1.Epidemiological characteristics analysis of tuberculosis among college students in Yangzhou during 2020-2024
Chinese Journal of School Health 2026;47(1):109-112
Objective:
To analyze the epidemiological characteristics of pulmonary tuberculosis (PTB) among college students in Yangzhou from 2020 to 2024, so as to provide a scientific basis for developing prevention and control strategies.
Methods:
An epidemiological investigation was conducted among 162 college students with PTB, and 7 134 of their contacts were screened. Data were obtained from the tuberculosis information management system and on campus screening records. Using descriptive epidemiological methods, trends in incidence, seasonal distribution, and bacteriological characteristics were analyzed.
Results:
From 2020 to 2024, the annual average incidence of pulmonary tuberculosis among college students in Yangzhou was 29.42 per 100 000, showing an overall fluctuating downward trend ( χ 2=12.36, P <0.01). Cases were mainly concentrated in summer and autumn, with the highest proportion in autumn (41.36%, 67/162), followed by summer (23.46%, 38/162). The proportion of etiologically positive cases increased from 37.21% in 2020 to 71.43% in 2024; among positive cases, the proportion of latent tuberculosis infection (LTBI) decreased from 66.67% (10/15) to 26.67% (4/15). The etiological positive rate was higher in females than in males ( χ 2= 11.76 , P <0.01). Comparison of screening methods showed that among index cases, the LTBI detection rate of the recombinant Mycobacterium tuberculosis fusion protein skin test (C-TST) was higher than that of the tuberculin skin test (TST), but the difference was not statistically significant ( χ 2=0.65, P =0.42); among close contacts, the detection rate of TST was higher than that of C-TST (15.1%,10.1%; χ 2=5.23, P <0.05).
Conclusion
From 2020 to 2024, the annual average incidence of pulmonary tuberculosis among college students in Yangzhou showed an overall fluctuating downward trend, with differences in TB infection screening methods and gender.
2.Inhibition of Epithelial-mesenchymal Transition Mechanism in Chronic Atrophic Gastritis Rats by Banxia Xiexintang via Regulating IL-17/ERK/C/EBPβ Signaling Pathway
Wenyu WU ; Xinyu ZENG ; Hao LI ; Weiqi SUN ; Jiahui REN ; Yang YU ; Tingting ZHOU ; Aili XU ; Wei WEI
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(4):1-10
ObjectiveThis study aimed to investigate the action mechanism by which Banxia Xiexintang (BXT) inhibits epithelial-mesenchymal transition (EMT) in chronic atrophic gastritis (CAG) rats by regulating the interleukin-17(IL-17)/extracellular regulated protein kinases(ERK)/CCAAT enhancer binding protein β(C/EBPβ)signaling pathway, thereby providing new theoretical evidence for the treatment of CAG with classic traditional Chinese medicine formulas. MethodsA CAG rat model was established by using the combined factor method. After successful modeling, the rats were randomly divided into the model group, low-, medium-, and high-dose groups (0.549, 1.098, 2.196 g·kg-1, respectively) of BXT, and the positive drug group (vitacoenzyme, 0.3 g·kg-1). A normal control group was also set up. After 8 weeks of intervention, the pathological changes of gastric tissue were evaluated. The enzyme-linked immunosorbent assay (ELISA) was used to detect the contents of IL-17, tumor necrosis factor-α (TNF-α), cyclooxygenase-2 (COX-2), and C/EBPβ in serum, as well as the contents of EMT markers in gastric mucosal tissue including E-cadherin, N-cadherin, and vimentin. The immunohistochemistry method was employed to determine the localization and protein expression levels of IL-17, p-ERK, and C/EBPβ in gastric mucosal tissue. Western blot was used to detect the protein expressions of C/EBPβ, ERK, and its phosphorylated form (p)-ERK in gastric mucosa. Real-time polymerase chain reaction (Real-time PCR) was applied to measure the mRNA expression levels of ERK, COX-2, and C/EBPβ in gastric mucosa. ResultsCompared with those in the normal control group, the rats in the model group showed gastric mucosal glandular atrophy and inflammatory cell infiltration. The protein and their related mRNA expressions of C/EBPβ, ERK, and p-ERK in gastric mucosa were significantly increased (P<0.05,P<0.01). The levels of IL-17, TNF-α, COX-2, and C/EBPβ in serum were significantly increased (P<0.01). The contents of N-cadherin and vimentin in gastric mucosal tissue were significantly increased, while the content of E-cadherin was significantly decreased (P<0.01). Compared with the model group, after intervention with different doses of BXT, the pathological damage of the gastric mucosa was improved to varying degrees. The protein and mRNA expressions of C/EBPβ, ERK, and p-ERK in gastric mucosa were significantly reduced (P<0.05,P<0.01). The levels of IL-17, TNF-α, COX-2, and C/EBP β in serum were significantly decreased (P<0.01). The contents of N-cadherin and vimentin in gastric mucosa tissue were decreased, while the content of E-cadherin was increased (P<0.05,P<0.01). ConclusionBXT can effectively improve the pathological damage of gastric mucosal tissue in CAG rats. Its action mechanism may be related to reducing the levels of IL-17 and TNF-α in serum, regulating the IL-17/ERK/C/EBPβ signaling pathway and inhibiting the EMT process.
3.Obesogenic effects of perinatal bisphenol AF exposure on prepubertal male offspring rats
Xi LIU ; Zhengli YANG ; Xueqing CHENG ; Jun YANG ; Jing XU ; Xinyu HONG
Shanghai Journal of Preventive Medicine 2026;38(2):139-145
ObjectiveTo investigate the disruptive effects of perinatal exposure to the environmental endocrine disruptor bisphenol AF (BPAF) on hepatic lipid metabolism in prepubertal (postnatal day 21, PND21) male offspring rats, and to provide scientific evidence for assessing the obesogenic effect of BPAF. MethodsSprague-Dawley (SD) rats aged 8 weeks were used in this study. Pregnant rats were divided into BPAF dose groups (2, 10, 50 mg·kg⁻¹) and a vehicle control group (corn oil), with 6 confirmed pregnant females per group. Gavage administration started from gestational day 0 and continued until the end of lactation. At PND21, one male offspring per litter was randomly selected. Serum concentrations of glucose (GLU), triglyceride (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), leptin (LEP), free fatty acid (FFA), as well as oxidative stress markers superoxide dismutase (SOD) and malondialdehyde (MDA), were measured. Pathological changes in liver and adipose tissues were evaluated, and the expression levels of genes related to hepatic lipid metabolism were measured. ResultsCompared to the vehicle control group, the 50 mg·kg⁻¹ group showed significantly increased serum LEP and MDA levels in male offspring (P<0.05), and significant upregulation of hepatic lipoprotein lipase (Lpl), fatty acid synthetase (Fas), and peroxisome proliferator-activated receptor γ (Pparg) gene expression (P<0.05). The 2 mg·kg⁻¹ group exhibited a significant increase in adipocyte length (P<0.05), while the 50 mg·kg⁻¹ group showed significant increases in both adipocyte area and length (P<0.05). No significant abnormalities were observed in liver histopathological examination. ConclusionPerinatal exposure to 50 mg·kg⁻1 BPAF induced adipocyte hypertrophy, elevated leptin levels, upregulation of lipid synthesis gene expression, and enhanced oxidative stress in prepubertal male offspring, suggesting that BPAF may exert environmental obesogenic effects by disrupting lipid metabolism pathways.
4.Mechanism of Taishan Panshisan in Inhibiting Oxidative Stress Injury of Trophoblast Cells by Regulating KEAP1/Nrf2/FoxO3 Signaling Pathway
Yangyang DUAN ; Xianglun JI ; Jiahong CHEN ; Jinghang YANG ; Xinyu XIAO ; Shutao CHEN ; Chaorui LIN ; Fan LIN ; Shu JIANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(10):12-22
ObjectiveTo explore the effect and mechanism of Taishan Panshi powder (TSPSP) on inhibiting oxidative stress injury in human chorionic trophoblast cells (HTR-8/SVneo), and to uelucidate the underlying mechanism of TSPSP in the treatment of spontaneous abortion (SA). MethodsGene differential analysis of SA was performed using the Gene Expression Omnibus (GEO) database and correlated with oxidative stress. Network pharmacology was employed to screen the active components of TSPSP, and a "Chinese medicine-component-target-disease" network was constructed to predict the mechanism of action of TSPSP. For in vitro validation experiments, HTR-8/SVneo cells were divided into blank group, model group, TSPSP-containing serum 2.5%, 5%, 10% groups, and nuclear factor E2-related factor 2 (Nrf2) inhibitor group (ML385, 30 μmol·L-1). Except for the blank group, other groups were stimulated with 150 μmol·L-1 H2O2 for 3 h to establish a cell oxidative stress injury model. After successful modeling, the blank group and model group were given 10% blank serum, each TSPSP-containing serum group was treated with the corresponding concentration of drug-containing serum, and the Nrf2 inhibitor group was additionally given 30 μmol·L-1 ML385 on the basis of 10% TSPSP-containing serum. All groups of cells were continuously cultured under the above conditions for 24 h, and then samples were collected for subsequent detection. Cell viability in each group was detected by CCK-8 assay. Cell migration rate was detected by scratch test. The contents of malondialdehyde (MDA), Fe2+, and Glutathione (GSH) were detected by enzyme-linked immunosorbent assay (ELISA). Intracellular reactive oxygen species (ROS) level was detected by a fluorescent probe (DCF-DA). The protein and mRNA expression levels of Kelch-like ECH-associated protein 1 (KEAP1), Nrf2, and forkhead box protein O3 (FoxO3) in cells were detected by immunofluorescence (IF) and real-time quantitative polymerase chain reaction (Real-time PCR). The protein expression levels of KEAP1, Nrf2, FoxO3, Glutathione peroxidase 4 (GPX4), and superoxide dismutase (SOD) in cells were detected by Western blot. ResultsThe GSE76862 and GSE22490 datasets were obtained from the GEO database. Differential gene analyses showed that the KEAP1, Nrf2, and FoxO3 genes were all associated with the disease. After matching with the oxidative stress pathway, nine significantly differential pathways were identified (P<0.05), among which three contained the target genes Nrf2 and FoxO3. A total of 246 active ingredient targets of TSPSP and 2 804 SA-related targets were obtained through network pharmacology, and 154 potential action targets were obtained after taking the intersection. Topological analysis showed that targets such as KEAP1 and Nrf2 exhibited high degree values. GO and KEGG enrichment analyses indicated that the intersection targets were mainly involved in oxidative stress response, FOXO and MAPK signaling pathways, etc. In in vitro experiments, compared with the blank group, the cell viability in the model group was significantly decreased (P<0.01). Compared with the model group, the cell viability in each TSPSP-containing serum group was significantly increased (P<0.01). Compared with the 10% TSPSP-containing serum group, the cell viability in the ML385 group decreased to approximately 70% (P<0.01). Compared with the blank group, the model group showed significantly increased contents of MDA, Fe2+, and ROS, decreased GSH expression (P<0.01), significantly reduced cell migration rate (P<0.01), and increased protein and mRNA expression levels of KEAP1 and FoxO3 (P<0.01), while decreased protein and mRNA expression levels of Nrf2, GPX4, and SOD (P<0.01). Compared with the model group, each TSPSP-containing serum group showed significantly decreased contents of MDA, Fe²⁺, and ROS, increased GSH expression (P<0.01), significantly increased migration rate (P<0.01), significantly decreased protein and mRNA expression levels of KEAP1 and FoxO3 (P<0.05, P<0.01), and significantly increased protein and mRNA expression levels of Nrf2, GPX4, and SOD (P<0.05, P<0.01). Compared with the 10% TSPSP-containing serum group, the ML385 group showed reversed trends in all indicators (P<0.05, P<0.01). ConclusionTSPSP can inhibit H2O2-induced oxidative stress injury of trophoblast cells, and its mechanism of action may be related to the drug activating the KEAP1/Nrf2/FoxO3 signaling pathway.
5.Mechanisms of Qizhujianwei Granules in Blocking Malignant Progression of Gastric Intraepithelial Neoplasia
Yuling YU ; Yanmin WANG ; Siqi WANG ; Yateng SUN ; Yunhe WANG ; Yonghuang YAN ; Xinyu YANG ; Siqi HAN ; Yuhong SONG ; Yuhan WANG ; Cai ZHANG ; Zeqi SU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(10):143-151
ObjectiveTo investigate the effects of Qizhujianwei granules (QZJW) on abnormal proliferation and malignant transformation of gastric mucosal cells in rats with gastric intraepithelial neoplasia (GIN) and to explore the related mechanisms. MethodsA total of 80 SPF male Wistar rats were used. A GIN rat model was established using a four-factor comprehensive method consisting of methylnitronitrosoguanidine (MNNG), ranitidine, irregular feeding patterns, and sodium salicylate. Except for the normal group, after successful modeling, the rats were randomly divided according to body weight into a model group, a Moluodan group (0.55 g·kg-1), and a QZJW group (7.34 g·kg-1), with 12 rats in each group. All groups were treated for 8 weeks. The general characteristics of the rats and morphological changes of the gastric mucosa were observed. Histopathological changes of the gastric mucosa were examined by hematoxylin-eosin (HE) staining. Enzyme-linked immunosorbent assay (ELISA) was used to detect serum levels of pepsinogenⅠ (PGⅠ), pepsinogenⅡ (PGⅡ), and gastrin (G-17), as well as the expression level of transforming growth factor-β1 (TGF-β1) in gastric mucosal tissue, and the PGⅠ/PGⅡ ratio was calculated. Immunohistochemistry (IHC) was used to detect the localization and expression levels of proliferating cell nuclear antigen (Ki-67) and Vimentin in gastric mucosal tissue. Western blot analysis was used to determine the protein expression levels of Wnt family member 3A (Wnt3a), β-catenin, CyclinD1, proto-oncogene Cmyc, transforming growth factor-β receptor Ⅰ (TGFβRⅠ), intracellular signaling transducers Smad2/3, phosphorylated (p)-Smad2/3, twist family transcription factor (Twist1), and Vimentin in gastric mucosal tissue. ResultsCompared with the normal group, the model group showed characteristic changes including dim eyes, pale ears and claws, dark-red tongue, and reduced luster of the tail. The gastric mucosa appeared pale, with surface congestion and erosion. The gastric mucosal glands were disordered, the nuclear-to-cytoplasmic ratio increased, and local tumor cells were observed. Serum PGⅠ and PGⅡ levels and the PGⅠ/PGⅡ ratio were significantly decreased (P<0.01), while the level of G-17 was significantly increased (P<0.01). The protein expression levels of Ki-67, Wnt3a, β-catenin, CyclinD1, Cmyc, TGF-β1, TGFβRⅠ, Smad2/3, Twist1, and Vimentin in gastric mucosal tissue were significantly increased (P<0.05, P<0.01), whereas the ratio of p-Smad2/3 to Smad2/3 was significantly decreased (P<0.05). Compared with the model group, the general characteristics and gastric mucosal conditions of rats in the Moluodan group and the QZJW group were improved. HE staining showed that QZJW could effectively block the malignant progression of GIN. Serum PGⅠ and PGⅡ levels and the PGⅠ/PGⅡ ratio were significantly increased (P<0.05, P<0.01), while the level of G-17 was significantly decreased (P<0.01). The protein expression levels of Ki-67, Wnt3a, β-catenin, CyclinD1, Cmyc, TGF-β1, TGFβRⅠ, Smad2/3, Twist1, and Vimentin in gastric mucosal tissue were significantly decreased (P<0.05, P<0.01). ConclusionQZJW have a therapeutic effect on rats with GIN. The mechanism may involve inhibition of the Wnt/β-catenin signaling pathway to regulate the cell cycle and suppress abnormal cell proliferation. Meanwhile, it may inhibit epithelial-mesenchymal transition by suppressing the TGF-β1/Smad/Twist1 signaling pathway, thereby blocking the malignant progression of GIN.
6.Mechanism of Taishan Panshisan in Inhibiting Oxidative Stress Injury of Trophoblast Cells by Regulating KEAP1/Nrf2/FoxO3 Signaling Pathway
Yangyang DUAN ; Xianglun JI ; Jiahong CHEN ; Jinghang YANG ; Xinyu XIAO ; Shutao CHEN ; Chaorui LIN ; Fan LIN ; Shu JIANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(10):12-22
ObjectiveTo explore the effect and mechanism of Taishan Panshi powder (TSPSP) on inhibiting oxidative stress injury in human chorionic trophoblast cells (HTR-8/SVneo), and to uelucidate the underlying mechanism of TSPSP in the treatment of spontaneous abortion (SA). MethodsGene differential analysis of SA was performed using the Gene Expression Omnibus (GEO) database and correlated with oxidative stress. Network pharmacology was employed to screen the active components of TSPSP, and a "Chinese medicine-component-target-disease" network was constructed to predict the mechanism of action of TSPSP. For in vitro validation experiments, HTR-8/SVneo cells were divided into blank group, model group, TSPSP-containing serum 2.5%, 5%, 10% groups, and nuclear factor E2-related factor 2 (Nrf2) inhibitor group (ML385, 30 μmol·L-1). Except for the blank group, other groups were stimulated with 150 μmol·L-1 H2O2 for 3 h to establish a cell oxidative stress injury model. After successful modeling, the blank group and model group were given 10% blank serum, each TSPSP-containing serum group was treated with the corresponding concentration of drug-containing serum, and the Nrf2 inhibitor group was additionally given 30 μmol·L-1 ML385 on the basis of 10% TSPSP-containing serum. All groups of cells were continuously cultured under the above conditions for 24 h, and then samples were collected for subsequent detection. Cell viability in each group was detected by CCK-8 assay. Cell migration rate was detected by scratch test. The contents of malondialdehyde (MDA), Fe2+, and Glutathione (GSH) were detected by enzyme-linked immunosorbent assay (ELISA). Intracellular reactive oxygen species (ROS) level was detected by a fluorescent probe (DCF-DA). The protein and mRNA expression levels of Kelch-like ECH-associated protein 1 (KEAP1), Nrf2, and forkhead box protein O3 (FoxO3) in cells were detected by immunofluorescence (IF) and real-time quantitative polymerase chain reaction (Real-time PCR). The protein expression levels of KEAP1, Nrf2, FoxO3, Glutathione peroxidase 4 (GPX4), and superoxide dismutase (SOD) in cells were detected by Western blot. ResultsThe GSE76862 and GSE22490 datasets were obtained from the GEO database. Differential gene analyses showed that the KEAP1, Nrf2, and FoxO3 genes were all associated with the disease. After matching with the oxidative stress pathway, nine significantly differential pathways were identified (P<0.05), among which three contained the target genes Nrf2 and FoxO3. A total of 246 active ingredient targets of TSPSP and 2 804 SA-related targets were obtained through network pharmacology, and 154 potential action targets were obtained after taking the intersection. Topological analysis showed that targets such as KEAP1 and Nrf2 exhibited high degree values. GO and KEGG enrichment analyses indicated that the intersection targets were mainly involved in oxidative stress response, FOXO and MAPK signaling pathways, etc. In in vitro experiments, compared with the blank group, the cell viability in the model group was significantly decreased (P<0.01). Compared with the model group, the cell viability in each TSPSP-containing serum group was significantly increased (P<0.01). Compared with the 10% TSPSP-containing serum group, the cell viability in the ML385 group decreased to approximately 70% (P<0.01). Compared with the blank group, the model group showed significantly increased contents of MDA, Fe2+, and ROS, decreased GSH expression (P<0.01), significantly reduced cell migration rate (P<0.01), and increased protein and mRNA expression levels of KEAP1 and FoxO3 (P<0.01), while decreased protein and mRNA expression levels of Nrf2, GPX4, and SOD (P<0.01). Compared with the model group, each TSPSP-containing serum group showed significantly decreased contents of MDA, Fe²⁺, and ROS, increased GSH expression (P<0.01), significantly increased migration rate (P<0.01), significantly decreased protein and mRNA expression levels of KEAP1 and FoxO3 (P<0.05, P<0.01), and significantly increased protein and mRNA expression levels of Nrf2, GPX4, and SOD (P<0.05, P<0.01). Compared with the 10% TSPSP-containing serum group, the ML385 group showed reversed trends in all indicators (P<0.05, P<0.01). ConclusionTSPSP can inhibit H2O2-induced oxidative stress injury of trophoblast cells, and its mechanism of action may be related to the drug activating the KEAP1/Nrf2/FoxO3 signaling pathway.
7.Mechanisms of Qizhujianwei Granules in Blocking Malignant Progression of Gastric Intraepithelial Neoplasia
Yuling YU ; Yanmin WANG ; Siqi WANG ; Yateng SUN ; Yunhe WANG ; Yonghuang YAN ; Xinyu YANG ; Siqi HAN ; Yuhong SONG ; Yuhan WANG ; Cai ZHANG ; Zeqi SU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(10):143-151
ObjectiveTo investigate the effects of Qizhujianwei granules (QZJW) on abnormal proliferation and malignant transformation of gastric mucosal cells in rats with gastric intraepithelial neoplasia (GIN) and to explore the related mechanisms. MethodsA total of 80 SPF male Wistar rats were used. A GIN rat model was established using a four-factor comprehensive method consisting of methylnitronitrosoguanidine (MNNG), ranitidine, irregular feeding patterns, and sodium salicylate. Except for the normal group, after successful modeling, the rats were randomly divided according to body weight into a model group, a Moluodan group (0.55 g·kg-1), and a QZJW group (7.34 g·kg-1), with 12 rats in each group. All groups were treated for 8 weeks. The general characteristics of the rats and morphological changes of the gastric mucosa were observed. Histopathological changes of the gastric mucosa were examined by hematoxylin-eosin (HE) staining. Enzyme-linked immunosorbent assay (ELISA) was used to detect serum levels of pepsinogenⅠ (PGⅠ), pepsinogenⅡ (PGⅡ), and gastrin (G-17), as well as the expression level of transforming growth factor-β1 (TGF-β1) in gastric mucosal tissue, and the PGⅠ/PGⅡ ratio was calculated. Immunohistochemistry (IHC) was used to detect the localization and expression levels of proliferating cell nuclear antigen (Ki-67) and Vimentin in gastric mucosal tissue. Western blot analysis was used to determine the protein expression levels of Wnt family member 3A (Wnt3a), β-catenin, CyclinD1, proto-oncogene Cmyc, transforming growth factor-β receptor Ⅰ (TGFβRⅠ), intracellular signaling transducers Smad2/3, phosphorylated (p)-Smad2/3, twist family transcription factor (Twist1), and Vimentin in gastric mucosal tissue. ResultsCompared with the normal group, the model group showed characteristic changes including dim eyes, pale ears and claws, dark-red tongue, and reduced luster of the tail. The gastric mucosa appeared pale, with surface congestion and erosion. The gastric mucosal glands were disordered, the nuclear-to-cytoplasmic ratio increased, and local tumor cells were observed. Serum PGⅠ and PGⅡ levels and the PGⅠ/PGⅡ ratio were significantly decreased (P<0.01), while the level of G-17 was significantly increased (P<0.01). The protein expression levels of Ki-67, Wnt3a, β-catenin, CyclinD1, Cmyc, TGF-β1, TGFβRⅠ, Smad2/3, Twist1, and Vimentin in gastric mucosal tissue were significantly increased (P<0.05, P<0.01), whereas the ratio of p-Smad2/3 to Smad2/3 was significantly decreased (P<0.05). Compared with the model group, the general characteristics and gastric mucosal conditions of rats in the Moluodan group and the QZJW group were improved. HE staining showed that QZJW could effectively block the malignant progression of GIN. Serum PGⅠ and PGⅡ levels and the PGⅠ/PGⅡ ratio were significantly increased (P<0.05, P<0.01), while the level of G-17 was significantly decreased (P<0.01). The protein expression levels of Ki-67, Wnt3a, β-catenin, CyclinD1, Cmyc, TGF-β1, TGFβRⅠ, Smad2/3, Twist1, and Vimentin in gastric mucosal tissue were significantly decreased (P<0.05, P<0.01). ConclusionQZJW have a therapeutic effect on rats with GIN. The mechanism may involve inhibition of the Wnt/β-catenin signaling pathway to regulate the cell cycle and suppress abnormal cell proliferation. Meanwhile, it may inhibit epithelial-mesenchymal transition by suppressing the TGF-β1/Smad/Twist1 signaling pathway, thereby blocking the malignant progression of GIN.
8.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
9.Therapeutic Effect of Wenweishu Granules on Functional Dyspepsia Rats with Spleen-stomach Deficiency Cold Syndrome Based on Bioinformatics Analysis and Experimental Validation
Xinyu YANG ; Xiaoyi JIA ; Zihua XUAN ; Shuangying GUI ; Yanfang WU ; Yuhan MA ; Qin RUAN ; Jia ZHENG ; Zhiyong JIAO
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(18):30-40
ObjectiveThis study aims to investigate the therapeutic effects of Wenweishu granule (WWSG) on functional dyspepsia (FD) with spleen-stomach deficiency cold syndrome in rats by integrating network pharmacology, molecular docking, and animal experiments. MethodsActive components and corresponding targets of WWSG were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and the Bioinformatics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine (BATMAN-TCM). Disease-related targets for FD with spleen-stomach deficiency cold syndrome were screened using GeneCards and the Integrative Pharmacology-based Research Platform of Traditional Chinese Medicine (TCMIP). Core therapeutic targets were identified via Cytoscape and validated by molecular docking. A rat model of FD with spleen-stomach deficiency cold syndrome was established using vinegar gavage combined with tail-clamping. The rats were randomly divided into a model group, low-, medium-, and high-dose WWSG groups (2.0, 4.0, 8.0 g·kg-1), a domperidone group (3.0 mg·kg-1), a Fuzi Lizhong pillwan (0.8 g·kg-1), and a normal control group (n=10 per group). Drugs were administered once daily by gavage for 14 consecutive days. After treatment, body weight, symptom scores, and gastrointestinal motility indices were recorded. Gastric and duodenal pathologies changes were observed via hematoxylin-eosin (HE) staining. Brain-gut peptides were measured in serum and tissue using enzyme-linked immunosorbent assay (ELISA). Immunohistochemistry and Western blot were performed to assess stem cell factor (SCF) and receptor tyrosine kinase (c-Kit) protein expression in gastric tissues. ResultsA total of 305 drug targets, 1 140 disease targets, and 116 overlapping targets were identified. Cytoscape analysis revealed 104 core targets. Enrichment analysis indicated that the SCF/c-Kit signaling pathway was the key mechanism. Molecular docking confirmed a strong binding affinity between active components of WWSG and SCF/c-Kit proteins (binding energy<-5.1 kcal·mol-1). Compared with the normal group, model rats exhibited slower weight gain (P<0.05), reduced gastric emptying and intestinal propulsion (P<0.01), mild gastric mucosal shedding, duodenal inflammatory cell infiltration, decreased levels of gastrin (GAS), 5-hydroxytryptamine (5-HT), and vasoactive intestinal peptide (VIP) (P<0.05, P<0.01), and elevated somatostatin (SS) expression (P<0.05, P<0.01). WWSG treatment ameliorated weight gain, symptom scores, and low-grade inflammation in gastric/duodenal tissues. High-dose WWSG significantly improved gastric emptying and intestinal propulsion, upregulated GAS, 5-HT, and VIP, and downregulated SS expression in serum and tissues (P<0.05, P<0.01). Immunohistochemistry and Western blot demonstrated that SCF and c-Kit protein expression was decreased in the model group (P<0.05, P<0.01), which was reversed by WWSG intervention (P<0.05). ConclusionWWSG exerts therapeutic effects on FD with spleen-stomach deficiency cold syndrome in rats, potentially by regulating the SCF/c-Kit signaling pathway to enhance gastrointestinal motility.
10.Effects of Rhizosphere Organic Acids on Metabolism of Hairy Roots of Salvia miltiorrhiza
Xinyu FU ; Wenying HAN ; Jidong JU ; Bingqian ZHOU ; Guohong YANG ; Xiao WANG ; Lanping GUO ; Wei LIU
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(18):166-174
ObjectiveTo investigate the effects of rhizosphere organic acids secreted by the roots of Salvia miltiorrhiza on continuous cropping obstacles. MethodsThe mixed solution of organic acids in the rhizosphere of S. miltiorrhiza in continuous cropping and rotation cropping was added to the hairy roots subcultured for 21 days, and samples were collected on days 0, 2, 4, 6, 8, and 10. The changes of biomass, effective components, primary metabolites, secondary metabolites, antioxidant enzymes, and hormones in hairy roots of S. miltiorrhiza were observed and determined. ResultsCompared with the rotation cropping group and the blank control group, the simulation of organic acid secretion from the roots of S. miltiorrhiza had a significant inhibitory effect on the growth of hairy roots and decreased the content of effective components as well as total sugar and total protein in primary metabolites. Compared with the blank control group, the rotation cropping group and the continuous cropping group showed total sugar and total protein content decreases of 33.9% and 5.1%, respectively. On the other hand, the secretion of organic acids from S. miltiorrhiza roots significantly promoted the accumulation of total phenolic acids and total tanshinone, which showed increases of 14.6% and 1.6%, respectively, in continuous cropping group and rotation cropping group compared with the blank control group. ConclusionThe organic acid environment under continuous cropping significantly inhibited the growth of hairy roots and the accumulation of primary metabolites, while promoting the synthesis and accumulation of secondary metabolites of S. miltiorrhiza.


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