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Suggested Citation:"Appendix A: References." National Academies of Sciences, Engineering, and Medicine. 2020. Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25627.
Page 101
Suggested Citation:"Appendix A: References." National Academies of Sciences, Engineering, and Medicine. 2020. Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25627.
Page 102
Suggested Citation:"Appendix A: References." National Academies of Sciences, Engineering, and Medicine. 2020. Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25627.
Page 103
Suggested Citation:"Appendix A: References." National Academies of Sciences, Engineering, and Medicine. 2020. Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting: Proceedings of a Workshop. Washington, DC: The National Academies Press. doi: 10.17226/25627.
Page 104

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Appendix A References Anderson, M. S., B. C. Martinson, and R. De Vries. 2007. Normative dissonance in science: Results from a national survey of U.S. scientists. Journal of Empirical Research on Human Research Ethics 2(4):3–14. Bik, E. M., A. Casadevall, and F. C. Fang. 2016. The prevalence of inappropriate image du- plication in biomedical research publications. mBio 7(3):e00809-16. Bik, E. M., F. C. Fang, A. L. Kullas, R. J. Davis, and A. Casadevall. 2018. Analysis and correc- tion of inappropriate image duplication: The Molecular and Cellular Biology experience. Molecular and Cellular Biology 38(20):e00309-18. Bosk, C. L., M. Dixon-Woods, C. A. Goeschel, and P. J. Pronovost. 2009. Reality check for checklists. Lancet 374(9688):444–445. Casadevall, A., and F. C. Fang. 2016. Rigorous science: A how-to guide. mBio 7(6):e01902-16. Chan, A.-W., A. Hróbjartsson, M. T. Haahr, P. C. Gøtzsche, and D. G. Altman. 2004. Empiri- cal evidence for selective reporting of outcomes in randomized trials: Comparison of protocols to published articles. JAMA 291:2457–2465. Chan, A.-W., A. Hróbjartsson, K. J. Jørgensen, P. C. Gøtzsche, and D. G. Altman. 2008. Dis- crepancies in sample size calculations and data analyses reported in randomized trials: Comparison of publications with protocols. BMJ 337:a2299. Chan, A.-W., J. M. Tetzlaff, D. G. Altman, K. Dickersin, and D. Moher. 2013a. SPIRIT 2013: New guidance for content of clinical trial protocols. Lancet 381(9861):91–92. Chan, A.-W., J. M. Tetzlaff, D. G. Altman, A. Laupacis, P. C. Gøtzsche, K. Krleža-Jeri c, ´ A. Hróbjartsson, H. Mann, K. Dickersin, J. A. Berlin, C. J. Doré, W. R. Parulekar, W. S. Summerskill, T. Groves, K. F. Schulz, H. C. Sox, F. W. Rockhold, D. Rennie, and D. Moher. 2013b. SPIRIT 2013 statement: Defining standard protocol items for clinical trials. Annals of Internal Medicine 158(3):200–207. Chan, A.-W., J. M. Tetzlaff, P. C. Gøtzsche, D. G. Altman, H. Mann, J. A. Berlin, K. Dickersin, A. Hróbjartsson, K. F. Schulz, W. R. Parulekar, K. Krleza-Jeric, A. Laupacis, and D. Mo- her. 2013c. SPIRIT 2013 explanation and elaboration: Guidance for protocols of clinical trials. BMJ 346:e7586. 101 PREPUBLICATION COPY—Uncorrected Proofs

102 ENHANCING SCIENTIFIC REPRODUCIBILITY Chan, A.-W., A. Pello, J. Kitchen, A. Axentiev, J. I. Virtanen, A. Liu, and E. Hemminki. 2017. Association of trial registration with reporting of primary outcomes in protocols and publications. JAMA 318(17):1709–1711. Chuang, K. V., and M. J. Keiser. 2018a. Adversarial controls for scientific machine learning. ACS Chemical Biology 13(10):2819–2821. Chuang, K. V., and M. J. Keiser. 2018b. Comment on “Predicting reaction performance in C-N cross-coupling using machine learning.” Science 362(6416). Collins, F. S., and L. A. Tabak. 2014. Policy: NIH plans to enhance reproducibility. Nature 505(7485):612–613. Fanelli, D., J. P. A. Ioannidis, and S. Goodman. 2018. Improving the integrity of published science: An expanded taxonomy of retractions and corrections. European Journal of Clinical Investigation 48(4). Gawande, A. 2009. The checklist manifesto: How to get things right. New York: Henry Holt and Company. Getz, K., R. Zuckerman, A. Cropp, A. Hindle, R. Krauss, and K. Kaitin. 2011. Measuring the incidence, causes, and repercussions of protocol amendments. Drug Information Journal 45:265–275. Hróbjartsson, A., J. Pildal, A.-W. Chan, M. T. Haahr, D. G. Altman, and P. C. Gøtzsche. 2009. Reporting on blinding in trial protocols and corresponding publications was often inadequate but rarely contradictory. Journal of Clinical Epidemiology 62:967–973. Hudson, K. L., M. S. Lauer, and F. S. Collins. 2016. Toward a new era of trust and transpar- ency in clinical trials. JAMA 316(13):1353–1354. Ioannidis, J. P. 2005. Why most published research findings are false. PLOS Medicine 2(8):e124. Jamieson, K. H., M. McNutt, V. Kiermer, and R. Sever. 2019. Signaling the trustworthiness of science. Proceedings of the National Academy of Sciences in the United States of America 116(39):19231–19236. Kiley, R., T. Peatfield, J. Hansen, and R. Reddington. 2017. Data sharing from clinical trials—a research funder’s perspective. New England Journal of Medicine 377:1990–1992. Landis, S. C., S. G. Amara, K. Asadullah, C. P. Austin, R. Blumenstein, E. W. Bradley, R. G. Crystal, R. B. Darnell, R. J. Ferrante, H. Fillit, R. Finkelstein, M. Fisher, H. E. Gendelman, R. M. Golub, J. L. Goudreau, R. A. Gross, A. K. Gubitz, S. E. Hes- terlee, D. W. Howells, J. Huguenard, K. Kelner, W. Koroshetz, D. Krainc, S. E. Lazic, M. S. Levine, M. R. Macleod, J. M. McCall, R. T. Moxley 3rd, K. Narasimhan, L. J. Noble, S. Perrin, J. D. Porter, O. Steward, E. Unger, U. Utz, and S. D. Silberberg. 2012. A call for transparent reporting to optimize the predictive value of preclinical research. Nature 490(7419):187–191. Macleod, M. R., H. B. van der Worp, E. S. Sena, D. W. Howells, U. Dirnagl, and G. A. Donnan. 2008. Evidence for the efficacy of NXY-059 in experimental focal cerebral ischaemia is confounded by study quality. Stroke 39(10):2824–2829. Mayo-Wilson, E., K. Vander Ley, K. Dickersin, and M. Helfand. 2017. Patient-Centered Out- comes Research Institute (PCORI) Methodology Standards to improve the design and reporting of research. Abstract for poster presentation at the Eighth International Congress on Peer Review and Scientific Publication, Chicago, IL. 0326 (accessed November 20, 2019). McNutt, M., 2014. Journals unite for reproducibility. Science 346(6210):679. Mhaskar, R., B. Djulbegovic, A. Magazin, H. P. Soares, and A. Kumar. 2012. Published meth- odological quality of randomized controlled trials does not reflect the actual quality assessed in protocols. Journal of Clinical Epidemiology 65:602–609. NASEM (National Academies of Sciences, Engineering, and Medicine). 2017. Fostering integ- rity in research. Washington, DC: The National Academies Press. NASEM. 2018. Open science by design: Realizing a vision for 21st century research. Washington, DC: The National Academies Press. PREPUBLICATION COPY—Uncorrected Proofs

APPENDIX A 103 NASEM. 2019. Reproducibility and replicability in science. Washington, DC: The National Academies Press. Nature Research. 2018. Nature reproducibility survey 2017. m9.figshare.6139937.v4. Nosek, B. A., G. Alter, G. C. Banks, D. Borsboom, S. D. Bowman, S. J. Breckler, S. Buck, C. D. Chambers, G. Chin, G. Christensen, M. Contestabile, A. Dafoe, E. Eich, J. Freese, R. Glennerster, D. Goroff, D. P. Green, B. Hesse, M. Humphreys, J. Ishiyama, D. Karlan, A. Kraut, A. Lupia, P. Mabry, T. Madon, N. Malhotra, E. Mayo-Wilson, M. McNutt, E. Miguel, E. Levy Paluck, U. Simonsohn, C. Soderberg, B. A. Spellman, J. Turitto, G. VandenBos, S. Vazire, E. J. Wagenmakers, R. Wilson, and T. Yarkoni, 2015. Promoting an open research culture. Science 348(6242):1422–1425. NPQIP Collaborative Group. 2019. Did a change in Nature journals’ editorial policy for life sciences research improve reporting? BMJ Open Science 3:e000035. PCORI (Patient-Centered Outcomes Research Institute). 2019. PCORI Methodology Standards. (accessed November 20, 2019). Pildal, J., A.-W. Chan, A. Hróbjartsson, E. Forfang, D. G. Altman, and P. C. Gøtzsche. 2005. Comparison of descriptions of allocation concealment in trial protocols and the pub- lished reports: Cohort study. BMJ 330:1049. Platt, J. R. 1964. Strong inference: Certain systematic methods of scientific thinking may produce much more rapid progress than others. Science 146(3642):347–353. Popper, K. 1963. Science as falsification. In Conjectures and refutations. London, UK: Routledge and Keagan Paul. Pp. 33–39. Prinz, F., T. Schlange, and K. Asadullah. 2011. Believe it or not: How much can we rely on published data on potential drug targets? Nature Review Drug Discovery 10(9):712. Russ, H., S. Busta, A. Riedel, G. Zöllner, and B. Jost. 2009. Evaluation of clinical trials by ethics committees in Germany: Experience of applicants with the review of requests for opinion of the ethics committees—results of a survey among members of the Ger- man Association of Research-Based Pharmaceutical Companies (VFA). German Medical Science 16;7:Doc07. Scharf, O., and A. D. Colevas. 2006. Adverse event reporting in publications compared with sponsor database for cancer clinical trials. Journal of Clinical Oncology 24:3933–3938. Sena, E. S., H. B. van der Worp, P. M. W. Bath, D. W. Howells, and M. R. Macleod, 2010. Publication bias in reports of animal stroke studies leads to major overstatement of efficacy. PLOS Biology 8(3):e1000344. Silberberg, S. D., D. C. Crawford, R. Finkelstein, W. J. Koroshetz, R. D. Blank, H. H. Freeze, H. H. Garrison, and Y. R. Seger. 2017. Shake up conferences. Nature 548(7666):153–154. Tang, Z., K. V. Chuang, C. DeCarli, L. W. Jin, L. Beckett, M. J. Keiser, and B. N. Dugger. 2019. Interpretable classification of Alzheimer’s disease pathologies with a convolutional neural network pipeline. Nature Communications 10(1):2173. Turner, L., L. Shamseer, D. G. Altman, L. Weeks, J. Peters, T. Kober, S. Dias, K. F. Schulz, A. C. Plint, and D. Moher. 2012. Consolidated standards of reporting trials (CONSORT) and the completeness of reporting of randomised controlled trials (RCTs) published in medical journals. Cochrane Database of Systematic Reviews 11:MR000030. Williams, C. L., A. Casadevall, and S. Jackson. 2019. Figure errors, sloppy science, and fraud: Keeping eyes on your data. Journal of Clinical Investigation 129(5):1805–1807. PREPUBLICATION COPY—Uncorrected Proofs


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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.

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