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In the English language, when a sentence contains all letters of the alphabet, such as "The/A quick brown fox jumps over the lazy dog", this is known as a pangram. Curiously, despite its odd meaning, this fox-dog pangram has found practical usage in some applications, mainly in text typography related to computer graphics, in linguistics, as a writing tutorial, or for testing computer keyboards. Even more curiously, it has been detected as a residual of template text in some academic papers. This unique linguistic curiosity was examined by screening Scopus and Web of Science, as well as Google Scholar from 2019–2023, to appreciate its practical use, as well as to assess whether there were any cases of residual template text, the main target of this exercise. In the latter case, this letter advocates for the removal of this residual text, in the form of a literary correction. [ABSTRACT FROM AUTHOR]

On occasion, following the publication of a paper, serious concerns might be raised, either about the study, the author(s), or background processes. When editors-in-chief (EiCs) have sufficient evidence in the case of a serious ethical offense or methodological errors that may invalidate the paper's findings or ethical standing, they can retract the paper rapidly. However, in the interim period between receiving a report and seeking a solution, several weeks, months or even years might pass, and readers need to be alerted to its potential unreliability. In such an instance, the current alternative (but not corrective) document takes the form of an editorial expression of concern (EoC). However, a case might be unresolved for a long time, with an EoC attached to it, so EiCs are encouraged to seek a resolution as promptly as possible because there are academics who might need to cite and/or rely on that paper. Curiously, even though a comprehensive debate is provided by COPE ethics guidelines and ICMJE recommendations, which refer to EoCs, guidance is not entirely clear. This paper makes an attempt to improve guidelines that editors could consider when faced with the dilemma of whether to issue an EoC, or not. [ABSTRACT FROM AUTHOR]

Lysine acetylation, an evolutionarily conserved post‐translational protein modification, is reversibly catalyzed by lysine acetyltransferases and lysine deacetylases. Lysine acetylation, which was first discovered on histones, mainly functions to configure the structure of chromatin and regulate gene transcriptional activity. Over the past decade, with advances in high‐resolution mass spectrometry, a vast and growing number of non‐histone proteins modified by acetylation in various plant species have been identified. Lysine acetylation of non‐histone proteins is widely involved in regulating biological processes in plants such as photosynthesis, energy metabolism, hormone signal transduction and stress responses. Moreover, in plants, lysine acetylation plays crucial roles in regulating enzyme activity, protein stability, protein interaction and subcellular localization. This review summarizes recent progress in our understanding of the biological functions and mechanisms of non‐histone protein acetylation in plants. Research prospects in this field are also noted. [ABSTRACT FROM AUTHOR]

Plant transcription factors (TFs) are integral proteins associated with gene transcription. That ability arises after TFs bind to specific DNA sequences, such as promoters, responding positively or negatively to a multitude of endogenous and exogenous factors or stressors. For this reason, in plants, the vast majority of TFs are associated with growth, development, and responses to biotic and abiotic stresses. As is commonly known, the genes coding for TFs are written in uppercase italics, whereas the resulting proteins are written in lowercase, such as OsWRKY28 and OsWRKY28, respectively for a member of the WRKY TF family in rice (Oryza sativa L.). However, despite the existence of some conventions for the nomenclature of TFs, some deviation from these norms has been observed in the literature. Several cases are highlighted, primarily related to NAC TFs. These cases emphasize the need for stricter quality control of literature pertaining to the nomenclature of plant TFs. [ABSTRACT FROM AUTHOR]

The B-box (BBX) family, which is a class of zinc finger transcription factors, exhibits special roles in plant growth and development as well as in plants' ability to cope with various stresses. Even though Rubus chingii is an important traditional medicinally edible plant in east Asia, there are no comprehensive studies of BBX members in R. chingii. In this study, 32 RcBBX members were identified, and these were divided into five groups. A collinearity analysis showed that gene duplication events were common, and when combined with a motif analysis of the RcBBX genes, it was concluded that group V genes might have undergone deletion of gene fragments or mutations. Analysis of cis-acting elements revealed that each RcBBX gene contained hormone-, light-, and stress-related elements. Expression patterns of the 32 RcBBX genes during fruit ripening revealed that highest expression occurred at the small green fruit stage. Of note, the expression of several RcBBX genes increased rapidly as fruit developed. These findings, combined with the expression profiles of anthocyanin biosynthetic genes during fruit ripening, allowed us to identify the nucleartargeted RcBBX26, which positively promoted anthocyanin production in R. chingii. The collective findings of this study shed light on the function of RcBBX genes in different tissues, developmental stages, and in response to two abiotic stresses. [ABSTRACT FROM AUTHOR]

In environmental science, it is necessary to accurately describe processes, methods and phenomena using established technical terms and jargon. Any significant deviation from such terms might leave readers and peers confused, while confusion can lead to misinterpretations, opening up the possibility of errors. During peer review and prior to publication in a peer-reviewed environmental journal, it is thus incumbent upon editors and peer reviewers, and to a lesser extent copy editors, to verify that terminology in a scientific paper is accurate. In this brief communication, 61 papers with cases of ‘tortured phrases’, which are terms that have-for some reason-come to replace established jargon, are described in indexed environmental literature, frequently in indexed journals that are generally associated with reputable publishers. Of the 61 papers, 13 have been retracted, suggesting an erosion of the papers’ integrity. Awareness of this phenomenon and these cases allows editors and peer reviewers of environmental journals to be more careful when screening and vetting submitted papers, but should also serve as a lesson for authors to be more careful when writing their papers, avoiding the temptation to automatically incorporate text that online text thesauruses may provide, or to use non-standard terms. [ABSTRACT FROM AUTHOR]

While guest or honourary authorship in academic papers is a broadly and widely discussed phenomenon in biomedical research, the issue of the use—or abuse—of article-processing charges (APCs) as a form of potential authorship exchange currency, that is, the 'APC ring,' is neither being considered nor discussed. The APC is central to the open-access (OA) movement, specifically the gold OA model. It is conceivable that, in a hyper-competitive academic publishing environment where the number of gold OA journals is growing, a segment of poorly funded researchers aiming to publish in ranked OA journals with out-of-reach APCs might turn to richer or well-funded researchers to cover the APC bill in exchange for authorship. Despite this, no published cases directly documenting APC-for-authorship schemes as a form of guest authorship appear to exist, which seems inconceivable. One possible explanation is that if such unethical behaviour were to be detected by APC-charging OA journals, it might not be reported as such. In this situation, APC-dependent OA journals would be conflicted between receiving a financial lifeline, the APC, and exposing authors that have abused the APC in their journals in exchange for authorship. How would publishers dependent on the APC-based OA model justify receiving APCs derived from an APC ring? Although this form of guest authorship is currently hypothetical, it seems highly likely, so this issue needs greater debate, and if actual case studies exist, these need to be openly and publicly debated to better appreciate how this phenomenon is taking place. [ABSTRACT FROM AUTHOR]

Due to their soft and hard skills, retirees in any field of study, including the arts, humanities, social, natural and biomedical sciences, mathematics and engineering, carry a wealth of experience, both personal and professional, could continue to be of benefit to students and early career researchers, even after they have retired. Their educational background and experience could enrich the education knowledge stream if their input, expertise and skills could be tapped after retirement, provided that they are physically and/or mentally healthy, able to communicate their ideas in a clear, lucid, and constructive way, and have accompanied support. Perspectives are offered about how retirees could benefit the research and education knowledge stream across disciplines in schools and institutes of higher education, such as universities. [ABSTRACT FROM AUTHOR]

Autumn daffodil (Sternbergia lutea) is a wild bulbous plant with tremendous ornamental value. Knowledge of the changes that occur during dormancy would be helpful to improve breeding strategies for this geophyte, its artificial cultivation for application in landscaping, and its commercialization. In a Mediterranean climate, the plant enters dormancy in June (stage 1, S1), dormancy proper, which lasts for two months [July and August; stage 2 (S2)], while September and October [stage 3 (S3); i.e., autumn] represent the exit from dormancy and the start of flowering. In this research, the biochemical changes in four tissues of bulbs (outer scales, inner scales, basal plate and bud) in the three stages (S1–S3), as well as in the leaves and roots of plants in two stages (S1, S3), were assessed. The total soluble protein, proline, phenolic and hydrogen peroxide (H2O2) contents in almost all tissues of the bulb increased from S1 to September (the first month of stage 3), but then decreased in October (the second month of stage 3). In contrast, total soluble carbohydrate content and superoxide dismutase (SOD) activity decreased during S2 but increased in S3. Malondialdehyde (MDA) content and peroxidase (POD) activity increased in S1–S3. In leaves and roots, proline, H2O2, and MDA content, as well as POD and SOD activity, were highest in S1. In contrast, total soluble carbohydrate and total soluble protein contents were highest in S3. The findings of this experiment will help to better understand autumn daffodil bulb dormancy from a biochemical perspective, allowing for more effective management of commercial bulb propagation and production, as well as transportation. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

This letter to the editor discusses the risks associated with relying on artificial intelligence (AI) text, specifically OpenAI's ChatGPT, for scientific writing. The authors conducted an experiment to test ChatGPT's ability to provide accurate estimates of the surface area of lakes worldwide. However, ChatGPT was unable to provide accurate information and did not acknowledge or reference the relevant scientific literature. These findings support previous concerns about the reliability and accountability of AI-generated text. [Extracted from the article]

The article discusses the use of "tortured phrases" in biomedical literature, specifically focusing on the term "bosom malignancy" in breast cancer literature. The author highlights how inaccurate or inappropriate terms can compromise the integrity of scientific output and emphasizes the importance of peer reviewers and editors in scrutinizing papers for such issues. The study conducted by an independent researcher identified instances of "bosom malignancy" in breast cancer literature, raising concerns about the impact of these phrases on the accuracy and integrity of scientific papers. The article also mentions the potential use of AI to detect and reverse such phrases, highlighting the need for effective detection methods in scientific writing. [Extracted from the article]

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. [ABSTRACT FROM AUTHOR]

Authors with compound family names face a constant set of challenges in having their names accurately represented in the scientific literature. In my personal case (Teixeira da Silva, JA), an as-yet-unquantified body of literature miscites me (and thus my work) as "da Silva, JAT", "Silva, JA", or other inaccurate forms. This paper provides evidence of the modification and thus misrepresentation of my professional publishing name in proofs of select papers eventually published in Springer Nature journals, despite the accuracy of metadata at the submission and acceptance stages. This record may also be helpful for other scientists with non-standard or compound family names, who may have had a similar experience. Springer Nature currently outsources the development of its proofs to Straive. Possible reasons as to why this misrepresentation might be occurring, and some solutions, are proposed. The misrepresentation of an author's professional publishing name may cause them reputational damage by distorting their publishing record, so publishers need to be aware of this issue and take appropriate measures to avoid such errors, correcting them whenever they are discovered and reported. [ABSTRACT FROM AUTHOR]

As a purely academic exercise of interest, and spurred by a curious debate in a blog entry over a decade ago, the purpose of this paper was to appreciate the incidence of select movie (film) titles in the titles of papers indexed in Scopus. Using 11 of the first 20 titles of a top 100 list of movie classics at the "Rotten Tomatoes" website, we assessed (January 2024) how frequently they appeared in the titles of those papers. While the vast majority of movie titles referred to the movie (or book version) itself, except for "The Wizard of Oz", which had 74.6% positive results for a software with this name, we found that some authors may have employed such titles to draw attention to their papers because readers would likely to be drawn to them due to familiarity with the movie title, or name recognition. To test this hypothesis, we assessed citation counts relative to the average of other papers published in the same journals and in the same years, finding that 83% of the 95 papers assessed had lower citation counts than the average of papers published in the same journal and in the same year. We also considered the ethics of the verbatim use of movie titles, especially of movies that may be copyrighted, when quotation marks are not used, or the absence of a note within the paper itself to indicate the source of the title's inspirational wording. Although we are cognizant of several limitations to this study, which serves as an initial springboard for additional future multidisciplinary studies, we suggest some additional research ideas to popularize the intersection between film studies, basic academic sciences, bibliometrics, and publishing. [ABSTRACT FROM AUTHOR]

The video assistant referee (VAR), popularized in football (soccer), has been decisive in many games played in several international and domestic competitions ever since the Fédération Internationale de Football Association (FIFA) formalized its use for the first time in the 2018 Men's Football World Cup. Serving as a support tool for on-field referees, it is not only a game unifier but also a conflict pacifier by using a technology-based method to objectively appreciate whether human decisions were accurate and fair or erroneous and thus in need of correction. Given the overwhelming support evidenced by its broad adoption, but also some criticisms and concerns about this technology, an objective assessment of the growing literature on VAR is timely to take stock of what is known and what is still unknown about its use and perception. Using primarily indexed English literature from 2018 to 2024, this narrative review aims to gauge four main talking points related to VAR, including, but not limited to, the technology used, why VAR is perceived as controversial, and its perception in a socio-cultural context. This review underscores the positive perception of referees towards VAR, highlighting improved decision accuracy and minimal match disruption. Fans and media express trust in VAR, but call for refinements. Concerns about in-stadium communication with spectators suggest a need for enhanced decision transparency. We also acknowledge limitations, including language bias, literature (un)availability and sex-based disparities, while proposing future research avenues. Overall, VAR has become integral to football, shaping its officiating landscape, and inviting continuous improvement. [ABSTRACT FROM AUTHOR]

The human factor in decision-making in tennis, like so many sports, plays a fundamental part of its ambience and/or drama or entertainment. This is because some line calls by some line umpires can be dubious, or even incorrect. In tennis events that allow for challenges to line calls, an artificial intelligence-based referee, in the form of electronic line calling (ELC), is then used to resolve the challenge, and the result is handed out by the chair umpire. This commentary debates the merits and demerits that may be associated with the total elimination of human line umpires by employing ELC. [ABSTRACT FROM AUTHOR]

A recent paper published in European Science Editing (ESE; https://doi.org/10.3897/ese.2023.e102691) assessed that journal's citations in 38 papers published between 2020 and 2022 using Dimensions and Scopus. The rationale for that study was that Dimensions, unlike Scopus, was "free", and thus a useful substitute for bibliometric analyses, but it is contended herein that the latter claim is not entirely accurate. To complement that analysis, citations of the same 38 papers, as well as 29 papers that had not been analyzed, giving the full complement of 67 papers published in ESE from 2020 to 2022, were reassessed (17 October 2023) using Scopus, Dimensions, and Google Scholar, since the latter is free. In addition, those papers' attention scores were appreciated from their Altmetrics scores, which were harvested from Dimensions. Although citation trends for the 38 papers were replicated, when the Altmetric scores of the additional 29 papers were also considered, the Altmetric score for ESE increased by 221 from 633 to give a total of 854. [ABSTRACT FROM AUTHOR]

A simple replacement—most likely due to a linguistic error—of the Greek letter beta (β) by the German letter Eszett (ß), has led to the introduction of an error in a body of literature related to beta (β)-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 β-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. [ABSTRACT FROM AUTHOR]

Four publishing-related organizations, the Committee on Publication Ethics (COPE), the Directory of Open Access Journals (DOAJ), the Open Access Scholarly Publishers Association (OASPA), and the World Association of Medical Editors (WAME), the first being dedicated specifically to the creation and dissemination of ethics policies, established a set of 16 principles related to journal and publisher transparency and “best” publishing practices. The first, second, third and fourth versions were published in 2013, 2015, 2018, and 2022, respectively. Membership of these organizations implies that members can only become such if they satisfy these principles. This paper compares the four versions to appreciate how the content has changed over time, as a historical endeavor to gather how publishing ethics has progressed over time. An assessment is also made to determine whether all principles are related to transparency and best principles, and if any may be missing. We concluded that the 16 principles offer broad guidance to several important aspects related to journal and publishing ethics and management. However, the vast majority are in general excessively broad, occasionally vague, or lack sufficient examples or specifics, despite the slight improvement between versions 3 and 4. We argue further that these weaknesses may limit their practical application. Until September 2022, there was no transparency regarding the consequences for any members that might violate, or not abide by, these principles. In the light of these arguments, we are of the opinion that the 16 principles of “best” publishing practices merit additional improvements. [ABSTRACT FROM AUTHOR]

In order to evaluate the effect of Glomus versiforme fungus on genes and metabolites related to the biosynthetic pathway of polyamines in pot marigold under drought stress, an experiment was conducted at three irrigation levels [100, 65, and 35% of field capacity (FC)] for 1, 2, 4, and 8 d in mycorrhizal (M) and non-mycorrhizal (NM) plants. At both 35 and 65% FC, putrescine (Put) accumulation peaked at 1 d. Accompanying the accumulation of Put at 1 d, there was an increase in the expression of ARG and ODC genes directly involved in the Put biosynthetic pathway, as well as the ADC, AIH, and CPA genes involved in the indirect Put biosynthetic pathway. At 1 d, M plants induced the accumulation of Put and increased the expression of ADC, AIH, and CPA, but had no significant effect on ODC expression. At both 35 and 65% FC, SAMDC gene expression increased from 1 to 8 d, and the expression of this gene was higher in M plants from 2 to 8 d. At both drought levels, highest Spd content and SPDS gene expression were observed at 2 d. Moreover, Spd accumulation from 2 to 8 d and SPDS gene expression from 4 to 8 d were higher in M plants than in NM plants. At both drought levels, Spm content and SPMS gene expression increased between 4 and 8 d, during which the accumulation and expression level of this gene in M plants was higher. [ABSTRACT FROM AUTHOR]

There are ample national, transnational, and international geopolitical conflicts around the world, the two most prominent likely being the current ongoing Russo-Ukrainian war, and the conflict between Taiwan (the Republic of China) and China (the People's Republic of China). To avoid criticism or the label of political bias, academics might refrain from using the term Taiwan or might not refer to it as a country. Similarly, they might not know whether they should refer to Crimea or the Donbas as being Ukrainian or Russian. Authors currently have little guidance and are somewhat left to their own devices when it comes to referring to these and other locations and territories, uncertain of the names that should be used to indicate them. They might also observe disclaimers on publishers' websites, in the footer of editorial board pages, or even as a small notice in their own manuscripts placed there by the publisher that distance the publisher from geopolitical conflicts and/or territorial claims, claiming neutrality, independent of whether those papers mention those conflicts, or not. Such disclaimers might be perceived as self-serving, placing the onus of responsibility of the choice of territorial term on authors' shoulders, so publishers should offer clearer advice to authors and editors on how to better handle this issue, that is, how to accurately name locations in geopolitically sensitive areas. There is a risk that papers that are insufficiently sensitive to such issues may be labelled as erroneous, and subjected to correction or retraction, or the authors may be subjected to public criticism or humiliation, so resolving this issue falls within the realm of academic publishing ethics. Currently, very little advice exists for geopolitical issues in the Committee on Publication Ethics and International Committee of Medical Journal Ethics ethics-related publishing guidelines. [ABSTRACT FROM AUTHOR]

Key points: Academia is already witnessing the abuse of authorship in papers with text generated by large language models (LLMs) such as ChatGPT.LLM‐generated text is testing the limits of publishing ethics as we traditionally know it.We alert the community to imminent risks of LLM technologies, like ChatGPT, for amplifying the predatory publishing 'industry'.The abuse of ChatGPT for the paper mill industry cannot be over‐emphasized.Detection of LLM‐generated text is the responsibility of editors and journals/publishers. [ABSTRACT FROM AUTHOR]

Purpose: The purpose of this paper is to reflect on the creation of safe academic (education and research) environments that offer proper protections to adult academics and staff, so that academia and society at large may benefit from the fruits of safe workplaces. Not all academic environments are entirely safe, and there are recorded cases of victims of harassment and sexual abuse. Design/methodology/approach: Given that co-workers in a laboratory, or research subjects in a research project, may be victims of harassment or sexual abuse, and that the same individuals may then become co-authors or anonymized research subjects, respectively, in academic papers, there is a need to appreciate what structural protection exists for such victims at the post-publication level. What should academia do with the literature of legally recognized sex offenders who have published in peer-reviewed and indexed academic journals? Findings: Currently, there is no specific guidance by ethics organizations (e.g., Committee on Publication Ethics and International Committee of Medical Journal Editors) to deal with this issue, so protective mechanisms for adult victims, as well as punitive measures against perpetrators at the post-publication stage, are needed. Originality/value: There may be career-altering repercussions – personal, professional and reputational – for co-authors of legally recognized sex offenders in papers published in peer-reviewed and indexed journals. There may also be life-altering outcomes to victims of sexual abuse who are the study subjects of such papers. Thus, a robust form of post-publication protection (and justice) based on unbiased and independent ethical and legal investigations, coordinated by editors, publishers and research institutes, needs to be established. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Knowledge pertaining to scholarly publishing is not limited to information held within academic papers, and within a complex publishing environment that is in constant flux due to challenges and threats, there is interest in knowing how journals are adjusting to these parameters. The Internet Archive is a free and easy way to archive information that is found on websites. We recently argued for its use in the archival of website-based citations, and expand those arguments herein to focus on the importance to archive journal editorial boards, for three reasons: first, journals might not have any formal mechanisms to register changes in the editorial constitution of the board; second, there is historical importance in appreciating changes to editorial board constituency, including changes to gender representation; and third, changes might be made opaquely to hide or masquerade information that is intricately linked to the historical aspect of that journal. Our interest is thus not only within a historical prism, but also from a bibliometric point of view, given that the editorial board defines—to some extent—the journal's content by serving as its gatekeepers of quality. We attempted to archive the editorial board pages of 46 journal editorial board URLs, achieving 100% mementos. [ABSTRACT FROM AUTHOR]

The Committee on Publication Ethics (COPE) is a leading ethics-promoting organization associated with academic publishing. COPE continuously fortifies its ethics guidelines, also serving as a warning portal of "predatory" publishing behavior. A 2019 COPE discussion document on "predatory publishing" lists 16 warning signs of predatory publishers/journals. Grounded in legitimacy theory, this study examines, by adopting COPE's 16 warning signs of "predatory publishing" as criteria, the case of a current COPE member publisher, Academic and Business Research Institute (AABRI). Our assessment reveals that, according to COPE's own stated criteria, AABRI would be considered as "predatory." The objective of this case study was to appreciate whether COPE's 16 warning signs may be insufficiently sensitive to detect a predatory journal or publisher, or whether those criteria require an adjustment if the journal/publisher is academically legitimate but is found to be otherwise. If such criteria were to be used widely by academics (and others) to characterize journals or publishers, but result in a surprising or undesired negative classification ("predatory"), then this may have widespread ramifications not only for global academia but also for scholarship and society at large. An incorrect classification could also negatively impact the COPE "brand" of ethical and scholarly legitimacy. [ABSTRACT FROM AUTHOR]

The letter to the editor discusses the implications of stricter regulations on the use and analysis of Twitter and other social media platforms in academic publishing. The authors argue that recent restrictions placed by Twitter on public access to tweets hinder open communication and go against the principles of open science. They suggest that researchers should be required to provide the raw data of their Twitter-based research as hard-copy evidence to ensure transparency and reproducibility. The authors also highlight the lack of specific guidelines for Twitter-based research in journal policies and recommend that journals make the raw tweet datasets publicly available. [Extracted from the article]

For data information scientists, librarians and academics alike, it is a worrisome sign when information or a file opaquely disappears from the body of scientific literature, even more so when it carries a digital object identifier (DOI). This is because the DOI typically offers a published paper a form of digital permanence. Preprints are being increasingly fused into the publication stream, serving as a prelude to submission to a peer-reviewed journal. One of the main preprint servers is Elsevier's SSRN. This paper, a rare case study, describes three preprints by the same authors related to peer review that were withdrawn (i.e., retracted). Apart from a short notice with identical text ("This paper has been removed from SSRN at the request of the author, SSRN, or the rights holder"), no date of the withdrawals and no explanation were publicly provided. Following queries to the authors and SSRN, the three preprints were reinstated around February 2023. Finally, the original title of two of the preprints was manipulated in the reinstated preprints. This historical case study not only highlights the risks of opaque preprint withdrawals, but also the ease with which information on preprint servers (in this case SSRN) can be modified and/or manipulated. [ABSTRACT FROM AUTHOR]

The debate on "predatory" publishing within academic scholarly communication continues. Blacklists (or watchlists) pertaining to "predatory" open access publishing by Jeffrey Beall, anonymous websites that cloned Beall's blacklists, with or without updates, as well as a now-defunct blacklist, Dolos list, contain classification errors. During a Google search in 2021–2022, we found that dozens of academic libraries around the world, primarily in the USA, had continued to promote those blacklists. The list was revisited on 23 February 2023, focusing on libraries in seven Anglophonic countries, noting that 37 libraries were still promoting the Beall-based blacklists. [ABSTRACT FROM AUTHOR]

In this paper, we reflect on how the principle of the 'right to be forgotten' (RTBF), specifically the right to erasure as enshrined in Article 17 (and to some extent Art. 19 and Art. 21) of the General Data Protection Regulation (GDPR; Regulation (EU) 2016/679), or the right to delete undesirable, unflattering or reputation‐damaging archived records of oneself from search engines or databases, might apply to academic publishing. In particular, we focus on archival (library and information) science, post‐publication peer review, and reflect on whether RTBF is compatible with open science principles. Even though RTBF became enshrined in EU law in 2018, its trans‐Atlantic export to the United States faces resistance because it is seen as being incompatible with First Amendment rights. We ponder the pertinence of the debate regarding local versus global applicability of RTBF when considering the transnational nature of some collaborative research. Although RTBF applies broadly to search engines such as Google, we question whether authors have this right and also whether publishers are subjected to this law with respect to science databases, or even 'local' (i.e., publisher‐controlled) archives, especially in the light of retractions or withdrawals, in which data and files are removed from a preprint or journal's website or, in extreme cases, where all or most bibliometric information is scrubbed clean, as in the case of 'silent retractions'. We extend our reflections further to appreciate whether authors or editors are entitled to RTBF in extreme instances of misconduct or fraud. The fundamental right to privacy and personal choice, as is suggested by (or enshrined in) RTBF, is not—in our view—compatible with several principles related to the integrity of data and information, or even their preservation, and may be diametrically opposed, depending on the situation. We encourage wider debate on this budding pertinent issue as a fundamental aspect of academic rights and freedoms. [ABSTRACT FROM AUTHOR]

The SCImago Journal Rank (SJR) ranks journals into four quartiles (Q1–Q4). SJR serves as a safelist for journal selection, when trying to avoid predatory journals, as journals that have been indexed by SJR are seen as having stringent publishing standards. An AI-based tool, the Academic Journal Predatory Checking System (AJPC), claims to be able to differentiate suspected predatory journals from normal journals. In this study, we asked (25 March 2023) AJPC to classify the top 2500 journals (based on SJR ranking). We found that 65.64% of these journals were classified as "suspected predatory", 33.28% were classified as "normal", while 1.08% of the journals could not be classified. A follow-up run (30 March 2023) returned different results (89.20%, 10.16% and 0.64%). This set of results is worrying, not only because of the number of SJR journals that are thought to be "predatory", but also because of the difference in results when using the same tool a matter of days apart. We extended our analysis and looked at seven stand-alone publishers (Elsevier, Frontiers, MDPI, OMICS, Springer Nature (incl. Nature Portfolio), Taylor & Francis and Wiley). In total, we asked AJPC to classify 17,721 journals. The results confirm that we should be concerned about the classifications provided by AJPC. For example, 100% (4756) of Elsevier journals were classified as "suspected predatory". Even Springer Nature (which includes the journal that published the AJPC paper) has journals which were classified at "suspected predatory". We thus urge caution against relying on AJPC at present. We also urge the AJPC's authors to provide an explanation as to why a journal is classified in a particular way, as part of their user interface. We are willing to conduct further analyses should AJPC be revised and updated as it could provide an important service to the scholarly community. [ABSTRACT FROM AUTHOR]

Acknowledgements are usually a minor part of scientific papers, but they serve a very important function. This section of the manuscript is normally reserved to thank those who offered assistance, but not enough to merit authorship, funders, or any other people or organizations or artificial intelligent tools that may have in any way been directly associated either with the research reported in that study, or with the published paper. Despite this, it is not uncommon to see wide disparities in ethics and author guidelines pertaining to acknowledgements, as was observed in 45 publishing-related entities (journals, publishers, preprints, ethics organizations, open access aggregators) that were assessed in this study. Greater standardization is required, especially among members of ethics policy groups such as the Committee on Publication Ethics or the International Committee of Medical Journal Editors. Moreover, even though verification is an essential step of this process, it is difficult to achieve. [ABSTRACT FROM AUTHOR]

Main conclusion: Santalum album (E,E)-α-farnesene synthase catalyzes FPP into (E,E)-α-farnesene. Overexpression of the SaAFS gene positively improved cold stress tolerance through JA biosynthesis and signaling pathways in Arabidopsis. Volatile terpenoids are released from plants that suffer negative effects following exposure to various biotic and abiotic stresses. Recent studies revealed that (E,E)-α-farnesene synthase (AFS) plays a significant role in a plant’s defence against biotic attack. However, little is known about whether AFS contributes to plant resistance to cold stress. In this study, a SaAFS gene was isolated from Indian sandalwood (Santalum album L.) and functionally characterized. The SaAFS protein mainly converts farnesyl diphosphate to (E,E)-α-farnesene. SaAFS was clustered into the AFS clade from angiosperms, suggesting a highly conserved enzyme. SaAFS displayed a significant response to cold stress and methyl jasmonate. SaAFS overexpression (OE) in Arabidopsis enhanced cold tolerance by increasing proline content, reducing malondialdehyde content, electrolyte leakage, and accumulating reactive oxygen species. Transcriptomic analysis revealed that upregulated genes related to stress response and JA biosynthesis and signaling were detected in SaAFS-OE lines compared with wild type plants that were exposed to cold stress. Endogenous JA and jasmonoyl-isoleucine content increased significantly in SaAFS-OE lines exposed to cold stress. Collectively considered, these results suggest that the SaAFS gene is a positive regulator during cold stress tolerance via JA biosynthesis and signaling pathways. [ABSTRACT FROM AUTHOR]

As the number of retractions of the academic literature increase, there is also a bibliometric interest in appreciating the volume of citations that retracted papers received prior to, and following, a retraction. We assessed the pre- and post-citation counts of one paper each of five classes of retracted papers using the Web of Science Core Collection (WOS-CC). The papers (and their respective DOIs) were: (C1) Data or classification error (https://doi.org/10.1371/journal.pone.0204076); (C2) fraud (https://doi.org/10.1007/s00265-011-1208-0); C3) paper mill (https://doi.org/10.1155/2017/2381482); C4) tortured phrase (https://doi.org/10.1007/s12652-020-02455-4); C5) plagiarism (https://doi.org/10.1016/j.neucom.2012.06.051). C1, C2, C3, C4 and C5 were cited (September 7, 2022) 43, 45, 35, 3, and 16 times, respectively. Separately, noting the shortcomings of the WOS-CC citation classification system for citations, we propose a new four-tier classification system for citation sentiment or use (background; supportive; contradictory; manipulative) that accommodates both the functionality and sentiment of a citation to assess how a retracted paper (or indeed, any paper), is cited. We tested this new classification system using C5. We envision that these two new systems (five classes of retracted papers; four tiers of citation behavior) can further be implemented in citation databases to improve the informative value of these resources. [ABSTRACT FROM AUTHOR]

Finding a niche journal for the submission of an academic paper can sometimes be a challenge for authors, and finding the right choice may involve a series of submissions and rejections. Emails from editors and journals related to the submission or rejection of a paper should be strictly related to these purposes, i.e., to inform authors that their paper has been received, outline the subsequent editorial handling or peer reviewer steps in the former, or the reasons for rejection in the latter. This paper highlights four cases of - in the author's opinion - the abuse of such emails by COPE member journals and publishers (Emerald Publishing Ltd., Springer Nature, Elsevier, Wiley) to advertise for-profit English revision and editing services and/or conferences, as a way to maximize these emails for a dual purpose, namely to inform authors of submission-related aspects (valid communication) while also trying to obtain clients and thus business for non-submission-related aspects (invalid communication). Since an abuse of email-based communication for non-academic purposes is an ethicsrelated matter, there is a need for systematic research of this potential abuse of emails from both COPE member and non-member journals. [ABSTRACT FROM AUTHOR]

Key points: Web‐based references form an integral part of academic culture and literature, as well as scientific communication.The preservation of web‐based references that are cited in‐text or in reference lists of academic papers is essential to ensure the integrity of knowledge preservation.When access or links to web‐based resources and references disappear, or if they are dysfunctional, these phenomena are collectively referred to as reference rot.Even though reference rot degrades the integrity of information in academic papers, no industry‐wide solutions currently exist.Given its prominence, we propose the Internet Archive as a possible solution to address reference rot, but also note its weaknesses and limitations. [ABSTRACT FROM AUTHOR]

Key points: The International Committee of Medical Journal Editors (ICMJE) recommendations for authorship are the dominant guidelines that guide who, and under what circumstances, an individual can be an author of an academic paper.Large language models (LLMs) and AI, like ChatGPT, given their ability and versatility, pose a challenge to the human‐based authorship model.Several journals and publishers have already prohibited the assignment of authorship to AI, LLMs, and even ChatGPT, not recognizing them as valid authors.We debate this premise, and asked ChatGPT to opine on this issue. ChatGPT considers itself as an invalid author.We applied the CRediT criteria to AI, finding that it was definitively able to satisfy three out of the 14 criteria, but only in terms of assistance. This was validated by ChatGPT itself. [ABSTRACT FROM AUTHOR]

In response to a letter by Ansorge, who questioned whether authors or science need the right not to want to be cited, we fully respect his opinion and choice to express that he believes that such a right is not needed. However, we counter that argument by noting that, even in the absence of concrete examples, to have a solid theoretical basis for arguing a right is essential, even if it is not always welcomed, or appreciated by all, or even many. The ability to have an equal right on any two sides of any argument or situation, including those related to the right to cite a paper, or to not cite a paper, or even to be cited, or to not want to be cited, is a fundamental right that we advocated for in our initial letter, and which we fortify in this follow-up letter. [ABSTRACT FROM AUTHOR]

Winter rye (Secale cereale L. cv. Rushnik) seeds were treated with thidiazuron (TDZ; 0.01–10 nmol/L), a plant growth regulator (PGR) with cytokinin-like activity, and grown hydroponically for 7 days. The aim of pretreatment with TDZ was to try and mitigate herbicide-induced stress in winter rye plants. The leaves of 7-days-old seedlings were sprayed with 100 μM of paraquat (PQ), a herbicide, and biochemical and physiological responses were assessed after 4 or 8 h in fully developed leaves. After 8 h, PQ treatment significantly increased H2O2 and lipid peroxidation levels (39% increase for both relative to 0 h) as well as APOX activity (35% increase), but significantly decreased total antioxidant activity (33% decrease) and photosynthetic apparatus activity (up to 38% decrease), as assessed by chlorophyll fluorescence parameters. Pretreatment with TDZ weakened the toxic effects of PQ on rye seedlings, especially 8 h after PQ treatment. This was most evident for low doses (0.01 to 1 nmol/L) of TDZ. An index of efficiency indicated that 0.1 nmol/L TDZ was the most effective concentration to reduce the toxic effect of PQ on winter rye seedlings. This research provides fundamental information about the practical use of TDZ as a means to diminish the toxic effects of a herbicide (PQ) on cultivated winter rye plants. [ABSTRACT FROM AUTHOR]

Bamboo, a fast growing plant, is a valuable and renewable bioresource with great socioeconomic value. Sustainable production is needed to combat industrial overexploitation by the paper, pulp, and fuel industries, as well as improper resource management that has widened the gap between supply and demand. Biotechnology applications, such as in vitro propagation and tissue culture, offer a range of solutions for improved and controlled growth, resulting in a more effective and reliable production chain. Seed propagation is ineffective for bamboo due to low seed viability, while vegetative propagation is limited to small-scale production. Genetic transformation of bamboo species remains limited, although the bamboo genome is now better understood and genetic improvement is possible. This review discusses protocols for in vitro propagation, in vitro flowering, synthetic seed production, and transgenic techniques used to improve bamboo. In addition, the application of next-generation sequencing technology to bamboo plants will be examined for fundamental processes related to growth and stress regulation, lignin and cellulose biosynthesis, secondary cell wall deposition, and flowering behavior. This review will provide researchers with a comprehensive overview and better understanding of bamboo biotechnology for better utilization and adaptation as a sustainable bioresource. Key message: Fast-growing bamboo has significant socioeconomic value. Due to industrial overexploitation and inadequate resource management, there is a growing gap between the supply and demand for bamboo. The use of biotechnology can enhance and regulate bamboo growth for environmentally friendly output. For improved use and adaption as a sustainable bioresource, this review offers a thorough overview of bamboo biotechnology. [ABSTRACT FROM AUTHOR]

Backgroud: Paeonia holds considerable value in medicinal, ornamental horticultural, and edible oil industries, but the incomplete state of phylogenetic research in this genus poses a challenge to the effective conservation and development of wild germplasm, and also impedes the practical utilization of existing cultivars. Due to its uniparental inheritance and lack of recombination, the plastome (i.e., plastid genome), which is a valuable molecular marker for phylogenetic analyses, is characterized by an appropriate rate of nucleotide evolution. Methods: In this study, 10 newly assembled data and available reported data were combined to perform a comparative genomics and phylogenetics analysis of 63 plastomes of 16 Paeonia species, primarily from East Asia, which is the origin and diversity center of Paeonia. Results: Ranging between 152,153 and 154,405 bp, most plastomes displayed a conserved structure and relatively low nucleotide diversity, except for six plastomes, which showed obvious IR construction or expansion. A total of 111 genes were annotated in the Paeonia plastomes. Four genes (rpl22, rps3, rps19 and ycf1) showed different copy numbers among accessions while five genes (rpl36, petN, psbI, rpl33 and psbJ) showed strong codon usage biases (ENC < 35). Additional selection analysis revealed that no genes were under positive selection during the domestication of tree peony cultivars whereas four core photosynthesis-related genes (petA, psaA, psaB and rbcL) were under positive selection in herbaceous peony cultivars. This discovery might contribute to the wide adaption of these cultivars. Two types of molecular markers (SSR and SNP) were generated from the 63 plastomes. Even though SSR was more diverse than SNP, it had a weaker ability to delimit Paeonia species than SNP. The reconstruction of a phylogenetic backbone of Paeonia in East Asia revealed significant genetic divergence within the P. ostii groups. Evidence also indicated that the majority of P. suffruticosa cultivars had a maternal origin, from P. ostii. The results of this research also suggest that P. delavayi var. lutea, which likely resulted from hybridization with P. ludlowii, should be classified as a lineage within the broader P. delavayi group. Conclusions: Overall, this study's research findings suggest that the Paeonia plastome is highly informative for phylogenetic and comparative genomic analyses, and could be useful in future research related to taxonomy, evolution, and domestication. [ABSTRACT FROM AUTHOR]

Malondialdehyde (MDA) is a product of lipid peroxidation that is often determined in abiotic stress-related phytoremediation research. This study assessed (July 14, 2022) the frequency of eight nomenclatural forms of MDA between 2001 and 2021 using three major databases (PubMed, Scopus, and Web of Science (WoS9). The most common form (75,060, 57,874, and 65,663 times in PubMed, Scopus, and WoS, respectively) of MDA was "malondialdehyde", followed by "malonaldehyde" (68,240, 3815, and 2337 times in these three databases, respectively). According to WoS, the journals that used "malondialdehyde" and "malonaldehyde" most frequently were Environmental Science and Pollution Research (Springer-Nature) (587 times) and The Journal of Chemical Physics (AIP Publishing) (57 times). Other less-frequent forms were: malonyldialdehyde, malonic dialdehyde, malon-dialdehyde, malone dialdehyde, malonic aldehyde, and malonodialdehyde. We recommend that the editors of journals that publish papers with themes that are closely associated with plant stress specify in their instructions for authors their journal's preferable nomenclatural form of MDA. The plant abiotic stress community, including phytoremediation specialists, need to debate this topic with the objective of seeking a standardized nomenclatural form of MDA, which would help to fortify the integrity of searches in major databases by allowing all relevant literature to be accurately identified. Novelty statement Malondialdehyde (MDA), a product of lipid peroxidation that is often determined in stress-related phytoremediation research, has various forms to its name. These nomenclatural variations were assessed in PubMed-, Scopus-, and Web of Science-indexed literature. This is the first study to detect, report, quantify and debate these forms of MDA. [ABSTRACT FROM AUTHOR]

Cancer research is occasionally described as being in a reproducibility crisis. The cancer literature has ample papers retracted due to misconduct, including the use of paper mills, invalid authorship, or fake data. The objective of this paper was to gain an appreciation of the balance of retractions and associated retraction notices of 23 retracted Cancer Biotherapy and Radiopharmaceuticals papers associated with paper mills. By 23 March 2023, these retracted papers had already accumulated 287 citations according to Web of Science Core Collection, 253 according to Scopus, and 365 according to Google Scholar, i.e., metrically speaking, they were highly rewarded. All authors had an affiliation (71% being a hospital) in China. Most (12/21; 57%) of corresponding authors had emails with a @163.com suffix. Four of the retraction notices (i.e., 17%) explicitly indicated paper mills as a reason for retraction although, in general, the retraction notices lacked details and background that could assist readers' understanding of the retractions. [ABSTRACT FROM AUTHOR]

ResearchGate (RG) is a popular academic social media networking platform for scientists, researchers, or academics (SRAs). RG automatically provides a metric, the RG Score, to each RG account holder that serves as a measure of that SRA's "academic" worth, productivity, and interaction with other SRAs. In 2017, this metric was described by RG as "the RG Score takes all your research and turns it into a source of reputation," indicating that "it is calculated based on the research in your profile and how other researchers interact with your content." However, the precise manner in which the RG Score is calculated was never made public because it is a proprietary algorithm, and requests to RG to disclose details of the equations used to calculate it were not met. Not unsurprisingly, RG announced that it would be phasing out the RG Score in June 2022. This article examines what is known in the literature about the RG Score, which may be perceived as a skewed metric because it may add excessive weighting to select aspects, such as questions and answers, rather than to the published literature of an SRA. The RG Interest Score is also critiqued. An author-based metric such as the RG Score that reflects a realistic balance between the most important academic factors while downplaying fairly redundant aspects such as the volume of answers might benefit SRAs. As for any metric, the RG Score should not be used in isolation, be gamed, or used as the basis of any financial remuneration schemes. [ABSTRACT FROM AUTHOR]

Flavonoids are important bioactive components in Dendrobium officinale, a medicinal orchid. They are involved in many biological activities, including protecting plants against biotic and abiotic stresses. Research on the key genes related to flavonoid biosynthesis in D. officinale is limited. In this study, one of the key flavonoid biosynthesis genes, flavanone 3-hydroxylase (F3H), was characterized from D. officinale. The open reading frame of DoF3H was 1 134 bp long and it encoded a 377-amino acid protein. The DoF3H protein showed considerably high homology with F3H proteins from other plant species and shared a common evolutionary ancestor with other F3Hs. DoF3H transcripts were detected in different organs of adult plants and mainly accumulated in flowers, followed by roots, stems and leaves, a pattern that was similar to the content of flavonoids. Recombinant DoF3H protein, which was localized in the cytosol, could convert naringenin to dihydrokaempferol. The mRNA levels of DoF3H were significantly induced by salt and cold stresses. Furthermore, the heterologous expression of DoF3H in Escherichia coli conferred it higher tolerance to salt and cold stresses. These results provide insight into the molecular function of DoF3H in the biosynthesis of flavonoids, and provide a new application for improvement of abiotic tolerance in D. officinale. [ABSTRACT FROM AUTHOR]