Publishing in the Open Access and Open Science era

Our research activities would be better served if they were communicated in a manner that is openly accessible to the public and all researchers. The research we share is often limited to representative data included in research papers-science would be much more efficient if all reproducible research data were shared alongside detailed methods and protocols, in the paradigm called Open Science. On the other hand, one primary function of research journals is to select manuscripts of good quality, verify the authenticity of the data and its impact, and deliver to the appropriate audience for critical evaluation and verification. In the current paradigm, where publication in a subset of journals is intimately linked to research evaluation, a hypercompetitive "market" has emerged where authors compete to access a limited number of top-tier journals, leading to high rejection rates. Competition among publishers and scientific journals for market dominance resulted in an increase in both the number of journals and the cost of publishing and accessing scientific papers. Here we summarize the current problems and potential solutions from the development of AI technology discussed in the seminar at the 46th Annual Meeting of the Molecular Biology Society of Japan.

Navigating the Seas of Publications in A Medical Journal: The Role of an Editor

The world of scientific publishing is a dynamic ecosystem where groundbreaking research and discoveries find their way into the public domain. Scientific journals play a pivotal role in disseminating new knowledge, shaping the healthcare landscape, and influencing clinical practice. Behind the scenes, editors serve as gatekeepers, meticulously reviewing and selecting articles to ensure the highest standards of quality and relevance. This article offers insights into the role of editors regarding publications in medical journals, shedding light on the challenges, responsibilities, and evolving trends in this crucial process.

[Predatory journals in Orthopedics and Traumatology]

Predatory journals are distinguished from legitimate journals by their lack of adequate reviews and editorial processes, compromising the quality of published content. These journals do not conduct peer reviews or detect plagiarism, and accept manuscripts without requiring substantial modifications. Their near 100% acceptance rate is driven by profit motives, regardless of the content they publish. While they boast a prestigious editorial board composed of renowned researchers, in most cases, it is a facade aimed at impressing and attracting investigators. Furthermore, these journals lack appropriate ethical practices and are non-transparent in their editorial processes. Predatory journals have impacted multiple disciplines, including Orthopedics and Traumatology, and their presence remains unknown to many researchers, making them unwitting victims. Their strategy involves soliciting articles via email from authors who have published in legitimate journals, promising quick, easy, and inexpensive publication. The implications and negative consequences of predatory journals on the scientific community and researchers are numerous. The purpose of this work is to provide general information about these journals, specifically in the field of Orthopedics and Traumatology, offering guidelines to identify and avoid them, so that authors can make informed decisions when publishing their manuscripts and avoid falling into the hands of predatory journals or publishers.

COVID-19 retracted publications on retraction watch: A systematic survey of their pre-prints and citations

Background

Studies related to the coronavirus disease 2019 (COVID-19) were frequently published as pre-prints prior to undergoing peer-review. However, several publications were later retracted due to ethical concerns or study misconduct. Although these studies have been retracted, the availability of their corresponding pre-prints has never been formally investigated, and may result in the spread of misinformation if they are being used to inform decision-making.

Methods

Our objective was to conduct a systematic survey of retracted COVID-19 publications listed on the Retraction Watch database as of August 15th, 2021. We assessed the availability of corresponding pre-prints for retracted publications, and documented the number of citations and online views.

Results

Our study included 140 retracted COVID-19 publications, and we could not retrieve corresponding pre-prints for 132 retracted publications in our study (94%). Although we were unable to find the majority of pre-prints, they had already been disseminated, with a maximal citation count of 593 and Altmetric score of 558,928.

Conclusion

While it is reassuring that most corresponding pre-prints could not be retrieved, our study highlights the need for online platforms and journals to employ quality assurance methods to prevent the spread of misinformation through citation of retracted papers.

Scientific contributions of citizen science applied to rare or threatened animals

Citizen science is filling important monitoring gaps and thus contributing to the conservation of rare or threatened animals. However, most researchers have used peer-reviewed publications to evaluate citizen science contributions. We quantified a larger spectrum of citizen science's contributions to the monitoring of rare or threatened animals, including contributions to the peer-reviewed publications, gray literature and to conservation measures (i.e., actions taken as a direct result of citizen science monitoring). We sought to provide broad information on how results of studies of citizen science monitoring is used. We also evaluated factors associated with success of citizen science projects. We conducted a web search to find citizen science projects focusing on rare and threatened species and surveyed citizen science project managers about their contributions and factors influencing their success. The number of projects increased rapidly after 2010. Almost one-half of the citizen science projects produced at least 1 peer-reviewed publication, 64% produced at least 1 gray literature publication, and 64% resulted in at least 1 conservation measure. Conservation measures covered a wide range of actions, including management and mitigation plans, modification of threat status, identification and establishment of protected areas, habitat restoration, control of invasive species, captive breeding programs, and awareness campaigns. Longevity, data quality, and collaboration type best explained quantities of all types of scientific contributions of citizen science. We found that citizen science contributed substantially to knowledge advancement and conservation, especially when programs were long term and had rigorous data collection and management standards, and multidisciplinary or transdisciplinary collaborations.

Clinical Images in Dermatology Manuscripts - A Study of Journal Submission Guidelines

BACKGROUND

Images are an important element of any scientific publication, more so for a very visual specialty such as dermatology. Dermatology journals generally include detailed instructions related to images submitted with the manuscripts, including technical aspects such as file format, resolution, and editing. We aimed to review and critically analyze instructions for images in the top 50 dermatology journals [as per the latest Clarivate journal citation report (JCR) ranking].

METHODS

The top 50 journals as per the latest Clarivate JCR were included in the study. Instructions for images were reviewed for each of the journals. The main points analyzed included file type, resolution, size limits, editing limits, support for post-processing of images and details regarding patient consent.

RESULTS

Only half the journals (25) had clear, detailed, and specific instructions for the images. Only one journal specifically mentioned pixels per inch (PPI) as the descriptive term, and the remaining used dots per inch (DPI), whereas 6 did not mention either. Twenty-three journals did not mention the recommended size of the image. The most common minimum resolution mentioned was 300 DPI (41 journals). Although 24 of the journals mentioned editing limits, none of the journals elaborated on image plagiarism in the instructions. Twenty-one of the fifty did not mention a clear policy on patient consent.

CONCLUSIONS

Image submission guidelines for dermatology journals need to be made more elaborate yet easier to understand. Developing a consensus, followed by standardization of these submission guidelines, can help both authors and journals.

Impact of COVID-19 on Otolaryngology Literature

Objectives/Hypothesis

To understand the effect of the COVID‐19 pandemic on the volume, quality, and impact of otolaryngology publications.

Study Design

Retrospective analysis.

Methods

Fifteen of the top peer‐reviewed otolaryngology journals were queried on PubMed for COVID and non‐COVID‐related articles from April 1, 2020 to March 31, 2021 (pandemic period) and pre‐COVID articles from the year prior. Information on total number of submissions and rate of acceptance were collected from seven top‐ranked journals.

Results

Our PubMed query returned 759 COVID articles, 4,885 non‐COVID articles, and 4,200 pre‐COVID articles, corresponding to a 34% increase in otolaryngology publications during the pandemic period. Meta‐analysis/reviews and miscellaneous publication types made up a larger portion of COVID publications than that of non‐COVID and pre‐COVID publications. Compared to pre‐COVID articles, citations per article 120 days after publication and Altmetric Attention Score were higher in both COVID articles (citations/article: 2.75 ± 0.45, P < .001; Altmetric Attention Score: 2.05 ± 0.60, P = .001) and non‐COVID articles (citations/article: 0.03 ± 0.01, P = .002; Altmetric Attention Score: 0.67 ± 0.28, P = .016). COVID manuscripts were associated with a 1.65 times higher acceptance rate compared to non‐COVID articles (P < .001).

Conclusions

COVID‐19 was associated with an increase in volume, citations, and attention for both COVID and non‐COVID articles compared to pre‐COVID articles. However, COVID articles were associated with lower evidence levels than non‐COVID and pre‐COVID articles.

Level of Evidence

3 Laryngoscope, 132:1364–1373, 2022

Transparent reporting of hypotheses and analyses in behavioral medicine research: An audit of publications in 2018 and 2008

Objective

We aimed to document the use of transparent reporting of hypotheses and analyses in behavioral medicine journals in 2018 and 2008. Design: We examined a randomly selected portion of articles published in 2018 and 2008 by behavioral medicine journals with the highest impact factor, excluding manuscripts that were reviews or purely descriptive. Main Outcome Measures: We coded whether articles explicitly stated if the hypotheses/outcomes/analyses were primary or secondary; if study was registered/pre-registered; if ‘exploratory’ or a related term was used to describe analyses/aims; and if power analyses were reported. Results: We coded 162 manuscripts published in 2018 (87% observational and 12% experimental). Sixteen percent were explicit in describing hypotheses/outcomes/analyses as primary or secondary, 51% appeared to report secondary hypotheses/outcomes/analyses but did not use term ‘secondary,’ and 33% were unclear. Registration occurred in 14% of studies, but 91% did not report which analyses were registered. ‘Exploratory’ or related term was used in 31% of studies. Power analyses were reported in 8% of studies. Compared to 2008 (n = 120), studies published in 2018 were more likely to be registered and less likely to be unclear if outcomes were primary or secondary. Conclusions: Behavioral medicine stakeholders should consider strategies to increase clarity of reporting, and particularly details that will inform readers if analyses were pre-planned or post-hoc.

Study registration

https://osf.io/39ztn

The Protocol Gap

Although peer review is considered one of the main pillars of modern science, experimental methods and protocols seem to be not a rigorous subject of this process in many papers. Commercial equipment, test kits, labeling kits, previously published concepts, and standard protocols are often considered to be not worth a detailed description or validation. Even more disturbing is the extremely biased citation behavior in this context, which sometimes leads to surrogate citations to avoid low-impact journals, preprints, or to indicate traditional practices. This article describes some of these surprising habits and suggests some measures to avoid the most unpleasant effects, which in the long term may undermine the credibility of science as a whole.

New investigator editorial: the osteopathic medical student perspective on research

Listen to this article’s corresponding podcast at https://ajpheart.podbean.com/e/behind-the-bench-episode7/ .

Bibliometric Analysis of Research on Telomere Length in Children: A Review of Scientific Literature

Telomere length in early life has been recently associated with biological aging and development of negative consequences in later adult life. A relevant area of research has emerged to understand the factors that impact telomere length in children. We conducted a bibliometric analysis to track research output and identify global trends and gaps in the knowledge of telomere length in children. Bibliographic data were retrieved from the Web of Science database and then analyzed by using Bibliometrix R package. A total of 840 publications were yielded from 1991 to 2019. The references were prominently published in journals, with 20 high ranked journals contributing to 30% of literature on telomere length in children. The USA was the most productive country (35.7%), followed by Europe (12.1%), and Asia (11.9%). A knowledge map of telomere length in children through keyword analyses revealed that there were two potential main lines of research based on two different approaches: genomic research and epidemiological research. This study shows that telomere length in children is a topic of research that has gained significant relevance in the last decade. This bibliometric study may be helpful in identifying research trends and finding research hot spots and gaps in this research field.

Adverse events related to biologicals used for patients with multiple sclerosis: a comparison between information originating from regulators and information originating from the scientific community

Background and purpose

Clinical decision making is facilitated by healthcare professionals’ and patients’ adequate knowledge of the adverse events. This is especially important for biologicals used for treating multiple sclerosis (MS). So far, little is known about whether different information sources report adverse events consistently.

Methods

Biologicals authorized by the European Medicines Agency for the treatment of MS were included in this study. Information on adverse events derived from phase 3 clinical trials from European Public Assessment Reports (EPARs) and from scientific publications was compared.

Results

In the study, eight biologicals used for the treatment of MS were included for which the EPAR and/or scientific publication reported a total of 707 adverse events. Approximately one‐third of the adverse events was reported in both the EPAR and scientific publication, one‐third was only reported in the EPAR and one‐third only in the scientific publication. Serious adverse events and adverse events that regulators classified as ‘important identified risk’ were significantly more often reported in both sources compared to adverse events not classified as such (respectively, 38% vs. 30% and 49% vs. 30%). Adverse events only reported in the EPAR or in the scientific publication were, in general, not described in the benefit–risk section or abstract, which were considered to be the most important sections of the documents.

Conclusions

This study showed that there is substantial discordance in the reporting of adverse events on the same phase 3 trials between EPARs and scientific publications. To support optimal clinical decision making, both documents should be considered.

SciPub-019-Getting Your Article Published in Scientific Journals- an Event Report

Introduction

The quantity and quality of published research from Nepal, though improving, are low. Among other factors, lack of knowledge about scientific writing is an important contributor. Thus, with the objective of improving knowledge about scientific writing, a one-day workshop was conducted, entitled, “SciPub-019-Getting your article published in scientific journals”.

Methods

The knowledge and attitude of participants were evaluated both before and immediately after the workshop.

Results

Thirty-three individuals participated with most (48.5%) being pharmacists, followed closely by doctors. 66.7% of the participants were males and 72.7% of participants had published one article as of the workshop date while the rest had published two. On specific questions, there was a significant difference between the responses regarding the abstract being the first part of the paper to be written, before and after the workshop. There was also a significant difference between the overall responses of the participants.

Conclusion

Improvement in the knowledge of the participants about scientific writing and publication was noted. Workshops of similar nature should be regularly conducted to improve the knowledge of new researchers about scientific writing.

Publication rates and reported results in a cohort of gene- and cell-based therapy trials

Aim: We investigated publication rates and reported results for gene- and cell-based therapy trials. Materials & methods: In a cohort of Institutional Review Board (IRB)-authorized trials during 2007-2017 in the Netherlands (n = 105), we examine publication rates and reported results in scientific papers and conference abstracts as well as associations with the occurrence of trial characteristics. Results: The publication rate for scientific papers was 27% and 17% for conference abstracts (median survival time: 1050 days). Academic hospitals published more in scientific papers whereas private sponsors published more in conference abstracts. Manufacturing protocols were underreported compared with clinical outcomes. Most publications reported positive results (78%). Conclusion: Publication rates are currently suboptimal indicating a need for enhanced knowledge sharing to stimulate gene- and cell-based therapy development.

Molecular Illustration in Research and Education: Past, Present, and Future

Two-dimensional illustration is used extensively to study and disseminate the results of structural molecular biology. Molecular graphics methods have been and continue to be developed to address the growing needs of the structural biology community, and there are currently many effective, turn-key methods for displaying and exploring molecular structure. Building on decades of experience in design, best-practice resources are available to guide creation of illustrations that are effective for research and education communities.

[Paramedical research, a long path towards autonomy]

An integral part of the care project of Versailles general hospital, paramedical research is facilitated and promoted by nursing management. It is also strongly encouraged and supported by medical professionals. Beyond the scientific interest in terms of the benefits for the quality of care, it is considered as an innovative project which unites and motivates staff, thereby favouring employee retention.

Citations increase with manuscript length, author number, and references cited in ecology journals

Most top impact factor ecology journals indicate a preference or requirement for short manuscripts; some state clearly defined word limits, whereas others indicate a preference for more concise papers. Yet evidence from a variety of academic fields indicates that within journals longer papers are both more positively reviewed by referees and more highly cited. We examine the relationship between citations received and manuscript length, number of authors, and number of references cited for papers published in 32 ecology journals between 2009 and 2012. We find that longer papers, those with more authors, and those that cite more references are cited more. Although paper length, author count, and references cited all positively covary, an increase in each independently predicts an increase in citations received, with estimated relationships positive for all the journals we examined. That all three variables covary positively with citations suggests that papers presenting more and a greater diversity of data and ideas are more impactful. We suggest that the imposition of arbitrary manuscript length limits discourages the publication of more impactful studies. We propose that journals abolish arbitrary word or page limits, avoid declining papers (or requiring shortening) on the basis of length alone (irrespective of content), and adopt the philosophy that papers should be as long as they need to be.

Accelerating scientific publication in biology

Scientific publications enable results and ideas to be transmitted throughout the scientific community. The number and type of journal publications also have become the primary criteria used in evaluating career advancement. Our analysis suggests that publication practices have changed considerably in the life sciences over the past 30 years. More experimental data are now required for publication, and the average time required for graduate students to publish their first paper has increased and is approaching the desirable duration of PhD training. Because publication is generally a requirement for career progression, schemes to reduce the time of graduate student and postdoctoral training may be difficult to implement without also considering new mechanisms for accelerating communication of their work. The increasing time to publication also delays potential catalytic effects that ensue when many scientists have access to new information. The time has come for life scientists, funding agencies, and publishers to discuss how to communicate new findings in a way that best serves the interests of the public and the scientific community.

Don't let spurious accusations of pseudoreplication limit our ability to learn from natural experiments (and other messy kinds of ecological monitoring)

Pseudoreplication is defined as the use of inferential statistics to test for treatment effects where treatments are not replicated and/or replicates are not statistically independent. It is a genuine but controversial issue in ecology particularly in the case of costly landscape-scale manipulations, behavioral studies where ethics or other concerns may limit sample sizes, ad hoc monitoring data, and the analysis of natural experiments where chance events occur at a single site. Here key publications on the topic are reviewed to illustrate the debate that exists about the conceptual validity of pseudoreplication. A survey of ecologists and case studies of experimental design and publication issues are used to explore the extent of the problem, ecologists' solutions, reviewers' attitudes, and the fate of submitted manuscripts. Scientists working across a range of ecological disciplines regularly come across the problem of pseudoreplication and build solutions into their designs and analyses. These include carefully defining hypotheses and the population of interest, acknowledging the limits of statistical inference and using statistical approaches including nesting and random effects. Many ecologists face considerable challenges getting their work published if accusations of pseudoreplication are made - even if the problem has been dealt with. Many reviewers reject papers for pseudoreplication, and this occurs more often if they haven't experienced the issue themselves. The concept of pseudoreplication is being applied too dogmatically and often leads to rejection during review. There is insufficient consideration of the associated philosophical issues and potential statistical solutions. By stopping the publication of ecological studies, reviewers are slowing the pace of ecological research and limiting the scope of management case studies, natural events studies, and valuable data available to form evidence-based solutions. Recommendations for fair and consistent treatment of pseudoreplication during writing and review are given for authors, reviewers, and editors.

Technology and Information Tool Preferences of Academics in the Field of Anaesthesiology

OBJECTIVE

Researchers use a large number of information technology tools from the beginning until the publication of a scientific study. The aim of the study is to investigate the technology and data processing tool usage preferences of academics who produce scientific publications in the field of anaesthesiology.

METHODS

A multiple-choice survey, including 18 questions regarding the use of technology to assess the preferences of academicians, was performed.

RESULTS

PubMed has been the most preferred article search portal, and the second is Google Academic. Medscape has become the most preferred medical innovation tracking website. Only 12% of academicians obtain a clinical trial registration number for their randomized clinical research. In total, 28% of respondents used the Consolidated Standards of Reporting Trials checklist in their clinical trials. Of all participants, 21% was using Dropbox and 9% was using Google-Drive for sharing files. Google Chrome was the most preferred internet browser (32.25%) for academic purposes. English language editing service was obtained from the Scribendi (21%) and Textcheck (12%) websites. Half of the academics were getting help from their specialist with a personal relationship, 27% was doing it themselves, and 24% was obtaining professional assistance for statistical requirements. Sixty percent of the participants were not using a reference editing program, and 21% was using EndNote. Nine percent of the academics were spending money for article writing, and the mean cost was 1287 Turkish Liras/year.

CONCLUSION

Academics in the field of anaesthesiology significantly benefit from technology and informatics tools to produce scientific publications.

[Not Available]

BACKGROUND

Honorary and ghost authorship, as well as competing interests, are well documented concerns related to the publication of scientific articles. Guidelines for writing and publishing scientific manuscripts are available, including those of the International Committee of Medical Journal Editors (ICMJE).

OBJECTIVES

The primary objective of this descriptive cross-sectional study was to identify, in the instructions for authors of pharmacy practice journals, guidance on authorship and competing interests. The secondary objective was to suggest suitable corrective measures for more transparent authorship.

METHODS

The first step of the project was to identify journals in the area of pharmacy practice. The instructions for authors of each journal were then reviewed to determine recommendations for avoiding problems related to authorship and competing interests. Finally, the members of the research team formulated potential corrective measures for researchers.

RESULTS

Of 232 pharmacy journals identified, 33 were deemed to focus on pharmacy practice. A total of 24 (73%) of these journals mentioned that they followed ICMJE policies, 14 (42%) asked authors to complete a competing interests disclosure form at the time of submission, 17 (52%) had a formal definition of authorship, and 5 (15%) asked for details of each author's contribution. A list of 40 criteria was developed to define authorship status.

CONCLUSION

Fewer than half of the journals asked authors to provide a competing interests disclosure form upon submission of an article, and only half had a formal definition of authorship. The scientific publication of papers relevant to pharmacy practice is not free from issues related to publication transparency. Publishing articles online and using a checklist to detail each author's contribution may help to limit the associated risks. [Publisher's translation].

EBUS-TBNA: popular but not universal

In recent years, the number of publications concerning interventional bronchoscopy has increased dramatically. The present paper focused on publications related to endobronchial ultrasound technique. Its aim was to provide an overview of the nature of publications about endobronchial ultrasound technique, especially with regard to the countries of origin of publications and the categories of journals in which these papers are published. Overall, the review demonstrates a limited use of endobronchial ultrasound technique in many countries.

Getting published well requires fulfilling editors' and reviewers' needs and desires

Publication in international scientific journals provides an unparalleled opportunity for authors to showcase their work. Where authors publish affects how the community values the work. This value directly determines the impact of the work on the field-papers must be read and cited to advance the field, and because the scientific literature is vast, only a subset of the literature is widely read and cited. Moreover, the value placed on the work also affects the authors' scientific reputation and career advancement. Consequently, it is essential that manuscripts receive the recognition they deserve by being published in one of the "best" journals that the scientific findings allow. Several factors determine where a paper is published: how well the topic of the paper fits the scope of the journal, the quality of the study and the manuscript describing it, the advance the paper makes in its field, the importance of the advance, and the extent to which the paper impacts the broader community of science. As scientists, we assume that our papers will be assessed objectively using only well defined scientific standards, but editors and reviewers also view papers subjectively, having biases of what defines a high-quality publication based on Western standards. Therefore, scientists trained in other parts of the world can be significantly disadvantaged in getting their papers published in the best journals. Here, I present concrete suggestions for improving the perception of a paper in the reader's minds, increasing the likelihood that it will get published well.

Does mentoring new peer reviewers improve review quality? A randomized trial

BACKGROUND

Prior efforts to train medical journal peer reviewers have not improved subsequent review quality, although such interventions were general and brief. We hypothesized that a manuscript-specific and more extended intervention pairing new reviewers with high-quality senior reviewers as mentors would improve subsequent review quality.

METHODS

Over a four-year period we randomly assigned all new reviewers for Annals of Emergency Medicine to receive our standard written informational materials alone, or these materials plus a new mentoring intervention. For this program we paired new reviewers with a high-quality senior reviewer for each of their first three manuscript reviews, and asked mentees to discuss their review with their mentor by email or phone. We then compared the quality of subsequent reviews between the control and intervention groups, using linear mixed effects models of the slopes of review quality scores over time.

RESULTS

We studied 490 manuscript reviews, with similar baseline characteristics between the 24 mentees who completed the trial and the 22 control reviewers. Mean quality scores for the first 3 reviews on our 1 to 5 point scale were similar between control and mentee groups (3.4 versus 3.5), as were slopes of change of review scores (-0.229 versus -0.549) and all other secondary measures of reviewer performance.

CONCLUSIONS

A structured training intervention of pairing newly recruited medical journal peer reviewers with senior reviewer mentors did not improve the quality of their subsequent reviews.

Published Articles in PubMed-indexed Journals from Tabriz University of Medical Sciences Faculty of Dentistry

BACKGROUND AND AIMS

This survey was conducted to provide statistical data regarding publications in PubMed-indexed journals from Tabriz University of Medical Sciences Faculty of Dentistry.

MATERIALS AND METHODS

The database used for this study was PubMed. The search was conducted using key words including the names of the heads of the departments. Papers published between January 1, 2005 and April 31, 2012 were considered. The retrieved abstracts were reviewed and unrelated articles were excluded. Data were transferred to Microsoft Excel software for descriptive statistical analyses.

RESULTS

A total of 158 papers matched the inclusion criteria, with the majority from the Department of Endodontics (49 articles). The highest proportion (48.3%) of papers was related to in vitro studies, followed by clinical trials, in vivo studies, and case reports. The number of publications showed a considerable increase over the studied period.

CONCLUSION

PubMed-indexed publications from different departments have increased steadily, suggesting that research has become an essential component in the evaluated institute.