The good, the bad and the rude peer-review

High-Performance Genome Annotation for a Safer and Faster-Developing Phage Therapy

Phage therapy, which uses phages to decrease bacterial load in an ecosystem, introduces a multitude of gene copies (bacterial and phage) into said ecosystem. While it is widely accepted that phages have a significant impact on ecology, the mechanisms underlying their impact are not well understood. It is therefore paramount to understand what is released in the said ecosystem, to avoid alterations with difficult-to-predict-but potentially huge-consequences. An in-depth annotation of therapeutic phage genomes is therefore essential. Currently, the average published phage genome has only 20-30% functionally annotated genes, which represents a hurdle to overcome to deliver safe phage therapy, for both patients and the environment. This study aims to compare the effectiveness of manual versus automated phage genome annotation methods. Twenty-seven phage genomes were annotated using SEA-PHAGE and Rime Bioinformatics protocols. The structural (gene calling) and functional annotation results were compared. The results suggest that during the structural annotation step, the SEA-PHAGE method was able to identify an average of 1.5 more genes per phage (typically a frameshift gene) and 5.3 gene start sites per phage. Despite this difference, the impact on functional annotation appeared to be limited: on average, 1.2 genes per phage had erroneous functions, caused by the structural annotation. Rime Bioinformatics' tool (rTOOLS, v2) performed better at assigning functions, especially where the SEA-PHAGE methods assigned hypothetical proteins: 7.0 genes per phage had a better functional annotation on average, compared to SEA PHAGE's 1.7. The method comparison detailed in this article indicate that (1) manual structural annotation is marginally superior to rTOOLS automated structural annotation; (2) rTOOLS automated functional annotation is superior to manual functional annotation. Previously, the only way to obtain a high-quality annotation was by using manual protocols, such as SEA-PHAGES. In the relatively new field of phage therapy, which requires support to advance, manual work can be problematic due to its high cost. Rime Bioinformatics' rTOOLS software allows for time and money to be saved by providing high-quality genome annotations that are comparable to manual results, enabling a safer and faster-developing phage therapy.

Beyond disclaimers: the need for a curation-based model of PubMed

According to its own description, the biomedical meta-database PubMed exists "with the aim of improving health-both globally and personally." Unfortunately, PubMed contains an increasing amount of low-quality research that may detract from this goal. Currently, PubMed warns its users and protects itself from such problems with a disclaimer stating that the presence of any article, book, or document in PubMed does not imply an endorsement of, or concurrence with, its contents by the NLM, the National Institutes of Health (NIH), or the U.S. Federal Government. However, we are critical of a "disclaimer-only" stance and encourage PubMed to take further action against low-quality research being found and indexed in its database, and thus available for use. To address this problem, we offer two lines of reasoning to argue that PubMed should not function merely as a passive index of health-related research. Instead, we first argue that only trustworthy published research is able to further PubMed's goal of health improvement. Secondly, on the basis of surveys, we argue that researchers place a high level of trust in articles that are referenced in this meta-database. We cannot expect any one set of actors to ensure trustworthy content on PubMed, which requires collective responsibility among authors, peer reviewers, editors, and indexers alike. Instead, we propose a curation-based model that incorporates three mechanisms of collaborative content curation: open expert feedback on indexed content, journal auditing, and constant transparent reassessment of indexed entities.

Redefining cancer research for therapeutic breakthroughs

Cancer research has played a pivotal role in improving patient outcomes. However, despite the significant investment in fundamental cancer research over the past few decades, the translation of funding into substantial advancements in cancer treatment has been limited. This perspective article employs a detailed analysis to outline strategies for promoting innovation and facilitating discoveries within the field of cancer research.

Editorial bullying: an exploration of acts impacting publication ethics and related environment

Bullying and misconduct in the realm of scientific and scholarly publishing have the potential to jeopardize the transparency and integrity of academic discourse. While misconduct issues among authors have been extensively discussed, the role of editors in perpetuating or mitigating such problems has garnered less attention. Scientific publishing serves as the gateway for disseminating innovative research findings globally, and the role of editors, especially Editor/s-in-chief, is pivotal in safeguarding the rigor and credibility of published research. Editor bullying and misconduct involve behaviors that undermine the scientific process, compromise research integrity, and harm the careers and wellbeing of individuals. These actions may manifest as biased decision-making, suppression of dissenting voices, or the exploitation of power dynamics in the peer review process. To address these issues, preventive and therapeutic approaches are suggested, including enhancing awareness, recognizing and mitigating exacerbating factors, and upholding professionalism. Moreover, the importance of a conflict-of-interest declaration for editors is highlighted to ensure transparency and integrity in the editorial process. The present mini-review aims to shed light on editor bullying, illuminating its gravity and the urgency to address these issues within the academic publishing domain/s. This review underscores the more subtle, yet equally significant, issue of professional misconduct in the editorial realm of scientific journals.

Exploring the Ethical, Legal, and Social Implications of ChatGPT in Urology

PURPOSE OF THE REVIEW

ChatGPT is programmed to generate responses based on pattern recognition. With this vast popularity and exponential growth, the question arises of moral issues, security and legitimacy. In this review article, we aim to analyze the ethical and legal implications of using ChatGPT in Urology and explore potential solutions addressing these concerns.

RECENT FINDINGS

There are many potential applications of ChatGPT in urology, and the extent to which it might improve healthcare may cause a profound shift in the way we deliver our services to patients and the overall healthcare system. This encompasses diagnosis and treatment planning, clinical workflow, patient education, augmenting consultations, and urological research. The ethical and legal considerations include patient autonomy and informed consent, privacy and confidentiality, bias and fairness, human oversight and accountability, trust and transparency, liability and malpractice, intellectual property rights, and regulatory framework. The application of ChatGPT in urology has shown great potential to improve patient care and assist urologists in various aspects of clinical practice, research, and education. Complying with data security and privacy regulations, and ensuring human oversight and accountability are some potential solutions to these legal and ethical concerns. Overall, the benefits and risks of using ChatGPT in urology must be weighed carefully, and a cautious approach must be taken to ensure that its use aligns with human values and advances patient care ethically and responsibly.

Common Interests Without Common Expertise: Reflections on Early-career Experiences in Cross-Disciplinary Research

Cross-disciplinary research enables us to tackle complex problems that require expertise from different fields. Such collaborations involve researchers who have different perspectives, communication styles, and knowledge bases, and can produce results far greater than the sum of their parts. However, in an era of increasing scientific specialization, there exist many barriers for students and early-career researchers (ECRs) interested in training and undertaking interdisciplinary research endeavors. This perspective examines the challenges that students and ECRs perceive and experience in cross-disciplinary work and proposes pathways to create more inclusive and welcoming research environments. This work emerges from a National Science Foundation (NSF)-funded workshop held during the Society for Integrative and Comparative Biology (SICB) Annual Meeting in January 2023 in Austin, TX. The workshop brought together seasoned interdisciplinary scientists with undergraduate and graduate students to identify and discuss perceived challenges through small group discussions and experience sharing. Through summarizing a range of student concerns about embarking on careers as interdisciplinary scientists and identifying ways to dismantle institutional and lab management-level barriers, we aim to promote an inclusive and collaborative problem-solving environment for scientists of all experience levels.

The Reviewer Academy of the Society of Critical Care Medicine: Key Principles and Strategic Plan

The Society of Critical Care Medicine (SCCM) Reviewer Academy seeks to train and establish a community of trusted, reliable, and skilled peer reviewers with diverse backgrounds and interests to promote high-quality reviews for each of the SCCM journals. Goals of the Academy include building accessible resources to highlight qualities of excellent manuscript reviews; educating and mentoring a diverse group of healthcare professionals; and establishing and upholding standards for insightful and informative reviews. This manuscript will map the mission of the Reviewer Academy with a succinct summary of the importance of peer review, process of reviewing a manuscript, and the expected ethical standards of reviewers. We will equip readers to target concise, thoughtful feedback as peer reviewers, advance their understanding of the editorial process and inspire readers to integrate medical journalism into diverse professional careers.

ChatGPT Utility in Healthcare Education, Research, and Practice: Systematic Review on the Promising Perspectives and Valid Concerns

ChatGPT is an artificial intelligence (AI)-based conversational large language model (LLM). The potential applications of LLMs in health care education, research, and practice could be promising if the associated valid concerns are proactively examined and addressed. The current systematic review aimed to investigate the utility of ChatGPT in health care education, research, and practice and to highlight its potential limitations. Using the PRIMSA guidelines, a systematic search was conducted to retrieve English records in PubMed/MEDLINE and Google Scholar (published research or preprints) that examined ChatGPT in the context of health care education, research, or practice. A total of 60 records were eligible for inclusion. Benefits of ChatGPT were cited in 51/60 (85.0%) records and included: (1) improved scientific writing and enhancing research equity and versatility; (2) utility in health care research (efficient analysis of datasets, code generation, literature reviews, saving time to focus on experimental design, and drug discovery and development); (3) benefits in health care practice (streamlining the workflow, cost saving, documentation, personalized medicine, and improved health literacy); and (4) benefits in health care education including improved personalized learning and the focus on critical thinking and problem-based learning. Concerns regarding ChatGPT use were stated in 58/60 (96.7%) records including ethical, copyright, transparency, and legal issues, the risk of bias, plagiarism, lack of originality, inaccurate content with risk of hallucination, limited knowledge, incorrect citations, cybersecurity issues, and risk of infodemics. The promising applications of ChatGPT can induce paradigm shifts in health care education, research, and practice. However, the embrace of this AI chatbot should be conducted with extreme caution considering its potential limitations. As it currently stands, ChatGPT does not qualify to be listed as an author in scientific articles unless the ICMJE/COPE guidelines are revised or amended. An initiative involving all stakeholders in health care education, research, and practice is urgently needed. This will help to set a code of ethics to guide the responsible use of ChatGPT among other LLMs in health care and academia.

Overcoming Language Barriers in Academia: Machine Translation Tools and a Vision for a Multilingual Future

Having a central scientific language remains crucial for advancing and globally sharing science. Nevertheless, maintaining one dominant language also creates barriers to accessing scientific careers and knowledge. From an interdisciplinary perspective, we describe how, when, and why to make scientific literature more readily available in multiple languages through the practice of translation. We broadly review the advantages and limitations of neural machine translation systems and propose that translation can serve as both a short- and a long-term solution for making science more resilient, accessible, globally representative, and impactful beyond the academy. We outline actions that individuals and institutions can take to support multilingual science and scientists, including structural changes that encourage and value translating scientific literature. In the long term, improvements to machine translation technologies and collective efforts to change academic norms can transform a monolingual scientific hub into a multilingual scientific network. Translations are available in the supplemental material.

Incorrect method for calculation of grey water footprint in several articles

The aim of research is to acquire new knowledge, discover new practices and methods, or simply improve existing ones. Sometimes these are dead ends, and the chosen direction of research is incorrect. This can even happen when the underlying assumptions may sound logical. Fu et al. use the incorrect method for the calculation of grey water footprint in their article "Measurement and driving factors of grey water footprint efficiency in Yangtze River Basin". Therefore, the results are biased. The results of greywater footprint for industry and households are underestimated, which emphasizes the contribution of agriculture to the total water footprint. In this Letter to Editors, numerical proof is provided that the used equation is incorrect. Unfortunately, there are three other articles which use the same incorrect equation. Two of these articles were published in the journal Science of the Total Environment. The editors are asked to initialize a correction process of these articles because a transparent corrections process is essential to assist in the maintenance of public confidence in research.

Individual integrity and public morality in scientific publishing

Science and science reporting are under threat. Knowingly or not, researchers and clinicians are part of this debacle. This is not due so much to the notorious replication crisis, as to our acceptance of lowering common morality for personal gains, including the widespread, deprecable phenomenon of predatory publishing. Rather than fiercefully countering this loathsome practice, academics are accepting, often supporting a masquerade solution: paying several thousand dollars to publish for all their own papers. This new policy will create a disparity across richer and poorer disciplines; will result in concentrating even more in the hands of large, rich, Western institutions, also penalising younger researchers; will kill observational studies and exploratory research; and will make disseminating science depending more on finances than on quality. This article calls for the full awareness of the academic community on the risks of the current situation in scientific publishing.

QUALITY PEER REVIEW IS ESSENTIAL FOR SCHOLARLY PUBLISHING

QUALITY PEER REVIEW IS ESSENTIAL FOR SCHOLARLY PUBLISHING

Writing for SICOT-J

Every time a paper is submitted to the journal, we realize the effort and amount of work it takes for performing the study, writing, formatting, and submitting the paper for peer review. However, how many of these papers are suitable for publication? Medical writing considerations, including an understandable text that does not confuse reading, formality, and ethics in writing, should be kept in mind when preparing and writing a paper to be submitted for publication to a journal. This editorial note offers useful advice for the authors submitting their papers to a journal on what to keep in mind before submission, how to prepare a quality submission, how to win the editor for their paper to avoid rejection, and how to make it to the review process and maybe to get published. It is our belief that these tips and advice on medical writing apply to any author and any journal.

Optimizing peer review to minimize the risk of retracting COVID-19-related literature

Retractions of COVID-19 literature in both preprints and the peer-reviewed literature serve as a reminder that there are still challenging issues underlying the integrity of the biomedical literature. The risks to academia become larger when such retractions take place in high-ranking biomedical journals. In some cases, retractions result from unreliable or nonexistent data, an issue that could easily be avoided by having open data policies, but there have also been retractions due to oversight in peer review and editorial verification. As COVID-19 continues to affect academics and societies around the world, failures in peer review might also constitute a public health risk. The effectiveness by which COVID-19 literature is corrected, including through retractions, depends on the stringency of measures in place to detect errors and to correct erroneous literature. It also relies on the stringent implementation of open data policies.

Peer review guidance: a primer for researchers

The peer review process is essential for quality checks and validation of journal submissions. Although it has some limitations, including manipulations and biased and unfair evaluations, there is no other alternative to the system. Several peer review models are now practised, with public review being the most appropriate in view of the open science movement. Constructive reviewer comments are increasingly recognised as scholarly contributions which should meet certain ethics and reporting standards. The Publons platform, which is now part of the Web of Science Group (Clarivate Analytics), credits validated reviewer accomplishments and serves as an instrument for selecting and promoting the best reviewers. All authors with relevant profiles may act as reviewers. Adherence to research reporting standards and access to bibliographic databases are recommended to help reviewers draft evidence-based and detailed comments.

How fast is the peer-review process for orthopaedic publications related to the Covid-19 pandemic?

PURPOSE

This study's primary objective is to evaluate the time spent in the peer-review process for orthopaedic publications related to the Covid-19 pandemic. The secondary objective is to evaluate the countries' and journals' contributions in these publications.

MATERIALS AND METHODS

We carried a search on August 1st, 2020, in one database (PubMed) using limited search terms to identify the orthopaedic publications related to the Covid-19 pandemic. After a filtration process, we evaluated the eligible article to identify the prevalence of different articles types, different countries, and journal contributions in these publications. The evaluation of the time spent in the peer-review process was done by obtaining the submission and acceptance dates.

RESULTS

Of the 231 articles eligible for initial assessment, review articles were the most common article type published (51%), 48 countries published articles in a unique 78 journals. Evaluation of the peer-review process in 147 articles revealed that the mean time from submission to acceptance was 14.3 ± 15.8 days (range from 0 to 74), the peer-review process took less than 30 days in 127 (86.4%) articles, 15 (10.2%) articles were accepted within the first day of submission.

CONCLUSION

Orthopaedic community contributed significantly to the publications related to the Covid-19 pandemic, with a contribution from many countries and journals. The peer-review process was notably shortened for some articles.

Using the peer review process to educate and empower emerging nurse scholars

Peer review, in various forms, is fundamental to research-based fields and scholarly publication. The integrity of the publication process is necessary to advance nursing science and support clinical nursing practice. The peer review process undergirds publication and grant funding. In theory, peer review should occur in a process that is unbiased with results providing a fair assessment of the scientific merit and credibility of the work being reviewed. The purpose of peer review is lost if reviewer comments are unprofessional. Budding nurse scholars may be demoralized and discouraged to revise and resubmit their work after receiving review feedback they perceive unprofessional and lacking constructive recommendations on how to improve their work. This "incivility" in the peer review process may discourage nursing authors from revising and resubmitting their work, thus robbing nursing of potentially meaningful contributions to nursing science. Often beginning doctorate nursing students have little or no experience in having their scholarly works evaluated and receiving feedback via the peer review process. Peer review provides an opportunity to educate emerging nurse scholars on ways to improve their writing skills and ways to receive and respond to constructive, meaningful feedback. This article aims to discuss: 1) peer review process, 2) challenges with peer review, 3) impact of unprofessional peer review comments and incivility in nursing peer review process can have on a budding scientists and nurse scholars, 4) ways the peer review process can be used to educate and empower emerging nurse scholars, 5) implications for nursing scholarship, 6) recommendations to address bias and how to provide supportive and constructive feedback and 7) finally provide readers with available resources where they can learn more about how to conduct a peer review.