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.Effect of cannabinoid type Ⅰ receptors on neuronal differentiation of human apical papilla stem cells
Ziwei LIU ; NIJATI·TURSUN ; Rui YIN ; Shuhui LI ; Jing ZHOU
Chinese Journal of Tissue Engineering Research 2026;30(1):93-100
BACKGROUND:Previous studies have demonstrated that the cannabinoid type Ⅰ receptor can enhance the proliferation and neural differentiation of neural stem cells and mesenchymal stem cells.Moreover,cannabinoid type Ⅰ also governs the proliferation and mineralization capacity of human apical papilla stem cells.However,there are relatively few investigations concerning the impact of cannabinoid type Ⅰ overexpression on the neural differentiation of human apical papilla stem cells.OBJECTIVE:To investigate the effect of cannabinoid type Ⅰ on neural differentiation of human apical papilla stem cells in vitro.METHODS:Healthy third molars with immature root tips that need to be removed for orthodontic treatment were collected,and human apical papilla stem cells were isolated and cultured by tissue block method combined with enzyme digestion method.Cannabinoid type Ⅰ gene was introduced into human apical papilla stem cells by lentivirus-mediated transfection technique.A blank control group,a negative control group,and cannabinoid type Ⅰ overexpression group were set up.The transfection effect of overexpression of cannabinoid type Ⅰ lentivirus on human apical papilla stem cells was verified by Western Blot.The control group,negative control group,cannabinoid type Ⅰ overexpression group and cannabinoid type Ⅰ overexpression+AM251(cannabinoid type Ⅰ receptor antagonist)group were set up.Cell proliferation was detected by CCK-8 assay at 1,5,and 10 days after neural induction.On day 10 of neural induction,the expression levels of TH,NeuroD-1,and NCAM1 genes were detected by qRT-PCR,and the protein expression levels of Nestin and TUBB3 were detected by immunofluorescence.RESULTS AND CONCLUSION:(1)Compared with the blank control group and the negative control group,the expression of cannabinoid receptor Ⅰ protein in the cannabinoid receptor Ⅰ overexpression group was significantly increased,and the difference was significant(P<0.05).(2)Compared with the blank control group and the negative control group,the proliferation ability of human apical papilla stem cells in the cannabinoid type Ⅰ overexpression group was the strongest at 5 and 10 days after neural induction(P<0.05).(3)Compared with the blank control group and the negative control group,the mRNA expression of NeuroD-1,NCAM1,and TH in the stem cells of the human apical papilla in the cannabinoid type Ⅰ overexpression group was significantly increased,and the fluorescence intensity of Nestin and TUBB3 was significantly enhanced(P<0.05).(4)Compared with the cannabinoid type Ⅰ overexpression group,the proliferation ability,mRNA expression level of NeuroD-1,NCAM1,and TH,as well as the fluorescence intensity of Nestin and TUBB3,were significantly decreased in the cannabinoid type Ⅰ overexpression+AM251 group(P<0.05).These findings conclude that overexpression of cannabinoid type Ⅰ promoted the proliferation and neural differentiation of human apical dentin papilla stem cells.
3.Expert Consensus on Blood Flow and Oxygen Delivery Phenotyping and Clinical Management of Septic Shock(2025)
Wei HUANG ; Xinchen WANG ; Wenzhao CHAI ; Keliang CUI ; Bo YAO ; Zhiqun XING ; Cui WANG ; Jingjing LIU ; Shiyi GONG ; Dongkai LI ; Wanhong YIN ; Xiaoting WANG ; Wei DU
Medical Journal of Peking Union Medical College Hospital 2026;17(1):40-58
Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. Septic shock is the primary cause of mortality in sepsis, with its core pathophysiological mechanism being severe ischemia and hypoxia in critical units—composed of microcirculation and the mitochondria of functional cells—resulting from disruptions in blood flow and oxygen flow following a dysregulated host response. Due to the systemically convergent yet clinically heterogeneous nature of the host response, current understanding and management strategies for hemodynamics remain inconsistent, often leading to inadequate resuscitation or overtreatment. To improve the quality of care, based on a systematic review of the "blood flow-oxygen flow" theory, an expert panel emphasizes reevaluating septic shock from an integrated perspective of blood flow and oxygen flow, and has formulated the
4.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.
5.Establishment of graded management standards for off-label use of Shenqi fuzheng injection
Min WU ; Mei YU ; Shengnan YIN ; Dongmei LIU
China Pharmacy 2026;37(5):650-654
OBJECTIVE To establish the graded management standards for off-label use of Shenqi fuzheng injection. METHODS Systematic searches were conducted in databases including CNKI, PubMed and the Cochrane Library to retrieve guidelines/consensuses, systematic reviews/meta-analyses, and randomized controlled trials (RCTs) of Shenqi fuzheng injection. The quality of evidence was evaluated using AGREE Ⅱ, AMSTAR Ⅱ, and the Risk of Bias 1.0 tool recommended by Cochrane Collaboration, and the graded management standard for off-label use of Shenqi fuzheng injection was developed by using the Thomson grading system. RESULTS A total of 534 articles were involved, including 11 guidelines, 22 systematic reviews/meta-analysis, and 501 RCTs. They covered 79 off-label indications for Shenqi fuzheng injection: cancer-related fatigue, colorectal cancer and breast cancer, all with high-quality evidence were classified under grade A management (grade Ⅰ commendation), allowing all physicians across the hospital to prescribe relevant treatments; five diseases, such as ovarian cancer, liver cancer, leukemia, heart failure and cerebral infarction, were classified under grade B management (grade Ⅱa commendation), with prescription restricted to physicians with intermediate or higher professional titles in specific departments; eleven diseases, including sepsis, cervical cancer, esophageal cancer, etc., were classified under grade C management (grade Ⅱb commendation), requiring strict evaluation by senior physicians before prescription; the use of Shenqi fuzheng injection for other conditions was explicitly prohibited due to a lack of sufficient evidence. CONCLUSIONS Off-label use of Shenqi fuzheng injection is prevalent. The graded management standard established by evidence-based medical approach provides a scientific basis for standardizing the clinical application of traditional Chinese medicine injections and offers an operable paradigm for implementing differentiated drug use supervision in medical institutions.
6.Preventive effect of LifePort combined with polymyxin B on donor-derived infections in kidney transplantation
Xiaomin LI ; Yuewei YIN ; Chenming ZHAO ; Yalin NIU ; Kailong LIU ; Pingying GUO ; Wei LI ; Baosai LU
Organ Transplantation 2026;17(2):227-234
Objective To evaluate the effect of LifePort combined with polymyxin B in preventing donor-derived infections caused by preservation solution contamination. Methods Clinical data of 110 kidney transplant recipients were retrospectively analyzed. According to the decontamination status of preservation solution, the recipients were divided into the decontamination group (n=62) and the non-decontamination group (n=48). The general data of the two groups were compared, and the preventive effect of polymyxin B on possible donor-derived infections (p-DDI) was analyzed, especially infections associated with multidrug-resistant Gram-negative bacteria (MDR GNB). Results There were no statistically significant differences in baseline data (gender, age, preservation solution contamination status, etc.) between the decontamination group and the non-decontamination group (all P > 0.05). The overall contamination rate of preservation solution was 80.0%, and 68 contaminated samples were with single microorganism and 20 with multiple microorganisms. Coagulase-negative staphylococci, Enterococcus and Klebsiella pneumoniae were the most common microorganisms in the positive samples. Fifteen cases of preservation solution were contaminated by MDR GNB, including 10 cases in the non-decontamination group and 5 cases in the decontamination group, with no statistically significant difference between the two groups (P = 0.053). Postoperative infection-related events occurred in 69 recipients, including 39 cases in the non-decontamination group and 30 cases in the decontamination group, with the incidence rate in the non-decontamination group significantly higher than that in the decontamination group (P < 0.001). Only 10 cases of infections were identified as p-DDI, all of which were positive for preservation solution culture, including 8 cases in the non-decontamination group and 2 cases in the decontamination group (P < 0.05). There were 5 cases of p-DDI related to MDR GNB in the non-decontamination group, while no such cases occurred in the decontamination group (P < 0.05). No adverse reactions related to polymyxin B were observed, and no recipient death or renal allograft dysfunction occurred in either group. Conclusions Adding polymyxin B to the preservation fluid during hypothermic machine perfusion with LifePort before renal transplantation may reduce p-DDI and its potential adverse consequences.
7.Preliminary application of histological evaluation of donor pancreas biopsy tissue in simultaneous pancreas-kidney transplantation
Jiao WAN ; Hui GUO ; Jiali FANG ; Guanghui LI ; Luhao LIU ; Yunyi XIONG ; Wei YIN ; Tong YANG ; Junjie MA ; Zheng CHEN
Organ Transplantation 2026;17(2):250-256
Objective To preliminarily investigate the safety and efficacy of donor pancreas needle biopsy in simultaneous pancreas-kidney transplantation. Methods Clinical data of 7 cases undergoing donor pancreas biopsy were collected retrospectively. All cases underwent donor pancreas biopsy before or during simultaneous pancreas-kidney transplantation. Frozen section or paraffin sectioning techniques were used for tissue preparation, and hematoxylin-eosin and Masson staining were performed to histologically evaluate the donor pancreas. The quality of donor pancreas was comprehensively assessed by combining histological findings with the donor's clinical data. Postoperative follow-up data of 5 simultaneous pancreas-kidney transplant recipients were collected to summarize the safety of donor pancreas biopsy and the prognosis of transplant recipients. Results The 7 pancreas donors were aged 28 to 62 years, with a body mass index ranging from 20.76 to 27.68 kg/m2. Liver ultrasound indicated fatty liver in 3 cases, while pancreatic ultrasound did not reveal any significant abnormalities. Among them, biopsy was performed on 2 donors after completion of pancreatic procurement and processing, and the frozen section histology showed moderate acute pancreatitis changes (edema of acinar cells, necrosis and inflammatory cell infiltration). Combined with a serum amylase level elevated more than 3 times the upper limit of normal value, these two donor pancreases were finally discarded. The remaining 5 cases underwent biopsy immediately after pancreatic vascular anastomosis during simultaneous pancreas-kidney transplantation, and histological evaluation was performed on paraffin-embedded sections. No biopsy-related complications (such as bleeding, pancreatic fistula, etc.) occurred after transplantation. One recipient died of severe infection 2 months after transplantation, while the other 4 recipients were followed up for more than 5 years, with well-functioning transplant kidneys and pancreases. Conclusions Donor pancreas biopsy is relatively safe, and the risk of biopsy-related complications after transplantation is controllable. Comprehensive assessment of donor pancreas quality by combining histological evaluation with the donor's clinical indicators is conducive to improving the accuracy of donor pancreas selection and organ utilization.
8.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.
9.Flavonoids Intervene in Diabetic Nephropathy by Regulating TGF-β/Smad Signaling Pathway: A Review
Qihui QIU ; Chang LIU ; Xiaotong YAN ; Jinwei HAN ; Hui SUN ; Fengting YIN ; Yuhang WANG ; Mengmeng WANG ; Xijun WANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(7):300-309
Diabetic nephropathy (DKD), as a common microvascular complication of diabetes mellitus (DM), is a major cause of end-stage renal disease (ESRD). Its clinical manifestations include increased urinary protein excretion, thickening of the glomerular basement membrane, and renal tubulointerstitial fibrosis. The pathogenesis of DKD is complex and involves multiple factors, including disordered glucose metabolism, hemodynamic alterations, and oxidative stress. Although modern medical approaches can alleviate certain symptoms, they still have limitations such as insufficient therapeutic targeting and prominent adverse effects. The transforming growth factor-β/Smad (TGF-β/Smad) signaling pathway is not only a tissue fibrosis pathway that has attracted considerable attention in recent years, but also regulates multiple protein molecules, including the glomerular podocyte slit diaphragm protein Podocin, interleukin-1β (IL-1β), and superoxide dismutase (SOD), thereby participating in various pathological processes and ultimately mediating renal injury. Flavonoid compounds, owing to their sustained pharmacological effects, broad spectrum of action, and high safety profile, have become ideal candidates for targeted therapy research in DKD. Existing studies have shown that these compounds can exert inhibitory effects on renal fibrosis, alleviate inflammatory responses, protect podocytes, and reduce oxidative stress by regulating the interactions between the TGF-β/Smad signaling pathway and the aforementioned protein molecules, thereby maintaining renal structure and function, reducing proteinuria, and significantly improving DKD lesions. This review briefly outlines the composition and functions of the TGF-β/Smad signaling pathway, elucidates the mechanisms by which this pathway regulates DKD, and focuses on summarizing major studies from the past decade on flavonoid-based interventions in DKD through targeted inhibition of the TGF-β/Smad signaling pathway. Furthermore, it discusses the considerable therapeutic potential of flavonoids in the treatment of this disease, aiming to provide a scientific basis for future clinical prevention and treatment of DKD and to promote the development of targeted drugs.
10.Targeted fluorescent imaging probes for detecting the spatial distribution of VEGF in the retinas of rats with radiation retinopathy
Yunhe DING ; Bin WANG ; Feng LIU ; Zhiyang ZHANG ; Haibei DONG ; Wenwen GUO ; Haitao YIN
International Eye Science 2026;26(4):567-572
AIM: To detect the distribution and expression of vascular endothelial growth factor(VEGF)in radiation retinopathy(RR)through fluorescence targeted imaging.METHODS:Covalent binding of fluorescein FITC with VEGF antibody ranibizumab to prepare targeted fluorescent imaging probe ranibizumab-FITC. SD rats were randomly divided into three groups based on the principle of weight balance: a normal control group(Con group), a low-dose radiation group(10 Gy group), and a high-dose radiation group(30 Gy group). Medical linear accelerators and lead blocks were used to locally irradiate the rat eyeballs for modeling. Western blot and qRT-PCR were used to detect the expression levels of VEGF-A in each group and to screen for appropriate modeling dose. The inverted fluorescence microscope and the confocal microscope were used to observe the distribution of VEGF and imaging probes in the retinas of control and RR model group rats, and to verify the effectiveness of targeted probes.RESULTS:The expression level of VEGF-A in the retina of rats in the high-dose radiation group(30 Gy group)was higher than that in the normal control group(Con group). In early RR, VEGF expression was observed to be associated with microaneurysms and abnormal microvessels in the retina. VEGF accumulation was observed at the site of capillary wall damage. When retinal capillary endothelial damage occurred, targeted probes gathered on the outer surface of the vessel wall.CONCLUSION:The expression level of VEGF in the retina of RR model rats is elevated, and fluorescent targeted molecular imaging probes can detect the spatial distribution of VEGF at the microvascular lesions in the retina of RR rats.

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