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.

Prevalence of helmintic infections in Brazilian Maxakali indigenous: a repeated cross-sectional design.

BACKGROUND: The prevalence of intestinal parasites is known to be high among Amerindian populations; further, there are serious problems in the healthcare of these populations in Brazil. The Maxakali, located in the northeastern region of Minas Gerais, Brazil, is an indigenous group that still preserves many of its cultural aspects. This study aimed to compare the positivity rate of schistosomiasis and soil-transmitted helminths in this ethnic group in epidemiological surveys conducted in 1972 and 2014. METHODS: Stool parasitological examinations were performed by the Kato-Katz technique during both periods in this population. In 2014, the parasitological diagnosis was also realized with the TF-Test® technique. RESULTS: In 1972, 270 inhabitants were examined. The positivity rates were 67.4% for Schistosoma mansoni, 72.9% for hookworms, 43.7% for Ascaris lumbricoides, and 23.7% for Trichuris trichiura. In 2014, 545 individuals were examined, and the positivity rates obtained were 45.7% for S. mansoni, 22.8% for hookworms, 0.6% for A. lumbricoides, and 2.8% for T. trichiura. CONCLUSIONS: The comparison of the parasitological surveys conducted in 1972 and 2014, indicates that the indigenous Maxakali remained neglected by the health and indigenous protection authorities during these four decades. The infection rate observed in 2014 for schistosomiasis and hookworm remains high, considering the current epidemiological view of these diseases in the Brazilian population.

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.

Editors and Authors of Medical Journals Should Be Mindful of the New ICMJE Disclosure Form and Updated Policies.

The International Committee of Medical Journal Editors (ICMJE) recommendations are used by medical journals worldwide to guide editors and authors regarding "best practices" related to the intersection between research and publishing. In this opinion paper, we bring two discussion points to the attention of readers and users of the ICMJE recommendations. The first pertains to journals' use of the old conflicts of interest form, replaced in 2021 with a new disclosure form. The second relates to inconsistent or outdated policies in journals' instructions for authors mismatching the current ICMJE recommendations. The ICMJE does not monitor how journals use or apply the ICMJE recommendations. Thus, the editors must be mindful of updates and changes relevant to the authors. Furthermore, authors should carefully examine journals before submission to ensure that journals use updated forms and policies and should be mindful of submitting to non-ICMJE-recommendations-conforming journals despite claiming to follow them.

The author expression ​of concern (AEOC): A proposed formal mechanism to allow authors' legitimate concerns to be heard, and their rights and voices to be respected.

We propose a type of DOI-based manuscript, the author expression of concern (AEOC), allowing authors to formally publish their concerns about legitimate procedural problems associated with editors, reviewers, journals or publishers. Managed by a neutral third-party arbitrator or moderator, AEOCs would be limited in size and subjected to fair but strict screening of presented evidence. When an AEOC is approved for publication by an arbitrator, the criticized party would also need to formally respond within a reasonable period, as a "letter to the author(s)", which is also screened by the same arbitrator. Expanding the range of publishing options for authors, as AEOCs, would allow them to voice their legitimate concerns related to a journal's procedures in a formalized format. Although implementation might be challenging at first, it could demonstrate the fairness of editorial policies and democratize the publication process by taking authors' legitimate expressions of discontent related to procedure, and their rights of expression into account, elevating them to a formal article status, allowing for a more balanced two-way system of accountability and openness. Author empowerment that matches editorial and publisher empowerment is essential for a journal to truly claim to be fair, just and accountable.