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E-raamat: Research in the Biomedical Sciences: Transparent and Reproducible

Edited by (Adjunct Professor, Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA), Edited by (Director, Corporate Liaison a), Edited by (Reader in Pharmacology, Kings College London, Rayne Institute, St. Thomas Hospital, London, UK)
  • Formaat: PDF+DRM
  • Ilmumisaeg: 20-Oct-2017
  • Kirjastus: Academic Press Inc
  • Keel: eng
  • ISBN-13: 9780128047262
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Research in the Biomedical Sciences: Transparent and ReproducibleSuurem pilt
  • Formaat: PDF+DRM
  • Ilmumisaeg: 20-Oct-2017
  • Kirjastus: Academic Press Inc
  • Keel: eng
  • ISBN-13: 9780128047262
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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

Muu info

Addresses experimentation, statistical analyses, and transparency and reproducibility issues from a didactic, pragmatic, and relevant standpoint in the biomedical sciences
List of Contributors
vii
Preface ix
1 Reproducibility in Biomedical Research
Kevin Mullane
Michael J. Curtis
Michael Williams
1.1 Introduction
2(1)
1.2 Defining Reproducibility
3(4)
1.3 Discipline Specific Terminology in the Biomedical Sciences?
7(1)
1.4 Experimental Factors in Addition to Statistics That Affect Reproducibility
8(6)
1.5 The Impact of the Internet on the Evolution of Research Practices---Databases and Third Party Analyses
14(4)
1.6 The Reproducibility Problem
18(8)
1.7 The Literature on Reproducibility in Biomedical Research
26(5)
1.8 Is There a Reproducibility Crisis?
31(1)
1.9 Trouble at the Laboratory?
32(1)
1.10 Retractions
32(12)
1.11 Reproducibility and Translational Medicine
44(7)
1.12 Conclusions
51(17)
References
54(14)
2 Experimental Planning and Execution
Kevin Mullane
Michael J. Curtis
Michael Williams
2.1 Introduction
68(1)
2.2 Hypothesis Generation
68(4)
2.3 Experimental Planning
72(6)
2.4 Addressing the Basics in Experimental Design
78(3)
2.5 Preclinical Experimental Systems
81(12)
2.6 Transparency and Accountability: Documenting Experimental Detail
93(1)
2.7 Pharmacokinetics
94(1)
2.8 Bias in Experimental Design
94(1)
2.9 Experimental Implementation
95(2)
2.10 Experimental Analysis
97(1)
2.11 Increasing the Probability of Generating Meaningful Results
98(10)
References
100(8)
3 Statistical Analysis in Preclinical Biomedical Research
Michael J. Marino
3.1 Introduction---Background to Statistics---Use and Misuse
108(8)
3.2 Exploratory Research and Exploratory Data Analysis
116(6)
3.3 Data Transformation and Normalization
122(2)
3.4 The Experimental Subject
124(1)
3.5 Determining Sample Size (n)
124(3)
3.6 Inferential or Frequentist Statistics
127(7)
3.7 Correlation
134(1)
3.8 Interpretation of Inferential Statistics
135(2)
3.9 Reporting of Results
137(2)
3.10 Bayesian Inference
139(1)
3.11 Big Data Issues
139(1)
3.12 P-Hacking
140(2)
3.13 Is There a Need for a Real-World Accommodation of the Statistical Ideal?
142(4)
References
143(3)
4 Reporting Results
Michael Williams
Kevin Mullane
Michael J. Curtis
4.1 Introduction
146(1)
4.2 Preparing the Manuscript
146(3)
4.3 The Manuscript Structure---IMRAD
149(2)
4.4 Instructions/Guidelines for Authors
151(1)
4.5 Assembling the Manuscript
152(4)
4.6 Results
156(16)
4.7 Discussion/Conclusions
172(2)
4.8 Materials and Methods
174(2)
4.9 Abstract
176(1)
4.10 Introduction
176(1)
4.11 Title Page
177(3)
4.12 Acknowledgments
180(1)
4.13 References
180(1)
4.14 The Cover Letter
181(1)
4.15 Practical Aspects of the Peer Review Process
181(17)
References
191(7)
5 Addressing Reproducibility: Peer Review, Impact Factors, Checklists, Guidelines, and Reproducibility Initiatives
Michael Williams
Kevin Mullane
Michael J. Curtis
5.1 Introduction
198(1)
5.2 Peer Review
199(11)
5.3 Practical Aspects of Peer Review
210(16)
5.4 Bias in Peer Review
226(5)
5.5 Grant Peer Review
231(3)
5.6 Open Access Publishing (OAP)
234(6)
5.7 The Journal Impact Factor (JIF)
240(9)
5.8 Addressing the Future of Peer Review and the JIF
249(8)
5.9 Deemphasizing the JIF?
257(1)
5.10 Guidelines and Checklists
257(20)
5.11 Checklists
277(4)
5.12 Reproducibility Initiatives (RIs)
281(2)
5.13 RIs in Practice: Concerns and Outcomes
283(3)
5.14 Reproducibility Initiatives---progress to date?
286(2)
5.15 Improving Reproducibility Outcomes---Where Are We?
288(20)
References
290(18)
6 Biomedical Research in the 21st Century: Multiple Challenges in Resolving Reproducibility Issues
Kevin Mullane
Michael J. Curtis
Michael Williams
6.1 Introduction
308(1)
6.2 Background
308(2)
6.3 Biomedical Research, Drug Discovery, and Development
310(7)
6.4 Drug Discovery: Technological Advances and Alternative Approaches
317(17)
6.5 Researchers---the Images, the Reality, the Incentives
334(3)
6.6 Reproducibility and the Research Culture
337(2)
6.7 Consequences---not
339(1)
6.8 Conclusions
340(15)
References
344(11)
Index 355
Michael Williams is an Adjunct Professor of Pharmacology with the Feinberg School of Medicine, Northwestern University in Chicago, IL, USA Michael Curtis is a Reader in Pharmacology, Kings College London, Rayne Institute, St. Thomas Hospital, London, UK Kevin Mullane is Director, Corporate Liaison and Ventures with J. David Gladstone Institutes, University of California, San Francisco in San Francisco, CA
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