Context-based task ontologies for clinical guidelines

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned in the WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up

Escaping death: Mitochondrial redox homeostasis in cancer cells

Reactive oxygen species (ROS) are important signaling molecules that act through the oxidation of nucleic acids, proteins, and lipids. Several hallmarks of cancer, including uncontrolled proliferation, angiogenesis, and genomic instability, are promoted by the increased ROS levels commonly found in tumor cells. To counteract excessive ROS accumulation, oxidative stress, and death, cancer cells tightly regulate ROS levels by enhancing scavenging enzymes, which are dependent on the reducing cofactor nicotinamide adenine dinucleotide phosphate (NADPH). This review focuses on mitochondrial ROS homeostasis with a description of six pathways of NADPH production in mitochondria and a discussion of the possible strategies of pharmacological intervention to selectively eliminate cancer cells by increasing their ROS levels

PAV ontology: provenance, authoring and versioning

Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple scientific claim with supportive evidence. Existing vocabularies such as DC Terms and the W3C PROV-O are domain-independent and general-purpose and they allow and encourage for extensions to cover more specific needs. We identify the specific need for identifying or distinguishing between the various roles assumed by agents manipulating digital artifacts, such as author, contributor and curator. We present the Provenance, Authoring and Versioning ontology (PAV): a lightweight ontology for capturing just enough descriptions essential for tracking the provenance, authoring and versioning of web resources. We argue that such descriptions are essential for digital scientific content. PAV distinguishes between contributors, authors and curators of content and creators of representations in addition to the provenance of originating resources that have been accessed, transformed and consumed. We explore five projects (and communities) that have adopted PAV illustrating their usage through concrete examples. Moreover, we present mappings that show how PAV extends the PROV-O ontology to support broader interoperability. The authors strived to keep PAV lightweight and compact by including only those terms that have demonstrated to be pragmatically useful in existing applications, and by recommending terms from existing ontologies when plausible. We analyze and compare PAV with related approaches, namely Provenance Vocabulary, DC Terms and BIBFRAME. We identify similarities and analyze their differences with PAV, outlining strengths and weaknesses of our proposed model. We specify SKOS mappings that align PAV with DC Terms.Comment: 22 pages (incl 5 tables and 19 figures). Submitted to Journal of Biomedical Semantics 2013-04-26 (#1858276535979415). Revised article submitted 2013-08-30. Second revised article submitted 2013-10-06. Accepted 2013-10-07. Author proofs sent 2013-10-09 and 2013-10-16. Published 2013-11-22. Final version 2013-12-06. http://www.jbiomedsem.com/content/4/1/3

Open semantic annotation of scientific publications using DOMEO

<p>Abstract</p> <p>Background</p> <p>Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model.</p> <p>Methods</p> <p>The Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of both the Annotation Framework and the open model was driven by requirements of several different types of alpha users, including bench scientists and biomedical curators from university research labs, online scientific communities, publishing and pharmaceutical companies.</p> <p>Several use cases were incrementally implemented by the toolkit. These use cases in biomedical communications include personal note-taking, group document annotation, semantic tagging, claim-evidence-context extraction, reagent tagging, and curation of textmining results from entity extraction algorithms.</p> <p>Results</p> <p>We report on the Domeo user interface here. Domeo has been deployed in beta release as part of the NIH Neuroscience Information Framework (NIF, <url>http://www.neuinfo.org</url><it/>) and is scheduled for production deployment in the NIF’s next full release.</p> <p>Future papers will describe other aspects of this work in detail, including Annotation Framework Services and components for integrating with external textmining services, such as the NCBO Annotator web service, and with other textmining applications using the Apache UIMA framework.</p

Unusual becoming Usual: recent persistent-rainstorm events and their implications for debris flow risk management in the northern Apennines of Italy

The alluvial events of Parma (13 October 2014) and Piacenza (13-14 September 2015) in the northern Apennines of Italy have had significant effects in terms of flooding and morphological changes along the main and secondary rivers of the affected areas. The paper presents a summary of the characteristics of the rainstorm events, as well as of the triggered debris flows and their consequences on infrastructures. In the perspective of an extremization of rainfall regimes as a consequence of ongoing climate changes, these phenomena might become quite usual in the future and should be further studied in order to define regional-specific triggering thresholds, analyse precursors from weather radar datasets and assess susceptibility on a regional scale basis

Commentary on: "Pityriasis Rosea Recurrence is Much Higher than Previously Known: A Prospective Study".

Abstract is missing (Correspondence

Controversies in adjuvant endocrine therapy for pre- and post-menopausal women with breast cancer

AbstractNearly 80% of breast cancer are hormone receptor positive. The efficacy of hormonal adjuvant therapy of breast cancer was expressed in the most recent EBCTG overview analysis of randomised trials using adjuvant tamoxifen. Five years of adjuvant tamoxifen led to proportional risk reduction, in terms of recurrence and mortality for hormone receptor positive patients, of 47% and 26%, respectively. This benefit was constant, regardless of menopausal status, age or whether or not chemotherapy was administered. More recent trials evaluating the use of aromatase inhibitors have challenged the standard of hormonal therapy in post-menopausal patients. However, many questions have been raised from these trials: (a) the optimal management of patients with hormone receptor positive breast cancer in terms of selection of hormonal agents and its sequence and duration; (b) the role of ovarian suppression in pre-menopausal patients; and (c) the actual role of biomolecular markers in clinical decision

Displacements of an Active Moderately Rapid Landslide\u2014A Dataset Retrieved by Continuous GNSS Arrays

This paper describes a dataset of continuous GNSS positioning solutions referring to slope movements in the Ca&rsquo; Lita landslide (Northern Apennines, Italy). The dataset covers the period from 24 March 2016 to 17 July 2019 and includes time-series of the daily position of three GNSS rovers located in different parts of the landslide: head zone, upper track zone, and lower track zone. Two different types of continuous GNSS arrays have been used: one is based on high-end Leica geodetic receivers, and the other is based on low-cost effective Emlid receivers. Displacements captured in the dataset are up to more than a hundred meters and are characterized by prolonged phases of slow movement and moderately rapid acceleration phases. The data presented in this contribution were used to underline slope processes and validate displacements retrieved by the application of digital image correlation to a stack of a satellite images

A case of drug rash with eosinophilia and systemic symptoms (DRESS) induced by telaprevir associated with HHV-6 active infection

Letter to the EditorA Case of Drug Rash with Eosinophilia and Systemic Symptoms (DRESS) In-duced by Telaprevir Associated with HHV-6 Active InfectionFrancesco Broccolo, Giulia Ciccarese, Antonino Picciotto, Francesco DragoPII: S0168-8278(14)00668-0DOI: http://dx.doi.org/10.1016/j.jhep.2014.09.014Reference: JHEPAT 5348To appear in