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.Integrating Transcriptomics and 3D Organoids to Investigate Mechanism of Periplaneta americana Extract Against Lung Adenocarcinoma
Qiong MA ; Chunxia HUANG ; Jiawei HE ; Yuting BAI ; Xingyue LIU ; Yuxuan XIONG ; Yang ZHONG ; Hengzhou LAI ; Yuling JIANG ; Xueke LI ; Qian WANG ; Yifeng REN ; Xi FU ; Funeng GENG ; Taoqing WU ; Ping XIAO ; Fengming YOU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(11):124-132
ObjectiveTo evaluate the antitumor activity of Periplaneta americana extract(PAE) against human-derived lung adenocarcinoma organoids(LUAD-PDOs) and to elucidate its potential mechanism based on transcriptomics. MethodsFresh tumor and adjacent normal tissues from patients with LUAD were collected to construct LUAD-PDOs and normal lung organoid(Nor-PDOs) models using 3D organoid culture technology. The effective intervention concentration of PAE was determined using the cell counting kit-8(CCK-8) assay. Experimental groups included the model group(LUAD-PDOs), normal group, model administration group(LUAD-PDOs+PAE), and normal administration group(Nor-PDOs+PAE). Hematoxylin-eosin(HE) staining was used to observe the pathological structures of PDOs, immunohistochemistry(IHC) was performed to detect the expressions of the proliferation marker Ki-67 and lung adenocarcinoma differentiation markers cytokeratin-7(CK-7) and Napsin A, TUNEL staining was applied to detect cell apoptosis. RNA sequencing(RNA-Seq) was conducted to identify differentially expressed genes(DEGs), followed by Gene Ontology(GO), Kyoto Encyclopedia of Genes and Genomes(KEGG), and Gene Set Enrichment Analysis(GSEA), alongside protein-protein interaction(PPI) network analysis to screen core mechanisms. Finally, key targets were validated by integrating external database analysis with immunofluorescence(IF). ResultsNor-PDOs and LUAD-PDOs that highly recapitulated the pathological characteristics of the primary tissues were successfully established. The CCK-8 assay determined that the effective intervention concentration of PAE was 16 g·L-1. Morphological observation showed that Nor-PDOs exhibited lumen-forming structures, whereas LUAD-PDOs displayed dense, solid structures. CCK-8 and TUNEL assays revealed that, compared with the model group, PAE intervention inhibited the proliferation of LUAD-PDOs and promoted apoptosis in LUAD cells, while showing no significant effect on the viability of Nor-PDOs. Transcriptomic analysis identified 719 DEGs that were significantly reversed after PAE intervention(347 up-regulated and 372 down-regulated)(P<0.05). GO enrichment analysis indicated that DEGs in the model administration group were significantly enriched in biological processes related to cell cycle regulation compared to the model group. KEGG pathway analysis revealed that PAE affected pathways related to proliferation and metabolism, including pathways in cancer and the p53 signaling pathway. GSEA further confirmed that PAE significantly enhanced the activity of the p53 signaling pathway(P<0.05). PPI network analysis indicated that breast cancer type 1 susceptibility protein(BRCA1) and checkpoint kinase 1(CHEK1) were the core down-regulated targets in the p53 pathway. IF verified the high expression of BRCA1 and CHEK1 in LUAD-PDOs and their significant downregulation after PAE intervention(P<0.05). Furthermore, survival analysis based on The Cancer Genome Atlas(TCGA) database indicated that low expression of BRCA1 and CHEK1 was significantly associated with prolonged overall survival in patients with LUAD(P<0.05). ConclusionPAE effectively inhibits proliferation of LUAD-PDOs and promotes their apoptosis, its anti-tumor mechanism is potentially associated with the activation of the p53 signaling pathway, with BRCA1 and CHEK1 genes likely serving as key downstream targets for the effects of PAE.
3.Construction and Application of "Source-Pivot-Convergence" Pattern Identification and Treatment Model for Malignant Tumors
Yuling JIANG ; Jiawei HE ; Yang ZHONG ; Chunxia HUANG ; Qiong MA ; Chuan ZHENG ; Xi FU ; Fengming YOU
Journal of Traditional Chinese Medicine 2026;67(9):956-960
Based on LI Gao's Academic Thought, focusing on the process of qi transformation and taking the regulation and restoration of metabolism and immunity as the entry point, a "source-pivot-convergence" diagnostic and therapeutic model for malignant tumors is constructed. In this model, spleen and stomach internal injury is the source of malignant tumor occurrence, while the disorder of ascending and descending is the pivot of the disease development, and the generation of yin fire is the convergence of malignant tumor progression. Based on this, the three major therapeutic methods of clearing the source, harmonizing the pivot, and resolving the convergence are established. To fortify spleen and boost qi, consolidate the root and clear the source, modified Buzhong Yiqi Decoction(补中益气汤)can be used. To raise the clear and direct the turbid downward, regulate qi and harmonize the pivot, modified Shengyang Yiwei Decoction (升阳益胃汤) is suggested. To restore balance and promote circulation, disperse accumulation and resolve convergence, modified Shengyang Sanhuo Decoction (升阳散火汤) is selected. In clinical practice, these formulas can be used in combination according to the complexity of the pathogenesis, and further adapted with prescriptions for promoting dispersion and penetrating pathogenic factors, resolving phlegm and promoting circulation, activating blood and eliminating concretions, which can provide a reference for the prevention and treatment of tumor diseases.
4.Construction and Application of "Source-Pivot-Convergence" Pattern Identification and Treatment Model for Malignant Tumors
Yuling JIANG ; Jiawei HE ; Yang ZHONG ; Chunxia HUANG ; Qiong MA ; Chuan ZHENG ; Xi FU ; Fengming YOU
Journal of Traditional Chinese Medicine 2026;67(9):956-960
Based on LI Gao's Academic Thought, focusing on the process of qi transformation and taking the regulation and restoration of metabolism and immunity as the entry point, a "source-pivot-convergence" diagnostic and therapeutic model for malignant tumors is constructed. In this model, spleen and stomach internal injury is the source of malignant tumor occurrence, while the disorder of ascending and descending is the pivot of the disease development, and the generation of yin fire is the convergence of malignant tumor progression. Based on this, the three major therapeutic methods of clearing the source, harmonizing the pivot, and resolving the convergence are established. To fortify spleen and boost qi, consolidate the root and clear the source, modified Buzhong Yiqi Decoction(补中益气汤)can be used. To raise the clear and direct the turbid downward, regulate qi and harmonize the pivot, modified Shengyang Yiwei Decoction (升阳益胃汤) is suggested. To restore balance and promote circulation, disperse accumulation and resolve convergence, modified Shengyang Sanhuo Decoction (升阳散火汤) is selected. In clinical practice, these formulas can be used in combination according to the complexity of the pathogenesis, and further adapted with prescriptions for promoting dispersion and penetrating pathogenic factors, resolving phlegm and promoting circulation, activating blood and eliminating concretions, which can provide a reference for the prevention and treatment of tumor diseases.
5.Compilation Explanation for Expert Consensus on Clinical Application of Ruyi Zhenbao Pills
Ming CHEN ; Jingling CHANG ; Shangquan WANG ; Gejia ZHONG ; Qiang DENG ; Hongxia CHEN ; Qi'en LI ; Yaming LIN ; Zujian XU ; Changkuan FU ; Yu'er HU ; Yanming XIE ; Yuanyuan LI
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(22):209-215
The compilation explanation for the Expert Consensus on Clinical Application of Ruyi Zhenbao pills systematically expounds the formulation methods and evidence-based basis of this consensus. In response to the weak clinical application evidence and ambiguous indications of Ruyi Zhenbao pills, the Institute of Basic Research in Clinical Medicine of China Academy of Chinese Medical Sciences, Wangjing Hospital of China Academy of Chinese Medical Sciences, and Dongzhimen Hospital of Beijing University of Chinese Medicine invited 39 experts from 31 medical institutions across China to complete the compilation through multi-disciplinary collaboration. The compilation strictly adheres to the World Health Organization (WHO) guidelines for guideline development and the GRADE evidence grading system. The work process covered the construction of clinical questions (a total of 30 clinical questions were determined based on expert voting results), evidence retrieval (covering Chinese and English databases and gray literature), safety assessment (integrating drug monitoring data and clinical research), and the formation of recommendation opinions and consensus suggestions (18 recommendation opinions were reached through the GRADE grid method, and 22 consensus suggestions were reached through majority voting rules). The results show that the consensus clearly states that this medicine is suitable for knee osteoarthritis, gouty arthritis, rheumatoid arthritis, neuropathic pain, and sequelae of stroke. In terms of safety, the adverse reactions are mainly gastrointestinal reactions such as nausea, vomiting, and abdominal pain. Pregnant women and those allergic to the ingredients of this medicine are contraindicated. The compilation process underwent three rounds of expert reviews and adopted methods such as nominal group technique and Delphi method to ensure the rigor of the consensus compilation process. It provides a paradigm for the formulation of expert consensus on clinical application of Tibetan medicine through the academic promotion and dynamic revision.
6.Changes in Astronaut Brain Function and Behavior Associated With Habitation on Low-Earth-orbit Space Stations
Hong-Ting JIANG ; You-Fu LUO ; Zheng-Jiang YANG ; Yuan YAO ; De-Zhong YAO ; Ke CHEN
Progress in Biochemistry and Biophysics 2026;53(10):2786-2796
During habitation on low-Earth-orbit (LEO) space stations, astronauts are exposed to a combination of orbital microgravity, space radiation, an enclosed and artificially controlled cabin environment, altered sleep-wake rhythms, and sustained operational and psychosocial demands. These factors can modify sensorimotor inputs, body-fluid distribution, arousal state, and task-related neural processing, thereby affecting brain function and behavior. Because evidence from real spaceflight remains limited by small samples, heterogeneous mission durations, and different measurement time points, this review integrates findings from real human spaceflight with relevant ground-based analog studies while treating real orbital studies as the primary source of evidence. We focus on electroencephalography (EEG) and event-related potentials (ERPs), structural and functional neuroimaging, and sensorimotor and cognitive outcomes, with particular attention to the direction, anatomical distribution, temporal course, and possible physiological significance of the reported changes. EEG studies indicate that long-duration spaceflight is associated with increased resting-state beta activity, particularly in sensorimotor and frontotemporal regions, together with state-dependent alterations in beta-band functional connectivity. In contrast, alpha source power and functional connectivity associated with the default mode network are reduced during long-duration missions, and some of these effects may persist into the early postflight period. Task-related electrophysiological findings further suggest that sustained mental workload can weaken frontocentral theta-temporoparietal gamma phase-amplitude coupling, whereas in-flight decision-making is accompanied by reduced P300 amplitude and reorganization of feedback-related potentials. Short-duration missions, however, have shown relative preservation of posterior dominant rhythms and some ERP measures, indicating that mission duration, recording state, and task demands substantially influence the observed electrophysiological phenotype. Neuroimaging provides complementary evidence at structural and network levels. Long-duration spaceflight has been associated with upward brain displacement, ventricular and cerebrospinal fluid expansion, regional gray- and white-matter remodeling, and alterations in white-matter structural connectivity. Functional magnetic resonance imaging (fMRI) studies further indicate reorganization of vestibular-sensorimotor, visual, and default mode networks. Some network changes recover after return to Earth, whereas others may remain detectable for months. Importantly, most MRI measurements are obtained after landing rather than in orbit; therefore, postflight findings may reflect a mixture of in-flight adaptation, the rapid transition back to 1 g, and subsequent readaptation rather than a single spaceflight effect. Behavioral evidence is most consistent for sensorimotor function. Early after return, astronauts frequently show impaired postural control, gait, spatial orientation, and coordination, consistent with reweighting among vestibular, visual, and proprioceptive information. By comparison, simple cognition and some critical operational tasks are often preserved. More subtle or high-load processes-including sustained attention, feedback evaluation, temporal processing, error monitoring, and metacognitive calibration may be more sensitive than global cognitive performance. This dissociation between neural change and preserved behavior suggests that altered brain activity should not automatically be interpreted as functional deterioration. Integrating the available modalities, we propose that LEO space-station habitation is better characterized by system-specific and stage-dependent neural adaptation than by a generalized increase or decline in brain function. The most coherent cross-modal pattern involves sensorimotor reorganization: reduced gravitational reference and weight-bearing feedback under microgravity may drive reweighting of vestibular, visual, and proprioceptive inputs, accompanied by changes in beta activity and vestibular-sensorimotor networks and followed by transient postflight sensorimotor deficits. A second major process involves fluid-related structural remodeling, in which cephalad fluid shifts and altered hydrostatic gradients may contribute to changes in cerebrospinal fluid spaces, ventricular volume, and brain tissue configuration. Resting-state and cognitive electrophysiological changes likely represent additional adjustments in network regulation and resource allocation, but their functional interpretation remains more dependent on sleep, workload, recording conditions, and individual differences. Future studies should move beyond isolated pre-post comparisons and group averages toward standardized longitudinal designs spanning preflight, multiple in-flight time points, and postflight recovery. Synchronized assessment of brain function, behavior, sleep, and key environmental parameters should be used to characterize individual adaptation trajectories and determine which neural changes reflect successful compensation, which predict delayed recovery, and which have genuine value for brain-health risk prediction and individualized countermeasures.
7.Advances in the application of deep learning for the diagnosis and treatment of osteonecrosis of the femoral head
Jia-Hao FU ; Hao CHEN ; Hong-Zhong XI ; Cheng-Lin LIU ; Yao-Kun WU ; Xin LIU ; Guang-Quan SUN
Medical Journal of Chinese People's Liberation Army 2025;50(10):1235-1242
With the rapid development of deep learning(DL)technology,its potential applications in the medical field have become increasingly prominent.As a refractory disease,osteonecrosis of the femoral head(ONFH)has certain limitations in traditional diagnostic and therapeutic approaches.The application of DL technology is expected to overcome these limitations and improve diagnosis and treatment outcomes.At present,the applications of DL models-including enhancing image clarity,improving diagnostic accuracy and efficiency,conducting prognostic evaluations,optimizing preoperative planning,assisting intraoperative imaging,and customizing personalized treatment plans-have fully demonstrated their tremendous potential in the diagnosis and treatment of ONFH.This review summarizes the current application status of DL in ONFH diagnosis and treatment,aiming to provide references and insights for future related research.
8.CURRENT DISTRIBUTION OF AEDES AEGYPTI IN LEIZHOU PENINSULA,ZHANJIANG CITY,GUANGDONG PROVINCE
Rui-Peng LU ; Jin-Hua DUAN ; Yu-Wen ZHONG ; Hui DENG ; Jun WU ; Li-Ping LIU ; Wei-Xiong YIN ; Feng XING ; Hui HUANG ; Chang-Jie FU ; Zong-Jing CHEN ; Ming-Ji CHENG ; Sheng-Jun HU ; Ya-Ting CHEN ; Wen-Ting GUO ; Li-Feng LIN
Acta Parasitologica et Medica Entomologica Sinica 2025;32(1):16-21
Objective To investigate the status of population dynamics and distribution changes of Aedes aegypti in Guangdong Province.Methods Continuous monitoring was conducted from May 2018 to July 2024 in Wushi Town and Qishui Town,Leizhou City,Zhanjiang City,Guangdong Province.Additionally,a survey of the distribution of Ae.aegypti along the Leizhou Peninsula coast was carried out.Results The density of Ae.aegypti in Zhanjiang showed a gradual decline from 2018 to 2024.The last detection of adult Ae.aegypti in Wushi Town was in September 2021,and the last larva was found in October 2023.No Ae.aegypti was detected in Qishui Town during surveys from 2021 to 2024.A survey of 18 coastal villages in the Leizhou Peninsula revealed no detections of Ae.aegypti.Conclusions This study provides a basis for understanding the distribution and population density fluctuations of Ae.aegypti,assessing its invasion risk,and scientifically conducting relevant prevention and control efforts.
9.Clinical Applications and Potential Mechanisms of Repetitive Transcranial Magnetic Stimulation in Prolonged Disorders of Consciousness
Jianlin PU ; Jing FU ; Zhong LI ; Qiuyue MAO ; Hongpeng LIU ; Yadong LIU ; Xuesong GAI
Journal of Kunming Medical University 2025;46(10):1-11
Prolonged disorders of consciousness(pDoC)are complex and prolonged conditions that severely impact patient prognosis and remain a clinical treatment challenge.In recent years,neural regulation-based awakening therapies have been widely applied in the assessment and treatment of pDoC patients.Repetitive transcranial magnetic stimulation(rTMS)technology can regulate neural activity and improve patients'consciousness states,demonstrating positive awakening effects for pDoC patients.However,the optimal stimulation parameters and awakening mechanisms of rTMS remain unclear.This article reviews the pathological mechanisms of pDoC,clinical applications of rTMS at different targeting sites and stimulation frequencies,and focuses on exploring how rTMS promotes consciousness recovery through neural mechanisms such as altering neural pathways,reshaping brain networks,promoting synaptic plasticity and neurotransmitter release,regulating neurotrophic factor expression,and modulating cerebral hemodynamics.Based on artificial intelligence,the article also prospects the future clinical research applications of rTMS.
10.Status and influencing factors of elevated blood pressure among manufacturing workers in Foshan City
Zhiheng XU ; Qinghua ZHONG ; Xudong LI ; Wei XU ; Fu CHEN ; Wanxia CHEN ; Qiang TAN
China Occupational Medicine 2025;52(6):637-642
Objective To analyze the elevated blood pressure status and its influencing factors among manufacturing workers in Foshan City. Methods A total of 565 795 manufacturing workers who underwent occupational medical examinations in Foshan City from 2017 to 2023 were included. Data of workers were obtained from the Guangdong Provincial Key Occupational Disease Monitoring and Management Platform. The influencing factors of elevated blood pressure were analyzed using descriptive epidemiological methods. Results A total of 89 526 cases of elevated blood pressure were detected among the 565 795 workers, with a detection rate of 15.82%. From 2017 to 2023, the annual detection rate of elevated blood pressure was 14.11%, 15.00%, 14.69%, 15.94%, 17.00%, 16.90%, and 16.68%, respectively, showing an overall upward trend (P<0.01). The top three industries with the highest detection rates of elevated blood pressure were instrument and meter manufacturing; wood processing and the manufacture of wood, bamboo, rattan, palm, and straw products; as well as agricultural and sideline food processing. Binary logistic regression analysis showed that male workers had a higher risk of elevated blood pressure than female workers (P<0.01). The risk of elevated blood pressure in workers increased with age, years of occupational hazard exposure, and duration of dust exposure (all P<0.05). Workers exposed to noise for more than three years had a higher risk of elevated blood pressure than those without noise exposure (P<0.05). The risk of elevated blood pressure among workers in Nanhai, Shunde, and Gaoming districts was higher than that in Chancheng District (all P<0.01). Workers originating from Northeast and Northwest China had a higher risk of elevated blood pressure than those from North China (all P<0.05). Workers from smaller-scale enterprises had higher risk of elevated blood pressure (all P<0.01). Conclusion Targeted blood pressure health interventions in Foshan City should be strengthened for male manufacturing workers who are older, have longer working years, and originate from Northeast and Northwest China. The development of exemplary health enterprises should be promoted, particularly among micro- and small-sized enterprises and key industries. Enhanced occupational health management is especially needed for positions with high intensity noise exposure and high concentration dust exposure.

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