bims-skolko Biomed News
on Scholarly communication
Issue of 2021‒03‒07
twenty-two papers selected by
Thomas Krichel
Open Library Society


  1. PLoS Biol. 2021 Mar 01. 19(3): e3001107
      Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic. We present an open-source, automated approach to identify 5 indicators of transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures, and protocol registration) and apply it across the entire open access biomedical literature of 2.75 million articles on PubMed Central (PMC). Our results indicate remarkable improvements in some (e.g., conflict of interest [COI] disclosures and funding disclosures), but not other (e.g., protocol registration and code sharing) areas of transparency over time, and map transparency across fields of science, countries, journals, and publishers. This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand, and promote transparency and reproducibility in science.
    DOI:  https://doi.org/10.1371/journal.pbio.3001107
  2. Nature. 2021 03;591(7848): 7
      
    Keywords:  Publishing; Research management; SARS-CoV-2
    DOI:  https://doi.org/10.1038/d41586-021-00527-9
  3. Nature. 2021 Mar;591(7849): 333-334
      
    Keywords:  Authorship; Careers; Publishing
    DOI:  https://doi.org/10.1038/d41586-021-00553-7
  4. Res Theory Nurs Pract. 2021 Mar 05. pii: RTNP-D-21-00020. [Epub ahead of print]
      
    DOI:  https://doi.org/10.1891/RTNP-D-21-00020
  5. World J Clin Cases. 2021 Feb 26. 9(6): 1247-1250
      Peer review is the cornerstone in scientific publication. Although peer review has paramount importance in ensuring the quality of the published literature, it still has a number of shortcomings. The present manuscript proposes a new method to improve the current peer review system by providing an interactive, dynamic platform that allows direct, anonymous interaction between the authors of submitted manuscripts and the reviewers. Such real-time interaction may help eliminate any problems related to misunderstanding or misinterpretation of the reviewer's comments or the authors' response, and would save time while keeping the identity of both parties anonymous.
    Keywords:  Improve; Interactive; Peer; Proposal; Review; System
    DOI:  https://doi.org/10.12998/wjcc.v9.i6.1247
  6. Eur Ann Otorhinolaryngol Head Neck Dis. 2021 Feb 25. pii: S1879-7296(21)00026-0. [Epub ahead of print]
      
    DOI:  https://doi.org/10.1016/j.anorl.2021.02.008
  7. Evid Based Nurs. 2021 Mar 04. pii: ebnurs-2021-103417. [Epub ahead of print]
      
    DOI:  https://doi.org/10.1136/ebnurs-2021-103417
  8. J Biomed Inform. 2021 Feb 26. pii: S1532-0464(21)00046-0. [Epub ahead of print] 103717
      OBJECTIVE: To annotate a corpus of randomized controlled trial (RCT) publications with the checklist items of CONSORT reporting guidelines and using the corpus to develop text mining methods for RCT appraisal.METHODS: We annotated a corpus of 50 RCT articles at the sentence level using 37 fine-grained CONSORT checklist items. A subset (31 articles) was double-annotated and adjudicated, while 19 were annotated by a single annotator and reconciled by another. We calculated inter-annotator agreement at the article and section level using MASI (Measuring Agreement on Set-Valued Items) and at the CONSORT item level using Krippendorff's α. We experimented with two rule-based methods (phrase-based and section header-based) and two supervised learning approaches (support vector machine and BioBERT-based neural network classifiers), for recognizing 17 methodology-related items in the RCT Methods sections.
    RESULTS: We created CONSORT-TM consisting of 10,709 sentences, 4,845 (45%) of which were annotated with 5,246 labels. A median of 28 CONSORT items (out of possible 37) were annotated per article. Agreement was moderate at the article and section levels (average MASI: 0.60 and 0.64, respectively). Agreement varied considerably among individual checklist items (Krippendorff's α= 0.06-0.96). The model based on BioBERT performed best overall for recognizing methodology-related items (micro-precision: 0.82, micro-recall: 0.63, micro-F1: 0.71). Combining models using majority vote and label aggregation further improved precision and recall, respectively.
    CONCLUSION: Our annotated corpus, CONSORT-TM, contains more fine-grained information than earlier RCT corpora. Low frequency of some CONSORT items made it difficult to train effective text mining models to recognize them. For the items commonly reported, CONSORT-TM can serve as a testbed for text mining methods that assess RCT transparency, rigor, and reliability, and support methods for peer review and authoring assistance. Minor modifications to the annotation scheme and a larger corpus could facilitate improved text mining models. CONSORT-TM is publicly available at https://github.com/kilicogluh/CONSORT-TM.
    Keywords:  CONSORT; corpus annotation; reporting guidelines; sentence classification; text mining
    DOI:  https://doi.org/10.1016/j.jbi.2021.103717
  9. J Oral Maxillofac Surg. 2021 Feb 02. pii: S0278-2391(21)00099-9. [Epub ahead of print]
      PURPOSE: Randomized controlled trials (RCTs) are the backbone of evidence-based medicine. Despite the widespread acceptance of Consolidated Standards of Reporting Trials (CONSORT), its use for reporting clinical trials in journals remains poor. The purpose of this study was to find out to what extent RCTs related to mandibular third molars have adhered to the CONSORT statement.METHODS: This study was carried out during April 2020 to June 2020. PubMed was used to retrieve RCTs related to mandibular third molars conducted during last 5 years. The search terms used were "mandibular third molar OR lower third molar OR impacted mandibular third molar AND randomized controlled trial." Each article was assessed for adherence to CONSORT statement.
    RESULTS: Eighty unique articles were retrieved. The mean percentage adherence to CONSORT statement noted was 60.26%. Of the 37 CONSORT items, only 4 items showed 100% adherence (2a, 2b, 4a, and 12a). The most underreported items were #10, 12b, 17a, 17b, 18, 19, 23 to 25. Of the 23 journals considered, 6 journals did not recommend CONSORT for reporting RCT in the "Instructions to Authors" guidelines.
    CONCLUSIONS: Within the limits of the study, it is clear that the RCTs related to third molar do not show 100% adherence to CONSORT checklist. The editorial policy, peer reviewers, and researchers should endorse the use of CONSORT checklist for transparent reporting of the RCTs.
    DOI:  https://doi.org/10.1016/j.joms.2021.01.032
  10. J Dent Res. 2021 Mar 03. 22034521998337
      An increasing number of studies on artificial intelligence (AI) are published in the dental and oral sciences. The reporting, but also further aspects of these studies, suffer from a range of limitations. Standards towards reporting, like the recently published Consolidated Standards of Reporting Trials (CONSORT)-AI extension can help to improve studies in this emerging field, and the Journal of Dental Research (JDR) encourages authors, reviewers, and readers to adhere to these standards. Notably, though, a wide range of aspects beyond reporting, located along various steps of the AI lifecycle, should be considered when conceiving, conducting, reporting, or evaluating studies on AI in dentistry.
    Keywords:  clinical studies/trials; computer vision; decision-making; deep learning; personalized medicine; software engineering
    DOI:  https://doi.org/10.1177/0022034521998337
  11. J Biomed Inform. 2021 Feb 05. pii: S1532-0464(21)00037-X. [Epub ahead of print] 103708
      
    DOI:  https://doi.org/10.1016/j.jbi.2021.103708
  12. J Allied Health. 2021 ;50(1): 1
      Scientific publications are an important medium for conveying new developments and important breakthroughs. As shown in the items that appear below, the realm in which periodicals operate also may be subjected to steady bouts of alteration.
  13. Nature. 2021 Mar 05.
      
    Keywords:  Careers; Lab life; Publishing
    DOI:  https://doi.org/10.1038/d41586-021-00593-z
  14. Int J Ther Massage Bodywork. 2021 Mar;14(1): 1-3
      Peer review is a mainstay of scientific publishing and, while peer reviewers and scientists report satisfaction with the process, peer review has not been without criticism. Within this editorial, the peer review process at the IJTMB is defined and explained. Further, seven steps are identified by the editors as a way to improve efficiency of the peer review and publication process. Those seven steps are: 1) Ask authors to submit possible reviewers; 2) Ask reviewers to update profiles; 3) Ask reviewers to "refer a friend"; 4) Thank reviewers regularly; 5) Ask published authors to review for the Journal; 6) Reduce the length of time to accept peer review invitation; and 7) Reduce requested time to complete peer review. We believe these small requests and changes can have a big effect on the quality of reviews and speed in which manuscripts are published. This manuscript will present instructions for completing peer review profiles. Finally, we more formally recognize and thank peer reviewers from 2018-2020.
  15. mBio. 2021 Mar 02. pii: e00117-21. [Epub ahead of print]12(2):
      The peer-reviewed scientific literature is the bedrock of science. However, scientific publishing is undergoing dramatic changes, which include the expansion of open access, an increased number of for-profit publication houses, and ready availability of preprint manuscripts that have not been peer reviewed. In this opinion article, we discuss the inequities and concerns that these changes have wrought.
    Keywords:  for-profit journals; impact factor; open access; preprint servers
    DOI:  https://doi.org/10.1128/mBio.00117-21
  16. Genet Med. 2021 Mar 01.
      From its earliest days, the field of human genetics has had a complex, and at times troubling, connection with racist ideologies. Although the modern field of human genetics and genomics has come a long way from those earlier errors, systemic racism remains ingrained in its institutions and practices. Although a variety of efforts are needed to excise systemic racism, we focus in this commentary on the work that must be done in scientific publishing in genetics and genomics. We propose eight principles that are both scientifically grounded and antiracist that we hope will serve as a foundation for the development of policies by publishers and editorial boards that address the unique needs of the field of genetics and genomics. Publishers and journals must go beyond mere policies, however. Editors and reviewers will need training on these policies and principles, and will benefit from resources like rubrics that can be used for evaluating the adherence of submissions to these guidelines.
    DOI:  https://doi.org/10.1038/s41436-021-01109-w