bims-skolko Biomed News
on Scholarly communication
Issue of 2022‒11‒27
24 papers selected by
Thomas Krichel
Open Library Society
  1. Why don't we share data and code? Perceived barriers and benefits to public archiving practices.
  2. Open science and conflict of interest policies of medical and health sciences journals before and during the COVID-19 pandemic: A repeat cross-sectional study: Open science policies of medical journals.
  3. Peer review? No thanks!
  4. Feedback as Dialogue for Faculty: From Peer Review to Peer-to-Peer Coaching.
  5. To fix peer review, break it into stages.
  6. Prediction Algorithms: Is Peer Review Enough?
  7. The art of peer review: Guidelines to become a credible and constructive peer reviewer.
  8. Peer Review, Confidential Comments to the Editor, and the Golden Rule.
  9. Peer-review: the pinnacle of scholarly communication.
  10. Urogynecology Early-Career Peer Reviewer Academy.
  11. Progressive and degenerative journals: on the growth and appraisal of knowledge in scholarly publishing.
  12. Changing patterns in reporting and sharing of review data in systematic reviews with meta-analysis of the effects of interventions: cross sectional meta-research study.
  13. Readership Awareness Series - Paper 2: Conflict of Interest.
  14. Awareness and knowledge of manuscript writing and research integrity: A cross sectional survey among graduate students.
  15. General Guide to Publish a Scientific Paper.
  16. Open Science Practices in Communication Sciences and Disorders: A Survey.
  17. Investing in the Academic Writing: Training Future Reviewers and Sustaining Efficient and Quality Peer Review.
  18. Scientific Publishing in Biomedicine: Information Literacy.
  19. The menace of self citation: An audit of two years from journals of Khyber Pakhtunkhwa.
  20. Authorship: Refusing what you know you don't deserve.
  21. Time to Publication in High-Impact General Medical Journals Differs Between Female and Male Researchers.
  22. Researcher, author and reviewer profiles.
  23. Marking the inclusion of the Korean Journal of Women Health Nursing in PubMed Central and strategies to be promoted to a top-tier journal in the nursing category.
  24. Fish and shellfish immunology reports: A new open access journal.
  1. Proc Biol Sci. 2022 Nov 30. 289(1987): 20221113
    Why don't we share data and code? Perceived barriers and benefits to public archiving practices.
    Dylan G E Gomes, Patrice Pottier, Robert Crystal-Ornelas, Emma J Hudgins, Vivienne Foroughirad, Luna L Sánchez-Reyes, Rachel Turba, Paula Andrea Martinez, David Moreau, Michael G Bertram, Cooper A Smout, Kaitlyn M Gaynor.
      The biological sciences community is increasingly recognizing the value of open, reproducible and transparent research practices for science and society at large. Despite this recognition, many researchers fail to share their data and code publicly. This pattern may arise from knowledge barriers about how to archive data and code, concerns about its reuse, and misaligned career incentives. Here, we define, categorize and discuss barriers to data and code sharing that are relevant to many research fields. We explore how real and perceived barriers might be overcome or reframed in the light of the benefits relative to costs. By elucidating these barriers and the contexts in which they arise, we can take steps to mitigate them and align our actions with the goals of open science, both as individual scientists and as a scientific community.
    Keywords:  code reuse‌; data reuse; data science; open science; reproducibility; transparency
    DOI:  https://doi.org/10.1098/rspb.2022.1113
  2. JRSM Open. 2022 Nov;13(11): 20542704221132139
    Open science and conflict of interest policies of medical and health sciences journals before and during the COVID-19 pandemic: A repeat cross-sectional study: Open science policies of medical journals.
    Antoni D Gardener, Ellen J Hick, Chloe Jacklin, Gifford Tan, Aidan G Cashin, Hopin Lee, David Nunan, Elaine C Toomey, Georgia C Richards.
      Objectives: To audit the transparent and open science standards of health and medical sciences journal policies and explore the impact of the COVID-19 pandemic.Design: Repeat cross-sectional study.
    Setting: 19 journals listed in Google Scholar's Top Publications for health and medical sciences.
    Participants: Blood, Cell, Circulation, European Heart Journal, Gastroenterology, Journal of Clinical Oncology, Journal of the American College of Cardiology, Nature Genetics, Nature Medicine, Nature Neuroscience, Neuron, PLoS ONE, Proceedings of the National Academy of Sciences, Science Translational Medicine, The British Medical Journal, The Journal of the American Medical Association, The Lancet, The Lancet Oncology, and The New England Journal of Medicine.
    Main outcome measures: We used the Transparency and Openness Promotion (TOP) guideline and the International Committee of Medical Journal Editors (ICMJE) requirements for disclosing conflicts of interest (COIs) to evaluate journals standards.
    Results: TOP scores slightly improved during the COVID-19 pandemic, from a median of 5 (IQR: 2-12.5) out of a possible 24 points in February 2020 to 7 (IQR: 4-12) in May 2021, but overall, scores were very low at both time points. Journal policies scored highest for their adherence to data transparency and scored lowest for preregistration of study protocols and analysis plans and the submission of replication studies. Most journals fulfilled all ICMJE provisions for reporting COIs before (84%; n  =  16) and during (95%; n  =  18) the COVID-19 pandemic.
    Conclusions: The COVID-19 pandemic has highlighted the importance of practising open science. However, requirements for open science practices in audited policies were overall low, which may impede progress in health and medical research. As key stakeholders in disseminating research, journals should promote a research culture of greater transparency and more robust open science practices.
    Keywords:  NON-CLINICAL; NONCLINICAL; epidemiology; journalology; public health; statistics and research methods
    DOI:  https://doi.org/10.1177/20542704221132139
  3. Climacteric. 2022 Nov 24. 1-2
    Peer review? No thanks!
    C Castelo-Branco.
      The peer review process is an inalienable necessity in the modern scientific world. Published manuscripts are founded on feedback, a process in which reviewers evaluate the scientific values of the submitted paper and provide comments and criticisms. The aim of this process is to assist authors by improving their papers, to promote good science. The peer-review process can be represented as a hurdle race with the ultimate prize of innovative accurate scientific knowledge being published. In this process, we have on the one side the authors and originators of ideas and on the other editors and reviewers. In the process of publishing a scientific article, it is important to respect the time and efforts of both actors.
    Keywords:  Peer-review; authors; editors; manuscript; reviewer; scientific journal
    DOI:  https://doi.org/10.1080/13697137.2022.2149006
  4. Med Educ. 2022 Nov 23.
    Feedback as Dialogue for Faculty: From Peer Review to Peer-to-Peer Coaching.
    Noam Margalit, Amber T Pincavage.
      
    DOI:  https://doi.org/10.1111/medu.14980
  5. Nature. 2022 Nov;611(7937): 637
    To fix peer review, break it into stages.
    Olavo B Amaral.
      
    Keywords:  Peer review; Publishing; Research data; Technology
    DOI:  https://doi.org/10.1038/d41586-022-03791-5
  6. Anesthesiology. 2022 Dec 01. 137(6): 661-663
    Prediction Algorithms: Is Peer Review Enough?
    Laurent G Glance, Laszlo Vutskits, Andrew Davidson.
      
    DOI:  https://doi.org/10.1097/ALN.0000000000004421
  7. Semin Vasc Surg. 2022 Dec;pii: S0895-7967(22)00069-2. [Epub ahead of print]35(4): 470-478
    The art of peer review: Guidelines to become a credible and constructive peer reviewer.
    M Libby Weaver, Rachael Sundland, Alexandra M Adams, Isabella Faria, Hope A Feldman, Hallbera Gudmundsdottir, Hannah Marmor, Victoria Miles, Brielle Ochoa, Samantha M Ruff, Celsa Tonelli, Maria S Altieri, Lisa Cannada, Karuna Dewan, Yana Etkin, Rebecca Marmor, Jennifer K Plichta, Chantal Reyna, Leah Tatebe, Laura M Drudi, Caitlin W Hicks.
      Peer review is a learned skill set that requires knowledge of study design, review construct, ethical considerations, and general expertise in a field of study. Participating in peer review is a rewarding and valuable experience in which all academic physicians are encouraged to partake. However, formal training opportunities in peer review are limited. In 2021, the Association of Women Surgeons and the journal Surgery collaborated to develop a Peer Review Academy. This academy is a 1-year longitudinal course that offers a select group of young women surgical trainees across all specialties a curriculum of monthly lectures and multiple formal mentored peer review opportunities to assist them in developing the foundation necessary to transition to independent peer review. The trainees and faculty mentors participating in the Association of Women Surgeons-Surgery Peer Review Academy compiled a summary of best peer review practices, which is intended to outline the elements of the skill set necessary to become a proficient peer reviewer.
    DOI:  https://doi.org/10.1053/j.semvascsurg.2022.10.002
  8. Ann Plast Surg. 2022 Nov 21.
    Peer Review, Confidential Comments to the Editor, and the Golden Rule.
    Eric Swanson.
      
    DOI:  https://doi.org/10.1097/SAP.0000000000003320
  9. Colorectal Dis. 2022 Nov;24(11): 1272
    Peer-review: the pinnacle of scholarly communication.
      
    DOI:  https://doi.org/10.1111/codi.16385
  10. Urogynecology (Hagerstown). 2022 Dec 01. 28(12): 795-796
    Urogynecology Early-Career Peer Reviewer Academy.
    Linda Brubaker.
      
    DOI:  https://doi.org/10.1097/SPV.0000000000001291
  11. Eur J Philos Sci. 2022 ;12(4): 61
    Progressive and degenerative journals: on the growth and appraisal of knowledge in scholarly publishing.
    Daniel J Dunleavy.
      Despite continued attention, finding adequate criteria for distinguishing "good" from "bad" scholarly journals remains an elusive goal. In this essay, I propose a solution informed by the work of Imre Lakatos and his methodology of scientific research programmes (MSRP). I begin by reviewing several notable attempts at appraising journal quality - focusing primarily on the impact factor and development of journal blacklists and whitelists. In doing so, I note their limitations and link their overarching goals to those found within the philosophy of science. I argue that Lakatos's MSRP and specifically his classifications of "progressive" and "degenerative" research programmes can be analogized and repurposed for the evaluation of scholarly journals. I argue that this alternative framework resolves some of the limitations discussed above and offers a more considered evaluation of journal quality - one that helps account for the historical evolution of journal-level publication practices and attendant contributions to the growth (or stunting) of scholarly knowledge. By doing so, the seeming problem of journal demarcation is diminished. In the process I utilize two novel tools (the mistake index and scite index) to further illustrate and operationalize aspects of the MSRP.
    Keywords:  Journalology; Meta-science; Methodology of scientific research programmes; Predatory publishing; Scholarly publishing; Sociology of science
    DOI:  https://doi.org/10.1007/s13194-022-00492-8
  12. BMJ. 2022 Nov 22. 379 e072428
    Changing patterns in reporting and sharing of review data in systematic reviews with meta-analysis of the effects of interventions: cross sectional meta-research study.
    Phi-Yen Nguyen, Raju Kanukula, Joanne E McKenzie, Zainab Alqaidoom, Sue E Brennan, Neal R Haddaway, Daniel G Hamilton, Sathya Karunananthan, Steve McDonald, David Moher, Shinichi Nakagawa, David Nunan, Peter Tugwell, Vivian A Welch, Matthew J Page.
      OBJECTIVES: To examine changes in completeness of reporting and frequency of sharing data, analytical code, and other review materials in systematic reviews over time; and factors associated with these changes.DESIGN: Cross sectional meta-research study.
    POPULATION: Random sample of 300 systematic reviews with meta-analysis of aggregate data on the effects of a health, social, behavioural, or educational intervention. Reviews were indexed in PubMed, Science Citation Index, Social Sciences Citation Index, Scopus, and Education Collection in November 2020.
    MAIN OUTCOME MEASURES: The extent of complete reporting and the frequency of sharing review materials in the systematic reviews indexed in 2020 were compared with 110 systematic reviews indexed in February 2014. Associations between completeness of reporting and various factors (eg, self-reported use of reporting guidelines, journal policies on data sharing) were examined by calculating risk ratios and 95% confidence intervals.
    RESULTS: Several items were reported suboptimally among 300 systematic reviews from 2020, such as a registration record for the review (n=113; 38%), a full search strategy for at least one database (n=214; 71%), methods used to assess risk of bias (n=185; 62%), methods used to prepare data for meta-analysis (n=101; 34%), and source of funding for the review (n=215; 72%). Only a few items not already reported at a high frequency in 2014 were reported more frequently in 2020. No evidence indicated that reviews using a reporting guideline were more completely reported than reviews not using a guideline. Reviews published in 2020 in journals that mandated either data sharing or inclusion of data availability statements were more likely to share their review materials (eg, data, code files) than reviews in journals without such mandates (16/87 (18%) v 4/213 (2%)).
    CONCLUSION: Incomplete reporting of several recommended items for systematic reviews persists, even in reviews that claim to have followed a reporting guideline. Journal policies on data sharing might encourage sharing of review materials.
    DOI:  https://doi.org/10.1136/bmj-2022-072428
  13. Semin Ophthalmol. 2022 Nov 21. 1-2
    Readership Awareness Series - Paper 2: Conflict of Interest.
    Mohammad Javed Ali, Ali Djalilian.
      
    DOI:  https://doi.org/10.1080/08820538.2022.2149080
  14. Heliyon. 2022 Nov;8(11): e11447
    Awareness and knowledge of manuscript writing and research integrity: A cross sectional survey among graduate students.
    Fadia Mayyas, Karem Alzoubi.
      Graduate students face a variety of barriers when writing manuscripts. The major barrier is inadequate writing experience and training. We aimed to evaluate the awareness and the knowledge of the basic principles in manuscript writing and research integrity among graduate students, and to assess the usefulness of workshops to improve their knowledge about manuscript writing process. A cross sectional survey was developed to evaluate the awareness and the knowledge about the manuscript writing steps and the research integrity among graduate students in Jordan. A one-day workshop about manuscript writing and research integrity was conducted. Students (n = 285) completed the questionnaire. Most participants were female masters'; students. Although 83.8% of the students were aware of the general manuscript structure, most of them were not aware of the basic concepts to write most manuscript sections. Only 22.5% of the students were aware of the authorship criteria. Data showed a lack of knowledge of different practices of scientific misconduct. Barriers in manuscript writing included the lack of focused research methodology courses and the lack of professional workshops and the absence constructive mentorship support. The workshop was useful in introducing the key concepts in manuscript writing. The present study revealed a lack of knowledge among graduate students about manuscript writing and scientific misconduct. Professional workshops are useful in improving students' knowledge.
    Keywords:  Graduate education; Manuscript; Scientific misconduct; Writing
    DOI:  https://doi.org/10.1016/j.heliyon.2022.e11447
  15. Recent Adv Drug Deliv Formul. 2022 ;16(3): 168-169
    General Guide to Publish a Scientific Paper.
    Brahma N Singh, Stefano Giovagnoli.
      
    DOI:  https://doi.org/10.2174/2667387816666220429093958
  16. J Speech Lang Hear Res. 2022 Nov 23. 1-20
    Open Science Practices in Communication Sciences and Disorders: A Survey.
    Mariam El Amin, James C Borders, Helen L Long, Mary Alice Keller, Elaine Kearney.
      PURPOSE: Open science is a collection of practices that seek to improve the accessibility, transparency, and replicability of science. Although these practices have garnered interest in related fields, it remains unclear whether open science practices have been adopted in the field of communication sciences and disorders (CSD). This study aimed to survey the knowledge, implementation, and perceived benefits and barriers of open science practices in CSD.METHOD: An online survey was disseminated to researchers in the United States actively engaged in CSD research. Four-core open science practices were examined: preregistration, self-archiving, gold open access, and open data. Data were analyzed using descriptive statistics and regression models.
    RESULTS: Two hundred twenty-two participants met the inclusion criteria. Most participants were doctoral students (38%) or assistant professors (24%) at R1 institutions (58%). Participants reported low knowledge of preregistration and gold open access. There was, however, a high level of desire to learn more for all practices. Implementation of open science practices was also low, most notably for preregistration, gold open access, and open data (< 25%). Predictors of knowledge and participation, as well as perceived barriers to implementation, are discussed.
    CONCLUSION: Although participation in open science appears low in the field of CSD, participants expressed a strong desire to learn more in order to engage in these practices in the future. Supplemental Material and Open Science Form: https://doi.org/10.23641/asha.21569040.
    DOI:  https://doi.org/10.1044/2022_JSLHR-22-00062
  17. Cureus. 2022 Oct;14(10): e30341
    Investing in the Academic Writing: Training Future Reviewers and Sustaining Efficient and Quality Peer Review.
    B M Munasinghe, Champa Chapman, Chinthaka Hewavitharane, Gayathri Hewawasam, T G Dissanayakege.
      Peer reviewers are considered gatekeepers in academic writing who play a pivotal and essential role during the publication process. Excellent manuscripts invariably need excellent reviewers. Producing peer reviewers with such caliber is time-consuming albeit necessary for the progress and continuity of academia. Despite the popular belief that an experienced author invariably makes a good reviewer, the reality is far-fetched. This suggests the need for peer reviewer training, which should be effective, logistically affordable, and demonstrate long-lasting positive impacts. Open review, co-review, and several reviewer training programs are already in place for this purpose with varying efficiencies. This narrative review discusses the current modalities available to a junior reviewer to improve his/her review skills and proposes a reviewer residency concept that could be adopted as a part of peer reviewer training.
    Keywords:  co-reviewing; junior reviewer; open review; peer review; peer reviewer; reviewer residency; trainee reviewer
    DOI:  https://doi.org/10.7759/cureus.30341
  18. Int J Endocrinol Metab. 2022 Jul;20(3): e128701
    Scientific Publishing in Biomedicine: Information Literacy.
    Zahra Bahadoran, Parvin Mirmiran, Khosrow Kashfi, Asghar Ghasemi.
      The literature review is an integral part of the research process, from developing research ideas to disseminating findings. It involves explaining, interpreting, and summarizing published materials around a topic to elaborate a research hypothesis/question, synthesize new concepts, identify knowledge gaps, develop new theories, and identify new research directions. Effective reading and processing of the literature (i.e., analyzing and synthesizing) and actual writing of the literature (verbal or non-verbal output, e.g., tables and figures) are essential stages of an effective literature review. This article provides a practical guide to conducting an effective literature review. In addition, literature search and evaluation are also briefly discussed.
    Keywords:  Information Literacy; Literature Review; Medical Writing; Publishing
    DOI:  https://doi.org/10.5812/ijem-128701
  19. Pak J Med Sci. 2022 Nov-Dec;38(8):38(8): 2284-2288
    The menace of self citation: An audit of two years from journals of Khyber Pakhtunkhwa.
    Mian Saad Ahmed, Umema Zafar, Hamna Zafar, Maryam Shahid Ullah, Feroz Ali Khan.
      Objective: To assess the author and journal self-citation amongst journals of Khyber Pakhtunkhwa.Methods: This is a cross-sectional study conducted from January 2021 to July 2021. In total, manuscript published in 10 journals of Khyber Pakhtunkhwa, either recognized by the Higher Education Commission or Pakistan Medical Commission, in the years 2018 and 2019 were included in the present research. All types of manuscripts were analyzed using a pre-designed data extraction table. Results were extracted, analyzed and appropriate statistics were applied.
    Results: About 1235 manuscripts published in 68 issues over a period of two years' time were analyzed. The majority of manuscripts were 1039 (84.1%) original articles followed by case reports 90 (7.3%). Author self-citation came out to be 11.26% and journal self-citation was 6.5%. The same institute's author affiliation came out to be 40.6%.
    Conclusion: The trend of author self-citation was found to be high while that of journal self-citation was low when compared with already prevalent literature.
    Keywords:  Audit; Author self-citation; Home authorship; Journal self-citation
    DOI:  https://doi.org/10.12669/pjms.38.8.6571
  20. Indian J Med Ethics. 2022 Sep 28.
    Authorship: Refusing what you know you don't deserve.
    Salik Ansari.
      Scientific writing and publishing are significant for an early-career researcher (ECR). For entry into doctoral studies, new jobs, or promotion, publications are among the essential requisites any selection committee will look for. Unlike interpersonal skills such as team building or communication, academic outputs are easier to assess and quantify but producing them may not always be easy for an ECR.
    DOI:  https://doi.org/10.20529/IJME.2022.073
  21. J Gen Intern Med. 2022 Nov 23.
    Time to Publication in High-Impact General Medical Journals Differs Between Female and Male Researchers.
    Paul Sebo.
      
    DOI:  https://doi.org/10.1007/s11606-022-07946-y
  22. J R Coll Physicians Edinb. 2022 Nov 25. 14782715221139591
    Researcher, author and reviewer profiles.
    Durga Prasanna Misra, Vinod Ravindran.
      
    Keywords:  ORCID; Publons; author profiles; name disambiguation; peer review; researcher profiles
    DOI:  https://doi.org/10.1177/14782715221139591
  23. Korean J Women Health Nurs. 2022 Sep;28(3): 165-168
    Marking the inclusion of the Korean Journal of Women Health Nursing in PubMed Central and strategies to be promoted to a top-tier journal in the nursing category.
    Sun Huh.
      
    DOI:  https://doi.org/10.4069/kjwhn.2022.08.19
  24. Fish Shellfish Immunol Rep. 2020 Dec;1 100001
    Fish and shellfish immunology reports: A new open access journal.
    Linsheng Song, Brian Dixon.
      
    DOI:  https://doi.org/10.1016/j.fsirep.2020.100001
This page is being maintained by Thomas Krichel. It was last updated on 2022‒11‒27 at 17:24:23.