1.Comparative study on methods for colon polyp endoscopic image segmentation and classification based on deep learning
Jian CHEN ; Zhenni WANG ; Kaijian XIA ; Ganhong WANG ; Luojie LIU ; Xiaodan XU
Journal of Shanghai Jiaotong University(Medical Science) 2024;44(6):762-772
Objective·To compare the performance of various deep learning methods in the segmentation and classification of colorectal polyp endoscopic images,and identify the most effective approach.Methods·Four colorectal polyp datasets were collected from three hospitals,encompassing 1 534 static images and 15 videos.All samples were pathologically validated and categorized into two types:serrated lesions and adenomatous polyps.Polygonal annotations were performed by using the LabelMe tool,and the annotated results were converted into integer mask formats.These data were utilized to train various architectures of deep neural networks,including convolutional neural network(CNN),Transformers,and their fusion,aiming to develop an effective semantic segmentation model.Multiple performance indicators for automatic diagnosis of colon polyps by different architecture models were compared,including mIoU,aAcc,mAcc,mDice,mFscore,mPrecision and mRecall.Results·Four different architectures of semantic segmentation models were developed,including two deep CNN architectures(Fast-SCNN and DeepLabV3plus),one Transformer architecture(Segformer),and one hybrid architecture(KNet).In a comprehensive performance evaluation of 291 test images,KNet achieved the highest mIoU of 84.59%,significantly surpassing Fast-SCNN(75.32%),DeepLabV3plus(78.63%),and Segformer(80.17%).Across the categories of"background","serrated lesions"and"adenomatous polyps",KNet's intersection over union(IoU)were 98.91%,74.12%,and 80.73%,respectively,all exceeding other models.Additionally,KNet performed excellently in key performance metrics,with aAcc,mAcc,mDice,mFscore,and mRecall reaching 98.59%,91.24%,91.31%,91.31%,and 91.24%,respectively,all superior to other models.Although its mPrecision of 91.46%was not the most outstanding,KNet's overall performance remained leading.In inference testing on 80 external test images,KNet maintained an mIoU of 81.53%,demonstrating strong generalization capabilities.Conclusion·The semantic segmentation model of colorectal polyp endoscopic images constructed by deep neural network based on KNet hybrid architecture,exhibits superior predictive performance,demonstrating its potential as an efficient tool for detecting colorectal polyps.
2.Constructing an artificial intelligence assisted system for colonoscopy quality control based on various deep learning architectures
Jian CHEN ; Zihao ZHANG ; Ganhong WANG ; Zhenni WANG ; Kaijian XIA ; Xiaodan XU
Chinese Journal of Medical Physics 2024;41(11):1443-1452
Objective To develop deep learning models for colonoscopy quality control using various deep learning architectures,and to delve into the decision-making mechanisms.Methods The colonoscopy images were selected from two datasets separately constructed by the HyperKvasir and Changshu Hospital Affiliated to Soochow University,encompassing intestines of varying degrees of cleanliness,polyps,and cecums.After image preprocessing and enhancement,transfer learning was carried out using the pre-trained models based on convolutional neural network(CNN)and Transformer.The model training adopted cross-entropy loss functions and Adam optimizer,and simultaneously implemented learning rate scheduling.To enhance model transparency,a thorough interpretability analysis was conducted using Grad-CAM,Guided Grad-CAM,and SHAP.The final model was converted to ONNX format and deployed on various equipment terminals to achieve real-time colonoscopy quality control.Results In a dataset of 3 831 colonoscopy images,EfficientNet model outperformed the other models on the test set,achieving an accuracy of 0.992 which was higher than those of the other models based on CNN(DenseNet121,ResNet50,VGG19)and Transformer(ViT,Swin,CvT),with a precision,recall rate,and F1 score of 0.991,0.989,and 0.990.On an external test set of 358 images,EfficientNet model had an average AUC,precision,and recall rate of 0.996,0.948,and 0.952,respectively.Although EfficientNet model is high-performing,some misjudgments still occurred.Interpretability analysis highlighted key image areas affecting decision-making.In addition,EfficientNet model was successfully converted to ONNX format and deployed on multiple platforms and devices,and it ensured real-time colonoscopy quality control with an inference speed of over 60 frames per second.Conclusion Among the 7 models developed for colonoscopy quality control based on CNN and Transformer,EfficientNet demonstrated exemplary performance across all categories and is deployed for real-time predictions on multiple terminals,aiming to provide patients with better medical care.
3.Study on the construction of modular and multidisciplinary nutrition innovation platform in Shanghai
Huachun WENG ; Gang XU ; Zhenni ZHU ; Lin ZHANG ; Yanfeng CHEN ; Jie SONG ; Saiqi QI ; Xiaoguang LI ; Linjun CHEN ; Jin SU ; Hui WANG
Shanghai Journal of Preventive Medicine 2022;34(11):1134-1140
ObjectiveTo determine the situation and challenges of innovation platforms in China, and to explore the construction strategy of Shanghai Nutrition Innovation Platform, which is suitable for Shanghai and may achieve the research and transformation of nutrition innovation and population health, so as to coordinate, unite and gather the superior resources of all parties and promote nutrition innovation. MethodsConstruction scheme and operational mechanism of Shanghai Nutrition Innovation Platform were explored by literature review, expert consultation and questionnaire. ResultsThere were various forms of innovation platforms in China. However, challenges were identified, such as decentralizing force, resource rearrangement and insufficient sharing effect. Shanghai Nutrition Innovation Platform adopted a modular organizational structure, which was divided into central group, node group, and subject group. Shanghai Center for Disease Control and Prevention, as the central organization, is responsible for the platform operation management. The expert database as an academic committee selected key organizations from nutrition-related universities, research institutes, academic associations, centers for disease control and prevention, hospitals and the industry. Based on the opening of its own innovation resources, the platform made effective use of external innovation resources and formed a closely integrated nutrition innovation network of multiple disciplines. ConclusionThis study promotes the construction of innovation platform model of cooperation, co-construction and resource sharing, and provides reference for the construction of innovation platform in China.
4.Genetic characteristics of Echovirus 11 circulating in Xiangyang, Hubei Province between 2016 and 2017
Zhenni WEI ; Shasha QIAN ; Yeqing TONG ; Changzheng XU ; Jia LU ; Jing GUO ; Wenhui WANG ; Yanping ZHOU ; Zejun WANG ; Shengli MENG ; Xiaoqi CHEN ; Xuhua GUAN ; Shuo SHEN
Chinese Journal of Microbiology and Immunology 2021;41(2):133-142
Objective:To analyze the molecular characteristics of Echovirus 11 (Echo11) strains isolated in Xiangyang, Hubei Province from 2016 to 2017 based on the sequences of VP1 gene.Methods:Rectal and throat swab specimens were collected from children with hand, foot and mouth disease (HFMD) in Xiangyang from 2016 to 2017. Echo11 strains were detected by real-time reverse transcriptase PCR (RT-PCR) and isolated after cultured in human rhabdosarcoma (RD) cells. The VP1 regions of Echo11 strains isolated from RD cells and the whole genomes of three representative Echo11 strains were amplified by conventional RT-PCR and the sequences were analyzed. DNAStar7.0 (MegAlign) and MEGA6.0 (Data) were used to analyze the homology and mutation sites in nucleotide and amino acid sequences. Neighbor-joining method was used to construct phylogenetic trees. Recombination analysis was performed with SimPlot software (BootScanning).Results:A total of 11 Echo11 strains were isolated from 3 494 HFMD cases, accounting for 0.31%. They were highly homologous in the VP1 gene. These strains shared 98.4%-100.0% homology in nucleotide sequences and 98.3%-100.0% homology in amino acid sequences. The homology between the 11 Echo11 strains and the prototype strain (Echo11/Gregory, X80059) was 73.9%-74.8% in nucleotide sequences and 87.7%-88.7% in amino acid sequences. All of the Echo11 strains circulating in Xiangyang were classified into lineage D, having a similarity to the strains circulating in some regions of mainland China since 2013. In multiple regions of the genome, the Echo11 strains isolated in Xiangyang were highly similar to the Henan Echo1 strains in 2010 and the Hubei Echo6 strains in 2015, suggesting there was recombination within the genome of Echo11 strains in Xiangyang.Conclusions:The Echo11 strains circulating in Xiangyang from 2016 to 2017 belonged to lineage D and were recombinant strains.
5.Correlation of damage-associated molecular pattern molecules with age and body mass index
Huan YANG ; Zhenni CHEN ; Xing CHEN ; Sijin LI ; Huiyang LI ; Fei XU ; Guofeng XU ; Biqiong REN
Chinese Journal of Preventive Medicine 2021;55(4):492-498
Objective:To explore the correlation of damage-associated molecular pattern molecules(DAMPs) serum S100, C-reactive protein (CRP), serum amyloid A (SAA) and uric acid (UA) with age and body mass index (BMI) to provide direction for further study of metabolic inflammation and inflammaging.Methods:The observational study method was used,and three hundred and sixty-six healthy people (131 males and 235 females) were selected from the physical examination center of the Second People′s Hospital of Hunan Province from May to October 2020. They were divided into three age groups according to the age interval of 20 years, including 156 (53 males and 103 females) aged 20-40 years, 110 (36 males and 74 females) aged 41-60 years, and 100 (42 males and 58 females) aged 61-80 years. Kruskal Wallis H test was used to compare the differences of serum S100, CRP, SAA and UA levels among different age groups. According to the Health Industry Standards of the People′s Republic of China-Weight Determination for Adults, the boundary is BMI =24 kg/m 2. The healthy people were divided into non overweight (BMI<24 kg/m 2) and overweight (BMI ≥ 24 kg/m 2) two groups. The 1∶1 propensity score was used to match the age and gender. There were 96 non overweight subjects [43 males, 53 females, age 52 (35, 66) years], 96 overweight subjects [44 males, 52 females, age 52 (36, 64) years]. The serum levels of S100, CRP, SAA and UA in different BMI groups were compared by Mann-Whitney U test. Results:The median serum UA concentrations in males and females were 356 and 277 μmol/L, and the levels of serum UA of male was significantly higher than that of female ( Z=-10.428, P<0.001); the median serum SAA concentrations in males and females were 3.1 mg/L and 4.4 mg/L, while the serum SAA level of female was significantly higher than that of male ( Z=3.652, P<0.001); for 20-40, 41-60, and 61-80 years old group, the median concentration of serum S100 was 0.058, 0.057, 0.070 μg/L, and the median concentration of serum CRP was 0.32, 0.58, 0.93 mg/L; the median serum SAA concentrations were 3.2, 4.0, 5.2 mg/L; serum uric acid concentrations were (301.8±61.5), (298.6±69.8), (329.0±77.8) μmol/L. The levels of serum S100, CRP, SAA, UA in 61-80 years group were significantly higher than those of 20-40 years group ( H=-2.749, H=-6.731, H=-5.033, H=-2.521, P=0.018, P<0.001, P<0.001, P=0.035) and 41-60 years old group ( H=-2.719, H=-2.539, H=-2.540, H=-2.486, P=0.020, P=0.033, P=0.033, P=0.039).The levels of serum CRP of 41-60 years group was significantly higher than that of 20-40 years group ( H=-4.108, P<0.001). There was no significant difference in levels of serum S100, SAA and UA between 20-40 years group and 41-60 years group ( H=0.189, H=-2.360, H=-0.165, P=1.000, P=0.055, P=1.000); the levels of serum CRP and SAA were positively correlated with age ( r s =0.342, r s =0.301, P<0.001, P<0.001); for overweight, non-overweight group, the median concentrations of serum S100 were 0.065 μg/L, 0.059 μg/L, the median concentrations of serum CRP were 0.92 mg/L, 0.47 mg/L, the median concentrations of serum SAA were 5.0 mg/L, 4.1 mg/L, the median concentrations of serum UA were 339.5 μmol/L, 301.5 μmol/L, the levels of CRP, SAA and UA in the overweight group were higher than those in the non-overweight group ( Z=4.278, Z=2.025, Z=3.787, P<0.001, P=0.043, P<0.001); the levels of S100 in the overweight group was higher than those in the non-overweight group, but there was no significant difference in S100 between the two groups ( Z=0.862, P=0.388); the levels of Serum CRP and UA were positively correlated with BMI ( r s =0.348, r s =0.264, P<0.001, P=0.009). Conclusions:With the increase of age, the serum S100, CRP, SAA and UA levels of healthy people may be on the rise, especially the serum CRP and SAA levels are positively correlated with age; the serum S100, CRP, SAA and UA levels of overweight people may be higher than those of non-overweight people, especially the serum CRP, UA levels are positively correlated with BMI.
6.Correlation of damage-associated molecular pattern molecules with age and body mass index
Huan YANG ; Zhenni CHEN ; Xing CHEN ; Sijin LI ; Huiyang LI ; Fei XU ; Guofeng XU ; Biqiong REN
Chinese Journal of Preventive Medicine 2021;55(4):492-498
Objective:To explore the correlation of damage-associated molecular pattern molecules(DAMPs) serum S100, C-reactive protein (CRP), serum amyloid A (SAA) and uric acid (UA) with age and body mass index (BMI) to provide direction for further study of metabolic inflammation and inflammaging.Methods:The observational study method was used,and three hundred and sixty-six healthy people (131 males and 235 females) were selected from the physical examination center of the Second People′s Hospital of Hunan Province from May to October 2020. They were divided into three age groups according to the age interval of 20 years, including 156 (53 males and 103 females) aged 20-40 years, 110 (36 males and 74 females) aged 41-60 years, and 100 (42 males and 58 females) aged 61-80 years. Kruskal Wallis H test was used to compare the differences of serum S100, CRP, SAA and UA levels among different age groups. According to the Health Industry Standards of the People′s Republic of China-Weight Determination for Adults, the boundary is BMI =24 kg/m 2. The healthy people were divided into non overweight (BMI<24 kg/m 2) and overweight (BMI ≥ 24 kg/m 2) two groups. The 1∶1 propensity score was used to match the age and gender. There were 96 non overweight subjects [43 males, 53 females, age 52 (35, 66) years], 96 overweight subjects [44 males, 52 females, age 52 (36, 64) years]. The serum levels of S100, CRP, SAA and UA in different BMI groups were compared by Mann-Whitney U test. Results:The median serum UA concentrations in males and females were 356 and 277 μmol/L, and the levels of serum UA of male was significantly higher than that of female ( Z=-10.428, P<0.001); the median serum SAA concentrations in males and females were 3.1 mg/L and 4.4 mg/L, while the serum SAA level of female was significantly higher than that of male ( Z=3.652, P<0.001); for 20-40, 41-60, and 61-80 years old group, the median concentration of serum S100 was 0.058, 0.057, 0.070 μg/L, and the median concentration of serum CRP was 0.32, 0.58, 0.93 mg/L; the median serum SAA concentrations were 3.2, 4.0, 5.2 mg/L; serum uric acid concentrations were (301.8±61.5), (298.6±69.8), (329.0±77.8) μmol/L. The levels of serum S100, CRP, SAA, UA in 61-80 years group were significantly higher than those of 20-40 years group ( H=-2.749, H=-6.731, H=-5.033, H=-2.521, P=0.018, P<0.001, P<0.001, P=0.035) and 41-60 years old group ( H=-2.719, H=-2.539, H=-2.540, H=-2.486, P=0.020, P=0.033, P=0.033, P=0.039).The levels of serum CRP of 41-60 years group was significantly higher than that of 20-40 years group ( H=-4.108, P<0.001). There was no significant difference in levels of serum S100, SAA and UA between 20-40 years group and 41-60 years group ( H=0.189, H=-2.360, H=-0.165, P=1.000, P=0.055, P=1.000); the levels of serum CRP and SAA were positively correlated with age ( r s =0.342, r s =0.301, P<0.001, P<0.001); for overweight, non-overweight group, the median concentrations of serum S100 were 0.065 μg/L, 0.059 μg/L, the median concentrations of serum CRP were 0.92 mg/L, 0.47 mg/L, the median concentrations of serum SAA were 5.0 mg/L, 4.1 mg/L, the median concentrations of serum UA were 339.5 μmol/L, 301.5 μmol/L, the levels of CRP, SAA and UA in the overweight group were higher than those in the non-overweight group ( Z=4.278, Z=2.025, Z=3.787, P<0.001, P=0.043, P<0.001); the levels of S100 in the overweight group was higher than those in the non-overweight group, but there was no significant difference in S100 between the two groups ( Z=0.862, P=0.388); the levels of Serum CRP and UA were positively correlated with BMI ( r s =0.348, r s =0.264, P<0.001, P=0.009). Conclusions:With the increase of age, the serum S100, CRP, SAA and UA levels of healthy people may be on the rise, especially the serum CRP and SAA levels are positively correlated with age; the serum S100, CRP, SAA and UA levels of overweight people may be higher than those of non-overweight people, especially the serum CRP, UA levels are positively correlated with BMI.
7.Study on the Effects of Costunolide on the Proliferation ,Migration and Apoptosis of Human Breast Cancer SK- BR-3 Cells and Its Mechanism
Qiang MA ; Shu XIONG ; Jiawei MIAO ; Jie CHEN ; Haiying ZHOU ; Jiao LUO ; Zhenni YANG ; Houliang SUN ; Xuesong DENG
China Pharmacy 2020;31(11):1342-1347
OBJECTIVE:To study the effects of costunolide on the proliferation ,migration and apoptosis of breast cancer SK-BR-3 cells and its mechanism. METHODS :SK-BR-3 cells in logarithmic growth period were collected and cultured with different concentrations (10,20,30,40,50 μmol/L)of costunolide for 24,48,72 h. Inhibitory rate of costunolide on cell proliferation was detected with CCK- 8. The cells were divided into blank control group and costunolide group (10,20,30 μmol/L). Hoechst 33258 fluorescence was used to observe the morphology and apoptosis of cells ,and apoptotic rate of cells were calculated. Cell scratch test was used to detect the migration ability of cells and calculate the migration rate. Western blotting was used to detect the relative expression level of Bcl- 2,Bax,Caspase-3 and Cleaved Caspase- 3 in cells. RESULTS :The proliferation of SK-BR-3 cells were significantly inhibited by costunolide (P<0.05 or P<0.01),and it shows a trend of concentration and time dependence. In the blank control group ,cells possessed clear contour ,regular shape and good adherence . Compared with blank control group,the number of cells were decreased significantly in 10,20,30 μmol/L costunolide groups,the cell structure was loose,the volume was reduced ,and the gap became larger ,and most of the cell contour disappeared and became round ,the cell adherence was poor ;cell migration rate and Bcl- 2 protein relative expression level were decreased significantly ,while apoptosis rate and the relative expression level of Bax ,Caspase-3 and Cleaved Caspase- 3 protein were significantly increased (P<0.05 or P<0.01). CONCLUSIONS : Costunolide can inhibit the proliferation and migration ,and induce apoptosis of human breast cancer SK-BR- 3 cells,mechanism of which may be through up-regulating the expression of Bax ,Caspase-3 and Cleaved Caspase- 3 while down-regulating the expression ofBcl-2.
8. The level and clinical significance of soluble ST2 in heart failure patients with atrial fibrillation
Yunping WANG ; Xinmei LIANG ; Xiaorong ZHENG ; Kegang JIA ; Zhenni CHEN ; Tian ZHOU ; Xuejing HAN ; Ping SHI
Chinese Journal of Laboratory Medicine 2019;42(11):933-941
Objective:
To determine the level of Soluble Suppression of Tumorigenicity-2 (sST2) in patients with heart failure(HF) and atrial fibrillation (AF), and to explore its diagnostic and prognostic value in patients with HF and AF.
Methods:
A prospective cohort study was carried out to investigate the data of 185 HF patients who were hospitalized between January 2018 and June 2018 in department of cardiology or department of cardiac care unit in TEDA International Cardiovascular Hospital. And according to whether they had atrial fibrillation before admission, we categorized patients into: HF with sinus rhythm (HF-SR, n=90) and HF with AF(HF-AF, n=95). Meanwhile, 40 healthy controls were collected. Baseline data of HF-SR and HF-AF groups and plasma sST2 levels in different ejection fraction groups were compared. Plasma sST2 level was determined by enzyme-linked immunosorbent assay(ELISA). Statistical methods such as nonparametric test and Spearman correlation analysis were used. The receiver operating characteristic curve was applied to evaluate the diagnostic value of sST2 in HF-SR and HF-AF groups. And by using the COX risk model, Multi-factor COX analysis was used to analyze the prognosis of patients.
Results:
Compared with healthy controls, the median (P25, P75) of Plasma sST2 levels in HF patients increased remarkably [32.93 (20.31-51.39) ng/mL
9.The imaging manifestation and pathological analysis of intracerebroventricular central neurocytoma
Hui CHEN ; Jingdong YAN ; Tao CHEN ; Zhenni LEI ; Wen CHEN
The Journal of Practical Medicine 2018;34(5):746-749
Objective To explore the radiological features of intracerebroventricular central neurocytoma and so as to improve the diagnosis of this disease. Methods Thirty patients with pathologically confirmed intra-cerebroventricular central neurocytoma in Nanfang Hospital in past 7 years were analyzed retrospectively for their clinical,radiological and pathological features combined with literatures review. Results Lesions of central neuro-cytoma located at the Monro's foramen areas,the anterior horns and bodies of lateral ventricles.Twenty eight of the patients underwent MRI(with 4 patients received MRS)and 11 patients underwent CT.All cases revealed unilateral or bilateral hydrocephalus of the lateral ventricles and ventriculomegaly.Plain CT revealed heterogeneous isodensity or slighly high density lesions with multiple cystic degeneration,necrosis and calcification while a few lesions(4 le-sions)showed hemorrhage.Heterogeneous isointense or mild hypointense were demonstrated on T1-weight MRI and heterogeneous isointense or slightly hyperintense on T2-weight MRI.Multiple cystic degeneration(always showed as distinctive "soap bubble sign"), necrosis and calcification could also be found within the tumor. The solid compo-nent of tumor revealed slightly high to high signal intensity on DWI while the cystic and necrosis components showed low signal intensity.Most of the tumors showed mild to moderate enhancement with vessels passing through on contrast scan. All cases with 1H MRS showed with obviously increased in Cho peak and decreased in Cr and NAA peaks.In immunohistochemical assay,most of the tumors revealed positive expressions of Neu-N,Synaptophy-sin, GFAP and hypo-level Ki-67. Conclusions The intracerebroventricular central neurocytoma has some typical imaging manifestations.Comprehensive analysis of CT and MRI can be conducive to preoperative diagnosis and dif-ferential diagnosis with other tumors in the lateral ventricle.
10.Lipid hepatoprotective effect of silibinin on fat-induced nonalcoholic fatty liver rat model
Huawu GAO ; Ming CHEN ; Zijiang LONG ; Zhenni WU ; Manyan HU ; Lina TIAN
Drug Evaluation Research 2017;40(6):773-777
Objective To investigate the lipid hepatoprotective effect of silibinin on high fat diet-induced nonalcoholic fatty liver (NAFL) rat model and provide a theoretical basis for the treatment of silibinin on NAFL.Methods The NAFL rat model was established by administration of high fat emulsion and high fat diet.Rats in control group was treated with saline and normal diet.The model rats were randomly divided into model group,simvastatin (positive drug,1.8 mg/kg) group,Silibinin groups with low,middle and high doses (18.9,37.8 and 75.6 mg/kg).From the fifth week,NAFLrats were treated with different drugsonce a day for eight weeks.All rats were anaesthetized after final administration,Livertissues were weighed for the calculation of hepatic coefficient The hepatic morphology was observed through HE staining.Serum was obtained from abdominal aortic blood for detection of triglyceride separation (TG),total cholesterol (TC),high density lipoprotein (HDL),low-density lipoprotein (LDL),aspartate aminotransferase (AST),and alanine aminotransferase (ALT) levels.Results After eight-week treatment,compared with model group,middle and high doses of silibinin could significantly improve the hepatic steatosis.The levels of hepatic coefficient,serum TC,TG,AST and ALT in rats treated with individual dose of Silibinin were significantly decreased (P < 0.05,0.01).Particularly,high dose of silibinin significantly reduced LDL level whereas elevated HDL level in serum (P < 0.01).Conclusion Silibinin has a therapeutic effect on nonalcoholic fatty liver rats,and possible mechanism is related to lipid-lowering and hepatic protection.

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