Article
Multidisciplinary Sciences
Leho Tedersoo, Rainer Kungas, Ester Oras, Kajar Koster, Helen Eenmaa, Ali Leijen, Margus Pedaste, Marju Raju, Anastasiya Astapova, Heli Lukner, Karin Kogermann, Tuul Sepp
Summary: The study found that while data sharing has improved over the past decade, differences in data availability and willingness to share data still exist among different disciplines. It is recommended to incentivize researchers to share data through benefits such as recognition and rewards, with funding agencies covering data management costs and enforcing data sharing surveillance.
Editorial Material
Biochemical Research Methods
Julian Matschinske, Nicolas Alcaraz, Arriel Benis, Martin Golebiewski, Dominik G. Grimm, Lukas Heumos, Tim Kacprowski, Olga Lazareva, Markus List, Zakaria Louadi, Josch K. Pauling, Nico Pfeifer, Richard Roettger, Veit Schwaemmle, Gregor Sturm, Alberto Traverso, Kristel Van Steen, Martiela Vaz de Freitas, Gerda Cristal Villalba Silva, Leonard Wee, Nina K. Wenke, Massimiliano Zanin, Olga Zolotareva, Jan Baumbach, David B. Blumenthal
Summary: The AIMe registry is a community-driven reporting platform for AI in biomedicine, aiming to improve the accessibility, reproducibility, and usability of biomedical AI models, and allowing future revisions by the community.
Editorial Material
Health Care Sciences & Services
Ioana A. Cristea, Florian Naudet, Laura Caquelin
Summary: Data sharing is becoming increasingly important in science, but there is a lack of focus on data sharing in metaresearch. It is necessary to improve and evaluate data sharing practices in metaresearch and provide tailored recommendations for improvement.
JOURNAL OF CLINICAL EPIDEMIOLOGY
(2022)
Article
Criminology & Penology
Jason M. Chin, Justin T. Pickett, Simine Vazire, Alex O. Holcombe
Summary: This study examines the prevalence of questionable research practices (QRPs) and open science practices (OSPs) in criminology, and explores researchers' opinions on these practices. The results show that both QRPs and OSPs are common in quantitative criminology, with researchers being more supportive of OSPs. Methodological training does not seem to be associated with the use of either QRPs or OSPs. The study also highlights the need for further reforms to reduce QRP use and promote the use of OSPs in order to improve the validity and reproducibility of criminological research.
JOURNAL OF QUANTITATIVE CRIMINOLOGY
(2023)
Article
Psychology, Multidisciplinary
Tom E. Hardwicke, Robert T. Thibault, Jessica E. Kosie, Joshua D. Wallach, Mallory C. Kidwell, John P. A. Ioannidis
Summary: A manual examination of 250 psychology articles published between 2014 and 2017 found that while over half of the articles were publicly available, sharing of research materials, preregistration, and other transparency and reproducibility-related research practices were rare. This suggests that these practices are far from routine in psychology research, highlighting the need for further efforts to increase credibility and utility.
PERSPECTIVES ON PSYCHOLOGICAL SCIENCE
(2022)
Article
Biology
Dylan G. E. Gomes, Patrice Pottier, Robert Crystal-Ornelas, Emma J. Hudgins, Vivienne Foroughirad, Luna L. Sanchez-Reyes, Rachel Turba, Paula Andrea Martinez, David Moreau, Michael G. Bertram, Cooper A. Smout, Kaitlyn M. Gaynor
Summary: The biological sciences community recognizes the importance of open, reproducible, and transparent research practices. However, researchers face barriers in sharing their data and code, including knowledge barriers, concerns about reuse, and misaligned career incentives. By identifying and addressing these barriers, we can promote open science goals.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Azza E. Ahmed, Joshua M. Allen, Tajesvi Bhat, Prakruthi Burra, Christina E. Fliege, Steven N. Hart, Jacob R. Heldenbrand, Matthew E. Hudson, Dave Deandre Istanto, Michael T. Kalmbach, Gregory D. Kapraun, Katherine Kendig, Matthew Charles Kendzior, Eric W. Klee, Nate Mattson, Christian A. Ross, Sami M. Sharif, Ramshankar Venkatakrishnan, Faisal M. Fadlelmola, Liudmila S. Mainzer
Summary: Genomics research and clinical practice require computational pipelines to efficiently handle complex analysis stages and large volumes of data. This study evaluates the key features of popular bioinformatics WfMSs such as Nextflow, CWL, WDL, and Swift/T, comparing their language expressiveness, modularity, scalability, robustness, reproducibility, interoperability, and ease of development for different computing environments. The choice of a WfMS depends on intrinsic language and engine features, as well as collaborations, adoption within consortia, and technical support. Evolution of WfMSs will continue to meet evolving community needs and computational infrastructure, with innovations focusing on big data technologies, interoperability, and provenance.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Andrew Delios, Elena Giulia Clemente, Tao Wu, Hongbin Tan, Yong Wang, Michael Gordon, Domenico Viganola, Zhaowei Chen, Anna Dreberb, Magnus Johannesson, Thomas Pfeiffer, Eric Luis Uhlmann
Summary: This study systematically examined the generalizability of a large set of archival research findings across different contexts. The findings showed that 45% of the replicated tests in different time periods and geographies matched the original reports. For the findings that could be directly reproduced, 84% were also observed in other available time periods and 57% were observed in other geographies. Overall, the study suggested limited empirical evidence for context sensitivity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Management
Alberto Galasso, Hong Luo, Brooklynn Zhu
Summary: This study examines the impact of safety regulations on research productivity by analyzing the case of increased safety regulations at the University of California after a tragic accident in 2008. The results suggest that wet labs, which conduct experiments using chemical and biological substances, did not experience significant changes in publication rates after the accident. However, wet labs that frequently used dangerous compounds before the accident reduced their reliance on flammable materials and unfamiliar hazardous compounds afterward. These findings indicate that laboratory safety practices may shape scientific production, but they do not impose a significant tax on research productivity.
Article
Chemistry, Multidisciplinary
Baudilio Coto, Inmaculada Suarez, Maria Jose Tenorio, Miguel Angel Gonzalez
Summary: The COVID-19 pandemic has led to the reorganization of learning methods, with remote learning playing a central role. Laboratory experiments have been heavily impacted, leading to the search for alternatives. This study proposes the use of simple programming in Excel to create calculation tools that simulate data acquisition in specific laboratory experiments. The results show that virtual experiments yield comparable grades and skills to in-person experiments.
JOURNAL OF CHEMICAL EDUCATION
(2023)
Review
Medicine, General & Internal
Werner Vach, Oke Gerke
Summary: Measurement procedures are not error-free, and scientific investigations often rely on replicates to study measurement errors. There is a lack of standardized terminology to support such research.
Article
Multidisciplinary Sciences
Sheeba Samuel, Birgitta Koenig-Ries
Summary: This article highlights the importance of research practices in different disciplines and the challenges faced by the "Reproducibility Crisis". The survey findings indicate a strong need for sharing data, code, methods, steps, and negative and positive results, while insufficient metadata, lack of publicly available data, and incomplete information in study methods are considered major reasons for poor reproducibility.
Review
Computer Science, Information Systems
Peter Kedron, Wenwen Li, Stewart Fotheringham, Michael Goodchild
Summary: The ability to reproduce and replicate research results, a cornerstone of the scientific method, has gained widespread attention and led to innovations. Geospatial researchers can learn and contribute from practices developed in other disciplines to enhance the reproducibility and replicability of research in their field.
INTERNATIONAL JOURNAL OF GEOGRAPHICAL INFORMATION SCIENCE
(2021)
Article
Dentistry, Oral Surgery & Medicine
Eneko Solaberrieta, Xabier Amezua, Mikel Iturrate, Xabier Garikano
Summary: The influence of facial scanning methods on the accuracy of transferring a maxillary digital scan to a 3D face scan in a virtual facebow technique was analyzed in this study. The results showed that different facial scanning methods had a significant impact on accuracy, with structured white light scanning method achieving higher levels of accuracy and precision.
JOURNAL OF PROSTHETIC DENTISTRY
(2022)
Review
Education & Educational Research
Emma Marsden, Kara Morgan-Short
Summary: Open research practices are relevant to all stages of research and they come with their own set of challenges. This article discusses the key aspects of open research, including its rationales, infrastructure, behaviors, and challenges. It argues that open research is an important part of the future, but significant changes are needed to overcome the challenges.
Article
Medicine, Legal
Fiona Sewell, Ian Ragan, Graham Horgan, David Andrew, Thomas Holmes, Irene Manou, Boris P. Mueller, Tim Rowan, Barbara G. Schmitt, Marco Corvaro
Summary: There are currently three test guidelines for acute oral toxicity studies, but the subjectivity of one guideline may be hindering its wider use. In order to address this, the NC3Rs and EPAA collaborated to analyze historical data and provide recommendations on the recognition of 'evident toxicity'.
REGULATORY TOXICOLOGY AND PHARMACOLOGY
(2024)
Article
Medicine, Legal
Michael DeVito, Bas Bokkers, Majorie B. M. van Duursen, Karin van Ede, Mark Feeley, Elsa Antunes Fernandes Gaspar, Laurie Haws, Sean Kennedy, Richard E. Peterson, Ron Hoogenboom, Keiko Nohara, Kim Petersen, Cynthia Rider, Martin Rose, Stephen Safe, Dieter Schrenk, Matthew W. Wheeler, Daniele S. Wikoff, Bin Zhao, Martin van den Berg
Summary: In October 2022, the World Health Organization reevaluated the toxic equivalency factors (TEFs) for chlorinated dioxin-like compounds in a panel convened in Lisbon. This effort utilized an updated database, Bayesian dose response modeling, and meta-analysis to derive Best-Estimate TEFs. Applying these new TEFs may result in lower total toxic equivalents for dioxin-like chemicals.
REGULATORY TOXICOLOGY AND PHARMACOLOGY
(2024)
