Citing/Referencing

As rightly pointed out earlier, research ethics advises authors to avoid plagiarism. Citing the used references in scientific works is the best way of preventing plagiarism. There are some guidelines on the internet that helps authors to observe ethical writing tips. We cite others' works in many different ways. Firstly, we should know that what is the difference between a reference and citation and why we cite

Keeping up with studies on covid-19: Systematic search strategies and resources

The reason I write this letter is to take a small step towards helping readers with evidence based decision making by keeping them up to date with the rapidly growing number of covid-19 studies in PubMed ..

T129. Pharmacological Interventions in Trials of People with Schizophrenia: A Register-Based Classification of Seventy Years of Research

BackgroundDrug development is a billion dollar business globally. It is crucial to stay up to date on drug developments all over the world any repetition will be irreversible waste of resources. The only way to keep up with all the development is to keep a living database of all trials running for each condition and covering all studies from every country in any language. An Information Specialist collects and classifies all pharmacological interventions from all schizophrenia trials.MethodsCochrane Schizophrenia’s Study-Based Register was developed and used as the source of trials, Emtree and MeSH for synonyms, AdisInsight and CT.gov for research drugs and WHO ATC for marketed drugs. This research took four years from 17 December 2014 and 6 January 2019 and involved 18,500 randomized controlled trial from 90 countries in 23 languages.ResultsOne third of tested interventions on patients with schizophrenia are pharmacological (816; belonging to 106 clinical classes) with antipsychotic drugs being the most researched (15.1%). Only 528 of these medications are listed in WHO ATC. Around one third of these drug interventions are seen only in research (236; from 21 pharmacological/biochemical classes). Within the pharmacological evaluations we identified 28 ‘qualifiers’ including dose, route, and timing of drug delivery. Using Data Science approaches, this research revealed unique antipsychotic drugs that are being prescribed only in certain countries such as Japan but the West is not aware of them. This research is also revealed all the research drugs and current trends in developing drugs in pharmaceutical companies.DiscussionClassification of medication interventions from trials requires use of many sources of information none of which are inclusive of all drugs. Without a global search in all languages the pharmaceutical companies and researchers are missing important successful developments from non-English speaking world. The cycle of developing research/withdrawn drugs does not stop and may end in veterinary medicine, doping agents in sports, and illicit drug market

Unsupervised annotation of regulatory domains by integrating functional genomic assays and Hi-C data

In each cell type, chromosomes are organized into a specific 3D structure that controls the function of a cell through different mechanisms including domain-scale regulation. Because of the correlation between genome structure and its function, different methods have been proposed to integrate 1D functional genomic and 2D Hi-C data to identify domain types. Existing methods rely on an assumption that directly connected genomic regions are more probable to have the same domain type, however, spatial clustering of genomic regions is based on both their first-order and second-order proximities. Here, we present an integrative approach that uses 1D functional genomic features and 3D interactions from Hi-C data to assign labels to genomic regions that can discriminate both spatial and functional genomic patterns. We use graph embedding to learn latent variables for nodes (genomic regions) that preserve the Hi-C graph second-order proximity. Such latent variables summarize spatial information in Hi-C data, and we feed them in addition to existing 1D functional features to the Segway, a genome annotation method, to infer domain states. We show that our labels distinguish a combination of the spatial and functional states of the genomic regions, for example, loci locating in the nucleus interior can be furthermore clustered into significantly and moderately expressed domains. We also found the importance of each of the spatial and functional features to explain different cell activities including replication timing and gene expression profile, and how coupling two feature types improve the prediction of such activities. Finally, we showed that incorporating spatial features allow finding domain types, which are co-regulated even in large genomic distance from each other. Our framework can be generalized to aggregate different 1D genomic assays and 3D interactions from Hi-C to find the mechanisms behind the association of genome 3D structure and epigenetic profile

Lessons from COVID-19 to Future Evidence Synthesis Efforts: First Living Search Strategy and Out of Date Scientific Publishing and Indexing Industry

Nussbaumer-Streit et al. reported a timely study on the exclusion of non-English language reports in systematic reviews [1] but cautiously generalised the implications to rapid reviews rather than systematic reviews. The results complement the guidance in the new edition of the Cochrane Handbook [2]. However, the time of publication of this report coincides with the COVID-19 outbreak that introduces a geographical bias towards the inclusion of non-English literature. Although many researchers will try to publish in English, literature in non-English should not be ignored. We also thought it will be an added value to share our other experiences on literature search for evidence synthesis on COVID-19

Citing/Referencing

As rightly pointed out earlier, research ethics advises authors to avoid plagiarism. Citing the used references in scientific works is the best way of preventing plagiarism. There are some guidelines on the internet that helps authors to observe ethical writing tips. We cite others' works in many different ways. Firstly, we should know that what is the difference between a reference and citation and why we cite

Designing the Structured Search Experience: Rethinking the Query-Builder Paradigm

Knowledge workers such as healthcare information professionals, legal researchers, and librarians need to create and execute search strategies that are comprehensive, transparent, and reproducible. The traditional solution is to use command-line query builders offered by proprietary database vendors. However, these are based on a paradigm that dates from the days when users could access databases only via text-based terminals and command-line syntax. In this paper, we present a new approach in which users express concepts as objects on a visual canvas and manipulate them to articulate relationships. This offers a more intuitive user experience (UX) that eliminates many sources of error, makes the query semantics more transparent, and offers new ways to collaborate, share, and optimize search strategies and best practice