ChatGPT and Corporations of Mega-journals Jeopardize the Norms That Underpin Academic Publishing.

Those who participate in and contribute to academic publishing are affected by its evolution. Funding bodies, academic institutions, researchers and peer-reviewers, junior scholars, freelance language editors, language-editing services, and journal editors are to enforce and uphold the ethical norms on which academic publishing is founded. Deviating from such norms will challenge and threaten the scholarly reputation, academic careers, and institutional standing; reduce the publishers' true impacts; squander public funding; and erode the public trust to the academic enterprise. Rigorous review is paramount because peer-review norms guarantee that scientific findings are scrutinized before being publicized. Volunteer peer-reviewers and guest journal editors devote an immense amount of unremunerated time to reviewing papers, voluntarily serving the scientific community, and benefiting the publishers. Some mega-journals are motivated to mass-produce publications and attract the funded projects instead of maintaining the scientific rigor. The rapid development of mega-journals may diminish some traditional journals by outcompeting their impacts. Artificial intelligence (AI) tools/algorithms such as ChatGPT may be misused to contribute to the mass-production of publications which may have not been rigorously revised or peer-reviewed. Maintaining norms that guarantee scientific rigor and academic integrity enable the academic community to overcome the new challenges such as mega-journals and AI tools.

Inhibition of GCN2 Reveals Synergy with Cell-Cycle Regulation and Proteostasis.

The integrated stress response is a signaling network comprising four branches, each sensing different cellular stressors, converging on the phosphorylation of eIF2α to downregulate global translation and initiate recovery. One of these branches includes GCN2, which senses cellular amino acid insufficiency and participates in maintaining amino acid homeostasis. Previous studies have shown that GCN2 is a viable cancer target when amino acid stress is induced by inhibiting an additional target. In this light, we screened numerous drugs for their potential to synergize with the GCN2 inhibitor TAP20. The drug sensitivity of six cancer cell lines to a panel of 25 compounds was assessed. Each compound was then combined with TAP20 at concentrations below their IC50, and the impact on cell growth was evaluated. The strongly synergistic combinations were further characterized using synergy analyses and matrix-dependent invasion assays. Inhibitors of proteostasis and the MEK-ERK pathway, as well as the pan-CDK inhibitors, flavopiridol, and seliciclib, were potently synergistic with TAP20 in two cell lines. Among their common CDK targets was CDK7, which was more selectively targeted by THZ-1 and synergized with TAP20. Moreover, these combinations were partially synergistic when assessed using matrix-dependent invasion assays. However, TAP20 alone was sufficient to restrict invasion at concentrations well below its growth-inhibitory IC50. We conclude that GCN2 inhibition can be further explored in vivo as a cancer target.

Passive Contribution of ChatGPT to Scientific Papers.

Arguably ChatGPT jeopardizes the integrity and validity of the academic publications instead of ethically facilitating them. ChatGPT can apparently fulfill a portion of one of the four authorship criteria set by the International Committee of Medical Journal Editors (ICMJE), i.e., "drafting." However, the authorship criteria by ICMJE must all be collectively met, not singly or partially. Many published manuscripts or preprints have credited ChatGPT by including it in the author byline, and the academic publishing enterprise seems to be unguided on how to handle such manuscripts. Interestingly, PLoS Digital Health removed ChatGPT off a paper which had ChatGPT listed initially in the author byline of the preprint version. Revised publishing policies are, thus, promptly required to guide a consistent stance regarding ChatGPT or similar artificial content generators. Publishing policies must accord among publishers, preprint servers ( https://asapbio.org/preprint-servers ), universities, and research institutions worldwide and across different disciplines. Ideally, considering any declaration of the contribution of ChatGPT to writing any scientific article should be recognized as publishing misconduct immediately and be retracted. Meanwhile, all parties involved in the scientific reporting and publishing must be educated about how ChatGPT fails to meet the essential authorship criteria, so that no author must submit a manuscript with ChatGPT contributing as a "co-author." Meanwhile, using ChatGPT for writing laboratory reports or short summaries of experiments may be acceptable, but not for academic publishing or formal scientific reporting.

ChatGPT and Publication Ethics.

Academic publishing is crucial for scientific communication, is governed by accepted ethical norms, and underpins the collective literature on basic science, and technological and medical principles and advances. In November 2022, the public and professional global communities, including the scientific community, witnessed the release of ChatGPT by OpenAI in San Francisco, California, USA. Excluding its public appeal and entertaining aspects but considering its diverse potential applications, some ethical concerns must be considered before establishing guidelines on using and including ChatGPT or similar platforms in scientific publishing. Some academic publishers and preprints have accepted manuscripts with ChatGPT listed as a "co-author". Though excluding such platforms from scientific publishing may not be practicable with time, establishing ethical principles is essential before ChatGPT could become a "co-author" in any scientific, published manuscript.

SARS-CoV-2 Infection, Inflammation, Immunonutrition, and Pathogenesis of COVID-19.

The COVID-19 pandemic, caused by the coronavirus, SARS-CoV-2, has claimed millions of lives worldwide in the past two years. Fatalities among the elderly with underlying cardiovascular disease, lung disease, and diabetes have particularly been high. A bibliometrics analysis on author's keywords was carried out, and searched for possible links between various coronavirus studies over the past 50 years, and integrated them. We found keywords like immune system, immunity, nutrition, malnutrition, micronutrients, exercise, inflammation, and hyperinflammation were highly related to each other. Based on these findings, we hypothesized that the human immune system is a multilevel super complex system, which employs multiple strategies to contain microorganism infections and restore homeostasis. It was also found that the behavior of the immune system is not able to be described by a single immunological theory. However, one main strategy is "self-destroy and rebuild", which consists of a series of inflammatory responses: 1) active self-destruction of damaged/dysfunctional somatic cells; 2) removal of debris and cells; 3) rebuilding tissues. Thus, invading microorganisms' clearance could be only a passive bystander response to this destroy-rebuild process. Microbial infections could be self-limiting and promoted as an indispensable essential nutrition for the vast number of genes existing in the microorganisms. The transient nutrition surge resulting from the degradation of the self-destroyed cell debris coupled with the existing nutrition state in the patient may play an important role in the pathogenesis of COVID-19. Finally, a few possible coping strategies to mitigate COVID-19, including vaccination, are discussed.

Identification of Streptococcus gallolyticus in tumor samples of Iranian patients diagnosed with colorectal cancer.

OBJECTIVE: Clinical outcomes of infection by S. gallolyticus have not been investigated extensively. We aimed to determine the prevalence of S. gallolyticus in tumor specimens obtained from Iranian patients diagnosed with colorectal cancer. Polymerase chain reaction was used to confirm the presence of S. gallolyticus in patients' tissue samples. RESULTS: Of 176 patients, 65 were diagnosed with colorectal cancer whereas 111 did not have any colon disease. No correlation was found between age, colonization with S. gallolyticus, gender, or risk factors. Overall, 72 (40%) patients carried S. gallolyticus; only 29% of the patients without colorectal cancer were positive for S. gallolyticus. Diagnosis of colorectal cancer and presence of S. gallolyticus significantly correlated (P = 0.006; odds ratio = 1.46; 95% CI = 1.21-3.87). Among the patients with colorectal cancer, 39 (60%) were positive with S. gallolyticus (P = 0.006) whereas 33 of 111 (29.7%) control subjects were positive for S. gallolyticus (P > 0.05); thus, 70.3% of the control subjects were not infected with S. gallolyticus. We found a high prevalence of S. gallolyticus among an Iranian cohort of patients with colorectal cancer. Despite previous reports, we report a positive correlation between colorectal cancer and S. gallolyticus colonization.

Learning from Retracted Papers Authored by the Highly Cited Iran-affiliated Researchers: Revisiting Research Policies and a Key Message to Clarivate Analytics.

Reasons underlying retractions of papers authored by the Iran-affiliated highly cited researchers (HCRs) have not been documented. Here, we report that 229 of the Iran-affiliated researchers were listed by the Clarivate Analytics as HCRs. We investigated the Retraction Watch Database and found that, in total, 51 papers authored by the Iran-affiliated HCRs were retracted from 2006 to 2019. Twenty-three of the 229 HCRs (10%) had at least one paper retracted. One of the listed HCRs had 22 papers retracted; 14 of the 23 (60.8%) had only one paper retracted. Among the 51 retracted papers, three had been authored by two female authors. Eight (16.8%) retracted papers had international co-authorships. The shortest and longest times from publication to retraction were 20 and 2610 (mean ± SD, 857 ± 616) days, respectively. Of the 51 papers, 43 (84%) had a single reason for retraction, whereas eight had multiple reasons. Among the 43 papers, 23 (53%) were retracted due to fake peer-review, eight (19%) were duplications, six (14%) had errors, four (9%) had plagiarism, and two (5%) were labelled as "limited or no information." Duplication of data, which is easily preventable, amounted to 27%. Any publishing oversight committed by an HCR may not be tolerated because they represent the stakeholders of the scientific literature and stand as role-models for other peer researchers. Future policies supporting the Iranian academia should radically change by implementation of educational and awareness programs on publishing ethics to reduce the rate of retractions in Iran.