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| 1 | A Chromosome-Scale Genome Assembly of Paper Mulberry(Bmussonetia papyrifera)Provides New Insights into Its Forage and Papermaking Usage显示文摘Paper mulberry(Broussonetia papyrifera)is a well-known woody tree historically used for Cai Lun papermaking,one of the four great inventions of ancient China.More recently,Paper mulberry has also been used as forage to address the shortage of feedstuff because of its digestible crude fiber and high protein contents.In this study,we obtained a chromosome-scale genome assembly for Paper mulberry using integrated approaches,including Illumina and PacBio sequencing platform as well as Hi-C,optical,and genetic maps.The assembled Paper mulberry genome consists of 386.83 Mb,which is close to the estimated size,and 99.25%(383.93 Mb)of the assembly was assigned to 13 pseudochromosomes.Comparative genomic analysis revealed the expansion and contraction in the flavonoid and lignin biosynthetic gene families,respectively,accounting for the enhanced flavonoid and decreased lignin biosynthesis in Paper mulberry.Moreover,the increased ratio of syringyl-lignin to guaiacyl-lignin in Paper mulberry underscores its suitability for use in medicine,forage,papermaking,and barkcloth making.We also identified the rootassociated microbiota of Paper mulberry and found that Pseudomonas and Rhizobia were enriched in its roots and may provide the source of nitrogen for its stems and leaves via symbiotic nitrogen fixation.Collectively,these results suggest that Paper mulberry might have undergone adaptive evolution and recruited nitrogen-fixing microbes to promote growth by enhancing flavonoid production and altering lignin monomer composition.Our study provides significant insights into genetic basis of the usefulness of Paper mulberry in papermaking and barkcloth making,and as forage.These insights will facilitate further domestication and selection as well as industrial utilization of Paper mulberry worldwide. | Xianjun Peng Hui Liu Peilin Chen Feng Tang Yanmin Hu Fenfen Wang Zhi Pi Meiling Zhao Naizhi Chen Hui Chen Xiaokang Zhang Xueqing Yan Min Liu Xiaojun Fu Guofeng Zhao Pu Yao Lili Wang He Dai Xuming Li Wei Xiong Wencai Xu Hongkun Zheng Haiyan Yu Shihua Shen | 2019 | Molecular Plant2019，12，5： | 18 |
| 2 | Data mining-based detection of acupuncture treatment on juvenile myopia显示文摘OBJECTIVE:We applied data mining techniques to the study of acupuncture as a treatment for juvenile myopia,with the aim of identifying hidden patterns in the data.METHODS:Fifty patients with juvenile myopia were selected and treated with acupuncture,and data mining was used to analyze the effects of treatment and the influence of behavioral variables.Clustering analysis was used to divide myopia patients into two classifications before acupuncture treatment.Artificial neural network BP algorithm was adopted to analyze the roles of different factors in changes in diopters.An association algorithm was used to analyze factors associated with the subjective experience of acupuncture and average diopter.RESULTS:The two classification results were fully consistent with the understandings of the ophthalmic circles.The duration of using the Internet and watching TV every day was the main factor that affected vision.Acupuncture feelings and therapeutic effect have a strong correlativity.A good or above experience's score of acupuncture could slow the progression of juvenile myopia.CONCLUSION:Collecting data from patients with juvenile myopia by using data mining can extract hidden potential rules and knowledge from the research evidence.The decision support can be provided to improve the doctor's clinical acupuncture treatment effects. | Xuming Yang Lingyu Xu Fei Zhong Ying Zhu | 2012 | Journal of Traditional Chinese Medicine2012，32，3： | 15 |
| 3 | Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies显示文摘Brassica rapa comprises several important cultivated vegetables and oil crops.Current reference genome assemblies of Brassica rapa are quite fragmented and not highly contiguous,thereby limiting extensive genetic and genomic analyses.Here,we report an improved assembly of the B.rapa genome(v3.0)using single-molecule sequencing,optical mapping,and chromosome conformation capture technologies(Hi-C).Relative to the previous reference genomes,our assembly features a contig N50 size of 1.45 Mb,representing a~30-fold improvement.We also identified a new event that occurred in the B.rapa genome~1.2 million years ago,when a long terminal repeat retrotransposon(LTR-RT)expanded.Further analysis refined the relationship of genome blocks and accurately located the centromeres in the B.rapa genome.The B.rapa genome v3.0 will serve as an important community resource for future genetic and genomic studies in B.rapa.This resource will facilitate breeding efforts in B.rapa,as well as comparative genomic analysis with other Brassica species. | Lei Zhang Xu Cai Jian Wu Min Liu Stefan Grob Feng Cheng Jianli Liang Chengcheng Cai Zhiyuan Liu Bo Liu Fan Wang Song Li Fuyan Liu Xuming Li Lin Cheng Wencai Yang Mai-he Li Ueli Grossniklaus Hongkun Zheng Xiaowu Wang | 2018 | Horticulture Research2018，5，1： | 10 |
| 4 | Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence显示文摘Rapeseed (Brassica napus),an important oilseed crop,has adapted to diverse climate zones and latitudes by forming three main ecotype groups,namely winter,semiwinter,and spring types. However,genetic variations underlying the divergence of these ecotypes are largely unknown. Here,we report the global pattern of genetic polymorphisms in rapeseed determined by resequencing a worldwide collection of 991 germplasm accessions.A total of 5.56 and 5.53 million singlenucleotide polymorphisms (SNPs)as Well as 1.86 and 1.92 million InDels were identified by mapping reads to the reference genomes of 'Darmor-bzh'and 'Tapidor,'respectively.We generated a map of allelic drift paths that shows splits and mixtures of the main populations,and revealed an asymmetric evolution of the two subgenomes of B.napus by calculating the genetic diversity and linkage disequilibrium parameters.Selective-sweep analysis revealed genetic changes in genes orthologous to those regulating various aspects of plant development and response to stresses.A genome-wide association study identified SNPs in the promoter regions of FLOWERING LOCUS T and FLOWERING LOCUS C orthologs that corresponded to the different rapeseed ecotype groups. Our study provides important insights into the genomic footprints of rapeseed evolution and flowering-time divergence among three ecotype groups,and will facilitate screening of molecular markers for accelerating rapeseed breeding. | Dezhi Wu Zhe Liang Tao Yan Ying Xu Lijie Xuan Juan Tang Gang Zhou Ulrike Lohwasser Shuijin Hua Haoyi Wang Xiaoyang Chen Qian Wang Le Zhu Antony Maodzeka Nazim Hussain Zhilan Li Xuming Li Imran Haider Shamsi Ghulam Jilani Linde Wu Hongkun Zheng Guoping Zhang Boulos Chalhoub Lisha Shen Hao Yu Lixi Jiang | 2019 | Molecular Plant2019，12，1： | 10 |
| 5 | A Plant Lectin Receptor-like Kinase Phosphorylates the Bacterial Effector AvrPtoB to Dampen Its Virulence in Arabidopsis显示文摘Plasma membrane-localized receptor-like kinases(RLKs)perceive conserved pathogen-associated molecular pattems(PAMPs)in plants,leading to PAMP-triggered immunity(PTI).TheArabidopsis thaliana lectin RLK LecRK-Ⅸ.2 has been shown to regulate the bacterial flagellin-derived peptide flg22-induced PTI.Here,we discover that Pseudomonas syringae effector AvrPtoB targets LecRK-Ⅸ.2 for degradation,which subsequently suppresses LecRK-Ⅸ.2-mediated PTI and disease resistance.However,LecRK-Ⅸ.2 can interact with and phosphorylate AvrPtoB at serine site 335(S335).AvrPtoB self-associates in vitro and in vivo,and the association appears to be essential for its E3 ligase activity in ubiquitinating substrate in plants.Phosphorylation of S335 disrupts the self-association and as a result,phosphomimetic AvrPtoBS335D cannot ubiquitinate LecRK-Ⅸ.2 efficiently,leading to the compromised virulence of AvrPtoB in suppressing PTI responses.fig22 enhances AvrPtoB S335 phosphorylation by inducing the expression and activating of LecRK-Ⅸ.2.Our study demonstrates that host RLKs can modify pathogen effectors to dampen their virulence and undermine their ability in suppressing PTI. | Ning Xu Xuming Luo Wei Wu Yingying Xing Yingbo Liang Yanzhi Liu Huasong Zou Hai-Lei Wei Jun Liu | 2020 | Molecular Plant2020，13，10： | 5 |
| 6 | A precise and accurate acupoint location obtained on the face using consistency matrix pointwise fusion method显示文摘OBJECTIVE: To develop a more precise and accurate method, and identified a procedure to measure whether an acupoint had been correctly located.METHODS: On the face, we used an acupoint location from different acupuncture experts and obtained the most precise and accurate values of acupoint location based on the consistency information fusion algorithm, through a virtual simulation of the facial orientation coordinate system.RESULTS: Because of inconsistencies in each acupuncture expert's original data, the system error could not be modified using the characteristics ofthe general weight calculation. First, we corrected each expert of acupoint location system error itself,to obtain a rational quantification for each expert of acupuncture and moxibustion acupoint location consistent support degree, to obtain pointwise variable precision fusion results, to put every expert's acupuncture acupoint location fusion error enhanced to pointwise variable precision. Then, we more effectively used the measured characteristics of different acupuncture expert's acupoint location, to improve the measurement information utilization efficiency and acupuncture acupoint location precision and accuracy.CONCLUSION: Based on using the consistency matrix pointwise fusion method on the acupuncture experts' acupoint location values, each expert's acupoint location information could be calculated, and the most precise and accurate values of each expert's acupoint location could be obtained. | Yang Xuming Ye Yijun Xia Yong Wei Xuanzhong Wang Zheyu Ni Hongmei Zhu Ying Xu Lingyu | 2015 | Journal of Traditional Chinese Medicine2015，35，1： | 4 |
| 7 | Microscopic view of phytoplankton along the Yangtze River显示文摘Phytoplankton play an important role in nutrient cycling and energy conversion. However, phytoplankton community is poorly understood in large river ecosystems. Based on the large-scale samplings conducted in spring and autumn of 2017, a systematic study has been made on seasonal and spatial distributions of phytoplankton community along the mainstream of the Yangtze River. As results, 6 phyla were identified and 59 phytoplankton species were detected using microscopy, including Bacillariophyta(29 species), Chlorophyta(13 species) and Cyanophyta(8 species) as the dominant group. Moreover, the density of phytoplankton was ranged 0.05×10^6–1.90×10^6 cells/L and the biomass was 0.01–1.01 mg/L, both reaching their maximum in the middle reach from Yichang to Wuhan. Significant seasonal difference of phytoplankton community was observed and spatial dissimilarity in spring was revealed. The cell abundance and biomass of phytoplankton could be fairly estimated by chlorophylla, and redundancy analysis indicated that water temperature, dissolved oxygen, biochemical oxygen demand, nitrite, and ammonia nitrogen were the most important explanatory environmental factors for phytoplankton compositions in the Yangtze River. | LIU YuXin XU XuMing WANG Ting NI JinRen | 2019 | Science China(Technological Sciences)2019，62，11： | 3 |
| 8 | Data mining-based study on sub-mentally healthy state among residents in eight provinces and cities in China显示文摘OBJECTIVE: To apply data mining methods to research on the state of sub-mental health among residents in eight provinces and cities in China and to mine latent knowledge about many conditions through data mining and analysis of data on 3970 sub-mentally healthy individuals selected from 13385 relevant question naires.METHODS: The strategic tree algorithm was used to identify the main mani festations of the state of sub-mental health. The backpropogation artificial neural network was used to analyze the main mani festations of sub-healthy mental states of three different degrees. A sub-mental health evaluation model was then established to achieve predictive evaluationresults.RESULTS: Using classifications from the Scale of Chinese Sub-healthy State, the main manifestations of sub-mental health selected using the strate gictree were F1101(Do you lack peace of mind?),F1102(Are you easily nervous when something comes up?), and F1002(Do you often sigh?). The relative intensity of manifestations of sub-mental health was highest for F1101, followed by F1102,and then F1002. Through study of the neural network, better differentiation could be made between moderate and severe and between mild and severe states of sub-mental health. The differentiation between mild and moderate sub-mental health states was less apparent. Additionally, the sub-mental health state evaluation model, which could be used to predict states of sub-mental health of different individuals, was established using F1101, F1102, F1002, and the mental self-assessment totals core.CONCLUSION: The main manifestations of the state of sub-mental health can be discovered using data mining methods to research and analyze the latent laws and knowledge hidden in research evidence on the state of sub-mental health. The state of sub-mental health of different individuals can be rapidly predicted using the model established here.This can provide a basis for assessment and intervention for sub-mental health. It can also replace the relatively outdated approaches to research on sub-health in the technical era of information and digitization by combining the study of states of sub-mental health with information techniques and by further quantifying the relevant information. | Hongmei Ni Xuming Yang Chengquan Fang Yingying Guo Mingyue Xu Yumin He | 2014 | Journal of Traditional Chinese Medicine2014，34，4： | 3 |
| 9 | The position of tree shrews in the mammalian tree:Comparing multi-gene analyses with phylogenomic results leaves monophyly of Euarchonta doubtful显示文摘The well-accepted Euarchonta grandorder is a pruned version of Archonta nested within the Euarchontoglires(or Supraprimates)clade.At present,it includes tree shrews(Scandentia),flying lemurs(Dermoptera)and primates(Primates).Here,a phylogenomic dataset containing 1912 exons from 22 representative mammals was compiled to investigate the phylogenetic relationships within this group.Phylogenetic analyses and hypothesis testing suggested that tree shrews can be classified as a sister group to Primates or to Glires or even as a basal clade within Euarchontoglires.Further analyses of both modified and original previously published datasets found that the phylogenetic position of tree shrews is unstable.We also found that two of three exonic indels reported as synapomorphies of Euarchonta in a previous study do not unambiguously support the monophyly of such a clade.Therefore,the monophyly of both Euarchonta and Sundatheria(Dermoptera+Scandentia)are suspect.Molecular dating and divergence rate analyses suggested that the ancestor of Euarchontoglires experienced a rapid divergence,which may cause the unresolved position of tree shrews even using the whole genomic data. | Xuming ZHOU Fengming SUN Shixia XU Guang YANG Ming LI | 2015 | Integrative Zoology2015，10，2： | 2 |
| 10 | Extraction, detection, and profiling of serum biomarkers using designed Fe3O4@SiO2@HA core-shell particles显示文摘 | Chandrababu Rejeeth Xuechao Pang Ru Zhang Wei Xu Xuming Sun Bin Liu Jiatao Lou Jingjing Wan Hongchen Gu Wei Yan Kun Qian | 2018 | Nano Research2018，11，1： | 2 |
| 11 | Characterization and Proteomic Analysis of Novel Rice Lesion Mimic Mutant with Enhanced Disease Resistance显示文摘Lesion mmic mutants(LMMs)are plants that spontaneously form lesions without pathogeninfection or external stimulus and exhibit resistance to pathogens.Here,a rice LMM was created by ethylmethane sulfonate mutagenesis,named as hpil(hydrogen peroxide induced lesion).Diaminobenzidineand trypan blue staining showed that large amounts of H_(2)O_(2) were produced and cell death was occurredat and around the parts of lesion mimic in the rice leaves.The phenotype of hpil is controlled by a singlerecessive gene,localized at a 2 Mb interval on chromosome 2.The data suggested that hpil is a novelLMM with enhanced bacterial and fungal disease resistance,and multiple pathogenesis-related proteins(PRs)were up-regulated.The proteomes of leaves at three positions(different degrees of lesion mimicseverity)were characterized in hpil compared with its wild type plant.Differentially expressed proteinswere detected by two dimensional difference gel electrophoresis and 274 proteins were identified byMALDITOF/TOFTM.These proteins were related to metabolic process,cellular process and response tostimulus,with mostly down-regulated in hpil leaves.Many of these proteins were related to the Calvincycle,photosynthetic electron transport chain,glycolysis/gluconeogenesis and phosphonates pathways.Some resistance-related proteins including 14-3-3 proteins,OsPR10 and antioxidases such asperoxidase,superoxide dismutase and ascorbate peroxidase were up-regulated in leaves with lesionmimic.These results provide the foundation for cloning of the target gene and shed light on themechanism involved in autaimmunity of rice. | Yang Yong Lin Qiujun Chen Xinyu Liang Weifang Fu Yuwen Xu Zhengjin Wu Yuanhua Wang Xuming Zhou Jie Yu Chulang Yan Chengqi Mei Qiong Chen Jianping | 2021 | Rice science2021，28，5： | 2 |
| 12 | Large Signal Statistical Model Oriented Parameter Extraction Method for GaN High Electron Mobility Transistors显示文摘Efficient parameter extraction method is essential to establish large signal statistical model. This paper presents an automatic parameter extraction method of I-V model for Gallium nitride(GaN) High electron mobility transistors(HEMTs) large signal statistical model. To accurate modeling the statistical characterization, all of 53 parameters in an I-V model are considered. In order to realize automatic parameter extraction, the model parameters are divided into blocks according to their physical meaning to reduce the complexity of the I-V model. Different parameter blocks are extracted separately by fitting the pulsed I-V transfer characteristic curves of the device at different quiescent bias points. A large signal statistical model for 0.25μm GaN HEMTs process has been established by using the proposed method after measuring 34 GaN HEMTs from 10 batches. The results show that the large-signal performances(Output power and Power added efficiency) can be reproduced with high accuracy by the proposed statistical model. | YU Xuming XU Yuehang WEN Zhang CHEN Zhikai HONG Wei | 2017 | Chinese Journal of Electronics2017，26，6： | 2 |
| 13 | Author Correction:Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies显示文摘Since the publication of this article,the authors have noticed that the total gene models(45,985),tandem arrays(2077),tandem genes(4963),redundancy removed(43,099),syntenic genes(39,858),nonsyntenic genes(3241),genes on chromosomes(45,411),genes on scaffolds(574)of B.rapa reference genome v3.0 were mistaken in the article. | Lei Zhang Xu Cai Jian Wu Min Liu Stefan Grob Feng Cheng Jianli Liang Chengcheng Cai Zhiyuan Liu Bo Liu Fan Wang Song Li Fuyan Liu Xuming Li Lin Cheng Wencai Yang Mai-he Li Ueli Grossniklaus Hongkun Zheng Xiaowu Wang | 2019 | Horticulture Research2019，6，1： | 2 |
| 14 | 3D printed fiber-optic nanomechanical bioprobe显示文摘Ultrasensitive nanomechanical instruments,e.g.atomic force microscopy(AFM),can be used to perform delicate biomechanical measurements and reveal the complex mechanical environment of biological processes.However,these instruments are limited because of their size and complex feedback system.In this study,we demonstrate a miniature fiber optical nanomechanical probe(FONP)that can be used to detect the mechanical properties of single cells and in vivo tissue measurements.A FONP that can operate in air and in liquids was developed by programming a microcantilever probe on the end face of a single-mode fiber using femtosecond laser two-photon polymerization nanolithography.To realize stiffness matching of the FONP and sample,a strategy of customizing the microcantilever’s spring constant according to the sample was proposed based on structure-correlated mechanics.As a proof-of concept,three FONPs with spring constants varying from 0.421 N m^(−1)to 52.6 N m^(−1)by more than two orders of magnitude were prepared.The highest microforce sensitivity was 54.5 nmμN^(−1)and the detection limit was 2.1 nN.The Young’s modulus of heterogeneous soft materials,such as polydimethylsiloxane,muscle tissue of living mice,onion cells,and MCF-7 cells,were successfully measured,which validating the broad applicability of this method.Our strategy provides a universal protocol for directly programming fiber-optic AFMs.Moreover,this method has no special requirements for the size and shape of living biological samples,which is infeasible when using commercial AFMs.FONP has made substantial progress in realizing basic biological discoveries,which may create new biomedical applications that cannot be realized by current AFMs. | Mengqiang Zou Changrui Liao Yanping Chen Lei Xu Shuo Tang Gaixia Xu Ke Ma Jiangtao Zhou Zhihao Cai Bozhe Li Cong Zhao Zhourui Xu Yuanyuan Shen Shen Liu Ying Wang Zongsong Gan Hao Wang Xuming Zhang Sandor Kasas Yiping Wang | 2023 | International Journal of Extreme Manufacturing2023，5，1： | 1 |
| 15 | Grain growth kinetics and densification mechanism of(TiZrHfVNbTa)C high-entropy ceramic under pressureless sintering显示文摘The grain growth kinetics and densification mechanism of(TiZrHfVNbTa)C high-entropy carbide ceramic are investigated in this work.A single phase carbide with a rock-salt structure is formed until 2300°C,below which an apparent aggregation of V,Zr and Hf exists.It is associated with the slow diffusion rate of V element as well as the relatively poor solubility of VC in HfC(as well as ZrC).The grain growth mechanism gradually changes from surface diffusion to volume diffusion and then grain boundary diffusion with increasing sintering temperature.This is attributed to the variation of activation energy of grain growth.The densification mechanism is principally dominated by the mass transport through lattice diffusion with the activation energy of 839±53 k J/mol.Through the design of two-step sintering,it is verified that the solid solution formation can effectively promote the densification process. | Wen Zhang Lei Chen Chenguang Xu Xuming Lv Yujin Wang Jiahu Ouyang Yu Zhou | 2022 | Journal of Materials Science & Technology2022，，15： | 1 |
| 16 | Short-term roxithromycin treatment attenuates airway inflammation via MAPK/NF-κB activation in a mouse model of allergic asthma显示文摘 | Xinxin Ci Xiao Chu Xue Xu Hongyu Li Xuming Deng | 2012 | Inflammation Research2012，，7： | 1 |
| 17 | Thiourea–thiocyanate leaching system for gold显示文摘 | Xiyun Yang Michael S. Moats Jan D. Miller Xuming Wang Xichang Shi Hui Xu | 2010 | Hydrometallurgy2010，，1： | 1 |
| 18 | A bidding model and cooperative game-based vertical handoff decision algorithm显示文摘 | LIU Xingwei FANG Xuming CHEN Xu | 2011 | Journal of Network and Computer Applications2011，34，： | 1 |
| 19 | Regulation of OsPRIOa Promoter Activity by Phytohormone and Pathogen Stimulation in Rice显示文摘OsPRIOa is one of the well known pathogenesis-related genes in rice,and is induced by multiple plant hormones and pathogens.However,the underlying transcriptional regulation mechanisms in response to differe nt signals and their crosstalks are still largely unknown.In order to find new players participated in the activation of OsPRIOa,we systematically analyzed the basal expression patterns as well as the expression responses of a 2.5 kb OsPRIOa promoter in rice transgenic plants after phytohormone and pathogen stimulations.In agreement with the native gene expression,the OsPRIOa promoter can drive glucuronidase(GUS)gene expressing in spots of leaf cells,leaf trichomes,lemmas and paleae,germinating embryos,calli and root tips.The leaf expression of OsPR10a::GUS was dramatically in creased upon jasm onic acid(JA)and cytoki nin(CK)treatme nts,or challe nges of the pathogen Magnaporthe grisea and Xanthomonas oryzae pv.oryzae.Thus,the OsPRIOa promoter reported here can faithfully reflect its native gene expression.The effects of several JA and CK responsive OsWRKY genes on the regulation of OsPRIOa promoter were then inspected by luciferase transient expression assay,and the JA inducible OsWRKYlO transcription factor was found as a new positive regulator of OsPRIOa.However,the key transcription factors of JA and CK signaling pathways,OsMYC2 and B-type response regulators,were not responsible for the activation of OsPRIOa promote Our findings provided new in sights into the regulation of OsPRIOa expression during plan t-hormone/pathoge n interactions,and the OsPRIOa reporter system can be useful to unravel novel regulators from both pathogen and host. | Zheng Ersong Wang Xuming Xu Rumeng Yu Feibo Zheng Chao Yang Yong Chen Yang Chen Jianping Yan Chengqi Zhou Jie | 2021 | Rice science2021，28，5： | 1 |
| 20 | Wettability of carbon fibers modified by acrylic acid and interface properties of carbon fiber/epoxy显示文摘 | Xu Zhiwei Chen Li Huang Yudong Li Jialu Wu Xiaoqing Li Xuming Jiao Yanan | 2008 | European Polymer Journal2008，44，2： | 1 |
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