Zero-shot Clinical Entity Recognition using ChatGPT

In this study, we investigated the potential of ChatGPT, a large language model developed by OpenAI, for the clinical named entity recognition task defined in the 2010 i2b2 challenge, in a zero-shot setting with two different prompt strategies. We compared its performance with GPT-3 in a similar zero-shot setting, as well as a fine-tuned BioClinicalBERT model using a set of synthetic clinical notes from MTSamples. Our findings revealed that ChatGPT outperformed GPT-3 in the zero-shot setting, with F1 scores of 0.418 (vs.0.250) and 0.620 (vs. 0.480) for exact- and relaxed-matching, respectively. Moreover, prompts affected ChatGPT's performance greatly, with relaxed-matching F1 scores of 0.628 vs.0.541 for two different prompt strategies. Although ChatGPT's performance was still lower than that of the supervised BioClinicalBERT model (i.e., relaxed-matching F1 scores of 0.628 vs. 0.870), our study demonstrates the great potential of ChatGPT for clinical NER tasks in a zero-shot setting, which is much more appealing as it does not require any annotation.Comment: 7 pages, 5 tables, 1 figur

The effectiveness of exercise on the symptoms in breast cancer patients undergoing adjuvant treatment: an umbrella review of systematic reviews and meta-analyses

BackgroundExercise has the potential to reduce symptoms for breast cancer patients during adjuvant treatment, and high-quality systematic reviews are essential for guiding clinical practice. The objective of this umbrella review is to examine current research evidence concerning the effectiveness of exercise on symptom management in breast cancer patients undergoing adjuvant treatment.MethodsAn umbrella review was conducted. We searched for eligible systematic reviews through 11 databases until August 13rd, 2023. Two authors independently screened titles and abstracts, assessing the full-text studies based on inclusion criteria. We used AMSTAR-2 to appraise the quality of the meta-analyses. The results would be presented with narrative summaries if the replication rate of the original study for a symptom was higher than 5% (calculated via the Corrected Covered Area, CCA). The protocol was documented in the PROSPERO registry (CRD42023403990).ResultsOf the 807 systematic reviews identified, 15 met the inclusion criteria, and 7 symptoms were the main focus. The main form of exercise mentioned was aerobic combined resistance exercise. The results of the quality assessment were mostly critically low (10/15). The repetition rate calculated by CCA showed moderate to very high repetition rates (10% to 18.6%). The findings of the included reviews indicated that the effects of exercise on relieving symptoms during breast cancer adjuvant treatment were mixed.ConclusionsResearch is still needed to confirm the majority of studies’ recommendations for exercise during adjuvant treatment for breast cancer patients, as it is crucial for managing symptoms in the rehabilitation process. To increase the efficiency of exercise in symptom management, future studies may focus more on the application of bridge symptoms, symptom networks, and ecological instantaneous assessment

Diabetic retinopathy risk in patients with unhealthy lifestyle: A Mendelian randomization study

PurposeThis study aimed to investigate the causal association between unhealthy lifestyle factors and diabetic retinopathy (DR) risk and to determine better interventions targeting these modifiable unhealthy factors.DesignTwo-sample Mendelian randomization (MR) analysis was performed in this study. The inverse variance-weighted method was used as the primary method.MethodOur study included 687 single-nucleotide polymorphisms associated with unhealthy lifestyle factors as instrumental variables. Aggregated data on individual-level genetic information were obtained from the corresponding studies and consortia. A total of 292,622,3 cases and 739,241,18 variants from four large consortia (MRC Integrative Epidemiology Unit [MRC-IEU], Genetic Investigation of Anthropometric Traits [GIANT], GWAS & Sequencing Consortium of Alcohol and Nicotine Use [GSCAN], and Neale Lab) were included.ResultIn the MR analysis, a higher body mass index (BMI) (odds ratio [OR], 95% confidence interval [CI] = 1.42, 1.30–1.54; P < 0.001] and cigarettes per day (OR, 95% CI = 1.16, 1.05–1.28; P = 0.003) were genetically predicted to be causally associated with an increased risk of DR, while patients with higher hip circumference (HC) had a lower risk of DR (OR, 95% CI = 0.85, 0.76–0.95; P = 0.004). In the analysis of subtypes of DR, the results of BMI and HC were similar to those of DR, whereas cigarettes per day were only related to proliferative DR (PDR) (OR, 95% CI = 1.18, 1.04–1.33; P = 0.009). In the MR-PRESSO analysis, a higher waist-to-hip ratio (WHR) was a risk factor for DR and PDR (OR, 95% CI = 1.24, 1.02–1.50, P = 0.041; OR, 95% CI = 1.32, 1.01–1.73, P = 0.049) after removing the outliers. Furthermore, no pleiotropy was observed in these exposures.ConclusionOur findings suggest that higher BMI, WHR, and smoking are likely to be causal factors in the development of DR, whereas genetically higher HC is associated with a lower risk of DR, providing insights into a better understanding of the etiology and prevention of DR

Transcriptome analysis of osmotic-responsive genes in ABA-dependent and -independent pathways in wheat (Triticum aestivum L.) roots

Bread wheat is one of the most important crops in the world. However, osmotic stress significantly inhibits wheat growth and development, and reduces crop yield and quality. Plants respond to osmotic stress mainly through abscisic acid (ABA)-dependent and -independent pathways. In this study, root transcriptome profiles of wheat seedlings exposed to osmotic stress and exogenous ABA were analysed to identify osmotic-responsive genes belonging to the ABA-dependent or -independent pathways. We found that osmotic stress promoted proline biosynthesis in the ABA-dependent pathway, and trehalose biosynthesis is likely promoted among soluble sugars to maintain protein bioactivity under osmotic stress. In wheat roots subjected to osmotic stress, calcium ions, and glutathione exert their functions mainly through calcium-binding protein (CaM/CML) and glutathione-S-transferase, respectively, depending on both pathways. In addition, a complex relationship among phytohormones signal transduction was observed in response to osmotic stress. The findings of this study deepen our understanding of the molecular mechanisms of osmotic-stress resistance, and provide several candidate osmotic-responsive genes for further study

Association between mobile phone addiction, sleep disorder and the gut microbiota: a short-term prospective observational study

Bidirectional communication between the gut microbiota and the brain has sparked interest in exploring the link between mobile phone addiction (MPA) and sleep disorders (SD) in microbiome research. However, investigating the role of gut microbiota in this relationship using animal models presents challenges due to the unique nature of MPA, and human research in this area is scarce. We recruited 99 healthy college students to evaluate the gut microbiome using 16S rRNA gene amplicon sequencing and assess MPA and SD at baseline and after a two-month follow-up. Multiple covariate-adjusted statistical models, including linear regression, permutational multivariate analysis of variance and so on, were employed to determine microbiome associations with MPA at baseline and changes in SD at follow-up. Our findings revealed negative associations between MPA and three alpha diversity metrics, along with alterations in bacterial composition. MPA showed negative associations with the relative abundance of Bacteroidetes, while displaying positive associations with Actinobacteria and Bifidobacteriales. Conversely, Actinobacteria exhibited a negative association with increased SD. This study has established a significant link between MPA and a decrease in the alpha diversity of the gut microbiota. Actinobacteria was associated with MPA and SD, respectively. Additional investigation is needed to fully comprehend the relationship between comorbid behavioral disorders and the gut microbiota

Infection status and risk factors of HIV, HBV, HCV, and syphilis among drug users in Guangdong, China - a cross-sectional study

<p>Abstract</p> <p>Background</p> <p>China has witnessed a remarkable increase in sexually transmitted infections (STIs) and HIV. The study is to assess the prevalence of HIV, HBV, HCV and syphilis and related risk factors among drug users in mandatory detoxification center Qingyuan, Guangdong, China.</p> <p>Method</p> <p>A cross-sectional study on drug use behaviors, sex behaviors, and presence of antibodies to HIV, HCV, Treponema pallidum, and surface antigen of HBV (HBsAg) was conducted among drug users recruited from 3 detoxification centers in Qingyuan, Guangdong, China. Risk factors for each of four infections were analyzed with logistic regression model.</p> <p>Results</p> <p>A total of 740 subjects were recruited, the median age was 31 years old (range 24-38). The seroprevalence rates of HIV, HBsAg, HCV and syphilis were 4.6%, 19.3%, 71.6% and 12.6%, respectively. Risk factors for HIV were intravenous drug use and co-infection with syphilis. Having a regular sexual partner who was a drug user was considered to be a risk factor for HBV. Intravenous drug use was a risk factor for HCV. However, the consistent use of condoms with commercial sex partners was protective for HCV infection. Compared to drug users living in urban area, those living in rural areas were more likely to be infected with syphilis, and there was an association between commercial sex and syphilis.</p> <p>Conclusion</p> <p>The prevalence of HIV, HBV, HCV and syphilis were high among drug users in detoxification centers in Qingyuan, thus, risk reduction programs for the drug user population is urgently required.</p

DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2

A subtelomeric region, 4q35.2, is implicated in facioscapulohumeral muscular dystrophy (FSHD), a dominant disease thought to involve local pathogenic changes in chromatin. FSHD patients have too few copies of a tandem 3.3-kb repeat (D4Z4) at 4q35.2. No phenotype is associated with having few copies of an almost identical repeat at 10q26.3. Standard expression analyses have not given definitive answers as to the genes involved. To investigate the pathogenic effects of short D4Z4 arrays on gene expression in the very gene-poor 4q35.2 and to find chromatin landmarks there for transcription control, unannotated genes and chromatin structure, we mapped DNaseI-hypersensitive (DH) sites in FSHD and control myoblasts. Using custom tiling arrays (DNase-chip), we found unexpectedly many DH sites in the two large gene deserts in this 4-Mb region. One site was seen preferentially in FSHD myoblasts. Several others were mapped >0.7 Mb from genes known to be active in the muscle lineage and were also observed in cultured fibroblasts, but not in lymphoid, myeloid or hepatic cells. Their selective occurrence in cells derived from mesoderm suggests functionality. Our findings indicate that the gene desert regions of 4q35.2 may have functional significance, possibly also to FSHD, despite their paucity of known genes

Aristolochic Acid I Induced Autophagy Extenuates Cell Apoptosis via ERK 1/2 Pathway in Renal Tubular Epithelial Cells

Autophagy is a lysosomal degradation pathway that is essential for cell survival and tissue homeostasis. However, limited information is available about autophagy in aristolochic acid (AA) nephropathy. In this study, we investigated the role of autophagy and related signaling pathway during progression of AAI-induced injury to renal tubular epithelial cells (NRK52E cells). The results showed that autophagy in NRK52E cells was detected as early as 3–6 hrs after low dose of AAI (10 µM) exposure as indicated by an up-regulated expression of LC3-II and Beclin 1 proteins. The appearance of AAI-induced punctated staining of autophagosome-associated LC3-II upon GFP-LC3 transfection in NRK52E cells provided further evidence for autophagy. However, cell apoptosis was not detected until 12 hrs after AAI treatment. Blockade of autophagy with Wortmannin or 3-Methyladenine (two inhibitors of phosphoinositede 3-kinases) or small-interfering RNA knockdown of Beclin 1 or Atg7 sensitized the tubular cells to apoptosis. Treatment of NRK52E cells with AAI caused a time-dependent increase in extracellular signal-regulated kinase 1 and 2 (ERK1/2) activity, but not c-Jun N-terminal kinase (JNK) and p38. Pharmacological inhibition of ERK1/2 phosphorylation with U0126 resulted in a decreased AAI-induced autophagy that was accompanied by an increased apoptosis. Taken together, our study demonstrated for the first time that autophagy occurred earlier than apoptosis during AAI-induced tubular epithelial cell injury. Autophagy induced by AAI via ERK1/2 pathway might attenuate apoptosis, which may provide a protective mechanism for cell survival under AAI-induced pathological condition

High Prevalence of Extended-Spectrum Beta Lactamases among Salmonella enterica Typhimurium Isolates from Pediatric Patients with Diarrhea in China

We investigated the extended-spectrum beta lactamases among 62 Salmonella enterica Typhimurium isolates recovered from children with diarrhea in a Chinese pediatric hospital. A large proportion of S. enterica Typhimurium isolates were resistant to multiple antimicrobial agents, including ampicillin (90.3%), tetracycline (80.6%), trimethoprim/sulfamethoxazole (74.2%), chloramphenicol (66.1%), cefotaxime (27.4%). Forty-nine (79.0%) of S. enterica Typhimurium isolates were positive for blaTEM-1b and resistant to ampicillin. Thirteen S. enterica Typhimurium isolates (21.0%) were positive for blaCTX-M-1-group and blaCTX-M-9-group, and all isolates harboring blaCTX-M genes were positive for ISEcp1. Two main clones (PFGE type A and D) accounted for nearly 70% of S. enterica Typhimurium isolates, and 7 CTX-M-producing isolates belonged to PFGE type D. Collectively, our data reveal multi-drug resistance and a high prevalence of extended spectrum beta lactamases among S. enterica Typhimurium isolates from children in China. In addition, we report the first identification of blaCTX-M-55 within Salmonella spp. Our data also suggest that clonal spread is responsible for the dissemination of S. enterica Typhimurium isolates