1.A digital droplet PCR detection technique based on filter faster R-CNN
Yipeng ZHANG ; Bo CHEN ; Jiaqi LI ; Yedong LIANG ; Huajian ZHANG ; Wenming WU ; Yu ZHANG
Journal of Southern Medical University 2024;44(2):344-353
Objective To propose a method for mitigate the impact of anomaly points(such as dust,bubbles,scratches on the chip surface,and minor indentations)in images on the results of digital droplet PCR(ddPCR)detection to achieve high-throughput,stable,and accurate detection.Methods We propose a Filter Faster R-CNN ddPCR detection model,which employs Faster R-CNN to generate droplet prediction boxes followed by removing the anomalies within the positive droplet prediction boxes using an outlier filtering module(Filter).Using a plasmid carrying a norovirus fragment as the template,we established a ddPCR dataset for model training(2462 instances,78.56%)and testing(672 instances,21.44%).Ablation experiments were performed to test the effectiveness of 3 filtering branches of the Filter for anomaly removal on the validation dataset.Comparative experiments with other ddPCR droplet detection models and absolute quantification experiments of ddPCR were conducted to assess the performance of the Filter Faster R-CNN model.Results In low-dust and dusty environments,the Filter Faster R-CNN model achieved detection accuracies of 98.23%and 88.35%for positive droplets,respectively,with composite F1 scores reaching 99.15%and 99.14%,obviously superior to the other models.The introduction of the filtering module significantly enhanced the positive accuracy of the model in dusty environments.In the absolute quantification experiments,a regression line was plotted using the results from commercial flow cytometry equipment as the standard concentration.The results show a regression line slope of 1.0005,an intercept of-0.025,and a determination coefficient of 0.9997,indicating high consistency between the two results.Conclusion The ddPCR detection technique using the Filter Faster R-CNN model provides a robust detection method for ddPCR under various environmental conditions.
2.A digital droplet PCR detection technique based on filter faster R-CNN
Yipeng ZHANG ; Bo CHEN ; Jiaqi LI ; Yedong LIANG ; Huajian ZHANG ; Wenming WU ; Yu ZHANG
Journal of Southern Medical University 2024;44(2):344-353
Objective To propose a method for mitigate the impact of anomaly points(such as dust,bubbles,scratches on the chip surface,and minor indentations)in images on the results of digital droplet PCR(ddPCR)detection to achieve high-throughput,stable,and accurate detection.Methods We propose a Filter Faster R-CNN ddPCR detection model,which employs Faster R-CNN to generate droplet prediction boxes followed by removing the anomalies within the positive droplet prediction boxes using an outlier filtering module(Filter).Using a plasmid carrying a norovirus fragment as the template,we established a ddPCR dataset for model training(2462 instances,78.56%)and testing(672 instances,21.44%).Ablation experiments were performed to test the effectiveness of 3 filtering branches of the Filter for anomaly removal on the validation dataset.Comparative experiments with other ddPCR droplet detection models and absolute quantification experiments of ddPCR were conducted to assess the performance of the Filter Faster R-CNN model.Results In low-dust and dusty environments,the Filter Faster R-CNN model achieved detection accuracies of 98.23%and 88.35%for positive droplets,respectively,with composite F1 scores reaching 99.15%and 99.14%,obviously superior to the other models.The introduction of the filtering module significantly enhanced the positive accuracy of the model in dusty environments.In the absolute quantification experiments,a regression line was plotted using the results from commercial flow cytometry equipment as the standard concentration.The results show a regression line slope of 1.0005,an intercept of-0.025,and a determination coefficient of 0.9997,indicating high consistency between the two results.Conclusion The ddPCR detection technique using the Filter Faster R-CNN model provides a robust detection method for ddPCR under various environmental conditions.
3.Fucoidan sulfate from Sargassum fusiforme regulates the SARS-CoV-2 receptor AXL expression in human embryonic lung diploid fibroblast cells.
Xuqiang ZHOU ; Weihua JIN ; Di JIANG ; Yipeng XU ; Sanying WANG ; Xinna WU ; Yunchuang CHANG ; Huili SU ; Tianjun ZHU ; Xiaogang XU ; Genxiang MAO
Journal of Zhejiang University. Science. B 2023;24(11):1047-1052
新冠病毒感染疫情严重威胁着世界各国人民的生命健康。目前,对病毒感染的防治研究主要集中在抑制病毒与分子受体的结合上。AXL作为新发现的严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)受体,在协助病毒感染人体呼吸系统中发挥着重要作用,是未来临床干预的潜在靶点。本研究对已发表的单细胞测序数据进行整理和分析,发现AXL在年轻人肺细胞中的表达水平明显高于老年人。人胚肺二倍体成纤维细胞(2BS)是衰老研究的公认细胞株。本文采用2BS细胞构建复制性细胞衰老模型,发现年轻细胞中AXL的蛋白水平明显高于衰老细胞,据此推测年轻人感染的风险可能更高,需要注意防护。我们发现一种羊栖菜褐藻多糖硫酸酯组分(SFW-3)可显著下调年轻2BS细胞中AXL的表达水平,表明SFW-3具有一定的抗SARS-CoV-2感染的研究价值,同时表明2BS细胞株也可作为潜在的SARS-CoV-2体外感染模型。
Humans
;
SARS-CoV-2
;
Sargassum/metabolism*
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Diploidy
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Sulfates/metabolism*
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COVID-19
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Polysaccharides/pharmacology*
;
Lung
4.Flap combined with 3D printed microporous tianium(tantalum)prosthesis in the treatment of lower extremity soft tissue defect with large bone defect
Yongqing XU ; Xinyu FAN ; Teng WANG ; Shaoquan PU ; Chuan LI ; Xingbo CAI ; Yi CUI ; Xiaoqing HE ; Wei LIN ; Yipeng WU ; Jian SHI ; Xia LI ; Dewei ZHAO ; Baoyi LIU ; Qiang FENG
Chinese Journal of Microsurgery 2022;45(1):21-27
Objective:To investigate the effect of flap combined with 3D printed microporous titanium(tantalum)prosthesis in the treatment of lower extremity soft tissue defect with large bone defect.Methods:From January 2019 to December 2020, 2 patients with large soft tissue defects on dorsal foot together with large metatarsal bone defect and 4 patients with soft tissue defects of calf with large tibial bone defect were treated. The areas of soft tissue defect were 5.0 cm×8.0 cm-15.0 cm×10.0 cm. The length of the bone defect were 3.8 cm to 7.0 cm, 5.75 cm in average. In the first stage, metatarsal bone defect or tibial bone defect was filled with vancomycin blended bone cement, meanwhile, soft tissue defect was repaired with anterolateral femoral flap(ALTF) with vascular anastomosis in 2 cases of feet, and local fascia flap was trans-positioned in 4 cases of lower extremity defects. The sizes of repairing flap were 6.0 cm×8.5 cm-16.0 cm×11.0 cm. Two to 7 months after the initial surgery, the customer designed microporous titanium prostheses were used(5 cases with microporous titanium and 1 with microporous tantalum) to repair the bone defects. The wound healing, the integration of metatarsal and tibial fractures with 3D printed microporous titanium(tantalum) prostheses, and the walking condition were observed after surgery. The follow-up lasted from 6 to 25 months, with an average of 12.7 months.Results:The wound healing in 5 patients was good. The patients stood on the foot in 2 months after surgery, started to walk with the assistance of crutch in 3 months after surgery, and took walk without assistance in 5-6 months after surgery. Good osseous integration were achieved. One diabetic patient had infection of foot wound 3 months after surgery. After removal of microporous titanium prosthesis and replacement of vancomycin blended interstitial substance of bone cement, the wound healed and the patient resumed walking.Conclusion:It is an effective method to encourage the patients to take early ambulation after the surgery for lower extremity soft tissue defect with large bone defect that was repaired by a flap and 3D printed microporous titanium(tantalum)prosthesis. Further observations are required to investigate the long-term efficacy, and the reduction of prosthesis infection rate requires further exploration.
5.An extended analysis of cardiovascular benefits of indoor air filtration intervention among elderly:a randomized crossover trial(Beijing indoor air purifier study,BIAPSY)
Chen JIE ; Wang TONG ; Xu HONGBING ; Zhu YUTONG ; Du YIPENG ; Liu BEIBEI ; Zhao QIAN ; Zhang YI ; Liu LINGYAN ; Yuan NINGMAN ; Fang JIAKUN ; Xie YUNFEI ; Liu SHUO ; Wu RONGSHAN ; Shao DANQING ; Song XIAOMING ; He BEI ; Brunekreef BERT ; Huang WEI
Global Health Journal 2022;6(1):30-34
Objective:Evidence on potential cardiovascular benefits of personal-level intervention among the elderly exposed to high levels of particulate matter(PM)remains limited.We aimed to assess improvements in surrogate markers of cardiovascular injury in vulnerable populations at risks by using indoor air filtration units.Methods:We conducted a randomized crossover trial for 2 separate 2-week air filtration interventions in 20 households of patients with stable chronic obstructive pulmonary disease and their partners in the winter of 2013,with concurrent measurements of indoor PM.The changes in biomarkers indicative of cardiac injury,atherosclerosis progression and systemic inflammation following intervention were evaluated using linear mixed-effect models.Results:In the analysis,average levels of indoor PM with aerodynamic diameters<2.5 μm(PM2.5)decreased significantly by 59.2%(from 59.6 to 24.3 μg/m3,P<0.001)during the active air filtration.The reduction was accompanied by improvements in levels of high-sensitivity cardiac troponin I by-84.6%(95%confidence interval[CI]:-90.7 to-78.6),growth differentiation factor-15 by-48.1%(95%CI:-31.2 to-25.6),osteoprotegerin by-65.4%(95%CI:-56.5 to-18.7),interleukin-4 by-46.6%(95%CI:-62.3 to-31.0)and myeloperoxidase by-60.3%(95%CI:-83.7 to-3.0),respectively.Conclusion:Indoor air filtration intervention may provide potential cardiovascular benefits in vulnerable popu-lations at risks.
6.Prognostic Evaluation of Prognostic Nutrition Index for Patients with Radical Cystectomy: A Meta-analysis
Wenchao TANG ; Yuanwei LI ; Jia CHEN ; Yipeng QIN ; Zhiying WU ; Huifeng FU
Cancer Research on Prevention and Treatment 2021;48(9):871-876
Objective To systematically evaluate the relation between prognostic nutrition index (PNI) and prognosis of bladder cancer (BC) patients treated with radical cystectomy (RC). Methods We searched the literatures about the relation between PNI and the prognosis of patients treated with radical cystectomy published from the inception to January 30, 2021 in PubMed, Embase, Web of Science, CNKI, Wanfang, VIP and Chinese Medical Journal Database, and used RevMan5.3 software for Meta analysis. Results We included six literatures which comprise a total of 1273 patients. The results showed that there was a significant correlation between low PNI and OS of BC patients treated with RC (
7.Retrospect and prospect of surgical treatment of pituitary adenoma in China from 1978-2019
Sen XIE ; Weiliang ZHAO ; Yipeng HAN ; Huayun WU ; Yahui YANG ; Guozhuan MIAO
Chinese Journal of Neuromedicine 2020;19(3):234-240
From 1978 to 2019, the cause of neurosurgery in China has developed rapidly, and the surgical treatment of pituitary adenoma has achieved good results.. This article focuses on the surgical treatment of pituitary adenomas from imaging techniques, surgical techniques and anesthesia techniques, and looks forward to the future.
8.Overexpression of CLPTM1L inhibits the sensitivity of 95-D lung cancer cells to gemcitabine
Yipeng SUN ; Zhenhua NI ; Yingying WU ; Qingge CHEN ; Junjie BI ; Yuhua LIN ; Xiongbiao WANG
Practical Oncology Journal 2019;33(6):486-490
Objective This study aimed to investigate the relationship between CLPTM1L gene and lung cancer 95-D cells sensitivity to gemcitabine,and to explore its potential mechanism of action. Methods Overexpression of lentivirus against CLPTM1L gene was constructed and infected with lung cancer 95-D cells;Cells were divided into the CLPTM1L overexpression group and con-trol group;The proliferation of cells in the overexpressing and control groups after gemcitabine treatment was detected by CCK-8;The changes of CLPTM1L gene and protein were detected by real-time PCR,Western blot and immunochemiluminescence;The changes of caspase-3/7 and caspase-9 activities were detected by bioluminescence;Western blot was used to detect the changes of p-4E-BP1 protein. Results The expression of CLPTM1L gene( P =0. 036) and its protein ( P <0. 01) was significantly increased after CLPTM1L overexpressed lentivirus-infected 95 -D cells;Compared with the control group,the proliferation of CLPTM1L overex-pressing group after gemcitabine treatment was increased(P <0. 01);The activity of caspase activity showed that the activities of caspase-3/7 and caspase-9 in the CLPTM1L overexpression group were significantly lower than those in the control group(P<0. 01);The phosphorylated level of 4E-BP1 protein in the CLPTM1L overexpression group was significantly higher than that in the control group. Conclusion Overexpression of CLPTM1L can reduce the sensitivity of lung cancer cells to gemcitabine. Its mechanism may be to increase the phosphorylation level of 4E-BP1.
9. Development of a quantitative serum assay of Golgi protein 73 in hepatocellular carcinoma using xMAP technology
Yun WU ; Yipeng WANG ; Jie MA ; Yonghong ZHANG ; Huanqin SUN ; Jianping SUN ; Zikang WANG ; Jie XU ; Yanchao DAI ; Ning LI
Chinese Journal of Oncology 2019;41(5):351-356
Objective:
To establish a quantitative assay of serum Golgi protein 73 (GP73) using xMAP technology and evaluate its performance.
Methods:
Monoclonal antibodies against GP73 were prepared and purified, and antibody pair screening was performed by double-antibody sandwich enzyme-linked immunosorbent assay. The screened antibodies were used to construct a Luminex liquid chip detection system, and the analysis performance of the detection system was evaluated. The serum levels of GP73 were detected in 90 clinical samples from healthy controls and patients with chronic hepatitis B infection (CHB) and hepatocellular carcinoma (HCC).
Results:
Five anti-GP73 monoclonal antibodies were prepared and purified, and 5 antibody pairs were successfully screened. The Luminex liquid chip detection system of GP73 was successfully constructed using 8F10D1 and 10B9F11 antibody pairs. The analytical performance evaluation showed that the sensitivity of this system was 0.25 ng/ml and the dynamic range was 0.25-100 ng/ml. No cross reactivity was observed. The intra- and inter-assay variation for GP73 was <8% and <11%, respectively. The recovery was 83%-92%. The linear regression equation was y=1.141x+ 6.436 (
10.Development of a quantitative serum assay of Golgi protein 73 in hepatocellular carcinoma using xMAP technology
Yun WU ; Yipeng WANG ; Jie MA ; Yonghong ZHANG ; Huanqin SUN ; Jianping SUN ; Zikang WANG ; Jie XU ; Yanchao DAI ; Ning LI
Chinese Journal of Oncology 2019;41(5):351-356
Objective To establish a quantitative assay of serum Golgi protein 73 ( GP73) using xMAP technology and evaluate its performance. Methods Monoclonal antibodies against GP73 were prepared and purified, and antibody pair screening was performed by double?antibody sandwich enzyme?linked immunosorbent assay. The screened antibodies were used to construct a Luminex liquid chip detection system, and the analysis performance of the detection system was evaluated. The serum levels of GP73 were detected in 90 clinical samples from healthy controls and patients with chronic hepatitis B infection ( CHB) and hepatocellular carcinoma ( HCC). Results Five anti?GP73 monoclonal antibodies were prepared and purified, and 5 antibody pairs were successfully screened.The Luminex liquid chip detection system of GP73 was successfully constructed using 8F10D1 and 10B9F11 antibody pairs. The analytical performance evaluation showed that the sensitivity of this system was 0.25 ng/ml and the dynamic range was 0.25?100 ng/ml. No cross reactivity was observed. The intra? and inter?assay variation for GP73 was <8% and <11%, respectively. The recovery was 83%?92%. The linear regression equation was y=1.141x+6.436 ( r2 =0.998 4, P<0.001). The GP73 concentrations in the serum samples of healthy control, CHB group, and HCC group were 42.8 (38.68, 55.90) ng/ml, 61.49 (43.59, 81) ng/ml, and 122.78 (49.36 liter, 264.55) ng/ml, respectively.The levels of GP73 in HCC group were significantly higher than those in CHB group and healthy controls (P<0.05). Moreover, the levels of GP73 in CHB group were significantly higher than those in healthy controls ( P<0.05). Conclusions A liquid chip detection system of GP73 was successfully constructed. It provides a powerful tool for the clinical application of GP73 in the future.

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