bims-skolko Biomed News
on Scholarly communication
Issue of 2022–09–11
24 papers selected by
Thomas Krichel, Open Library Society
  1. Preprints in Chemistry: a Research Team's Journey.
  2. The score after 10 years of registration of systematic review protocols.
  3. Postponed, non-competitive peer review for research funding.
  4. Peer Review in Urologic Journals: What is the Best Peer Review Model?
  5. Advances in transparency and reproducibility in the social sciences.
  6. Recommendations for the extraction, analysis, and presentation of results in scoping reviews.
  7. How to Develop an Evidence-Based Project Into a Manuscript for Publication.
  8. Clinical EEG and Neuroscience Editorial Board Announces New Criteria for Studies Reporting on Data-Driven Classifiers, and on Novel Interventions and Treatments.
  9. Gender and Geographic Origin as Determinants of Manuscript Publication Outcomes: JBMR® Bibliometric Analysis from 2017 to 2019.
  10. When open data closes the door: A critical examination of the past, present and the potential future for open data guidelines in journals.
  11. Open science and data sharing in trauma research: Developing a trauma-informed protocol for archiving sensitive qualitative data.
  12. Neither carrots nor sticks? Challenges surrounding data sharing from the perspective of research funding agencies-A qualitative expert interview study.
  13. Tackling the politicisation of COVID-19 data reporting through open access data sharing.
  14. Without appropriate metadata, data-sharing mandates are pointless.
  15. Reasons for qualitative psychologists to share human data.
  16. Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future.
  17. Readership Awareness Series - Paper 1: Ghost Authorship.
  18. The rise and rise of the impact factor.
  19. The need for editorial fellowships in Indian medical journals.
  20. The Importance of Mentoring for Publication.
  21. Best Practices for Citing Scientific Publications.
  22. How do we prevent scientific fraud?
  23. Medical Journal Websites Include Online-Only Content Plus Intriguing and Unique Features.
  24. Addressing Diversity, Equity, and Inclusion at the JNCI Journals.
  1. ChemistryOpen. 2022 Sep 06. e202200150
    Preprints in Chemistry: a Research Team's Journey.
    Rosaria Ciriminna, Mario Pagliaro.
      The benefits of publishing research papers first in preprint form are substantial and long-lasting also in chemistry. Recounting the outcomes of our team's nearly six-year journey through preprint publishing, we show evidence that preprinting research substantially benefits both early career and senior researchers in today's highly interdisciplinary chemical research. These findings are of general value, as shown by analyzing the case of four more research teams based in economically developed and developing countries.
    Keywords:  open access; open science; preprint; preprints in chemistry; research impact
    DOI:  https://doi.org/10.1002/open.202200150
  2. Syst Rev. 2022 Sep 05. 11(1): 191
    The score after 10 years of registration of systematic review protocols.
    Kim van der Braak, Mona Ghannad, Claudia Orelio, Pauline Heus, Johanna A A Damen, René Spijker, Karen Robinson, Hans Lund, Lotty Hooft.
       BACKGROUND: With the exponential growth of published systematic reviews (SR), there is a high potential for overlapping and redundant duplication of work. Prospective protocol registration gives the opportunity to assess the added value of a new study or review, thereby potentially reducing research waste and simultaneously increasing transparency and research quality. The PROSPERO database for SR protocol registration was launched 10 years ago. This study aims to assess the proportion SRs of intervention studies with a protocol registration (or publication) and explore associations of SR characteristics with protocol registration status.
    METHODS: PubMed was searched for SRs of human intervention studies published in January 2020 and January 2021. After random-stratified sampling and eligibility screening, data extraction on publication and journal characteristics, and protocol registration status, was performed. Both descriptive and multivariable comparative statistical analyses were performed.
    RESULTS: A total of 357 SRs (2020: n = 163; 2021: n = 194) were included from a random sample of 1267 publications. Of the published SRs, 38% had a protocol. SRs that reported using PRISMA as a reporting guideline had higher odds of having a protocol than publications that did not report PRISMA (OR 2.71; 95% CI: 1.21 to 6.09). SRs with a higher journal impact factor had higher odds of having a protocol (OR 1.12; 95% CI 1.04 to 1.25). Publications from Asia had a lower odds of having a protocol (OR 0.43; 95% CI 0.23 to 0.80, reference category = Europe). Of the 33 SRs published in journals that endorse PROSPERO, 45% did not have a protocol. Most SR protocols were registered in PROSPERO (n = 129; 96%).
    CONCLUSIONS: We found that 38% of recently published SRs of interventions reported a registered or published protocol. Protocol registration was significantly associated with a higher impact factor of the journal publishing the SR and a more frequent self-reported use of the PRISMA guidelines. In some parts of the world, SR protocols are more often registered or published than others. To guide strategies to increase the uptake of SR protocol registration, further research is needed to gain understanding of the benefits and informativeness of SRs protocols among different stakeholders.
    SYSTEMATIC REVIEW REGISTRATION: osf.io/9kj7r/.
    Keywords:  Implementation; Open science; Protocol registration; Systematic review
    DOI:  https://doi.org/10.1186/s13643-022-02053-9
  3. Eur J Neurosci. 2022 Sep 09.
    Postponed, non-competitive peer review for research funding.
    Martin Dresler.
      Receiving research grants is among the highlights of an academic career, affirming previous accomplishments and enabling new research endeavors. Much of the process of acquiring research funding, however, belongs to the less favorite duties of many researchers: it is time consuming, often stressful, and, in the majority of cases, unsuccessful. This resentment toward funding acquisition is backed up by empirical research: the current system to distribute research funding, via competitive calls for extensive research applications that undergo peer review, has repeatedly been shown to fail in its task to reliably rank proposals according to their merit, while at the same time being highly inefficient. The simplest, fairest, and broadly supported alternative would be to distribute funding more equally across researchers e.g. by an increase of universities' base funding, thereby saving considerable time that can be spent on research instead. Here, I propose how to combine such a 'funding flat rate' model - or other efficient distribution strategies - with quality control through postponed, non-competitive peer-review using open science practices.
    Keywords:  funding; meta science; peer review; research
    DOI:  https://doi.org/10.1111/ejn.15818
  4. J Urol. 2022 Sep 08. 101097JU0000000000002961
    Peer Review in Urologic Journals: What is the Best Peer Review Model?
    Elie Kaplan-Marans, Jacob Khurgin.
      
    Keywords:  double-anonymous review; open peer review; peer review; single-anonymous review
    DOI:  https://doi.org/10.1097/JU.0000000000002961
  5. Soc Sci Res. 2022 Sep;pii: S0049-089X(22)00076-X. [Epub ahead of print]107 102770
    Advances in transparency and reproducibility in the social sciences.
    Jeremy Freese, Tamkinat Rauf, Jan Gerrit Voelkel.
      Worries about a "credibility crisis" besieging science have ignited interest in research transparency and reproducibility as ways of restoring trust in published research. For quantitative social science, advances in transparency and reproducibility can be seen as a set of developments whose trajectory predates the recent alarm. We discuss several of these developments, including preregistration, data-sharing, formal infrastructure in the form of resources and policies, open access to research, and specificity regarding research contributions. We also discuss the spillovers of this predominantly quantitative effort towards transparency for qualitative research. We conclude by emphasizing the importance of mutual accountability for effective science, the essential role of openness for this accountability, and the importance of scholarly inclusiveness in figuring out the best ways for openness to be accomplished in practice.
    Keywords:  Open science; Reproducibility; Transparency
    DOI:  https://doi.org/10.1016/j.ssresearch.2022.102770
  6. JBI Evid Synth. 2022 Sep 08.
    Recommendations for the extraction, analysis, and presentation of results in scoping reviews.
    Danielle Pollock, Micah D J Peters, Hanan Khalil, Patricia McInerney, Lyndsay Alexander, Andrea C Tricco, Catrin Evans, Érica Brandão de Moraes, Christina M Godfrey, Dawid Pieper, Ashrita Saran, Cindy Stern, Zachary Munn.
       ABSTRACT: Scoping reviewers often face challenges in the extraction, analysis, and presentation of scoping review results. Using best-practice examples and drawing on the expertise of the JBI Scoping Review Methodology Group and an editor of a journal that publishes scoping reviews, this paper expands on existing JBI scoping review guidance. The aim of this article is to clarify the process of extracting data from different sources of evidence; discuss what data should be extracted (and what should not); outline how to analyze extracted data, including an explanation of basic qualitative content analysis; and offer suggestions for the presentation of results in scoping reviews.
    DOI:  https://doi.org/10.11124/JBIES-22-00123
  7. Prog Transplant. 2022 Sep 07. 15269248221123864
    How to Develop an Evidence-Based Project Into a Manuscript for Publication.
    Rebecca P Winsett.
      
    DOI:  https://doi.org/10.1177/15269248221123864
  8. Clin EEG Neurosci. 2022 Sep 06. 15500594221123461
    Clinical EEG and Neuroscience Editorial Board Announces New Criteria for Studies Reporting on Data-Driven Classifiers, and on Novel Interventions and Treatments.
    Dean F Salisbury.
      
    DOI:  https://doi.org/10.1177/15500594221123461
  9. J Bone Miner Res. 2022 Sep 05.
    Gender and Geographic Origin as Determinants of Manuscript Publication Outcomes: JBMR® Bibliometric Analysis from 2017 to 2019.
    Fernando Rivadeneira, Randall T Loder, Anthony C McGuire, Joseph R Chitwood, Katie Duffy, Roberto Civitelli, Melissa A Kacena, Jennifer J Westendorf.
      The Journal of Bone and Mineral Research (JBMR®), the flagship journal of the ASBMR, enjoys a premiere position in its field and has a global reach. The journal uses a single-blind peer-review process whereby three editors are typically involved in assessing each submission for publication, in addition to external reviewers. While emphasizing fairness, rigor, and transparency, this process is not immune to the influence of unconscious biases. The gender and geographic diversity of JBMR® authors, editors and reviewers has increased over the last three decades, but whether such diversity has affected peer-review outcomes is unknown. We analyzed manuscript acceptance rates based on the gender and geographic origin of authors, reviewers, and Associate Editors. The analysis included 1,662 original research articles submitted to JBMR® from September 2017 through December 2019. Gender was assigned using probabilities from an online tool and manually validated through internet searches. Predictor variables of manuscript outcome were determined with multivariate logistic regression analysis. The acceptance rate was highest when the first and last authors were of different genders, and lowest when both authors were men. Reviewer gender did not influence the outcome regardless of the genders of the first and last authors. Associate Editors from all geographical regions tended to select reviewers from their same region. The acceptance rate was highest when the Associate Editor was from Europe. Manuscripts with authors from North America and Australia/New Zealand had greater overall odds of acceptance than those from Europe and Asia. Manuscripts reviewed only by Editorial Board (EB) members had a lower acceptance rate than those refereed by non-EB reviewers or a mix of EB and non-EB reviewers. Overall, the geographical origin of authors, reviewers, and editors, as well as reviewers' EB membership may influence manuscript decisions. Yet, the JBMR® peer-review process remains largely free from gender bias.
    Keywords:  Authorship Trends; Bibliometrics; Country; Gender; Peer Review
    DOI:  https://doi.org/10.1002/jbmr.4696
  10. Br J Soc Psychol. 2022 Sep 08.
    When open data closes the door: A critical examination of the past, present and the potential future for open data guidelines in journals.
    Annayah M B Prosser, Richard J T Hamshaw, Johanna Meyer, Ralph Bagnall, Leda Blackwood, Monique Huysamen, Abbie Jordan, Konstantina Vasileiou, Zoe Walter.
      Opening data promises to improve research rigour and democratize knowledge production. But it also presents practical, theoretical, and ethical considerations for qualitative researchers in particular. Discussion about open data in qualitative social psychology predates the replication crisis. However, the nuances of this ongoing discussion have not been translated into current journal guidelines on open data. In this article, we summarize ongoing debates about open data from qualitative perspectives, and through a content analysis of 261 journals we establish the state of current journal policies for open data in the domain of social psychology. We critically discuss how current common expectations for open data may not be adequate for establishing qualitative rigour, can introduce ethical challenges, and may place those who wish to use qualitative approaches at a disadvantage in peer review and publication processes. We advise that future open data guidelines should aim to reflect the nuance of arguments surrounding data sharing in qualitative research, and move away from a universal "one-size-fits-all" approach to data sharing. This article outlines the past, present, and the potential future of open data guidelines in social-psychological journals. We conclude by offering recommendations for how journals might more inclusively consider the use of open data in qualitative methods, whilst recognizing and allowing space for the diverse perspectives, needs, and contexts of all forms of social-psychological research.
    Keywords:  content analysis; ethics; journal guidelines; journals; open data; open science; psychology; qualitative; qualitative methods; quantitative; social psychology; social sciences
    DOI:  https://doi.org/10.1111/bjso.12576
  11. Psychol Trauma. 2022 Sep 08.
    Open science and data sharing in trauma research: Developing a trauma-informed protocol for archiving sensitive qualitative data.
    Rebecca Campbell, Rachael Goodman-Williams, Jasmine Engleton, McKenzie Javorka, Katie Gregory.
       OBJECTIVE: The open science movement seeks to make research more transparent, and to that end, researchers are increasingly expected or required to archive their data in national repositories. In qualitative trauma research, data sharing could compromise participants' safety, privacy, and confidentiality because narrative data can be more difficult to de-identify fully. There is little guidance in the traumatology literature regarding how to discuss data-sharing requirements with participants during the informed consent process. Within a larger research project in which we interviewed assault survivors, we developed and evaluated a protocol for informed consent for qualitative data sharing and engaging participants in data de-identification.
    METHOD: We conducted qualitative interviews with N = 32 adult sexual assault survivors regarding (a) how to conduct informed consent for data sharing, (b) whether participants should have input on sharing their data, and (c) whether they wanted to redact information from their transcripts prior to archiving.
    RESULTS: No potential participants declined participation after learning about the archiving mandate. Survivors indicated that they wanted input on archiving because the interview is their story of trauma and abuse and it would be disempowering not to have control over how this information was shared and disseminated. Survivors also wanted input on this process to help guard their privacy, confidentiality, and safety. None of the participants elected to redact substantive data prior to archiving.
    CONCLUSIONS: Engaging participants in the archiving process is a feasible practice that is important and empowering for trauma survivors. (PsycInfo Database Record (c) 2022 APA, all rights reserved).
    DOI:  https://doi.org/10.1037/tra0001358
  12. PLoS One. 2022 ;17(9): e0273259
    Neither carrots nor sticks? Challenges surrounding data sharing from the perspective of research funding agencies-A qualitative expert interview study.
    Michael Anger, Christian Wendelborn, Eva C Winkler, Christoph Schickhardt.
       BACKGROUND: Data Sharing is widely recognised as crucial for accelerating scientific research and improving its quality. However, data sharing is still not a common practice. Funding agencies tend to facilitate the sharing of research data by both providing incentives and requiring data sharing as part of their policies and conditions for awarding grants. The goal of our article is to answer the following question: What challenges do international funding agencies see when it comes to their own efforts to foster and implement data sharing through their policies?
    METHODS: We conducted a series of sixteen guideline-based expert interviews with representatives of leading international funding agencies. As contact persons for open science at their respective agencies, they offered their perspectives and experiences concerning their organisations' data sharing policies. We performed a qualitative content analysis of the interviews and categorised the challenges perceived by funding agencies.
    RESULTS: We identify and illustrate six challenges surrounding data sharing policies as perceived by leading funding agencies: The design of clear policies, monitoring of compliance, sanctions for non-compliance, incentives, support, and limitations for funders' own capabilities. However, our interviews also show how funders approach potential solutions to overcome these challenges, for example by coordinating with other agencies or adjusting grant evaluation metrics to incentivise data sharing.
    DISCUSSION AND CONCLUSION: Our interviews point to existing flaws in funders' data sharing policies, such as a lack of clarity, a lack of monitoring of funded researchers' data sharing behaviour, and a lack of incentives. A number of agencies could suggest potential solutions but often struggle with the overall complexity of data sharing and the implementation of these measures. Funders cannot solve each challenge by themselves, but they can play an active role and lead joint efforts towards a culture of data sharing.
    DOI:  https://doi.org/10.1371/journal.pone.0273259
  13. Lancet Infect Dis. 2022 Aug 31. pii: S1473-3099(22)00505-9. [Epub ahead of print]
    Tackling the politicisation of COVID-19 data reporting through open access data sharing.
    Chad R Wells, Alison P Galvani.
      
    DOI:  https://doi.org/10.1016/S1473-3099(22)00505-9
  14. Nature. 2022 09;609(7926): 222
    Without appropriate metadata, data-sharing mandates are pointless.
    Mark A Musen.
      
    Keywords:  Research data; Research management
    DOI:  https://doi.org/10.1038/d41586-022-02820-7
  15. Br J Soc Psychol. 2022 Sep 06.
    Reasons for qualitative psychologists to share human data.
    Veli-Matti Karhulahti.
      Qualitative data sharing practices in psychology have not developed as rapidly as those in parallel quantitative domains. This is often explained by numerous epistemological, ethical and pragmatic issues concerning qualitative data types. In this article, I provide an alternative to the frequently expressed, often reasonable, concerns regarding the sharing of qualitative human data by highlighting three advantages of qualitative data sharing. I argue that sharing qualitative human data is not by default 'less ethical', 'riskier' and 'impractical' compared with quantitative data sharing, but in some cases more ethical, less risky and easier to manage for sharing because (1) informed consent can be discussed, negotiated and validated; (2) the shared data can be curated by special means; and (3) the privacy risks are mainly local instead of global. I hope this alternative perspective further encourages qualitative psychologists to share their data when it is epistemologically, ethically and pragmatically possible.
    Keywords:  epistemology; ethics; meta science; open science; practice; qualitative
    DOI:  https://doi.org/10.1111/bjso.12573
  16. Proteomics. 2022 Sep 08. e2200014
    Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future.
    Andrew R Jones, Eric W Deutsch, Juan Antonio Vizcaíno.
      Data independent acquisition (DIA) proteomics techniques have matured enormously in recent years, thanks to multiple technical developments in e.g. instrumentation and data analysis approaches. However, there are many improvements that are still possible for DIA data in the area of the FAIR (Findability, Accessibility, Interoperability and Reusability) data principles. These include more tailored data sharing practices and open data standards, since public databases and data standards for proteomics were mostly designed with DDA data in mind. Here we first describe the current state of the art in the context of FAIR data for proteomics in general, and for DIA approaches in particular. For improving the current situation for DIA data, we make the following recommendations for the future: (i) development of an open data standard for spectral libraries; (ii) make mandatory the availability of the spectral libraries used in DIA experiments in ProteomeXchange resources; (iii) improve the support for DIA data in the data standards developed by the Proteomics Standards Initiative; and (iv) improve the support for DIA datasets in ProteomeXchange resources, including more tailored metadata requirements. This article is protected by copyright. All rights reserved.
    Keywords:  Data Independent Acquisition; data repositories; data standards; proteomics data; spectral libraries
    DOI:  https://doi.org/10.1002/pmic.202200014
  17. Semin Ophthalmol. 2022 Sep 06. 1-2
    Readership Awareness Series - Paper 1: Ghost Authorship.
    Mohammad Javed Ali, Ali Djalilian.
      
    DOI:  https://doi.org/10.1080/08820538.2022.2112852
  18. Eur J Emerg Med. 2022 Oct 01. 29(5): 321-322
    The rise and rise of the impact factor.
    Yonathan Freund.
      
    DOI:  https://doi.org/10.1097/MEJ.0000000000000971
  19. Diabetes Metab Syndr. 2022 Aug 27. pii: S1871-4021(22)00218-1. [Epub ahead of print]16(9): 102604
    The need for editorial fellowships in Indian medical journals.
    Asmita Chakrabarti, Sumit Roy Chowdhury.
      
    Keywords:  Editorial review; Journals; Peer review; Publication
    DOI:  https://doi.org/10.1016/j.dsx.2022.102604
  20. Nurs Womens Health. 2022 Sep 01. pii: S1751-4851(22)00183-0. [Epub ahead of print]
    The Importance of Mentoring for Publication.
    Heidi Collins Fantasia.
      Mentorship for manuscript preparation and publication is important for the success of novice authors.
    DOI:  https://doi.org/10.1016/j.nwh.2022.08.002
  21. Optom Vis Sci. 2022 Sep 01. 99(9): 677-678
    Best Practices for Citing Scientific Publications.
    Michael D Twa.
      
    DOI:  https://doi.org/10.1097/OPX.0000000000001934
  22. Brain Commun. 2022 ;4(5): fcac217
    How do we prevent scientific fraud?
    Tara L Spires-Jones.
      Our editor discusses scientific fraud and ways we can discourage it.
    DOI:  https://doi.org/10.1093/braincomms/fcac217
  23. Arthroscopy. 2022 Sep;pii: S0749-8063(22)00418-2. [Epub ahead of print]38(9): 2589-2592
    Medical Journal Websites Include Online-Only Content Plus Intriguing and Unique Features.
    James H Lubowitz, Jefferson C Brand, Michael J Rossi.
      Arthroscopy; Arthroscopy Techniques; and Arthroscopy, Sports Medicine, and Rehabilitation (ASMAR) websites include content that is available only online. Every time we visit the websites, we discover new content and educational features worth exploring. From meeting abstracts to multimedia, and from research pearls collections to world maps indicating the reach of our journals, a tour of our websites is enthralling. You can even take a bite of a hamburger.
    DOI:  https://doi.org/10.1016/j.arthro.2022.07.005
  24. J Natl Cancer Inst. 2022 Sep 06. pii: djac124. [Epub ahead of print]
    Addressing Diversity, Equity, and Inclusion at the JNCI Journals.
    Patricia A Ganz, Ronald C Chen, Amanda L Boehm.
      
    DOI:  https://doi.org/10.1093/jnci/djac124
This page is being maintained by Thomas Krichel. It was last updated on 2024‒11‒22 at 4:28.