1.Mining molecular biomarkers regulating the occurrence of kidney renal clear cell carcinoma based on bioinformatics methods
Feng GUO ; Chenyu WANG ; Zhenfeng SHI ; Jianhua ZHAO ; Wenlong FAN ; Kadeer AIHEMAITI ; Zecheng NI
Journal of Modern Urology 2025;30(3):215-222
Objective: To identify biomolecular markers closely related to the occurrence of kidney renal clear cell carcinoma (KIRC) and verify their expression levels in clinical samples. Methods: Stage Ⅰ KIRC mRNA sequencing data were obtained from The Cancer Genome Atlas (TCGA).Principal component analysis (PCA) was used for dimensionality reduction to screen differentially expressed genes (DEGs),which then underwent GO and KEGG analyses.Weighted gene co-expression network analysis (WGCNA) was used to screen genes significantly related to KIRC,and a protein-protein interaction (PPI) network was constructed to screen hub genes.The diagnostic value of hub genes was evaluated with receiver operating characteristic (ROC) curve,and their prognostic value was analyzed using survival curve plots.The correlation between the mRNA expressions of hub genes and the pathological stages of KIRC was analyzed.Clinical samples of 20 patients with stage Ⅰ KIRC treated in our hospital were included,and the expressions of the hub genes in cancerous and adjacent tissues were detected with reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR),Western blotting,and enzyme-linked immunosorbent assay (ELISA). Results: A total of 8223 DEGs were screened out,including 4092 up-regulated ones and 4131 down-regulated ones.GO analysis showed that DEGs were related to bioadhesion,plasma membrane composition,and transporter activity.KEGG analysis showed that DEGs were related to pathways such as cell adhesion molecules,cytokine-cytokine receptor interactions,and interactions between viral proteins and cytokines and cytokine receptors.WGCNA analysis obtained 171 genes that were significantly related to stage Ⅰ KIRC.The hub gene,lymphocyte cytosolic protein 2 (LCP2),screened out by the PPI network,was significantly related to stage Ⅰ KIRC.The area under the ROC curve was 0.96.The expression level was negatively correlated with the overall survival rate of patients.The expression of LCP2 was related to the stage and lymph node metastasis.Clinical verification showed that the mRNA and protein relative expressions of LCP2 in KIRC tissues were significantly higher than those in adjacent tissues (P<0.000 1). Conclusion: LCP2 is significantly up-regulated in stage Ⅰ KIRC tissues and can be used as a potential biomarker for the early diagnosis and treatment of KIRC.
2.Establishment and evaluation of the model for predicting lung cancer occurrence in COPD patients based on XGBoost
Jing YANG ; Tong JIAO ; Yujiao DONG ; Chenyu YAO ; Qunyu KONG ; Jie SHI ; Shuanying YANG
Journal of Xi'an Jiaotong University(Medical Sciences) 2025;46(2):345-352
Objective To construct an XGBoost predictive model using clinical characteristic data from patients with chronic obstructive pulmonary disease(COPD)and evaluate the efficacy of the predictive model in early risk prediction of lung cancer occurrence in COPD patients.Methods In this retrospective cross-sectional study,cluster sampling was used.We selected clinically diagnosed COPD patients admitted to The Second Affiliated Hospital of Xi'an Jiaotong University from January 1,2018,to December 31,2022.A total of 4 008 patients with complete data were included.First,the baseline of each characteristic was analyzed,and then XGBoost was used to construct the lung cancer risk prediction model for COPD patients,and SHAP(SHapley Additive exPlanation)value was used to quantify and attribute the importance of each characteristic.DC A curve was used to evaluate the clinical application value.Results After constructing a lung cancer risk model for COPD patients using 28 variables,eight variables were selected according to the importance of the variables and clinical experience,and the prediction model was reconstructed.The model efficacy in the training set and the test set was 0.948(0.938,0.958)and 0.797(0.738,0.856),respectively.SHAP diagram showed that elevated CEA,CA125,FIB,eosinophils,PLT and D-dimer and reduced TT all contributed to an increased risk of lung cancer in COPD patients.DCA curve showed that the prediction model had clinical application value,which could help doctors make more accurate prognosis prediction and treatment decisions.Conclusion The successful establishment of an XGBoost predictive model,utilizing a subset of features,enables early prediction of lung cancer occurrence in COPD patients.
3.Antimicrobial resistance surveillance in the bacterial strains isolated from pediatric intensive care units in China:results from 2020 to 2022
Jing LIU ; Huiyuan YAN ; Gangfeng YAN ; Guoping LU ; Pan FU ; Chuanqing WANG ; Danqun JIN ; Wenjia TONG ; Chenyu ZHANG ; Jianli CHEN ; Yi LIN ; Jia LEI ; Yibing CHENG ; Qunqun ZHANG ; Kaijie GAO ; Yuanyuan CHEN ; Shufang XIAO ; Juan HE ; Li JIANG ; Huimin XU ; Yuxia LI ; Hanghai DING ; Hehe CHEN ; Yao ZHENG ; Qunying CHEN ; Ying WANG ; Hong REN ; Chenmei ZHANG ; Zhenjie CHEN ; Mingming ZHOU ; Yucai ZHANG ; Yiping ZHOU ; Zhenjiang BAI ; Saihu HUANG ; Lili HUANG ; Weiguo YANG ; Weike MA ; Qing MENG ; Pengwei ZHU ; Yong LI ; Yan XU ; Yi WANG ; Yanqiang DU ; Huijun CAI ; Bizhen ZHU ; Huixuan SHI ; Shaoxian HONG ; Yukun HUANG ; Meilian HUANG
Chinese Journal of Infection and Chemotherapy 2025;25(3):303-311
Objective This study aimed to investigate the antimicrobial resistance profiles of bacterial strains isolated from pediatric intensive care units(PICU)in China for better antimicrobial therapy.Methods Clinical isolates were collected from 17 institutions,including tertiary care children's hospitals and pediatric department of tertiary general hospitals in China from January 1,2020 to December 31,2022.Antimicrobial susceptibility testing was carried out according to a unified protocol using Kirby-Bauer method or automated systems.Results were interpreted according to the breakpoints released by the Clinical and Laboratory Standards Institute(CLSI)in 2020.Results A total of 10 688 isolates were collected,including gram-positive organisms(39.2%)and gram-negative organisms(60.8%).The top three organisms were S.aureus(13.6%,1 453/10 688),A.baumannii(10.0%,1 067/10 688),and coagulase-negative Staphylococcus(9.9%,1 058/10 688).Multi-drug resistant organisms(MDROs)were very common in children.The prevalence of methicillin-resistant Staphylococcus aureus(MRSA),carbapenem-resistant Enterobacterales(CRE),carbapenem-resistant E.coli,carbapenem-resistant K.pneumoniae(CRKP),carbapenem-resistant A.baumannii(CRAB),and carbapenem-resistant P.aeruginosa(CRPA)was 41.1%,19.4%,8.8%,30.9%,67.4%,and 28.8%,respectively.Overall,more than 50%of Enterobacteriales isolates were resistant to cephalosporins,while nearly 25%of Enterobacteriales isolates were resistant to carbapenems.MDROs were highly resistant to commonly used antibiotics.More than 80%of CRE and CRAB strains were resistant to all beta-lactam antibiotics.CRE and CRAB showed low resistance rates to tigecycline and polymyxin.CRPA showed lower resistance rates to piperacillin,beta-lactamase inhibitor combinations than the resistance rates to third and fourth generation cephalosporins.All of the Staphylococcus and Enterococcus isolates were susceptible to vancomycin and tigecycline.None of PRSP strains isolated from meningitis and nonmeningitis samples were resistant to rifampicin,vancomycin,or linezolid.The prevalence of β-lactamase-negative ampicillin-resistant(BLNAR)strains was 43.3%in Haemophilus influenzae.Conclusions MDROs were prevalent in PICU.It is necessary to establish an effective multidisciplinary team(MDT)to control the antimicrobial resistance.
4.Establishment and evaluation of the model for predicting lung cancer occurrence in COPD patients based on XGBoost
Jing YANG ; Tong JIAO ; Yujiao DONG ; Chenyu YAO ; Qunyu KONG ; Jie SHI ; Shuanying YANG
Journal of Xi'an Jiaotong University(Medical Sciences) 2025;46(2):345-352
Objective To construct an XGBoost predictive model using clinical characteristic data from patients with chronic obstructive pulmonary disease(COPD)and evaluate the efficacy of the predictive model in early risk prediction of lung cancer occurrence in COPD patients.Methods In this retrospective cross-sectional study,cluster sampling was used.We selected clinically diagnosed COPD patients admitted to The Second Affiliated Hospital of Xi'an Jiaotong University from January 1,2018,to December 31,2022.A total of 4 008 patients with complete data were included.First,the baseline of each characteristic was analyzed,and then XGBoost was used to construct the lung cancer risk prediction model for COPD patients,and SHAP(SHapley Additive exPlanation)value was used to quantify and attribute the importance of each characteristic.DC A curve was used to evaluate the clinical application value.Results After constructing a lung cancer risk model for COPD patients using 28 variables,eight variables were selected according to the importance of the variables and clinical experience,and the prediction model was reconstructed.The model efficacy in the training set and the test set was 0.948(0.938,0.958)and 0.797(0.738,0.856),respectively.SHAP diagram showed that elevated CEA,CA125,FIB,eosinophils,PLT and D-dimer and reduced TT all contributed to an increased risk of lung cancer in COPD patients.DCA curve showed that the prediction model had clinical application value,which could help doctors make more accurate prognosis prediction and treatment decisions.Conclusion The successful establishment of an XGBoost predictive model,utilizing a subset of features,enables early prediction of lung cancer occurrence in COPD patients.
5.Antimicrobial resistance surveillance in the bacterial strains isolated from pediatric intensive care units in China:results from 2020 to 2022
Jing LIU ; Huiyuan YAN ; Gangfeng YAN ; Guoping LU ; Pan FU ; Chuanqing WANG ; Danqun JIN ; Wenjia TONG ; Chenyu ZHANG ; Jianli CHEN ; Yi LIN ; Jia LEI ; Yibing CHENG ; Qunqun ZHANG ; Kaijie GAO ; Yuanyuan CHEN ; Shufang XIAO ; Juan HE ; Li JIANG ; Huimin XU ; Yuxia LI ; Hanghai DING ; Hehe CHEN ; Yao ZHENG ; Qunying CHEN ; Ying WANG ; Hong REN ; Chenmei ZHANG ; Zhenjie CHEN ; Mingming ZHOU ; Yucai ZHANG ; Yiping ZHOU ; Zhenjiang BAI ; Saihu HUANG ; Lili HUANG ; Weiguo YANG ; Weike MA ; Qing MENG ; Pengwei ZHU ; Yong LI ; Yan XU ; Yi WANG ; Yanqiang DU ; Huijun CAI ; Bizhen ZHU ; Huixuan SHI ; Shaoxian HONG ; Yukun HUANG ; Meilian HUANG
Chinese Journal of Infection and Chemotherapy 2025;25(3):303-311
Objective This study aimed to investigate the antimicrobial resistance profiles of bacterial strains isolated from pediatric intensive care units(PICU)in China for better antimicrobial therapy.Methods Clinical isolates were collected from 17 institutions,including tertiary care children's hospitals and pediatric department of tertiary general hospitals in China from January 1,2020 to December 31,2022.Antimicrobial susceptibility testing was carried out according to a unified protocol using Kirby-Bauer method or automated systems.Results were interpreted according to the breakpoints released by the Clinical and Laboratory Standards Institute(CLSI)in 2020.Results A total of 10 688 isolates were collected,including gram-positive organisms(39.2%)and gram-negative organisms(60.8%).The top three organisms were S.aureus(13.6%,1 453/10 688),A.baumannii(10.0%,1 067/10 688),and coagulase-negative Staphylococcus(9.9%,1 058/10 688).Multi-drug resistant organisms(MDROs)were very common in children.The prevalence of methicillin-resistant Staphylococcus aureus(MRSA),carbapenem-resistant Enterobacterales(CRE),carbapenem-resistant E.coli,carbapenem-resistant K.pneumoniae(CRKP),carbapenem-resistant A.baumannii(CRAB),and carbapenem-resistant P.aeruginosa(CRPA)was 41.1%,19.4%,8.8%,30.9%,67.4%,and 28.8%,respectively.Overall,more than 50%of Enterobacteriales isolates were resistant to cephalosporins,while nearly 25%of Enterobacteriales isolates were resistant to carbapenems.MDROs were highly resistant to commonly used antibiotics.More than 80%of CRE and CRAB strains were resistant to all beta-lactam antibiotics.CRE and CRAB showed low resistance rates to tigecycline and polymyxin.CRPA showed lower resistance rates to piperacillin,beta-lactamase inhibitor combinations than the resistance rates to third and fourth generation cephalosporins.All of the Staphylococcus and Enterococcus isolates were susceptible to vancomycin and tigecycline.None of PRSP strains isolated from meningitis and nonmeningitis samples were resistant to rifampicin,vancomycin,or linezolid.The prevalence of β-lactamase-negative ampicillin-resistant(BLNAR)strains was 43.3%in Haemophilus influenzae.Conclusions MDROs were prevalent in PICU.It is necessary to establish an effective multidisciplinary team(MDT)to control the antimicrobial resistance.
6.Evaluation of Habitat Suitability of Prunella vulgaris L.Based on MaxEnt Model and ArcGIS
Ru PEI ; Zhaohua SHI ; Lei XU ; Junjie HU ; Hengjian XIA ; Shengjun WANG ; Chenyu WANG ; Lichun YE
Chinese Journal of Information on Traditional Chinese Medicine 2024;31(11):1-6
Objective To screen the main environmental factors affecting the growth of Prunella vulgaris L.based on MaxEnt model and ArcGIS;To predict its potential suitable habitats in China;To provide reference for the artificial cultivation of Prunella vulgaris L.Methods Totally 346 pieces of sample point data of Prunella vulgaris L.were collected.Combined with data of 38 ecological factors,the main environmental factors affecting the distribution of Prunella vulgaris L.were screened using MaxEnt model.ArcGIS software was used to evaluate the habitat suitability of Prunella vulgaris L.and analyze the distribution of suitable areas for Prunella vulgaris L.worldwide and in China.Results The main ecological factors affecting the distribution of Prunella vulgaris L.were upper(0-30 cm)soil gravel volume percentage,soil effective water content,upper(0-30 cm)soil exchangeable sodium salt,specific soil types related to agricultural use in soil units and upper(0-30 cm)soil sand content.The highly suitable areas of Prunella vulgaris L.were mainly in Yunnan,Heilongjiang,eastern Inner Mongolia and central Sichuan.Conclusion The predicted results can provide a reference for the introduction of cultivation and sustainable resource utilization of Prunella vulgaris L.
7.Patent Analysis of Galla Chinensis Based on Incopat Patent Database
Chenyu WANG ; Chiqing CHEN ; Jie XIANG ; Zhiwei CHEN ; Lei XU ; Junjie HU ; Lichun YE ; Zhaohua SHI
World Science and Technology-Modernization of Traditional Chinese Medicine 2024;26(6):1505-1514
Wubeizi(Galla Chinensis)is a commonly used traditional Chinese medicine in modern clinical practice,which is widely used to treat hemorrhoids,bleeding,mouth ulcers and other diseases.Based on the incopat patent database,the global Galla Chinensis sub-patent search in the past 20 years was conducted,and a total of 8123 related patents were retrieved;Using the basic chart analysis method,the pattern analysis of Galla Chinensis sub-patents was carried out from the aspects of application trend,patent value,technical field,legal status,etc.The analysis results show that the development of Galla Chinensis is in the rapid development stage,Galla Chinensis has in-depth research in the treatment of hemorrhoids,oral ulcers,bleeding,Chinese herbal medicine,Chinese patent medicine and cosmetics are the hot spot of research and development at present,China and South Korea are the main distribution countries of Galla Chinensis patents.The number of Chinese Galla Chinensis patents is large,but the patent quality,value and patent level of the world have a certain gap.In view of the current development trend of Galla Chinensis,there is still a large amount of patent application space in this field.Chinese Galla Chinensis patent applicants can combine their own advantages,development trend and short board to formulate scientific development strategy,thus improving the core competitiveness of Galla Chinensis industry fundamentally.
8.Patent Analysis of Artemsia Argyi Based on Incopat Patent Database
Lichun YE ; Chenyu WANG ; Qin YUAN ; Junjie HU ; Guohua ZHENG ; Benda XIAO ; Xinan LIAO ; Zhaohua SHI
World Science and Technology-Modernization of Traditional Chinese Medicine 2023;25(6):1881-1894
Artemsia argyi Levl.et Vant is a commonly used Chinese herbal medicine and moxibustion raw material plant,so far has more than two thousand years of medicinal history,as one of the most commonly used Chinese medicinal materials.The incopat patent database was used to search the worldwide patent data of the last 20 years,and a total of 25279 argyi related patents were retrieved.The pattern of argyi patents was analyzed from the perspectives of global application trend,main technical fields,national economy composition,applicant ranking,patent value and other aspects by means of graph combination.The analysis shows that the innovation and development of argyi is in the stage of rapid development;The medical,Chinese patent medicine,cosmetics and physiotherapy of argyi are the hot research and development of current technology;There are a large number of patents related to argyi in the world,but they are mainly distributed in China and South Korea.Among them,the number of patents related to argyi in China reaches 20381,far higher than that in other countries,but the number of high-value patents is not very large,and the value and quality of patents are still insufficient compared with other countries.From the perspective of the current development trend of argyi,with the deepening of clinical application recognition and scientific research of argyi,there is a large patent space in the field of argyi.Patent applicants can formulate corresponding patent application strategies according to the global development opportunities,technological development status and existing weaknesses.
9.Mentor-mentee dual evaluation of current clinical and translational research mentor competency and mentor training needs
Bei TAN ; Yizhen WEI ; Yue LI ; Yuqian SHI ; Dantong ZHU ; Chenyu ZHU ; Huijuan ZHU ; Linzhi LUO
Chinese Journal of Medical Education Research 2022;21(12):1642-1647
Objective:To investigate mentor-mentee dual evaluation of the current status of mentor competency of clinical and translational research mentors, and provide the basis for mentor training focused on the mentor competences.Methods:A total of 121 clinical and translational research mentors and 170 mentees from Peking Union Medical College Hospital were enrolled. The Chinese version of the Mentor Competency Assessment (MCA) questionnaire was used to evaluate the mentor competency, including maintaining effective communication, aligning expectations, assessing understanding, fostering independence, addressing diversity, promoting professional development total 6 parts with 26 sub-items. The Likert scale was used to quantitatively evaluate the clinical and translational research mentor competency by mentor-mentee dual evaluations. And the composition and training needs of clinical and translational research mentors were investigated. SPSS 25.0 was used for t-test. Results:Seventy percent (119/170) of mentees considered the mentor guidance was very helpful, and 78.5% (95/121) of the mentors considered it necessary to carry out the mentor training. The mentee evaluation of mentor competency was significantly higher than that of mentor self-evaluation [total score (162.35±23.59) vs. (154.80±19.81), P < 0.01]. And the excellent rate of 26 sub-items by mentees and mentors were 100.0%(170/170) and 46.3%(56/121) respectively. The mentors and mentees shared the agreement of the strengths on trust-based relationship and encouraging mentees, and weaknesses on taking into account the possible prejudices in mentor-mentee relationship. Conclusion:The clinical and translational research mentors have already had good competences, but mentor training is still highly warranted. It's expected that to carry out targeted mentor training and assessment according to the mentor's competences will help to improve the construction of the medical talents training system.
10.Research progress on tissue engineering in repairing tempomandibular joint.
Jiejun SHI ; Huiming WANG ; Yingnan WANG ; Chenyu WANG ; Cunyi WANG
Journal of Zhejiang University. Medical sciences 2021;50(2):212-221
Temporomandibular joint osteoarthritis (TMJOA) is mainly manifested as perforation of temporomandibular joint disc (TMJD) and destruction of condylar osteochondral complex (COCC). In recent years, tissue engineering technology has become one of the effective strategies in repairing this damage. With the development of scaffold material technology, composite scaffolds have become an important means to optimize the performance of scaffolds with the combined advantages of natural materials and synthetic materials. The gelling method with the minimally invasive concept can greatly solve the problems of surgical trauma and material anastomosis, which is beneficial to the clinical transformation of temporomandibular joint tissue engineering. Extracellular matrix scaffolds technology can solve the problem of scaffold source and maximize the simulation of the extracellular environment, which provides an important means for the transformation of temporo joint tissue engineering to animal level. Due to the limitation of the source and amplification of costal chondrocytes, the use of mesenchymal stem cells from different sources has been widely used for temporomandibular joint tissue engineering. The fibrochondral stem cells isolated from surface layer of articular cartilage may provide one more suitable cell source. Transforming growth factor β superfamily, due to its osteochondrogenesis activity has been widely used in tissue engineering, and platelet-rich derivative as a convenient preparation of compound biological factor, gradually get used in temporomandibular joint tissue engineering. With the deepening of research on extracellular microenvironment and mechanical stimulation, mesenchymal stem cells, exosomes and stress stimulation are increasingly being used to regulate the extracellular microenvironment. In the future, the combination of complex bioactive factors and certain stress stimulation may become a trend in the temporomandibular joint tissue engineering research. In this article, the progress on tissue engineering in repairing COCC and TMJD, especially in scaffold materials, seed cells and bioactive factors, are reviewed, so as to provide information for future research design and clinical intervention.
Animals
;
Mesenchymal Stem Cells
;
Temporomandibular Joint/surgery*
;
Temporomandibular Joint Disc/surgery*
;
Tissue Engineering
;
Tissue Scaffolds

Result Analysis
Print
Save
E-mail