1.Bioinformatics Analysis and Validation of Cuproptosis-related Genes in Wilson Disease
Zhuang TAO ; Meixia WANG ; Shuai KANG ; Jipeng LIU ; Rui WANG ; Jiafeng ZHOU ; Wenming YANG
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(15):124-131
ObjectiveTo explore the role of cuproptosis and identify cuproptosis-related genes in Wilson disease (WD) through bioinformatics analysis and clinical validation,providing implications and directions for the diagnosis and treatment of WD. Methods(1) Screening of target genes: The differentially expressed genes (DEGs) between WD and healthy control were obtained from GeneCards,and the cuproptosis-related genes were obtained from Gene Expression Omnibus (GEO) and published literature.The cuproptosis-related genes in WD were obtained by intersection.Through gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses,the specific biological process,functions or metabolic pathways of cuproptosis-related genes in WD were predicted.Molecular docking and PyMOL visualization were then performed to analyze and verify the potential regulatory mechanism of Gandou Fumu Decoction for cuproptosis.(2)Validation of target genes: The blood samples of 15 WD patients treated in the department of encephalopathy and 15 healthy volunteers undergoing physical examinations in the health management center were randomly collected from the First Affiliated Hospital of Anhui University of Chinese Medicine.The expression levels of target genes were determined by Western blot and real-time PCR. Results(1) A total of 3 607 DEGs in WD were obtained from GSE107323 in GEO,and 68 cuproptosis-related genes were obtained from GeneCards and published literature.Twelve common target genes were obtained by intersection,including three up-related genes(SQSTM1,MIF1,and TAX1BP1) and nine down-regulated genes(CP,SERPINE1,AOC3,GPX4,SLC27A5,VEGF-A,PDHB,PDK1,and ATP7B).The common target genes were mainly enriched in monocarboxylic acid metabolism,oxidoreductase activity,negative regulation of molecular functions,which mainly involved HIF-1,ferroptosis and other signaling pathways.Molecular docking and PyMOL visualization results showed Gandou Fumu Decoction had good binding ability with the cuproptosis-related genes PDK1,SERPINE1,VEGFA,and AOC3 in WD.(2)A total of 30 blood samples were collected,including 15 WD patients and 15 health volunteers.Western blot results showed that expression levels of target genes were consistent with the results obtained by bioinformatics analysis.RT-qPCR results showed that compared with healthy volunteers,WD patients had down-regulated mRNA levels of SERPINE1,GPX4,SLC27A5,and VEGF-A and up-regulated mRNA levels of SQSTM1 and MIF1(P<0.05). ConclusionThe expression levels of cuproptosis-related genes in WD patients are consistent with the results predicted by bioinformatics analysis.The characteristic preparation Gandou Fumu Decoction of Xin'an Medicine showed good binding abilities with the cuproptosis-related genes in WD.Cuproptosis may play a key role in the pathophysiological mechanism of WD,which can provide a new target for the diagnosis and treatment of WD.
2.Research status of traditional Chinese medicine monomer mediating related signaling pathways in treatment of intervertebral disc degeneration
Yunyun YANG ; Qiqing CHEN ; Jirong ZHAO ; Bao ZHU ; Dong MA ; Junkai HUANG ; Dehao AN ; Jipeng ZOU ; Weihang LIU
Chinese Journal of Tissue Engineering Research 2024;28(18):2918-2924
BACKGROUND:Intervertebral disk degeneration is a pathological change caused by a series of complex molecular mechanisms that result in the aging and damage of intervertebral discs,ultimately leading to severe clinical symptoms.Traditional Chinese medicine has unique advantages in the treatment of intervertebral disk degeneration due to its low cost,non-addictive nature,multi-target effects,minimally toxic and side effects,and high patient acceptance. OBJECTIVE:To review the latest research results of traditional Chinese medicine monomer intervention-related signaling pathways in the treatment of intervertebral disk degeneration,describe and analyze the action mechanism of traditional Chinese medicine monomer on intervertebral disk degeneration,and provide a new approach and theoretical basis for future basic research and clinical treatment. METHODS:The first author searched for relevant literature from January 2018 to February 2023 in CNKI,PubMed,VIP,and WanFang using the search terms"intervertebral disc,signal pathway".The articles that did not meet the criteria were excluded after preliminary screening of the titles and abstracts.Finally,72 articles were selected for review and analysis. RESULTS AND CONCLUSION:Traditional Chinese medicine monomers can regulate multiple classical signaling pathways such as Wnt/β-catenin,PI3K/Akt,mTOR,NF-κB,and MAPK.They achieve this by regulating oxidative stress,adjusting the expression of pro/anti-apoptotic proteins in cells,stimulating cellular autophagy function,reducing stimulation of cell inflammatory factors,increasing the expression of extracellular matrix markers,reducing the production of matrix-degrading enzymes,maintaining the synthesis and stability of extracellular matrix,inducing differentiation of mesenchymal stem cells in the nucleus pulposus into nucleus pulposus cells,promoting endogenous repair and reconstruction,controlling apoptosis and aging of nucleus pulposus cells,and increasing the activity of nucleus pulposus cells.These actions improve the microenvironment within the intervertebral disc,maintain the normal physiological function of the intervertebral disc,and delay intervertebral disc degeneration.
3.Identification of Chinese Herb Pieces Based on YOLOv4
Cong GUO ; Yujia TIAN ; Yang LI ; Yang LIU ; Jun ZHANG ; Jipeng DI ; Aixia YAN ; An LIU
Chinese Journal of Experimental Traditional Medical Formulae 2023;29(14):133-140
Chinese herbal piece is an important component of the traditional Chinese medicine (TCM) system, and identifying their quality and grading can promote the development and utilization of Chinese herbal pieces. Utilizing deep learning for intelligent identification of Chinese herbal pieces can save time, effort, and cost, while also reasonably avoiding the constraints of human subjectivity, providing a guarantee for efficient identification of Chinese herbal pieces. In this study, a dataset containing 108 kinds of Chinese herbal pieces (14 058 images) was constructed,the basic YOLOv4 algorithm was employed to identify the 108 kinds of Chinese herbal pieces of our database The mean average precision (mAP) of the developed basic YOLOv4 model reached 85.3%. In addition, the receptive field block was introduced into the neck network of YOLOv4 algorithm, and the improved YOLOv4 algorithm was used to identify Chinese herbal pieces. The mAPof the improved YOLOv4 model achieved 88.7%, the average precision of 80 kinds of decoction pieces exceeded 80%, the average precision of 48 kinds of decoction pieces exceeded 90%. These results indicate that adding the receptive field module can help to some extent in the identification of Chinese herbal medicine pieces with different sizes and small volumes. Finally, the average precision of each kind of Chinese herbal medicine piece by the improved YOLOv4 model was further analyzed. Through in-depth analysis of the original images of Chinese herbal medicine pieces with low prediction average precision, it was clarified that the quantity and quality of original images of Chinese herbal medicine pieces are key to performing intelligent object detection. The improved YOLOv4 model constructed in this study can be used for the rapid identification of Chinese herbal pieces, and also provide reference guidance for the manual authentication of Chinese herbal medicine decoction pieces.
4.Research on classification of benign and malignant lung nodules based on three-dimensional multi-view squeeze-and-excitation convolutional neural network.
Yang YANG ; Xiaoqin LI ; Zhenbo HAN ; Jipeng FU ; Bin GAO
Journal of Biomedical Engineering 2022;39(3):452-461
Lung cancer is the most threatening tumor disease to human health. Early detection is crucial to improve the survival rate and recovery rate of lung cancer patients. Existing methods use the two-dimensional multi-view framework to learn lung nodules features and simply integrate multi-view features to achieve the classification of benign and malignant lung nodules. However, these methods suffer from the problems of not capturing the spatial features effectively and ignoring the variability of multi-views. Therefore, this paper proposes a three-dimensional (3D) multi-view convolutional neural network (MVCNN) framework. To further solve the problem of different views in the multi-view model, a 3D multi-view squeeze-and-excitation convolution neural network (MVSECNN) model is constructed by introducing the squeeze-and-excitation (SE) module in the feature fusion stage. Finally, statistical methods are used to analyze model predictions and doctor annotations. In the independent test set, the classification accuracy and sensitivity of the model were 96.04% and 98.59% respectively, which were higher than other state-of-the-art methods. The consistency score between the predictions of the model and the pathological diagnosis results was 0.948, which is significantly higher than that between the doctor annotations and the pathological diagnosis results. The methods presented in this paper can effectively learn the spatial heterogeneity of lung nodules and solve the problem of multi-view differences. At the same time, the classification of benign and malignant lung nodules can be achieved, which is of great significance for assisting doctors in clinical diagnosis.
Humans
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Lung/pathology*
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Lung Neoplasms/pathology*
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Neural Networks, Computer
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Tomography, X-Ray Computed/methods*
5.Research progress of Guizhi Shaoyao Zhimu Decoction in the treatment of rheumatoid arthritis
Zhijiao ZHANG ; Yonghong XIAO ; Shuang ZHU ; Jipeng QI ; Yang WU
International Journal of Traditional Chinese Medicine 2022;44(6):704-707
Guizhi Shaoyao Zhimu Decoction combined with drugs taken internally or external therapy show the benefits for rheumatoid arthritis patients. It can control the clinical symptoms such as swelling and pain of the joints, reduce inflammatory indicators, and has less adverse reactions. Modern pharmacological researches show that it can regulate a variety of inflammatory signaling pathways to achieve anti-inflammatory and analgesic effects, induce apoptosis of synovial cells, resist bone damage, and regulate immunity with multiple treatment targets to rheumatoid arthritis.
6.Establishing prediction model of community-acquired pneumonia complicated with acute respiratory distress syndrome based on artificial neural network
Jipeng MO ; Zhongzhi JIA ; Yan TANG ; Mingxia YANG ; Hui QIN
Chinese Critical Care Medicine 2022;34(4):367-372
Objective:To investigate the independent risk factors of community-acquired pneumonia (CAP) complicated with acute respiratory distress syndrome (ARDS), and the accuracy and prevention value of ARDS prediction based on artificial neural network model in CAP patients.Methods:A case-control study was conducted. Clinical data of 414 patients with CAP who met the inclusion criteria and were admitted to the comprehensive intensive care unit and respiratory department of Changzhou Second People's Hospital Affiliated to Nanjing Medical University from February 2020 to February 2021 were analyzed. They were divided into two groups according to whether they had complicated with ARDS. The clinical data of the two groups were collected within 24 hours after admission, the influencing factors of ARDS were screened out by univariate analysis, and the artificial neural network model was constructed. Through the artificial neural network model, the importance of input layer independent variables (that was, the influence factors obtained from univariate analysis) on the output layer dependent variables (whether ARDS occurred) was drawn. The artificial neural network modeling data pairs were randomly divided into training group ( n = 290) and verification group ( n = 124) in a ratio of 7∶3. The overall prediction accuracy of the training group and the verification group was calculated respectively. At the same time, the receiver operator characteristic curve (ROC curve) was drawn, and the area under the ROC curve (AUC) was calculated. Results:All 414 patients were enrolled in the analysis, including 82 patients with ARDS and 332 patients without ARDS. Univariate analysis showed that gender, age, heart rate (HR), maximum systolic blood pressure (MSBP), maximum respiratory rate (MRR), source of admission, C-reactive protein (CRP), procalcitonin (PCT), erythrocyte sedimentation rate (ESR), neutrophil count (NEUT), eosinophil count (EOS), fibrinogen equivalent unit (FEU), activated partial thromboplastin time (APTT), total bilirubin (TBil), albumin (ALB), lactate dehydrogenase (LDH), serum creatinine (SCr), hemoglobin (Hb) and blood glucose (GLU) were significantly different between the two groups, which might be the risk factors of CAP patients complicated with ARDS. Taking the above 19 risk factors as the input layer and whether ARDS occurred as the output layer, the artificial neural network model was constructed. Among the input layer independent variables, the top five indicators with the largest influence weight on the neural network model were LDH (100.0%), PCT (74.4%), FEU (61.5%), MRR (56.9%), and APTT (51.6%), indicating that that these five indicators had a greater impact on the occurrence of ARDS in patients with CAP. The overall prediction accuracy of the artificial neural network model in the training group was 94.1% (273/290), and that of the verification group was 89.5% (111/124). The AUC predicted by the aforementioned artificial neural network model for ARDS in CAP patients was 0.977 (95% confidence interval was 0.956-1.000).Conclusion:The prediction model of ARDS in CAP patients based on artificial neural network model has good prediction ability, which can be used to calculate the accuracy of ARDS in CAP patients, and specific preventive measures can be given.
7.3DSlicer software assisted microsurgery for parafalcine meningioma through contralateral longitudinal fissure approach
Jipeng YANG ; Xiaotong LI ; Tongju WANG ; Xiaofeng SUN ; Zhaohui LI ; Hongchao HU ; Chen LI
Clinical Medicine of China 2021;37(5):420-425
Objective:To evaluate the effect of microsurgery for parafalcine meningioma through contralateral longitudinal fissure approach assisted by 3DSlicer software.Methods:From January 2020 to January 2021, 18 patients with parafalcine meningioma in The second hospital of Hebei Medical University were randomly selected as the observation group.The contralateral longitudinal fissure was treated by microsurgery assisted by 3DSlicer software.Before operation, improve the imaging examinations such as brain CT plain and enhancement, magnetic resonance angiography and magnetic resonance venography, establish the models of tumor, superior sagittal sinus and superior cerebral artery by using 3DSlicer software, analyze the positional relationship between tumor and superior sagittal sinus and superior cerebral vein, and remove the tumor by contralateral longitudinal fissure approach.Nineteen patients with parafalx meningioma treated by traditional ipsilateral longitudinal fissure approach from January to December 2019 were selected as the control group.The differences in operation time, intraoperative bleeding, limb muscle strength recovery rate, headache and dizziness relief rate were compared between the two groups.Results:In the observation group, the positional relationship between the reconstructed tumor and the superior cerebral vein above its base was completely consistent with the actual situation during the operation.All patients underwent Simpson grade I resection, and there was no injury to the superior cerebral vein and venous sinus during the operation.The recovery rate of limb muscle strength in the observation group (75%(9/12)) was higher than that in the control group (23%(3/13))( P=0.009). There was no significant difference in the operation time, intraoperative bleeding and the remission rate of headache and dizziness one week after operation in the observation group ( P>0.05). Conclusion:3DSlicer software was helpful for preoperative evaluation of the positional relationship between parafalcine meningioma and the anatomic structures such as superior cerebral vein and superior sagittal sinus.Under the guiding of 3DSlicer software, surgeon removed the tumor totally through the contralateral longitudinal fissure approach, which effectively reduced the operative side injury of the important structures such as superior cerebral vein and functional cerebral cortex, and contributed highly to the recovery of limb muscle strength of patients.
8.Preliminary report of preclinical trial of multi-genome engineering pig-to-macaque heart, liver and kidney transplantation
Xuan ZHANG ; Lin WANG ; Hongtao ZHANG ; Zhaoxu YANG ; Shuqiang YUE ; Yanling YANG ; Hailong DONG ; Min CHEN ; Zhihong LU ; Liang CHENG ; Jincheng LIU ; Shiqiang YU ; Geng ZHANG ; Weijun QIN ; Jipeng LI ; Hongjiang WEI ; Luhan YANG ; Liang ZHOU ; Enwu LONG ; Kaishan TAO ; Kefeng DOU
Organ Transplantation 2021;12(1):51-
Objective To investigate the application prospect of the most extensive genome engineering pig internationally in preclinical xenotransplantation. Methods Porcine endogenous retrovirus (PERV) knockout combined with 3 major heterologous antigen gene knockouts and 9 humanized genes for inhibition of complement activation, regulation of coagulation disorders, anti-inflammatory and anti-phagocytosis were transferred into a pig (PERV-KO/3-KO/9-TG) as a donor, and the heart, liver and kidney were obtained and transplanted to 3 Rhesus macaque recipients respectively to establish a preclinical research model of pig-to-Rhesus macaque xenotransplantation. The functional status of xenografts after blood flow reconstruction was observed and the survival of recipients was summarized. The hemodynamics of xenografts were monitored. The change of hematological indexes of each recipient was compared. The histopathological manifestation of xenografts was observed. Results After the blood flow was reconstructed, all xenografts showed ruddy color, soft texture and good perfusion. The transplant heart, liver and kidney showed full arterial and venous blood flow and good perfusion at 1 d after operation. The postoperative survival time of heart, liver, and kidney transplant recipients was 7, 26, and 1 d, respectively. The levels of creatine kinase, creatine kinase isoenzyme, and lactate dehydrogenase increased in heart transplant recipient at 1 d after operation, and gradually recovered to near normal levels at 6 d after operation. All indexes increased sharply at 7 d after operation. The level of aspartate aminotransferase increased in liver transplant recipients at 2 d after operation, and the alanine aminotransferase basically returned to normal at 10 d after operation, but the total bilirubin continued to increase. Both aspartate aminotransferase and alanine aminotransferase increased at 12 d after operation, and reached a peak at 15 d after operation. The kidney transplant recipient developed mild proteinuria at 1 d after operation, and died of sudden severe arrhythmia. Histopathology showed that the tissue structure of cardiac and renal xenografts was close to normal, and liver xenografts presented with patchy necrosis, the liver tissue structure was disordered, accompanied by inflammatory damage, interstitial hemorrhage and thrombotic microangiopathy. Conclusions PERV-KO/3-KO/9-TG pig shows advantages in overcoming hyperacute rejection, mitigating humoral rejection and coagulation dysregulation. However, whether it can be used as potential donor for clinical xenotransplantation needs further evaluation.
9.Verification of method for microbial limit test on diatomite and pearlite
Qiming ZHANG ; Yali WANG ; Yonghao XU ; Lin ZHANG ; Congcong HAN ; Zhidong WANG ; Jipeng ZHANG ; Fujun YANG ; Xiao LIU
Chinese Journal of Blood Transfusion 2021;34(10):1147-1149
【Objective】 To establish a microbial limit test method for diatomite and pearlite, and verify its applicability. 【Methods】 According to the requirements of general rule 1105, Microbial Limit Test for Non Sterile Products of Pharmacopoeia of the People′s Republic of China (2020 Edition), the applicability test of microbial counting methods for three batches of perlite and diatomite was conducted before the microbial limit test of samples. The microbial growth of filter aid was analyzed and the recovery rate of each test bacterium was calculated. 【Results】 The ratio of the colony number of the test group minus the colony number of the test sample control group to the bacterial liquid control group was in the range of 0.5~2.0. 【Conclusion】 The method is accurate, reliable and can be used for microbial limit test of diatomite and perlite.
10.MiR-128-3p Regulates Proliferation, Migration and Apoptosis of Glioblastoma Multiforme by Targeting HOXA5
Jipeng YANG ; Xiang QIU ; Chen LI ; Jiankai YANG ; Hongjiang LIU ; Baohua JIAO
Cancer Research on Prevention and Treatment 2021;48(1):12-18
Objective To investigate the reasons of HOXA5 overexpression in GBM and the molecular mechanism of miR-128-3p regulating the proliferation, invasion and apoptosis of glioblastoma multiforme. Methods After increasing and decreasing miR-128-3p expression in U87 cell lines by lentivirus transfection, the changes of HOXA5 expression were detected by Western blot, to explore the correlation between miR-128-3p and HOXA5 in GBM. The dual-luciferase reporter tests were performed to detect the target interaction of miR-128-3p with HOXA5. Through CCK-8 test, Transwell test, flow cytometric assay and tumor cell xenograft in nude mice, we verified molecular mechanism of miR-128-3p regulating the proliferation, invasion and apoptosis of GBM

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