bims-skolko Biomed News
on Scholarly communication
Issue of 2020‒10‒11
sixteen papers selected by
Thomas Krichel
Open Library Society


  1. J Med Syst. 2020 Oct 06. 44(11): 196
    Mielke C, Kuballa S, Schulze M, Haux R.
      Open Access is an upcoming paradigm to communicate scientific knowledge. The Trans-O-MIM Project works on strategies, models, and evaluation metrics for the goal-oriented, stepwise, sustainable, and fair transformation of established subscription-based scientific journals into open-access-based journals. This research intends to present an evaluation metric and the associated identified appropriate parameters for such transformations. To develop the evaluation metric, it has been implemented in the context of a business management method for planning, steering and controlling action and corporate strategies. The central element was a 3-step procedure for developing the metric. In stage 1 necessary preconditions for a transformation were considered. Stage 2 is the actual elaboration of the evaluation metric by means of a scenario analysis and stage 3 comprises the exemplary testing at the journal Methods of Information in Medicine. The three methodological steps have primarily resulted in 5 scenarios with 9 different final states from the scenario analysis. Thus, the metric is now composed of these 5 scenarios, which can be used to evaluate the success or failure of a transformation. A list of 65 suitable parameters to measure changes in scenario were compiled. So, it is possible to evaluate the transformation and to find the current final state. Parameters like submissions, publications, and time as well as the scenario states could be applied to the transformation process of the Methods of Information in Medicine journal. The proposed evaluation metric can be used to evaluate the transformation processes of subscription-based journals into open-access-based journals.
    Keywords:  Evaluation metric; Medical informatics; Open access; Transformation
    DOI:  https://doi.org/10.1007/s10916-020-01651-1
  2. F1000Res. 2020 ;9 415
    Cortegiani A, Ippolito M, Ingoglia G, Manca A, Cugusi L, Severin A, Strinzel M, Panzarella V, Campisi G, Manoj L, Gregoretti C, Einav S, Moher D, Giarratano A.
      Background: Scopus is a leading bibliometric database. It contains the largest number of articles cited in peer-reviewed publications . The journals included in Scopus are periodically re-evaluated to ensure they meet indexing criteria and some journals might be discontinued for publication concerns. These journals remain indexed and can be cited. Their metrics have yet to be studied. This study aimed  to evaluate the main features and metrics of journals discontinued from Scopus for publication concerns, before and after their discontinuation, and to determine the extent of predatory journals among the discontinued journals. Methods: We surveyed the list of discontinued journals from Scopus (July 2019). Data regarding metrics, citations and indexing were extracted from Scopus or other scientific databases, for the journals discontinued for publication concerns.  Results: A total of 317 journals were evaluated. Ninety-three percent of the journals (294/318) declared they published using an Open Access model. The subject areas with the greatest number of discontinued journals were  Medicine (52/317; 16%),  Agriculture and Biological Science (34/317; 11%), and  Pharmacology, Toxicology and Pharmaceutics (31/317; 10%). The mean number of citations per year after discontinuation was significantly higher than before (median of difference 64 citations, p<0.0001), and so was the number of citations per document (median of difference 0.4 citations, p<0.0001). Twenty-two percent (72/317) were included in the Cabell's blacklist. The DOAJ currently included only 9 journals while 61 were previously included and discontinued, most for 'suspected editorial misconduct by the publisher'. Conclusions: The citation count of journals discontinued for publication concerns increases despite discontinuation and predatory behaviors seemed common. This paradoxical trend can inflate scholars' metrics prompting artificial career advancements, bonus systems and promotion. Countermeasures should be taken urgently to ensure the reliability of Scopus metrics both at the journal- and author-level for the purpose of scientific assessment of scholarly publishing.
    Keywords:  Scopus; citation count; indexing; journal; metrics; predatory
    DOI:  https://doi.org/10.12688/f1000research.23847.1
  3. PLoS One. 2020 ;15(10): e0240288
    Heßler N, Rottmann M, Ziegler A.
      Successful publishing of an article depends on several factors, including the structure of the main text, the so-called introduction, methods, results and discussion structure (IMRAD). The first objective of our work is to provide recent results on the number of paragraphs (pars.) per section used in articles published in major medical journals. Our second objective is the investigation of other structural elements, i.e., number of tables, figures and references and the availability of supplementary material. We analyzed data from randomly selected original articles published in years 2005, 2010 and 2015 from the journals The BMJ, The Journal of the American Medical Association, The Lancet, The New England Journal of Medicine and PLOS Medicine. Per journal and year 30 articles were investigated. Random effect meta-analyses were performed to provide pooled estimates. The effect of time was analyzed by linear mixed models. All articles followed the IMRAD structure. The number of pars. per section increased for all journals over time with 1.08 (95% confidence interval (CI): 0.70-1.46) pars. per every two years. The largest increase was observed for the methods section (0.29 pars. per year; 95% confidence interval (CI): 0.19-0.39). PLOS Medicine had the highest number of pars. The number of tables did not change, but number of figures and references increased slightly. Not only the standard IMRAD structure should be used to increase the likelihood for publication of an article but also the general layout of the target journal. Supplementary material has become standard. If no journal-specific information is available, authors should use 3/10/9/8 pars. for the introduction/methods/results/discussion sections.
    DOI:  https://doi.org/10.1371/journal.pone.0240288
  4. Int J Womens Dermatol. 2020 Sep;6(4): 255-256
    Maghfour J, Olson J, Jacob SE.
      
    Keywords:  Academia; COVID-19; Dermatology journals
    DOI:  https://doi.org/10.1016/j.ijwd.2020.07.009
  5. PLoS One. 2020 ;15(10): e0240123
    Gianola S, Jesus TS, Bargeri S, Castellini G.
      The COVID-19 pandemic has unleashed a deluge of publications. For this cross-sectional study we compared the amount and reporting characteristics of COVID-19-related academic articles and preprints and the number of ongoing clinical trials and systematic reviews. To do this, we searched the PubMed database of citations and abstracts for published life science journals by using appropriate combinations of medical subject headings (MeSH terms), and the COVID-19 section of the MedRxiv and BioRxiv archives up to 20 May 2020 (21 weeks). In addition, we searched Clinicaltrial.gov, Chinese Clinical Trial Registry, EU Clinical Trials Register, and 15 other trial registers, as well as PROSPERO, the international prospective register of systematic reviews. The characteristics of each publication were extracted. Regression analyses and Z tests were used to detect publication trends and their relative proportions. A total of 3635 academic publications and 3805 preprints were retrieved. Only 8.6% (n = 329) of the preprints were already published in indexed journals. The number of academic and preprint publications increased significantly over time (p<0.001). Case reports (6% academic vs 0.9% preprints; p<0.001) and letters (17.4% academic vs 0.5% preprints; p<0.001) accounted for a greater share of academic compared to preprint publications. Differently, randomized controlled trials (0.22% vs 0.63%; p<0.001) and systematic reviews (0.08% vs 5%) made up a greater share of the preprints. The relative proportion of clinical studies registered at Clinicaltrials.gov, Chinese Clinical Trial Registry, and EU Clinical Trials Register was 57.9%, 49.5%, and 98.9%, respectively, most of which were still "recruiting". PROSPERO listed 962 systematic review protocols. Preprints were slightly more prevalent than academic articles but both were increasing in number. The void left by the lack of primary studies was filled by an outpour of immediate opinions (i.e., letters to the editor) published in PubMed-indexed journals. Summarizing, preprints have gained traction as a publishing response to the demand for prompt access to empirical, albeit not peer-reviewed, findings during the present pandemic.
    DOI:  https://doi.org/10.1371/journal.pone.0240123
  6. J Breath Res. 2020 10 06. 14(4): 040202
    Pleil JD, Beauchamp JD, Dweik RA, Risby TH.
      In contrast to blood and urine samples, breath is invisible and ubiquitous in the environment. Different precautions are now necessary beyond the usual 'Universal Precautions'. In the era of COVID-19, breath (especially the aerosol fraction) can no longer be considered as harmless in the clinic or laboratory. As Journal of Breath Research is a primary resource for breath-related research, we (the editors) are presently developing safety guidance applicable to all breath research , not just for those projects that involve known COVID-19 infected subjects. We are starting this process by implementing requirements on reporting safety precautions in research papers and notes. This editorial announces that authors of all new submissions to JBR henceforth must state clearly the procedures undertaken for assuring laboratory and clinical safety, much like the existing requirements for disclosing Ethics Committee or Institutional Review Board protocols for studies on human subjects. In the following, we additionally make some recommendations based on best practices drawn from our experience and input from the JBR Editorial Board.
    DOI:  https://doi.org/10.1088/1752-7163/abb99a
  7. J Cardiovasc Comput Tomogr. 2020 Oct 01. pii: S1934-5925(20)30449-4. [Epub ahead of print]
    Nieman K.
      
    DOI:  https://doi.org/10.1016/j.jcct.2020.09.010
  8. J Crit Care. 2020 Sep 17. pii: S0883-9441(20)30687-0. [Epub ahead of print]
    Greiner B, Corcoran A, Wheeler D.
      PURPOSE: Publication bias has a significant impact on the results of systematic reviews. Clinical trial registry searches, which include unpublished research, should be conducted when performing systematic reviews to reduce publication bias. We aimed to analyze the use of clinical trial registry searches in critical care systematic reviews.METHODS: Systematic reviews published between 01/01/2010-02/18/2020 from the top 5 critical care journals were extracted from PubMed and screened for trial registry use. Additionally, of the studies not performing registry searches, we assessed ClinicalTrials.gov for potentially relevant trials that were missed by not performing a registry search.
    RESULTS: Three hundred and twenty six systematic reviews were analyzed, of which 37 (11.3%) performed trial registry searches. Of the studies not performing clinical trial registry searches, 56% had at least 1 potentially relevant trial that was missed.
    CONCLUSIONS: The omission of relevant, unpublished clinical trial results may be negatively impacting the accuracy of critical care systematic reviews. We recommend all systematic reviewers conduct clinical trial registry searches to reduce publication bias.
    Keywords:  Clinical trial registry; Critical care medicine; Publication bias; Systematic review
    DOI:  https://doi.org/10.1016/j.jcrc.2020.09.010
  9. JAMA Netw Open. 2020 Oct 01. 3(10): e2014661
    Wang F, Schilsky RL, Page D, Califf RM, Cheung K, Wang X, Pang H.
      Importance: Adherence to the Consolidated Standards of Reporting Trials (CONSORT) for randomized clinical trials is associated with improvingquality because inadequate reporting in randomized clinical trials may complicate the interpretation and the application of findings to clinical care.Objective: To evaluate an automated reporting checklist generation tool that uses natural language processing (NLP), called CONSORT-NLP.
    Design, Setting, and Participants: This study used published journal articles as training, testing, and validation sets to develop, refine, and evaluate the CONSORT-NLP tool. Articles reporting randomized clinical trials were selected from 25 high-impact-factor journals under the following categories: (1) general and internal medicine, (2) oncology, and (3) cardiac and cardiovascular systems.
    Main Outcomes and Measures: For an evaluation of the performance of this tool, an accuracy metric defined as the number of correct assessments divided by all assessments was calculated.
    Results: The CONSORT-NLP tool uses the widely used Portable Document Format as an input file. Of the 37 CONSORT reporting items, 34 (92%) were included in the tool. Of these 34 reporting items, 30 were fully implemented; 28 (93%) of the fully implemented CONSORT reporting items had an accuracy of more than 90% for the validation set. The remaining 2 (7%) had an accuracy between 80% and 90% for the validation set. Two to 5 articles were selected from each of these journals for a total of 158 articles to establish a training set of 111 articles to train CONSORT-NLP for CONSORT reporting items, a testing set of 25 articles to refine CONSORT-NLP, and a validation set of 22 articles to assess the performance of CONSORT-NLP. The CONSORT-NLP tool used the Portable Document Format of the articles as input files. A CONSORT-NLP graphical user interface was built using Java in 2019. The time required to complete the CONSORT checklist manually vs using the CONSORT-NLP tool was compared for 30 articles. Two case studies for randomized clinical trials are provided as an illustration for the CONSORT-NLP tool. For the 30 articles investigated, CONSORT-NLP required a mean (SD) 23.0 (4.1) seconds, whereas the manual reviewer required a mean (SD) 11.9 (2.2), 22.6 (4.6), and 57.6 (7.1) minutes, for 3 reviewers, respectively.
    Conclusions and Relevance: The CONSORT-NLP tool is designed to assist in the reporting of randomized clinical trials. Potential users of CONSORT-NLP include clinicians, researchers, and scientists who plan to publish a randomized trial study in a peer-reviewed journal. The use of CONSORT-NLP may help them save substantial time when generating the CONSORT checklist. This tool may also be useful for manuscript reviewers and journal editors who review these articles.
    DOI:  https://doi.org/10.1001/jamanetworkopen.2020.14661
  10. Front Physiol. 2020 ;11 1073
    Coronel R.
      Productivity in science has increased and it is becoming more important for scientists to publish, to publish frequently, and to accumulate citations to their work. However, the peer review system may not only promote and advance but also hinder, prevent, or delay publication. In this personal perspective, confirmatory, consensual, competitive, and controversial publication strategies are described that they may meet with various degrees of approval or disapproval from the author's peers. The selected publication strategy may impact on the development of a career. Resolving controversies helps science advance efficiently. Therefore, controversies should be sought and addressed, although preferably not at the start of a career.
    Keywords:  competition; confirmation; consensus; controversy; publication; strategy
    DOI:  https://doi.org/10.3389/fphys.2020.01073
  11. Eur J Microbiol Immunol (Bp). 2020 Oct 03.
    Behzadi P, Gajdács M.
      To have a successful publication in a peer-reviewed journal, a collection of factors and items is needed. Some of them directly and the others indirectly have important roles in scholarly publication. However, a well-designed scientific investigation together with a powerful academic English language may guarantee the publication of a manuscript. In other words, a standard and professional methodology which is expressed by an influent academic English language constitutes the soul of the manuscript's body. Obviously, the accuracy and fluency of the English language of the manuscript is the author(s)' responsibility and neither the reviewers' nor the editor's and the journal's. As publication of a research paper is the complementary section of a scientific study, it is recognized as an academic criterion for academicians. Thus, this review focuses on the all of items which are necessary and vital for a successful scholarly publication.
    Keywords:  abstracting and indexing; immunology publications; medical manuscripts; microbiology publications; peer-review; research
    DOI:  https://doi.org/10.1556/1886.2020.00023
  12. J Med Libr Assoc. 2020 Oct 01. 108(4): 523-526
    Akers KG, Barr-Walker J, Amos K.
      As the premier journal in health sciences librarianship, the Journal of the Medical Library Association (JMLA) continuously strives to publish high-quality work that advances research and practice and to provide irreplaceable value for readers, authors, and reviewers. This editorial reflects on the state of JMLA in 2020 by describing our editorial team and volume of submissions, highlighting recent initiatives that strengthen the journal's position in the profession, and sharing future plans to enrich JMLA's content and promote open science. Committed to ending structural racism and other inequities in the field, we also issue an ongoing call for submissions pertaining to social justice and critical perspectives on health sciences librarianship.
    DOI:  https://doi.org/10.5195/jmla.2020.1075