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• Human immunodeficiency virus (HIV) drug resistance has implications for antiretroviral treatment strategies and for containing the HIV pandemic because the development of HIV drug resistance leads to the requirement for antiretroviral drugs that may be less effective, less well-tolerated, and more expensive than those used in first-line regimens.  • HIV drug resistance studies are designed to determine which HIV mutations are selected by antiretroviral drugs and, in turn, how these mutations affect antiretroviral drug susceptibility and response to future antiretroviral treatment regimens.  • Such studies collectively form a vital knowledge base essential for monitoring global HIV drug resistance trends, interpreting HIV genotypic tests, and updating HIV treatment guidelines.  • Although HIV drug resistance data are collected in many studies, such data are often not publicly shared, prompting the need to recommend best practices to encourage and standardize HIV drug resistance data sharing.  • In contrast to other viruses, sharing HIV sequences from phylogenetic studies of transmission dynamics requires additional precautions as HIV transmission is criminalized in many countries and regions.  • Our recommendations are designed to ensure that the data that contribute to HIV drug resistance knowledge will be available without undue hardship to those publishing HIV drug resistance studies and without risk to people living with HIV.

Social media and new tools for engagement offer democratic platforms for enhancing constructive scientific criticism which had previously been limited. Constructive criticism can now be massive, timely and open. However, new options have also enhanced obsessive criticism. Obsessive criticism tends to focus on one or a handful of individuals and their work, often includes ad hominem aspects, and the critics often lack field-specific skills and technical expertise. Typical behaviours include: repetitive and persistent comments (including sealioning), lengthy commentaries/tweetorials/responses often longer than the original work, strong degree of moralizing, distortion of the underlying work, argumentum ad populum, calls to suspend/censor/retract the work or the author, guilt-by-association, reputational tarnishing, large gains in followers specifically through attacks, finding and positing sensitive personal information, anonymity or pseudonymity, social media campaigning, and unusual ratio of criticism to pursuit of one's research agenda. These behaviours may last months or years. Prevention and treatment options may include awareness, identifying and working around aggravating factors, placing limits on the volume by editors, constructive pairing of commissioned editorials, incorporation of some hot debates from unregulated locations such as social media or PubPeer to the pages of scientific journals, preserving decency and focusing on evidence and arguments and avoiding personal statements, or (in some cases) ignoring. We need more research on the role of social media and obsessive criticism on an evolving cancel culture, the social media credibility, the use/misuse of anonymity and pseudonymity, and whether potential interventions from universities may improve or further weaponize scientific criticism.

BackgroundIn this paper, we argue for Gender as a Sociocultural Variable (GASV) as a complement to Sex as a Biological Variable (SABV). Sex (biology) and gender (sociocultural behaviors and attitudes) interact to influence health and disease processes across the lifespan-which is currently playing out in the COVID-19 pandemic. This study develops a gender assessment tool-the Stanford Gender-Related Variables for Health Research-for use in clinical and population research, including large-scale health surveys involving diverse Western populations. While analyzing sex as a biological variable is widely mandated, gender as a sociocultural variable is not, largely because the field lacks quantitative tools for analyzing the influence of gender on health outcomes.MethodsWe conducted a comprehensive review of English-language measures of gender from 1975 to 2015 to identify variables across three domains: gender norms, gender-related traits, and gender relations. This yielded 11 variables tested with 44 items in three US cross-sectional survey populations: two internet-based (N = 2051; N = 2135) and a patient-research registry (N = 489), conducted between May 2017 and January 2018.ResultsExploratory and confirmatory factor analyses reduced 11 constructs to 7 gender-related variables: caregiver strain, work strain, independence, risk-taking, emotional intelligence, social support, and discrimination. Regression analyses, adjusted for age, ethnicity, income, education, sex assigned at birth, and self-reported gender identity, identified associations between these gender-related variables and self-rated general health, physical and mental health, and health-risk behaviors.ConclusionOur new instrument represents an important step toward developing more comprehensive and precise survey-based measures of gender in relation to health. Our questionnaire is designed to shed light on how specific gender-related behaviors and attitudes contribute to health and disease processes, irrespective of-or in addition to-biological sex and self-reported gender identity. Use of these gender-related variables in experimental studies, such as clinical trials, may also help us understand if gender factors play an important role as treatment-effect modifiers and would thus need to be further considered in treatment decision-making.

Recent, high-profile, large-scale, preregistered failures to replicate uncover that many highly-regarded experiments are "false positives"; that is, statistically significant results of underlying null effects. Large surveys of research reveal that statistical power is often low and inadequate. When the research record includes selective reporting, publication bias and/or questionable research practices, conventional meta-analyses are also likely to be falsely positive. At the core of research credibility lies the relation of statistical power to the rate of false positives. This study finds that high (>50%-60%) median retrospective power (MRP) is associated with credible meta-analysis and large-scale, preregistered, multi-lab "successful" replications; that is, with replications that corroborate the effect in question. When median retrospective power is low (<50%), positive meta-analysis findings should be interpreted with great caution or discounted altogether.

We introduce and evaluate three tests for publication selection bias based on excess statistical significance (ESS). The proposed tests incorporate heterogeneity explicitly in the formulas for expected and ESS. We calculate the expected proportion of statistically significant findings in the absence of selective reporting or publication bias based on each study's SE and meta-analysis estimates of the mean and variance of the true-effect distribution. A simple proportion of statistical significance test (PSST) compares the expected to the observed proportion of statistically significant findings. Alternatively, we propose a direct test of excess statistical significance (TESS). We also combine these two tests of excess statistical significance (TESSPSST). Simulations show that these ESS tests often outperform the conventional Egger test for publication selection bias and the three-parameter selection model (3PSM).

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

We present a consensus-based checklist to improve and document the transparency of research reports in social and behavioural research. An accompanying online application allows users to complete the form and generate a report that they can submit with their manuscript or post to a public repository.

Publication interests should not limit access to public data

Selective cutoff reporting in primary diagnostic accuracy studies with continuous or ordinal data may result in biased estimates when meta-analyzing studies. Collecting individual participant data (IPD) and estimating accuracy across all relevant cutoffs for all studies can overcome such bias but is labour intensive. We meta-analyzed the diagnostic accuracy of the Patient Health Questionnaire-9 (PHQ-9) depression screening tool. We compared results for two statistical methods proposed by Steinhauser and by Jones to account for missing cutoffs, with results from a series of bivariate random effects models (BRM) estimated separately at each cutoff. We applied the methods to a dataset that contained information only on cutoffs that were reported in the primary publications and to the full IPD dataset that contained information for all cutoffs for every study. For each method, we estimated pooled sensitivity and specificity and associated 95% confidence intervals for each cutoff and area under the curve (AUC). The full IPD dataset comprised data from 45 studies, 15 020 subjects, and 1972 cases of major depression and included information on every possible cutoff. When using data available in publications, using statistical approaches outperformed the BRM applied to the same data. AUC was similar for all approaches when using the full IPD dataset, though pooled estimates were slightly different. Overall, using statistical methods to fill in missing cutoff data recovered the receiver operating characteristic (ROC) curve from the "full IPD dataset" well when using only the "published" subset. All methods performed similarly when applied to the full IPD dataset. [This article was written with the DEPRESsion Screening Data (DEPRESSD) Collaboration.]

Effective data management is crucial for scientific integrity and reproducibility, a cornerstone of scientific progress. Well-organized and well-documented data enable validation and building on results. Data management encompasses activities including organization, documentation, storage, sharing, and preservation. Robust data management establishes credibility, fostering trust within the scientific community and benefiting researchers' careers. In experimental biomedicine, comprehensive data management is vital due to the typically intricate protocols, extensive metadata, and large datasets. Low-throughput experiments, in particular, require careful management to address variations and errors in protocols and raw data quality. Transparent and accountable research practices rely on accurate documentation of procedures, data collection, and analysis methods. Proper data management ensures long-term preservation and accessibility of valuable datasets. Well-managed data can be revisited, contributing to cumulative knowledge and potential new discoveries. Publicly funded research has an added responsibility for transparency, resource allocation, and avoiding redundancy. Meeting funding agency expectations increasingly requires rigorous methodologies, adherence to standards, comprehensive documentation, and widespread sharing of data, code, and other auxiliary resources. This review provides critical insights into raw and processed data, metadata, high-throughput versus low-throughput datasets, a common language for documentation, experimental and reporting guidelines, efficient data management systems, sharing practices, and relevant repositories. We systematically present available resources and optimal practices for wide use by experimental biomedical researchers. [ABSTRACT FROM AUTHOR]

Publication selection bias undermines the systematic accumulation of evidence. To assess the extent of this problem, we survey over 68,000 meta-analyses containing over 700,000 effect size estimates from medicine (67,386/597,699), environmental sciences (199/12,707), psychology (605/23,563), and economics (327/91,421). Our results indicate that meta-analyses in economics are the most severely contaminated by publication selection bias, closely followed by meta-analyses in environmental sciences and psychology, whereas meta-analyses in medicine are contaminated the least. After adjusting for publication selection bias, the median probability of the presence of an effect decreased from 99.9% to 29.7% in economics, from 98.9% to 55.7% in psychology, from 99.8% to 70.7% in environmental sciences, and from 38.0% to 29.7% in medicine. The median absolute effect sizes (in terms of standardized mean differences) decreased from d = 0.20 to d = 0.07 in economics, from d = 0.37 to d = 0.26 in psychology, from d = 0.62 to d = 0.43 in environmental sciences, and from d = 0.24 to d = 0.13 in medicine. [ABSTRACT FROM AUTHOR]

We propose to change the default P-value threshold for statistical significance for claims of new discoveries from 0.05 to 0.005.