1,960 research outputs found

    Clonal Complexes in Biomedical Ontologies

    Get PDF
    An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Se-quence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies

    Constructing a lattice of Infectious Disease Ontologies from a Staphylococcus aureus isolate repository

    Get PDF
    A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology

    Experience of cardiac rehabilitation after coronary artery surgery: effects on health and risk factors

    Get PDF
    Objective:Cardiac rehabilitation (CR) programs are provided to support the recovery process following acute myocardial infarction and coronary artery bypass grafting (CABG). Attendance varies. We related attendance following CABG to severity of cardiac symptoms, general health status (Short Form-36) and prevalence of modifiable coronary artery disease (CAD) risk factors. METHODS: 209 patients due to undergo CABG were recruited and assessed preoperatively as well as at a mean of 16.4 months postoperatively. General health status was measured using the Short Form-36 questionnaire. Severity of cardiac symptoms was assessed on a visual analogue scale. Modifiable coronary artery disease risk factors (smoking, body mass index, hypertension and elevated cholesterol) and social deprivation index were noted

    The Infectious Disease Ontology in the Age of COVID-19

    Get PDF
    The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

    The Australian corporate closet, why it\u27s still so full: a review of incidence rates for sexual orientation discrimination gender identity discrimination in the workplace

    Get PDF
    The paper reviews the extant Australian literature on sexual orientation (SO) discrimination within the Australian workplace. In the research, there is variation in organisational workplace and a bias towards health and educational sectors as a research setting, which raises some methodological considerations such as poor generalisability to other organisational contexts. The small body of Australian research into SO discrimination encompasses; (i) varied methodological and theoretical approaches, (ii) disparate authors selecting a varied range of aspects of discrimination thus absenting a unifying framework to guide research and lacking as yet seminal authorship providing focus, iii) limited sampling of participants making comparisons difficult and further indicating the absence of a unifying framework with which to focus the research and iv) limited studies exclusively investigating workplace discrimination. In this paper, the Australian literature is presented chronologically, and where possible, it has linked studies together to indicate the commensurate nature of the studies to illustrate the incidence rates of SO discrimination in the Australian labour market as a rationale for GLBTIQ employees remaining in the corporate closet

    Homophobia to heterosexism: constructs in need of re-visitation

    Get PDF
    Although the concept of homophobia has been used extensively in the literature since the early 1960s, researchers have shown growing concern for its relevance in present day research. Additionally, there has been variance in its definition leading to an array of ambiguities resulting in methodological limitations in empirical studies with a disregard for ensuring that definitions used match the focus of study. There have been numerous attempts to locate the construct within a theoretical framework and this has also resulted in weak empirical design. These weaknesses in research on homophobia have resulted in the coining of the construct heterosexism as a more contemporary and more appropriate definition than that of homophobia to indicate anti-gay discrimination. This review considers both terms with regard to their appropriateness and distinction and the utility of the construct heterosexism as it is applied to contemporary research on non-heterosexual communities. It is concluded that homophobia can no longer be framed as a straightforward function of individual psyches or irrational fear and loathing and that heterosexism is more appropriate in defining prejudiced behaviours and their consequences for non-heterosexual communities

    NuSTAR detection of X-ray heating events in the quiet Sun

    Get PDF
    The explanation of the coronal heating problem potentially lies in the existence of nanoflares, numerous small-scale heating events occurring across the whole solar disk. In this Letter, we present the first imaging spectroscopy X-ray observations of three quiet Sun flares during the Nuclear Spectroscopic Telescope ARray (NuSTAR) solar campaigns on 2016 July 26 and 2017 March 21, concurrent with the Solar Dynamics Observatory/Atmospheric Imaging Assembly (SDO/AIA) observations. Two of the three events showed time lags of a few minutes between peak X-ray and extreme ultraviolet emissions. Isothermal fits with rather low temperatures in the range 3.2–4.1 MK and emission measures of (0.6–15) × 1044 cm−3 describe their spectra well, resulting in thermal energies in the range (2–6) × 1026 erg. NuSTAR spectra did not show any signs of a nonthermal or higher temperature component. However, as the estimated upper limits of (hidden) nonthermal energy are comparable to the thermal energy estimates, the lack of a nonthermal component in the observed spectra is not a constraining result. The estimated Geostationary Operational Environmental Satellite (GOES) classes from the fitted values of temperature and emission measure fall between 1/1000 and 1/100 A class level, making them eight orders of magnitude fainter in soft X-ray flux than the largest solar flares

    An improved ontological representation of dendritic cells as a paradigm for all cell types

    Get PDF
    The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’
    • 

    corecore