1.Key gene screening and prediction model construction of gastric cancer based on machine learning
Zepeng WANG ; Kunpeng LI ; Yu ZHOU ; Sihai LI
Chinese Journal of Medical Physics 2024;41(1):115-124
Objective To verify the genetic characteristics associated with gastric cancer,and to propose a hybrid feature selection method for identifying target genes,further analyzing their significance and establishing a new diagnostic prediction model.Methods Analysis of variance in bioinformatics was performed on the original gastric cancer data,and then machine learning methods such as random forest,recursive feature elimination of support vector machine,and LASSO algorithm were used to screen gastric cancer associated genes,and the intersection of results was taken as the key gene set.The key genes were identified and verified through enrichment analysis.The diagnosis and prediction models based on 8 kinds of machine learning classification algorithms such as multi-layer perceptron,logistic regression and decision tree,were constructed using the key genes.Results The key genes selected by the hybrid feature selection method were closely related to the tumorigenesis and development.Eight key genes(TXNDC5,BMP8A,ONECUT2,COL10A1,JCHAIN,INHBA,LCTL and TRIM59)were identified as potential markers of good diagnostic efficacy in gastric cancer.The ROC curve and accuracy results demonstrated that among the 8 classification models,MLP is the best gastric cancer prediction model,with an accuracy of 97.77%,which was 3.83%higher than that of Xgboost gastric cancer prediction model.Conclusion The study identifies 8 key genes for the diagnosis and prevention of gastric cancer,and establishes the optimal prognosis model.
2.Review on application of artificial intelligence in tumor gene expression data analysis
Kunpeng LI ; Zepeng WANG ; Yu ZHOU ; Sihai LI
Chinese Journal of Medical Physics 2024;41(3):389-396
Tumors are serious diseases threatening human health,and the early diagnosis is essential to improve treatment success and patient survival.The study of tumor gene expression data has become a major tool for revealing tumor disease mechanisms,in which artificial intelligence plays an important role.The potential advantages of supervised learning,unsupervised learning and deep learning in tumor prediction and classification are explored from the perspective of machine learning methods.Special attention is paid to the impact of feature selection algorithms on gene screening and their importance in high-dimensional gene expression data.By providing a comprehensive overview of the application and development of artificial intelligence in the analysis of tumor gene expression data,the study aims to provide an outlook for future research directions and promote further development.
3.Analysis of current situation of cognition of high-alert medications among medical staffs in Chongming District of Shanghai
Xian SHEN ; Xingxing YU ; Liuhua GU ; Kunpeng YU ; Yunda JIANG
Chinese Journal of Pharmacoepidemiology 2024;33(3):291-300
Objective To understand the cognition status of high-alert medications among medical staffs in Chongming District of Shanghai,and to explore its influencing factors and improvement countermeasures,so as to provide references for safe clinical use and effective control of such drugs.Methods Convenient sampling method was used to investigate among medical staffs in 9 hospitals in Chongming District from March to May 2022,the survey content included general information of medical staff and their awareness of high-alert medications.The orderly multi-classification logistic regression was used to analyze the influencing factors of the cognition of high-alert medications among medical staffs.Results A total of 605 valid questionnaires were collected,including 263 from doctors and 342 from nurses.The results of univariate analysis showed that there were significant differences in the grade distribution of high-alert medications management knowledge scores among doctors of different gender,education background and whether to partcipate in in-hospital training(P<0.05).There were significant differences in the grade distribution of high-alert medications management knowledge scores among nurses with different education background,hospital level and whether to partcipate in in-hospital training(P<0.05).There was significant differences in the grade distribution of high-alert medications pharmacy knowledge scores whether doctors participated in in-hospital training(P<0.05).There were significant differences in the grade distribution of high-alert medications pharmacy knowledge scores among nurses with different education background,professional title,working years and whether to partcipate in in-hospital training(P<0.05).The results of multi-factor Logistic analysis showed that whether doctors had participated in in-hospital training was an influential factor for and high-alert medications management knowledge score level(OR=0.003,95%CI 0.000 to 0.023,P<0.001),high-alert medications pharmacy knowledge score level(OR=0.252,95%CI 0.147 to 0.431,P<0.001).Whether nurses participated in in-hospital training(OR=0.022,95%CI 0.010 to 0.048,P<0.001)and hospital level(OR=3.353,95%CI 1.639 to 6.855,P=0.001)were the influencing factors of nurses'high-alert medications management knowledge score level,and education background(OR=4.933,95%CI 1.452 to 16.760,P=0.011)and whether nurses participated in in-hospital training(OR=0.414,95%CI 0.239 to 0.717,P=0.002)were the influencing factors of nurses'high-alert medications pharmacy knowledge score level.Conclusion The cognition of high-alert medications among medical staffs in Chongming District is at a medium level on the whole.It is suggested to improve their cognitive ability and risk prevention awareness by improving their education,strengthening the knowledge education and training of high-alert medications,and homogenizing management,so as to ensure the safety of clinical drugs.
4.Correlation analysis between MRI parameters and molecular pathology of primary central nervous system lymphoma
Zhang DONGYANG ; Wang SHUYE ; Liu YUE ; Yang KUNPENG ; Yu HONGJUAN ; Wang YUE
Chinese Journal of Clinical Oncology 2024;51(8):401-405
Objective:To investigated the relationship between magnetic resonance imaging(MRI)parameters and the molecular pathology of primary central nervous system lymphoma(PCNSL).Methods:We retrospectively analyzed 26 patients from The First Affiliated Hospital of Harbin Medical University between January 2020 and June 2023 classified into germinal center B-cell like(GCB)and non-germinal center B-cell like(non-GCB)groups based on cell origin,into Ki-67≥75%and<75%groups based on the Ki-67 index,into BCL-2+and BCL-2-groups based on BCL-2 expression,and into responsive and non-responsive groups based on their response to MAP+Bruton's tyrosine kinase inhib-itor(BTKi)treatment.We extracted and compared first-order parameters between the groups,including mean value,standard deviation,variance,coefficient of variation,skewness,kurtosis,and entropy from baseline MRI images.Results:Four parameters(variance,kurtosis,skewness,and coefficient of variation)showed no significant differences between groups.However,three parameters(mean,standard devi-ation,and entropy)significantly differed between the groups based on Ki-67 and BCL-2 expression.For the Ki-67 index,the three parameters'areas under the curve(AUC)were 0.731,0.831,and 0.913,respectively.For BCL-2 expression,the mean and standard deviation AUCs were 0.889 and 0.938,respectively.In addition,the mean and entropy parameters significantly differed between the groups categorized by cell origin and treatment responsiveness(P<0.05).Multi-parameter joint analysis demonstrated greater identification accuracy compared to util-izing individual quantitative parameters from texture analysis.Conclusions:The mean,standard deviation,and entropy MRI parameters can help predict Ki-67 and BCL-2 expression in patients with PCNSL and have evaluative functions for treatment.They are beneficial for preoper-ative non-invasive assessment of tumor malignancy,providing vidence for prognosis and treatment planning.
5.Expression of β-xylosidase An-xyl from Aspergillus niger and characterization of its xylose tolerance.
Le LI ; Cheng PENG ; Kunpeng YU ; Yiling TANG ; Yanling LIN ; Lijun LI ; Hui NI ; Qingbiao LI
Chinese Journal of Biotechnology 2023;39(11):4593-4607
The hydrolysis of xylo-oligosaccharides catalyzed by β-xylosidase plays an important role in the degradation of lignocellulose. However, the enzyme is easily inhibited by its catalytic product xylose, which severely limits its application. Based on molecular docking, this paper studied the xylose affinity of Aspergillus niger β-xylosidase An-xyl, which was significantly differentially expressed in the fermentation medium of tea stalks, through cloning, expression and characterization. The synergistic degradation effect of this enzyme and cellulase on lignocellulose in tea stems was investigated. Molecular docking showed that the affinity of An-xyl to xylose was lower than that of Aspergillus oryzae β-xylosidase with poor xylose tolerance. The Ki value of xylose inhibition constant of recombinant-expressed An-xyl was 433.2 mmol/L, higher than that of most β-xylosidases of the GH3 family. The Km and Vmax towards pNPX were 3.6 mmol/L and 10 000 μmol/(min·mL), respectively. The optimum temperature of An-xyl was 65 ℃, the optimum pH was 4.0, 61% of the An-xyl activity could be retained upon treatment at 65 ℃ for 300 min, and 80% of the An-xyl activity could be retained upon treatment at pH 2.0-8.0 for 24 h. The hydrolysis of tea stem by An-xyl and cellulase produced 19.3% and 38.6% higher reducing sugar content at 2 h and 4 h, respectively, than that of using cellulase alone. This study showed that the An-xyl mined from differential expression exhibited high xylose tolerance and higher catalytic activity and stability, and could hydrolyze tea stem lignocellulose synergistically, which enriched the resource of β-xylosidase with high xylose tolerance, thus may facilitate the advanced experimental research and its application.
Aspergillus niger/genetics*
;
Xylose/metabolism*
;
Molecular Docking Simulation
;
Xylosidases/genetics*
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Cellulases
;
Tea
;
Hydrogen-Ion Concentration
;
Substrate Specificity
6.Expression of β-glucosidase An-bgl3 from Aspergillus niger for conversion of scopolin.
Kunpeng YU ; Cheng PENG ; Yanling LIN ; Lijun LI ; Hui NI ; Qingbiao LI
Chinese Journal of Biotechnology 2023;39(3):1232-1246
Scopoletin is a coumarin compound with various biological activities including detumescence and analgesic, insecticidal, antibacterial and acaricidal effects. However, interference with scopolin and other components often leads to difficulties in purification of scopoletin with low extraction rates from plant resource. In this paper, heterologous expression of the gene encoding β-glucosidase An-bgl3 derived from Aspergillus niger were carried out. The expression product was purified and characterized with further structure-activity relationship between it and β-glucosidase analyzed. Subsequently, its ability for transforming scopolin from plant extract was studied. The results showed that the specific activity of the purified β-glucosidase An-bgl3 was 15.22 IU/mg, the apparent molecular weight was about 120 kDa. The optimum reaction temperature and pH were 55 ℃ and 4.0, respectively. Moreover, 10 mmol/L metal ions Fe2+ and Mn2+ increased the enzyme activity by 1.74-fold and 1.20-fold, respectively. A 10 mmol/L solution containing Tween-20, Tween-80 and Triton X-100 all inhibited the enzyme activity by 30%. The enzyme showed affinity towards scopolin and tolerated 10% methanol and 10% ethanol solution, respectively. The enzyme specifically hydrolyzed scopolin into scopoletin from the extract of Erycibe obtusifolia Benth with a 47.8% increase of scopoletin. This demonstrated that the β-glucosidase An-bgl3 from A. niger shows specificity on scopolin with good activities, thus providing an alternative method for increasing the extraction efficiency of scopoletin from plant material.
Aspergillus niger/genetics*
;
beta-Glucosidase/chemistry*
;
Scopoletin
;
Polysorbates
;
Coumarins
7.Sinogram interpolation combined with unsupervised image-to-image translation network for CT metal artifact correction.
Jiahong YU ; Kunpeng ZHANG ; Shuang JIN ; Zhe SU ; Xiaotong XU ; Hua ZHANG
Journal of Southern Medical University 2023;43(7):1214-1223
OBJECTIVE:
To propose a framework that combines sinogram interpolation with unsupervised image-to-image translation (UNIT) network to correct metal artifacts in CT images.
METHODS:
The initially corrected CT image and the prior image without artifacts, which were considered as different elements in two different domains, were input into the image transformation network to obtain the corrected image. Verification experiments were carried out to assess the effectiveness of the proposed method using the simulation data, and PSNR and SSIM were calculated for quantitative evaluation of the performance of the method.
RESULTS:
The experiment using the simulation data showed that the proposed method achieved better results for improving image quality as compared with other methods, and the corrected images preserved more details and structures. Compared with ADN algorithm, the proposed algorithm improved the PSNR and SSIM by 2.4449 and 0.0023 when the metal was small, by 5.9942 and 8.8388 for images with large metals, and by 8.8388 and 0.0130 when both small and large metals were present, respectively.
CONCLUSION
The proposed method for metal artifact correction can effectively remove metal artifacts, improve image quality, and preserve more details and structures on CT images.
Artifacts
;
Algorithms
;
Computer Simulation
;
Tomography, X-Ray Computed
8.Clinical efficacy and prognosis of different laparoscopic hiatal hernia repair
Weigang WANG ; Kunpeng QU ; Xiaoyong TANG ; Xiaobei ZHANG ; Chenghui REN ; Baoshun YANG ; Yongjiang YU
Chinese Journal of General Surgery 2022;37(11):830-833
Objective:To compare the effectiveness and recurrence rate of different types of mesh or without mesh in laparoscopic hiatal hernia repair.Methods:From Jan 2016 to Mar 2022 at the three hospital 90 patients with hiatal hernia, including 26 cases without mesh, 29 cases using synthetic mesh, and 35 cases using biological mesh underwent laparoscopic hiatal hernia repair.Results:The surgical procedures was successful in all the 90 cases without conversion to open surgeny. There were no statistically significant differences in operative time, intraoperative blood loss and postoperative hospital stay among the three groups ( P>0.05), and there were statistically significant differences in hospital cost between the group without mesh and synthetic mesh and biological mesh ( P<0.05). Long-term follow-up was achieved in 87 patients, with a follow-up rate of 96.7% (87/90), and a median follow-up time of 44 months. There were no significant differences in the incidence of postoperative complications (diarrhea, dysphagia, abdominal distension, chest pain), recurrence rate of symptoms (acid reflux, heartburn) and patient satisfaction among the three groups ( P>0.05). Conclusion:In laparoscopic hiatal hernia repair, the mesh should be carefully selected according to the specific intraoperative situation for a satisfactory clinical efficacy.
9.Status of HVPG clinical application in China in 2021
Wen ZHANG ; Fuquan LIU ; Linpeng ZHANG ; Huiguo DING ; Yuzheng ZHUGE ; Jitao WANG ; Lei LI ; Guangchuan WANG ; Hao WU ; Hui LI ; Guohong CAO ; Xuefeng LU ; Derun KONG ; Lin SUN ; Wei WU ; Junhui SUN ; Jiangtao LIU ; He ZHU ; Dongliang LI ; Wuhua GUO ; Hui XUE ; Yu WANG ; Jiancuo GENGZANG ; Tian ZHAO ; Min YUAN ; Shirong LIU ; Hui HUAN ; Meng NIU ; Xin LI ; Jun MA ; Qingliang ZHU ; Wenbo GUO ; Kunpeng ZHANG ; Xiaoliang ZHU ; Birun HUANG ; Jianan LI ; Weidong WANG ; Hongfeng YI ; Qi ZHANG ; Long GAO ; Guo ZHANG ; Zhongwei ZHAO ; Kai XIONG ; Zexin WANG ; Hong SHAN ; Mingsheng LI ; Xueqiang ZHANG ; Haibin SHI ; Xiaogang HU ; Kangshun ZHU ; Zhanguo ZHANG ; Hong JIANG ; Jianbo ZHAO ; Mingsheng HUANG ; Wenyong SHEN ; Lin ZHANG ; Feng XIE ; Zhiwei LI ; Changlong HOU ; Shengjuan HU ; Jianwei LU ; Xudong CUI ; Ting LU ; Shaoqi YANG ; Wei LIU ; Junping SHI ; Yanming LEI ; Jinlun BAO ; Tao WANG ; Weixin REN ; Xiaoli ZHU ; Yong WANG ; Lei YU ; Qiang YU ; Huiling XIANG ; Wenqiang LUO ; Xiaolong QI
Chinese Journal of Hepatology 2022;30(6):637-643
Objective:The investigation and research on the application status of Hepatic Venous Pressure Gradient (HVPG) is very important to understand the real situation and future development of this technology in China.Methods:This study comprehensively investigated the basic situation of HVPG technology in China, including hospital distribution, hospital level, annual number of cases, catheters used, average cost, indications and existing problems.Results:According to the survey, there were 70 hospitals in China carrying out HVPG technology in 2021, distributed in 28 provinces (autonomous regions and municipalities directly under the central Government). A total of 4 398 cases of HVPG were performed in all the surveyed hospitals in 2021, of which 2 291 cases (52.1%) were tested by HVPG alone. The average cost of HVPG detection was (5 617.2±2 079.4) yuan. 96.3% of the teams completed HVPG detection with balloon method, and most of the teams used thrombectomy balloon catheter (80.3%).Conclusion:Through this investigation, the status of domestic clinical application of HVPG has been clarified, and it has been confirmed that many domestic medical institutions have mastered this technology, but it still needs to continue to promote and popularize HVPG technology in the future.
10.Research progress in endoscopic retrograde cholangiopancreatography-mediated photodynamic therapy for cholangiocarcinoma.
Kunpeng WANG ; Li XIONG ; Zijian ZHANG ; Kai LIU ; Yunpeng HUANG ; Xin YANG ; Qinglong LI ; Wei CHEN ; Heng ZOU ; Yu WEN
Journal of Central South University(Medical Sciences) 2019;44(11):1275-1280
The malignant degree of cholangiocarcinoma is high, and the early diagnosis is difficult. The vast majority of patients are unresectable when they are diagnosed. The patients have low quality of life and short survival cycle. Traditional radiotherapy and chemotherapy have poor efficacy and lead to side effects, and thus lack effective control measures for cholangiocarcinoma. Endoscopic retrograde cholangiopancreatography (ERCP) is an important method for diagnosing and treating biliary tract diseases. Photodynamic therapy (PDT) is a new local treatment for cholangiocarcinoma. In recent years, ERCP-mediated PDT treatment of cholangiocarcinoma has gradually emerged. ERCP-mediated PDT can effectively relieve the symptoms of patients with cholangiocarcinoma, improve the patients' quality of life, prolong the survival cycle, and is expected to become a new treatment for cholangiocarcinoma.
Bile Duct Neoplasms
;
diagnosis
;
Bile Ducts, Intrahepatic
;
Cholangiocarcinoma
;
diagnosis
;
Cholangiopancreatography, Endoscopic Retrograde
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Humans
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Photochemotherapy
;
Quality of Life

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