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This list reflects the citations made throughout the SPIRIT 2013 Checklist section of the website, and replicates the published SPIRIT 2013 Explanation & Elaboration paper.

(1)   World Medical Association. WMA Declaration of Helsinki – Ethical principles for medical research involving human subjects. 2008. [Cited 2012 Sept 25]. Available from: http://www.wma.net/en/30publications/10policies/b3/index.html

(2)   Pildal J, Chan A-W, Hróbjartsson A, Forfang E, Altman DG, Gøtzsche PC. Comparison of descriptions of allocation concealment in trial protocols and the published reports: cohort study. BMJ 2005;330:1049.

(3)   Hróbjartsson A, Pildal J, Chan A-W, Haahr MT, Altman DG, Gøtzsche PC. Reporting on blinding in trial protocols and corresponding publications was often inadequate but rarely contradictory. J Clin Epidemiol 2009;62:967-973.

(4)   Chan A-W, Hróbjartsson A, Haahr MT, Gøtzsche PC, Altman DG. Empirical evidence for selective reporting of outcomes in randomized trials: comparison of protocols to published articles. JAMA 2004;291:2457-2465.

(5)   Scharf O, Colevas AD. Adverse event reporting in publications compared with sponsor database for cancer clinical trials. J Clin Oncol 2006;24:3933-3938.

(6)   Chan A-W, Hróbjartsson A, Jørgensen KJ, Gøtzsche PC, Altman DG. Discrepancies in sample size calculations and data analyses reported in randomised trials: comparison of publications with protocols. BMJ 2008;337:a2299.

(7)   Al-Marzouki S, Roberts I, Evans S, Marshall T. Selective reporting in clinical trials: analysis of trial protocols accepted by the Lancet. Lancet 2008;372:201.

(8)   Hernández AV, Steyerberg EW, Taylor GS, Marmarou A, Habbema JD, Maas AI. Subgroup analysis and covariate adjustment in randomized clinical trials of traumatic brain injury: a systematic review. Neurosurgery 2005;57:1244-1253.

(9)   Gøtzsche PC, Hróbjartsson A, Johansen HK, Haahr MT, Altman DG, Chan A-W. Ghost authorship in industry-initiated randomised trials. PLoS Med 2007;4:e19.

(10)   Gøtzsche PC, Hróbjartsson A, Johansen HK, Haahr MT, Altman DG, Chan A-W. Constraints on publication rights in industry-initiated clinical trials. JAMA 2006;295:1645-1646.

(11)   Mhaskar R, Djulbegovic B, Magazin A, Soares HP, Kumar A. Published methodological quality of randomized controlled trials does not reflect the actual quality assessed in protocols. J Clin Epidemiol 2012;65:602-609.

(12)   Smyth RM, Kirkham JJ, Jacoby A, Altman DG, Gamble C, Williamson PR. Frequency and reasons for outcome reporting bias in clinical trials: interviews with trialists. BMJ 2011;342:c7153.

(13)   Tetzlaff JM, Chan A-W, Kitchen J, Sampson M, Tricco AC, Moher D. Guidelines for randomized controlled trial protocol content: a systematic review. Syst Rev 2012;1:43.

(14)   Chan A-W, Tetzlaff JM, Altman DG, Laupacis A, Gøtzsche PC, Krleža-Jerić K et al. SPIRIT 2013 Statement: Defining standard protocol items for clinical trials. Ann Intern Med 2013. In press (Online First version).

(15)   Tetzlaff JM, Moher D, Chan A-W. Developing a guideline for reporting clinical trial protocols: Delphi consensus survey. Trials 2012;13:176.

(16)   Moher D, Schulz KF, Simera I, Altman DG. Guidance for developers of health research reporting guidelines. PLoS Med 2010;7:e1000217.

(17)   Moher D, Hopewell S, Schulz KF, Montori V, Gøtzsche PC, Devereaux PJ et al. CONSORT 2010 Explanation and Elaboration: updated guidelines for reporting parallel group randomised trials. BMJ 2010;340:c869.

(18)   Liberati A, Altman DG, Tetzlaff J, Mulrow C, Gøtzsche PC, Ioannidis JP et al. The PRISMA statement for reporting systematic reviews and meta-analyses of studies that evaluate health care interventions: explanation and elaboration. J Clin Epidemiol 2009;62:e1-34.

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(20)   Dickersin K, Manheimer E, Wieland S, Robinson KA, Lefebvre C, McDonald S. Development of the Cochrane Collaboration’s CENTRAL Register of controlled clinical trials. Eval Health Prof 2002;25:38-64.

(21)   Shaw L, Price C, McLure S, Howel D, McColl E, Ford GA. Paramedic Initiated Lisinopril For Acute Stroke Treatment (PIL-FAST): study protocol for a pilot randomised controlled trial [protocol]. Trials 2011;12:152.

(22)   Sim I, Chan A-W, Gülmezoglu AM, Evans T, Pang T. Clinical trial registration: transparency is the watchword. Lancet 2006;367:1631-1633.

(23)   Dickersin K, Rennie D. Registering clinical trials. JAMA 2003;290:516-523.

(24)   Krleža-Jerić K, Chan A-W, Dickersin K, Sim I, Grimshaw J, Gluud C for the Ottawa Group. Principles for international registration of protocol information and results from human trials of health related interventions: Ottawa statement (part 1). BMJ 2005;330:956-958.

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(26)   Mathieu S, Boutron I, Moher D, Altman DG, Ravaud P. Comparison of registered and published primary outcomes in randomized controlled trials. JAMA 2009;302:977-984.

(27)   Bourgeois FT, Murthy S, Mandl KD. Outcome reporting among drug trials registered in ClinicalTrials.gov. Ann Intern Med 2010;153:158-166.

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(30)   European Commission. Communication from the Commission regarding the guideline on the data fields contained in the clinical trials database provided for in Article 11 of Directive 2001/20/EC to be included in the database on medicinal products provided for in Article 57 of Regulation (EC) No 726/2004 (2008/C 168/02). Official Journal of the European Union 2008;51:3-4.

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(32)   Bernhard Nocht Institute for Tropical Medicine. Probiotic saccharomyces boulardii for the prevention of antibiotic-associated diarrhoea (SacBo). In: ClinicalTrials.gov [Internet]. Bethesda (MD): National Library of Medicine (US). 2000. [cited 2012 Sept 25]. Available from: http://clinicaltrials.gov/ct2/show/NCT01143272 NLM Identifier: NCT01143272.

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(36)   Lexchin J, Bero LA, Djulbegovic B, Clark O. Pharmaceutical industry sponsorship and research outcome and quality: systematic review. BMJ 2003;326:1167-1170.

(37)   Als-Nielsen B, Chen W, Gluud C, Kjaergard LL. Association of funding and conclusions in randomized drug trials: a reflection of treatment effect or adverse events? JAMA 2003;290:921-928.

(38)   Bekelman JE, Li Y, Gross CP. Scope and impact of financial conflicts of interest in biomedical research: a systematic review. JAMA 2003;289:454-465.

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(41)   Etter J-F, Burri M, Stapleton J. The impact of pharmaceutical company funding on results of randomized trials of nicotine replacement therapy for smoking cessation: a meta-analysis. Addiction 2007;102:815-822.

(42)   Golder S, Loke YK. Is there evidence for biased reporting of published adverse effects data in pharmaceutical industry-funded studies? Br J Clin Pharmacol 2008;66:767-773.

(43)   Min Y-I, Unalp-Arida A, Scherer R, Dickersin K. Assessment of equipoise using a cohort of randomized controlled trials [abstract]. International Congress on Peer Review and Biomedical Publication; 2005 Sept 16-18; Chicago, Illinois, USA 2005.

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(45)   Ahmer S, Arya P, Anderson D, Faruqui R. Conflict of interest in psychiatry. Psychiatr Bull 2005;29:302-304.

(46)   The Danish National Committee on Biomedical Research Ethics. Guidelines about Notification etc. of a Biomedical Research Project to the Committee System on Biomedical Research Ethics No 9154, 5 May 2011. 2011. [Cited 2012 Sept 25]. Available from: http://www.cvk.sum.dk/English/guidelinesaboutnotification.aspx

(47)   Lester RT, Mills EJ, Kariri A, Ritvo P, Chung M, Jack W, et al. The HAART cell phone adherence trial (WelTel Kenya1): a randomized controlled trial protocol [protocol]. Trials 2009;10:87.

(48)   Rennie D, Yank V, Emanuel L. When authorship fails. A proposal to make contributors accountable. JAMA 1997;278:579-585.

(49)   Trials.  Instructions for authors – study protocols. 2012. [Cited 2012 Sept 25]. Available from: http://www.trialsjournal.com/authors/instructions/studyprotocol#formatting-contributions

(50)   Williams H. The Bullous Pemphigoid Steroids and Tetracyclines (BLISTER) Study. A randomised controlled trial to compare the safety and effectiveness of doxycycline (200 mg/day) with prednisolone (0.5 mg/kg/day) for initial treatment of bullous pemphigoid [protocol]. Version 4.0 (July 20, 2011).  [Cited 2012 Sept 25]. Available from: http://www.spirit-statement.org/wp-content/uploads/2012/12/Blister-Protocol-v4-20July2011.pdf

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(53)   World Health Organization. Handbook for good clinical research practice (GCP): Guidance for implementation. 2002. [Cited 2012 Sept 25]. Available from: http://apps.who.int/prequal/info_general/documents/GCP/gcp1.pdf

(54)   Pierce MA, Hess EP, Kline JA, Shah ND, Breslin M, Branda ME, et al. The Chest Pain Choice trial: a pilot randomized trial of a decision aid for patients with chest pain in the emergency department [protocol]. Trials 2010;11:57.

(55)   Vlad SC, LaValley MP, McAlindon TE, Felson DT. Glucosamine for pain in osteoarthritis: why do trial results differ? Arthritis Rheum 2007;56:2267-2277.

(56)   Kjaergard LL, Als-Nielsen B. Association between competing interests and authors’ conclusions: epidemiological study of randomised clinical trials published in the BMJ. BMJ 2002;325:249.

(57)   Liss H. Publication bias in the pulmonary/allergy literature: effect of pharmaceutical company sponsorship. Isr Med Assoc J 2006;8:451-454.

(58)   Montgomery JH, Byerly M, Carmody T, Li B, Miller DR, Varghese F et al. An analysis of the effect of funding source in randomized clinical trials of second generation antipsychotics for the treatment of schizophrenia. Control Clin Trials 2004;25:598-612.

(59)   Perlis RH, Perlis CS, Wu Y, Hwang C, Joseph M, Nierenberg AA. Industry sponsorship and financial conflict of interest in the reporting of clinical trials in psychiatry. Am J Psychiatry 2005;162:1957-1960.

(60)   Jagsi R, Sheets N, Jankovic A, Motomura AR, Amarnath S, Ubel PA et al. Frequency, nature, effects, and correlates of conflicts of interest in published clinical cancer research. Cancer 2009;115:2783-2791.

(61)   Mello MM, Clarridge BR, Studdert DM. Academic medical centers’ standards for clinical-trial agreements with industry. N Engl J Med 2005;352:2202-10.

(62)   European Vasculitis Study Group (EUVAS). RITUXVAS Clinical Trial Protocol: An international, randomised, open label trial comparing a rituximab based regimen with a standard cyclophosphamide/azathioprine regimen in the treatment of active, ‘generalised’ ANCA associated vasculitis [protocol]. Version 1b (November 15, 2005). [Cited 2012 Sept 25]. Available from: http://www.vasculitis.nl/media/documents/rituxvas.pdf

(63)   Delgado-Rodriguez M, Ruiz-Canela M, De Irala-Estevez J, Llorca J, Martinez-Gonzalez MA. Participation of epidemiologists and/or biostatisticians and methodological quality of published controlled clinical trials. J Epidemiol Community Health 2001;55:569-572.

(64)   Llorca J, Martinez-Sanz F, Prieto-Salceda D, Fariñas-Alvarez C, Chinchon MV, Quinones D et al. Quality of controlled clinical trials on glaucoma and intraocular high pressure. J Glaucoma 2005;14:190-195.

(65)   CRASH2 Clinical Randomisation of an Antifibrinolytic in Significant Haemorrhage: A large randomised placebo controlled trial among trauma patients with or at risk of significant haemorrhage, of the effects of antifibrinolytic treatment on death and transfusion requirement [protocol]. Version 3 (July 2, 2005). [Cited 2012 Sept 25]. Available from: http://www.crash2.lshtm.ac.uk/

(66)   Clarke M. Doing new research? Don’t forget the old. PLoS Med 2004;1:e35.

(67)   Prescott RJ, Counsell CE, Gillespie WJ, Grant AM, Russell IT, Kiauka S et al. Factors that limit the quality, number and progress of randomised controlled trials. Health Technol Assess 1999;3:1-143.

(68)   Centre for Reviews and Dissemination. Systematic review of barriers, modifiers and benefits involved in participation in cancer trials. CRD Report 31. York: University of York. 2006.

(69)   Tournoux C, Katsahian S, Chevret S, Levy V. Factors influencing inclusion of patients with malignancies in clinical trials. Cancer 2006;106:258-270.

(70)   Clarke M, Hopewell S, Chalmers I. Clinical trials should begin and end with systematic reviews of relevant evidence: 12 years and waiting. Lancet 2010;376:20-21.

(71)   Canadian Institutes of Health Research. RCT evaluation criteria and headings. 2010. [Cited 2012 Sept 25]. Available from: http://www.cihr.ca/e/39187.html

(72)   National Institute for Health Research. Efficacy and mechanism evaluation program. Important information & guidance notes – preliminary application. 2012. [Cited 2012 Sept 25]. Available from: http://www.eme.ac.uk/funding/Researcher-led.asp

(73)   Jüni P, Nartey L, Reichenbach S, Sterchi R, Dieppe PA, Egger M. Risk of cardiovascular events and rofecoxib: cumulative meta-analysis. Lancet 2004;364:2021-2029.

(74)   Puhan MA, Vollenweider D, Steurer J, Bossuyt PM, ter Riet G. Where is the supporting evidence for treating mild to moderate chronic obstructive pulmonary disease exacerbations with antibiotics? A systematic review. BMC Med 2008;6:28.

(75)   Fergusson D, Glass KC, Hutton B, Shapiro S. Randomized controlled trials of aprotinin in cardiac surgery: could clinical equipoise have stopped the bleeding? Clin Trials 2005;2:218-229.

(76)   Lau J, Antman EM, Jimenez-Silva J, Kupelnick B, Mosteller F, Chalmers TC. Cumulative meta-analysis of therapeutic trials for myocardial infarction. N Engl J Med 1992;327:248-254.

(77)   Robinson KA, Goodman SN. A systematic examination of the citation of prior research in reports of randomized, controlled trials. Ann Intern Med 2011;154:50-55.

(78)   Goudie AC, Sutton AJ, Jones DR, Donald A. Empirical assessment suggests that existing evidence could be used more fully in designing randomized controlled trials. J Clin Epidemiol 2010;63:983-991.

(79)   Cooper NJ, Jones DR, Sutton AJ. The use of systematic reviews when designing studies. Clin Trials 2005;2:260-264.

(80)   Song F, Parekh S, Hooper L, Loke YK, Ryder J, Sutton AJ et al. Dissemination and publication of research findings: an updated review of related biases. Health Technol Assess 2010;14:iii-193.

(81)   Ross JS, Tse T, Zarin DA, Xu H, Zhou L, Krumholz HM. Publication of NIH funded trials registered in ClinicalTrials.gov: cross sectional analysis. BMJ 2012;344:d7292.

(82)   Ross JS, Mulvey GK, Hines EM, Nissen SE, Krumholz HM. Trial publication after registration in ClinicalTrials.Gov: a cross-sectional analysis. PLoS Med 2009;6:e1000144.

(83)   Hopewell S, Loudon K, Clarke MJ, Oxman AD, Dickersin K. Publication bias in clinical trials due to statistical significance or direction of trial results. Cochrane Database of Systematic Reviews 2009, Issue 1. Art. No.: MR000006. DOI:10.1002/14651858.MR000006.pub3.

(84)   Chan A-W. Out of sight but not out of mind: how to search for unpublished clinical trial evidence. BMJ 2012;344:d8013.

(85)   A phase III multi-centre, randomised, double-blind, double-dummy, comparative clinical study to assess the safety and efficacy of a fixed-dose formulation of oral pyronaridine artesunate (180:60 mg tablet) versus chloroquine (155 mg tablet), in children and adult patients with acute Plasmodium vivax malaria [protocol]. Version 2.0 (March 5, 2007). [Cited 2012 Sept 25]. Available from: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0014501#s5

(86)   Dawson L, Zarin DA, Emanuel EJ, Friedman LM, Chaudhari B, Goodman SN. Considering usual medical care in clinical trial design. PLoS Med 2009;6:e1000111.

(87)   Van Luijn JCF, Van Loenen AC, Gribnau FWJ, Leufkens HGM. Choice of comparator in active control trials of new drugs. Ann Pharmacother 2008;42:1605-1612.

(88)   Johansen HK, Gøtzsche PC. Problems in the design and reporting of trials of antifungal agents encountered during meta-analysis. JAMA 1999;282:1752-1759.

(89)   Stang A, Hense H-W, Jöckel K-H, Turner EH, Tramèr MR. Is it always unethical to use a placebo in a clinical trial? PLoS Med 2005;2:e72.

(90)   Emanuel EJ, Miller FG. The ethics of placebo-controlled trials — A middle ground. N Engl J Med 2001;345:915-919.

(91)   Ross S, Grant A, Counsell C, Gillespie W, Russell I, Prescott R. Barriers to participation in randomised controlled trials: a systematic review. J Clin Epi 1999;52:1143-1156.

(92)   Mills EJ, Seely D, Rachlis B, Griffith L, Wu P, Wilson K et al. Barriers to participation in clinical trials of cancer: a meta-analysis and systematic review of patient-reported factors. Lancet Oncol 2006;7:141-148.

(93)   Rochon PA, Gurwitz JH, Simms RW. A study of manufacturer supported trials of non-steroidal anti-inflammatory drugs in the treatment of arthritis. Archives of Int Med 1994;9:157-163.

(94)   Rutherford BR, Sneed JR, Roose SP. Does study design influence outcome? The effects of placebo control and treatment duration in antidepressant trials. Psychother Psychosom 2009;78:172-181.

(95)   Sneed JR, Rutherford BR, Rindskopf D, Lane DT, Sackeim HA, Roose SP. Design makes a difference: a meta-analysis of antidepressant response rates in placebo-controlled versus comparator trials in late-life depression. Am J Geriatr Psychiatry 2008;16:65-73.

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(98)   A phase 3, active (Warfarin) controlled, randomized, double-blind, parallel arm study to evaluate efficacy and safety of Apixaban in preventing stroke and systemic embolism in subjects with nonvalvular atrial fibrillation (ARISTOTLE: Apixaban for Reduction In STroke and Other ThromboemboLic Events in Atrial Fibrillation) [protocol]. Version 4 (August 4, 2010). [Cited 2012 Sept 25]. Available from: http://www.nejm.org/doi/full/10.1056/NEJMoa1107039

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(100)   Heger U, Voss S, Knebel P, Doerr-Harim C, Neudecker J, Schuhmacher C,  et al. Prevention of abdominal wound infection (PROUD trial, DRKS00000390): study protocol for a randomized controlled trial [protocol]. Trials 2011;12:245.

(101)   Hopewell S, Dutton S, Yu L-M, Chan A-W, Altman DG. The quality of reports of randomised trials in 2000 and 2006: comparative study of articles indexed in PubMed. BMJ 2010;340:c723.

(102)   Dumville JC, Hahn S, Miles JN, Torgerson DJ. The use of unequal randomisation ratios in clinical trials: a review. Contemp Clin Trials 2006;27:1-12.

(103)   Gilbody S, Bower P, Torgerson D, Richards D. Cluster randomized trials produced similar results to individually randomized trials in a meta-analysis of enhanced care for depression. J Clin Epidemiol 2008;61:160-168.

(104)   Lathyris D, Trikalinos TA, Ioannidis JPA. Evidence from crossover trials: Empirical evaluation and comparison against parallel arm trials. Int J Epidemiol 2007;36:422-430.

(105)   Khan KS, Daya S, Collins JA, Walter SD. Empirical evidence of bias in infertility research: overestimation of treatment effect in crossover trials using pregnancy as the outcome measure. Fertil Steril 1996;65:939-945.

(106)   Katz J, Finnerup NB, Dworkin RH. Clinical trial outcome in neuropathic pain: relationship to study characteristics. Neurology 2008;70:263-272.

(107)   Le Henanff A, Giraudeau B, Baron G, Ravaud P. Quality of reporting of noninferiority and equivalence randomized trials. JAMA 2006;295:1147-1151.

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(109)   Krysan DJ, Kemper AR. Claims of equivalence in randomized controlled trials of the treatment of bacterial meningitis in children. Pediatr Infect Dis J 2002;21:753-758.

(110)   Tinmouth JM, Steele LS, Tomlinson G, Glazier GH. Are claims of equivalency in digestive diseases trials supported by the evidence. Gastroenterol 2004;126:1700-1710.

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(113)   Project Accept Study Group. Project Accept (HPTN 043): A phase III randomized controlled trial of community mobilization, mobile testing, same-day results, and post-test support for HIV in Sub-Saharan Africa and Thailand [protocol]. Version 2.4 (April 15, 2011). [Cited 2012 Sept 25]. Available from: http://www.hptn.org/research_studies/hptn043.asp

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(120)   Sood A, Knudsen K, Sood R, Wahner-Roedler DL, Barnes SA, Bardia A et al. Publication bias for CAM trials in the highest impact factor medicine journals is partly due to geographical bias. J Clin Epi 2007;60:1123-1126.

(121)   Wu T, Li Y, Bian Z, Liu G, Moher D. Randomized trials published in some Chinese journals: how many are randomized? Trials 2009;10:46.

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(125)   Blümle A, Meerpohl JJ, Rücker G, Antes G, Schumacher M, von Elm E. Reporting of eligibility criteria of randomised trials: cohort study comparing trial protocols with subsequent articles. BMJ 2011;342:d1828.

(126)   Cook JA. The challenges faced in the design, conduct and analysis of surgical randomised controlled trials. Trials 2009;10:9.

(127)   Simpson F, Sweetman EA, Doig GS. Systematic review of techniques and interventions for improving adherence to inclusion and exclusion criteria during enrolment into randomised controlled trials.  Trials 2010;11:17.

(128)   Rendell JM, Merritt RK, Geddes JR. Incentives and disincentives to participation by clinicians in randomised controlled trials. Cochrane Database of Systematic Reviews 2007, Issue 2. Art. No.: MR000021. DOI: 10.1002/14651858.MR000021.pub3.

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(130)   Townsley CA, Selby R, Siu LL. Systematic review of barriers to the recruitment of older patients with cancer onto clinical trials. J Clin Oncol 2005;23:3112-3124.

(131)   Uchino K, Billheimer D, Cramer SC. Entry criteria and baseline characteristics predict outcome in acute stroke trials. Stroke 2001;32:909-916.

(132)   Van Spall HGC, Toren A, Kiss A, Fowler RA. Eligibility criteria of randomized controlled trials published in high-impact general medical journals: a systematic sampling review. JAMA 2007;297:1233-1240.

(133)   Shapiro SH, Weijer C, Freedman B. Reporting the study populations of clinical trials. Clear transmission or static on the line? J Clin Epi 2000;53:973-979.

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