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The effect of journal guidelines on the reporting of antibody validation.

ABSTRACT: Background:Despite the widespread use of antibodies as a research tool, problems with specificity, lot-to-lot consistency and sensitivity commonly occur and may be important contributing factors to the 'replication crisis' in biomedical research. This makes the validation of antibodies and accurate reporting of this validation in the scientific literature extremely important. Therefore, some journals now require authors to comply with antibody reporting guidelines. Methods:We used a quasi-experimental approach to assess the effectiveness of such journal guidelines in improving antibody reporting in the scientific literature. In a sample of 120 publications, we compared the reporting of antibody validation and identification information in two journals with guidelines (Nature and the Journal of Comparative Neurology) with two journals without guidelines (Science and Neuroscience), before and after the introduction of these guidelines. Results:Our results suggest that the implementation of antibody reporting guidelines might have some influence on the reporting of antibody validation information. The percentage of validated antibodies per article slightly increased from 39% to 57% in journals with guidelines, whereas this percentage decreased from 23% to 14% in journals without guidelines. Furthermore, the reporting of validation information of all primary antibodies increased by 23 percentage points in the journals with guidelines (OR = 2.80, 95% CI = 0.96-INF; adjusted p = 1, one-tailed), compared to a decrease of 13 percentage points in journals without guidelines. Fortunately, the guidelines seem to be more effective in improving the reporting of antibody identification information. The reporting of identification information of all primary antibodies used in a study increased by 58 percentage points (OR = 17.8, 95% CI = 4.8-INF; adjusted p = 0.0003, one-tailed) in journals with guidelines. This percentage also slightly increased in journals without guidelines (by 18 percentage points), suggesting an overall increased awareness of the importance of antibody identifiability. Moreover, this suggests that reporting guidelines mostly have an influence on the reporting of information that is relatively easy to provide. A small increase in the reporting of validation by referencing the scientific literature or the manufacturer's data also indicates this. Conclusion:Combined with the results of previous studies on journal guidelines, our study suggests that the effect of journal antibody guidelines on validation practices by themselves may be limited, since they mostly seem to improve antibody identification instead of actual experimental validation. These guidelines, therefore, may require additional measures to ensure effective implementation. However, due to the explorative nature of our study and our small sample size, we must remain cautious towards other factors that might have played a role in the observed change in antibody reporting behaviour.

SUBMITTER: Hoek JM

PROVIDER: S-EPMC7275675 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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The effect of journal guidelines on the reporting of antibody validation.

Hoek Joyce M JM Hepkema Wytske M WM Halffman Willem W

PeerJ 20200603

<h4>Background</h4>Despite the widespread use of antibodies as a research tool, problems with specificity, lot-to-lot consistency and sensitivity commonly occur and may be important contributing factors to the 'replication crisis' in biomedical research. This makes the validation of antibodies and accurate reporting of this validation in the scientific literature extremely important. Therefore, some journals now require authors to comply with antibody reporting guidelines.<h4>Methods</h4>We used ...[more]

PMID: 32547887

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Project description:BackgroundReporting of health research is often inadequate and incomplete. Complete and transparent reporting is imperative to enable readers to assess the validity of research findings for use in healthcare and policy decision-making. To this end, many guidelines, aimed at improving the quality of health research reports, have been developed for reporting a variety of research types. Despite efforts, many reporting guidelines are underused. In order to increase their uptake, evidence of their effectiveness is important and will provide authors, peer reviewers and editors with an important resource for use and implementation of pertinent guidance. The objective of this study was to assess whether endorsement of reporting guidelines by journals influences the completeness of reporting of health studies.MethodsGuidelines providing a minimum set of items to guide authors in reporting a specific type of research, developed with explicit methodology, and using a consensus process will be identified from an earlier systematic review and from the EQUATOR (Enhancing the QUAlity and Transparency Of health Research) Network's reporting guidelines library. MEDLINE, EMBASE, the Cochrane Methodology Register and Scopus will be searched for evaluations of those reporting guidelines; relevant evaluations from the recently conducted CONSORT systematic review will also be included. Single data extraction with 10% verification of study characteristics, 20% of outcomes and complete verification of aspects of study validity will be carried out. We will include evaluations of reporting guidelines that assess the completeness of reporting: (1) before and after journal endorsement, and/or (2) between endorsing and non-endorsing journals. For a given guideline, analyses will be conducted for individual and the total sum of items. When possible, standard, pooled effects with 99% confidence intervals using random effects models will be calculated.DiscussionEvidence on which guidelines have been evaluated and which are associated with improved completeness of reporting is important for various stakeholders, including editors who consider which guidelines to endorse in their journal editorial policies.

Project description:ObjectiveTo investigate the effect of an additional review based on reporting guidelines such as STROBE and CONSORT on quality of manuscripts.DesignMasked randomised trial. Population Original research manuscripts submitted to the Medicina Clínica journal from May 2008 to April 2009 and considered suitable for publication.InterventionControl groupconventional peer reviews alone. Intervention group: conventional review plus an additional review looking for missing items from reporting guidelines. Outcomes Manuscript quality, assessed with a 5 point Likert scale (primary: overall quality; secondary: average quality of specific items in paper). Main analysis compared groups as allocated, after adjustment for baseline factors (analysis of covariance); sensitivity analysis compared groups as reviewed. Adherence to reviewer suggestions assessed with Likert scale.ResultsOf 126 consecutive papers receiving conventional review, 34 were not suitable for publication. The remaining 92 papers were allocated to receive conventional reviews alone (n=41) or additional reviews (n=51). Four papers assigned to the conventional review group deviated from protocol; they received an additional review based on reporting guidelines. We saw an improvement in manuscript quality in favour of the additional review group (comparison as allocated, 0.25, 95% confidence interval -0.05 to 0.54; as reviewed, 0.33, 0.03 to 0.63). More papers with additional reviews than with conventional reviews alone improved from baseline (22 (43%) v eight (20%), difference 23.6% (3.2% to 44.0%), number needed to treat 4.2 (from 2.3 to 31.2), relative risk 2.21 (1.10 to 4.44)). Authors in the additional review group adhered more to suggestions from conventional reviews than to those from additional reviews (average increase 0.43 Likert points (0.19 to 0.67)).ConclusionsAdditional reviews based on reporting guidelines improve manuscript quality, although the observed effect was smaller than hypothesised and not definitively demonstrated. Authors adhere more to suggestions from conventional reviews than to those from additional reviews, showing difficulties in adhering to high methodological standards at the latest research phases. To boost paper quality and impact, authors should be aware of future requirements of reporting guidelines at the very beginning of their study. Trial registration and protocol Although registries do not include trials of peer review, the protocol design was submitted to sponsored research projects (Instituto de Salud Carlos III, PI081903).

Project description:BackgroundThe reporting of machine learning (ML) prognostic and diagnostic modeling studies is often inadequate, making it difficult to understand and replicate such studies. To address this issue, multiple consensus and expert reporting guidelines for ML studies have been published. However, these guidelines cover different parts of the analytics lifecycle, and individually, none of them provide a complete set of reporting requirements.ObjectiveWe aimed to consolidate the ML reporting guidelines and checklists in the literature to provide reporting items for prognostic and diagnostic ML in in-silico and shadow mode studies.MethodsWe conducted a literature search that identified 192 unique peer-reviewed English articles that provide guidance and checklists for reporting ML studies. The articles were screened by their title and abstract against a set of 9 inclusion and exclusion criteria. Articles that were filtered through had their quality evaluated by 2 raters using a 9-point checklist constructed from guideline development good practices. The average κ was 0.71 across all quality criteria. The resulting 17 high-quality source papers were defined as having a quality score equal to or higher than the median. The reporting items in these 17 articles were consolidated and screened against a set of 6 inclusion and exclusion criteria. The resulting reporting items were sent to an external group of 11 ML experts for review and updated accordingly. The updated checklist was used to assess the reporting in 6 recent modeling papers in JMIR AI. Feedback from the external review and initial validation efforts was used to improve the reporting items.ResultsIn total, 37 reporting items were identified and grouped into 5 categories based on the stage of the ML project: defining the study details, defining and collecting the data, modeling methodology, model evaluation, and explainability. None of the 17 source articles covered all the reporting items. The study details and data description reporting items were the most common in the source literature, with explainability and methodology guidance (ie, data preparation and model training) having the least coverage. For instance, a median of 75% of the data description reporting items appeared in each of the 17 high-quality source guidelines, but only a median of 33% of the data explainability reporting items appeared. The highest-quality source articles tended to have more items on reporting study details. Other categories of reporting items were not related to the source article quality. We converted the reporting items into a checklist to support more complete reporting.ConclusionsOur findings supported the need for a set of consolidated reporting items, given that existing high-quality guidelines and checklists do not individually provide complete coverage. The consolidated set of reporting items is expected to improve the quality and reproducibility of ML modeling studies.

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The effect of journal guidelines on the reporting of antibody validation.

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The effect of journal guidelines on the reporting of antibody validation.

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