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Reporting all results efficiently: A RARE proposal to open up the file drawer.

ABSTRACT: While the social sciences have made impressive progress in adopting transparent research practices that facilitate verification, replication, and reuse of materials, the problem of publication bias persists. Bias on the part of peer reviewers and journal editors, as well as the use of outdated research practices by authors, continues to skew literature toward statistically significant effects, many of which may be false positives. To mitigate this bias, we propose a framework to enable authors to report all results efficiently (RARE), with an initial focus on experimental and other prospective empirical social science research that utilizes public study registries. This framework depicts an integrated system that leverages the capacities of existing infrastructure in the form of public registries, institutional review boards, journals, and granting agencies, as well as investigators themselves, to efficiently incentivize full reporting and thereby, improve confidence in social science findings. In addition to increasing access to the results of scientific endeavors, a well-coordinated research ecosystem can prevent scholars from wasting time investigating the same questions in ways that have not worked in the past and reduce wasted funds on the part of granting agencies.

SUBMITTER: Laitin DD

PROVIDER: S-EPMC8719896 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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Reporting all results efficiently: A RARE proposal to open up the file drawer.

Laitin David D DD Miguel Edward E Alrababa'h Ala' A Bogdanoski Aleksandar A Grant Sean S Hoeberling Katherine K Hyunjung Mo Cecilia C Moore Don A DA Vazire Simine S Weinstein Jeremy J Williamson Scott S

Proceedings of the National Academy of Sciences of the United States of America 20211201 52

While the social sciences have made impressive progress in adopting transparent research practices that facilitate verification, replication, and reuse of materials, the problem of publication bias persists. Bias on the part of peer reviewers and journal editors, as well as the use of outdated research practices by authors, continues to skew literature toward statistically significant effects, many of which may be false positives. To mitigate this bias, we propose a framework to enable authors t ...[more]

PMID: 34933997

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Project description:Infection experiments are critical for understanding wildlife disease dynamics. Although infection experiments are typically designed to reduce complexity, disease outcomes still result from complex interactions between host, pathogen, and environmental factors. Cryptic variation across factors can lead to decreased repeatability of infection experiments within and between research groups and hinder research progress. Furthermore, studies with unexpected results are often relegated to the "file drawer" and potential insights gained from these experimental outcomes are lost. Here, we report unexpected results from an infection experiment studying the response of two differentially-susceptible but related frogs (American Bullfrog Rana catesbeiana and the Mountain yellow-legged frog Rana muscosa) to the amphibian-killing chytrid fungus (Batrachochytrium dendrobatidis, Bd). Despite well-documented differences in susceptibility between species, we found no evidence for antibody-mediated immune response and no Bd-related mortality in either species. Additionally, during the study, the sham-inoculated R. catesbeiana control group became unexpectedly Bd-positive. We used a custom genotyping assay to demonstrate that the aberrantly-infected R. catesbeiana carried a Bd genotype distinct from the inoculation genotype. Thus R. catesbeiana individuals were acquired with low-intensity infections that could not be detected with qPCR. In the Bd-inoculated R. catesbeiana treatment group, the inoculated genotype appeared to out-compete the cryptic infection. Thus, our results provide insight into Bd coinfection dynamics, a phenomenon that is increasingly relevant as different pathogen strains are moved around the globe. Our experiment highlights how unexpected experimental outcomes can serve as both cautionary tales and opportunities to explore unanswered research questions. We use our results as a case study to highlight common sources of anomalous results for infection experiments. We argue that understanding these factors will aid researchers in the design, execution, and interpretation of experiments to understand wildlife disease processes.

Project description:BackgroundStandardized methods for reporting surgical quality have been described for all the major urological procedures apart from radical nephroureterectomy (RNU).ObjectiveTo propose a tetrafecta criterion for assessing the quality of RNU based on a consensus panel within the Young Association of Urology (YAU) Urothelial Group, and to test the impact of this tetrafecta in a multicenter, large contemporary cohort of patients treated with RNU for upper tract urothelial carcinoma (UTUC).Design setting and participantsThis was a retrospective analysis of 1765 patients with UTUC treated between 2000 and 2021.Outcome measurements and statistical analysisWe interviewed the YAU Urothelial Group to propose and score a list of items to be included in the "RNU-fecta." A ranking was generated for the criteria with the highest sum score. These criteria were applied to a large multicenter cohort of patients. Kaplan-Meier curves were built to evaluate differences in overall survival (OS) rates between groups, and a multivariable logistic regression model was used to find the predictors of achieving the RNU tetrafecta.Results and limitationsThe criteria with the highest score included three surgical items such as negative soft tissue surgical margins, bladder cuff excision, lymph node dissection according to guideline recommendations, and one oncological item defined by the absence of any recurrence in ≤12 mo. These items formed the RNU tetrafecta. Within a median follow-up of 30 mo, 52.6% of patients achieved the RNU tetrafecta. The 5-yr OS rates were significantly higher for patients achieving tetrafecta than for their counterparts (76% vs 51%). Younger age, lower body mass index, and robotic approach were found to be independent predictors of tetrafecta achievement. Conversely, a higher Eastern Cooperative Oncology Group score, higher clinical stage, and bladder cancer history were inversely associated with tetrafecta.ConclusionsHerein, we present a "tetrafecta" composite endpoint that may serve as a potential tool to assess the overall quality of the RNU procedure. Pending external validation, this tool could allow a comparison between surgical series and may be useful for assessing the learning curve of the procedure as well as for evaluating the impact of new technologies in the field.Patient summaryIn this study, a tetrafecta criterion was developed for assessing the surgical quality of radical nephroureterectomy in patients with upper tract urothelial carcinoma. Patients who achieved tetrafecta had higher 5-yr overall survival rates than those who did not.

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Reporting all results efficiently: A RARE proposal to open up the file drawer.

Publications

Reporting all results efficiently: A RARE proposal to open up the file drawer.

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