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Zhang Y, Feng T, Wang S, Dong R, Yang J, Su J, Wang B. A Novel XGBoost Method to Identify Cancer Tissue-of-Origin Based on Copy Number Variations. Front Genet 2020; 11:585029. [PMID: 33329723 PMCID: PMC7716814 DOI: 10.3389/fgene.2020.585029] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/05/2020] [Indexed: 01/18/2023] Open
Abstract
The discovery of cancer of unknown primary (CUP) is of great significance in designing more effective treatments and improving the diagnostic efficiency in cancer patients. In the study, we develop an appropriate machine learning model for tracing the tissue of origin of CUP with high accuracy after feature engineering and model evaluation. Based on a copy number variation data consisting of 4,566 training cases and 1,262 independent validation cases, an XGBoost classifier is applied to 10 types of cancer. Extremely randomized tree (Extra tree) is used for dimension reduction so that fewer variables replace the original high-dimensional variables. Features with top 300 weights are selected and principal component analysis is applied to eliminate noise. We find that XGBoost classifier achieves the highest overall accuracy of 0.8913 in the 10-fold cross-validation for training samples and 0.7421 on independent validation datasets for predicting tumor tissue of origin. Furthermore, by contrasting various performance indices, such as precision and recall rate, the experimental results show that XGBoost classifier significantly improves the classification performance of various tumors with less prediction error, as compared to other classifiers, such as K-nearest neighbors (KNN), Bayes, support vector machine (SVM), and Adaboost. Our method can infer tissue of origin for the 10 cancer types with acceptable accuracy in both cross-validation and independent validation data. It may be used as an auxiliary diagnostic method to determine the actual clinicopathological status of specific cancer.
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Zhou L, Wang J, Liu G, Lu Q, Dong R, Tian G, Yang J, Peng L. Probing antiviral drugs against SARS-CoV-2 through virus-drug association prediction based on the KATZ method. Genomics 2020; 112:4427-4434. [PMID: 32745502 PMCID: PMC7832256 DOI: 10.1016/j.ygeno.2020.07.044] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/04/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022]
Abstract
It is urgent to find an effective antiviral drug against SARS-CoV-2. In this study, 96 virus-drug associations (VDAs) from 12 viruses including SARS-CoV-2 and similar viruses and 78 small molecules are selected. Complete genomic sequence similarity of viruses and chemical structure similarity of drugs are then computed. A KATZ-based VDA prediction method (VDA-KATZ) is developed to infer possible drugs associated with SARS-CoV-2. VDA-KATZ obtained the best AUCs of 0.8803 when the walking length is 2. The predicted top 3 antiviral drugs against SARS-CoV-2 are remdesivir, oseltamivir, and zanamivir. Molecular docking is conducted between the predicted top 10 drugs and the virus spike protein/human ACE2. The results showed that the above 3 chemical agents have higher molecular binding energies with ACE2. For the first time, we found that zidovudine may be effective clues of treatment of COVID-19. We hope that our predicted drugs could help to prevent the spreading of COVID.
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Yang W, Liu Y, Dong R, Liu J, Lang J, Yang J, Wang W, Li J, Meng B, Tian G. Accurate Detection of HPV Integration Sites in Cervical Cancer Samples Using the Nanopore MinION Sequencer Without Error Correction. Front Genet 2020; 11:660. [PMID: 32714374 PMCID: PMC7344299 DOI: 10.3389/fgene.2020.00660] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/29/2020] [Indexed: 12/14/2022] Open
Abstract
During the carcinogenesis of cervical cancer, the DNA of human papillomavirus (HPV) is frequently integrated into the human genome, which might be a biomarker for the early diagnosis of cervical cancer. Although the detection sensitivity of virus infection status increased significantly through the Illumina sequencing platform, there were still disadvantages remain for further improvement, including the detection accuracy and the complex integrated genome structure identification, etc. Nanopore sequencing has been proven to be a fast yet accurate technique of detecting pathogens in clinical samples with significant longer sequencing length. However, the identification of virus integration sites, especially HPV integration sites was seldom carried out by using nanopore platform. In this study, we evaluated the feasibility of identifying HPV integration sites by nanopore sequencer. Specifically, we re-sequenced the integration sites of a previously published sample by both nanopore and Illumina sequencing. After analyzing the results, three points of conclusions were drawn: first, 13 out of 19 previously published integration sites were found from all three datasets (i.e., nanopore, Illumina, and the published data), indicating a high overlap rate and comparability among the three platforms; second, our pipeline of nanopore and Illumina data identified 66 unique integration sites compared with previous published paper with 13 of them being verified by Sanger sequencing, indicating the higher integration sites detection sensitivity of our results compared with published data; third, we established a pipeline which could be used in HPV integration site detection by nanopore sequencing data without doing error correction analysis. In summary, a new nanopore data analysis method was tested and proved to be reliable in integration sites detection compared with methods of existing Illumina data analysis pipeline with less sequencing data required. It provides a solid evidence and tool to support the potential application of nanopore in virus status identification.
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Yu XP, Jin ZN, Li Y, Wu CY, He JQ, Luo YW, Sun LZ, Dong R. [Long-term outcome comparison of ostial/shaft lesions in unprotected left main coronary artery treated by PCI or CABG]. ZHONGHUA XIN XUE GUAN BING ZA ZHI 2020; 48:484-488. [PMID: 32842258 DOI: 10.3760/cma.j.cn112148-20191226-00769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To evaluate long-term clinical outcomes of consecutive patients treated with coronary artery bypass grafting (CABG) and percutaneous coronary intervention(PCI) with drug-eluting stents(DES) for ostial/shaft lesions in unprotected left main coronary artery(ULMCA). Method: A total of 259 patients with isolated ostial/midshaft lesions in unprotected left main coronary artery were enrolled consecutively who received DES implantation or underwent CABG between January 2003 and July 2009 in Beijing Anzhen Hospital. The endpoints of the study were death, repeat revascularization, myocardial infarction (MI) and stroke. Time to the primary endpoint was evaluated according to the Kaplan-Meier method, and the log-rank test was applied to compare the incidence of the endpoint. Adjusted risks for adverse outcomes were compared by multivariate Cox proportional hazard regression analyses. Results: A total of 259 patients were included, including 149 in PCI group and 110 in CABG group. And 193(74.5%) cases were males.The age was (61.4±9.8) years old. The median follow-up was 10.1 years (interquartile range 8.3 to 11.2 years) in the overall patients. There were no significant difference for the incidence of death [37.0% vs. 43.1% ,P=0.143] , MI [34.0% vs. 19.4% ,P=0.866], stroke [6.4% vs. 11.7% , P=0.732], repeart revascularization [33.6% vs. 39.9% ,P=0.522] between PCI group and CABG group before multivariate adjusting,according to the incidence calculated with Kaplan-Meier. After adjusting covariates such as age, left ventricular ejection fraction(LVEF) and serum creatine with multivariate Cox hazard regression model, there was still no significant difference between the two groups. Conclusions: PCI with DES is as effective and safe as CABG in patients with left main ostium/shaft lesion during a median follow-up of 10.1 years.
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Quan L, Dong R, Yang W, Chen L, Lang J, Liu J, Song Y, Ma S, Yang J, Wang W, Meng B, Tian G. Simultaneous detection and comprehensive analysis of HPV and microbiome status of a cervical liquid-based cytology sample using Nanopore MinION sequencing. Sci Rep 2019; 9:19337. [PMID: 31852945 PMCID: PMC6920169 DOI: 10.1038/s41598-019-55843-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/21/2019] [Indexed: 02/06/2023] Open
Abstract
Human papillomavirus (HPV) is a major pathogen that causes cervical cancer and many other related diseases. HPV infection related cervical microbiome could be an induce factor of cervical cancer. However, it is uncommon to find a single test on the market that can simultaneously provide information on both HPV and the microbiome. Herein, a novel method was developed in this study to simultaneously detect HPV infection and microbiota composition promptly and accurately. It provides a new and simple way to detect vaginal pathogen situation and also provide valuable information for clinical diagnose. This approach combined multiplex PCR, which targeted both HPV16 E6E7 and full-length 16S rRNA, and Nanopore sequencing to generate enough information to understand the vagina condition of patients. One HPV positive liquid-based cytology (LBC) sample was sequenced and analyzed. After comparing with Illumina sequencing, the results from Nanopore showed a similar microbiome composition. An instant sequencing evaluation showed that 15 min sequencing is enough to identify the top 10 most abundant bacteria. Moreover, two HPV integration sites were identified and verified by Sanger sequencing. This approach has many potential applications in pathogen detection and can potentially aid in providing a more rapid clinical diagnosis.
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Wu LS, Dong R, Dang HM, Song Y, Cao J, Liu D, Huang Q, Fu W, Ma XL. [Short-term outcomes of sequential radial artery grafting in patients with coronary artery disease]. ZHONGHUA YI XUE ZA ZHI 2019; 99:3308-3312. [PMID: 31715666 DOI: 10.3760/cma.j.issn.0376-2491.2019.42.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the short-term outcomes of patients with coronary artery disease (CAD) who underwent coronary artery bypass graft (CABG) with sequential radial artery graft. Methods: Clinical data of patients with CAD who underwent CABG with sequential radial artery graft from August to December 2018 in Beijing Anzhen Hospital was retrospectively analyzed. Computer tomography angiography was employed to evaluate the patency of grafts and the incidence of adverse cardiovascular events was followed up 3 months after surgery. Results: A total of thirty patients were included, with an average age of (60.2±7.3) years old, among whom 83.3% were male, and 93.3% had three-vessel disease detected by coronary angiography. All patients had left internal mammary artery (LIMA) anastomosed to the left anterior descending (LAD) and sequential radial artery graft. Among sequential radial artery grafts, the most frequent anastomosis of sequential radial artery graft was aortic artery (AO)-first diagonal branch (D1)-first obtuse marginal branch (OM1) (13 patients, 43.3%), followed by AO-OM1-second obtuse marginal branch (OM2) (9 patients, 30.0%), and 18 patients also underwent saphenous vein graft. None of 30 patients experienced adverse cardiovascular events during postoperative period in hospital. Three-months follow-up outcomes showed that LIMA-LAD in 1 patient (3.3%) occluded, 3 patients had occluded anastomosis of sequential radial artery graft, 1 patient (3.3%) had heart failure, and 1 patient (3.3%) had recurrent angina. Conclusion: The radial artery could be used as the second arterial graft for CAD patients undergoing CABG with a sequential anastomosis technique, and these patients need regular anti-arterial spasm drug treatment after CABG.
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Zhou J, Zhang W, Liu W, Sheng J, Li M, Chen X, Dong R. Histological study of intestinal goblet cells, IgA, and CD3+ lymphocyte distribution in Huang-huai white goat. Folia Morphol (Warsz) 2019; 79:303-310. [PMID: 31322724 DOI: 10.5603/fm.a2019.0082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/10/2019] [Indexed: 11/25/2022]
Abstract
BACKGROUND Ten healthy adult Huang-huai white goats were selected and sacrificed by jugular vein bleeding after anaesthesia to observe the distribution characteristics of the histological structure of the intestinal mucosa, goblet cells, IgA, and CD3+ lymphocytes. MATERIALS AND METHODS Three sections of the duodenum, the jejunum, and the ileum were immediately collected and fixed with 4% paraformaldehyde for 72 h to prepare tissue sections. After haematoxylin and eosin, periodic acid Schiff, and immunohistochemical staining was performed, the distribution characteristics of goblet cells, IgA-positive cells, and CD3+ lymphocytes were observed. Results showed high columnar epithelial cells in the duodenum and jejunum of Huang-huai white goat and low columnar epithelial cells in the ileum mucosa. RESULTS Mucopolysaccharides secreted by intestinal goblet cells were mainly neutral, and the number of ileum goblet cells was significantly higher than that of the duodenum and the jejunum (p < 0.05). IgA-positive cells were distributed in the lamina propria of the duodenum, and the number of cells was significantly higher than that in the jejunum and the ileum (p < 0.01). The significant difference was found between the jejunum and the ileum (p < 0.01). The CD3+ cells in the intestinal mucosa were distributed in the lamina propria mucosae, and some of the positive cells in the jejunum were distributed between epithelial cells. CD3+ cells had the largest number in the jejunal lamina propria but had the lowest number in the ileum. CONCLUSIONS The jejunum was significantly higher than the duodenum (p < 0.05), and the ileum was much less than the jejunum (p < 0.01).
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Meng B, Quan L, Yang W, Lang J, Chen L, Dong R, Zhao J, Tian G. Discovering HPV16 and HPV18 infection status and cancer gene variations in cervical cancer patient specimens by using Next-generation sequencing. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e13040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e13040 Background: Human papillomavirus (HPV) infection has been reported as an important cause of cervical cancer for many years. HPV16 and HPV18 are the two most prevalent types in cervical cancer5. Integration of HPV DNA is a crucial genetic event in cervical carcinogenesis. Therefore, it is important to know the HPV integration hot spots in human genome to predict the cervical cancer development status of patients. Although many studies have addressed the HPV integration sites in human genome, it is still a technique barrier to precisely determine the HPV integration sites of each patient, especially at early disease development stage with limited integration sites existing. Methods: To solve this problem, we first designed HPV probes to capture HPV integrated sequences of genome using next generation sequencing (NGS). And then we analyzed the integration sites by two methods with the NGS results, HPV Detector. We applied the study on 17 patient samples, 15 of them were found HPV16 positive and 2 of them were found HPV18 positive. Among them 16 were detected with HPV integration sites. Results: The results indicated that different samples showed different numbers of integration sites with limited overlapped positions in genome. The integrated positions of HPV16/18 located in all the genes of the virus, but mostly distributed in gene E1, L1 and L2. We identified integration sites HPV16 E6/GATC, E6/WWTR1, L2/DGKB, E1/EHHADH, ect. Some of the integrated sites in human genome are belong to intergenic region. We also used cancer gene panel, which cover 143 cancer related genes exon regions, to identify the mutation sites of each samples. We summed up a highly occurred mutated cancer gene list, which include ALK, NF1, PIK3R1, ROS1, TSC1, TSC2, ect. Most of them are either cancer driver genes or have been found highly related to cervical cancer. Further study is still carrying on. Conclusions: In conclusion, our HPV probe could successfully detect HPV16 and HPV18 in patient samples and enrich HPV integration sites in human genome of cervical samples significantly. It could provide detailed information for cervical cancer discovery and early detection.
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Wang S, Dong R. Feature selection with improved binary artificial bee colony algorithm for microarray data. INTERNATIONAL JOURNAL OF COMPUTATIONAL SCIENCE AND ENGINEERING 2019. [DOI: 10.1504/ijcse.2019.10022757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Han YJ, Partington J, Chhantyal-Pun R, Henry M, Auriacombe O, Rawlings T, Li LH, Keeley J, Oldfield M, Brewster N, Dong R, Dean P, Davies AG, Ellison BN, Linfield EH, Valavanis A. Gas spectroscopy through multimode self-mixing in a double-metal terahertz quantum cascade laser. OPTICS LETTERS 2018; 43:5933-5936. [PMID: 30547973 DOI: 10.1364/ol.43.005933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/10/2018] [Indexed: 06/09/2023]
Abstract
A multimode self-mixing terahertz-frequency gas absorption spectroscopy is demonstrated based on a quantum cascade laser. A double-metal device configuration is used to expand the laser's frequency tuning range, and a precision-micromachined external waveguide module is used to enhance the optical feedback. Methanol spectra are measured using two laser modes at 3.362 and 3.428 THz, simultaneously, with more than eight absorption peaks resolved over a 17 GHz bandwidth, which provide the noise-equivalent absorption sensitivity of 1.20×10-3 cm-1 Hz-1/2 and 2.08×10-3 cm-1 Hz-1/2, respectively. In contrast to all previous self-mixing spectroscopy, our multimode technique expands the sensing bandwidth and duty cycle significantly.
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Xiao HJ, Huang XX, Liu Z, Dong R, Song DY, Zhang X, Wang SY, Dai HP. [Metformin protects against bleomycin-induced pulmonary fibrosis in mice]. ZHONGHUA YI XUE ZA ZHI 2018; 98:1951-1955. [PMID: 29996289 DOI: 10.3760/cma.j.issn.0376-2491.2018.24.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the effect of metformin on murine model of bleomycin (BLM)-induced lung injury and fibrosis. Methods: A total of 30 mice were divided into 3 groups: control, BLM, and BLM with metformin, in accordance with the random number table and each group had 10 mice. To induce the pulmonary fibrosis model, a concentration of 2 mg/ml bleomycin was intratracheally administered in the BLM group and BLM with metformin group with a volume of 1.75 μl/g, while the control group accepted saline with the same volume. Metformin (200 mg/kg) was given to the mice orally once a day from the day before intratracheal instillation of bleomycin to day 14. The daily survival condition of mice was recorded during 14 days. At day 14, HE-staining was used to assess the severity of fibrosis according to the method proposed by Ashcroft. Total lung collagen content was determined by hydroxyproline assay and Masson's trichrome staining. To examine the expression of fibronectin we used the method of immunohistochemistry staining. The changes of Transforming Growth Factor beta 1 (TGF-β(1)) in plasm, bronchoalveolar lavage fluid (BALF) and lung were measured by ELISA. Results: The survival rates of control group, BLM group and BLM with metformin group at day 14 were 10/10, 4/10 and 7/10 respectively. According to the method proposed by Ashcroft the score of metformin treated mice was significantly lower than that of the bleomycin model mice[(3.82±0.58) vs (7.79±0.06), (P<0.05)]. The hydroxyproline level in lung tissue were markedly attenuated in metformin treated mice compared with bleomycin model mice [(0.40±0.05) vs (0.73±0.10) μg/mg, (P<0.05)]. The level of TGF-β(1) in plasma, BALF and lung tissue were also decreased in mice treated with metformin compared with bleomycin model mice [(2.32±0.68) vs (4.59±0.45) ng/ml, (0.81±0.09) vs (1.40±0.06) ng/ml, (17.12±0.83) vs (21.25±0.69) ng/mg, all P<0.05]. Conclusion: Metformin can reduce the severity of pulmonary fibrosis in mice induced by bleomycin.
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Papadopoulos K, Harb W, Lu N, Ma X, He Y, Yuan L, Fu M, Lin Y, Xu W, Wang X, Wang P, Xu T, Dong R, Gong J. Phase I study of KN035, a novel fusion Anti-PD-L1 antibody administered subcutaneously in patients with advanced solid tumors in the USA. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy288.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Dong R, Liu M, Huang XX, Liu Z, Jiang DY, Xiao HJ, Dai HP. [Effect of water-soluble C(60) fullerenes on pulmonary fibrosis induced by bleomycin in mice]. ZHONGHUA YI XUE ZA ZHI 2018; 97:1740-1744. [PMID: 28606286 DOI: 10.3760/cma.j.issn.0376-2491.2017.22.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To evaluate the role of water-soluble C(60) fullerenes in mice model of lung injury and fibrosis that induced by bleomycin. Methods: A total of 20 healthy C57BL/6J mice were randomly divided into normal control group, bleomycin group, high dose C(60) group, low dose C(60) group, each group with 5 mice. Mice were induced pulmonary fibrosis by intratracheal injection of bleomycin except the normal control group, which was induced by saline instead. In low dose C(60) group and high dose C(60) group, 1 mg·kg(-1)·d(-1) and 10 mg·kg(-1)·d(-1) water-soluble C(60) fullerenes was injected into mice intraperitoneally every day, which began from one day before intratracheal instillation of bleomycin until the end of observation. Saline was given to mice in the same way in normal control and bleomycin group. This study investigated the variation of weight and survival rate of mice for 14 d. HE-staining and Masson's trichrome staining were used to assess the severity of fibrosis according to the method proposed by Ashcroft at 14th day. Total lung collagen content was determined by hydroxyproline assay. The changes of transforming growth factor-β(1) (TGF-β(1)) and tumor necrosis factor α (TNF-α) in plasma, bronchial alveolar lavage fluid (BALF) and lung tissue were measured by enzyme-linked immunosorbent assay (ELISA). And, the amount of reactive oxygen species (ROS) was tested by 2, 7-dichlorofuorescin diacetate (DCFH-DA), and determined by the ratio of fluorescence intensity and protein content (OD/μg). Results: C(60) can protect mice that injured by bleomycin from weight loss. According the method proposed by Ashcroft et al.HE and Masson's trichrome staining showed that collagen deposition in lung tissue were markedly attenuated in C(60) (1 mg·kg(-1)·d(-1) and 10 mg·kg(-1)·d(-1)) treated mice compared with bleomycin model mice[(4.08±0.52), (3.00±0.41) vs (6.75±0.75) points, both P<0.01]. In low dose C(60) group and high dose C(60) group, the content of hydroxyproline in lung tissue were significantly lower than that in bleomycin group[(0.36±0.06), (0.35±0.08) vs (0.55±0.16) μg/mg, both P<0.05]. The level of TGF-β(1) in BALF and lung tissue were also decreased in mice treated with C(60) (10 mg·kg(-1)·d(-1)) compared with bleomycin model mice, but the difference had no statistical significance[(9.38±5.32) vs (23.60±8.96) pg/ml, (2.89±0.35) vs (6.44±2.95) pg/mg, both P>0.05]. Also, in high dose C(60) group, the content of TNF-α in plasma, BALF and lung tissue were significantly lower than those in bleomycin group[(4.56±0.73) vs (7.21±2.26) pg/ml, (34.58±23.30) vs (151.00±27.34) pg/ml, (22.99±5.83) vs (122.90±22.04) pg/mg, all P<0.05]. In addition, Compared with bleomycin group, ROS in lung tissue was significantly decreased after treatment with C(60) (10 mg·kg(-1)·d(-1))[(19.68±0.91) vs (22.92±1.71) OD/μg, P<0.05]. Conclusion: Water-soluble C(60) fullerenes reduce the severity of pulmonary fibrosis induced by bleomycin in mice.
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Hua K, Liu TS, Li Y, Zhao Y, Zheng JB, Zhou N, Zhou SY, Dong R. [Short-term clinical safety and efficacy of No-touch great saphenous vein harvesting technique for off-pump coronary artery bypass grafting]. ZHONGHUA YI XUE ZA ZHI 2018; 98:1601-1604. [PMID: 29886653 DOI: 10.3760/cma.j.issn.0376-2491.2018.20.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To evaluated early clinical outcomes of saphenous vein grafts harvested with a No-touch technique in off-pump coronary artery bypass graft (OPCABG) surgery. Methods: A total of 124 patients with three-vessel disease undergoing OPCABG by No-touch technique between June and November 2017 in Beijing An Zhen Hospital were respectively reviewed. Results: The average age of patients was (60.7±10.3) years, and 80 cases (64.5%) were male, with the average body mass index (BMI)of (25.4±2.5) kg/m(2,) the mean preoperative left ventricular ejection fraction (LVEF) of (58.0±7.0%). The operative time was (4.0±0.4) hours, and 16 cases (12.9%) were harvested for whole vein grafts. The number of vein grafts and venous anastomoses was 144 and 284, respectively. There were 16 cases of single bridge NTSVG-LAD, 4 cases of single bridge NTSVG-D, 99 cases of sequential bridge NTSVG-OM-PDA, 5 cases of sequential bridge NTSVG-OM-PLV, 4 cases of sequential bridge NTSVG-OM-RCA, 16 cases of sequential bridge NTSVG-D-OM-PDA. The mean flow volume of No-touch vein grafts was (51.9±2.4) ml/min. There was no death case in hospital. Postoperative re-exploration for hemorrhage of anastomosis happened in 1 case (0.8%), which was caused by pericardial tamponade due to insufficiency of hemostasis in internal mammary bed. There were 1 case of bad wound healing of lower extremity incision (0.8%). A total of 124 cases were followed up after operation, and the follow-up rate was 100%. There was one all-cause death (0.8%) 27 days after the operation. Conclusion: The short-term clinical observation of the application of No-touch great saphenous vein harvesting technique for OPCABG is safe and effective.
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Wang J, Zhou M, Dong R, Cong X, Zhang R, Wang X. Simultaneous Determination of Peroxide Hydrogen and Ascorbic Acid by Capillary Electrophoresis with Platinum Nanoparticles Modified Micro-disk Electrode. ELECTROANAL 2017. [DOI: 10.1002/elan.201600407] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hua K, Sheng JJ, Dong R. [Short-term clinical outcomes and risk factors associated with in-hospital mortality in patients undergoing off-pump coronary artery bypass grafting]. ZHONGHUA YI XUE ZA ZHI 2017; 97:1218-1221. [PMID: 28441848 DOI: 10.3760/cma.j.issn.0376-2491.2017.16.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore short-term clinical outcomes and risk factors associated with in-hospital mortality in patients undergoing off-pump coronary artery bypass grafting (OPCABG) and establish a prediction model for in-hospital mortality. Methods: The clinical data of patients undergoing OPCABG in Beijing Anzhen Hospital between January 2014 and January 2016 was retrospectively studied. Univariate analysis and logistic regression were applied to determine the potential risk factors, and then a prediction model for mortality was confirmed. The calibration and discrimination of the prediction model was finally tested. Results: A total of 2 546 patients who underwent OPCABG were recruited. In-hospital mortality of OPCABG was 0.7% (17 cases). Seven variables: female, age, left main disease >50%, low left ventricular ejection fraction (LVEF), acute myocardial infarction before surgery, operative status (selective or emergent), moderate concomitant mitral valve regurgitation were independently correlated with OPCABG mortality (all P<0.05). The result of Hosmer-Lemeshow test was χ(2)=5.912, P=0.676. The area under receiver-operating characteristic curve (ROC) was 0.881. Conclusions: OPCABG is safe and effective for myocardial revascularization in a short term. The following risk factors are associated with an increased operative mortality of OPCABG: male, age, left main disease >50%, low LVEF, acute myocardial infarction before surgery, operative status (selective or emergent), moderate concomitant mitral valve regurgitation. The prediction model established by above-mentioned potential risk factors was proven to perform well by statistical tests.
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Dong R, Weng L, Guo T, Zhu TN, Zhao JL, Wu QJ, Zeng XF. [The 455th case: swollen leg, jaundice and mental disturbance]. ZHONGHUA NEI KE ZA ZHI 2017; 56:316-320. [PMID: 28355731 DOI: 10.3760/cma.j.issn.0578-1426.2017.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A 17-year-old young man with a history of swollen leg and intermittent jaundice was presented to Peking Union Medical College Hospital with acute fever and mental disturbance. He developed deep venous thrombosis, acute myocardial infarction and plantar skin necrosis during the past four years, and was presented with an acute episode of fever, thrombocytopenia, acute kidney injury, acute myocardial infarction, mental disturbance, and obstructive jaundice. Laboratory tests showed schistocytes on peripheral blood smear.High titer of antiphospholipid antibodies was detected.Strikingly, the activity of a disintegrin and metalloprotease with a thrombospondin type 1 motif, member 13 (ADAMTS13)was significantly decreased without the production of inhibitors. Images indicated stenosis of the common bile duct, common hepatic duct, and cystic duct, which caused dilation of bile ducts and the gall bladder. Corticosteroids and anticoagulation therapy were effective at first, but the disease relapsedonce the corticosteroids tapered down. Plasma exchange was administrated for 17 times, which was effective temporarily during this episode. Methylprednisolone pulse therapy, intravenous immunoglobulin, rituximab, anticoagulation therapy, and bile drainage, were all tried but still could not control the disease. The patient's family agreed to withdraw treatment after he developed septic shock.
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Zhang S, Ma L, Dong R, Zhang CY, Sun WJ, Fan MJ, Yang DS, Zhou F, Liu W. Study on the synthesis and tribological properties of anti-corrosion benzotriazole ionic liquid. RSC Adv 2017. [DOI: 10.1039/c6ra27376a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Anti-corrosion benzotriazole ionic liquid (IL, BTAP4444) was synthesized by neutralizing 1H-benzotriazole (BTAH) with terabutylphosphonium hydroxide (P4444OH).
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Liu TS, Chen BT, Dong R, Li Y, Zhao Y, Hua K. [Safety and efficacy of off-pump coronary artery bypass grafting in octogenarians]. ZHONGHUA YI XUE ZA ZHI 2016; 96:2903-2905. [PMID: 27760636 DOI: 10.3760/cma.j.issn.0376-2491.2016.36.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To discuss the clinical safety and efficacy about off-pump coronary artery bypass grafting (OPCABG) in octogenarians. Methods: From June 2005 to July 2014, 252 patients (male 208, female 44, with a mean age of 81.7 years old) underwent OPCABG in Beijing Anzhen Hospital who were aged 80 years or older were enrolled. Results: Eight (3.2%) patients were diagnosed as single vessel coronary artery disease (CAD), 29 cases (11.5%) were diagnosed as bifurcation vessel CAD, and 215 cases (85.3%) were multivessel CAD. One hundred and one cases (40.1%) were diagnosed as left main artery disease, among which 51 cases (20.2%) had old myocardial infarction. Two hundred and forty-eight patients belonged to Canadian Cardiovascular Society (CCS) classⅠ-Ⅲ and 4 cases to CCS class Ⅳ. One hundred and forty-five cases belonged to New York Heart Association (NYHA) classⅠ-Ⅱ and 107 cases to NYHA class Ⅲ-Ⅳ. Mean graft number was 3. Two hundred and six patients (81.7%) received total vein graft operation. Intra-aortic balloon pump (IABP) was used in 43 patients (17.1%). In-hospital death occurred in 15 cases (6.0%). Major in-hospital complications included reoperation (16 cases), re-intubation (16 cases), dialysis (11 cases), sternum infection (2 cases), atrial fibrillation (63 cases). The follow-up time was from 1 to 11 years (with a mean time of 6 years). All-cause mortality was 18.1% (43 cases). The major out-of-hospital complications included recurrent myocardial infarction (3 cases), stroke (3 cases), re-admission (27 cases) and recurrent angina pectoris (20 cases). Conclusion: OPCABG is safe and effective for myocardial revascularization in patients aged 80 years and over.
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Zhu DD, Yu XJ, Zheng XH, Dong R, Liu YW, Xue CY, Wang KL. [Antimicrobial resistance analysis of salmonella from broiler cultivation and processing production in Heilongjiang Province]. ZHONGHUA YU FANG YI XUE ZA ZHI [CHINESE JOURNAL OF PREVENTIVE MEDICINE] 2016; 50:833-835. [PMID: 27655608 DOI: 10.3760/cma.j.issn.0253-9624.2016.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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Dong R, Liu GB, Liu BH, Chen G, Li K, Zheng S, Dong KR. Targeting long non-coding RNA-TUG1 inhibits tumor growth and angiogenesis in hepatoblastoma. Cell Death Dis 2016; 7:e2278. [PMID: 27362796 PMCID: PMC5108331 DOI: 10.1038/cddis.2016.143] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/11/2016] [Accepted: 04/11/2016] [Indexed: 02/07/2023]
Abstract
Hepatoblastoma is the most common liver tumor of early childhood, which is usually characterized by unusual hypervascularity. Recently, long non-coding RNAs (lncRNA) have emerged as gene regulators and prognostic markers in several cancers, including hepatoblastoma. We previously reveal that lnRNA-TUG1 is upregulated in hepatoblastoma specimens by microarray analysis. In this study, we aim to elucidate the biological and clinical significance of TUG1 upregulation in hepatoblastoma. We show that TUG1 is significantly upregulated in human hepatoblastoma specimens and metastatic hepatoblastoma cell lines. TUG1 knockdown inhibits tumor growth and angiogenesis in vivo, and decreases hepatoblastoma cell viability, proliferation, migration, and invasion in vitro. TUG1, miR-34a-5p, and VEGFA constitutes to a regulatory network, and participates in regulating hepatoblastoma cell function, tumor progression, and tumor angiogenesis. Overall, our findings indicate that TUG1 upregulation contributes to unusual hypervascularity of hepatoblastoma. TUG1 is a promising therapeutic target for aggressive, recurrent, or metastatic hepatoblastoma.
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Yuan L, Liu J, Dong R, Zhu J, Tao C, Zheng R, Zhu S. 14,15-epoxyeicosatrienoic acid promotes production of brain derived neurotrophic factor from astrocytes and exerts neuroprotective effects during ischaemic injury. Neuropathol Appl Neurobiol 2016; 42:607-620. [PMID: 26526810 DOI: 10.1111/nan.12291] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 10/09/2015] [Accepted: 10/27/2015] [Indexed: 02/06/2023]
Abstract
AIMS 14,15-Epoxyeicosatrienoic acid (14,15-EET) is abundantly expressed in brain and exerts protective effects against ischaemia. 14,15-EET is hydrolysed by soluble epoxide hydrolase (sEH). sEH-/- mice show a higher level of 14,15-EET in the brain. Astrocytes play a pivotal role in neuronal survival under ischaemic conditions. However, it is unclear whether the neuroprotective effect of 14,15-EET is associated with astrocytes. METHODS A mouse model of focal cerebral ischaemia was induced by middle cerebral artery occlusion. Oxygen-glucose deprivation/reoxygenation (OGD/R) was performed on cultured murine astrocytes, neurons and a human cell line. Cell viabilities were measured by 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyl-2H-tetrazolium bromide (MTT) assay. The mRNA expressions were quantified by real-time PCR. Brain derived neurotrophic factor (BDNF) concentration was measured by ELISA. Protein expressions were quantified by Western blotting. BDNF and peroxisome proliferators-activated receptor gamma (PPAR-γ) expressions were analysed by confocal microscopy. RESULTS Decreased infarct volumes, elevated BDNF expression and increased numbers of BDNF/GFAP Glial Fibrillary Acidic Protein double-positive cells were observed in the ischaemic penumbra of sEH-/- mice. The decreased infarct volumes of sEH-/- mice were diminished by intracerebroventricular injection of a blocker of BDNF receptor. 14,15-EET increases BDNF expression and cell viability of murine astrocytes and U251 cells by BDNF-TrkB Tyrosine receptor kinase-B-extracellular signal-regulated kinase 1/2 signalling during OGD/R. 14,15-EET protects neurons from OGD/R by stimulating the production of astrocyte-derived BDNF. 14,15-EET stimulates the production of astrocyte-derived BDNF through PPAR-γ/p-cAMP-response element binding protein signal pathways. CONCLUSIONS Our study demonstrates the importance of 14,15-EET-mediated production of astrocyte-derived BDNF for enhancing viability of astrocytes and protecting neurons from the ischaemic injury and provides insights into the mechanism by which 14,15-EET is involved in neuroprotection.
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Han P, Zhao J, Guo Q, Wang J, Zhang W, Shen S, Wang X, Dong R, Ma Y, Kang L, Fu L, Jia L, Han X, He Z, Bao Y, Wang L, Niu K. Incidence, Risk Factors, and the Protective Effect of High Body Mass Index against Sarcopenia in Suburb-Dwelling Elderly Chinese Populations. J Nutr Health Aging 2016; 20:1056-1060. [PMID: 27925147 DOI: 10.1007/s12603-016-0704-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Few studies have explored the risk factors of sarcopenia in certain cohorts. The objective of this study was to examine the incidence of sarcopenia and associated factors over a 1-year period in an elderly Chinese suburban population. METHODS This study was conducted on 356 Chinese suburb-dwelling participants aged ≥60 years, for whom detailed information regarding sociodemographics, behavioral characteristics, and medical conditions had been documented. Sarcopenia was defined according to the Asian Working Group for Sarcopenia (AWGS) criteria. Sarcopenia incidence was documented after one year of follow-up, and correlated with several possible factors. RESULTS At baseline, 64 (9.7%) of the initial 657 participants had sarcopenia. The prevalence of sarcopenia was 10.4% after one year. Between baseline and 1-year follow-up, 13 of the participants without sarcopenia at baseline had developed sarcopenia. After multivariate adjustments, it was found that the incidence of sarcopenia increased with age and high body mass index (BMI) is associated with less incidence of sarcopenia. Incidence was also higher among women. CONCLUSIONS We found sarcopenia incidence increased with age, and women were more likely to have sarcopenia. A higher BMI is also associated with a lower incidence of sarcopenia. Maintaining a healthy weight could be beneficial in the prevention of sarcopenia.
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Macintosh B, Graham JR, Barman T, De Rosa RJ, Konopacky Q, Marley MS, Marois C, Nielsen EL, Pueyo L, Rajan A, Rameau J, Saumon D, Wang JJ, Patience J, Ammons M, Arriaga P, Artigau E, Beckwith S, Brewster J, Bruzzone S, Bulger J, Burningham B, Burrows AS, Chen C, Chiang E, Chilcote JK, Dawson RI, Dong R, Doyon R, Draper ZH, Duchêne G, Esposito TM, Fabrycky D, Fitzgerald MP, Follette KB, Fortney JJ, Gerard B, Goodsell S, Greenbaum AZ, Hibon P, Hinkley S, Cotten TH, Hung LW, Ingraham P, Johnson-Groh M, Kalas P, Lafreniere D, Larkin JE, Lee J, Line M, Long D, Maire J, Marchis F, Matthews BC, Max CE, Metchev S, Millar-Blanchaer MA, Mittal T, Morley CV, Morzinski KM, Murray-Clay R, Oppenheimer R, Palmer DW, Patel R, Perrin MD, Poyneer LA, Rafikov RR, Rantakyrö FT, Rice EL, Rojo P, Rudy AR, Ruffio JB, Ruiz MT, Sadakuni N, Saddlemyer L, Salama M, Savransky D, Schneider AC, Sivaramakrishnan A, Song I, Soummer R, Thomas S, Vasisht G, Wallace JK, Ward-Duong K, Wiktorowicz SJ, Wolff SG, Zuckerman B. Discovery and spectroscopy of the young jovian planet 51 Eri b with the Gemini Planet Imager. Science 2015; 350:64-7. [DOI: 10.1126/science.aac5891] [Citation(s) in RCA: 391] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 08/03/2015] [Indexed: 11/02/2022]
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Li S, Tang X, Peng L, Luo Y, Dong R, Liu J. The diagnostic performance of CT-derived fractional flow reserve for evaluation of myocardial ischaemia confirmed by invasive fractional flow reserve: a meta-analysis. Clin Radiol 2015; 70:476-86. [DOI: 10.1016/j.crad.2014.12.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 11/28/2022]
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