1.Applications of artificial intelligence in the research of molecular mechanisms of traditional Chinese medicine formulas.
Hongyu CHEN ; Ruotian TANG ; Mei HONG ; Jing ZHAO ; Dong LU ; Xin LUAN ; Guangyong ZHENG ; Weidong ZHANG
Chinese Journal of Natural Medicines (English Ed.) 2025;23(11):1329-1341
Traditional Chinese medicine formula (TCMF) represents a fundamental component of Chinese medical practice, incorporating medical knowledge and practices from both Han Chinese and various ethnic minorities, while providing comprehensive insights into health and disease. The foundation of TCMF lies in its holistic approach, manifested through herbal compatibility theory, which has emerged from extensive clinical experience and evolved into a highly refined knowledge system. Within this framework, Chinese herbal medicines exhibit intricated characteristics, including multi-component interactions, diverse target sites, and varied biological pathways. These complexities pose significant challenges for understanding their molecular mechanisms. Contemporary advances in artificial intelligence (AI) are reshaping research in traditional Chinese medicine (TCM), offering immense potential to transform our understanding of the molecular mechanisms underlying TCMFs. This review explores the application of AI in uncovering these mechanisms, highlighting its role in compound absorption, distribution, metabolism, and excretion (ADME) prediction, molecular target identification, compound and target synergy recognition, pharmacological mechanisms exploration, and herbal formula optimization. Furthermore, the review discusses the challenges and opportunities in AI-assisted research on TCMF molecular mechanisms, promoting the modernization and globalization of TCM.
Artificial Intelligence
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Drugs, Chinese Herbal/pharmacokinetics*
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Humans
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Medicine, Chinese Traditional
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Animals
2.Oral health-related quality of life status and risk factors in patients with mental disorders.
Xuemei YANG ; Hongyu WANG ; Yonghua TANG ; Chengjun YIN ; Jingya YU ; Xiaoqin BI
West China Journal of Stomatology 2025;43(1):84-91
OBJECTIVES:
This study aims to explore the current status and risk factors of oral health-related quality of life OHRQoL in patients with mental disorders and provide evidence for effective intervention measures.
METHODS:
A total of 397 patients diagnosed with mental illness were selected by convenience sampling, and investigation was carried out using general data questionnaire, health literacy in dentistry-14 (HeLD-14), oral health impact profile-14 (OHIP-14), and oral health status checklist.
RESULTS:
The total score of OHIP-14 in patients with mental disorders was 8(2, 14). The score of HeLD-14 was negatively correlated with the score of OHIP-14 (r=-0.142, P<0.01). The results of multiple linear regression showed that six variables including annual family income, schizophrenia, sweets, frequency of visits to the dentist, dental caries, and missing teeth affected OHRQoL of patients with mental disorders (P<0.05).
CONCLUSIONS
The poor OHRQoL of psychiatric patients is associated with many factors. Medical personnel should pay attention to their oral health problems and develop targeted oral care programs throughout the course of disease to improve oral health and related quality of life of patients.
Humans
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Quality of Life
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Oral Health
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Mental Disorders
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Risk Factors
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Surveys and Questionnaires
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Male
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Female
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Dental Caries
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Adult
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Middle Aged
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Schizophrenia
3.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*
4.Effect of enriched environment combined with acupuncture at head points on behavior in rats with autism spectrum disorder
Zichen MU ; Qiang TANG ; Yunqiu SHI ; Yan WANG ; Shuwei ZHU ; Ya'nan ZHUANG ; Danshuang XU ; Hongyu LI ; Baolong LI ; Chunyan ZHANG ; Mengke YUAN
Chinese Journal of Rehabilitation Theory and Practice 2024;30(2):176-182
ObjectiveTo observe the effect of enriched environment (EE) combined with acupuncture at head point (HA) on behavior in rats with autism spectrum disorder. MethodsHealthy female Wistar rats were given peritoneal injection of sodium valproate at 12.5 days of gestation. Twenty-four male offspring rats were randomly selected and then randomly divided into model group (n = 6), EE group (n = 6), HA group (n = 6) and EE combined with HA group (the combined group, n = 6). Six male offspring rats born from female mice injected with the same amount of saline intraperitoneally were as control group. After four weeks of treatment, all the five groups were tested with three-chamber test and marble burying test, and the sociability index, the social novelty index and the number of buried marbles were recorded. The levels of interleukin (IL)-1β and IL-6 in peripheral blood were determined by enzyme-linked immunosorbent assay (ELISA). ResultsAfter treatment, compared with the model group, the sociability index and the social novelty index improved (P < 0.05), the number of buried marbles reduced (P < 0.05), and the levels of IL-6 and IL-1β in peripheral blood decreased in EE group, HA group and the combined group (P < 0.05); while the combined group was the best (P < 0.01). ConclusionBoth EE or acupuncture at HA could improve behavioral symptoms, and reduce the expression of inflammatory factors in rats with autism spectrum disorder. The combination of the two methods showed the best result.
5.Effect of Xiaoxuming decoction on OGD/R-induced synaptic plasticity in HT22 cells
Manman WANG ; Rui LAN ; Yong ZHANG ; Xueqin FU ; Xuhuan ZOU ; Weiwei WANG ; Hongyu LI ; Chen TANG ; Shuang LIU
Chinese Journal of Pathophysiology 2024;40(1):126-133
AIM:To explore the protective effect of Xiaoxuming decoction(XXMD)on synaptic plasticity in the context of cerebral ischemia-reperfusion injury following ischemic stroke.METHODS:An oxygen-glucose depriva-tion/reoxygenation(OGD/R)model was employed in vitro using mouse hippocampal neurons(HT22 cells)to simulate ischemia-reperfusion injury.Cell viability was assessed using a CCK-8 assay to determine the optimal XXMD concentra-tion.The HT22 cells were divided into two groups:control and model(OGD/R).Cellular morphological changes were ob-served using an inverted microscope.The levels of IL-1β,IL-6 and TNF-α in the supernatant were quantified by ELISA.Ultrastructural changes were examined by transmission electron microscopy.Immunofluorescence staining was used to de-tect neuron markers NeuN and synaptic proteins NF200 and MAP2.The protein levels of NF200 and MAP2 were analyzed by Western blot.RESULTS:The highest cell survival rate occurred at an XXMD concentration of 100 mg/L(P<0.05).Compared with control group,the cells in model group exhibited round shape and shrinkage,mitochondrial swelling or vacuolization,and a marked decrease in survival rate.There were significant increases in IL-1β,IL-6 and TNF-α levels(P<0.05).Immunofluorescence intensity and protein levels of NeuN,NF200 and MAP2 were notably reduced(P<0.05).Treatment with XXMD improved cell morphology,ultrastructure and survival rate(P<0.05),and decreased in-flammatory factor levels(P<0.05).Compared with model group,the cells in OGD/R+XXMD group showed significantly increased immunofluorescence intensity and protein levels of NeuN,NF200 and MAP2(P<0.05).CONCLUSION:Xiaoxuming decoction may mitigate OGD/R-induced injury,potentially by inhibiting inflammatory responses and enhanc-ing synaptic plasticity.
6.Research progress of berberine in the field of neuroprotection in ischemic stroke
Hongyu LI ; Rui LAN ; Manman WANG ; Weiwei WANG ; Yong ZHANG ; Chen TANG ; Shuang LIU
Chinese Journal of Comparative Medicine 2024;34(2):129-136
Berberine is a natural isoquinoline alkaloid that was initially used as a broad-spectrum antibacterial agent in clinical treatment of enteritis,peptic ulcers,chronic gastritis,pneumonia,and other diseases.In recent years,in-depth study of the pharmacological effects of berberine has provided increasing evidence that berberine has neuroprotective effects on ischemic stroke.In this review,we introduce the effect of berberine on risk factors of ischemic stroke and discuss the neuroprotective effects of berberine on various mechanisms of ischemic stroke in detail to provide a reference for clinical and basic research in this field.
7.Analysis of co-expressed genes in myocardial ischemia-reperfusion injury and necrotic apoptosis utilizing bioinformatics
Yaowei ZHAO ; Hongyu LI ; Xiyuan MA ; Xianghong MENG ; Qiang TANG
Journal of China Medical University 2024;53(1):67-74
Objective To identify and validate co-expressed genes associated with myocardial ischemia/reperfusion injury(MI/RI)and necrotic apoptosis by bioinformatics analysis.Methods Gene expression profile data for MI/RI were obtained by GSE67308 and GSE19875 datasets from the Gene Expression Omnibus(GEO)database.Differential expression analysis was conducted on the GSE67308 dataset to identify differentially expressed genes(DEGs),followed by gene set enrichment analysis and biological pathway analysis.More-over,immune cell infiltration analysis was performed on the GSE67308 dataset.Necrotic apoptosis-related genes were retrieved from the Molecular Signatures Database and the Kyoto Encyclopedia of Genes and Genomes(KEGG).A protein-protein interaction(PPI)network was constructed by overlapping DEGs with these necrotic apoptosis-related genes to identify key genes.Furthermore,the expression pat-terns of these key genes across various cardiac cell types were analyzed using a single-cell sequencing analysis platform,and validation of key gene expression was performed using the GSE19875 dataset.Results A total of 1054 DEGs were identified,comprising 363 upregu-lated and 691 downregulated genes.Gene enrichment analysis revealed that DEGs were primarily associated with processes related to apoptosis,immune responses,and intracellular signaling regulation.Moreover,biological pathway analysis demonstrated that DEGs were predominantly involved in the regulation of signaling pathways such as tumor necrosis factor(TNF)and NF-κB.Immune infiltration anal-ysis indicated a high degree of immune infiltration,particularly with natural killer cells and monocytes,in MI/RI myocardial tissue.PPI network analysis identified Il1b,TNF,Birc3,and Ripk1as crucial genes in the context of necrotic apoptosis.Single-cell sequencing anal-ysis showed the elevated expression of key genes within white blood cells.In comparison to the control group,the MI/RI model group in the GSE19875 dataset exhibited significantly increased expression of Il1b,TNF,Birc3,and Ripk1(P<0.01).Conclusion MI/RI is strongly correlated with the TNF signaling pathway and the NF-κB signaling pathway,both of which play pivotal roles in regulating necrotic apop-tosis.Il1b,TNF,Birc3,and Ripk1emerge as key genes that concurrently regulate both MI/RI and necrotic apoptosis.It is plausible that IL-1b,TNF,Birc3,and Ripk1 may serve as critical regulatory factors in the context of necrotic apoptosis during MI/RI.
8.Research advances in the pathogenesis of abnormal copper metabolism in Parkinson's disease
Huijie YANG ; Rui LAN ; Manman WANG ; Weiwei WANG ; Hongyu LI ; Chen TANG ; Shuang LIU ; Jieli YANG ; Xiaoming SHEN
Chinese Journal of Comparative Medicine 2024;34(10):118-124
Parkinson's disease is a neurodegenerative disease associated with abnormal copper metabolism in the brain,which leads to misfolding and aggregation of α-synuclein-copper complexes,which is an important pathological sign of Parkinson's disease.Copper metabolism,i.e.,cellular metabolic processes involving copper ions,is closely related to the pathogenesis of α-synuclein aggregation,dopamine metabolism,mitochondrial dysfunction,oxidative stress,and ferroptosis in Parkinson's disease.In this review,we summarize the molecular metabolic mechanism of copper toxicity by studying the pathological role of copper metabolism in Parkinson's disease,to support our further understanding of the mechanism of action and drug development.
9.Hip joint movement during a step′s swing phase is cases of hemiplegia with foot drop
Luping CHEN ; Qing XIA ; Lingling DU ; Hongyu ZHANG ; Lu WEI ; Zewen TANG
Chinese Journal of Physical Medicine and Rehabilitation 2024;46(7):635-640
Objective:To analyze hip joint movement during the swing phase of the strides of stroke survivors with hemiplegia and foot drop.Methods:Thirty stroke survivors with hemiplegia and foot drop formed the observation group, while thirty matched healthy counterparts were the control group. A three-dimensional gait analysis system was used to compare the hip and ankle joint kinematics on the hemiplegic side of the observation group members with those on the corresponding side of a matched control. Pearson correlation related the maximum plantar flexion angle of the ankle and hip joints in the observation group.Results:Compared with the control group, there was a significant increase in the maximum abduction and external rotation of the hip joint during the swing phase, but a significant decrease in the maximum extension, flexion, adduction, internal rotation. The range of motion of the hip joint in the sagittal, frontal and horizontal planes was significantly smaller, as was the maximum dorsiflexion and sagittal range of motion of the ankle joint. The maximum plantar flexion angle of the ankle was positively correlated with the hip joint′s maximum flexion, maximum external rotation and sagittal joint motion, but negatively correlated with the hip′s horizontal motion.Conclusion:In stroke survivors with hemiplegia and ptosis, significant changes are observed in the three-dimensional motion during the swing phase of a stride. The mode of hip joint compensation changes depending on the severity of the foot drop.
10.Study on the relationship between anti-gp210, anti-sp100 antibodies and clinical features and prognosis of patients with primary biliary cholangitis
Jingyi ZHANG ; Juan FENG ; Hongyu ZHANG ; Jing NIE ; Hong YU ; Yingmei TANG
Chinese Journal of Rheumatology 2023;27(8):505-512
Objective:To study the correlation between anti-gp210 antibody, anti-sp100 antibody with clinical features and prognosis of patients with PBC.Methods:A total of 992 patients with PBC from 9 medical centers in Yunnan Province from January 1, 2015 to December 31, 2021 were included retrospectively. The demographic data, medical history, UDCA treatment, laboratory and imaging data were collected, and telephone follow-up was conducted. The positive rates of anti-gp210 antibody and anti-sp100 antibody in PBC patients with different clinical characteristics were compared, and the differences of laboratory parameters and prognosis between the anti-gp210 and anti-sp100 antibodies positive and negative groups were compared. T test, rank sum test, variance analysis were used for statistical analysis.Results:The positive rate of anti-gp210 antibody in Han patients was significantly higher than that in minority patients (21.5% vs 9.9%, χ2=6.88, P=0.009), but there was no significant difference in the positive rate of anti-sp100 antibody between the two groups (10.9% vs 6.6%, χ2=1.62, P=0.204).There were no significant differences in the positive rates of anti-gp210 antibody and anti-sp100 antibody among different genders ( χ2=0.50, P=0.478)( Z=-0.41, P=0.682)and ages( χ2=0.01, P=0.951)( Z=-0.60, P=0.549). There was no significant difference in the positive rate of anti-gp210 antibody between AMA M2 antibody positive and negative patients ( χ2=3.45, P=0.063), PBC patients with Sj?gren′s syndrome compared with those without Sj?gren′s syndrome (21.3% vs 20.4%, χ2=0.05, P=0.828), and PBC patients with viral hepatitis compared with those without viral hepatitis(19.6% vs 20.5%, χ2=0.02, P=0.877). The positive rate of anti-gp210 antibody was significantly increased in patients with PBC confirmed by liver biopsy with unknown diagnosis (25.6% vs 18.4%, χ2=6.52, P=0.011), patients with AIH (26.6% vs 18.9%, χ2=5.82, P=0.016), cirrhosis (23.3% vs 11.3%, χ2=16.00, P<0.001), decompensation of cirrhosis (23.9% vs 18.2%, χ2=4.66, P=0.031), jaundice (29.7% vs 17.1%, χ2=18.59, P<0.001) and hyperlipidemia (24.9% vs 18.1%, χ2=6.30, P=0.012). The positive rate of anti-sp100 antibody was significantly increased in patients with negative AMA M2 antibody PBC patients (20.9% vs 7.2%, χ2=36.54, P<0.001)and patients with PBC confirmed by liver biopsy with unknown diagnosis (17.9% vs 7.5%, χ2=23.40, P<0.001), while in patients with AIH (11.1% vs 10.3%, χ2=0.09, P=0.769), Sj?gren′s syndrome (15.7% vs 10.0%, χ2=2.87, P=0.090), viral hepatitis (4.3% vs 10.8%, χ2=1.94, P=0.164), cirrhosis(10.5% vs 10.5%, χ2<0.01, P=0.991), decompensated symptoms of cirrhosis (10.3% vs 10.6%, χ2=0.03, P=0.868), jaundice (12.5% vs 9.7%, χ2=1.62, P=0.203)and hyperlipidemia (8.7% vs 11.5%, χ2=1.86, P=0.172), the positive rate was not significantly increased. The levels of ALT [71.00(48.00, 111.00)U/L vs 58.00 (31.00,112.75)U/L, Z=-2.63, P=0.009], AST [92.00 (54.00, 133.00)U/L vs 76.00(42.00, 128.00)U/L, Z=-2.73, P=0.006], ALP[306.00(176.00, 528.00)U/L vs 204.00(126.25, 350.75)U/L, Z=-4.78, P<0.001], GGT[284.00(131.00, 524.00)U/L vs 165.00(53.63, 389.00)U/L, Z=-4.36, P<0.001], TBIL[33.60(16.60, 82.10)mmol/L vs 23.45 (14.80, 61.13)mmol/L, Z=-3.00, P=0.003], DBIL [20.30 (6.60, 66.40)mmol/L vs 11.60 (5.90, 45.00)mmol/L, Z=-3.13, P=0.002], bile acid[53.40(19.50, 148.00)mmol/L vs 39.30(11.70, 118.58)mmol/L, Z=-2.26, P=0.024], IgM[3.61(2.03,5.26)g/L vs 2.39(1.37, 3.67)g/L, Z=-5.38, P<0.001] and APTT[37.40(33.10, 41.30)s vs 35.70 (31.30, 41.30)s, Z=-3.28, P=0.001])were significantly increased in patients with positive anti-gp210 antibody compared patients with negative anti-gp210 antibody, while the IgG level was significantly increased in patients with positive anti-sp100 antibody compared with patients with negative anti-gp210 antibody( Z=-2.25, P=0.025), but no other indexes were significantly increased. The Mayo risk score[3.48(2.46, 5.01) vs 3.18 (2.20, 4.64), Z=-2.052, P=0.04] and mortality at the end of follow-up (24.6% vs 16.7%, χ2=6.57, P=0.0.038)in patients with positive anti-gp210 antibody were much higher than those in patients with negative anti-gp210 antibody, but there were no significant differences in Mayo risk score [3.16 (2.21, 4.53) vs 3.28 (2.23,4.71), Z=-0.86, P=0.392] and mortality at the end of follow-up (13.5% vs 18.9%, χ2=2.12, P=0.346) between anti-sp100 antibody positive and negative patients. Conclusion:PBC patients with positive anti-gp210 antibody may have more serious liver pathologic damage and extra-hepatic complications, more serious liver function impairment, more obvious cholestasis, and worse prognosis. Anti-sp100 antibody has been shown to have no significant correlation with disease severity and prognosis.

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