At the Nomenclature Section of the XVIII International Botanical Congress in Melbourne, Australia (IBC), the botanical community voted to allow electronic publication of nomenclatural acts for algae, fungi and plants, and to abolish the rule requiring Latin descriptions or diagnoses for new taxa. Since the 1st January 2012, botanists have been able to publish new names in electronic journals and may use Latin or English as the language of description or diagnosis.Using data on vascular plants from the International Plant Names Index (IPNI) spanning the time period in which these changes occurred, we analysed trajectories in publication trends and assessed the impact of these new rules for descriptions of new species and nomenclatural acts. The data show that the ability to publish electronically has not “opened the floodgates” to an avalanche of sloppy nomenclature, but concomitantly neither has there been a massive expansion in the number of names published, nor of new authors and titles participating in publication of botanical nomenclature.The e-publication changes introduced in the Melbourne Code have gained acceptance, and botanists are using these new techniques to describe and publish their work. They have not, however, accelerated the rate of plant species description or participation in biodiversity discovery as was hoped.The online version of this article (doi:10.1186/s12862-017-0961-8) contains supplementary material, which is available to authorized users. Publication of results is one of the cornerstones of the scientific endeavour. Differences between scientific and general publishing were first articulated by Henry Oldenburg, who as Secretary of the Royal Society, established the first English-language scientific journal, Philosophical Transactions of the Royal Society . OldenbeInternational Code of Nomenclature for algae, fungi and plants ) d plants , hereaftd plants , 8.Discussions about electronic publication in the botanical community began in the 1990s, formal proposals at the 1999 XVI IBC in St Louis  to allow30A.2. To aid availability through time and place, authors publishing nomenclatural novelties should give preference to periodicals that regularly publish taxonomic articles, or else printed copies of a publication  should be deposited in at least ten, but preferably more, botanical or other generally accessible libraries throughout the world including a name-indexing centre appropriate to the taxonomic group. .www.zoobank.org; for description of ZooBank see   8] for dpublication channel: to indicate if the work was published on paper or as an e-publication. This is set to e-publication if the article containing the nomenclatural act is either published online before print or is published online only. The default value of the flag indicates paper publication.language: indicates that the description or diagnosis is written in English. The default value of the flag indicates use of Latin language.Digital Object Identifiers (DOIs) - these can be resolved to access metadata about the publication and to navigate to the reference online (if available).The authorship of the nomenclatural act is standardised using the principles laid out in Authors of Plant Names   were analysed. The years 2009 - 2011 represent the three years before the changes in the ICN agreed at the Melbourne Congress, which came into effect on 1st January 2012; 2012–2014 represent the three years after. Although we conducted our analysis in 2017, the most recent data included in the dataset are two years old - this was to ensure that more obscure titles have had a chance to be seen by the IPNI editorial team. The lag time for some types of publications  can be up to a year or more. Three years after the implementation of the ICN change date gives us a valuable range of samples, because at least some of the work published in 2012 would have been already in the publication system and thus done using the previous rules; thus authors would have been unable to fully take advantage of the changes in the ICN which came into effect on 1st January of that year.Emergence trends for authors and publications were created, in order to see if more people were participating in the publication of new vascular plant names, and if the range of places available in which to publish have expanded. To get a better view of underlying trends, a longer timescale was chosen for this part of the analysis - the full decade between 2005 and 2014 (inclusive).We recognised that taxon-specific communities of botanists may exist, such as those working in plant families with considerable horticultural interest. To assess the degree to which these communities were using e-publication in different ways, we drilled down into the flowering plant data to collate information on the rate of take-up of e-publication in particular families. For this analysis we compared three families with considerable horticultural and collector interest – Orchidaceae (orchids), Cactaceae (cacti) and Bromeliaceae (airplants and pineapples) – with three families that are of less horticultural interest – Fabaceae (beans), Solanaceae (nightshades) and Cyperaceae (sedges). We performed the same analyses on these smaller datasets as were done for the whole dataset (see above).tax. nov. (names of new taxa) - tax. novcomb. nov. (new combinations) - comb. nov, stat. nov, comb. et stat. nov.nom. nov. (replacement names and names at new rank) - nom. nov., nom. et stat. nov.The nomenclatural acts recorded in the IPNI database were classified into three broad groupings:SQL queries were executed against the underlying IPNI database on 2017-04-28, these were scripted in the Python programming language.Volume of nomenclatural acts: numbers of nomenclatural acts were grouped by publication year and citation type  for acts representing new names: numbers of nomenclatural acts representing new names (tax. nov.) were grouped by year, and then by language and publication channel combined.Authors - number active: the unique number of authors specified as members of the publishing author team in nomenclatural acts between 2005 and 2014 were counted, broken down by year.Authors - number emergent: for all the authors active in the selected period (2005-2014), their date of emergence was calculated - this is the date when they were first recorded as a member of the publishing team of a nomenclatural act. This dataset was grouped by year of emergence to give a count for each year.Publications - number active: as per the analysis for authors described above, this is the unique number of serial publications recorded as containing nomenclatural acts published between 2005 and 2014 were counted, broken down by year. A serial publication is defined as a multi-volume work.Publications - number emergent:  - for all serial publications active in the selected period, their date of emergence was calculated - this is when they were first recorded as containing a nomenclatural act. This dataset was grouped by year of emergence to give a count for each year of the study.The volume of nomenclatural acts – excluding lectotypifications - has remained relatively constant  shows that almost half (48.3%) of all acts recorded were using e-publication Fig. , data inWhen looking at only the publication of new names for taxa, the previous status quo  is steadily diminishing, with almost three quarters (74.7%) of the new taxonomic descriptions in the final year of the study utilising at least one of the major ICN changes introduced Fig. , data inThe data show no sudden difference in the emergence or participation of either authors or serials after the starting date for e-publication in 2012  , and to increase the communities working in taxonomy through adoption of e-dimensions to their work [Underlying many of the hopes regarding e-publication is a recognition of a potential opportunity to overcome the so-called “taxonomic impediment”  by previous authors [ authors . AnecdotModernity: This is difficult to assess with the data we have assembled. The results of our analyses show no perceptible change in numbers of publications pre and post the permitted use of e-publication, suggesting that the changes are seen as part of the normal publication process. Also discussed under modernity was the wish to improve the visibility and opinion of taxonomy - electronic publication and the use of English rather than Latin for the diagnosis or descriptions, is on the rise .Date of publication: The principle of priority is dependent upon the retrieval of an effective date of publication for any nomenclatural act, be it a new species, new combination, name at new rank or lectotypification. Over the course of the 3 years of data we assembled, there have been a handful of cases requiring investigation, these are not common and in fact are no different than any other nomenclatural problem needing investigation to resolve. It is, however, an issue that many journals still do not place the date of effective publication in the required PDF of the publication, but instead place it elsewhere, for example in the table of contents for the journal. It is imperative that botanists work with publishers to ensure that e-publications best serve future generations of botanists – this will be an on-going conversation [ersation  and we hArchiving: Access to past literature is fundamental for systematics, as it is for all of science. At the current point in time - just five years after the first e-published works - we are too early to fully assess issues regarding archival storage and long term accessibility. Because archiving of works is not part of the requirements for effective publication under the ICN (for either print or e-publications), resolution of this concern does not lie in the rules of the ICN, but rather, in continued dialogue with publishers of works that contain botanical nomenclature.If the hopes have not been fully realised, what of the fears? The fears expressed about the acceptance of e-publication are underpinned by concerns about the potential for fragmentation of the community - either geographically or through time - and a consequent lessening in taxonomic quality. Our analysis of families with considerable horticultural interest versus those without such associated communities showed no difference in the rates of use of e-publication (see Additional file Our analysis shows that in the time frame we have analysed, three years after the implementation date for e-publication, nomenclature as applied to vascular plants continues to be in a steady state - both in terms of the number and quality of nomenclatural acts recorded, and the participation of those doing the science that results in these acts. We can therefore conclude that one of the more modest hopes - that e-publication is seen as part of the normal publication process - has been realised. In fact, we did not need to run for our lives : the issThe result that the acceptance of e-publication has not elevated the rate of species description nor increased the numbers of people involved in naming new taxa means that as a community, botanists must consider other ways to speed up taxonomy. Some issues that have been raised include the large numbers of specimens now available for examination before a decision can be reached about the novelty of a taxon, the advent of a perception that molecular as well as morphological data are necessary for making a taxonomic decision, and the rigour of the peer-review process that accompanies modern publication. It still takes as long to make a decision about the identity of a specimen as it always has done, and if a botanist has 3000 specimens to look at it necessarily will take longer. Human resource issues are likely to be crucial for increasing the rate of taxonomy; our efforts perhaps should be focusing on this rather than on technological quick fixes.International Code of Nomenclature for algae, fungi and plants shows that treating e-publication as an instance of publication, rather than something special to be regulated differently has been a good decision that still has the potential to help the botanical community both publish and access work describing life on Earth.It is clear that much discussion remains to be had with the publishers of nomenclature about some of the issues that have arisen, such as display of the date of effective publication, access and archiving. The results of this analysis of one part of the names governed by the


Open science has received a great deal of attention across the academic community. Open science has been defined in many ways, but the central principle is to make methods, results and the underpinning data (publicly) available. The aim of this editorial is to outline the key issues that the nutrition and physical activity fields need to consider in relation to making the research within the field as transparent and reproducible as possible. We provide a brief overview of the key issues to consider and provide open science recommendations for publications within IJBNPA and the wider field. Open science has received a great deal of attention across the academic community. Open science has been defined in many ways, but the central principle is to make methods, results and the underpinning data (publicly) available. Open science principles are receiving key support from national funding agencies . InteresIn terms of steps that can be taken now, it is a requirement for IJBNPA that all trials should be registered and although IJBNPA does not publish protocol papers there are many excellent journals within our publisher’s (BMC) portfolio such as Trials and Pilot and Feasibility Studies that accept protocol papers. We therefore strongly encourage publication of protocols in these journals or other appropriate venues. As outlined in the author guidelines, we also expect all authors to use the appropriate reporting checklists  for allMaking data fully available to facilitate replication should be a core aspiration of our field. We recognise that there can be challenges in making data available and while this is a requirement for some funding agencies, it is not for all. However, there are many repositories and institutional portals that are simple to use, and we encourage all authors to make data available where possible. We also think that providing analysis code  for new techniques or methods along with detailed descriptions of what the code is trying to do would be a relatively easy goal for the field. While providing code for standard commands would be unnecessary, code for novel applications such as the creation of food groups from national dietary surveys or new means of processing raw accelerometer data would be of great help to the field. While we recognise that code often represents huge amounts of thought and work by statisticians that often do not get sufficient credit for their invaluable contributions, providing code as a supplementary file that is citable would provide the justifiable credit and allow the field to learn from each other, and make our research more efficient. We therefore encourage all authors to consider if code could be made available in supplementary files and we will actively promote data sharing for the journal.It is important to recognise that there are other strategies that could be adopted by the field to facilitate open science such as the use of registered reports and pre-prints. Registered reports, in which publication decisions are taken on the methods and importance of the research question posed before data are collected have drawn interest from many fields including psychology and associated behavioural health fields such as addiction research  and coulIn conclusion, we encourage all authors to consider the issues presented in this editorial, to adopt the steps that can be taken now and rapidly move to data and code sharing as means of advancing the fields of nutrition and physical activity research.


This Editorial describes PLOS Biology's experiment with contextualised publication, whereby potentially controversial studies are published with an Editor’s Note and an accompanying Primer in which the Academic Editor guides the reader, dissects the study, and lays out the thinking behind the decision to publish. PLOS Biology feel this is great news; opening up peer review is a natural progression in the movement that recognizes both the utility and moral mandate for open access publication and for making both data and code as well as unique research materials available. Publishing the reviews will provide important context for decisions and help others interpret the research. For a small subset of papers, however, we’re finding that the route to publication can benefit from some very special additional treatment. For these particular manuscripts, it is clear that the claims are potentially intriguing and important, but the reviewers’ comments indicate that simple publication might lead to misunderstanding or misinterpretation. We believe that such cases benefit from contextualised publication with an Editor’s Note on the article and an accompanying Primer in which the Academic Editor carefully guides the reader, dissects the study, and lays out the thinking behind the decision to publish.PLOS journals are today launching optional published peer review, in which authors can elect to publish, alongside their papers, the decision letters, reviewer comments, and their own responses. We at PLOS Biology always like to run experiments, taking opportunities to push the boundaries of openness. Our editorial model is already quite unique and consists of discussing a submitted manuscript with an Academic Editor, seeking the opinions of several expert reviewers, and then discussing the reviewers’ comments with the Academic Editor as we formulate a decision. To recognise this effort, the Academic Editor’s name is published within any accepted manuscripts as an imprimatur.Even if we don’t advertise them widely, as former scientists we at Our experience as editors has taught us that for the vast majority of manuscripts, this model tends to converge (perhaps after revisions) on a relatively straightforward decision—to publish, to invite revision, or to reject. But what if this resolution doesn’t happen? What if, after one or two rounds of review, there are still deep divisions between the opinions of conscientious and constructive reviewers, or individual reviewers are themselves in two minds as to whether to recommend publication? At such an impasse, the problems are exacerbated if the claims of the paper concerned are potentially important and contentious for the field.Simply publishing such a paper as-is might run the risk of mis- or over-interpretation. On the other hand, rejecting it would not only be potentially unfair to the authors, but would also render unpredictable how that paper might eventually be published and promoted. Moreover, the substantial time and effort already spent by multiple well-qualified academics in reviewing the manuscript and providing their expert opinions might go to waste. And crucially, by publishing the study, we have the opportunity to work with the authors to determine how the results of a study are communicated, as opposed to leaving it to the vagaries of publication elsewhere.This has happened to us three times in the past year see , and it In the three cases that we describe here, the need for contextualisation became gradually apparent during the process. We’ve now formalised how we might identify such cases in the future and devised a recommended workflow, to try to ensure that this occurs in a more structured way. By doing this, we hope to be able to publish more provocative science in a more contextualised environment, giving readers a more nuanced understanding of the research as well as its limitations and promise. The initiative seems to have largely been well received by readers, reviewers and authors. And once reviews are made openly available, readers will be privy to the underlying concerns that drove our decisions and this particular mode of publication.Below are three instances in which a research paper has been published on the condition of co-publication with a Primer specially commissioned to contextualise the work, to explain the decision to publish, and to caveat some of the conclusions.What the paper said:Results obtained from a mitochondrion-targeted temperature-sensitive fluorescent probe suggest that the internal mitochondrial temperature is substantially higher by 10°C) than the surrounding intracellular space [0°C than What the Primer said:Nick Lane: While these conclusions are surprising, readers should bear in mind that other factors than temperature might be affecting the probe, and that the implied temperature gradient across the mitochondrial membrane is hard to explain. That said, mitochondria do produce substantial amounts of heat, and the study raises interesting questions about the meaning of “temperature” in tiny volumes and non-equilibrium turbulent conditions .What the paper said:Studies using fruit flies and cultured mammalian cells suggest that low-intensity electromagnetic fields can influence biological systems by triggering the production of reactive oxygen species (ROS) via a mechanism that is dependent on cryptochromes, proteins implicated in magnetoreception .What the Primer said:Lukas Landler and David Keays: Previous studies in this field have been justifiably viewed with scepticism, and the topic lies at the heart of a controversy about alleged adverse health effects of power lines. The current paper represents a substantial improvement, but the implementation of zero magnetic field controls remains problematical, and the role of cryptochromes may be indirect .What the paper said:Experiments using cleaner wrasse suggest that they are able to identify their reflection in a mirror as themselves, and will attempt to remove marks only visible in the mirror by scraping their bodies on stones. This suggests that these fish exhibit a level of self-awareness that has only been demonstrated in a handful of species .What the Primer said:Frans de Waal: These findings are intriguing, but there remains a question about the control invisible mark, which may have a tactile component, and about what this so-called “mark test” really tells us about animals’ sense of self. The study supports the case for a more gradualist approach to animal self-consciousness .


Journal of Cachexia, Sarcopenia and Muscle (JCSM) and its two daughter journals JCSM Rapid Communication and JCSM Clinical Reports. We request of all author sending to the journal a paper for consideration that at the time of submission to JCSM, the corresponding author, on behalf of all co‐authors, needs to certify adherence to these principles. The principles are as follows:JCSM as provided;all authors listed on a manuscript considered for publication have approved its submission and (if accepted) approve publication in each named author has made a material and independent contribution to the work submitted for publication;no person who has a right to be recognized as author has been omitted from the list of authors on the submitted manuscript;the submitted work is original and is neither under consideration elsewhere nor that it has been published previously in whole or in part other than in abstract form;all authors certify that the submitted work is original and does not contain excessive overlap with prior or contemporaneous publication elsewhere, and where the publication reports on cohorts, trials, or data that have been reported on before the facts need to be acknowledged and these other publications must be referenced;all original research work has been approved by the relevant bodies such as institutional review boards or ethics committees;all relevant conflicts of interest, financial or otherwise, that may affect the authors' ability to present data objectively, and relevant sources of funding of the research in question have been duly declared in the manuscript;JCSM as a valid publication only as long as all statements in the guidelines on ethical publishing remain true.the manuscript in its published form will be maintained on the servers of JCSM, JCSM Rapid Communication, and JCSM Clinical Reports, respectively, so that the available information regarding the published article can be updated and/or the manuscript can be withdrawn.If any of the aforementioned statements ceases to be true, the authors have a duty to notify as soon as possible the Editors of This article details an updated version of the principles of ethical authorship and publishing in the  Journal of Cachexia, Sarcopenia and Muscle (JCSM) is a peer‐reviewed international journal dedicated to publishing materials that are related to cachexia and sarcopenia as well as to body composition and its physiological and pathophysiological changes during the life span and in different illnesses from all fields of the life sciences. JCSM was founded in 2010 and has attracted interest by both clinicians and researchers, which is buttressed by increasing download numbers, citations, and submissions and by an increasing impact factor.JCSM are now coming from and interest in the field of body wasting is embracing the entire globe.The JCSM—the Journal of the American Medical Directors Association, ESC Heart Failure, and the two new daughter journals JCSM Clinical Reports and JCSM Rapid Communications, share the view that academic publishing depends, to a great extent, on trust between authors, reviewers, editors, and the academic and lay public.JCSM see it as their duty to promote transparency and research integrity. And, as this is an ongoing effort, we wish to recall the validity and update the statements on ethical publishing made by us before.The authors of these ethical guidelines, who are editing five peer‐reviewed journals including—besides JCSM and its two daughter journals JCSM Clinical Reports and JCSM Rapid Communications are required to certify that they comply with the guidelines of publishing in JCSM outlined in the succeeding text. This should be performed by stating as part of the published manuscript that ‘All authors of this manuscript comply with the guidelines of ethical authorship and publishing in the Journal of Cachexia, Sarcopenia and Muscle’, providing reference to these guidelines by referencing this article. Specifically, the corresponding author, on behalf of all co‐authors,JCSM as provided;certifies that all authors listed on a manuscript considered for publication have approved its submission and (if accepted) approve publication in certifies that each named author has made a material and independent contribution to the work submitted for publication—authorship credit should be based only on, first, a substantial contribution to conception and design, or acquisition of data, or analysis and interpretation of data, and second, drafting the article or revising it critically for important intellectual content;certifies that no person who has a right to be recognized as author has been omitted from the list of authors on the submitted manuscript;certifies that the submitted work is original and is neither under consideration elsewhere nor that it has been published previously in whole or in part other than in abstract form;certifies that all authors certify that the submitted work is original and does not contain excessive overlap with prior or contemporaneous publication elsewhere, and where the publication reports on cohorts, trials, or data that have been reported on before the facts need to be acknowledged and these other publications must be referenced ;certifies that all original research work has been approved by the relevant bodies such as institutional review boards or ethics committees ;certifies that all relevant conflicts of interest, financial or otherwise, that may affect the authors' ability to present data objectively, and relevant sources of funding of the research in question have been duly declared in the manuscript;JCSM as a valid publication only as long as all statements in the guidelines on ethical publishing remain true.certifies that the manuscript in its published form will be maintained on the servers of JCSM, JCSM Rapid Communication, and JCSM Clinical Reports, respectively, so that the available information regarding the published article can be updated and/or the manuscript can be withdrawn.If any of the aforementioned statements ceases to be true, the authors have a duty to notify as soon as possible the Editors of All authors wishing to publish in JCSM journal family, and the increasing number of submissions underscores the continuing need for such a niche journal and its two daughter journals, JCSM Rapid Communication and JCSM Clinical Reports.We will continue our editorial work for the JCSM aim to continue to keep a close eye on these issues, and we need reviewers to help in this. We simply ask that authors play fair to the academic community and the public at large and then none of this will ever be an issue. We want to take a lead in identifying, notifying, investigating, and reporting all occurrences of scientific misconduct related to JCSM. We will withdraw papers, if significant problems come to our attention. This shall be no surprise to anyone when it has to occur. Hence, we request that these ethical guidelines for publishing in JCSM and its two daughter journals are cited in each article. As stated before, academic publishing is built on trust. We want JCSM to be a trusted and valued source of best available scientific knowledge in the field. We hope that, together, we can achieve this objective and our journal can succeed in this ambition.Despite the existing wish to advance our knowledge, we recognize that the world is not free of scientific misconduct, which can come in many ways. We are happy to report that only very few problems have arisen in the past seven years, and no published paper had to be withdrawn so far. The Editors of


An a priori design is essential to reduce the risk of bias in systematic reviews (SRs). To this end, authors can register their SR with PROSPERO, and/or publish a SR protocol in an academic journal. The latter has the advantage that the manuscript for the SR protocol is usually peer-reviewed. However, since authors ought not to begin/continue the SR before their protocol has been accepted for publication, it is crucial that SR protocols are processed in a timely manner.‘BMC Systematic Reviews’ from 2012 to 2017.Our main aim was to descriptively analyse the peer review process of SR protocols published in ‘BMC Systematic Reviews’ between 2012 and 2017, except for protocols for overviews, scoping reviews or realist reviews. Data were extracted from the SR protocols and Open Peer Review reports. For each round of peer review, two researchers judged the extent of revision (minor/major) based on the reviewer reports. Their content was further investigated by two researchers in a random 10%-sample using PRISMA-P as a guideline. All data were analysed descriptively.We systematically searched MEDLINE via PubMed for all SR protocols published in ‘BMC Systematic Reviews’ between 2012 and 2017. Of those, 485 (89.2%) also registered the SR in PROSPERO, the majority (87.4%) before first submission of the manuscript for the SR protocol (median 49 days). The absolute number of published SR protocols increased from 2012 to 2017 (21 vs 145 protocols), as did the median processing time (61 vs 142 days from submission to acceptance) and the proportion of protocols requiring a major revision after first peer review (19.1% vs 52.4%). Reviewer comments most frequently addressed the PRISMA-P item ‘Eligibility criteria’. Overall, 76.0% of the reviewer comments suggested more transparency.We identified 544 eligible protocols published in The number of published SR protocols increased over the years, but so did the processing time. In 2017, it took several months from submission to acceptance, which is critical from an author’s perspective. New models of peer review such as post publication peer review for SR protocols should be investigated. This could probably be realized with PROSPERO.The online version of this article (10.1186/s12874-019-0698-8) contains supplementary material, which is available to authorized users. Systematic reviews (SRs) are conducted to inform clinical practice and decision-making by synthesising and contextualising all relevant evidence that is available regarding a specific research question. Since SRs are typically retrospective in nature , it is cOne way to establish one’s methods a priori is to develop a SR protocol, that is ‘[ …] a document that presents an explicit scientific ‘road map’ of a planned, uninitiated systematic review’ (p. 3) . If SR pAuthors can also register their SR free of charge with the International Prospective Register of Systematic Reviews, PROSPERO, to establish their methods a priori. To date, over 30,000 SRs are registered in PROSPERO . RegistrBoth, publishing protocols or registering SRs, helps to avoid unnecessary duplication as it allows other researchers to systematically search for them , 13. TheA good peer review takes time. In the context of SR protocols, having a manuscript peer-reviewed means a delay in the generation of new knowledge. This is because it is not advisable for authors to begin or continue conducting their SR before the protocol has been accepted for publication as changes to the planned methods (protocol amendments) may be required. A delay in the generation of new knowledge consequently causes a delay in the dissemination of new knowledge. This is costly for the research community and general public  and may ‘BMC Systematic Reviews’ is an open peer review journal established in 2012. As we have recently shown, it is among the journals publishing the majority of SR protocols ’.We searched for SR protocols published in ‘BMC Systematic Reviews’ up to and including 2017 regardless of their topic area. Protocols for overviews, scoping- or realist reviews as well as articles that were not SR protocols were excluded.We included all SR protocols that were labelled as such and published in All records retrieved by the literature search were managed in EndNote . To accelerate the screening process, we used an approach described by Khangura et al. : One resData were extracted from the protocols and Open Peer Review reports (reviewer reports and author comments) into a piloted Excel spreadsheet by one researcher (TR). Where TR was in doubt and in a 10%-sample of all protocols (every tenth protocol), another researcher (KA/TM/DP) double-checked the data. Discrepancies were resolved by discussion. For data items requiring our judgement (e.g. the topic area), we a priori set a cut-off value for the minimum level of inter-rater reliability of 0.8. Items in which the minimum level was not achieved in the 10%-sample were double-checked by another researcher (KA/TM/DP) in every protocol.The following characteristics were extracted for every protocol: publication year, country of first author’s first affiliation, topic area, whether the authors reported information on competing interests, whether the protocol had already undergone full external peer review as part of an external and non-industry funding process, source of funding (with regard to review), number of authors, date protocol received, number of reviewers, number of revisions, date authors responded (for each revision), date protocol was accepted, date protocol was published and date of PROSPERO registration (if available). The date peer review was completed, level of interest, quality of written English and competing interests were extracted for each reviewer and each revision. We did not investigate any revisions required by the editors.‘major’ if changes to the planned methods (protocol amendments) had to be made which would have prevented to begin or continue the review. It was classified as ‘minor’ if more transparency was required, e.g. by justifying or describing any of the planned methods in greater detail. These judgements were made independently by two researchers  for every protocol.In addition, we judged the extent of each revision by assessing the reviewer reports in detail. As a rule of thumb, the extent of a revision was classified as In a randomly selected 10%-sample of the included protocols, one researcher  allocated every methods-related comment the PRISMA-P item (no. 8 to 17) that best described it . For eacAll data were descriptively analysed. For continuous data, we calculated means and standard deviations (SDs), medians and its interquartile ranges (IQRs). For categorical data, we calculated frequencies and proportions.We used the dates a protocol was first submitted, peer-reviewed (for each reviewer), the authors responded (for each revision), accepted and published to calculate the following durations: Submission to first peer review, submission to acceptance, submission to publication, acceptance to publication.All statistical analyses were performed using SAS for Windows, version 9.4 .Our literature search resulted in 693 records, of which 544 (78.5%) were SR protocols that fulfilled the inclusion criteria of our study. The remaining records were either not a protocol or were protocols for primary studies, overviews, scoping- or realist reviews.n = 269) were published in 2016 or 2017, and most first authors were affiliated with an institution from Canada or the UK . Nearly half the protocols (44.1%) were for therapeutic reviews. There was a competing interest statement in every protocol (100%). Ten protocols (1.8%) had already undergone full external peer review, which means they only underwent editorial peer review as per the journal policy [Almost half of the 544 protocols  peer-review (7.2%), no revision was required by the reviewer(s) (4.0%), or the reviewer report was missing (0.9%). After the second round of peer review, 9.3% of the 162 protocols that were not accepted after the first revision required a major revision. 50.6% required a minor revision and 40.1% did not require a further revision. Ten protocols were peer-reviewed three times or more often. Overall, there were 1.3 ± 0.7 reviewers and 1.1 ± 0.6 revisions per protocol. For 50.0% of all protocols, we classified the extent of revision after the first round of peer-review as In 6.4% of the protocols, at least one reviewer indicated that the protocol was of limited interest. The quality of written English was found to need some language corrections or not suitable by at least one reviewer in 30.4% , with a peak in 2016 with 96% (Table n = 424).There was a steady increase in the number of protocols published in 6% Table . Of thosThe mean number of reviewers almost doubled between 2012 and 2017  although it did not increase continuously over time. However, there was a large difference between 2016 and 2017 (increase from 1.1 to 1.7). There were no apparent trends in the proportion of protocols which did not require a revision, nor in the proportion of protocols that require one revision, two revisions and three or more revisions , while in 2017 it was 52 days. The median duration from submission to acceptance was 2.5 times higher in 2017 (142 days) than in 2012 (61 days) and the median duration from submission to publication of 86 days in 2012 almost doubled to 158 days in 2017. For the time between acceptance and publication, there was no consistent trend over the years (ranging from 12 to 16 days).‘BMC Systematic Reviews’ in 2017 was 168 days and 16 days from acceptance to publication [For comparison, the time from submission to acceptance across all manuscripts submitted to lication .From our random 10%-sample, we had to exclude one protocol for which no reviewer comments were available, resulting in 53 protocols for further analyses based on PRISMA-P. Overall, there were 450 comments (on average 8.5 ± 9.0 per protocol), 342 of which suggested more transparency (76.0%) and 108 which suggested a protocol amendment (24.0%). Suggestions for more transparency were implemented in 85.1% and protocol amendments in 73.7%; non-implementation was justified by the authors for all but two comments, both which suggested a protocol amendment.‘Eligibility criteria’  and item 9 ‘Information source’ (52.8%). With 13.2% each, comments on ‘Data management’, Criteria for quantitative synthesis’ and ‘Confidence in cumulative evidence’ were least common  and item 9 ‘Information sources’ (39.6%). They were implemented in 56.3, 100 and 93.8% of the time, respectively.The proportion of comments suggesting protocol amendments was highest for PRISMA-P item 10 ‘BMC Systematic Reviews’ has increased tremendously since the journal’s launch, from n = 21 in 2012 to n = 145 in 2017 . The proportion of protocols requiring a major revision was 37.9% and has also increased with time. Three quarters of reviewer comments suggested more transparency. Most protocols were also registered with PROSPERO (89.2%), an increasing proportion before the manuscript had been submitted (reaching 94.0% in 2017).Our study shows that the number of protocols published in While the time from acceptance to publication was constantly about two weeks over the years, the time from submission to publication almost doubled and went from just under three months in 2012 to over five months in 2017. This is how long it takes for a primary study from first submission to acceptance , the timFrom an author’s perspective, long processing times might have far-reaching implications. Although authors should wait until their protocol is accepted for publication, they might choose to continue working on their SR in the meanwhile. This holds the risk that valuable comments from the peer review might not lead to changes in the SR’s methodology, which might be critical unless the part requiring a revision has not been commenced or finished by then. For example, a revision of the eligibility criteria might result in a new search strategy.Waiting for the protocol to be accepted causes a delay in the conduct of the SR and consequently in the dissemination of new knowledge . MoreoveThe most likely reason for the increased duration from submission to publication is the increase in the proportion of protocols that required major revisions. As we have shown, protocols requiring a major revision after the first round of peer review took about a month longer (median 29 days) to get published than those requiring a minor revision. But why did more protocols require a major revision?One explanation might be that the quality of initially submitted manuscripts for SR protocols became slightly worse over time, perhaps due to a change in the authors who submit SR protocols. One can assume that publishing protocols has become more popular over the years, while in the beginning only groups which are experienced in performing SRs submitted protocols. This is supported by the fact that the geographical scope in PROSPERO , as well‘BMC Systematic Reviews’ that the authors follow the checklist and submit it as an additional file [Another explanation why more and more protocols required a major revision might be the introduction of PRISMA-P in 2015. Nowadays, it is required by nal file . OtherwiBecause the time from submission to first peer review has also steadily increased from 2015 onwards, another explanation might be the increasing difficulties in finding appropriate peer reviewers given the increase in scientific publications in general . HoweverAbout 9 out of 10 protocols were also registered in PROSPERO. It is known, that SRs with published protocols are more often registered with PROSPERO than SRs without . But thiOne major argument for publishing a protocol of a SR is to receive input regarding the review scope and review methodology from independent peer reviewers, who themselves are experienced researchers. However, in a recent study we found that SRs with published protocols had older searches compared to SRs without a published protocol; in 52.2% of the SRs, the final search had already been performed before submitting the protocol for publication . This fiNaturally, authors play an important role in the peer review process, too. We found that most of the reviewer’s comments on methodological issues suggested more transparency, not amendments to the protocol. The former could be avoided to some extent if authors paid more attention to this matter in the preparation of their manuscript, and described and justified their methods more carefully in the initial submission.One could argue that for protocols, which did not require any amendments, the registration in PROSPERO would have been sufficient. That is because all potential advantages of publishing SR protocols, apart from peer review, could also be achieved through registering the SR with PROSPERO (provided that information is presented in the same amount of detail as they would have been in a protocol). Furthermore, a recent study found that registered reviews were of higher quality than non-registered reviews . However‘abandoned’ including details on reasons for that, although this is seldom done [An advantage of PROSPERO is that the registration and status of the SR can be easily updated and details or the reference for the published review can be added. If the SR has never been completed, another possibility is to switch its status to dom done . Since a‘BMC Systematic Reviews’ since it was launched in 2012 up to and including 2017. Despite the large number of analysed protocols (n = 544), the journal only served an example. However, it is the open peer review journal, in which most SR protocols are published (39.7%), followed by BMJ Open (23.4%) [This was a study of all SR protocols published in blished 3.7%, follAlthough most endpoints of this study were based on data like dates and frequencies, we had to make judgements regarding some endpoints. To be as objective as possible, we did not check back with any peer reviewers, protocol authors or the editors, which means that our judgements might vary from the original ones. To increase internal validity, the reviewer reports for each protocol were assessed by two researchers independently regarding their extent of revision, though.We used PRISMA-P as a simplified method of content analysis and we might have misclassified some comments. Moreover, the 10%-sample of protocols might be too small for meaningful analysis. However, we had the opportunity to include a total of 450 reviewer comments. Lastly, we did not analyse whether changes in PROSPERO were made after the protocol had been finally approved. Status updates are not often done in PROSPERO , though,The increasing number of published protocols can be interpreted as a desirable trend, but the long and steadily increasing processing time is not acceptable from an author’s perspective. When protocols are submitted, a timely and well-performing peer review system is needed. It has been stressed that due to the increasing number of scientific articles the workload imposed on individual reviewers appears to be reaching a `breaking point’; for protocols of SRs it has already been reached . New modAdditional file 1: Time trends in judgement of level of interest and quality of written English. (PDF 16 kb)Additional file 2: Time trends in basic and peer-review characteristics and processing times – additional data. (PDF 19 kb)


Following eight years at the helm of Biology Open (BiO), Founding Editor-in-Chief Jordan Raff this year made the decision to stand down from the role . As I taIn addition to increasing our outputs, scientific publication in the biological/biomedical sciences is becoming more international. The number of countries listed in authors’ affiliations has increased by ∼1% per year D and theSupplemental File 1). Inspection of these words revealed changes in the occurrence of experimental techniques, such as a decrease in the use of chromatography . This is readily visible from the increase in ‘redness’ of the heatmap between successive years as time progresses  their portfolio of Open Access journals, keeping publication costs low and returning any profits to the scientific community in the form of research, travel or conference grants. The third option is that funders will become the publishers of the future and set up Open Access platforms to disseminate their funded results. Such platforms have already begun to emerge, such as Open Research from the Wellcome Trust, and Gates Open Research from the Bill and Melinda Gates foundation. The question that we as authors need to ask is: where do we want our grant money to go? We can choose to give our money either to a commercial publishing company (who will in turn give it to its shareholders) or we can give it to a society or a research funder (who will reinvest any profits in supporting future research and researchers). Only the latter options are both sustainable and contribute to the future of science, so the choice should be easy.My most sincere thanks to Jordan, who brought Biology Open into existence and created a journal that gives back to the biological sciences community. I look forward to building on what Jordan started. Biology Open already provides an Open Access platform for publishing all aspects of biological research, from polar bears to cell polarity and everything in between. As a publication from the not-for-profit The Company of Biologists, it also already supports research and researchers around the world and reduces barriers to publication while maintaining scientific integrity. However, there is more to be done to improve the publication process and I very much look forward to the opportunity I now have as the new Editor-in-Chief of BiO.


In this 20th anniversary theme issue, we are celebrating how JMIR Publications, an innovative publisher deeply rooted in academia and created by scientists for scientists, pioneered the open access model, is advancing digital health research, is disrupting the scholarly publishing world, and is helping to empower patients. All this has been made possible by the disintermediating power of the internet. And we are not done innovating: Our new series of “superjournals,” called JMIRx, will provide a glimpse into what we see as the future and end goal in scholarly publishing: open science. In this model, the vast majority of papers will be published on preprint servers first, with “overlay” journals then competing to peer review and publish peer-reviewed “versions of record” of the best papers. Journal of Medical Internet Research, the journal; now, JMIR Publications, the publisher) started an unprecedented journey to disrupt the medical informatics and publishing world with a new kind of journal and a new type of business model. The term “open access” was not invented back in 1999; most journals were still published and distributed on paper, and I remember the days of having to courier 10 copies of a manuscript on paper to a journal office, which then sent out the same hardcopies by postal mail to peer-reviewers. Creative Commons was in its infancy, and authors routinely signed away their copyright to publishers. A paper I submitted to a medical informatics journal took 2 years to be published. In this environment I was excited about the possibilities of the internet but also frustrated by the obvious inefficiencies and anachronisms of how we communicate in science. Having already worked as editor and book author in my student days, I decided to create a radically different, new journal for the internet age, with the intention of innovating on form, content, and business model.Twenty years ago, JMIR . This new form also opened up content to nontraditional audiences, ultimately contributing to a shift in the power distribution between doctors versus patients  to preprint servers for discussion and peer-review, and journal editors and publishers would pick and bid for the best papers they want to see as “type-2 papers” [version of record] in their journal. JMIR Research Protocols journal, which increases accountability and transparency in research through registered protocols and registered reports, we are confident that once again, we are at the at cutting edge of an open-science revolution, and we look forward to take that journey in the next 20 years with our growing base of readers, editors and reviewers.This is what I still believe may be the future of publishing, and JMIRx may illustrate this. Combined with other innovations, such as our


We live in a time of “now,” when we can pretty much find anything we need at the click of a button, have it delivered to our door within hours, and often without the need to compromise on quality. The market place is more competitive than ever – as a supplier, if you can't deliver a quality product in a timely manner, then somebody else will step into the gap and, before you know it, the opportunity has closed.Just like every other aspect of modern life, endocrinology, diabetes and metabolism are fast moving with new, often ground‐breaking, developments emerging every week, if not every day. Technological advances mean that many basic scientific and clinical questions can now be addressed in a way that could only have been dreamt about as recently as five years ago. However, identifying which are the important questions to ask, and working out how best to address these, remains as big a challenge as ever.So, when we complete a piece of work, irrespective of whether the findings are “positive” or “negative,” we quite rightly want to get our message out and into the public domain – but then the next challenge appears – how best to do this? For most of us, publishing in scientific journals remains important – yes, there are alternative ways to “publish” our findings, especially if we are sufficiently adept to exploit the opportunities presented by social media – but, at the end of the day, the traditional model, whereby our work is subjected to pre‐publication scrutiny by our peers , remains as important as ever. Indeed, good peer review often adds to the quality of the final product – who hasn't been grateful for the insightful comments of a reviewer or editor that have improved the quality of an article, and for which we can take the credit!However, publishing in scientific journals remains as competitive as ever, with researchers aspiring to see their labours rewarded with acceptance by one of the “higher ranked” journals. Of course, such an approach is not without its challenges. The acceptance rates in many journals remain relatively low – and often this isn't simply a reflection of the quality of the material submitted, but rather a “lack of space” such that many worthy articles are turned away, especially if they are not deemed sufficiently novel or are viewed as simply confirming the work of others. However, this strategy is flawed because good quality confirmatory papers, or indeed studies that refute the findings of previous manuscripts, may be just as important as the original work. Indeed, the topic of reproducibility of medical scientific discovery is currently a “live debate” as public and other funding bodies seek to ensure they are securing full value for money from their investments.Another issue facing the modern researcher is how to navigate the challenge of Open Access – again many funding bodies and host institutions demand that their grant holders/employees make their work available as soon as possible using the Open Access model.So, when approached by Wiley to consider the introduction of a new journal, into what already seems a congested market place, the most important question to ask was whether the model proposed would create a journal that could meet the demands of publishing in the modern era. I'm pleased to say that Endocrinology, Diabetes & Metabolism has been designed to be just that. Like other journals, ultimately the quality of material submitted will be the key factor in deciding whether an article is accepted for publication – so, for a primary data manuscript the validity of the hypothesis/aims, methods, results and discussion will all remain central to journal decision making, and similarly for reviews and other articles, quality will be the key watchword. However, while novelty will still remain important, it will not be an essential requirement for publication in the journal.Endocrinology, Diabetes & Metabolism will accept manuscripts from across the full breadth of our specialty, ranging from basic science to clinical practice, and in so doing will hopefully offer something for everyone.As an Open Access journal one of our priorities will be to ensure timely publication in a manner that allows authors to readily meet their obligations to funding bodies and host institutions.Finally, although the on‐line environment offers the option to “do away” with word and figure limits, the Editorial Team believes strongly that the ability to distil a message into a compact format remains an essential skill and one that benefits all – in the modern world everyone is busy, our attention spans limited, and so delivering our message rapidly, in a readily digestible format, is likely to pay significant dividends all round.


If you are reading this commentary then it is most probable that you have been invited and even participated in the review of submissions to a scientific journal at some point in your career. For those of you who have performed reviews, thank you for your contribution to the advancement of high quality science. The purpose of this commentary is to encourage and recruit additional reviewers as this is the critical fuel that makes a journal successful. As journal or section editors, we recognize that reviewers are perhaps more critical than authors and much more difficult to recruit.Scientists sometimes forget that they exist within a closed cycle system. They are funded to carry out research, which they must publish, to hopefully obtain tenure and additional funding with which they are funded to carry out research….and while most scientists see reviewing grant proposals as a duty and honor and rarely refuse, many neglect to see reviewing journal submissions in the same light. Without a continuous stream of reviewers and reviews, your submission can be significantly delayed in the first step of write–revise–publish, and negatively impact tenure and promotion decisions and supporting material for grant submissions. Perhaps this has even contributed to the incredible increase in the number of predatory journals because of the ability to exchange paying unwarranted page charges for rapid, but poorly regulated publication.SOX 2, a new genomic marker in patients presenting with (ICD10) S10.87XA where BRCA1 status provides guidance for treatment?” (contrafaco)…“I am writing to invite you to serve to review the manuscript: “Let’s examine the most common reasons that editors receive for refusing an invitation to review a journal submission, but first, the invitation:“It’s not my area of expertise”….The likelihood that you are an expert in this work (NB: S10.87XA is a condition known commonly as “hickey”) is incredibly small (p ≪ 0.00000001) but, as a scientist, you can objectively review many components of the study, e.g. methods, data, analysis, and also state what you specifically have or have not reviewed. This can still be very valuable to both the editor and the author in evaluating and improving the manuscript and the research. In addition, if structured appropriately, the opportunity exists for you to also gain insights into methodologies and diseases, etc. that could prove useful in expanding your own research perspective.Potential solution There should be a “checklist” provided to and completed by the author upon submission that goes beyond the current general classification being used, and that provides more detail about the methodologies and/or analytics, data source/collection, disease/condition being studied, public/private healthcare/population environment, etc. A similar checklist, to be completed by potential reviewers, and that should definitely include any and all authors who have published in that journal, could be used to better evaluate and match manuscript to reviewer. General categorizations, e.g. “cardiovascular”, do not adequately address this issue.2.“I am busy…I don’t have time”Of course you are busy…. A successful career in science has become increasingly challenging because of funding issues and coopertition between academia and industry, especially academic spin-out companies. And some potential reviewers sit in more than one world at the same time. The scientific community, however, exists as a somewhat closed group defined by essential requirements of both advanced training and experience. We all need to remember that this system maintains a form of symmetry…if everyone is to busy working and writing papers (or grants) to review a limited number of manuscripts, then we should expect that our submissions also will meet reviewers who “are too busy”. It is perhaps appropriate to consider the responsibility to perform reviews as a “professional tax”…and it is also appropriate to expect not to be over-taxed.Potential solution Journal editors can “assign” credits for performing reviews, with the total points being stored in the reviewer’s “account” and maintained by an honest broker i.e. an academic institution or non-profit organization/professional society, across the scientific community. Reviewers could be appropriately acknowledged, annually, for their contributed activity and possibly, some publishers might offer reduced publication fee opportunities. This documentation could/should be further considered in academic promotion and review procedures.And if you are “on vacation” or “travel”, it is also appropriate to suggest when you might be able to return the review, even if after the proposed date, so that the editor can respond accordingly.3.‘Invited but no response”Unfortunately, this category is larger than can be justified and the total lack of response is inappropriate and unprofessional. An editor appreciates having a response and commitment, either to review or not to review. And editors and publishing systems do keep track of their reviewer pools. This is a list where you likely may not wish to be included.We welcome your response and thoughts…and even more importantly, your potential interest in joining the group of active reviewers who help to advance the science in a responsible and quality manner.


Randy Schekman reflects on the origins of the journal, the eLife approach to peer review, and current challenges in scientific publishing.As he prepares to step down as the Editor-in-Chief of eLife,  In December 2010 the Howard Hughes Medical Institute (HHMI), the Max Planck Society and the Wellcome Trust invited leading figures in the life and biomedical sciences to a meeting at the HHMI Janelia Research Campus to consider the creation of a new open-access journal that would publish outstanding research in these fields. Many of those present expressed impatience with the delays and difficulties they had experienced in publishing what they considered to be excellent work in the pages of three journals: Cell, Nature and Science.Mark Walport, the director of the Wellcome Trust at the time, memorably remarked that "the process of science peer review needs to be owned by professional scientists" in order to curtail the "endless iterations of nit-picking" that were common during peer review at the most selective journals . The conThe situation was particularly toxic for early-career researchers, who felt that they had to publish in one of these journals in order to secure a permanent research position . AlthougAt the time of the meeting I was coming to the end of a five-year term as Editor-in-Chief of the Proceedings of the National Academy of Sciences (PNAS), and had been prepared to stay for a second term. However, Robert Tjian, my colleague at UC Berkeley and president of HHMI at the time, urged me to consider leading this new effort. I was intrigued by the possibility of this new venture, particularly given its solid financial foundation and the opportunity of starting afresh. Harold Varmus, then director of the National Cancer Institute, advised that a new journal would have to do something different in order to distinguish it from other journals in the evolving publishing landscape. Thus, when offered the position, I accepted with enthusiasm and took Varmus’s sage advice to "think different" to heart.My first steps were to appoint two Deputy Editors (Fiona Watt and Detlef Weigel), a team of Senior Editors who were all active scientists in the major areas of the life sciences, and a manager for the editorial office (Mark Patterson). At a meeting in New York in December 2011 we agreed on a peer-review process for the journal. All new submissions would be assigned to a Senior Editor, who would decide (often in consultation with a member of our soon-to-be established Board of Reviewing Editors) whether or not to invite a full submission that would be sent to referees for full peer review: this initial decision is taken by professional editors at the most selective journals.Thinking about ways to improve the peer-review process for manuscripts that survive this initial stage, I recalled how editorial staff at PNAS were able to consult with one another online as submissions moved through the peer-review process, so we agreed that eLife editors and reviewers should discuss a manuscript and their reports on it before reaching a consensus decision. This consultation – which is overseen by the Reviewing Editor who is handling the manuscript – has become a central element of the eLife peer-review process: once the last report has been received, each reviewer receives an email asking them to read and comment on the other reports (which include the name of each reviewer). If the reviewers broadly support publication, they agree on the revisions that need to be made in order for the manuscript to be accepted. This is a significant change to the standard approach because the reviewers, in collaboration with the editor, focus on identifying the most important revisions for the author. In addition, the consultation allows the reviewers to learn from each other and, if necessary, to revise their views on a manuscript in the light of comments from reviewers who might know more about a particular topic or technique.One of my goals had been to make the peer-review process more open and constructive: over the years I felt that peer review had become somewhat toxic and destructive, with reviewers taking advantage of the veil of anonymity to make more and more unnecessarily negative comments about the papers they were reviewing. In the eLife process reviewers know that they will have to defend their views in an open discussion with the other reviewers before an editorial decision is rendered on a manuscript, and I am convinced that this has fostered a more positive approach to peer review, and am pleased to see that a number of other journals have experimented with similar approaches .One of my goals had been to make the peer-review process more open and constructiveIt is worth emphasizing three other points about the eLife approach to peer review: i) in the case of a positive decision the individual referee reports are normally not sent to the authors: rather authors are sent a detailed decision letter that contains a list of the essential revisions agreed by the Reviewing Editor and the reviewers during the consultation  and a list of minor revisions; ii) extra experiments are only requested if they are essential to support the major claims in the manuscript and can be completed within two months; iii) in most cases the revised manuscript is assessed by just the Reviewing Editor, rather than sending it back to all the reviewers: this, combined with our practice of only requesting essential revisions, helps to speed up the publication process.Other important aspects of the eLife peer-review process include: there is no target acceptance rate for eLife – editors accept all the papers that reach the standard we expect ; there is no limit on the length of papers – authors can have as many words and figures as they need; and the decision letter and the authors' response to this letter are published with the paper, along with the names of those referees who are happy for their identities to be made public. Unlike the most selective journals, eLife is not in the business of selling magazines or subscriptions. Instead, our editors are selected for their expertise, and they are encouraged to accept for publication those papers that combine true scholarship and responsible behavior, rather than identifying papers on the latest fads that may help to increase our impact factor. We have opposed the use of the impact factor since day one because we feel it is meaningless, particularly when it is used to assess individual papers or scientists .By the time we opened for submissions in June 2012 we had 15 Senior Editors  and 175 Reviewing Editors, and by the end of 2012 we had published 27 Research Articles. Fast forward to the present and we received 7671 submissions in 2018 and published over 1250 research papers . We now have over 340 Reviewing Editors, 43 Senior Editors and three Deputy Editors .We are also committed to improving both the gender and geographical balance among our Editors: this is important to us because an analysis of all submissions to eLife between 2012 and 2017 found that "women and authors from nations outside of North America and Europe were underrepresented both as gatekeepers (editors and peer reviewers) and last authors" . Sadly, We have opposed the use of the impact factor since day one because we feel it is meaningless, particularly when it is used to assess individual papers or scientists.Setting a fee for publication for further details).Given the generous support we received from our funders, we did not charge a publication fee until the end of 2016. However, as we knew we would eventually have to go it alone, we introduced a publication fee of $2500 per paper in January 2017. The fee was set at this level to cover our marginal publication costs, with the funds we receive from HHMI, the Max Planck Society, Wellcome and the Knut and Alice Wallenberg Foundation largely being used to support fixed publishing costs and the development of our journal infrastructure  that explains the content and context of the paper for the general reader . Fortunately, the ground is now shifting rapidly, most notably with a far-reaching proposal in Europe called Another positive development in scientific publishing over the past few years has been the growth of preprint servers in the life and biomedical sciences, notably bioRxiv, which allow researchers to make their results available as quickly and as widely as possible. A number of journals had been exploring new approaches to scientific publishing before the launch of eLife, notably journals published by BMC, BMJ, EMBO and PLOS, and this spirit of innovation has continued with these publishers and others: examples include the development of the Open Research publishing platform by F1000Research , and an open-source platform for scientific publishing. We have started to build a submission and peer-review platform in collaboration with a number of other like-minded organizations, and are also in the process of adapting our publishing platform so that it can be used by other journals and publishers. The hope is that this platform could be adopted by society publishers and other non-profits to reduce their costs, and thus reduce their reliance on the income from journal subscriptions. I see this as a crucial development as it will help societies and non-profits survive in an environment that is dominated by the large commercial publishers and societies with substantial publishing operations.Looking ahead, I see several challenges and opportunities for eLife. One is for the journal to continue to grow and to continue to advocate for change in peer review and scientific publishing more generally, both individually and as part of organizations such as DORA. Another is to continue to build an end-to-end research on Parkinson’s Disease. When my wife died, I was asked by the Brin Foundation to chair an effort to identify and support key elements of basic research focused on understanding the origin(s) and mechanism(s) of disease progression, and I am now helping to build an international network of Parkinson’s Disease geneticists, cell and molecular biologists, neuroscientists and physicians to tackle this scourge. Our goal is to advance our basic understanding as an essential prelude to the development of new drugs and surgical procedures. I am eager to take on this challenge and am grateful to the Brin Foundation for helping to turn my personal grief into something constructive.Although I am enormously gratified by the success and future promise of eLife, I decided to step down for personal reasons. My wife of 44 years died in September 2017 of complications from Parkinson’s Disease. At the time of her death, I had been in casual conversation with a representative of the Sergey Brin Family Foundation, which has generously supported


Engineering in Life Sciences will be a full Gold Open Access journal starting January 1st, 2020.All papers are now freely accessible for everybody to read, directly upon publication.Authors may share their articles with anyone, on any platform or via any communication channel.Copyright will remain with the authors under a Creative Commons Attribution (CC‐BY) License which permits use, distribution, and reproduction in any medium .With Open Access, visibility is significantly increased and research reaches a larger audience; this usually also leads to increased downloads and citations.We are very happy to announce that The publishing landscape is currently undergoing significant changes. More and more funders and countries now mandate Open Access. They are convinced, similarly to more and more researchers, that science should not be locked behind paywalls, but freely available to read for everyone. So are we! Especially biochemical engineering has a lot to offer and provides numerous solutions for the most driving questions of today for a sustainable future: this science should be easy to find and open to access for anyone.Of course, the move to Open Access will not affect the editorial process — the scientific evaluation of manuscripts is independent of our publication model. We intend to keep the quality of published papers at the highest scientific level.https://authorservices.wiley.com/author-resources/Journal-Authors/open-access/affiliation-policies-payments/institutional-funder-payments.html.Although there are many advantages of Open Access, we understand that there are also potential concerns. To cover the costs of publishing, Article Processing Charges (APC) will be levied for articles that are accepted and published in the journal. However, APCs are covered by many funders, institutions, or national agreements. Please read more https://authorservices.wiley.com/open-research/open-access/for-authors/waivers-and-discounts.html).The most prominent agreement is the one with “Projekt DEAL” in Germany, covering the costs for Open Access publishing in Wiley journals for the eligible authors from German institutes. Additionally, waivers and discounts are in place, e.g. for authors from developing countries Thomas Bley(Editor‐in‐Chief)Ralf Takors(Editor‐in‐Chief)Danielle Flemming(Managing Editor)


Unrestricted access to journal publications speeds research progress, productivity, and knowledge translation, which in turn develops and promotes the efficient dissemination of content. We describe access to the 500 most-cited emergency medicine (EM) articles (published between 2012 and 2016) in terms of publisher-based access (open access or subscription), alternate access routes (self-archived or author provided), and relative cost of access.Academia.edu, and the Unpaywall and Open Access Button browser plugins to locate self-archived copies. We contacted corresponding authors of the remaining inaccessible studies for a copy of each of their articles. We collected article processing and access costs from the journal publishers, and then calculated relative cost differences using the World Bank purchasing power parity index for the United States (U.S.), Germany, Turkey, China, Brazil, South Africa, and Australia. This allows costs to be understood relative to the economic context of the countries from which they originated.We used the Scopus database to identify the 500 most-cited EM articles published between 2012 and 2016. Access status was collected from the journal publisher. For studies not available via open access, we searched on Google, Google Scholar, Researchgate, We identified 500 articles for inclusion in the study. Of these, 167 (33%) were published in an open access format. Of the remaining 333 (67%), 204 (61%) were available elsewhere on the internet, 18 (4%) were provided by the authors, and 111 (22%) were accessible by subscription only. The mean article processing and access charges were $2,518.62 and $44.78, respectively. These costs were 2.24, 1.75, 2.28 and 1.56 times more expensive for South African, Chinese, Turkish, and Brazilian authors, respectively, than for U.S. authors .Despite the advantage of open access publication for knowledge translation, social responsibility, and increased citation, one in five of the 500 EM articles were accessible only via subscription. Access for scientists from upper-middle income countries was significantly hampered by cost. It is important to acknowledge the value this has for authors from low- and middle-income countries. Authors should also consider the citation advantage afforded by open access publishing when deciding where to publish. Access to key academic literature is vital for authors, scientists and clinicians, especially those working in low- and middle-income countries.6Unrestricted access to research improves research progress, productivity, and knowledge translation. These in turn develop and promote the efficient dissemination of content in an ever-expanding knowledge cycle.This was a retrospective, cross-sectional study using secondary, published data. We searched for articles via Scopus and SciVal  to identify the 500 most-cited EM articles published between 2012 and 2016. Scopus is the largest abstract and citation database of peer-reviewed literature. SciVal is a powerful data engine that can be used (amongst a vast number of other functions) to interrogate the Scopus database. We used it to perform an automated keyword search for EM articles, along with citation counts and journal, author and publisher details. Articles were then ranked using their citation count to allow selection of the sample.https://scholar.google.co.za/), Researchgate (https://www.researchgate.net/) and Academia (https://www.academia.edu/) to determine whether an archived copy existed. Unpaywall  and the Open Access Button (https://openaccessbutton.org/) browser plugins were also used for this purpose. We did not include a search of any of the shadow libraries (Libgen or Sci-Hub).Each of the included articles was manually checked to identify their open access status via the publisher’s websites. Where articles were not available open access from the publisher’s website (subscription-based articles), we used the article title to interrogate Google, Google Scholar  and asked to provide a copy of his or her article for a university research project. Corresponding authors were given 14 days to reply and were provided with full details of the study aims if they were requested. We collected article processing and access costs from each respective journal’s publisher. Publishers were contacted via email where cost information was not available on their public website.We used the World Bank’s purchasing power parity (PPP) index to calculate the relative journal article processing and access cost differences for selected countries. PPP is based on the hypothesis that similar items cost the same no matter where in the world it is purchased. For instance, a tall Starbucks caffé latte will not just cost $2.95 in the United States (U.S.), but anywhere in the world; the only difference would be the expression of $2.95 in a foreign currency (R40.90 in South Africa). In reality, however, parity doesn’t exist. The PPP index describes this deviation from parity and uses the U.S. dollars as its baseline. A tall Starbucks caffé latte in South Africa actually costs R27.00 ($1.95) and not R40.90 ($2.95). For an American tourist ordering a tall Starbucks caffé latte in South Africa, this will result in a 33% cost saving, but for a South African tourist in the U.S. this will result in a 50% cost increase. Although not directly applicable to publication cost, the PPP index offers a simplified, hypothetical comparison of the relative article processing and access cost between countries, as it does for other goods. For our analysis we included only the top publishing countries of each global publication region, as per Scopus .We employed Microsoft Excel  for data analysis. Article accessibility was presented descriptively. The PPP index was used to calculate the factor by which publication costs differed between the included publishing countries, relative to the U.S. dollar. These were compared using a paired t-test, with significance defined as a p-value of less than 0.05. To provide an understanding of the economic burden of scientific publishing for scientists and clinicians living in middle-income countries, we calculated an equivalent local cost of article processing and access for the four middle-income countries included  to the U.S. cost of publishing and access, by applying the PPP index in reverse. Essentially this calculation allowed us to describe a similar out-of-pocket expense for a researcher earning in one of these four countries and the U.S.The study protocol was reviewed and approved by both the Human Research Ethics committees of Stellenbosch University and the University of Cape Town, Cape Town, South Africa (largely due to involvement of an undergraduate researcher in the project).Critical Care and Resuscitation, levies no article processing cost for open access publishing. However, as a society journal, access is restricted to members of the society for the first three months following publication, after which it is made universally accessible. There were 471 (94.2%) articles with first authors from high-income countries and 25 (5%) from upper-middle income countries, with the remaining four (0.8%), split equally between articles with first authors from lower-middle and lower-income countries.We collected the 501 top-ranked EM articles by citation count. After excluding one article due to its retraction from circulation, we were left with 500 articles published over 29 journals. Of these journals, 22 (76%) were hybrid open access journals , six (21%) were open access-only journals, and one was a subscription-only journal. One journal, While two out of three of the top 500 cited EM articles were subscription based, only one in five were eventually found to need subscription for access. This figure broadly compares with the global open access rate, which is estimated at around 28% of peer-reviewed articles;3upper-middle income status.13The cost of access to non-open access articles was significantly prohibitive for the low- and middle-income countries included in our sample. It is notable that waivers and discounts would not apply to any of these countries, as they are specifically excluded by publishers due to their Upper-middle income countries aside, the African EM open-access study showed that the relative cost of access was much higher for low- and lower-middle income countries. Relative to the U.S., costs were 3.5 and 2.8 times more for Ghanaian and Tanzanian authors, respectively.9Apart from the social responsibility, publishing open access presents authors from high-income countries with an evidence-based opportunity to improve their citation counts (which is important for promotion and grant applications). Studies have shown that publishing open access improves discovery and citation of articles, offering a significant advantage.14Although applications like Unpaywall and Open Access Button make it easier to find archived publications, it is more complicated than locating an open access article directly through its publisher’s website. Archiving is also dependent on publisher regulations, which often prohibit archiving for up to 12 months, and restricts which versions of an article can be archived.Author responses to publication requests were less than half of what was observed in the African open access study. As the two cohorts differed substantially we did not explore this finding further. It is possible that the philanthropic nature of African authors played a role.There are a number of limitations to this study. It is likely that many, or all, of these papers would be accessible through the shadow library SciHub. Publishers are clear that SciHub’s business model contravenes copyright. However, research has shown that scientists are often willing to view SciHub use in less black-and-white terms.Our study only included articles from the Scopus database. A different database might have altered the findings of the study. However, Scopus does provide the largest abstract and citation database of peer-reviewed literature (including EM) globally, which explains our choice to use it. Finally, we only included articles from EM journals, which limits the list of top papers. Many top emergency care papers are published in leading non-EM journals with different access policies. This may also have affected the findings.In conclusion, this study showed that one in every five of the top 500 EM papers published in EM journals over a five-year period were not accessible without a subscription, and that access for scientists from low- and middle-income countries is significantly hampered by cost. It would be useful to view the uptake of open access over time to see if it is improving, as is happening in other specialties. Describing EM journals in terms of their accessibility  and then linking this to journal impact might help guide authors select more accessible journals. Authors, specifically those from high-income countries, should consider the citation advantage afforded by open access publishing when deciding where to publish. It is also important to acknowledge the value this has for authors from low- and middle-income countries.


The recent replication crisis has caused several scientific disciplines to self-reflect on the frequency with which they replicate previously published studies and to assess their success in such endeavours. The rate of replication, however, has yet to be assessed for ecology and evolution. Here, I survey the open-access ecology and evolution literature to determine how often ecologists and evolutionary biologists replicate, or at least claim to replicate, previously published studies. I found that approximately 0.023% of ecology and evolution studies are described by their authors as replications. Two of the 11 original-replication study pairs provided sufficient statistical detail for three effects so as to permit a formal analysis of replication success. Replicating authors correctly concluded that they replicated an original effect in two cases; in the third case, my analysis suggests that the finding by the replicating authors was consistent with the original finding, contrary the conclusion of “replication failure” by the authors. Replicability is the cornerstone of science yet its importance has gained widespread support only in recent years . The “reThere is much debate and confusion surrounding what constitutes a replication . EcologiAnimal Behaviour, Behavioural Ecology and Sociobiology, and Behavioural Ecology) were partial/conceptual replications whereas no exact replications were found.The replication of research studies (or at least the publication of replications) has been rather poor across disciplines in the social and natural sciences despite its need. For example, only 1% of papers published in the top 100 psychology journals were partial replications  and estiNot only are scientists failing to conduct (or publish) replications, but more worryingly, we are failing to replicate original research findings when studies are repeated. Two separate studies conducted by The Many Labs project successfully replicated 77%  and 54% Perhaps the apparent low success of replication studies stems from the manner in which success is judged. There is no single standard for evaluating replication success  but mostEcology, Evolution, Behavior, and Systematics studies claiming to be true replications and then compare this rate with that of a general biology open access publication (PeerJ). Second, I calculate the success rate of replications found in these journals.We do not know if there is a ‘replication crisis’ in ecology and evolution. However, in order to make informed decisions on whether we need to change our views and behaviour toward replications, we need, as a first step, an empirical assessment of their frequency and success in the published literature. My aim in this paper is two-fold. First, I attempt to quantify the frequency of Ecology, Evolution, Behavior, and Systematics within the “Agricultural and Biological Sciences” subject area of the SCImago Journal & Country Rank portal (https://www.scimagojr.com/). This resulted in a subset of 38,730 papers from 160 journals  to text-mine this subset of papers for any permutation of the word “replicate”  in the Introduction and Discussion  that provided an open access publishing option as well as open access journals . In order to compare rates of study replication in discipline-specific  open access (and hybrid) journals with a multidisciplinary open access journal I also text-mined 3,343 papers published in PeerJ.I used code written in the Python language  required to calculate an effect size (Cohen’s d). In cases where the original effect size differs from zero but the replicate does not, I used d33%). A replication having an effect size significantly smaller than d33% is inconsistent with the studied effect being big enough to have been detectable with the original sample size, which then casts doubt on the validity of the original finding . I did not include quasireplications  or studi finding .n = 11 papers that claimed to have replicated a previously published study  to that observed in Ecology, Evolution, Behavior, and Systematics journals.Examination of lication  out of 3Ecology, Evolution, Behavior, and Systematics literature suggests that approximately 0.023% of studies in ecology and evolutionary biology truly replicated (or at least claimed to have) a previosuly published study. Although this rate is on par with other disciplines in the natural and social sciences  and that in Ecology, Evolution, Behavior, and Systematics journals. Finally, perhaps the rate of replication observed here is not representative of the field as a whole because publication rates of replications might be higher in non-open access Ecology, Evolution, Behavior, and Systematics journals. This seems counter-intuitive, however, as anecdotal evidence suggests that open access journals are expected to have the highest likelihood of publishing a replication. Given these caveats it is important to emphasize that 0.023% likely underestimates the actual rate of study replication in ecology and evolution.I do not know of any study examining whether exact replications are more likely to be called a replication within the paper than a conceptual replication or the likelihhod that an author conducting a true replication will even label their study as such. It seems unlikely that an author who is explicitly conducting a replication, particualrly an exact replication, would not use the word “replication” somewhere in their article. However, perhaps authors are reticent to claim their study as a replication because the stigma of study replication persists and thus reduces publication success. Alternatively, perhaps the low rate observed here is due to a higher likelihood of replications being published in multidisciplinary biology journals rather than more targeted sources such as those in n = 10 replication studies  in their replication study. d33% = 0.29 (n = 113 thus n = 56.5 per group) was not rejected (p = 0.09). This is consistent with the notion that the effect found by In contrast, Ecology, Evolution, Behavior, and Systematics; however, that authors provided the relevant information to calculate an effect size in only three of 11 cases is cause for concern. I recommend that future authors either include a detectability analysis (This formal analysis of three replicated effect sizes shows that the replicate study supported the original conclusion in two-thirds of cases. This sample size is too small to support sweeping generalizations of the efficacy of replications in analysis  as part 10.7717/peerj.7654/supp-1Supplemental Information 1Click here for additional data file.