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.

BACKGROUND:The morphological indexes of ankle point may change after ankle fracture,and there is a certain correlation between the coronal angle change of ankle point and the functional recovery of ankle joint.Most previous studies have studied the height recovery of ankle point after surgery,so the correlation between the fluctuation of coronal angle of ankle point and the functional recovery of ankle joint after ankle fracture has certain reference significance. OBJECTIVE:To investigate the effect of coronal angle change of ankle point on joint function recovery after ankle fracture. METHODS:A total of 86 patients with ankle fracture who underwent surgical treatment were selected as the study objects,and were divided into excellent group(n=45)and poor group(n=41)according to the results of American Orthopaedic Foot&Ankle Society(AOFAS)hindfoot-ankle score during the last follow-up,and the general data of the two groups were compared.The morphological indexes of ankle points on the affected side and healthy side were compared after surgery based on ankle acupoints and lateral X-rays of the ankle joint,including the width and depth of ankle points,coronal angle and sagittal angle,and the difference of ankle points between the affected side and healthy side,and further comparison and analysis were conducted in each group.A joint model was constructed and Cox regression analysis was used to evaluate the relationship between coronal angle fluctuation and joint function recovery.Least absolute shrinkage and selection operator regression method and multivariate Logistic regression were used to analyze the risk factors affecting the recovery of joint function.The patients were divided into 5-quartile array(Q1-Q5)according to the angle of coronal position at ankle point from low to high.The clinical data characteristics of the five groups were compared,and the correlation between the change of coronal position at ankle point and the risk of poor recovery of joint function was analyzed by multivariate Logistic regression.A restricted cubic spline Logistic regression model was established to analyze the dose-response relationship.The prediction model of regression equation y=1-1/(1+e-z)was established and verified. RESULTS AND CONCLUSION:(1)The width and depth of ankle point on the affected side,coronal angle and sagittal angle were significantly higher than those on the healthy side(all P<0.05),and compared with the excellent group,the difference of ankle point width,depth difference,coronal angle difference and sagittal angle difference were greater in the poor group(P<0.05).(2)The combined model showed that the risk of poor joint function was increased by 3%for every 1? increase in coronal angle,regardless of whether the angle was within the normal range.(3)Least absolute shrinkage and selection operator regression and multivariate Logistics regression analysis showed that after adjusting for potential confounding factors,it was found that age,lack of functional exercise in early stage,no calcaneal traction,failure to remove internal fixation,postoperative complications,and increased ankle coronal angle were independent risk factors for joint function recovery(P<0.05).(4)The coronal angle within 3 months after surgery was independently correlated with the risk of poor joint function recovery(OR=1.57,95%CI:1.38-1.76,P=0.002),and the trend test of the coronal angle from low to high quintile in each postoperative period had statistical significance(Ptrend<0.001).(5)Restricted cubic spline model analysis showed that there was no nonlinear relationship between the coronal angle change of ankle point and the risk of poor joint function recovery in males or females.Through Bootstrap self-sampling,the prediction model has good differentiation and accuracy.(6)The reduction of coronal angle of ankle point after ankle fracture plays a significant role in promoting the recovery of joint function.Therefore,the detection of coronal angle of ankle point after ankle fracture is helpful to understand the recovery of joint function of patients.

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 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.

Knee osteoarthritis(OA)is a primary cause of joint dysfunction.Knee osteotomy has garnered significant attention due to its potential to delay the progression of knee OA and enhance joint function.As a pivotal biomechanical factor in the onset and progression of OA,the accurate correction of abnormal knee alignment is the central objective of knee osteotomy.This article systematically reviews the biomechanical research progress related to knee osteotomy,with a focus on the precision and personalized correction of force line.The development of new classification system and measurement technology of force line is summarized,the biomechanical mechanism of knee OA induced by abnormal mechanical load is analyzed,and the goal of force line and clinical application progress of knee osteotomy is discusses,so as to provide a new perspective and idea for the clinical treatment of knee OA with knee osteotomy.

To analyze the standard establishment approach and compilation rationale for metallic pharmaceutical packaging standard development in the 2025 edition of the Pharmacopeia of the People's Republic of China.This article systematically explained the background and process of establishing the guiding principles for metallic materials and containers used in pharmaceutical packaging in the Chinese Pharmacopoeia through basic information,relevant domestic and international standards,the establishment of key quality attributes of metallic pharmaceutical packaging materials,and the construction of metallic pharmaceutical packaging material standards.The newly established guidelines,the Pharmacopeia of the People's Republic of China 9625,prioritized product critical quality attributes(CQAs)and real-world applicability.This dual emphasis on rigidity and adaptability enhances drug safety,meets the regulatory requirements,and promotes the globalization and scientific advancement of China's pharmaceutical packaging industry.

This study aims to investigate the anti-inflammatory and anti-apoptotic effects of total flavonoids of hawthorn leaves(TFHL)on lipopolysaccharide(LPS)-induced inflammatory injury in rat intestinal epithelial(IEC-6)cells,as well as the underlying mechanisms.An in vitro inflam-mation model was first established by treating IEC-6 cells with lipopolysaccharide(LPS).IEC-6 cells were then incubated with three concentrations of TFHL for 24 h prior to a further 24 h LPS treatment.RT-qPCR was used to quantify mRNA levels of the inflammatory genes COX-2 and iN-OS,while Western blotting was used to assess protein levels of the apoptotic markers Bax,cleaved Caspase-3,Bcl-2,and the JNK/p-JNK signaling pathway.Finally,cells were pretreated with TFHL and/or the JNK inhibitor SP600125 for 24 h before LPS exposure for 24 h,in order to evaluate the combined effects of TFHL and SP600125 on LPS-induced inflammatory cytokine expression and apoptotic protein levels in IEC-6 cells.The results showed that,compared with the LPS group,the mRNA level of COX-2 and iNOS in the 2.5,5.0,10.0 mg/L TFHL group and the Bax and Caspase-3 protein levels decreased significantly(P＜0.01),and the Bcl-2 protein level was significantly higher(P＜0.01),p-JNK protein level and p-JNK/JNK ratio decreased significantly(P＜0.01);compared with the LPS group,the COX-2 and iNOS mRNA levels of the TFHL+LPS group de-creased significantly(P＜0.01),Bax,and Caspase-3 protein levels decreased significantly(P＜0.01),and the level of Bcl-2 protein increased significantly(P＜0.05);compared with the LPS group,the COX-2 and iNOS mRNA levels of the TFHL+SP600125 group decreased significantly(P＜0.01),Bax and Caspase-3 protein levels decreased significantly(P＜0.01),and Bcl-2 protein level increased significantly(P＜0.01).These findings indicate that TFHL exerts anti-inflammato-ry and anti-apoptotic effects in LPS-challenged IEC-6 cells by inhibiting the JNK signaling path-way.

Objective To investigate the effect of perindopril on the nicotinamide adenine dinucleotide phosphate(NADPH)oxidase 4(NOX4)/NOD-like receptor protein 3(NLRP3)signaling pathway in rat liver fibrosis induced by thioacetamide(TAA).Methods Thirty-two SD rats were randomly divided into the blank group,the model group(TAA 200 mg/kg,twice a week for 6 weeks)and the low/high dose group(TAA+perindopril 2/8 mg/kg),with 8 rats in each group.Two weeks after modeling,the administration group was given the corresponding dose of perindopril by gavage(for 4 weeks).At the end of the 6th week,liver pathological sections were used to observe pathological changes of liver tissue and degrees of fibrosis and inflammation.The biochemical analyzer was used to detect alanine aminotransferase(ALT)and aspartate aminotransferase(AST).Enzyme-linked immunosorbent assay(ELISA)was used to detect NLRP3 and IL-1β.Immunohistochemistry was used to detect NOX4,NLRP3,Caspase-1,IL-1β protein and α-smooth muscle agonist protein(α-SMA).Results Compared with the blank group,liver collagen fibers were significantly proliferated in the model group,a large number of inflammatory cells infiltrated,and serum levels of ALT and AST,as well as NLRP3 and IL-1β in rats were significantly increased.The average optical density values of positive proteins such as NOX4,NLRP3,Caspase-1,IL-1β and α-SMA in rat liver tissue increased significantly(P<0.05).Compared with the model group,the proliferation of collagen fibers and inflammatory infiltration were significantly reduced in both the low-dose and high-dose groups,and serum levels of ALT and AST,NLRP3 and IL-1β in rats were significantly decreased.The average optical density values of positive proteins such as NOX4,NLRP3,Caspase-1,IL-1β and α-SMA in rat liver tissue decreased significantly(P<0.05).Moreover,the degree of liver fibrosis reduction in rats was better in the high-dose group than that in the low-dose group.Conclusion Perindopril may regulate the NLRP3 signaling pathway by inhibiting the expression of NOX4,thereby reducing oxidative stress damage and inflammatory responses and thus delaying the process of liver fibrosis.