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https://www.readbyqxmd.com/read/27913348/automatic-refinement-strategies-for-manual-initialization-of-object-trackers
#1
Hao Zhu, Fatih Porikli
Tracking objects across multiple frames is a wellinvestigated problem in computer vision. The majority of the existing algorithms assume an accurate initialization is readily available. However, in many real-life settings, in particular for applications where the video is streaming in real-time, the initialization has to be provided by a human operator. This limitation raises an inevitable uncertainty issue. Here, we first collect a large and new dataset of inputs that consists of more than 20K human initialization clicks, called as HIC, by several subjects under three practical user interface scenarios for the popular TB50 tracking benchmark...
December 1, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/27909418/risk-and-ambiguity-in-information-seeking-eye-gaze-patterns-reveal-contextual-behavior-in-dealing-with-uncertainty
#2
Peter Wittek, Ying-Hsang Liu, Sándor Darányi, Tom Gedeon, Ik Soo Lim
Information foraging connects optimal foraging theory in ecology with how humans search for information. The theory suggests that, following an information scent, the information seeker must optimize the tradeoff between exploration by repeated steps in the search space vs. exploitation, using the resources encountered. We conjecture that this tradeoff characterizes how a user deals with uncertainty and its two aspects, risk and ambiguity in economic theory. Risk is related to the perceived quality of the actually visited patch of information, and can be reduced by exploiting and understanding the patch to a better extent...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27907895/mutlbsgenedb-mutated-ligand-binding-site-gene-database
#3
Pora Kim, Junfei Zhao, Pinyi Lu, Zhongming Zhao
Mutations at the ligand binding sites (LBSs) can influence protein structure stability, binding affinity with small molecules, and drug resistance in cancer patients. Our recent analysis revealed that ligand binding residues had a significantly higher mutation rate than other parts of the protein. Here, we built mutLBSgeneDB (mutated Ligand Binding Site gene DataBase) available at http://zhaobioinfo.org/mutLBSgeneDB We collected and curated over 2300 genes (mutLBSgenes) having ∼12 000 somatic mutations at ∼10 000 LBSs across 16 cancer types and selected 744 drug targetable genes (targetable_mutLBSgenes) by incorporating kinases, transcription factors, pharmacological genes, and cancer driver genes...
October 7, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903906/eupathdb-the-eukaryotic-pathogen-genomics-database-resource
#4
Cristina Aurrecoechea, Ana Barreto, Evelina Y Basenko, John Brestelli, Brian P Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S Harb, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C Kissinger, Cris Lawrence, Wei Li, Deborah F Pinney, Jane A Pulman, David S Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J Stoeckert, Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27900953/feedback-control-policies-employed-by-people-using-intracortical-brain-computer-interfaces
#5
Francis R Willett, Chethan Pandarinath, Beata Jarosiewicz, Brian A Murphy, William D Memberg, Christine H Blabe, Jad Saab, Benjamin L Walter, Jennifer A Sweet, Jonathan P Miller, Jaimie M Henderson, Krishna V Shenoy, John D Simeral, Leigh R Hochberg, Robert F Kirsch, A Bolu Ajiboye
OBJECTIVE: When using an intracortical BCI (iBCI), users modulate their neural population activity to move an effector towards a target, stop accurately, and correct for movement errors. We call the rules that govern this modulation a 'feedback control policy'. A better understanding of these policies may inform the design of higher-performing neural decoders. APPROACH: We studied how three participants in the BrainGate2 pilot clinical trial used an iBCI to control a cursor in a 2D target acquisition task...
November 30, 2016: Journal of Neural Engineering
https://www.readbyqxmd.com/read/27899905/effects-of-individual-differences-in-working-memory-on-plan-presentational-choices
#6
Nava Tintarev, Judith Masthoff
This paper addresses research questions that are central to the area of visualization interfaces for decision support: (RQ1) whether individual user differences in working memory should be considered when choosing how to present visualizations; (RQ2) how to present the visualization to support effective decision making and processing; and (RQ3) how to evaluate the effectiveness of presentational choices. These questions are addressed in the context of presenting plans, or sequences of actions, to users. The experiments are conducted in several domains, and the findings are relevant to applications such as semi-autonomous systems in logistics...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27899692/jenkins-ci-an-open-source-continuous-integration-system-as-a-scientific-data-and-image-processing-platform
#7
Ioannis K Moutsatsos, Imtiaz Hossain, Claudia Agarinis, Fred Harbinski, Yann Abraham, Luc Dobler, Xian Zhang, Christopher J Wilson, Jeremy L Jenkins, Nicholas Holway, John Tallarico, Christian N Parker
High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS)...
November 29, 2016: Journal of Biomolecular Screening
https://www.readbyqxmd.com/read/27899678/virus-variation-resource-improved-response-to-emergent-viral-outbreaks
#8
Eneida L Hatcher, Sergey A Zhdanov, Yiming Bao, Olga Blinkova, Eric P Nawrocki, Yuri Ostapchuck, Alejandro A Schäffer, J Rodney Brister
The Virus Variation Resource is a value-added viral sequence data resource hosted by the National Center for Biotechnology Information. The resource is located at http://www.ncbi.nlm.nih.gov/genome/viruses/variation/ and includes modules for seven viral groups: influenza virus, Dengue virus, West Nile virus, Ebolavirus, MERS coronavirus, Rotavirus A and Zika virus Each module is supported by pipelines that scan newly released GenBank records, annotate genes and proteins and parse sample descriptors and then map them to controlled vocabulary...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899676/transportdb-2-0-a-database-for-exploring-membrane-transporters-in-sequenced-genomes-from-all-domains-of-life
#9
Liam D H Elbourne, Sasha G Tetu, Karl A Hassan, Ian T Paulsen
All cellular life contains an extensive array of membrane transport proteins. The vast majority of these transporters have not been experimentally characterized. We have developed a bioinformatic pipeline to identify and annotate complete sets of transporters in any sequenced genome. This pipeline is now fully automated enabling it to better keep pace with the accelerating rate of genome sequencing. This manuscript describes TransportDB 2.0 (http://www.membranetransport.org/transportDB2/), a completely updated version of TransportDB, which provides access to the large volumes of data generated by our automated transporter annotation pipeline...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899670/the-new-nhgri-ebi-catalog-of-published-genome-wide-association-studies-gwas-catalog
#10
Jacqueline MacArthur, Emily Bowler, Maria Cerezo, Laurent Gil, Peggy Hall, Emma Hastings, Heather Junkins, Aoife McMahon, Annalisa Milano, Joannella Morales, Zoe May Pendlington, Danielle Welter, Tony Burdett, Lucia Hindorff, Paul Flicek, Fiona Cunningham, Helen Parkinson
The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation interface. These developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. The range of available Catalog data has also been extended with structured ancestry and recruitment information added for all studies...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899668/cyanobase-%C3%A2-a-large-scale-update-on-its-20th-anniversary
#11
Takatomo Fujisawa, Rei Narikawa, Shin-Ichi Maeda, Satoru Watanabe, Yu Kanesaki, Koichi Kobayashi, Jiro Nomata, Mitsumasa Hanaoka, Mai Watanabe, Shigeki Ehira, Eiji Suzuki, Koichiro Awai, Yasukazu Nakamura
The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase (http://genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently. Since then, CyanoBase has constantly been extended and has received several updates. Here, we describe a new large-scale update of the database, which coincides with its 20th anniversary. We have expanded the number of cyanobacterial genomic sequences from 39 to 376 species, which consists of 86 complete and 290 draft genomes...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899660/cebs-a-comprehensive-annotated-database-of-toxicological-data
#12
Isabel A Lea, Hui Gong, Anand Paleja, Asif Rashid, Jennifer Fostel
The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in recent years and currently contains over 11 000 test articles (exposure agents) and over 8000 studies including all available NTP carcinogenicity, short-term toxicity and genetic toxicity studies...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899627/improvements-to-patric-the-all-bacterial-bioinformatics-database-and-analysis-resource-center
#13
Alice R Wattam, James J Davis, Rida Assaf, Sébastien Boisvert, Thomas Brettin, Christopher Bun, Neal Conrad, Emily M Dietrich, Terry Disz, Joseph L Gabbard, Svetlana Gerdes, Christopher S Henry, Ronald W Kenyon, Dustin Machi, Chunhong Mao, Eric K Nordberg, Gary J Olsen, Daniel E Murphy-Olson, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon D Pusch, Maulik Shukla, Veronika Vonstein, Andrew Warren, Fangfang Xia, Hyunseung Yoo, Rick L Stevens
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899624/microscope-in-2017-an-expanding-and-evolving-integrated-resource-for-community-expertise-of-microbial-genomes
#14
David Vallenet, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Aurélie Lajus, Adrien Josso, Jonathan Mercier, Alexandre Renaux, Johan Rollin, Zoe Rouy, David Roche, Claude Scarpelli, Claudine Médigue
The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899619/the-nextprot-knowledgebase-on-human-proteins-2017-update
#15
Pascale Gaudet, Pierre-André Michel, Monique Zahn-Zabal, Aurore Britan, Isabelle Cusin, Marcin Domagalski, Paula D Duek, Alain Gateau, Anne Gleizes, Valérie Hinard, Valentine Rech de Laval, JinJin Lin, Frederic Nikitin, Mathieu Schaeffer, Daniel Teixeira, Lydie Lane, Amos Bairoch
The neXtProt human protein knowledgebase (https://www.nextprot.org) continues to add new content and tools, with a focus on proteomics and genetic variation data. neXtProt now has proteomics data for over 85% of the human proteins, as well as new tools tailored to the proteomics community.Moreover, the neXtProt release 2016-08-25 includes over 8000 phenotypic observations for over 4000 variations in a number of genes involved in hereditary cancers and channelopathies. These changes are presented in the current neXtProt update...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899616/the-tissuenet-v-2-database-a-quantitative-view-of-protein-protein-interactions-across-human-tissues
#16
Omer Basha, Ruth Barshir, Moran Sharon, Eugene Lerman, Binyamin F Kirson, Idan Hekselman, Esti Yeger-Lotem
Knowledge of the molecular interactions of human proteins within tissues is important for identifying their tissue-specific roles and for shedding light on tissue phenotypes. However, many protein-protein interactions (PPIs) have no tissue-contexts. The TissueNet database bridges this gap by associating experimentally-identified PPIs with human tissues that were shown to express both pair-mates. Users can select a protein and a tissue, and obtain a network view of the query protein and its tissue-associated PPIs...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899614/suba4-the-interactive-data-analysis-centre-for-arabidopsis-subcellular-protein-locations
#17
Cornelia M Hooper, Ian R Castleden, Sandra K Tanz, Nader Aryamanesh, A Harvey Millar
The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) is a comprehensive collection of manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from 22 prediction programs. SUBA4 contains an additional 35 568 localizations totalling more than 60 000 experimental protein location claims as well as 37 new suborganellar localization categories. The experimental PPI data has been expanded to 26 327 PPI pairs including 856 PPI localizations from experimental fluorescent visualizations...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899613/nsdna-a-manually-curated-database-of-experimentally-supported-ncrnas-associated-with-nervous-system-diseases
#18
Jianjian Wang, Yuze Cao, Huixue Zhang, Tianfeng Wang, Qinghua Tian, Xiaoyu Lu, Xiaoyan Lu, Xiaotong Kong, Zhaojun Liu, Ning Wang, Shuai Zhang, Heping Ma, Shangwei Ning, Lihua Wang
The Nervous System Disease NcRNAome Atlas (NSDNA) (http://www.bio-bigdata.net/nsdna/) is a manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDs represent a common group of disorders, some of which are characterized by high morbidity and disabilities. The pathogenesis of NSDs at the molecular level remains poorly understood. ncRNAs are a large family of functionally important RNA molecules. Increasing evidence shows that diverse ncRNAs play a critical role in various NSDs...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899586/r-loopdb-a-database-for-r-loop-forming-sequences-rlfs-and-r-loops
#19
Piroon Jenjaroenpun, Thidathip Wongsurawat, Sawannee Sutheeworapong, Vladimir A Kuznetsov
R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899581/hmtdb-2016-data-update-a-better-performing-query-system-and-human-mitochondrial-dna-haplogroup-predictor
#20
Rosanna Clima, Roberto Preste, Claudia Calabrese, Maria Angela Diroma, Mariangela Santorsola, Gaetano Scioscia, Domenico Simone, Lishuang Shen, Giuseppe Gasparre, Marcella Attimonelli
The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release...
November 28, 2016: Nucleic Acids Research
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