The undeclared use of third-party service providers in academic publishing is unethical: an epistemic reflection and scoping review.

There is a substantial body of scientific literature on the use of third-party services (TPS) by academics to assist as "publication consultants" in scholarly publishing. TPS provide a wide range of scholarly services to research teams that lack the equipment, skills, motivation, or time to produce a paper without external assistance. While services such as language editing, statistical support, or graphic design are common and often legitimate, some TPS also provide illegitimate services and send unsolicited e-mails (spam) to academics offering these services. Such illegitimate types of TPS have the potential to threaten the integrity of the peer-reviewed scientific literature. In extreme cases, for-profit agencies known as "paper mills" even offer fake scientific publications or authorship slots for sale. The use of such illegitimate services as well as the failure to acknowledge their use is an ethical violation in academic publishing, while the failure to declare support for a TPS can be considered a form of contract fraud. We discuss some literature on TPS, highlight services currently offered by ten of the largest commercial publishers and expect authors to be transparent about the use of these services in their publications. From an ethical/moral (i.e., non-commercial) point of view, it is the responsibility of editors, journals, and publishers, and it should be in their best interest to ensure that illegitimate TPS are identified and prohibited, while publisher-employed TPS should be properly disclosed in their publications.

Clarifying middle authorship contributions to reduce abuses in science publishing and assessment of top-ranked SJR biochemistry and pharmacology journals' authorship criteria.

So-called "middle authors," being neither the first, last, nor corresponding author of an academic paper, have made increasing relative contributions to academic scholarship over recent decades. No work has specifically and explicitly addressed the roles, rights, and responsibilities of middle authors, an authorship position which we believe is particularly vulnerable to abuse via growing phenomena such as paper mills. Responsible middle authorship requires transparent declarations of intellectual and other scientific contributions that journals can and should require of co-authors and established guidelines and criteria to achieve this already exist (ICMJE/CRediT). Although publishers, editors, and authors need to collectively uphold a situation of shared responsibility for appropriate co-authorship, current models have failed science since verification of authorship is impossible, except through blind trust in authors' statements. During the retraction of a paper, while the opinion of individual co-authors might be noted in a retraction notice, the retraction itself practically erases the relevance of co-author contributions and position/status (first, leading, senior, last, co-corresponding, etc.). Paper mills may have successfully proliferated because individual authors' roles and responsibilities are not tangibly verifiable and are thus indiscernible. We draw on a historical example of manipulated research to argue that authors and editors should publish publicly available, traceable contributions to the intellectual content of an article-both classical authorship or technical contributions-to maximize both visibility of individual contributions and accountability. To make our article practically more relevant to this journal's readership, we reviewed the top 50 Q1 journals in the fields of biochemistry and pharmacology, as ranked by the SJR, to appreciate which journals adopted the ICMJE or CRediT schools of authorship contribution, finding significant variation in adhesion to ICMJE guidelines nor the CRediT criteria and wording of author guidelines.

ChatGPT as an "author": Bibliometric analysis to assess the validity of authorship.

Background: Following the 2023 surge in popularity of large language models like ChatGPT, significant ethical discussions emerged regarding their role in academic authorship. Notable ethics organizations, including the ICMJE and COPE, alongside leading publishers, have instituted ethics clauses explicitly stating that such models do not meet the criteria for authorship due to accountability issues.Objective: This study aims to assess the prevalence and ethical implications of listing ChatGPT as an author on academic papers, in violation of existing ethical guidelines set by the ICMJE and COPE.Methods: We conducted a comprehensive review using databases such as Web of Science and Scopus to identify instances where ChatGPT was credited as an author, co-author, or group author.Results: Our search identified 14 papers featuring ChatGPT in such roles. In four of those papers, ChatGPT was listed as an "author" alongside the journal's editor or editor-in-chief. Several of the ChatGPT-authored papers have accrued dozens, even hundreds of citations according to Scopus, Web of Science, and Google Scholar.Discussion: The inclusion of ChatGPT as an author on these papers raises critical questions about the definition of authorship and the accountability mechanisms in place for content produced by artificial intelligence. Despite the ethical guidelines, the widespread citation of these papers suggests a disconnect between ethical policy and academic practice.Conclusion: The findings suggest a need for corrective measures to address these discrepancies. Immediate review and amendment of the listed papers is advised, highlighting a significant oversight in the enforcement of ethical standards in academic publishing.

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.

Against "silent" retractions in neuroscience.

When an academic paper is published in a journal that assigns a digital object identifier (DOI) to papers, this is a de facto fait accompli. Corrections or retractions are supposed to follow a specific protocol, especially in journals that claim to follow the Committee on Publication Ethics (COPE) guidelines. In this paper, we highlight a case of a new, fully open access neuroscience journal that claims to be COPE-compliant, yet has silently retracted two papers since all records, bibliometrics, and PDF files related to their existence have been deleted from the journal's website. Although this phenomenon does not seem to be common in the neurosciences, we consider that any opaque corrective measures in journals whose papers could be cited may negatively impact the wider neuroscience literature and community. Instead, we encourage transparency in retraction to promote truthfulness and trustworthiness.

A switch in letters leads to the "creation" of Eszett (ß)-catenin rather than beta (ß)-catenin.

A simple replacement-most likely due to a linguistic error-of the Greek letter beta (ß) by the German letter Eszett (ß), has led to the introduction of an error in a body of literature related to beta (ß)-catenin, resulting in the "creation" of a non-existent compound and false positive, Eszett (ß)-catenin. A search on 9 December 2023 in PubMed for ß-catenin and ß-catenin revealed 395 and 45,919 results, respectively. The 25 results of ß-catenin published in 2023 were examined in more detail to appreciate the location(s) in each paper where this error had occurred. While the scientific findings of these studies do not seem to be impacted by this error, authors and editors would need to weigh the need or benefit of correcting this error.

Against Over-reliance on PRISMA Guidelines for Meta-analytical Studies.

The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were elaborated to allow authors of such papers to identify quality articles for inclusion in their scholarly work. However, we have identified several issues that point to an over-reliance on the PRISMA guidelines. Firstly, we question the rigor of implementation by authors and the rigor of verification by peer reviewers and editors, and whether they have screened papers to ensure adherence to the PRISMA guidelines. Secondly, we have identified cases where the PRISMA criteria led to as much as 99.97% of the published literature being ignored, suggesting that valid publications meeting these criteria might be at risk of being ignored. Thirdly, we have noted that exclusion is not only a quantitative problem-it is also a qualitative one, since the screening procedure groups all non-conforming literature into one basket. Fourthly, we have noted that seven copies of the PRISMA guidelines exist. This being the case, which one should be cited? To replace over-reliance on PRISMA screening, we encourage authors, peer reviewers, and editors to publish systematic reviews and meta-analyses that respect the dual criteria of scientific plausibility and diversity of included papers.

Linguistic precision, and declared use of ChatGPT, needed for radiology literature.

There is a need to ensure the accuracy of linguistic descriptors in the medical literature, including that related to radiology, to allow peers and professionals to communicate ideas and scientific results in a clear and unambiguous manner. This letter highlights an issue that could undermine the clarity of scientific writing in radiology literature, namely the presence of non-standard terminology for established jargon, and emphasizes the need for authors to transparently declare the use of language editing services and AI-driven tools, such as ChatGPT, if these have been used to formulate text and ideas in their papers. Ultimately, clear radiology papers that are compliant with current publishing ethics will serve radiologists and patients well.

An artificial intelligence tool misclassifies sport science journals as predatory.

OBJECTIVES: The choice of a scholarly journal, as opposed to a predatory journal, might impact a sport scientist's career negatively if the wrong choice is made, especially at an early stage of their research and publishing careers. Artificial intelligence (AI) is increasingly impacting sport science and academia. In this study, we tested the accuracy and sensitivity of an AI-driven tool, applied specifically to sport science. DESIGN: Our research relies on the use of a new and free online AI-driven tool, the AJPC System, which claims the ability to distinguish "normal" (scholarly) from "suspected predatory" (unscholarly) journals. METHODS: The AJPC System was used to assess (1 December 2023) the classification of all ranked sport journals (n = 124), namely those in all four quartiles (Q1-Q4) of SCImago Journal Rank (SJR), in the "Sports Science" category. RESULTS: The AJPC System considered 47/124 journals to be "suspected predatory", mostly in Q4 journals (54.8 % of total), casting a negative image on their academic standing. CONCLUSIONS: Sport scientists are likely to consider SJR Q1-Q4 journals to be relatively safe to publish in, reliable and reputable, and might be confused with the "suspected predatory" label assigned to 37.9 % of those journals. The AJPC System is thus misleading sport scientists.

What does ChatGPT advise about predatory publishing?

The debate surrounding "predatory publishing" continues to be unable to find entirely effective solutions to dealing with this problem, despite fervent efforts by many academics and policy makers around the world. Given this situation, we were interested in appreciating whether ChatGPT would be able to offer insight and solutions, to complement current human-based efforts.

Identification of the CONSTANS-like family in Cymbidium sinense, and their functional characterization.

BACKGROUND: Cymbidium sinense is an orchid that is typically used as a potted plant, given its high-grade ornamental characteristics, and is most frequently distributed in China and SE Asia. The inability to strictly regulate flowering in this economically important potted and cut-flower orchid is a bottleneck that limits its industrial development. Studies on C. sinense flowering time genes would help to elucidate the mechanism regulating flowering. There are very few studies on the genetic regulation of flowering pathways in C. sinense. Photoperiod significantly affects the flowering of C. sinense, but it was unknown how the CONSTANS gene family is involved in regulating flowering. RESULTS: In this study, eight CONSTANS-like genes were identified and cloned. They were divided into three groups based on a phylogenetic analysis. Five representative CsCOL genes (CsCOL3/4/6/8/9) were selected from the three groups to perform expression characterization and functional study. CsCOL3/4/6/8/9 are nucleus-localized proteins, and all five CsCOL genes were expressed in all organs, mainly in leaves followed by sepals. The expression levels of CsCOL3/4 (group I) were higher in all organs than other CsCOL genes. Developmental stage specific expression revealed that the expression of CsCOL3/4/9 peaked at the initial flowering stage. In contrast, the transcript level of CsCOL6/8 was highest at the pedicel development stage. Photoperiodic experiments demonstrated that the transcripts of the five CsCOL genes exhibited distinct diurnal rhythms. Under LD conditions, the overexpression of CsCOL3/4 promoted early flowering, and CsCOL6 had little effect on flowering time, whereas CsCOL8 delayed flowering of Arabidopsis thaliana. However, under SD conditions, overexpression of CsCOL4/6/8 promoted early flowering and the rosette leaves growth, and CsCOL3 induced flower bud formation in transgenic Arabidopsis. CONCLUSION: The phylogenetic analysis, temporal and spatial expression patterns, photoperiodic rhythms and functional study indicate that CsCOL family members in C. sinense were involved in growth, development and flowering regulation through different photoperiodic pathway. The results will be useful for future research on mechanisms pertaining to photoperiod-dependent flowering, and will also facilitate genetic engineering-based research that uses Cymbidium flowering time genes.

Improved chromosome-level genome assembly of Indian sandalwood (Santalum album).

Santalum album is a well-known aromatic and medicinal plant that is highly valued for the essential oil (EO) extracted from its heartwood. In this study, we present a high-quality chromosome-level genome assembly of S. album after integrating PacBio Sequel, Illumina HiSeq paired-end and high-throughput chromosome conformation capture sequencing technologies. The assembled genome size is 207.39 M with a contig N50 of 7.33 M and scaffold N50 size of 18.31 M. Compared with three previously published sandalwood genomes, the N50 length of the genome assembly was longer. In total, 94.26% of the assembly was assigned to 10 pseudo-chromosomes, and the anchor rate far exceeded that of a recently released value. BUSCO analysis yielded a completeness score of 94.91%. In addition, we predicted 23,283 protein-coding genes, 89.68% of which were functionally annotated. This high-quality genome will provide a foundation for sandalwood functional genomics studies, and also for elucidating the genetic basis of EO biosynthesis in S. album.