Opinion: Is science really facing a reproducibility crisis, and do we need it to?

Proteomics: An In-Depth Review on Recent Technical Advances and Their Applications in Biomedicine

Proteins hold pivotal importance since many diseases manifest changes in protein activity. Proteomics techniques provide a comprehensive exploration of protein structure, abundance, and function in biological samples, enabling the holistic characterization of overall changes in organisms. Nowadays, the breadth of emerging methodologies in proteomics is unprecedentedly vast, with constant optimization of technologies in sample processing, data collection, data analysis, and its scope of application is steadily transitioning from the bench to the clinic. Here, we offer an insightful review of the technical developments in proteomics and its applications in biomedicine over the past 5 years. We focus on its profound contributions in profiling disease spectra, discovering new biomarkers, identifying promising drug targets, deciphering alterations in protein conformation, and unearthing protein-protein interactions. Moreover, we summarize the cutting-edge technologies and potential breakthroughs in the proteomics pipeline and provide the principal challenges in proteomics. Based on these, we aspire to broaden the applicability of proteomics and inspire researchers to enhance our understanding of complex biological systems by utilizing such techniques.

Public engagement with research reproducibility

Public engagement with reproducibility is crucial for fostering trust in science. This Community Page outlines, through the example of baking Christmas tree meringues, how scientists can effectively engage and educate the public about the importance of reproducibility in research.

A systematic review of human odometry

Human odometry refers to an individual's ability to travel between locations without eyesight and without designating a conscious effort toward spatially updating themselves as they travel through the environment. A systematic review on human odometry was completed for the purpose of establishing the state-of-the-art of the topic, and based on this information, develop meaningful hypotheses using Strong Inference. The following databases were searched up to February 16, 2023, and accessed through University of Nebraska at Omaha proxied databases: IEEEXplore, PsycArticles, PsycInfo, PubMed Central, SCOPUS, and Web of Science. Of the 7,060 articles reviewed, 23 met our inclusion criteria and were accumulated for their contents and quality. Methodologies, limitations, strengths, and future solutions based on those 23 articles are discussed. In summary, young healthy adults are the typical population examined, and distance perception can be manipulated with distance or gait type. Odometry can be studied using simple measurement tools, participants are often given 3-4 attempts to correctly perceive an average distance of 14.3 m, and the average article is of moderate quality with a mean score of 6.13. Many literature gaps, variability in methodology, and insufficient detail, can be amended by the addition of slightly more detailed manuscripts in future publications.

Housing and Husbandry Factors Affecting Zebrafish (Danio rerio) Novel Tank Test Responses: A Global Multi-Laboratory Study

The reproducibility crisis in bioscience, characterized by inconsistent study results, impedes our understanding of biological processes and global collaborative studies offer a unique solution. This study is the first global collaboration using the zebrafish (Danio rerio) novel tank test, a behavioral assay for anxiety-like responses. We analyzed data from 20 laboratories worldwide, focusing on housing conditions and experimental setups. Our study included 488 adult zebrafish, tested for 5 min, focusing on a variety of variables. Key findings show females exhibit more anxiety-like behavior than males, underscoring sex as a critical variable. Housing conditions, including higher stocking densities and specific feed types, influenced anxiety levels. Optimal conditions (5 fish/L) and nutritionally rich feeds (e.g., rotifers), mitigated anxiety-like behaviors. Environmental stressors, like noise and transportation, significantly impacted behavior. We recommend standardizing protocols to account for sex differences, optimal stocking densities, nutritionally rich feeds, and minimizing stressors to improve zebrafish behavioral study reliability.

Spider's Silk as a Potential Source of Antibiotics: An Integrative Review

Spiders produce webs, which are still a largely unexplored source of antibacterial compounds, although the reports of its application in the medical field. Therefore, this study aims to present an integrative review of the antibacterial activity of spider webs. The research was conducted using Google Scholar, Scielo, Web of Science, PubMed, ScienceDirect, Medline EBSCO, LILACS, and Embase. The inclusion criteria were original articles written in English that studied the antibiotic properties of the web or isolated compounds tested. The studies were compared according to the spider species studied, the type of web, treatment of the sample, type of antimicrobial test, and the results obtained. Nine hundred and seventy-three publications were found, and after applying the inclusion and exclusion criteria, sixteen articles were selected. Bacterial inhibition was found in seven studies against various species of bacteria such as Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Salmonella Typhi, Bacillus megaterium, Listeria monocytogenes, Acinetobacter baumannii, Streptococcus pneumoniae, Pasteurella multocida, and Bacillus subtilis. Additionally, there was no apparent relationship between the proximity of the spider species evaluated in the studies and the presence or absence of activity. Methodological problems detected may affected the reproducibility and reliability of the results in some studies, such as the lack of description of the web or microorganism strain, as well as the absence of adequate controls and treatments to sterilize the sample. Spider webs can be a valuable source of antibiotics; however, more studies are needed to confirm the real activity of the web or components involved.

Decatastrophizing research irreproducibility

The reported inability to replicate research findings from the published literature precipitated extensive efforts to identify and correct perceived deficiencies in the execution and reporting of biomedical research. Despite these efforts, quantification of the magnitude of irreproducible research or the effectiveness of associated remediation initiatives, across diverse biomedical disciplines, has made little progress over the last decade. The idea that science is self-correcting has been further challenged in recent years by the proliferation of unverified or fraudulent scientific content generated by predatory journals, paper mills, pre-print server postings, and the inappropriate use of artificial intelligence technologies. The degree to which the field of pharmacology has been negatively impacted by these evolving pressures is unknown. Regardless of these ambiguities, pharmacology societies and their associated journals have championed best practices to enhance the experimental rigor and reporting of pharmacological research. The value of transparent and independent validation of raw data generation and its analysis in basic and clinical research is exemplified by the discovery, development, and approval of Highly Effective Modulator Therapy (HEMT) for Cystic Fibrosis (CF) patients. This provides a didactic counterpoint to concerns regarding the current state of biomedical research. Key features of this important therapeutic advance include objective construction of basic and translational research hypotheses, associated experimental designs, and validation of experimental effect sizes with quantitative alignment to meaningful clinical endpoints with input from the FDA, which enhanced scientific rigor and transparency with real world deliverables for patients in need.

Estimating the replicability of highly cited clinical research (2004-2018)

INTRODUCTION

Previous studies about the replicability of clinical research based on the published literature have suggested that highly cited articles are often contradicted or found to have inflated effects. Nevertheless, there are no recent updates of such efforts, and this situation may have changed over time.

METHODS

We searched the Web of Science database for articles studying medical interventions with more than 2000 citations, published between 2004 and 2018 in high-impact medical journals. We then searched for replications of these studies in PubMed using the PICO (Population, Intervention, Comparator and Outcome) framework. Replication success was evaluated by the presence of a statistically significant effect in the same direction and by overlap of the replication's effect size confidence interval (CIs) with that of the original study. Evidence of effect size inflation and potential predictors of replicability were also analyzed.

RESULTS

A total of 89 eligible studies, of which 24 had valid replications (17 meta-analyses and 7 primary studies) were found. Of these, 21 (88%) had effect sizes with overlapping CIs. Of 15 highly cited studies with a statistically significant difference in the primary outcome, 13 (87%) had a significant effect in the replication as well. When both criteria were considered together, the replicability rate in our sample was of 20 out of 24 (83%). There was no evidence of systematic inflation in these highly cited studies, with a mean effect size ratio of 1.03 [95% CI (0.88, 1.21)] between initial and subsequent effects. Due to the small number of contradicted results, our analysis had low statistical power to detect predictors of replicability.

CONCLUSION

Although most studies did not have eligible replications, the replicability rate of highly cited clinical studies in our sample was higher than in previous estimates, with little evidence of systematic effect size inflation. This estimate is based on a very select sample of studies and may not be generalizable to clinical research in general.

Promoting Data Sharing: The Moral Obligations of Public Funding Agencies

Sharing research data has great potential to benefit science and society. However, data sharing is still not common practice. Since public research funding agencies have a particular impact on research and researchers, the question arises: Are public funding agencies morally obligated to promote data sharing? We argue from a research ethics perspective that public funding agencies have several pro tanto obligations requiring them to promote data sharing. However, there are also pro tanto obligations that speak against promoting data sharing in general as well as with regard to particular instruments of such promotion. We examine and weigh these obligations and conclude that all things considered funders ought to promote the sharing of data. Even the instrument of mandatory data sharing policies can be justified under certain conditions.

Reproducibility of arterial spin labeling cerebral blood flow image processing: A report of the ISMRM open science initiative for perfusion imaging (OSIPI) and the ASL MRI challenge

PURPOSE

Arterial spin labeling (ASL) is a widely used contrast-free MRI method for assessing cerebral blood flow (CBF). Despite the generally adopted ASL acquisition guidelines, there is still wide variability in ASL analysis. We explored this variability through the ISMRM-OSIPI ASL-MRI Challenge, aiming to establish best practices for more reproducible ASL analysis.

METHODS

Eight teams analyzed the challenge data, which included a high-resolution T1-weighted anatomical image and 10 pseudo-continuous ASL datasets simulated using a digital reference object to generate ground-truth CBF values in normal and pathological states. We compared the accuracy of CBF quantification from each team's analysis to the ground truth across all voxels and within predefined brain regions. Reproducibility of CBF across analysis pipelines was assessed using the intra-class correlation coefficient (ICC), limits of agreement (LOA), and replicability of generating similar CBF estimates from different processing approaches.

RESULTS

Absolute errors in CBF estimates compared to ground-truth synthetic data ranged from 18.36 to 48.12 mL/100 g/min. Realistic motion incorporated into three datasets produced the largest absolute error and variability between teams, with the least agreement (ICC and LOA) with ground-truth results. Fifty percent of the submissions were replicated, and one produced three times larger CBF errors (46.59 mL/100 g/min) compared to submitted results.

CONCLUSIONS

Variability in CBF measurements, influenced by differences in image processing, especially to compensate for motion, highlights the significance of standardizing ASL analysis workflows. We provide a recommendation for ASL processing based on top-performing approaches as a step toward ASL standardization.

Unveiling the ethical void: Bias in reference citations and its academic ramifications

Citation bias receives scant attention in discussions of ethics. However, inaccurate citation may lead to significant distortions in scientific understanding. Although ethnical and gender citation disparities have been proposed as critical aspects, there are other contributors to citation distortions, like region-based citation bias, that, although less recognized within the scientific community, are equally important. While the foundations of scientific citation include acknowledging pioneers, giving credit to related work, and providing background reading, other more subjective or even questionable criteria are often used when constructing a reference lists. Here, we discuss the potential causes and ethical concerns of citation bias, emphasizing the role of international- or region-based citation bias as one of the most harmful aspects of this ethical breach. We argue that the international scientific community should be aware of this problem and recognize its consequences, which include hindering the accurate dissemination of science, marginalizing underrepresented voices in academia, and impeding scientific progress. We advocate that scientists should compile their reference lists with the same seriousness and integrity they apply to all other aspects of their research.

MAATrica: a measure for assessing consistency and methods in medicinal and nutraceutical chemistry papers

The growing number of scientific papers and document sources underscores the need for methods capable of evaluating the quality of publications. Researchers who are looking for relevant papers for their studies need ways to assess the scientific value of these documents. One approach involves using semantic search engines that can automatically extract important knowledge from the growing body of text. In this study, we introduce a new metric called "MAATrica," which serves as the foundation for an innovative method designed to evaluate research papers. MAATrica offers a new way to analyze and categorize text, focusing on the consistency of research documents in the life sciences, particularly in the fields of medicinal and nutraceutical chemistry. This method utilizes semantic descriptions to cover in silico experiments, as well as in vitro and in vivo essays. Created to aid in evaluation processes like peer review, MAATrica uses toolkits and semantic applications to build the proposed measure, identify scientific entities, and gather information. We have applied MAATrica to roughly 90,000 papers and present our findings here.

Analytical code sharing practices in biomedical research

Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten articles organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability. Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses. In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

A survey of researchers' methods sharing practices and priorities

Missing or inaccessible information about the methods used in scientific research slows the pace of discovery and hampers reproducibility. Yet little is known about how, why, and under what conditions researchers share detailed methods information, or about how such practices vary across social categories like career stage, field, and region. In this exploratory study, we surveyed 997 active researchers about their attitudes and behaviors with respect to methods sharing. The most common approach reported by respondents was private sharing upon request, but a substantial minority (33%) had publicly shared detailed methods information independently of their research findings. The most widely used channels for public sharing were connected to peer-reviewed publications, while the most significant barriers to public sharing were found to be lack of time and lack of awareness about how or where to share. Insofar as respondents were moderately satisfied with their ability to accomplish various goals associated with methods sharing, we conclude that efforts to increase public sharing may wish to focus on enhancing and building awareness of existing solutions-even as future research should seek to understand the needs of methods users and the extent to which they align with prevailing practices of sharing.

Computational reproducibility of Jupyter notebooks from biomedical publications

BACKGROUND

Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows, including for research publications. The reproducibility of computational aspects of research is a key component of scientific reproducibility but has not yet been assessed at scale for Jupyter notebooks associated with biomedical publications.

APPROACH

We address computational reproducibility at 2 levels: (i) using fully automated workflows, we analyzed the computational reproducibility of Jupyter notebooks associated with publications indexed in the biomedical literature repository PubMed Central. We identified such notebooks by mining the article's full text, trying to locate them on GitHub, and attempting to rerun them in an environment as close to the original as possible. We documented reproduction success and exceptions and explored relationships between notebook reproducibility and variables related to the notebooks or publications. (ii) This study represents a reproducibility attempt in and of itself, using essentially the same methodology twice on PubMed Central over the course of 2 years, during which the corpus of Jupyter notebooks from articles indexed in PubMed Central has grown in a highly dynamic fashion.

RESULTS

Out of 27,271 Jupyter notebooks from 2,660 GitHub repositories associated with 3,467 publications, 22,578 notebooks were written in Python, including 15,817 that had their dependencies declared in standard requirement files and that we attempted to rerun automatically. For 10,388 of these, all declared dependencies could be installed successfully, and we reran them to assess reproducibility. Of these, 1,203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones. Running the other notebooks resulted in exceptions.

CONCLUSIONS

We zoom in on common problems and practices, highlight trends, and discuss potential improvements to Jupyter-related workflows associated with biomedical publications.

Early life stress aggravates disease pathogenesis in mice with experimental autoimmune encephalomyelitis: Support for a two-hit hypothesis of multiple sclerosis etiology

Vision problems are one of the earliest diagnosed symptoms of multiple sclerosis (MS). The onset and progression of vision loss and the underlying pathogenesis in MS may be influenced by cumulative psychophysiological stress. Here, we used a two-hit model of stress in female mice to determine if early life stress (ELS, the first hit) influences the response to an immunization that induces experimental autoimmune encephalomyelitis (EAE, the second hit) later in life. We hypothesized that ELS caused by animal transportation from a vendor during early postnatal development represents a co-factor which can exacerbate the clinical severity of EAE. Indeed, adult EAE mice with a history of ELS displayed more severe clinical signs and delayed recovery compared to non-stressed EAE mice. ELS also diminished visual acuity measured by optokinetic responses, as well as locomotion and exploratory behaviours in EAE mice. Notably, ELS accelerated vision loss and caused earlier onset of visual impairments in EAE. Exacerbated functional impairments in stressed EAE mice were highly correlated with circulating corticosterone levels. The findings show that the progression of induced EAE in adulthood can be significantly impacted by adverse early life experiences. These observations emphasize the importance of comprehensive behavioural testing, including non-motor functions, to enhance the translational value of preclinical animal models of MS. Moreover, shipment stress of laboratory animals should be considered a necessary variable in preclinical MS research. The consideration of cumulative lifetime stresses provides a new perspective of MS pathogenesis within a personalized medicine framework.

Antiphospholipid antibodies are enriched post-acute COVID-19 but do not modulate the thrombotic risk

BACKGROUND AND OBJECTIVES

COVID-19-associated coagulopathy, shown to increase the risk for the occurrence of thromboses and microthromboses, displays phenotypic features of the antiphospholipid syndrome (APS), a prototype antibody-mediated autoimmune disease. Several groups have reported elevated levels of criteria and non-criteria antiphospholipid antibodies (aPL), assumed to cause APS, during acute or post-acute COVID-19. However, disease heterogeneity of COVID-19 is accompanied by heterogeneity in molecular signatures, including aberrant cytokine profiles and an increased occurrence of autoantibodies. Moreover, little is known about the association between autoantibodies and the clinical events. Here, we first aim to characterise the antiphospholipid antibody, anti-SARS-CoV-2 antibody, and the cytokine profiles in a diverse collective of COVID-19 patients (disease severity: asymptomatic to intensive care), using vaccinated individuals and influenza patients as comparisons. We then aim to assess whether the presence of aPL in COVID-19 is associated with an increased incidence of thrombotic events in COVID-19.

METHODS AND RESULTS

We conducted anti-SARS-CoV-2 IgG and IgA microELISA and IgG, IgA, and IgM antiphospholipid line immunoassay (LIA) against 10 criteria and non-criteria antigens in 155 plasma samples of 124 individuals, and we measured 16 cytokines and chemokines in 112 plasma samples. We additionally employed clinical and demographic parameters to conduct multivariable regression analyses within multiple paradigms. In line with recent results, we find that IgM autoantibodies against annexin V (AnV), β2-glycoprotein I (β2GPI), and prothrombin (PT) are enriched upon infection with SARS-CoV-2. There was no evidence for seroconversion from IgM to IgG or IgA. PT, β2GPI, and AnV IgM as well as cardiolipin (CL) IgG antiphospholipid levels were significantly elevated in the COVID-19 but not in the influenza or control groups. They were associated predominantly with the strength of the anti-SARS-CoV-2 antibody titres and the major correlate for thromboses was SARS-CoV-2 disease severity.

CONCLUSION

While we have recapitulated previous findings, we conclude that the presence of the aPL, most notably PT, β2GPI, AnV IgM, and CL IgG in COVID-19 are not associated with a higher incidence of thrombotic events.

Transforming health and well-being through publishing computable biomedical knowledge (CBK)

Computable biomedical knowledge artifacts (CBKs) are software programs that transform input data into practical output. CBKs are expected to play a critical role in the future of learning health systems. While there has been rapid growth in the development of CBKs, broad adoption is hampered by limited verification, documentation, and dissemination channels. To address these issues, the Learning Health Systems journal created a track dedicated to publishing CBKs through a peer-review process. Peer review of CBKs should improve reproducibility, reuse, trust, and recognition in biomedical fields, contributing to learning health systems. This special issue introduces the CBK track with four manuscripts reporting a functioning CBK, and another four manuscripts tackling methodological, policy, deployment, and platform issues related to fostering a healthy ecosystem for CBKs. It is our hope that the potential of CBKs exemplified and highlighted by these quality publications will encourage scientists within learning health systems and related biomedical fields to engage with this new form of scientific discourse.

Fifty years of research on questionable research practises in science: quantitative analysis of co-citation patterns

Questionable research practises (QRPs) have been the focus of the scientific community amid greater scrutiny and evidence highlighting issues with replicability across many fields of science. To capture the most impactful publications and the main thematic domains in the literature on QRPs, this study uses a document co-citation analysis. The analysis was conducted on a sample of 341 documents that covered the past 50 years of research in QRPs. Nine major thematic clusters emerged. Statistical reporting and statistical power emerged as key areas of research, where systemic-level factors in how research is conducted are consistently raised as the precipitating factors for QRPs. There is also an encouraging shift in the focus of research into open science practises designed to address engagement in QRPs. Such a shift is indicative of the growing momentum of the open science movement, and more research can be conducted on how these practises are employed on the ground and how their uptake by researchers can be further promoted. However, the results suggest that, while pre-registration and registered reports receive the most research interest, less attention has been paid to other open science practises (e.g. data sharing).

Empirical evidence of widespread exaggeration bias and selective reporting in ecology

In many scientific disciplines, common research practices have led to unreliable and exaggerated evidence about scientific phenomena. Here we describe some of these practices and quantify their pervasiveness in recent ecology publications in five popular journals. In an analysis of over 350 studies published between 2018 and 2020, we detect empirical evidence of exaggeration bias and selective reporting of statistically significant results. This evidence implies that the published effect sizes in ecology journals exaggerate the importance of the ecological relationships that they aim to quantify. An exaggerated evidence base hinders the ability of empirical ecology to reliably contribute to science, policy, and management. To increase the credibility of ecology research, we describe a set of actions that ecologists should take, including changes to scientific norms about what high-quality ecology looks like and expectations about what high-quality studies can deliver.

Commentary: Visual Cultures, Publication Technologies, and Legitimation in the Life Sciences

This paper comments on five articles in the special issue "Circulating Images in the Life Sciences." It sees the papers as unified by two themes. The first is their attention to the processes of legitimation. The second is the embedding of the images in textual cultures, which changed over time from the mid-nineteenth century to the very recent past, most notably with the recent advent of digital culture.

Methods for Heart Rate Variability Biofeedback (HRVB): A Systematic Review and Guidelines

Heart Rate Variability Biofeedback (HRVB) has been widely used to improve cardiovascular health and well-being. HRVB is based on breathing at an individual's resonance frequency, which stimulates respiratory sinus arrhythmia (RSA) and the baroreflex. There is, however, no methodological consensus on how to apply HRVB, while details about the protocol used are often not well reported. Thus, the objectives of this systematic review are to describe the different HRVB protocols and detect methodological concerns. PsycINFO, CINALH, Medline and Web of Science were searched between 2000 and April 2021. Data extraction and quality assessment were based on PRISMA guidelines. A total of 143 studies were finally included from any scientific field and any type of sample. Three protocols for HRVB were found: (i) "Optimal RF" (n = 37), each participant breathes at their previously detected RF; (ii) "Individual RF" (n = 48), each participant follows a biofeedback device that shows the optimal breathing rate based on cardiovascular data in real time, and (iii) "Preset-pace RF" (n = 51), all participants breathe at the same rate rate, usually 6 breaths/minute. In addition, we found several methodological differences for applying HRVB in terms of number of weeks, duration of breathing or combination of laboratory and home sessions. Remarkably, almost 2/3 of the studies did not report enough information to replicate the HRVB protocol in terms of breathing duration, inhalation/exhalation ratio, breathing control or body position. Methodological guidelines and a checklist are proposed to enhance the methodological quality of future HRVB studies and increase the information reported.

Estimating the false discovery risk of (randomized) clinical trials in medical journals based on published p-values

The influential claim that most published results are false raised concerns about the trustworthiness and integrity of science. Since then, there have been numerous attempts to examine the rate of false-positive results that have failed to settle this question empirically. Here we propose a new way to estimate the false positive risk and apply the method to the results of (randomized) clinical trials in top medical journals. Contrary to claims that most published results are false, we find that the traditional significance criterion of α = .05 produces a false positive risk of 13%. Adjusting α to.01 lowers the false positive risk to less than 5%. However, our method does provide clear evidence of publication bias that leads to inflated effect size estimates. These results provide a solid empirical foundation for evaluations of the trustworthiness of medical research.

Analytical code sharing practices in biomedical research

Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten papers organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability (p=2.71×10-9). Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses (p=1.15*10-07). In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

Unraveling controversies over civic honesty measurement: An extended field replication in China

Cohn et al. (2019) conducted a wallet drop experiment in 40 countries to measure "civic honesty around the globe," which has received worldwide attention but also sparked controversies over using the email response rate as the sole metric of civic honesty. Relying on the lone measurement may overlook cultural differences in behaviors that demonstrate civic honesty. To investigate this issue, we conducted an extended replication study in China, utilizing email response and wallet recovery to assess civic honesty. We found a significantly higher level of civic honesty in China, as measured by the wallet recovery rate, than reported in the original study, while email response rates remained similar. To resolve the divergent results, we introduce a cultural dimension, individualism versus collectivism, to study civic honesty across diverse cultures. We hypothesize that cultural differences in individualism and collectivism could influence how individuals prioritize actions when handling a lost wallet, such as contacting the wallet owner or safeguarding the wallet. In reanalyzing Cohn et al.'s data, we found that email response rates were inversely related to collectivism indices at the country level. However, our replication study in China demonstrated that the likelihood of wallet recovery was positively correlated with collectivism indicators at the provincial level. Consequently, relying solely on email response rates to gauge civic honesty in cross-country comparisons may neglect the vital individualism versus collectivism dimension. Our study not only helps reconcile the controversy surrounding Cohn et al.'s influential field experiment but also furnishes a fresh cultural perspective to evaluate civic honesty.

Research Animal Behavioral Management Programs for the 21st Century

Behavioral management programs have been developed commonly for research dogs and primates but rarely has program consideration been expanded to include all research species worked with. This is necessary to reduce animal stress and promote natural behaviors, which can promote good animal welfare and result in more robust and reproducible scientific data. We describe the evolution of consideration for research animal needs and define an umbrella-based model of research animal behavioral management programs, which may be used for all research species. In addition to developing a more comprehensive program, we emphasize the need for regular welfare assessments to determine whether the program is working cohesively and whether any aspects require modification.

PreprintMatch: A tool for preprint to publication detection shows global inequities in scientific publication

Preprints, versions of scientific manuscripts that precede peer review, are growing in popularity. They offer an opportunity to democratize and accelerate research, as they have no publication costs or a lengthy peer review process. Preprints are often later published in peer-reviewed venues, but these publications and the original preprints are frequently not linked in any way. To this end, we developed a tool, PreprintMatch, to find matches between preprints and their corresponding published papers, if they exist. This tool outperforms existing techniques to match preprints and papers, both on matching performance and speed. PreprintMatch was applied to search for matches between preprints (from bioRxiv and medRxiv), and PubMed. The preliminary nature of preprints offers a unique perspective into scientific projects at a relatively early stage, and with better matching between preprint and paper, we explored questions related to research inequity. We found that preprints from low income countries are published as peer-reviewed papers at a lower rate than high income countries (39.6% and 61.1%, respectively), and our data is consistent with previous work that cite a lack of resources, lack of stability, and policy choices to explain this discrepancy. Preprints from low income countries were also found to be published quicker (178 vs 203 days) and with less title, abstract, and author similarity to the published version compared to high income countries. Low income countries add more authors from the preprint to the published version than high income countries (0.42 authors vs 0.32, respectively), a practice that is significantly more frequent in China compared to similar countries. Finally, we find that some publishers publish work with authors from lower income countries more frequently than others.

On the Role of Theory and Modeling in Neuroscience

In recent years, the field of neuroscience has gone through rapid experimental advances and a significant increase in the use of quantitative and computational methods. This growth has created a need for clearer analyses of the theory and modeling approaches used in the field. This issue is particularly complex in neuroscience because the field studies phenomena that cross a wide range of scales and often require consideration at varying degrees of abstraction, from precise biophysical interactions to the computations they implement. We argue that a pragmatic perspective of science, in which descriptive, mechanistic, and normative models and theories each play a distinct role in defining and bridging levels of abstraction, will facilitate neuroscientific practice. This analysis leads to methodological suggestions, including selecting a level of abstraction that is appropriate for a given problem, identifying transfer functions to connect models and data, and the use of models themselves as a form of experiment.

Large inherent variability in data derived from highly standardised cell culture experiments

Cancer drug development is hindered by high clinical attrition rates, which are blamed on weak predictive power by preclinical models and limited replicability of preclinical findings. However, the technically feasible level of replicability remains unknown. To fill this gap, we conducted an analysis of data from the NCI60 cancer cell line screen (2.8 million compound/cell line experiments), which is to our knowledge the largest depository of experiments that have been repeatedly performed over decades. The findings revealed profound intra-laboratory data variability, although all experiments were executed following highly standardised protocols that avoid all known confounders of data quality. All compound/ cell line combinations with > 100 independent biological replicates displayed maximum GI50 (50% growth inhibition) fold changes (highest/ lowest GI50) > 5% and 70.5% displayed maximum fold changes > 1000. The highest maximum fold change was 3.16 × 10¹⁰ (lowest GI50: 7.93 ×10^-10 µM, highest GI50: 25.0 µM). FDA-approved drugs and experimental agents displayed similar variation. Variability remained high after outlier removal, when only considering experiments that tested drugs at the same concentration range, and when only considering NCI60-provided quality-controlled data. In conclusion, high variability is an intrinsic feature of anti-cancer drug testing, even among standardised experiments in a world-leading research environment. Awareness of this inherent variability will support realistic data interpretation and inspire research to improve data robustness. Further research will have to show whether the inclusion of a wider variety of model systems, such as animal and/ or patient-derived models, may improve data robustness.

Decreased sensitivity to antidepressant drugs in Wistar Hannover rats submitted to two animal models of depression

The Wistar Hannover rat (WHR) is a strain commonly used for toxicity studies but rarely used in studies investigating depression neurobiology. In this study, we aimed to characterise the behavioural responses of WHR to acute and repeated antidepressant treatments upon exposure to the forced swim test (FST) or learned helplessness (LH) test. WHR were subjected to forced swimming pre-test and test with antidepressant administration (imipramine, fluoxetine, or escitalopram) at 0, 5 h and 23 h after pre-test. WHR displayed high immobility in the test compared to unstressed controls (no pre-swim) and failed to respond to the antidepressants tested. The effect of acute and repeated treatment (imipramine, fluoxetine, escitalopram or s-ketamine) was then tested in animals not previously exposed to pre-test. Only imipramine (20 mg/kg, 7 days) and s-ketamine (acute) reduced the immobility time in the test. To further investigate the possibility that the WHR were less responsive to selective serotonin reuptake inhibitors, the effect of repeated treatment with fluoxetine (20 mg/kg, 7 days) was investigated in the LH model. The results demonstrated that fluoxetine failed to reduce the number of escape failures in two different protocols. These data suggest that the WHR do not respond to the conventional antidepressant treatment in the FST or the LH. Only s-ketamine and repeated imipramine were effective in WHR in a modified FST protocol. Altogether, these results indicate that WHR may be an interesting tool to investigate the mechanisms associated with the resistance to antidepressant drugs and identify more effective treatments.

Improving evidence-based practice through preregistration of applied research: Barriers and recommendations

Preregistration is the practice of publicly publishing plans on central components of the research process before access to, or collection, of data. Within the context of the replication crisis, open science practices like preregistration have been pivotal in facilitating greater transparency in research. However, such practices have been applied nearly exclusively to basic academic research, with rare consideration of the relevance to applied and consultancy-based research. This is particularly problematic as such research is typically reported with very low levels of transparency and accountability despite being disseminated as influential gray literature to inform practice. Evidence-based practice is best served by an appreciation of multiple sources of quality evidence, thus the current review considers the potential of preregistration to improve both the accessibility and credibility of applied research toward more rigorous evidence-based practice. The current three-part review outlines, first, the opportunities of preregistration for applied research, and second, three barriers - practical challenges, stakeholder roles, and the suitability of preregistration. Last, this review makes four recommendations to overcome these barriers and maximize the opportunities of preregistration for academics, industry, and the structures they are held within - changes to preregistration templates, new types of templates, education and training, and recognition and structural changes.

Strategic priorities for reproducibility reform

Increasing the reproducibility of research should be a top priority. Great work is being done, but more work is needed to combine efforts and maximize our actions to enable true reproducibility reform.

Valuation regimes in academia: Researchers’ attitudes towards their diversity of activities and academic performance

Evaluation systems have been long criticized for abusing and misusing bibliometric indicators. This has created a culture by which academics are constantly exposing their daily work to the standards they are expected to perform. In this study, we investigate whether researchers’ own values and expectations are in line with the expectations of the evaluation system. We conduct a multiple case study of five departments in two Dutch universities to examine how they balance between their own valuation regimes and the evaluation schemes. For this, we combine curriculum analysis with a series of semi-structured interviews. We propose a model to study the diversity of academic activities and apply it to the multiple case study to understand how such diversity is shaped by discipline and career stage. We conclude that the observed misalignment is not only resulting from an abuse of metrics but also by a lack of tools to evaluate performance in a contextualized and adaptable way.

Realizing the potential of restoration science

Restoration science is growing fast. The restoration of habitats is increasingly part of the discussion over how to tackle the challenges of climate change, biodiversity loss and rural development. With this increasing role and attendant visibility, restoration science has seen increasing controversy. Here I describe six aspects of robust restoration science that should be kept in mind to help realize its potential: do data-driven studies; focus on robust results; improve reproducibility; contextualize the results; give attention to economics; consider the wider goals of restoration. Realizing the potential of restoration science, via robust scientific studies, will provide society with the knowledge and tools to make better choices about which habitats to restore and where. This article is part of the theme issue 'Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration'.

"The elephant in the room": social responsibility in the production of sociogenomics research

Sociogenomics examines the extent to which genetic differences between individuals relate to differences in social and economic behaviors and outcomes. The field evokes mixed reactions. For some, sociogenomics runs the risk of normalizing eugenic attitudes and legitimizing social inequalities. For others, sociogenomics brings the promise of more robust and nuanced understandings of human behavior. Regardless, a history of misuse and misapplication of genetics raises important questions about researchers' social responsibilities. This paper draws on semi-structured interviews with sociogenomics researchers who investigate intelligence and educational attainment. It does so to understand how researcher's motivations for engaging in a historically burdened field connect to their views on social responsibility and the challenges that come with it. In interviews, researchers highlighted the trade-off between engaging in socially contested research and the potential benefits their work poses to the social sciences and clinical research. They also highlighted the dilemmas of engaging with the public, including the existence of multiple publics. Finally, researchers elucidated uncertainties over what social responsibility is in practice and whether protecting against the misuse and misinterpretation of their research is wholly possible. This paper concludes by offering ways to address some of the challenges of social responsibility in the production of knowledge.

Systematic assessment of the replicability and generalizability of preclinical findings: Impact of protocol harmonization across laboratory sites

The influence of protocol standardization between laboratories on their replicability of preclinical results has not been addressed in a systematic way. While standardization is considered good research practice as a means to control for undesired external noise (i.e., highly variable results), some reports suggest that standardized protocols may lead to idiosyncratic results, thus undermining replicability. Through the EQIPD consortium, a multi-lab collaboration between academic and industry partners, we aimed to elucidate parameters that impact the replicability of preclinical animal studies. To this end, 3 experimental protocols were implemented across 7 laboratories. The replicability of results was determined using the distance travelled in an open field after administration of pharmacological compounds known to modulate locomotor activity (MK-801, diazepam, and clozapine) in C57BL/6 mice as a worked example. The goal was to determine whether harmonization of study protocols across laboratories improves the replicability of the results and whether replicability can be further improved by systematic variation (heterogenization) of 2 environmental factors (time of testing and light intensity during testing) within laboratories. Protocols were tested in 3 consecutive stages and differed in the extent of harmonization across laboratories and standardization within laboratories: stage 1, minimally aligned across sites (local protocol); stage 2, fully aligned across sites (harmonized protocol) with and without systematic variation (standardized and heterogenized cohort); and stage 3, fully aligned across sites (standardized protocol) with a different compound. All protocols resulted in consistent treatment effects across laboratories, which were also replicated within laboratories across the different stages. Harmonization of protocols across laboratories reduced between-lab variability substantially compared to each lab using their local protocol. In contrast, the environmental factors chosen to introduce systematic variation within laboratories did not affect the behavioral outcome. Therefore, heterogenization did not reduce between-lab variability further compared to the harmonization of the standardized protocol. Altogether, these findings demonstrate that subtle variations between lab-specific study protocols may introduce variation across independent replicate studies even after protocol harmonization and that systematic heterogenization of environmental factors may not be sufficient to account for such between-lab variation. Differences in replicability of results within and between laboratories highlight the ubiquity of study-specific variation due to between-lab variability, the importance of transparent and fine-grained reporting of methodologies and research protocols, and the importance of independent study replication.

The Dilemma of Reproducibility of Gating Isotherms for Flexible MOFs

Porous materials receive a high level of scientific and technological interest due to their applications in various fields such as adsorption, separation and storage, catalysis, ion exchange, nanotechnology, etc. Gas adsorption is a well-established tool for the characterization of the texture of porous solids. Physisorption isotherms are generally expected to be well reproducible for rigid adsorbents, but this is not always the case for nonrigid (flexible) materials. The presence of a metastability region and sensitivity of the activation barriers to the material's texture often influence the isotherms' run. Here, we address the complexity that arises in terms of reproducibility and sample handling for flexible metal-organic frameworks, with the example of DUT-8(Ni). It belongs to the group of "gate opening" metal-organic frameworks and is a typical representative of the pillared layer compounds. We propose characteristic parameters for the analysis and comparison of adsorption isotherms, showing the "gate opening" step, associated with the adsorption-induced solid-state phase transition. A set of 50 nitrogen physisorption isotherms measured at 77 K were analyzed and correlated with the synthetic and outgassing conditions. The study highlights the importance of accurate descriptions and record-keeping of experimental details and their role in the replication of scientific results.

Do studies published in two leading reproduction journals between 2011 and 2020 demonstrate that they followed WHO5 recommendations for basic semen analysis?

STUDY QUESTION

Do publications that involve the interpretation of the results of a basic semen analysis, published in Human Reproduction and Fertility & Sterility between 2011 and 2020, give sufficient evidence in their methodology to demonstrate that they followed the technical methods recommended in the fifth edition of the World Health Organization (WHO) laboratory manual, entitled WHO Laboratory Manual for the Examination and Processing of Human Semen (WHO5)?

SUMMARY ANSWER

Evidence of methodological agreement of studies with the WHO5 recommendations was low, despite 70% of papers stating that they followed WHO5 recommendations.

WHAT IS KNOWN ALREADY

A basic semen analysis is currently an integral part of infertility investigations of the male, but method standardization in laboratories remains an issue. The different editions of the WHO manual for the basic semen analysis (WHO1-6) have attempted to address this by providing increasingly rigorous methodological protocols to reduce experimental error. However, to what extent these methods are followed by studies that involve the interpretation of the results of basic semen analysis remains unknown.

STUDY DESIGN, SIZE, DURATION

A survey of the technical methods used to perform a basic semen analysis was conducted on studies published in two leading reproduction journals (Human Reproduction and Fertility & Sterility) between 2011 and 2020.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The literature search was performed on the electronic databases PUBMED and MEDLINE Ovid between January 2021 and March 2021. The MeSH terms included in the search were 'sperm concentration' OR 'sperm motility' OR 'sperm morphology' OR 'sperm vitality' OR 'male fertility' AND 'human spermatozoa' NOT 'animals'. A total of 122 studies were available for analysis.

MAIN RESULTS AND THE ROLE OF CHANCE

In total, 70% of the studies cited WHO5 in their methods section. Of the remaining studies, 10% cited the fourth edition of the WHO laboratory manual (WHO4), 7% cited both WHO4 and WHO5, 1% cited the third edition of the WHO laboratory manual (WHO3), and 12% did not cite the WHO at all. Overall methodological agreement with WHO5 recommendations was poor, with the main reason for this lack of agreement being that the research studies did not disclose specific details of the technical methods and equipment used.

LIMITATIONS, REASONS FOR CAUTION

In the case of studies that did not disclose any specific technical methods that they used, we did not attempt to contact these authors and so were unable to confirm the agreement between their technical methods and WHO5 recommendations.

WIDER IMPLICATIONS OF THE FINDINGS

Our findings suggest there is an urgent need to develop strategies to address standardization in reporting the results of a semen analysis for publication. This is particularly timely given the recent publication of WHO6 and ISO standard 23162 for the basic examination of human semen.

STUDY FUNDING/COMPETING INTEREST(S)

There was no funding for this project. C.L.R.B., as an employee of the University of Dundee, serves on the Scientific Advisory board of ExSeed Health (from October 2021, financial compensation to the University of Dundee) and is a scientific consultant for Exscientia (from September 2021, financial compensation to the University of Dundee). C.L.R.B. has previously received a fee from Cooper Surgical for lectures on scientific research methods outside the submitted work (2020) and Ferring for a lecture on male reproductive health (2021). C.L.R.B. is Editor for RBMO.

TRIAL REGISTRATION NUMBER

N/A.

Sex-specific stress and biobehavioral responses to human experimenters in rats

Important factors influencing the outcome of animal experiments in preclinical research are often overlooked. In the current study, the reaction of female and male rats toward the biological sex of a human experimenter was investigated in terms of anxiety-like behaviors and physiological stress responses, as measured by infrared (IR) thermography, circulating corticosterone (CORT) and oxytocin levels. Female rats displayed consistently exacerbated anxiety-related behaviors along with elevated body surface temperature during repeated exposure to male experimenters. Experimental stress further intensified thermal responses to a male experimenter, especially in female rats. The behavioral responses to a male experimenter in females were associated with higher circulating CORT and lower oxytocin levels. Similar responses were induced by a T-shirt worn by a human male. The findings suggest that psychophysiological responses of female rats to a male experimenter are influenced by both visual and olfactory cues. The results emphasize the need to not only consider sex differences in experimental animals, but also standardize and report the experimenter’s biological sex to avoid ambiguity in the generation and interpretation of results.

How Reproducibility Will Accelerate Discovery Through Collaboration in Physio-Logging

What new questions could ecophysiologists answer if physio-logging research was fully reproducible? We argue that technical debt (computational hurdles resulting from prioritizing short-term goals over long-term sustainability) stemming from insufficient cyberinfrastructure (field-wide tools, standards, and norms for analyzing and sharing data) trapped physio-logging in a scientific silo. This debt stifles comparative biological analyses and impedes interdisciplinary research. Although physio-loggers (e.g., heart rate monitors and accelerometers) opened new avenues of research, the explosion of complex datasets exceeded ecophysiology’s informatics capacity. Like many other scientific fields facing a deluge of complex data, ecophysiologists now struggle to share their data and tools. Adapting to this new era requires a change in mindset, from “data as a noun” (e.g., traits, counts) to “data as a sentence”, where measurements (nouns) are associate with transformations (verbs), parameters (adverbs), and metadata (adjectives). Computational reproducibility provides a framework for capturing the entire sentence. Though usually framed in terms of scientific integrity, reproducibility offers immediate benefits by promoting collaboration between individuals, groups, and entire fields. Rather than a tax on our productivity that benefits some nebulous greater good, reproducibility can accelerate the pace of discovery by removing obstacles and inviting a greater diversity of perspectives to advance science and society. In this article, we 1) describe the computational challenges facing physio-logging scientists and connect them to the concepts of technical debt and cyberinfrastructure, 2) demonstrate how other scientific fields overcame similar challenges by embracing computational reproducibility, and 3) present a framework to promote computational reproducibility in physio-logging, and bio-logging more generally.

Re-evaluating methods reporting practices to improve reproducibility: an analysis of methodological rigor for the Langendorff whole-heart technique

In recent decades, the scientific community has seen an increased interest in rigor and reproducibility. In 2017, concerns of methodological thoroughness and reporting practices were implicated as significant barriers to reproducibility within the preclinical cardiovascular literature, particularly in studies employing animal research. The Langendorff, whole-heart technique has proven to be an invaluable research tool, being modified in a myriad of ways to probe questions across the spectrum of physio- and pathophysiologic function of the heart. As a result, significant variability in the application of the Langendorff technique exists. This literature review quantifies the different methods employed in the implementation of the Langendorff technique and provides brief examples of how individual parametric differences can impact the outcomes and interpretation of studies. From 2017-2020, significant variability of animal models, anesthesia, cannulation time, and perfusate composition, pH, and temperature demonstrate that the technique has diversified to meet new challenges and answer different scientific questions. The review also reveals which individual methods are most frequently reported, even if there is no explicit agreement upon which parameters should be reported. The analysis of methods related to the Langendorff technique suggests a framework for considering methodological approach when interpreting seemingly contradictory results, rather than concluding that results are irreproducible.

Dynamics of cross-platform attention to retracted papers

Scientific retraction has been on the rise recently. Retracted papers are frequently discussed online, enabling the broad dissemination of potentially flawed findings. Our analysis spans a nearly 10-y period and reveals that most papers exhaust their attention by the time they get retracted, meaning that retractions cannot curb the online spread of problematic papers. This is striking as we also find that retracted papers are pervasive across mediums, receiving more attention after publication than nonretracted papers even on curated platforms, such as news outlets and knowledge repositories. Interestingly, discussions on social media express more criticism toward subsequently retracted results and may thus contain early signals related to unreliable work.

Retracted papers often circulate widely on social media, digital news, and other websites before their official retraction. The spread of potentially inaccurate or misleading results from retracted papers can harm the scientific community and the public. Here, we quantify the amount and type of attention 3,851 retracted papers received over time in different online platforms. Comparing with a set of nonretracted control papers from the same journals with similar publication year, number of coauthors, and author impact, we show that retracted papers receive more attention after publication not only on social media but also, on heavily curated platforms, such as news outlets and knowledge repositories, amplifying the negative impact on the public. At the same time, we find that posts on Twitter tend to express more criticism about retracted than about control papers, suggesting that criticism-expressing tweets could contain factual information about problematic papers. Most importantly, around the time they are retracted, papers generate discussions that are primarily about the retraction incident rather than about research findings, showing that by this point, papers have exhausted attention to their results and highlighting the limited effect of retractions. Our findings reveal the extent to which retracted papers are discussed on different online platforms and identify at scale audience criticism toward them. In this context, we show that retraction is not an effective tool to reduce online attention to problematic papers.

The Reproducibility Movement in Psychology: Does Researcher Gender Affect How People Perceive Scientists With a Failed Replication?

The reproducibility movement in psychology has resulted in numerous highly publicized instances of replication failures. The goal of the present work was to investigate people’s reactions to a psychology replication failure vs. success, and to test whether a failure elicits harsher reactions when the researcher is a woman vs. a man. We examined these questions in a pre-registered experiment with a working adult sample, a conceptual replication of that experiment with a student sample, and an analysis of data compiled and posted by a psychology researcher on their public weblog with the stated goal to improve research replicability by rank-ordering psychology researchers by their “estimated false discovery risk.” Participants in the experiments were randomly assigned to read a news article describing a successful vs. failed replication attempt of original work from a male vs. female psychological scientist, and then completed measures of researcher competence, likability, integrity, perceptions of the research, and behavioral intentions for future interactions with the researcher. In both working adult and student samples, analyses consistently yielded large main effects of replication outcome, but no interaction with researcher gender. Likewise, the coding of weblog data posted in July 2021 indicated that 66.3% of the researchers scrutinized were men and 33.8% were women, and their rank-ordering was not correlated with researcher gender. The lack of support for our pre-registered gender-replication hypothesis is, at first glance, encouraging for women researchers’ careers; however, the substantial effect sizes we observed for replication outcome underscore the tremendous negative impact the reproducibility movement can have on psychologists’ careers. We discuss the implications of such negative perceptions and the possible downstream consequences for women in the field that are essential for future study.

A Brief Guide to Statistical Analysis and Presentation for the Plant Pathology Journal

Statistical analysis of data is an integral part of research projects in all scientific disciplines including the plant pathology. Appropriate design, application and interpretation of statistical analysis are also, therefore, at the center of publishing and properly evaluating studies in plant pathology. A survey of research works published in the Plant Pathology Journal, however, cast doubt on high standard of statistical analysis required for scientific rigor and reproducibility in the journal. Here I first describe, based on the survey of published works, what mistakes are commonly made and what components are often lacking during statistical analysis and interpretation of its results. Next, I provide possible remedies and suggestions to help guide researchers in preparing manuscript and reviewers in evaluating manuscripts submitted to the Plant Pathology Journal. This is not aiming at delineating technical and practical details of particular statistical methods or approaches.

Social Class Priming Effect on Prosociality: Evidence from Explicit and Implicit Measures

Although abundant research has explored the relationship between social class and prosociality, it remains controversial. This study aimed to investigate the effect of social class priming on prosociality among college students. Experiment 1 was an explicit experiment in which we employed the MacArthur scale to prime participants’ social class and then used a donation task. The results showed that students in a low social class priming group had more donation behaviors compared to ones in a high social class priming group. Experiment 2 was an implicit experiment in which we used a single category implicit association test (SC-IAT) to investigate the relationship between the self-concepts of different social classes and prosociality after priming participants’ social class. The results indicated that students in a low social class priming condition had a stronger connection between self-concepts and prosocial inclinations than ones in a high social class priming condition. Thus, our study demonstrated that students primed with low social class were more prosocial than those primed with high social class, and supported the empathy-altruism theory of prosocial behavior. These findings are of great practical significance to promote prosocial behavior of individuals of different social classes.

Preliminary Evidence for an Association between Journal Submission Requirements and Reproducibility of Published Findings: A Pilot Study

Systemic efforts have been employed to improve the reproducibility of published findings in psychology. To date, little research has been conducted evaluating how well these efforts work. In an effort to bridge this gap, the current study looked at journal submission requirements intended to encourage authors to engage in best practices for facilitating reproducible science and offers preliminary evidence for their potential efficacy. We calculated reproducibility indices (p-curves) for three randomly selected empirical studies published in each of 23 psychology journals in 2019 and correlated quantitative results from those analyzes with the number of submission requirements for each journal that intended to ensure compliance with best reporting practices. Results indicated a greater number of submission requirements at a given outlet was associated with indices indicating greater likelihood of reproducibility of findings. We frame findings as impetus for future, more extensive, research to identify causal links between submission requirements and reproducibility.

Transforming Academic Drug Discovery

A drug accelerator that partners the creative power of academic scientists with drug discovery professionals to consistently advance groundbreaking biological discoveries towards patients in need would be transformational. One such model, the Tri-Institutional Therapeutics Discovery Institute, evolved a series of best practices for identifying, selecting, executing, and completing academic-initiated drug discovery projects, as evidenced by licensing successes, is described.

The "'Crisis' Crisis" in psychology

The recent trend to label dilemmas in psychology as "crises" is insidious. The "'Crisis' Crisis" in psychology can distract us from actionable practices. As a case in point, "The Generalizability Crisis" offers the valuable central thesis that verbal-quantitative gaps imperil psychological science. Focusing on the key issues rather than crisis narratives can lead to progress in our discourse and research.