bims-skolko Biomed News
on Scholarly communication
Issue of 2021‒12‒26
twenty-five papers selected by
Thomas Krichel
Open Library Society

  1. Acta Dermatovenerol Alp Pannonica Adriat. 2021 Dec;30(4): 127-128
      Next spring, we will celebrate 30 years since the first issue of Acta Dermatovenerologica Alpina, Pannonica et Adriatica (Acta Dermatovenerol APA) was published and, to our astonishment and disappointment, it seems that the goal we have long awaited (and worked hard for)-obtaining an official impact factor (IF)-is nowhere in sight. Every application for an IF has been met with various reasons why our journal does not fulfill the criteria for inclusion in the Science Citation Index Expanded (SCIE). Given the highly non-transparent evaluation process, we conclude that there probably really is no room for small and independent journals in the world of publishing giants and commercial interests. Although disheartened, we will continue our long-established tradition of providing open-access and quality content in dermatology and sexually transmitted infections for researchers and clinicians in the region and worldwide because science should be open and committed to teamwork.
  2. J Mass Spectrom Adv Clin Lab. 2021 Nov;22 8-16
      Introduction: With the rising complexity of modern multimarker analytical techniques and notable scientific publication retractions required for erroneous statistical analysis, there is increasing awareness of the importance of research transparency and reproducibility. The development of mature open-source tools for literate programming in multiple langauge paradigms has made fully-reproducible authorship possible.Objectives: We describe the procedure for manuscript preparation using RMarkdown and the R statistical programming language with application to JMSACL or any other Elsevier journal.
    Methods: An instructional manuscript has been prepared in the RMarkdown markup language with stepwise directions on preparing sections, subsections, lists, tables, figures and reference management in an entirely reproducible format.
    Results: From RMarkdown code, a submission-ready PDF is generated and JMSACL-compatible LaTeX code is generated. These can be uploaded to the Editorial Manager.
    Conclusion: A completely reproducible manuscript preparation pipeline using the R and RMarkdown is described.
    Keywords:  Data science; Executable document; LaTeX; Literate programming; Markdown; R language; RMarkdown; Reproducible research
  3. SICOT J. 2021 ;7 64
      BACKGROUND: The internet has changed the way we access and publish Orthopaedic literature. Traditional subscription journals have been challenged by the open access method of publication which permits the author to make their article available to all readers for free, often at a cost to the author. This has also been adopted in part by traditional subscription journals forming hybrid journals. One of the criticisms of open access publications is that it provides the author with a "pay to publish" opportunity. We aimed to determine if access to the journals impacts their influence.METHODS: We selected the top 40 Trauma and Orthopaedic Journals as ranked by the SCImago Rank. Each journal was reviewed and assessed for the journal quality, defined by reviewing the journal impact factor and SCImago rank; influence, defined by reviewing the top 10 articles provided by the journal for the number of citations; and cost of open access publication.
    RESULTS: Of the top 40 journals, 10 were subscription, 10 were open access, and 20 were hybrid journals. Subscription journals had the highest mean impact factor, and SCImago rank with a significant difference in the impact factor (p = 0.001) and SCImago rank (p = 0.021) observed between subscription and open access journals. No significant difference was seen between citation numbers of articles published in subscription and open access journals (p = 0.168). There was a positive correlation between the cost of publishing in an open access journal and the impact factor (r = 0.404) but a negative correlation between cost and the number of citations (r = 0.319).
    CONCLUSION: Open access journals have significantly lower quality measures in comparison to subscription journals. Despite this, we found no difference between the number of citations, suggestive of there being no difference in the influence of these journals in spite of the observed difference in quality.
    Keywords:  Citations; Open access; Orthopaedic Literature; Publications
  4. DNA Cell Biol. 2021 Dec 23.
      Grant writing, science policy and public engagement (PE) activities are forms of science communication, and all are essential for research to function and benefit our society. Scientists rely on competitive grant funding to finance their research; this is an opportunity for researchers to communicate their scientific vision and engage funders, major players in defining how public funds and government policies are prioritized to drive research and innovation. PE is often still seen as a box-ticking or persuasion exercise, yet establishing the right communication channels with the public is pivotal for a scientist's job to impact society. We believe that evidence-based communication is becoming essential in a world dominated by an excess of information, where verified sources are under pressure. Support in the form of dedicated training and allocated resources, particularly for early career researchers, can help establish what we describe as a long-lasting virtuous circle, in which public funds are spent effectively toward scientific advances that the public and policy makers can embrace.
    Keywords:  funding; policy; public engagement; science communication
  5. BMJ Evid Based Med. 2021 Dec 21. pii: bmjebm-2021-111826. [Epub ahead of print]
    Keywords:  conflict of interest; ethics; health services research; policy
  6. Health Info Libr J. 2021 Dec;38(4): 245-247
      This editorial discusses the emergence of visual abstracts within journals to disseminate findings. Published alongside Aggarwal's retrospective study reporting that visual abstracts do not increase impact scores more than conventional abstracts of clinical research, it is suggested that visual abstracts may have a greater impact for smaller, specialty journals.
    Keywords:  information dissemination; publishers and publishing; research impact; social media
  7. J Biol Chem. 2021 Dec 16. pii: S0021-9258(21)01282-5. [Epub ahead of print]298(1): 101473
  8. Pediatr Obes. 2021 Dec 20. e12879
      BACKGROUND: Stigma towards children with obesity can begin as early as 3 years old, leading to increased risk for poorer mental health outcomes and lower quality of life. This includes discriminatory language used by peers and adults, which may be compounded by use within the medical community and in published research.OBJECTIVES: Our primary objective was to investigate adherence to person-centred language (PCL) in childhood obesity-related medical publications.
    METHODS: We searched PubMed for childhood obesity-related articles from 2018 through 2020, from journals frequently publishing childhood-obesity-related research. Articles were randomized and searched for a list of predetermined, stigmatizing terms.
    RESULTS: Of the sample of 300 articles, only 21.7% were adherent to PCL guidelines. The most frequent labels found were 'obese' appearing in 70.33% of articles and 'overweight' in 63.7%. Labels such as 'chubby', 'large', and 'fat' were less common, but still appeared in the medical literature.
    CONCLUSIONS: A majority of childhood obesity-related articles did not adhere to PCL guidelines. Given the negative effects of stigma among children with obesity, it is imperative to advocate for PCL use within the medical community. Increased stringency by journal editors and publishers may be the next step in this process.
    Keywords:  childhood obesity; person-centred language; stigma; weight
  9. PLoS One. 2021 ;16(12): e0261622
      The skill of analyzing and interpreting research data is central to the scientific process, yet it is one of the hardest skills for students to master. While instructors can coach students through the analysis of data that they have either generated themselves or obtained from published articles, the burgeoning availability of preprint articles provides a new potential pedagogical tool. We developed a new method in which students use a cognitive apprenticeship model to uncover how experts analyzed a paper and compare the professional's cognitive approach to their own. Specifically, students first critique research data themselves and then identify changes between the preprint and final versions of the paper that were likely the results of peer review. From this activity, students reported diverse insights into the processes of data presentation, peer review, and scientific publishing. Analysis of preprint articles is therefore a valuable new tool to strengthen students' information literacy and understanding of the process of science.
  10. Proc Natl Acad Sci U S A. 2021 Dec 28. pii: e2106178118. [Epub ahead of print]118(52):
      While the social sciences have made impressive progress in adopting transparent research practices that facilitate verification, replication, and reuse of materials, the problem of publication bias persists. Bias on the part of peer reviewers and journal editors, as well as the use of outdated research practices by authors, continues to skew literature toward statistically significant effects, many of which may be false positives. To mitigate this bias, we propose a framework to enable authors to report all results efficiently (RARE), with an initial focus on experimental and other prospective empirical social science research that utilizes public study registries. This framework depicts an integrated system that leverages the capacities of existing infrastructure in the form of public registries, institutional review boards, journals, and granting agencies, as well as investigators themselves, to efficiently incentivize full reporting and thereby, improve confidence in social science findings. In addition to increasing access to the results of scientific endeavors, a well-coordinated research ecosystem can prevent scholars from wasting time investigating the same questions in ways that have not worked in the past and reduce wasted funds on the part of granting agencies.
    Keywords:  file drawer problem; null findings; publication bias; registries; research transparency
  11. Patterns (N Y). 2021 Dec 10. 2(12): 100368
      Numerous arguments strongly support the practice of open science, which offers several societal and individual benefits. For individual researchers, sharing research artifacts such as data can increase trust and transparency, improve the reproducibility of one's own work, and catalyze new collaborations. Despite a general appreciation of the benefits of data sharing, research data are often only available to the original investigators. For data that are shared, lack of useful metadata and documentation make them challenging to reuse. In this paper, we argue that a lack of incentives and infrastructure for making data useful is the biggest barrier to creating a culture of widespread data sharing. We compare data with code, examine computational environments in the context of their ability to facilitate the reproducibility of research, provide some practical guidance on how one can improve the chances of their data being reusable, and partially bridge the incentive gap. While previous papers have focused on describing ideal best practices for data and code, we focus on common-sense ideas for sharing tabular data for a target audience of academics working in data science adjacent fields who are about to submit for publication.
    Keywords:  DSML 4: Production: Data science output is validated, understood, and regularly used for multiple domains/platforms
  12. DNA Cell Biol. 2021 Dec 23.
      In this commentary, we focus on the ethical challenges of data sharing and its potential in supporting biomedical research. Taking human genomics (HG) and European governance for sharing genomic data as a case study, we consider how to balance competing rights and interests-balancing protection of the privacy of data subjects and data security, with scientific progress and the need to promote public health. This is of particular relevancy in light of the current pandemic, which stresses the urgent need for international collaborations to promote health for all. We draw from existing ethical codes for data sharing in HG to offer recommendations as to how to protect rights while fostering scientific research and open science.
    Keywords:  European Union; data sharing; digital ethics; human genomics; privacy; public health; rights
  13. Chemistry. 2021 Dec 21. e202104280
      Science and scholarly publishing are transforming! Chemistry-A European Journal, the flagship of the Chemistry Europe family of journals has been transforming and evolving too. We have been working hard over the last year to adapt and improve our processes and workflows to meet the changing requirements of our authors, referees and readers. Read all about these changes, and much more about the journal and Chemistry Europe portfolio in this Editorial.
  14. Qatar Med J. 2021 ;2021(3): 43
      It is with great pride that we celebrate the 50th issue of Qatar Medical Journal (QMJ) that has achieved significant growth recently. Our mission is to encourage authors to submit high-quality and innovative research promoting medical advancements. In the past two years, manuscripts submissions have tripled in number and were enriched by a more diverse pool of authors with global representation, resulting in an increase in the number of published issues moving from being a biannual to a triannual journal. Additionally, the number of articles published in an issue has doubled. QMJ continues to be an open-access peer-reviewed journal, publishing original research work, reviews, editorials, and case reports that are particularly relevant to medicine and free of charge to authors. It is indexed in several renowned and highly ranked platforms such as PubMed Central, Scopus, Scimago, Google Scholar, and the Directory of Open Access Journals. It was also recently indexed in the World Health Organization's Index Medicus for the Eastern Mediterranean Region (IMEMR). We look forwards to becoming the highest-rated medical journal, in terms of impact factor, regionally.
  15. FEBS Open Bio. 2021 Dec 20.
      Takashi Gojobori was one of the original founding members of the Editorial Board of FEBS Open Bio, and is easily one of our most hard-working editors, having carefully evaluated hundreds of manuscripts on bioinformatics for us over the last decade. Takashi Gojobori received his doctorate at Kyushu University, Japan, before joining the University of Texas Health Science Center as a Research Associate and then Research Assistant Professor. Takashi was formerly the Vice-Director and Professor of National Institute of Genetics (NIG), Mishima, Japan, and at present, he is Distinguished Professor of Bioscience and Bioscience Acting Director of the Computational Bioscience Research Center at King Abdullah University of Science and Technology (KAUST), Saudi Arabia. Takashi was formerly the Editor-in-Chief of the journal Gene, and is also a long-term member of the Editorial Board of FEBS Letters, among other editorial appointments. In honour of his ten years (and counting!) of service to the journal, we present here this interview with him on his research and experiences.