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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.

Due to COVID-19, Japan’s GDP decreased by 4.5% in 2020 from 0.7% in 2019. The economy increased by 1.7% in 2021, stagnated at 1.4% in 2022, and is expected to grow at 1.8% in 2023 and to slowdown to 0.9% in 2024, based on the January 2023 forecasts of the International Monetary Fund (IMF). IMF’s January 2023 report is based on inflation peaking with low growth due to rising interest rates. In January 2021, a year into the COVID-19 pandemic period, the IMF was hopeful, predicting a V-shaped growth pattern of 3.1% for 2021 and 2.4% for 2022 due to policy stimulus and the availability of vaccines. However, this did not materialize due to various geopolitical and economic shocks. The economic costs of the COVID-19 pandemic relative to its absence are estimated to be at least US$1.1 trillion (¥160 trillion) until 2030 under a continued low economic growth future path. Moreover, the estimated US$1.1 trillion economic loss is equivalent to the erasure of approximately 30% of GDP produced in 2019 during the Abenomics era. If in the absence of the pandemic, the economy was assumed to have a high growth, the losses would reach US$ 4.8 trillion (¥706 trillion) due to the lost opportunity of a high-growth counterfactual trajectory.

This commentary abridges three closely related aspects of scholarly publishing, copyright transfer to publishers in the subscription-based model, posting of author-accepted versions to preprint servers, and publishing embargoes, to appreciate how each might impact the dissemination of information. We found no direct evidence showing that either copyright transfer or the posting of early (i.e., author-submitted or journal-accepted) versions of works to preprint servers stifle academics’ ability to share their papers openly. However, some key structural issues and incompatibilities in policies may dampen the wider adoption of preprints despite their widely promoted advantages for scientists. We found a 6- to 36-month embargo period in place by 10 of the world’s top largest publishers, depending on the version of the record. These embargoes may constrain the dissemination of knowledge.

A recent disruptive innovation to scientific publishing is OpenAI’s ChatGPT, a large language model. The International Committee of Medical Journal Editors and COPE, and COPE member journals or publishers, set limitations to ChatGPT’s involvement in academic writing, requesting authors to declare its use. Those guidelines are practically useless because they ignore two fundamentals: first, academics who cheat to achieve success will not declare the use of ChatGPT; second, they fail to explicitly assign the responsibility of detection to editors, journals, and publishers. Using two primers, i.e., residual text that may reflect traces of ChatGPT’s output but that authors may have forgotten to remove from their articles, this commentary draws readers’ attention to 46 open-access examples sourced from PubPeer. Even though editors should be obliged to investigate such cases, a primer-based detection of ChatGPT’s textual crumb trails is only a temporary measure and not a sustainable solution because it relies on the detection of carelessness.

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.

The ongoing Russo-Ukrainian war is affecting Ukrainian agriculture. For example, Ukraine is no longer able to export agricultural products such as grains and cereals by sea to regional (European) and international markets, although this has been partially mitigated by the creation of a "grain corridor". As a result, food security in Ukraine, and to some extent, in the region (EU) and globally, is at some risk, especially in countries that rely heavily on agricultural imports from Ukraine. About 70% of the land in Ukraine is used for agricultural production. This paper provides an overview of Ukrainian agricultural production using statistics for 2018-2022, based on available literature, as well as FAO and official Ukrainian government statistics. Global production of the main grain crops and cereals (wheat, maize, barley, rapeseed, and sunflower), ranging between 2.9 and 6.6%, showed an upward trend in 2017-2021. Ukraine accounted for 9, 12, 12, 14, and 50% of the global trade market (import + export) in 2020/2021 for wheat, maize, barley, rapeseed, and sunflower oil, respectively. About 75% of agricultural products and services (892,852 million UAH in total) come from the crop industry, with the remainder from the livestock industry. Fertilizer export was banned in 2022.

In academic publishing, there is a need to be able to discern scholarly from unscholarly, deceptive, and/or predatory journals. Predatory journals are not expected among highly ranked journals in reputable databases. SCImago Journal Rank (SJR), which ranks journals into four quartiles (Q1–Q4), acts as a whitelist or safelist for journal selection. Q1 SJR-ranked journals are likely not “predatory.” An artificial intelligence (AI)-based tool Academic Journal Predatory Checking (AJPC) system launched in February 2023 claims to differentiate suspected predatory journals (SPJs) from normal journals. AJPC system classified, in a 2 June 2023 assessment, 27 (or 42%) of the 64 Q1 SJR-ranked library and information science journals, most (48%) published by Taylor & Francis, as SPJs. This output is unlikely to be accurate (or is likely to be inaccurate) and may suggest that this free online AI-driven tool, whose output can be independently verified by anybody, may be providing erroneous output, and thus misleading information.

Retractions are on the rise as a result of a surge in post-publication peer review and an emboldened anonymous whistle-blowing movement. Cognizant that their brand may be damaged as a result of not correcting problematic literature, journals and publishers that are loosely considered to be non-"predatory" are trying to contain the deluge of reports on flawed research that has flooded the biomedical and scientific literature. Within this climate, many studies have started to be retracted and corrected, reinforcing the stigmatization associated with retractions, i.e., having a retraction is considered to be a bad or negative thing. Negative retraction stigmatization has mainly been borne by authors, whereas journals and publishers, except for headline-grabbing reports, have thus far largely avoided this stigma. One of the efforts to destigmatize retractions, at least those for honest errors, has been to try to relabel or rebrand retractions. The terms "self-retraction", "amendment", "publisher-caused error", and others have emerged, but such a diverse lexicon may complicate the publishing landscape more than it resolves the stigma. Seeking euphemistic terms to represent a truth within a toxic context of negative stigmatization only politicizes the issue, and does not resolve it. We suggest that a change is needed in the culture within the biomedical community, to acceptance of critique, and that the culture of shaming needs to be halted in order to achieve this. Only then can academics assume greater responsibility, without the risk of being shamed, of retracting their faulty literature, "honestly", when they feel that this is needed.

Preprints are not only a raw form of research presentation, but also increasingly used as a gateway of entry into peer-reviewed journals. Several preprint servers are in existence, and some serve specific thematic groups or specialties, while others have a broader thematic scope. In this letter, we examined 36 preprint servers in March of 2023, noting that the majority (27/36 or 75%) accept opinion papers, two have an unclear, unstated, or unknown set of policies, while seven, including some of the most popular (biorXiv, medRxiv, Research Square), do not explicitly accommodate opinion papers. We opine that it would be in the interests of those preprint servers that do not publish opinion papers or evidence-based opinion papers to modify their scope of manuscript types in order to expand their user base and attract more participating scientists, but also to provide a more holistic set of scientific publishing objectives that accommodates a wider and more inclusive range of views.

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]

Tumor Biology, owned by the International Society of Oncology and BioMarkers and currently published by IOS Press, lost its Clarivate impact factor of 3.650 in 2017. It has been plagued by over 100 retractions due to paper mills (including a batch of 15 papers published between 2014 and 2016 that were retracted at the end of 2021), faked peer reviews, and forged research. According to PubMed, the number of papers published by Tumor Biology has been reduced to a mere trickle, dropping from 707 in 2017 to 66 in 2018. It is unclear how Tumor Biology will be able to recover from such disastrous reputational damage and whether there is even merit in continuing its publication. Other journals for cancer and oncology research would do well to observe this case closely and learn from its mistakes.

With increasing cases of fraud in submission, peer review, and publication processes, some by authors with fake identities and who use concocted emails, including the use of web-based emails, editors and publishers are looking for ways to try and stem the tide of fraud. In some journals, editors and publishers mistakenly believe that this might be possible by implementing a policy that mandates submitting authors to have an institutional email. However, this may be discriminatory at various levels, the most obvious of which is unfairness, i.e., no right to “entry” to a journal based exclusively on the type of email used, even more so when the submitting author is not fake. Such policies might, very ironically, even violate stated journal or publisher policies on discrimination and inclusivity. Editors and publishers that employ such tactics, as a way to attempt to reduce fraudulent submissions, need to rethink this potentially discriminatory strategy. In a publishing world that is becoming increasingly litigious, it would not be surprising if legal action would one day be taken against a journal or publisher by a valid author using a web-based email such as @gmail.com, @yahoo.com, or @163.com, but who may have been unfairly barred entry to that journal based on such a policy. Two real case examples are provided, Tumor Biology, a struggling journal published by IOS Press, and Journal of Business Ethics, a journal published by Springer Nature.

Without peer reviewers, the entire scholarly publishing system as we currently know it would collapse. However, as it currently stands, publishing is an extremely exploitative system, relative to other business models, in which trained and specialized labor is exploited, in the form of editors and peer reviewers, primarily by for-profit publishers, in return for a pat on the back, and a public nod of thanks. This is the "standardized" and "accepted" form for deriving mainstream peer reviewed literature. However, except for open peer review, where reports are open and identities are known, traditional peer review is closed, and the content of peer reports is known only to the authors and editors involved. Publons launched in 2012 as a platform that would offer recognition to peer reviewers for their work. In 2016, Publons rewarded the most productive reviewers with a "Sentinels of Science" award, accompanied by a dismal monetary reward (38 US cents/review) for their efforts. A site aimed at registering pre- and post-publication peer efforts, Publons was perceived as a positive step towards a more transparent peer review system. However, the continued presence of fake peer reviews and a spike in retractions, even among publishers that were Publons sponsors, suggests that perhaps peers may be exploiting Publons to get recognition for superficial or poor peer review. Since all reviews are not public, their content and quality cannot be verified. On 1 June 2017, Clarivate™ Analytics, which owns the journal impact factor--most likely the most gamed non-academic factor in academic publishing--which is a measure of the number of citations of papers in journals, many of which are published by the for-profit publishers--including Publons sponsors--that "employ" free peer reviewers to quality check the literature they then sell for profit, purchased Publons. Touting the purchase as a way to increase transparency, and stamp out fake peer review, some who had supported Publons felt betrayed, even cancelling their Publons accounts immediately when learning of this purchase. Their concerns included the possible "gaming" of peer review as had taken place with the journal impact factor. This commentary examines possible positive and negative aspects of this business transaction, and what it might mean to academics and publishers.

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]

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]

In publishing ethics, self-plagiarism or text recycling is subject to a correction or retraction. This paper examines a high-profile case of ethical exceptionalism in the publishing status quo. Jennifer Couzin-Frankel, a science writer for the magazine Science, published by The American Association for the Advancement of Science (AAAS), was the first reporter to publicly reveal the identity of Brandon Stell, the President of The PubPeer Foundation, which owns PubPeer, a science whistle-blower website. The AAAS is a Committee on Publication Ethics (COPE) member publisher. Couzin-Frankel published two articles, one of which self-plagiarized (i.e., the use of text written by the same person but not properly cited, or acknowledged) about 25% of text in the other article. Couzin-Frankel has also employed nested self-citation, which is the citation of a separate part of a paper such as a table or text box, to give the impression of a separate publication. These aspects call into question how strictly information is vetted and edited at AAAS’s Science. Despite alerting the AAAS, this heavily self-plagiarized paper has not been corrected or retracted. How then do the AAAS and COPE justify the continued publication of both texts?