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Knowledge representation

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https://www.readbyqxmd.com/read/29218395/inferring-phylogenetic-trees-from-the-knowledge-of-rare-evolutionary-events
#1
Marc Hellmuth, Maribel Hernandez-Rosales, Yangjing Long, Peter F Stadler
Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters. In this contribution we analyze the phylogenetic information content from a combinatorial point of view by considering the binary relation on the set of taxa defined by the existence of a single event separating two taxa. We show that the graph-representation of this relation must be a tree. Moreover, we characterize completely the relationship between the tree of such relations and the underlying phylogenetic tree...
December 7, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/29218267/radiomics-in-precision-medicine-for-lung-cancer
#2
REVIEW
Julie Constanzo, Lise Wei, Huan-Hsin Tseng, Issam El Naqa
With the improvement of external radiotherapy delivery accuracy, such as intensity-modulated and stereotactic body radiation therapy, radiation oncology has recently entered in the era of precision medicine. Despite these precise irradiation modalities, lung cancers remain one of the most aggressive human cancers worldwide, possibly because of diverse genotypic alterations that drive and maintain lung tumorigenesis. It has been long recognized that imaging could aid in the diagnosis, tumor delineation, and monitoring of lung cancer...
December 2017: Translational Lung Cancer Research
https://www.readbyqxmd.com/read/29215557/indoors-locality-positioning-using-cognitive-distances-and-directions
#3
Yankun Wang, Hong Fan, Ruizhi Chen
Spatial relationships are crucial to spatial knowledge representation, such as positioning localities. However, minimal attention has been devoted to positioning localities indoors with locality description. Distance and direction relations are generally used when positioning localities, namely, translating descriptive localities into spatially explicit ones. We propose a joint probability function to model locality distribution to address the uncertainty of positioning localities. The joint probability function consists of distance and relative direction membership functions...
December 7, 2017: Sensors
https://www.readbyqxmd.com/read/29214571/preparing-data-at-the-source-to-foster-interoperability-across-rare-disease-resources
#4
Marco Roos, Estrella López Martin, Mark D Wilkinson
The ability to combine heterogeneous data distributed across the globe is critically important to boost research on rare diseases, but it presents a number of methodological, representational and automation challenges. In this scenario, biomedical ontologies are of critical importance for enabling computers to aid in information retrieval and analysis across data collections.This chapter presents an approach to preparing rare disease data for integration through the application of a global standard for computer-readable data and knowledge...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29214177/linked-registries-connecting-rare-diseases-patient-registries-through-a-semantic-web-layer
#5
Pedro Sernadela, Lorena González-Castro, Claudio Carta, Eelke van der Horst, Pedro Lopes, Rajaram Kaliyaperumal, Mark Thompson, Rachel Thompson, Núria Queralt-Rosinach, Estrella Lopez, Libby Wood, Agata Robertson, Claudia Lamanna, Mette Gilling, Michael Orth, Roxana Merino-Martinez, Manuel Posada, Domenica Taruscio, Hanns Lochmüller, Peter Robinson, Marco Roos, José Luís Oliveira
Patient registries are an essential tool to increase current knowledge regarding rare diseases. Understanding these data is a vital step to improve patient treatments and to create the most adequate tools for personalized medicine. However, the growing number of disease-specific patient registries brings also new technical challenges. Usually, these systems are developed as closed data silos, with independent formats and models, lacking comprehensive mechanisms to enable data sharing. To tackle these challenges, we developed a Semantic Web based solution that allows connecting distributed and heterogeneous registries, enabling the federation of knowledge between multiple independent environments...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29212542/a-framework-to-find-the-logic-backbone-of-a-biological-network
#6
Parul Maheshwari, Réka Albert
BACKGROUND: Cellular behaviors are governed by interaction networks among biomolecules, for example gene regulatory and signal transduction networks. An often used dynamic modeling framework for these networks, Boolean modeling, can obtain their attractors (which correspond to cell types and behaviors) and their trajectories from an initial state (e.g. a resting state) to the attractors, for example in response to an external signal. The existing methods however do not elucidate the causal relationships between distant nodes in the network...
December 6, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29212411/geriatric-traumatic-brain-injury-epidemiology-outcomes-knowledge-gaps-and-future-directions
#7
Raquel C Gardner, Kristen Dams-O'Connor, Molly Rose Morrissey, Geoffrey Manley
This review of the literature on traumatic brain injury (TBI) in older adults focuses on incident TBI sustained in older adulthood ("geriatric TBI") rather than on the separate, but related, topic of older adults with a history of earlier-life TBI. We describe the epidemiology of geriatric TBI, the impact of comorbidities and pre-injury function on TBI risk and outcomes, diagnostic testing, management issues, outcomes, and critical directions for future research. The highest incidence of TBI-related emergency department visits, hospitalizations, and deaths occur in older adults...
December 6, 2017: Journal of Neurotrauma
https://www.readbyqxmd.com/read/29211807/null-diffusion-based-enrichment-for-metabolomics-data
#8
Sergio Picart-Armada, Francesc Fernández-Albert, Maria Vinaixa, Miguel A Rodríguez, Suvi Aivio, Travis H Stracker, Oscar Yanes, Alexandre Perera-Lluna
Metabolomics experiments identify metabolites whose abundance varies as the conditions under study change. Pathway enrichment tools help in the identification of key metabolic processes and in building a plausible biological explanation for these variations. Although several methods are available for pathway enrichment using experimental evidence, metabolomics does not yet have a comprehensive overview in a network layout at multiple molecular levels. We propose a novel pathway enrichment procedure for analysing summary metabolomics data based on sub-network analysis in a graph representation of a reference database...
2017: PloS One
https://www.readbyqxmd.com/read/29210882/fluency-in-nursing-education-and-simulation-a-concept-analysis
#9
Audra Lewis
AIM: The aim of the study was to realign how nurses view simulation in nursing education as a means of facilitating fluency in knowledge and action to promote expertise in practice. BACKGROUND: Nursing expertise is attained by translating complex phenomena across multiple representations and by constructing meaning through experience. Simulation provides learners the experiences necessary to develop fluency in thought and action. METHOD: Procedures outlined by Hupcey and Penrod (2005) and Walker and Avant (2011) were used to identify uses, defining attributes, philosophical assumptions, contextual factors, and values of the concept...
November 27, 2017: Nursing Education Perspectives
https://www.readbyqxmd.com/read/29210012/the-invisibility-of-fisheries-in-the-process-of-hydropower-development-across-the-amazon
#10
Carolina Rodrigues da Costa Doria, Simone Athayde, Elineide E Marques, Maria Alice Leite Lima, Jynessa Dutka-Gianelli, Mauro Luis Ruffino, David Kaplan, Carlos E C Freitas, Victoria N Isaac
We analyze the invisibility of fisheries and inadequacy of fishers' participation in the process of hydropower development in the Amazon, focusing on gaps between legally mandated and actual outcomes. Using Ostrom's institutional design principles for assessing common-pool resource management, we selected five case studies from Brazilian Amazonian watersheds to conduct an exploratory comparative case-study analysis. We identify similar problems across basins, including deficiencies in the dam licensing process; critical data gaps; inadequate stakeholder participation; violation of human rights; neglect of fishers' knowledge; lack of organization and representation by fishers' groups; and lack of governmental structure and capacity to manage dam construction activities or support fishers after dam construction...
December 5, 2017: Ambio
https://www.readbyqxmd.com/read/29209023/motor-cortical-activity-changes-during-neuroprosthetic-controlled-object-interaction
#11
John E Downey, Lucas Brane, Robert A Gaunt, Elizabeth C Tyler-Kabara, Michael L Boninger, Jennifer L Collinger
Brain-computer interface (BCI) controlled prosthetic arms are being developed to restore function to people with upper-limb paralysis. This work provides an opportunity to analyze human cortical activity during complex tasks. Previously we observed that BCI control became more difficult during interactions with objects, although we did not quantify the neural origins of this phenomena. Here, we investigated how motor cortical activity changed in the presence of an object independently of the kinematics that were being generated using intracortical recordings from two people with tetraplegia...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29206841/auditory-word-recognition-of-verbs-effects-of-verb-argument-structure-on-referent-identification
#12
Mònica Sanz-Torrent, Llorenç Andreu, Javier Rodriguez Ferreiro, Marta Coll-Florit, John C Trueswell
Word recognition includes the activation of a range of syntactic and semantic knowledge that is relevant to language interpretation and reference. Here we explored whether or not the number of arguments a verb takes impinges negatively on verb processing time. In this study, three experiments compared the dynamics of spoken word recognition for verbs with different preferred argument structure. Listeners' eye movements were recorded as they searched an array of pictures in response to hearing a verb. Results were similar in all the experiments...
2017: PloS One
https://www.readbyqxmd.com/read/29202761/hilbert-schmidt-and-sobol-sensitivity-indices-for-static-and-time-series-wnt-signaling-measurements-in-colorectal-cancer-part-a
#13
Shriprakash Sinha
BACKGROUND: Ever since the accidental discovery of Wingless [Sharma R.P., Drosophila information service, 1973, 50, p 134], research in the field of Wnt signaling pathway has taken significant strides in wet lab experiments and various cancer clinical trials, augmented by recent developments in advanced computational modeling of the pathway. Information rich gene expression profiles reveal various aspects of the signaling pathway and help in studying different issues simultaneously. Hitherto, not many computational studies exist which incorporate the simultaneous study of these issues...
December 4, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29200981/semantic-specificity-in-one-year-olds-word-comprehension
#14
Elika Bergelson, Richard Aslin
The present study investigated infants' knowledge about familiar nouns. Infants (n = 46, 12-20-month-olds) saw two-image displays of familiar objects, or one familiar and one novel object. Infants heard either a matching word (e.g. "foot' when seeing foot and juice), a related word (e.g. "sock" when seeing foot and juice) or a nonce word (e.g. "fep" when seeing a novel object and dog). Across the whole sample, infants reliably fixated the referent on matching and nonce trials. On the critical related trials we found increasingly less looking to the incorrect (but related) image with age...
2017: Language Learning and Development
https://www.readbyqxmd.com/read/29199547/from-ships-to-robots-the-social-relations-of-sensing-the-world-ocean
#15
Jessica Lehman
The dominant practices of physical oceanography have recently shifted from being based on ship-based ocean sampling and sensing to being based on remote and robotic sensing using satellites, drifting floats and remotely operated and autonomous underwater vehicles. What are the implications of this change for the social relations of oceanographic science? This paper contributes to efforts to address this question, pursuing a situated view of ocean sensing technologies so as to contextualize and analyze new representations of the sea, and interactions between individual scientists, technologies and the ocean...
December 1, 2017: Social Studies of Science
https://www.readbyqxmd.com/read/29198880/aureowiki-%C3%AC%C2%B5-the-repository-of-the-staphylococcus-aureus-research-and-annotation-community
#16
Stephan Fuchs, Henry Mehlan, Jörg Bernhardt, André Hennig, Stephan Michalik, Kristin Surmann, Jan Pané-Farré, Anne Giese, Stefan Weiss, Linus Backert, Alexander Herbig, Kay Nieselt, Michael Hecker, Uwe Völker, Ulrike Mäder
In light of continuously accumulating data and knowledge on major human pathogens, comprehensive and up-to-date sources of easily accessible information are urgently required. The AureoWiki database (http://aureowiki.med.uni-greifswald.de) provides detailed information on the genes and proteins of clinically and experimentally relevant S. aureus strains, currently covering NCTC 8325, COL, Newman, USA300_FPR3757, and N315. By implementing a pan-genome approach, AureoWiki facilitates the transfer of knowledge gained in studies with different S...
November 24, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/29196280/search-and-graph-database-technologies-for-biomedical-semantic-indexing-experimental-analysis
#17
Isabel Segura Bedmar, Paloma Martínez, Adrián Carruana Martín
BACKGROUND: Biomedical semantic indexing is a very useful support tool for human curators in their efforts for indexing and cataloging the biomedical literature. OBJECTIVE: The aim of this study was to describe a system to automatically assign Medical Subject Headings (MeSH) to biomedical articles from MEDLINE. METHODS: Our approach relies on the assumption that similar documents should be classified by similar MeSH terms. Although previous work has already exploited the document similarity by using a k-nearest neighbors algorithm, we represent documents as document vectors by search engine indexing and then compute the similarity between documents using cosine similarity...
December 1, 2017: JMIR Medical Informatics
https://www.readbyqxmd.com/read/29191207/medical-subdomain-classification-of-clinical-notes-using-a-machine-learning-based-natural-language-processing-approach
#18
Wei-Hung Weng, Kavishwar B Wagholikar, Alexa T McCray, Peter Szolovits, Henry C Chueh
BACKGROUND: The medical subdomain of a clinical note, such as cardiology or neurology, is useful content-derived metadata for developing machine learning downstream applications. To classify the medical subdomain of a note accurately, we have constructed a machine learning-based natural language processing (NLP) pipeline and developed medical subdomain classifiers based on the content of the note. METHODS: We constructed the pipeline using the clinical NLP system, clinical Text Analysis and Knowledge Extraction System (cTAKES), the Unified Medical Language System (UMLS) Metathesaurus, Semantic Network, and learning algorithms to extract features from two datasets - clinical notes from Integrating Data for Analysis, Anonymization, and Sharing (iDASH) data repository (n = 431) and Massachusetts General Hospital (MGH) (n = 91,237), and built medical subdomain classifiers with different combinations of data representation methods and supervised learning algorithms...
December 1, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/29187927/our-chairman-is-very-efficient-community-participation-in-the-delivery-of-primary-health-care-in-ibadan-southwest-nigeria
#19
Omowunmi Folake Iyanda, Oluwaseun Oladapo Akinyemi
Introduction: Community participation is rapidly being viewed as a requirement for the successful acceptance of health services; it integrates a complicated process which involves customs, beliefs, culture and power relations, not only structures and policies. Yet, there is a wide knowledge gap and changes favouring community participation in primary health care is still minimal. This study aims to assess the process indicators and other factors influencing community participation in the delivery of primary health care...
2017: Pan African Medical Journal
https://www.readbyqxmd.com/read/29187333/toward-a-clinic-of-temporality
#20
Thérèse Rivasseau Jonveaux, Martine Batt, Alain Trognon
The discovery of time cells has expanded our knowledge in the field of spatial and temporal information coding and the key role of the hippocampus. The internal clock model complemented with the attentional gate model allows a more in-depth understanding of the perception of time. The motor representation of duration is ensured by the basal ganglia, while the cerebellum synchronizes short duration for the movement. The right prefrontal cortex seemingly intervenes in the handling of temporal information in working memory...
December 1, 2017: Gériatrie et Psychologie Neuropsychiatrie du Vieillissement
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