Publishing in the Open Access and Open Science era.

Our research activities would be better served if they were communicated in a manner that is openly accessible to the public and all researchers. The research we share is often limited to representative data included in research papers-science would be much more efficient if all reproducible research data were shared alongside detailed methods and protocols, in the paradigm called Open Science. On the other hand, one primary function of research journals is to select manuscripts of good quality, verify the authenticity of the data and its impact, and deliver to the appropriate audience for critical evaluation and verification. In the current paradigm, where publication in a subset of journals is intimately linked to research evaluation, a hypercompetitive "market" has emerged where authors compete to access a limited number of top-tier journals, leading to high rejection rates. Competition among publishers and scientific journals for market dominance resulted in an increase in both the number of journals and the cost of publishing and accessing scientific papers. Here we summarize the current problems and potential solutions from the development of AI technology discussed in the seminar at the 46th Annual Meeting of the Molecular Biology Society of Japan.

David versus Goliath: Early career researchers in an unethical publishing system.

The publish-or-perish culture in academia has catalysed the development of an unethical publishing system. This system is characterised by the proliferation of journals and publishers-unaffiliated with learned societies or universities-that maintain extremely large revenues and profit margins diverting funds away from the academic community. Early career researchers (ECRs) are particularly vulnerable to the consequences of this publishing system because of intersecting factors, including pressure to pursue high impact publications, rising publication costs and job insecurity. Moving towards a more ethical system requires that scientists advocate for structural change by making career choices that come with risks, many of which disproportionately impact ECRs. We illuminate major issues facing ECRs in Ecology and Evolution under the current publishing system, and propose a portfolio of actions to promote systemic change that can be implemented by ECRs and established researchers.

Evaluating early intervention in smoldering myeloma clinical trials: a systematic review.

BACKGROUND: Smoldering multiple myeloma (SMM), an asymptomatic precursor of multiple myeloma (MM), carries a variable risk of progression to MM. There is little consensus on the efficacy or optimal timing of treatment in SMM. We systematically reviewed the landscape of all clinical trials in SMM. We compared the efficacy of treatment regimens studied in SMM to results from these regimens when used in newly diagnosed multiple myeloma (NDMM), to determine whether the data suggest deeper responses in SMM versus NDMM. METHODS: All prospective interventional clinical trials for SMM, including published studies, meeting abstracts, and unpublished trials listed on ClinicalTrials.gov up to April 1, 2023, were identified. Trial-related variables were captured, including treatment strategy and efficacy results. Relevant clinical endpoints were defined as overall survival (OS) and quality of life. RESULTS: Among 45 SMM trials identified, 38 (84.4%) assessed active myeloma drugs, while 7 (15.6%) studied bone-modifying agents alone. Of 18 randomized trials in SMM, only one (5.6%) had a primary endpoint of OS; the most common primary endpoint was progression-free survival (n = 7, 38.9%). Among 32 SMM trials with available results, 9 (28.1%) met their prespecified primary endpoint, of which 5 were single-arm studies. Six treatment regimens were tested in both SMM and NDMM; 5 regimens yielded a lower rate of very good partial response rate or better (≥VGPR) in SMM compared to the corresponding NDMM trial (32% vs 63%, 43% vs 53%, 40% vs 63%, 86% vs 89%, 92% vs 95%, and 94% vs 87%, respectively). CONCLUSION: In this systematic review of all prospective interventional clinical trials in SMM, we found significant variability in trial design, including randomization status, primary endpoints, and types of intervention used. Despite the statistical limitations, comparison of treatment regimens revealed no compelling evidence that the treatment is more effective when introduced early in SMM compared to NDMM.

Renewing an author-centric publication process.

Immunology & Cell Biology celebrated its 100-year birthday as a journal with an editorial workshop focused on how we can improve the author experience. In our renewed editorial policies, we articulate our editorial focus on the quality of the scientific question and the robustness of the conclusions, including a new "scoop protection" policy to live our values. The journal is dedicated to maintaining its relationship with reviewers, enabling rapid quality peer review, but is also opening new lines of submission with expedited cross-platform assessment of reviews and incorporation into the Review Commons submission pipeline. In 2024 we will expand our social media promotion of articles and build on the career development resource of Immunology Futures. Here we lay out the ethos, numbers and rationale behind ICB's renewed author-centric publication policies for 2024.

OncoPubMiner: a platform for mining oncology publications.

Updated and expert-quality knowledge bases are fundamental to biomedical research. A knowledge base established with human participation and subject to multiple inspections is needed to support clinical decision making, especially in the growing field of precision oncology. The number of original publications in this field has risen dramatically with the advances in technology and the evolution of in-depth research. Consequently, the issue of how to gather and mine these articles accurately and efficiently now requires close consideration. In this study, we present OncoPubMiner (https://oncopubminer.chosenmedinfo.com), a free and powerful system that combines text mining, data structure customisation, publication search with online reading and project-centred and team-based data collection to form a one-stop 'keyword in-knowledge out' oncology publication mining platform. The platform was constructed by integrating all open-access abstracts from PubMed and full-text articles from PubMed Central, and it is updated daily. OncoPubMiner makes obtaining precision oncology knowledge from scientific articles straightforward and will assist researchers in efficiently developing structured knowledge base systems and bring us closer to achieving precision oncology goals.

Protecting and promoting editorial independence.

We argue that editorial independence, through robust practice of publication ethics and research integrity, promotes good science and prevents bad science. We elucidate the concept of research integrity, and then discuss the dimensions of editorial independence. Best practice guidelines exist, but compliance with these guidelines varies. Therefore, we make recommendations for protecting and strengthening editorial independence.

Unpublished trials of alprazolam XR and their influence on its apparent efficacy for panic disorder.

OBJECTIVE: To test for publication bias with alprazolam, the most widely prescribed benzodiazepine, by comparing its efficacy for panic disorder using trial results from (1) the published literature and (2) the US Food and Drug Administration (FDA). METHODS: From FDA reviews, we included data from all phase 2/3 efficacy trials of alprazolam extended-release (Xanax XR) for the treatment of panic disorder. A search for matching publications was performed using PubMed and Google Scholar. Publication bias was examined by comparing: (1) overall trial results (positive or not) according to the FDA v. corresponding publications; (2) effect size (Hedges's g) based on FDA data v. published data. RESULTS: The FDA review showed that five trials were conducted, only one of which (20%) was positive. Of the four not-positive trials, two were published conveying a positive outcome; the other two were not published. Thus, according to the published literature, three trials were conducted and all (100%) were positive. Alprazolam's effect size calculated using FDA data was 0.33 (CI95% 0.07-0.60) v. 0.47 (CI95% 0.30-0.65) using published data, an increase of 0.14, or 42%. CONCLUSIONS: Publication bias substantially inflates the apparent efficacy of alprazolam XR.

Delayed publication of clinical trials in gynecologic oncology.

OBJECTIVES: Delays in clinical trial publication can hinder timely implementation of evidence-based practices. We sought to determine publication rates and time to publication for clinical trials addressing gynecologic malignancies. METHODS: All clinical trials addressing gynecologic cancers in the ClinicalTrials.gov registry with a primary completion date between 1/1/2018 and 1/1/2020 were identified. The primary outcome was publication rate. All included studies had been completed for at least 3 years. Secondary outcomes were time to publication and associations between publication rate and sponsor, cancer type, and the number and location of primary study sites. RESULTS: Of the 290 trials included, 161 (55.5%) had a peer-reviewed publication for the primary outcome within at least 3 years after completion. Of these, 123 had positive results (76.4%) and 38 were negative (23.6%). The average duration from primary completion to manuscript publication was 23.6 months (SD 13.9; median 21.4, IQR 15.1-32.4). Only 73 had results posted on the ClinicalTrials.gov registry (25.2%). Studies with positive findings had a significantly faster time to publication than those with negative results (22.0 mo vs 29.0 mo, p = 0.009). There was no significant difference between publication rate and funding source, cancer type, or location and number of primary sites. CONCLUSIONS: Timely publication of clinical trials addressing gynecologic cancers remains an issue. Studies with positive findings were published faster than those with negative results, but the average publication time was still almost 2 years from trial completion. Further efforts should be made to identify and address barriers to clinical trial publication.

The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes.

The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the 'Code of Nomenclature of Prokaryotes Described from DNA Sequence Data' ('SeqCode'), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.

Valid publication of names of two domains and seven kingdoms of prokaryotes.

The International Code of Nomenclature of Prokaryotes (ICNP) now includes the categories domain and kingdom. For the purpose of the valid publication of their names under the ICNP, we consider here the two known domains, 'Bacteria' and 'Archaea', as well as a number of taxa suitable for the rank of kingdom, based on previous phylogenetic and taxonomic studies. It is proposed to subdivide the domain Bacteria into the kingdoms Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati. This arrangement reflects contemporary phylogenetic hypotheses as well as previous taxonomic proposals based on cell wall structure, including 'diderms' vs. 'monoderms', Gracilicutes vs. Firmicutes, 'Negibacteria' vs. 'Unibacteria', 'Hydrobacteria' vs. 'Terrabacteria', and 'Hydrobacterida' vs. 'Terrabacterida'. The domain Archaea is proposed to include the kingdoms Methanobacteriati, Nanobdellati and Thermoproteati, reflecting the previous division into 'Euryarchaeota', 'DPANN superphylum' and 'TACK superphylum'.

Nonparametric worst-case bounds for publication bias on the summary receiver operating characteristic curve.

The summary receiver operating characteristic (SROC) curve has been recommended as one important meta-analytical summary to represent the accuracy of a diagnostic test in the presence of heterogeneous cutoff values. However, selective publication of diagnostic studies for meta-analysis can induce publication bias (PB) on the estimate of the SROC curve. Several sensitivity analysis methods have been developed to quantify PB on the SROC curve, and all these methods utilize parametric selection functions to model the selective publication mechanism. The main contribution of this article is to propose a new sensitivity analysis approach that derives the worst-case bounds for the SROC curve by adopting nonparametric selection functions under minimal assumptions. The estimation procedures of the worst-case bounds use the Monte Carlo method to approximate the bias on the SROC curves along with the corresponding area under the curves, and then the maximum and minimum values of PB under a range of marginal selection probabilities are optimized by nonlinear programming. We apply the proposed method to real-world meta-analyses to show that the worst-case bounds of the SROC curves can provide useful insights for discussing the robustness of meta-analytical findings on diagnostic test accuracy.

Sensitivity analysis for publication bias in meta-analysis of sparse data based on exact likelihood.

Meta-analysis is a powerful tool to synthesize findings from multiple studies. The normal-normal random-effects model is widely used to account for between-study heterogeneity. However, meta-analyses of sparse data, which may arise when the event rate is low for binary or count outcomes, pose a challenge to the normal-normal random-effects model in the accuracy and stability in inference since the normal approximation in the within-study model may not be good. To reduce bias arising from data sparsity, the generalized linear mixed model can be used by replacing the approximate normal within-study model with an exact model. Publication bias is one of the most serious threats in meta-analysis. Several quantitative sensitivity analysis methods for evaluating the potential impacts of selective publication are available for the normal-normal random-effects model. We propose a sensitivity analysis method by extending the likelihood-based sensitivity analysis with the $t$-statistic selection function of Copas to several generalized linear mixed-effects models. Through applications of our proposed method to several real-world meta-analyses and simulation studies, the proposed method was proven to outperform the likelihood-based sensitivity analysis based on the normal-normal model. The proposed method would give useful guidance to address publication bias in the meta-analysis of sparse data.

Dissemination and outcome reporting bias in clinical malaria intervention trials: a cross-sectional analysis.

BACKGROUND: Dissemination and outcome reporting biases are a significant problem in clinical research, with far-reaching implications for both scientific understanding and clinical decision-making. This study investigates the prevalence of dissemination- and outcome reporting biases in registered interventional malaria research. METHODS: All malaria interventional trials registered on ClinicalTrials.gov from 2010 to 2020 were identified. Subsequently, publications that matched the registration were searched. The primary outcome measures were the percentage of registered studies that resulted in subsequent publication of study results, the concordance between registered outcomes, and reported outcomes. Secondary outcomes were compliance with WHO standards for timely publication (issued in 2017) of summary study results in the respective trial registry (within 12 months of study completion) or peer-reviewed publication (within 24 months of study completion) was evaluated. RESULTS: A total of 579 trials were identified on ClinicalTrials.gov, of which 544 met the inclusion criteria. Notably, almost 36.6% of these trials (199/544) were registered retrospectively, with 129 (23.7%) registered after the first patient enrolment and 70 (12.9%) following study completion. Publications were identified for 351 out of 544 registered trials (64.5%), involving 1,526,081 study participants. Conversely, publications were not found for 193 of the 544 registrations (35.5%), which aimed to enrol 417,922 study participants. Among these 544 registrations, 444 (81.6%) did not meet the WHO standard to post summary results within 12 months of primary study completion (the last visit of the last subject for collection of data on the primary outcome), while 386 out of 544 registrations (71.0%) failed to publish their results in a peer-reviewed journal within 24 months of primary study completion. Discrepancies were noted in the reported primary outcomes compared to the registered primary outcomes in 47.6% (222/466) of the published trials, and an even higher discordance rate of 73.2% (341/466 publications) for secondary outcomes. CONCLUSIONS: Non-dissemination remains a significant issue in interventional malaria research, with most trials failing to meet WHO standards for timely dissemination of summary results and peer-reviewed journal publications. Additionally, outcome reporting bias is highly prevalent across malaria publications. To address these challenges, it is crucial to implement strategies that enhance the timely reporting of research findings and reduce both non-dissemination and outcome reporting bias.

A Review of Meta-Analyses in Plastic Surgery: Need for Adequate Assessment of Publication Bias.

INTRODUCTION: Publication bias describes a phenomenon in which significant positive results have a higher likelihood of being published compared to negative or nonsignificant results. Publication bias can confound the estimated therapeutic effect in meta-analyses and needs to be adequately assessed in the surgical literature. METHODS: A review of meta-analyses published in five plastic surgery journals from 2002 to 2022 was conducted. The inclusion criteria for meta-analyses were factors that demonstrated an obligation to assess publication bias, such as interventions with comparable treatment groups and enough power for statistical analysis. Acknowledgment of publication bias risk, quality of bias assessment, methods used in assessment, and individual article factors were analyzed. RESULTS: 318 unique meta-analyses were identified in literature search, and after full-text reviews, 143 met the inclusion criteria for obligation to assess publication bias. 64% of eligible meta-analyses acknowledged the confounding potential of publication bias, and only 46% conducted a formal assessment. Of those who conducted an assessment, 49% used subjective inspection of funnel plots alone, while 47% used any statistical testing in analysis. Overall, only 9/143 (6.3%) assessed publication bias and attempted to correct for its effect. Journals with a higher average impact factor were associated with mention and assessment of publication bias, but more recent publication year and higher number of primary articles analyzed were not. CONCLUSIONS: This review identified low rates of proper publication bias assessment in meta-analyses published in five major plastic surgery journals. Assessment of publication bias using objective statistical testing is necessary to ensure quality literature within surgical disciplines.

Reporting of core outcomes in gastric cancer surgery trials over the past 25 years (systematic review).

BACKGROUND: Gastric cancer, a leading cause of cancer-related mortality worldwide, has seen limited improvement in survival over the past 3 decades. Surgical resection is the cornerstone of curative management but the optimal approach remains unclear. Decision-making is hindered by inconsistent outcome reporting limiting data synthesis between trials. International consensus between healthcare professionals and patients has formed a core outcome set to be reported as a minimum. We appraised outcomes previously reported. METHODS: Evidence Based Medicine Reviews, MEDLINE, EMBASE and CINAHL were searched for randomised controlled trials (RCTs) and systematic reviews of RCTs during years 1995-2021. We searched trial registries for protocols of ongoing and future trials. RESULTS: Ninety-nine articles from 64 studies and 69 trial protocols were included. No study reported all core outcomes: average reported per trial was 4 (interquartile range: 2). 'Serious' adverse events were reported by 98%, completeness of tumour removal by 85% and surgery-related death by 74%. Outcomes important to patients were reported least: quality of life (22%) and nutritional effects (15%). Defining outcomes and time frames used was variable. CONCLUSIONS: Critically important outcomes are poorly reported in the literature and the status has not improved in future trials. Further work is required to improve uptake.

Questionnaire survey for the International Journal of Legal Medicine on the occassion of the 26th triennal meeting of the International Academy of Legal Medicine.

A questionnaire was prepared in advance of the 26th triennial conference of the International Academy of Legal Medicine (IALM) and sent to 474 email addresses included in the IALM mailing list. The questionnaire addressed three current challenges faced by the International Journal of Legal Medicine (IJLM): the publication of guidelines and validation studies in the field of legal medicine, the publication ethics of case reports, and the recruitment of new reviewers for the IJLM. The response rate was 20%. The survey results highlight the need for international guidelines in various areas of legal medicine. Some desired guidelines already exist. To provide visibility and knowledge of the existing national guidelines, the IJLM has launched a Topical Collection on Quality Assurance in Legal Medicine. This collection aims to inform readers about country-specific characteristics of legal medicine structures and the existing national guidelines.Around 80% of the participants stated that there are legal or ethical requirements for the publication of forensic case reports or case series. Various options for obtaining consent for publication are discussed. Eighty-six of the 97 participants indicated their willingness to review manuscripts for the IJLM. It is emphasized that the contributions of reviewers should be duly recognized and valued.

Reporting of interventional clinical trial results in an academic center: a survey of completed studies.

BACKGROUND: The dissemination of clinical trial results is an important scientific and ethical endeavour. This survey of completed interventional studies in a French academic center describes their reporting status. METHODS: We explored all interventional studies sponsored by Rennes University Hospital identified on the French Open Science Monitor which tracks trials registered on EUCTR or clinicaltrials.gov, and provides an automatic assessment of the reporting of results. For each study, we ascertained the actual reporting of results using systematic searches on the hospital internal database, bibliographic databases (Google Scholar, PubMed), and by contacting all principal investigators (PIs). We describe several features (including total budget and numbers of trial participants) of the studies that did not report any results. RESULTS: The French Open Science Monitor identified 93 interventional studies, among which 10 (11%) reported results. In contrast, our survey identified 36 studies (39%) reporting primary analysis results and an additional 18 (19%) reporting results for secondary analyses (without results for their primary analysis). The overall budget for studies that did not report any results was estimated to be €5,051,253 for a total of 6,735 trial participants. The most frequent reasons for the absence of results reported by PIs were lack of time for 18 (42%), and logistic difficulties (e.g. delay in obtaining results or another blocking factor) for 12 (28%). An association was found between non-publication and negative results (adjusted Odds Ratio = 4.70, 95% Confidence Interval [1.67;14.11]). CONCLUSIONS: Even allowing for the fact that automatic searches underestimate the number of studies with published results, the level of reporting was disappointingly low. This amounts to a waste of trial participants' implication and money. Corrective actions are needed. TRIAL REGISTRATION: https://osf.io/q5hcs.

Exploring trial publication and research waste in COVID-19 randomised trials of hydroxychloroquine, corticosteroids, and vitamin D: a meta-epidemiological cohort study.

BACKGROUND: The global research response to the COVID-19 pandemic was impressive, but also led to an infodemic and considerable research waste. Registered, but unpublished trials added to this noise. We aimed to determine the proportion of registered randomised trials of common COVID-19 treatments that were published and to describe the characteristics of these trials to examine the association between trial characteristics, publication status and research waste. METHODS: This meta-epidemiological cohort study used a sample of randomised trials of corticosteroids, hydroxychloroquine or vitamin D as treatments for COVID-19, registered between 1 November 2019 and 31 December 2021 and available via the WHO ICTRP portal. We searched for the trials' published results up to 20 October 2022. We extracted the trial characteristics, analysing with descriptive statistics. We performed univariate logistic regression to examine the association between trials' characteristics and publication status, followed by multiple logistic regression using significant characteristics to assess the association between trial characteristics and publication status. RESULTS: We identified 357 eligible trials on ICTRP. Of these, 107 (30%) had published or made their results available publicly by 20 October 2022, while 250 (70%) had not been published or shared their results publicly. Multiple logistic regression analysis showed that a larger target sample size was a significant positive predictor of publication with target sample sizes above 300 almost tripling the odds of publication (aOR: 2.75, 95% CI: 1.35 to 5.62). CONCLUSIONS: Less than one third of registered trials made their results public and our findings identified that many trialists had not updated their trial registry entry with the trial status, results or both. Failure to share trial results publicly is a disservice to patients, clinicians and policy makers and adds to research waste.

Effects of mixed nuts as part of a Brazilian Cardioprotective diet on LDL-cholesterol in adult patients after myocardial infarction: a multicenter randomized controlled clinical trial.

BACKGROUND: Nuts consumption is related to cardioprotective effects on primary cardiovascular prevention, but studies conducted in secondary prevention are small, scarce and controversial. The objective of this trial was to evaluate the effects of a regional and sustainable cardioprotective diet added or not with an affordable mixed nuts on cardiometabolic features in patients with previous myocardial infarction. METHODS: DICA-NUTS study is a national, multi-center, and superiority-parallel randomized clinical trial. Males and females over 40 years old diagnosed with previous myocardial infarction in the last 2 to 6 months were included. Patients were allocated into two groups: the Brazilian Cardioprotective diet (DICA Br) supplemented with 30 g/day of mixed nuts (10 g of peanuts; 10 g of cashew; 10 g of Brazil nuts) (intervention group, n = 193); or only DICA Br prescription (control group, n = 195). The primary outcome was low-density lipoprotein cholesterol means (in mg/dL) after 16 weeks. Secondary outcomes were other lipid biomarkers, glycemic and anthropometric data and diet quality. RESULTS: After adjustment for baseline values, participating study site, time since myocardial infarction and statin treatment regimen (high potency, moderate and low potency/no statins), no significant difference was found between the groups in low-density lipoprotein cholesterol concentrations (intervention-control difference: 3.48 mg/dL [-3.45 to 10.41], P = 0.32). Both groups improved their overall diet quality at the end of the study without differences between them after 16 weeks (intervention-control difference: 1.05 (-0.9 to 2.99); P = 0.29). Other lipids, glycemic profile and anthropometrics were also not different between study groups at the end of the study. CONCLUSION: Adding 30 g/day of mixed nuts to the DICA Br for 16 weeks did not change lipid, glycemic and anthropometric features in the post-myocardial infarction setting. TRIAL REGISTRATION: This study is registered on ClinicalTrials.gov website under number NCT03728127 and its World Health Organization Universal Trial Number (WHO-UTN) is U1111-1259-8105.

Publication Bias and Selective Outcome Reporting in Randomized Controlled Trials Related to Rehabilitation: A Literature Review.

OBJECTIVE: To investigate the rate of registered protocols published as research papers as a measure of publication bias, and the concordance rates of the primary outcomes between research protocol and published papers as a measure of selective outcome reporting bias in randomized controlled trials (RCTs) related to rehabilitation. DATA SOURCES: Protocols related to RCTs were extracted from electronic databases, the University Hospital Medical Information Network (UMIN), International Standard Research Clinical Trial Number (ISRCTN), ClinicalTrials.gov, and MEDLINE. Published papers were retrieved from MEDLINE. STUDY SELECTION: The inclusion criteria were as follows: (1) initial registration (UMIN, ISRCTN, ClinicalTrials.gov) within the designated period; (2) published as a paper from a research protocol in MEDLINE (PubMed); and (3) written in English or Japanese. The search period was from January 1, 2013, to December 31, 2020. DATA EXTRACTION: The outcome of this study was set as the rate of published papers that were consistent with the extracted research protocol and the concordance rate between the primary outcomes in published papers and in protocols. The concordance rate of the primary outcomes was evaluated by checking whether the description in the research protocol matched that in the paper's abstract and main text. DATA SYNTHESIS: Out of the 5597 research protocols registered, only 727 were published (13.0%). The concordance rates of the primary outcomes were 48.7% and 72.6% in the abstract and main text, respectively. CONCLUSIONS: This study revealed major discrepancies between the number of research protocols and published papers, and difference of description regarding the primary outcomes in published papers which were already defined in the research protocols.