1.Pathogenesis Reasoning Chain-of-thought Supervision for Large Language Models: Syndrome Manifestation Recognition and Multidimensional Evaluation in Spleen-stomach Disorders
Shu-Han YANG ; Yu-Xin HU ; Xin-Yu YU ; Yu-Ying TU ; Yi-Chang ZANG ; Pan-Fei LI
Progress in Biochemistry and Biophysics 2026;53(5):1240-1263
ObjectiveThe essence of syndrome manifestation recognition in traditional Chinese medicine (TCM) is to infer the body’s latent pathogenesis state from clinical observational information, rather than to perform simple label matching. However, previous studies have largely modeled this task as syndrome pattern classification within a fixed label space, which does not adequately reflect the cognition process of TCM syndrome differentiation centered on pathogenesis reasoning, and is also insufficient to capture the openness, semantic variability, and cross-disease reusability of syndrome manifestation expression. This study aimed to investigate whether introducing pathogenesis reasoning chain-of-thought (PR-CoT) supervision into large language models (LLMs) could improve the quality and cognitive consistency of syndrome manifestation recognition and support cross-disease transfer. MethodsSyndrome manifestation recognition was formulated as a conditional generation task under the framework of clinical observational information (X)→pathogenesis structure (Z)→syndrome pattern output (Y), where Z serves as an explicit intermediate structural variable linking the clinical evidence and syndrome judgment. Within this framework, a PR-CoT-supervised dataset for syndrome manifestation recognition was constructed based on medical case records of spleen-stomach disorders. After preprocessing, information extraction, manual proofreading, and data cleaning, the dataset comprised 4 800 training cases, 400 development cases, and 400 test cases. Each sample was annotated with a structured PR-CoT consisting of three progressive levels: clinical information summarization, comprehensive pathogenesis analysis, and syndrome pattern output. Supervised fine-tuning was conducted on open-source LLMs, with an end-to-end model serving as the baseline. Qwen3-32B was used as the primary experimental model, and Qwen3-14B as the scale comparison model. A progressive multidimensional evaluation framework was further established, comprising a structural parsing level, a semantic similarity level, and an expert blind review level. At the structural parsing level, syndrome pattern expressions were decomposed into structural elements and evaluated using Precision, Recall, F1 score, and Jaccard similarity. At the semantic similarity level, independent LLMs scored the theoretical proximity between predicted and reference syndrome patterns. At the expert blind review level, three TCM experts independently evaluated model outputs on two dimensions: syndrome differentiation consistency and terminology standardization of syndrome patterns. In addition, zero-shot cross-disease transfer evaluation was conducted on gynecological and heart-system disorder test sets. ResultsAt the structural parsing level, PR-CoT supervision did not lead to a stable improvement in the element-wise overlap of syndrome pattern structural components. Compared with the corresponding baselines, neither Qwen3-32B nor Qwen3-14B showed consistent advantages in structural matching metrics after the introduction of PR-CoT supervision. In contrast, at the semantic similarity level, PR-CoT supervision produced stable positive gains across different model scales and evaluation systems. The average semantic score of Qwen3-32B increased from 6.425 8 in the baseline model to 6.585 0 after PR-CoT supervision, and that of Qwen3-14B increased from 5.870 0 to 5.964 2. At the expert blind review level, the overall score of Qwen3-32B (PR-CoT) was 7.026 0±0.107 7, higher than 6.416 3±0.288 9 for its baseline. In zero-shot cross-disease testing, the PR-CoT model still showed advantages in semantic evaluation and expert evaluation on both gynecological and heart-system disorder test sets, indicating a certain degree of transferability. ConclusionThe benefits of PR-CoT supervision are mainly reflected in TCM semantic consistency and clinical plausibility, rather than in improved hard matching of structural elements. These findings support understanding syndrome manifestation recognition as a process of generating and expressing latent pathogenesis structures, rather than as a classification task within a traditional fixed label space. By introducing pathogenesis reasoning as an explicit intermediate structure into the modeling process and combining it with a progressive multidimensional evaluation framework, this study provides a methodological pathway for intelligent TCM syndrome differentiation that integrates theoretical alignment, interpretability, and multi-level evaluation.
2.Pathogenesis Reasoning Chain-of-thought Supervision for Large Language Models: Syndrome Manifestation Recognition and Multidimensional Evaluation in Spleen-stomach Disorders
Shu-Han YANG ; Yu-Xin HU ; Xin-Yu YU ; Yu-Ying TU ; Yi-Chang ZANG ; Pan-Fei LI
Progress in Biochemistry and Biophysics 2026;53(5):1240-1263
ObjectiveThe essence of syndrome manifestation recognition in traditional Chinese medicine (TCM) is to infer the body’s latent pathogenesis state from clinical observational information, rather than to perform simple label matching. However, previous studies have largely modeled this task as syndrome pattern classification within a fixed label space, which does not adequately reflect the cognition process of TCM syndrome differentiation centered on pathogenesis reasoning, and is also insufficient to capture the openness, semantic variability, and cross-disease reusability of syndrome manifestation expression. This study aimed to investigate whether introducing pathogenesis reasoning chain-of-thought (PR-CoT) supervision into large language models (LLMs) could improve the quality and cognitive consistency of syndrome manifestation recognition and support cross-disease transfer. MethodsSyndrome manifestation recognition was formulated as a conditional generation task under the framework of clinical observational information (X)→pathogenesis structure (Z)→syndrome pattern output (Y), where Z serves as an explicit intermediate structural variable linking the clinical evidence and syndrome judgment. Within this framework, a PR-CoT-supervised dataset for syndrome manifestation recognition was constructed based on medical case records of spleen-stomach disorders. After preprocessing, information extraction, manual proofreading, and data cleaning, the dataset comprised 4 800 training cases, 400 development cases, and 400 test cases. Each sample was annotated with a structured PR-CoT consisting of three progressive levels: clinical information summarization, comprehensive pathogenesis analysis, and syndrome pattern output. Supervised fine-tuning was conducted on open-source LLMs, with an end-to-end model serving as the baseline. Qwen3-32B was used as the primary experimental model, and Qwen3-14B as the scale comparison model. A progressive multidimensional evaluation framework was further established, comprising a structural parsing level, a semantic similarity level, and an expert blind review level. At the structural parsing level, syndrome pattern expressions were decomposed into structural elements and evaluated using Precision, Recall, F1 score, and Jaccard similarity. At the semantic similarity level, independent LLMs scored the theoretical proximity between predicted and reference syndrome patterns. At the expert blind review level, three TCM experts independently evaluated model outputs on two dimensions: syndrome differentiation consistency and terminology standardization of syndrome patterns. In addition, zero-shot cross-disease transfer evaluation was conducted on gynecological and heart-system disorder test sets. ResultsAt the structural parsing level, PR-CoT supervision did not lead to a stable improvement in the element-wise overlap of syndrome pattern structural components. Compared with the corresponding baselines, neither Qwen3-32B nor Qwen3-14B showed consistent advantages in structural matching metrics after the introduction of PR-CoT supervision. In contrast, at the semantic similarity level, PR-CoT supervision produced stable positive gains across different model scales and evaluation systems. The average semantic score of Qwen3-32B increased from 6.425 8 in the baseline model to 6.585 0 after PR-CoT supervision, and that of Qwen3-14B increased from 5.870 0 to 5.964 2. At the expert blind review level, the overall score of Qwen3-32B (PR-CoT) was 7.026 0±0.107 7, higher than 6.416 3±0.288 9 for its baseline. In zero-shot cross-disease testing, the PR-CoT model still showed advantages in semantic evaluation and expert evaluation on both gynecological and heart-system disorder test sets, indicating a certain degree of transferability. ConclusionThe benefits of PR-CoT supervision are mainly reflected in TCM semantic consistency and clinical plausibility, rather than in improved hard matching of structural elements. These findings support understanding syndrome manifestation recognition as a process of generating and expressing latent pathogenesis structures, rather than as a classification task within a traditional fixed label space. By introducing pathogenesis reasoning as an explicit intermediate structure into the modeling process and combining it with a progressive multidimensional evaluation framework, this study provides a methodological pathway for intelligent TCM syndrome differentiation that integrates theoretical alignment, interpretability, and multi-level evaluation.
3.Construction and Optimization of Alzheimer's Disease Classification Model Based on Brain Mixed Function Network Topology Parameters and Machine Learning
Xiao-yu HAN ; Xiu-zhu JIA ; Yang LI ; Meng-ying LOU ; Yong-qi NIE ; Xin-ping GUO ; Lu YU ; Zhi-yuan LI ; Lian-zheng SU
Progress in Modern Biomedicine 2025;25(11):1770-1778
Objective:To explore the interrelationship between brain functional networks and features in functional magnetic resonance imaging(fMRI)of patients with Alzheimer's disease(AD),and to construct mixed-function networks(MFN),and apply them in machine learning classification models to improve the accuracy of AD classification.Methods:102 AD patients and 227 healthy subjects in the Alzheimer's Neuroimaging Initiative(ADNI)dataset were retrospectively analyzed.The partial correlation brain network of the blood oxygen level dependent(BOLD)signal was calculated and fused with low-frequency wave amplitude(ALFF),fractional low-frequency wave amplitude(fALFF)and local consistency(ReHo)features to construct MFN.Network topology parameters were extracted,and a variety of machine learning classification models were constructed based on MFN topological parameters,accuracy,precision,recall and area under the curve(AUC)were used to evaluate the predictive efficiency of the models.Results:By constructed MFN and calculated intra group to inter group ratio(IIGR),35 features could be obtained from ALFF,fALFF and ReHo feature topological parameter analysis,after rank sum test and FDR correction,there were statistical differences among 28 features(P<0.05).The classification results show that,all the five classifiers have high classification performance on the test data set.The accuracy,precision and recall rates of random forest(RF),adaptive lifting algorithm(AdaBoost),guided aggregation algorithm(Bagging)and support vector machine(SVM)were all 99.7%,and the AUC values were up to 100%,99.5%,99.1%and 99.5%,respectively.The accuracy(98.5%),precision(98.5%),recall(98.5%),and AUC(99.1%)of the multi-layer perceptron(MLP)were slightly lower than other models,but remained excellent.It was worth noting that RF has the highest AUC value of all models at 100.0%,while Bagging has the lowest AUC value(99.1%)in the integrated approach.The results of performance comparison show that,MFN classification model can significantly improve the recognition and classification of AD disease,and greatly improve the performance of various indicators of the classifier.The results showed that,MFN classification model was superior to intelligent classification based fusion,DBN-based multitask learning,PVT-TSVM,unsupervised learning and clustering,SVM and SVM of degree 3 polynomial kernel function in key indicators such as accuracy(99.13%),AUC(99.42%),recall rate(99.46%)and specificity(99.42%)with plasma proteins,machine learning algorithms.It was further proved that MFN classification model has good generalization ability and robustness in AD disease classification.Conclusion:The AD classification model constructed based on brain mixed function network topology parameters and machine learning can improve the accuracy of AD classification.
4.A study on the practical effect of critical value management based on the goal and key result approach
Qing GUO ; Jie ZHOU ; Xiaoshuang YU ; Mingyang YANG ; Mengqi HAN ; Xin SONG ; Jing LI ; Jiaoqian YING
Modern Hospital 2025;25(6):865-868
Objective To explore the effectiveness of the OKR method in improving the efficiency of the whole process of critical value management,and to provide new ideas for the implementation of medical quality improvement in other medical insti-tutions.Methods A hospital in Tianjin was selected as the study object,which used the OKR method to reform the management of critical value since January 2024.The core goal of"improving the effectiveness of critical value management"was set,and the goal was broken down into quantitative key results such as"the rate of receiving the critical value system is over 95%"and"the rate of completing the standardised writing of medical records is up to 85%".Results After the reform,several quantitative key results,such as the completion rate of critical care medical record writing,the rate of standardised medical record writing,and the rate of overtime acceptance,were all better than before.Conclusion Through the OKR method to unify the whole hospital's strategic objectives,and the dynamic adjustment of the program based on data review,the hospital's critical value management efficiency has been significantly improved,effectively guaranteeing the safety of patients,and providing new perspectives and methods for the management of critical value in other medical institutions.
5.Astragaloside Ⅳ inhibits LPS-induced RAW 264.7 macrophage polarization and regulates their migration via cGAS/STING/NF-κB pathway
Chang-chao YANG ; Guo-ting LI ; Lin LIU ; Zi-xian ZHAO ; Wei-kang LI ; Qing-xin SUN ; Yu-ying ZHAO ; Jing-shan ZHAO
Chinese Pharmacological Bulletin 2025;41(7):1290-1297
Aim To explore the effect of astragalosideⅣ(AS-Ⅳ)on lipopolysaccharide(LPS)-induced po-larization and migration of RAW 264.7 macrophages and the underlying mechanism.Methods 1 mg·L-1 LPS was used to construct cell migration model.Scratch assay was utilized to determine cell migration rate.Immunofluorescence staining was utilized to de-tect the expression and location of F4/80,iNOS and Arg-1.CCK-8 assay was used to determine the viabili-ty of RAW 264.7 cells.Griess assay was used to measure NO content.Molecular docking was used to analyze the interaction between AS-Ⅳ and the core tar-gets such as cGAS and STING protein.Western blot was employed to detect the expression of iNOS,Arg-1,cGAS,STING,NF-κB p65 and p-NF-κB p65 protein.Results AS-Ⅳ significantly inhibited the migration and M1 polarization of RAW 264.7 cells induced by LPS.Moreover,AS-Ⅳ could interact with cGAS and STING protein,especially cGAS.Further Western blot assay showed that AS-Ⅳ significantly downregulated the expression of iNOS,cGAS,STING and p-NF-κB p65 protein.Conclusions AS-Ⅳ could promote mac-rophage M1 to M2 polarization,thereby inhibited mac-rophage migration through restraining the cGAS/STING/NF-κB signaling pathway,which provides a new therapeutic target for AS-Ⅳ to improve the early inflammatory response of AS.
6.CRISPR/Cas9 Technology:Exploring The Functions of lncRNAs and Their Roles in Cancer Progression
Xin LI ; Ying HU ; Yu-Ming WANG
Chinese Journal of Biochemistry and Molecular Biology 2025;41(3):364-375
The emergence of CRISPR/Cas system has greatly promoted the progress in the field of gene editing,especially CRISPR/Cas9 system,which has become a core tool in biomedical research.Long noncoding RNAs(lncRNAs)play a key role in gene regulation,cell differentiation and the development of a variety of diseases.Especially in cancer research,lncRNAs have important application prospects as cancer biomarkers and therapeutic targets.However,lncRNAs are generally characterized by low abun-dance and poor conservation,which limits the study of their functions by traditional means.CRISPR/Cas9 technology provides an efficient,flexible and accurate tool for lncRNA research,which significantly accelerates the progress in this field.This paper first reviews the basic principles of CRISPR/Cas9 system and its wide applications in gene editing,including CRISPR knockout,knock-in,interference,activation and other functional systems.These technologies can not only screen key lncRNAs in specific biological processes,but also be used for gene function research to explore their roles in diseases.This article focu-ses on the analysis of CRISPR/Cas9 technology in the study of lncRNA functions,regulatory mecha-nisms,and its key applications in tumor research.In addition,the article also summarizes the methods of genome-wide screening by CRISPR/Cas9 to identify functional lncRNAs,and discusses the roles of these lncRNAs in cancer cell proliferation,migration,invasion and drug resistance.CRISPR/Cas9 knockout system can efficiently knock down lncRNA genes and reveal their specific functions in gene regulation.At the same time,CRISPR activation and interference technology provide a new idea for the research of non-coding genes,and further explore its clinical application in cancer and other diseases by regulating the expression level of lncRNAs.The article also discusses the potential of CRISPR technology in future ln-cRNA research,especially the progress in solving technical problems such as genome complexity,targe-ting efficiency and off-target effects.As mentioned in the review,CRISPR/Cas9 technology not only pro-vides a powerful tool for studying lncRNAs,but also provides new ideas and opportunities for developing new means of cancer diagnosis and treatment in the future.
7.circHERC4_041 Inhibits the Fibrotic Phenotype of Cardiac Fibroblasts by Encoding Protein
Yuan GAO ; Chuan-Meng ZHOU ; Hua-Yan WU ; Ya WANG ; Ru-Shi WU ; Pei-Ying GUAN ; Jun-Tao FANG ; Jin-Dong XU ; Yu-Peng LIU ; Zhi-Qin HU ; Zhi-Xin SHAN
Chinese Journal of Biochemistry and Molecular Biology 2025;41(3):393-403
A mounting body of research suggests that circRNAs significantly contribute to the develop-ment of myocardial fibrosis.The microarray results of human circular RNA expression profile indicated that circHERC4_041 expression increased in the myocardium of patients with heart failure,RT-qPCR a-nalysis confirmed that the myocardial expression level of circHERC4_041 in individuals with heart failure were considerably elevated compared to that in healthy organ donors.Fluorescence in situ hybridization(FISH)confirmed that circHERC4_041 was abundant in the cytoplasm of human cardiomyocyte AC16.Overexpression of circHERC4_041 in mouse myocardial fibroblasts(mCFs)mediated by adenovirus in-hibited the expression of fibrosis-related proteins in mCFs.Experiments involving cell proliferation,wound healing,and Transwell assays demonstrated that overexpression of circHERC4_041 suppressed the growth and mobility of mCFs(P<0.001).Sequence analysis results suggested that circHERC4_041 con-tains potential ribosome entry sequence(IRES)and open reading frame(ORF).Western blot confirmed that circHERC4_041 could translate the 516 amino acid HERC4-516aa protein,which was mainly located in the cytoplasm of the cell.Cell functional experiments confirmed that circHERC4_041 inhibited the fi-brotic phenotype of mCFs by specifically translating HERC4-516aa(P<0.05).The specific interaction between HERC4-516aa and transglutaminase 2(TGM2)was confirmed by IP-MS screening and Co-IP i-dentification.Further results found that the degradation of TGM2 was promoted through proteasome path-way.The overexpression of TGM2 in mCFs facilitated by adenoviral vectors could counteract the suppres-sive effects of HERC4-516aa on the fibrotic phenotype of mCFs.Therefore,this study confirmed that the HERC4-516aa protein translated by circHERC4_041 can specifically bind to TGM2 to inhibit the fibrotic phenotype of myocardial fibroblasts.
8.MR ultrashort echo time and T1W sequences for detecting bone erosions of gouty arthritis
Tong YU ; Xiaoli LI ; Pei NIE ; Ying CHEN ; Lin HAN ; Meihan CHEN ; Fengjiao LI ; Xin HUANG ; Changgui LI ; Wenjian XU
Chinese Journal of Medical Imaging Technology 2025;41(3):452-456
Objective To compare the value of ultrashort echo time(UTE)and T1W sequences for detecting bone erosions of gouty arthritis.Methods Forty-four gouty patients were prospectively enrolled,including 32 cases with affected feet and 12 cases with affected knee.MR UTE and T1W sequence scanning of the affected area were performed,and subjectively scoring of imaging quality of 2 kinds of MRI were evaluated,respectively.Then total number and total score of bone erosions of each case were calculated according to all affected bones.Taken DECT as reference standard,the efficacy of UTE and T1WI for detecting bone erosions was assessed through comparing with DECT using Kappa coefficient.Results The imaging quality score of T1WI was lower than that of DECT(all P<0.05),while no significant difference was found between UTE and DECT(all P>0.05).There was high agreement between UTE and DECT for detecting bone erosions(κ=0.949),while the agreement between T1WI and DECT ranged from good to high(κ=0.718 to 0.805).The total number and total score of bone erosions based on T1WI were significantly lower than those based on DECT(all P<0.05),while no significant difference was found between UTE and DECT(all P>0.05).Conclusion UTE was better than T1WI for detecting bone erosions of gouty arthritis.
9.Research hotspots and trends of functional cure of hepatitis B based on bibliometric analysis
Qi-ran ZHANG ; Bing CAO ; Ji-bin XIN ; Li-jun WU ; Yu-lei SUN ; Jun YING ; Wen-hong ZHANG
Fudan University Journal of Medical Sciences 2025;52(2):159-170
Objective To analyze the global literature related to functional cure of hepatitis B from 2019 to 2023 by using bibliometric analysis methods,so as to help researchers understand the research hotspots and trends in this field.Methods The literature related to the topic of functional cure of hepatitis B included in the Science Citation Index Expanded(SCI-Expanded)of the Web of Science Core Collection from 2019 to 2023 was searched.By using VOSviewer and CiteSpace visual analysis tools,analyses were conducted from the perspectives of publication trends,international research cooperation networks,and keyword emergence,and were elaborated with the specific contents of the related literature to elucidate research hotspots and trends.Results A total of 600 eligible papers in this field were included.Keyword co-occurrence and thematic clustering suggested that the main research directions of functional cure were:serum biomarkers for prediction and monitoring of functional cure,functional cure and immunity,nucleoside analog discontinuation,interferon therapy,and long-term prognosis of functional cure.The research contents of the ESI highly cited original research papers were similar to the clustering of the above,but showed more attention on the novel agents for functional cure.The content of the keyword emergence map showed that hotspots of interest changed from virologic mechanisms and serum markers,to nucleoside analog discontinuation and interferon therapy,and finally to immunologic mechanisms and new drug.Conclusion The research hotspots and trends of functional cure of hepatitis B were focused on virological mechanism,serum markers,immunological mechanism,nucleoside analog discontinuation,interferon therapy,and long-term prognosis after cure.
10.Current status,hotspots and prospects of research on liver failure caused by viral hepatitis:a bibliometric and visualization-based analysis
Xiang-yu QIN ; Bing CAO ; Ji-bin XIN ; Li-jun WU ; Jian-ming ZHENG ; Jun YING
Fudan University Journal of Medical Sciences 2025;52(2):180-189
Objective To conduct a bibliometric analysis of relevant literature on liver failure caused by viral hepatitis from the past five years,and to help researchers understand the current status and hotspots in this field,and to provide insights into future research trends.Methods Based on the Science Citation Index Expanded(SCI-Expanded)data from Web of Science Core Collection,visualization analysis and mapping were conducted through VOSviewer and CiteSpace software to generate visual representations of international research collaboration networks,keyword co-occurrence clustering,and keyword bursts.Results From 2019 to 2023,a total of 873 relevant literature were included,with a total citation frequency of 7 364 and an average citation frequency of 8.44.Among them,China had the highest number of publications(458 articles,52.46%)and had the most cooperation with the United States.The research hotspots of viral hepatitis induced liver failure were mainly divided into three categories:basic and clinical research on liver failure caused by non-hepatitis B virus(HBV),the pathogenesis of HBV related liver failure,and treatment and prediction models of liver failure.The keyword time overlay map and burst map showed that the research hotspots had gradually shifted from the prevention and control of new infections to the treatment and prognosis assessment of patients with chronic infection.Conclusion China is a major international research entity in liver failure caused by viral hepatitis and actively participates in international scientific collaborations.The research hotspots on liver failure caused by viral hepatitis have gradually shifted from preventing viral hepatitis infections and expanding treatment options to the treatment of chronic infection patients and prognostic prediction.

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