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Li Liu, Zijia Lin, Ling Shao, Fumin Shen, Guiguang Ding, Jungong Han
With the dramatic development of the Internet, how to exploit large-scale retrieval techniques for multimodal web data has become one of the most popular but challenging problems in computer vision and multimedia. Recently, hashing methods are used for fast nearest neighbor search in large-scale data spaces, by embedding high-dimensional feature descriptors into a similarity-preserving Hamming space with a low dimension. Inspired by this, in this paper, we introduce a novel supervised cross-modality hashing framework which can generate unified binary codes for instances represented in different modalities...
October 19, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Marcela Suárez-Esquivel, Nazareth Ruiz-Villalobos, Amanda Castillo-Zeledón, César Jiménez-Rojas, R Martin Roop Ii, Diego J Comerci, Elías Barquero-Calvo, Carlos Chacón-Díaz, Clayton C Caswell, Kate S Baker, Esteban Chaves-Olarte, Nicholas R Thomson, Edgardo Moreno, Jean J Letesson, Xavier De Bolle, Caterina Guzmán-Verri
Brucellosis is a bacterial infectious disease affecting a wide range of mammals and a neglected zoonosis caused by species of the genetically homogenous genus Brucella. As in most studies on bacterial diseases, research in brucellosis is carried out by using reference strains as canonical models to understand the mechanisms underlying host pathogen interactions. We performed whole genome sequencing analysis of the reference strain B. abortus 2308 routinely used in our laboratory, including manual curated annotation accessible as an editable version through a link at https://en...
2016: Frontiers in Microbiology
Kersten Döring, Björn A Grüning, Kiran K Telukunta, Philippe Thomas, Stefan Günther
Information extraction from biomedical literature is continuously growing in scope and importance. Many tools exist that perform named entity recognition, e.g. of proteins, chemical compounds, and diseases. Furthermore, several approaches deal with the extraction of relations between identified entities. The BioCreative community supports these developments with yearly open challenges, which led to a standardised XML text annotation format called BioC. PubMed provides access to the largest open biomedical literature repository, but there is no unified way of connecting its data to natural language processing tools...
2016: PloS One
Gang Xie, Anne Roiko, Helen Stratton, Charles Lemckert, Peter K Dunn, Kerrie Mengersen
For dose-response analysis in quantitative microbial risk assessment (QMRA), the exact beta-Poisson model is a two-parameter mechanistic dose-response model with parameters α>0 and β>0, which involves the Kummer confluent hypergeometric function. Evaluation of a hypergeometric function is a computational challenge. Denoting PI(d) as the probability of infection at a given mean dose d, the widely used dose-response model PI(d)=1-(1+dβ)-α is an approximate formula for the exact beta-Poisson model. Notwithstanding the required conditions α<β and β>1, issues related to the validity and approximation accuracy of this approximate formula have remained largely ignored in practice, partly because these conditions are too general to provide clear guidance...
October 5, 2016: Risk Analysis: An Official Publication of the Society for Risk Analysis
G Droege, K Barker, O Seberg, J Coddington, E Benson, W G Berendsohn, B Bunk, C Butler, E M Cawsey, J Deck, M Döring, P Flemons, B Gemeinholzer, A Güntsch, T Hollowell, P Kelbert, I Kostadinov, R Kottmann, R T Lawlor, C Lyal, J Mackenzie-Dodds, C Meyer, D Mulcahy, S Y Nussbeck, É O'Tuama, T Orrell, G Petersen, T Robertson, C Söhngen, J Whitacre, J Wieczorek, P Yilmaz, H Zetzsche, Y Zhang, X Zhou
Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today's ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way...
2016: Database: the Journal of Biological Databases and Curation
Max Klein, Rati Sharma, Chris Bohrer, Cameron Avelis, Elijah Roberts
: Data-parallel programming techniques can dramatically decrease the time needed to analyze large data sets. While these methods have provided significant improvements for sequencing-based analyses, other areas of biological informatics have not yet adopted them. Here, we introduce Biospark, a new framework for performing data-parallel analysis on large numerical data sets. Biospark builds upon the open source Hadoop and Spark projects, bringing domain-specific features for biology. AVAILABILITY AND IMPLEMENTATION: Source code is licensed under the Apache 2...
September 22, 2016: Bioinformatics
Ola Spjuth, Patrik Rydberg, Egon L Willighagen, Chris T Evelo, Nina Jeliazkova
Xenobiotic metabolism is an active research topic but the limited amount of openly available high-quality biotransformation data constrains predictive modeling. Current database often default to commonly available information: which enzyme metabolizes a compound, but neither experimental conditions nor the atoms that undergo metabolization are captured. We present XMetDB, an open access database for drugs and other xenobiotics and their respective metabolites. The database contains chemical structures of xenobiotic biotransformations with substrate atoms annotated as reaction centra, the resulting product formed, and the catalyzing enzyme, type of experiment, and literature references...
2016: Journal of Cheminformatics
Nina M Trocky, Kathleen M Buckley
Although wikis appear to have been reported as effective tools for educators, uncertainty exists as to their effectiveness in achieving student learning outcomes. The aim of this integrative review was to examine the current evidence on the impact of wikis on student learning in courses requiring collaborative or co-developed assignments or activities. The authors searched several electronic databases for relevant articles and used R. Whittemore and K. Knafl's (2005) integrative review method to analyze and synthesize the evidence...
September 2016: Journal of Professional Nursing: Official Journal of the American Association of Colleges of Nursing
Juliane Fluck, Sumit Madan, Sam Ansari, Alpha T Kodamullil, Reagon Karki, Majid Rastegar-Mojarad, Natalie L Catlett, William Hayes, Justyna Szostak, Julia Hoeng, Manuel Peitsch
Success in extracting biological relationships is mainly dependent on the complexity of the task as well as the availability of high-quality training data. Here, we describe the new corpora in the systems biology modeling language BEL for training and testing biological relationship extraction systems that we prepared for the BioCreative V BEL track. BEL was designed to capture relationships not only between proteins or chemicals, but also complex events such as biological processes or disease states. A BEL nanopub is the smallest unit of information and represents a biological relationship with its provenance...
2016: Database: the Journal of Biological Databases and Curation
Meghan J Elliott, Sharon E Straus, Neesh Pannu, Sofia B Ahmed, Andreas Laupacis, George C Chong, David R Hillier, Kate T Huffman, Andrew C Lei, Berlene V Villanueva, Donna M Young, Helen Tam-Tham, Maoliosa Donald, Erin Lillie, Braden J Manns, Brenda R Hemmelgarn
BACKGROUND: Few studies have evaluated stakeholder engagement in chronic kidney disease (CKD) research prioritization. In this two-arm, parallel group randomized controlled trial, we sought to compare an in-person nominal group technique (NGT) approach with an online wiki-inspired alternative to determining the top 10 CKD research priorities, and to evaluate stakeholder engagement and satisfaction with each process. METHODS: Eligible participants included adults ≥18 years with access to a computer and Internet, high health literacy, and from one of the following stakeholder groups: patients with CKD not on dialysis, their caregivers, health care providers who care for patients with CKD, or CKD-related health policymakers...
2016: BMC Medical Informatics and Decision Making
Ei-Wen Yang, Tao Jiang
MOTIVATION: Differential transcript expression (DTE) analysis without predefined conditions is critical to biological studies. For example, it can be used to discover biomarkers to classify cancer samples into previously unknown subtypes such that better diagnosis and therapy methods can be developed for the subtypes. Although several DTE tools for population data, i.e., data without known biological conditions, have been published, these tools either assume binary conditions in the input population or require the number of conditions as a part of the input...
August 13, 2016: Bioinformatics
In Seok Yang, Hyeonju Son, Sora Kim, Sangwoo Kim
BACKGROUND: Alternative splicing events that result in the production of multiple gene isoforms reveals important molecular mechanisms. Gene isoforms are often differentially expressed across organs and tissues, developmental stages, and disease conditions. Specifically, recent studies show that aberrant regulation of alternative splicing frequently occurs in cancer to affect tumor cell transformation and growth. While analysis of isoform expression is important for discovering tumor-specific isoform signatures and interpreting relevant genomic mutations, there is currently no web-based, easy-to-use, and publicly available platform for this purpose...
2016: BMC Genomics
Magdalena A Tkacz, Kornel Chromiński, Dominika Idziak-Helmcke, Ewa Robaszkiewicz, Robert Hasterok
This paper presents ChroTeMo, a tool for chromosome territory modelling, accompanied by ChroTeVi-a chromosome territory visualisation software that uses the data obtained by ChroTeMo. These tools have been developed in order to complement the molecular cytogenetic research of interphase nucleus structure in a model grass Brachypodium distachyon. Although the modelling tool has been initially created for one particular species, it has universal application. The proposed version of ChroTeMo allows for generating a model of chromosome territory distribution in any given plant or animal species after setting the initial, species-specific parameters...
2016: PloS One
Natalie Cooper, Gavin H Thomas, Richard G FitzJohn
Phylogenetic comparative methods are becoming increasingly popular for investigating evolutionary patterns and processes. However, these methods are not infallible - they suffer from biases and make assumptions like all other statistical methods.Unfortunately, although these limitations are generally well known in the phylogenetic comparative methods community, they are often inadequately assessed in empirical studies leading to misinterpreted results and poor model fits. Here, we explore reasons for the communication gap dividing those developing new methods and those using them...
June 2016: Methods in Ecology and Evolution
A Schuster, D Brachthäuser, M Mansour, H Alfke
In times of RIS (radiology information system) and KIS (hospital information system) systems, patient-related data are at the radiologist's disposal at the push of a button. However, this is not the case for other important data. The increasing complexity of modern medicine demands that up-to-date information like protocols, SOPs (Standards of Practice), news and modifications are constantly accessible to all employees. This aspect of quality assurance becomes increasingly important in the context of certification...
September 2016: Der Radiologe
Mark M Hammer, Gavriel D Kohlberg
BACKGROUND: Despite widespread calls for its use, there are challenges to the implementation of evidence-based medicine (EBM) in clinical practice. METHODS: In response to the challenges of finding timely, pertinent information on diagnostic test accuracy, we developed an online, crowd-sourced Wiki on diagnostic test accuracy called Get the Diagnosis (GTD, RESULTS: Since its launch in November 2008 till October 2015, GTD has accumulated information on 300 diagnoses, with 1617 total diagnostic entries...
August 3, 2016: Postgraduate Medical Journal
D G Howe, Y M Bradford, A Eagle, D Fashena, K Frazer, P Kalita, P Mani, R Martin, S T Moxon, H Paddock, C Pich, S Ramachandran, L Ruzicka, K Schaper, X Shao, A Singer, S Toro, C Van Slyke, M Westerfield
The Zebrafish Model Organism Database (ZFIN; serves as the central repository for genetic and genomic data produced using zebrafish (Danio rerio). Data in ZFIN are either manually curated from peer-reviewed publications or submitted directly to ZFIN from various data repositories. Data types currently supported include mutants, transgenic lines, DNA constructs, gene expression, phenotypes, antibodies, morpholinos, TALENs, CRISPRs, disease models, movies, and images. The rapidly changing methods of genomic science have increased the production of data that cannot readily be represented in standard journal publications...
2016: Methods in Cell Biology
Marjorie A Vogt, Barbara H Schaffner
Nursing education is challenged to prepare students for complex healthcare needs through the integration of teamwork and informatics. Technology has become an important teaching tool in the blended classroom to enhance group based learning experiences. Faculty evaluation of classroom technologies is imperative prior to adoption. Few studies have directly compared various technologies and their impact on student satisfaction and learning. The purpose of this study was to evaluate technology enhanced teaching methods on the learning and satisfaction of graduate students in an advanced pharmacology class using an unfolding case study...
July 2016: Nurse Education in Practice
Giovanni Stracquadanio, Kun Yang, Jef D Boeke, Joel S Bader
: Synthetic biology has become a widely-used technology, and expanding applications in research, education, and industry require progress tracking for team-based DNA synthesis projects. Although some vendors are beginning to supply multi-kilobase sequence-verified constructs, synthesis workflows starting with short oligos remain important for cost savings and pedagogical benefit. We developed BioPartsDB as an open-source, extendable workflow management system for synthetic biology projects with entry points for oligos and larger DNA constructs and ending with sequence-verified clones...
July 13, 2016: Bioinformatics
Imad Abugessaisa, Hisashi Shimoji, Serkan Sahin, Atsushi Kondo, Jayson Harshbarger, Marina Lizio, Yoshihide Hayashizaki, Piero Carninci, Alistair Forrest, Takeya Kasukawa, Hideya Kawaji
The Functional Annotation of the Mammalian Genome project (FANTOM5) mapped transcription start sites (TSSs) and measured their activities in a diverse range of biological samples. The FANTOM5 project generated a large data set; including detailed information about the profiled samples, the uncovered TSSs at high base-pair resolution on the genome, their transcriptional initiation activities, and further information of transcriptional regulation. Data sets to explore transcriptome in individual cellular states encoded in the mammalian genomes have been enriched by a series of additional analysis, based on the raw experimental data, along with the progress of the research activities...
2016: Database: the Journal of Biological Databases and Curation
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