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1.  The Relationship of Previous Training and Experience of Journal Peer Reviewers to Subsequent Review Quality 
PLoS Medicine  2007;4(1):e40.
Peer review is considered crucial to the selection and publication of quality science, but very little is known about the previous experiences and training that might identify high-quality peer reviewers. The reviewer selection processes of most journals, and thus the qualifications of their reviewers, are ill defined. More objective selection of peer reviewers might improve the journal peer review process and thus the quality of published science.
Methods and Findings
306 experienced reviewers (71% of all those associated with a specialty journal) completed a survey of past training and experiences postulated to improve peer review skills. Reviewers performed 2,856 reviews of 1,484 separate manuscripts during a four-year study period, all prospectively rated on a standardized quality scale by editors. Multivariable analysis revealed that most variables, including academic rank, formal training in critical appraisal or statistics, or status as principal investigator of a grant, failed to predict performance of higher-quality reviews. The only significant predictors of quality were working in a university-operated hospital versus other teaching environment and relative youth (under ten years of experience after finishing training). Being on an editorial board and doing formal grant (study section) review were each predictors for only one of our two comparisons. However, the predictive power of all variables was weak.
Our study confirms that there are no easily identifiable types of formal training or experience that predict reviewer performance. Skill in scientific peer review may be as ill defined and hard to impart as is “common sense.” Without a better understanding of those skills, it seems unlikely journals and editors will be successful in systematically improving their selection of reviewers. This inability to predict performance makes it imperative that all but the smallest journals implement routine review ratings systems to routinely monitor the quality of their reviews (and thus the quality of the science they publish).
A survey of experienced reviewers, asked about training they had received in peer review, found there are no easily identifiable types of formal training and experience that predict reviewer performance.
Editors' Summary
When medical researchers have concluded their research and written it up, the next step is to get it published as an article in a journal, so that the findings can be circulated widely. These published findings help determine subsequent research and clinical use. The editors of reputable journals, including PLoS Medicine, have to decide whether the articles sent to them are of good quality and accurate and whether they will be of interest to the readers of their journal. To do this they need to obtain specialist advice, so they contact experts in the topic of the research article and ask them to write reports. This is the process of scientific peer review, and the experts who write such reports are known as “peer reviewers.” Although the editors make the final decision, the advice and criticism of these peer reviewers to the editors is essential in making decisions on publication, and usually in requiring authors to make changes to their manuscript. The contribution that peer reviewers have made to the article by the time it is finally published may, therefore, be quite considerable.
Although peer review is accepted as a key part of the process for the publishing of medical research, many people have argued that there are flaws in the system. For example, there may be an element of luck involved; one author might find their paper being reviewed by a reviewer who is biased against the approach they have adopted or who is a very critical person by nature, and another author may have the good fortune to have their work considered by someone who is much more favorably disposed toward their work. Some reviewers are more knowledgeable and thorough in their work than others. The editors of medical journals try to take in account such biases and quality factors in their choice of peer reviewers or when assessing the reviews. Some journals have run training courses for experts who review for them regularly to try to make the standard of peer review as high as possible.
Why Was This Study Done?
It is hard for journal editors to know who will make a good peer reviewer, and there is no proven system for choosing them. The authors of this study wanted to identify the previous experiences and training that make up the background of good peer reviewers and compare them with the quality of the reviews provided. This would help journal editors select good people for the task in future, and as a result will affect the quality of science they publish for readers, including other researchers.
What Did the Researchers Do and Find?
The authors contacted all the regular reviewers from one specialist journal (Annals of Emergency Medicine). A total of 306 of these experienced reviewers (71% of all those associated with the journal) completed a survey of past training and experiences that might be expected to improve peer review skills. These reviewers had done 2,856 reviews of 1,484 separate manuscripts during a four-year study period, and during this time the quality of the reviews had been rated by the journal's editors. Surprisingly, most variables, including academic rank, formal training in critical appraisal or statistics, or status as principal investigator of a grant, failed to predict performance of higher-quality reviews. The only significant predictors of quality were working in a university-operated hospital versus other teaching environment and relative youth (under ten years of experience after finishing training), and even these were only weak predictors.
What Do These Findings Mean?
This study suggest that there are no easily identifiable types of formal training or experience that predict peer reviewer performance, although it is clear that some reviewers (and reviews) are better than others. The authors suggest that it is essential therefore that journals routinely monitor the quality of reviews submitted to them to ensure they are getting good advice (a practice that is not universal).
Additional Information.
Please access these Web sites via the online version of this summary at
• WAME is an association of editors from many countries who seek to foster international cooperation among editors of peer-reviewed medical journals
• The Fifth International Congress on Peer Review and Biomedical Publication is one of a series of conferences on peer review
• The PLoS Medicine guidelines for reviewers outline what we look for in a review
• The Council of Science Editors promotes ethical scientific publishing practices
• An editorial also published in this issue of PLoS Medicine discusses the peer review process further
PMCID: PMC1796627  PMID: 17411314
2.  Multi-Stage Open Peer Review: Scientific Evaluation Integrating the Strengths of Traditional Peer Review with the Virtues of Transparency and Self-Regulation 
The traditional forms of scientific publishing and peer review do not live up to all demands of efficient communication and quality assurance in today’s highly diverse and rapidly evolving world of science. They need to be advanced and complemented by interactive and transparent forms of review, publication, and discussion that are open to the scientific community and to the public. The advantages of open access, public peer review, and interactive discussion can be efficiently and flexibly combined with the strengths of traditional scientific peer review. Since 2001 the benefits and viability of this approach are clearly demonstrated by the highly successful interactive open access journal Atmospheric Chemistry and Physics (ACP, and a growing number of sister journals launched and operated by the European Geosciences Union (EGU, and the open access publisher Copernicus ( The interactive open access journals are practicing an integrative multi-stage process of publication and peer review combined with interactive public discussion, which effectively resolves the dilemma between rapid scientific exchange and thorough quality assurance. Key features and achievements of this approach are: top quality and impact, efficient self-regulation and low rejection rates, high attractivity and rapid growth, low costs, and financial sustainability. In fact, ACP and the EGU interactive open access sister journals are by most if not all standards more successful than comparable scientific journals with traditional or alternative forms of peer review (editorial statistics, publication statistics, citation statistics, economic costs, and sustainability). The high efficiency and predictive validity of multi-stage open peer review have been confirmed in a series of dedicated studies by evaluation experts from the social sciences, and the same or similar concepts have recently also been adopted in other disciplines, including the life sciences and economics. Multi-stage open peer review can be flexibly adjusted to the needs and peculiarities of different scientific communities. Due to the flexibility and compatibility with traditional structures of scientific publishing and peer review, the multi-stage open peer review concept enables efficient evolution in scientific communication and quality assurance. It has the potential for swift replacement of hidden peer review as the standard of scientific quality assurance, and it provides a basis for open evaluation in science.
PMCID: PMC3389610  PMID: 22783183
open evaluation; public peer review; open access publishing; interactive discussion; open peer commentary; transparency; self-regulation
3.  A survey of authors publishing in four megajournals 
PeerJ  2014;2:e365.
Aim. To determine the characteristics of megajournal authors, the nature of the manuscripts they are submitting to these journals, factors influencing their decision to publish in a megajournal, sources of funding for article processing charges (APCs) or other fees and their likelihood of submitting to a megajournal in the future.
Methods. Web-based survey of 2,128 authors who recently published in BMJ Open, PeerJ, PLOS ONE or SAGE Open.
Results. The response rate ranged from 26% for BMJ Open to 47% for SAGE Open. The authors were international, largely academics who had recently published in both subscription and Open Access (OA) journals. Across journals about 25% of the articles were preliminary findings and just under half were resubmissions of manuscripts rejected by other journals. Editors from other BMJ journals and perhaps to a lesser extent SAGE and PLOS journals appear to be encouraging authors to submit manuscripts that were rejected by the editor’s journals to a megajournal published by the same publisher. Quality of the journal and speed of the review process were important factors across all four journals. Impact factor was important for PLOS ONE authors but less so for BMJ Open authors, which also has an impact factor. The review criteria and the fact the journal was OA were other significant factors particularly important for PeerJ authors. The reputation of the publisher was an important factor for SAGE Open and BMJ Open. About half of PLOS ONE and around a third of BMJ Open and PeerJ authors used grant funding for publishing charges while only about 10% of SAGE Open used grant funding for publication charges. Around 60% of SAGE Open and 32% of PeerJ authors self-funded their publication fees however the fees are modest for these journals. The majority of authors from all 4 journals were pleased with their experience and indicated they were likely to submit to the same or similar journal in the future.
Conclusions. Megajournals are drawing an international group of authors who tend to be experienced academics. They are choosing to publish in megajournals for a variety of reasons but most seem to value the quality of the journal and the speed of the review/publication process. Having a broad scope was not a key factor for most authors though being OA was important for PeerJ and SAGE Open authors. Most authors appeared pleased with the experience and indicated they are likely to submit future manuscripts to the same or similar megajournal which seems to suggest these journals will continue to grow in popularity.
PMCID: PMC4006221  PMID: 24795855
Open access; Megajournals; Survey; Authors
4.  Open, single-blind, double-blind: which peer review process do you prefer? 
BMC Pharmacology and Toxicology was created from the merger of two journals within the BMC series published by BioMed Central: BMC Pharmacology and BMC Clinical Pharmacology. BMC Pharmacology operated anonymous peer review whereas BMC Clinical Pharmacology operated a fully open peer review policy where the identity of the reviewers was known to the editors, authors and readers. The merged journal also adopted a fully open peer review policy. Two years on we discuss the views and experiences of our Editorial Board Members towards open peer review on this biomedical journal.
PMCID: PMC4191873  PMID: 25266119
5.  A Study of Innovative Features in Scholarly Open Access Journals 
The emergence of the Internet has triggered tremendous changes in the publication of scientific peer-reviewed journals. Today, journals are usually available in parallel electronic versions, but the way the peer-review process works, the look of articles and journals, and the rigid and slow publication schedules have remained largely unchanged, at least for the vast majority of subscription-based journals. Those publishing firms and scholarly publishers who have chosen the more radical option of open access (OA), in which the content of journals is freely accessible to anybody with Internet connectivity, have had a much bigger degree of freedom to experiment with innovations.
The objective was to study how open access journals have experimented with innovations concerning ways of organizing the peer review, the format of journals and articles, new interactive and media formats, and novel publishing revenue models.
The features of 24 open access journals were studied. The journals were chosen in a nonrandom manner from the approximately 7000 existing OA journals based on available information about interesting journals and include both representative cases and highly innovative outlier cases.
Most early OA journals in the 1990s were founded by individual scholars and used a business model based on voluntary work close in spirit to open-source development of software. In the next wave, many long-established journals, in particular society journals and journals from regions such as Latin America, made their articles OA when they started publishing parallel electronic versions. From about 2002 on, newly founded professional OA publishing firms using article-processing charges to fund their operations have emerged. Over the years, there have been several experiments with new forms of peer review, media enhancements, and the inclusion of structured data sets with articles. In recent years, the growth of OA publishing has also been facilitated by the availability of open-source software for journal publishing.
The case studies illustrate how a new technology and a business model enabled by new technology can be harnessed to find new innovative ways for the organization and content of scholarly publishing. Several recent launches of OA journals by major subscription publishers demonstrate that OA is rapidly gaining acceptance as a sustainable alternative to subscription-based scholarly publishing.
PMCID: PMC3278101  PMID: 22173122
Scholarly publishing; open access; Internet; peer review
6.  F1000Research: Tics welcomes you to 21st century biomedical publishing 
F1000Research  2014;3:272.
Tics are repeated, usually suppressible movements or vocalizations. They are the defining features of tic disorders including Tourette syndrome, but many people have them for shorter durations at some point in childhood. This editorial marks the beginning of the F1000Research: Tics specialty section, an effort to provide a single portal to modern research on tics and tic disorders. Publications in F1000Research: Tics benefit from F1000Research’s novel approach to publishing, in which articles can be published within days of submission. Peer review happens after publication and is fully open. When the submitted article or a revision is approved, it is promptly submitted to repositories including NIH’s PubMed Central. In addition to research articles and reviews, F1000Research: Tics will publish study protocols, clinical practice articles, case reports, and data notes. The home page will also provide links to expert recommendations of articles that have appeared elsewhere, and to relevant posters from scientific meetings ( F1000Research’s approach is enabled by the capabilities of internet publication, including space to publish the full results of a study rather than just a few graphs selected from the data. Publishing methodologically sound studies without requiring subjective editorial judgments of novelty or broad appeal brings numerous advantages, including minimizing publication bias and shining the light of openness on peer review. To celebrate the launch of the Tics section, F1000Research is offering discounted article processing charges for manuscripts submitted by March 1st 2015. I have had good experiences publishing in F1000Research, and look forward to seeing a wide range of tic-related manuscripts submitted.
PMCID: PMC4288402  PMID: 25580234
7.  The Open Science Peer Review Oath 
F1000Research  2014;3:271.
One of the foundations of the scientific method is to be able to reproduce experiments and corroborate the results of research that has been done before. However, with the increasing complexities of new technologies and techniques, coupled with the specialisation of experiments, reproducing research findings has become a growing challenge. Clearly, scientific methods must be conveyed succinctly, and with clarity and rigour, in order for research to be reproducible. Here, we propose steps to help increase the transparency of the scientific method and the reproducibility of research results: specifically, we introduce a peer-review oath and accompanying manifesto. These have been designed to offer guidelines to enable reviewers (with the minimum friction or bias) to follow and apply open science principles, and support the ideas of transparency, reproducibility and ultimately greater societal impact. Introducing the oath and manifesto at the stage of peer review will help to check that the research being published includes everything that other researchers would need to successfully repeat the work. Peer review is the lynchpin of the publishing system: encouraging the community to consciously (and conscientiously) uphold these principles should help to improve published papers, increase confidence in the reproducibility of the work and, ultimately, provide strategic benefits to authors and their institutions. Future incarnations of the various national Research Excellence Frameworks (REFs) will evolve away from simple citations towards measurable societal value and impact. The proposed manifesto aspires to facilitate this goal by making transparency, reproducibility and citizen-scientist engagement (with the knowledge-creation and dissemination processes) the default parameters for performing sound research.
PMCID: PMC4304228  PMID: 25653839
8.  An Open Science Peer Review Oath 
F1000Research  2015;3:271.
One of the foundations of the scientific method is to be able to reproduce experiments and corroborate the results of research that has been done before. However, with the increasing complexities of new technologies and techniques, coupled with the specialisation of experiments, reproducing research findings has become a growing challenge. Clearly, scientific methods must be conveyed succinctly, and with clarity and rigour, in order for research to be reproducible. Here, we propose steps to help increase the transparency of the scientific method and the reproducibility of research results: specifically, we introduce a peer-review oath and accompanying manifesto. These have been designed to offer guidelines to enable reviewers (with the minimum friction or bias) to follow and apply open science principles, and support the ideas of transparency, reproducibility and ultimately greater societal impact. Introducing the oath and manifesto at the stage of peer review will help to check that the research being published includes everything that other researchers would need to successfully repeat the work. Peer review is the lynchpin of the publishing system: encouraging the community to consciously (and conscientiously) uphold these principles should help to improve published papers, increase confidence in the reproducibility of the work and, ultimately, provide strategic benefits to authors and their institutions.
PMCID: PMC4304228  PMID: 25653839
9.  AoB PLANTS: origins and features 
AoB Plants  2009;2009:plp002.
The reasons that lie behind starting AoB PLANTS and the ambitions and principal features of the new journal are explained in detail by the Chief Editor.
AoB PLANTS is a peer reviewed, Open Access (OA) journal owned and run by plant biologists and published by Oxford University Press. The journal publishes research papers, reviews and opinion papers on all aspects of land based plant biology. They are made available rapidly online and can be accessed without the need for subscriptions or payment.
Several difficulties in conventional publishing of peer-reviewed manuscripts encouraged AoB PLANTS to adopt OA. Open Access helps sidestep library budgets which are struggling to purchase the increasing numbers of journals. Open Access makes research freely available both to the academic community and beyond while publishing online only eliminates the need to reject good manuscripts simply to control the size of the printed journal. Finally, the journal chose to go OA to ensure the widest possible international readership for the growing amount of high-quality plant science research being carried out worldwide in response to problems such as climate change and food shortages. Responses to a wide-ranging online questionnaire indicated strong international support for a journal such as AoB PLANTS.
Principal features
AoB PLANTS strives for fair and rapid peer review followed by fast publication of accepted papers. For an initial period, there will be no OA fees, and fees will remain modest once introduced. AoB PLANTS adopts double-blind peer review using published criteria for acceptability as a basis for decision-making. Accepted papers are published shortly after acceptance together with referees' analyses using Stanford University Libraries High Wire Press H2O platform. Authors retain ownership of the copyright in their papers.
PMCID: PMC2982705  PMID: 22476111
10.  Why training and specialization is needed for peer review: a case study of peer review for randomized controlled trials 
BMC Medicine  2014;12(1):128.
The purpose and effectiveness of peer review is currently a subject of hot debate, as is the need for greater openness and transparency in the conduct of clinical trials. Innovations in peer review have focused on the process of peer review rather than its quality.
The aims of peer review are poorly defined, with no evidence that it works and no established way to provide training. However, despite the lack of evidence for its effectiveness, evidence-based medicine, which directly informs patient care, depends on the system of peer review. The current system applies the same process to all fields of research and all study designs. While the volume of available health related information is vast, there is no consistent means for the lay person to judge its quality or trustworthiness. Some types of research, such as randomized controlled trials, may lend themselves to a more specialized form of peer review where training and ongoing appraisal and revalidation is provided to individuals who peer review randomized controlled trials. Any randomized controlled trial peer reviewed by such a trained peer reviewer could then have a searchable ‘quality assurance’ symbol attached to the published articles and any published peer reviewer reports, thereby providing some guidance to the lay person seeking to inform themselves about their own health or medical treatment.
Specialization, training and ongoing appraisal and revalidation in peer review, coupled with a quality assurance symbol for the lay person, could address some of the current limitations of peer review for randomized controlled trials.
PMCID: PMC4243268  PMID: 25285376
Peer review; Evidence based medicine; EBM; Randomized controlled trials; RCT; Clinical training; Medical education; Reporting guidelines; CONSORT
11.  A retrospective analysis of submissions, acceptance rate, open peer review operations, and prepublication bias of the multidisciplinary open access journal Head & Face Medicine 
Head & Face Medicine  2007;3:27.
Head & Face Medicine (HFM) was launched in August 2005 to provide multidisciplinary science in the field of head and face disorders with an open access and open peer review publication platform. The objective of this study is to evaluate the characteristics of submissions, the effectiveness of open peer reviewing, and factors biasing the acceptance or rejection of submitted manuscripts.
A 1-year period of submissions and all concomitant journal operations were retrospectively analyzed. The analysis included submission rate, reviewer rate, acceptance rate, article type, and differences in duration for peer reviewing, final decision, publishing, and PubMed inclusion. Statistical analysis included Mann-Whitney U test, Chi-square test, regression analysis, and binary logistic regression.
HFM received 126 articles (10.5 articles/month) for consideration in the first year. Submissions have been increasing, but not significantly over time. Peer reviewing was completed for 82 articles and resulted in an acceptance rate of 48.8%. In total, 431 peer reviewers were invited (5.3/manuscript), of which 40.4% agreed to review. The mean peer review time was 37.8 days. The mean time between submission and acceptance (including time for revision) was 95.9 days. Accepted papers were published on average 99.3 days after submission. The mean time between manuscript submission and PubMed inclusion was 101.3 days. The main article types submitted to HFM were original research, reviews, and case reports. The article type had no influence on rejection or acceptance. The variable 'number of invited reviewers' was the only significant (p < 0.05) predictor for rejection of manuscripts.
The positive trend in submissions confirms the need for publication platforms for multidisciplinary science. HFM's peer review time comes in shorter than the 6-weeks turnaround time the Editors set themselves as the maximum. Rejection of manuscripts was associated with the number of invited reviewers. None of the other parameters tested had any effect on the final decision. Thus, HFM's ethical policy, which is based on Open Access, Open Peer, and transparency of journal operations, is free of 'editorial bias' in accepting manuscripts.
Original data
Provided as a downloadable tab-delimited text file (URL and variable code available under section 'additional files').
PMCID: PMC1913501  PMID: 17562003
12.  Maintaining Live Discussion in Two-Stage Open Peer Review 
Open peer review has been proposed for a number of reasons, in particular, for increasing the transparency of the article selection process for a journal, and for obtaining a broader basis for feedback to the authors and for the acceptance decision. The review discussion may also in itself have a value for the research community. These goals rely on the existence of a lively review discussion, but several experiments with open-process peer review in recent years have encountered the problem of faltering review discussions. The present article addresses the question of how lively review discussion may be fostered by relating the experience of the journal Electronic Transactions on Artificial Intelligence (ETAI) which was an early experiment with open peer review. Factors influencing the discussion activity are identified. It is observed that it is more difficult to obtain lively discussion when the number of contributed articles increases, which implies difficulties for scaling up the open peer review model. Suggestions are made for how this difficulty may be overcome.
PMCID: PMC3282940  PMID: 22363282
open peer review; community peer review; two-stage peer review; live discussion
13.  Open Evaluation: A Vision for Entirely Transparent Post-Publication Peer Review and Rating for Science 
The two major functions of a scientific publishing system are to provide access to and evaluation of scientific papers. While open access (OA) is becoming a reality, open evaluation (OE), the other side of the coin, has received less attention. Evaluation steers the attention of the scientific community and thus the very course of science. It also influences the use of scientific findings in public policy. The current system of scientific publishing provides only journal prestige as an indication of the quality of new papers and relies on a non-transparent and noisy pre-publication peer-review process, which delays publication by many months on average. Here I propose an OE system, in which papers are evaluated post-publication in an ongoing fashion by means of open peer review and rating. Through signed ratings and reviews, scientists steer the attention of their field and build their reputation. Reviewers are motivated to be objective, because low-quality or self-serving signed evaluations will negatively impact their reputation. A core feature of this proposal is a division of powers between the accumulation of evaluative evidence and the analysis of this evidence by paper evaluation functions (PEFs). PEFs can be freely defined by individuals or groups (e.g., scientific societies) and provide a plurality of perspectives on the scientific literature. Simple PEFs will use averages of ratings, weighting reviewers (e.g., by H-index), and rating scales (e.g., by relevance to a decision process) in different ways. Complex PEFs will use advanced statistical techniques to infer the quality of a paper. Papers with initially promising ratings will be more deeply evaluated. The continual refinement of PEFs in response to attempts by individuals to influence evaluations in their own favor will make the system ungameable. OA and OE together have the power to revolutionize scientific publishing and usher in a new culture of transparency, constructive criticism, and collaboration.
PMCID: PMC3473231  PMID: 23087639
peer review; publishing; ratings; social web; open evaluation
14.  Qualitative Analysis of Peer Coaches’ Experiences with Counseling African Americans About Reducing Heart Disease Risk 
Despite mounting evidence that peer coaches can make significant contributions to patient health, little is known about factors that must be addressed to engage and retain them in their role.
To identify motivators and barriers to serving as a peer coach.
Open ended semi-structured interviews.
In a randomized trial of peer support, patients with well controlled hypertension and good interpersonal skills were recruited and trained to serve as peer coaches for African-American patients from the same practices who had poorly controlled hypertension. Peer coaches spoke by telephone at least three times with their same sex patient–clients on alternate months during the 6-month intervention and counseled about medication adherence as well as other healthy lifestyles.
Of 15 trained peer coaches, ten were contacted and agreed to participate in the qualitative interview. Peer coaches had a mean age of 66 years, 50% were women, and 80% were African-American. Themes regarding favorable aspects of the peer coach experience included: meaning and satisfaction derived from contributing to community health and the personal emotional and physical benefits derived from serving as a peer coach. Negative aspects centered on: challenges in establishing the initial telephone contact and wanting more information about their patient–clients’ personal health conditions and status. Peer coaches endorsed gender matching but were less clear about race-matching.
Programs that utilize peer support to enhance positive health behaviors should recognize that a spirit of volunteerism motivates many successful peer coaches. Program planners should acknowledge the special characteristics required of successful peer coaches when selecting, motivating and training individuals for this role.
Electronic supplementary material
The online version of this article (doi:10.1007/s11606-011-1883-6) contains supplementary material, which is available to authorized users.
PMCID: PMC3270244  PMID: 21953326
peer coach; peer counseling; navigator; risk counseling
15.  Views on the peer review system of biomedical journals: an online survey of academics from high-ranking universities 
Peer review is the major method used by biomedical journals for making the decision of publishing an article. This cross-sectional survey assesses views concerning the review system of biomedical journals among academics globally.
A total of 28,009 biomedical academics from high-ranking universities listed by the 2009 Times Higher Education Quacquarelli Symonds (THE-QS) World University Rankings were contacted by email between March 2010 and August 2010. 1,340 completed an online survey which focused on their academic background, negative experiences and views on biomedical journal peer review and the results were compared among basic scientists, clinicians and clinician scientists.
Fewer than half of the respondents agreed that the peer review systems of biomedical journals were fair (48.4%), scientific (47.5%), or transparent (25.1%). Nevertheless, 58.2% of the respondents agreed that authors should remain anonymous and 64.4% agreed that reviewers should not be disclosed. Most, (67.7%) agreed to the establishment of an appeal system. The proportion of native English-speaking respondents who agreed that the “peer review system is fair” was significantly higher than for non-native respondents (p = 0.02). Similarly, the proportion of clinicians stating that the “peer review system is fair” was significantly higher than that for basic scientists and clinician-scientists (p = 0.004). For females, (β = −0.1, p = 0.03), the frequency of encountering personal attacks in reviewers’ comments (β = −0.1, p = 0.002) and the frequency of imposition of unnecessary references by reviewers (β = −0.06, p = 0.04) were independently and inversely associated with agreement that “the peer review system is fair”.
Academics are divided on the issue of whether the biomedical journal peer review system is fair, scientific and transparent. A majority of academics agreed with the double-blind peer review and to the establishment of an appeal system. Female academics, experience of personal attacks and imposition of unnecessary references by reviewers were related to disagreement about fairness of the peer review system of biomedical journals.
PMCID: PMC3685540  PMID: 23758823
Academics; Peer review; Biomedical journal; Online survey
16.  OpenKnowledge for peer-to-peer experimentation in protein identification by MS/MS 
Traditional scientific workflow platforms usually run individual experiments with little evaluation and analysis of performance as required by automated experimentation in which scientists are being allowed to access numerous applicable workflows rather than being committed to a single one. Experimental protocols and data under a peer-to-peer environment could potentially be shared freely without any single point of authority to dictate how experiments should be run. In such environment it is necessary to have mechanisms by which each individual scientist (peer) can assess, locally, how he or she wants to be involved with others in experiments. This study aims to implement and demonstrate simple peer ranking under the OpenKnowledge peer-to-peer infrastructure by both simulated and real-world bioinformatics experiments involving multi-agent interactions.
A simulated experiment environment with a peer ranking capability was specified by the Lightweight Coordination Calculus (LCC) and automatically executed under the OpenKnowledge infrastructure. The peers such as MS/MS protein identification services (including web-enabled and independent programs) were made accessible as OpenKnowledge Components (OKCs) for automated execution as peers in the experiments. The performance of the peers in these automated experiments was monitored and evaluated by simple peer ranking algorithms.
Peer ranking experiments with simulated peers exhibited characteristic behaviours, e.g., power law effect (a few dominant peers dominate), similar to that observed in the traditional Web. Real-world experiments were run using an interaction model in LCC involving two different types of MS/MS protein identification peers, viz., peptide fragment fingerprinting (PFF) and de novo sequencing with another peer ranking algorithm simply based on counting the successful and failed runs. This study demonstrated a novel integration and useful evaluation of specific proteomic peers and found MASCOT to be a dominant peer as judged by peer ranking.
The simulated and real-world experiments in the present study demonstrated that the OpenKnowledge infrastructure with peer ranking capability can serve as an evaluative environment for automated experimentation.
PMCID: PMC3377912  PMID: 22192521
17.  Issue Information 
Aims and Scope: Molecular Genetics & Genomic Medicine is a peer reviewed journal for rapid dissemination of high-quality research related to the dynamically developing areas of human, molecular and medical genetics. The journal publishes original research articles covering novel findings in phenotypic, molecular, biological, and genomic aspects of genomic variation, inherited disorders and birth defects. The broad publishing spectrum of Molecular Genetics & Genomic Medicine includes rare and common disorders from diagnosis to treatment. Examples of appropriate articles include reports of novel disease genes, functional studies of genetic variants, in-depth genotype-phenotype studies, genomic analysis of inherited disorders, molecular diagnostic methods, medical bioinformatics, ethical, legal, and social implications (ELSI), and novel approaches to clinical diagnosis. We anticipate that Molecular Genetics & Genomic Medicine will provide a high quality scientific home for next generation sequencing studies of rare and common disorders, which will make novel findings in this fascinating area easily and rapidly accessible to the scientific community. This will serve as the basis for translating next generation sequencing studies into individualized diagnostics and therapeutics, for day-to-day medical care.
Molecular Genetics & Genomic Medicine publishes original research articles, reviews, and research methods papers, along with invited editorials and commentaries. Original research papers must report well-conducted research with conclusions supported by the data presented.
Molecular Genetics & Genomic Medicine is a Wiley Open Access journal, one of a series of peer reviewed titles publishing quality research with speed and efficiency. For further information visit the Wiley Open Access website.
PMCID: PMC3907910  PMID: 24498632
18.  Misrepresentation of Randomized Controlled Trials in Press Releases and News Coverage: A Cohort Study 
PLoS Medicine  2012;9(9):e1001308.
A study conducted by Amélie Yavchitz and colleagues examines the factors associated with “spin” (specific reporting strategies, intentional or unintentional, that emphasize the beneficial effect of treatments) in press releases of clinical trials.
Previous studies indicate that in published reports, trial results can be distorted by the use of “spin” (specific reporting strategies, intentional or unintentional, emphasizing the beneficial effect of the experimental treatment). We aimed to (1) evaluate the presence of “spin” in press releases and associated media coverage; and (2) evaluate whether findings of randomized controlled trials (RCTs) based on press releases and media coverage are misinterpreted.
Methods and Findings
We systematically searched for all press releases indexed in the EurekAlert! database between December 2009 and March 2010. Of the 498 press releases retrieved and screened, we included press releases for all two-arm, parallel-group RCTs (n = 70). We obtained a copy of the scientific article to which the press release related and we systematically searched for related news items using Lexis Nexis.
“Spin,” defined as specific reporting strategies (intentional or unintentional) emphasizing the beneficial effect of the experimental treatment, was identified in 28 (40%) scientific article abstract conclusions and in 33 (47%) press releases. From bivariate and multivariable analysis assessing the journal type, funding source, sample size, type of treatment (drug or other), results of the primary outcomes (all nonstatistically significant versus other), author of the press release, and the presence of “spin” in the abstract conclusion, the only factor associated, with “spin” in the press release was “spin” in the article abstract conclusions (relative risk [RR] 5.6, [95% CI 2.8–11.1], p<0.001). Findings of RCTs based on press releases were overestimated for 19 (27%) reports. News items were identified for 41 RCTs; 21 (51%) were reported with “spin,” mainly the same type of “spin” as those identified in the press release and article abstract conclusion. Findings of RCTs based on the news item was overestimated for ten (24%) reports.
“Spin” was identified in about half of press releases and media coverage. In multivariable analysis, the main factor associated with “spin” in press releases was the presence of “spin” in the article abstract conclusion.
Editors' Summary
The mass media play an important role in disseminating the results of medical research. Every day, news items in newspapers and magazines and on the television, radio, and internet provide the general public with information about the latest clinical studies. Such news items are written by journalists and are often based on information in “press releases.” These short communications, which are posted on online databases such as EurekAlert! and sent directly to journalists, are prepared by researchers or more often by the drug companies, funding bodies, or institutions supporting the clinical research and are designed to attract favorable media attention to newly published research results. Press releases provide journalists with the information they need to develop and publish a news story, including a link to the peer-reviewed journal (a scholarly periodical containing articles that have been judged by independent experts) in which the research results appear.
Why Was This Study Done?
In an ideal world, journal articles, press releases, and news stories would all accurately reflect the results of health research. Unfortunately, the findings of randomized controlled trials (RCTs—studies that compare the outcomes of patients randomly assigned to receive alternative interventions), which are the best way to evaluate new treatments, are sometimes distorted in peer-reviewed journals by the use of “spin”—reporting that emphasizes the beneficial effects of the experimental (new) treatment. For example, a journal article may interpret nonstatistically significant differences as showing the equivalence of two treatments although such results actually indicate a lack of evidence for the superiority of either treatment. “Spin” can distort the transposition of research into clinical practice and, when reproduced in the mass media, it can give patients unrealistic expectations about new treatments. It is important, therefore, to know where “spin” occurs and to understand the effects of that “spin”. In this study, the researchers evaluate the presence of “spin” in press releases and associated media coverage and analyze whether the interpretation of RCT results based on press releases and associated news items could lead to the misinterpretation of RCT results.
What Did the Researchers Do and Find?
The researchers identified 70 press releases indexed in EurekAlert! over a 4-month period that described two-arm, parallel-group RCTs. They used Lexis Nexis, a database of news reports from around the world, to identify associated news items for 41 of these press releases and then analyzed the press releases, news items, and abstracts of the scientific articles related to each press release for “spin”. Finally, they interpreted the results of the RCTs using each source of information independently. Nearly half the press releases and article abstract conclusions contained “spin” and, importantly, “spin” in the press releases was associated with “spin” in the article abstracts. The researchers overestimated the benefits of the experimental treatment from the press release as compared to the full-text peer-reviewed article for 27% of reports. Factors that were associated with this overestimation of treatment benefits included publication in a specialized journal and having “spin” in the press release. Of the news items related to press releases, half contained “spin”, usually of the same type as identified in the press release and article abstract. Finally, the researchers overestimated the benefit of the experimental treatment from the news item as compared to the full-text peer-reviewed article in 24% of cases.
What Do These Findings Mean?
These findings show that “spin” in press releases and news reports is related to the presence of “spin” in the abstract of peer-reviewed reports of RCTs and suggest that the interpretation of RCT results based solely on press releases or media coverage could distort the interpretation of research findings in a way that favors experimental treatments. This interpretation shift is probably related to the presence of “spin” in peer-reviewed article abstracts, press releases, and news items and may be partly responsible for a mismatch between the perceived and real beneficial effects of new treatments among the general public. Overall, these findings highlight the important role that journal reviewers and editors play in disseminating research findings. These individuals, the researchers conclude, have a responsibility to ensure that the conclusions reported in the abstracts of peer-reviewed articles are appropriate and do not over-interpret the results of clinical research.
Additional Information
Please access these Web sites via the online version of this summary at
The PLOS Hub for Clinical Trials, which collects PLOS journals relating to clinical trials, includes some other articles on “spin” in clinical trial reports
EurekAlert is an online free database for science press releases
The UK National Health Service Choices website includes Beyond the Headlines, a resource that provides an unbiased and evidence-based analysis of health stories that make the news for both the public and health professionals
The US-based organization HealthNewsReview, a project supported by the Foundation for Informed Medical Decision Making, also provides expert reviews of news stories
PMCID: PMC3439420  PMID: 22984354
19.  The scholarship of critical review: improving quality and relevance 
To describe the process of scientific peer review as it is used in the manuscript submission process, assess threats and challenges to the peer review process, and to offer suggestions for enhancing its effectiveness.
Peer review is often seen as one of the hallmarks of scientific publication. The primary goal of peer review is to improve the science within papers that are ultimately published, by helping an editor better understand the strengths and weaknesses of a given paper. This process, while fairly well studied within the medical field, has received almost no attention at all within chiropractic. This paper provides guidance to reviewers and potential reviewers which can help them to understand both the scientific and the human aspects of peer review. This is designed to elevate this function to one trusted by the profession rather than seen as simply another hurdle to overcome. Several future directions are offered, including unblinding the review process for transparency, conducting rigorous studies looking at peer review, and developing formal training programs for potential reviewers.
Peer review is likely to remain in force as a means to provide guidance to authors and editors about the rigor of submitted papers. However, the nature of peer review may be changing and editors and authors need to stay aware of the implications of these changes. Recommendations to open the process, study it and develop training programs are designed to ensure that the process remains as impartial as possible.
PMCID: PMC2597885  PMID: 19066695
Peer Review; Periodicals; Chiropractic
20.  The Open Medicine student peer review program 
Open Medicine  2011;5(1):e55-e56.
Open Medicine has provided an opportunity to acquire experience in peer review for a group of graduate students in the Department of Community Health Sciences at the University of Calgary. To date, approximately 40 students have regularly participated in the peer review of manuscripts for Open Medicine. Participating students attend group sessions on the practicalities of reviewing papers, the revision and resubmission process, and specific topic areas that arise from particular papers. Through these experiences, the students have gained insight into the importance of quality peer review, Open Access publication and research reporting guidelines. Open Medicine encourages the proliferation of similar programs at other universities, as this valuable part of medical research is not formally taught in most graduate health research programs.
PMCID: PMC3205806  PMID: 22046221
21.  Developing PeerLink to engage out-of-care HIV+ substance users: Training peers to deliver a peer-led motivational intervention with fidelity 
AIDS care  2012;25(7):10.1080/09540121.2012.748169.
Substance use among HIV+ individuals can be a barrier to HIV care, resulting in poor health outcomes. Motivational interviewing (MI) is an effective intervention to reduce substance abuse and increase HIV-related health. Healthcare workers from various backgrounds can be effectively trained in delivering MI interventions; however, there has been limited evidence that peers can effectively deliver MI interventions with fidelity. Peers have traditionally worked in HIV care settings and represent a valid context for a peer-delivered intervention focused on motivational issues. We trained four peers in MI. In this paper, we describe the intervention, explain the MI training methods, and investigate whether peers can be trained in MI with fidelity. The MI training included didactic instruction, group workshops, and individual feedback sessions. Two of four peers achieved MI treatment fidelity as measured by the Motivational Interviewing Treatment Integrity Code Version 3.0. Overall, peers had difficulty using open-ended questions and querying pros and cons, skills thought necessary to elicit change talk. They also tended to give too much direct advice where reflections would have been appropriate. A challenge was training peers to change familiar ways of communicating. Nonetheless, they did well at assessing and highlighting motivation to change. The total training hours (40 h) was long compared with other published MI studies. However, the intervention included several components with two targeted change behaviors. It is likely that peers can be trained in MI with fidelity in less time given a more streamlined intervention. When working with peers who have life stressors similar to the target group, it is important to be flexible in the training.
PMCID: PMC3817565  PMID: 23230862
motivational interviewing; peer training; substance use; HIV/AIDS; MITI
22.  Virtual slides in peer reviewed, open access medical publication 
Diagnostic Pathology  2011;6:124.
Application of virtual slides (VS), the digitalization of complete glass slides, is in its infancy to be implemented in routine diagnostic surgical pathology and to issues that are related to tissue-based diagnosis, such as education and scientific publication.
Electronic publication in Pathology offers new features of scientific communication in pathology that cannot be obtained by conventional paper based journals. Most of these features are based upon completely open or partly directed interaction between the reader and the system that distributes the article. One of these interactions can be applied to microscopic images allowing the reader to navigate and magnify the presented images. VS and interactive Virtual Microscopy (VM) are a tool to increase the scientific value of microscopic images.
Technology and Performance
The open access journal Diagnostic Pathology has existed for about five years. It is a peer reviewed journal that publishes all types of scientific contributions, including original scientific work, case reports and review articles. In addition to digitized still images the authors of appropriate articles are requested to submit the underlying glass slides to an institution (, and for digitalization and documentation. The images are stored in a separate image data bank which is adequately linked to the article. The normal review process is not involved. Both processes (peer review and VS acquisition) are performed contemporaneously in order to minimize a potential publication delay. VS are not provided with a DOI index (digital object identifier). The first articles that include VS were published in March 2011.
Results and Perspectives
Several logistic constraints had to be overcome until the first articles including VS could be published. Step by step an automated acquisition and distribution system had to be implemented to the corresponding article. The acceptance of VS by the reader is high as well as by the authors. Of specific value are the increased confidence to and reputation of authors as well as the presented information to the reader. Additional associated functions such as access to author-owned related image collections, reader-controlled automated image measurements and image transformations are in preparation.
Virtual Slides
The virtual slide(s) for this article can be found here:
PMCID: PMC3275477  PMID: 22182763
Virtual slide; virtual microcopy; open access publication; image interpretation; image content information
23.  Effect on peer review of telling reviewers that their signed reviews might be posted on the web: randomised controlled trial 
Objectives To see whether telling peer reviewers that their signed reviews of original research papers might be posted on the BMJ’s website would affect the quality of their reviews.
Design Randomised controlled trial.
Setting A large international general medical journal based in the United Kingdom.
Participants 541 authors, 471 peer reviewers, and 12 editors.
Intervention Consecutive eligible papers were randomised either to have the reviewer’s signed report made available on the BMJ’s website alongside the published paper (intervention group) or to have the report made available only to the author—the BMJ’s normal procedure (control group). The intervention was the act of revealing to reviewers—after they had agreed to review but before they undertook their review—that their signed report might appear on the website.
Main outcome measures The main outcome measure was the quality of the reviews, as independently rated on a scale of 1 to 5 using a validated instrument by two editors and the corresponding author. Authors and editors were blind to the intervention group. Authors rated review quality before the fate of their paper had been decided. Additional outcomes were the time taken to complete the review and the reviewer’s recommendation regarding publication.
Results 558 manuscripts were randomised, and 471 manuscripts remained after exclusions. Of the 1039 reviewers approached to take part in the study, 568 (55%) declined. Two editors’ evaluations of the quality of the peer review were obtained for all 471 manuscripts, with the corresponding author’s evaluation obtained for 453. There was no significant difference in review quality between the intervention and control groups (mean difference for editors 0.04, 95% CI −0.09 to 0.17; for authors 0.06, 95% CI −0.09 to 0.20). Any possible difference in favour of the control group was well below the level regarded as editorially significant. Reviewers in the intervention group took significantly longer to review (mean difference 25 minutes, 95% CI 3.0 to 47.0 minutes).
Conclusion Telling peer reviewers that their signed reviews might be available in the public domain on the BMJ’s website had no important effect on review quality. Although the possibility of posting reviews online was associated with a high refusal rate among potential peer reviewers and an increase in the amount of time taken to write a review, we believe that the ethical arguments in favour of open peer review more than outweigh these disadvantages.
PMCID: PMC2982798  PMID: 21081600
24.  BioLit: integrating biological literature with databases 
Nucleic Acids Research  2008;36(Web Server issue):W385-W389.
BioLit is a web server which provides metadata describing the semantic content of all open access, peer-reviewed articles which describe research from the major life sciences literature archive, PubMed Central. Specifically, these metadata include database identifiers and ontology terms found within the full text of the article. BioLit delivers these metadata in the form of XML-based article files and as a custom web-based article viewer that provides context-specific functionality to the metadata. This resource aims to integrate the traditional scientific publication directly into existing biological databases, thus obviating the need for a user to search in multiple locations for information relating to a specific item of interest, for example published experimental results associated with a particular biological database entry. As an example of a possible use of BioLit, we also present an instance of the Protein Data Bank fully integrated with BioLit data. We expect that the community of life scientists in general will be the primary end-users of the web-based viewer, while biocurators will make use of the metadata-containing XML files and the BioLit database of article data. BioLit is available at
PMCID: PMC2447735  PMID: 18515836
25.  How to write an article: Preparing a publishable manuscript! 
CytoJournal  2012;9:1.
Most of the scientific work presented as abstracts (platforms and posters) at various conferences have the potential to be published as articles in peer-reviewed journals. This DIY (Do It Yourself) article on how to achieve that goal is an extension of the symposium presented at the 36th European Congress of Cytology, Istanbul, Turkey (presentation available on net at The criteria for manuscript authorship should be based on the ICMJE (International Committee of Medical Journal Editors) Uniform Requirements for Manuscripts. The next step is to choose the appropriate journal to submit the manuscript and review the ‘Instructions to the authors’ for that journal. Although initially it may appear to be an insurmountable task, diligent organizational discipline with a little patience and perseverance with input from mentors should lead to the preparation of a nearly perfect publishable manuscript even by a novice. Ultimately, the published article is an excellent track record of academic productivity with contribution to the general public good by encouraging the exchange of experience and innovation. It is a highly rewarding conduit to the personal success and growth leading to the collective achievement of continued scientific progress. Recent emergences of journals and publishers offering the platform and opportunity to publish under an open access charter provides the opportunity for authors to protect their copyright from being lost to conventional publishers. Publishing your work on this open platform is the most rewarding mission and is the recommended option in the current modern era.
[This open access article can be linked (copy-paste link from HTML version of this article) or reproduced FREELY if original reference details are prominently identifiable].
PMCID: PMC3280045  PMID: 22363390
Author; cytopathology; manuscript; publish; research; reviewer

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