Facilitating open science without sacrificing IP rights: A novel tool for improving replicability of published research: A novel tool for improving replicability of published research.
Ontology highlight
ABSTRACT:
SUBMITTER: Cohen-Sasson O
PROVIDER: S-EPMC9442283 | biostudies-literature | 2022 Sep
REPOSITORIES: biostudies-literature
Publications
Facilitating open science without sacrificing IP rights: A novel tool for improving replicability of published research: A novel tool for improving replicability of published research.
Cohen-Sasson Or O Tur-Sinai Ofer O
EMBO reports 20220816 9
Conditional Access Agreements could improve replicability of research and enhance Open Science without jeopardizing intellectual property rights. ...[more]
Similar Datasets
Project description:Biomarkers that can guide cancer therapy based on patients' individual cancer molecular signature can enable a more effective treatment with fewer adverse events. Data on actionable somatic mutations and germline genetic variants, studied by personalized medicine and pharmacogenomics, can be obtained from tumor tissue or blood samples. As tissue biopsy cannot reflect the heterogeneity of the tumor or its temporal changes, liquid biopsy is a promising alternative approach. In recent years, extracellular vesicles (EVs) have emerged as a potential source of biomarkers in liquid biopsy. EVs are a heterogeneous population of membrane bound particles, which are released from all cells and accumulate into body fluids. They contain various proteins, lipids, nucleic acids (miRNA, mRNA, and DNA) and metabolites. In cancer, EV biomolecular composition and concentration are changed. Tumor EVs can promote the remodeling of the tumor microenvironment and pre-metastatic niche formation, and contribute to transfer of oncogenic potential or drug resistance during chemotherapy. This makes them a promising source of minimally invasive biomarkers. A limited number of clinical studies investigated EVs to monitor cancer progression, tumor evolution or drug resistance and several putative EV-bound protein and RNA biomarkers were identified. This review is focused on EVs as novel biomarker source for personalized medicine and pharmacogenomics in oncology. As several pharmacogenes and genes associated with targeted therapy, chemotherapy or hormonal therapy were already detected in EVs, they might be used for fine-tuning personalized cancer treatment.
| S-EPMC8120271 | biostudies-literature
Project description:This article examines why many studies fail to replicate statistically significant published results. We address this issue within a general statistical framework that also allows us to include various questionable research practices (QRPs) that are thought to reduce replicability. The analyses indicate that the base rate of true effects is the major factor that determines the replication rate of scientific results. Specifically, for purely statistical reasons, replicability is low in research domains where true effects are rare (e.g., search for effective drugs in pharmacology). This point is under-appreciated in current scientific and media discussions of replicability, which often attribute poor replicability mainly to QRPs.
| S-EPMC7561355 | biostudies-literature
Project description:BackgroundIn the USA, firearms are commonly involved in many incidents of serious interpersonal harm. Federal law prohibits the purchase and possession of firearms by certain high-risk groups including those with prior felony or domestic violence misdemeanor convictions. Evidence supports the effectiveness of these prohibitions, but little is known about how often prohibited persons later seek to have their firearm rights restored.Main bodyFor this commentary, we systematically searched the empirical literature for information about who requests firearm rights restoration in the USA, how often it is granted, and what its consequences are. We found a dearth of empirical literature on this topic.ConclusionWe call for attention to this gap in the research. There is a need to build an evidence base that can help inform state policy and courtroom practices regarding the eligibility, appropriateness, and risk for subsequent harm following firearm rights restoration among persons who are prohibited based on a criminal conviction history.
| S-EPMC10768349 | biostudies-literature
Project description:Previous work suggests that key factors for replicability, a necessary feature for theory building, include statistical power and appropriate research planning. These factors are examined by analyzing a collection of 12 standardized meta-analyses on language development between birth and 5 years. With a median effect size of Cohen's d = .45 and typical sample size of 18 participants, most research is underpowered (range = 6%-99%; median = 44%); and calculating power based on seminal publications is not a suitable strategy. Method choice can be improved, as shown in analyses on exclusion rates and effect size as a function of method. The article ends with a discussion on how to increase replicability in both language acquisition studies specifically and developmental research more generally.
| S-EPMC6282795 | biostudies-literature
Project description:IntroductionPrevious 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.MethodsWe 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.ResultsA 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.ConclusionAlthough 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.
| S-EPMC11305584 | biostudies-literature
Project description:Systems epidemiology offers a more comprehensive and holistic approach to studies of cancer in populations by considering high dimensionality measures from multiple domains, assessing the inter-relationships among risk factors, and considering changes over time. These approaches offer a framework to account for the complexity of cancer and contribute to a broader understanding of the disease. Therefore, NCI sponsored a workshop in February 2019 to facilitate discussion about the opportunities and challenges of the application of systems epidemiology approaches for cancer research. Eight key themes emerged from the discussion: transdisciplinary collaboration and a problem-based approach; methods and modeling considerations; interpretation, validation, and evaluation of models; data needs and opportunities; sharing of data and models; enhanced training practices; dissemination of systems models; and building a systems epidemiology community. This manuscript summarizes these themes, highlights opportunities for cancer systems epidemiology research, outlines ways to foster this research area, and introduces a collection of papers, "Cancer System Epidemiology Insights and Future Opportunities" that highlight findings based on systems epidemiology approaches.
| S-EPMC8719747 | biostudies-literature
Project description:Alzheimer disease (AD) research faces challenges to successful enrollment, especially to clinical trials and biomarker studies. Failure to recruit the planned number of participants in a timely manner threatens the internal validity and success of clinical research, raising concerns about external validity and generalizability of results, and possibly leading to disparities in disease treatment. Methods to improve recruitment exist, but require varying levels of staff effort and financial resources, and evidence of effectiveness is often lacking or inconsistent. In this review, we summarize some of the available methods to improve AD research recruitment, the available literature to support or refute these strategies, and some of the experiences at the authors' AD Research Centers. We discuss the use of community-based participatory research principles and participant registries as a means to enhance research enrollment and increase diversity of research samples.
| S-EPMC3945167 | biostudies-literature
Project description:The VEGAS platform is not suitable for mammalian directed evolution
| PRJEB47639 | ENA
Project description:BackgroundThe objective of this study was to evaluate the nature and extent of reproducible and transparent research practices in neurology publications.MethodsThe NLM catalog was used to identify MEDLINE-indexed neurology journals. A PubMed search of these journals was conducted to retrieve publications over a 5-year period from 2014 to 2018. A random sample of publications was extracted. Two authors conducted data extraction in a blinded, duplicate fashion using a pilot-tested Google form. This form prompted data extractors to determine whether publications provided access to items such as study materials, raw data, analysis scripts, and protocols. In addition, we determined if the publication was included in a replication study or systematic review, was preregistered, had a conflict of interest declaration, specified funding sources, and was open access.ResultsOur search identified 223,932 publications meeting the inclusion criteria, from which 400 were randomly sampled. Only 389 articles were accessible, yielding 271 publications with empirical data for analysis. Our results indicate that 9.4% provided access to materials, 9.2% provided access to raw data, 0.7% provided access to the analysis scripts, 0.7% linked the protocol, and 3.7% were preregistered. A third of sampled publications lacked funding or conflict of interest statements. No publications from our sample were included in replication studies, but a fifth were cited in a systematic review or meta-analysis.ConclusionsCurrently, published neurology research does not consistently provide information needed for reproducibility. The implications of poor research reporting can both affect patient care and increase research waste. Collaborative intervention by authors, peer reviewers, journals, and funding sources is needed to mitigate this problem.
| S-EPMC7049215 | biostudies-literature
Project description:PurposeThe ongoing replication crisis within and beyond psychology has revealed the numerous ways in which flexibility in the research process can affect study outcomes. In speech research, examples of these "researcher degrees of freedom" include the particular syllables, words, or sentences presented; the talkers who produce the stimuli and the instructions given to them; the population tested; whether and how stimuli are matched on amplitude; the type of masking noise used and its presentation level; and many others. In this research note, we argue that even seemingly minor methodological choices have the potential to affect study outcomes. To that end, we present a reanalysis of six existing data sets on spoken word identification in noise to assess how differences in talkers, stimulus processing, masking type, and listeners affect identification accuracy.ConclusionsOur reanalysis revealed relatively low correlations among word identification rates across studies. The data suggest that some of the seemingly innocuous methodological details that differ across studies-details that cannot possibly be reported in text given the idiosyncrasies inherent to speech-introduce unknown variability that may affect replicability of our findings. We therefore argue that publicly sharing stimuli is a crucial step toward improved replicability in speech research.Supplemental materialhttps://doi.org/10.23641/asha.21985907.
| S-EPMC10465150 | biostudies-literature