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Open peer review (OPR), as with other elements of open science and open research, is on the rise. It aims to bring greater transparency and participation to formal and informal peer review processes. But what is meant by `open peer review', and what advantages and disadvantages does it have over standard forms of review? How do authors or reviewers approach OPR? And what pitfalls and opportunities should you look out for? Here, we propose ten considerations for OPR, drawing on discussions with authors, reviewers, editors, publishers and librarians, and provide a pragmatic, hands-on introduction to these issues. We cover basic principles and summarise best practices, indicating how to use OPR to achieve best value and mutual benefits for all stakeholders and the wider research community., Competing Interests: Competing interests: BS is head of Open Science projects at Göttingen State and University Library. She contributes to several committees, e.g. the EC's Horizon2020 expert group on Future of Scholarly Publishing and scholarly Communication and Knowledge Exchange's Open Access Expert Group. BS and TRH are affiliated with OpenUP, an EC funded project which addresses key aspects and challenges of the currently transforming science landscape and aspires to come up with a cohesive framework for the review-disseminate-assess phases of the research life cycle that is fit to support and promote Open Science. BS is, and TRH was, affiliated with the OpenAIRE2020 project, an EC-funded initiative to implement and monitor Open Access and Open Science policies in Europe and beyond. TRH is Editor-in-Chief of Publications (ISSN 2304-6775), an open access journal on scholarly publishing published quarterly by MDPI and Senior Researcher at Know-Center GmbH, Graz, Austria, a research centre for data-driven business innovative information and communication technologies. XvE is business development manager at Copernicus GmbH, and open-access publisher (Copernicus Publications) and professional congress organizer (Copernicus Meetings). Since September 2015 she has been a member of the board of directors of the Open Access Scholarly Publishers Association (OASPA). ECM supported and initiated the development and implementation of new approaches to peer review and related policy at BMC (part of Springer Nature) until June 2018. She is also an Editorial Board Member for Research Integrity and Peer Review and a member of the Advisory Board for EnTIRE (an EU proposal for Mapping the research ethics and research integrity framework).

Objectives: We examined major issues associated with sharing of individual clinical trial data and developed a consensus document on providing access to individual participant data from clinical trials, using a broad interdisciplinary approach., Design and Methods: This was a consensus-building process among the members of a multistakeholder task force, involving a wide range of experts (researchers, patient representatives, methodologists, information technology experts, and representatives from funders, infrastructures and standards development organisations). An independent facilitator supported the process using the nominal group technique. The consensus was reached in a series of three workshops held over 1 year, supported by exchange of documents and teleconferences within focused subgroups when needed. This work was set within the Horizon 2020-funded project CORBEL (Coordinated Research Infrastructures Building Enduring Life-science Services) and coordinated by the European Clinical Research Infrastructure Network. Thus, the focus was on non-commercial trials and the perspective mainly European., Outcome: We developed principles and practical recommendations on how to share data from clinical trials., Results: The task force reached consensus on 10 principles and 50 recommendations, representing the fundamental requirements of any framework used for the sharing of clinical trials data. The document covers the following main areas: making data sharing a reality (eg, cultural change, academic incentives, funding), consent for data sharing, protection of trial participants (eg, de-identification), data standards, rights, types and management of access (eg, data request and access models), data management and repositories, discoverability, and metadata., Conclusions: The adoption of the recommendations in this document would help to promote and support data sharing and reuse among researchers, adequately inform trial participants and protect their rights, and provide effective and efficient systems for preparing, storing and accessing data. The recommendations now need to be implemented and tested in practice. Further work needs to be done to integrate these proposals with those from other geographical areas and other academic domains., Competing Interests: Competing interests: TG is the editor-in-chief of BMJ Open, the journal that publishes this article. During the paper evaluation she recused herself from the peer review and decision-making process. BB reports various unrestricted gifts (see) supporting travel and effort; grants from Laura and John Arnold Foundation and the Greenwall Foundation during the conduct of the study; and non-financial support from Vivli, outside the submitted work. RK reports she was Founder of CDISC and President during the development of the submitted work. DaS was employed by BioMed Central at the time of the consensus process., (© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

Introduction: Systematic reviews evaluating the impact of interventions to improve the quality of peer review for biomedical publications highlighted that interventions were limited and have little impact. This study aims to compare the accuracy of early career peer reviewers who use an innovative online tool to the usual peer reviewer process in evaluating the completeness of reporting and switched primary outcomes in completed reports., Methods and Analysis: This is a cross-sectional study of individual two-arm parallel-group randomised controlled trials (RCTs) published in the BioMed Central series medical journals, BMJ , BMJ Open and Annals of Emergency Medicine and indexed with the publication type 'Randomised Controlled Trial'. First, we will develop an online tool and training module based (a) on the Consolidated Standards of Reporting Trials (CONSORT) 2010 checklist and the Explanation and Elaboration document that would be dedicated to junior peer reviewers for assessing the completeness of reporting of key items and (b) the Centre for Evidence-Based Medicine Outcome Monitoring Project process used to identify switched outcomes in completed reports of the primary results of RCTs when initially submitted. Then, we will compare the performance of early career peer reviewers who use the online tool to the usual peer review process in identifying inadequate reporting and switched outcomes in completed reports of RCTs at initial journal submission. The primary outcome will be the mean number of items accurately classified per manuscript. The secondary outcomes will be the mean number of items accurately classified per manuscript for the CONSORT items and the sensitivity, specificity and likelihood ratio to detect the item as adequately reported and to identify a switch in outcomes. We aim to include 120 RCTs and 120 early career peer reviewers., Ethics and Dissemination: The research protocol was approved by the ethics committee of the INSERM Institutional Review Board (21 January 2016). The study is based on voluntary participation and informed written consent., Trial Registration Number: NCT03119376., Competing Interests: Competing interests: None declared., (© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

Objectives: To assess why articles are retracted from BioMed Central journals, whether retraction notices adhered to the Committee on Publication Ethics (COPE) guidelines, and are becoming more frequent as a proportion of published articles., Design/setting: Retrospective cross-sectional analysis of 134 retractions from January 2000 to December 2015., Results: 134 retraction notices were published during this timeframe. Although they account for 0.07% of all articles published (190 514 excluding supplements, corrections, retractions and commissioned content), the rate of retraction is rising. COPE guidelines on retraction were adhered to in that an explicit reason for each retraction was given. However, some notices did not document who retracted the article (eight articles, 6%) and others were unclear whether the underlying cause was honest error or misconduct (15 articles, 11%). The largest proportion of notices was issued by the authors (47 articles, 35%). The majority of retractions were due to some form of misconduct (102 articles, 76%), that is, compromised peer review (44 articles, 33%), plagiarism (22 articles, 16%) and data falsification/fabrication (10 articles, 7%). Honest error accounted for 17 retractions (13%) of which 10 articles (7%) were published in error. The median number of days from publication to retraction was 337.5 days., Conclusions: The most common reason to retract was compromised peer review. However, the majority of these cases date to March 2015 and appear to be the result of a systematic attempt to manipulate peer review across several publishers. Retractions due to plagiarism account for the second largest category and may be reduced by screening manuscripts before publication although this is not guaranteed. Retractions due to problems with the data may be reduced by appropriate data sharing and deposition before publication. Adopting a checklist (linked to COPE guidelines) and templates for various classes of retraction notices would increase transparency of retraction notices in future., Competing Interests: Both authors have completed the ICMJE uniform disclosure form and declare we are employed by BioMed Central. Since the manuscript has been revised ECM has been co-opted as a COPE Council Member, but this study did not involve COPE. We declare no other relationships or activities that could appear to have influenced the submitted work., (Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.)

Open access, open data, open source and other open scholarship practices are growing in popularity and necessity. However, widespread adoption of these practices has not yet been achieved. One reason is that researchers are uncertain about how sharing their work will affect their careers. We review literature demonstrating that open research is associated with increases in citations, media attention, potential collaborators, job opportunities and funding opportunities. These findings are evidence that open research practices bring significant benefits to researchers relative to more traditional closed practices.

In this experiment, the authors were interested in testing the effect of a small molecule inhibitor on the ratio of males and females in the offspring of their model Dipteran species. The authors report that in a wild-type population, ~50 % of offspring are male. They then test the effect of treating females with the chemical, which they think might affect the male:female ratio compared with the untreated group. They claim that there is a statistically significant increase in the percentage of males produced and conclude that the drug affects sex ratios.

Protein X is a signalling molecule that stimulates apoptosis. Treatment of cells with Protein X results in five times higher levels of cell death than those seen in untreated cells (wild type), as measured by Caspase-positive cells. Based on previous work, the authors identify Protein Y as the putative receptor for Protein X and here try to test whether this is indeed the case. They claim that in a geneY mutant, where no receptor is expressed, treatment with Protein X no longer results in increased cell death, supporting the hypothesis that Protein Y is the receptor for signalling molecule X.

Background: Due to problems of publication bias and selective reporting, the ICMJE requires prospective registration of all clinical trials with an appropriate registry before the first participant is enrolled. Previous research has shown that not all clinical trials are registered at this time (prospectively). This study investigated the extent and timing of trial registration. The aims were to determine 1) the proportion of clinical trials that were registered prospectively or retrospectively and 2) when retrospective registration took place in relation to submission to the journal in which they were published., Methods: All clinical trials published in the BMC series in 2013 were identified. All articles that met the study's inclusion criteria were categorised into one of three categories: 1) prospectively registered, 2) retrospectively registered before submission to the journal in which they were published or 3) retrospectively registered after submission to the journal in which they were published., Results: One hundred and eight eligible studies were identified. Of these, 33 (31 %) reported studies that were registered prospectively, 72 reported studies that were registered retrospectively (67 %) and three articles (3 %) did not include a trial registration number. Of the 72 studies that were registered retrospectively, 66 (92 %) were registered before the article was submitted to the journal and six (8 %) were registered after the article was submitted to the journal., Conclusions: Ten years after the ICMJE requirements for prospective registration of clinical trials this study found that the majority of included clinical trials were registered retrospectively but before submission to a journal for publication. This highlights the need for organisations other than journals, such as research institutions and grant giving bodies, to be more involved in enforcing prospective trial registration.

The authors of this paper were interested to see whether the expression of three proteins (A, B and C) was altered in a knockout mouse model of a gene encoding Protein X. Each experiment measured the expression of a different protein and the results seem to show a clear increase in protein expression in the mutant mouse compared with the control. The results are reported as statistically significant, with impressive 'n' values in each condition: the authors say that n = 7 in each case. They confidently conclude that the level of each of the three proteins is increased in the knockout mutant.

Background. The Journal Citation Reports journal impact factors (JIFs) are widely used to rank and evaluate journals, standing as a proxy for the relative importance of a journal within its field. However, numerous criticisms have been made of use of a JIF to evaluate importance. This problem is exacerbated when the use of JIFs is extended to evaluate not only the journals, but the papers therein. The purpose of this study was therefore to investigate the relationship between the number of citations and journal IF for identical articles published simultaneously in multiple journals. Methods. Eligible articles were consensus research reporting statements listed on the EQUATOR Network website that were published simultaneously in three or more journals. The correlation between the citation count for each article and the median journal JIF over the published period, and between the citation count and number of article accesses was calculated for each reporting statement. Results. Nine research reporting statements were included in this analysis, representing 85 articles published across 58 journals in biomedicine. The number of citations was strongly correlated to the JIF for six of the nine reporting guidelines, with moderate correlation shown for the remaining three guidelines (median r = 0.66, 95% CI [0.45-0.90]). There was also a strong positive correlation between the number of citations and the number of article accesses (median r = 0.71, 95% CI [0.5-0.8]), although the number of data points for this analysis were limited. When adjusted for the individual reporting guidelines, each logarithm unit of JIF predicted a median increase of 0.8 logarithm units of citation counts (95% CI [-0.4-5.2]), and each logarithm unit of article accesses predicted a median increase of 0.1 logarithm units of citation counts (95% CI [-0.9-1.4]). This model explained 26% of the variance in citations (median adjusted r (2) = 0.26, range 0.18-1.0). Conclusion. The impact factor of the journal in which a reporting statement was published was shown to influence the number of citations that statement will gather over time. Similarly, the number of article accesses also influenced the number of citations, although to a lesser extent than the impact factor. This demonstrates that citation counts are not purely a reflection of scientific merit and the impact factor is, in fact, auto-correlated.

Male crickets (Gryllus bimaculatus) establish dominance hierarchies within a population by fighting with one another. Larger males win fights more frequently than their smaller counterparts, and a previous study found that males recognise one another primarily through sensory input from the antennae. This study therefore investigated whether the success of larger crickets is influenced by sensory input from the antennae, in part by assessing the number of fights that large 'antennectomized' crickets won against small crickets, compared with the number that large, intact crickets won. The success rate was significantly lower in antennectomized males, though they still won the majority of fights (73/100 versus 58/100, Fisher's exact test P < 0.05); the authors thus conclude that sensory input from the antennae affects the fighting success of large males, but that other size-related factors also play a part.

Zebrafish are able to regenerate various organs and tissues after damage or amputation. To understand better the genetic controls of this process, the authors of this study investigated the expression of two genes previously implicated in fin regeneration using semi-quantitative RT-PCR, at three time points after fin amputation (T1, T2, and T3 in Fig. 1, corresponding to the initiation, middle, and end of fin regeneration, respectively). Briefly, the RT-PCR procedure involved isolating messenger RNA (mRNA) from a matched amount of zebrafish cells from the site of fin regeneration at the three time points, and using primers specific to each gene to selectively detect mRNA as an indicator of gene expression levels. The authors used total genomic DNA isolated from zebrafish cells as a positive control, and no RNA or DNA template as a negative control. They found that Gene 1 was only expressed early on in the process, while Gene 2 expression gradually increased during fin regeneration, reaching a peak of expression toward the end of the process. This provides some detailed information that could be useful in elucidating the function of these genes in fin regeneration.

Oat plants grown at an agricultural research facility produce higher yields in Field 1 than in Field 2, under well fertilised conditions and with similar weather exposure; all oat plants in both fields are healthy and show no sign of disease. In this study, the authors hypothesised that the soil microbial community might be different in each field, and these differences might explain the difference in oat plant growth. They carried out a metagenomic analysis of the 16 s ribosomal 'signature' sequences from bacteria in 50 randomly located soil samples in each field to determine the composition of the bacterial community. The study identified >1000 species, most of which were present in both fields. The authors identified two plant growth-promoting species that were significantly reduced in soil from Field 2 (Student's t-test P < 0.05), and concluded that these species might have contributed to reduced yield.

Oat plants grown at an agricultural research facility produce higher yields in Field 1 than in Field 2, under well fertilised conditions and with similar weather exposure; all oat plants in both fields are healthy and show no sign of disease. In this study, the authors hypothesised that the soil microbial community might be different in each field, and these differences might explain the difference in oat plant growth. They carried out a metagenomic analysis of the 16 s ribosomal 'signature' sequences from bacteria in 50 randomly located soil samples in each field to determine the composition of the bacterial community. The study identified >1000 species, most of which were present in both fields. The authors identified two plant growth-promoting species that were significantly reduced in soil from Field 2 (Student's t-test P < 0.05), and concluded that these species might have contributed to reduced yield.

The pea aphid Acyrthosiphon pisum is an agriculturally important pest of leguminous plants including peas and broad beans. The widespread use of chemical pesticides impacts heavily on the environment, and increases pesticide-resistant pea aphid populations, so alternative strategies are being actively sought. Pseudomonas syringae bacteria are known to infect and kill the pea aphid, and offer a possible control strategy. In this study, the authors measured the effects of injecting P. syringae on the survival of pea aphid populations at 24 and 48 hours. The pea aphid population was killed more rapidly (98 % after 24 hours) with a higher concentration of injected bacteria than in the control or with lower concentrations, indicating that a P. syringae-based control strategy may be a useful alternative to conventional pesticides.

Objectives: To assess whether reports from reviewers recommended by authors show a bias in quality and recommendation for editorial decision, compared with reviewers suggested by other parties, and whether reviewer reports for journals operating on open or single-blind peer review models differ with regard to report quality and reviewer recommendations., Design: Retrospective analysis of the quality of reviewer reports using an established Review Quality Instrument, and analysis of reviewer recommendations and author satisfaction surveys., Setting: BioMed Central biology and medical journals. BMC Infectious Diseases and BMC Microbiology are similar in size, rejection rates, impact factors and editorial processes, but the former uses open peer review while the latter uses single-blind peer review. The Journal of Inflammation has operated under both peer review models., Sample: Two hundred reviewer reports submitted to BMC Infectious Diseases, 200 reviewer reports submitted to BMC Microbiology and 400 reviewer reports submitted to the Journal of Inflammation., Results: For each journal, author-suggested reviewers provided reports of comparable quality to non-author-suggested reviewers, but were significantly more likely to recommend acceptance, irrespective of the peer review model (p<0.0001 for BMC Infectious Diseases, BMC Microbiology and the Journal of Inflammation). For BMC Infectious Diseases, the overall quality of reviewer reports measured by the Review Quality Instrument was 5% higher than for BMC Microbiology (p=0.042). For the Journal of Inflammation, the quality of reports was the same irrespective of the peer review model used., Conclusions: Reviewers suggested by authors provide reports of comparable quality to non-author-suggested reviewers, but are significantly more likely to recommend acceptance. Open peer review reports for BMC Infectious Diseases were of higher quality than single-blind reports for BMC Microbiology. There was no difference in quality of peer review in the Journal of Inflammation under open peer review compared with single blind., (Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.)

Virus B is a newly emerged viral strain for which there is no current treatment. Drug A was identified as a potential treatment for infection with virus B. In this pre-clinical phase of drug testing, the effects of drug A on survival after infection with virus B was tested. There was no difference in survival between control (dark blue) and drug A-treated, virus B-infected mice (green), but a significant difference in survival between control and virus B-infected mice without drug treatment (light blue, z-test for proportions P < 0.05, n = 30 in each group). The authors therefore concluded that drug A is effective in reducing mouse mortality due to virus B.

Some steroid drugs are designed for clinical use to combat muscle-wasting diseases, but are also used by athletes to improve their performance by increasing muscle strength or endurance. This study investigated the effect of one steroid drug on the number of times a weight could be lifted by healthy male subjects as a measure of endurance. The ratio of number of lifts performed with a steroid-injected arm versus a sham-injected control arm increased with the drug dose; the authors therefore concluded that the drug improved endurance.

Shear stress in arteries, which is a measure of the force exerted by blood flow on the arterial wall, is associated with the location of lipid plaques that cause heart disease. In this study, a mathematical model of shear stress was combined with cross-sectional x-ray images of an artery taken using Computed Tomography (CT) scanning, allowing the authors to explore patterns of shearing stress and shed light on the role of arterial architecture in heart disease.

Probiotic treatments are thought to increase the levels of commensal bacterial species that populate the human gut, causing no harm to their host and playing an important role in maintaining gut health. This study is an investigation of the effect of a probiotic treatment on the level of a known commensal bacterium in the guts of healthy human subjects, which was significantly increased with probiotic treatment compared with a control. The authors concluded that the probiotic may thus help to promote gut health.