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GenOrigin: A comprehensive protein-coding gene origination database on the evolutionary timescale of life

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Journal of Genetics and Genomics 2021年第12期48卷 1122-1129页

作者： yi-Bo Tong Meng-wei Shi sheng Hu Qian yu-jie chen Zhi-Hui Luo yi-Xuan Tu yu-Li xiong ying-jie Geng chunyan chen Zhen-xia chen Hubei Hongshan Laboratory College of Biomedicine and HealthHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Center for Ecological and Environmental Sciences Northwestern Polytechnical UniversityXi’an 710072China Interdisciplinary Sciences Institute Huazhong Agricultural UniversityWuhan 430070China Shenzhen Institute of Nutrition and health Huazhong Agricultural UniversityShenzhen 518000China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China

The origination of new genes contributes to the biological diversity of life. New genes may quickly build their network, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific genes, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates across species is available. here,we systematically date the age of 9,102,113 protein-coding genes from 565 species in the Ensembl and Ensembl Genomes databases, including 82 bacteria, 57 protists, 134 fungi, 58 plants, 56 metazoa, and 178 vertebrates, using a protein-family-based pipeline with Wagner parsimony algorithm. We also collect gene age estimate data from other studies and uniformly distribute the gene age estimates to time ranges in a million years for comparison across studies. All the data are cataloged into Gen Origin(http://***/), a user-friendly new database of gene age estimates, where users can browse gene age estimates by species, age, and gene ontology. In Gen Origin, the information such as gene age estimates,annotation, gene ontology, ortholog, and paralog, as well as detailed gene presence/absence views for gene age inference based on the species tree with evolutionary timescale, is provided to researchers for exploring gene functions.

关键词： Gene age Gene family Comparative analysis

Follicular carcinoma of the thyroid with a single metastatic lesion in the lumbar spine:A case report

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World Journal of Clinical Cases 2022年第26期10卷 9493-9501页

作者： Yao-Kun chen yu-chun chen wei-Xun Lin jie-Hua Zheng yi-yuan Liu Juan Zou jie-Hui Cai Ze-Qi Ji Ling-Zhi chen Zhi-yang Li Ye-xi chen Department of Thyroid Breast and Hernia SurgeryThe Second Affiliated Hospital of Shantou University Medical CollegeShantou 515000Guangdong ProvinceChina Department of Bone Joint and Spine SurgeryThe Second Affiliated Hospital of Shantou University Medical CollegeShantou 515000Guangdong ProvinceChina

BACKGROUND The bone is the second most common site of thyroid cancer metastasis,after the *** options for bone metastasis of thyroid cancer include surgery,radioiodine therapy(RAIT),external radiation therapy,thyroid-stimulating hormone(TSH)inhibition,bisphosphonates,and small-molecule targeted *** most cases,thyroid carcinoma is found in the thyroid tissue;reports of follicular thyroid carcinoma with a single metastasis to the lumbar spine are *** SUMMARY We report a case of bone metastasis as the only clinical manifestation of thyroid *** patient was a 67-year-old woman with lumbar pain for 7 years and aggravation with intermittent claudication who had previously undergone partial thyroidectomy of a benign thyroid *** abnormal nodules were found in the bilateral thyroid ***,imaging studies were consistent with a spinal tumor,and the lesion was diagnosed as a metastatic follicular carcinoma of thyroid *** adopted a multidisciplinary collaboration and comprehensive treatment *** patient underwent lumbar spine surgery,total resection of the thyroid,postoperative TSH suppression therapy,and *** were no complications associated with the operation,and the patient had good postoperative *** has experienced no *** Follicular thyroid carcinoma is associated with early hematogenous metastasis,and the bone is a typical site of *** bone metastasis is not a contraindication to medical procedures,and providing the appropriate therapy can result in better outcomes and quality of life for these patients.

关键词： Case report Thyroid carcinoma Lumbar spine Metastasis Surgery

Simulation and test of the SLEGS TOF spectrometer at SSRF

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Nuclear Science and Techniques 2023年第3期34卷 171-184页

作者： Kai-jie chen Long-xiang Liu Zi-Rui Hao yu-Gang Ma Hong-wei Wang Gong-Tao Fan xi-Guang Cao Hang-Hua Xu yi-Fei Niu xin-xiang Li xin-Rong Hu yu-Xuan yang sheng jin Pan Kuang School of Physical Science and Technology ShanghaiTech UniversityShanghai 201210China Shanghai Institute of Applied Physics Chinese Academy of SciencesShanghai 201800China Shanghai Advanced Research Institute Chinese Academy of SciencesShanghai 201210China University of Chinese Academy of Science Beijing 100080China Key Laboratory of Nuclear Physics and Ion-beam Application(MOE) Institute of Modern PhysicsFudan UniversityShanghai 200433China School of Nuclear Science and Technology Lanzhou UniversityLanzhou 730000China School of Nuclear Science and Technology University of South ChinaHengyang 421001China School of Physics and Microelectronics Zhengzhou UniversityZhengzhou 450052China

The Shanghai laser electron gamma source(SLEGS)is a powerful tool for exploring photonuclear physics,such as giant dipole resonance(GDR)and pygmy dipole resonance,which are the main mechanisms of collective nuclear *** goal of the SLEGS neutron time-of-flight(TOF)spectrometer is to measure GDR and specific nuclear structures in the energy region above the neutron *** SLEGS TOF spectrometer was designed to hold 20 sets of EJ301 and LaBr3 ***4 was used to simulate the efficiency of each detector and the entire spectrometer,which provides a reference for the selection of detectors and layout of the SLEGS TOF *** the events of 208Pb,implementations of coincidence and time-of-flight technology for complex experiments are available;thus,and neutron decay events can be *** performance of SLEGS TOF spectrometer was systematically evaluated using offline experiments,in which the time resolution reached approximately 0.9 ns.

关键词： SLEGS Time-of-flight Photoneutron nuclear reaction

Data analysis guidelines for single‑cell RNA‑seq in biomedical studies and clinical applications

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Military Medical Research 2023年第4期10卷 529-553页

作者： Min Su Tao Pan Qiu‑Zhen chen wei‑wei Zhou yi Gong Gang Xu Huan‑yu Yan Si Li Qiao‑Zhen Shi Ya Zhang xiao he chun‑jie Jiang Shi‑Cai Fan xia Li Murray J.Cairns xi Wang Yong‑sheng Li State Key Laboratory of Reproductive Medicine Nanjing Medical UniversityNanjing 211166China College of Biomedical Information and Engineering the First Affiliated Hospital of Hainan Medical UniversityHainan Medical UniversityHaikou 571199HainanChina College of Bioinformatics Science and Technology Harbin Medical UniversityHarbin 150081HeilongjiangChina Department of Immunology Nanjing Medical UniversityNanjing 211166China Department of Laboratory Medicine Women and Children’s Hospital of Chongqing Medical UniversityChongqing 401174China Baylor College of Medicine HoustonTX 77030USA Shenzhen Institute for Advanced Study University of Electronic Science and Technology of ChinaShenzhen 518110GuangdongChina School of Biomedical Sciences and Pharmacy Faculty of Health and Medicinethe University of NewcastleUniversity DriveCallaghanNSW 2308Australia Precision Medicine Research Program Hunter Medical Research InstituteNew Lambton HeightsNSW 2305Australia

The application of single-cell RNA sequencing(scRNA-seq)in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic *** the expansion of capacity for high-throughput scRNA-seq,including clinical samples,the analysis of these huge volumes of data has become a daunting prospect for researchers entering this ***,we review the workflow for typical scRNA-seq data analysis,covering raw data processing and quality control,basic data analysis applicable for almost all scRNA-seq data sets,and advanced data analysis that should be tailored to specific scientific *** summarizing the current methods for each analysis step,we also provide an online repository of software and wrapped-up scripts to support the *** and caveats are pointed out for some specific analysis tasks and *** hope this resource will be helpful to researchers engaging with scRNA-seq,in particular for emerging clinical applications.

关键词： Single-cell RNA-sequencing(scRNA-seq) Data analysis Biomedical research Clinical applications

hepatocellular carcinoma: Can LI-RADS v2017 with gadoxetic-acid enhancement magnetic resonance and diffusion-weighted imaging improve diagnostic accuracy?

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World Journal of Gastroenterology 2019年第5期25卷 622-631页

作者： Tong Zhang Zi-xing Huang yi wei Han-yu Jiang jie chen xi-Jiao Liu Li-Kun Cao Ting Duan xiao-Peng he chun-Chao xia Bin Song Department of Radiology Sichuan University West China Hospital

BACKGROUND The Liver Imaging Reporting and Data System(LI-RADS), supported by the American College of Radiology(ACR), has been developed for standardizing the acquisition, interpretation, reporting, and data collection of liver imaging examinations in patients at risk for hepatocellular carcinoma(HCC). Diffusionweighted imaging(DWI), which is described as an ancillary imaging feature of LI-RADS, can improve the diagnostic efficiency of LI-RADS v2017 with gadoxetic acid-enhanced magnetic resonance imaging(MRI) for *** To determine whether the use of DWI can improve the diagnostic efficiency of LIRADS v2017 with gadoxetic acid-enhanced magnetic resonance MRI for *** In this institutional review board-approved study, 245 observations of high risk of HCC were retrospectively acquired from 203 patients who underwent gadoxetic acid-enhanced MRI from October 2013 to April 2018. Two readers independently measured the maximum diameter and recorded the presence of each lesion and assigned scores according to LI-RADS v2017. The test was used to determine the agreement between the two readers with or without DWI. In addition, the sensitivity(SE), specificity(SP), accuracy(AC), positive predictive value(PPV), and negative predictive value(NPV) of LI-RADS were *** index values were used to compare the diagnostic performance of LIRADS with or without *** Almost perfect interobserver agreement was obtained for the categorization of observations with LI-RADS(kappa value: 0.813 without DWI and 0.882 with DWI). For LR-5, the diagnostic SE, SP, and AC values were 61.2%, 92.5%, and71.4%, respectively, with or without DWI; for LR-4/5, they were 73.9%, 80%, and75.9% without DWI and 87.9%, 80%, and 85.3% with DWI; for LR-4/5/M, they were 75.8%, 58.8%, and 70.2% without DWI and 87.9%, 58.8%, and 78.4% with DWI; for LR-4/5/TIV, they were 75.8%, 75%, and 75.5% without DWI and 89.7%,75%, and 84.9% with DWI. The Youden index values of the LI-RADS classification

关键词： hepatocellular carcinoma Liver Imaging Reporting and Data System Magnetic resonance imaging Diffusion-weighted imaging Diagnosis

Measurement of Br(n,γ)cross sections up to stellar s-process temperatures at the CSNS Back‑n

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Nuclear Science and Techniques 2023年第11期34卷 226-241页

作者： Gao‑Le yang Zhen‑Dong An wei Jiang xian‑Kai Li wei‑wei Qiu Zheng‑Fa Liao Zi‑yue Zhuang xiao‑Ping Zhang sheng‑Li chen chen‑chen Guo Er‑xi xiao xiao Fang xin‑xiang Li xin‑Rong Hu Bing Jiang jin‑cheng Wang jie Ren Wen Luo Zhi‑Chao Zhu Hao‑yang Lan Zong‑wei Cao Xu Ma ying‑Du Liu Pu‑Sen Wang yi yang Ping Su xian‑Gai Deng Wan‑Bing he chun‑Wang Ma yu‑Ting Wang Zhi‑Tao Dai Peng‑Qin he Ren‑Guang Tang Tao Zhou jing Wang Han yi yue Zhang Yong‑Hao chen Rui‑Rui Fan Ke‑Qing Gao Qiang Li Kang Sun Zhi‑xin Tan Min‑Hao Gu Han‑Tao jing jing‑yu Tang School of Physics and Astronomy Sun Yat-sen UniversityZhuhai 519082China Shanghai Institute of Applied Physics Chinese Academy of SciencesShanghai 201800China State Key Laboratory of Lunar and Planetary Sciences Macao University of Science and TechnologyMacao 999078China CNSA Macao Center for Space Exploration and Science Macao 999078China Institute of High Energy Physics Chinese Academy of SciencesBeijing 100049China Spallation Neutron Source Science Center Dongguan 523803China School of Nuclear Science and Technology University of South ChinaHengyang 421001China Sino‑French Institute of Nuclear Engineering and Technology Sun Yat-sen UniversityZhuhai 519082China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of Nuclear Data China Institute of Atomic EnergyBeijing 102413China School of Materials Science and Engineering Xiangtan UniversityXiangtan 411100China Key Laboratory of Nuclear Physics and Ion‑beam Application(MOE) Institute of Modern PhysicsDepartment of Nuclear Science and TechnologyFudan UniversityShanghai 200433China Institute of Particle and Nuclear Physics Henan Normal UniversityXinxiang 453007China School of Physics Henan Normal UniversityXinxiang 453007China Shenzhen Center Cancer hospitalChinese Academy of Medical SciencesShenzhen 518100China School of Nuclear Science and Technology University of Science and Technology of ChinaHefei 230027China

The neutron capture cross sections(n,γ)of bromine were obtained using the time-of-flight technique at the Back-n facility of the China Spallation Neutron ***γ-rays originating from neutron-induced capture events were detected using four C_(6)D_(6) *** pulse-height weighting technique and double-bunch unfolding method based on Bayesian theory were used in the data *** deductions,normalization,and corrections were carefully considered to obtain reliable measurement *** multilevel R-matrix Bayesian code SAMMY was used to extract the resonance parameters in the resolved resonance region(RRR).The average cross sections in the unresolved resonance region(URR)were obtained from 10 to 400 *** experimental results were compared with data from several evaluated libraries and previous experi-ments in the RRR and *** TALYS code was used to describe the average cross sections in the *** astrophysical Maxwell average cross sections(MACSs)of ^(79,81)Br from kT=5 to 100 keV were calculated over a sufficiently wide range of neutron *** a thermal energy of kT=30 keV,the MACS value for ^(79)Br 682±68 mb was in good agreement with the KADoNiS v1.0 recommended *** contrast,the value of 293±29 mb for ^(81)Br was substantially higher than that of the evaluated database and the KADoNiS v1.0 recommended value.

关键词： Time-of-flight technique Neutron capture cross sections Maxwell average cross sections

SARS-CoV-2 envelope protein impairs airway epithelial barrier function and exacerbates airway inflammation via increased intracellular Cl^(-)concentration

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Signal Transduction and Targeted Therapy 2024年第4期9卷 1745-1759页

作者： Jian-Bang Xu wei-jie Guan yi-Lin Zhang Zhuo-Er Qiu Lei chen xiao-chun Hou Junqing yue yu-yun Zhou jie sheng Lei Zhao yun-xin Zhu jing Sun jincun Zhao Wen-Liang Zhou Nan-Shan Zhong State Key Laboratory of Respiratory Disease National Clinical Research Center for Respiratory DiseaseNational Center for Respiratory MedicineDepartment of Respiratory and Critical Care MedicineGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouP.R.China Department of Thoracic Surgery Guangzhou Institute for Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouP.R.China Guangzhou National Laboratory GuangzhouP.R.China School of Life Sciences Sun Yat-sen UniversityGuangzhouP.R.China Guangdong Provincial Key Laboratory of Pharmaceutical Functional Genes School of Life SciencesSun Yat-sen UniversityGuangzhouP.R.China Department of Physiology School of Basic Medical SciencesGuangzhou Medical UniversityGuangzhouP.R.China

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection disrupts the epithelial barrier and triggers airway *** envelope(E)protein,a core virulence structural component of coronaviruses,may play a role in this *** could interfere with transepithelial Cl^(-)transport via impairment of the cystic fibrosis transmembrane conductance regulator(CFTR),which modulates nuclear factor kB(NF-kB)***,the pathological effects of SARS-CoV-2 E protein on airway epithelial barrier function,Cl^(-)transport and the robust inflammatory response remain to be ***,we have demonstrated that E protein down-regulated the expression of tight junctional proteins,leading to the disruption of the airway epithelial *** addition,E protein triggered the activation of Toll-like receptor(TLR)2/4 and downstream c-Jun N-terminal kinase(JNK)signaling,resulting in an increased intracellular Cl^(-)concentration([Cl^(-)]_(i))via up-regulating phosphodiesterase 4D(PDE4D)expression in airway epithelial *** elevated[Cl^(-)]_(i);contributed to the heightened airway inflammation through promoting the phosphorylation of serum/glucocorticoid regulated kinase 1(SGK1).Moreover,blockade of SGK1 or PDE4 alleviated the robust inflammatory response induced by E ***,these findings provide novel insights into the pathogenic role of SARS-CoV-2 E protein in airway epithelial damage and the ongoing airway inflammation during SARS-CoV-2 infection.

关键词： airway inflammation elevated

Comparison of acute pneumonia caused by SARS-CoV-2 and other respiratory viruses in children:a retrospective multi-center cohort study during COVID-19 outbreak

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Military Medical Research 2021年第4期8卷 468-480页

作者： Guang-Li Ren xian-Feng Wang Jun Xu Jun Li Qiong Meng Guo-Qiang xie Bo Huang wei-chun Zhu jing Lin cheng-he Tang sheng Ye Zhuo Li jie Zhu Zhen Tang Ming-xin Ma Cong xie ying-Wen Wu chen-xi Liu Fang yang yu-Zong Zhou ying Zheng Shu-Ling Lan Jian-Feng chen Feng Ye yu he BenQing Wu Long chen Si-Mao Fu cheng-Zhong Zheng yuan Shi Department of Pediatrics General Hospital of Southern Theater Command of PLA111 Liuhua RoadYuexiu DistrictGuangzhou 510010GuangdongChina. Department of Pediatrics the Third People’s Hospital of ShenzhenShenzhen 518100GuangdongChina. Pediatric Intensive Care Unit Wuhan Children’s HospitalTongji Medical CollegeHuazhong University of Science&TechnologyWuhan 430010China. Pediatric Intensive Care Unit Maternal and Child Health Hospital of HuangshiHuangshi 435000HubeiChina. Department of Pediatrics the Second People’s Hospital of Guangdong ProvinceGuangzhou 510317China. Department of Pediatrics the Third Affiliated Hospital of Zunyi Medical University(the First People’s Hospital of Zunyi)Guizhou 563000China. Department of Pediatrics the Eighth People’s Hospital of GuangzhouGuangzhou 510440China. Department of Pediatrics the First Affiliated Hospital of Xinxiang Medical UniversityXinxiang 453100HenanChina. Pediatric Intensive Care Unit the Children’s Hospital Zhejiang University School of MedicineHangzhou 310000China. Department of Emergency/Critical Medicine Children’s Hospital of Nanjing Medical UniversityNanjing 210008China. Department of Pediatrics the Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510260China. Department of Medical information date room General Hospital of Southern Theater Command of PLAGuangzhou 510010China. Department of Pediatrics the First Affiliated Hospital of Jinan UniversityGuangzhou 510632China. Department of Pediatrics Maternal and Child Health Hospital of YangjiangYangjiang 529500GuangdongChina. Department of Pediatrics Shenzhen Hospital Affiliated to the University of Chinese Academy of SciencesShenzhen 518107GuangdongChina. Department of Pediatrics Nanfang Hospital of Southern Medical UniversityGuangzhou 510515China. Department of Pediatrics Zhujiang Hospital of Southern Medical UniversityGuangzhou 510280China. Department of Pediatrics Military Hospital of 74 Group of PLAGuangzhou 510318China. Department of Neonatology

Background:Until January 18,2021,coronavirus disease-2019(COVID-19)has infected more than 93 million individuals and has caused a certain degree of *** pneumonia caused by common viruses such as respiratory syncytial virus,rhinovirus,human metapneumovirus,human bocavirus,and parainfluenza viruses have been more common in ***,the incidence of COVID-19 in children was significantly lower than that in *** purpose of this study was to describe the clinical manifestations,treatment and outcomes of COVID-19 in children compared with those of other sources of viral pneumonia diagnosed during the COVID-19 ***:Children with COVID-19 and viral pneumonia admitted to 20 hospitals were enrolled in this retrospective multi-center cohort study.A total of 64 children with COVID-19 were defined as the COVID-19 cohort,of which 40 children who developed pneumonia were defined as the COVID-19 pneumonia *** 284 children with pneumonia caused by other viruses were defined as the viral pneumonia *** epidemiologic,clinical,and laboratory findings were compared by Kolmogorov-Smirnov test,t-test,Mann-Whitney U test and Contingency table *** usage,immunotherapy,blood transfusion,and need for oxygen support were collected as the treatment ***,intensive care needs and symptomatic duration were collected as the outcome ***:Compared with the viral pneumonia cohort,children in the COVID-19 cohort were mostly exposed to family members confirmed to have COVID-19(53/64 vs.23/284),were of older median age(6.3 years vs.3.2 years),and had a higher proportion of ground-glass opacity(GGO)on computed tomography(18/40 vs.0/38,Phe COVID-19 pneumonia cohort had a lower proportion of severe cases(1/40 vs.38/284,P=0.048),and lower cases with high fever(3/40 vs.167/284,Phe propor

关键词： Children Severe acute respiratory syndrome Coronavirus disease-2019 Viral pneumonia

Chronic Intracerebroventricular Infusion of Metformin Inhibits Salt-Sensitive Hypertension via Attenuation of Oxidative Stress and Neurohormonal Excitation in Rat Paraventricular Nucleus

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Neuroscience Bulletin 2019年第1期35卷 57-66页

作者： xiao-jing yu Ya-Nan Zhao yi-Kang Hou Hong-Bao Li Wen-jie xia Hong-Li Gao Kai-Li Liu Qing Su Hui-yu yang Bin Liang Wen-sheng chen wei Cui ying Li Guo-Qing Zhu Zhi-Ming yang yu-Ming Kang Department of Physiology and Pathophysiology Xi’an Jiaotong University School of Basic Medical SciencesMinistry of Education Key Laboratory of Environment and Genes Related to DiseasesXi’an Jiaotong UniversityXi’an 710061China Department of Cardiology Second Affiliated Hospital of Shanxi Medical UniversityTaiyuan 030001China Department of Respiratory Medicine Affiliated Jiangyin Hospital of Southeast University Medical SchoolJiangyin 214400China Department of Cardiovascular Surgery Xijing HospitalFourth Military Medical UniversityXi’an 710032China Department of Endocrinology and Metabolism First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an Jiaotong University Health Science CenterXi’an 710061China Department of Plastic and Cosmetic Surgery Gansu Provincial HospitalLanzhou 730000China Key Laboratory of Cardiovascular Disease and Molecular Intervention Department of PhysiologyNanjing Medical UniversityNanjing 210029China

Metformin(MET), an antidiabetic agent, also has antioxidative effects in metabolic-related *** study was designed to determine whether MET has anti-hypertensive effects in salt-sensitive hypertensive rats by inhibiting oxidative stress in the hypothalamic paraventricular nucleus(PVN). Salt-sensitive rats received a highsalt(HS) diet to induce hypertension, or a normal-salt(NS)diet as control. At the same time, they received intracerebroventricular(ICV) infusion of MET or vehicle for 6 weeks. We found that HS rats had higher oxidative stress levels and mean arterial pressure(MAP) than NS rats. ICV infusion of MET attenuated MAP and reduced plasma norepinephrine levels in HS rats. It also decreased reactive oxygen species and the expression of subunits of NAD(P)H oxidase, improved the superoxide dismutase activity,reduced components of the renin-angiotensin system, and altered neurotransmitters in the PVN. Our findings suggest that central MET administration lowers MAP in saltsensitive hypertension via attenuating oxidative stress,inhibiting the renin-angiotensin system, and restoring the balance between excitatory and inhibitory neurotransmitters in the PVN.

关键词： Hypertension Paraventricular nucleus Sympathoexcitation Metformin Oxidative stress