Automating generation of textual class definitions from OWL to English

Text definitions for entities within bio-ontologies are a cornerstone of the effort to gain a consensus in understanding and usage of those ontologies. Writing these definitions is, however, a considerable effort and there is often a lag between specification of the main part of an ontology (logical descriptions and definitions of entities) and the development of the text-based definitions. The goal of natural language generation (NLG) from ontologies is to take the logical description of entities and generate fluent natural language. The application described here uses NLG to automatically provide text-based definitions from an ontology that has logical descriptions of its entities, so avoiding the bottleneck of authoring these definitions by hand

Linked data authority records for Irish place names

Linked Data technologies are increasingly being implemented to enhance cataloguing workflows in libraries, archives and museums. We review current best practice in library cataloguing, how Linked Data is used to link collections and provide consistency in indexing, and briefly describe the relationship between Linked Data, library data models and descriptive standards. As an example we look at the Logainm.ie dataset, an online database holding the authoritative hierarchical list of Irish and English language place names in Ireland. This paper describes the process of creating the new Linked Logainm dataset, including the transformation of the data from XML to RDF and the generation of links to external geographic datasets like DBpedia and the Faceted Application of Subject Terminology. This dataset was then used to enhance the National Library of Ireland's metadata MARCXML metadata records for its Longfield maps collection. We also describe the potential benefits of Linked Data for libraries, focusing on the use of the Linked Logainm dataset and its future potential for Irish heritage institutions

Trace amine-associated receptor 1 (TAAR1) agonists for psychosis: protocol for a living systematic review and meta-analysis of human and non-human studies

Background: There is an urgent need to develop more effective and safer antipsychotics beyond dopamine 2 receptor antagonists. An emerging and promising approach is TAAR1 agonism. Therefore, we will conduct a living systematic review and meta-analysis to synthesize and triangulate the evidence from preclinical animal experiments and clinical studies on the efficacy, safety, and underlying mechanism of action of TAAR1 agonism for psychosis. Methods: Independent searches will be conducted in multiple electronic databases to identify clinical and animal experimental studies comparing TAAR1 agonists with licensed antipsychotics or other control conditions in individuals with psychosis or animal models for psychosis, respectively. The primary outcomes will be overall psychotic symptoms and their behavioural proxies in animals. Secondary outcomes will include side effects and neurobiological measures. Two independent reviewers will conduct study selection, data extraction using predefined forms, and risk of bias assessment using suitable tools based on the study design. Ontologies will be developed to facilitate study identification and data extraction. Data from clinical and animal studies will be synthesized separately using random-effects meta-analysis if appropriate, or synthesis without meta-analysis. Study characteristics will be investigated as potential sources of heterogeneity. Confidence in the evidence for each outcome and source of evidence will be evaluated, considering the summary of the association, potential concerns regarding internal and external validity, and reporting biases. When multiple sources of evidence are available for an outcome, an overall conclusion will be drawn in a triangulation meeting involving a multidisciplinary team of experts. We plan trimonthly updates of the review, and any modifications in the protocol will be documented. The review will be co-produced by multiple stakeholders aiming to produce impactful and relevant results and bridge the gap between preclinical and clinical research on psychosis

Secondary injury and inflammation after intracerebral haemorrhage: a systematic review and meta-analysis of molecular markers in patient brain tissue

BACKGROUND: Inflammatory responses to intracerebral haemorrhage (ICH) are potential therapeutic targets. We aimed to quantify molecular markers of inflammation in human brain tissue after ICH compared with controls using meta-analysis. METHODS: We searched OVID MEDLINE (1946–) and Embase (1974–) in June 2020 for studies that reported any measure of a molecular marker of inflammation in brain tissue from five or more adults after ICH. We assessed risk of bias using a modified Newcastle-Ottawa Scale (mNOS; mNOS score 0–9; 9 indicates low bias), extracted aggregate data, and used random effects meta-analysis to pool associations of molecules where more than two independent case–control studies reported the same outcome and Gene Ontology enrichment analysis to identify over-represented biological processes in pooled sets of differentially expressed molecules (International Prospective Register of Systematic Reviews ID: CRD42018110204). RESULTS: Of 7501 studies identified, 44 were included: 6 were case series and 38 were case–control studies (median mNOS score 4, IQR 3–5). We extracted data from 21 491 analyses of 20 951 molecules reported by 38 case–control studies. Only one molecule (interleukin-1β protein) was quantified in three case–control studies (127 ICH cases vs 41 ICH-free controls), which found increased abundance of interleukin-1β protein after ICH (corrected standardised mean difference 1.74, 95% CI 0.28 to 3.21, p=0.036, I(2)=46%). Processes associated with interleukin-1β signalling were enriched in sets of molecules that were more abundant after ICH. CONCLUSION: Interleukin-1β abundance is increased after ICH, but analyses of other inflammatory molecules after ICH lack replication. Interleukin-1β pathway modulators may optimise inflammatory responses to ICH and merit testing in clinical trials

Digital Cinemas

Digital technologies have altered the terms of all the major areas of film: finance, production and post-production, distribution and consumption.  This chapter looks at these through the lens of debates over historical continuities and discontinuities in each area, looking especially at the variety of production and dissemination formats from blockbusters to zero-budget film-making, the impact of technical standardisation, the affordances of different digital technologies, notably bitmap and vector, and the role of platforms like YouTube and their alternatives. The possibilities and challenges of 'world cinema' as a concept in this terrain will be the central them

Ethics in extracorporeal life support:a narrative review

Abstract During 50 years of extracorporeal life support (ECLS), this highly invasive technology has left a considerable imprint on modern medicine, and it still confronts researchers, clinicians and policymakers with multifarious ethical challenges. After half a century of academic discussion about the ethics of ECLS, it seems appropriate to review the state of the argument and the trends in it. Through a comprehensive literature search on PubMed, we identified three ethical discourses: (1) trials and evidence accompanying the use of ECLS, (2) ECLS allocation, decision-making and limiting care, and (3) death on ECLS and ECLS in organ donation. All included articles were carefully reviewed, arguments extracted and grouped into the three discourses. This article provides a narrative synthesis of these arguments, evaluates the opportunities for mediation and substantiates the necessity of a shared decision-making approach at the limits of medical care

Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles

Purpose. This paper introduces the Research Articles in Simplified HTML (or RASH), which is a Web-first format for writing HTML-based scholarly papers; it is accompanied by the RASH Framework, a set of tools for interacting with RASH-based articles. The paper also presents an evaluation that involved authors and reviewers of RASH articles submitted to the SAVE-SD 2015 and SAVE-SD 2016 workshops. Design. RASH has been developed aiming to: be easy to learn and use; share scholarly documents (and embedded semantic annotations) through the Web; support its adoption within the existing publishing workflow. Findings. The evaluation study confirmed that RASH is ready to be adopted in workshops, conferences, and journals and can be quickly learnt by researchers who are familiar with HTML. Research Limitations. The evaluation study also highlighted some issues in the adoption of RASH, and in general of HTML formats, especially by less technically savvy users. Moreover, additional tools are needed, e.g., for enabling additional conversions from/to existing formats such as OpenXML. Practical Implications. RASH (and its Framework) is another step towards enabling the definition of formal representations of the meaning of the content of an article, facilitating its automatic discovery, enabling its linking to semantically related articles, providing access to data within the article in actionable form, and allowing integration of data between papers. Social Implications. RASH addresses the intrinsic needs related to the various users of a scholarly article: researchers (focussing on its content), readers (experiencing new ways for browsing it), citizen scientists (reusing available data formally defined within it through semantic annotations), publishers (using the advantages of new technologies as envisioned by the Semantic Publishing movement). Value. RASH helps authors to focus on the organisation of their texts, supports them in the task of semantically enriching the content of articles, and leaves all the issues about validation, visualisation, conversion, and semantic data extraction to the various tools developed within its Framework