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| 1 | A Data-Driven Clustering Recommendation Method for Single-Cell RNA-Sequencing Data显示文摘Recently,the emergence of single-cell RNA-sequencing(scRNA-seq)technology makes it possible to solve biological problems at the single-cell resolution.One of the critical steps in cellular heterogeneity analysis is the cell type identification.Diverse scRNA-seq clustering methods have been proposed to partition cells into clusters.Among all the methods,hierarchical clustering and spectral clustering are the most popular approaches in the downstream clustering analysis with different preprocessing strategies such as similarity learning,dropout imputation,and dimensionality reduction.In this study,we carry out a comprehensive analysis by combining different strategies with these two categories of clustering methods on scRNA-seq datasets under different biological conditions.The analysis results show that the methods with spectral clustering tend to perform better on datasets with continuous shapes in two-dimension,while those with hierarchical clustering achieve better results on datasets with obvious boundaries between clusters in two-dimension.Motivated by this finding,a new strategy,called QRS,is developed to quantitatively evaluate the latent representative shape of a dataset to distinguish whether it has clear boundaries or not.Finally,a data-driven clustering recommendation method,called DDCR,is proposed to recommend hierarchical clustering or spectral clustering for scRNA-seq data.We perform DDCR on two typical single cell clustering methods,SC3 and RAFSIL,and the results show that DDCR recommends a more suitable downstream clustering method for different scRNA-seq datasets and obtains more robust and accurate results. | Yu Tian Ruiqing Zheng Zhenlan Liang Suning Li Fang-Xiang Wu Min Li | 2021 | Tsinghua Science and Technology2021，26，5： | 3 |
| 2 | Synthesis and biological activities of 2-oxocycloalkylsulfonamides显示文摘 | XINGHAI LI XINLING YANG XIAOMEI LIANG ZHENPENG KAI HUIZU YUAN DEKAIYUAN JIANJUN ZHANG RUIQING WANG FUXIANG RAN SHUHUA QI YUN LING FUHENG CHEN DAOQUAN WANG | | 0，，08： | 1 |
| 3 | GL9 from Oryza glumaepatula controls grain size and chalkiness in rice显示文摘Grain size is a key factor influencing grain yield and appearance quality in rice.We identified twelve quantitative trait loci(QTL)for grain length(GL),nine for grain width(GW),and nine for 1000-kernel weight(TKW)using GLU-SSSLs,which are single-segment substitution lines with Oryza glumaepatula as donor parent and Huajingxian 74(HJX74)as recipient parent.Among the QTL,qGL1-2,qGL1-4,qGL9-2,qGW2-2,qGW9-1 and qTKW9-2 contributed to high grain yield.GL9 was identified as a candidate gene for qGL9-2 by map-based cloning and sequencing,and is a novel allele of GS9.The kernel of NIL-gl9was slenderer and longer than that of HJX74,and the TKW and grain yield per plant of NIL-gl9 were higher than those of HJX74.The proportion of grain chalkiness of NIL-gl9 was much lower than that of HJX74.Thus,gl9 increased grain yield and appearance quality simultaneously.Three pyramid lines,NIL-gs3/gl9,NIL-GW7/gl9 and NIL-gw8/gl9,were developed and the kernel of each was longer than that of the corresponding recipient parent lines.The gl9 allele may be beneficial for breeding rice varieties with high grain yield and good appearance quality. | Shaojun Lin Zupei Liu Kui Zhang Weifeng Yang Penglin Zhan Quanya Tan Yajun Gou Shuaipeng Ma Xin Luan Chubing Huang Zhili Xiao Yuanyuan Liu Bihuang Zhu Ruiqing Liang Wenqi Zhou Haitao Zhu Suhong Bu Guifu Liu Guiquan Zhang Shaokui Wang | 2023 | The Crop Journal2023，11，1： | 1 |
| 4 | Serological Prevalence Survey Among the High-Risk Populations of Brucellosis-Endemic Areas-China,2019−2020显示文摘What is already known about this topic?Timely screening of high-risk population is important to improve the early detection of brucellosis among the endemic areas during the high incidence seasons,which is also required by the National Brucellosis Prevention and Control Plan(2016–2020)(NBPCP).What is added by this report?Seroepidemiological characteristics of brucellosis in high-risk populations were obtained and special occupational populations were found.The seroprevalence of brucellosis has been decreasing compared with that reported in the recent years due to the ongoing implementation of control measures in endemic areas.What are the implications for public health practice?Special occupational populations could be promptly detected using routine screening,which makes it possible to initiate standardized treatment for infected patients as early as possible.It also reminds us to pay attention to special occupational populations to improve their knowledge of brucellosis and reduce the risk of infection. | Shenghong Lin Zhe Wang Xinrong Liu Aizhi Yu Muhtar·Hasan Jiensi·Bayidawulieti Haitan·Aximujiang Ruiqing Li Guoxing Zheng Xinwang Liang Xiaoling Fan Biqiao Hou Xiaolong Fan Dilxat·Abuliti Lusha Shi Cuihong Zhang Yifei Wang Pengjing Ning Caixiong Liu Zhongjie Li Liping Wang | 2021 | China CDC weekly2021，3，6： | 1 |
| 5 | Brucellosis Knowledge and Personal Protective Equipment Usage Among High-Risk Populations in Brucellosis-Endemic Areas-China,2019−2020显示文摘What is already known about this topic?According to the National Brucellosis Prevention and Control Plan(2016–2020)(NBPCP),the awareness rate of high-risk populations in brucellosis-endemic areas should reach 90%by 2020.But the updated results have not been reported.What is added by this report?This report determined the awareness rate of brucellosis(17.74%),utilization of personal protective equipment(PPE)(20.13%),and their relationship with seroprevalence,which provides evidence for the effectiveness of the implementation of NBPCP.What are the implications for public health practice?The results suggest that health education should be conducted for high-risk populations to improve their brucellosis and protection knowledge. | Zhe Wang Shenghong Lin Xinrong Liu Aizhi Yu Muhtar·Hasan Jiensi·Bayidawulieti Haitan·Aximujiang Ruiqing Li Guoxing Zheng Xinwang Liang Xiaoling Fan Biqiao Hou Xiaolong Fan Dilxat·Abuliti Lusha Shi Cuihong Zhang Yifei Wang Pengjing Ning Caixiong Liu Zhongjie Li Liping Wang | 2021 | China CDC weekly2021，3，6： | 1 |
| 6 | SSRE:Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement显示文摘Accurate identification of cell types from single-cell RNA sequencing(scRNA-seq)data plays a critical role in a variety of scRNA-seq analysis studies.This task corresponds to solving an unsupervised clustering problem,in which the similarity measurement between cells affects the result significantly.Although many approaches for cell type identification have been proposed,the accuracy still needs to be improved.In this study,we proposed a novel single-cell clustering framework based on similarity learning,called SSRE.SSRE models the relationships between cells based on subspace assumption,and generates a sparse representation of the cell-to-cell similarity.The sparse representation retains the most similar neighbors for each cell.Besides,three classical pairwise similarities are incorporated with a gene selection and enhancement strategy to further improve the effectiveness of SSRE.Tested on ten real scRNA-seq datasets and five simulated datasets,SSRE achieved the superior performance in most cases compared to several state-of-the-art single-cell clustering methods.In addition,SSRE can be extended to visualization of scRNA-seq data and identification of differentially expressed genes.The matlab and python implementations of SSRE are available at https://github.com/CSUBioGroup/SSRE. | Zhenlan Liang Min Li Ruiqing Zheng Yu Tian Xuhua Yan Jin Chen Fang-Xiang Wu Jianxin Wang | 2021 | Genomics, Proteomics & Bioinformatics2021，19，2： | 0 |
| 7 | Oriented Generation of Novel Thermo-Sensitive Genic Male Sterile Lines with Improved Grain Shape and Outcrossing Rate in Early-Season Rice显示文摘Two-line hybrid rice with excellent quality is preferred in the Chinese market.However,there is a trade-off between reducing costs for hybrid seed production and lowering the outcrossing rate of the sterile line,which is largely determined by the stigma exsertion rate(SER).In this study,we constructed mutants of male sterility lines with improved grain length(GL)and SER in three elite early-season indica rice varieties through targeted manipulation of the TMS5 and GS3 genes using CRISPR/Cas9-mediated multiplex systems.We obtained a series of marker-free gs3 single mutants and gs3tms5 double mutants with significantly higher SER,longer grains,and increased 1000-grain weight compared with the wild type(WT).Importantly,the typically thermo-sensitive genic male sterile(TGMS)trait with a higher SER was observed in gs3tms5 mutants,and their F1 hybrids exhibited remarkable improvements in grain shape and yield-related traits.Our findings provided an efficient method to generate new valuable TGMS germplasm with improved SER through the mutagenesis of GS3 and TMS5 synergistically,and demonstrated that GS3 had pleiotropic effects on grain size,SER,and grain quality in early-season indica rice. | ZHANG Huali CHEN Junyu LI Ruiqing WANG Huimei DAI Dongqing LIANG Minmin WU Mingyue MA Liangyong | 2024 | Rice science2024，31，2： | 0 |
| 8 | Multilayer Porous Vanadium Nitride Microsheets Anodes for Highly Stable Na-ion Batteries显示文摘Sodiumion batteries(SIBs)have attracted intensive attention as promising alternative to lithium-ionbatteries(LIBs)for large scale energy storage systems because of low cost of sodium,similar energy storage mechanism and the reasonable performance.However,it is still a great challenge to search and design a robust structure of anode materials with excellent cycling stability and high rate capability for SIBs.Herein,multilayer porous vanadium nitride(VN)microsheets are synthesized through a facile and scalable hydrothermal synthesis-nitrogenization strategy as an effective anode material for SIBs.The multilayer porous VN microsheets not only offer more active sites for fast Na+insertion/extraction process and short diffusion pathway,but also effectively buffer the volume change of anode due to more space in the multilayer porous structure.The large proportions of capacitive behavior imply that the Na+charge storage depends on the intercalation pseudocapacitive mechanism.The multilayer porous VN microsheets electrodes manifest excellent cycling stability and rate capability,delivering a discharge capacity of 156.1 mA·h/g at 200 mA/g after 100 cycles,and a discharge capacity of 111.9 mA·h/g at 1.0 A/g even after 2300 cycles with the Coulombic efficiency of nearly 100%. | HU Tao YANG Weiwei WANG Cheng BU Yali JIN Feng ZHANG Dongwen GU Min LIU Wenhui LIANG Qinghua LIU Ruiqing FENG Xiaomiao MA Yanwen | 2021 | Chemical Research in Chinese Universities2021，37，2： | 0 |
| 9 | Regulation of cell morphology and viability using anodic aluminum oxide with custom-tailored structural parameters显示文摘Anodic aluminum oxide(AAO)with independently controlled period,porosity,and height is used as the model surface to study the single structural parameter effect on breast cancer cell behaviors,including cell polarity and cell viability.It is found that the quantity of multipolar cells and cell viability increases as the nanodent period increases from 100 to 300 nm,while the number of bipolar cells has almost no change until there is a dramatic decrease as the period increases to 3oo nm.After anodizing nanodents into nanopores,the numbers of both bipolar cells and the cell viability increase significantly with the porosity increase.However,as the porosity further increases and the nanopore changes into a nanocone pillar,most of the cells become nonpolar spheres and the cell viability decreases.Increasing the height of the nanocone pillar has little effect on the cell polarity;the cell viability increases slightly with the increase of the nanocone pillar height.These results reveal the influence of individual nanostructure parameters on the cell behavior,especially the cell polarity and the cell viability,which can help to design the surface to make the cell grow as desired. | Zhiying ZHANG Ting LIU Juan LI Yiyan GUO Ruiqing LIANG Jiangbo LU Runguang SUN Jun DONG | 2022 | Frontiers of Materials Science2022，16，4： | 0 |
| 10 | Application of BeiDou navigation satellite system in emergency rescue of natural hazards: a case study for field geological survey of Qinghai−Tibet plateau显示文摘In recent years,geological and mineral resources exploration in China has expanded to deep hinterland of the Qinghai−Tibet Plateau and other regions with complex geological conditions.The special natural conditions of Qinghai−Tibet Plateau determine the characteristics of“life-forbidden zone”that is characterized by alpine hypoxia,changeable weather,complex road conditions,and beast attack.In particular,the work in wild depopulated zones with severe environment and poor communications imposes serious threats to the life safety of geological personnel.Therefore,how to guarantee the safety of geological personnel working on the Qinghai−Tibet Plateau and how to reduce or even avoid casualty of geological personnel have currently become the urgent challenge.In this study,an emergency rescue information system for field geological survey is constructed based on BeiDou Navigation Satellite System.A case study of emergency rescue has been conducted in the depopulated zone of the Qinghai−Tibet Plateau and good effects have been achieved,providing security assurance for personnel engaged in field geological survey on the Qinghai−Tibet Plateau and technical support for the emergency rescue in case of natural hazards on the Qinghai−Tibet Plateau.The BeiDou Navigation Satellite System(BDS)can be effectively used to locate and communicate in the emergency rescue for rigorous Geological survey task where there is no network signal for the mobile phone,and the emergency rescue guarantee system is independent,reliable,and relatively cheap.The application value of BDS is demonstrated in the geological field. | Ming Hao Jianlong Zhang Ruiqing Niu Changrong Deng Hong Liang | 2018 | Geo-Spatial Information Science2018，21，4： | 0 |
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