An extensive benchmark study on biomedical text generation and mining with ChatGPT.

MOTIVATION: In recent years, the development of natural language process (NLP) technologies and deep learning hardware has led to significant improvement in large language models (LLMs). The ChatGPT, the state-of-the-art LLM built on GPT-3.5 and GPT-4, shows excellent capabilities in general language understanding and reasoning. Researchers also tested the GPTs on a variety of NLP-related tasks and benchmarks and got excellent results. With exciting performance on daily chat, researchers began to explore the capacity of ChatGPT on expertise that requires professional education for human and we are interested in the biomedical domain. RESULTS: To evaluate the performance of ChatGPT on biomedical-related tasks, this article presents a comprehensive benchmark study on the use of ChatGPT for biomedical corpus, including article abstracts, clinical trials description, biomedical questions, and so on. Typical NLP tasks like named entity recognization, relation extraction, sentence similarity, question and answering, and document classification are included. Overall, ChatGPT got a BLURB score of 58.50 while the state-of-the-art model had a score of 84.30. Through a series of experiments, we demonstrated the effectiveness and versatility of ChatGPT in biomedical text understanding, reasoning and generation, and the limitation of ChatGPT build on GPT-3.5. AVAILABILITY AND IMPLEMENTATION: All the datasets are available from BLURB benchmark https://microsoft.github.io/BLURB/index.html. The prompts are described in the article.

Analgesic efficacy of an opioid-free postoperative pain management strategy versus a conventional opioid-based strategy following laparoscopic radical gastrectomy: an open-label, randomized, controlled, non-inferiority trial.

OBJECTIVE: In patients undergoing laparoscopic radical gastrectomy, the use of subcostal transversus abdominis plane block (STAPB) for completely opioid-free postoperative pain management lacks convincing clinical evidence. METHODS: This study included 112 patients who underwent laparoscopic radical gastrectomy at the 900TH Hospital of the Joint Logistics Support Force from October 2020 to March 2022. Patients were randomly divided into (1:1) continuous opioid-free STAPB (C-STAPB) group and conventional group. In the C-STAPB group, 0.2% ropivacaine (bilateral, 20 ml per side) was injected intermittently every 12 h through a catheter placed on the transverse abdominis plane for postoperative pain management. The conventional group was treated with a conventional intravenous opioid pump (2.5 µg/kg sufentanil and 10 mg tropisetron, diluted to 100 ml with 0.9% NS). The primary outcomes were the accumulative area under the curve of the numeric rating scale (NRS) score at 24 and 48 h postoperatively at rest and during movement. The secondary outcomes were postoperative recovery outcomes, postoperative daily food intake, and postoperative complications. RESULTS: After exclusion (n = 16), a total of 96 patients (C-STAPB group, n = 46; conventional group, n = 49) were included. We found there were no significant differences in the cumulative AUC of NRS score PACU-24 h and PACU-48 h between the C-STAPB group and conventional group at rest [(mean difference, 1.38; 95% CI, - 2.21 to 4.98, P = 0.447), (mean difference, 1.22; 95% CI, - 6.20 to 8.65, P = 0.744)] and at movement [(mean difference, 2.90; 95% CI, - 3.65 to 9.46; P = 0.382), (mean difference, 4.32; 95% CI, - 4.46 to 13.1; P = 0.331)]. The 95% CI upper bound of the difference between rest and movement in the C-STAPB group was less than the inferior margin value (9.5 and 14 points), indicating the non-inferiority of the analgesic effect of C-STPAB. The C-STAPB group had faster postoperative recovery profiles including earlier bowel movement, defecation, more volume of food intake postoperative, and lower postoperative nausea and vomiting compared to conventional groups (P < 0.001). CONCLUSIONS: After laparoscopic radical gastrectomy, the analgesic effect of C-STAPBP is not inferior to the traditional opioid-based pain management model. TRIAL REGISTRATION: ChiCTR2100051784.

RNAi-Mediated Suppression of OsBBTI5 Promotes Salt Stress Tolerance in Rice.

This study explores the impact of RNAi in terms of selectively inhibiting the expression of the OsBBTI5 gene, with the primary objective of uncovering its involvement in the molecular mechanisms associated with salt tolerance in rice. OsBBTI5, belonging to the Bowman-Birk inhibitor (BBI) family gene, is known for its involvement in plant stress responses. The gene was successfully cloned from rice, exhibiting transcriptional self-activation in yeast. A yeast two-hybrid assay confirmed its specific binding to OsAPX2 (an ascorbate peroxidase gene). Transgenic OsBBTI5-RNAi plants displayed insensitivity to varying concentrations of 24-epibrassinolide in the brassinosteroid sensitivity assay. However, they showed reduced root and plant height at high concentrations (10 and 100 µM) of GA3 immersion. Enzyme activity assays revealed increased peroxidase (POD) and superoxide dismutase (SOD) activities and decreased malondialdehyde (MDA) content under 40-60 mM NaCl. Transcriptomic analysis indicated a significant upregulation of photosynthesis-related genes in transgenic plants under salt stress compared to the wild type. Notably, this study provides novel insights, suggesting that the BBI gene is part of the BR signaling pathway, and that OsBBTI5 potentially enhances stress tolerance in transgenic plants through interaction with the salt stress-related gene OsAPX2.

Comprehensively Analyze the Prognosis Significance and Immune Implication of PTPRO in Lung Adenocarcinoma.

Immunotherapy for lung adenocarcinoma (LUAD) is considered to be a promising treatment option, but only a minority of patients benefit from it. Therefore, it is essential to clarify the regulation mechanism of the tumor immune microenvironment (TIM) of the LUAD. Receptor-type protein tyrosine phosphatase (PTPRO) has been shown to be a tumor suppressor in a variety of tumor; however, its role in LUAD has never been reported. In this study, we first found that PTPRO was lowly expressed in LUAD and positively correlated with patient prognosis. Next, we investigated the relationship between PTPRO and clinical characteristics, and the results showed that gender, age, T, and stage were closely related to the expression level of PTPRO. Moreover, we performed univariate and multivariate analyses, and the results revealed that PTPRO was a protective factor for LUAD. By constructing a nomogram based on the expression level of PTPRO and various clinical characteristics, it was proved that the nomogram has a good predictive capacity. Furthermore, we analyzed the coexpression network of PTPRO through multiple databases and performed GO and KEGG enrichment analyses. The results demonstrated that PTPRO was involved in the regulation of multiple immune pathways. In addition, we analyzed whether PTPRO expression of LUAD regulate immune cell infiltration and the results demonstrated that PTPRO was closely related to the infiltration of various immune cells. Finally, we predicted LUAD sensitivity to chemotherapeutics and response to immunotherapy by PTPRO expression levels. The results showed that PTPRO expression level affect the sensitivity of various chemotherapeutic drugs and may be involved in the efficacy of immunotherapy. These results we obtained suggested that PTPRO is closely related to the prognosis and TIM of LUAD, which may be a potential immunotherapeutic target for LUAD.

Unlocking the Potential of Carbon Quantum Dots for Cell Imaging, Intracellular Localization, and Gene Expression Control in Arabidopsis thaliana (L.) Heynh.

Utilizing carbon quantum dots (CQDs) as biomaterials for delivering small substances has gained significant attention in recent research. However, the interactions and mechanisms of action of CQDs on plants have received relatively little focus. Herein, we investigated the transportation of CQDs into various organs of Arabidopsis thaliana (L.) Heynh. via the vessel system, leading to the epigenetic inheritance of Argonaute family genes. Our findings reveal that CQDs may interact with microRNAs (miRNAs), leading to the repression of post-transcriptional regulation of target genes in the cytoplasm. Transcriptome and quantitative PCR analyses demonstrated consistent gene expression levels in offspring. Moreover, microscopic observations illustrated rapid CQD localization on cell membranes and nuclei, with increased nuclear entry at higher concentrations. Notably, our study identified an alternative regulatory microRNA, microRNA172D, for the Argonaute family genes through methylation analysis, shedding light on the connection between CQDs and microRNAs.

Fast and High-Efficiency Synthesis of Capsanthin in Pepper by Transient Expression of Geminivirus.

The color of the chili fruit is an important factor that determines the quality of the chili, as red chilies are more popular among consumers. The accumulation of capsanthin is the main cause of reddening of the chili fruit. Capsanthin is an important metabolite in carotenoid metabolism, and its production level is closely linked to the expression of the genes for capsanthin/capsorubin synthase (CCS) and carotenoid hydroxylase (CrtZ). We reported for the first time that the synthesis of capsanthin in chili was enhanced by using a geminivirus (Bean Yellow Dwarf Virus). By expressing heterologous ß-carotenoid hydroxylase (CrtZ) and ß-carotenoid ketolase (CrtW) using codon optimization, the transcription level of the CCS gene and endogenous CrtZ was directly increased. This leads to the accumulation of a huge amount of capsanthin in a very short period of time. Our results provide a platform for the rapid enhancement of endogenous CCS activity and capsanthin production using geminivirus in plants.

Transcriptome Analysis Reveals the Molecular Regularity Mechanism Underlying Stem Bulblet Formation in Oriental Lily 'Siberia'; Functional Characterization of the LoLOB18 Gene.

The formation of underground stem bulblets in lilies is a complex biological process which is key in their micropropagation. Generally, it involves a stem-to-bulblet transition; however, the underlying mechanism remains elusive. It is important to understand the regulatory mechanism of bulblet formation for the reproductive efficiency of Lilium. In this study, we investigated the regulatory mechanism of underground stem bulblet formation under different conditions regarding the gravity point angle of the stem, i.e., vertical (control), horizontal, and slanting. The horizontal and slanting group displayed better formation of bulblets in terms of quality and quantity compared with the control group. A transcriptome analysis revealed that sucrose and starch were key energy sources for bulblet formation, auxin and cytokinin likely promoted bulblet formation, and gibberellin inhibited bulblet formation. Based on transcriptome analysis, we identified the LoLOB18 gene, a homolog to AtLOB18, which has been proven to be related to embryogenic development. We established the stem bud growth tissue culture system of Lilium and silenced the LoLOb18 gene using the VIGS system. The results showed that the bulblet induction was reduced with down-regulation of LoLOb18, indicating the involvement of LoLOb18 in stem bulblet formation in lilies. Our research lays a solid foundation for further molecular studies on stem bulblet formation of lilies.

A novel and efficient method to induce allospecific CD8+ memory T lymphocytes.

The aim of the current study was to establish a simple method for effectively inducing memory T lymphocytes by the intraperitoneal injection of spleen lymphocytes into mice. In total, 75 mice were divided into the following groups: an injection group administered three doses of spleen lymphocytes (1 × 106 , 5 × 106 , and 1 × 107 cells), a transplantation group in which a 0.25-cm2 skin section from C57BL/6 mice was transplanted onto the back of the recipient, and a control group in which an equal volume of phosphate-buffered saline was injected. At 1, 2, or 3 months following transplantation, the following parameters were evaluated: quantity of T lymphocytes, percentage of cluster of differentiation 8+ (CD8+ ) memory T cells, and proliferation index of purified CD8+ memory T cells. No significant differences among groups were detected at 1 month (p > .05). However, the injection group administered 1 × 106 cells exhibited the highest proportion of CD8+ memory T cells among all groups at 2 months, and the proportions of CD8+ T cells were higher in the three injection groups than in the skin transplantation and control groups at 3 months. The proportions of memory T cells were higher in the injection groups administered 5 × 106 or 1 × 107 cells than in the skin transplantation and control groups at 3 months. The newly established method effectively induces memory T lymphocytes via the intraperitoneal injection of spleen lymphocytes in vivo and has potential applications in the field of immunotherapy.

Efficacy of convalescent plasma for the treatment of severe influenza.

BACKGROUND: Convalescent plasma administration may be of clinical benefit in patients with severe influenza, but reports on the efficacy of this therapy vary. METHODS: We conducted a systematic review and meta-analysis assessing randomized controlled trials (RCTs) involving the administration of convalescent plasma to treat severe influenza. Healthcare databases were searched in February 2020. All records were screened against eligibility criteria, and the risks of bias were assessed. The primary outcome was the fatality rate. RESULTS: A total of 2861 studies were retrieved and screened. Five eligible RCTs were identified. Pooled analyses yielded no evidence that using convalescent plasma to treat severe influenza resulted in significant reductions in mortality (odds ratio, 1.06; 95% CI, 0.51-2·23; P = 0.87; I2 = 35%), number of days in the intensive care unit, or number of days on mechanical ventilation. This treatment may have the possible benefits of increasing hemagglutination inhibition titers and reducing influenza B viral loads and cytokine levels. No serious adverse events were reported. The included studies were generally of high quality with a low risk of bias. CONCLUSIONS: The administration of convalescent plasma appears safe but may not reduce the mortality, number of days in the intensive care unit, or number of days on mechanical ventilation in patients with severe influenza.

Diabetic Foot Limb Salvage-A Series of 809 Attempts and Predictors for Endovascular Limb Salvage Failure.

BACKGROUND: To review patient characteristics and outcomes of in-patient diabetic foot limb salvage and identify risk factors predicting for endovascular limb salvage failure. METHODS: Retrospective study of limb salvage attempts in 809 patients between August 2013 and July 2015. RESULTS: Sixty-eight percent of our study population were male with mean age at 65 years and 73% presented with Rutherford grade 6 critical limb ischemia, with the remaining 27% Rutherford grade 5. Eighty-one percent had toe pressures of less than 50 mm Hg, 64% had infrainguinal trans-Atlantic inter-society consensus (TASC II) C or D lesions while 78% had infrapopliteal TASC II C or D lesions. Seven hundred seventy-seven patients (96%) underwent endovascular-first approach limb salvage, with 95% requiring infrapopliteal angioplasty, with 84% of them requiring 2-vessel or 3-vessel revascularization. Thirty-two patients (4%) underwent surgical bypass limb salvage, with 63% performed as salvage procedures for failed angioplasties. The mean in-patient stay was 12.3 days within the endovascular group and 31.1 days within the bypass group (P < 0.01). One-year limb salvage was successful in 88% of endovascular group, as compared with 72% in bypass group (P = 0.01). Overall 1-year survival was 93% within the endovascular group and 88% within the bypass group (P = 0.27). The mean in-patient cost was SGD$5,518 within the endovascular group and SGD$15,141 within the bypass group (P < 0.01). Multivariate analysis showed that independent predictors for failure of endovascular limb salvage include end-stage renal failure (ESRF) (odds ratio [OR] 2.04, P = 0.01), toe pressures <50 mm Hg (OR 2.15, P = 0.01), infrainguinal TASC II patterns C or D (OR 1.99, P = 0.03), and indirect angiosome revascularization (OR 2.03, P = 0.02). CONCLUSIONS: Within our study population of Asian ethnicity, most in-patient diabetic foot peripheral arterial disease presented with Rutherford grade 6 disease, with mostly TASC II C or D lesions and required infrapopliteal revascularization. As most patients had multiple comorbidities and were poor surgical candidates, the majority underwent endovascular-first approach revascularization. Independent predictors of endovascular limb salvage failure include ESRF, toe pressures <50 mm Hg, infrainguinal TASC II patterns C or D, and indirect angiosome revascularization.

Reduced weed seed shattering by silencing a cultivated rice gene: strategic mitigation for escaped transgenes.

Transgene flow form a genetically engineered (GE) crop to its wild relatives may result in unwanted environmental consequences. Mitigating transgenes via introducing a gene that is disadvantageous to wild relatives but beneficial to crops, and is tightly-linked with the target transgenes, may provide a promising solution to limit the spread of transgenes in wild/weedy populations. Here we demonstrate a novel system with significantly reduced seed shattering in crop-weed hybrid descendants by partially silenced expression of the seed-shattering gene SH4 in cultivated rice, using artificial microRNA and antisense RNA techniques. Accordingly, fewer seeds were found in the soil of the field plots where transgenic hybrid lineages were grown. However, no differences in productivity-related traits were detected between GE and non-GE cultivated rice. To silence seed-shattering genes provides a useful strategy to reduce the potential environmental impacts caused by transgene flow from commercial GE rice to weedy rice, in addition to the control of weedy rice.

Aetiology of bronchiectasis in Guangzhou, southern China.

BACKGROUND AND OBJECTIVE: Aetiologies of bronchiectasis in mainland China and their comparisons with those in western countries are unknown. We aimed to investigate bronchiectasis aetiologies in Guangzhou, southern China, and to determine ethnic or geographic differences with reports from western countries. METHODS: Consecutive patients with steady-state bronchiectasis were randomly recruited. Past history was meticulously extracted. Patients underwent physical examination, saccharine test, humoral immunity assays, gastroesophageal reflux scoring and sputum culture. Fiberoptic bronchoscopy, total immunoglobin E (IgE) and Aspergillus fumigatus-specific IgE measurement, 24-h gastroesophageal pH monitoring and miscellaneous screening tests were performed, if indicated. This entailed comparisons on aetiologies with literature reports. RESULTS: We enrolled 148 patients (44.6 ± 13.8 years, 92 females), most of whom had mild to moderate bronchiectasis. Idiopathic (46.0%), post-infectious (27.0%) and immunodeficiency (8.8%) were the most common aetiologies. Miscellaneous aetiologies consisted of asthma (5.4%), gastroesophageal reflux (4.1%), aspergillosis (2.7%), congenital lung malformation (2.0%), Kartagener syndrome (1.4%), rheumatoid arthritis (1.4%), chronic obstructive pulmonary disease (0.7%), Young's syndrome (0.7%), yellow nail's syndrome (0.7%), eosinophilic bronchiolitis (0.7%) and foreign bodies (0.7%). No notable differences in clinical characteristics between idiopathic and known aetiologies were found. Ethnic or geographic variations of aetiologies were overall unremarkable. CONCLUSIONS: Idiopathic, post-infectious and immunodeficiency constitute major bronchiectasis aetiologies in Guangzhou. Clinical characteristics of patients between known aetiologies and idiopathic bronchiectasis were similar. Ethnicity and geography only account for limited differences in aetiologic spectra. These findings will offer rationales for early diagnosis and management of bronchiectasis in future studies and clinical practice in China.

[Effects of JAZF1 overexpression on proinflammatory cytokines in hepatocytes induced by palmitic acid].

OBJECTIVE: To investigate the effects of JAZF1 overexpression on the pro-inflammatory cytokines in hepatic steatosis. METHODS: The model of hepatic steatosis was established by incubating hepatocytes with palmitic acid (PA) at 0, 0.125, 0.25, 0.5 and 1 mM dose and for 0, 6, 12, 24 and 48 hours, after which recombinant adenovirus expressing JAZF1 (Ad-JAZF1) was introduced to up-regulate expression. Triglyceride level was measured by GOD. Cell viability was detected by CCK-8. The mRNA and protein expression of TNF-alpha, MCP-1, IL-8 and JAZF1 was examined by RT-PCR, ELISA, and western blotting. RESULTS: The PA-treated hepatocytes showed dose-dependent significant increases in TNF-alpha, MCP-1 and IL-8 mRNA expression for doses up to 0.25 mM; there were no significant increases for the highest doses of 0.5 and 1 mM. The 0.25 mM PA-treated hepatocytes showed time-dependent significant increases in TNF-alpha, MCP-1 and IL-8 mRNA expressions (FTNF-alpha = 26.51, FMCP-1 = 57.20, FIL-8 = 353.85, P less than 0.01), with the maximum level reached at 12 h and followed by a gradual decrease with longer treatment times. JAZF1 mRNA and protein expression was markedly increased in hepatocytes infected with Ad-JAZF1 (P less than 0.01). However, the AP-treated hepatocytes with JAZF1 overexpression showed down-regulation of TNF-alpha, MCP-1 and IL-8 mRNA expression (decreased by 89.69%, 77.68%, and 83.21%, respectively) and secretion (37%, 37% and 41%, respectively, P less than 0.01). CONCLUSION: Stimulation of hepatocytes by the PA fatty acid in vitro promotes mRNA expression of TNF-alpha, MCP-1 and IL-8, but overexpression of JAZF1 inhibits the PA-induced expression and secretion of these factors.

Different dosage regimens of zuranolone in the treatment of major depressive disorder: A meta-analysis of randomized controlled trials.

OBJECTIVE: To investigate the efficacy and safety of different dosage regimens of zuranolone in the treatment of patients with major depressive disorder (MDD). METHODS: PubMed, Embase, The Cochrane Library and other databases were searched from inception until July 2019. Randomized controlled trials (RCTs) related to the efficacy and safety of zuranolone in the treatment of MDD were included. The data were extracted independently by 2 investigators and assessed the study quality by the Cochrane risk-of-bias tool. The primary outcome includes the 17-item HAMILTON total score (HAMD-17) and the incidence of adverse events (AEs). RESULTS: Six high-quality RCTs with 1593 patients were finally included in our analysis. Zuranolone group achieve a notable treatment effect at day15 in HAMD-17 compared with placebo group (MD = -2.69, 95 % CI: -4.45 to -0.94, P < 0.05). For safety, no significant differences existed in the proportion of patients with AEs between zuranolone with placebo (RR = 1.25, 95 % CI: 0.99 to 1.58, P = 0.06). CONCLUSION: Zuranolone has a significant efficacy in improving depressive symptoms in the short term and is positively correlated with the dosage administered. However, the efficacy of zuranolone decreased significantly when the time of administration was extended. Zuranolone demonstrated a controllable safety issue. But adverse effects increased as the dose of zuranolone was gradually increased to 50 mg.