1.Computational pathology in precision oncology: Evolution from task-specific models to foundation models.
Yuhao WANG ; Yunjie GU ; Xueyuan ZHANG ; Baizhi WANG ; Rundong WANG ; Xiaolong LI ; Yudong LIU ; Fengmei QU ; Fei REN ; Rui YAN ; S Kevin ZHOU
Chinese Medical Journal 2025;138(22):2868-2878
With the rapid development of artificial intelligence, computational pathology has been seamlessly integrated into the entire clinical workflow, which encompasses diagnosis, treatment, prognosis, and biomarker discovery. This integration has significantly enhanced clinical accuracy and efficiency while reducing the workload for clinicians. Traditionally, research in this field has depended on the collection and labeling of large datasets for specific tasks, followed by the development of task-specific computational pathology models. However, this approach is labor intensive and does not scale efficiently for open-set identification or rare diseases. Given the diversity of clinical tasks, training individual models from scratch to address the whole spectrum of clinical tasks in the pathology workflow is impractical, which highlights the urgent need to transition from task-specific models to foundation models (FMs). In recent years, pathological FMs have proliferated. These FMs can be classified into three categories, namely, pathology image FMs, pathology image-text FMs, and pathology image-gene FMs, each of which results in distinct functionalities and application scenarios. This review provides an overview of the latest research advancements in pathological FMs, with a particular emphasis on their applications in oncology. The key challenges and opportunities presented by pathological FMs in precision oncology are also explored.
Humans
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Precision Medicine/methods*
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Medical Oncology/methods*
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Artificial Intelligence
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Neoplasms/pathology*
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Computational Biology/methods*
2.Expert consensus on evaluation index system construction for new traditional Chinese medicine(TCM) from TCM clinical practice in medical institutions.
Li LIU ; Lei ZHANG ; Wei-An YUAN ; Zhong-Qi YANG ; Jun-Hua ZHANG ; Bao-He WANG ; Si-Yuan HU ; Zu-Guang YE ; Ling HAN ; Yue-Hua ZHOU ; Zi-Feng YANG ; Rui GAO ; Ming YANG ; Ting WANG ; Jie-Lai XIA ; Shi-Shan YU ; Xiao-Hui FAN ; Hua HUA ; Jia HE ; Yin LU ; Zhong WANG ; Jin-Hui DOU ; Geng LI ; Yu DONG ; Hao YU ; Li-Ping QU ; Jian-Yuan TANG
China Journal of Chinese Materia Medica 2025;50(12):3474-3482
Medical institutions, with their clinical practice foundation and abundant human use experience data, have become important carriers for the inheritance and innovation of traditional Chinese medicine(TCM) and the "cradles" of the preparation of new TCM. To effectively promote the transformation of new TCM originating from the TCM clinical practice in medical institutions and establish an effective evaluation index system for the transformation of new TCM conforming to the characteristics of TCM, consensus experts adopted the literature research, questionnaire survey, Delphi method, etc. By focusing on the policy and technical evaluation of new TCM originating from the TCM clinical practice in medical institutions, a comprehensive evaluation from the dimensions of drug safety, efficacy, feasibility, and characteristic advantages was conducted, thus forming a comprehensive evaluation system with four primary indicators and 37 secondary indicators. The expert consensus reached aims to encourage medical institutions at all levels to continuously improve the high-quality research and development and transformation of new TCM originating from the TCM clinical practice in medical institutions and targeted at clinical needs, so as to provide a decision-making basis for the preparation, selection, cultivation, and transformation of new TCM for medical institutions, improve the development efficiency of new TCM, and precisely respond to the public medication needs.
Medicine, Chinese Traditional/standards*
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Humans
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Consensus
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Drugs, Chinese Herbal/therapeutic use*
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Surveys and Questionnaires
3.Research progresses on the mechanism of macrophages in tendon bone healing.
Liang WANG ; Yinshuan DENG ; Tao QU ; Chaoming DA ; Yunfei HE ; Rui LIU ; Weimin NIU ; Weishun YAN ; Zhen CHEN ; Shuo LI ; Zhiyun YANG ; Binbin GUO ; Xueqian LAI
Chinese Journal of Cellular and Molecular Immunology 2025;41(2):183-187
The connection between tendons and bones is called the tendon bone connection. With the continuous improvement of national sports awareness, excessive exercises and the related intensity are prone to damage the tendon bone connection. Tendon bone healing is a complex repair and healing process involving multiple factors, and good tendon bone healing is a prerequisite for its physiological function. The complexity of tendon bone structure also poses great challenges to the repair of tendon bone injuries. In recent years, researches have found that stem cells, growth factors, macrophages, and other factors are closely related to the healing process of tendon bone injuries, among which macrophages play an important role in the healing process. The authors reviewed relevant research literature in recent years and summarized the role of macrophages in tendon bone healing, in order to provide new ideas and directions for treatment strategies to promote tendon bone healing.
Humans
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Macrophages/metabolism*
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Wound Healing
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Animals
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Tendons/physiology*
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Bone and Bones/injuries*
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Tendon Injuries
4.Expression and Clinical Significance of Co-inhibitory Molecules TIGIT/CD155 and PD-1 in Chronic Lymphocytic Leukemia.
Rui ZHANG ; Shuang CHEN ; Ting-Ting LUO ; Jian-Hua QU
Journal of Experimental Hematology 2025;33(1):54-61
OBJECTIVE:
To investigate the expression of co-inhibitory molecules TIGIT/CD155 and PD-1 on CD4+T cells and Treg cells in peripheral blood of patients with chronic lymphocytic leukemia (CLL) and analyze their clinical significance.
METHODS:
The expression of PD-1 and TIGIT on CD4+T cells and Treg cells was detected by flow cytometry in 40 CLL patients and 20 healthy controls. Additionally, the expression of CD155 on peripheral blood B cells and DC cells of the enrolled subjects was detected.
RESULTS:
The proportions of PD-1+TIGIT+CD4+T cells, PD-1+TIGIT+Treg cells and CD155+DC cells in peripheral blood of CLL patients were significantly higher than those of healthy controls ( P < 0.05). The proportions of PD-1+TIGIT+CD4+T cells and PD-1+TIGIT+Treg cells in CLL patients were significantly higher than those of PD-1+TIGIT-CD4+T cells and PD-1+TIGIT-Treg cells, respectively ( P < 0.05). Both PD-1+TIGIT+CD4+T cells and PD-1+TIGIT+Treg cells were positively correlated with the level of CD155+DC cells (r =0.742, r =0.766). With the progression of Binet stage, the proportions of PD-1+TIGIT+CD4+T cells, PD-1+TIGIT+Treg cells, and CD155+DC cells gradually increased ( P < 0.05), and the aforementioned three types cells were all increased in patients with CD38≥30%, IGVH unmutated, or poor prognosis due to chromosomal abnormalities ( P < 0.05).
CONCLUSION
Co-inhibitory molecules PD-1 and TIGIT may be involved in immunodepletion in patients with advanced CLL, which has clinical prognostic value. Dual inhibitor molecular targeted therapy provides a new direction for the individualized treatment of CLL.
Humans
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Leukemia, Lymphocytic, Chronic, B-Cell/immunology*
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Receptors, Immunologic/metabolism*
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Programmed Cell Death 1 Receptor/metabolism*
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T-Lymphocytes, Regulatory/metabolism*
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Receptors, Virus/metabolism*
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CD4-Positive T-Lymphocytes/metabolism*
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Male
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Female
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Middle Aged
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Flow Cytometry
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Clinical Relevance
5.Genetic and clinical phenotypic analysis of Usher syndrome-associated gene variants.
Heng ZHAO ; Xiuli MA ; Yanli QU ; Guo LI ; Ken LIN ; Rui HUANG ; Lijuan ZHOU ; Jing MA
Journal of Clinical Otorhinolaryngology Head and Neck Surgery 2025;39(8):736-742
Objective:To investigate the molecular characteristics and clinical heterogeneity of Usher syndrome(USH) -related gene variants in patients with hereditary hearing loss in southwest China, providing a basis for early diagnosis and clinical management. Methods:Thirteen patients from twelve families with hearing loss who attended the Affiliated Children's Hospital of Kunming Medical University between January 2017 and March 2021 were enrolled. All patients were identified as carrying USH-related gene variants through next-generation sequencing. Sanger sequencing was performed for all patients and their parents to validate the pathogenic variants. Comprehensive clinical evaluations, including medical history collection, otologic and ophthalmologic examinations, and vestibular function assessments, were conducted. Results:Among the 13 patients, 4 were diagnosed with USH type 1 and 2 with USH type 2. A total of 19 pathogenic or likely pathogenic variants were detected in USH-related genes, including MYO7A,CDH23,USH1C, and USH2A. The causative gene was MYO7A in 3 probands, CDH23 in 5, USH1C in 3, and USH2Ain 2. All patients exhibited an autosomal recessive inheritance pattern. Vestibular dysfunction was observed in 4 patients, and retinitis pigmentosa(RP) in 3 patients. Based on the genotype-phenotype correlation, 6 patients were initially diagnosed with USH, while 7 were classified as having non-syndromic hearing loss(NSHL). Conclusion:This study revealed the clinical heterogeneity of USH-related gene variants in patients with hereditary deafness in southwest China. Although the clinical manifestations of USH are complex and there are overlapping characteristics between different subtypes, genetic testing provides an important basis for early diagnosis and precise clinical management. Especially for those with typical hearing loss, early genetic diagnosis can provide a window of time for early detection and intervention of retinitis pigmentosa.
Humans
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Usher Syndromes/genetics*
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Myosin VIIa
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Phenotype
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Male
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Female
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Myosins/genetics*
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Mutation
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Cadherins/genetics*
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Child
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Extracellular Matrix Proteins/genetics*
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Adolescent
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Pedigree
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High-Throughput Nucleotide Sequencing
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Cadherin Related Proteins
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Cytoskeletal Proteins
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Cell Cycle Proteins
6.Identification and expression analysis of β-amylase gene family members in alfalfa under saline-alkali stress.
Hongyu QU ; Lishuang ZHANG ; Yahui TANG ; Lei LIU ; Rui GUO ; Weileng GUO ; Changhong GUO
Chinese Journal of Biotechnology 2025;41(2):719-735
Beta-amylases (BAMs), key enzymes in starch hydrolysis, play an important role in plant growth, development, and resistance to abiotic stress. To mine the saline-alkali tolerance-related BAM genes in alfalfa (Medicago sativa L.), we identified MsBAM genes in the whole genome. The physicochemical properties, phylogeny, gene structures, conserved motifs, secondary structures, promoter cis-acting elements, chromosome localization, and gene replication relationships of BAM gene family members were analyzed. RNA-seq and quantitative real-time PCR (qRT-PCR) were employed to analyze the expression patterns of BAM family members under saline-alkali stress. The results showed that 54 BAM genes were identified in the genome, which were classified into 8 subgroups according to the phylogenetic tree. The members of the same subgroup had similar gene structures except that those of subgroups 1 and 7 had large differences. Conserved motif analysis showed that all MsBAM proteins had a typical glycohydrolysis domain. The chromosome localization analysis showed that MsBAM gene family members were unevenly distributed on 27 chromosomes. The duplication of gene segments led to the increase in BAM gene number in alfalfa. The promoters of BAM genes contained a large number of elements in response to plant hormones and stress. Transcriptome data and qRT-PCR results showed that the expression levels of most MsBAM genes were up-regulated in response to saline-alkali stress. Under the saline-alkali stress, the expression levels of 28 genes, including MsBAM6, were up-regulated on days 1 and 7, and those of 5 genes, including MsBAM9, were up-regulated by over 2 folds. In addition, under salt-alkali stress, BAM activity and soluble sugar content were significantly increased. These results indicate that BAM genes play a key role in alfalfa in response to saline-alkali stress, laying a foundation for further research in this field.
Medicago sativa/physiology*
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beta-Amylase/metabolism*
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Phylogeny
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Gene Expression Regulation, Plant
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Stress, Physiological/genetics*
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Multigene Family
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Alkalies
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Plant Proteins/genetics*
7.The taste correction process of ibuprofen oral solution based on the combination of electronic tongue technology and artificial taste comprehensive evaluation
Rui YUAN ; Yun-ping QU ; Yan WANG ; Ya-xuan ZHANG ; Wan-ling ZHONG ; Xiao-yu FAN ; Hui-juan SHEN ; Yun-nan MA ; Jin-hong YE ; Jie BAI ; Shou-ying DU
Acta Pharmaceutica Sinica 2024;59(8):2404-2411
This experiment aims to study the taste-masking effects of different kinds of corrigent used individually and in combination on ibuprofen oral solution, in order to optimize the taste-masking formulation. Firstly, a wide range of corrigent and the mass fractions were extensively screened using electronic tongue technology. Subsequently, a combination of sensory evaluation, analytic hierarchy process (AHP)-fuzzy mathematics evaluation, and Box-Behnken experimental design were employed to comprehensively assess the taste-masking effects of different combinations of corrigent on ibuprofen oral solution, optimize the taste-masking formulation, and validate the results. The study received ethical approval from the Review Committee of the Beijing University of Chinese Medicine (ethical code: 2024BZYLL0102). The results showed that corrigent fractions and types were screened separately through single-factor experiments. Subsequently, a Box-Behnken response surface design combined with AHP and fuzzy mathematics evaluation was used to fit a functional model:
8.Visualization of nasal powder distribution using biomimetic human nasal cavity model.
Jiawen SU ; Yan LIU ; Hongyu SUN ; Abid NAEEM ; Huipeng XU ; Yue QU ; Caifen WANG ; Zeru LI ; Jianhua LU ; Lulu WANG ; Xiaofeng WANG ; Jie WU ; Lixin SUN ; Jiwen ZHANG ; Zhigang WANG ; Rui YANG ; Li WU
Acta Pharmaceutica Sinica B 2024;14(1):392-404
Nasal drug delivery efficiency is highly dependent on the position in which the drug is deposited in the nasal cavity. However, no reliable method is currently available to assess its impact on delivery performance. In this study, a biomimetic nasal model based on three-dimensional (3D) reconstruction and three-dimensional printing (3DP) technology was developed for visualizing the deposition of drug powders in the nasal cavity. The results showed significant differences in cavity area and volume and powder distribution in the anterior part of the biomimetic nasal model of Chinese males and females. The nasal cavity model was modified with dimethicone and validated to be suitable for the deposition test. The experimental device produced the most satisfactory results with five spray times. Furthermore, particle sizes and spray angles were found to significantly affect the experimental device's performance and alter drug distribution, respectively. Additionally, mometasone furoate (MF) nasal spray (NS) distribution patterns were investigated in a goat nasal cavity model and three male goat noses, confirming the in vitro and in vivo correlation. In conclusion, the developed human nasal structure biomimetic device has the potential to be a valuable tool for assessing nasal drug delivery system deposition and distribution.
9.Changes in serum immunoglobulin levels in children with thalassemia who undergo repeated blood transfusions and their correlation with delayed hemolytic transfusion reactions
Xiaohong JIN ; Meikun HU ; Rui CHEN ; Lilan GAO ; Shuxia WANG ; Mengxing LYU ; Kexuan QU
Chinese Journal of Blood Transfusion 2024;37(5):548-555
Objective To study the changes in serum immunoglobulin levels in children with thalassemia who undergo repeated blood transfusions and explore their correlation with delayed hemolytic transfusion reactions(DHTR).Methods Serum samples from children with thalassemia who received blood transfusion treatment from June 2022 to April 2023(ob-servation group)and healthy children who underwent physical examination(control group)in our hospital were collected.The levels of serum immunoglobulins(IgG subtype,IgM,IgA,IgE and IgD)were detected using flow cytometry CBA multi-factor quantitative detection technology,and the differences between the two groups were compared.The children were divided into 4 groups according to different transfusion numbers:≤10 numbers,11-30 numbers,31-50 numbers and>50 numbers,and the differences between different blood transfusion numbers and serum immunoglobulin levels in each group were compared using one-way analysis of variance(ANOVA).Children with thalassemia with DHTR were in the hemolysis group,and children with thalassemia who did not experience DHTR were in the non-hemolysis group.The changes in serum immunoglobulins(IgG subtypes,IgM,IgA,IgE and IgD)between the two groups were compared to explore the correlation between serum immunoglobulins in thalassemia children with repeated transfusion and DHTR.Results The levels of IgG1,IgG3,IgG4 and IgA in the observation group were significantly higher than those in the control group,with the increase of(2.07±2.12),(0.67±2.03),(0.30±0.37)and(6.04±11.40)mg/mL,respectively,while the level of IgD in observation group was significantly lower than that in the control group,with a decrease of(0.03±0.01)mg/mL,P<0.05.No significant difference was noticed in IgG2,IgM and IgE between the groups(P>0.05).IgG1 and IgG4 both significantly increased with the number of blood transfusions.The IgG1 in the 4 groups increased sequentially as(0.30±0.62),(0.41±0.51)and(3.60±3.48)mg/mL,and IgG4 increased sequentially as(0.12±0.13),(0.22±0.07)and(0.21±0.38)mg/mL.IgG2,IgM and IgD showed a significant decrease,with IgG 2,IgM,and IgD in four groups decreased as(0.91±1.50),(0.14±0.10)and(0.05±0.05)mg/mL,respectively,showing significant differences with the number of blood transfusions(P<0.05).No sig-nificant difference was found in IgG3,IgA and IgE with different number of transfusions(P>0.05).IgG1,IgG3 and IgG4 in the hemolysis group were significantly higher than those in the non-hemolysis group,with an increase of(4.44±3.41),(0.73±1.26)and(0.52±0.40),respectively(P<0.05).IgD in the hemolysis group was significantly lower than that in the non-hemolysis group,with a decrease of(0.00±0.06)mg/mL,P<0.05.No significance was noticed in IgG2,IgM,IgA and IgE between the hemolysis group and the non-hemolysis group(P>0.05).Conclusion The serum immunoglobulin levels of children with thalassemia who undergo repeated blood transfusions are abnormal.There are differences in correlation between the number of blood transfusions and serum immunoglobulin levels among children with thalassemia who undergo repeated blood transfusions.The relevant serum immunoglobulins for DHTR in children with thalassemia who undergo repeated blood transfusions are IgG1,IgG3 and IgG4.
10.IL2rg-/- rats support prolonged infection of human RSV
Rui XIONG ; Yong WU ; Yanwei YANG ; Zhe QU ; Susu LIU ; Yuya WANG ; Liying MA ; Rui FU ; Yihong PENG ; Chunnan LIANG ; Changfa FAN
Acta Laboratorium Animalis Scientia Sinica 2024;32(1):17-24
Objective To overcome the limitations of existing human respiratory syncytial virus(hRSV)animal models,such as semi-permissiveness and short duration of infection,this study established an IL2rg gene knockout(IL2rg-/-)rat model using TALEN gene editing technology.Methods The animal model was infected with hRSV intranasally.Clinical characteristics,body weight,and temperature changes were observed over the infection period(0~35 days).The total viral loads in respiratory organs,such as the nasal tissue,trachea,and lungs,were measured at various time points(4,11,20,and 35 days post-infection).Pathological analysis was conducted on target organs at the endpoint of observation(35 days post-infection).Changes in peripheral blood T,B,NK,and NKT cells and various cytokines were assessed at various time points(4,20,and 35 days post-infection).Results(1)IL2rg/-knockout rats sustained high viral loads in the nasal cavity upon intranasal inoculation with hRSV.The average peak titer rapidly reached 1 × 1010 copies/g in nasal tissue and 1 × 107 copies/g up to 5 weeks post-infection.(2)However,no significant pathological changes were noted in nasal,tracheal,or lung tissues.(3)An increase was observed in the content of peripheral blood B cells in hRSV-infected IL2rg--rats.(4)IL-6 and MCP-1 were increased in the early stage of infection and then decreased at the end of the observation period.Conclusions This study established a new IL2rg-/-rat model using TALEN technology and found that this model effectively supported high-level replication and long-term infection of hRSV,providing a good basis for antiviral drug screening and in vivo efficacy evaluation of anti-hRSV antibodies.

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