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.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.
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.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.
7.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.
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.Effect of early thoracic paracentesis drainage on acute lung injury in severe acute pancreatitis
Xuyang WANG ; Zhangpeng WANG ; Jun WU ; Guangxu JING ; Zhu HUANG ; Hongyu SUN ; Lijun TANG
Journal of Clinical Hepatology 2023;39(7):1633-1642
Objective To investigate the effect of early thoracic paracentesis drainage for pleural effusion with a small or moderate volume on acute lung injury in patients with severe acute pancreatitis (SAP). Methods A retrospective analysis was performed for the clinical data of 107 patients with SAP who were admitted to The General Hospital of Western Theater Command from January 2015 to December 2021, and according to whether thoracic paracentesis drainage was performed within the first three days after admission, the patients were divided into thoracic paracentesis drainage group (TPD group with 51 patients) and non-thoracic paracentesis drainage group (N-TPD group with 56 patients).The two groups were compared in terms of laboratory markers and clinical outcome on days 5 and 10 after admission.The independent-samples t test was used for comparison of normally distributed continuous data between two groups, and the Mann-Whitney U test was used for comparison of non-normally distributed continuous data between two groups; the chi-square test was used for comparison of categorical data between two groups. Results Compared with the N-TPD group, the TPD group had a significantly shorter length of stay in the intensive care unit, a significantly shorter length of hospital stay, and significantly lower hospital costs (all P < 0.05), while there were no significant differences between the TPD group and the N-TPD group in mortality rate (9.8% vs 14.3%, χ 2 =0.502, P =0.478) and the incidence rate of sepsis (29.4% vs 44.6%, χ 2 =2.645, P =0.104).The TPD group had a significant reduction in the incidence rate of acute respiratory distress syndrome (ARDS)( χ 2 =6.038, P =0.043), as well as a significantly lower incidence rate of moderate ARDS than the N-TPD group (7.8% vs 21.4%, χ 2 =3.874, P =0.049).Compared with the N-TPD group, the TPD group had a significantly lower rate of use of mechanical ventilation (35.3% vs 57.2%, χ 2 =6.735, P =0.034) and a significantly lower proportion of patients receiving invasive mechanical ventilation (9.8% vs 26.8%, χ 2 =5.065, P =0.024).Compared with the N-TPD group, the TPD group had a significantly lower incidence rate of pulmonary infection (23.5% vs 42.9%, χ 2 =4.466, P =0.035) and a significantly shorter duration of systemic inflammatory response syndrome (11.2±5.0 days vs 16.8±4.7 days, t =5.949, P < 0.001).Compared with the N-TPD group, the TPD group had significantly better laboratory markers (high-sensitivity C-reactive protein, interleukin-1, interleukin-6, interleukin-8, tumor necrosis factor-α, arterial partial pressure of oxygen, oxygen saturation, and oxygenation index) and incidence rate of respiratory failure on days 5 and 10 after admission (all P < 0.05).On day 10 after admission, the TPD group had significantly better APACHE Ⅱ score and modified Mashall score than the N-TPD group (both P < 0.05). Conclusion For SAP patients with a small or moderate volume of pleural effusion, early thoracic paracentesis drainage can effectively improve acute lung injury, alleviate systemic inflammatory response, shorten the length of hospital stay, and reduce hospital costs.

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