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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):1709â1711. Chuang, K. V., and M. J. Keiser. 2018a. Adversarial controls for scientific machine learning. ACS Chemical Biology 13(10):2819â2821. Chuang, K. V., and M. J. Keiser. 2018b. Comment on âPredicting reaction performance in C-N cross-coupling using machine learning.â Science 362(6416). Collins, F. S., and L. A. Tabak. 2014. Policy: NIH plans to enhance reproducibility. Nature 505(7485):612â613. 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 45:265â275. HrÃ³bjartsson, A., J. Pildal, A.-W. Chan, M. T. Haahr, D. G. Altman, and P. C. GÃ¸tzsche. 2009. Reporting on blinding in trial protocols and corresponding publications was often inadequate but rarely contradictory. Journal of Clinical Epidemiology 62:967â973. 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):1353â1354. 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):19231â19236. Kiley, R., T. Peatfield, J. Hansen, and R. Reddington. 2017. Data sharing from clinical trialsâa research funderâs perspective. New England Journal of Medicine 377:1990â1992. 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):187â191. 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):2824â2829. 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. https://peerreviewcongress.org/prc17- 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 65:602â609. 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 COPYâUncorrected Proofs
APPENDIX A 103 NASEM. 2019. Reproducibility and replicability in science. Washington, DC: The National Academies Press. Nature Research. 2018. Nature reproducibility survey 2017. https://doi.org/10.6084/ 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):1422â1425. NPQIP Collaborative Group. 2019. Did a change in Nature journalsâ editorial policy for life sciences research improve reporting? BMJ Open Science 3:e000035. PCORI (Patient-Centered Outcomes Research Institute). 2019. PCORI Methodology Standards. https://www.pcori.org/methodology-standards (accessed November 20, 2019). Pildal, J., A.-W. Chan, A. HrÃ³bjartsson, E. Forfang, D. G. Altman, and P. C. GÃ¸tzsche. 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):347â353. Popper, K. 1963. Science as falsification. In Conjectures and refutations. London, UK: Routledge and Keagan Paul. Pp. 33â39. 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. ZÃ¶llner, 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 committeesâresults 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 24:3933â3938. 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):153â154. Tang, Z., K. V. Chuang, C. DeCarli, L. W. Jin, L. Beckett, M. J. Keiser, and B. N. Dugger. 2019. Interpretable classification of Alzheimerâs 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):1805â1807. PREPUBLICATION COPYâUncorrected Proofs
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