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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.

Academic publishing is undergoing a highly transformative process, and many established rules and value systems that are in place, such as traditional peer review (TPR) and preprints, are facing unprecedented challenges, including as a result of post-publication peer review. The integrity and validity of the academic literature continue to rely naively on blind trust, while TPR and preprints continue to fail to effectively screen out errors, fraud, and misconduct. Imperfect TPR invariably results in imperfect papers that have passed through varying levels of rigor of screening and validation. If errors or misconduct were not detected during TPR's editorial screening, but are detected at the post-publication stage, an opportunity is created to correct the academic record. Currently, the most common forms of correcting the academic literature are errata, corrigenda, expressions of concern, and retractions or withdrawals. Some additional measures to correct the literature have emerged, including manuscript versioning, amendments, partial retractions and retract and replace. Preprints can also be corrected if their version is updated. This paper discusses the risks, benefits and limitations of these forms of correcting the academic literature., Author(s): Jaime A. Teixeira da Silva [sup.1] Author Affiliations: (1) Independent researcher, 761-0799, , PO Box 7, Ikenobe 3011-2, Kagawa-ken, Japan The Preprinted and Published Literature Is Imperfect and Is [...]