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
;
Phenotype
;
Biological Ontologies
;
Language
;
Software
;
Large Language Models
2.Expert Consensus on Neurocritical Care Monitoring and Management in Beijing and Tibet(2025)
Drolma PHURBU ; Wenjin CHEN ; Heng ZHANG ; Jian ZHANG ; Xiaomeng WANG ; Guoying LIN ; Wenjun PAN ; Xiying GUI ; Xin CAI ; Chodron TENZIN ; Jianlei FU ; Qianwei LI ; TSEYANG ; Yijun LIU ; Bo LIU ; Tsering DROLMA ; Yudron SONAM ; KYILV ; Samdrup TSERING ; Wa DA ; Juan GUO ; Cheng QIU ; Huan CHEN ; Xiaoting WANG ; Yangong CHAO ; Dawei LIU ; Wenzhao CHAI ; Chenggong HU ; Wanhong YIN ; Shihong ZHU
Medical Journal of Peking Union Medical College Hospital 2026;17(1):59-72
Neurocritical care involves complex pathophysiological mechanisms, and its incidence is higher, injuries are more severe, and treatment is more challenging in high-altitude environments. This consensus, based on the latest domestic and international evidence-based medical data, establishes a standardized, goal-oriented framework for neurocritical care management applicable in high-altitude regions and nationwide. The consensus was developed following international standards for evidence quality assessment and underwent two rounds of Delphi expert consultation, resulting in 32 recommendation statements covering three parts: management systems, monitoring and assessment, and core strategies. Key updates include: advocating for the establishment of independent neurocritical care units and implementing precise tiered diagnosis and treatment based on the "Five Differences in Critical Care" concept; constructing a "trinity" multimodal brain monitoring system centered on cerebral blood flow, cerebral oxygenation, and brain function, emphasizing routine bedside transcranial Doppler ultrasound, cerebral oximetry, and continuous electroencephalography monitoring; shifting management strategies from mild hypothermia therapy to targeted temperature management, and defining the "446" target management pathway for the supercritical stage; emphasizing the assessment of static and dynamic cerebrovascular autoregulation functions through multimodal methods to achieve individualized optimal mean arterial pressure management; elevating cerebrospinal fluid management goals to the level of "glymphatic system" function maintenance; implementing a multidisciplinary collaborative, whole-process management model focusing on patients' long-term neurological functional outcomes; de-escalation criteria include multidimensional indicators such as recovery of brain structure, restoration of cerebrovascular autoregulation, improvement in cerebrospinal fluid dynamics, and reduction in biomarker levels; and integrating cutting-edge technologies like artificial intelligence into post-critical care management and rehabilitation planning. This consensus systematically integrates the entire process of neurocritical care management, reflecting the modern connotation of goal-oriented, dynamic, and multimodal integration in neurocritical care medicine. It aims to adapt to new trends such as deepening understanding of pathophysiological mechanisms, the integration of medicine and engineering, and the empowerment of artificial intelligence, thereby further advancing the discipline of critical care medicine.
3.The role of British social workers in health and elderly care and its implications for China
Chinese Medical Ethics 2026;39(1):138-142
The report of the 20th National Congress of the Communist Party of China proposed to implement the strategy of actively responding to population aging, charting a clear direction for China’s elderly care initiatives. Under this background, social workers serve as vital human resources in the elderly care service system, and the full realization of their roles and functions is of great importance. British social workers, through long-term practice in the field of health and elderly care, have developed multifaceted roles, such as providers of personalized care, defenders of rights and interests, educators of health, protectors under special circumstances, collaborators of innovation and development, and supporters in the field of health and elderly care, offering valuable insights for China. Combined with the realities of an aging society, efforts should be advanced from four aspects, including enhancing the recognition of social workers, strengthening their professional skills, promoting cooperation with the elderly care industry, and safeguarding the rights of the elderly, with a view to enabling social workers to better provide high-quality services for Chinese elderly groups in the field of health and elderly care.
4.Differences in deltamethrin resistance and kdr gene mutation in Culex tritaeniorhynchus population in and outside the Yellow Sea wetland
Xiao-er ZHANG ; Zhi-ming WU ; Ye TIAN ; Qian CUI ; Yu-qian JI ; Huan WANG ; Shu-juan YANG ; Yi-chao ZHAO ; Yu WANG ; Hua-yu YIN ; Yu DING ; Guo-jin YAN ; Min-sen ZHAO ; Shou-gang ZHANG ; Bing-dong SONG ; Hong-na CHEN ; Jian GAO ; Wei-fang YANG ; Yu-fu ZHANG ; Hui LIU ; Hong-liang CHU
Acta Parasitologica et Medica Entomologica Sinica 2026;33(2):101-107
Objective To gain insights into the biological characteristics of different populations of Culex tritaeniorhynchus within and around the Yellow Sea wetland from the perspective of the occurrence of resistance, we investigated the levels of resistance to deltamethrin and kdr gene mutation in the wetland and its peripheral areas. Methods Specimens were collected from Cx. tritaeniorhynchus populations at two monitoring sites in the Rare Bird National Nature Reserve and Tiaozi Ni Wetland Scenic Area, and also from two populations in Yancheng City and the Liuhe District of Nanjing, and the resistance of these mosquitoes to deltamethrin was determined using the CDC biotest bottle method. For each concentration of deltamethrin assessed, a random subset of exposed specimens was selected for amplification of the kdr gene fragment, followed by Sanger sequencing to identify and analyze resistance-associated mutations. Results The LC50 levels of deltamethrin among mosquitoes from the four populations in Luhe, Yancheng, the Rare Bird National Nature Reserve and the Tiaozi Ni Wetland Scenic Area were 2.048 5, 7.798 2, 3.473 3, and 17.695 5 mg/mL, respectively, with corresponding concentrations of deltamethrin ranging from 0.005 to 5.000,0.050 to 50.000,0.050 to 25.000 and 0.050 to 50.000 mg/mL, respectively. Furthermore, the ranges of the KT50 values were 11.76-107.43, 67.05-216.30,29.77-107.43 and 28.40-329.51 min; the 1-h knockdown rates were 34.58%-99.15%, 9.52%-43.80%, 55.09%-73.01%, and 10.09%-68.07%; and the 24-h mortality rates were 12.15%-67.52%,9.52%-79.56%,13.17%-82.21%, and 11.01%-78.99%, respectively. With respect to kdr gene mutation, we assayed a total of 63,70,59, and 57 mosquitoes for the four populations, for which we detected L1014F mutation frequencies of 14.29%, 35.00%, 20.34%, and 31.58%, respectively, with a majority of these mutations being heterozygous for resistance. In addition, five adult mosquitoes were identified has having synonymous mutations at site 1011[i. e. , AAT(asparagine)mutation to AAC(asparagine)]. Conclusions Our findings revealed the clear resistance of Cx. tritaeniorhynchus to deltamethrin in the Yancheng region of the Yellow Sea wetland, and the resistance phenotype and kdr frequency of Cx. tritaeniorhynchus in the wetland environment were comparable to those of Cx. tritaeniorhynchus in the wetland environment, thereby indicating that the resistance of different populations of Cx. tritaeniorhynchus was homogeneous under the pressure of different insecticide selection within and around the wetland. However, the underlying mechanisms need to be further studied.
5.Impact of DRG payment reform on the length of stay and expenses of patients in pilot medical institutions of Beijing
Moning GUO ; Yin CHEN ; Xue WU ; Yelong QIU ; Airan DONG ; Tinghui FU ; Yi WANG
Chinese Journal of Hospital Administration 2025;41(8):587-592
Objective:To analyse the impact of diagnosis-related groups (DRG) payment reform on the length of stay and hospitalisation expenses of patients in pilot medical institutions of Beijing, for references for the formulation and optimisation of DRG payment related policies.Methods:The home page data of inpatient medical records from 56 medical institutions that implemented DRG payment in Beijing from April to October 2021 (before DRG payment reform) and April to October 2022 (after DRG payment reform). Patients participating in the basic medical insurance for urban employees in Beijing were selected as the reform group, and others served as the control group. The difference-in-differences model (DID) were used to analyse the related indicators, to evaluate the effectiveness of the reform.Results:This study comprised a total of 3 294 003 inpatients. Of them, 1 714 134 cases were in the control group (911 100 cases before the reform and 803 034 cases after) and 1 579 869 cases were in the study group (802 899 cases before the reform and 776 970 cases after). The gender, age composition and treatment methods of patients changed little before and after the reform. But the proportion of patients with severe comorbidities or complications rose from 11.11% before the reform to 13.19% after the reform. Through the analysis of the DID model, the DRG payment reform could reduce the length of stay ( P=0.001) and hospitalization expenses of patients ( P<0.001), and played a certain optimising role in the cost structure. Among them, the proportion of medical service expenses did not change significantly ( P=0.977), the proportion of inspection and testing expenses, as well as drug expenses decreased slightly ( P=0.001, P=0.004), and the proportion in consumable expenditures increased slightly ( P=0.001). Conclusions:DRG payment reform played a positive role in shortening the length of stay and hospitalization expenses. It was suggested that medical institutions in Beijing should further optimize the structure of patient hospitalization expenses, with a focus on exploring effective ways to increase the medical service revenue and reasonably control the consumables costs.
6.Research on Discrimination of Degradation Levels in Shipwreck Archaeological Wood Based on Microscale Attenuated Total Reflection Fourier Transform Infrared Spectroscopy
Ren LI ; Man-Li SUN ; Li-Chao JIAO ; Ya-Fang YIN ; Zhi-Guo ZHANG ; Fu-De TIE
Chinese Journal of Analytical Chemistry 2025;53(6):967-975
After the wooden shipwreck was recovered from the marine underwater environment,the wooden components undergo varying degrees of degradation,therefore,accurately determining the extent of degradation is a fundamental scientific issue for implementing effective preservation strategies.In this work,the wooden remains of Pinus massoniana excavated from the"Nanhai No.1"shipwreck(Southern Song Dynasty)were investigated and compared with the modern wood to discriminate the degradation levels of archaeological wood using attenuated total reflection Fourier transform infrared(ATR-FTIR)spectroscopy.The residual sugar content within wood cell walls was determined using a non-invasive automated microscale ATR-FTIR method to extract chemical information from the wood tangential section.Microstructural characterization of wood samples was conducted by super depth of field microscopy and scanning electron microscopy.FTIR spectral analysis was performed to evaluate the degradation state and elucidate changes in cellulose crystallinity.Finally,the combination of FTIR spectroscopy with the sparse partial least squares discriminant analysis(sPLS-DA)model facilitated the rapid discrimination of degradation levels in shipwreck archaeological wood,and the performance of the model was evaluated using receiver operating characteristic(ROC)curves and area under the curve(AUC).The results showed that the higher the degree of wood degradation,the lower the residual sugar content in the wood cell wall,and the residual glucose content of highly degraded wood was only 4.7%.Significant differences were observed in both the tangential section microstructure and FTIR characteristic absorption patterns across degradation levels,and as the degradation advanced,progressive cell wall loosening occurred alongside selective removal of polysaccharide components,and the relative lignin content was increased,resulting in an elevated A1509/A1370 ratio in FTIR spectra.The sPLS-DA model achieved excellent discrimination performance with AUC values exceeding 0.9,confirming that the combination of FTIR spectroscopy with sPLS-DA enabled accurate assessment of degradation levels in shipwreck archaeological wood.This study developed a rapid and accurate methodology for assessing degradation levels in shipwreck archaeological wood based on microscale ATR-FTIR spectroscopy,which would help to promote the accurate assessment of the preservation state of waterlogged wooden artifacts.
7.Diagnosis and Treatment of a Case of Spironolactone-Associated Asymptomatic Hyperuricemia After Renal Transplantation
Yun XIAO ; Xiaoyu HAN ; Chao ZHENG ; Yu FU ; Hanbin XIONG ; Bin ZOU ; Baolin WANG ; Hua ZOU ; Chenglong YIN ; Zhengyao JIANG ; Sheng ZOU ; Anle DU ; Guohui LI ; Xiaohui GUO ; Lin ZHONG ; Jiake HE
Herald of Medicine 2025;44(10):1562-1565
Objective To explore the identification method,pathogenesis,clinical characteristics and individualized pharmacotherapy of asymptomatic hyperuricemia after renal transplantation.Methods The pharmacist was on duty at the organ transplant outpatient clinic.During this time,they analyzed and sorted out the medications,identified and differentiated a case of asymptomatic hyperuricemia related to spironolactone in a patient who had undergone a renal transplant,and provided comprehensive care throughout the entire process.Results The asymptomatic hyperuricemia in this patient might be associated with spironolactone,and the adverse reactions of the patient were alleviated by pharmacists through optimizing clinical treatment.Up to now,no hyperuricemia occurred.Conclusions Pharmacists are required to collaborate closely with clinicians to establish medication profiles for patients under long-term follow-up and to closely monitor and evaluate drug-related adverse reactions.Additionally,they should assess the renal function and immune status of transplant recipients promptly and formulate individualized treatment plans in order to enhance the long-term survival of both the transplanted kidneys and the recipients.
8.Effectiveness of Pentavalent Rotavirus Vaccine - a Propensity Score Matched Test Negative Design Case-Control Study Using Medical Big Data in Three Provinces of China.
Yue Xin XIU ; Lin TANG ; Fu Zhen WANG ; Lei WANG ; Zhen LI ; Jun LIU ; Dan LI ; Xue Yan LI ; Yao YI ; Fan ZHANG ; Lei YU ; Jing Feng WU ; Zun Dong YIN
Biomedical and Environmental Sciences 2025;38(9):1032-1043
OBJECTIVE:
The objective of our study was to evaluate the vaccine effectiveness (VE) of the pentavalent rotavirus vaccine (RV5) among < 5-year-old children in three provinces of China during 2020-2024 via a propensity score-matched test-negative case-control study.
METHODS:
Electronic health records and immunization information systems were used to obtain data on acute gastroenteritis (AGE) cases tested for rotavirus (RV) infection. RV-positive cases were propensity score matched with RV-negative controls for age, visit month, and province.
RESULTS:
The study included 27,472 children with AGE aged 8 weeks to 4 years at the time of AGE diagnosis; 7.98% (2,192) were RV-positive. The VE (95% confidence interval, CI) of 1-2 and 3 doses of RV5 against any medically attended RV infection (inpatient or outpatient) was 57.6% (39.8%, 70.2%) and 67.2% (60.3%, 72.9%), respectively. Among children who received the 3rd dose before turning 5 months of age, 3-dose VE decreased from 70.4% (53.9%, 81.1%) (< 5 months since the 3rd dose) to 63.0% (49.1%, 73.0%) (≥ 1 year since the 3rd dose). The three-dose VE rate was 69.4% (41.3%, 84.0%) for RVGE hospitalization and 57.5% (38.9%, 70.5%) for outpatient-only medically attended RVGE.
CONCLUSION
Three-dose RV5 VE against rotavirus gastroenteritis (RVGE) in children aged < 5 years was higher than 1-2-dose VE. Three-dose VE decreased with time since the 3rd dose in children who received the 3rd dose before turning five months of age, but remained above 60% for at least one year. VE was higher for RVGE hospitalizations than for medically attended outpatient visits.
Humans
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Rotavirus Vaccines/immunology*
;
China/epidemiology*
;
Case-Control Studies
;
Child, Preschool
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Infant
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Rotavirus Infections/epidemiology*
;
Male
;
Propensity Score
;
Female
;
Vaccine Efficacy
;
Gastroenteritis/virology*
;
Vaccines, Attenuated
;
Rotavirus
9.Patient-specific quality assurance for non-normal radiotherapy plans based on statistical process control
Juan DENG ; Gaoyuan LIU ; Chuou YIN ; Jiang LIU ; Guojian MEI ; Ling HUA ; Shutong YU ; Xinhui FU ; Chen LIN ; Tian LI ; Yibao ZHANG
Chinese Journal of Radiological Medicine and Protection 2025;45(4):296-301
Objective:To apply statistical process control (SPC) techniques to the quality assurance of non-normal radiotherapy plans through Johnson transformation, establishing patient-specific tolerance and action limits based on treatment sites and dose/distance assessment criteria, thereby enhancing the intensity-modulated radiation therapy (IMRT) verification accuracy and dose delivery precision.Methods:In this study, 951 gamma analysis data of patient-specific quality assurance (PSQA) executed on the Halcyon accelerator platform were selected and categorized into six groups based on treatment sites, including brain (102 cases), head and neck (100 cases), breast (229 cases), lung (154 cases), esophagus (223 cases), and pelvic (143 cases) groups. The six groups of data were statistically analyzed through Anderson-Darling normality tests ( α = 0.05) using Minitab 21 software. Non-normal data were transformed into normal data through Johnson transformation and then were used to establish treatment site-specific tolerance and action limits, which were compared with the Shewhart control charts based on normal distributions. Results:The PSQA result of the six groups all exhibited non-normal distributions ( P < 0.05). Through Johnson transformation, the tolerance and action limits for the head and neck, breast, lung, esophagus, and pelvic areas under the 3%/2 mm criterion ranged from 95.13% to 96.16% and 94.19% to 95.91%, respectively. In contrast, the tolerance and action limits ranged from 91.15% to 94.86% and 89.94% to 94.78% under the 2%/2 mm criterion. Directly applying Shewhart control charts without normality assumptions yielded higher tolerance limits compared to the application of Johnson transformation, increasing the false positive rate in the non-normal PSQA process. Conclusions:Applying the SPC techniques directly to a non-normal process can lead to an increased false alarm rate and wrong process interpretation. The SPC techniques combined with Johnson transformation enable more effective monitoring of a non-normal PSQA process, facilitating timely identification of potential factors that may lead to an out-of-control process based on the treatment site-specific limits.
10.Expert Consensus on the Ethical Requirements for Generative AI-Assisted Academic Writing
You-Quan BU ; Yong-Fu CAO ; Zeng-Yi CHANG ; Hong-Yu CHEN ; Xiao-Wei CHEN ; Yuan-Yuan CHEN ; Zhu-Cheng CHEN ; Rui DENG ; Jie DING ; Zhong-Kai FAN ; Guo-Quan GAO ; Xu GAO ; Lan HU ; Xiao-Qing HU ; Hong-Ti JIA ; Ying KONG ; En-Min LI ; Ling LI ; Yu-Hua LI ; Jun-Rong LIU ; Zhi-Qiang LIU ; Ya-Ping LUO ; Xue-Mei LV ; Yan-Xi PEI ; Xiao-Zhong PENG ; Qi-Qun TANG ; You WAN ; Yong WANG ; Ming-Xu WANG ; Xian WANG ; Guang-Kuan XIE ; Jun XIE ; Xiao-Hua YAN ; Mei YIN ; Zhong-Shan YU ; Chun-Yan ZHOU ; Rui-Fang ZHU
Chinese Journal of Biochemistry and Molecular Biology 2025;41(6):826-832
With the rapid development of generative artificial intelligence(GAI)technologies,their widespread application in academic research and writing is continuously expanding the boundaries of sci-entific inquiry.However,this trend has also raised a series of ethical and regulatory challenges,inclu-ding issues related to authorship,content authenticity,citation accuracy,and accountability.In light of the growing involvement of AI in generating academic content,establishing an open,controllable,and trustworthy ethical governance framework has become a key task for safeguarding research integrity and maintaining trust within the academic community.This expert consensus outlines ethical requirements across key stages of AI-assisted academic writing-including topic selection,data management,citation practices,and authorship attribution.It aims to clarify the boundaries and ethical obligations surrounding AI use in academic writing,ensuring that technological tools enhance efficiency without compromising in-tegrity.The goal is to provide guidance and institutional support for building a responsible and sustainable research ecosystem.


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