There have been tremendous developments in the field of Journalology during the last two decades and now it has emerged as an important discipline with numerous sub-specialties. Most of the editors have so far learnt this art through on the job training. The professional competencies required to be an Editor of a biomedical journal to act as an effective scientific editor has a very broad range and often it is not possible for an individual to fulfill all the requirements and he/she has to depend on the teamwork in which people with expertise in different areas put together their efforts to produce a good quality peer reviewed biomedical journal. They are most often members of the Editorial Board or work in an advisory capacity. The editors are supposed to have some knowledge in areas like research methods, publication ethics, different peer review processes, their advantages and disadvantages, how to protect integrity of their journal/professionalism, they must possess sound knowledge to be able to make good decisions, proficiency in language skills and indexing of the journal in different databases. All this certainly is beyond the capability of an individual and most often these editors have to rely on their other team members.th in 2011. Basically it was meant to train the trainers hence one editor was invited from all the EMRO countries. The first author was one of the participants in this course from Pakistan and as per WHO mandatory requirements, on return to Pakistan, organized the training course for the editors under the auspicious of Pakistan Association of Medical Editors (PAME). These courses were organized at Karachi, Lahore, Rawalpindi-Islamabad and Peshawar.Associations of Medical Editors in different countries have been organizing different workshops, training courses for their members. WHO EMRO also organized a training course for editors at Shiraz University of Medial Sciences, Shiraz Islamic Republic of Iran from November 14-17World Association of Medical Editors (WAME) came up with a Syllabus for prospective and newly appointed editorsFor Pakistan we suggested starting a Certificate Course in Medical JournalismQuality and standard of most of the biomedical journals published by professional specialty organizations or medical colleges, universities in Pakistan also leaves much to be desired. One of the important reasons is that most of the faculty members are working as editors in honorary capacity as an additional responsibility. Not only that they do not have any contract appointment and they can be removed anytime. Hence, under such working environment one cannot expect these editors to work with devotion and dedication, concentrating on improving the quality of their journals. It is in the interest of the stake holder’s editors as well as the owner institutions, specialty organizations that the editors should be offered contract appointment clearly defining their role, duties and responsibilities which will be a step in the right direction. The sooner the importance of such a step is realized, better it will be.More recently Moher et al and their colleagues which included distinguished medical editors from different countries, representatives of various associations of medical editors, scientific publishers have proposed some core competences for scientific editors of biomedical journals.3Editors should be able to demonstrate experience and have broad knowledge of the fields covered by their journal.They should be able to synthesize information and views form a wide range of sources and make informed decisions.They should practice lifelong learning related to their role as an editor and within their areas of experience.They should be able to communicate clearly and effectively manage communications and relationship with authors, peer reviewers, other editors, staff, journal owners, readers, publishers and other related individuals, groups.Editors should act with leadership and integrity and be accountable to authors, peer reviewers, fellow editors, readers, journal owners, publishers and other relevant individual and groups.They should demonstrate knowledge related to the integrity of research and publishing and apply best practices in dealing with research or publication misconduct, misbehavior and questionable practices.They should be able to identify and uphold the principles of ethical research involving humans and animals, when appraising manuscripts.They should apply their responsibilities and rights as a journal editor.They should be able to identify and use trustworthy resources.They should be able to select journal contents that reflect the goals and scope of the journal.They should be capable of analyzing journal policies, practices and performance metrics to improve journal performance.Editors should be able to evaluate the scientific rigor and integrity of manuscripts and make editorial decisions after consideration of reviewers and other editor’s comments.They should be capable of applying best practices for research and other manuscript presentation when evaluating and requesting revision of manuscripts.They should be able to manage and assure the integrity of the peer review process.The above fourteen broad core competences includes different sub-sets like identifying situations where skills required exceeds their level of competency and they need to seek advice from others, exercising sound judgment in making decisions, reconsider decisions when necessary and respond promptly, set personal learning goals, ensure clear instructions for authors and peer reviewers, effective use of all communication channels i.e. correspondence, e mail and social media, mentor, educate train and provide feedback to other editor colleagues, monitor and safeguard fairness and timeliness, know what constitutes a publication ethics, identify conflict of interest on the part of authors and peer reviewers, editors and publishers, manage redundant or duplicate submissions, identify and apply principles of confidentiality, comply with licensing and copy right regulations, ensure best practices as regards advertising policy, identify and use resources for technical editing for authors, editors and peer reviewers, analyze journal performance, formal rational opinion about the submitted manuscripts, practice triage of manuscripts thoroughly and in a timely manner, apply best practices in evaluating citation and references, describe different models of peer review, select peer reviewers who are competent and identify those with conflict of interest, provide feedback to the reviewers, express gratitude to the reviewers besides regularly monitoring and auditing the journal’s performance looking at the acceptance, rejection of manuscripts. They should not hesitate to review their decisions if sound explanation is given with proper references by authors whose manuscripts are first rejected during peer review.The whole thing is continuously evolving and in the years to come, it is expected that proper training manuals may be developed and a core competency based curriculum will be finalized. Later on the evaluation of these competencies will be possible which could be in the form of some certification. Moher and their colleagues in their consensus statement has also suggested the above in short term and long term goals.


January 2016. We have already published the reviewer comments and author responses of over 2000 papers, whose authors have opted in to our transparent peer review scheme.Our fundamental belief as a journal is that science benefits from openness, whether it be open access to the published literature, to data and materials, or to work that has not yet been peer reviewed in the form of preprints. Our belief in openness also motivated us to offer our authors the option to publish their peer-review reports alongside their papers, a service we have been offering since Nature Communications, we recognise that this process and the resulting revisions take time. Preprint servers provide a valuable service by allowing authors to lay claim to exciting findings and alert the field without delay, to the benefit of scientific discovery. Preprints should, of course, be interpreted with caution until they have been subject to the scrutiny of peer review. However, rapid dissemination in a preprint server and high-quality peer review and promotion through publication in a scientific journal should, in our view, go hand in hand.While we take pride in the thoroughness of peer review at Nature Communications. The list, which will appear on our dedicated website and will be freely accessible to all without registration, will provide a link to the preprint on the recognized preprint server. Only preprints that are currently under peer review at Nature Communications or are being revised for further consideration will be listed on the site, and, once a final decision has been made, papers will be removed from the list. Authors can opt to deposit their work on a preprint server and join the service at any time and we will update our site accordingly, and they can also ask to be removed at any time. This service will initially run as a trial during which we will assess the level of uptake and any feedback we receive from authors and readers.With this spirit in mind, we are now offering authors whose submitted manuscript has been deposited in a preprint server, and is selected for peer review, the option of including their paper on a public list of articles under review at We hope that by offering additional visibility to preprints that are under consideration in our journal, we will not only be able to accelerate the dissemination of potentially exciting science, but also complement our peer review process by promoting wider scrutiny of preprints and thus a more holistic review procedure. Preprint servers provide a means for scientists to solicit informal feedback on their work, and we anticipate that our authors will continue to take such feedback into account to strengthen their findings during the peer review process.Promoting preprints under peer review represents for us another small step towards a more open and transparent peer review process in which preprints and the community’s feedback on them play an important part.th, 2017 and we will be offering any authors whose papers are sent out for review the opportunity to have their preprint listed on our website. Further information on the trial can be found here.We are excited to start this trial on September 12‘‘…rapid dissemination in a preprint server and high quality peer review and promotion through publication in a scientific journal should, in our view, go hand in hand.’’


The theme of this year's Peer Review Week is transparency. During the last few decades, I believe that a lack of transparency in the review process has degraded the field of scientific publishing. Authors were frequently left confused and angry when conflicting reviews lead to a rejection or when their paper received an obscure rejection and was not reviewed at all. Some journals still use the infamous box “confidential remarks to the editor.” These practices led to a growing sense of dissatisfaction among all scientists, myself included.eNeuro is proud to be among these journals. At eNeuro the decisions and the reviews are based on facts that are communicated to the authors and there are no confidential remarks to the editor. What would be the point? If there is something wrong in the paper or a doubt about the work, it is conveyed directly to the authors. Also, because our editors at eNeuro are actively engaged in research in the field, they are well positioned to assess the validity of the reviewers’ comments. Just like the conclusions we draw from our own research, decisions at eNeuro are thoroughly justified and based on facts.Fortunately, times have changed. There is now a growing number of journals that have a more transparent peer-review system, and eLife led the way. They set up a consultation process between reviewers and the reviewing editor , who work together until a consensus is reached. This consensual decision is then conveyed to the authors. This is a very good way to ensure transparency and restore confidence in the peer-review process. Reviewers and Reviewing Editor speak with one voice, nothing is hidden and the decision does not accompany contradictory suggestions for improving the paper. This is the solution that we have also adopted at eNeuro.Inconsistency between reviews has also been a problem. When there are both positive and negative reviews, the final decision is often negative. Why? As authors, we rarely got a justification. Again, the solution is simple. One document–one voice–should be conveyed to the authors. What if the Peer Review Process was Painless’ currently shown on eNeuro’s homepage.And it does work. How do we know? Since 2014, we have received less than a handful of appeals. This means that authors received enough facts to understand why their papers were rejected. Both authors and reviewers who have experienced the consultation-consensus process report how much they enjoy the procedure and its transparency and clarity. You can hear a few of our editors and an author discuss this process in our latest video ‘Of course, transparency can (and should) be continually improved. Ideally, the names of the reviewers could be disclosed whether the paper is accepted or rejected. Although, this may pose problems, one being that reviewers may fear future retribution from unhappy authors. Going for full transparency, and agreeing on what that means, should be a collegial decision and involve discussions among all stakeholders and with many journals.eNeuro, we are striving to increase transparency, and we are constantly thinking about novel ways to improve it . We are about to begin an initiative to allow authors to “review” the reviewing process for their paper. Authors who submit with eNeuro will find a survey in their decision letter that allows them to provide us feedback. These responses will increase transparency by informing our reviewing editors and me how authors experience our reviewing process. We are here to help authors, and authors can help us to make a better journal. Stay tuned!At Cheers,


This means that authors do not have to spend time responding to confusing or conflicting requests for revisions. Peer review is a topic that most scientists have strong opinions on. Many recognize that constructive and insightful comments from reviewers can strengthen manuscripts. Yet the process is criticized for being too slow, for being biased and for quashing revolutionary ideas while, at the same time, letting all sorts of flawed papers get published. There are also two concerns that come up time and again: requests for additional experiments that are beyond the scope of the original manuscript , and repEditors and reviewers are also aware of these problems. Raymond Goldstein is a biophysicist at the University of Cambridge who has served on the editorial boards of several journals: "It was often very frustrating as an editor not to be able to provide authors with a clear description of what they needed to do to advance to publication."collaborative approach to peer review in which referees, editors and authors could interact directly with each other in order to speed up the decision-making process. And since 2010, The EMBO Journal has asked reviewers to give feedback on each other's reviews the day before the editor makes the decision  agree that the consultation process at eLife adds value for authors. "It gets the authors actual intelligible and unified feedback on their work," says Vosshall, who has reviewed nine manuscripts for eLife and published one paper in the journal. Alexey Merz, an associate professor in biochemistry at the University of Washington, has also experienced the process from both sides and thinks it is the best peer-review process of those he has encountered: "Not all decision letters will achieve their intended goal equally well, but it is great to see a process designed to encourage a constructive, actionable report rather than a laundry list."Most reviewers , Carey feels that she got a better result in the end than if she had submitted to another journal. Also, because the decision letter and author response from the original rejection and eventual acceptance are published alongside the paper, Carey likes the fact that "readers can actually decide for themselves about the fairness of the process".Carey has since reviewed four more papers for eLife and says her experience as a reviewer influenced her decision to submit a paper to the journal in 2015. She describes Though authors generally appreciate a clear decision, some have suggested that having the reviewers reach a consensus might not always be the best way to improve the manuscript. Reviewers will interpret the same paper in different ways and some authors appreciate seeing any feedback that could help them to strengthen their manuscript. As Merz puts it: "divergence among referees can be useful too."The benefits of the consultation do, of course, come with a cost. "Because each step in the process involves several scientists, there can be delays," says Ng. To compensate for this extra time, eLife editors aim to rapidly triage initial submissions to decide which papers should move forward to full peer review. Culham points out that, while this process is not always perfect, it helps to preserve the time of editors and reviewers for those manuscripts that show the most promise. "It also," she adds, "reduces the likelihood that authors waste time waiting for a negative outcome."Between them, Culham, Parsons and Ng have been consulted on over 400 initial submissions and always aim to put aside blocks of time to read new manuscripts and share their thoughts on them as soon as possible. Parsons often looks at initial submissions on the train during her 40-minute commute to and from work. "You need to respond quickly to requests when they drop into your inbox," she says, "which includes saying if you feel you are not qualified to judge the science. Senior Editors and authors really appreciate fast, honest responses."While the consultation about a manuscript inevitably delays the decision by several days or more, Parsons believes that spending time to clarify exactly what is needed in the revision is an efficient use of time. "It actually speeds up the process later on, by preventing endless rounds of miscommunication and re-reviewing," she says. Indeed, over 70% of the papers published in eLife were accepted after a single round of peer review.Editors can also take steps to minimize the delay caused by the consultation itself. After reading all the reviews, Parsons tries to structure the online consultation to make the most effective use of the reviewers' time. She assembles a list of the core points from all the reviews, and identifies potentially unnecessary or unreasonable requests that should probably be excluded from the decision letter. She then uses these summaries to begin her discussion with the reviewers. Parsons says that, in her experience, this proactive approach "helps to steer the consultation process in the direction of a timely and well-rounded response". She adds that the process is also "smoother for everyone" when all the reviewers are communicative and prompt to engage in the discussion.Beyond the extra time required for the eLife peer review process, some have expressed concern about reviewers being identified to one another during the consultation . For exaresponses to a survey, most reviewers agree that openness benefits the consultation process.Culham disagrees with the suggestion that consultative peer review disadvantages early-career reviewers. "Generally, I've found reviewers very respectful of one another regardless of career stage," she says. "Like the other reviewers, junior investigators can give their honest opinion in their reviews before seeing other reviewers' reports or knowing their identities." Culham also watches out for salient points from any reviewer that might get "ignored or drowned out in the discussion" and makes sure to include them in the decision letter. Based on their over 600 new submissions each month. This means that, either as reviewers or authors, more and more scientists are experiencing consultative peer review. Parsons feels that this exposure is helping to change the landscape of peer review.In its first five years eLife has published more than 3,500 manuscripts (and reviewed around twice this number), and now receives Culham adds that her role at eLife has already changed the way she writes reviews for all journals: "I aim to be decisive and clear about necessary versus optional changes; I also admit when I'm less certain about something and would appreciate discussing it with others." Going forward, her biggest hope is that as the approach becomes more widespread, the culture of peer review will change to make it better for all involved and better for science.– have already adopted a consultative review process, in one form or another, and others are experimenting with it (Indeed, some journals – including Development, The Plant Cell and eNeuro  with it . And aft with it .In recent years, physicists introduced – or reintroduced  – biologcollection of articles on peer review.This Feature Article is part of a


Genome Biology as reviewers. The first interview is with Hyongbum (Henry) Kim, an Associate Professor at Yonsei University College of Medicine in South Korea.Peer reviewers are the unsung heroes of science. We celebrate reviewers through a series of interviews with people who have made particularly strong recent contributions to  Since 2010, when I become an independent researcher, the primary focus of our lab has been to develop efficient and robust methods that enable genome engineering in various cell types and organisms, including mammalian cells and mice. The ultimate goal of our research is to contribute to the development of novel therapeutic modalities for various diseases using genome engineering methods.Back in 2010, zinc finger nucleases were the only type of programmable nuclease available for genome editing. The efficiency of generating knockout cells was often low, necessitating significant effort and time for making knockout cell lines. To overcome this problem, Jin-Soo Kim’s group at Seoul National University and our group developed and tested a reporter for zinc finger nuclease activity .Our group also showed the possibility of “safer” genome editing using cell-penetrating peptides to achieve plasmid-free delivery of Cas9 protein and guide RNA. This approach reduces off-target effects and avoids mutagenesis caused by insertion of delivery vectors . Based oCurrently, we are trying to improve and/or develop genome-wide nuclease libraries for disruption of coding and noncoding elements. Other ongoing projects in the lab include potential therapeutic applications of CRISPR-Cas9 to genetic eye and liver diseases. We are also interested in high-throughput approaches for evaluating the activity of CRISPR-Cas9 based on target sequences. We will continue our research to improve or develop genome editing tools for biomedical research and biotechnology and apply these advanced genome editing methods as therapeutic modalities for various diseases.I expect that genome-editing technology will be continuously improved. The efficiency of genome editing will be enhanced and the range of tools will be widened. Currently, CRISPR-Cas9 is the dominant method for genome editing. However, new genome editing tools may emerge, which could be alternative or complementary to CRISPR-Cas9.I expect that issues associated with off-target nuclease activity may be a less significant problem in the future. We already have unbiased methods for detecting off-target effects and more sensitive methods will be available in the near future. After identifying potential off-target effects, we will be able to predict their potential adverse effects. If a nuclease has off-target effects that could cause significant problems, such as cancer development, then we can choose another nuclease. Furthermore, there are already methods available for reducing off-target effects, such as the use of high fidelity Cas9 nucleases, paired nickases, truncated guide RNAs, or a combination of FokI nuclease with dead Cas9, as well as decreasing the duration of nuclease activity (reviewed in ). I woulEfficient delivery of genome-editing factors to somatic cells in vivo may remain challenging; a large amount of effort will probably be needed to increase efficiency. Similarly, delivery of RNA interference-inducing factors, such as small interfering RNA (siRNA) or small hairpin RNA (shRNA), is one of the biggest road blocks for the application of this technology. However, transient delivery of genome-editing factors is sufficient for genome editing, in contrast to siRNA or shRNA, which often require continuous delivery. Thus, the burden or difficulty of genome-editing factor delivery to achieve a therapeutic or biotechnological goal may be lower than that for RNA interference.First, the peer review process gives me a good feeling that I am serving the scientific community. When I click the “agree” button to accept the review request, I feel like that I am donating something to the community. Second, in some cases, during the review process, I can get the latest scientific information, which can indirectly affect my research. Third, the improvement of the manuscript by my comments gives me positive satisfaction that I have indirectly contributed to the paper. Given that the number of papers that readers can read is limited, it is important to publish papers that are sufficiently novel, logical, and complete. My comments often improve the manuscript significantly and correct errors in the paper, which will eventually give better information to its readers.First, I would like to suggest an establishment of a manuscript transfer system across different journal groups. This system could reduce the burden on reviewers and accelerate the publication of the paper. There are good internal transfer systems within some big journal groups. However, transfer of manuscripts between different journal groups is currently difficult.Second, I would suggest publication of reviewers’ comments even if a paper is rejected from a journal, if the authors want to share with others. There are some journals that publish reviewers’ comments when the paper is accepted. To reduce the probability of unfair review, I would suggest online publication of the rejected manuscript together with the comments when authors choose this option after the paper undergoes peer review. These online publications may be made available at preprint servers or at the journal sites themselves if the editors agree.I think that these two suggestions may also have some adverse effects. However, given that such changes would be expected to make manuscript publication faster and fairer, they would be cost-effective approaches for facilitating the development of science.I have had one particularly good experience as a peer reviewer. I was requested to review a paper that was a creative and novel work in this field. However, the manuscript had many errors and there were a lot of points that needed to be addressed before publication. I commented on those issues in detail. Several months later, a much improved version of the paper was sent to me and I was happy to see the improvement. I felt like I was involved in the study.I had a bad experience regarding peer review as an author, as most scientists have. I submitted a presubmission inquiry about my paper to a journal. The editor sent me positive feedback and I decided to submit my paper to that journal. During the submission, I found that I had the option for double-blind review, in which the authors are anonymous to the reviewers. Because I thought that double-blind review would lead to fairer review, I selected that option. Subsequently, my paper was severely and, in some aspects, unfairly criticized by the reviewers. My guess is that the reviewers may have thought that the anonymous authors would not have sufficient experience to discover something important and new in the research field. Although it is not clear whether double-blind review was a part of the reason for the severe criticisms, I believe that fairer and less biased reviews will be performed if double-blind reviews are mandatory rather than optional.


Arquivos Brasileiros de Cardiologia for the 2018-2021 period. Inthis first editorial, I would like to thank my peers and colleagues, who have manifestedsincere and total support to my indication. It is undoubtedly a great challenge tocontribute to the most important scientific journal of Cardiology in South America.It was a great honor and privilege to be appointed to serve as the new editor-in-chief ofthe Arquivos Brasileiros de Cardiologia. And it will go on likethis. Thus, I ask for the support of all involved in the task in the coming years.Moreover, it is on the shoulders of the previous editors-in-chief that I humbly makemyself available to collaborate with this communication channel of the BrazilianCardiology. The work here developed is monumental and was only possible because of thecollaboration of the associate editors and reviewers, who are part of the great familyof the Arquivos Brasileiros de Cardiologia was Dr. Jairo Ramos, whosuggested the journal’s name, which has persisted since 1948. The histories of theBrazilian Cardiology, of the Brazilian Society of Cardiology and of the ArquivosBrasileiros de Cardiologia have mingled for decades. It is worth notingthat the first study published, entirely written in English, was "Theelectrocardiographic evidence of local ventricular ischemia", by Robert H.Bayley and Jolm S. La Due, from Oklahoma City, United States (1 Thisclearly shows that the internationalization potential of the ArquivosBrasileiros de Cardiologia has always been in its DNA. It is up to us, as aSociety of Cardiology, to fully develop it.The constitution of a writing committee for the Brazilian Society of Cardiology journalwas proposed by Dante Pazzanese and Luiz V. Décourt, and the first “director” ofthe d States .1 Thisc2 What I learned during his management, aswell as his support, substantiated my decision of applying for editor-in-chief of theArquivos Brasileiros de Cardiologia.I am especially grateful to our former editor-in-chief Dr. Luiz Felipe P. Moreira for itsexcellent management and for handing on a well-structured and organized journal to me.His editorial from last December revisits the accomplishments of the past eight years, aperiod when I was associate editor of diagnostic and imaging methods.Arquivos Brasileiros de Cardiologia need to beprepared to keep up with such changes and innovations.Several actions have been planned to speed up the article review process of our journaland make it more attractive to authors. With the constant progress of science and of itsoutreach channels, the In the 2018-2021 period, two master beams will provide the base for that innovation: ourjournal’s internationalization and its impact factor improvement. Those two master beamswere chosen because of the stability, in the past years, of our journal’s impact factorslightly above 1 and non-adherence to the internationalization issues recommended byScielo.ArquivosBrasileiros de Cardiologia in the form of original articles. Reviewarticles will maintain the tradition of reviewing Cardiology topics and its limits withother specialties, always indicating the future steps in the area, such as the reviewarticle of the January issue.3 We arerenewing our associate editors, the international reviewers and our editorial boardaiming at both speeding up the publication of articles in the ArquivosBrasileiros de Cardiologia and improving their quality.The first master beam has been championed by Scielo for a while and will be emphasized incoming the championed years. One aspect of internationalization is the participation ofinternational associate editors. In 2018 we will begin with two new internationaleditors and one international co-editor, thus meeting the Scielo recommendation ofhaving approximately 30% of international associate editors. We aim at getting moreinternational visibility and attracting “good science” for the ArquivosBrasileiros de Cardiologia. Our two major objectives are obviouslysynergistic.International collaboration has been a mechanism to enhance the impact factor of someEuropean international journals. I believe we need to refine our performance in thatarea, having, thus, to adopt internationalization measures for the Arquivos Brasileiros de Cardiologia. We wantto increase the satisfaction of the authors and reviewers during the editorial processesin our journal. The first important step is the adoption of a new electronic system ofsubmission, most likely the ScholarOne, which will allow a faster andmore practical management of the articles from the viewpoints of all involved: authors,associate editors, editor-in-chief, reviewers and editorial assistants. In addition, wewill work close to authors and reviewers to obtain a rapid and effective review,allowing the editors to decide more accurately and efficiently.In addition, measures to speed up and modernize the article review process areprogrammed, in an attempt to rapidly notify the authors about the acceptance or refusalof their articles in the How do you do it?”, and the answer was“Keep it simple!!”. I believe we should listen to that advice andfollow it. Thus, mini-editorials for the original articles and a Some changes in the formats of the articles are being planned to make them more concise,direct and pragmatic. In a recent visit of Prof. Valentin Fuster, JACC’seditor-in-chief, we asked “Arquivos Brasileiros deCardiologia has to undergo a deep and thorough discussion. Likewise, andpossibly even more controversial, “open science” proposes accepting the articles in the“preprint” format. Briefly, there are online repositories that accept scientificarticles before undergoing peer review. This ensures the authors maintain “property” ofthe idea and data immediately, allowing them to be cited by other authors, but this cangenerate the exposure of low-quality articles. However, during exposure, similarly to anInternet forum, comments can be made, and the authors can use them to improve theirpublication quality. Several journals already accept the submission of articles that hadbeen published as preprint. Should the Arquivos Brasileiros deCardiologia accept that too? Again, this has to be thoroughly discussed,and we have to face a new challenge to adapt to the new digital reality of our virtualworld. Scielo seems to strongly support those measures that will soon be mandatory.There is evidence in the literature that the movement towards “open science” increasesthe impact factor of the journals.5 Ibelieve we have to go along with the change of times.However, not everything is planned linearly as described above. New challenges will askfor the participation of all players in this scientific process, including our BrazilianSociety of Cardiology members. In a recent meeting, Scielo has determined new guidelinesto be followed by Latin American journals, some of which with disruptive characteristicsand unpredictable final effects. The most important examples are the continuingpublication and the concept of “open science”. The latter includes the publication inrepositories of source data that generated the manuscript’s results. Such publicationmakes data public and available to be used, checked and re-analyzed by groups other thanthe original authors. Although extremely controversial, that mechanism seems to increasethe number of citations of the articles, and, thus, the impact of the articles and ofthe journal, in addition to adding credibility to them. Would this function in the sameway in the Brazilian scientific environment? This response can only be provided by thescientific community, and its adoption by the Arquivos Brasileiros de Cardiologia content. There is evidence inthe literature that the presence of journals in Twitter significantly increases thenumber of citations of articles and their impact.6In addition, we have planned to use more intensively the social media to disseminate theArquivos Brasileiros de Cardiologia over seven decadesof existence, and because it represents the science of one of the major societies ofCardiology in the world, I am sure that the future of our Arquivos Brasileirosde Cardiologia is brilliant and will continue to merge with the history ofthe Brazilian Cardiology.However, some things never change, and the “good science” and the relevance of thearticles continue to depend on traditional scientific aspects, such as the changes inclinical practice and the generation of new knowledge or ideas on the pathophysiology,natural history or treatment of a disease. Based on the “good science” that has beenfostered by the


Genome Biology has always had a strong enthusiasm for open research policies. For example, we were among the first to mandate publicly available supporting data and open source code. Naturally, then, we have watched with close interest as other journals have experimented with—or in some cases wholeheartedly embraced—open or transparent peer review. Among the pioneers in this area were The BMJ  and open peer review (in which the reviewer reports are published together with the reviewers’ names) increase the accountability of the peer review process; the latter also provides a mechanism for reviewers to obtain credit for their efforts . In addiNature Communications pilot has seen a favorable response from authors, with the majority opting for transparent review [Nevertheless, many other researchers feel that the risks associated with totally open peer review still outweigh the benefits. One often-discussed reservation is that early-career researchers will be reluctant to criticize the work of more senior researchers in their field, in case there are negative implications for future grant applications or peer review of their own publications. This could lead to watered-down reviewer reports that hold back on useful criticisms and/or could make it harder to secure reviewers, resulting in extended peer review times. Transparent peer review retains the benefits of open reviewer reports but, because reviewers retain anonymity, some of the drawbacks of open peer review are likely to be diminished. The t review .With these pros and cons in mind, we conducted a poll of our editorial board to solicit their views on openness in peer review. A large minority of board members  were in favor of fully open review, with a slightly larger proportion  being broadly in favor but with some caveats or equivocacy. The most common suggestion was that anonymous, rather than signed, reviewer reports should be published.Genome Biology transparent peer review trial, we will be assessing the degree of support for this approach in our community as well as the impact on peer review times. Half of the manuscripts that are peer reviewed will be assigned to the trial, and the other half will serve as a control arm. For the manuscripts selected for the trial, authors will be offered the option of transparent peer review or standard single-blind review. We are not yet proposing fully open review, but we will give the reviewers the option to reveal their identity.For the We will track the time taken to send decisions to the authors of the transparently reviewed manuscripts and will compare these time with those in the control arm of the trial. We will also look at the effect of transparent peer review on the quality of reports, although that is harder to measure. Over the next few weeks, we will be able to establish whether transparent review delays review time, and how much support there is among our author and reviewer communities for the introduction of transparent peer review on a permanent basis.We will report the results over the coming months. If you have any comments on these proposals, please email us using editorial@genomebiology.com.


The funding statement for this article should read as follows:https://www.nih.gov) GM079804, GM126558, AI126308-01A1 and the Chicago Biomedical Consortium  with support from the Searle Funds at The Chicago Community Trust. We also thank the Research Open Access Publishing (ROAAP) Fund of the University of Illinois at Chicago for financial support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.”“This work is supported by National Institute of Health (


Science paper :84-87, 1927a). Despite being well acclimated into the scientific world of peer-review, Muller choose to avoid the peer-review process on his most significant publication. It appears that Muller’s actions were strongly influenced by his desire to claim primacy for the discovery of gene mutation. The actions of Muller have important ethical lessons and implications today, when self-interest trumps one’s obligations to society and the scientific culture that supports the quest for new knowledge and discovery.This historical analysis indicates that it is highly unlikely that the Nobel Prize winning research of Hermann J. Muller was peer-reviewed. The published paper of Muller lacked a research methods section, cited no references, and failed to acknowledge and discuss the work of Gager and Blakeslee  that claimed to have induced gene mutation via ionizing radiation six months prior to Muller’s non-data  Science under the title, “The Artificial Transmutation of the Gene” [Science permitted Muller with their vehicle to manipulate the scientific community, ignoring the standard protocols/rules of scientific publication, has never been clarified by this journal, nor by Muller based on a review of publications and letter correspondence. So bizarre was this deviation from accepted protocol that Muller’s former Ph.D. advisor at Columbia University, Thomas H. Morgan, suggested that perhaps Muller did not have the data to support his claims [Hermann J. Muller’s reporting that X-rays induced gene mutations in the fruit fly has long been considered an interesting one . Muller he Gene” . Since ts claims .Science publication at the 5th International Genetics Congress  in Berlin, finally silencing the critics. He showed that X-rays produced transgenerational phenotypic changes in the fruit fly, which he asserted were due to gene mutations. These changes were also induced with striking frequency. Muller became a highly recognized scientific leader within days as the media quickly grasped the potential significance of his discovery. However, he still had not published these research findings. These data, which would provide the basis for his eventual Nobel Prize in 1946, were subsequently published in 1928 in the Proceedings of the International Genetics Congress [Science publication became the publication of note, even today, based on citation frequency. The data-based proceedings paper would be cited only about once/year in the basic Web of Science search until his Nobel Prize in 1946 and even less frequently thereafter.The rampant speculation came to a head when Muller presented the data some three months after the Congress . DespiteScience statements. However, this paper proved to be problematic as it failed to include a methods section, nor a normal discussion section that places his findings within the context of other relevant work, failing to cite any references. This omission was particularly glaring since Gager and Blakeslee [Proceedings of the National Academy of Sciences (PNAS) evidence for the first time of true gene mutations (via the use of ionizing radiation), some six months prior to Muller’s Science paper. These same researchers also presented their mutation data at the Berlin conference with Muller and are also published in the same International Genetics Congress proceedings. The failure of Muller to acknowledge the January 1927 PNAS Gager and Blakeslee findings/claims is a serious issue, since both groups were claiming primacy for the induction of gene mutation.Nearly a decade ago I obtained the Muller’s 1928 Genetics Congress proceedings paper, being interested to learn more precisely how he verified the 1927 lakeslee  had repoOf further relevance was Muller’s failure to address the possibility that his “gene” mutation findings could have been simply due to heritable chromosomal mutation, via the deleting of large gene segments. This issue was a crucial, yet initially hidden, concern of Muller. It was discussed privately by Muller and his colleague/friend Edgar Altenburg during the late summer/fall of 1927. He would eventually publicly discuss the matter at the annual American Association for the Advancement of Science (AAAS) meeting in December 1927  as he trIn addition to the above issues, Muller’s paper also seemed poorly constructed, requiring revision and clarification to enhance readability. The paper had other limitations of a more specific nature that could have been raised in a review process. While the purpose of the present paper is not to retrospectively review Muller’s paper some 90 years later, but to present a few additional issues that may have warranted responses from contemporary peer-reviewers such as: failure to include a control group for experiment #3, and the use of only two doses, especially when using doses that were very high for experiments #2 and #3 with his new, more sensitive and then unvalidated fruit fly model. Furthermore, the initial experiment (#1) with a standard fruit model was performed with four doses, with the upper doses inducing substantial sterility while the lowest dose, which was still quite high, showed no evidence of transgenerational phenotypic  changes. These points were either only casually addressed, or ignored.“This is to answer your question about when I first suggested the making of cytogenetic maps. In my paper given to the 1927 Congress in Berlin, it is stated on page 245 that the structural changes produced by x-rays should make it possible to obtain more direct evidence of the physical correctness of the linage maps. This paper, though printed first in 1928, was printed from a manuscript given (in) at the time of the Congress in 1927 where it was presented exactly as finally printed.”Upon reflection, it appeared that there was very little, if any, possibility that this paper had been peer reviewed due to its multiple critical information omissions, experimental design and evaluation questions and a lack of clarity in writing style. Despite its extraordinary gene mutational claims, the manuscript required considerable improvement prior to being acceptable for publication. These issues led to my obtaining a copy of Muller’s research notebook, containing the data for his Nobel Prize research during the time period for the respective experiments. I also obtained numerous communications between Muller and colleagues to explore whether the manuscript was peer reviewed and if it was, what the evaluations were. The information revealed evidence within a letter from Muller to Edgar Altenburg on July 8, 1946  that theMuller indicates that his presentation at the Congress in 1927 was published exactly as presented with no changes made. This statement reveals that the editor(s) of the Congress very likely published it without peer-review.A legitimate peer-review may have highlighted important methodological/study design concerns such as the requirement for a methods section, the need to discuss relevant research such as the claims of Gager and Blakeslee  for geneScience and publication of his critical data paper in a non-peer reviewed conference proceeding allowed Muller to side-step normal protocols by which the scientific community polices itself, to weed out inferior manuscripts and to enhance the quality of those deemed acceptable. These procedures not only aid society, they are intended to educate the researcher. Muller’s actions were clearly manipulative and self-serving within a context of high stress and excitement. Further, his actions were unfair to the other competitors chasing the gene mutation prize and harmful to society that needs scientists to follow the procedure, even though the entire review process can be frustrating, time-consuming, and very imperfect.The failure to receive appropriate peer review created the opportunity for Muller to quickly gain attention and fame, at the expense of others. It also seriously affected the direction of the field since he incorrectly linked the induction of transgenerational phenotypic changes induced by very high doses of X-rays with gene mutation and then to linear dose response modeling for risk assessment without convincing evidence. This critical belief came to dominate the field, misdirecting radiation genetics, environmental mutagenesis and cancer risk assessment until finally shown to be incorrect decades later , 3, 5–7.British Medical Journal reports a modern sounding peer review process as early as 1893 [Surgery, Gynecology and Obstetrics in 1905 [The issue of peer review is relevant to Muller’s Nobel Prize research activities. The question may be raised as to what was the nature of the peer review in the early decades of the twentieth century. While the history of peer in the early part of the twentieth century is not particularly clear due to inadequate record keeping, various biological/medical journals of the early twentieth century conducted their peer-review via a committee/editorial board system, which progressively expanded to include reviewers outside the Editorial Board. The American Journal of Botany (AJB). Gager, who was the co-author of the first paper to show gene mutation as noted above, was on the editorial board of the AJB starting in 1915, being its business manager for 21 years (until 1936). During this time, the journal developed a modern peer-review process with the goal of providing “a hopeful means of preventing publication of inferior papers and improving the quality of others”. This process was in place by 1933. Of significance is that the AJB editorial board had representatives from a broad spectrum of affiliated professional societies, including the American Phytopathological Society, the Ecological Society of America, The American Society of Plant Physiologists, The Mycological Society of America and the Genetics Society of America. Referees were typically selected by an editorial board member with the closest subject matter expertise to the paper. Rejection of a paper had to be approved by at least one member of the board along with the editor-in-chief [An insight into how radiation geneticists viewed peer-review may be gained by a consideration of the actions/leadership of Stewart Gager and the activities of the in-chief . This hiJournal of Experimental Zoology. This journal was created in 1903 with the first issue published in 1904. Amongst the founding and longstanding editorial board members was Thomas H. Morgan, who would become Muller’s Ph.D. advisor a decade later. In a retrospective recounting of the journal, the managing editor Ross G. Harrison [Journal of Experimental Zoology [Genetics, which T.H. Morgan also helped create in 1916 [Advances in Genetics over a dispute with the editor M. Dermerc. In this case, Muller was angry because a manuscript was published as a result of a favorable peer-review. Muller was frustrated that Demerec had not selected him as a reviewer. In their exchange of letters, Demerec ended up accusing Muller of attempting to impose his version of censorship [The earliest historical linkage of peer-review to Muller may be seen with the Harrison  indicate Zoology –17. This in 1916 , with Munsorship . There wWith respect to Muller, it was clear that he knew where his gene mutation interpretational weakness lay. In fact, the gene mutation criticism of Stadler , 25 was Science journal discussion only and the non-peer-reviewed Congress proceedings) were directed toward being first, even if it meant skirting the protocol of the publication process. Muller also cited the date of publication of his key Proceedings paper incorrectly, making it 1927 rather than 1928. He did this in other subsequent publications, influencing many others to adopt the same publication date error, but all pointing to the notion that Muller was first. In the end, what this meant was that Muller won the race, got the prize and yet would have his key finding, that he produced gene mutations, recognized as incorrect even by his closest colleagues long after his death [Muller was focused on being the first to produce gene mutation. He knew it was critically important and so did others. The publication actions of Muller (i.e., is death  for a deWould a professional peer-review had detected the error of Muller’s gene mutation interpretation? While this is not known it is likely that reviewers would have demanded that Muller include a methods section, and a legitimate discussion component to the paper at the least. These would have involved delays. What would have happened in a review process will remain speculative. However, one can see in Muller’s actions how they were not fair to this competitors as well as the scientific community and society who need scientific contributions vetted in an objective manner that ensures an appropriate evaluation of the submitted manuscript.This paper reveals that the strategy of Hermann J. Muller to obtain primacy for his discovery of radiation-induced gene mutations led to his avoiding peer-review, publishing a paper that had significant limitations despite its Nobel Prize award quality. Muller’s actions were troubling as he placed his prize-seeking goals ahead of his responsibility to the field and social obligation of playing by the same publication rules as other researchers. The peer-review process is important and even Muller’s Nobel Prize winning research would have profited from this. Furthermore, we have now learned with modern nucleotide assessment technology, that his Nobel Prize winning findings of producing gene mutations by high doses of X-rays were not gene mutations, but gross gene deletions and other major chromosome rearrangements, a finding that confirmed the doubts of some leading geneticists of his era who had clearly suspected that he had incorrectly interpreted his findings.


Formally, they announced a war against open access journals, but, in reality, they announced a war against publishers who do not retain subscription journals.Before the Internet, libraries played a crucial role in the dissemination of information and ruled the publishing industry: publishers begged librarians to subscribe to their journals. Publishers maintained official and personal contacts to ensure that librarians subscribed to their journals. Librarians were the bosses, with real power. But the internet and other technological advances changed the game. Librarians lost power and funding. Essentially, traditional libraries were becoming obsolete. Scientists could read journals, especially open access journals, at their workplace without going to a library. Open access papers cost many times less for society. Libraries are trying to adapt to this new reality by assuming new functions. Unfortunately, some older generations of librarians have worked to turn back technological progress and are fighting to regain their power. For example, to the best of my knowledge, Jeffrey Beall, a librarian, did not put on his blacklist prominent publishers of open access journals who also publish subscription journals. He does not care about open access journals, per se. It is simple: if publishers retain subscription journals, if they remain on their knees asking librarians to subscribe to their journal at enormous cost to society (in addition to fee charged the authors for publication), they are not put on the blacklist. In that situation, a librarian, such as Jeffrey Beall, is the boss. Moreover, a question that has puzzled people for a decade is, why are all of a publisher’s journals blacklisted, regardless of substantial differences among those journals? Why the entire publisher? Never half the journals of the publisher: either all the journals or no journal is blacklisted (there may be exceptions I am not aware of).The common thread is this: these journals are both published by the same publisher, who does not publish subscription journals, and therefore does not beg on its knees for libraries to subscribe. Beall is losing power and therefore chose Oncotarget as a principle target for an attack. Oncotarget was extremely successful, easily competing with other cancer journals, including mega-journals (see Oncotarget Home page). This was likely seen as a very bad example to others. It shows that a new type of journal can be extremely successful, and it was therefore decided that it should be destroyed. Over a period of two years, Beall and anonymous bloggers have harassed Oncotarget and its Editor–in-Chief personally. We were harassed on many levels, daily, including defamation in a Wikipedia controlled by Beall’s co-fighters.For example, all the publications of Impact Journals LLC were put on Beall’s blacklist without explanation in 2015. What is the common thread between Oncotarget and Oncoscience? Oncotarget is a large and prominent journal, whereas Oncoscience is a small journal that is free for readers and authors alike. It is a kind of charity journal, so to speak, and cannot possibly be predatory because it is intentionally losing money for the benefit of humanity. according to the statement from the MEDLINE reviewers on 6/22/2017, “This journal [Oncotarget] continues to play a major role in the publication of important basic science research papers. Editorial practices are consistently high. Ethical guidelines are consistently followed. This is an important research journal for the field.” The journal was described as “excellent.” It is noteworthy that MEDLINE’s decision to delete Oncotarget was based in part on incorrect information. For example, they stated that we do not publish clinical papers, which of course we do. The MEDLINE decision was invalid for many reasons, including technicalities.Despite this harassment, Oncotarget flourished, showing how resilient an honest journal can be. The main attack occurred in August 2017: several librarians at the National Library of Medicine (NLM), including J. Backus, decided to selectively re-evaluate Oncotarget without warning. They requested no information from us before deleting Oncotarget from MEDLINE. It is an unprecedented case for such a prominent journal. Remarkably, Ultimately, MEDLINE deleted Oncotarget from PubMed Central and PubMed even without re-evaluation. They merely incorrectly informed us that we had never been accepted to PubMed Central, although we had been and we posted all our issues there. Numerous papers in Oncotarget were cynically deleted from PubMed based solely on the date of acceptance, thereby hurting science and the scientists, wasting taxpayer money (as these papers re-appeared on PubMed later), and preventing scientists from disseminating their research. Later Backus and Beall gave a misleading interview that appeared online. Pro-Beall bloggers filled the Internet with misinformation about the event. Only the actions of the leadership of the NLM stopped this injustice and restored our PubMed and PubMed Central status, but they did not have enough power to immediately reverse the MEDLINE decision. We remain hopeful that the decision will be reversed.Web of Science  recently chose Oncotarget as the best journal in their rubric “Rising Star” out of 10 thousand journals, based on their serious analysis of data. Unexpectedly, however, in January 2018 we started to hear rumors from China that Clarivate Analytics had stopped indexing Oncotarget after the November 10, 2017 issue. Once again, this action was taken without informing Oncotarget and without asking for any information from us. We sent several emails in January and did not get a response. Finally, we were able to reach high level executives, who agreed to index Oncotarget up to January 2018, but would stop indexing for 2018. When asked for their concerns, they failed to respond to our rebuttal, despite their promises to do so. Clarivate benefits from libraries’ subscriptions, so the entire system works together. The action of Clarivate was cynical, and once again the authors are suffering. We are hopeful that we can work with Clarivate so that the indexing of Oncotarget can be expeditiously resumed.Despite these attacks, Oncotarget has continued to serve as a well-recognized and respected international journal, and has continued to flourish. As an example, For thousands of years libraries served science and scientists. Indexes were created to disseminate information, not to suppress it. For the first time in history, in response to rapid technological progress, librarians are suppressing science and refusing to serve science. Of course, this not true of all librarians. The new generation of librarians resist Beall’ s ideas, including Beall’s supervisor, whose recent article should be read by everyone.We, the scientists, should change the situation and change the policies of Indexes such as Clarivate’s Web of Science and MEDLINE, and make indexes work for us. Otherwise, why should these organizations exist?The link to this Editorial was sent to Retraction Watch as a referral to their inquiry about de-listing Oncotarget from Web of Science.


Maximilian Muenke, Founding Editor‐in‐ChiefSuzanne Hart, Editor‐in‐ChiefMolecular Genetics & Genomic Medicine (MGGM) turns 5 years old. For the editors of this journal it is time for some reflection, “looking back and looking forward”. The first issue appeared in May of 2013, 60 years after the publication by Watson and Crick's discovery of the double‐helical structure of DNA and 10 years after the completion of the Human Genome Project.This year Human & Medical Genetics, Medical Genetics & Genomic Medicine, and a few others, before Molecular Genetics & Genomic Medicine became the top choice. Suzanne Hart was chosen as Deputy Editor‐in‐Chief in part because of her expertise that is different from the EIC. Twenty‐four colleagues  with a wide range of expertise from 15 different countries were invited to serve on the MGGM Editorial Board.The work for this journal began 1 year earlier with the selection of the Founding Editor‐in‐Chief (EIC) Max Muenke, choice of a journal title, and the Aims and Scope of the journal. Initial options for titles included Aims and Scope of MGGM were and are broad, to encompass a wide range of topics including basic and translational science, technological advances, human and medical genetics, animal models of human disease, pharmacogenomics and translational medicine , comparative genomics . As submissions have grown since 2013, the number of accepted articles has also steadily increased. Dedicated peer review and editorial evaluation ensures that all published articles meet rigorous scientific standards. As was our hope when the journal started, the topics of the unsolicited, peer‐reviewed articles are broad, ranging from diagnosis to treatment as is well illustrated by the titles of the 10 most highly cited manuscripts  and are indexed and discoverable in PubMed/MEDLINE. MGGM is now in Web of Science (WoS) via indexing in Clarivate Analytics’ Science Citation Index Expanded (SCIE).All MGGM became the third Editor‐in‐Chief of the American Journal of Medical Genetics Part A (AJMG)  technological advances leading to progress in (2) pharmacogenomics, (3) precision medicine in general, and (4) cancer genomics specifically.http://exac.broadinstitute.org), ClinVar (http://www.ncbi.nlm.nih.gov/clinvar), and others , high throughput functional validation of variants of unknown significance will continue to be critical in order to determine mechanisms of disease  (Johnson & Weitzel, “The essential job of precision medicine is to match the right drugs to the right patients” Letai, . PrecisiMolecular Genetics & Genomic Medicine proudly finds its home. Our journal's Open Access publication policy fully supports the public sharing of scientific knowledge aimed at advancing these admirable goals. As the editors of MGGM, we are honored to be able to publish, and make publicly available, papers representing the widest possible range of human and medical genetics research, and to provide valuable commentaries and global insights on new research and treatment trends. We sincerely thank the Editorial Board, our esteemed peer reviewers, and most of all, the authors and readers of MGGM for this honor.Looking back has been inspiring, but looking forward is exciting! If the past five years are any indication of the rapid pace of future research, then the next five years in the allied fields of molecular genetics and genomic medicine will be full of new discoveries that will facilitate an improved understanding of the genetic etiology of disease. Such discoveries could in turn provide tools for better patient understanding and disease prevention, or stimulate investment in applied research that might speed the delivery of targeted treatments to the patient bedside. It is within this exciting research environment that the journal MGGM over the past five years and are looking forward to continuing to publish high quality articles in the field in both the American Journal of Medical Genetics and Molecular Genetics & Genomic Medicine. We wish our readers the very best in 2018.So, at the start of 2018, we are proud of the accomplishments of Max and Suzanne


Journals are exploring new approaches to peer review in order to reduce bias, increase transparency and respond to author preferences. Funders are also getting involved. Can we trust peer review?, Is peer review just a crapshoot? and It's time to overhaul the secretive peer review process. Read some more and you will learn that despite its many shortcomings – it is slow, it is biased, and it lets flawed papers get published while rejecting work that goes on to win Nobel Prizes – the practice of having your work reviewed by your peers before it is published is still regarded as the 'gold standard' of scientific research. Carry on reading and you will discover that peer review as currently practiced is a relatively new phenomenon and that, ironically, there have been remarkably few peer-reviewed studies of peer review.If you start reading about the subject of peer review, it won't be long before you encounter articles with titles like For many years peer review meant only one thing for many journals – single-blind peer review. In this approach an author submits a manuscript to a journal, an editor assigns it to anonymous referees for peer review and, if the referee reports are favourable, a revised version of the manuscript is accepted for publication. However, irrespective of whether the manuscript is ultimately accepted or rejected, the identities of the reviewers remain hidden from authors and readers, and their reports are only ever seen by the editor and authors. 'Single blind' means that the reviewers can see who the authors are, but the authors cannot see who the reviewers are.In recent years, however, the picture has changed and journals have started to experiment with other forms of peer review – such as double-blind peer review, open or transparent peer review, interactive public peer review, results-free peer review and, brace yourself, post-publication author-led invited open peer review. At the same time there have been dramatic changes in other areas of scientific publishing such as the growth of open access, the rise of mega-journals, the increasing popularity of preprints in the life sciences and the involvement of funders in various aspects of scholarly communication see .Box 1.Funders get involvedWellcome Open Research on the F1000 platform, and the Gates Foundation and the UCL Great Ormond Street Institute of Child Health (which is part of University College London) have announced plans to launch similar titles – Gates Open Research and UCL Child Health Open Research – later this year.Another emerging trend is the increasing involvement of funders in scientific publishing. In 2016 the Wellcome Trust  launched European Union has also announced that it is investigating the possibility of funding an open-access platform that will allow the rapid publication of both preprints and peer-reviewed articles for research funded by its Horizon 2020 programme (which has a budget of €80 billion). More details are expected later this year, but the EU has announced that the platform will "contain mechanisms for open/collaborate/public peer review".The 100 articles since it was launched in late 2016, making it one of the most popular titles for Wellcome-funded authors. A survey of authors carried out in April found that publication speed and the ability to share a variety of research outputs were the primary reasons why authors published on the platform. Non-traditional article formats published by Wellcome Open Research include Software Tool Articles, Data Notes and Research Notes (which can include 'single-finding papers').Wellcome Open Research was set up for three main reasons says Robert Kiley, Head of Open Research at Wellcome: "to speed up the publication of research, to improve research reproducibility, and to encourage the sharing of all research outputs". The platform has published more than blog post at the time, "but it is worth noting that reviewers have been prepared to 'not approve' papers and that the reviews – all publicly available – are on occasions highly critical".The survey also explored attitudes to open peer review and the ways referees were selected: when asked "what effect has authors choosing their own referees had on the peer review?", a third felt that this might result in the referees being less critical, 45% thought that there is no difference between authors and editors choosing referees, and 64% thought that the process allows authors to ensure that the referees have the right expertise. (Authors were able to agree with more than one statement in response to this question.) It is impossible to determine if authors selecting referees results in reviews being less critical, wrote Michael Markie of F1000 in a At present Wellcome Open Research only accepts submissions from researchers who are funded by the Wellcome Trust. However, the platform's website also states: "We hope that other funders will follow our lead and that, over time, funder-specific platforms will merge into a single international platform, open to all researchers."Many of these developments are interlinked: a key feature of mega-journals, for example, is that peer reviewers are asked to not pass judgment on the potential importance or significance of a manuscript; rather, at PLOS ONE for example, their role is "to determine whether a paper is technically sound and worthy of inclusion in the published scientific record". Preprints, on the other hand, are not peer reviewed at all, although many go on to be reviewed and published by journals.Publishing Research Consortium conducted a survey in which more than 3000 academics were asked a series of questions about peer review. One of the clearest messages to emerge from the survey was a lack of support for single-blind peer review: 56% of respondents reported a preference for double-blind peer review, with just 25% preferring single-blind peer review, and only 13% preferring open peer review. "The overwhelmingly most popular reason for preferring double-blind review," the authors of the report explained, "was that it was seen as a more objective process, removing potential biases due for example to the author's institution, race or country, or personal biases."The pressure to move away from single-blind peer review has been building for a number of years. In 2008 the Taylor & Francis also found a "strong preference for double blind review" when it surveyed more than 7000 authors, reviewers and editors in 2015. However, there was also relatively little appetite for radical change among the respondents: "Overall this study still found a fairly conservative researcher view, demonstrating a wish for tweaks to the current systems rather than a radically new way of assessing the quality and validity of research outputs."The publisher Congress on Peer Review, held September 10–12 in Chicago, two publishers – Springer Nature and IOP Publishing – reported the results of experiments in which authors were offered the option of single-blind or double-blind peer review for their manuscripts.Journals and publishers have been slow to react to these messages. However, at the recent Eighth International Springer Nature trial involved over 100,000 submissions to Nature, Nature Communications and 23 other Nature journals (such as Nature Cell Biology) over a two-year period. Presenting the results in Chicago, Elisa De Ranieri of Springer Nature reported that 12% of authors had opted for double-blind review, and that there was no significant difference in the proportion of male and female corresponding authors selecting this option. This was surprising as it has long been thought that single-blind peer review was prone to gender bias. The The Springer Nature study also found that authors from the most prestigious institutions were the least likely to opt for double-blind review: only 4% of corresponding authors from institutions ranked in the top 10 of the 2016 Times Higher Education (THE) ranking opted for double-blind review, whereas the figure for institutions ranked 101 or below was 13%. And of the 10 countries that submitted the most manuscripts, authors from the US and China were the least and most likely, respectively, to select double-blind review.De Ranieri and colleagues also studied whether the manuscripts in their sample were accepted or rejected. Nature journals use professional editors to make initial decisions on manuscripts: these editors typically reject about 80% of submissions without review, and send the remaining 20% to external referees. The Springer Nature study found that editors were less likely to send double-blind manuscripts to external referees (8% vs 23%), and that double-blind manuscripts were also less likely to be accepted after external peer review (25% vs 44%).IOP Publishing pilot study offers the option of single- or double-blind review to authors submitting to two journals – Materials Research Express and Biomedical Physics & Engineering Express. Presenting preliminary results from the first seven months of the study (which will last a year), Simon Harris of IOP Publishing reported that 20% of authors had opted for double-blind review on both journals. Moreover, as with the Springer Nature study, the rejection rate for double-blind submissions was significantly higher than the rejection rate for single-blind submissions (roughly 70% vs 50%).The One of the next challenges, De Ranieri told the meeting in Chicago, is to determine if the different rejection rates are due to differences in quality or to bias on the part of editors and/or referees. To explore the possibility of bias by editors a number of Nature journals are thinking of experimenting with 'triple-blind review', which would involve professional editors making initial decisions on manuscripts without knowing who the authors were. It is also possible that the fact that an author has opted for double-blind review might bias referees against a manuscript: De Ranieri suggested that one way to overcome this form of bias, if it exists, would be to make double-blind review mandatory rather than optional. Another challenge for supporters of double-blind is that as preprints become more popular it will be increasingly difficult to stop referees knowing who the authors are.While single-blind and double-blind peer review are fairly well defined, the same is not true for open or 'transparent' peer review , followed by open reports (publishing referee reports), and open participation . The other traits include open pre-review manuscripts , and open interaction (which can involve the referees discussing their reports before a decision is reached). eLife employs a form of open interaction during which the editors and referees agree on the points that the authors need to address in order to have their paper accepted; the decision letter that contains this list of points is published with accepted papers, but the individual reports are not .BMJ is probably the highest-profile journal to employ open peer review and for each research article it publishes, it also publishes a 'prepublication history' that includes all previous versions of the article, signed referee reports, comments from BMJ editors and the authors' responses to these comments and reports. In 2011 the BMJ Group told a parliamentary committee looking into peer review that it had been using "signed open review [...] for more than a decade with no significant problems". However, it also noted that "PLOS Medicine tried and then discontinued this practice in late 2007 citing reviewers' reluctance to sign their reports".The EMBO Journal also publishes a 'peer review process file' that includes referee reports and decision letters, among other things, but it is not compulsory for referees to reveal their identity. And Elsevier, one of the world's biggest scientific publishers, has plans to make open peer review an option on 1800 of its journals by 2020. "We've had positive feedback from our pilot titles," Philippe Terheggen, managing director of the company's journals group, told Research Information earlier this year, "so we now want to roll out open peer review across all Elsevier-owned journals."The BMC employ open peer review and publish named referee reports alongside papers."There are strong ethical arguments for open peer review," says Elizabeth Moylan, a senior editor at BioMed Central (BMC), which is part of Springer Nature. These include making editors and referees more accountable for the decisions made by journals, and providing credit for peer reviewers. Moylan adds that open peer review may help to train early-career researchers about the peer review process. More than 70 journals at recent study of how often researchers accepted invitations to review papers for a sample of BMC and SpringerOpen journals found that the accept rate was highest (60%) for double-blind journals and lowest (42%) for journals that used open review. The rate for single-blind journals in the sample was 53%. This echoes the findings of a study at the BMJ in the late 1990s which found that open peer review increased the likelihood of reviewers declining to review, but had "no important effect on the quality of the review, the recommendation regarding publication, or the time taken to review".So why is open peer review not more popular? One reason , is that journals find it more difficult to recruit reviewers. A It's time to overhaul the secretive peer review process: "Some reviewers, especially junior scientists, fear that critical but honest reviews of work by senior scientists in the field would subject them to retribution by these senior figures, who might someday be asked to review their grants, papers, or promotions. Faced with such fears," Flier continues, "they might decline requests to do peer reviews, or provide less honest reviews seeking to pander to the authors. This isn't just a hypothetical concern – I have heard it from many faculty members at Harvard Medical School, as well as from some journal editors. To the extent it is real, this brings shame on a profession committed at its core to the pursuit of knowledge and truth."The biggest concern, however, is that reviewers may be reluctant to be sufficiently critical. As Jeffrey Flier, a former dean of Harvard Medical School, puts it in In the same article Flier argues in favour of open peer review, with all referee names and reports being made public. "When peer review is cloaked in secrecy, there are limited incentives for performing high-quality reviews," he writes. "That allows bias, carelessness, conflict of interest, and other deficiencies to persist without a way to penalize those who generate inadequate reviews" .interactive public peer review'. In this approach a submitted manuscript is first subject to 'initial access peer review' to ensure that it falls within the scope of the journal and meets certain scientific and technical standards. The manuscript is then published as a 'discussion paper' to allow interactive discussion and public commenting by at least two designated referees (who can be anonymous or named) and other members of the scientific community. This 'open discussion' phase typically lasts eight weeks and the authors are expected to respond to comments as they appear. If all goes well the authors are asked to submit a revised manuscript, which the co-editor handling the paper can accept for publication in the journal or reject. In 2001 the journal Atmospheric Chemistry and Physics introduced a twist to the peer review process called 'When a paper is accepted, the previous versions, comments and author responses to comments remain on the site, although some referees opt to remain anonymous. In 2012 the journal's chief executive editor, Ulrich Pöschl of the Max Planck Institute for Chemistry, wrote that the journal's scientific reputation and low rejection rate (~15% at the time) "confirm that anticipation of public peer review and discussion deters authors from submitting low-quality manuscripts and, thus, relieves editors and referees from spending too much time on deficient submissions" .post-publication author-led invited open peer review' and considers itself to be a 'platform' rather than a journal. Articles submitted to the platform are published as soon as they have passed certain basic checks , and then undergo post-publication peer review by referees who are suggested by the authors. "The editorial team checks the referee suggestions, and will only formally invite them to review the article if they fit our criteria – that is, if they are not close collaborators, have appropriate level of expertise, have no competing interests," says Sabina Alam, editorial director at F1000Research. "We believe that authors are best placed to identify appropriate experts for their paper, but we also believe it’s important that we check the suggestions carefully (including email addresses), and remain as the central point of contact between authors and referees, to ensure that our peer review standards are maintained."F1000Research employs a similar form of peer review called 'At first articles are labelled as 'Awaiting peer review', with this label changing to a green tick (meaning a referee has 'approved' the manuscript), a green question mark (meaning an 'approved with reservations' rating) or a red 'x' (meaning a 'not approved' rating) when the first referee report is received. Further ratings are added as more reports are received, with the named referee reports being published shortly after they are received. Referee reports also have their own DOI, which means that they can be cited and included in the referee's ORCID profile: somewhat surprisingly, some journals that publish referee reports do not assign DOIs to them.As with a traditional journal, authors can submit a revised version to address the points made by the referees and, they hope, convert question marks into ticks. An article is considered as accepted – and therefore suitable for indexing in PubMed and other bibliographic databases – when it receives two 'approved' ratings or one 'approved' and two 'approved with reservations' ratings. All versions of the article are available on the site, and when a new version is published, a summary is provided as to how that version differs from the previous version.What advice does Alam have for any existing journal thinking of introducing an F1000-style peer review process? "The largest challenge is the technical infrastructure required to run the model," she says. "We had to build our own editorial management system and structure the underlying database in a very different way to most publishing systems, to enable us to incorporate the versioning and the referee reports being associated with specific versions. A skilled editorial team is also required."A number of research funders have also started to use the F1000 platform for their own titles, or have plans to do so see .The tendency of authors and journals to publish positive results at the expense of negative or inconclusive results – a phenomenon known as publication bias – is also driving change in peer review. Two similar approaches, registered reports and results-free peer review, are trying to address this problem by focusing on the methods used in experiments rather than the results obtained.In the registered reports approach the authors submit a 'stage 1 manuscript' that describes the hypotheses they plan to test and the methods they will use . When thOnce the experiments have been completed and the data analysed, the authors submit a 'stage 2 manuscript' which also includes a results section and a discussion section. If the authors have performed the experiments and analyses as described in the stage 1 manuscript, if any pre-specified quality checks (such as positive controls) have been passed, and if the conclusions of the study are justified by the data, the manuscript is accepted for publication.BMC Psychology since late 2016 .The results-free approach to peer review has been available as an option to authors submitting to ate 2016  and, as over 60 papers have been published in 12 journals via the registered report route, with the majority appearing in psychology journals. Chris Chambers of Cardiff University – who is the editor for registered reports at Cortex, the European Journal of Neuroscience and Royal Society Open Science – estimates that another 100–200 have been provisionally accepted. All told, more than 60 journals now offer registered reports for regular issues, with others using the format for special issues. eLife, for example, employs a modified version of the format for the Reproducibility Project: Cancer Biology.To date outcome switching' . BMC Medicine recently became the first medical journal to offer a registered reports track for clinical trials.So what can be done to increase the use of this approach? "The most important practical step is for more journals to offer them," says Chambers. "All journals in all scientific fields that publish at least some articles reporting the outcomes of hypothesis testing should offer registered reports. This means we need thousands more journals to adopt the format." Chambers also argues that registered reports should be adopted in clinical trials to prevent publication bias and a practice known as 'Exploratory Reports for such research.And do registered reports have any disadvantages? "Perhaps the most common criticism is that they limit creativity or exploration in science, but this is not true," says Chambers. "Registered reports can, and often do, include extensive exploratory analyses, which are clearly labelled as exploratory so that readers can make informed judgments, but they are not designed to replace purely exploratory, non-hypothesis driven science." Cortex has plans to launch a new article type called In another development the journal Nicotine & Tobacco Research and the medical charity Cancer Research UK are collaborating on a pilot project that aligns decisions about funding and publication, with the journal agreeing, in principle, to publish the results of research that the funder decides to support. In the first stage of the 'registered reports funding' process a researcher submitting a standard application for funding to the charity's Tobacco Advisory Group can opt into the scheme: an editor from the journal who has been co-opted into the funding review process then checks that the work is within the scope of the journal, although the decision to fund remains solely with the funder. To begin just a small number of applications (randomly selected from those who have opted in) are being included in the pilot.GRAND  that is funded by Pfizer.In the second stage the researcher submits a registered report about the work they have been funded to do, and the editor oversees the review of the report, using the same referees who reviewed the grant where possible. "Combining grant funding and publication decisions into a single, two-stage process promises to dramatically reduce the burden on reviewers, and also serve to reduce questionable research practices and publication bias," explained an editorial in the journal . NicotinSo how will we know if the pilot has been successful? "Initially we just want to see what proportion of applicants are interested in this approach, and what their experiences of it are, and what proportion of grant reviewers agree to also review the registered report," says Marcus Munafò of Bristol University, who is the editor of Nicotine & Tobacco Research. "If the initial signs are positive we would like to run something similar again, and over time see whether it leads to improvements in the efficiency and quality of research published, if it protects against publication bias, and so on."Peer review: a flawed process at the heart of science and journals, published in 2006, he wrote that peer review's "defects are easier to identify than its attributes. Yet it shows no sign of going away"  to find suitable referees for papers; encourage more diversity in the reviewer pool; experiment with new models of peer review; invest in reviewer training programmes; encourage publishers to work together; develop ways to give reviewers credit for their work; and make greater use of technology .So, where next for peer review? In May this year Digital Science and BioMed Central released a report called Some of the recommendations are driven by the growth in the number of papers being submitted to journals, and the concomitant need to find more reviewers: increasing the numbers of referees from groups that are currently under-represented in the reviewer pool could help solve two problems at the same time. Concerns about the 'burden' of peer review could also be addressed if publishers worked together to make it easier for referee names and reports to be transferred between journals.PEERE project, which is funded by the EU, and journals dedicated to peer review, such as Research Integrity and Peer Review.""Personally, I find it interesting that there is more research into peer-review itself, with interventions designed to improve the efficiency, transparency and accountability of peer review being more rigorously evaluated," says Anna Clark, who is now an assistant editor at BMJ Open. "Two good examples are the Can we trust peer review?, but the domination of single-blind peer review is certainly under assault from a range of alternatives.It is common to read about actors, writers and directors who don't read reviews of their plays or films, and to hear novelists say that they don't pay attention to what the critics have said about their latest book. Scientists don't have this option: they have to read their reviews and to take on board what the reviewers have said, whether they agree with them or not. Nonetheless, if the system works as intended, the authors will benefit from the wisdom of their peers, readers will benefit from knowing that what they are reading has been subject to a form of quality control, and some small corner of science will take a small step forward. However, even when working as intended, it is clear that the peer review system remains prone to a range of biases, with particular fields wrestling with specific challenges, such as publication bias in psychology and outcome switching in the reporting of clinical trials. It is unlikely that we have seen the end of articles with titles like collection of articles on peer review.This Feature Article is part of a


The publication of this issue of the Journal of Applied Clinical Medical Physics marks the conclusion of my first year as Editor‐in‐Chief. The experience of editing a scientific journal has been a rewarding one for me, placing me in contact with many of my clinical and scientific colleagues in a collaborative venture that, we hope, contributes to the quality of medical physics practice throughout the world. I have interacted in previous years with the JACMP as an author. Finding myself on the other side of the fence has given me a greater appreciation of the role of an editor and, in particular, a greater appreciation for the fine contributions my predecessors in the position as Editor‐in‐Chief have made to our profession of medical physics.I am pleased that the JACMP has established itself in, what is to the best of my knowledge, a unique role as an open access, online journal in the medical physics community. There is no need to repeat our journal's philosophy regarding open access; my predecessors have articulated this philosophy very well. Open access appears to be the wave of the future. The National Institutes of Health, for example, has mandated that“…all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer‐reviewed manuscripts upon acceptance for publication…”More recently, on February 12 of this year, Harvard University's Faculty of Arts and Sciences adopted a policy that requires that scholarly articles by faculty members be available free to the public online.As of October 1 of this year, over 3500 journals are listed in the Directory of Open Access Journals.Now that my first year as Editor‐in‐Chief is coming to a close, I would like to share with you a few statistics about the JACMP, some of which are presented in Table It should be noted that the number of acceptances plus the number of rejections does not equal the number of submissions, as papers are sometimes withdrawn (as is the case with 3 papers from the 3rd quarter of 2007), and many papers, especially recent submissions, are still in review. The number of submissions appears to be steady at around 33 per quarter, although we saw a substantial increase during the second quarter of 2008. It appears that approximately 1/3 of submissions are declined; the low value for the 3rd quarter of 2008 is simply a result of the fact that most manuscripts submitted during that period are still under review. A rejection rate of approximately 1/3 is a rate that I am presently comfortable with, although increases in the number of submissions may result in a change in the bar. The mean time to complete the first round of review appears to be steady at around 25 days, which is also, I believe, a good figure, attesting to the diligence of our Associate Editors and Reviewers.A journal such as the JACMP would not exist without the cooperation of our Associate Editors and Reviewers. These are the heroes who are charged with reading the manuscripts and critically assessing their suitability for the JACMP. Associate Editors are listed below:Associate Editors (including Guest Associate Editors): Nzhde Agazaryan, Salahuddin Ahmad, John Antolak, Peter Balter, Pat Cadman, Marco Carlone, Nathan Childress, Geoff Clarke, Laurence Court, Jianrong Dai, Larry DeWerd, Gino Fallone, John Gibbons, Michael Gossman, Stephen Kry, Eduardo Moros, Firas Mourtada, Ben Nelms, Niko Papanikolaou, Bill Pavlicek, Matt Podgorsak, Chet Ramsey, Jim Rodgers, John Rong, Bill Salter, Mehrdad Sarfaraz, Tim Solberg, Frank Van Den Heuvel, Sastry Vedam, Lu Wang, Chuck Willis, Al Zacarias, Ron ZhuOver 200 individuals served as Reviewers, and they are listed in a Supplementary File. Please refer to this file to acknowledge their immense contribution to the JACMP. Thanks, of course, to the many scientists and clinicians who submitted manuscripts. Without a continuous stream of good manuscripts, our Associate Editors and Reviewers would have nothing to do. And, finally, I would be remiss if I did not thank you, the readers of this journal. Without a readership, we would have no journal. Thank you for your continued support. Please join me in looking forward to our Tenth Anniversary Volume.George Starkschall, PhDEditor‐in‐ChiefNovember 15, 2008