1.Development and validation of PhenoRAG: A visualization tool for automated human phenotype ontology term annotation based on large language models and retrieval-augmented generation technology.
Wei ZHONG ; Yousheng YAN ; Kai YANG ; Yan LIU ; Xinyu FU ; Zhengyang YAO ; Chenghong YIN
Chinese Journal of Medical Genetics 2026;43(1):36-43
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
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Phenotype
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Biological Ontologies
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Language
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Software
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Large Language Models
2.A randomized,double-blind,placebo-controlled,multicenter clinical study of Shengxuebao Mixture in treating cancer-related anemia
Zhu LIU ; Xiangrong LI ; Xiaojun DAI ; Yanjun WANG ; Xiao LI ; Keqiong WANG ; Tao WU ; Miaowen ZHONG ; Hongjiang YU ; Ji FENG ; Zuowei HU ; Kainan LI ; Shaowei CHEN ; Chunhua LI ; Zhengchuan FU ; Rui ZHANG ; Yongfa CHEN ; Hongyu XU ; Tao REN ; Yibo YAO ; Jianxu JIN ; Pengyin WANG ; Zhijiang HE ; Jian SHEN ; Lei WANG ; Min LI ; Wenming CHANG ; Xinyi CHEN ; Li HOU
Journal of Beijing University of Traditional Chinese Medicine 2025;48(10):1447-1459
Objective We aimed to evaluate the efficacy and safety of Shengxuebao Mixture in the treatment of cancer-related anemia(CRA)presenting with syndrome of deficiency of liver and kidney combined with syndrome of deficiency of both qi and blood.Methods A randomized,double-blind,placebo-controlled,multicenter clinical trial was conducted.Eligible patients with malignant tumors meeting the inclusion and exclusion criteria were enrolled from 26 hospitals,including Dongzhimen Hospital,Beijing University of Chinese Medicine,Xiaogan Central Hospital,and Yangzhou Hospital of Traditional Chinese Medicine,from June 1,2022,to September 30,2024.Patients were allocated 1:1 to either the experimental group receiving Shengxuebao Mixture or the control group receiving its simulator(placebo)using a block randomization method under double-blind conditions.Both groups received 15 mL orally three times daily for 28 consecutive days.The primary efficacy indicators included the hemoglobin(Hb)improvement rate(RHb)and the traditional Chinese medicine(TCM)syndrome improvement rate(RTCM)at week 4 of treatment.The secondary efficacy indicators encompassed Hb and red blood cell(RBC)count,Karnofsky Performance Status(KPS)score,TCM syndrome score,individual TCM symptom scores,and changes in each of these indicators compared to the baseline period at weeks 2,4,and 6 of treatment.Safety evaluations were conducted at week 4 of treatment.Results A total of 239 patients were enrolled,with 225 cases included in the Full Analysis Set(FAS)(109 in the experimental group vs.116 control group),163 in the Per Protocol Set(PPS)(77 vs.86),and 225 in the Safety Set(SS)(109 vs.116).Baseline characteristics between groups showed no significant differences.Significant differences were observed between the experimental and control groups in RHb at week 4(FAS:49.51%vs.35.24%,P<0.05;PPS:53.25%vs.36.05%,P<0.05)and RTCM at week 4(FAS:61.54%vs.39.62%,P<0.01;PPS:64.94%vs.40.70%,P<0.01).At weeks 2,4,and 6,the experimental group showed greater improvements in Hb and RBC counts than the control group.Additionally,the TCM syndrome scores were lower in the experimental group than in the control group at these time points.Except for week 2 in PPS,the KPS improvement was better in the experimental group than in the control group(P<0.05).The experimental group also demonstrated a greater reduction in scores for individual TCM symptoms such as spiritlessness and weakness,poor appetite and reduced food intake at weeks 4 and 6 compared to the control group(P<0.05,P<0.01).Furthermore,the reduction in vertigo score was more pronounced in the experimental group at week 6(P<0.01).For the score of pale and lusterless complexion,only in the PPS was the reduction from baseline more significant in the experimental group than in the control group at weeks 4 and 6(P<0.05).No significant differences were observed between the experimental and control groups in the incidence of all adverse events or drug-related adverse reactions.Conclusion Shengxuebao Mixture demonstrates significant efficacy in patients with CRA presenting syndrome of deficiency of liver and kidney combined with syndrome of deficiency of both qi and blood,effectively increasing Hb levels,ameliorating TCM syndromes,alleviating clinical symptoms,and enhancing functional status,with no significant difference in adverse drug reactions compared to the placebo.
3.Therapeutic efficacy and mechanism of artesunate for mouse model of polycystic ovary syndrome
Xueling WANG ; Peiling ZHONG ; Zhipeng ZHAO ; Fei CHEN ; Xin LIU ; Sijia LIU ; Lie YUAN ; Lu FANG ; Qianyi YAO ; Xiong YANG ; Chao LIU ; Jiakun CHENG ; Yongqing CAI ; Xiaoli LI ; Weihong LI
Journal of Army Medical University 2025;47(3):193-204
Objective To investigate the therapeutic efficacy of artesunate(AS)on polycystic ovary syndrome(PCOS)in mice and explore the potential mechanism primarily.Methods Twenty-five female C57BL/6J mice were randomly divided into Control group,model group(PCOS group),low-and high-dose AS groups(AS15 and AS30 groups)and metformin group(Met group).In addition to the Control group,the mouse model of PCOS was established by subcutaneous injection of dehydroepiandrosterone(DHEA,60 mg/kg)following by a high-fat diet for 21 d.After modeling,AS of 15 and 30 mg/kg was intraperitoneally injected into the mice of the AS 15 and AS30 groups,respectively,and 200 mg/kg Met was given to those of the Met group by gavage,once per day,for 6 weeks.ELISA was used to detect serum testosterone(T),fasting insulin(FINS),luteinizing hormone(LH)and follicle-stimulating hormone(FSH),and the LH/FSH ratio was calculated.The levels of fasting blood glucose(FBG),triglyceride(TG)and total cholesterol(TC)were detected by automatic biochemical analyzer,and the homeostasis model assessment of insulin resistance(HOMA-IR)was calculated.The estrous cycle was observed,and HE staining was performed for pathological changes in the ovary and uterus.Immunofluorescence assay was employed to measure the expression of p-eIF2α,ATF4 and CHOP in the ovarian tissue.After steroidogenic human granulosa-like tumor cell line KGN were exposed to 100 μmol/L DHEA to simulate the hyperandrogen environment of PCOS,and then treated with 5 and 10 μg/mL AS for 24 h,the protein levels of endoplasmic reticulum stress signaling pathway was detected by Western blotting.Results Compared with the Control group,the PCOS mice had disturbed estrous cycle,polycystic changes in the ovaries,and significantly increased serum T level and LH/FSH ratio(P<0.05),and obviously elevated HOMA-IR,TC and TG levels in terms of metabolism(P<0.01).The expression levels of p-eIF2α,ATF4 and CHOP were notably up-regulated in the ovarian granulosa cells of PCOS mice and KGN cells after DHEA exposure(P<0.05).Additionally,AS treatment attenuated the pathological changes of ovary and uterine expression,decreased the serum T level and the LH/FSH ratio(P<0.05),and reduced HOMA-IR,TC and TG levels(P<0.05)when compared with the PCOS mice.Moreover,the expression levels of p-eIF2α,ATF4 and CHOP were significantly down-regulated after AS treatment in both ovarian granulosa cells of PCOS mice and KGN cells(P<0.05).Conclusion AS significantly improves glycolipid metabolic disorder and reproductive dysfunction in PCOS mice,which may be associated with its suppressing endoplasmic reticulum stress by inhibiting the PERK/eIF2α/ATF4/CHOP pathway.
4.Research progress on the correlation between Alzheimer's disease and hearing loss
Junrui LI ; Yuhong WANG ; Moxian CHEN ; Li JIN ; Guangxiang ZHONG ; Shaochun CHEN ; Zhao-ying CHU ; Yao LIU ; Lijuan AO
Journal of Audiology and Speech Pathology 2025;33(6):596-601
Alzheimer's disease(AD)is an age-related neurodegenerative disease with an increasing incidence worldwide.A large number of studies have shown that the incidence rates of hearing loss is high in patients with mild cognitive impairment and Alzheimer's disease,and may be a risk factor for the occurrence and development of cognitive impairment.There is an interaction between the two,but the causal mechanism is still unclear.Early screening and management of hearing impairment may play an important role in the early diagnosis,symptom im-provement and disease progression of Alzheimer's disease.This paper reviews relevant clinical and basic research to discuss the correlation between hearing loss and Alzheimer's disease,and the possible causal mechanism between them.
5.Mechanism of silibinin derivative Sil-1 modulating MAPK signaling pathway to inhibit acute myocardial infarction in rats
Yi-fan LIU ; Meng LI ; De-yu CUI ; Xiao-yan LU ; Ting-bo NING ; Chun-xiu XU ; Jing-chun YAO ; Ji-dong ZHOU ; Zhong LIU
Chinese Pharmacological Bulletin 2025;41(8):1453-1462
Aim To study the protective effect of the silibinin derivative Sil-1 on acute myocardial ischemia in SD rats and its mechanism of action.Methods Af-ter 18 hours of oxygen-glucose deprivation and treat-ment of H9c2 cells,the protective effect of Sil-1 on rat cardiomyocytes was examined.SD rats were treated 30 minutes before surgery,followed by 24 h ligation of the left anterior descending coronary artery.The cardiopro-tective effects of Sil-1 and its mechanisms for improving myocardial ischemic injury were investigated using pro-teomics technology.Results In vitro,compared with the control group,the activity of H9c2 cells in the mod-el group showed reduced cell viability,increased dead cells,elevated ROS and higher levels of LDH and in-flammatory cytokines TNF-α,IL-1β and IL-6 in the culture medium.Sil-1 could improve the above condi-tions to different degrees.In vivo,compared with the control group,rats in the model group showed signifi-cantly higher T waves on electrocardiogram,significant ischemic areas in the heart section,disorganized ar-rangement of cardiomyocytes,increased inflammatory factor infiltration and elevated CK,CK-MB,LDH and inflammatory factors TNF-α,IL-6 and IL-1β.Besides,NF-κB phosphorylation levels in myocardial tissue in-creased.Sil-1 improved the above conditions to varying degrees.The results of proteomics showed that 90 pro-teins were found between the control vs model group and the Sil-1 vs model group,and KEGG enrichment a-nalysis showed that MAPK,chemokines,VEGF and other signaling pathways were abundant.Western blot results showed that Sil-1 blocked the phosphorylation of ERK,JNK and p38 MAPK.Conclusions Sil-1 inhib-its the MAPK pathway by blocking the phosphorylation of JNK,ERK,and p38 MAPK,and achieves a protec-tive effect on rats with acute myocardial infarction.
6.Pathways and effectiveness of medical humanities education in internship from the perspective of the hidden curriculum:an empirical study based on the HPAS-HSP scale
Jie LI ; Zhijie LI ; Xueping LIU ; Qian WU ; Liying ZHONG ; Chuanyu YAO ; Qiyuan QIN
Modern Hospital 2025;25(11):1800-1804
Objective This study aims to establish a hidden curriculum-based medical humanities teaching pathway within surgical internship education and evaluate its effectiveness in enhancing students' humanistic care competence.Methods A single-group pre-test and post-test design was adopted.A total of 76 interns from a tertiary teaching hospital in 2024 were in-cluded.A five-dimensional hidden curriculum framework—material,spiritual,behavioral,faculty,and institutional—was con-structed.Humanistic competence was assessed before and after the intervention using the Humanistic Professional Awareness Scale for Healthcare Students and Providers(HPAS-HSP).Results Post-intervention scores significantly improved compared to pre-intervention across the total scale in the three dimensions:personal integrity and responsibility,sensitivity to others,and pro-fessional competence(P<0.05),with the greatest improvement observed in sensitivity to others.Conclusion The structured hidden curriculum is effective in enhancing medical students' humanistic qualities,especially in fostering emotional resonance and professional identity.Future work should focus on verifying behavioral transformation and developing multi-source evaluation sys-tems to improve effectiveness and applicability.
7.Analysis on application of new anti-tumor drugs for respiratory system in 121 hospitals in China from 2019 to 2022
Yue XING ; Tong LIU ; Lu ZHONG ; Yao JIN ; Xue TENG
Chinese Journal of Pharmacoepidemiology 2025;34(1):27-34
Objective To investigating the usage and changing trend of new anti-tumor drugs for respiratory system of 121 hospitals after the implementation of relevant policies insurance negotiation in China from 2019 to 2022,explore the development tendency of new anti-tumor drugs in hospitals under the medical reform policy and provide references for the rational use and standardized management of new anti-tumor drugs.Methods Based on the anti-tumour drug for respiratory system varieties in the Guidelines for the Clinical Application of Novel Anti-tumour Drugs Version 2022,descriptive statistical analysis was applied to retrieve data on the use of new anti-tumour drugs for respiratory system in 121 hospitals from 2019 to 2022,and drug dosage form,amount,drug frequency(DDDs),average daily cost(DDC)and drug ranking ratio(B/A)were statistically analyzed.Results The number of users and the proportion of new anti-tumour drugs for respiratory system used in 121 hospitals in China showed a year-on-year increasing trend from 2019 to 2022.In different cities of China,the drug use amount of Guangzhou,Beijing,Hangzhou and Zhengzhou was relatively large.In terms of drug use,small-molecule targeted drugs were still the main new anti-tumor drugs,while macromolecule targeted drugs showed a downward trend,and immunotherapy drugs showed a gradual upward trend.In terms of the amount of use,the top drugs in the four years were ecitinib,aletinib,gefitinib and oxitinib.The small molecule targeted drugs included in the national insurance negotiations showed increasing use and a decreasing amount of money spent.The ranking of DDDs was basically stable,with fluctuations in individual varieties.The DDC values of small molecule targeted drugs had significantly decreased,while the DDC values of immunotherapy drugs were relatively high.From 2021 to 2022,the B/A value of the novel anti-tumor drugs was most respiratory tumors was close to 1,and the varieties located at 0.8 to 1.2 accounted for 61.5%of the total drugs.Conclusion At present,the selection of new anti-tumor drugs for respiratory system is still dominated by small molecule targeted drugs and the use of immunotherapy drugs is increasing.The synchronization of the amount and frequency of most drugs has increased.The adjustment of the medical insurance catalog and the implementation of policies such as national negotiation effectively promote the decrease of the amount of drug use and the improvement of drug trend.
8.Party building-guided initiatives in colorectal cancer screening and support for primary healthcare in-stitutions
Xueqing YAO ; Chengzhi HUANG ; Zhiyuan LIU ; Zhanyan GUO ; Yue ZHOU ; Weixian HU ; Xiaowu LI ; Zhenbin LIN ; Yuemei ZHONG ; Dailan XIONG ; Zejian LYU ; Junjiang WANG
Modern Hospital 2025;25(8):1274-1276
With the advancement of China's healthcare reform,enhancing the capacity of primary healthcare services has become a pivotal task.Colorectal cancer,one of the most prevalent malignancies in China,highlights the critical importance of early screening and diagnosis to improve patient survival rates.This study,guided by the principles of Party building and Xi Jinping Thought on Socialism with Chinese Characteristics,examines the implementation and outcomes of a rural outreach program focused on colorectal cancer screening and diagnostic technologies.By promoting the dissemination of colorectal cancer screening initiatives,the paper aims to provide empirical evidence to support the deepening of primary-care services,foster high-quality ad-vancement of grassroots health services,and align with the national Healthy China Initiative,thereby more effectively safeguarding population health.
9.Clinical characteristics analysis of peptic ulcers caused by eosinophilic gastrointestinal disorders in children
Meng JIN ; Mingran MI ; Wenwen LIU ; Kunyu YAO ; Ran ZHANG ; Xuemei ZHONG
International Journal of Pediatrics 2025;52(4):268-273
Objective:To analyze the clinical characteristics,laboratory tests,endoscopic features,treatment,and follow-up of peptic ulcers caused by eosinophilic gastrointestinal disorders(EGIDs)in children,with the aim of improving the level of understanding,diagnosis and treatment of EGIDs in children with the onset of peptic ulcers.Methods:A retrospective analysis was conducted on children admitted to the Department of Gastroenterology,Capital Center for Children's Health,Capital Medical University from January 1st,2019 to October 31st,2023,who underwent complete endoscopic examination. The first examination showed the presence of peptic ulcers(gastric or duodenal ulcers)under the endoscope,and were ultimately diagnosed with peptic ulcers caused by EGIDs through examination and follow-up. The clinical characteristics,laboratory tests,endoscopic results,and treatment follow-up were analyzed.Results:Thirty-five children were EGIDs,22 males and 13 females.Twenty-two cases(62.9%)had abdominal pain as the main symptom.Laboratory tests:17 cases(48.6%)showed a decrease in hemoglobin,15 cases(42.9%)showed an increase in eosinophil count,20 cases(57.1%)tested gastro positive for food allergen specific IgE,and 17 cases(48.6%)showed thickening of the intestinal wall on gastrointestinal ultrasound. Endoscopic features:8 cases(22.9%)showed gastric antral ulcers,including 7 cases(20.0%)with multiple gastric antral ulcers,and 25 cases(71.4%)showed duodenal bulb ulcers.There were 15 cases(42.9%)showed huge ulcers,and 14 cases(40.0%)were located in the duodenal bulb. Comparison of clinical characteristics between children with EGIDs(EGIDs group)and those with peptic ulcers caused by Helicobacter pylori infection(Hp group):the first clinical symptom in both groups was mainly abdominal pain,but the incidence rate in the EGIDs group was lower(62.9% vs 93.5%),and the weigth for length Z score in the EGIDs group was lower[0(-1.6,0.8)vs 1.1(0,1.9)],with statistical significance(all P<0.05). Comparison of laboratory tests:the EGIDs group showed a statistically significant difference in hemoglobin levels[120(101,124)g/L vs 130(100,138)g/L],eosinophil count[0.28(0.13,0.71)× 10 9/L vs 0.16(0.08,0.22)×10 9/L],a positive rate of food allergen specific IgE detection(57.1% vs 32.3%),and a positive rate of intestinal wall thickening detected by gastrointestinal ultrasound(48.6% vs 16.1%)compared with the Hp group(all P<0.05). Comparison of endoscopic examinations:multiple ulcers in the gastric antrum were more common in the EGIDs group than in the Hp group(20.0% vs 0),and the difference was statistically significant( P<0.05). Conclusion:For children with peptic ulcers with onset of abdominal pain,with anemia or malnutrition,or multiple ulcers in the gastric antrum and huge ulcers in the duodenal bulb detected by endoscopy,it is recommended to perform multi site biopsies to help diagnose EGIDs early.
10.Advances in regulation of dysregulated bone remodeling by immune cells within rheumatoid arthritis synovial microenvironment
Jun-jie HE ; Zhong-liu YAO ; Ming-yue HU ; Hong HUANG ; Xiong CAI
Chinese Pharmacological Bulletin 2025;41(10):1801-1807
Rheumatoid arthritis(RA)is characterized by bidi-rectional bone remodeling imbalance,clinically termed the "high resorption-low formation" paradox,stemming not only from osteoclast hyperactivation but also critically involving pro-found suppression of osteoblast differentiation and function.No-tably,this suppression cannot be fully attributed to osteoclast hyperactivity;synovium-resident immune cells exert a pivotal regulatory influence through distinct mechanisms.This review systematically examines how synovial immune cells orchestrate bone remodeling in RA through both paracrine cytokine networks and direct cell-cell communication with bone lineage cells,thereby perturbing physiological homeostasis and driving patho-logical progression.These mechanistic revelations yield innova-tive perspectives on RA pathogenesis,positioning immune-medi-ated osteoimmune dysregulation as a promising therapeutic fron-tier for targeted intervention.

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