Approximation algorithms; clustering; privacy

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

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.

Alignment and clustering of phylogenetic markers - implications for microbial diversity studies - White,James R; Navlakha,Saket; Nagarajan,Niranjan; Ghodsi,Mohammad-Reza; Kingsford, Carl; Pop, Mihai (BMC Bioinformatics, 2010)
Molecular studies of microbial diversity have provided many insights into the bacterial communities inhabiting the human body and the environment. A common first step in such studies is a survey of conserved marker genes (primarily 16S rRNA) to characterize the taxonomic composition and diversity of these communities. To date, however, there exists significant variability in analysis methods employed in these studies.

Applications of Parameterized st-Orientations - Charalampos Papamanthou; Tollis, Ioannis G. (Journal of Graph Algorithms and Applications, 2010)

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

Assembly complexity of prokaryotic genomes using short reads - Kingsford, Carl; Schatz,Michael C; Pop, Mihai (BMC Bioinformatics, 2010)
De Bruijn graphs are a theoretical framework underlying several modern genome assembly programs, especially those that deal with very short reads. We describe an application of de Bruijn graphs to analyze the global repeat structure of prokaryotic genomes.

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

Automatic target recognition based on simultaneous sparse representation - Patel, Vishal M.; Nasrabadi,N.M.; Chellapa, Rama (Image Processing (ICIP), 2010 17th IEEE International Conference on, 2010)
In this paper, an automatic target recognition algorithm is presented based on a framework for learning dictionaries for simultaneous sparse signal representation and feature extraction. The dictionary learning algorithm is based on class supervised simultaneous orthogonal matching pursuit while a matching pursuit-based similarity measure is used for classification. We show how the proposed framework can be helpful for efficient utilization of data, with the possibility of developing real-time, robust target classification. We verify the efficacy of the proposed algorithm using confusion matrices on the well known Comanche forward-looking infrared data set consisting of ten different military targets at different orientations.
Keywords: (artificial; algorithm; feature; based; classification; iterative; classification; learning; Comanche; data; dictionary; matching; extraction; image; forward-looking; infrared; intelligence); military; learning; MATCHING; matrix; dictionary; measure; military; methods; learning; orthogonal; pursuit; pursuit; confusion; recognition; class; recognition; target; representation; feature; representation; sparse; set; automatic; signal; similarity; simultaneous; sparse; supervised; systems; object; target; target; simultaneous; tracking

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.

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.

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

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

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

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

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

Computational Approaches for Genome Assembly Validation - Choi,J.H.; Tang,H.; Kim,S.; Pop, Mihai (Biological Data Mining, 2010)

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.

COSI: Cloud Oriented Subgraph Identification in Massive Social Networks - Bröcheler,M.; Pugliese, A.; V.S. Subrahmanian (Advances in Social Networks Analysis and Mining (ASONAM), 2010 International Conference on, 2010)
Subgraph matching is a key operation on graph data. Social network (SN) providers may want to find all subgraphs within their social network that match certain query graph patterns. Unfortunately, subgraph matching is NP-complete, making its application to massive SNs a major challenge. Past work has shown how to implement subgraph matching on a single processor when the graph has 10-25M edges. In this paper, we show how to use cloud computing in conjunction with such existing single processor methods to efficiently match complex subgraphs on graphs as large as 778M edges. A cloud consists of one master compute node and k slave compute nodes. We first develop a probabilistic method to estimate probabilities that a vertex will be retrieved by a random query and that a pair of vertices will be successively retrieved by a random query. We use these probability estimates to define edge weights in an SN and to compute minimal edge cuts to partition the graph amongst k slave nodes. We develop algorithms for both master and slave nodes that try to minimize communication overhead. The resulting COSI system can answer complex queries over real-world SN data containing over 778M edges very efficiently.
Keywords: (online); answering; social; complexity; data; computing; edge; data; graph; estimation; query; handling; graph; matching; Internet; computational; matching; probability; query; network; subgraph; networking; NP-complete; cloud; pattern; probability; processing; social; theory; pattern; weight; graph

Cyberinfrastructure for Social Action on National Priorities - Pirolli,Peter; Preece,Jenny; Shneiderman, Ben (Computer, 2010)
Extensive research is needed to build upon currently used media and tools to foster wider participation, address national priorities, and deal with potential dangers associated with technology-mediated social participation.
Keywords: Collaborative tools; Peer to peer computing; Public policy; Research initiatives; Social network services; Special issues and sections; Technology-mediated social participation

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.

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

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

Energy-driven distribution of signal processing applications across wireless sensor networks - Chung-Ching Shen; Plishker, William L.; Ko,Dong-Ik; Bhattacharyya, Shuvra S.; Goldsman,Neil (ACM Trans. Sen. Netw., 2010)
Wireless sensor network (WSN) applications have been studied extensively in recent years. Such applications involve resource-limited embedded sensor nodes that have small size and low power requirements. Based on the need for extended network lifetimes in WSNs in terms of energy use, the energy efficiency of computation and communication operations in the sensor nodes becomes critical. Digital Signal Processing (DSP) applications typically require intensive data processing operations and as a result are difficult to implement directly in resource-limited WSNs. In this article, we present a novel design methodology for modeling and implementing computationally intensive DSP applications applied to wireless sensor networks. This methodology explores efficient modeling techniques for DSP applications, including data sensing and processing; derives formulations of Energy-Driven Partitioning (EDP) for distributing such applications across wireless sensor networks; and develops efficient heuristic algorithms for finding partitioning results that maximize the network lifetime. To address such an energy-driven partitioning problem, this article provides a new way of aggregating data and reducing communication traffic among nodes based on application analysis. By considering low data token delivery points and the distribution of computation in the application, our approach finds energy-efficient trade-offs between data communication and computation.
Keywords: DSP; Energy efficiency; network lifetime; Speech recognition; Wireless sensor networks

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

Evaluation of the Interaction of Cyclin-Dependent Kinase 5 with Activator p25 and with p25-Derived Inhibitor CIP - Cardone, Antonio; Albers,R.W.; Sriram,R.D.; Pant,H.C. (Journal of Computational Biology, 2010)

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

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

Exploring temporal patterns with information visualization: keynote - Plaisant, Catherine (Proceedings of Graphics Interface 2010, 2010)
After an overview of visualizations to explore temporal patterns, we will focus on interfaces for discovering temporal event patterns in electronic health records. Specifying event sequence queries is challenging even for skilled computer professionals familiar with SQL. Our novel interactive search strategies allow for aligning records on important events, ranking, and filtering combined with grouping of results to find common or rare events. A second approach is to use query-by-example, in which users specify a pattern and see a similarity-ranked list of results, but the similarity measure needs to be customized for different needs. Temporal summaries allow comparisons between groups. We will discuss the methods we use to evaluate the usefulness of our interfaces through collaborations with clinicians and hospital administrators on case studies. Finally, application of the techniques to other domains will be discussed.
Keywords: electronic health records; search interfaces

Face Recognition by Computers and Humans - Chellapa, Rama; Sinha, P.; Phillips,P.J. (Computer, 2010)
This article talks about how the study of how humans perceive faces can be used to help design practical systems for face recognition. Besides applications related to identification and verification-such as access control, law enforcement, ID and licensing, and surveillance-face recognition has also proven useful in applications such as human-computer interaction, virtual reality, database retrieval, multimedia, and computer entertainment. Continuing research into face recognition will provide scientists and engineers with many vital projects, in areas such as homeland security, human-computer interaction, and numerous consumer applications. The areas we are considering pursuing are recognition from unconstrained video sequences, incorporating familiarity into algorithms, modeling effects of aging, and developing biologically plausible models for human face recognition ability.
Keywords: access; Computer; control; aging; computer; control; face; entertainment; database; interaction; national; interaction; unconstrained; reality; access; recognition; homeland; recognition; human; retrieval; face; security; security; human; sequences; virtual; video