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

Objective:To explore the impact of air pollution on hospital visits for mental and behavioral disorders among residents in an industrial area in Henan Province from 2016 to 2021.Methods:Daily outpatient visits data for mental and behavioral disorders were collected from Angang General Hospital in Angang Industrial Area at Anyang City between January 2016 and December 2021. And air pollutants and meteorological data during the same period were also collected. A generalized additive model was used for time-series analysis to examine the relationship between daily average concentrations of nitrogen dioxide (NO 2), sulfur dioxide (SO 2), fine particulate matter (PM 2.5), inhalable particulate matter (PM 10), carbon monoxide (CO), and ozone (O 3) with a lag of 0 to 7 days on the number of visits for mental and behavioral disorders among residents. The single-day lag effect (lag0-lag7 d) and cumulative lag effect (lag01-lag07 d) were analyzed. The smooth cubic spline function was used to fit the exposure-response relationship, and subgroup analysis was performed according to different genders, seasons and ages. Results:A total of 26 268 hospital visits for mental and behavioral disorders were collected from the industrial area between 2016 and 2021. The daily average concentrations of SO 2, NO 2, PM 2.5, PM 10, and CO were (27.50±27.33), (43.11±18.33), (73.87±60.30), (134.01±83.81) μg/m 3, and (1.72±1.03) mg/m 3, respectively. The daily maximum 8-hour average concentration of O 3 was (82.18±53.70) μg/m 3. After controlling for long-term trends, temperature, relative humidity, day of the week effects, and holiday effects, the generalized additive model analysis showed that NO 2 had a statistically significant impact on the hospital visits for mental and behavioral disorders at lag0 d, lag2 d and lag01-lag05 d and CO had a statistically significant impact at lag0-lag3 d and lag01-lag06 d (all P<0.05). NO 2 at lag02-lag04 d and CO at lag0-lag2 d and lag01-lag04 d had statistically significant effects on the visits for neurasthenia (both P<0.05). The impacts of NO 2 at lag03-lag04 d, PM 2.5 at lag3 d and lag03-lag04 d, PM 10 at lag3 d and lag03 d, and CO at lag3 d and lag01-lag05 d on visits for generalized anxiety disorder were also statistically significant (all P<0.05). After false discovery rate (FDR) correction, it was shown that for every 10 μg/m 3 increase in NO 2 and every 0.1 mg/m 3 increase in CO, the percentage increase in visits for mental and behavioral disorders and its 95% confidence interval (95% CI) were 3.38% (0.95%-5.87%) and 0.78% (0.38%-1.17%), respectively. For every 0.1 mg/m 3 increase in CO, the visits for neurasthenia increased by 0.78% (0.27%-1.29%). For every 10 μg/m 3 increase in PM 2.5 and every 0.1 mg/m 3 increase in CO, the visits for generalized anxiety disorder increased by 1.07% (0.46%-1.68%) and 1.17% (0.37%-1.97%), respectively (adjusted P<0.05). There was a linear exposure-response relationship between NO 2 and CO and the hospital visits for mental and behavioral disorders, CO and the hospital visits for neurasthenia, and CO and PM 2.5 and the hospital visits for generalized anxiety disorder ( P<0.05 for the overall association test and P>0.05 for the non-linearity test). Stratified analysis showed that air pollutants had an impact on male patients with neurasthenia, female patients with generalized anxiety disorder, individuals aged <45 years with mental and behavioral disorders, and individuals aged ≥65 years with generalized anxiety disorder. The impact of air pollutants was greater during the cold season or winter. Conclusion:Exposure to air pollution can increase hospital visits for mental and behavioral disorders among residents in industrial areas, with a higher risk among those aged<45 years old and during the cold season.

Objective:This study systematically summarized the construction experience of the immunology platform at the Institute of Basic Medical Sciences, Peking University Third Hospital, aiming to provide theoretical references and practical guidance for research-oriented hospitals in building high-quality research platforms.Methods:This study employed case study analysis to elaborate on the platform development initiatives, integrating literature analysis and in-depth interviews to conduct a horizontal comparison of management models among peer research platforms.Results:Through five years of development, the platform had achieved remarkable outcomes via a model integrating ″Talent cultivation-Technological innovation-Equipment procurement″ Research talents had demonstrated breakthroughs in securing national-level research grants, publishing high-impact papers, and obtaining scientific awards. The technical service system had achieved enhancement in both service scope and professional depth, fostering robust interdisciplinary synergy. The platform had effectively expanded its societal engagement capacity.Conclusions:The sustainable advancement of research-oriented hospital immunology platform necessitates establishing standardized flow cytometry databases and implementing high-dimensional data integration. Building upon multidisciplinary convergence, it is imperative to pioneer innovative operational mechanisms characterized by efficiency, open-access, and shared frameworks.

Objective To explore the role of pseudogene AC106872.1 in maintaining the self-renewal capacity of human embryonic stem cells(hESCs).Methods AC106872.1 was knocked out in hESCs and knockout effi-ciency was validated by PCR and agarose gel electrophoresis.The colony formation of hESCs was assessed through colony formation assays and alkaline phosphatase(AP)staining.The expression level of pluripotency and differ-entiation marker genes was analyzed by qPCR and flow cytometry.RNA sequencing(RNA-seq)was performed to assess transcriptomic changes upon AC106872.1 knockout.Results Knockout of AC106872.1 significantly in-hibited the colony formation of hESCs(P＜0.05).The expression level of pluripotency marker genes was signifi-cantly reduced(P＜0.000 1),while the expression of differentiation marker genes was markedly increased(P＜0.000 1).Conclusions The pseudogene AC 1 06872.1 plays a crucial role in maintaining human embryonic stem cell self-renewal through regulation of pluripotency genes expression.

This study investigated the role of the nuclear factor of activated T cells c3 (NFATc3) in vascular smooth muscle cells (VSMCs) during aortic aneurysm and dissection (AAD) progression and the underlying molecular mechanisms. Cytoplasmic and nuclear NFATc3 levels were elevated in human and mouse AAD. VSMC-NFATc3 deletion reduced thoracic AAD (TAAD) and abdominal aortic aneurysm (AAA) progression in mice, contrary to VSMC-NFATc3 overexpression. VSMC-NFATc3 deletion reduced extracellular matrix (ECM) degradation and maintained the VSMC contractile phenotype. Nuclear NFATc3 targeted and transcriptionally upregulated matrix metalloproteinase 9 (MMP9) and MMP2, promoting ECM degradation and AAD development. NFATc3 promoted VSMC phenotypic switching by binding to eukaryotic elongation factor 2 (eEF2) and inhibiting its phosphorylation in the VSMC cytoplasm. Restoring eEF2 reversed the beneficial effects in VSMC-specific NFATc3-knockout mice. Cabamiquine-targets eEF2 and inhibits protein synthesis-inhibited AAD development and progression in VSMC-NFATc3-overexpressing mice. VSMC-NFATc3 promoted VSMC switch and ECM degradation while exacerbating AAD development, making it a novel potential therapeutic target for preventing and treating AAD.

Myocardial fibrosis is a serious cause of heart failure and even sudden cardiac death. However, the mechanisms underlying myocardial ischemia-induced cardiac fibrosis remain unclear. Here, we identified that the expression of sterile alpha and TIR motif containing 1 (SARM1), was increased significantly in the ischemic cardiomyopathy patients, dilated cardiomyopathy patients (GSE116250) and fibrotic heart tissues of mice. Additionally, inhibition or knockdown of SARM1 can improve myocardial fibrosis and cardiac function of myocardial infarction (MI) mice. Moreover, SARM1 fibroblasts-specific knock-in mice had increased deposition of extracellular matrix and impaired cardiac function. Mechanically, elevated expression of SARM1 promotes the deposition of extracellular matrix by directly modulating P4HA1. Notably, by using the Click-iT reaction, we identified that the increased expression of ZDHHC17 promotes the palmitoylation levels of SARM1, thereby accelerating the fibrosis process. Based on the fibrosis-promoting effect of SARM1, we screened several drugs with anti-myocardial fibrosis activity. In conclusion, we have unveiled that palmitoylated SARM1 targeting P4HA1 promotes collagen deposition and myocardial fibrosis. Inhibition of SARM1 is a potential strategy for the treatment of myocardial fibrosis. The sites where SARM1 interacts with P4HA1 and the palmitoylation modification sites of SARM1 may be the active targets for anti-fibrosis drugs.

Objective To observe the value of machine learning(ML)models based on ultrasound radiomics for preoperatively distinguishing atypical parathyroid tumor(APT)/parathyroid carcinoma(PC)and parathyroid adenoma(PA).Methods Totally 330 primary hyperparathyroidism patients who underwent surgical treatments were retrospectively enrolled and categorized into APT/PC group(n=78)and PA group(n=252)according to surgical pathology and clinical follow-up results,also divided into training set(n=231)and test set(n=99)at the ratio of 7∶3.Based on preoperative ultrasound,545 radiomics features were extracted,and recursive feature elimination(RFE),Kruskal-Wallis or analysis of variance methods were used to screen the features,respectively.Support vector machine(SVM),linear discriminant analysis(LDA),least absolute shrinkage and selection operator logistic regression(LRLASSO),also random forest(RF)and decision tree(DT)algorithms were adopted to construct ML models for differentiating APT/PC and PA,respectively.Then the models were trained in training set,their performance were verified in test set,and a 5-fold cross-validation was adopted to screen out the better combinations.Results Compared with Kruskal-Wallis and analysis of variance methods,the distinguishing efficacy of SVM,LDA,LRLASSO,RF and DT models constructed based on features screened out using RFE method in training set(area under the curve[AUC]=0.870,0.878,0.850,0.847,1.000)and test set(AUC=0.856,0.842,0.827,0.847 and 0.704)were all relatively higher.In test set,the AUC of SVM,LDA,LRLASSO and RF models constructed based on the features screened out using RFE method(included 25,23,17 and 23 features)were all higher than that of DT model(8 features)(all P＜0.001).No significant difference of AUC was found between SVM,LRLASSO or RF models and LDA model(all P＞0.05).The AUC of SVM and RF models were higher than that of LRLASSO model(both P＜0.05),while of SVM and RF models were not significantly different(P＞0.05),indicating that SVM,LDA and RF models were better ones.Conclusion SVM,LDA,LRLASSO,RF and DT models based on ultrasound radiomics could effectively distinguish APT/PC and PA preoperatively,among which SVM,LDA and RF models had better diagnostic efficacy.

Objective:To analyze the clinical characteristics of locally advanced rectal cancer patients with pathological complete response (pCR) after neoadjuvant chemoradiotherapy combined with immunotherapy.Methods:The retrospective cohort study was conducted. The clinicopatholo-gical data of 46 patients with locally advanced rectal cancer who were admitted to 6 medical centers, including Beijing Friendship Hospital of Capital Medical University et al, from June 2021 to November 2022 were collected. There were 29 males and 17 females, aged (61±4)years. Patients received neoadjuvant chemoradiotherapy combined with immune checkpoint inhibitor therapy, and under-went radical total mesorectal excision during 6-12 weeks after radiotherapy. Observation indicators: (1) comparison of clinical characteristics between pCR and non-pCR patients;(2) postoperative complications and adverse reactions of pCR and non-pCR patients. Comparison of measurement data with normal distribution between groups was conducted using the t test. Comparison of measurement data with skewed distribution between groups was conducted using the Mann-Whitney U test. Comparison of count data between groups was conducted using the chi-square test or Fisher exact probability. Comparison of ordinal data between groups was conducted using the Mann-Whitney U test. Results:(1) Comparison of clinical characteristics between pCR and non-pCR patients. Before neoadjuvant therapy, there were 14 cases aged ≥50 years and 6 cases aged <50 years in pCR patients, versus 25 cases and 1 case in non-pCR patients, showing a significant difference between the two groups ( P<0.05). After neoadjuvant therapy, cases in clinical stage T0, T1, T2, T3, T4 were 11, 1, 5, 3, 0 for pCR patients versus 7, 4, 2, 11, 2 for non-pCR patients, cases of tumor regression grade 1, 2, 3, 4 were 11, 8, 1, 0 for pCR patients versus 7, 14, 4, 1 for non-pCR patients, cases in low-risk, medium-risk, high-risk of neoadjuvant rectal scoring and grading were 20, 0, 0 for pCR patients versus 4, 18, 4 for non-pCR patients, respectively, showing significant differences in above indicators between the two groups ( Z=-2.256, -2.104, -5.458, P<0.05). (2) Postoperative complications and adverse reactions of pCR and non-pCR patients. Postoperative complications occurred in 2 cases of pCR patients and 5 cases of non-pCR patients, postoperative adverse reactions occurred in 11 cases of pCR patients and 10 cases of non-pCR patients, showing no significant difference between the two groups ( P>0.05). Conclusion:Compared with locally advanced rectal cancer patients aged ≥50 years, those aged <50 years have significant benefits from neoadjuvant chemoradiotherapy combined with immunotherapy. Clinical T staging and magnetic resonance imaging-detected tumor regression grade after neoadjuvant therapy have predictive value for patients with pCR .

Objective:To explore the impact of air pollution on hospital visits for mental and behavioral disorders among residents in an industrial area in Henan Province from 2016 to 2021.Methods:Daily outpatient visits data for mental and behavioral disorders were collected from Angang General Hospital in Angang Industrial Area at Anyang City between January 2016 and December 2021. And air pollutants and meteorological data during the same period were also collected. A generalized additive model was used for time-series analysis to examine the relationship between daily average concentrations of nitrogen dioxide (NO 2), sulfur dioxide (SO 2), fine particulate matter (PM 2.5), inhalable particulate matter (PM 10), carbon monoxide (CO), and ozone (O 3) with a lag of 0 to 7 days on the number of visits for mental and behavioral disorders among residents. The single-day lag effect (lag0-lag7 d) and cumulative lag effect (lag01-lag07 d) were analyzed. The smooth cubic spline function was used to fit the exposure-response relationship, and subgroup analysis was performed according to different genders, seasons and ages. Results:A total of 26 268 hospital visits for mental and behavioral disorders were collected from the industrial area between 2016 and 2021. The daily average concentrations of SO 2, NO 2, PM 2.5, PM 10, and CO were (27.50±27.33), (43.11±18.33), (73.87±60.30), (134.01±83.81) μg/m 3, and (1.72±1.03) mg/m 3, respectively. The daily maximum 8-hour average concentration of O 3 was (82.18±53.70) μg/m 3. After controlling for long-term trends, temperature, relative humidity, day of the week effects, and holiday effects, the generalized additive model analysis showed that NO 2 had a statistically significant impact on the hospital visits for mental and behavioral disorders at lag0 d, lag2 d and lag01-lag05 d and CO had a statistically significant impact at lag0-lag3 d and lag01-lag06 d (all P<0.05). NO 2 at lag02-lag04 d and CO at lag0-lag2 d and lag01-lag04 d had statistically significant effects on the visits for neurasthenia (both P<0.05). The impacts of NO 2 at lag03-lag04 d, PM 2.5 at lag3 d and lag03-lag04 d, PM 10 at lag3 d and lag03 d, and CO at lag3 d and lag01-lag05 d on visits for generalized anxiety disorder were also statistically significant (all P<0.05). After false discovery rate (FDR) correction, it was shown that for every 10 μg/m 3 increase in NO 2 and every 0.1 mg/m 3 increase in CO, the percentage increase in visits for mental and behavioral disorders and its 95% confidence interval (95% CI) were 3.38% (0.95%-5.87%) and 0.78% (0.38%-1.17%), respectively. For every 0.1 mg/m 3 increase in CO, the visits for neurasthenia increased by 0.78% (0.27%-1.29%). For every 10 μg/m 3 increase in PM 2.5 and every 0.1 mg/m 3 increase in CO, the visits for generalized anxiety disorder increased by 1.07% (0.46%-1.68%) and 1.17% (0.37%-1.97%), respectively (adjusted P<0.05). There was a linear exposure-response relationship between NO 2 and CO and the hospital visits for mental and behavioral disorders, CO and the hospital visits for neurasthenia, and CO and PM 2.5 and the hospital visits for generalized anxiety disorder ( P<0.05 for the overall association test and P>0.05 for the non-linearity test). Stratified analysis showed that air pollutants had an impact on male patients with neurasthenia, female patients with generalized anxiety disorder, individuals aged <45 years with mental and behavioral disorders, and individuals aged ≥65 years with generalized anxiety disorder. The impact of air pollutants was greater during the cold season or winter. Conclusion:Exposure to air pollution can increase hospital visits for mental and behavioral disorders among residents in industrial areas, with a higher risk among those aged<45 years old and during the cold season.

Objective:To analyze the clinical characteristics of locally advanced rectal cancer patients with pathological complete response (pCR) after neoadjuvant chemoradiotherapy combined with immunotherapy.Methods:The retrospective cohort study was conducted. The clinicopatholo-gical data of 46 patients with locally advanced rectal cancer who were admitted to 6 medical centers, including Beijing Friendship Hospital of Capital Medical University et al, from June 2021 to November 2022 were collected. There were 29 males and 17 females, aged (61±4)years. Patients received neoadjuvant chemoradiotherapy combined with immune checkpoint inhibitor therapy, and under-went radical total mesorectal excision during 6-12 weeks after radiotherapy. Observation indicators: (1) comparison of clinical characteristics between pCR and non-pCR patients;(2) postoperative complications and adverse reactions of pCR and non-pCR patients. Comparison of measurement data with normal distribution between groups was conducted using the t test. Comparison of measurement data with skewed distribution between groups was conducted using the Mann-Whitney U test. Comparison of count data between groups was conducted using the chi-square test or Fisher exact probability. Comparison of ordinal data between groups was conducted using the Mann-Whitney U test. Results:(1) Comparison of clinical characteristics between pCR and non-pCR patients. Before neoadjuvant therapy, there were 14 cases aged ≥50 years and 6 cases aged <50 years in pCR patients, versus 25 cases and 1 case in non-pCR patients, showing a significant difference between the two groups ( P<0.05). After neoadjuvant therapy, cases in clinical stage T0, T1, T2, T3, T4 were 11, 1, 5, 3, 0 for pCR patients versus 7, 4, 2, 11, 2 for non-pCR patients, cases of tumor regression grade 1, 2, 3, 4 were 11, 8, 1, 0 for pCR patients versus 7, 14, 4, 1 for non-pCR patients, cases in low-risk, medium-risk, high-risk of neoadjuvant rectal scoring and grading were 20, 0, 0 for pCR patients versus 4, 18, 4 for non-pCR patients, respectively, showing significant differences in above indicators between the two groups ( Z=-2.256, -2.104, -5.458, P<0.05). (2) Postoperative complications and adverse reactions of pCR and non-pCR patients. Postoperative complications occurred in 2 cases of pCR patients and 5 cases of non-pCR patients, postoperative adverse reactions occurred in 11 cases of pCR patients and 10 cases of non-pCR patients, showing no significant difference between the two groups ( P>0.05). Conclusion:Compared with locally advanced rectal cancer patients aged ≥50 years, those aged <50 years have significant benefits from neoadjuvant chemoradiotherapy combined with immunotherapy. Clinical T staging and magnetic resonance imaging-detected tumor regression grade after neoadjuvant therapy have predictive value for patients with pCR .