January 16, 2021

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Reproducibility in Biomedical Research

Reproducibility in Biomedical Research
Author : Erwin B. Montgomery
Publisher : Academic Press
Release Date : 2019-03-14
Category : Medical
Total pages :356
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Reproducibility in Biomedical Research: Epistemological and Statistical Problems explores the ideas and conundrums inherent in scientific research. It explores factors of reproducibility, including logic, distinguishing productive from unproductive irreproducibility, the scientific method, and the use of statistics. In multiple examples and six detailed case studies, the book demonstrates the misuse of logic resulting in unproductive irreproducibility, allowing researchers to develop their own logic and planning abilities. Biomedical researchers, clinicians, administrators of scientific institutions and funding agencies, journal editors, philosophers of science and medicine will find the arguments and explorations a valuable addition to their libraries. Considers the meaning and purpose of reproducibility to help design research Reviews famous case studies of alleged irreproducibility to determine if these could be reproducible Provides a theoretical aspect to practical issues surrounding research design and conduct

Research in the Biomedical Sciences

Research in the Biomedical Sciences
Author : Michael Williams,Michael Curtis,Kevin Mullane
Publisher : Academic Press
Release Date : 2017-10-20
Category : Science
Total pages :382
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Research in the Biomedical Sciences: Transparent and Reproducible documents the widespread concerns related to reproducibility in biomedical research and provides a best practices guide to effective and transparent hypothesis generation, experimental design, reagent standardization (including validation and authentication), statistical analysis, and data reporting. The book addresses issues in the perceived value of the existing peer review process and calls for the need for improved transparency in data reporting. It reflects new guidelines for publication that include manuscript checklists, replication/reproducibility initiatives, and the potential consequences for the biomedical research community and societal health and well-being if training, mentoring, and funding of new generations of researchers and incentives for publications are not improved. This book offers real world examples, insights, and solutions to provide a thought-provoking and timely resource for all those learning about, or engaged in, performing and supervising research across the biomedical sciences. Provides a “big picture perspective on the scope of reproducibility issues and covers initiatives that have potential as effective solutions Offers real-world research context for transparent, reproducible experimental design, execution and reporting of biomedical research with the potential to address aspects of the translational gap in drug discovery Highlights the importance of reproducibility and the necessary changes in biomedical and pharmaceutical research training and incentives to ensure sustainability

Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting

Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting
Author : National Academies of Sciences, Engineering, and Medicine,Health and Medicine Division,Board on Health Care Services,Board on Health Sciences Policy,Roundtable on Genomics and Precision Health,National Cancer Policy Forum,Forum on Neuroscience and Nervous System Disorders,Forum on Drug Discovery, Development, and Translation
Publisher : National Academies Press
Release Date : 2020-05-28
Category : Medical
Total pages :142
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Sharing knowledge is what drives scientific progress - each new advance or innovation in biomedical research builds on previous observations. However, for experimental findings to be broadly accepted as credible by the scientific community, they must be verified by other researchers. An essential step is for researchers to report their findings in a manner that is understandable to others in the scientific community and provide sufficient information for others to validate the original results and build on them. In recent years, concern has been growing over a number of studies that have failed to replicate previous results and evidence from larger meta-analyses, which have pointed to the lack of reproducibility in biomedical research. On September 25 and 26, 2019, the National Academies of Science, Engineering, and Medicine hosted a public workshop in Washington, DC, to discuss the current state of transparency in the reporting of preclinical biomedical research and to explore opportunities for harmonizing reporting guidelines across journals and funding agencies. Convened jointly by the Forum on Drug Discovery, Development, and Translation; the Forum on Neuroscience and Nervous System Disorders; the National Cancer Policy Forum; and the Roundtable on Genomics and Precision Health, the workshop primarily focused on transparent reporting in preclinical research, but also considered lessons learned and best practices from clinical research reporting. This publication summarizes the presentation and discussion of the workshop.

Research in the Biomedical Sciences

Research in the Biomedical Sciences
Author : Michael Curtis,Michael Williams
Publisher : Academic Press
Release Date : 2017-06-01
Category :
Total pages :356
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Research in the Biomedical Sciences: Transparent and Reproducible documents the widespread concerns related to reproducibility in biomedical research and provides a best practices guide to effective and transparent hypothesis generation, experimental design, reagent standardization (including validation and authentication), statistical analysis, and data reporting. The book addresses issues in the perceived value of the existing peer review process and calls for the need for improved transparency in data reporting. It reflects new guidelines for publication that include manuscript checklists, replication/reproducibility initiatives, and the potential consequences for the biomedical research community and societal health and well-being if training, mentoring, and funding of new generations of researchers and incentives for publications are not improved. This book offers real world examples, insights, and solutions to provide a thought-provoking and timely resource for all those learning about, or engaged in, performing and supervising research across the biomedical sciences. Provides a "big picture" perspective that includes the scope of the replicability issue and covers initiatives that have the potential to act as effective solutions Offers real world research context for transparent, replicable experimental design and execution and reporting of biomedical research with the potential to address aspects of the translational gap in drug discovery Highlights the importance of reproducibility and the necessary changes in biomedical and pharmaceutical research training and incentives to ensure sustainability

Reproducibility and Replicability in Science

Reproducibility and Replicability in Science
Author : National Academies of Sciences, Engineering, and Medicine,Policy and Global Affairs,Committee on Science, Engineering, Medicine, and Public Policy,Board on Research Data and Information,Division on Engineering and Physical Sciences,Committee on Applied and Theoretical Statistics,Board on Mathematical Sciences and Analytics,Division on Earth and Life Studies,Nuclear and Radiation Studies Board,Division of Behavioral and Social Sciences and Education,Committee on National Statistics,Board on Behavioral, Cognitive, and Sensory Sciences,Committee on Reproducibility and Replicability in Science
Publisher : National Academies Press
Release Date : 2019-10-20
Category : Science
Total pages :256
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One of the pathways by which the scientific community confirms the validity of a new scientific discovery is by repeating the research that produced it. When a scientific effort fails to independently confirm the computations or results of a previous study, some fear that it may be a symptom of a lack of rigor in science, while others argue that such an observed inconsistency can be an important precursor to new discovery. Concerns about reproducibility and replicability have been expressed in both scientific and popular media. As these concerns came to light, Congress requested that the National Academies of Sciences, Engineering, and Medicine conduct a study to assess the extent of issues related to reproducibility and replicability and to offer recommendations for improving rigor and transparency in scientific research. Reproducibility and Replicability in Science defines reproducibility and replicability and examines the factors that may lead to non-reproducibility and non-replicability in research. Unlike the typical expectation of reproducibility between two computations, expectations about replicability are more nuanced, and in some cases a lack of replicability can aid the process of scientific discovery. This report provides recommendations to researchers, academic institutions, journals, and funders on steps they can take to improve reproducibility and replicability in science.

Reproducibility in A.I. for Biomedical Research: an Application to Parkinson's Disease

Reproducibility in A.I. for Biomedical Research: an Application to Parkinson's Disease
Author : Christian Lee McDaniel
Publisher : Unknown
Release Date : 2019
Category :
Total pages :162
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Deep learning-based data analysis techniques have found many uses in biomedical re- search. Recent expansion of open source databases and computational tools has fostered distributed and explorative research. Under these conditions, reproducibil- ity and experimental rigor must be ensured. Developing explicit analysis pipelines exposes the scientific process and yields reproducible results. In this thesis, we look at the case of deep learning-based data analysis for Parkinson's disease (PD) research. We develop end-to-end pipelines in two PD-related fields: accelerometer data analysis and neuroimage analysis. First, we construct a simple yet robust recurrent neural network for classifying motor activity from accelerometer data alone; this has applications for identifying the mo- tor symptoms of PD. Next, we propose a novel graph convolutional network architecture for distinguishing PD patients vs. healthy controls from multimodal neuroimage data. Our pipelines standardize the data preprocessing and analysis steps, fostering reproducibility and deliberate progression of their respective fields.

Rigor Mortis

Rigor Mortis
Author : Richard Harris
Publisher : Basic Books
Release Date : 2018-05-01
Category : Medical
Total pages :288
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"A rewarding read for anyone who wants to know the unvarnished truth about how science really gets done."--Financial Times American taxpayers spend $30 billion annually funding biomedical research, but over half of these studies can't be replicated due to poor experimental design, improper methods, and sloppy statistics. Bad science doesn't just hold back medical progress, it can sign the equivalent of a death sentence for terminal patients. In Rigor Mortis, Richard Harris explores these urgent issues with vivid anecdotes, personal stories, and interviews with the top biomedical researchers. We need to fix our dysfunctional biomedical system--before it's too late.

Interpreting Biomedical Science

Interpreting Biomedical Science
Author : Ülo Maiväli
Publisher : Academic Press
Release Date : 2015-06-12
Category : Science
Total pages :416
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Interpreting Biomedical Science: Experiment, Evidence, and Belief discusses what can go wrong in biological science, providing an unbiased view and cohesive understanding of scientific methods, statistics, data interpretation, and scientific ethics that are illustrated with practical examples and real-life applications. Casting a wide net, the reader is exposed to scientific problems and solutions through informed perspectives from history, philosophy, sociology, and the social psychology of science. The book shows the differences and similarities between disciplines and different eras and illustrates the concept that while sound methodology is necessary for the progress of science, we cannot succeed without a right culture of doing things. Features theoretical concepts accompanied by examples from biological literature Contains an introduction to various methods, with an emphasis on statistical hypothesis testing Presents a clear argument that ties the motivations and ethics of individual scientists to the success of their science Provides recommendations on how to safeguard against scientific misconduct, fraud, and retractions Arms young scientists with practical knowledge that they can use every day

The Genetics of Pain

The Genetics of Pain
Author : Jeffrey Steven Mogil
Publisher : International Assn for the Study of Pain
Release Date : 2004
Category : Medical
Total pages :349
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No field of biology has engendered so much interest, hope, and hype as genetics. Advances in molecular, statistical and behavioral methodologies have suddenly allowed genetic investigations of complex biological phenomena, including pain. Genetic studies of pain are already showing their power to identify new molecular targets for drug development and create new animal models of pain pathology. Alone among biological approaches, pain genetics can explain why we're not all alike with respect to pain - why some people hurt more, and receive less benefit from existing analgesics. The knowledge gained holds the promise of allowing truly individualized pain therapy.

The Practice of Reproducible Research

The Practice of Reproducible Research
Author : Justin Kitzes,Daniel Turek,Fatma Deniz
Publisher : Univ of California Press
Release Date : 2017-10-17
Category : Science
Total pages :368
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The Practice of Reproducible Research presents concrete examples of how researchers in the data-intensive sciences are working to improve the reproducibility of their research projects. In each of the thirty-one case studies in this volume, the author or team describes the workflow that they used to complete a real-world research project. Authors highlight how they utilized particular tools, ideas, and practices to support reproducibility, emphasizing the very practical how, rather than the why or what, of conducting reproducible research. Part 1 provides an accessible introduction to reproducible research, a basic reproducible research project template, and a synthesis of lessons learned from across the thirty-one case studies. Parts 2 and 3 focus on the case studies themselves. The Practice of Reproducible Research is an invaluable resource for students and researchers who wish to better understand the practice of data-intensive sciences and learn how to make their own research more reproducible.

Interpreting Biomedical Science

Interpreting Biomedical Science
Author : Ülo Maiväli
Publisher : Academic Press
Release Date : 2015-06-12
Category : Science
Total pages :416
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Interpreting Biomedical Science: Experiment, Evidence, and Belief discusses what can go wrong in biological science, providing an unbiased view and cohesive understanding of scientific methods, statistics, data interpretation, and scientific ethics that are illustrated with practical examples and real-life applications. Casting a wide net, the reader is exposed to scientific problems and solutions through informed perspectives from history, philosophy, sociology, and the social psychology of science. The book shows the differences and similarities between disciplines and different eras and illustrates the concept that while sound methodology is necessary for the progress of science, we cannot succeed without a right culture of doing things. Features theoretical concepts accompanied by examples from biological literature Contains an introduction to various methods, with an emphasis on statistical hypothesis testing Presents a clear argument that ties the motivations and ethics of individual scientists to the success of their science Provides recommendations on how to safeguard against scientific misconduct, fraud, and retractions Arms young scientists with practical knowledge that they can use every day

Animal Models in Biomedical Research

Animal Models in Biomedical Research
Author : Anonim
Publisher : DIANE Publishing
Release Date : 1993-07
Category :
Total pages :80
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Statistical Challenges in Assessing and Fostering the Reproducibility of Scientific Results

Statistical Challenges in Assessing and Fostering the Reproducibility of Scientific Results
Author : National Academies of Sciences, Engineering, and Medicine,Division on Engineering and Physical Sciences,Board on Mathematical Sciences and Their Applications,Committee on Applied and Theoretical Statistics
Publisher : National Academies Press
Release Date : 2016-03-29
Category : Mathematics
Total pages :132
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Questions about the reproducibility of scientific research have been raised in numerous settings and have gained visibility through several high-profile journal and popular press articles. Quantitative issues contributing to reproducibility challenges have been considered (including improper data measurement and analysis, inadequate statistical expertise, and incomplete data, among others), but there is no clear consensus on how best to approach or to minimize these problems. A lack of reproducibility of scientific results has created some distrust in scientific findings among the general public, scientists, funding agencies, and industries. While studies fail for a variety of reasons, many factors contribute to the lack of perfect reproducibility, including insufficient training in experimental design, misaligned incentives for publication and the implications for university tenure, intentional manipulation, poor data management and analysis, and inadequate instances of statistical inference. The workshop summarized in this report was designed not to address the social and experimental challenges but instead to focus on the latter issues of improper data management and analysis, inadequate statistical expertise, incomplete data, and difficulties applying sound statistic inference to the available data. Many efforts have emerged over recent years to draw attention to and improve reproducibility of scientific work. This report uniquely focuses on the statistical perspective of three issues: the extent of reproducibility, the causes of reproducibility failures, and the potential remedies for these failures.

Reproducibility

Reproducibility
Author : Harald Atmanspacher,Sabine Maasen
Publisher : John Wiley & Sons
Release Date : 2016-07-05
Category : Education
Total pages :600
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A review of the scientific method. In the scientific method, results must be capable of being reproduced to be valid.

Metabolomics for Biomedical Research

Metabolomics for Biomedical Research
Author : Jerzy Adamski
Publisher : Academic Press
Release Date : 2020-03-20
Category : Medical
Total pages :266
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Metabolomics for Biomedical Research brings together recent progress on study design, analytics, biostatistics and bioinformatics for the success of metabolomics research. Metabolomics represents a very interdisciplinary research prominent in the functional analyses of living systems; hence, this book focuses on translation and medical aspects. The book discusses topics such as biomarkers and their requirements to be used in medical research, with the parameters and approaches on how to validate their quality; and animal models and other approaches, as stem cells and organoid culture. Additionally, it explains how metabolomics may be applied in prediction of individual response to drug or disease progression. This book is a valuable source for researchers on systems biology and other members of biomedical field interested in metabolism-oriented studies for medical research. Focuses on metabolomics in translational and medical research Provides basics for, and concepts of, contemporary translational personalized medicine research with metabolomics Brings the major recent progresses on design, analytics, biostatistics and bioinformatics relating to the success of metabolomics research