@article {20369, title = {Quantification of Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae in French Mediterranean coastal lagoons}, journal = {Research in Microbiology}, volume = {164}, year = {2013}, month = {Jan-10-2013}, pages = {867 - 874}, abstract = {Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae are human pathogens. Little is known about these Vibrio spp. in the coastal lagoons of France. The purpose of this study was to investigate their incidence in water, shellfish and sediment of three French Mediterranean coastal lagoons using the most probable number-polymerase chain reaction (MPN-PCR). In summer, the total number of V. parahaemolyticus in water, sediment, mussels and clams collected from the three lagoons varied from 1 to >1.1 {\texttimes} 103 MPN/l, 0.09 to 1.1 {\texttimes} 103 MPN/ml, 9 to 210 MPN/g and 1.5 to 2.1 MPN/g, respectively. In winter, all samples except mussels contained V. parahaemolyticus, but at very low concentrations. Pathogenic (tdh- or trh2-positive) V. parahaemolyticus were present in water, sediment and shellfish samples collected from these lagoons. The number of V. vulnificus in water, sediment and shellfish samples ranged from 1 to 1.1 {\texttimes} 103 MPN/l, 0.07 to 110 MPN/ml and 0.04 to 15 MPN/g, respectively, during summer. V. vulnificus was not detected during winter. V. cholerae was rarely detected in water and sediment during summer. In summary, results of this study highlight the finding that the three human pathogenic Vibrio spp. are present in the lagoons and constitute a potential public health hazard.}, issn = {09232508}, doi = {10.1016/j.resmic.2013.06.005}, url = {https://linkinghub.elsevier.com/retrieve/pii/S092325081300106X}, author = {Cantet, Franck and Hervio-Heath, Dominique and Caro, Audrey and Le Mennec, C{\'e}cile and Monteil, Caroline and Qu{\'e}m{\'e}r{\'e}, Catherine and Jolivet-Gougeon, Anne and Rita R Colwell and Monfort, Patrick} } @article {20376, title = {Detection, Isolation, and Identification of Vibrio cholerae from the Environment}, journal = {Current Protocols in Microbiology}, volume = {26}, year = {2012}, month = {08/2012}, publisher = {John Wiley \& Sons, Inc.}, chapter = {Unit 6A.5}, address = {Hoboken, NJ, USA}, abstract = {Recent molecular advances in microbiology have greatly improved the detection of bacterial pathogens in the environment. These improvements and a downward trend in the cost of molecular detection methods have contributed to increased frequency of detection of pathogenic microorganisms where traditional culture-based detection methods have failed. Culture methods also have been greatly improved, and the confluence of the two suites of methods provides a powerful tool for detection, isolation, and characterization of pathogens. While molecular detection provides data on the presence and type of pathogens, culturing methods allow a researcher to preserve the organism of interest for {\textquotedblleft}-omics{\textquotedblright} studies, such as genomic, metabolomic, secretomic, and transcriptomic analysis, which are rapidly becoming more affordable. This has yielded a clearer understanding of the ecology and epidemiology of microorganisms that cause disease. In this unit, we present commonly accepted methods for isolation, detection, and characterization of V. cholerae, providing more extensive knowledge of the ecology and epidemiology of this organism. This unit has been fully revised and updated from the earlier version with the latest knowledge and additional information not previously included. Curr. Protoc. Microbiol. 26:6A.5.1-6A.5.51. {\textcopyright} 2012 by John Wiley \& Sons, Inc. }, doi = {10.1002/9780471729259.mc06a05s26}, url = {http://doi.wiley.com/10.1002/9780471729259.mc06a05s26}, author = {Huq, Anwar and Haley, Bradd J. and Taviani, Elisa and Chen, Arlene and Hasan, Nur A. and Rita R Colwell}, editor = {Coico, Richard and Kowalik, Tim and Quarles, John and Stevenson, Brian and Taylor, Ron} } @article {19721, title = {InterPro in 2011: new developments in the family and domain prediction database.}, journal = {Nucleic Acids Res}, volume = {40}, year = {2012}, month = {2012 Jan}, pages = {D306-12}, abstract = {

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}, issn = {1362-4962}, doi = {10.1093/nar/gkr948}, author = {Hunter, Sarah and Jones, Philip and Mitchell, Alex and Apweiler, Rolf and Attwood, Teresa K and Bateman, Alex and Bernard, Thomas and Binns, David and Bork, Peer and Burge, Sarah and de Castro, Edouard and Coggill, Penny and Corbett, Matthew and Das, Ujjwal and Daugherty, Louise and Duquenne, Lauranne and Finn, Robert D and Fraser, Matthew and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Kahn, Daniel and Kelly, Elizabeth and Letunic, Ivica and Lonsdale, David and Lopez, Rodrigo and Madera, Martin and Maslen, John and McAnulla, Craig and McDowall, Jennifer and McMenamin, Conor and Mi, Huaiyu and Mutowo-Muellenet, Prudence and Mulder, Nicola and Natale, Darren and Orengo, Christine and Pesseat, Sebastien and Punta, Marco and Quinn, Antony F and Rivoire, Catherine and Sangrador-Vegas, Amaia and Jeremy D Selengut and Sigrist, Christian J A and Scheremetjew, Maxim and Tate, John and Thimmajanarthanan, Manjulapramila and Thomas, Paul D and Wu, Cathy H and Yeats, Corin and Yong, Siew-Yit} } @conference {12436, title = {Sparse dictionary-based representation and recognition of action attributes}, booktitle = {2011 IEEE International Conference on Computer Vision (ICCV)}, year = {2011}, month = {2011/11/06/13}, pages = {707 - 714}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present an approach for dictionary learning of action attributes via information maximization. We unify the class distribution and appearance information into an objective function for learning a sparse dictionary of action attributes. The objective function maximizes the mutual information between what has been learned and what remains to be learned in terms of appearance information and class distribution for each dictionary item. We propose a Gaussian Process (GP) model for sparse representation to optimize the dictionary objective function. The sparse coding property allows a kernel with a compact support in GP to realize a very efficient dictionary learning process. Hence we can describe an action video by a set of compact and discriminative action attributes. More importantly, we can recognize modeled action categories in a sparse feature space, which can be generalized to unseen and unmodeled action categories. Experimental results demonstrate the effectiveness of our approach in action recognition applications.}, keywords = {action attributes, appearance information, class distribution, Dictionaries, dictionary learning process, Encoding, Entropy, Gaussian process model, Gaussian processes, Histograms, HUMANS, Image coding, image representation, information maximization, learning (artificial intelligence), modeled action categories, Mutual information, Object recognition, probabilistic logic, sparse coding property, sparse dictionary-based recognition, sparse dictionary-based representation, sparse feature space, unmodeled action categories}, isbn = {978-1-4577-1101-5}, doi = {10.1109/ICCV.2011.6126307}, author = {Qiang Qiu and Zhuolin Jiang and Chellapa, Rama} } @article {17462, title = {Usability and Accessibility in Consumer Health Informatics: Current Trends and Future Challenges}, journal = {American Journal of Preventive Medicine}, volume = {40}, year = {2011}, month = {2011/05//}, pages = {S187-S197 - S187-S197}, abstract = {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.}, isbn = {0749-3797}, doi = {10.1016/j.amepre.2011.01.009}, url = {http://www.sciencedirect.com/science/article/pii/S0749379711000869}, author = {Goldberg,Larry and Lide,Bettijoyce and Lowry,Svetlana and Massett,Holly A. and O{\textquoteright}Connell,Trisha and Preece,Jennifer and Quesenbery,Whitney and Shneiderman, Ben} } @conference {16824, title = {Determining the spatial reader scopes of news sources using local lexicons}, booktitle = {Proceedings of the 18th SIGSPATIAL International Conference on Advances in Geographic Information Systems}, series = {GIS {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {43 - 52}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Information sources on the Internet (e.g., Web versions of newspapers) usually have an implicit spatial reader scope, which is the geographical location for which the content has been primarily produced. Knowledge of the spatial reader scope facilitates the construction of a news search engine that provides readers a set of news sources relevant to the location in which they are interested. In particular, it plays an important role in disambiguating toponyms (e.g., textual specifications of geographical locations) in news articles, as the process of selecting an interpretation for the toponym often reduces to one of selecting an interpretation that seems natural in the context of the spatial reader scope. The key to determining the spatial reader scope of news sources is the notion of local lexicon, which for a location s is a set of concepts such as, but not limited to, names of people, landmarks, and historical events, that are spatially related to s. Techniques to automatically generate the local lexicon of a location by using the link structure of Wikipedia are described and evaluated. A key contribution is the improvement of existing methods used in the semantic relatedness domain to extract concepts spatially related to a given location from the Wikipedia. Results of experiments are presented that indicate that the knowledge of the spatial reader scope significantly improves the disambiguation of textually specified locations in news articles and that using local lexicons is an effective method to determine the spatial reader scopes of news sources.}, keywords = {geotagging, local lexicon, news search engine, spatial reader scope, spatial relatedness}, isbn = {978-1-4503-0428-3}, doi = {10.1145/1869790.1869800}, url = {http://doi.acm.org/10.1145/1869790.1869800}, author = {Quercini,Gianluca and Samet, Hanan and Sankaranarayanan,Jagan and Lieberman,Michael D.} } @conference {16692, title = {Improving translation via targeted paraphrasing}, booktitle = {Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing}, year = {2010}, month = {2010///}, pages = {127 - 137}, author = {Resnik, Philip and Buzek,O. and Hu,C. and Kronrod,Y. and Quinn,A. and Bederson, Benjamin B.} } @article {15300, title = {Natural language annotations for the Semantic Web}, journal = {On the Move to Meaningful Internet Systems 2002: CoopIS, DOA, and ODBASE}, year = {2010}, month = {2010///}, pages = {1317 - 1331}, author = {Katz,B. and Jimmy Lin and Quan,D.} } @conference {13916, title = {Designing the reading experience for scanned multi-lingual picture books on mobile phones}, booktitle = {Proceedings of the 9th ACM/IEEE-CS joint conference on Digital libraries}, year = {2009}, month = {2009///}, pages = {305 - 308}, author = {Bederson, Benjamin B. and Quinn,A. and Druin, Allison} } @article {13780, title = {Generating surveys of scientific paradigms}, journal = {Proceedings of HLT-NAACL}, year = {2009}, month = {2009///}, abstract = {The number of research publications in var-ious disciplines is growing exponentially. Researchers and scientists are increasingly finding themselves in the position of having to quickly understand large amounts of tech- nical material. In this paper we present the first steps in producing an automatically gen- erated, readily consumable, technical survey. Specifically we explore the combination of citation information and summarization tech- niques. Even though prior work (Teufel et al., 2006) argues that citation text is unsuitable for summarization, we show that in the frame- work of multi-document survey creation, cita- tion texts can play a crucial role. }, author = {Mohammad,S. and Dorr, Bonnie J and Egan,M. and Hassan,A. and Muthukrishan,P. and Qazvinian,V. and Radev,D. and Zajic, David} } @article {13895, title = {The Maryland Modular Method: An Approach to Doctoral Education in Information Studies}, journal = {Journal of education for library and information science}, volume = {50}, year = {2009}, month = {2009///}, pages = {293 - 301}, author = {Druin, Allison and Jaeger,P. T and Golbeck,J. and Fleischmann,K.R. and Jimmy Lin and Qu,Y. and Wang,P. and Xie,B.} } @article {17990, title = {Mesh-of-Trees and Alternative Interconnection Networks for Single-Chip Parallelism}, journal = {Very Large Scale Integration (VLSI) Systems, IEEE Transactions on}, volume = {17}, year = {2009}, month = {2009/10//}, pages = {1419 - 1432}, abstract = {In single-chip parallel processors, it is crucial to implement a high-throughput low-latency interconnection network to connect the on-chip components, especially the processing units and the memory units. In this paper, we propose a new mesh of trees (MoT) implementation of the interconnection network and evaluate it relative to metrics such as wire complexity, total register count, single switch delay, maximum throughput, tradeoffs between throughput and latency, and post-layout performance. We show that on-chip interconnection networks can provide higher bandwidth between processors and shared first-level cache than previously considered possible, facilitating greater scalability of memory architectures that require that. MoT is also compared, both analytically and experimentally, to some other traditional network topologies, such as hypercube, butterfly, fat trees and butterfly fat trees. When we evaluate a 64-terminal MoT network at 90-nm technology, concrete results show that MoT provides higher throughput and lower latency especially when the input traffic (or the on-chip parallelism) is high, at comparable area. A recurring problem in networking and communication is that of achieving good sustained throughput in contrast to just high theoretical peak performance that does not materialize for typical work loads. Our quantitative results demonstrate a clear advantage of the proposed MoT network in the context of single-chip parallel processing.}, keywords = {90, cache;single, complexity;multiprocessor, delay;single-chip, first-level, high-throughput, interconnection, low-latency, network;memory, network;shared, networks;network-on-chip;parallel, nm;wire, Parallel, parallelism;size, processing;, processor;single-chip, switch, topologies;on-chip, units;mesh-of-trees;network}, isbn = {1063-8210}, doi = {10.1109/TVLSI.2008.2003999}, author = {Balkan,A.O. and Gang Qu and Vishkin, Uzi} } @article {14640, title = {Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians}, journal = {Clinical Endocrinology}, volume = {70}, year = {2009}, month = {2009/05/01/}, pages = {698 - 705}, abstract = {Objective Resistin causes insulin resistance and diabetes in mice whereas in humans it is linked to inflammation and atherosclerosis. Few human genetic studies of resistin in inflammation and atherosclerosis have been performed. We hypothesized that the {\textendash}420C>G putative gain-of-function resistin variant would be associated with inflammatory markers and atherosclerosis but not with metabolic syndrome or adipokines in humans.Design and methods We examined the association of three resistin polymorphisms, {\textendash}852A>G, {\textendash}420C>G and +157C>T, and related haplotypes with plasma resistin, cytokines, C-reactive protein (CRP), adipokines, plasma lipoproteins, metabolic syndrome and coronary artery calcification (CAC) in nondiabetic Caucasians (n~=~851). Results Resistin levels were higher, dose-dependently, with the {\textendash}420G allele (CC 5{\textperiodcentered}9~{\textpm}~2{\textperiodcentered}7~ng/ml, GC 6{\textperiodcentered}5~{\textpm}~4{\textperiodcentered}0~ng/ml and GG 7{\textperiodcentered}2~{\textpm}~4{\textperiodcentered}8~ng/ml, trend P~=~0{\textperiodcentered}04) after age and gender adjustment [fold higher for GC~+~GG vs. CC; 1{\textperiodcentered}07~(1{\textperiodcentered}00{\textendash}1{\textperiodcentered}15), P~<~0{\textperiodcentered}05)]. The {\textendash}852A>G single nucleotide polymorphism (SNP) was associated with higher soluble tumour necrosis factor-receptor~2 (sol-TNFR2) levels in fully adjusted models [1{\textperiodcentered}06~(95\%~CI 1{\textperiodcentered}01{\textendash}1{\textperiodcentered}11), P~=~0{\textperiodcentered}01)]. The estimated resistin haplotype (GGT) was associated with sol-TNFR2 (P~=~0{\textperiodcentered}04) and the AGT haplotype was related to CRP (P~=~0{\textperiodcentered}04) in the fully adjusted models. Resistin SNPs and haplotypes were not associated with body mass index (BMI), fasting glucose, insulin resistance, metabolic syndrome, adipokines or CAC scores. Conclusions Despite modest associations with plasma resistin and inflammatory biomarkers, resistin 5' variants were not associated with metabolic parameters or coronary calcification. This suggests that resistin is an inflammatory cytokine in humans but has little influence on adiposity, metabolic syndrome or atherosclerosis. }, isbn = {1365-2265}, doi = {10.1111/j.1365-2265.2008.03375.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2265.2008.03375.x/abstract;jsessionid=3EAA174C4993EDEE1267334CDA36E086.d01t01}, author = {Qasim,Atif N and Metkus,Thomas S and Tadesse,Mahlet and Lehrke,Michael and Restine,Stephanie and Wolfe,Megan L and Hannenhalli, Sridhar and Cappola,Thomas and Rader,Daniel J and Reilly,Muredach P} } @conference {13888, title = {Using citations to generate surveys of scientific paradigms}, booktitle = {Proceedings of Human Language Technologies: The 2009 Annual Conference of the North American Chapter of the Association for Computational Linguistics}, series = {NAACL {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {584 - 592}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {The number of research publications in various disciplines is growing exponentially. Researchers and scientists are increasingly finding themselves in the position of having to quickly understand large amounts of technical material. In this paper we present the first steps in producing an automatically generated, readily consumable, technical survey. Specifically we explore the combination of citation information and summarization techniques. Even though prior work (Teufel et al., 2006) argues that citation text is unsuitable for summarization, we show that in the framework of multi-document survey creation, citation texts can play a crucial role.}, isbn = {978-1-932432-41-1}, url = {http://dl.acm.org/citation.cfm?id=1620754.1620839}, author = {Mohammad,Saif and Dorr, Bonnie J and Egan,Melissa and Hassan,Ahmed and Muthukrishan,Pradeep and Qazvinian,Vahed and Radev,Dragomir and Zajic, David} } @article {17491, title = {Visual overviews for discovering key papers and influences across research fronts}, journal = {Journal of the American Society for Information Science and Technology}, volume = {60}, year = {2009}, month = {2009/11/01/}, pages = {2219 - 2228}, abstract = {Gaining a rapid overview of an emerging scientific topic, sometimes called research fronts, is an increasingly common task due to the growing amount of interdisciplinary collaboration. Visual overviews that show temporal patterns of paper publication and citation links among papers can help researchers and analysts to see the rate of growth of topics, identify key papers, and understand influences across subdisciplines. This article applies a novel network-visualization tool based on meaningful layouts of nodes to present research fronts and show citation links that indicate influences across research fronts. To demonstrate the value of two-dimensional layouts with multiple regions and user control of link visibility, we conducted a design-oriented, preliminary case study with 6 domain experts over a 4-month period. The main benefits were being able (a) to easily identify key papers and see the increasing number of papers within a research front, and (b) to quickly see the strength and direction of influence across related research fronts.}, isbn = {1532-2890}, doi = {10.1002/asi.21160}, url = {http://onlinelibrary.wiley.com/doi/10.1002/asi.21160/abstract}, author = {Aris,Aleks and Shneiderman, Ben and Qazvinian,Vahed and Radev,Dragomir} } @conference {16069, title = {Aligning temporal data by sentinel events: discovering patterns in electronic health records}, booktitle = {Proceedings of the twenty-sixth annual SIGCHI conference on Human factors in computing systems}, series = {CHI {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {457 - 466}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Electronic Health Records (EHRs) and other temporal databases contain hidden patterns that reveal important cause-and-effect phenomena. Finding these patterns is a challenge when using traditional query languages and tabular displays. We present an interactive visual tool that complements query formulation by providing operations to align, rank and filter the results, and to visualize estimates of the intervals of validity of the data. Display of patient histories aligned on sentinel events (such as a first heart attack) enables users to spot precursor, co-occurring, and aftereffect events. A controlled study demonstrates the benefits of providing alignment (with a 61\% speed improvement for complex tasks). A qualitative study and interviews with medical professionals demonstrates that the interface can be learned quickly and seems to address their needs.}, keywords = {electronic health record, Evaluation, Information Visualization, search, temporal data, Uncertainty}, isbn = {978-1-60558-011-1}, doi = {10.1145/1357054.1357129}, url = {http://doi.acm.org/10.1145/1357054.1357129}, author = {Wang,Taowei David and Plaisant, Catherine and Quinn,Alexander J. and Stanchak,Roman and Murphy,Shawn and Shneiderman, Ben} } @conference {17998, title = {An area-efficient high-throughput hybrid interconnection network for single-chip parallel processing}, booktitle = {Proceedings of the 45th annual Design Automation Conference}, series = {DAC {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {435 - 440}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Single-chip parallel processing requires high bandwidth between processors and on-chip memory modules. A recently proposed Mesh-of-Trees (MoT) network provides high throughput and low latency at relatively high area cost. In this paper, we introduce a hybrid MoT-BF network that combines MoT network with the area efficient butterfly network. We prove that the hybrid network reduces MoT network{\textquoteright}s area cost. Cycle-accurate simulation and post-layout results all show that significant area reduction can be achieved with negligible performance degradation, when operating at same clock rate.}, keywords = {hybrid networks, mesh-of-trees, on-chip networks}, isbn = {978-1-60558-115-6}, doi = {10.1145/1391469.1391583}, url = {http://doi.acm.org/10.1145/1391469.1391583}, author = {Balkan,Aydin O. and Gang Qu and Vishkin, Uzi} } @article {17021, title = {Community response grid (CRG) for a university campus: Design requirements and implications}, journal = {Proceedings of the 5th International ISCRAM Conference}, year = {2008}, month = {2008///}, pages = {34 - 43}, abstract = {This paper describes the initial stages of the participatory design of a community-oriented emergency responsesystem for a university campus. After reviewing related work and the current University emergency response system, this paper describes our participatory design process, discusses initial findings from a design requirement survey and from our interactions with different stakeholders, and proposes a Web interface design for a community response grid system. The prototyping of the system demonstrates the possibility of fostering a social-network-based community participation in emergency response, and also identifies concerns raised by potential users and by the professional responder community. }, author = {Wu,P.F. and Qu,Y. and Preece,J. and Fleischmann,K. and Golbeck,J. and Jaeger,P. and Shneiderman, Ben} } @article {17063, title = {Designing community-based emergency communication system: A preliminary study}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {45}, year = {2008}, month = {2008///}, pages = {1 - 3}, author = {Fei Wu,P. and Qu,Y. and Fleischmann,K. and Golbeck,J. and Jaeger,P. and Preece,J. and Shneiderman, Ben} } @conference {18212, title = {Extended abstract: A hardware-assisted data hiding based approach in building high performance secure execution systems}, booktitle = {Hardware-Oriented Security and Trust, 2008. HOST 2008. IEEE International Workshop on}, year = {2008}, month = {2008/06//}, pages = {93 - 96}, abstract = {Recently, a novel data hiding technique was proposed to embed information into compiled binary codes in order to enhance system performance. Using this technique as a vehicle, we propose a framework to build high-performance secure execution systems by embedding data for security and trust purposes. We illustrate this approach in a mobile computing environment by an instruction-block level data hiding technique, which can be used to defend against malicious attacks (such as Trojan injection). This improves the trustworthiness of mobile codes. It also protects the code providerpsilas intellectual property because the code can be executed only on the designated device. When combined with the existing approach in [4], the proposed data hiding framework can provide trust and high-performance simultaneously. Finally, we conduct a proof-of-the-concept FPGA prototyping to validate the data hiding technique and evaluate the hardware cost in terms of gate count, power consumption, and gate delay.}, keywords = {arrays;invasive, attacks;mobile, codes;data, codes;mobile, computing;, computing;power, consumption;proof-of-the-concept, count;gate, data, delay;hardware-assisted, embedding;gate, embedding;instruction-block, encapsulation;distributed, execution, FPGA, gate, hiding;information, injection;binary, level;malicious, programmable, programming;field, prototyping;secure, software;mobile, systems;binary, Trojan}, doi = {10.1109/HST.2008.4559062}, author = {Taylor,M. and Yin,Chi-En and M. Wu and Gang Qu} } @conference {12173, title = {Readability of scanned books in digital libraries}, booktitle = {Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems}, year = {2008}, month = {2008///}, pages = {705 - 714}, author = {Quinn,A.J. and Hu,C. and Arisaka,T. and Rose,A. and Bederson, Benjamin B.} } @article {14556, title = {Cell breathing in wireless LANs: Algorithms and evaluation}, journal = {IEEE Transactions on Mobile Computing}, volume = {6}, year = {2007}, month = {2007///}, pages = {164 - 178}, author = {Hajiaghayi, Mohammad T. and Mirrokni,S. V. and Saberi,A. and Bahl,P. and Jain,K. and Qiu,L.} } @article {17023, title = {Community response grids: E-government, social networks, and effective emergency management}, journal = {Telecommunications Policy}, volume = {31}, year = {2007}, month = {2007/11//}, pages = {592 - 604}, abstract = {This paper explores the concept of developing community response grids (CRGs) for community emergency response and the policy implications of such a system. CRGs make use of the Internet and mobile communication devices, allowing residents and responders to share information, communicate, and coordinate activities in response to a major disaster. This paper explores the viability of using mobile communication technologies and the Web, including e-government, to develop response systems that would aid communities before, during, and after a major disaster, providing channels for contacting residents and responders, uploading information, distributing information, coordinating the responses of social networks, and facilitating resident-to-resident assistance. Drawing upon research from computer science, information studies, public policy, emergency management, and several other disciplines, the paper elaborates on the concept of and need for CRGs, examines related current efforts that can inform the development of CRGs, discusses how research about community networks can be used to instill trust and social capital in CRGs, and examines the issues of public policy, telecommunications, and e-government related to such a system.}, keywords = {Community response grid, E-government, Emergency response, Mobile communications, Public policy, social networks}, isbn = {0308-5961}, doi = {10.1016/j.telpol.2007.07.008}, url = {http://www.sciencedirect.com/science/article/pii/S0308596107000699}, author = {Jaeger,Paul T. and Shneiderman, Ben and Fleischmann,Kenneth R. and Preece,Jennifer and Qu,Yan and Fei Wu,Philip} } @article {17022, title = {Community response grids for older adults: Motivations, usability, and sociability}, journal = {Proceedings of the 13th Americas Conference on Information Systems}, year = {2007}, month = {2007///}, abstract = {This paper discusses the motivation for a Community Response Grid (CRG) to helpolder adults improve their capability for coping with emergency situations. We define and discuss the concept of a CRG, briefly review the limits of current emergency response systems, and identify usability and sociability guidelines for CRGs for older adults based on existing research. The paper ends with a call to action and suggestions for future research directions. }, author = {Wu,P.F. and Preece,J. and Shneiderman, Ben and Jaeger,P. T and Qu,Y.} } @article {17024, title = {Community Response Grids: Using Information Technology to Help Communities Respond to Bioterror Emergencies}, journal = {Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science}, volume = {5}, year = {2007}, month = {2007/12//}, pages = {335 - 346}, abstract = {Access to accurate and trusted information is vital in preparing for, responding to, and recovering from an mergency. To facilitate response in large-scale emergency situations, Community Response Grids (CRGs) integrate Internet and mobile technologies to enable residents to report information, professional emergency responders to disseminate instructions, and residents to assist one another. CRGs use technology to help residents and professional emergency responders to work together in community response to emergencies, including bioterrorism events. In a time of increased danger from bioterrorist threats, the application of advanced information and communication technologies to community response is vital in confronting such threats. This article describes CRGs, their underlying concepts, development efforts, their relevance to biosecurity and bioterrorism, and future research issues in the use of technology to facilitate community response.}, isbn = {1538-7135, 1557-850X}, doi = {10.1089/bsp.2007.0034}, url = {http://www.liebertonline.com/doi/abs/10.1089/bsp.2007.0034}, author = {Jaeger,Paul T. and Fleischmann,Kenneth R. and Preece,Jennifer and Shneiderman, Ben and Fei Wu,Philip and Qu,Yan} } @article {16261, title = {Evolution of genes and genomes on the Drosophila phylogeny}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007/11/08/}, pages = {203 - 218}, abstract = {Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.}, isbn = {0028-0836}, doi = {10.1038/nature06341}, url = {http://www.nature.com/nature/journal/v450/n7167/full/nature06341.html}, author = {Clark,Andrew G. and Eisen,Michael B. and Smith,Douglas R. and Bergman,Casey M. and Oliver,Brian and Markow,Therese A. and Kaufman,Thomas C. and Kellis,Manolis and Gelbart,William and Iyer,Venky N. and Pollard,Daniel A. and Sackton,Timothy B. and Larracuente,Amanda M. and Singh,Nadia D. and Abad,Jose P. and Abt,Dawn N. and Adryan,Boris and Aguade,Montserrat and Akashi,Hiroshi and Anderson,Wyatt W. and Aquadro,Charles F. and Ardell,David H. and Arguello,Roman and Artieri,Carlo G. and Barbash,Daniel A. and Barker,Daniel and Barsanti,Paolo and Batterham,Phil and Batzoglou,Serafim and Begun,Dave and Bhutkar,Arjun and Blanco,Enrico and Bosak,Stephanie A. and Bradley,Robert K. and Brand,Adrianne D. and Brent,Michael R. and Brooks,Angela N. and Brown,Randall H. and Butlin,Roger K. and Caggese,Corrado and Calvi,Brian R. and Carvalho,A. Bernardo de and Caspi,Anat and Castrezana,Sergio and Celniker,Susan E. and Chang,Jean L. and Chapple,Charles and Chatterji,Sourav and Chinwalla,Asif and Civetta,Alberto and Clifton,Sandra W. and Comeron,Josep M. and Costello,James C. and Coyne,Jerry A. and Daub,Jennifer and David,Robert G. and Delcher,Arthur L. and Delehaunty,Kim and Do,Chuong B. and Ebling,Heather and Edwards,Kevin and Eickbush,Thomas and Evans,Jay D. and Filipski,Alan and Findei|[szlig]|,Sven and Freyhult,Eva and Fulton,Lucinda and Fulton,Robert and Garcia,Ana C. L. and Gardiner,Anastasia and Garfield,David A. and Garvin,Barry E. and Gibson,Greg and Gilbert,Don and Gnerre,Sante and Godfrey,Jennifer and Good,Robert and Gotea,Valer and Gravely,Brenton and Greenberg,Anthony J. and Griffiths-Jones,Sam and Gross,Samuel and Guigo,Roderic and Gustafson,Erik A. and Haerty,Wilfried and Hahn,Matthew W. and Halligan,Daniel L. and Halpern,Aaron L. and Halter,Gillian M. and Han,Mira V. and Heger,Andreas and Hillier,LaDeana and Hinrichs,Angie S. and Holmes,Ian and Hoskins,Roger A. and Hubisz,Melissa J. and Hultmark,Dan and Huntley,Melanie A. and Jaffe,David B. and Jagadeeshan,Santosh and Jeck,William R. and Johnson,Justin and Jones,Corbin D. and Jordan,William C. and Karpen,Gary H. and Kataoka,Eiko and Keightley,Peter D. and Kheradpour,Pouya and Kirkness,Ewen F. and Koerich,Leonardo B. and Kristiansen,Karsten and Kudrna,Dave and Kulathinal,Rob J. and Kumar,Sudhir and Kwok,Roberta and Lander,Eric and Langley,Charles H. and Lapoint,Richard and Lazzaro,Brian P. and Lee,So-Jeong and Levesque,Lisa and Li,Ruiqiang and Lin,Chiao-Feng and Lin,Michael F. and Lindblad-Toh,Kerstin and Llopart,Ana and Long,Manyuan and Low,Lloyd and Lozovsky,Elena and Lu,Jian and Luo,Meizhong and Machado,Carlos A. and Makalowski,Wojciech and Marzo,Mar and Matsuda,Muneo and Matzkin,Luciano and McAllister,Bryant and McBride,Carolyn S. and McKernan,Brendan and McKernan,Kevin and Mendez-Lago,Maria and Minx,Patrick and Mollenhauer,Michael U. and Montooth,Kristi and Mount, Stephen M. and Mu,Xu and Myers,Eugene and Negre,Barbara and Newfeld,Stuart and Nielsen,Rasmus and Noor,Mohamed A. F. and O{\textquoteright}Grady,Patrick and Pachter,Lior and Papaceit,Montserrat and Parisi,Matthew J. and Parisi,Michael and Parts,Leopold and Pedersen,Jakob S. and Pesole,Graziano and Phillippy,Adam M and Ponting,Chris P. and Pop, Mihai and Porcelli,Damiano and Powell,Jeffrey R. and Prohaska,Sonja and Pruitt,Kim and Puig,Marta and Quesneville,Hadi and Ram,Kristipati Ravi and Rand,David and Rasmussen,Matthew D. and Reed,Laura K. and Reenan,Robert and Reily,Amy and Remington,Karin A. and Rieger,Tania T. and Ritchie,Michael G. and Robin,Charles and Rogers,Yu-Hui and Rohde,Claudia and Rozas,Julio and Rubenfield,Marc J. and Ruiz,Alfredo and Russo,Susan and Salzberg,Steven L. and Sanchez-Gracia,Alejandro and Saranga,David J. and Sato,Hajime and Schaeffer,Stephen W. and Schatz,Michael C and Schlenke,Todd and Schwartz,Russell and Segarra,Carmen and Singh,Rama S. and Sirot,Laura and Sirota,Marina and Sisneros,Nicholas B. and Smith,Chris D. and Smith,Temple F. and Spieth,John and Stage,Deborah E. and Stark,Alexander and Stephan,Wolfgang and Strausberg,Robert L. and Strempel,Sebastian and Sturgill,David and Sutton,Granger and Sutton,Granger G. and Tao,Wei and Teichmann,Sarah and Tobari,Yoshiko N. and Tomimura,Yoshihiko and Tsolas,Jason M. and Valente,Vera L. S. and Venter,Eli and Venter,J. Craig and Vicario,Saverio and Vieira,Filipe G. and Vilella,Albert J. and Villasante,Alfredo and Walenz,Brian and Wang,Jun and Wasserman,Marvin and Watts,Thomas and Wilson,Derek and Wilson,Richard K. and Wing,Rod A. and Wolfner,Mariana F. and Wong,Alex and Wong,Gane Ka-Shu and Wu,Chung-I and Wu,Gabriel and Yamamoto,Daisuke and Yang,Hsiao-Pei and Yang,Shiaw-Pyng and Yorke,James A. and Yoshida,Kiyohito and Zdobnov,Evgeny and Zhang,Peili and Zhang,Yu and Zimin,Aleksey V. and Baldwin,Jennifer and Abdouelleil,Amr and Abdulkadir,Jamal and Abebe,Adal and Abera,Brikti and Abreu,Justin and Acer,St Christophe and Aftuck,Lynne and Alexander,Allen and An,Peter and Anderson,Erica and Anderson,Scott and Arachi,Harindra and Azer,Marc and Bachantsang,Pasang and Barry,Andrew and Bayul,Tashi and Berlin,Aaron and Bessette,Daniel and Bloom,Toby and Blye,Jason and Boguslavskiy,Leonid and Bonnet,Claude and Boukhgalter,Boris and Bourzgui,Imane and Brown,Adam and Cahill,Patrick and Channer,Sheridon and Cheshatsang,Yama and Chuda,Lisa and Citroen,Mieke and Collymore,Alville and Cooke,Patrick and Costello,Maura and D{\textquoteright}Aco,Katie and Daza,Riza and Haan,Georgius De and DeGray,Stuart and DeMaso,Christina and Dhargay,Norbu and Dooley,Kimberly and Dooley,Erin and Doricent,Missole and Dorje,Passang and Dorjee,Kunsang and Dupes,Alan and Elong,Richard and Falk,Jill and Farina,Abderrahim and Faro,Susan and Ferguson,Diallo and Fisher,Sheila and Foley,Chelsea D. and Franke,Alicia and Friedrich,Dennis and Gadbois,Loryn and Gearin,Gary and Gearin,Christina R. and Giannoukos,Georgia and Goode,Tina and Graham,Joseph and Grandbois,Edward and Grewal,Sharleen and Gyaltsen,Kunsang and Hafez,Nabil and Hagos,Birhane and Hall,Jennifer and Henson,Charlotte and Hollinger,Andrew and Honan,Tracey and Huard,Monika D. and Hughes,Leanne and Hurhula,Brian and Husby,M Erii and Kamat,Asha and Kanga,Ben and Kashin,Seva and Khazanovich,Dmitry and Kisner,Peter and Lance,Krista and Lara,Marcia and Lee,William and Lennon,Niall and Letendre,Frances and LeVine,Rosie and Lipovsky,Alex and Liu,Xiaohong and Liu,Jinlei and Liu,Shangtao and Lokyitsang,Tashi and Lokyitsang,Yeshi and Lubonja,Rakela and Lui,Annie and MacDonald,Pen and Magnisalis,Vasilia and Maru,Kebede and Matthews,Charles and McCusker,William and McDonough,Susan and Mehta,Teena and Meldrim,James and Meneus,Louis and Mihai,Oana and Mihalev,Atanas and Mihova,Tanya and Mittelman,Rachel and Mlenga,Valentine and Montmayeur,Anna and Mulrain,Leonidas and Navidi,Adam and Naylor,Jerome and Negash,Tamrat and Nguyen,Thu and Nguyen,Nga and Nicol,Robert and Norbu,Choe and Norbu,Nyima and Novod,Nathaniel and O{\textquoteright}Neill,Barry and Osman,Sahal and Markiewicz,Eva and Oyono,Otero L. and Patti,Christopher and Phunkhang,Pema and Pierre,Fritz and Priest,Margaret and Raghuraman,Sujaa and Rege,Filip and Reyes,Rebecca and Rise,Cecil and Rogov,Peter and Ross,Keenan and Ryan,Elizabeth and Settipalli,Sampath and Shea,Terry and Sherpa,Ngawang and Shi,Lu and Shih,Diana and Sparrow,Todd and Spaulding,Jessica and Stalker,John and Stange-Thomann,Nicole and Stavropoulos,Sharon and Stone,Catherine and Strader,Christopher and Tesfaye,Senait and Thomson,Talene and Thoulutsang,Yama and Thoulutsang,Dawa and Topham,Kerri and Topping,Ira and Tsamla,Tsamla and Vassiliev,Helen and Vo,Andy and Wangchuk,Tsering and Wangdi,Tsering and Weiand,Michael and Wilkinson,Jane and Wilson,Adam and Yadav,Shailendra and Young,Geneva and Yu,Qing and Zembek,Lisa and Zhong,Danni and Zimmer,Andrew and Zwirko,Zac and Jaffe,David B. and Alvarez,Pablo and Brockman,Will and Butler,Jonathan and Chin,CheeWhye and Gnerre,Sante and Grabherr,Manfred and Kleber,Michael and Mauceli,Evan and MacCallum,Iain} } @conference {18000, title = {Layout-Accurate Design and Implementation of a High-Throughput Interconnection Network for Single-Chip Parallel Processing}, booktitle = {High-Performance Interconnects, 2007. HOTI 2007. 15th Annual IEEE Symposium on}, year = {2007}, month = {2007/08//}, pages = {21 - 28}, abstract = {A mesh of trees (MoT) on-chip interconnection network has been proposed recently to provide high throughput between memory units and processors for single-chip parallel processing (Balkan et al., 2006). In this paper, we report our findings in bringing this concept to silicon. Specifically, we conduct cycle-accurate Verilog simulations to verify the analytical results claimed in (Balkan et al., 2006). We synthesize and obtain the layout of the MoT interconnection networks of various sizes. To further improve throughput, we investigate different arbitration primitives to handle load and store, the two most common memory operations. We also study the use of pipeline registers in large networks when there are long wires. Simulation based on full network layout demonstrates that significant throughput improvement can be achieved over the original proposed MoT interconnection network. The importance of this work lies in its validation of performance features of the MoT interconnection network, as they were previously shown to be competitive with traditional network solutions. The MoT network is currently used in an eXplicit multi-threading (XMT) on-chip parallel processor, which is engineered to support parallel programming. In that context, a 32-terminal MoT network could support up to 512 on-chip XMT processors. Our 8-terminal network that could serve 8 processor clusters (or 128 total processors), was also accepted recently for fabrication.}, keywords = {description, design;mesh, interconnection, languages;multi-threading;multiprocessor, MoT, multi-threading;layout-accurate, network;on-chip, network;Verilog, networks;parallel, of, on-chip, Parallel, processing;, processing;hardware, processor;parallel, processors;on-chip, programming;pipeline, registers;single-chip, simulations;eXplicit, TREES, XMT}, doi = {10.1109/HOTI.2007.11}, author = {Balkan,A.O. and Horak,M.N. and Gang Qu and Vishkin, Uzi} } @article {12362, title = {Probabilistic design of multimedia embedded systems}, journal = {ACM Transactions on Embedded Computing Systems (TECS)}, volume = {6}, year = {2007}, month = {2007///}, pages = {15{\textendash}es - 15{\textendash}es}, author = {Hua,S. and Qu,G. and Bhattacharyya, Shuvra S.} } @inbook {19622, title = {Time and Space Efficient Algorithms for Two-Party Authenticated Data Structures}, booktitle = {Information and Communications Security}, series = {Lecture Notes in Computer Science}, year = {2007}, month = {2007/01/01/}, pages = {1 - 15}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Authentication is increasingly relevant to data management. Data is being outsourced to untrusted servers and clients want to securely update and query their data. For example, in database outsourcing, a client{\textquoteright}s database is stored and maintained by an untrusted server. Also, in simple storage systems, clients can store very large amounts of data but at the same time, they want to assure their integrity when they retrieve them. In this paper, we present a model and protocol for two-party authentication of data structures. Namely, a client outsources its data structure and verifies that the answers to the queries have not been tampered with. We provide efficient algorithms to securely outsource a skip list with logarithmic time overhead at the server and client and logarithmic communication cost, thus providing an efficient authentication primitive for outsourced data, both structured (e.g., relational databases) and semi-structured (e.g., XML documents). In our technique, the client stores only a constant amount of space, which is optimal. Our two-party authentication framework can be deployed on top of existing storage applications, thus providing an efficient authentication service. Finally, we present experimental results that demonstrate the practical efficiency and scalability of our scheme.}, keywords = {Algorithm Analysis and Problem Complexity, Computer Communication Networks, computers and society, Data Encryption, Management of Computing and Information Systems, Systems and Data Security}, isbn = {978-3-540-77047-3, 978-3-540-77048-0}, url = {http://link.springer.com/chapter/10.1007/978-3-540-77048-0_1}, author = {Charalampos Papamanthou and Tamassia, Roberto}, editor = {Qing, Sihan and Imai, Hideki and Wang, Guilin} } @article {12355, title = {Energy-efficient embedded software implementation on multiprocessor system-on-chip with multiple voltages}, journal = {ACM Transactions on Embedded Computing Systems (TECS)}, volume = {5}, year = {2006}, month = {2006///}, pages = {321 - 341}, author = {Hua,S. and Qu,G. and Bhattacharyya, Shuvra S.} } @conference {19493, title = {Eye of the Beholder: Phone-Based Text-Recognition for the Visually-Impaired}, booktitle = {2006 10th IEEE International Symposium on Wearable Computers}, year = {2006}, month = {2006///}, pages = {145 - 146}, abstract = {Blind and visually-impaired people cannot access essential information in the form of written text in our environment (e.g., on restaurant menus, street signs, door labels, product names and instructions, expiration dates). In this paper, we present and evaluate a mobile text-recognition system capable of extracting written information from a wide variety of sources and communicating it on-demand to the user. The user needs no additional hardware except an ordinary, Internet- enabled mobile camera-phone - a device that many visually-impaired individuals already own. This approach fills a gap in assistive technologies for the visually- impaired because it makes users aware of textual information not available to them through any other means.}, keywords = {CAMERAS, data mining, handicapped aids, Hardware, Image quality, Internet, Land mobile radio cellular systems, Mobile computing, mobile handsets, mobile text-recognition system, Optical character recognition software, phone-based text-recognition, Product safety, Text recognition, visually-impaired}, author = {Tudor Dumitras and Lee, M. and Quinones, P. and Smailagic, A. and Siewiorek, Dan and Narasimhan, P.} } @article {18010, title = {Mesh-of-Trees and Alternative Interconnection Networks for Single Chip Parallel Processing (Extended Abstract)}, year = {2006}, month = {2006/06//}, abstract = {Many applications have stimulated the recent surge of interest single-chip parallel processing. In such machines, it is crucial to implement a high-throughput low-latency interconnection network to connect the on-chip components, especially the processing units and the memory units. In this paper, we propose a new mesh of trees (MoT) implementation of the interconnection network and evaluate it relative to metrics such as wire area, register count, total switch delay, maximum throughput, latency-throughput relation and delay effects of long wires. We show that on-chip interconnection networks can facilitate higher bandwidth between processors and shared first-level cache than previously considered possible. This has significant impact for chip multiprocessing. MoT is also compared, both analytically and experimentally, to some other traditional network topologies, such as hypercube, butterfly, fat trees and butterfly fat trees. When we evaluate a 64-terminal MoT network at 65nm technology, concrete results show that MoT provides higher throughput and lower latency especially when the input traffic (or the on-chip parallelism) is high, at the cost of larger area. A recurring problem in networking and communication is that of achieving good sustained throughput in contrast to just high theoretical peak performance that does not materialize for typical work loads. Our quantitative results demonstrate a clear advantage of the proposed MoT network in the context of single-chip parallel processing.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/3678}, author = {Balkan,Aydin O. and Gang Qu and Vishkin, Uzi} } @article {12661, title = {Bayesian algorithms for simultaneous structure from motion estimation of multiple independently moving objects}, journal = {Image Processing, IEEE Transactions on}, volume = {14}, year = {2005}, month = {2005/01//}, pages = {94 - 109}, abstract = {The problem of simultaneous structure from motion estimation for multiple independently moving objects from a monocular image sequence is addressed. Two Bayesian algorithms are presented for solving this problem using the sequential importance sampling (SIS) technique. The empirical posterior distribution of object motion and feature separation parameters is approximated by weighted samples. The first algorithm addresses the problem when only two moving objects are present. A singular value decomposition (SVD)-based sample clustering algorithm is shown to be capable of separating samples related to different objects. A pair of SIS procedures is used to track the posterior distribution of the motion parameters. In the second algorithm, a balancing step is added into the SIS procedure to preserve samples of low weights so that all objects have enough samples to propagate empirical motion distributions. By using the proposed algorithms, the relative motions of all the moving objects with respect to the camera can be simultaneously estimated. Both algorithms have been tested on synthetic and real- image sequences. Improved results have been achieved.}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Bayesian algorithm;clustering algorithm;empirical posterior distribution;feature separation parameter;monocular image sequence;motion estimation;multiple independently moving object;object motion;real-image sequence;sequential importance sampling techniqu, Biological;Models, Computer-Assisted;Imaging, Computer-Assisted;Pattern Recognition, Computer-Assisted;Subtraction Technique;Video Recording;Walking;, Statistical;Movement;Numerical Analysis, Three-Dimensional;Information Storage and Retrieval;Models}, isbn = {1057-7149}, doi = {10.1109/TIP.2004.837551}, author = {Qian,Gang and Chellapa, Rama and Qinfen Zheng} } @conference {12388, title = {CASPER: an integrated energy-driven approach for task graph scheduling on distributed embedded systems}, booktitle = {Application-Specific Systems, Architecture Processors, 2005. ASAP 2005. 16th IEEE International Conference on}, year = {2005}, month = {2005/07//}, pages = {191 - 197}, abstract = {For multiprocessor embedded systems, the dynamic voltage scaling (DVS) technique can be applied to scheduled applications for energy reduction. DVS utilizes slack in the schedule to slow down processes and save energy. Therefore, it is generally believed that the maximal energy saving is achieved on a schedule with the minimum makespan (maximal slack). Most current approaches treat task assignment, scheduling, and DVS separately. In this paper, we present a framework called CASPER (combined assignment, scheduling, and power-management) that challenges this common belief by integrating task scheduling and DVS under a single iterative optimization loop via genetic algorithm. We have conducted extensive experiments to validate the energy efficiency of CASPER. For homogeneous multiprocessor systems (in which all processors are of the same type), we consider a recently proposed slack distribution algorithm (PDP-SPM) by S. Hua and G. Qu (2005): applying PDP-SPM on the schedule with the minimal makespan gives an average of 53.8\% energy saving; CASPER finds schedules with slightly larger makespan but a 57.3\% energy saving, a 7.8\% improvement. For heterogeneous systems, we consider the power variation DVS (PV-DVS) algorithm by Schmitz et al. (2004), CASPER improves its energy efficiency by 8.2\%. Finally, our results also show that the proposed single loop CASPER framework saves 23.3\% more energy over GMA+EE-GLSA by Schmitz et al. (2002), the only other known integrated approach with a nested loop that combines scheduling and power management in the inner loop but leaves assignment in the outer loop.}, keywords = {CASPER, combined-assignment-scheduling-and-power-management, computational complexity, distributed system, dynamic voltage scaling, embedded systems, energy reduction, genetic algorithm, Genetic algorithms, graph theory, homogeneous multiprocessor system, maximal energy saving, Multiprocessing systems, multiprocessor embedded system, optimization loop, power management, power variation, Processor scheduling, slack distribution algorithm, task assignment, task graph scheduling}, doi = {10.1109/ASAP.2005.23}, author = {Kianzad,V. and Bhattacharyya, Shuvra S. and Gang Qu} } @conference {12342, title = {DSP address optimization using evolutionary algorithms}, booktitle = {Proceedings of the 2005 workshop on Software and compilers for embedded systems}, year = {2005}, month = {2005///}, pages = {91 - 98}, author = {Leventhal,S. and Yuan,L. and Bambha,N. K and Bhattacharyya, Shuvra S. and Qu,G.} } @conference {18017, title = {Arbitrate-and-move primitives for high throughput on-chip interconnection networks}, booktitle = {Circuits and Systems, 2004. ISCAS {\textquoteright}04. Proceedings of the 2004 International Symposium on}, volume = {2}, year = {2004}, month = {2004/05//}, pages = {II - 441-4 Vol.2 - II - 441-4 Vol.2}, abstract = {An n-leaf pipelined balanced binary tree is used for arbitration of order and movement of data from n input ports to one output port. A novel arbitrate-and-move primitive circuit for every node of the tree, which is based on a concept of reduced synchrony that benefits from attractive features of both asynchronous and synchronous designs, is presented. The design objective of the pipelined binary tree is to provide a key building block in a high-throughput mesh-of-trees interconnection network for Explicit Multi Threading (XMT) architecture, a recently introduced parallel computation framework. The proposed reduced synchrony circuit was compared with asynchronous and synchronous designs of arbitrate-and-move primitives. Simulations with 0.18 mu;m technology show that compared to an asynchronous design, the proposed reduced synchrony implementation achieves a higher throughput, up to 2 Giga-Requests per second on an 8-leaf binary tree. Our circuit also consumes less power than the synchronous design, and requires less silicon area than both the synchronous and asynchronous designs.}, keywords = {8, arbiter, arbitrate-and-move, architecture;, asynchronous, balanced, binary, circuit, circuit;, circuits;, consumption;, data, explicit, interconnection, interconnections;, leaf, mesh-of-trees, multi-threading;, Multithreading, n-leaf, network;, pipeline, pipelined, power, primitive, processing;, reduced, simulation;, structures;, synchronous, synchrony, system-on-chip;, tree, tree;}, doi = {10.1109/ISCAS.2004.1329303}, author = {Balkan,A.O. and Gang Qu and Vishkin, Uzi} } @article {12689, title = {Bayesian self-calibration of a moving camera}, journal = {Computer Vision and Image Understanding}, volume = {95}, year = {2004}, month = {2004/09//}, pages = {287 - 316}, abstract = {In this paper, a Bayesian self-calibration approach using sequential importance sampling (SIS) is proposed. Given a set of feature correspondences tracked through an image sequence, the joint posterior distributions of both camera extrinsic and intrinsic parameters as well as the scene structure are approximated by a set of samples and their corresponding weights. The critical motion sequences are explicitly considered in the design of the algorithm. The probability of the existence of the critical motion sequence is inferred from the sample and weight set obtained from the SIS procedure. No initial guess for the calibration parameters is required. The proposed approach has been extensively tested on both synthetic and real image sequences and satisfactory performance has been observed.}, keywords = {self-calibration, Sequential Monte Carlo methods, structure from motion, video analysis}, isbn = {1077-3142}, doi = {10.1016/j.cviu.2004.03.009}, url = {http://www.sciencedirect.com/science/article/pii/S1077314204000396}, author = {Qian,Gang and Chellapa, Rama} } @conference {12686, title = {Robust Bayesian cameras motion estimation using random sampling}, booktitle = {Image Processing, 2004. ICIP {\textquoteright}04. 2004 International Conference on}, volume = {2}, year = {2004}, month = {2004/10//}, pages = {1361 - 1364 Vol.2 - 1361 - 1364 Vol.2}, abstract = {In this paper, we propose an algorithm for robust 3D motion estimation of wide baseline cameras from noisy feature correspondences. The posterior probability density function of the camera motion parameters is represented by weighted samples. The algorithm employs a hierarchy coarse-to-fine strategy. First, a coarse prior distribution of camera motion parameters is estimated using the random sample consensus scheme (RANSAC). Based on this estimate, a refined posterior distribution of camera motion parameters can then be obtained through importance sampling. Experimental results using both synthetic and real image sequences indicate the efficacy of the proposed algorithm.}, keywords = {3D, baseline, Bayesian, CAMERAS, cameras;, coarse-to-fine, consensus, density, estimation;, feature, function;, hierarchy, image, images;, importance, matching;, MOTION, posterior, probability, probability;, processing;, random, RANSAC;, real, realistic, sample, sampling;, scheme;, sequences;, stereo, strategy;, synthetic, wide}, doi = {10.1109/ICIP.2004.1419754}, author = {Qian, G. and Chellapa, Rama and Qinfen Zheng} } @article {12714, title = {Structure from Motion Using Sequential Monte Carlo Methods}, journal = {International Journal of Computer Vision}, volume = {59}, year = {2004}, month = {2004///}, pages = {5 - 31}, abstract = {In this paper, the structure from motion (SfM) problem is addressed using sequential Monte Carlo methods. A new SfM algorithm based on random sampling is derived to estimate the posterior distributions of camera motion and scene structure for the perspective projection camera model. Experimental results show that challenging issues in solving the SfM problem, due to erroneous feature tracking, feature occlusion, motion/structure ambiguity, mixed-domain sequences, mismatched features, and independently moving objects, can be well modeled and effectively addressed using the proposed method.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1023/B:VISI.0000020669.68126.4b}, author = {Qian,Gang and Chellapa, Rama} } @conference {12705, title = {Vehicle detection and tracking using acoustic and video sensors}, booktitle = {Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP {\textquoteright}04). IEEE International Conference on}, volume = {3}, year = {2004}, month = {2004/05//}, pages = {iii - 793-6 vol.3 - iii - 793-6 vol.3}, abstract = {Multimodal sensing has attracted much attention in solving a wide range of problems, including target detection, tracking, classification, activity understanding, speech recognition, etc. In surveillance applications, different types of sensors, such as video and acoustic sensors, provide distinct observations of ongoing activities. We present a fusion framework using both video and acoustic sensors for vehicle detection and tracking. In the detection phase, a rough estimate of target direction-of-arrival (DOA) is first obtained using acoustic data through beam-forming techniques. This initial DOA estimate designates the approximate target location in video. Given the initial target position, the DOA is refined by moving target detection using the video data. Markov chain Monte Carlo techniques are then used for joint audio-visual tracking. A novel fusion approach has been proposed for tracking, based on different characteristics of audio and visual trackers. Experimental results using both synthetic and real data are presented. Improved tracking performance has been observed by fusing the empirical posterior probability density functions obtained using both types of sensors.}, keywords = {acoustic, applications;, audio, audio-visual, beam-forming, Carlo, chain, density, detection;, direction-of-arrival, DOA, empirical, estimation;, framework;, functions;, fusion, fusion;, joint, Markov, methods;, Monte, moving, multimodal, object, optical, posterior, probability, probability;, processes;, processing;, sensing;, sensor, sensors;, signal, Surveillance, surveillance;, systems;, target, techniques;, tracking;, vehicle, video}, doi = {10.1109/ICASSP.2004.1326664}, author = {Chellapa, Rama and Qian,Gang and Qinfen Zheng} } @article {12955, title = {A 4-Year Study of the Epidemiology of Vibrio Cholerae in Four Rural Areas of Bangladesh}, journal = {Journal of Infectious DiseasesJ Infect Dis.}, volume = {187}, year = {2003}, month = {2003/01/01/}, pages = {96 - 101}, abstract = {How Vibrio cholerae spreads around the world and what determines its seasonal peaks in endemic areas are not known. These features of cholera have been hypothesized to be primarily the result of environmental factors associated with aquatic habitats that can now be identified. Since 1997, fortnightly surveillance in 4 widely separated geographic locations in Bangladesh has been performed to identify patients with cholera and to collect environmental data. A total of 5670 patients (53\% <5 years of age) have been studied; 14.3\% had cholera (10.4\% due to V. cholerae O1 El Tor, 3.8\% due to O139). Both serogroups were found in all locations; outbreaks were seasonal and often occurred simultaneously. Water-use patterns showed that bathing and washing clothes in tube-well water was significantly protective in two of the sites. These data will be correlated with environmental factors, to develop a model for prediction of cholera outbreaks}, isbn = {0022-1899, 1537-6613}, doi = {10.1086/345865}, url = {http://jid.oxfordjournals.org/content/187/1/96}, author = {Sack,R. Bradley and Siddique,A. Kasem and Longini,Ira M. and Nizam,Azhar and Yunus,Md and M. Sirajul Islam and Morris,Jr and Ali,Afsar and Huq,Anwar and Nair,G. Balakrish and Qadri,Firdausi and Faruque,Shah M. and Sack,David A. and Rita R Colwell} } @conference {12322, title = {Energy reduction techniques for multimedia applications with tolerance to deadline misses}, booktitle = {Proceedings of the 40th annual Design Automation Conference}, year = {2003}, month = {2003///}, pages = {131 - 136}, author = {Hua,S. and Qu,G. and Bhattacharyya, Shuvra S.} } @conference {12381, title = {Exploring the probabilistic design space of multimedia systems}, booktitle = {14th IEEE International Workshop on Rapid Systems Prototyping, 2003. Proceedings}, year = {2003}, month = {2003/06/09/11}, pages = {233 - 240}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we propose the novel concept of probabilistic design for multimedia systems and a methodology to quickly explore such design space at an early design stage. The probabilistic design is motivated by the challenge of how to design, but not over-design, multimedia embedded systems while systematically incorporating such application{\textquoteright}s performance requirements, uncertainties in execution time, and tolerance for reasonable execution failures. Our goal is to bridge the gap between real-time analysis and embedded software implementation for rapid and economic (multimedia) system prototyping. Our method takes advantage of multimedia system{\textquoteright}s unique features mentioned above to relax the rigid hardware requirements for software implementation and eventually avoid over-designing the system.}, keywords = {economic system prototyping, embedded software implementation, Embedded system, Energy consumption, execution time uncertainties, Hardware, multimedia embedded systems, multimedia system prototyping, multimedia systems, performance requirements, probabilistic design space, rapid system prototyping, Real time systems, real-time analysis, reasonable execution failure tolerance, Resource management, software prototyping, Space exploration, Streaming media, systems analysis, Timing, Uncertainty}, isbn = {0-7695-1943-1}, doi = {10.1109/IWRSP.2003.1207053}, author = {Shaoxiong Hua and Gang Qu and Bhattacharyya, Shuvra S.} } @conference {15285, title = {What makes a good answer? The role of context in question answering}, booktitle = {Human-Computer Interaction, Interact {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {25 - 25}, author = {Jimmy Lin and Quan,D. and Sinha,V. and Bakshi,K. and Huynh,D. and Katz,B. and Karger,D. R} } @article {12759, title = {A Bayesian Approach to Simultaneous Motion Estimation of Multiple Independently Moving Objects}, journal = {INTERNATIONAL CONFERENCE ON PATTERN RECOGNITION}, volume = {16}, year = {2002}, month = {2002///}, pages = {309 - 314}, abstract = {In this paper, the problem of simultaneous motion estima-tion of multiple independently moving objects is addressed. A novel Bayesian approach is designed for solving this prob- lem using the sequential importance sampling (SIS) method. In the proposed algorithm, a balancing step is added into the SIS procedure to preserve samples of low weights so that all objects have enough samples to propagate empirical motion distributions. By using the proposed algorithm, the relative motions of all moving objects with respect to camera can be simultaneously estimated . This algorithm has been tested on both synthetic and real image sequences. Improved re- sults have been achieved. }, author = {Qian, G. and Chellapa, Rama and Zheng,Q.} } @conference {12758, title = {Bayesian structure from motion using inertial information}, booktitle = {Image Processing. 2002. Proceedings. 2002 International Conference on}, volume = {3}, year = {2002}, month = {2002///}, pages = {III-425 - III-428 vol.3 - III-425 - III-428 vol.3}, abstract = {A novel approach to Bayesian structure from motion (SfM) using inertial information and sequential importance sampling (SIS) is presented. The inertial information is obtained from camera-mounted inertial sensors and is used in the Bayesian SfM approach as prior knowledge of the camera motion in the sampling algorithm. Experimental results using both synthetic and real images show that, when inertial information is used, more accurate results can be obtained or the same estimation accuracy can be obtained at a lower cost.}, keywords = {3D, analysis;, Bayes, Bayesian, camera, estimation;, image, images;, importance, inertial, information;, methods;, MOTION, motion;, parameter, processing;, real, reconstruction;, sampling;, scene, sensors;, sequence;, sequences;, sequential, signal, structure-from-motion;, synthetic, systems;, video}, doi = {10.1109/ICIP.2002.1038996}, author = {Qian,Gang and Chellapa, Rama and Qinfen Zheng} } @article {16270, title = {Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii}, journal = {Nature}, volume = {419}, year = {2002}, month = {2002/10/03/}, pages = {512 - 519}, abstract = {Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.}, isbn = {0028-0836}, doi = {10.1038/nature01099}, url = {http://www.nature.com/nature/journal/v419/n6906/full/nature01099.html}, author = {Carlton,Jane M. and Angiuoli,Samuel V and Suh,Bernard B. and Kooij,Taco W. and Pertea,Mihaela and Silva,Joana C. and Ermolaeva,Maria D. and Allen,Jonathan E and Jeremy D Selengut and Koo,Hean L. and Peterson,Jeremy D. and Pop, Mihai and Kosack,Daniel S. and Shumway,Martin F. and Bidwell,Shelby L. and Shallom,Shamira J. and Aken,Susan E. van and Riedmuller,Steven B. and Feldblyum,Tamara V. and Cho,Jennifer K. and Quackenbush,John and Sedegah,Martha and Shoaibi,Azadeh and Cummings,Leda M. and Florens,Laurence and Yates,John R. and Raine,J. Dale and Sinden,Robert E. and Harris,Michael A. and Cunningham,Deirdre A. and Preiser,Peter R. and Bergman,Lawrence W. and Vaidya,Akhil B. and Lin,Leo H. van and Janse,Chris J. and Waters,Andrew P. and Smith,Hamilton O. and White,Owen R. and Salzberg,Steven L. and Venter,J. Craig and Fraser,Claire M. and Hoffman,Stephen L. and Gardner,Malcolm J. and Carucci,Daniel J.} } @article {12760, title = {Structure from Motion/Stereoscopic Vision/Surface Geometry/Shape-Bayesian Self-Calibration of a Moving Camera}, journal = {Lecture Notes in Computer Science}, volume = {2351}, year = {2002}, month = {2002///}, pages = {277 - 293}, author = {Qian, G. and Chellapa, Rama} } @article {14089, title = {The African trypanosome genome}, journal = {International Journal for Parasitology}, volume = {30}, year = {2000}, month = {2000/04//}, pages = {329 - 345}, abstract = {The haploid nuclear genome of the African trypanosome, Trypanosoma brucei, is about 35 Mb and varies in size among different trypanosome isolates by as much as 25\%. The nuclear DNA of this diploid organism is distributed among three size classes of chromosomes: the megabase chromosomes of which there are at least 11 pairs ranging from 1 Mb to more than 6 Mb (numbered I-XI from smallest to largest); several intermediate chromosomes of 200-900 kb and uncertain ploidy; and about 100 linear minichromosomes of 50-150 kb. Size differences of as much as four-fold can occur, both between the two homologues of a megabase chromosome pair in a specific trypanosome isolate and among chromosome pairs in different isolates. The genomic DNA sequences determined to date indicated that about 50\% of the genome is coding sequence. The chromosomal telomeres possess TTAGGG repeats and many, if not all, of the telomeres of the megabase and intermediate chromosomes are linked to expression sites for genes encoding variant surface glycoproteins (VSGs). The minichromosomes serve as repositories for VSG genes since some but not all of their telomeres are linked to unexpressed VSG genes. A gene discovery program, based on sequencing the ends of cloned genomic DNA fragments, has generated more than 20 Mb of discontinuous single-pass genomic sequence data during the past year, and the complete sequences of chromosomes I and II (about 1 Mb each) in T. brucei GUTat 10.1 are currently being determined. It is anticipated that the entire genomic sequence of this organism will be known in a few years. Analysis of a test microarray of 400 cDNAs and small random genomic DNA fragments probed with RNAs from two developmental stages of T. brucei demonstrates that the microarray technology can be used to identify batteries of genes differentially expressed during the various life cycle stages of this parasite.}, isbn = {0020-7519}, doi = {16/S0020-7519(00)00015-1}, url = {http://www.sciencedirect.com/science/article/pii/S0020751900000151}, author = {El-Sayed, Najib M. and Hegde,Priti and Quackenbush,John and Melville,Sara E. and Donelson,John E.} }