bims-skolko Biomed News
on Scholarly communication
Issue of 2023–02–12
twenty-two papers selected by
Thomas Krichel, Open Library Society



  1. Nature. 2023 Feb 10.
      
    Keywords:  Careers; Genetics; Publishing; Research data
    DOI:  https://doi.org/10.1038/d41586-023-00385-7
  2. Scientometrics. 2023 Jan 30. 1-33
      The development of network technique and open access has made numerous research results freely obtained online, thereby facilitating the growth of the emerging evaluation methods of Altmetrics. However, it is unknown whether the time interval from reception to publication has an impact on the evaluation indicators of articles in the social network environment. We construct a range of time-series indexes that represent the features of the evaluation indicators and then explore the correlation of acceptance delay, technical delay, and overall delay with the relevant indicators of citations, usage, sharing and discussions, and collections that are obtained from the open access journal platform PLOS. Moreover, this research also explores the differences in the correlations of the delays for the literature in six subject areas with the corresponding indicators and the discrepancies of the correlations of delays and indexes in various metric quartiles. The results of the Mann-Whitney U test reveal that the length of delays affects the performance of the literature on some indicators. This study indicates that reducing the acceptance time and final publication time of articles can improve the efficiency of knowledge diffusion through the formal academic citation channel, but in the context of social networking communication, an appropriate interval at a particular stage in the publishing process can enhance the heat of sharing, discussion, and collection of articles to a small extent, hence boosting the influence and attention received by the literature on the internet.
    Keywords:  Acceptance delay; Correlation analysis; Measurement indicators; Publication delay; Technical delay
    DOI:  https://doi.org/10.1007/s11192-023-04640-6
  3. PLoS One. 2023 ;18(2): e0281110
      Publication and related biases constitute serious threats to the validity of research synthesis. If research syntheses are based on a biased selection of the available research, there is an increased risk of producing misleading results. The purpose fo this study is to explore the extent of positive outcome bias, time-lag bias, and place-of-publication bias in published research on the effects of psychological, social, and behavioral interventions. The results are based on 527 Swedish outcome trials published in peer-reviewed journals between 1990 and 2019. We found no difference in the number of studies reporting significant compared to non-significant findings or in the number of studies reporting strong effect sizes in the published literature. We found no evidence of time-lag bias or place-of-publication bias in our results. The average reported effect size remained constant over time as did the proportion of studies reporting significant effects.
    DOI:  https://doi.org/10.1371/journal.pone.0281110
  4. Nature. 2023 Feb;614(7947): 214-216
      
    Keywords:  Machine learning; Mathematics and computing; Publishing
    DOI:  https://doi.org/10.1038/d41586-023-00340-6
  5. Account Res. 2023 Feb 07.
      This letter to the editor suggests adding a technical point to the new editorial policy expounded by Hosseini et al. on the mandatory disclosure of any use of natural language processing (NLP) systems, or generative AI, in writing scholarly publications. Such AI systems should naturally also be forbidden from being named as authors, because they would not have fulfilled prevailing authorship guidelines (such as the widely adopted ICMJE authorship criteria).
    Keywords:  Authorship; ChatGPT; ICMJE guidelines; generative AI
    DOI:  https://doi.org/10.1080/08989621.2023.2177160
  6. bioRxiv. 2023 Jan 23. pii: 2023.01.21.525030. [Epub ahead of print]
      In this work we investigate how models with advanced natural language processing capabilities can be used to reduce the time-consuming process of writing and revising scholarly manuscripts. To this end, we integrate large language models into the Manubot publishing ecosystem to suggest revisions for scholarly text. We tested our AI-based revision workflow in three case studies of existing manuscripts, including the present one. Our results suggest that these models can capture the concepts in the scholarly text and produce high-quality revisions that improve clarity. Given the amount of time that researchers put into crafting prose, we anticipate that this advance will revolutionize the type of knowledge work performed by academics.
    DOI:  https://doi.org/10.1101/2023.01.21.525030
  7. PNAS Nexus. 2022 Jul;1(3): pgac106
      The Open Science movement aims at ensuring accessibility, reproducibility, and transparency of research. The adoption of Open Science practices in animal science, however, is still at an early stage. To move ahead as a field, we here provide seven practical steps to embrace Open Science in animal science. We hope that this paper contributes to the shift in research practices of animal scientists towards open, reproducible, and transparent science, enabling the field to gain additional public trust and deal with future challenges to guarantee reliable research. Although the paper targets primarily animal science researchers, the steps discussed here are also applicable to other research domains.
    Keywords:  animal research; open access; open data; open peer-review; preregistration
    DOI:  https://doi.org/10.1093/pnasnexus/pgac106
  8. Perspect Psychol Sci. 2023 Feb 06. 17456916221141357
      There is growing evidence that the published psychological literature is marred by multiple errors and inaccuracies and often fails to reflect the changing nature of the knowledge base. At least four types of error are common-citation error, methodological error, statistical error, and interpretation error. In the face of the apparent inevitability of these inaccuracies, core scientific values such as openness and transparency require that correction mechanisms are readily available. In this article, I reviewed standard mechanisms in psychology journals and found them to have limitations. The effects of more widely enabling open postpublication critique in the same journal in addition to conventional peer review are considered. This mechanism is well established in medicine and the life sciences but rare in psychology and may assist psychological science to correct itself.
    Keywords:  citation; error; peer review; publication
    DOI:  https://doi.org/10.1177/17456916221141357
  9. R Soc Open Sci. 2023 Feb;10(2): 221460
      Open Research aims to make research more accessible, transparent, reproducible, shared and collaborative. Doing so is meant to democratize and diversify access to knowledge and knowledge production, and ensure that research is useful outside of academic contexts. Increasing equity is therefore a key aim of the Open Research movement, yet mounting evidence demonstrates that the practices of Open Research are implemented in ways that undermine this. In response, we convened a diverse community of researchers, research managers and funders to co-create actionable recommendations for supporting the equitable implementation of Open Research. Using a co-creative modified Delphi method, we generated consensus-driven recommendations that address three key problem areas: the resource-intensive nature of Open Research, the high cost of article processing charges, and obstructive reward and recognition practices at funders and research institutions that undermine the implementation of Open Research. In this paper, we provide an overview of these issues, a detailed description of the co-creative process, and present the recommendations and the debates that surrounded them. We discuss these recommendations in relation to other recently published ones and conclude that implementing ours requires 'global thinking' to ensure that a systemic and inclusive approach to change is taken.
    Keywords:  equity in science; meta-science; open research; open science; open science policy; open science recommendations
    DOI:  https://doi.org/10.1098/rsos.221460
  10. Clin Imaging. 2023 Feb 02. pii: S0899-7071(23)00021-9. [Epub ahead of print]96 31-33
       OBJECTIVE: To gain more insight in scientific integrity in the field of cardiovascular imaging research by conducting a survey among all corresponding authors who published in cardiovascular imaging journals.
    METHODS: Corresponding authors who published in one of eight major cardiovascular imaging journals in 2021 were requested to complete a questionnaire about scientific integrity in the field of cardiovascular imaging.
    RESULTS: Responses from 160 corresponding authors were received. The majority of respondents had a medical doctor degree (81.1%), held an academic position (93.8%, of which 44.0% as full professor), and had >10 years of research experience (72.5%). Overall confidence in the integrity of published scientific work in cardiovascular imaging was high, with a median score of 8 out of 10 (IQR 2). 5 respondents (3.1%) declared having committed scientific fraud in the past 5 years and 38 respondents (23.8%) declared having witnessed or suspected scientific fraud by anyone from their department in the past 5 years. 85.6% of respondents think that publication bias is present. 50% of respondents declared that any of their publications in the past 5 years had a co-author who actually did not deserve this co-authorship.
    CONCLUSION: Experts in the field report that several forms of scientific fraud, publication bias, and honorary authorship are present in cardiovascular imaging research. Despite these reports of academic dishonesty, overall confidence in the integrity of cardiovascular imaging research is deemed high.
    Keywords:  Cardiology; Fraud; Medical imaging; Research; Scientific misconduct; Trust
    DOI:  https://doi.org/10.1016/j.clinimag.2023.01.011
  11. Nature. 2023 Feb;614(7947): 227
      
    Keywords:  Communication; Ethics; Research management
    DOI:  https://doi.org/10.1038/d41586-023-00329-1
  12. Methods Inf Med. 2023 Feb 07.
       BACKGROUND:  During the last decades, the Open Access paradigm has become an important approach for publishing new scientific knowledge. From 2015 to 2020, the Trans-O-MIM research project was undertaken with the intention to identify and to explore solutions in transforming subscription-based journals into Open Access journals. Trans-O-MIM stands for 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 with Methods of Information in Medicine as an example.
    OBJECTIVES:  To present an overview of the outcomes of the Trans-O-MIM research project as a whole and to share our major lessons learned.
    METHODS:  As an approach for transforming journals, a Tandem Model has been proposed and implemented for Methods of Information in Medicine. For developing a metric to observe and assess journal transformations, scenario analysis has been used. A qualitative and a two-tier quantitative study on drivers and obstacles of Open Access publishing for medical informatics researchers was designed and conducted. A project setup with a research team, a steering committee, and an international advisory board was established. Major international medical informatics events have been used for reporting and for receiving feedback.
    RESULTS:  Based on the Tandem Model, the journal Methods of Information in Medicine has been transformed into a journal where, in addition to its subscription-based track, from 2017 onwards a Gold Open Access track has been successfully added. An evaluation metric, composed of 5 scenarios and 65 parameters, has been developed, which can assist respective decision makers in assessing such transformations. The studies on drivers and obstacles of Open Access publishing showed that, while most researchers support the idea of making scientific knowledge freely accessible to everyone, they are hesitant about actually living this practice by choosing Open Access journals to publish their own work. Article-processing charges and quality issues are perceived as the main obstacles in this respect, revealing a two-sided evaluation of Open Access models, reflecting the different viewpoints of researchers as authors or readers. Especially researchers from low-income countries benefit from a barrier-free communication mainly in their role as readers and much less in their role as authors of scientific information. This became also evident at the institutional level, as Open Access policies or financial support through funding bodies are most prevalent in Europe and North America.
    CONCLUSIONS:  With Trans-O-MIM, an international research project was performed. An existing journal has been transformed. In addition, with the support of the International Medical Informatics Association, as well as of the European Federation for Medical Informatics and of the German Association for Medical Informatics, Biometry and Epidemiology as European and German medical informatics organizations, we did run an international experiment on Open Access incentives. Both together are, as far as the authors know, unique. We therefore expect that this research could add new knowledge on Open Access transformation.
    DOI:  https://doi.org/10.1055/s-0043-1761499
  13. R Soc Open Sci. 2023 Feb;10(2): 221093
      The Transparency and Openness Promotion (TOP) Guidelines provide a framework to help journals develop open science policies. Theories of behaviour change can guide understanding of why journals do (not) implement open science policies and the development of interventions to improve these policies. In this study, we used the Theoretical Domains Framework to survey 88 journal editors on their capability, opportunity and motivation to implement TOP. Likert-scale questions assessed editor support for TOP, and enablers and barriers to implementing TOP. A qualitative question asked editors to provide reflections on their ratings. Most participating editors supported adopting TOP at their journal (71%) and perceived other editors in their discipline to support adopting TOP (57%). Most editors (93%) agreed their roles include maintaining policies that reflect current best practices. However, most editors (74%) did not see implementing TOP as a high priority compared with other editorial responsibilities. Qualitative responses expressed structural barriers to implementing TOP (e.g. lack of time, resources and authority to implement changes) and varying support for TOP depending on study type, open science standard, and level of implementation. We discuss how these findings could inform the development of theoretically guided interventions to increase open science policies, procedures and practices.
    Keywords:  Top Guidelines; behaviour change; journal editors; open science; reproducibility; transparency
    DOI:  https://doi.org/10.1098/rsos.221093
  14. Curr Med Res Opin. 2023 Feb 07. 1-7
       OBJECTIVES: Although diversity, equity, and inclusion (DEI) initiatives are progressively being implemented across various arenas in academic medicine, biomedical research, and healthcare, significant inequities throughout medicine and biomedical research remain. One means by which to rectify these long-standing inequities is through the implementation of a position dedicated to DEI among journal editorial boards; thus, we sought to assess the extent to which this position has been implemented among high-impact biomedical research journals.
    METHODS: We performed a cross-sectional analysis of the editorial boards of the top 100 journals by impact factor (IF) across 30 medical specialties. All editorial board positions (editors-in-chief, deputy, associate, and assistant editors, as well as editorial and advisory board members) were included. We also assessed the proportion of other named-position editors (i.e., social media and statistics editors), and compared these to the proportion of DEI editors.
    RESULTS: Among the 100 highest IF biomedical journals (range: 12.035 - 508.702), 6 (6%) have a DEI editorial position. In contrast, 25 (25%) and 35 (35%) journals have at least 1 social media or statistics editorial position, respectively. The DEI editorial position comprises 0.086% of the 6,974 total editorial positions, while social media (60/6,974) and statistical (196/6,974) editors comprise 0.86% and 2.81% of total journal editorial board positions, respectively.
    CONCLUSIONS: Few of the most influential biomedical journals have implemented a formal, named position dedicated to DEI. Biomedical journals should consider establishing a dedicated DEI editorial position, and ensure this individual position is publicly denoted on the editorial board.
    Keywords:  Biomedical publishing; Diversity; Equity; Inclusion; Research
    DOI:  https://doi.org/10.1080/03007995.2023.2177381
  15. Am J Physiol Regul Integr Comp Physiol. 2023 Feb 07.
      In Part 1 of this Perspective, I share my thoughts on several key issues related to publishing in academic biomedical research for early career stage investigators. Among the topics discussed are the importance of publishing peer-reviewed manuscripts, considerations associated with different types of publications, how frequently you should publish, how to select a scientific journal for your manuscript, and navigating authorship questions, including who should be an author, authorship order, and who should write a manuscript.
    Keywords:  career development; manuscript writing; professional skills; publishing
    DOI:  https://doi.org/10.1152/ajpregu.00265.2022
  16. Am J Physiol Regul Integr Comp Physiol. 2023 Feb 07.
      In Part 2 of this Perspective on Publishing Particulars, I share several recommendations with early career stage investigators for how to successfully develop a competitive manuscript for publication. In the initial section, I first discuss how to organize content most effectively for an original research article by creating a "storyboard" of the key results, including the sequence in which they will be presented. I then emphasize the importance of rigorously outlining all the information to be presented in the manuscript before attempting to write the text. In the second section, I comprehensively discuss tactical approaches for developing the specific component parts of an original research paper, including the Abstract, Introduction, Methods, Results and illustrations, and Discussion, as well as strategies for referencing the text. In the final section, I provide suggestions for how to best develop a compelling review article. The topics discussed include how to view the opportunity; selecting authors and defining their respective roles; identifying the foundational components of the text; conducting a comprehensive review of the target published literature; and organizing, writing, and illustrating the article.
    Keywords:  career development; manuscript writing; professional skills; publishing
    DOI:  https://doi.org/10.1152/ajpregu.00267.2022
  17. Am J Physiol Regul Integr Comp Physiol. 2023 Feb 07.
      In Part 3 of this Perspective on Publishing Particulars I begin by providing several general writing tips to consider when developing a manuscript for publication. I then discuss the process involved in rigorously editing research papers and advance some important considerations for manuscript submission. I next share my thoughts and recommendations when attempting to interpret and respond to comments from the manuscript peer review process. Lastly, I discuss author responsibilities after a manuscript is accepted for publication. Overall, this portion of the 3-part commentary seeks to complete a broader discussion on publishing in the biomedical sciences aimed at better informing early-stage investigators about many of the nuances of this critical area of professional development.
    Keywords:  biomedical research; career development; manuscript writing; professional skills
    DOI:  https://doi.org/10.1152/ajpregu.00270.2022
  18. Ocul Surf. 2023 Feb 03. pii: S1542-0124(23)00015-0. [Epub ahead of print]28 56-57
      
    Keywords:  Authorship; Paper mills; Publication ethics; Scientific ethics; Unethical
    DOI:  https://doi.org/10.1016/j.jtos.2023.02.001
  19. BMJ Open Sport Exerc Med. 2023 ;9(1): e001460
       Background: Research evidence is commonly compiled into expert-agreed consensus statements or guidelines, with an increasing trend towards their publication in peer-reviewed journals. Prominent among these has been the publication of several International Olympic Committee (IOC) tatements to help inform sport and exercise medicine (SEM) practice. This study aimed to assess the citation impact and reach of the IOC statements published between 2003 and 2020.
    Method: Bibliometric analysis focused on identifying core publications (original statement and linked publications) and quantifying their academic citations (number and Field-Weighted Citation Impact (FWCI)) in journal articles up to February 2022. The analysis includes descriptive data on the country of IOC statement authorship affiliations, where they were published and by whom. The extent to which the IOC statements have been cited in the peer-reviewed literature is presented, together with information about the country of authorship of the citing papers as a measure of international academic reach.
    Results: 29 IOC statements were composed of 61 core publications. The IOC statements have had 9535 citations from 7863 citing publications. Individual FWCI ranged from 1.2 to 24.3 for core publications. The IOC statements were coauthored by multiple authors, mostly affiliated to countries with well-resourced SEM Authors of citing publications reflected the same geographical regions (ie, the USA, Canada, Australia, UK and western Europe.).
    Conclusion: Disseminating the IOC statements as open access papers in peer-reviewed journals has resulted in strong citation impact. However, this impact is centred on well-resourced academic circles that may not represent the diversity of SEM. Further research is required to identify if, and to what extent, the IOC statements have impacted SEM practice worldwide.
    Keywords:  consensus statement; knowledge translation; position statement; sports & exercise medicine; sports medicine
    DOI:  https://doi.org/10.1136/bmjsem-2022-001460
  20. Microbiology (Reading). 2022 Dec;168(12):
      This is the final paper in a series of three historical reviews marking the 75th anniversary of the launch of the Journal of General Microbiology (JGM), now Microbiology. It looks at some of the factors involved in the physical, and the electronic, production of the Journal, and how those factors have evolved since the Journal was launched in 1947. There have, of course, been massive changes in all aspects of production over the past 75 years. Microbiology started with manual typewriters, literal (rather than electronic) cutting and pasting of text at the editing stage, retyping and rechecking, hot-metal setting and printing, and finally postal distribution of complete bound issues. Illustrations, figures and tables presented special challenges. And there was also the considerable chore of having to duplicate and mail out multiple paper copies at the refereeing stage. It was all perfectly manageable, but it took a great deal of time and effort, and became all the more demanding as the Journal grew in scale and geographical reach. The dramatic rate of technical change since then is obvious to all. The technology has allowed each aspect of journal publishing to be done in new and far more convenient ways; and in some important respects it has also changed how we think about the very idea of journal publishing. Through all this, publishing has remained central to what the Microbiology Society is and does.
    DOI:  https://doi.org/10.1099/mic.0.001273