OBJECTIVE: To develop a user-friendly visualization application for the automatic annotation of Human Phenotype Ontology (HPO) terms based on large language models and retrieval-augmented generation (RAG) technology, and to validate its performance in an authoritative case dataset. METHODS: By integrating the domestic open-source large language model DeepSeek-V3 with RAG technology, an interactive web application was deployed on the Streamlit cloud platform. Using only the latest official HPO dataset as the data source, the lightweight sentence-embedding model BAAI/bge-small-en-v1.5 was employed to construct a FAISS vector index. During the online phase, a four-step closed-loop process is automatically completed: multilingual translation, phenotype phrase extraction, RAG candidate retrieval, term mapping, and official database validation. 121 English case reports publicly released by BMJ Case Reports and Oxford Medical Case Reports (with a gold-standard HPO set of 1 794 terms) were selected for application validation. Precision, recall, and F1 score were calculated and compared horizontally with traditional dictionary tools, standalone large language models, and the similar application "RAG-HPO". Finally, replace the model with the more advanced ChatGPT-5 and evaluate its performance on the newly extracted dataset. RESULTS: An HPO term automatic annotation visualization application named PhenoRAG, based on large language models and RAG technology, was successfully developed. Users can access it directly via a web link. Across the 112 cases, a total of 2 150 HPO terms were generated; 2,064 (96.0%) were fully validated by the official database, with a hallucination rate of 1.3% and an HPO ID-name mismatch rate of 2.7%. After deduplication, 1,906 terms remained for testing. The overall precision was 63.65%, recall was 67.34%, and F1 was 65.44%, significantly outperforming traditional annotation tools (F1: 0.45-0.49, P < 0.001). Although PhenoRAG's F1 was lower than that of RAG-HPO (F1 = 0.78, P < 0.001), which relies on a manually constructed synonym database of 54 000 entries plus the HPO dataset, it requires no additional dictionary maintenance and can be used without any background in computer programming. Moreover, after switching to the GPT-5 model, PhenoRAG exhibited no hallucination rate on the new dataset, and its F1 score significantly increased (P = 0.038). CONCLUSION Without constructing a synonym database, the PhenoRAG achieved high-accuracy automatic mapping from clinical text to standard HPO terms. It features a low usage threshold, free access, and a Chinese-language interface, and can directly serve rare disease diagnosis, genetic counseling, and research scenarios in China and worldwide, warranting further clinical promotion and multicenter validation.
Humans ; Phenotype ; Biological Ontologies ; Language ; Software ; Large Language Models

Background/Aims: Acetyl coenzyme A (acetyl-CoA) is one of the most essential metabolites in cell metabolism but its function and concentration in hepatocellular carcinoma (HCC) remain elusive and controversial. Methods: A comprehensive analysis of acetyl-CoA levels and acetyl-CoA synthetase 2 (ACSS2) expression across a range of samples, including patient specimens from both hepatitis B virus (HBV) positive and HBV negative HCC individuals, HBV-transgenic mouse HCC models, and multiple cell lines. Furthermore, to evaluate the functional significance of ACSS2 in HBV-related HCC, we implemented both genetic and pharmacological inhibition strategies targeting ACSS2. Molecular mechanism and mitophagy assessment were revealed by cleavage under target and tagmentation sequencing, RNA sequencing, bioinformatic analyses, transmission electron microscopy and JC-1 staining. Results: Our study revealed a distinct metabolic signature of HBV-related HCC, marked by elevated acetyl-CoA, which was driven by ACSS2. ACSS2 was upregulated by the carbohydrate response element-binding protein in HBV-related HCC. Furthermore, ACSS2 improved tumor cell proliferation, an effect that was dependent on its enzymatic activity. Mechanistically, ACSS2-induced acetyl-CoA accumulation activated voltage-dependent anion channels 1 transcription through increased H3K27ac occupancy, which subsequently promoted mitophagy and HBV-related HCC tumorigenesis. Notably, targeting ACSS2 by depletion or inhibition with a catalytic inhibitor significantly suppressed tumor growth. Conclusions These findings not only illustrate the interplay between metabolic reprogramming, epigenetic modification, and tumorigenesis in the context of HBV infection, but also highlight ACSS2 as a novel metabolic vulnerability in HBV-related HCC. Therefore, targeting ACSS2 could be a novel strategy against HBV-related HCC.

Background/Aims: Liver transplantation (LT) following total hepatectomy is a life-saving treatment for hepatocellular carcinoma (HCC). The HCC recurrence after LT hinders the effectiveness of the procedure. The objective of this study is to develop a pre-operative risk stratification model based on a liquid biopsy. Methods: We conducted a comprehensive multi-omics study of 260 HCC patients from three centers, including clinical data, low-coverage whole-genome sequencing of cell-free DNA (cfDNA) from plasma, as well as whole-exome, single-nucleus RNA, and spatial transcriptomics from matched tumor and non-tumor tissues. Results: We identified cfDNA-derived copy number alteration (CNA) signatures associated with post-transplant recurrence. By integrating cfDNA-derived CNA profiles with single-cell transcriptomic data, we traced recurrence-associated cfDNA to a distinct subpopulation of malignant cells within the primary tumor. These cells were embedded in a pro-metastatic microenvironment of specialized endothelial subtypes and cancer-associated fibroblasts. Notably, most recurrence-associated lesions were detectable in cfDNA prior to liver transplantation (LT). Building on these insights, we developed the ZJU Criteria based on CNA fragments and tumor markers, a pre-LT risk prediction tool that integrates conventional clinical factors with cfDNA-derived CNA signatures, and validated it using internal and independent external cohorts. Conclusion Our findings suggest that post-transplant recurrence commonly originates from advanced subclones that emerge late during tumor evolution. The ZJU Criteria provides an accurate, non-invasive strategy that significantly improves pre-LT risk stratification and clinical decision-making for patients with HCC.

ObjectiveFrozen shoulder (FS) is a debilitating musculoskeletal disorder characterized by persistent inflammation and progressive fibrosis of the glenohumeral joint capsule, leading to pain and severely restricted range of motion. Given the limited efficacy of current pharmacotherapies, there is an urgent need for novel anti-fibrotic agents. Guyanxiao Tincture (GYX), a traditional Chinese herbal formula, has shown clinical benefits in alleviating FS symptoms. However, its bioactive constituents and the molecular mechanisms underlying its therapeutic effects remain poorly defined. This study aimed to systematically evaluate the therapeutic efficacy of GYX against FS and to elucidate the mechanisms by which GYX attenuates capsular fibrosis. MethodsA Sprague-Dawley (SD) rat model of FS was established by immobilizing the unilateral shoulder with a plaster cast for 21 d. Following model induction, animals were administered with GYX or its serum-identified bioactive component, icariside F2. The absorbed prototype compounds of GYX in FS rat serum were profiled using ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Therapeutic effects were assessed by measuring shoulder range of motion (ROM), histopathological evaluation of the capsule via hematoxylin-eosin staining, and quantification of transforming growth factor‑β1 (TGF-β1) content by ELISA. To explore the underlying mechanisms, transcriptomic profiling of the shoulder capsule was performed using RNA sequencing, and differentially expressed genes were validated by real-time quantitative PCR. Protein expression and localization were examined through immunohistochemistry, immunofluorescence, and Western blot. Protein-protein interaction networks were constructed to identify key regulatory hubs. In vitro, primary shoulder capsule fibroblasts were stimulated with TGF‑β1 to induce a fibrotic phenotype and then treated with icariside F2. The expression of alpha cardiac muscle 1 (ACTC1), α‑smooth muscle actin, and collagen I was subsequently measured. ResultsSerum pharmacochemistry analysis identified icariside F2 as the predominant circulating bioactive component of GYX in FS rats. Both GYX and icariside F2 treatment significantly improved the ROM and ameliorated histopathological lesions, including the attenuation of synovial hyperplasia, inflammatory infiltration, and excessive collagen deposition in the shoulder capsule. Consistently, elevated TGF‑β1 levels in the model group were markedly reduced after the interventions. RNA sequencing revealed that actin ACTC1 was dramatically upregulated in the fibrotic capsule, accompanied by the enrichment of fibrosis-associated pathways such as TGF‑β signaling, focal adhesion, and ECM-receptor interaction. Protein-protein interaction network analysis demonstrated that ACTC1 directly interacts with core fibrotic genes, including Col1a1, Col1a2, Thbs2, and Fn1. Critically, icariside F2 administration significantly reversed the aberrant overexpression of ACTC1 and suppressed the activation of the aforementioned fibrosis-related pathways in vivo. In TGF‑β1-stimulated fibroblasts, icariside F2 dose-dependently downregulated ACTC1 at both the mRNA and protein levels and concurrently decreased the expression of the fibrotic markers α‑smooth muscle actin and collagen I. Immunofluorescence and Western blot further confirmed that icariside F2 attenuated stress fiber formation and collagen production in vitro. ConclusionGYX and its bioactive component icariside F2 effectively alleviate the progression of frozen shoulder by inhibiting capsular fibrosis. Mechanistically, the therapeutic action is functionally linked to the suppression of ACTC1 and its downstream profibrotic signaling cascade, highlighting ACTC1 as a promising therapeutic target for the management of frozen shoulder.

[Objective] To evaluate the efficacy and safety of sacral neuromodulation (SNM) in the treatment of patients with benign prostatic hyperplasia (BPH) complicated with underactive bladder (UAB) who respond poorly to transurethral resection of the prostate (TURP). [Methods] A retrospective analysis was performed on 10 patients with BPH and UAB treated with TURP by the same surgeon in Zhongda Hospital Southeast University during Jan.2018 and Jan.2023.The residual urine volume was not significantly relieved after operation, and the maximum urine flow rate and urine volume per discharge were not significantly improved.All patients underwent phase I SNM, and urinary diaries were recorded before and after surgery to observe the average daily frequency of urination, volume per urination, maximum urine flow rate, and residual urine volume. [Results] The operation time was (97.6±11.2) min.During the postoperative test of 2-4 weeks, if the residual urine volume reduction by more than 50% was deemed as effective, SNM was effective in 6 patients (60.0%). Compared with preoperative results, the daily frequency of urination [(20.2±3.8) times vs. (13.2±3.2) times], volume per urination [(119.2±56.7) mL vs. (246.5±59.2) mL], maximum urine flow rate [(8.7±1.5) mL/s vs. (16.5±2.6) mL/s], and residual urine volume [(222.5±55.0) mL vs. (80.8±16.0) mL] were significantly improved, with statistical significance (P<0.05). There were no complications such as bleeding, infection, fever or pain.The 6 patients who had effective outcomes successfully completed phase II surgery, and the fistula was removed.During the follow-up of 1 year, the curative effect was stable, and there were no complications such as electrode displacement, incision infection, or pain in the irritation sites.The residual urine volume of the other 4 unsuccessful patients did not improve significantly, and the electrodes were removed and the vesicostomy tube was retained. [Conclusion] SNM is safe and effective in the treatment of BPH with UAB patients with poor curative effects after TURP.

Objective To explore the diagnostic value of exhaled volatile organic compounds (VOCs) for cystic fibrosis (CF). Methods A systematic search was conducted in PubMed, EMbase, Web of Science, Cochrane Library, CNKI, Wanfang, VIP, and SinoMed databases up to August 7, 2024. Studies that met the inclusion criteria were selected for data extraction and quality assessment. The quality of included studies was assessed by the Newcastle-Ottawa Scale (NOS), and the risk of bias and applicability of included prediction model studies were assessed by the prediction model risk of bias assessment tool (PROBAST). Results A total of 10 studies were included, among which 5 studies only identified specific exhaled VOCs in CF patients, and another 5 developed 7 CF risk prediction models based on the identification of VOCs in CF. The included studies reported a total of 75 exhaled VOCs, most of which belonged to the categories of acylcarnitines, aldehydes, acids, and esters. Most models (n=6, 85.7%) only included exhaled VOCs as predictive factors, and only one model included factors other than VOCs, including forced expiratory flow at 75% of forced vital capacity (FEF75) and modified Medical Research Council scale for the assessment of dyspnea (mMRC). The accuracy of the models ranged from 77% to 100%, and the area under the receiver operating characteristic curve ranged from 0.771 to 0.988. None of the included studies provided information on the calibration of the models. The results of the Prediction Model Risk of Bias Assessment Tool (PROBAST) showed that the overall bias risk of all predictive model studies was high, and the overall applicability was unclear. Conclusion The exhaled VOCs reported in the included studies showed significant heterogeneity, and more research is needed to explore specific compounds for CF. In addition, risk prediction models based on exhaled VOCs have certain value in the diagnosis of CF, but the overall bias risk is relatively high and needs further optimization from aspects such as model construction and validation.

Objective To evaluate the advantages of powder-liquid double-chamber bag products compared with traditional powder injection. Methods The systematic review method was used to collect the literature on powder-liquid double-chamber bag, extract common evaluation indicators, evaluate the use value of powder-liquid double-chamber bag products, and conduct a comprehensive comparison with traditional powder injection products. Results A total of 23 articles were included in the literature. The effectiveness indicators used for evaluation were the stability of the liquid medicine, the accuracy of the preparation concentration, and the residual amount of the liquid medicine; the safety indicators were the incidence of insoluble particles and the incidence of punctures and scratches. The economic indicators were preparation cost, occupied volume of preparation supplies, waste weight, hospitalization cost and incidence of blood infection. The applicability indicators were preparation time, average occupation of medical staff, packaging weight and storage and transportation volume, environmental adaptability, and ease of waste disposal. Accessibility indicators are the number of manufacturers, raw material supply capacity, and patient affordability. Through the evaluation of literature evidence, it was found that the stability and concentration accuracy of the powder-liquid double-chamber bag were higher than those of the traditional powder injection, and the domestic supply had been achieved. The double-chamber bag method can reduce the infusion reaction and shorten the preparation time of the liquid medicine. Conclusion Compared with traditional powder injectabler products, powder-liquid double-chamber bags have advantages in the dimensions of effectiveness, safety, economy, suitability and innovation, and the accessibility dimension meets the requirements.

ObjectiveAutism spectrum disorder (ASD) is a neurodevelopmental condition characterized by difficulties with communication and social interaction, restricted and repetitive behaviors. Previous studies have indicated that individuals with ASD exhibit early and lifelong attention deficits, which are closely related to the core symptoms of ASD. Basic visual attention processes may provide a critical foundation for their social communication and interaction abilities. Therefore, this study explores the behavior of children with ASD in capturing attention to changes in topological properties. MethodsOur study recruited twenty-seven ASD children diagnosed by professional clinicians according to DSM-5 and twenty-eight typically developing (TD) age-matched controls. In an attention capture task, we recorded the saccadic behaviors of children with ASD and TD in response to topological change (TC) and non-topological change (nTC) stimuli. Saccadic reaction time (SRT), visual search time (VS), and first fixation dwell time (FFDT) were used as indicators of attentional bias. Pearson correlation tests between the clinical assessment scales and attentional bias were conducted. ResultsThis study found that TD children had significantly faster SRT (P<0.05) and VS (P<0.05) for the TC stimuli compared to the nTC stimuli, while the children with ASD did not exhibit significant differences in either measure (P>0.05). Additionally, ASD children demonstrated significantly less attention towards the TC targets (measured by FFDT), in comparison to TD children (P<0.05). Furthermore, ASD children exhibited a significant negative linear correlation between their attentional bias (measured by VS) and their scores on the compulsive subscale (P<0.05). ConclusionThe results suggest that children with ASD have difficulty shifting their attention to objects with topological changes during change detection. This atypical attention may affect the child’s cognitive and behavioral development, thereby impacting their social communication and interaction. In sum, our findings indicate that difficulties in attentional capture by TC may be a key feature of ASD.

Objective To analyze the epidemiological characteristics and trends of the incidence and mortality of biliary tract cancer in Shanghai from 2002 to 2020. Methods Data on new cases and deaths of malignant tumors of the gallbladder, extrahepatic bile ducts, and other biliary tract organs from 2002 to 2020 were obtained from the Population-based Cancer Registry and Vital Statistics System of Shanghai Municipal Center for Disease Control and Prevention. Cases or deaths, proportion, crude rate, age-specific rate, age-standardized rate (ASR) and others were calculated stratified by year of diagnosis or death, gender and age-group. ASRs were calculated using Segi′s 1960 world standard population. Trends of the annual percent change (APC) of ASRs, age-specific rates and proportions of new cases with selected diagnostic character of biliary tract cancer stratified by different groups were analyzed by Joinpoint analysis software. Results Annual new cases of biliary tract cancer in Shanghai increased from 963 in 2002 to 1 537 in 2020, with ASR of incidence changing from 3.91/10⁵ to 3.59/10⁵. Annual deaths increased from 830 to 1 225, with ASR of mortality decreased from 3.36/10⁵ to 2.69/10⁵. In 2020, the crude rate of incidence of biliary tract cancer was 10.43/10⁵ (9.54/10⁵ in males and 11.30/10⁵ in females) in Shanghai, and the ASR was 3.59/10⁵ (3.54/10⁵ in males and 3.61/10⁵ in females), with no statistically significant gender difference (P=0.731). The crude rate of mortality was 8.31/10⁵ (7.60/10⁵ in males and 9.00/10⁵ in females), and the ASR was 2.69/10⁵ (2.69/10⁵ in males and 2.66/10⁵ in females), also with no significant gender difference (P=0.874). Age-specific nunbers and rates of incidence and mortality generally increased with aging. Stratified by gender, the trend of ASRs of incidence of biliary tract cancer in Shanghai in males showed no significant change (P=0.179) from 2002 to 2020, nor did that of ASRs of mortality (P=0.738). In females, the ASRs of incidence decreased at an average annual rate of 1.58% (P<0.001), while the trend of ASRs of mortality showed no significant change from 2002 to 2011 (P=0.774), but ASRs decreased at an average annual rate of 3.72% from 2011 to 2020 (P<0.001). Among new cases, the proportions of morphological verification increased, while the proportions of imaging verification decreased. The gallbladder was the most common site, but its proportions decreased significantly, whereas the proportions of extrahepatic bile duct increased from 25.75% to 42.88%. Over 60% of cases were unknown stage at diagnosis, while the combined proportions of stages Ⅰ-Ⅲ remained less than that of stage Ⅳ. Conclusions The ASRs for incidence and mortality of biliary tract cancer in Shanghai remain relatively high, with distinct epidemiological characteristics. The improvement in the diagnosis and treatment of biliary diseases maybe have impact on the incidence patterns of biliary tract cancer in Shanghai, but the effect on increasing survival rates and reducing mortality rates is relatively lagging. It needs a big progress to advance the screening, diagnosis, and survival of biliary tract cancer in Shanghai. This study provides a foundation for further research and prevention strategies for biliary tract cancer.

Gastric cancer with peritoneal metastasis (GCPM) is a common and lethal manifestation of advanced gastric cancer, with a median survival of only 5-11 months. This consensus was developed by 30 experts from Asia (China, Japan, Korea, and Singapore) using the Delphi method and the GRADE evidence grading system. A total of 29 statements were formulated, covering the diagnosis and assessment of GCPM, indications for laparoscopic exploration and NIPS (normothermic intraperitoneal and systemic treatment), treatment regimens, prevention and management of complications, criteria for conversion surgery, and postoperative intraperitoneal therapy. The consensus aims to standardize clinical practice and improve the prognosis of patients with GCPM.