Article
Biology
Patrick Bodilly Kane, Jonathan Kimmelman
Summary: The Reproducibility Project: Cancer Biology aims to provide evidence on reproducibility in cancer research and identify factors influencing reproducibility. Results suggest the current diagnostic machine in cancer research recommends many non-reproducible findings for further advancement, raising concerns. However, further evaluation is needed, with unanswered questions on the machine's accuracy, societal costs of false positives and negatives, and interpretation of its outputs by scientists and others.
Editorial Material
Microbiology
A. Murat Eren, Evan Kiefl, Alon Shaiber, Iva Veseli, Samuel E. Miller, Matthew S. Schechter, Isaac Fink, Jessica N. Pan, Mahmoud Yousef, Emily C. Fogarty, Florian Trigodet, Andrea R. Watson, Ozcan C. Esen, Ryan M. Moore, Quentin Clayssen, Michael D. Lee, Veronika Kivenson, Elaina D. Graham, Bryan D. Merrill, Antti Karkman, Daniel Blankenberg, John M. Eppley, Andreas Sjodin, Jarrod J. Scott, Xabier Vazquez-Campos, Luke J. McKay, Elizabeth A. McDaniel, Sarah L. R. Stevens, Rika E. Anderson, Jessika Fuessel, Antonio Fernandez-Guerra, Lois Maignien, Tom O. Delmont, Amy D. Willis
Summary: In microbiology, there is an abundance of big data, but the workflows designed to interpret the data may constrain the biological questions that can be asked. Anvi'o, a community-led multi-omics platform, is maturing into an open software ecosystem that reduces constraints in 'omics data analyses.
NATURE MICROBIOLOGY
(2021)
Editorial Material
Biotechnology & Applied Microbiology
Andreas Gollner, Markus Koester, Paul Nicklin, Thomas Trieselmann, Elliott Klein, Jaromir Vlach, Claudia Heine, Marc Grundl, Juergen Ramharter, David Wyatt, Menorca Chaturvedi, Alessio Ciulli, Katharine C. Carter, Susanne Mueller, Daniel Bischoff, Peter Ettmayer, Eric Haaksma, Juergen Mack, Darryl McConnell, Dirk Stenkamp, Harald Weinstabl, Matthias Zentgraf, Clive R. Wood, Florian Montel
Summary: Pharmacological probes are essential for studying disease biology and developing new therapies. The Boehringer Ingelheim open innovation portal opnMe.com addresses the issue of using inadequate molecules by sharing extensively validated probes with the scientific community.
NATURE REVIEWS DRUG DISCOVERY
(2022)
Article
Computer Science, Theory & Methods
Anna L. Smith, Tian Zheng, Andrew Gelman
Summary: The paper aims to compare two studies using predictive models and address the replication crisis in the behavioral sciences. By utilizing prediction scoring, the researchers are able to quantitatively assess the agreement between datasets and uncover differences between populations and settings.
STATISTICS AND COMPUTING
(2023)
Editorial Material
Neurosciences
Timothy Daly
Summary: The Journal of Alzheimer's Disease (JAD) is not only a platform for cutting-edge science and ethical reflection but also for philosophical discussions in science. It is suggested that interdisciplinary researchers should publish their innovative questions and findings about Alzheimer's disease in JAD.
JOURNAL OF ALZHEIMERS DISEASE
(2023)
Article
Biotechnology & Applied Microbiology
Danying Shao, Gretta D. Kellogg, Ali Nematbakhsh, Prashant K. Kuntala, Shaun Mahony, B. Franklin Pugh, William K. M. Lai
Summary: Reproducibility is a significant challenge in (epi)genomic research, especially with the rapid generation of high-throughput sequencing data. We have developed a web-based project management platform called PEGR that tracks and quality controls experiments, compatible with multiple assays and bioinformatic pipelines, supporting rigor and reproducibility for biochemists and bioinformaticians.
Review
Biochemical Research Methods
Verena Heise, Constance Holman, Hung Lo, Ekaterini Maria Lyras, Mark Christopher Adkins, Maria Raisa Jessica Aquino, Konstantinos I. Bougioukas, Katherine O. Bray, Martyna Gajos, Xuanzong Guo, Corinna Hartling, Rodrigo Huerta-Gutierrez, Miroslava Jindrova, Joanne P. M. Kenney, Adrianna P. Kepinska, Laura Kneller, Elena Lopez-Rodriguez, Felix Muehlensiepen, Angela Richards, Gareth Richards, Maximilian Siebert, James A. Smith, Natalie Smith, Nicolai Stransky, Sirpa Tarvainen, Daniela Sofia Valdes, Kayleigh L. Warrington, Nina-Maria Wilpert, Disa Witkowska, Mirela Zaneva, Jeanette Zanker, Tracey L. Weissgerber
Summary: Open, reproducible, and replicable research practices are crucial in scientific research. Grassroots-level training, often conducted by early career researchers for early career researchers, can provide a platform for learning new practices. This study outlines ten simple rules for participants of such training courses to implement robust research practices in their own projects. These rules include prioritizing and planning the implementation process, managing implementation problems, and integrating reproducible research and open science practices into future research careers. Strategies for course organizers to prepare and support participants during the implementation process are also discussed.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Neurosciences
Taiga Abe, Ian Kinsella, Shreya Saxena, E. Kelly Buchanan, Joao Couto, John Briggs, Sian Lee Kitt, Ryan Glassman, John Zhou, Liam Paninski, John P. Cunningham
Summary: A key aspect of neuroscience research is the development of powerful, general-purpose data analyses that process large datasets. This article introduces Neuroscience Cloud Analysis As a Service (NeuroCAAS), an automated open-source analysis platform that offers infrastructure reproducibility, simplifies data analyses, and accelerates their dissemination and use in neuroscientific discovery.
Article
Biochemistry & Molecular Biology
Nicole Y. Souren, Norbert E. Fusenig, Stefanie Heck, Wilhelm G. Dirks, Amanda Capes-Davis, Franca Bianchini, Christoph Plass
Summary: Misidentification of cell lines is a serious threat to scientific reproducibility. Strict multi-layered quality control, collaborations between journals, research institutions, and funders, as well as regular authentication schemes and staff training, are essential to address this issue. Future steps should focus on enhancing good cell culture practices.
Article
Environmental Sciences
Donele Wilkins, Amy J. Schulz
Summary: Communities affected by environmental exposures and health disparities recognize the role of racism in shaping these risks. More researchers are focusing on racism as a fundamental driver of racial inequities in environmental health. Research and funding institutions are committed to addressing structural racism. This article discusses strategies for taking explicitly antiracist approaches to community engagement in environmental health research.
ENVIRONMENTAL HEALTH PERSPECTIVES
(2023)
Article
Biodiversity Conservation
Facundo X. Palacio, Corey T. Callaghan, Pedro Cardoso, Emma J. Hudgins, Marta A. Jarzyna, Gianluigi Ottaviani, Federico Riva, Caio Graco-Roza, Vaughn Shirey, Stefano Mammola
Summary: The widespread use of species traits in ecology has led to a rapid increase in functional diversity analyses. Researchers can utilize an eight-step protocol to conduct and report functional diversity analyses, aiming to improve reproducibility, transparency, and comparability in research.
Review
Public, Environmental & Occupational Health
Roger D. Peng, Stephanie C. Hicks
Summary: Advancements in computing technology have led to significant progress in scientific discovery, but have also raised concerns about the reproducibility of data analyses and the replicability of scientific findings. These issues highlight the importance of ensuring transparency and rigor in research practices to improve the reliability of public health research in the future.
ANNUAL REVIEW OF PUBLIC HEALTH, VOL 42, 2021
(2021)
Article
Environmental Sciences
C. Kelly, M. Wynants, A. Patrick, A. Taylor, F. Mkilema, M. Nasseri, S. Lewin, L. Munishi, K. Mtei, P. Ndakidemi, W. Blake
Summary: Pastoralist communities worldwide are facing challenges in food and feed productivity, with East African agro-pastoral systems approaching a tipping point in land degradation. The lack of high spatial resolution soil health data is a key barrier, but bridging this gap through community-led initiatives and using portable soil scanner technology can improve decision-making and mitigate land degradation threats.
ENVIRONMENTAL RESEARCH LETTERS
(2022)
Article
Biology
Alejandro de la Vega, Roberta Rocca, Ross W. Blair, Christopher J. Markiewicz, Jeff Mentch, James D. Kent, Peer Herholz, Satrajit S. Ghosh, Russell A. Poldrack, Tal Yarkoni
Summary: Neuroscout is an end-to-end platform for analyzing naturalistic fMRI data, which automatically annotates stimuli from multiple ecologically-valid datasets and reduces the burden of reproducible research. Through validating the automatic feature extraction approach, it has the potential to support more robust fMRI research and democratize fMRI research.
Article
Computer Science, Information Systems
Anna Ostropolets, Yasser Albogami, Mitchell Conover, Juan M. Banda, William A. Baumgartner Jr, Clair Blacketer, Priyamvada Desai, Scott L. DuVall, Stephen Fortin, James P. Gilbert, Asieh Golozar, Joshua Ide, Andrew S. Kanter, David M. Kern, Chungsoo Kim, Lana Y. H. Lai, Chenyu Li, Feifan Liu, Kristine E. Lynch, Evan Minty, Maria Ines Neves, Ding Quan Ng, Tontel Obene, Victor Pera, Nicole Pratt, Gowtham Rao, Nadav Rappoport, Ines Reinecke, Paola Saroufim, Azza Shoaibi, Katherine Simon, Marc A. Suchard, Joel N. Swerdel, Erica A. Voss, James Weaver, Linying Zhang, George Hripcsak, Patrick B. Ryan
Summary: Objective observational studies should be robust and reproducible, but nonreproducibility is often caused by unclear reporting. This study aimed to assess how different interpretations of study logic can impact patient characteristics.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2023)
Article
Biochemistry & Molecular Biology
Scott Ferguson, Ashley Jones, Kevin Murra, Benjamin Schwessinger, Justin O. Borevitz
Summary: Synteny loss, primarily caused by unequal homologous recombination, is commonly observed when comparing closely related species. In this study, the genomes of three closely related Eucalyptus species were analyzed, revealing that approximately 48% of the genomes remained syntenic while approximately 36% underwent rearrangements. It was found that rearrangements highly fragmented microsynteny and potentially altered the phenotypes of the Eucalyptus species. This study highlights the importance of using an unbiased framework in genomic variation studies and emphasizes the potential impact of rearrangements on species differentiation and adaptation.
Editorial Material
Biochemistry & Molecular Biology
Ulrich Mansmann, Clara Locher, Fabian Prasser, Tracey Weissgerber, Ulrich Sax, Martin Posch, Evelyne Decullier, Ioana A. A. Cristea, Thomas P. A. Debray, Leonhard Held, David Moher, John P. A. Ioannidis, Joseph S. S. Ross, Christian Ohmann, Florian Naudet
Summary: Data sharing improves the value of medical research and promotes trust in clinical trials, but more biomedical researchers need training in approaches such as meta-research, data science, and ethical, legal, and social issues.
Article
Multidisciplinary Sciences
Ashley Jones, David Stanley, Scott Ferguson, Benjamin Schwessinger, Justin Borevitz, Norman Warthmann
Summary: This study presents a cost-conscious protocol for generating multiplexed short-read DNA libraries using a bead-linked transposome from Illumina, which reduces costs and labor time compared to conventional methods.
Review
Biochemical Research Methods
Verena Heise, Constance Holman, Hung Lo, Ekaterini Maria Lyras, Mark Christopher Adkins, Maria Raisa Jessica Aquino, Konstantinos I. Bougioukas, Katherine O. Bray, Martyna Gajos, Xuanzong Guo, Corinna Hartling, Rodrigo Huerta-Gutierrez, Miroslava Jindrova, Joanne P. M. Kenney, Adrianna P. Kepinska, Laura Kneller, Elena Lopez-Rodriguez, Felix Muehlensiepen, Angela Richards, Gareth Richards, Maximilian Siebert, James A. Smith, Natalie Smith, Nicolai Stransky, Sirpa Tarvainen, Daniela Sofia Valdes, Kayleigh L. Warrington, Nina-Maria Wilpert, Disa Witkowska, Mirela Zaneva, Jeanette Zanker, Tracey L. Weissgerber
Summary: Open, reproducible, and replicable research practices are crucial in scientific research. Grassroots-level training, often conducted by early career researchers for early career researchers, can provide a platform for learning new practices. This study outlines ten simple rules for participants of such training courses to implement robust research practices in their own projects. These rules include prioritizing and planning the implementation process, managing implementation problems, and integrating reproducible research and open science practices into future research careers. Strategies for course organizers to prepare and support participants during the implementation process are also discussed.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Neurosciences
Abi Fukami-Gartner, Ana A. Baburamani, Ralica Dimitrova, Prachi A. Patkee, Olatz Ojinaga-Alfageme, Alexandra F. Bonthrone, Daniel Cromb, Alena U. Uus, Serena J. Counsell, Joseph Hajnal, Jonathan O'Muircheartaigh, Mary A. Rutherford
Summary: Down syndrome (DS) is a common genetic cause of intellectual disability. In this study, researchers analyzed the brain volumes of neonates with DS using neuroimaging techniques. They found that the DS brain showed significant reductions in overall volume, cerebral white matter, and cerebellar volumes, as well as differences in relative lobar volumes. Furthermore, certain features such as enlarged deep gray matter volume and lateral ventricle enlargement were observed. Assessing phenotypic severity at the neonatal stage may help guide early interventions and improve neurodevelopmental outcomes in children with DS.
Article
Agronomy
Susann Auer, Jutta Ludwig-Mueller
Summary: The commercial aspect of growing Brassica crops is influenced by the worldwide occurrence of the clubroot pathogen, Plasmodiophora brassicae, which causes significant crop yield reduction and is difficult to eradicate. Chemical treatments are not widely available, and the majority of control is through resistant crops. Biocontrol agents have shown some effectiveness in reducing clubroot, but commercial application is limited. Bacterial and fungal endophytes hold great potential for biocontrol, but further research is needed before field-scale application can be achieved.
EUROPEAN JOURNAL OF PLANT PATHOLOGY
(2023)
Article
Plant Sciences
Lily Chen, Diep R. Ganguly, Sarah H. Shafik, Florence Danila, Christopher P. L. Grof, Robert E. Sharwood, Robert T. Furbank
Summary: The localization of SWEET4 protein in the seed and stem of Setaria viridis suggests its involvement in supplying sugars to carbon sink tissues. SWEET proteins play a crucial role in apoplastic sugar transport during phloem unloading and the post-phloem pathway in developing seeds. The study provides evidence for the role of SWEET proteins in the apoplastic transport pathway and proposes a pathway for post-phloem sugar transport into the seed.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Biochemistry & Molecular Biology
Wil Prall, Diep R. Ganguly, Brian D. Gregory
Summary: Although covalent nucleotide modifications were first identified on tRNAs and rRNAs, they have also been found on mRNAs. These modifications have significant effects on the processing and functionality of these protein-encoding molecules. This article focuses on the understanding, detection, and study of covalent nucleotide modifications on mRNAs in plants, as well as the outstanding future questions in this field.
Article
Nutrition & Dietetics
Lauren Hurley, Jesse Jauhal, Sharadyn Ille, Kasey Pull, Olga V. Malysheva, Nafisa M. Jadavji
Summary: Maternal dietary deficiencies of folic acid and choline during pregnancy do not affect offspring behavior after ischemic stroke, but do impact brain histology and plasma levels of one-carbon metabolites. Sex differences in stroke outcomes were observed. This study highlights the importance of maternal nutrition and sex in stroke outcomes.
Article
Ecology
Daniel Powell, Benjamin Schwessinger, Celine H. Frere
Summary: Researchers uncover new information on the evolutionary relationship of emerging fungal pathogens through mitochondrial genome sequencing and phylogenetic analysis of seven species. They also develop a species-specific qPCR assay for rapid detection and demonstrate its application in a wild urban population of a dragon lizard.
ECOLOGY AND EVOLUTION
(2023)
Article
Neurosciences
Chaofei Bao, Xiaoyue Zhu, Joshua Moller-Mara, Jingjie Li, Sylvain Dubroqua, Jeffrey C. Erlich
Summary: This study reveals that the frontal orienting field (FOF) is a crucial node in the neural circuit for the dynamic representation of action values during decision-making under risk in rats. Silencing the FOF caused a change in the curvature of the rats' utility function and reduced lottery choices.
NATURE NEUROSCIENCE
(2023)
Article
Plant Sciences
Yunfei Hu, Li Zeng, Xiaodong Lv, Junhua Guo, Xiaoyan Li, Xiaohua Zhang, Dan Wang, Jingya Wang, Jinlong Bi, Magdalena M. M. Julkowska, Bo Li
Summary: This study identified NIGT1.4 as a novel contributor to maintained root growth under salt stress through analyzing natural variation of primary root length in Arabidopsis. NIGT1.4 was shown to promote primary root growth in response to salt stress through interaction with SnRK2.2 and 2.3. Moreover, NIGT1.4 was found to induce the expression of ERF1, which regulates downstream functional genes for maintained primary root elongation.
Review
Nutrition & Dietetics
Sapna Virdi, Abbey M. Mckee, Manogna Nuthi, Nafisa M. Jadavji
Summary: Dietary supplementation of 1C components such as folic acid, vitamin B12, and choline has positive effects on healthy aging by integrating nutritional signals with multiple processes in the human body. Considerations for promoting healthy aging through dietary supplementation include using precision medicine for individualized plans, avoiding over-supplementation, and combining therapies.
Article
Biodiversity Conservation
Martina Huber, Magdalena M. M. Julkowska, L. Basten Snoek, Hans van Veen, Justine Toulotte, Virender Kumar, Kaisa Kajala, Rashmi Sasidharan, Ronald Pierik
Summary: This study aims to improve weed suppression in rice farming by enhancing the crop's shading capacity, thus reducing the reliance on herbicide application and promoting environmental sustainability.
PLANTS PEOPLE PLANET
(2023)
Article
Public, Environmental & Occupational Health
Robyn N. Hall, Ashley Jones, Emma Crean, Victoria Marriott, Nevada Pingault, Alexandra Marmor, Timothy Sloan-Gardner, Karina Kennedy, Kerryn Coleman, Vanessa Johnston, Benjamin Schwessinger
Summary: The Australian Capital Territory (ACT) detected an incursion of the SARS-CoV-2 Delta variant. Public health interventions, including a territory-wide lockdown and comprehensive contact tracing, were rapidly implemented. Genomic sequencing revealed at least 13 independent incursions with onward spread in the community, and different incursions affected distinct cohorts.
EPIDEMIOLOGY AND INFECTION
(2023)
