bims-librar Biomed News
on Biomedical librarianship
Issue of 2021‒04‒11
twelve papers selected by
Thomas Krichel
Open Library Society
  1. Learning about COVID-19: a qualitative interview study of Australians' use of information sources.
  2. REDASA: A Secure Continually Updating Web-Source Processing Pipeline supporting a REaltime DAta Synthesis and Analysis of Scientific Literature.
  3. A Novel Web Application for Rapidly Searching the Diagnostic Case Archive.
  4. A Comparative Analysis of System Features Used in the TREC-COVID Information Retrieval Challenge.
  5. Search, access, and explore life science nanopublications on the Web.
  6. TransforMED: End-to-End Transformers for Evidence-Based Medicine and Argument Mining in medical literature.
  7. Citation.js: a format-independent, modular bibliography tool for the browser and command line.
  8. Influence of tweets and diversification on serendipitous research paper recommender systems.
  9. Which Resources Are Better: Sales or Scholarly? An Assessment on the Readability, Quality, and Technical Features of Online Chemical Peel Websites.
  10. The readability of general practice websites: a cross-sectional analysis of all general practice websites in Scotland.
  11. A READABILITY COMPARISON OF ONLINE SPANISH AND ENGLISH PATIENT EDUCATION MATERIALS ABOUT VISION HEALTH.
  12. Predatory Journals, Fake Conferences and Misleading Social Media: The Dark Side of Medical Information.
  1. BMC Public Health. 2021 Apr 07. 21(1): 662
    Learning about COVID-19: a qualitative interview study of Australians' use of information sources.
    Deborah Lupton, Sophie Lewis.
      BACKGROUND: A multitude of information sources are available to publics when novel infectious diseases first emerge. In this paper, we adopt a qualitative approach to investigate how Australians learnt about the novel coronavirus and COVID-19 and what sources of information they had found most useful and valuable during the early months of the pandemic.METHODS: In-depth semi-structured telephone interviews were conducted with a diverse group of 40 Australian adults in mid-2020 about their experiences of the COVID-19 crisis. Participants were recruited through Facebook advertising. Detailed case studies were created for each participant, providing the basis of a thematic analysis which focused on the participants' responses to the questions about COVID-19-related information sources.
    RESULTS: Diverse sources of COVID-19-related information, including traditional media, online media and in-person interactions, were actively accessed, appraised and engaged with by participants. There was a high level of interest in COVID-19 information as people grappled with uncertainty, anxiety and feeling overwhelmed. Certain key events or experiences made people become aware that the outbreak was threatening Australia and potentially themselves. Most people demonstrated keen awareness that misinformation was rife in news outlets and social media sites and that they were taking steps to determine the accuracy of information. High trust was placed in health experts, scientists and government sources to provide reliable information. Also important to participants were informal discussions with friends and family members who were experts or working in relevant fields, as well as engaging in-person in interactions and hearing from friends and family who lived overseas about what COVID-19 conditions were like there.
    CONCLUSION: A constantly changing news environment raises challenges for effective communication of risk and containment advice. People can become confused, distressed and overwhelmed by the plethora of information sources and fast-changing news environment. On the other hand, seeking out information can provide reassurance and comfort in response to anxiety and uncertainty. Clarity and consistency in risk messaging is important, as is responding quickly to changes in information and misinformation. Further research should seek to identify any changes in use of and trust in information sources as time goes by.
    DOI:  https://doi.org/10.1186/s12889-021-10743-7
  2. J Med Internet Res. 2021 Apr 03.
    REDASA: A Secure Continually Updating Web-Source Processing Pipeline supporting a REaltime DAta Synthesis and Analysis of Scientific Literature.
    Uddhav Vaghela, Simon Rabinowicz, Paris Bratsos, Guy Martin, Epameinondas Fritzilas, Sheraz Markar, Sanjay Purkayastha, Karl Stringer, Harshdeep Singh, Charlie Llewellyn, Debabrata Dutta, Jonathan M Clarke, Matthew Howard, Ovidiu Serban, James Kinross.
      BACKGROUND: The scale and quality of the global scientific response to the COVID-19 pandemic has unquestionably saved lives. However, COVID-19 has also triggered an unprecedented "infodemic"; the velocity and volume of data production has overwhelmed many key stakeholders such as clinicians and policymakers who have been unable to process structured and unstructured data for evidence-based decision making. Current solutions which aim to alleviate this data synthesis challenge are unable to capture heterogeneous web data in "real-time" for the production of concomitant answers and are not based on the high-quality information in response to a free-text query.OBJECTIVE: : The main objective of this project is to build a generic real-time continuously updating curation platform that could support a data synthesis and analysis of scientific literature framework. Our secondary objective is to validate this pipeline and the curation methodology on COVID-19 related medical literature, by expanding the CORD19 dataset by adding new, unstructured data.
    METHODS: To realise an infrastructure that addresses the objectives, the PanSurg Collaborative at Imperial College London has developed a unique data pipeline based on a web crawler extraction methodology. This data pipeline converges with a novel curation methodology that adopts a "human in the loop" methodology for the characterisation of quality, relevance and key evidence across a range of scientific literature sources.
    RESULTS: REDASA is now one of the world's largest and most current COVID-19 source of evidence consisting of 104,000 documents. By capturing curators' critical appraisal methodology through the application of discrete labelling and rating of information, REDASA has rapidly developed a foundational data science dataset of over 1400 articles in the realm of pooled COVID-19 information, representing ∼10% of the papers written worldwide on COVID-19 in under two weeks.
    CONCLUSIONS: This dataset can act as ground-truth for future implementation of a live, automated systematic review. The benefits of the current design are threefold: 1) adoption of a friendlier "human in the loop" methodology by embedding an efficient user-friendly curation platform into an NLP search engine; 2) provides a curated dataset in JSON (JavaScript Object Notation) format for experienced academic reviewers' critical appraisal choices and decision-making methodology; 3) due to the wide scope and depth of the web-crawling, REDASA has already captured one of the world's largest COVID-19 data corpora for search and curation. This dataset can act as ground-truth for future implementation of a live, automated systematic review.
    DOI:  https://doi.org/10.2196/25714
  3. J Pathol Inform. 2020 ;11 39
    A Novel Web Application for Rapidly Searching the Diagnostic Case Archive.
    Scott Robertson.
      Academic pathologists must have the ability to search their institution's archive of diagnostic case data. This ability is foundational for research, education, and other academic activities. However, the built-in search functions of commercial laboratory information systems are not always optimized for this activity, leading to delays between an initial search request, and eventual results delivery. To solve this problem, a novel web-based search platform was developed, named Pathtools, which allows our staff and trainees to directly and rapidly search our diagnostic case archive. Pathtools was built with open-source components and features a web-based user-interface. Pathtools uses an SQL database which was populated with anatomic pathology case data going back to 1980, and contains 4.2 million cases (as of July 31, 2020). Pathtools has two major modes of operation, "Preview Mode" and "Research Mode." Since deployment in February of 2019, Pathtools carried out 33,817 searches in Preview Mode, averaging 0.72 s (standard deviation = 1.7) between search submission, and on-screen display of search results. In Research Mode, Pathtools has also been used to produce data sets for research activity, providing the data used in many abstracts and manuscripts our investigators submitted recently. Interestingly, 75% of search activity is from trainees during their preview time. In a survey of residents and fellows, 83% used Pathtools during the majority of their preview sessions, demonstrating an important role for this resource in trainee education. In conclusion, a web-based search tool can rapidly and securely provide search capability directly to end-users, which has augmented trainee education and research activity in our department.
    Keywords:  Education; pathology reports; python; text search; web application
    DOI:  https://doi.org/10.4103/jpi.jpi_43_20
  4. J Biomed Inform. 2021 Apr 05. pii: S1532-0464(21)00074-5. [Epub ahead of print] 103745
    A Comparative Analysis of System Features Used in the TREC-COVID Information Retrieval Challenge.
    Jimmy Chen, William R Hersh.
      The COVID-19 pandemic has resulted in a rapidly growing quantity of scientific publications from journal articles, preprints, and other sources. The TREC-COVID Challenge was created to evaluate information retrieval methods and systems for this quickly expanding corpus. Using the COVID-19 Open Research Dataset (CORD-19), several dozen research teams participated in over 5 rounds of the TREC-COVID Challenge. While previous work has compared IR techniques used on other test collections, there are no studies that have analyzed the methods used by participants in the TREC-COVID Challenge. We manually reviewed team run reports from Rounds 2 and 5, extracted features from the documented methodologies, and used a univariate and multivariate regression-based analysis to identify features associated with higher retrieval performance. We observed that fine-tuning datasets with relevance judgments, MS-MARCO, and CORD-19 document vectors was associated with improved performance in Round 2 but not in Round 5. Though the relatively decreased heterogeneity of runs in Round 5 may explain the lack of significance in that round, fine-tuning has been found to improve search performance in previous challenge evaluations by improving a system's ability to map relevant queries and phrases to documents. Furthermore, term expansion was associated with improvement in system performance, and the use of the narrative field in the TREC-COVID topics was associated with decreased system performance in both rounds. These findings emphasize the need for clear queries in search. While our study has some limitations in its generalizability and scope of techniques analyzed, we identified some IR techniques that may be useful in building search systems for COVID-19 using the TREC-COVID test collections.
    DOI:  https://doi.org/10.1016/j.jbi.2021.103745
  5. PeerJ Comput Sci. 2021 ;7 e335
    Search, access, and explore life science nanopublications on the Web.
    Fabio Giachelle, Dennis Dosso, Gianmaria Silvello.
      Nanopublications are Resource Description Framework (RDF) graphs encoding scientific facts extracted from the literature and enriched with provenance and attribution information. There are millions of nanopublications currently available on the Web, especially in the life science domain. Nanopublications are thought to facilitate the discovery, exploration, and re-use of scientific facts. Nevertheless, they are still not widely used by scientists outside specific circles; they are hard to find and rarely cited. We believe this is due to the lack of services to seek, find and understand nanopublications' content. To this end, we present the NanoWeb application to seamlessly search, access, explore, and re-use the nanopublications publicly available on the Web. For the time being, NanoWeb focuses on the life science domain where the vastest amount of nanopublications are available. It is a unified access point to the world of nanopublications enabling search over graph data, direct connections to evidence papers, and scientific curated databases, and visual and intuitive exploration of the relation network created by the encoded scientific facts.
    Keywords:  Data access; Data citation; Data exploration; Data search; Graph exploration; Nanopublication; Scientific data
    DOI:  https://doi.org/10.7717/peerj-cs.335
  6. J Biomed Inform. 2021 Mar 31. pii: S1532-0464(21)00096-4. [Epub ahead of print] 103767
    TransforMED: End-to-End Transformers for Evidence-Based Medicine and Argument Mining in medical literature.
    Nikolaos Stylianou, Ioannis Vlahavas.
      Argument Mining (AM) refers to the task of automatically identifying arguments in a text and finding their relations. In medical literature this is done by identifying Claims and Premises and classifying their relations as either Support or Attack. Evidence-Based Medicine (EBM) refers to the task of identifying all related evidence in medical literature to allow medical practitioners to make informed choices and form accurate treatment plans. This is achieved through the automatic identification of Population, Intervention, Comparator and Outcome entities (PICO) in the literature to limit the collection to only the most relevant documents. In this work, we combine EBM with AM in medical literature to increase the performance of the individual models and create high quality argument graphs, annotated with PICO entities. To that end, we introduce a state-of-the-art EBM model, used to predict the PICO entities and two novel Argument Identification and Argument Relation classification models that utilize the PICO entities to enhance their performance. Our final system works in a pipeline and is able to identify all PICO entities in a medical publication, the arguments presented in them and their relations.
    Keywords:  Argument Mining; Deep Learning; Evidence Based Medicine; Natural Language Processing
    DOI:  https://doi.org/10.1016/j.jbi.2021.103767
  7. PeerJ Comput Sci. 2019 ;5 e214
    Citation.js: a format-independent, modular bibliography tool for the browser and command line.
    Lars G Willighagen.
      Background: Given the vast number of standards and formats for bibliographical data, any program working with bibliographies and citations has to be able to interpret such data. This paper describes the development of Citation.js (https://citation.js.org/), a tool to parse and format according to those standards. The program follows modern guidelines for software in general and JavaScript in specific, such as version control, source code analysis, integration testing and semantic versioning.Results: The result is an extensible tool that has already seen adaption in a variety of sources and use cases: as part of a server-side page generator of a publishing platform, as part of a local extensible document generator, and as part of an in-browser converter of extracted references. Use cases range from transforming a list of DOIs or Wikidata identifiers into a BibTeX file on the command line, to displaying RIS references on a webpage with added Altmetric badges to generating "How to cite this" sections on a blog. The accuracy of conversions is currently 27% for properties and 60% for types on average and a typical initialization takes 120 ms in browsers and 1 s with Node.js on the command line.
    Conclusions: Citation.js is a library supporting various formats of bibliographic information in a broad selection of use cases and environments. Given the support for plugins, more formats can be added with relative ease.
    Keywords:  Bibliography; Javascript
    DOI:  https://doi.org/10.7717/peerj-cs.214
  8. PeerJ Comput Sci. 2020 ;6 e273
    Influence of tweets and diversification on serendipitous research paper recommender systems.
    Chifumi Nishioka, Jörn Hauke, Ansgar Scherp.
      In recent years, a large body of literature has accumulated around the topic of research paper recommender systems. However, since most studies have focused on the variable of accuracy, they have overlooked the serendipity of recommendations, which is an important determinant of user satisfaction. Serendipity is concerned with the relevance and unexpectedness of recommendations, and so serendipitous items are considered those which positively surprise users. The purpose of this article was to examine two key research questions: firstly, whether a user's Tweets can assist in generating more serendipitous recommendations; and secondly, whether the diversification of a list of recommended items further improves serendipity. To investigate these issues, an online experiment was conducted in the domain of computer science with 22 subjects. As an evaluation metric, we use the serendipity score (SRDP), in which the unexpectedness of recommendations is inferred by using a primitive recommendation strategy. The results indicate that a user's Tweets do not improve serendipity, but they can reflect recent research interests and are typically heterogeneous. Contrastingly, diversification was found to lead to a greater number of serendipitous research paper recommendations.
    Keywords:  Digital library; Experimental study; Recommender system; Scholarly articles; Serendipity; User study
    DOI:  https://doi.org/10.7717/peerj-cs.273
  9. Aesthet Surg J Open Forum. 2021 Jan;3(1): ojab008
    Which Resources Are Better: Sales or Scholarly? An Assessment on the Readability, Quality, and Technical Features of Online Chemical Peel Websites.
    Jeffrey Alex Varghese, Anooj A Patel, Chitang Joshi, Brendan Alleyne, Robert D Galiano.
      Background: Chemical peels are an exceedingly popular cosmetic treatment with a wide variety of suppliers, each with its own online health resource describing the procedure. With increasing reliance on the internet for medical information, it is crucial that these resources provide reliable information for patients to make informed decisions.Objectives: The aim of this study was to examine popular chemical peel resources and determine if those that offered chemical peel treatments (Sales) had lower readability, quality of information, and technical features compared with those that did not (Scholarly).
    Methods: The term "chemical peel" was searched in July 2020 and the top 50 websites were retrieved for analysis. Each resource's readability, quality, and technical features were measured through 8 readability formulas, the DISCERN and Health on the Net Code (HONcode), and 2 website performance monitors.
    Results: The 50 websites were analyzed with an average Fry readability score of 13th grade. Scholarly websites displayed higher readability than Sales (Flesch Reading Ease 54.4 > 47.4, P = 0.047 and Coleman-Liau Index 10.6 < 11.7, P = 0.04). Scholarly resources surpassed Sales both in quality (DISCERN 56.4 > 39.7, P < 0.001 and HONcode 11.8 > 9.5, P = 0.032) and technical features (WooRank 76.9 > 68.6, P = 0.0082).
    Conclusions: The average readability of chemical peel resources is too difficult, and their quality must be improved. Scholarly resources exhibited higher readability, quality, and technical features than Sales websites.
    DOI:  https://doi.org/10.1093/asjof/ojab008
  10. Br J Gen Pract. 2021 Jan 05. pii: BJGP.2020.0820. [Epub ahead of print]
    The readability of general practice websites: a cross-sectional analysis of all general practice websites in Scotland.
    Guy Rughani, Peter Hanlon, Neave Corcoran, Frances S Mair.
      BACKGROUND: General practice websites are an increasingly important point of interaction, but their readability is largely unexplored. One in four adults struggle with basic literacy, and there is a socioeconomic gradient. Readable content is a prerequisite to promoting health literacy.AIM: To assess general practice website readability by analysing text and design factors, and to assess whether practices adapted their website text to the likely literacy levels of their populations.
    DESIGN AND SETTING: Websites for all general practices across Scotland were analysed from March to December 2019, using a cross-sectional design.
    METHOD: Text was extracted from five webpages per website and eight text readability factors were measured, including the Flesch Reading Ease and the Flesch-Kincaid Grade Level. The relationship between readability and a practice population's level of deprivation, measured using the Scottish Index of Multiple Deprivation (SIMD), was assessed. Overall, 10 design factors contributing to readability and accessibility were scored.
    RESULTS: In total, 86.4% (n = 813/941) of Scottish practices had a website; 22.9% (n = 874/3823) of webpages were written at, or below, the government-recommended reading level for online content (9-14 years old), and the content of the remaining websites, 77.1% (n = 2949/3823), was suitable for a higher reading age. Of all webpages, 80.5% (n = 3077/3823) were above the recommended level for easy-to-understand 'plain English'. There was no statistically significant association between webpage reading age and SIMD. Only 6.7% (n = 51/764) of websites achieved all design and accessibility recommendations.
    CONCLUSION: Changes to practice websites could improve readability and promote health literacy, but practices will need financial resources and ongoing technical support if this is to be achieved and maintained. Failure to provide readable and accessible websites may widen health inequalities; the topic will become increasingly important as online service use accelerates.
    Keywords:  digital divide; general practice; health literacy; online systems; primary health care
    DOI:  https://doi.org/10.3399/BJGP.2020.0820
  11. Ophthalmic Epidemiol. 2021 Apr 08. 1-7
    A READABILITY COMPARISON OF ONLINE SPANISH AND ENGLISH PATIENT EDUCATION MATERIALS ABOUT VISION HEALTH.
    Naveen Karthik, Kayvan Barekatain, Hoang Vu, Danny T Y Wu, Joshua R Ehrlich.
      Purpose: Current United States national guidelines recommend patient education materials (PEMs) be written at a 5th-6th grade level. The objective of this study was to compare the readability of Spanish vision and eye health PEMs to nationally recommended reading levels and to English versions of the same PEMs.Methods: PEMs were collected from seven online websites of vision-related organizations that provided PEMs with Spanish and English versions. PEMs were downloaded for text to be extracted and analyzed. Readability scoring was performed with Índice Flesch-Szigriszt, Spanish and English Lexile Text Analyzers, and Flesch-Kincaid Grade Level.Results: A total of 484 PEMs with Spanish and English versions were analyzed. Readability for Spanish PEMs was reported at or above the 6th grade level for 57% of articles based on Spanish Lexile scoring and 63% based on Índice Flesch-Szigriszt scoring. Readability for English PEMs was reported at or above the 6th grade level for 66% of articles based on English Lexile scoring and 75% based on Flesch-Kincaid Grade Level scoring. Wilcoxon signed-rank test comparing grade levels translated from Lexile scores for Spanish and English versions of PEMs revealed that Spanish versions of PEMs required higher grade reading levels compared to English versions of PEMs (p < .001).Conclusion: Spanish and English PEMs were written above nationally recommended reading levels. Online sources providing multilingual vision and eye health education should consider routinely monitoring PEMs to ensure reading levels meet the literacy needs of their audiences.
    Keywords:  Readability; health literacy; internet; patient education; vision and eye health
    DOI:  https://doi.org/10.1080/09286586.2021.1910316
  12. Zdr Varst. 2021 Jun;60(2): 79-81
    Predatory Journals, Fake Conferences and Misleading Social Media: The Dark Side of Medical Information.
    Suzana Kert, Igor Švab.
      We live in an age of information revolution, where trends in informing physicians and the lay public bring new challenges that must be faced by healthcare professionals. Predatory journals and fake conferences are common. Social media is full of false information, which results in serious public health damage. Therefore, it is important that health professionals communicate properly with the public and patients and that they address the education of both the public and other health professionals.
    Keywords:  evidence-based medicine; fake medicine; infodemic; misinformation; predatory journals
    DOI:  https://doi.org/10.2478/sjph-2021-0012
This page is being maintained by Thomas Krichel. It was last updated on 2021‒07‒23 at 09:38:59.