Recent years have led to dramatic progress in both experimental and clinical research. Based on a much better and continuously increasing understanding of disease mechanisms, progression and pathophysiology, new therapies with an improved translational potential to protect tissue either against acute or chronic degeneration and even approaches potentially capable of repairing damaged brain tissue are emerging. Importantly, the field has learned from previous translational setbacks as the internal and external validity of experimental studies are continuously improving. This is paralleled by an increase in the number of clinical trials aimed at establishing new therapeutic approaches.For instance, neuroprotection is currently seeing a renaissance in the areas of stroke and traumatic brain injury research and treatment. The translational failure of early neuroprotective paradigms for stroke which rely on systemic administration of neuroprotectants during acute and subacute stages has been reported and analyzed in detail. Whereas previous preclinical research and the translation of results obtained therein into clinical treatments were often impaired by shortcomings in experimental design, research quality in the field has improved substantially and methodological rigor applied today is outstanding across many fields.Similar progress is reported in other fields. For example, a recent double‐blind and randomized phase II clinical trial in multiple sclerosis (MS) revealed preliminary evidence for a modest yet clinically meaningful therapeutic effect of mesenchymal stem cell (MSC) transplantation.Recent studies have evaluated the therapeutic potential of rasagiline, a monoamine oxidase B inhibitor, regarding its neuroprotective potential in Parkinson's disease (PD) and in amylotrophic lateral sclerosis (ALS). In PD, rasagiline was used as an add‐on to the standard levodopa treatment in a Japanese cohort enrolled into a randomized, double‐blind, placebo‐controlled, Phase II/III clinical trial. Rasagiline reduced OFF‐time and improved symptoms in ON‐time as measured by the Movement Disorder Society‐Unified Parkinson's Disease Rating Scale scores.Over the past decade, we have experienced an acceleration in the development of new classes of therapeutic agents. While the previous wave of neuroprotective agents in the early 2000s was driven mainly by small molecule drugs, we now live in an age of biopharmaceutical drugs that are beginning to dominate the clinical realm, including antibodies, nanobodies, viral vectors, antisense oligonucleotides, or various gene‐editing solutions. Biopharmaceuticals offer an unprecedented sophistication in therapeutic mechanism and specificity. The challenge, however, is their size, which on average exceeds the size of small molecules by at least three orders of magnitude. The blood–brain barrier is a major obstacle and there is still an unmet need to deliver these very large biologics to reach their targets in the brain. To address this, dedicated delivery techniques such as invasive but highly effective convection‐enhanced deliveryIndeed, suboptimal drug access to the brain after systemic administration is believed to be one of the major reasons for the failure of all previous neuroprotective clinical trials for stroke.Neuroprotection.However, the entire field is still at its infancy, and the clinical impact of novel neuroprotective and neurorestorative approaches remains limited and modest. Additional research efforts, both preclinically and clinically, are required to increase this impact and generate strong evidence for the efficacy of new neuroprotective approaches in large‐scale clinical trials. This is likely to come in part from continued back‐translation of what we have learnt clinically as well as future paralleled preclinical and clinical studies to gain better mechanistic insight. Nevertheless, it is not unreasonable to claim that there was rarely a better time to enter the neuroprotection and neurorestoration fields, and to work in translational neuroscience. What is still missing though is a platform to bundle and share the knowledge generated in the field. Cooperating with Wiley, a renowned scientific publisher, and partnering with the Chinese Medical Association we intend to fill this gap by launching the new journal Neuroprotection publishes original research and reviews reporting recent advances and breakthroughs in the fields of neuroprotection and nervous system repair. The journal is not restricted to any particular condition but focuses on the entire spectrum of central and peripheral nervous system diseases. Neuroprotection is an open‐access journal and has a strong interdisciplinary approach including areas such as neurobiology, neuropharmacology, neurology, neurosurgery, neuroimaging, neurorehabilitation, and basic as well as translational neuroscience. The journal's audience, including basic researchers, translational scientists and clinicians, reflects this interdisciplinarity. Neuroprotection is dedicated to a rigorous peer‐review process and outstanding quality of publications from the start. As a welcoming gift to the neuroscience community, but also to facilitate a large number of submissions to select the very best manuscripts for publication, we decided to waive all article processing and publication fees during the first 2 years after the journal's launch. Neuroprotection is now accepting manuscripts, applying a free format submission policy. This means that authors can submit articles in their format of choice, and particular formatting requirements do not need to be met at this stage. This makes the submission process smoother and less time‐consuming. The journal's website can be found at https://onlinelibrary.wiley.com/journal/2770730x.Neuroprotection! We do look forward to your contribution!Please join us on an amazing scientific journey into neuroprotection in research and clinics, and submit your manuscript to All authors listed have made a substantial, direct, and intellectual contribution to the work and approved it for publication.The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Xunming Ji, Piotr Walczak, and Johannes Boltze are Co‐Editors in Chief of Neuroprotection, Shen Li is the journal's executive editor. All other authors are members of the editorial board. They were blinded from reviewing or making decisions on the manuscript. The article was subject to the journal's standard procedures, with peer review handled independently of this Editorial Board member and their research groups. Piotr Walczak is a founder and holds equity IntraArt, LLC. Ti‐com, LLC.This article does not contain any studies with human participants or animals performed by any of the authors.


Plant‐Environment Interactions (P‐EI) is happy to announce a new article category called Methods and Techniques. P‐EI is still a young journal, although we have now published two full volumes (in 2021 and 2022). Over these past 2 years, we have recognized that some submitted studies may not be focused primarily on a research question or hypothesis, but instead they may be describing the invention, development, or improvement of methodological approaches or equipment that can be used to better understand how plants interact with the abiotic and biotic environment. In response to this, in 2023, we will be launching Methods and Techniques as an article category that the authors can choose on submission of their manuscripts.The Editorial Board of Methods and Techniques will be the same as those for research articles, with the same limit on total number of figures and tables combined (maximum of 10). However, the structure of Methods and Techniques does not have to adhere to the traditional Introduction—Methods—Results—Discussion format of research articles. Manuscripts submitted under this new category should still have an abstract and will need to provide evidence that the new methods/equipment work as intended. This evidence can involve comparison with other established approaches, presentation of statistical analyses that quantify precision, accuracy and/or repeatability, and visual aids, depending on the method and its applications. In the interest of transparency and reproducible sound science, we also ask that where new protocols, workflows. or equipment are described, all details are made available at submission that would be needed by a third party to reproduce the method. This may include design plans, programming code, or detailed lab protocols, and these details can be submitted as supplementary materials for review. Finally, as with all other article categories in our journal, Methods and Techniques submissions need to involve interactions between plants and their abiotic or biotic environment for us to consider the submission for publication.The guidelines for preparation of manuscripts to be considered under P‐EI is an ideal venue for publication of studies introducing new or improved methodologies, because there is great potential for those new approaches to reach and be used by a wide range of plant and environmental scientists across the globe. We look forward to receiving and reading your Methods and Techniques submissions soon.As an open‐access journal,


With the rapidly increasing amount of scientific literature, it is getting continuously more difficult for researchers in different disciplines to keep up-to-date with the recent findings in their field of study. Processing scientific articles in an automated fashion has been proposed as a solution to this problem, but the accuracy of such processing remains very poor for extraction tasks beyond the most basic ones (like locating and identifying entities and simple classification based on predefined categories). Few approaches have tried to change how we publish scientific results in the first place, such as by making articles machine-interpretable by expressing them with formal semantics from the start. In the work presented here, we propose a first step in this direction by setting out to demonstrate that we can formally publish high-level scientific claims in formal logic, and publish the results in a special issue of an existing journal. We use the concept and technology of nanopublications for this endeavor, and represent not just the submissions and final papers in this RDF-based format, but also the whole process in between, including reviews, responses, and decisions. We do this by performing a field study with what we call formalization papers, which contribute a novel formalization of a previously published claim. We received 15 submissions from 18 authors, who then went through the whole publication process leading to the publication of their contributions in the special issue. Our evaluation shows the technical and practical feasibility of our approach. The participating authors mostly showed high levels of interest and confidence, and mostly experienced the process as not very difficult, despite the technical nature of the current user interfaces. We believe that these results indicate that it is possible to publish scientific results from different fields with machine-interpretable semantics from the start, which in turn opens countless possibilities to radically improve in the future the effectiveness and efficiency of the scientific endeavor as a whole. Considering the abundance of scientific articles that are published every day , keepinge.g., A range of approaches have been proposed to address some of these problems by making scientific texts machine-readable, allowing for automatic summarising, finding and retrieving information easier and even the ability to  reason on the scientific texts themselves. Text mining approaches work reasonably well when it comes to simple entity extraction with techniques like named-entity recognition to extract the main concepts from a text e.g., , but accgenuine semantic publishing (The vast majority of existing approaches of making scientific texts machine-readable have one thing in common: they take the current paradigm of scientific articles for granted and therefore take them as their starting point to extract information. While it is important to try to process the vast amount of existing scientific literature that has the form of long English texts (and sometimes long texts in other languages), we should also think about how we can improve the way how we publish scientific insights in the first place. An important aspect of this is the vision of semantic publishing, which we mean here in the sense of blishing , where tblishing , which asuper-pattern, a semantic template to represent the meaning of scientific claims in formal logic , that instance of stress has the relation of affecting an instance of Pgp expression. Formally, it directly maps to this logic formula: ciplines .affects-relation holds in the given condition), and does not stand for the certainty or validity of the statement as a whole. Expressing the (un)certainty of the statement can be done with models such as ORCA  at an established publisher (IOS Press). This special issue consists of what we call formalization papers, which are nanopublication-based semantic publications whose novelty lies in the formalization of a previously published scientific claim.In the work to be presented below, the main research goal is to combine all the elements we have previously worked on—namely semantic representation of reviews , scientiIn this research we therefore aim to answer the following research question: •Can nanopublications and the super-pattern enable a new paradigm of scientific communication where authors publish their scientific findings with formal semantics from the start?The rest of this article is structured as follows. In ‘Background’ we describe the current state of the art in the field of scientific publishing with regard to scientific knowledge representation, semantic publishing and semantic articles and also alternative proposed machine-readable approaches like nanopublications. In ‘Methodology’ we describe our approach with regard to a new way of publishing, starting from a formal way of representing the content of scientific claims and ending with the representation of the publication process itself in what we call “formalization papers”. We then report and discuss the results of the field study we performed using formalization papers in ‘Results’. Future work and conclusion of the present research are outlined in ‘Discussion and Conclusion’.We provide here the background on scientific knowledge representation, scientific publishing, nanopublications, and genuine semantic publishing in particular.Novel proposals for the current “Disruption Era”  include A range of methods have been proposed to make scientific articles more machine-readable: from structuring scientific works as Research Objects (RO)  to usinge.g., A significant number of vocabularies and ontologies in many various domains have been developed, which are now ready to be used for scientific knowledge representation. But, even though practical problems like finding, accessing and versioning among other things have been reported , these ve.g., for the representation and discovery of concepts, their relations and associated supporting evidence in order to integrate distributed repositories  , an initTo conclude, apart from very few exceptions such as the work done in the biodiversity data field and the SKGO project, hence on restricted fields and restricted kinds of claims, genuine semantic publishing remains a vision for which we have little practical evidence as of now on how it can work in practice. So, there is still a huge gap with regard to making scientific knowledge machine interpretable, despite all these useful attempts and approaches that aim towards machine interpretability. As such, for a publication to be genuinely semantic, not only the semantic representation from the start of the structure and content of a fine-grained and authentic primary component of a publication entity needs to be considered, but also all the aspects that pertain to its publication. And, as we noticed in the projects mentioned above, the combination of all these requirements together is not present in current research.In this section we describe the approach and methods we followed to investigate whether nanopublications and the super-pattern are suitable to achieve genuine semantic publishing.In our approach, we committed to a number of features. First, we wanted the final contributions to be published as “real” papers in a real established journal. They should be fully semantically represented (in RDF) but also have classical views that makes them look like other papers. Like that, they should also seamlessly integrate with the existing bibliometric system and it should be straightforward to cite them in the classical way.e.g., information about the used methods among many other things, but for the purpose of the study to be presented, we focus only on the main claims.Second, we decided to fully focus on arguably the most interesting element of scientific articles, which happens to also be one of the most challenging to formally represent: the main scientific claims the article is making. Scientific articles have a large number of other interesting pieces of information, Third, in order to retain the flexibility and power of nanopublications, we decided to refrain from providing a custom-built and optimized user interface that hides the complexity and limits the flexibility. By using generic template-based nanopublication tools and by customizing them solely by providing the templates, we hoped to get a better understanding of how the nanopublication technology works for such kinds of content and workflows in general, and not just for our specific case. On the other hand, this also means that we were looking for a bit more technically minded authors who can handle interfaces that do not come with all the comfort of polished specific applications.could be used to publish novel claims, but decided for practical reasons to focus on formalizing claims from previously published articles. Our approach is therefore based on what we call formalization papers that contribute novel formalizations of existing claims.Fourth, we wanted to test a system that Finally, we wanted to cover not just these main claims, but the whole publishing workflow that involves the initial submission of contributions, their reviewing, the responses to the reviews, the updated versions, and the final decision, and represent these as independent but interlinked nanopublications.Our approach builds upon our new concept of formalization papers. A formalization paper contributes a semantic formalization of one of the main claims of an already published scientific article. Its novelty therefore lies solely in the formalization of a claim, not the claim itself. The authors of such formalization papers consequently take credit for the way how the formalization is done, but not for the original claim (unless that claim happens to come from the same authors).e.g., in HTML or PDF, but these are just views of the same underlying RDF content. Our formalization papers consist of nanopublications in which the assertion contains the formalization of the scientific claim using the super-pattern (https://larahack.github.io/linkflows_superpattern/doc/sp/index-en.html). In the process of coming up with such a formalization, one often realizes that for some of the class slots of the super-pattern  the class that should be filled in to arrive at a correct formalization is not directly defined in any existing vocabulary or ontology and as such, this class might need to be minted as well. The provenance part of the nanopublication describes the “formalization activity” that was conducted in order arrive at this formalization from what is written in the source publication. The precise phrase from that source publication that was used can be quoted too.The content of a formalization paper is fully expressed in RDF in the form of nanopublications. Such a formalization paper can be shown in other formats to users, -pattern , the prohttps://github.com/peta-pico/nanobench). In order to publish formalization papers, class definitions, and all the other kinds of nanopublications , we use Nanobench  (https:/https://github.com/peta-pico/tapas) is equally generic. It is a simple user interface component built on top of grlc .The second tool that we are using, Tapas   by IOS Press. The goal of this was to demonstrate for the first time that scientific articles can be formalized and therefore machine-interpretable including the main scientific claims. As a secondary goal, we wanted to find out whether nanopublications are a good technology for that, and whether it is feasible to represent also the entire submission and reviewing process within the same framework.In order to test our approach, we devised a field study where interested authors could submit formalization papers, which upon acceptance are to be published as a special issue in the journal Data Science  using our previously proposed reviewing ontology . Upon acThe authors received close guidance on how to represent a claim of their choosing in RDF using the super-pattern and nanopublications, and on the various stages of the publication process. Authors took part in several information sessions and discussion meetings and were provided at each step with helper materials, videos, and even direct assistance if needed. In total, 24 such individual sessions were organized from May to December 2021.i.e., context, subject, and object slots) of the super-pattern should be filled in with classes that are not yet defined in any existing vocabulary or ontology. In this case the authors first had to define these themselves, and they could do that also with the Nanobench tool loading a template for class definition.  The assertion of a nanopublication defining a new class may look for example as follows (link to full nanopublication):In order to define a formalization, sometimes some of the class slots  is declared as super-class of the newly minted class “STX1B mutation”, and “STX1B” (Q18048867) is linked as a related class.link to full nanopublication):Then the authors can publish their formalization in the form of a nanopublication using Nanobench see , and aft    <http://purl.org/np/RAGo62Hb_Bx1klF4pn1q1Ty40860e3A7Sz4hr2vojZ2wA>     pso:withStatus pso:submitted ;     frbr:partOf fpsi:DataScienceSpecialIssue .    link to full nanopublication):All submitted formalizations were subsequently reviewed. All authors were encouraged to review other submissions, and these reviews were semantic, open, and non-anonymous. These reviews were again done in nanopublications with the Nanobench tool. Such an example of a nanopublication assertion that contains a review modeled using the reviewing ontology can be seen below , it is link to full nanopublication):Subsequently, authors of the submissions could respond to the received review comments, again in nanopublications, and update their submissions based on these review comments. This is an example of a response to a review comment  and if that point was addressed, partially addressed or not addressed at all by the author. Moreover, a link to the respective review is given using the link to full nanopublication):Finally, the authors updated their formalizations with the same template as depicted in     <http://purl.org/np/RAeRSya2qIYymsBxiqOZP_oaQpHXUVXiydKvPCFM-7DDQ>     dct:description "All review comments were addressed and the formalization looks                      good." ;     pso:withStatus pso:accepted-for-publication ;     frbr:partOf fpsi:DataScienceSpecialIssue .    All formalizations reached a satisfactory level of quality, as indicated by the reviews and the authors’ responses, and we therefore accepted all 15 submissions for publication.In order to show the accepted papers in the special issue as if they were classical papers, to integrate them in the publisher’s content management system, and to make them connect to the existing bibliometric system, we semi-automatically created “classical views” in the form of HTML and PDF versions of the nanopublications, as can be seen in In order to evaluate the general idea of formalization papers, all participants to the field study were asked to give us their opinion and report on their experiences about the involved processes and concepts. This evaluation was performed by means of a structured questionnaire consisting of four main parts, each one evaluating different aspects of the workflow.In the first part, we are interested in assessing the difficulty of conceptually understanding the formalization paper idea and the super-pattern, and of performing the formalization tasks. In part two, we focus on the difficulty of the technical aspects in the various submission, reviewing and revision stages. Part three addresses some more general aspects about the authors’ experience and preferences. Authors were asked about their confidence in the formalization they published and about their interest of publishing such formalizations along their scientific publications in the future. We also asked them how important they think it is that all these steps are performed by the authors themselves (as they did). Moreover, in this part, authors could give us their opinion with regard to the importance of having a “classical view” along with the nanopublication representation of their formalization paper. The fourth and final part of the questionnaire asked for the technical background of the authors. At the very end, the respondents could give further free-text feedback. The full questionnaire is available in our In this section we present the formalizations that resulted from our field study. We present a descriptive analysis of the generated data and analyze it also with the help of a network visualization. Finally, we report on the results from the user feedback questionnaire.https://github.com/LaraHack/formalization_papers_supplemental/tree/main/nanopubs), while the nanopublication index containing all these nanopublications has also been published (Nanopublication index: http://purl.org/np/RAkLJW7vIsnKKJDf1iswdgtFPQSo3lEG_z8DhHfD7dofE). Also, the final submissions for the special issue with formalization papers at the Data Science journal that was released in March 2022  can be found online .All the nanopublications that were created for all the submissions, formalization paper versions, the review comments, the responses to the review comments and the newly minted classes used in the formalizations together with the decisions are accessible online  from 12 different institutions from the United States of America, Germany, Luxembourg, Bulgaria, and The Netherlands from fields like biomedicine, bioinformatics, health sciences, ecology, data science, and computer science. After an initial information session, out of the 20 authors that responded to the call for papers, 18 decided to continue their participation. All these 18 authors that responded to the call for formalization papers managed in the end to publish (upon acceptance) their articles in a special issue at the Data Science journal.In total, we had an initial number of 20 people that replied to our call for articles  and made available online after serialization in trig files .In this field experiment we used nanopublications to embed, not only the formalizations created, but also the entire publication process that these formalizations underwent. As such, the entire formalization papers creation and publication process was thoroughly documented and published in a formal and machine-interpretable way, made possible by making use of nanopublications as “FAIR data containers”. All the nanopublications pertaining to the special issue with formalization papers at the Data Science journal have been retrieved from the nanopublication network  of the graph indicate when a nanopublication is referring to another one by using its identifier in the assertion. The edges shown in red are superseding relations, pointing from a new version of a nanopublication to its previous version. This is how nanopublications, being immutable, are dealing with representing new versions.In The 18 authors and co-authors of the formalization papers were asked to fill in the user feedback questionnaire. It was important for this questionnaire to be fully and reliably anonymous, as the authors needed to be able to give their honest opinions. This meant that we had to send reminders without knowing who already filled it in. After several rounds of reminders, we ended up getting 19 responses, meaning that at least one of the authors submitted two responses. Due to the anonymous nature of this questionnaire, it was not possible find out which responses were affected, and we have therefore to deal with such a dataset of slightly imperfect representation.very difficult and very easy. These results seem to suggest that the authors were able to understand the main formalization papers idea together with the super-pattern that comprises it, but when it came to the actual instantiation of the super-pattern , this was considered a little more difficult, but still on average far from very difficult.In In The authors indicated that they have, on average, a high level of knowledge on the topics of knowledge representation, knowledge graphs, Linked Data, and ontologies/vocabularies, with scores from 3.89 to 4.00. Their background in nanopublications, formal logic, and programming languages was significantly lower, on average, but still relatively high, with scores between 3.05 and 3.47.A total of 10 out of the 18 authors used the free text feedback of the questionnaire. Eight of these 10 respondents expressed their excitement about the field study and found the formalization paper concept and the whole publication process interesting and useful. However, half of these respondents also mentioned that the overall process proved to be a little more difficult than they expected, due to the tools used maybe being too technical. One author also pointed out that multiple formalizations can be written for the same claim by choosing the context, subject and object classes differently and expressed the worry that this would decrease the interoperatibility or utility of formalizations especially when aggregating or mining them. This is a reasonable point to make, but due to the fully formal semantics, syntactic differences are in principle not hindering this kind of interoperability. Overall, the super-pattern, the formalization paper concept, and the nanopublication-based publication workflow seem to have been well-accepted and understood by the participants, and many of them showed an enthusiastic reaction.The publication of the special issue with formalization papers at the Data Science journal shows not only that nanopublications and the super-pattern can be used to implement the basic steps and entities of a journal workflow, but also that authors of such formalization papers can be taught to use these in order to publish in a novel journal publication workflow as the publication of the special issue demonstrates. Our results show that the super-pattern can be well understood conceptually and despite the fact that from a practical standpoint applying it seems to be more difficult, its application remains perfectly feasible. Furthermore, we saw in our field study that even if the current general-purpose tools can be considered a viable solution, these are not necessarily easy to use, but they still remain a good tool for the purpose of publishing formalization papers. Moreover, considering the formalization papers, authors seem confident with regard to the quality of their publications and seem interested in publishing such formalizations in the future.In future work, we plan to take the next logical step by publishing novel claims in this way from the start, and not depend on claims from already-published papers. These contributions will then also have to be accompanied by statements about the methods, equipment, and all other relevant scientific concepts, and can include not just the high-level claim but more lower-level ones, possibly all the way down to the raw data. This representation would then ideally cover the entire scientific workflow, starting from a motivation, leading to the design and execution of a study, and ending in new scientific insights. Such fully formalized scientific contributions can be seen as a major step—even a breakthrough—for the Semantic Web and Open Science movements and will bring us closer to a world where machines can interpret scientific knowledge and help us organize and understand it in a reliable and transparent manner.10.7717/peerj-cs.1159/supp-1Supplemental Information 1https://github.com/LaraHack/fpsi_analyticsThis repository contains data and code (SPARQL queries and scripting) to extract the published formalization articles (in the form of nanopublications) from the nanopublication decentralized network. It also contains the scripts made for the automatic visualization of these nanopublications in the form of a graph and a script to create the index for these nanopublications.These formalization articles will be published in the IOS Press journal Data Science, in a special issue with formalization articles in late March 2022. See Click here for additional data file.10.7717/peerj-cs.1159/supp-2Supplemental Information 2Click here for additional data file.


Radiologia Brasileira(RB), the official scientific publication of the Brazilian Collegeof Radiology and Diagnostic Imaging, was established as one of the most importantmedical imaging journals of Latin America.Since its first issue in 1958, RB . Despite his busy academic schedule, Professor Marchiori dedicated his heart andsoul to ensure the progress of this journal. In the past decade, RBexperienced unprecedent advances in editorial office organization as well as in theindexation database, as mentioned by him in the last editorial.This successful history is the result of more than six decades of contributions by manypeople, including the authors, reviewers, editorial office members, and editors. It isundeniable, though, that much of this trajectory can be directly linked to theleadership of Professor Edson Marchiori who was the Editor-in-Chief ofRB. As an academicradiologist, I have been a member of the editorial boards of several of the majorinternational radiological journals, and have served as an associated editor ofRB for five years. These past experiences prepared me for this newrole, and I am looking forward to working with and for the Brazilian radiologycommunity.I’m honored to serve as the next Editor-in-Chief of RB but also ofradiology practice in Brazil. RB articles are reviewed, edited, andpublished within the planned timeframe, following the highest ethical standards andguaranteeing scientific integrity. Personally, I have no words to express how grateful Iam for his patience and willingness to mentor me all these years on theRB Editorial Board. These are big shoes to fill!First, though, I must express the gratitude of the entire radiological community inBrazil to Professor Marchiori for the tremendous accomplishments during his tenure,which contributed to elevating not only the quality of There are challenges ahead, and now it is time to face them. It is essential to mentiontwo herein.RB in the Web of Sciencedatabase . This is arguably the most relevantindexation process for a scientific journal. It is from the Web of Science that theJournal Citation Reports (JCR) is derived, along with the journal’s impactfactor. The indexation formwas filled in late June 2022 and it is currently being evaluated by the ClarivateAnalytics team.The first is to complete the indexation of RB intends to be a platform for disseminatinghigh-quality and practical knowledge. For accomplishing this goal, we must providestate-of-art evidence-based articles with a focus on best practices in radiology, e.g.critical reviews and, occasionally, illustrated pictorial articles. At the same time,RB is committed to disseminating new science through originalarticles. New scientific content will continue to be our focus, and manuscripts will beassessed and curated under the highest scientific standards to ensure a fair peer reviewprocess. We must emphasize the importance of the contributing authors for a scientificpublication, as they are the main supporters of any journal. To meet our authors’expectations, RB is continuously working to improve the editorialprocess to provide a quick and accurate response to all submissions, ultimatelyshortening the time interval between the submission and publication.Equally important is the need to strengthen the relationship with our target audience,readers and authors. The RB editorial office to ourreviewers, many of whom have selflessly served our society for many years. I would alsolike to take this opportunity to encourage young researchers who might be interested injoining our group as RB reviewers to apply by e-mail(radiologiabrasileira@cbr.org.br) stating their field of interest andincluding an abbreviated curriculum vitae.The peer-review process must be fair and consistently demonstrate high quality to attractthe best manuscripts and meet authors’ expectations. Needless to say, this is anenormous job that requires time and dedication. Therefore, I would like to express inthis editorial the gratitude of the whole RB to maintain the trajectory of a high-quality, peer-reviewed,international, and open-access publication, committed to improving science and the bestpractices in radiology, always with a patient-driven focus.In conclusion, I am committed, along with the entire new Editorial Board of


The ethics of generative artificial intelligence (AI) use in scientific manuscript content creation has become a serious matter of concern in the scientific publishing community. Generative AI has computationally become capable of elaborating research questions; refining programming code; generating text in scientific language; and generating images, graphics, or figures. However, this technology should be used with caution. In this editorial, we outline the current state of editorial policies on generative AI or chatbot use in authorship, peer review, and editorial processing of scientific and scholarly manuscripts. Additionally, we provide JMIR Publications’ editorial policies on these issues. We further detail JMIR Publications’ approach to the applications of AI in the editorial process for manuscripts in review in a JMIR Publications journal. Technology tools are useful for making the scientific writing process more timely and effective. Many advances have been made in terms of the tools available to help conduct more sophisticated statistical analysis, manage references, and check grammar. Among these advances, large language model (LLMs) are neural networks trained on large corpora of textual information that can be fine-tuned to respond to natural language queries in a conversational fashion. In late 2022, OpenAI released ChatGPT, an artificial intelligence (AI) chatbot  that useJournal of Medical Internet Research showed that ChatGPT was able to generate a highly convincing, fraudulent scientific manuscript article in approximately 1 hour [The ethics of generative AI use in scientific manuscript content creation has become a serious matter of concern in the scientific publishing community ,3. More y 1 hour . The autFor authors of academic manuscripts, key issues of concern include the need to fact-check AI-generated content of any form ; assign accountability for AI-generated information; and disclose transparently the use of generative AI in producing any scholarly or scientific work, especially when it impacts the meaning and content of the information submitted for potential publication . For peeIn this editorial, we outline the current state of editorial policies on generative AI or chatbot use in authorship, peer review, and editorial processing of scientific and scholarly manuscripts. Additionally, we provide JMIR Publications’ editorial policies on these issues, with the goal of ensuring the integrity of the science published and the publishing process. We further detail JMIR Publications’ approach to the applications of AI in the editorial process for manuscripts in review in a JMIR Publications journal.Recommendations on Chatbots and Generative Artificial Intelligence in Relation to Scholarly Publication that “Chatbots cannot be authors” [In scientific publishing, there is already historical precedent that the transparency of authorship is essential to the integrity of scientific publication . Regardiauthors” . One exaauthors”  noted thauthors” . Unfortuauthors” .Journal of Medical Internet Research, which now has a section on generative language models (including ChatGPT), where it may be appropriate to submit work that uses such technology as a core component of the work , then providing acknowledgment of the use of generative AI in writing or creating text, figures, or other content for scientific publication is required -19. We wthe work . If an aSuch acknowledgements must be fully transparent, precise, and complete throughout the submission, editorial, and production processes and will be disclosed upon the publication of a manuscript, if accepted for publication after the disclosure has been provided . In addiunintentional plagiarism (because the AI may not be able to properly source or cite literature) [AI plagiarism (the authors passing off or taking credit for the production of statements that were generated by AI). Either form of plagiarism is deemed not acceptable and would be examined carefully in accordance with COPE guidance [Authors must also be cautious of the use of generative AI because of its predispositions to hallucination information and references -22. Becaerature)  or overtguidance . Authorsguidance . FurtherJMIR Preprints [For peer reviewers, JMIR Publications adheres to expectations similar to that for authors: specifically, peer reviewers are accountable for the content of AI-generated comments submitted in a peer review. Consequently, peer reviewers are strongly advised to still ensure that the quality and content of the peer review meet the recommended standards described elsewhere in JMIR Publications policies . Howeverreprints ), informreprints . HoweverIn addition to accountability and confidentiality, transparency is essential to ensure the integrity of the peer review process. Agencies such as the US National Institutes of Health (NIH) have issued clear guidance that the use of AI in assisting a review with the grant peer review process is prohibited due to a breach of their confidentiality and nondisclosure agreements . Some puAt JMIR Publications, we adhere to this guidance of transparency and disclosure; we do not endorse a ban on generative AI in peer review, which can be counterproductive in various ways ,35. Peernot permit the use of the free version of ChatGPT for assisting with peer review comment generation.Importantly, when peer reviewers use generative AI to support their peer review, they are accountable to ensuring the confidentiality of the peer review process. Detailed and careful review of the terms of use of any generative AI is strongly advised, if not required. Furthermore, if the peer reviewer has any doubts about potential information leakage after a careful review of the terms of use of a generative AI tool, then they should not engage in its use for this task. For example, in the free version of Open AI’s ChatGPT, their March 14, 2023, Terms of Use  do not enot permit the use of the free version of Claude for assisting with peer review comment generation.In another example, Anthropic’s Claude also has clearly stated language in their July 8, 2023, Terms of Service : “You rePeer reviewers for JMIR Publications journals are advised to carefully review the content of the Peer Reviewer Hub for guidance , includiAI is already in use by some publishers, as an attempt to optimize the editorial workflow. For instance, some publishers have publicly available tools where the authors can add the title, keywords, and abstract of their manuscript, and the AI tool will list the journals that this work is more suitable for. This approach could be time-saving for both the editors and the authors.Similar to peer reviewers and authors, editors evaluating and issuing decisions about manuscripts are accountable for the content of their decisions and the final decision on the manuscript, whether it is accepted or rejected . This inWhen editors evaluate peer reviews of a manuscript that they are assigned to, the editor should follow JMIR Publications policies in evaluating the quality, validity, relevance, and professional language use of a peer review. In a recommendation from the WAME, similar to peer reviewers, editors are also accountable for the generated content, the transparency of the disclosure of use, and maintaining confidentiality during the peer review process . RoutineThe accountability of parties using generative AI, transparency regarding complete disclosure, and the maintenance of confidentiality are fundamental in maintaining the integrity of the scientific record and are key components of JMIR Publications’ editorial policies. Because of the rapidly evolving nature of AI technologies, related policies, regulations , investi


Over the course of civilization, humans have increasingly expanded their freedom to live a better life. In comparison with the primitive society, our modern society has many more choices of life-supporting resources, such as year-round food supply, permanent shelters, diverse energy sources, and effective preventive and curing medicine. However, our society is currently still heavily relying on the resources provided by Mother Nature, which cannot meet the future global needs in terms of both quantity and quality under the pressure of population growth, natural resource reduction, and environmental deterioration. For example, the food sources originating from plants, animals, or microbes do not have the nutrition balance for optimal human health –3. ClBiodesign in living organisms deals with the structure of the particular organism and the interactions between the biomolecules encoded in their genomes. In the broadest sense, biodesign is concerned with the nature and properties of the information required to create biological behavior at the ecological, organism, cellular, organelle, and molecular levels and how biological systems interface with the environment and devices. The explosion of omics data , the rapid advance in computational modeling and machine learning, the reduced cost of omics data generation and analysis and DNA/RNA and protein synthesis, and the disruptive genome editing technology based on CRISPR-  Cas (CRISPR-associated) systems have accelerated the evolution of biodesign as a next-generation discipline of biology, as best reflected by a rapid increase in the number of publications related to biodesign since a decade ago Figure. As a cWith unlimited potential in fundamental research, broad practical applications, and ever-increasing amount of R&D funding support from government agencies, industries, and government/industry consortia around the world, biodesign is growing into a new interdisciplinary field that integrates a wide range of research areas, including molecular biology, genetics, biochemistry, genomics, chemical engineering, computational biology, bioinformatics, synthetic biology, systems biology, physiology, ecology, breeding, medical science, animal science, microbiology, crop science, horticulture, and forestry. To embrace the promise of this fast-growing research discipline, this journal was launched to advance both fundamental and applied research, foster multidisciplinary collaboration, and promote dissemination of scientific information and knowledge in the field of biosystems design. This new journal will emphasize the rational or automated design of engineered organisms to address global challenges in health, agriculture, bioenergy, and the environment. It will promote research, with the increasing sophistication and greater social responsibility, on the predictable conduct of (1) engineered biological parts in an exogenous genomic context, (2) engineered part assemblies  in an exogenous compartment context, (3) engineered assemblies in an exogenous cell, (4) engineered cells in an exogenous tissue, and (5) engineered tissues in an exogenous organism.de novoorganism biodesign; and (3) social responsibility dimension: biodesign security and ethics  scientific dimension: biodesign theory, principles, methodology, tools, and applications; 2) organismal dimension: animal, human, microbial, plant, and organismAs a vigorously peer-reviewed, open-access online-only journal, it is dedicated to rapid, efficient, and free worldwide dissemination of scientific discoveries, technological advancements, and social responsibilities in the format of research articles, reviews, editorials, and perspectives. We are honored and humbled to serve the biodesign community as the founding editors-in-chief and executive editor and are extremely grateful to highly reputable experts to serve as associate editors. This journal welcomes high-quality manuscripts from researchers around the world. We hope that this journal will grow fast and healthy to become a leading journal in the field of biodesign through collective efforts of the editorial board, authors, reviewers, and readers.


I would like to thank the authors for their commentary on the publication “ChatGPT Utility in Healthcare Education, Research, and Practice: Systematic Review on the Promising Perspectives and Valid Concerns” ,2. I valAs highlighted in the review and the commentary, the significance of AI, particularly large language models (LLMs) like ChatGPT, in healthcare education, research, and practice cannot be understated . TherefoRegarding the concerns raised in the commentary, I fully acknowledge the potential limitations of the review, which stem from the methodology used for the systematic search and the inclusion of various types of research records , as well as from the evolving nature of the research subject with subsequent inherent challenge in accurate assessment of the long-term impact of LLMs. Additionally, I would like to highlight that the necessity for further elaboration on the review limitations was raised and addressed during the peer review process, including the issues of single authorship, absence of quality assessment of the included records, and the rapid evolution of the research subject. These issues were missing from the initial preprint and were included in the final published form of the review ,7. FurthWhile I hold the PROSPERO registration in high regard as a valuable component of systematic reviews, it is pertinent to acknowledge that the nature of the review did not involve human subjects, thus rendering PROSPERO registration non-mandatory in this particular context ,10. Addihttps://pubmed.ncbi.nlm.nih.gov/?term=chatgpt&size=200, accessed on 19 October 2023). Given this context, a focused search term would yield the most relevant and comprehensive results for the specific review objectives in line with the PRISMA guidelines. The comprehensiveness of the review was also the basis for the inclusion of various types of content . Additionally, the use of Google Scholar besides PubMed, given its rapid comprehensive indexing of a wide range of scholarly and non-scholarly literature, ensured that the likelihood of missing relevant references would be negligible [Contrary to the commentary’s claim, the search strategy employed was meticulously outlined in the published manuscript . The spegligible .The issue of missing a priori qualitative analysis methodology in the review should be interpreted in light of the review’s focus on ChatGPT’s implications rather than methodological intricacies. Thus, a broad categorization of ChatGPT’s implications in healthcare was considered in order not to miss important peculiar observations of ChatGPT’s benefits/concerns in the included records. Thus, it is important to contextualize this consideration within the specific objectives of the review.Two important points that appear to be overlooked in the commentary are related to the publication comprising me as a single author and the absence of quality assessment of the included records. These issues were addressed during the peer review process and were also mentioned explicitly in the limitations sub-section of the publication, as mentioned earlier in this letter .While I recognize the essential role of post-publication scholarly critique, I firmly believe that such exchanges should adhere to the highest standards of accuracy and respect for context . In lighNevertheless, I have to re-emphasize that I truly acknowledge the role of scholarly collaboration, which undoubtedly enriches research, and this will be considered in my future work.Finally, I have to acknowledge that it is my sincere belief that academic discourse thrives on constructive engagement. Therefore, I would like to thank the authors of the commentary for their notable level of interest in the review, which signifies the scholarly relevance and potential real-world implications of its findings.


Early in the pandemic, pre-print servers sped rapid evidence sharing. A collaborative of major medical journals supported their use to ensure equitable access to scientific advancements. In the intervening three years, we have made major advancements in the prevention and treatment of COVID-19 and learned about the benefits and limitations of pre-prints as a mechanism for sharing and disseminating scientific knowledge.Pre-prints increase attention, citations, and ultimately impact policy, often before findings are verified. Evidence suggests that pre-prints have more spin relative to peer-reviewed publications. Clinical trial findings posted on pre-print servers do not change substantially following peer-review, but other study types  often undergo substantial revision or are never published.Nuanced policies about sharing results are needed to balance rapid implementation of true and important advancements with accuracy. Policies recommending immediate posting of COVID-19-related research should be re-evaluated, and standards for evaluation and sharing of unverified studies should be developed. These may include specifications about what information is included in pre-prints and requirements for certain data quality standards ; requirements for code release and sharing; and limiting early postings to methods, results, and limitations sections.Academic publishing needs to innovate and improve, but assessments of evidence quality remains a critical part of the scientific discovery and dissemination process. Throughout the COVID-19 pandemic, dramatic press headlines about new pandemic “discoveries” related to the novel virus have driven practice carried out by clinicians, fear experienced by the public, and sometimes policy enacted by public health and governmental authorities. For the first time on a large scale, reports of scientific findings were commonly disseminated based on information gleaned from unpublished observational, laboratory, and modeling studies posted on pre-print servers without vetting or substantive quality evaluations.Early in the pandemic, pre-print servers played an important role in speeding the rapid dissemination of evidence and allowed for widespread access to findings by the public and those without access to published articles behind a paywall. Recognizing the importance of emerging research to guide practice, a collaborative of major medical journals supported the use of pre-print servers to ensure equitable access to scientific advancements. should the practice of sharing and disseminating these unvetted studies continue? Will pre-prints be one of the pandemic innovations that stands the test of time? If so, how does the pre-print process need to evolve to safely support clinical advancements?Now that the WHO has declared the end of the COVID-19 public health emergency,Preprint servers are sites where authors can post their scientific papers prior to submission, review, or acceptance in a traditional journal Fig. . They exAs the year 2020 dawned, the established mechanisms by which research findings are made available were too slow to keep pace with the needs of the healthcare and scientific communities. Even for studies that go on to be accepted, the editorial process for publication in a peer reviewed journal, which includes multiple reviews and revisions, easily takes many months, and sometimes more than a year. Clearly, with a deadly and unknown disease ravaging the globe, and new discoveries being made every day, business as usual would have been inadequate and inappropriate. The pre-print servers offered a solution to these problems.For the first time, pre-print servers became important sources of medical information, with the papers therein amplified in traditional and non-traditional news outlets and even included in deliberations about important public health decisions, like school policy, mask mandates, and vaccine recommendations. Studies posted on pre-print servers impacted citation and alt-metric scores—two measures of research impact—and some had substantial impacts on clinical care decisions and policy without high-quality—or occasionally even verified—data to back up their claims.There are a number of benefits associated with posting manuscripts to pre-print servers prior to publication, including (1) the findings are immediately widely available for viewing and citing and, unlike many journal sites, without a pay wall; (2) feedback received from the research community and (unlike what scientists might otherwise get when they present their work at conferences) the general public can be used to improve the quality of the manuscript prior to submission to journals and/or during the revision process; (3) leveraging the timestamp on the posting can avoid disputes about originality of research or the timing of findings compared to that of other researchers, and (4) because the sites include information about version numbers and revisions, they can serve as a mechanism for promoting transparency and accountability. As noted above, authors benefit from increased visibility and alt-metric scores, which are a measure of publication impact. Researchers can also benefit by using pre-print servers as a mechanism for sharing preliminary research findings used to support grant proposals. However, the same cannot be said for other study designs, or for clinical trial results that never go on to get published. A recent study found that one in five randomized controlled trials remained unpublished 12 months after posting, and those that were not published were less complete and more highly spun than those that had undergone the peer review process and were ultimately published in a journal. Findings are even more stark for other study designs. Although published literature on the topic is inconsistent, estimates are that only approximately two-thirds of pre-prints go on to get published of these, about 17% undergo major changes during the revision process, meaning that almost half of the papers posted to pre-print servers are either changed substantially or never make it through peer-review.Although dissemination of COVID-19-related research through pre-prints was widely accepted and adopted before major therapeutic and preventative milestones were reached, the approach has many limitations, which have important implications for public health and science communication. Quality checks are limited, and there is no standardized process for ensuring accuracy. Among clinical trials that are ultimately published, findings do not change substantially following peer-review, although presentation of results tends to be more complete and with less perceived spin. Disclaimers are insufficient to overcome this basic human instinct. Many early reports are later debunked by better quality research, and promising interventions tested in laboratory or modeling settings often are found to be ineffective when tested in human populations. This tension is amplified because laboratory, modeling, and simulation studies are inherently faster to conduct. Human subjects are protected, drugs are regulated before they can be tested, and recruitment, outcomes assessments, and data analysis all take time.Anchoring bias is a well-described concept in psychology and refers to the strong tendency of humans to weight the first piece of information they receive more heavily than future information.Once data are available, findings and early presentations are widely shared on social and traditional media outlets, impacting perceptions and, at times, policy-making decisions. Pre-print servers do not create these information dissemination problems, but they do accelerate them. Thus, even updated policy about the use of pre-print servers is unlikely to be sufficient on its own to change the problems posed by factors inherent to the speed of the scientific discovery process or to how data are shared and discussed in public forums. Effects were strongest early in the pandemic, when there were few treatment options, and waned as time went on. Studies on the efficacy of the bivalent COVID-19 vaccine in human subjects have been presented at regulatory meetings before peer review, allowing for expedited authorization and guideline development, potentially benefiting society by reducing delays. On the other hand, even after a pre-print purportedly demonstrating efficacy was withdrawn from the server due to serious ethical infractions, ivermectin has continued to be prescribed despite a preponderance of evidence demonstrating lack of efficacy. Other examples of practice changes driven by early studies with major limitations include “gaiter-gate”. Despite rapidly available contradictory evidence, the damage was done. Gaiters were widely banned in schools based on an early report that they were inferior to other cloth masks and subsequent dissemination via traditional and social media sources. In another example, a research group using publicly available CDC data published a pre-print in May 2022 that calculated that COVID-19 was the 4th highest cause of death in children under the age of 19. This analysis was shared in both the FDA’s VRBPAC meeting and the CDC’s ACIP meeting to inform discussion about COVID-19 vaccination policy for children. Findings were also widely shared in traditional and social media outlets. A revised version of the pre-print, however, listed COVID-19 as the 7th highest cause of death, and in the final publication, COVID-19 was calculated to be the 8th highest cause of death. During the revision process, the estimated crude mortality rate of COVID-19 for children changed quite dramatically, from 7.2 down to 1.0 per 100,000 from the first version of the pre-print to the final, peer-reviewed published version of the manuscript.These concerns are not just theoretical but supported by empirical evidence. Likely driven in part by anchoring bias, despite these well-documented limitations of different study designs and analyses, by the time contradictory or higher-quality evidence became available, the first report has already made its lasting mark. For example, a study by one of the authors (WBE) measured the speed and scope of COVID-19 prescribing practices in the Veterans Health System and found that practice patterns changed rapidly after data release via pre-print servers and press releases, with limited additional change after peer-reviewed publication. First, given the aforementioned data demonstrating that one of the biggest impacts of peer-review is to change framing and reduce spin, a pre-print policy change that could be trialed is presentation of methods, results, and limitations sections only without background and discussion sections, which are fundamentally more prone to personal opinion and political viewpoints. Another possibility is for pre-print servers to be re-organized, such that limitations are a required element that are presented before the results section. This would ensure that limitations are highlighted so that the public can view and comment on them; reading limitations first might also change the reader’s perceptions about the implications of the results, partially (if not completely) addressing anchoring bias tendencies. Additional requirements for quality checks and release of underlying methodology  would also be options for improving pre-print transparency and evaluations. Development and application of advanced technology to identify falsified images, calculation errors, and plagiarism are additional considerations that should be considered, supported, and evaluated to improve evidence quality.Recognizing the limitations of pre-prints, their benefits, and their real-world impacts raises important questions about how the use of pre-print servers for disseminating medical evidence should evolve as we move into the next phase of living with COVID-19 (Table The influence of pre-prints has not occurred in a vacuum. They are one piece of the puzzle and changes at many levels of the system are needed to improve data dissemination. Before pre-prints are widely shared by influencers, covered by the media, and communicated to the public as “truth,” uncertainty about the study’s eventual conclusions and implications of the work needs to be acknowledged by those who are responsible for sharing and spreading the information. Peer review is slow, biased, and often does not lead to major changes even when they are needed, as occurred with the Surgisphere debacle, in which the underlying data supporting the harms of hydroxychloroquine for COVID-19 treatment could not be verified. For topics of critical public health importance, rapid review pathways should be adopted to ensure that data from high-quality randomized controlled trials are quickly available to inform clinical care decisions. Peer-reviewed manuscripts in traditional journals should be readily available and accessible without a subscription, and access needs to be expanded; Plan S in Europe and the White House Office of Science and Technology policy on free, immediate, and equitable access are important policy changes aimed to address these barriers. Open access should be the standard, and The Journal of the American Medical Association took big steps in this direction in December 2022. The National Library of Medicine could require indexed journals to, at a minimum, make methods, results, and limitations openly accessible to the public and set quality standards to encourage expansion of open-access models.Although pre-prints in their current iteration may not be the ultimate solution, innovation in medical publishing and dissemination of research findings is badly needed. Academic publishing is strongly biased toward publishing papers—and questioning findings less—if authored by those who are already “famous.”quid pro quo. However, given the rise of for-profit journals and major publishing enterprises, some of which boast profit margins higher than those of Apple or Google, due in part to the free labor and expertise provided by reviewers—the compensation structure, or lack thereof, needs reevaluation. However, despite all of these caveats and limitations, recent data suggest that the speed and quality of peer review may actually have increased during the pandemic.The financial incentives of academic publishing also inherently create challenges. Academic journals rely on the donated time of unpaid reviewers, which may limit review quality. Journals requesting peer-review are asking for time and expertise—things that outside of academia are always compensated. The practice of donated reviews may be defensible for society journals that do not have publication fees and therefore providing an expert review free-of-charge is a What is the best path forward? Evidence of quality and our willingness to act upon findings need to be balanced Table . Data frMainstream and social media outlets should wait for observational and laboratory-based research to undergo a vetting process. Denise-Marie Ordway wrote in The Journalist’s Resource in April 2020 that there are 6 things journalists must know before covering biomedical research pre-prints about COVID-19:Policies recommending immediate posting of COVID-19-related research should be re-considered—case reports, observational, and modeling studies should be made publicly and freely available after an evaluation process and with quality standards. Academic publishing needs to innovate and improve—but evidence of quality assessments remain a critical part of the scientific discovery process. We need to take a step back and digest the data before it is disseminated and implemented. To achieve real improvement, we also need to re-think how and when information is shared.


Getting to a net-zero emissions economy requires faster development and diffusion of novel clean energy technologies. We exploit a rare natural experiment to study the impact of an open-access mandate on the diffusion of scientific research into patented technologies. From 2014 onwards, the U.S. Department of Energy (DOE) required its 17 National Laboratories (NLs) to publish all peer-reviewed scientific articles without a paywall. Using data from more than 300,000 scientific publications between 2012 and 2018, we show that scientific articles subject to the mandate were used on average 42% more in patents, despite embargo periods of up to 12 months. We also show that articles subject to the mandate were not cited more frequently by other academic articles. Our findings suggest that the mandate primarily contributed to technological development but has not led to additional academic research. Lastly, we show that small firms were the primary beneficiaries of the increased diffusion of scientific knowledge.  •We examine the impact of the U.S. Department of Energy’s open-access mandate•Scientific articles subject to the mandate were utilized on average 42% more in patents•Articles subject to the mandate were not cited more frequently by other academic papers•Small firms were the primary beneficiaries of the increased knowledge diffusion Social sciences; Research methodology social science Achieving net-zero emissions by the second half of this century as envisaged by the Paris AgreementFor inventors, the importance of accessing scientific literature has grown over time as scientific research is playing an increasingly critical role in shaping technological progress. The share of U.S. patents reliant on federally funded science has increased steadily over the last century, with nearly one-third of patented inventions in the United States (U.S.) citing federally funded science since the 2000s. In the U.S., federal agencies play a key role in funding and conducting scientific research like the federal executive departments , the National Science Foundation, and NASA.,Over the past five years, several universities and other public research institutions ranging from the University of California to the Max Planck Institute have voiced increasing discontent with the subscription-based system adopted by most academic journals. Reasons for this resistance include perceptions of unfair pricing and the assertion that the results of publicly funded science should be available to the public.,,,As scientific journals provide a central diffusion pathway of scientific knowledge to firms,st of October 2014.We exploit a rare natural experiment to study the impact of the increased availability of scientific research on the diffusion of scientific knowledge into patented technologies. The U.S. DOE mandated that all scientific, peer-reviewed articles resulting from its 17 NLs must be made available without a paywall within a year if published on or after the 1The mandate allows us to study three interrelated questions. First, we analyze how NL researchers changed their publication strategy based on the mandate. If researchers choose to deposit accepted manuscripts in free repositories, many journals impose an embargo period, which is the time lag before it can be made publicly available in a repository. In our sample, 11 out of 16 paywalled journals had embargo periods of at least 6 months, thereby increasing access hurdles to the diffusion of research. If researchers pay for gold open access, this could divert funds away from key research activities as open access fees of 10,000 USD per article are not unusual.Second, we analyze whether treated articles  were used more in other scientific articles and patented technologies. We investigate whether articles subject to the mandate were cited more by other academic research and patents . Lastly, we investigate whether the mandate primarily helped those firms with historically low access to scientific research .Exploring whether small firms are affected by the mandate is critical for several reasons. Research scientists at universities or large, R&D-intensive firms typically have a greater awareness, access, and ability to effectively exploit scientific knowledge originating outside of their direct research vicinity. In contrast, non-academic professionals and small-and-medium-sized enterprises (SMEs) are more likely to struggle with effective knowledge exploitation. Ware and Monkman,To explore the effect of this mandate, we first build a unique dataset of more than 300,000 scientific articles from the top 20 journals (in terms of the number of DOE-funded publications) in which DOE-funded research has appeared according to the DOE’s own PAGES database. We then check for each article whether it is available without a paywall,The public sector in the U.S. plays a distinct role in advancing innovation, particularly through different ways of funding research and development (R&D) activities.Reviews of the NL’s performance have highlighted several areas of weak organizational design, specifically on technology transfer. Most troubling is the declining engagement with the private sector, which ultimately must adopt, develop, and deploy the energy technologies invented with public R&D. Anadon et al.OSTI.GOV within 12 months after publication in a journal.”A potential avenue to increase the uptake of scientific advances in the private sector is to lower access costs. The DOE’s OA mandate is part of a larger plan by the U.S. federal government to increase access to federally funded science. In 2013, the White House Office of Science and Technology Policy published a memo that government-funded science should be freely accessible.In addition, it stated that “The OA version may be a copy of the published version of the paper if the journal permits it, a link to permanent OA version at a journal or other repository, or the author’s final peer-reviewed manuscript”.This section provides an overview of our main results, placebo tests, and robustness checks performed in our analysis. We first discuss the changes to the publishing strategy of scientists caused by the mandate. Next, we highlight changes to the uptake of scientific knowledge by patent holders as a proxy for technological applications of the increased diffusion of science from the NLs. Lastly, we investigate who benefited primarily from the increased openness of NL studies.We analyze to what extent the likelihood of different OA types changed through the OA mandate , which has important implications for our results and the impact of the policy itself. Hybrid and gold OA allow for immediate, free, and public access to research articles, yet depositing accepted articles in repositories (green OA) commonly comes with the requirement of an embargo period of several months to over one year.Our estimates of the NL mandate’s impact on downstream inventions should therefore be seen as the likely lower bound as impacts would likely even be higher if articles were free to read upon publication. We also observe imperfect compliance with the mandate, suggesting that our estimated impacts could even be larger in the case of full compliance (around 10% of NL authors do not comply with the mandate in our study period).,Lastly, we also document an increase in Bronze OA, which are articles that have no clearly identifiable license but are free to read on the publishers’ website. While these articles can be accessed without cost, the lack of a clear license means that they cannot be re-used.Our results hold important implications for policymakers. First, the exact policy design significantly influences the diffusion of scientific knowledge. Given that scholars strive to minimize the cost of complying with the mandate, the imposed embargo periods further delay public access to scientific publications. Therefore, the U.S. government’s decision to require immediate public access to federally funded publications from 2026 onwards is a critical step toward ensuring timely access.,Scientific knowledge entails both tacit and explicit knowledge and various diffusion channels, which makes it difficult to investigate. In our study, we leverage a range of recent advances in data availability by Marx and FuegiOur results indicate that the OA mandate is most useful in spurring additional technical inventions but not additional scientific research . Our results suggest that at least on average researchers do not struggle to access scientific research, though there might be inequities that our results do not fully reflect . The application of NL research in patented inventions is particularly important for the NLs as they have historically struggled with increasing the outflow of knowledge to more applied domains.Lastly, we find that particularly small firms (those with below-median patent portfolios) benefited from the OA mandate. After the mandate, small firms cite NL research around 50% more (compared to articles that were not subject to the mandate). This change indicates that particularly smaller firms are adversely affected by the journals’ paywalls. Several survey-based studies indicate access barriers, but we are the first study to demonstrate the effect of an OA mandate on downstream patented inventions by smaller firms. We, therefore, make an important extension to the work of Galasso and Schankerman (2015) who show that patent invalidation particularly helps small firms. Yet, we document that this also holds for the diffusion of scientific knowledge, which tends to be further removed from the actual application than the patent-to-patent citations that Galasso and Schankerman (2015) draw on for their analysis.,SMEs play an integral role in driving economic development in Europe and the U.S. but appear to be particularly affected by difficult access to scientific publications.Our work can be extended in several ways. First, it would be critical to investigate more closely how OA mandates impact other forms of knowledge diffusion.While we show that the mandate primarily affected patented inventions by small firms, studying whether academics from low- and middle-income countries benefited from the mandate, leading to spillovers outside of the U.S. would be an important addition to the literature.,,Our work draws on one diffusion channel of scientific research, namely, scientific publications. Yet, there are many ways that scientific knowledge can diffuse, including co-supervision of students between industry and academia, licensing, and consulting.bprobst@ethz.ch).Further information requests should be directed to the lead contact Benedict Probst  model for two main reasons. First, to address selection bias, which is a key concern in causal inference. In our case, researchers could pay to make their best articles published open access. This self-selection can confound the estimates of the mandate’s effect. A DID-model controls for time-invariant confounders that simultaneously influence the selection into open access and the outcome. Second, to tackle time-varying confounders. Before and after the implementation of the policy, there might be concurrent changes in the wider political, technical, and funding landscape. By comparing changes in the treatment group (subject to the mandate) to a credible control group , the DID model can isolate the causal effect of the policy by addressing these time-varying confounders.:st October 2014, the date from which NL articles had to be published OA. The DID estimator . Results are presented in


Physiological Reports (PR), the world of publishing was already very different from what I had grown used to during most of my research career. There was growing opposition to the model in which publication was funded by institutions subscribing to journals. This meant that only those with the funds required to subscribe could read the science, at least without waiting for an embargo period of 6 months or more. The Open Access movement argued that since research was generally funded by the public, it should be available for all to read.When I was appointed as the first Editor‐in‐Chief of Physiological Reports was established as a cooperative venture between the American Physiological Society (APS) and The Physiological Society (TPS). So, the Editor‐in‐Chief had two mistresses to serve! The societies had many years' experience of publishing, with The Journal of Physiology (JP) founded in 1878 and The American Journal of Physiology (AJP) in 1898. Neither Society, however, had published an Open Access journal. Terra Nova—exciting, challenging and at times, daunting.Physiological Reports was also different from its better‐established sister journals in the way in which it received manuscripts. While some were submitted by the conventional route, a large fraction were “cascaded” from JP and AJP. These were scientifically sound manuscripts, but which had not met the criterion of impact demanded by those journals. This process demanded good links between PR and the other journals. I remember going to many APS Editorial Board meetings, trying to persuade the longer established journals that PR was indeed respectable, and being rewarded with doughnuts, submissions, and enduring friendships. Acta Physiologica became another supporting journal for cascading to PR and brought in good relations with the Scandinavian Physiological Society.One frustration was the time it took for PR to be indexed on PubMed and other platforms. Indeed, it took three Editors‐in‐Chief and 10 years for it to be awarded the cherished Impact Factor. This does make me reflect on the power of the Impact Factor, an arbitrary metric relating to the number of citations garnered by the average paper in a 2‐year period after publication.Another issue that is still evolving is the way in which academic journal publishing is funded. The traditional, subscription‐based model has been criticized, not only because of the requirement to pay to read, but also because the profits accrue to the publishers, and scientists give their time freely, as authors and reviewers. Of course, in the case of JP and APS, the publishers are scientific societies and the income supports their charitable activities. The move to Open Access poses a threat to such organizations, as subscription income falls are not matched by article processing charges. Another problem with Open Access is that it has replaced a system where one needs money to read, with one where money is required to publish, perhaps not as big an improvement as the founders of Open Access envisaged.Physiological Reports and many other Open Access journals make a major positive contribution to the scientific landscape. The same cannot, however, be said for the outputs of several “predatory” publishers. Since Open Access is funded by authors, the more articles that are published, the more profit is made. In order to publish as many papers as possible, there may be little or no reviewing of the content. Thus, PR sometimes felt on the back foot, as some physiologists considered all open access journals tarnished.The real success and achievements of PR, and its establishment in the ranks of good physiological journals, is down to the past and present dedicated editorial teams, the belief and support of APS and TPS, and the publisher Wiley, who all tirelessly promoted the journal and delivered on editorial promises of efficiency and transparency. In public and private conversations, I referred to PR as the “author's friend,” as we were not looking for reasons to reject their submissions. This has become an enduring characteristic of PR, and one that will contribute to its success in the next 10 years and beyond.Happy birthday PR and congratulations to Jo and her team.


There is a power imbalance between authors and reviewers in single-blind peer review. We explored how switching from single-blind to double-blind peer review affected 1) the willingness of experts to review, 2) their publication recommendations, and 3) the quality of review reports.The Finnish Medical Journal switched from single-blind to double-blind peer review in September 2017. The proportion of review invitations that resulted in a received review report was counted. The reviewers’ recommendations of “accept as is”, “minor revision”, “major revision” or “reject” were explored. The content of the reviews was assessed by two experienced reviewers using the Review Quality Instrument modified to apply to both original research and review manuscripts. The study material comprised reviews submitted from September 2017 to February 2018. The controls were the reviews submitted between September 2015 and February 2016 and between September 2016 and February 2017. The reviewers’ recommendations and the scorings of quality assessments were tested with the Chi square test, and the means of quality assessments with the independent-samples t test.P = 0.010). For the quality assessment, 116 reviews from the double-blind period were compared with 104 reviews conducted between September 2016 and February 2017. On a 1–5 scale , double-blind reviews received higher overall proportion of ratings of 4 and 5 than single-blind reviews . Means for the overall quality of double-blind reviews were 3.38  vs. 3.22  for single-blind reviews.A total of 118 double-blind first-round reviews of 59 manuscripts were compared with 232 single-blind first-round reviews of 116 manuscripts. The proportion of successful review invitations when reviewing single-blinded was 67%, and when reviewing double-blinded, 66%. When reviewing double-blinded, the reviewers recommended accept as is or minor revision less often than during the control period (59% vs. 73%), and major revision or rejection more often (41% vs 27%, The quality of the reviews conducted double-blind was better than of those conducted single-blind. Switching to double-blind review did not alter the reviewers’ willingness to review. The reviewers became slightly more critical. Peer review is considered a key element of a scientific journal, but many flaws have been identified. It is slow, poor in detecting fraud, highly subjective, prone to bias, expensive, and easily abused , 2. The In addition to the weaknesses described above, there is a serious power imbalance in single-blind peer review. There is plenty of evidence that author characteristics, such as prestige, affiliation, nationality, language, and gender may affect the reviewers’ opinions and assessments of the manuscripts , 5. The Innovations aiming to tackle at least some of these biases include two opposite formats of peer review: double-blind peer review and open peer review. In double-blind peer review neither authors nor reviewers know the identity of the others. Double-blinding should reduce the status bias and other biases of single-blind peer review , 3–6. ThThe Finnish Medical Journal is one of the two major general medical journals in Finland. The journal is published by the Finnish Medical Association, and the members receive the journal as member benefit. Other health care professionals and institutions can subscribe for the journal. The journal is published in Finnish, with English summaries online. As a journal published in a national language, it is not indexed internationally and, thus, has no impact factor. The journal annually publishes c. 120 peer-reviewed articles, including original research articles, review articles and case reports. In addition to those, editorials, opinion pieces and letters to the editor, as well as news and feature articles are published. There are no article processing charges.Most review articles are commissioned and both non-commissioned and commissioned reviews, as well as original research articles and case-reports, are externally peer reviewed by at least two reviewers. The reviewers are medical or other professionals with scientific training, and they are selected by the journal’s associate editors. Due to the language, the pool of potential reviewers is limited to Finnish speaking experts. There are c. 30,000 licensed physicians in Finland, about 25% of them with a doctorate .In September 2017, the Finnish Medical Journal switched from single-blind to double-blind peer review. After the switch to double-blind peer review, a separate title page including the names and affiliations of the authors was required, and the main text without this information was instructed to be submitted as a separate file. The authors were instructed to avoid such expressions as “our previous study” and “our hospital”. Any acknowledgements that might have revealed, e.g., the institutions of the authors were removed before peer review by the editorial staff.We explored how switching to double-blind peer review affected 1) the willingness of experts to review, 2) their publication recommendations, and 3) the quality of review reports.st, 2017, and February 28th, 2018. The controls were the reviews submitted between September 2015 and February 2016 and between September 2016 and February 2017, i.e., the corresponding months of the respective years. The reviews on all manuscripts with at least 2 first-round reviews were included. In cases where there were more than 2 reviews for the manuscript, the first 2 reviews received were included  using the Review Quality Instrument (RQI) . Thus, wThe reviewers’ recommendations were tested with the Chi square test. We assessed inter-rater reliability of two reviewers’ recommendations for the same manuscript with Fleiss’ Kappa , which iFor the review report scorings by the two reviewers (TH and MM), we assessed consistency of their scores with intraclass correlation coefficient (ICC) using a two-way mixed-effects model. ICC reflects a degree of correlation and agreement between two raters’ measurements of same group of subjects, and values > 0.75 indicate good reliability .P < 0.05 was considered statistically significant. Data analysis was performed using IBM SPSS Statistics v29 (RRID:SCR_016479).We classified the review report scorings to high (4 and 5) and others. The proportions on high scorings were tested with the Chi square test. The means of quality assessments were tested with the independent-samples t test. Reviews for 294 manuscripts had been submitted to the journal’s web server during the study and control periods. For 85 manuscripts, only 1 review had been submitted, and these were excluded. In addition, 34 manuscripts were excluded for various reasons: review was incomplete, one of the reviewers was an associate editor for the journal, or the reviewer clearly knew the author during the double-blind period. In our analysis, 118 reviews of 59 original research manuscripts and review manuscripts conducted double-blind by 114 individual reviewers were included. These were compared with 232 reviews of 116 manuscripts conducted single-blind by 213 reviewers, i.e., the reviewers knew the identity of the authors  during the double-blind period, and 3 (IQR 2–4) during the control periods. The range was 2 to 7 in both groups.P = 0.02). When performing a double-blinded review, the reviewers’ recommendations were slightly more negative than those of single-blinded reviewers’, but the difference in the distribution of recommendations was not statistically significant  (Table P = 0.040). Combined, accept as is or minor revision were recommended for 70 (59%) manuscripts during the double-blind period and for 169 (73%) during the single-blind period (P = 0.010). 54 (92%) manuscripts from the double-blind period and 106 (91%) from the single-blind period led to a published article.The level of agreement between two reviewers’ recommendations for the same manuscripts was positive indicating slight agreement  ranging from highest in item 4  to lowest in item 8 .For the quality assessment 116 reviews were included (in 2 cases there was no written review) and compared to 104 reviews conducted between September 2016 and February 2017. We calculated the inter-rater reliability ICC of RQI scorings between the two independent reviewers (TH and MM). The ICC was moderate for all RQI items  (Table P = 0.003) (Table P < 0.001). The means were 3.38  vs 3.22 .The proportions of high quality scorings for RQI item 2 and overall were significantly higher when reviewing double-blinded. The reviewers more often discussed the originality of the manuscript (item 2) when reviewing double-blinded than when reviewing single-blinded: the proportions of scorings 4 and 5 on a 1–5 scale  were 39% and 26%, respectively . Another study in a setting when anonymization was voluntary found no evidence that the policy affected reviewer recruitment [There are only few studies specifically exploring reviewers’ willingness to review in single- vs. double-blind setting. Huber et al. found that the reviewers significantly more often accepted the review invitation when the prominent researcher was shown as corresponding author . On the ruitment . Accordiruitment . In a Brruitment .Interestingly, one study found that when reviewing double-blind, the reviewers less often recommended rejection . In a stPrevious studies on double-blind peer review looking at the quality of peer review reports have given variable results. One study showed that blinding improved the quality of reviews  but, conThe short study period which resulted to a relatively small material is a limitation of our study. It is uncertain if a larger data would have given different results, e.g., about the reviewers’ willingness to review. The time-window was limited because in March 2018 we changed our peer review platform, and the findings after that would not have been comparable to the earlier findings. On the other hand, we collected control data from two previous comparable periods, which data suggest that the changes in our peer review parameters were indeed associated with the switch. For the comparison, we chose the same months as the study months, in order to avoid seasonal variation, e.g., due to vacations of the reviewers, which might have affected the results.Blinding probably failed in some cases, and the reviewers may have recognised the authors. Previous studies have shown that this may happen in up to 50% of cases –16, commAlthough being a validated tool , RQI alsWe found that after switching from single-blind to double-blind peer review the quality of review reports, measured using the modified RQI, improved. The double-blinded reviewers more often discussed the originality of manuscripts, and the overall quality of reviews conducted double-blind was significantly better than those conducted single-blind. When performing a double-blind review, the reviewers’ recommendations were slightly more negative than those of single-blinded reviewers’, but the difference in the distribution of recommendations was not statistically significant. However, major revision was recommended more often during the double-blind period than during the control period (33% vs 23%). The reviewers’ willingness to review did not change.We introduced double-blind peer review to the Finnish Medical Journal, in order to tackle the power imbalance between authors and reviewers, and the biases well-known in single-blind peer review. Our results indicate that double-blind peer review is a feasible model to a journal in a small language area without major downsides.