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.

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.

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.

Prevalence of Primary Multidrug-resistant Helicobacter pylori in Children: A Systematic Review and Meta-analysis.

BACKGROUND: The emergence and global spread of multidrug-resistant Helicobacter pylori (MDR H. pylori) is a major health problem in children, which can increase the risk of serious complications such as gastric cancer. The aim of this study was to determine the prevalence of primary MDR H. pylori in children via a comprehensive systematic literature review and meta-analysis. METHODS: All potential studies were collected from international databases like: ISI Web of Science, Embase, PubMed, Google Scholar, and Scopus from 2011-July 24, 2022. Ultimately, primary MDR H. pylori in children was measured as an event rate with corresponding 95% confidence intervals. RESULTS: A total of 19 studies met the inclusion criteria. The overall prevalence of primary MDR H. pylori in children was measured at 6.0% (95% CI: 3.1-11.6); There was a significant difference in primary MDR H. pylori resistance rates between Asian populations and Western countries. CONCLUSIONS: The global spread of MDR H. pylori strains could significantly limit the options of anti-H. pylori treatment regimens. The frequency of primary MDR H. pylori infection differs between various geographical regions. Thus, drug susceptibility testing and the eradication of H. pylori infection can effectively reduce and control the spread of H. pylori antibiotic resistance throughout the world.

Clinical relevance of the cagA and vacA s1m1 status and antibiotic resistance in Helicobacter pylori: a systematic review and meta-analysis.

BACKGROUND: The role of Helicobacter pylori (H. pylori) virulence factors of such as vacA s1m1 and cagA in designating clinical outcomes and eradication rate has been deeply challenged in the last decade. The goal of this analysis was to identify the potential relevance between cagA and vacA genotypes with reported antibiotic resistance observed in clinical H. pylori isolates. METHODS: This literature search was conducted in databases such as Clarivate analytics, PubMed, Scopus, EMBASE, DOAJ, and Google Scholar by April 2022, regardless of language restrictions and publication date. Quality of the included studies was assessed by the Newcastle-Ottawa scale. Statistical analysis of retrieved studies was fulfilled using Comprehensive Meta-Analysis software version 2.2. Following quality appraisal of eligible studies, potential association between the status of cagA and vacA genes with resistance to clarithromycin, metronidazole, amoxicillin, tetracycline, and levofloxacin was measured using odds ratio with 95% confidence interval. We also used sensitivity analyses and meta-regression to eliminate the source of heterogeneity from the overall estimates. Publication bias was assessed using funnel plot, Egger's test, Begg's test with the trim and fill procedure to assess the presence and magnitude of publication bias in the included studies. RESULTS: Our findings suggested that a significant relationship between cagA status and increase resistance to metronidazole (OR: 2.69; 95% CI: 1.24-5.83 ). In subgroup analysis, we found that in the Western population, infection with cagA-positive strains could be led to increase in the resistance to metronidazole (OR: 1.59; 95% CI: 0.78-3.21 ), amoxicillin (OR: 19.68 ; 95% CI: 2.74- 141.18), and levofloxacin (OR: 11.33; 95% CI: 1.39- 91.85). After implementation of trim and fill method, the adjusted OR was not significantly differed from original estimates which in turn represented our subgroup analysis was statistically robust. On the other hand, vacA genotypes usually reduce the antibiotic resistance of this bacterium, so that vacA s1m1 significantly reduces the resistance to metronidazole (OR: 0.41; 95% CI: 0.20-0.86 ). Surprisingly, resistance of vacA s2m2 strains to antibiotics was low, the reason may be due to the non-inflammatory properties of strains containing vacA s2m2. The meta-regression and sensitivity analyses successfully reduced the effect of heterogeneity from the overall estimates. In addition, although the pooled OR is reduced after trim and fill adjustment but results do not change the conclusion regarding vacA genotypes and antibiotic resistance. CONCLUSIONS: According to our findings, it was clearly demonstrated that cagA-positive strains are resistance to metronidazole, especially in Western countries. In Western countries, vacA s1m1 increases resistance to amoxicillin and levofloxacin. Based on the present findings, the vacA s1m1 genotype significantly increases resistance to metronidazole, while the vacA s1m2 decreases resistance to clarithromycin and metronidazole. Resistance to antibiotics in less virulent (vacA s2m2) strains is statistically significant lower than others.

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.

Is Omicron the last SARS-CoV-2 Variant of Concern?

Millions have died due to the COVID-19 pandemic. The irrepressible propensity of the pandemic, which was highlighted by the outbreak of the Delta variant, should not be underestimated. The Omicron SARS-CoV-2 variant is thought to have originated from Africa. Sequences of the omicron variant show that it carries the highest number of point mutations detected in a betacoronavirus. High hospitalization numbers due to the Omicron variant has retriggered precautionary restrictions and border closures even in countries which have attained herd immunity by mass vaccinations. Surveillance systems for accurate screening of the Omicron variant are needed to guide implementation of hygiene principles and restrictions. Development of vaccines against the variants is important as the pandemic evolves. Whether Omicron is the last variant depends on the success of the local and global public-health strategies against SARS-CoV-2.