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| 1 | Recent Progress Using High-throughput Sequencing Technologies in Plant Molecular Breeding显示文摘High-throughput sequencing is a revolutionary technological innovation in DNA sequencing.This technology has an ultra-low cost per base of sequencing and an overwhelmingly high data output.High-throughput sequencing has brought novel research methods and solutions to the research fields of genomics and post-genomics.Furthermore,this technology is leading to a new molecular breeding revolution that has landmark significance for scientific research and enables us to launch multi-level,multi-faceted,and multi-extent studies in the fields of crop genetics,genomics,and crop breeding.In this paper,we review progress in the application of high-throughput sequencing technologies to plant molecular breeding studies. | Qiang Gao Guidong Yue Wenqi Li Junyi Wang Jiaohui Xu Ye Yin | 2012 | Journal of Integrative Plant Biology2012，54，4： | 15 |
| 2 | Numerical analysis on noise of rotor with unconventional blade tips based on CFD/Kirchhoff method显示文摘A solver is developed aiming at efficiently predicting rotor noise in hover and forward flight. In this solver, the nonlinear near-field solutions are calculated by a hybrid approach which includes the Navier-Stokes and Euler equations based on a moving-embedded grid system and adaptive grid methodology. A combination of the third-order upwind scheme and flux-difference splitting scheme, instead of the second-order center-difference scheme which may cause larger wake dissipation, has been employed in the present computational fluid dynamics (CFD) method. The sound pressure data in the near field can be calculated directly by solving the Navier-Stokes equations, and the sound propagation can be predicted by the Kirchhoff method. A harmonic expansion approach is presented for rotor far-field noise prediction, which gives an analytical expression for the integral function in the Kirchhoff formula. As a result, the interpolation process is simplified and the efficiency and accuracy of the interpolation are improved. Then, the high-speed impulsive (HIS) noise of a helicopter rotor at different tip Mach numbers and on different observers is calculated and analyzed in hover and forward flight, which shows a highly directional characteristic of the rotor HIS noise with a maximum value in the rotor plane, and the HSI noise weakens rapidly with the increasing of the directivity angle. In order to investigate the effects of the rotor blade-tip shape on its aeroacoustic characteristics, four kinds of blade tips are designed and their noise characteristics have been simulated. At last, a new unconventional CLOR-II blade tip has been designed, and the noise characteristics of the presented CLOR-II model rotor have been simulated and measured compared to the reference rotors with a rectangular or swept-back platform blade tip. The results demonstrate that the unconventional CLOR-II blade tip can significantly reduce the HSI noise of a rotor. | Wang Bo Zhao Qijun Xu Guohua Ye Liang Wang Junyi | 2013 | Chinese Journal of Aeronautics2013，26，3： | 8 |
| 3 | A new distinct geminivirus causes soybean stay-green disease显示文摘Dear Editor,Plant viruses make up almost half of the plant disease-causing pathogens,affecting crop yields and the global economy(Savary et al.,2019).Soybean(Glycine max)is one of the most valuable legume crops in the world,supplying 25%of the global edible oil and two-thirds of the global concentrated protein for livestock feeding.Recently,the outbreak of soybean stay-green syndrome with delayed leaf senescence(stay-green),flat pods,and increased number of abnormal seeds has swept the soybean production in the Huang-Huai-Hai region of China,resulting in huge yield losses(Xu et al.,2019).This disease has become an epidemic and prominent problem in soybean production and is still expanding its geography,including North America,posing a serious threat to soybean production(Harbach et al.,2016;Zhang et al.,2016;Li et al.,2019).However,the cause of soybean stay-green syndrome remains obscure. | Ruixiang Cheng Ruoxin Mei Rong Yan Hongyu Chen Dan Miao Lina Cai Jiayi Fan Gairu Li Ran Xu Weiguo Lu Yu Gao Wenwu Ye Shuo Su Tianfu Han Junyi Gai Yuanchao Wang Xiaorong Tao Yi Xu | 2022 | Molecular Plant2022，15，6： | 6 |
| 4 | An all-round AI-Chemist with a scientific mind显示文摘The realization of automated chemical experiments by robots unveiled the prelude to an artificial intelligence(AI)laboratory.Several AI-based systems or robots with specific chemical skills have been demonstrated,but conducting all-round scientific research remains challenging.Here,we present an all-round AI-Chemist equipped with scientific data intelligence that is capable of performing basic tasks generally required in chemical research.Based on a service platform,the AI-Chemist is able to automatically read the literatures from a cloud database and propose experimental plans accordingly.It can control a mobile robot in-house or online to automatically execute the complete experimental process on 14 workstations,including synthesis,characterization and performance tests.The experimental data can be simultaneously analysed by the computational brain of the AI-Chemist through machine learning and Bayesian optimization,allowing a new hypothesis for the next iteration to be proposed.The competence of the AI-Chemist has been scrutinized by three different chemical tasks.In the future,the more advanced all-round AI-Chemists equipped with scientific data intelligence may cause changes to the landscape of the chemical laboratory. | Qing Zhu Fei Zhang Yan Huang Hengyu Xiao LuYuan Zhao XuChun Zhang Tao Song XinSheng Tang Xiang Li Guo He BaoChen Chong JunYi Zhou YiHan Zhang Baicheng Zhang JiaQi Cao Man Luo Song Wang GuiLin Ye WanJun Zhang Xin Chen Shuang Cong Donglai Zhou Huirong Li Jialei Li Gang Zou WeiWei Shang Jun Jiang Yi Luo | 2022 | National Science Review2022，9，10： | 5 |
| 5 | Prevalence and clinical significance of pathogenic germline BRCA1/2 mutations in Chinese non-small cell lung cancer patients显示文摘Objective: Germline alterations in the breast cancer susceptibility genes type 1 and 2, BRCA1 and BRCA2, predispose individuals to hereditary cancers, including breast, ovarian, prostate, pancreatic, and stomach cancers.Accumulating evidence suggests inherited genetic susceptibility to lung cancer.The present study aimed to survey the prevalence of pathogenic germline BRCA mutations(gBRCAm) and explore the potential association between gBRCAm and disease onset in Chinese advanced non-small cell lung cancer(NSCLC) patients.Methods: A total of 6,220 NSCLC patients were screened using capture-based ultra-deep targeted sequencing to identify patients harboring germline BRCA1/2 mutations.Results: Out of the 6,220 patients screened, 1.03%(64/6,220) of the patients harbored the pathogenic gB RCAm, with BRCA2 mutations being the most predominant mutations(49/64, 76.5%).Patients who developed NSCLC before 50 years of age were more likely to carry gBRCAm(P = 0.036).Among the patients harboring classic lung cancer driver mutations, those with concurrent gBRCAm were significantly younger than those harboring the wild-type gBRCA(P = 0.029).By contrast, the age of patients with or without concurrent gBRCAm was comparable to those of patients without the driver mutations(P = 0.972).In addition, we identified EGFR-mutant patients with concurrent gBRCAm who showed comparable progression-free survival but significantly longer overall survival(P = 0.002) compared to EGFR-mutant patients with wild-type germline BRCA.Conclusions: Overall, our study is the largest survey of the prevalence of pathogenic gBRCAm in advanced Chinese NSCLC patients.Results suggested a lack of association between germline BRCA status and treatment outcome of EGFR-TKI.In addition,results showed a positive correlation between pathogenic gB RCAm and an early onset of NSCLC. | Xingsheng Hu Dongyong Yang Yalun Li Li Li Yan Wang Peng Chen Song Xu Xingxiang Pu Wei Zhu Pengbo Deng Junyi Ye Hanhan Zhang Analyn Lizaso Hao Liu Xinru Mao Hai Huang Qian Chu Chengping Hu | 2019 | Cancer Biology & Medicine2019，16，3： | 4 |
| 6 | The draftgenome of a diploid cotton gossypium raimondii 显示文摘 | Kunbo Wang Zhiwen Wang Fuguang Li Wuwei Ye Junyi Wang Guoli Song Zhen Yue Lin Cong Haihong Shang Shilin Zhu Changsong Zou Qin Li Youlu Yuan Cairui Lu Hengling Wei Caiyun Gou Zequn Zheng Ye Yin Xueyan Zhang Kun Liu Bo Wang Chi Song Nan Shi Russell J Kohel Richard G Percy John Z Yu Yu-xian Zhu Jun Wang Shuxun Yu | 2012 | Nat Genet2012，，44： | 1 |
| 7 | Erratum to Prevalence and clinical significance of pathogenic germline BRCA1/2 mutations in Chinese non-small cell lung cancer patients显示文摘In the published article1,the affiliation for the first author,Xingshcng Hu,is'Department of Medical Oncology,Cancer Hospital,Chinese Academy of Medical Sciences',we would like to update it to'Department of Medical Oncology,National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College,Beijing,100021,China'.We apologize for the errors and for any confusion it may have caused. | Xingsheng Hu Dongyong Yang Yalun Li Li Li Yan Wang Peng Chen Song Xu Xingxiang Pu Wei Zhu Pengbo Deng Junyi Ye Hanhan Zhang Analyn Lizaso Hao Liu Xinru Mao Hai Huang Qian Chu Chengping Hu | 2020 | Cancer Biology & Medicine2020，17，2： | 1 |
| 8 | A study of long-term sea level variability in the East China Sea显示文摘From the analyses of the satellite altimeter Maps of Sea Level Anomaly(MSLA) data, tidal gauge sea level data and historical sea level data, this paper investigates the long-term sea level variability in the East China Sea(ECS).Based on the correlation analysis, we calculate the correlation coefficient between tidal gauge and the closest MSLA grid point, then generate the map of correlation coefficient of the entire ECS. The results show that the satellite altimeter MSLA data is effective to observe coastal sea level variability. An important finding is that from map of correlation coefficient we can identify the Kuroshio. The existence of Kuroshio decreases the correlation between coastal and the Pacific sea level. Kurishio likes a barrier or a wall, which blocks the effect of the Pacific and the global change. Moreover, coastal sea level in the ECS is mainly associated with local systems rather than global change. In order to calculate the long-term sea level variability trend, the empirical mode decomposition(EMD) method is applied to derive the trend on each MSLA grid point in the entire ECS. According to the 2-D distribution of the trend and rising rate, the sea level on the right side of the axis of Kuroshio rise faster than in its left side. This result supports the barrier effect of Kuroshio in the ECS. For the entire ECS, the average sea level rose 45.0 mm between 1993 and 2010, with a rising rate of(2.5±0.4) mm/a which is slower than global average.The relatively slower sea level rising rate further proves that sea level rise in the ECS has less response to global change due to its own local system effect. | XU Ying LIN Mingsen ZHENG Quanan YE Xiaomin LI Junyi ZHU Benlu | 2015 | Acta Oceanologica Sinica2015，34，11： | 1 |
| 9 | Increasing Prevalence of Type 2 Diabetes in Chinese Adults in Shanghai显示文摘 | Li Rui Lu Wei Jiang Qing Wu Li Yan Yun Zhao Gen Ming Shi Liang Yang Qu Di Ruan Ye Jiang Junyi Zhang Sheng Nian Xu Wang Hong Zhong Wei Jian | 2012 | EN2012，，5： | 1 |
| 10 | stAPAminer:Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies显示文摘Alternative polyadenylation(APA)contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases.Singlecell RNA sequencing(scRNA-seq)has enabled the profiling of APA at the single-cell level;however,the spatial information of cells is not preserved in scRNA-seq.Alternatively,spatial transcriptomics(ST)technologies provide opportunities to decipher the spatial context of the transcriptomic landscape.Pioneering studies have revealed potential spatially variable genes and/or splice isoforms;however,the pattern of APA usage in spatial contexts remains unappreciated.In this study,we developed a toolkit called stAPAminer for mining spatial patterns of APA from spatially barcoded ST data.APA sites were identified and quantified from the ST data.In particular,an imputation model based on the k-nearest neighbors algorithm was designed to recover APA signals,and then APA genes with spatial patterns of APA usage variation were identified.By analyzing wellestablished ST data of the mouse olfactory bulb(MOB),we presented a detailed view of spatial APA usage across morphological layers of the MOB.We compiled a comprehensive list of genes with spatial APA dynamics and obtained several major spatial expression patterns that represent spatial APA dynamics in different morphological layers.By extending this analysis to two additional replicates of the MOB ST data,we observed that the spatial APA patterns of several genes were reproducible among replicates.stAPAminer employs the power of ST to explore the transcriptional atlas of spatial APA patterns with spatial resolution.This toolkit is available at http://gffzz188fe103f8f1460asuxu6ouxwkk5969of.ffgz.tsg.suse.edu.cn/BMILAB/stAPAminer and http://gffzz77e3413bc06540edsuxu6ouxwkk5969of.ffgz.tsg.suse.edu.cn/biocode/tools/BT007320. | Guoli Ji Qi Tang Sheng Zhu Junyi Zhu Pengchao Ye Shuting Xia Xiaohui Wu | 2023 | Genomics, Proteomics & Bioinformatics2023，21，3： | 1 |
| 11 | Stem cell niche-inspired microcarriers with ADSCs encapsulation for diabetic wound treatment显示文摘Stem cell therapies have made great progress in the treatment of diabetic wounds during recent decades,while their short in vivo residence,alloimmune reactions,undesired behaviors,and dramatic losses of cell functions still hinder the translation of them into clinic.Here,inspired by the natural components of stem cell niches,we presented novel microfluidic hydrogel microcarriers with extracellular matrix(ECM)-like composition and adipose-derived stem cells(ADSCs)encapsulation for diabetic wound healing.As the hydrogel was synthesized by conjugating hyaluronic acid methacryloyl(HAMA)onto the Fibronectin(FN)molecule chain(FN-HAMA),the laden ADSCs in the microcarriers showed improved bioactivities and pro-regenerative capabilities.Based on these features,we have demonstrated that these ADSCs microcarriers exhibited significant promotion of neovascularization,follicular rejuvenation,and collagen deposition in a mouse diabetic wound model.These results indicated that the stem cell niche-inspired FN-HAMA microcarriers with ADSCs encapsulation have great clinical potential for diabetic wound treatment. | Xiangyi Wu Haofang Zhu Junyi Che Ye Xu Qian Tan Yuanjin Zhao | 2023 | Bioactive Materials2023，，8： | 1 |
| 12 | Engineering J-aggregates for NIR-induced meso-CF_(3)-BODIPY nanoparticles by activated apoptosis mechanism in photothermal therapy显示文摘Forming J-aggregates by organic monomer is a fascinating strategy to urge spectroscopic redshift with respect to that of the monomer.Herein,we designed 1,7-diphenyl-substituted meso–CF_(3)-BDP monomer confirmed by X-ray crystallographic analysis.The low-barrier rotation of the–CF_(3)group in meso–CF_(3)-BDP1 significantly enhances the non-radiative efficiency,and the photothermal conversion efficiency(PCE)of the self-assembled nanoparticles(1-NPs:λ_(abs)=746 nm)by J-aggregates was 82%.1-NPs could effectively block cell cycle progression,inhibit cancer cell proliferation and trigger cell apoptosis under low power laser irradiation(0.2 W/cm^(2)).This study proposes an alternate molecular design platform by J-aggregates to promote PCE through the insertion of rotating segment and trigger the cancer cells apoptosis in photothermal therapy at low power laser density. | Chujing Ye Shan Zhang Dongxiang Zhang Yue Shen Zhan Wang Huan Wang Junyi Ren Xin-Dong Jiang Jianjun Du Rong Shang Guiling Wang | 2023 | Chinese Chemical Letters2023，34，9： | 0 |
| 13 | Anisodine hydrobromide alleviates oxidative stress caused by hypoxia/reoxygenation in human cerebral microvascular endothelial cells predominantly via inhibition of muscarinic acetylcholine receptor 4显示文摘Background:Anisodine hydrobromide(AT3),an anti-cholinergic agent,could be delivered to the brain across the blood-brain barrier and has been used clinically for the treatment of cerebral ischemia/reperfusion injury.Endothelial dysfunction can be caused by hypoxia/reoxygenation(H/R)via oxidative stress and metabolic alterations.The present study investigated whether AT3 regulates the production of nitric oxide(NO)and reactive oxygen species(ROS),and the HIF-1αpathway via regulation of muscarinic acetylcholine receptors(mAChRs)in brain microvascular endothelial cells after H/R exposure.Methods:Under H/R conditions,hCMEC/D3 cerebral microvascular endothelial cells were treated with AT3.Specific inhibitors of M2-and M4-mAChRs were used to explore the mechanism by which AT3 influences oxidative stress in endothelial cells.Then,mAChRs expression was detected by western blotting and NO production was detected by Greiss reaction.The intracellular ROS level was measured using DCFH-DA probes.The expression of hypoxia-inducible transcription factor 1α(HIF-1α)was also detected.Results:While H/R induced the expression of M2-and M4-mAChRs,AT3 suppressed the H/R-upregulated M2-and M4-mAChRs.H/R also induced the production of NO,ROS,and apoptosis.AT3 and M4-mAChR inhibitors inhibited the H/R-induced production of NO and ROS and apoptosis.HIF-1αwas induced by H/R,but was suppressed by AT3.Conclusion:Thus,the in vitro evidence shows that AT3 protects against H/R injury in cerebral microvascular endothelial cells via inhibition of HIF-1α,NO and ROS,predominantly through the downregulation of M4-mAChR.The findings offer novel understandings regarding AT3-mediated attenuation of endothelial cell apoptosis and cerebral ischemia/reperfusion injury. | WENLI JIANG JUNYI SHEN XIAOQIANG DU YAN QIU JIAN ZHONG ZHI OUYANG BINGMEI M.FU YE ZENG | 2023 | BIOCELL2023，47，10： | 0 |
| 14 | A novel nine gene signature integrates stemness characteristics associated with prognosis in hepatocellular carcinoma显示文摘Cancer stem cells(CSCs)are heterogeneous with self-renewal and differentiation ability.The mRNA expression-based stemness index(mRNAsi)described the similarity between tumor cells and CSCs,which is positively associated with the poor prognosis of cancer patients.However,the key prognostic genes related to mRNAsi in hepatocellular carcinoma(HCC)remains unclear.A 9-gene signature related to mRNAsi and HCC prognosis including PSMG3,SNRPD1,DTYMK,PIGU,NME1,TXNL4A,IPO4,PES1,and REXO4 was obtained.High expression of this signature indicates poor prognosis of HCC.PIGU was an independent prognostic factor of HCC,which was significantly associated with progression of HCC.Among them,DTYMK and NME1 enriched in pyrimidine metabolism,SNRPD1 and TXNL4A enriched in spliceosome and PIGU enriched in glycosyl phosphatidylinositol(GPI)-anchor biosynthesis pathways.High levels of IPO4,NME1,PES1,PIGU and SNRPD1 were closely associated with metastasis of HCC,and low levels of IPO4,PIGU and REOX4 were significantly associated with sorafenib resistance of HCC.High expression of the 9-gene signature was negatively correlated with the stromal cell infiltration,and positively correlated with specific immune subtypes-related to angiogenesis,M1/M2 macrophage polarization,and M2 response.The 9-gene signature was negatively correlated with the stroma,and SNRPD1 and TXNL4 were positively correlated with immune infiltrate.NME1 was negatively correlated with tumor purity.Therefore,a 9-gene signature related to mRNAsi and poor prognosis in HCC were identified,which can be used as biomarkers for the diagnosis of HCC and functional mechanism exploration of CSCs in HCC.These genes such as IPO4 and PIGU might drive the transition of tumor cells into CSCs which possibly controls the balance between metastasis and drug resistance in HCC.The challenge on balance between metastasis and drug resistance for tumor therapy was firstly reported by the present study. | XINGHONG YAO CHENGQUAN LU JUNYI SHEN WENLI JIANG YAN QIU YE ZENG LIANG LI | 2021 | BIOCELL2021，45，6： | 0 |
| 15 | Finite Series Representation of Rician Shadowed Channel with Integral Fading Parameter and the Associated Exact Performance Analysis显示文摘With the deployment of small cells and device to device communications in future heterogeneous networks,in many situations we would encounter mobile radio channels with partly blocked line of sight component,which are well modeled by the Rician shadowed(RS) fading channel.In this paper,by the usage of Kummer transformation,a simplified representation of the RS fading channel with integral fading parameter is given.It is a finite series representation involving only exponential function and low order polynomials.This allows engineers not only the closed-form expressions for exact performance analysis over RS fading channel,but also the insights on the system design tactics. | JIAN Xin ZENG Xiaoping YU Anning YE Changrong YANG Junyi | 2015 | China Communications2015，12，3： | 0 |
| 16 | NEW ORGANIC SYSTEM FOR PHOTON-GATED PERSISTENT SPECTRAL HOLE BURNING显示文摘We report a new system of organic materials for photon-gated persistent spectral hole burning by donor-acceptor electron transfer:a tetrabenzoporphyrin derivative as donor and one of several aromatic cyanides as an acceptor in a poly(methyl methacrylate)(FMMA)host matrix.Up to 50C%deep spectral holes in transmission were burnt and appeared very high hole burning efficiency. | WANG Duoyuan HU Lingzhi HE Huizhu XIE Jie ZHANG Junyi ZHAO Lizeng ZHANG Xiulan ZHANG Dongxiang MI Xin NIE Yuxin YE Peixian | 1990 | Chinese Physics Letters1990，7，12： | 0 |
| 17 | Differential regulation of JAK1 expression by ETS1 associated with predisposition to primary biliary cholangitis显示文摘Primary biliary cholangitis(PBC)is an autoimmune liver disease characterized by the destruction of intrahepatic small bile ducts and progressive cholestasis,eventually leading to liver cirrhosis and hepatic failure without appropriate treatment(Terziroli Beretta-Piccoli et al.,2019). | Peng Jiang Chan Wang Mingming Zhang Ye Tian Weifeng Zhao Junyi Xin Yexi Huang Zhibin Zhao Wenjuan Sun Jie Long Ruqi Tang Fang Qiu Xingjuan Shi Yi Zhao Li Zhu Na Dai Lei Liu Xudong Wu Jinshan Nie Bo Jiang Youlin Shao Yueqiu Gao Jianjiang Yu Zhigang Hu Zhidong Zang Yuhua Gong Yaping Dai Lan Wang Ningling Ding Ping Xu Sufang Chen Lu Wang Jing Xu Luyao Zhang Junyan Hong Ruonan Qian Hu Li Xuan Jiang Congwei Chen Wenyan Tian Jian Wu Yuzhang Jiang Chongxu Han Kui Zhang Hong Qiu Li Li Hong Fan Liming Chen Jianqiong Zhang Zhongsheng Sun Xiao Han Zhenhua Dai Erguang Li M.Eric Gershwin Zhexiong Lian Xiong Ma Michael F.Seldin Weichang Chen Meilin Wang Xiangdong Liu | 2023 | Journal of Genetics and Genomics2023，50，10： | 0 |
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