The perceived feasibility of methods to reduce publication bias

Discontinuation and nonpublication analysis of chronic pain randomized controlled trials

Introduction

The primary objective of this cross-sectional analysis is to evaluate rates of discontinuation and nonpublication of Randomized controlled trials (RCTs) of therapeutic interventions to treat chronic pain.

Methods

Using ClinicalTrials.gov, a sample was obtained which included clinical trials pertaining to chronic pain. Trials were analyzed for publication status and completion status of each trial. If information was unavailable on the trial registry database, or could not be allocated through a systematic search, the corresponding trialist was contacted and data points were gathered.

Results

In our final analysis of the 408 RCTs, we found that 281 (68.9%) were published in a peer-reviewed journal and 127 (31.1%) were unpublished trials. Of 112 discontinued trials, 59 (52.7%) reached publication. In addition, 221 of 296 completed trials (74.7%) were published, and 75 (25.3%) remained unpublished after trial completion. The most common listed reason for trial discontinuation was administrative recommendations (41 of 71 trials [57.7%]), while not receiving an email reply to our standardized email from the corresponding trialist was the most common result for trial nonpublication (49 of 88 trials [55.7%]). Clinical trials funded by nonindustry sponsors were more likely to reach publication than industry-funded clinical trials (unadjusted odds ratio 1.86 [95% CI, 1.18-2.95]; adjusted odds ratio 3.01 [95% CI, 1.76-5.14]).

Conclusion

The rate of discontinuation of RCTs involving patients with chronic pain is concerning. Chronic pain affects many patients; thus, the importance of having quality data from clinical trials cannot be overstated. Our study indicates that chronic pain RCTs are frequently discontinued and their findings often go unpublished - all of which could provide crucial information to providers and patients regarding the treatment of chronic pain. We offer suggestions to enhance chronic pain RCT completion, thereby reducing the waste of resources in chronic pain research.

Recent Updates to CSE Recommendations for Promoting Integrity in Scientific Journal Publications: 7 Ways to Integrate Diversity, Equity, and Inclusion Into Scholarly Publishing

The Council of Science Editors' (CSE) Recommendations for Promoting Integrity in Scientific Journal Publications was first published in 2006, and the full document was updated in 2009 and again in 2012. In 2018, the CSE Editorial Policy Committee (EPC) began making updates on a rolling basis as new sections were added or existing sections updated to reflect new information or best practices. This updated method for amending the document allows for more rapid dissemination of its contents so that recommendations can be quickly put into practice in journal operations. In this column, the reader is advised of a recent update that provides guidance on the importance of advancing best practices in scholarly publishing. Content in this update, while condensed, was taken largely verbatim from the CSE's Recommendations for Promoting Integrity in Scientific Journal Publications. However, readers are encouraged to visit the full set of Recommendations for Promoting Integrity in Scientific Journal Publications at https://www.councilscienceeditors.org/resource-library/editorial-policies/publication-ethics/.

Institutionalizing Open Science in Africa: Limitations and Prospects

The advancement of scientific research and raising the next-generation scientists in Africa depend largely on science access. The COVID-19 pandemic has caused discussions around open science (OS) to reemerge globally, especially in resource-poor settings like Africa, where the practice of OS is low. The authors highlighted the elements, benefits, and existing initiatives of OS in Africa. More importantly, the article critically appraised the challenges, opportunities, and future considerations of OS in Africa. Addressing challenges of funding and leadership at different levels of educational, research, and government parastatals may be pivotal in charting a new course for OS in Africa. This review serves as an advocacy strategy and an informative guide to policymaking and institutionalization of OS in Africa.

Autonomous design of new chemical reactions using a variational autoencoder

Artificial intelligence based chemistry models are a promising method of exploring chemical reaction design spaces. However, training datasets based on experimental synthesis are typically reported only for the optimal synthesis reactions. This leads to an inherited bias in the model predictions. Therefore, robust datasets that span the entirety of the solution space are necessary to remove inherited bias and permit complete training of the space. In this study, an artificial intelligence model based on a Variational AutoEncoder (VAE) has been developed and investigated to synthetically generate continuous datasets. The approach involves sampling the latent space to generate new chemical reactions. This developed technique is demonstrated by generating over 7,000,000 new reactions from a training dataset containing only 7,000 reactions. The generated reactions include molecular species that are larger and more diverse than the training set.

Association of Accuracy, Conclusions, and Reporting Completeness With Acceptance by Radiology Conferences and Journals

BACKGROUND

Preferential publication of studies with positive findings can lead to overestimation of diagnostic test accuracy (i.e. publication bias). Understanding the contribution of the editorial process to publication bias could inform interventions to optimize the evidence guiding clinical decisions.

PURPOSE/HYPOTHESIS

To evaluate whether accuracy estimates, abstract conclusion positivity, and completeness of abstract reporting are associated with acceptance to radiology conferences and journals.

STUDY TYPE

Meta-research.

POPULATION

Abstracts submitted to radiology conferences (European Society of Gastrointestinal and Abdominal Radiology (ESGAR) and International Society for Magnetic Resonance in Medicine (ISMRM)) from 2008 to 2018 and manuscripts submitted to radiology journals (Radiology, Journal of Magnetic Resonance Imaging [JMRI]) from 2017 to 2018. Primary clinical studies evaluating sensitivity and specificity of a diagnostic imaging test in humans with available editorial decisions were included.

ASSESSMENT

Primary variables (Youden's index [YI > 0.8 vs. <0.8], abstract conclusion positivity [positive vs. neutral/negative], number of reported items on the Standards for Reporting of Diagnostic Accuracy Studies [STARD] for Abstract guideline) and confounding variables (prospective vs. retrospective/unreported, sample size, study duration, interobserver agreement assessment, subspecialty, modality) were extracted.

STATISTICAL TESTS

Multivariable logistic regression to obtain adjusted odds ratio (OR) as a measure of the association between the primary variables and acceptance by radiology conferences and journals; 95% confidence intervals (CIs) and P-values were obtained; the threshold for statistical significance was P < 0.05.

RESULTS

A total of 1000 conference abstracts (500 ESGAR and 500 ISMRM) and 1000 journal manuscripts (505 Radiology and 495 JMRI) were included. Conference abstract acceptance was not significantly associated with YI (adjusted OR = 0.97 for YI > 0.8; CI = 0.70-1.35), conclusion positivity (OR = 1.21 for positive conclusions; CI = 0.75-1.90) or STARD for Abstracts adherence (OR = 0.96 per unit increase in reported items; CI = 0.82-1.18). Manuscripts with positive abstract conclusions were less likely to be accepted by radiology journals (OR = 0.45; CI = 0.24-0.86), while YI (OR = 0.85; CI = 0.56-1.29) and STARD for Abstracts adherence (OR = 1.06; CI = 0.87-1.30) showed no significant association. Positive conclusions were present in 86.7% of submitted conference abstracts and 90.2% of journal manuscripts.

DATA CONCLUSION

Diagnostic test accuracy studies with positive findings were not preferentially accepted by the evaluated radiology conferences or journals.

EVIDENCE LEVEL

3 TECHNICAL EFFICACY: Stage 2.

Musculoskeletal pain and sedentary behaviour in occupational and non-occupational settings: a systematic review with meta-analysis

BACKGROUND

Sedentary behaviour (SB; time spent sitting) is associated with musculoskeletal pain (MSP) conditions; however, no prior systematic review has examined these associations according to SB domains. We synthesised evidence on occupational and non-occupational SB and MSP conditions.

METHODS

Guided by a PRISMA protocol, eight databases (MEDLINE, CINAHL, PsycINFO, Web of Science, Scopus, Cochrane Library, SPORTDiscus, and AMED) and three grey literature sources (Google Scholar, WorldChat, and Trove) were searched (January 1, 2000, to March 17, 2021) for original quantitative studies of adults ≥ 18 years. Clinical-condition studies were excluded. Studies' risk of bias was assessed using the QualSyst checklist. For meta-analyses, random effect inverse-variance pooled effect size was estimated; otherwise, best-evidence synthesis was used for narrative review.

RESULTS

Of 178 potentially-eligible studies, 79 were included [24 general population; 55 occupational (incuding15 experimental/intervention)]; 56 studies were of high quality, with scores > 0.75. Data for 26 were meta-synthesised. For cross-sectional studies of non-occupational SB, meta-analysis showed full-day SB to be associated with low back pain [LBP - OR = 1.19(1.03 - 1.38)]. Narrative synthesis found full-day SB associations with knee pain, arthritis, and general MSP, but the evidence was insufficient on associations with neck/shoulder pain, hip pain, and upper extremities pain. Evidence of prospective associations of full-day SB with MSP conditions was insufficient. Also, there was insufficient evidence on both cross-sectional and prospective associations between leisure-time SB and MSP conditions. For occupational SB, cross-sectional studies meta-analysed indicated associations of self-reported workplace sitting with LBP [OR = 1.47(1.12 - 1.92)] and neck/shoulder pain [OR = 1.73(1.46 - 2.03)], but not with extremities pain [OR = 1.17(0.65 - 2.11)]. Best-evidence synthesis identified inconsistent findings on cross-sectional association and a probable negative prospective association of device-measured workplace sitting with LBP-intensity in tradespeople. There was cross-sectional evidence on the association of computer time with neck/shoulder pain, but insufficient evidence for LBP and general MSP. Experimental/intervention evidence indicated reduced LBP, neck/shoulder pain, and general MSP with reducing workplace sitting.

CONCLUSIONS

We found cross-sectional associations of occupational and non-occupational SB with MSP conditions, with occupational SB associations being occupation dependent, however, reverse causality bias cannot be ruled out. While prospective evidence was inconclusive, reducing workplace sitting was associated with reduced MSP conditions. Future studies should emphasise prospective analyses and examining potential interactions with chronic diseases.

PROTOCOL REGISTRATION

PROSPERO ID # CRD42020166412 (Amended to limit the scope).

A Systematic Review of Interventions for Multilingual Preschoolers With Speech and Language Difficulties

Purpose There is a shortage of information on evidence-based interventions for supporting young multilingual children. The purpose of this review was to identify interventions that have been evaluated with preschool-age multilingual children with a speech and/or language disorder or who are at risk of poor speech, language, literacy, and/or educational outcomes. Method This review considered speech, language, and early literacy interventions evaluated with preschool-age multilingual children with a speech and/or language disorder or who have been identified as being at risk of language difficulties (PROSPERO ID: 165892). The following electronic databases were searched: EBSCO (CINAHL Plus, ERIC, PsycINFO, Medline, Education) and Linguistics, Language, and Behavior Abstracts. Data were extracted describing article, participant, methodological, and intervention variables, and effect sizes. The Council for Exceptional Children's (CEC) standards for evidence-based practice were used to examine the quality of studies. Results Fifty-six relevant studies were identified in 52 articles and these studies described 4,551 participants who had speech sound disorder (six articles), developmental language disorder (11 articles), or were considered to be at risk (36 articles). The interventions targeted speech production (seven studies), language (45 studies), and early literacy (11 studies) skills. Most studies reported positive effects. Only 15 studies met all quality indicators specified by the CEC (2014) and these described 18 interventions targeting language and literacy skills. The only intervention with sufficient evidence to be considered an evidence-based practice was Nuestros Niños [Our Children] for children's early literacy and phonological awareness skills. Conclusions A number of high-quality studies exist that describe speech, language and/or literacy interventions for preschool-age multilingual children with a speech and/or language disorder, or who have been identified as being at risk of language difficulties. However, there remains limited evidence for specific interventions as to their ability to inform evidence-based practices. Supplemental Material https://doi.org/10.23641/asha.16632649.

Objectivity for the research worker

In the last decade, many problematic cases of scientific conduct have been diagnosed; some of which involve outright fraud (e.g., Stapel, 2012) others are more subtle (e.g., supposed evidence of extrasensory perception; Bem, 2011). These and similar problems can be interpreted as caused by lack of scientific objectivity. The current philosophical theories of objectivity do not provide scientists with conceptualizations that can be effectively put into practice in remedying these issues. We propose a novel way of thinking about objectivity for individual scientists; a negative and dynamic approach.We provide a philosophical conceptualization of objectivity that is informed by empirical research. In particular, it is our intention to take the first steps in providing an empirically and methodologically informed inventory of factors that impair the scientific practice. The inventory will be compiled into a negative conceptualization (i.e., what is not objective), which could in principle be used by individual scientists to assess (deviations from) objectivity of scientific practice. We propose a preliminary outline of a usable and testable instrument for indicating the objectivity of scientific practice.

The Impact of Choosing Wisely Interventions on Low-Value Medical Services: A Systematic Review

Policy Points Dissemination of Choosing Wisely guidelines alone is unlikely to reduce the use of low-value health services. Interventions by health systems to implement Choosing Wisely guidelines can reduce the use of low-value services. Multicomponent interventions targeting clinicians are currently the most effective types of interventions.

CONTEXT

Choosing Wisely aims to reduce the use of unnecessary, low-value medical services through development of recommendations related to service utilization. Despite the creation and dissemination of these recommendations, evidence shows low-value services are still prevalent. This paper synthesizes literature on interventions designed to reduce medical care identified as low value by Choosing Wisely and evaluates which intervention characteristics are most effective.

METHODS

We searched peer-reviewed and gray literature from the inception of Choosing Wisely in 2012 through June 2019 to identify interventions in the United States motivated by or using Choosing Wisely recommendations. We also included studies measuring the impact of Choosing Wisely on its own, without interventions. We developed a coding guide and established coding agreement. We coded all included articles for types of services targeted, components of each intervention, results of the intervention, study type, and, where applicable, study quality. We measured the success rate of interventions, using chi-squared tests or Wald tests to compare across interventions.

FINDINGS

We reviewed 131 articles. Eighty-eight percent of interventions focused on clinicians only; 48% included multiple components. Compared with dissemination of Choosing Wisely recommendations only, active interventions were more likely to generate intended results (65% vs 13%, p < 0.001) and, among those, interventions with multiple components were more successful than those with one component (77% vs 47%, p = 0.002). The type of services targeted did not matter for success. Clinician-based interventions were more effective than consumer-based, though there is a dearth of studies on consumer-based interventions. Only 17% of studies included a control arm.

CONCLUSIONS

Interventions built on the Choosing Wisely recommendations can be effective at changing practice patterns to reduce the use of low-value care. Interventions are more effective when targeting clinicians and using more than one component. There is a need for high-quality studies that include active controls.

Full Abstract to Published Manuscript: Evaluation of the Scientific Impact of the American Society of Breast Surgeons Conference

Background

The scientific rigor of the abstracts presented at the American Society of Breast Surgeons (ASBrS) annual meeting has not been recently evaluated. In this study, we sought to determine the rate at which abstracts presented at the 2017 and 2018 ASBrS meetings were published in peer-reviewed journals, and compared the rates with breast abstracts presented at the 2018 Society of Surgical Oncology (SSO) meeting.

Methods

Abstracts from the 2017 and 2018 ASBrS and 2018 SSO conferences were searched in PubMed for published manuscripts using the abstract title and/or first or last author.

Results

In 2017, 21.6% of the 268 abstracts presented at the ASBrS conference resulted in full publication, compared with 36.6% of the 273 abstracts presented at the 2018 ASBrS conference, resulting in a significant difference in the publication rate (p < 0.001). Of the 158 abstracts published from the 2017 and 2018 meetings, 75 (47.8%) were published in Annals of Surgical Oncology (ASO). There was no correlation between impact factor and time to publication. Oral presentations and quick shots were more likely to be published than poster presentations, and oral presentations were more likely to be published in higher-impact journals. The 2018 SSO meetings resulted in 54 of 111 (48.6%) breast abstracts leading to full publication.

Conclusion

Approximately 29.2% of the abstracts presented at the ASBrS 2017 and 2018 conferences resulted in a published manuscript. A higher publication rate in higher impact journals for oral presentations indicates that the abstract review process properly stratifies the research.

Supplementary Information

The online version contains supplementary material available at 10.1245/s10434-021-10493-1.

How to Conduct Responsible Research: A Guide for Graduate Students

Researchers must conduct research responsibly for it to have an impact and to safeguard trust in science. Essential responsibilities of researchers include using rigorous, reproducible research methods, reporting findings in a trustworthy manner, and giving the researchers who contributed appropriate authorship credit. This "how-to" guide covers strategies and practices for doing reproducible research and being a responsible author. The article also covers how to utilize decision-making strategies when uncertain about the best way to proceed in a challenging situation. The advice focuses especially on graduate students, but is appropriate for undergraduates and experienced researchers. It begins with an overview of responsible conduct of research, research misconduct, and ethical behavior in the scientific workplace. The takeaway message is that responsible conduct of research requires a thoughtful approach to doing research in order to ensure trustworthy results and conclusions, and that researchers receive fair credit. © 2021 Wiley Periodicals LLC.

A Systematic Review and Meta-Analysis of the Association between Personality and Cognitive Failures / Complaints

This systematic review examined the associations of personality traits with cognitive failures and cognitive complaints across the adult lifespan. We first present three conceptual models (cognitive abilities, mental processes, and reporting bias) that could explain why personality is related to such behaviors. We then conducted five separate meta-analyses with 10-17 cross-sectional samples (N = 7,642 - 10,564) that were identified through a systematic literature search following the MOOSE guidelines. Higher neuroticism (r = .39, 95% CI [0.32, 0.45]) and lower conscientiousness (r = -.36, 95% CI [-.42, -.29]) were related to more cognitive failures and complaints. Lower scores on the remaining traits were also associated with more cognitive failures and complaints, yet to a weaker extent (extraversion: r = -.14, 95% CI [-.20, -.08]; openness: r = -.07, 95% CI [-.11, -.03]; agreeableness: r = -.13, 95% CI [-.21, -.05]). With the current empirical evidence, it is not possible to tell which of the three conceptual models explains how much of the associations. For neuroticism, there is more support for the mental processes than the reporting bias model, but more research is needed to fully test mechanistic models. We provide several suggestions for future research to address existing limitations of the literature on personality and cognitive failures and complaints.

A Systematic Review and Meta-Analysis of Hospitalised Current Smokers and COVID-19

SARS-CoV-2 is a new coronavirus that has caused a worldwide pandemic. It produces severe acute respiratory disease (COVID-19), which is fatal in many cases, characterised by the cytokine release syndrome (CRS). According to the World Health Organization, those who smoke are likely to be more vulnerable to infection. Here, in order to clarify the epidemiologic relationship between smoking and COVID-19, we present a systematic literature review until 28th April 2020 and a meta-analysis. We included 18 recent COVID-19 clinical and epidemiological studies based on smoking patient status from 720 initial studies in China, the USA, and Italy. The percentage of hospitalised current smokers was 7.7% (95% CI: 6.9-8.4) in China, 2.3% (95% CI: 1.7-2.9) in the USA and 7.6% (95% CI: 4.2-11.0) in Italy. These percentages were compared to the smoking prevalence of each country and statistically significant differences were found in them all (p < 0.0001). By means of the meta-analysis, we offer epidemiological evidence showing that smokers were statistically less likely to be hospitalised (OR = 0.18, 95% CI: 0.14-0.23, p < 0.01). In conclusion, the analysis of data from 18 studies shows a much lower percentage of hospitalised current smokers than expected. As more studies become available, this trend should be checked to obtain conclusive results and to explore, where appropriate, the underlying mechanism of the severe progression and adverse outcomes of COVID-19.

Association between complement 4 copy number variation and systemic lupus erythematosus: a meta-analysis

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by multiple genetic mutations. Complement 4 (C4) copy number variation (CNV) is a target-of-interest located on chromosome 6. C4 encodes for either of the two C4 paralogs, C4A or C4B, and low C4 levels have been associated with SLE activity. In this study, we conducted a meta-analysis to comprehensively understand the role of C4 CNV in SLE. Three databases (PubMed, Embase, and Web of Science) were searched for relevant studies. Two investigators independently extracted and evaluated data from eligible studies. Associations between C4 CNV and SLE were estimated by odds ratios (OR) and 95% confidence intervals (95% CI). Further analysis was conducted using the STATA 12.0 software. A total of eight case-control studies were included in the analysis with 4107 SLE patients and 5889 healthy controls. Six studies used TaqMan real-time PCR to genotype C4 CNV, with 1 study used paralog ratio test and other one used multiplex ligation-dependent probe amplification (MLPA). Lower total C4 CNV and C4A CNV were associated with SLE in the overall analysis (pooled OR: 1.55, 95% CI: 1.23-1.95; pooled OR: 1.86, 95% CI: 1.51-2.29). The subgroup analysis found that total C4 CNV and lower C4A CNV were significantly associated with SLE in Caucasians (pooled OR: 1.84, 95% CI: 1.60-2.12; pooled OR: 2.23, 95% CI:1.92-2.59). However, the association was not detected in East Asians. Lastly, SLE was not associated with C4B CNV, long C4 CNV, or short C4 CNV. The meta-analysis confirmed that lower total C4 CNV and lower C4A CNV are associated with SLE in certain populations. Future studies should consider other ethnic groups to further investigate the relationship between the C4 gene and SLE.

Potential publication bias in chiropractic and spinal manipulation research listed on clinicaltrials.gov

INTRODUCTION

Clinical trial registries are used to help improve transparency in trial reporting. Our study aimed to identify potential publication bias in chiropractic and spinal manipulation research by assessing data drawn from published studies listed in clinincaltrials.gov.

METHODS

We searched the clinicaltrials.gov registry database for completed trials tagged with the key indexing terms chiropractic or spinal manipulation. We assessed if the trial registry had been updated with data, then searched for publications corresponding to the registered trials. Finally, the frequency of positive or negative results was determined from published studies.

RESULTS

For the term 'chiropractic', 63% of studies supported the intervention and 52% supported the intervention for the term 'spinal manipulation'.

DISCUSSION

Publication bias in chiropractic and spinal manipulation research listed in clinicaltrials.gov appears to occur. Further work may help understand why this happens and what may be done to mitigate this moving forward.

Attitudes towards animal study registries and their characteristics: An online survey of three cohorts of animal researchers

OBJECTIVES

Prospective registration of animal studies has been suggested as a new measure to increase value and reduce waste in biomedical research. We sought to further explore and quantify animal researchers' attitudes and preferences regarding animal study registries (ASRs).

DESIGN

Cross-sectional online survey.

SETTING AND PARTICIPANTS

We conducted a survey with three different samples representing animal researchers: i) corresponding authors from journals with high Eigenfactor, ii) a random Pubmed sample and iii) members of the CAMARADES network.

MAIN OUTCOME MEASURES

Perceived level of importance of different aspects of publication bias, the effect of ASRs on different aspects of research as well as the importance of different research types for being registered.

RESULTS

The survey yielded responses from 413 animal researchers (response rate 7%). The respondents indicated, that some aspects of ASRs can increase administrative burden but could be outweighed by other aspects decreasing this burden. Animal researchers found it more important to register studies that involved animal species with higher levels of cognitive capabilities. The time frame for making registry entries publicly available revealed a strong heterogeneity among respondents, with the largest proportion voting for "access only after consent by the principal investigator" and the second largest proportion voting for "access immediately after registration".

CONCLUSIONS

The fact that the more senior and experienced animal researchers participating in this survey clearly indicated the practical importance of publication bias and the importance of ASRs underscores the problem awareness across animal researchers and the willingness to actively engage in study registration if effective safeguards for the potential weaknesses of ASRs are put into place. To overcome the first-mover dilemma international consensus statements on how to deal with prospective registration of animal studies might be necessary for all relevant stakeholder groups including animal researchers, academic institutions, private companies, funders, regulatory agencies, and journals.

Bacterial antibiotic resistance development and mutagenesis following exposure to subminimal inhibitory concentrations of fluoroquinolones in vitro: a systematic literature review protocol

INTRODUCTION

Antibiotic resistance (AR) is among the most pressing global health challenges. Fluoroquinolones are a clinically important group of antibiotics that have wide applicability in both humans and animals. While many drivers of AR are known, the impact of medicine quality on AR remains largely unknown. The aim of this review is to systematically evaluate the evidence of the impact of in vitro subinhibitory antibiotic exposure, a major tenet of substandard antibiotics, on the development of AR and mutagenesis, using fluoroquinolones as a case study.

METHODS AND ANALYSIS

EMBASE, Web of Science and PubMed will be systematically searched for primary experimental in vitro studies, from earliest available dates within each database (1947, 1965 and 1966, respectively) through 2018, related to subinhibitory fluoroquinolone exposure and AR. A specifically developed non-weighted tool will be used to critically assess the evidence. Subgroup analyses will be performed for different variables and outcomes.

ETHICS AND DISSEMINATION

Ethical approval is not required as no primary data are to be collected. The completed systematic review will be disseminated through conference meeting presentations and a peer-reviewed publication.

Anthropogenic biases in chemical reaction data hinder exploratory inorganic synthesis

Most chemical experiments are planned by human scientists and therefore are subject to a variety of human cognitive biases¹, heuristics² and social influences³. These anthropogenic chemical reaction data are widely used to train machine-learning models⁴ that are used to predict organic⁵ and inorganic^6,7 syntheses. However, it is known that societal biases are encoded in datasets and are perpetuated in machine-learning models⁸. Here we identify as-yet-unacknowledged anthropogenic biases in both the reagent choices and reaction conditions of chemical reaction datasets using a combination of data mining and experiments. We find that the amine choices in the reported crystal structures of hydrothermal synthesis of amine-templated metal oxides⁹ follow a power-law distribution in which 17% of amine reactants occur in 79% of reported compounds, consistent with distributions in social influence models^10-12. An analysis of unpublished historical laboratory notebook records shows similarly biased distributions of reaction condition choices. By performing 548 randomly generated experiments, we demonstrate that the popularity of reactants or the choices of reaction conditions are uncorrelated to the success of the reaction. We show that randomly generated experiments better illustrate the range of parameter choices that are compatible with crystal formation. Machine-learning models that we train on a smaller randomized reaction dataset outperform models trained on larger human-selected reaction datasets, demonstrating the importance of identifying and addressing anthropogenic biases in scientific data.

Data Dissemination: Shortening the Long Tail of Traumatic Brain Injury Dark Data

Translation of traumatic brain injury (TBI) research findings from bench to bedside involves aligning multi-species data across diverse data types including imaging and molecular biomarkers, histopathology, behavior, and functional outcomes. In this review we argue that TBI translation should be acknowledged for what it is: a problem of big data that can be addressed using modern data science approaches. We review the history of the term big data, tracing its origins in Internet technology as data that are "big" according to the "4Vs" of volume, velocity, variety, veracity and discuss how the term has transitioned into the mainstream of biomedical research. We argue that the problem of TBI translation fundamentally centers around data variety and that solutions to this problem can be found in modern machine learning and other cutting-edge analytical approaches. Throughout our discussion we highlight the need to pull data from diverse sources including unpublished data ("dark data") and "long-tail data" (small, specialty TBI datasets undergirding the published literature). We review a few early examples of published articles in both the pre-clinical and clinical TBI research literature to demonstrate how data reuse can drive new discoveries leading into translational therapies. Making TBI data resources more Findable, Accessible, Interoperable, and Reusable (FAIR) through better data stewardship has great potential to accelerate discovery and translation for the silent epidemic of TBI.

Open laboratory notebooks: good for science, good for society, good for scientists

The fundamental goal of the growing open science movement is to increase the efficiency of the global scientific community and accelerate progress and discoveries for the common good. Central to this principle is the rapid disclosure of research outputs in open-access peer-reviewed journals and on pre-print servers. The next bold step in this direction is open laboratory notebooks, where research scientists share their research - including detailed protocols, negative and positive results - online and in near-real-time to synergize with their peers. Here, we highlight the benefits of open lab notebooks to science, society and scientists, and discuss the challenges that this nascent movement is facing. We also present the implementation and progress of our own initiative at openlabnotebooks.org, with more than 20 active contributors after one year of operation.

Open laboratory notebooks: good for science, good for society, good for scientists

The fundamental goal of the growing open science movement is to increase the efficiency of the global scientific community and accelerate progress and discoveries for the common good. Central to this principle is the rapid disclosure of research outputs in open-access peer-reviewed journals and on pre-print servers. The next bold step in this direction is open laboratory notebooks, where research scientists share their research — including detailed protocols, negative and positive results — online and in near-real-time to synergize with their peers. Here, we highlight the benefits of open lab notebooks to science, society and scientists, and discuss the challenges that this nascent movement is facing. We also present the implementation and progress of our own initiative at openlabnotebooks.org, with more than 20 active contributors after one year of operation.

Effectiveness of online learning on health researcher capacity to appropriately integrate sex, gender, or both in grant proposals

BACKGROUND

To describe the effectiveness of online learning to augment academic capacity to consider sex and gender in the conduct of basic science, clinical research, and population health studies.

METHOD

The analysis compares pre- and post-test scores from 1441 individuals who completed the Canadian Institutes of Health Research Institute of Gender and Health's interactive e-learning modules between February 2016 and May 2017. The tests measured knowledge, self-efficacy, and self-reported intent to change behavior for three competencies: (1) the ability to appropriately define and distinguish between sex-related versus gender-related variables, (2) the application of methods for integrating sex and gender, and (3) the critical appraisal of sex and gender integration in the design, methods, and analysis plan of research proposals and publications.

RESULTS

Of the 543 individuals who completed the basic science module, 62% demonstrated improved knowledge, and 86% increased self-efficacy across all competencies. Gains in knowledge and self-efficacy also occurred among 84% and 77% of completers of the human data collection module (n = 463) and among 73% and 82% of those who completed the secondary data analysis module (n = 435). In aggregate, 95% of participants reported an intent to change their behavior with respect to sex and gender in health research.

CONCLUSIONS

Interactive online learning combined with feedback and self-assessment results in improved knowledge and self-efficacy for integrating sex and gender in health research.

Biases Inherent in Studies of Coffee Consumption in Early Pregnancy and the Risks of Subsequent Events

Consumption of coffee by women early in their pregnancy has been viewed as potentially increasing the risk of miscarriage, low birth weight, and childhood leukemias. Many of these reports of epidemiologic studies have not acknowledged the potential biases inherent in studying the relationship between early-pregnancy-coffee consumption and subsequent events. I discuss five of these biases, recall bias, misclassification, residual confounding, reverse causation, and publication bias. Each might account for claims that attribute adversities to early-pregnancy-coffee consumption. To what extent these biases can be avoided remains to be determined. As a minimum, these biases need to be acknowledged wherever they might account for what is reported.

Publication of Randomized Clinical Trials in Pediatric Research: A Follow-up Study

IMPORTANCE

Nonpublication of research results in considerable research waste and compromises medical evidence and the safety of interventions in child health.

OBJECTIVE

To replicate, compare, and contrast the findings of a study conducted 15 years ago to determine the impact of ethical, editorial, and legislative mandates to register and publish findings.

DESIGN, SETTING, AND PARTICIPANTS

In this cohort study, abstracts accepted to the Pediatric Academic Societies (PAS) meetings from May 2008 to May 2011 were screened in duplicate to identify phase 3 randomized clinical trials enrolling pediatric populations. Subsequent publication was ascertained through a search of electronic databases in 2017. Study internal validity was measured using the Cochrane Risk of Bias Tool, the Jadad scale, and allocation concealment, and key variables (eg, trial design and study stage) were extracted. Associations between variables and publication status, time to publication, and publication bias were examined.

MAIN OUTCOMES AND MEASURES

Publication rate, trial registration rate, study quality, and risk of bias.

RESULTS

A total of 177 787 abstracts were indexed in the PAS database. Of these, 3132 were clinical trials, and 129 met eligibility criteria. Of these, 93 (72.1%; 95% CI, 53.8%-79.1%) were published. Compared with the previous analysis, the current analysis showed that fewer studies remained unpublished (183 of 447 [40.9%] vs 36 of 129 [27.9%], respectively; odds ratio [OR], 0.56; 95% CI, 0.36-0.86; P = .008). Fifty-one of 129 abstracts (39.5%) were never registered. Abstracts with larger sample sizes (OR, 1.92; 95% CI, 1.15-3.18; P = .01) and those registered in ClinicalTrials.gov (OR, 13.54; 95% CI, 4.78-38.46; P < .001) were more likely to be published. There were no differences in quality measures, risk of bias, or preference for positive results (OR, 1.60; 95% CI, 0.58-4.38; P = .34) between published and unpublished studies. Mean (SE) time to publication following study presentation was 26.48 (1.97) months and did not differ between studies with significant and nonsignificant findings (25.61 vs 26.86 months; P = .93). Asymmetric distribution in the funnel plot (Egger regression, -2.77; P = .04) suggests reduced but ongoing publication bias among published studies. Overall, we observed a reduction in publication bias and in preference for positive findings and an increase in study size and publication rates over time.

CONCLUSIONS AND RELEVANCE

These results suggest a promising trend toward a reduction in publication bias and nonpublication rates over time and positive impacts of trial registration. Further efforts are needed to ensure the entirety of evidence can be accessed when assessing treatment effectiveness.