1.Advances and prospects of the integration of multi-omics and artificial intelligence in traditional Chinese medicine research
Guicheng Liu ; Xi Long ; Qinghua PENG ; Sainan Tian ; Shujuan Hu
Digital Chinese Medicine 2025;8(3):300-312
Objective:
To map the research hotspots, developmental trends, and existing challenges in the integration of artificial intelligence (AI) with multi-omics in traditional Chinese medicine (TCM) through comprehensive bibliometric analysis.
Methods:
China National Knowledge Infrastructure (CNKI), Wanfang Data, China Science and Technology Journal Database (VIP), Chaoxing Journal Database, PubMed, and Web of Science were searched to collect literature on the theme of AI in TCM multi-omics research from the inception of each database to December 31, 2024. Eligible records were required to simultaneously address AI, TCM, and multi-omics. Quantitative and visual analyses of publication growth, core authorship networks, institutional collaboration patterns, and keyword co-occurrence were performed using Microsoft Excel 2021, NoteExpress v4.0.0, and Cite Space 6.3.R1. AI application modes in TCM multi-omics research were also categorized and summarized.
Results:
A total of 1 106 articles were enrolled (932 Chinese and 174 English). Publication output has increased continuously since 2010 and accelerated after 2016. Region-specific collaboration clusters were identified, dominated by Beijing University of Chinese Medicine, China Academy of Chinese Medical Sciences, Shanghai University of Traditional Chinese Medicine, and Nanjing University of Chinese Medicine. Keyword co-occurrence analysis revealed that current AI applications predominantly centered on metabolomics and algorithms such as cluster analysis and data mining. Research foci mainly ranked as follows: single herbs, herbal formulae, and disease-syndrome differentiation.
Conclusion
Machine learning methods are the predominant integrative modality of AI in the realm of TCM multi-omics research at present, utilized for processing omics data and uncovering latent patterns therein. The domain of TCM, in addition to investigating omics information procured through high-throughput technologies, also integrates data on traditional Chinese medicinal substances and clinical phenotypes, progressing towards joint analysis of multi-omics, high-dimensionality of data, and multi-modality of information. Deep learning approaches represent an emerging trend in the field.
2.Effect of berberine on regulating NF-κB p65/TGF-β1/CTGF signaling pathway in reducing renal fibrosis injury in mice
Guang-Yao LI ; Jia-Min LIANG ; Meng-Tong JIN ; Duan XI ; Peng LIU ; Peng WANG ; Rui-Hua WANG ; Qing-Qing LIU
Chinese Pharmacological Bulletin 2024;40(11):2042-2047
Aim To investigate the protective effect of berberine(BBR)on mice with unilateral ureteral obstr-uction(UUO)and explore its mechanism.Methods C57BL/6 mice were randomly divided into the sham group,UUO group,and BBR treatment groups(50,100 and 200 mg·kg-1),with eight mice in each group.Except the sham group,the other groups were subjected to left ureteral ligation to establish the UUO model.Af-ter modeling,the mice in the sham and UUO groups were fed normal saline,and the mice in the BBR treat-ment groups were fed(50,100,200)mg·kg-1 BBR by gavage for 14 days,respectively.Biochemical analy-zer was employed to detect the levels of serum creati-nine(Scr)and blood urea nitrogen(BUN).HE,Mas-son,TUNEL and immunohistochemical staining were used to observe the pathological changes of renal tis-sue.ELISA was employed to detect the expression of pro-inflammatory cytokines in renal tissue homogenate.Western blot was used to detect the protein levels of NF-κB p65,TGF-β1 and CTGF in mouse kidney.Re-sults Compared with the UUO group,the levels of Scr and BUN in the BBR group were significantly reduced.Renal injury and interstitial fibrosis were alleviated.The expression of pro-inflammatory cytokines decreased in kidney.The expression of NF-κB p65,TGF-β1 and CTGF decreased.All results showed some degree of dose dependence.Conclusion Berberine has a sig-nificant protective effect on unilateral ureteral obstruc-tion mice,and the mechanism may be that BBR has the potential to inhibit NF-κB p65/TGF-β1/CTGF signa-ling pathway,thus reducing renal inflammation and fi-brosis.
3.Prediction and identification of B-cell epitopes of SARS-CoV-2 E protein
Peng-Fei ZHANG ; Jun LIU ; Zi-Yang ZOU ; Xi-Long KANG ; Li SONG ; Xin-An JIAO ; Chuang MENG ; Zhi-Ming PAN
Chinese Journal of Zoonoses 2024;40(9):807-813
This work was aimed at predicting and verifying B-cell epitopes of SARS-CoV-2 E protein through bioinformatics methods,and clarifying the dominant B cell epitopes with mouse polyclonal antibody serum prepared through SARS-CoV-2 re-combinant E protein immunization and human positive serum vaccinated with inactivated SARS-CoV-2 vaccine.The structural and B-cell linear epitopes of SARS-CoV-2 E protein were predicted with SOPMA,Expasy,SWISS-MODEL,IEDB database,and Bepid-2.0 software.Candidate epitopes were expressed as GST-tagged recombinant protein fragments in an E.coli sys-tem,and their immunoreactivity with mouse and human poly-clonal positive serum against SARS-CoV-2 E protein was de-tected by western blotting and indirect ELISA,respectively.The epitope prediction results showed that E protein contained linear B cell epitopes Ser6-Val14 and Tyr57-Pro71,and the conformational epitopes of Glu8-Val12,Leu39-Tyr59,and Ser60-Leu65.The GST tagged recombinant E protein fragments of E1 and E3,containing Ser6-Val14 and Tyr57-Pro71 epitopes,respectively,as well as E2 without an epitope sequence as a control,were expressed in an E.coli expression system and successfully purified with an Ni-NTA column.Western blotting and indirect ELISA analysis indicated that all mouse and human SARS-CoV-2 positive sera positively reacted with only E1 and E3 proteins,but negatively reacted with E2 protein,thus indicating that the corresponding epitope prediction with Ser6-Val14 and Tyr57-Pro71 was correct.This study successfully predicted and preliminarily identified two linear B cell epitopes of SARS-CoV-2 E protein,thus providing a reference for the preparation of new coronavirus vaccines and the analysis of immune response characteristics.
4.MTHFD2 Is a Negative Regulatory Molecule for the Formation of Heterotypic Cell-in-Cell Structures
Peng-Fei FENG ; Chen-Yu LIU ; Yi-Nuo HUANG ; Zhuo-Ran SUN ; Yang-Yi ZHANG ; Hong-Yan HUANG ; Chen-Xi WANG ; Xiao-Ning WANG
Chinese Journal of Biochemistry and Molecular Biology 2024;40(6):819-826
Heterotypic cell-in-cell structures(heCICs)mediate unique non-autonomous cell death,which are widely involved in a variety of important pathological processes,such as tumorigenesis,pro-gression and clinical prognosis.Methylenetetrahydrofolata dehydrogenase 2(MTHFD2),one of the key enzymes of one-carbon metabolism,is highly expressed in a variety of tumor cells.In this study,in order to investigate the effect of MTHFD2 on the formation of heCICs,liver cancer cells and immune cells were first labeled separately by live cell dyes,and the heCIC model was established by using fluorescence mi-croscopy for cell imaging and analysis.After transiently knocking down MTHFD2 in cells by RNAi,we found that the ability of PLC/PRF/5 and Hep3B to form heCICs with immune cells was significantly in-creased(all P<0.01).MTHFD2 recombinant expression plasmid was constructed by the homologous re-combination method,and MTHFD2 overexpression cell lines were further constructed.Then,the effect of MTHFD2 overexpression on the ability to form heCICs was detected by co-culturing the overexpression cell lines with immune cells.The results showed that the rate of heCIC formation was significantly re-duced after overexpression of MTHFD2(all P<0.001).In conclusion,this study demonstrated that MTHFD2 is a negative regulator of heCIC formation,providing a research basis for targeting MTHFD2 to promote heCIC formation and enhance the in-cell killing of immune cells.
5.Research Progress on Permanent Pacemaker Implantation After Transcatheter Aortic Valve Replacement
Nan CHEN ; Xi PENG ; Junpeng LIU ; Huiping ZHANG
Chinese Circulation Journal 2024;39(9):924-930
Indications of transcatheter aortic valve replacement(TAVR)are extending to lower risk population.High atrioventricular block is one of the common complication of TAVR,permanent pacemaker implantation is receiving high recognition now.This review summarizes research progress on the anatomy,indicators,predictors and prognosis of permanent pacemaker implantation after TAVR.
6.The Association between the Gut Microbiota and Erectile Dysfunction
Tianle ZHU ; Xi LIU ; Peng YANG ; Yukuai MA ; Pan GAO ; Jingjing GAO ; Hui JIANG ; Xiansheng ZHANG
The World Journal of Men's Health 2024;42(4):772-786
Purpose:
Explore the causal relationship between the gut microbiota and erectile dysfunction (ED) at phylum, class, order, family, and genus levels, and identify specific pathogenic bacteria that may be associated with the onset and progression of ED.
Materials and Methods:
The genetic variation data of 196 human gut microbiota incorporated in our study came from the human gut microbiome Genome Wide Association Studies (GWAS) dataset released by the MiBioGen Consortium. The GWAS statistics for ED were extracted from one study by Bovijn et al., which included 223,805 participants of European ancestry, of whom 6,175 were diagnosed with ED. Subsequently, Mendelian randomization (MR) analysis was carried out to explore whether a causal relationship exists between the gut microbiota and ED. Additionally, bidirectional MR analysis was performed to examine the directionality of the causal relationship.
Results:
Through MR analysis, we found that family Lachnospiraceae (odds ratio [OR]: 1.27, 95% confidence interval [CI]: 1.05–1.52, p=0.01) and its subclass genus LachnospiraceaeNC2004 group (OR: 1.17, 95% CI: 1.01–1.37, p=0.04) are associated with a higher risk of ED. In addition, genus Oscillibacter (OR: 1.17, 95% CI: 1.02–1.35, p=0.03), genus Senegalimassilia (OR: 1.32, 95% CI: 1.06–1.64, p=0.01) and genus Tyzzerella3 (OR: 1.14, 95% CI: 1.02–1.27, p=0.02) also increase the risk of ED. In contrast, the inverse variance weighted estimate of genus RuminococcaceaeUCG013 (OR: 0.77, 95% CI: 0.61–0.96, p=0.02) suggests that it has a protective effect against the occurrence of ED.
Conclusions
This study preliminarily identified 6 bacterial taxa that may have a causal relationship with ED, including family Lachnospiraceae, genus Lachnospiraceae NC2004 group, Oscillibacter, Senegalimassilia, Tyzzerella 3 and Ruminococcaceae UCG013. These identified important bacterial taxa may serve as candidates for microbiome intervention in future ED clinical trials.
7.Analysis of problems and countermeasures in the construction of geriatric department in hospitals of China
Peng QIAN ; Zhi LIU ; Liwei JING ; Xi GAO
Chinese Journal of Hospital Administration 2024;40(6):415-418
Developing geriatric department is an important measure to address the aging population. In recent years, there had been some progress in the construction of geriatric departments in hospitals of China, but there was still significant room for improvement in the context of rapid aging. At present, the geriatric departments in hospitals were mainly facing problems and difficulties such as low attention within the hospital, shortage of geriatric medical professionals, imperfect payment systems, inapplicable performance evaluation indicators, and low social awareness. This study suggested that we should further strengthen the construction of geriatric departments in hospitals, accelerate the construction of geriatric medicine talent teams, promote the reform of payment methods related to geriatric medicine services, optimize the performance evaluation methods of geriatric medicine departments, and enhance the social identity of geriatric medicine departments, so as to provide references for promoting the sustainable and high-quality development of geriatric medicine departments in hospitals of China.
8.Effects of fast-advancing short-term high altitude exposure on different systems in young and middle-aged men
Zehong PENG ; Jianglong WEN ; Wenzhuo ZHU ; Xi ZHU ; Chao LIU ; Heng CHENG ; Qi ZHANG ; Lili ZHU
China Modern Doctor 2024;62(26):15-19
Objective To observe the changes of liver function,blood cell,and lung function of healthy young and middle-aged men before and after fast-advancing short-term high altitude exposure(FSHAE);and to explore the effects and possible mechanisms of FSHAE on the function of liver,blood cells,and lung tissues.Methods This study included 48 healthy young and middle-aged male volunteers,who collected physiological indicators,tested liver function indicators,blood cell indicators,and lung function-related indicators 1 day before entering the plateau(100m above sea level),and 15 days after FSHAE(3000m above sea level).Differences in the relevant parameters of each system were compared before and after FSHAE.Results Compared with those before entering the plateau,the physiological parameters of young and middle-aged men after 15 days of FSHAE heart rate increased significantly,respiratory rate increased,systolic blood pressure increased,mean arterial blood pressure increased,oxygen saturation decreased(P<0.01),and diastolic blood pressure increased(P<0.05),all of which were statistically significant;and the indicators of liver function:glutamic oxaloacetic aminotransferase,glutamic alanine aminotransferase increased(P<0.01),glutamylamine aminotransferase,glutamate aminotransferase,glutaminase,and pulmonary function were increased(P<0.01),glutamyl transpeptidase,alkaline phosphatase,and total bile acids were elevated,and total protein decreased(P<0.05),and the differences were statistically significant.Hemocyte-related indexes:erythrocyte count,erythrocyte pressure volume,mean erythrocyte volume,mean hemoglobin volume,mean hemoglobin concentration,and hemoglobin were elevated,and platelet count decreased(P<0.01),and the differences were statistically significant.although there was an elevation of leukocyte count(P>0.05);Lung function-related indexes:decreased exertion lung volume(P<0.05).There were decreased exertion expiratory volume in the first second,increased one-second rate(P>0.05).Conclusion FSHAE can lead to oxidative stress in the organism,and acute hypoxic multisystemic injury will occur,with the simultaneous emergence of hypoxic adaptive regulation of various systems,self-compensatory repair of various organs of the organism,and there may be the possibility of interactions between various systems.
9.Design of intelligent horizontal rotating cell culture device
Li-Fei YANG ; Ye-Rong QIAN ; Jun-Xi XIANG ; Ai-Hua SHI ; Xin LIU ; Sha-Sha WEI ; Yi LYU ; Peng LIU
Chinese Medical Equipment Journal 2024;45(9):41-45
Objective To develop an intelligent horizontal rotating cell culture device with high modularity,easy operation,easy disinfection,low cost and high stability.Methods The cell culture device consisted of a rotating culture module,a dirve module,a control module and control software,with the shells of all the modules being manufactured by 3D printing.The rotating culture module was composed of a tubular electrospun scaffold,a cell culture chamber,a magnetic coupling rotor and polypropylene pipeline;the drive module was made up of a N20 reduction motor and a magnetic coupling rotor;the control module included an ESP-8266 chip and a printed circuit board;the control software was developed with Blinker IoT platform and C++language.The device was used to culture human intrahepatic bile duct epithelial cells to verify its effects.Results Light microscopy and scanning electron microscopy images showed that a uniform and continuous cell layer was formed on the surface of the tubular electrospun scaffold.Conclusion The intelligent horizontal rotating cell culture device achieves uniform growth of cells on the inner surface of tubular electrospun scaffolds,and can be used as an effective platform for cell culture on tubular scaffolds.[Chinese Medical Equipment Journal,2024,45(9):41-45]
10.Research status of key technologies and equipment for dynamic perception of battlefield casualties
Zi-Jian WANG ; Chen SU ; Xin-Xi XU ; Xin LIU ; Zhen-Bao WANG ; Pei-Peng LIU ; Jie-Feng GUO ; Xiu-Guo ZHAO
Chinese Medical Equipment Journal 2024;45(9):95-108
The research progress in key technologies for dynamic perception of battlefield casualties was reviewed,including unmanned equipment dynamic mapping,dynamic environment semantic segmentation and casualty detection and identification.The discussion also covered the current state of research on casualty dynamic perception equipment in aerial and ground domains.The development trends of key technologies and equipment for dynamic perception of battlefield casualties were pointed out,and references were provided for enhancing the efficacy of battlefield casualty care and improving medical service support capabilities.[Chinese Medical Equipment Journal,2024,45(9):95-108]

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