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https://www.readbyqxmd.com/read/28077170/prosodic-processing-post-traumatic-brain-injury-a-systematic-review
#1
Gabriela Ilie, Michael D Cusimano, Wenshan Li
BACKGROUND: Traumatic brain injury (TBI) survivors often report difficulties with understanding and producing paralinguistic cues, as well as understanding and producing basic communication tasks. However, a large range of communicative deficits in this population cannot be adequately explained by linguistic impairment. The review examines prosodic processing performance post-TBI, its relationship with injury severity, brain injury localization, recovery and co-occurring psychiatric or mental health issues post-TBI METHODS: A systematic review using several databases including MEDLINE, EMBASE, Cochrane, LLBA (Linguistics and Language Behaviour Abstract) and Web of Science (January 1980 to May 2015), as well as a manual search of the cited references of the selected articles and the search cited features of PubMed was performed...
January 4, 2017: Systematic Reviews
https://www.readbyqxmd.com/read/28062448/ontologyx-a-suite-of-r-packages-for-working-with-ontological-data
#2
Daniel Greene, Sylvia Richardson, Ernest Turro
: Ontologies are widely used constructs for encoding and analyzing biomedical data, but the absence of simple and consistent tools has made exploratory and systematic analysis of such data unnecessarily difficult. Here we present three packages which aim to simplify such procedures. The ontologyIndex package enables arbitrary ontologies to be read into R, supports representation of ontological objects by native R types, and provides a parsimonius set of performant functions for querying ontologies...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28060704/segnet-a-deep-convolutional-encoder-decoder-architecture-for-scene-segmentation
#3
Vijay Badrinarayanan, Alex Kendall, Roberto Cipolla
We present a novel and practical deep fully convolutional neural network architecture for semantic pixel-wise segmentation termed SegNet. This core trainable segmentation engine consists of an encoder network, a corresponding decoder network followed by a pixel-wise classification layer. The architecture of the encoder network is topologically identical to the 13 convolutional layers in the VGG16 network [1]. The role of the decoder network is to map the low resolution encoder feature maps to full input resolution feature maps for pixel-wise classification...
January 2, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28059689/an-integrated-health-neighbourhood-framework-to-optimise-the-use-of-ehr-data
#4
Siaw-Teng Liaw, Simon De Lusignan
 General practice should become the hub of integrated health neighbourhoods (IHNs), which involves sharing of information to ensure that medical homes are also part of learning organisations that use electronic health record (EHR) data for care, decision making, teaching and learning, quality improvement and research. The IHN is defined as the primary and ambulatory care services in a locality that relates largely to a single hospital-based secondary care service provider and is the logical denominator and unit of comparison for the optimal use of EHR data and health information exchange (HIE) to facilitate integration and coordination of care...
October 4, 2016: Journal of Innovation in Health Informatics
https://www.readbyqxmd.com/read/28057566/semanticsco-a-platform-to-support-the-semantic-composition-of-services-for-gene-expression-analysis
#5
Gabriela D A Guardia, Luís Ferreira Pires, Eduardo G da Silva, Cléver R G de Farias
Gene expression studies often require the combined use of a number of analysis tools. However, manual integration of analysis tools can be cumbersome and error prone. To support a higher level of automation in the integration process, efforts have been made in the biomedical domain towards the development of semantic web services and supporting composition environments. Yet, most environments consider only the execution of simple service behaviours and requires users to focus on technical details of the composition process...
January 2, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28035214/easy-extraction-of-terms-and-definitions-with-owl2tl
#6
John Judkins, Joseph Utecht, Mathias Brochhausen
Facilitating good communication between semantic web specialists and domain experts is necessary to efficient ontology development. This development may be hindered by the fact that domain experts tend to be unfamiliar with tools used to create and edit OWL files. This is true in particular when changes to definitions need to be reviewed as often as multiple times a day. We developed "OWL to Term List" (OWL2TL) with the goal of allowing domain experts to view the terms and definitions of an OWL file organized in a list that is updated each time the OWL file is updated...
August 2016: CEUR Workshop Proceedings
https://www.readbyqxmd.com/read/28031284/drug-drug-interaction-discovery-and-demystification-using-semantic-web-technologies
#7
Adeeb Noor, Abdullah Assiri, Serkan Ayvaz, Connor Clark, Michel Dumontier
OBJECTIVE: To develop a novel pharmacovigilance inferential framework to infer mechanistic explanations for asserted drug-drug interactions (DDIs) and deduce potential DDIs. MATERIALS AND METHODS: A mechanism-based DDI knowledge base was constructed by integrating knowledge from several existing sources at the pharmacokinetic, pharmacodynamic, pharmacogenetic, and multipathway interaction levels. A query-based framework was then created to utilize this integrated knowledge base in conjunction with 9 inference rules to infer mechanistic explanations for asserted DDIs and deduce potential DDIs...
December 28, 2016: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28019640/semantic-dementia-a-mini-review
#8
Blanka Klimova, Michal Novotny, Kamil Kuca
BACKGROUND: At present there are about 47.5 million people suffering from different types of dementia and by 2030 this number should reach 75.6 million. This obviously brings about serious social and economic burden for people suffering from any kind of dementia. OBJECTIVE: The purpose of this article is to explore only semantic dementia (SD) as one of the forms of frontotemporal dementia (FTD) and provide the latest information on its diagnosis and treatment which play a significant role in the maintenance of quality of life of both patients and their caregivers...
December 23, 2016: Mini Reviews in Medicinal Chemistry
https://www.readbyqxmd.com/read/27992262/the-kit-motion-language-dataset
#9
Matthias Plappert, Christian Mandery, Tamim Asfour
Linking human motion and natural language is of great interest for the generation of semantic representations of human activities as well as for the generation of robot activities based on natural language input. However, although there have been years of research in this area, no standardized and openly available data set exists to support the development and evaluation of such systems. We, therefore, propose the Karlsruhe Institute of Technology (KIT) Motion-Language Dataset, which is large, open, and extensible...
December 2016: Big Data
https://www.readbyqxmd.com/read/27936706/computational-chemistry-data-management-platform-based-on-the-semantic-web
#10
Bing Wang, Paul A Dobosh, Stuart Chalk, Mirek Sopek, Neil S Ostlund
This paper presents a formal data publishing platform for computational chemistry using semantic web technologies. This platform encapsulates computational chemistry data from a variety of packages in an Extensible Markup Language (XML) file called CSX (Common Standard for eXchange). On the basis of a Gainesville Core (GC) ontology for computational chemistry, a CSX XML file is converted into the JavaScript Object Notation for Linked Data (JSON-LD) format using an XML Stylesheet Language Transformation (XSLT) file...
December 22, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27932908/lifewatch-greece-data-services-discovering-biodiversity-data-using-semantic-web-technologies
#11
Nikos Minadakis, Yannis Marketakis, Martin Doerr, Chryssoula Bekiari, Panagiotis Papadakos, Alexandros Gougousis, Nicolas Bailly, Christos Arvanitidis
BACKGROUND: Biodiversity data is characterized by its cross-disciplinary character, the extremely broad range of data types and structures, and the variety of semantic concepts that it encompasses. Furthermore there is a plethora of different data sources providing resources for the same piece of information in a heterogeneous way. Even if we restrict our attention to Greek biodiversity domain, it is easy to see that biodiversity data remains unconnected and widely distributed among different sources...
2016: Biodiversity Data Journal
https://www.readbyqxmd.com/read/27927232/publication-of-nuclear-magnetic-resonance-experimental-data-with-semantic-web-technology-and-the-application-thereof-to-biomedical-research-of-proteins
#12
Masashi Yokochi, Naohiro Kobayashi, Eldon L Ulrich, Akira R Kinjo, Takeshi Iwata, Yannis E Ioannidis, Miron Livny, John L Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara
BACKGROUND: The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. FINDINGS: To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data...
May 5, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27924010/dna-data-bank-of-japan
#13
Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Toshiaki Katayama, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration with the US National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). The DDBJ Center also services Japanese Genotype-phenotype Archive (JGA), with the National Bioscience Database Center to collect human-subjected data from Japanese researchers...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899668/cyanobase-%C3%A2-a-large-scale-update-on-its-20th-anniversary
#14
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...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899649/protein-ontology-pro-enhancing-and-scaling-up-the-representation-of-protein-entities
#15
Darren A Natale, Cecilia N Arighi, Judith A Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R Christie, Julie Cowart, Peter D'Eustachio, Alexander D Diehl, Harold J Drabkin, William D Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed, Cathy H Wu
The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899636/the-monarch-initiative-an-integrative-data-and-analytic-platform-connecting-phenotypes-to-genotypes-across-species
#16
Christopher J Mungall, Julie A McMurry, Sebastian Köhler, James P Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J P Gourdine, Julius O B Jacobsen, Dan Keith, Bryan Laraway, Suzanna E Lewis, Jeremy NguyenXuan, Kent Shefchek, Nicole Vasilevsky, Zhou Yuan, Nicole Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N Robinson, Melissa A Haendel
The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27875201/categorical-colormap-optimization-with-visualization-case-studies
#17
H Fang, S Walton, E Delahaye, J Harris, D A Storchak, M Chen
Mapping a set of categorical values to different colors is an elementary technique in data visualization. Users of visualization software routinely rely on the default colormaps provided by a system, or colormaps suggested by software such as ColorBrewer. In practice, users often have to select a set of colors in a semantically meaningful way (e.g., based on conventions, color metaphors, and logological associations), and consequently would like to ensure their perceptual differentiation is optimized. In this paper, we present an algorithmic approach for maximizing the perceptual distances among a set of given colors...
January 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/27861505/content-based-discovery-for-web-map-service-using-support-vector-machine-and-user-relevance-feedback
#18
Kai Hu, Zhipeng Gui, Xiaoqiang Cheng, Kunlun Qi, Jie Zheng, Lan You, Huayi Wu
Many discovery methods for geographic information services have been proposed. There are approaches for finding and matching geographic information services, methods for constructing geographic information service classification schemes, and automatic geographic information discovery. Overall, the efficiency of the geographic information discovery keeps improving., There are however, still two problems in Web Map Service (WMS) discovery that must be solved. Mismatches between the graphic contents of a WMS and the semantic descriptions in the metadata make discovery difficult for human users...
2016: PloS One
https://www.readbyqxmd.com/read/27853445/semantic-differential-scale-method-can-reveal-multi-dimensional-aspects-of-mind-perception
#19
Hideyuki Takahashi, Midori Ban, Minoru Asada
As humans, we tend to perceive minds in both living and non-living entities, such as robots. From a questionnaire developed in a previous mind perception study, authors found that perceived minds could be located on two dimensions "experience" and "agency." This questionnaire allowed the assessment of how we perceive minds of various entities from a multi-dimensional point of view. In this questionnaire, subjects had to evaluate explicit mental capacities of target characters (e.g., capacity to feel hunger)...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27849523/videostory-embeddings-recognize-events-when-examples-are-scarce
#20
Amirhossein Habibian, Thomas Mensink, Cees G M Snoek
This paper aims for event recognition when video examples are scarce or even completely absent. The key in such a challenging setting is a semantic video representation. Rather than building the representation from individual attribute detectors and their annotations, we propose to learn the entire representation from freely available web videos and their descriptions using an embedding between video features and term vectors. In our proposed embedding, which we call Video2vec, the correlations between the words are utilized to learn a more effective representation by optimizing a joint objective balancing descriptiveness and predictability...
November 10, 2016: IEEE Transactions on Pattern Analysis and Machine Intelligence
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