Abstract
Poor quality of reporting in published scientific manuscripts has been identified as a major contributor to the low reproducibility of research outcomes. Improved author compliance to a journal’s submission guidelines, rigorous editorial vigilance by competent reviewers and journal editors, and revamped research practices and policies by research institutes can raise the reporting quality of submitted manuscripts. In this chapter, we describe the current requirements of scholarly publishing and the responsibilities of authors, peer reviewers, journal editors, scientific journals, and academic institutions. We propose that scientific reproducibility can be improved by (a) upgrading editorial vigilance to assure the quality and accuracy of the scientific record; (b) institutional training in writing in the sciences for research trainees; and (c) institutional adoption of existing standards of quality control in manufacturing and commercial research organizations to develop good publishing and research practices and integrity.
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References
Levitan KB. Scientific societies and their journals: biomedical scientists assess the relationship. Soc Stud Sci. 1979;9:393–400.
Tenopir C, King DW, Boyce P, et al. Patterns of journal use by scientists through three evolutionary phases. D-Lib Mag. 2003;9:1082.
Niu X, Hemminger BM. A study of factors that affect the information-seeking behavior of academic scientists. J Am Soc Inf Sci Technol. 2011;63:336–53.
Nicholas D, Watkinson A, Volentine R, et al. Trust and authority in scholarly communications in the light of the digital transition: setting the scene for a major study. Learn Publ. 2014;27:121–34.
Jubb M. Communication or competition: what motivates researchers to write articles for journals? Learn Publ. 2014;27:251–2.
Shamseer L, Moher D, Maduekwe O, et al. Potential predatory and legitimate biomedical journals: can you tell the difference? a cross-sectional comparison. BMC Med. 2017;15:28.
Peer review in scientific publications. London: Science and Technology Committee, House of Commons; 2011.
Byrne DW. Common reasons for rejecting manuscripts at medical journals: a survey of editors and peer reviewers. Science. 2000;23:39–44.
Sugimoto CR, Lariviere V, Ni C, Cronin B. Journal acceptance rates: a cross-disciplinary analysis of variability and relationships with journal measures. J Informetr. 2013;7:897–906.
Lamb CR, Mai W. Acceptance rate and reasons for rejection of manuscripts submitted to Veterinary Radiology & Ultrasound during 2012. Vet Radiol Ultrasound. 2014;56:103–8.
Reich ES. The golden club. Nature. 2013;502:291–3.
Casadevall A, Fang FC. Reproducible science. Infect Immun. 2010;78:4972–5.
Begley CG, Ioannidis JPA. Reproducibility in science. Circ Res. 2015;116:116–26.
Baker M. Is there a reproducibility crisis? Nature. 2016;533:452–4.
Fanelli D. Opinion: Is science really facing a reproducibility crisis, and do we need it to? Proc Natl Acad Sci USA. 2008;115:2628–31
Goodman SN, Fanelli D, Ioannidis JPA. What does research reproducibility mean? Sci Transl Med. 2016;8:341ps12.
Barba LA. Terminologies for reproducible research. arXiv. 2018;1802 03311v1 [cs DL].
Plesser HE. Reproducibility vs. replicability: a brief history of a confused terminology. Front Neuroinform. 2018;11:76.
Drummond C. Replicability is not reproducibility: nor is it good science. In: Proceedings of the Evaluation Methods for Machine Learning Workshop at the 26th ICML. Montreal, Canada: National Research Council of Canada; 2009.
Ioannidis JPA. Why most published research findings are false. PLoS Med. 2005;2:e124.
Prinz F, Schlange T, Asadullah K. Believe it or not: how much can we rely on published data on potential drug targets? Nat Rev Drug Discov. 2011;10:712.
Peng R. The reproducibility crisis in science: a statistical counterattack. Significance. 2015;12:30–2.
Loken E, Gelman A. Measurement error and the replication crisis. Science. 2017;355:584–5.
Munafo MR, Nosek BA, Bishop DVM, et al. A manifesto for reproducible science. Nat Hum Behav. 2017;1:0021.
Enserink M. Sloppy reporting on animal studies proves hard to change. Science. 2017;357:1337–8.
Nuffield Council of Bioethics. The culture of scientific research in the UK. London: Nuffield Council of Bioethics; 2014.
Research integrity. London: Science and Technology Commitee, House of Commons; 2018
Day RA. The origins of the scientific paper: the IMRAD format. J Am Med Writ Assoc. 1989;4:16–8.
Sollaci LB, Pereira MG. The introduction, methods, results, and discussion (IMRAD) structure: a fifty-year survey. J Med Libr Assoc. 2004;92:364–71.
International Committee of Medical Journal Editors. Recommendations for the conduct, reporting, editing, and publication of scholarly work in medical journals. 2018. http://www.icmje.org/icmje-recommendations.pdf.
Malicki M, Aalbersberg IJ, Bouter L, ter Riet G. Journals’ instructions to authors: A cross-sectional study across scientific disciplines. PLoS One. 2019;14:e0222157.
Baker D, Lidster K, Sottomayor A, Amor S. Two years later: journals are not yet enforcing the ARRIVE guidelines on reporting standards for pre-clinical animal studies. PLoS Biol. 2014;12:e1001756.
McGrath JC, Lilley E. Implementing guidelines on reporting research using animals (ARRIVE etc.): new requirements for publication in BJP. Br J Pharmacol. 2015;172:3189–93.
Hooijmans CR, Leenaars M, Ritskes-Hoitinga M. A gold standard publication checklist to improve the quality of animal studies, to fully integrate the three Rs, and to make systematic reviews more feasible. Alt Lab Anim. 2010;38:167–82.
Battisti WP, Wager E, Baltzer L. Good publication practice for communicating company-sponsored medical research: GPP3. Ann Intern Med. 2015;163:461–4.
Stevens A, Shamseer L, Weinstein E, et al. Relation of completeness of reporting of health research to journals’ endorsement of reporting guidelines: systematic review. Br Med J. 2014;348:g3804.
Bezdjian A, Klis SFL, Peters JPM, et al. Quality of reporting of otorhinolaryngology articles using animal models with the ARRIVE statement. Lab Anim. 2017;52:79–87.
Leung V, Rousseau-Blass F, Beauchamp G, Pang DSJ. ARRIVE has not ARRIVEd: support for the ARRIVE (Animal Research: reporting of in vivo Experiments) guidelines does not improve the reporting quality of papers in animal welfare, analgesia or anesthesia. PLoS One. 2018;13:e0197882.
Hair K, Macleod MR, Sena ES, et al. A randomised controlled trial of an intervention to improve compliance with the ARRIVE guidelines (IICARus). Res Integr Peer Rev. 2019;4:12.
Nicholas D, Watkinson A, Jamali HR, et al. Peer review: still king in the digital age. Learn Publ. 2015;28:15–21.
Bornmann L. Scientific peer review. Ann Rev Info Sci Technol. 2011;45:197–245.
Smith R. Peer review: a flawed process at the heart of science and journals. J R Soc Med. 2006;99:178–82.
Smith R. Classical peer review: an empty gun. Breast Cancer Res. 2010;12:S13.
Smith R. Roger Bacon on ignorance and peer review. 2017. https://blogs.bmj.com/bmj/2017/05/04/richard-smith-roger-bacon-on-ignorance-and-peer-review/.
Wagner PD, Bates JHT. Maintaining the integrity of peer review. J Appl Physiol. 2016;120:479–80.
Black N, van RS, Godlee F, et al. What makes a good reviewer and a good review for a general medical journal? JAMA. 1998;280:231–3.
Albert KM. Open access: implications for scholarly publishing and medical libraries. J Med Libr Assoc. 2006;94:253–62.
Bartholomew RE. Science for sale: the rise of predatory journals. J R Soc Med. 2014;107:384–5.
Laakso M, Welling P, Bukvova H, et al. The development of open access journal publishing from 1993 to 2009. PLoS One. 2011;6:e20961.
Johnson R, Watkinson A, Mabe M. An overview of scientific and scholarly publishing. 5th ed. The Hague: International Association of Scientific, Technical and Medical Publishers; 2018. https://www.stm-assoc.org/2018_10_04_STM_Report_2018.pdf.
Bjork BC, Welling P, Laakso M, et al. Open access to the scientific journal literature: situation 2009. PLoS One. 2010;5:e11273.
Guedj D, Ramjoue C. European Commission policy on open-access to scientific publications and research data in Horizon 2020. Biomed Data J. 2015;1:11–4.
Schiltz M. Science without publication paywalls: cOAlition S for the realisation of full and immediate open access. PLoS Med. 2018;15:e1002663.
Horton R. The future of scientific knowledge. Lancet. 2018;392:2337.
Bordage G. Reasons reviewers reject and accept manuscripts: the strengths and weaknesses in medical education reports. Acad Med. 2001;76:889–96
Pierson DJ. The top 10 reasons why manuscripts are not accepted for publication. Respir Care. 2004;49:1246–52.
Ehara S, Takahashi K. Reasons for rejection of manuscripts submitted to AJR by international authors. Am J Roentgenol. 2007;188:W113–6.
Harris AHS, Reeder R, Hyun JK. Common statistical and research design problems in manuscripts submitted to high-impact psychiatry journals: what editors and reviewers want authors to know. J Psychiatr Res. 2009;43:1231–4.
Johnson C, Green B. Submitting manuscripts to biomedical journals: common errors and helpful solutions. J Manip Physiol Ther. 2009;32:1–12.
Wyness T, McGhee CN, Patel DV. Manuscript rejection in ophthalmology and visual science journals: identifying and avoiding the common pitfalls. Clin Exp Ophthalmol. 2009;37:864–7.
Ali J. Manuscript rejection: causes and remedies. J Young Pharm. 2010;2:3–6.
Harris AHS, Reeder RN, Hyun JK. Survey of editors and reviewers of high-impact psychology journals: statistical and research design problems in submitted manuscripts. J Psychol. 2011;145:195–209.
Pimm J. Dear editor, why have you rejected my article? Psychiatrist. 2013;37:313–4.
Garg A, Das S, Jain H. Why we say no! A look through the editor’s eye. J Clin Diagn Res. 2015;9:JB01–5.
Meyer HS, Durning SJ, Sklar DP, Maggio LA. Making the first cut: an analysis of academic medicine editors’ reasons for not sending manuscripts out for external peer review. Acad Med. 2018;93:464–70.
Chew FS. Fate of manuscripts rejected for publication in the AJR. Am J Roentgenol. 1991;156:627–32.
Ray J, Berkwits M, Davidoff F. The fate of manuscripts rejected by a general medical journal. Am J Med. 2000;109:131–5.
Wijnhoven BPL, Dejong CHC. Fate of manuscripts declined by the British Journal of Surgery. Br J Surg. 2010;97:450–4.
Khosla A, McDonald RJ, Bornmann L, Kallmes DF. Getting to yes: the fate of neuroradiology manuscripts rejected by Radiology over a 2-year period. Radiology. 2011;260:3–5.
Okike K, Kocher MS, Nwachukwu BU, et al. The fate of manuscripts rejected by the Journal of Bone and Joint Surgery (American Volume). J Bone Joint Surg AM. 2012;94:e130
Grant WD, Cone DC. If at first you don’t succeed: the fate of manuscripts rejected by Academic Emergency Medicine. Acad Emerg Med. 2015;22:1213–7.
Docherty AB, Klein AA. The fate of manuscripts rejected from Anaesthesia. Anaesthesia. 2017;72:427–30.
Cronin B. Language matters. J Am Soc Inf Sci Technol. 2011;63:217.
Wager E, Jefferson T. Shortcomings of peer review in biomedical journals. Learn Publ. 2001;14:257–63.
Vale RD. Accelerating scientific publication in biology. Proc Natl Acad Sci USA. 2015;112:13439–46.
Allison DB, Brown AW, George BJ, Kaiser KA. A tragedy of errors. Nature. 2016;530:27–9.
Kravitz RL, Franks P, Feldman MD, et al. Editorial peer reviewers’ recommendations at a general medical journal: are they reliable and do editors care? PLoS One. 2010;5:e10072.
Baethge C, Franklin J, Mertens S. Substantial agreement of referee recommendations at a general medical journal – a peer review evaluation at Deutsches Arzteblatt International. PLoS One. 2013;8:e61401.
Rothwell PM, Martyn CN. Reproducibility of peer review in clinical neuroscienceIs agreement between reviewers any greater than would be expected by chance alone? Brain. 2000;123:1964–9.
Bornmann L, Mutz R, Daniel H-D. A reliability-generalization study of journal peer reviews: a multilevel meta-analysis of inter-rater reliability and its determinants. PLoS One. 2010;5:e14331.
Jirschitzka J, Oeberst A, Gollner R, Cress U. Inter-rater reliability and validity of peer reviews in an interdisciplinary field. Scientometrics. 2017;113:1059–92.
Siler K, Lee K, Bero L. Measuring the effectiveness of scientific gatekeeping. Proc Natl Acad Sci USA. 2015;112:360–5.
Publons. Global State of Peer Review. 2018.
Kovanis M, Porcher R, Ravaud P, Trinquart L. The global burden of journal peer review in the biomedical literature: strong imbalance in the collective enterprise. PLoS One. 2016;11:e0166387.
Breuning M, Backstrom J, Brannon J, et al. Reviewer fatigue? Why scholars decline to review their peers’ work. PS: Polit Sci Polit. 2015;48:595–600.
D’Andrea R, O’Dwyer JP. Can editors save peer review from peer reviewers? PLoS One. 2017;12:e0186111.
Gannon F. The essential role of peer review. EMBO Rep. 2001;2:743.
Jackson JL, Srinivasan M, Rea J, et al. The validity of peer review in a general medicine journal. PLoS One. 2011;6:e22475.
Galipeau J, Barbour V, Baskin P, et al. A scoping review of competencies for scientific editors of biomedical journals. BMC Med. 2016;14:16.
Moher D, Galipeau J, Alam S, et al. Core competencies for scientific editors of biomedical journals: consensus statement. BMC Med. 2017;15:167.
Young NS, Ioannidis JPA, Al-Ubaydli O. Why current publication practices may distort science. PLoS Med. 2008;5:e201.
van Lent M, Overbeke J, Out HJ. Role of editorial and peer review processes in publication bias: analysis of drug trials submitted to eight medical journals. PLoS One. 2014;9:e104846.
Beall J. Predatory publishers are corrupting open access. Nature. 2012;489:179.
Butler D. Investigating journal: the dark side of publishing. Nature. 2013;495:433–5.
Bert F, Paget DZ. Scaioli G. A social way to experience a scientific event: Twitter use at the 7th European Public Health Conference. Scand J Public Health. 1999;44:130–3.
Kiernan M, Wigglesworth N. The use of social media in the dissemination of information from scientific meetings. J Infect Prev. 2011;12:224–5.
Kapp JM, Hensel B, Schnoring KT. Is Twitter a forum for disseminating research to health policy makers? Ann Epidemiol. 2015;25:883–7.
Allen CG, Andersen B, Chambers DA, et al. Twitter use at the 2016 conference on the science of dissemination and implementation in health: analyzing #DIScience16. Implement Sci. 2018;13:34.
McClain CR. Practices and promises of Facebook for science outreach: becoming a “Nerd of Trust”. PLoS Biol. 2017;15:e2002020.
Science is social. Nat Genet. 2018;50:1619.
Lee CJ, Sugimoto CR, Zhang G, Cronin B. Bias in peer review. J Am Soc Inf Sci Technol. 2012;64:2–17.
Munafo M, Neill J. Null is beautiful: on the importance of publishing null results. J Psychopharmacol. 2016;30:585.
Gaston T, Smart P. What influences the regional diversity of reviewers: a study of medical and agricultural/biological sciences journals. Learn Publ. 2018;31:189–97.
Lerback J, Hanson B. Journals invite too few women to referee. Nature. 2017;541:455–7.
Garfield E. Citation analysis as a tool in journal evaluation. Science. 1972;178:471–9.
Rogers LF. Impact factor; the numbers game. Am J Roentgenol. 2002;178:541–2.
Tsikliras AC. Chasing after the high impact. ESEP. 2008;8:45–7.
Seglen PO. Why the impact factor of journals should not be used for evaluating research. Br Med J. 1997;314:498–502.
Hecht F, Hecht BK, Sandberg AA. The journal “Impact Factor”: A misnamed, misleading, misused measure. Cancer Genet Cytogenet. 1998;104:77–81.
Bertuzzi S, Drubin DG. No shortcuts for research assessment. Mol Biol Cell. 2013;24:1505–6.
Hirsch JE. An index to quantify an individual’s scientific research output. Proc Natl Acad Sci USA. 2005;102:16569–72.
Egghe L. Theory and practise of the g-index. Scientometrics. 2006;69:131–52.
Patel VM, Ashrafian H, Bornmann L, et al. Enhancing the h index for the objective assessment of healthcare researcher performance and impact. J R Soc Med. 2013;106:19–29.
Lawrence PA. The politics of publication. Nature. 2003;422:259–61.
Lawrence PA. The mismeasurement of science. Curr Biol. 2007;17:R583–5.
Lawrence PA. Lost in publication: how measurement harms science. Ethics Sci Environ Polit. 2008;8:9–11.
Campbell P. Escape from the impact factor. Ethics Sci Environ Polit. 2008;8:5–7.
Boutron I, Ravaud P. Misrepresentation and distortion of research in biomedical literature. Proc Natl Acad Sci USA. 2018;115:2613–9.
Angell M, Relman AS. Redundant publication. N Engl J Med. 1989;320:1212–4.
Budd JM. Stewart KN. Is there such a thing as “least publishable unit”? an empirical investigation. LIBRES 2015;25:78–85.
Day NE. The silent majority: manuscript rejection and its impact on scholars. Acad Man Learn Edu. 2011;10:704–18.
Wager E. Coping with scientific misconduct. Br Med J. 2011;343:d6586.
Brainard J. Rethinking retractions. Science. 2018;362:390–3.
Grieneisen ML, Zhang M. A comprehensive survey of retracted articles from the scholarly literature. PLoS One. 2012;7:e44118.
Drubin DG, Kellogg DR. English as the universal language of science: opportunities and challenges. Mol Biol Cell. 2012;23:1399.
Wicherts MJ. The weak spots in contemporary science (and how to fix them). Animals. 2017;7:90.
McNutt M. Journals unite for reproducibility. Science. 2014;346:679.
Cruz-Castro L, Sanz-Menendez L. Autonomy and authority in public research organisations: structure and funding factors. Minerva. 2018;56:135–60.
Tartari V, Perkmann M, Salter A. In good company: the influence of peers on industry engagement by academic scientists. Res Policy. 2014;43:1189–203.
Munafo MR, Hollands GJ, Marteau TM. Open science prevents mindless science. Br Med J. 2018;363:k4309.
Review of Wellcome Trust PhD research training: the supervisor perspective. London: Wellcome Trust; 2001.
Boulbes DR, Costello TJ, Baggerly KA, et al. A survey on data reproducibility and the effect of publication process on the ethical reporting of laboratory research. Clin Cancer Res. 2018;24:3447–55.
Nosek BA, Alter G, Banks GC, et al. Promoting an open research culture. Science. 2015;348:1422–5.
Wren JD, Kozak KZ, Johnson KR, et al. The write position. A survey of perceived contributions to papers based on byline position and number of authors. EMBO Rep. 2007;8:988–91.
McNutt MK, Bradford M, Drazen JM, et al. Transparency in authors’ contributions and responsibilities to promote integrity in scientific publication. Proc Natl Acad Sci USA. 2018;115:2557–60.
Laurance WF. Second thoughts on who goes where in author lists. Nature. 2006;442:26.
Greene M. The demise of the lone author. Nature. 2007;450:1165.
Glonti K, Cauchi D, Cobo E, et al. A scoping review protocol on the roles and tasks of peer reviewers in the manuscript review process in biomedical journals. BMJ Open. 2017;7:e017468
Pinto da Costa M, Oliveira J, Abdulmalik J. Where can early career researchers learn how to peer review a scientific paper? Eur Sci Editing. 2018;44:4–7, 18.
Tokalic R, Marusic A. A peer review card exchange game. Eur Sci Editing. 2018;44:52–5.
Yosten GLC, Adams JC, Bennett CN, et al. Editorial: revised guidelines to enhance the rigor and reproducibility of research published in American Physiological Society Journals. Am J Physiol Regul Integr Comp Physiol. 2018;315:R1251–R1253
Freedman LP, Cockburn IM, Simcoe TS. The economics of reproducibility in preclinical research. PLoS Biol. 2015;13:e1002165.
Schneider K. Faking it: the case against industrial bio-test laboratories. Amicus J. 1983;Spring edition:14–26.
Baldeshwiler AM. History of FDA good laboratory practices. Qual Assur J. 2003;7:157–61.
Cooper-Hannan R, Harbell JW, Coecke S, et al. The principles of good laboratory practice: application to in vitro toxicology studies. Alt Lab Anim. 1999;27:539–77.
Seiler JP. Good laboratory practice: the why and the how. Berlin: Springer; 2006.
Glick JL, Shamoo AE. A call for the development of “good research practices” (GRP) guidelines. Account Res. 1993;2:231–5.
Murray GD. Promoting good research practice. Stat Methods Med Res. 2000;9:17–24.
Davies R. Good research practice: it is time to do what others think we do. Quasar. 2013;124:21–3.
Pedro-Roig L, Emmerich CH. The reproducibility crisis in preclinical research – lessons to be learnt from clinical research. Med Writ. 2017;26:28–32.
Dickersin K, Mayo-Wilson E. Standards for design and measurement would make clinical research reproducible and usable. Proc Natl Acad Sci USA. 2018;115:2590–4.
Whitlock MC, McPeek MA, Rausher MD, et al. Data archiving. Am Nat. 2010;175:145–6.
Mannheimer S, Yoon A, Greenberg J, et al. A balancing act: the ideal and the realistic in developing Dryad’s preservation policy. First Monday. 2014;19
Vines TH, Albert AYK, Andrew RL, et al. The availability of research data declines rapidly with article age. Curr Biol. 2014;24:94–7.
Gopen GD. Expectations: teaching writing from the reader’s perspective. London: Pearson Longman; 2004.
Acknowledgements
The authors thank Dr. Eoghan McAlpine and Dr. Ze’ev Bomzon for their constructive criticisms and helpful suggestions. The authors also thank Statler and Waldorf for encouraging and inspiring us to write this chapter.
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Bomzon, A., Tobin, G. (2021). Scholarly Publishing and Scientific Reproducibility. In: Sánchez Morgado, J.M., Brønstad, A. (eds) Experimental Design and Reproducibility in Preclinical Animal Studies . Laboratory Animal Science and Medicine, vol 1. Springer, Cham. https://doi.org/10.1007/978-3-030-66147-2_9
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