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| 1 | Whole-genome sequencing of 508 patients identifies key molecular features associated with poor prognosis in esophageal squamous cell carcinoma显示文摘Esophageal squamous cell carcinoma(ESCC)is a poor-prognosis cancer type with limited understanding of its molecular etiology.Using 508 ESCC genomes,we identified five novel significantly mutated genes and uncovered mutational signature clusters associated with metastasis and patients’outcomes.Several functional assays implicated that NFE2L2 may act as a tumor suppressor in ESCC and that mutations in NFE2L2 probably impaired its tumor-suppressive function,or even conferred oncogenic activities.Additionally,we found that the NFE2L2 mutations were significantly associated with worse prognosis of ESCC.We also identified potential noncoding driver mutations including hotspot mutations in the promoter region of SLC35E2 that were correlated with worse survival.Approximately 5.9%and 15.2%of patients had high tumor mutation burden or actionable mutations,respectively,and may benefit from immunotherapy or targeted therapies.We found clinically relevant coding and noncoding genomic alterations and revealed three major subtypes that robustly predicted patients’outcomes.Collectively,we report the largest dataset of genomic profiling of ESCC useful for developing ESCC-specific biomarkers for diagnosis and treatment. | Yongping Cui Hongyan Chen Ruibin Xi Heyang Cui Yahui Zhao Enwei Xu Ting Yan Xiaomei Lu Furong Huang Pengzhou Kong Yang Li Xiaolin Zhu Jiawei Wang Wenjie Zhu Jie Wang Yanchun Ma Yong Zhou Shiping Guo Ling Zhang Yiqian Liu Bin Wang Yanfeng Xi Ruifang Sun Xiao Yu Yuanfang Zhai Fang Wang Jian Yang Bin Yang Caixia Cheng Jing Liu Bin Song Hongyi Li Yi Wang Yingchun Zhang Xiaolong Cheng Qimin Zhan Yanhong Li Zhihua Liu-Show | 2020 | Cell Research2020，30，10： | 19 |
| 2 | The heterogeneity of islet autoantibodies and the progression of islet failure in type 1 diabetic patients显示文摘Type 1 diabetes mellitus is heterogeneous in many facets. The patients suffered from type 1 diabetes present several levels of islet function as well as variable number and type of islet-specific autoantibodies. This study was to investigate prevalence and heterogeneity of the islet autoantibodies and clinical phenotypes of type 1 diabetes mellitus; and also discussed the process of islet failure and its risk factors in Chinese type 1 diabetic patients. A total of 1,291 type 1 diabetic patients were enrolled in this study. Demographic information was collected. Laboratory tests including mixed-meal tolerance test, human leukocyte antigen alleles, hemoglobin A1 c, lipids, thyroid function and islet autoantibodies were conducted. The frequency of islet-specific autoantibody in newly diagnosed T1 DM patients(duration shorter than half year) was 73% in East China. According to binary logistic regressions, autoantibody positivity, longer duration and lower Body Mass Index were the risk factors of islet failure. As the disease developed, autoantibodies against glutamic acid decarboxylase declined as well as the other two autoantibodies against zinc transporter 8 and islet antigen 2. The decrease of autoantibodies was positively correlated with aggressive beta cell destruction. Autoantibodies can facilitate the identification of classic T1 DM from other subtypes and predict the progression of islet failure. As there were obvious heterogeneity in autoantibodies and clinical manifestation in different phenotypes of the disease, we should take more factors into consideration when identifying type 1 diabetes mellitus. | Jin Liu Lingling Bian Li Ji Yang Chen Heng Chen Yong Gu Bingqin Ma Wei Gu Xinyu Xu Yun Shi Jian Wang Dalong Zhu Zilin Sun Jianhua Ma Hui Jin Xing Shi Heng Miao Bing Xin Yan Zhu Zhenwen Zhang Ruifang Bu Lan Xu Guangde Shi Wei Tang Wei Li Dongmei Zhou Jun Liang Xingbo Cheng Bimin Shi Jixiang Dong Ji Hu Chen Fang Shao Zhong Weinan Yu Weiping Lu Chenguang Wu Li Qian Jiancheng Yu Jialin Gao Xiaoqiang Fei Qingqing Zhang Xueqin Wang Shiwei Cui Jinluo Cheng Ning Xu Guofeng Wang Guoqing Han Chunrong Xu Yun Xie Minmin An Wei Zhang Zhixiao Wang Yun Cai Qi Fu Yu Fu Shuai Zheng Fan Yang Qingfang Hu Hao Dai Yu Jin Zheng Zhang Kuanfeng Xu Yifan Li Jie Shen Hongwen Zhou Wei He Xuqin Zheng Xiao Han Liping Yu Jinxiong She Mei Zhang Tao Yang | 2016 | Science China(Life Sciences)2016，59，9： | 5 |
| 3 | A Self-certified Cross-Cluster Asymmetric Group Key Agreement for Wireless Sensor Networks显示文摘Wireless sensor networks have some obvious characteristics, such as communication range is limited, computing power is limited and energy is limited. Group key agreement in this environment requires a cross-cluster, computation and communication overhead are lightweight and highly safe group key agreement protocol. Aiming at these demands, the paper proposes a Self-certified cross-cluster Asymmetric group key agreement(SC-AGKA). To establish a lightweight and efficient group communication channel among sensor nodes. According to the cluster head as the bridge node to realize the sensor nodes in different cluster have the same group key information, and negotiate a pair of asymmetric group keys to realize the cross cluster secure communication. The group communication adopts asymmetric encryption mechanism. It realizes the group security communication mechanism of message sender unconstraint. The asymmetric group key agreement has the key self-certified, which does not need additional rounds to verify the correctness of group key. Proven and analysis show that the proposed protocol has the advantages of in security and energy consumption. | ZHANG Qikun LI Yongjiao ZHANG Quanxin YUAN Junling WANG Ruifang GAN Yong TAN Yu'an | 2019 | Chinese Journal of Electronics2019，28，2： | 5 |
| 4 | Modeling of void closure in diffusion bonding process based on dynamic conditions显示文摘The dynamic conditions for plastic deformation mechanism,surface source mechanism,interface source mechanism and creep mechanism in the diffusion bonding process are proposed.Based on these dynamic conditions,a model for void closure in the diffusion bonding process is derived.The effects of diffusion bonding parameters on the bonding mechanisms are analyzed.For the diffusion bonding process of TC4 alloy,at a low diffusion bonding temperature or pressure,or for a short time,the interface source mechanism plays a main role.But,the creep mechanism is the dominant mechanism and operates until the diffusion bonding is fulfilled.As the diffusion bonding time increases,the surface source and interface source mechanism enhance and then stop at a certain stage of diffusion bonding,while the creep mechanism enhances continuously.As the diffusion bonding temperature or pressure increases,the interface source mechanism weakens and the other mechanisms enhance.The maximum and average errors between the calculated and the experimental results in the diffusion bonding for TC4 alloy are 12.86% and 5.79%,respectively. | MA RuiFang LI MiaoQuan LI Hong YU WeiXin | 2012 | Science China(Technological Sciences)2012，55，9： | 5 |
| 5 | Single-cell RNA-seq analysis of testicular somatic cell development in pigs显示文摘Spermatogenesis is the process by which diploid male germ cells propagate and differentiate into haploid flagellated spermatozoa.This highly complicated process is dependent on testicular somatic cells maturation.While the role of these somatic cells in spermatogenesis is relatively well established,knowledge about their development and maturation,particularly at the molecular level,is limited.In this study,we profiled the testicular single-cell transcriptomes of Guanzhong black pigs at the age of 7,30,60,90,and 150 days.Five types of Sertoli cells,five types of Leydig cells,and four types of peritubular myoid cells were identified.Histological analysis revealed the changes in proliferation levels and marker gene expressions,and the prion-like protein gene(PRND)was identified as a novel marker for Sertoli cells.Additionally,integrated analyses of porcine and human datasets revealed similarities between human and pig testicular somatic cells.Overall,the data obtained in this study contribute to the understanding of testicular development in pigs as a model species. | Lingkai Zhang Ming Guo Zidong Liu Ruifang Liu Yi Zheng Taiyong Yu Yinghua Lv Hongzhao Lu Wenxian Zeng Tao Zhang Chuanying Pan | 2022 | Journal of Genetics and Genomics2022，49，11： | 4 |
| 6 | Identification of Differentially-expressed Genes in Intestinal Gastric Cancer by Microarray Analysis显示文摘Gastric cancer(GC) is one of the most frequent malignant tumors. In order to systematically characterize the cellular and molecular mechanisms of intestinal GC development,in this study, we used 22 K oligonucleotide microarrays and bioinformatics analysis to evaluate the gene expression profiles of GC in 45 tissue samples, including 20 intestinal GC tissue samples,20 normal appearing tissues(NATs) adjacent to tumors and 5 noncancerous gastric mucosa tissue samples. These profiles allowed us to explore the transcriptional characteristics of GC and determine the change patterns in gene expression that may be of clinical significance. 1519 and 1255 differentially-expressed genes(DEGs) were identified in intestinal GC tissues and NATs, respectively,as determined by Bayesian analysis(P < 0.001). These genes were associated with diverse functions such as mucosa secretion, metabolism, proliferation, signaling and development, which occur at different stages of GC development. | Shizhu Zang Ruifang Guo Rui Xing Liang Zhang Wenmei Li Min Zhao Jingyuan Fang Fulian Hu Bin Kang Yonghong Ren Yonglong Zhuang Siqi Liu Rong Wang Xianghong Li Yingyan Yu Jing Cheng Youyong Lu | 2014 | Genomics, Proteomics & Bioinformatics2014，12，6： | 4 |
| 7 | MULTI-TILLERING DWARF1, a new allele of BRITTLE CULM 12, affects plant height and tiller in rice显示文摘Plant height and tillering are crucial factors determining rice plant architecture and influencing rice grain production. In this study, multi-tillering dwarf1(mtd1), a stable multi-tiller and dwarf mutant, was screened from the ethylmethane sulfonate-treated japonica rice variety Wuyunging7. Compared with the wild type, mtd1 mutant exhibited pleiotropic phenotypes, including dwarfism, more tillers, brittle culms and delayed heading date.By employing map-based cloning strategy, the gene MTD1 was finally mapped to an approximately 66-kb region on the short arm of chromosome 9. Sequencing results showed that the gene LOC_Os09g02650(BC12) in mtd1 mutant had a single nucleotide substitution(G to A), which generated a premature translation stop. Over-expressing MTD1/BC12 coding sequence rescued all the phenotypes of mtd1 mutants including plant height and tillers, which confirms that BC12 is the mutated gene in mtd1 mutant.Quantitative reverse transcription-PCR analysis showed that MTD1/BC12 could negatively regulate the expression of MONOCULM 1, IDEAL PLANT ARCHITECTURE1 and Tillering and Dwarf 1, and control rice tillering. Remarkably, a-amylase activity analysis and gibberellic acid(GA)treatment showed that the dwarf phenotype of mtd1 mutant was dependent on GA biosynthesis pathway. These results facilitated to further uncover the molecular mechanism of the growth and development in rice. | Haiping Yu Deyong Ren Yangzhou Zhu Jiangmin Xu Yuexing Wang Ruifang Liu Yunxia Fang Zhenyuan Shi Jiangjie Pan Mei Lu Bojun Ma Jiang Hu Yuchun Rao | 2016 | Science Bulletin2016，61，23： | 3 |
| 8 | Adjunctive sepsis therapy with aminophylline(STAP):a randomized controlled trial显示文摘Background:Sepsis is a serious disease caused by infection.Aminophylline has anti-asthma and anti-inflammatory effects.We aimed to explore the safety and effect of aminophylline in sepsis.Methods:We conducted a clinical randomized controlled trial involving 100 patients diagnosed with sepsis within 48 h after intensive care unit(ICU)admission in two sites.All patients were randomized in a 1:1 ratio to receive standard therapy with or without aminophylline.The primary clinical outcome was all-cause mortality at 28 days.Results:From September 27,2018 to February 12,2020,we screened 277 septic patients and eventually enrolled 100 patients,with 50 assigned to the aminophylline group and 50 to the usual-care group.At 28 days,7 of 50 patients(14.0%)in the aminophylline group had died,compared with 16 of 50(32.0%)in the usual-care group(P=0.032).Cox regression showed that the aminophylline group had a lower hazard of death(hazard ratio=0.312,95%confidence interval:0.129–0.753).Compared with the usual-care group,patients in the aminophylline group had a longer survival time(P=0.039 by the log-rank test).The effects of aminophylline on vasopressor dose,oxygenation index,and sequential organ failure assessment score were timedependent with treatment.There were no significant differences in total hospitalization days,ICU hospitalization days,and rates of serious adverse events(all P>0.05).No adverse events were observed in the trial.Conclusions:Aminophylline as an adjunct therapy could significantly reduce the risk of death and prolong the survival time of patients with sepsis.Trial registration:ChiCTR.org.cn,ChiCTR1800019173. | Ruifang Zhang Huan Liu Dongmei Dai Xianfei Ding Dong Wang Yan Wang Xuexiu Shi Shuguang Zhang Xiaoguang Duan Haixu Wang Yonggang Luo Shaohua Liu Bing Han Xiaojuan Zhang Yu Fang Jing Yang Wangbin Xu Tongwen Sun | 2022 | Chinese Medical Journal2022，135，23： | 2 |
| 9 | Single-cell RNA-sequencing reveals the dynamic process and novel markers in porcine spermatogenesis显示文摘Background:Spermatogenesis is the process by which male gametes are formed from spermatogonial stem cells and it is essential for the reliable transmission of genetic information between generations.To date,the dynamic transcriptional changes of defined populations of male germ cells in pigs have not been reported.Results:To characterize the atlas of porcine spermatogenesis,we profiled the transcriptomes of~16,966 testicular cells from a 150-day-old pig testis through single-cell RNA-sequencing(scRNA-seq).The scRNA-seq analysis identified spermatogonia,spermatocytes,spermatids and three somatic cell types in porcine testes.The functional enrichment analysis demonstrated that these cell types played diverse roles in porcine spermatogenesis.The accuracy of the defined porcine germ cell types was further validated by comparing the data from scRNA-seq with those from bulk RNA-seq.Since we delineated four distinct spermatogonial subsets,we further identified CD99 and PODXL2 as novel cell surface markers for undifferentiated and differentiating spermatogonia,respectively.Conclusions:The present study has for the first time analyzed the transcriptome of male germ cells and somatic cells in porcine testes through scRNA-seq.Four subsets of spermatogonia were identified and two novel cell surface markers were discovered,which would be helpful for studies on spermatogonial differentiation in pigs.The datasets offer valuable information on porcine spermatogenesis,and pave the way for identification of key molecular markers involved in development of male germ cells. | Lingkai Zhang Fuyuan Li Peipei Lei Ming Guo Ruifang Liu Ling Wang Taiyong Yu Yinghua Lv Tao Zhang Wenxian Zeng Hongzhao Lu Yi Zheng | 2022 | Journal of Animal Science and Biotechnology2022，13，2： | 2 |
| 10 | Clay nanosheet-mediated delivery of recombinant plasmids expressing artificial miRNAs via leaf spray to prevent infection by plant DNA viruses显示文摘Whitefly-transmitted begomoviruses are economically important plant pathogens that cause severe problems in many crop plants,such as tomato,papaya,cotton,and tobacco.Tomato yellow leaf curl virus(TYLCV)is a typical monopartite begomovirus that has been extensively studied,but methods that can efficiently control begomoviruses are still scarce.In this study,we combined artificial microRNA(amiRNA)-mediated silencing technology and clay nanosheetmediated delivery by spraying and developed a method for efficiently preventing TYLCV infection in tomato plants.We designed three amiRNAs that target different regions of TYLCV to silence virus-produced transcripts.Three plant expression vectors expressing pre-amiRNAs were constructed,and recombinant plasmid DNAs(pDNAs)were loaded onto nontoxic and degradable layered double hydroxide(LDH)clay nanosheets.LDH nanosheets containing multiple pDNAs were sprayed onto plant leaves.We found that the designed amiRNAs were significantly accumulated in leaves 7 days after spraying,while the pDNAs were sustainably detected for 35 days after the spray,suggesting that the LDH nanosheets released pDNAs in a sustained manner,protected pDNAs from degradation and efficiently delivered pDNAs into plant cells.Importantly,when the LDH nanosheets coated with pDNAs were sprayed onto plants infected by TYLCV,both the disease severity and TYLCV viral concentration in sprayed plants were significantly decreased during the 35 days,while the levels of H_(2)O_(2) were significantly increased in those plants.Taken together,these results indicate that LDH nanosheets loaded with pDNAs expressing amiRNAs can be a sustainable and promising tool for begomovirus control. | Qili Liu Yanpeng Li Kedong Xu Dongxiao Li Haiyan Hu Feng Zhou Puwen Song Yongang Yu Qichao Wei Qian Liu Weipeng Wang Ruifang Bu Haili Sun Xiaohui Wang Jianjun Hao Honglian Li Chengwei Li | 2020 | Horticulture Research2020，7，1： | 1 |
| 11 | Muntz Rational Approximation for Special Function Classes in Orlicz Spaces显示文摘Using the method of construction,with the help of inequalities,we research the Muntz rational approximation of two kinds of special function classes,and give the corresponding estimates of approximation rates of these classes under widely conditions.Because of the Orlicz Spaces is bigger than continuous function space and the Lp space,so the results of this paper has a certain expansion significance. | Ruifang Yu Garide Wu | 2017 | Analysis in Theory and Applications2017，33，1： | 1 |
| 12 | Partial P-Type Metal Ions Doping Induced Variation of Both Crystal Structure and Oxygen Vacancy Within Cu/SnO_(2) Metastable Solid Solution Nanofibers for Highly Sensitive C_(2)H_(2) Sensor显示文摘Partial P-type metal ions doping(PPMID)is an alternative method to further enhance the gas sensing performance of N-type metal oxides(NMOs)in contrast to that of P-N metal oxides heterojunctions,but the influences of the introduction of PPMID on the grain size and oxygen vacancies of NMOs have been rarely investigated.Herein,a simple and effective route has been demonstrated to address this problem with Cu^(2+)-doped SnO_(2) metastable solid solution nanofibers(CSMSSNs)as model and C_(2)H_(2) as target molecule by combining electrospinning and calcination technique.It seems that the introduction of PPMID can also affect crystal structure and oxygen vacancies of NMOs,proven by combining X-ray diffraction(XRD)and X-ray photoelectron spectra(XPS).Thus,PPD,crystal structure and oxygen vacancies have been combined to clarify the enhanced sensing performance of Cu-doped SnO_(2) metastable solid solution nanofibers angainst C_(2)H_(2). | WANG Ruifang YU Xi LI Zhenyu CHEN Jingyu JIANG Tingting | 2021 | Chemical Research in Chinese Universities2021，37，3： | 1 |
| 13 | In vivo biocompatibility and biodegradation of a Mg-15%Ca 3 (PO 4 ) 2 composite as an implant material显示文摘 | Kun Yu Liangjian Chen Jun Zhao Ruifang Wang Yilong Dai Qiao Huang | 2013 | Materials Letters2013，，： | 1 |
| 14 | P-glycoprotein associates with Anxa2 and promotes invasion in multidrug resistant breast cancer cells显示文摘 | Fei Zhang Haichang Zhang Zhiyong Wang Man Yu Ran Tian Wei Ji Yi Yang Ruifang Niu | 2013 | Biochemical Pharmacology2013，，： | 1 |
| 15 | Experimental study on the vitrification and xenotransplantation of human ovarian tissue显示文摘Background:Cryopreservation of ovarian tissue is a promising method for preserving fertility.Transmission electron microscopy(TEM)is an evaluation system for cryo-injury during the cooling and warming process which is very laborious and needs to be optimized.Objective:In this study,we evaluated that serum 17β-oestradiol(E2)may be used as an indicator of vitrified ovarian tissue.Methods:Immunodeficient nude mice were used as hosts for xenografting of vitrified-warmed human ovarian tissues.A total of 54 mice were divided into two group:vitrified ovarian xenotransplant(VOX)group(n?45)and non-transplant control group(n?9).The transplanted mice were grouped into vitrified/warmed grafted-4 weeks(VOX-4w,n?15),vitrified/warmed grafted-6weeks(VOX-6w n?15)and vitrified/warmed grafted-12 weeks(VOX-12w n?15)according to the time after transplantation.The viable and functional recovery of grafted ovarian tissue was assessed by light microscopy,transmission electron microscopy,and hormone(E2)assays.Results:Serum E2 concentration was significantly higher in VOX-6w(group(21.07 pg/ml)than that of VOX-12w group(15.59 pg/ml).VOX-12w group showed a lower value(12.61 pg/ml)for E2 concentration.The trend for E2 concentration was consistent with the morphological identification of the grafts.Conclusion:In vivo serum hormone E2 released by cortical biopsies can be used as a functional marker for xenotransplanted vitrified-warmed human ovarian tissue reserve. | Jinghui Zhao Yuping Ge Jingyi Li Yucui Zeng Guoyi Dong Liping Zeng Juanjuan Dai Hui Du Mumin Shao Xuewen Yu Huan Li Fang He Zhouchun Shang Chun Wang Gabor Vajt Huiru Tang Ruifang Wu Yutao Du | 2022 | Gynecology and Obstetrics Clinical Medicine2022，2，1： | 1 |
| 16 | Complex mode superposition algorithm for seismic responses of nonclassically damped linear MDOF system显示文摘 | ZHOU Xiyuan YU Ruifang DONG Di | 2004 | Journal of Earthquake Engineering2004，8，4： | 1 |
| 17 | Complex mode superposition algorithm for seismic response of non- classically damped linear MDOF system显示文摘 | Zhou Xiyuan Yu Ruifang Dong di | 2004 | Journal of Earthquake Engineering2004，8，4： | 1 |
| 18 | Panicle-3D: A low-cost 3D-modeling method for rice panicles based on deep learning, shape from silhouette, and supervoxel clustering显示文摘Self-occlusions are common in rice canopy images and strongly influence the calculation accuracies of panicle traits. Such interference can be largely eliminated if panicles are phenotyped at the 3 D level.Research on 3 D panicle phenotyping has been limited. Given that existing 3 D modeling techniques do not focus on specified parts of a target object, an efficient method for panicle modeling of large numbers of rice plants is lacking. This paper presents an automatic and nondestructive method for 3 D panicle modeling. The proposed method integrates shoot rice reconstruction with shape from silhouette, 2 D panicle segmentation with a deep convolutional neural network, and 3 D panicle segmentation with ray tracing and supervoxel clustering. A multiview imaging system was built to acquire image sequences of rice canopies with an efficiency of approximately 4 min per rice plant. The execution time of panicle modeling per rice plant using 90 images was approximately 26 min. The outputs of the algorithm for a single rice plant are a shoot rice model, surface shoot rice model, panicle model, and surface panicle model, all represented by a list of spatial coordinates. The efficiency and performance were evaluated and compared with the classical structure-from-motion algorithm. The results demonstrated that the proposed method is well qualified to recover the 3 D shapes of rice panicles from multiview images and is readily adaptable to rice plants of diverse accessions and growth stages. The proposed algorithm is superior to the structure-from-motion method in terms of texture preservation and computational efficiency. The sample images and implementation of the algorithm are available online. This automatic, cost-efficient, and nondestructive method of 3 D panicle modeling may be applied to high-throughput 3 D phenotyping of large rice populations. | Dan Wu Lejun Yu Junli Ye Ruifang Zhai Lingfeng Duan Lingbo Liu Nai Wu Zedong Geng Jingbo Fu Chenglong Huang Shangbin Chen Qian Liu Wanneng Yang | 2022 | The Crop Journal2022，10，5： | 1 |
| 19 | Complex mode superpostion algorithm for seismic response of non-classically damped linear MDOF system 显示文摘 | Xiyuan Yu Ruifang Dong Di | 2004 | Journal of Earthquake Engineering2004，8，4： | 1 |
| 20 | Complex mode superposition algorithm for seismic responses of nonclassically damped linear MDOF system显示文摘 | Zhou Xiyuan Yu Ruifang Dong Di | 2004 | Journal of Earthquake Engineering2004，8，4： | 1 |
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