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| 1 | The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb显示文摘 | Liang Yan Xiao Wang Hui Liu Yang Tian Jinmin Lian Ruijuan Yang ShumeiHao Xuanjun Wang Shengchao Yang Qiye Li Shuai Qi Ling Kui Moses Okpekum Xiao Ma Jiajin Zhang Zhaoli Ding Guojie Zhang Wen Wang Yang Dong Jun Sheng | 2015 | Molecular Plant2015，8，6： | 64 |
| 2 | Circulating tumor DNA 5-hydroxymethylcytosine as a novel diagnostic biomarker for esophageal cancer显示文摘 | Xin Tian Baofa Sun Chuanyuan Chen Chunchun Gao Ji Zhang XingYu Lu Linchen Wang Xiangnan Li Yurong Xing Ruijuan Liu Xiao Han Zheng Qi Xiaojian Zhang Chuan He Dali Han Yun-Gui Yang Quancheng Kan | 2018 | Cell Research2018，28，5： | 12 |
| 3 | Data mining-aided materials discovery and optimization显示文摘Recent developments in data mining-aided materials discovery and optimization are reviewed in this paper,and an introduction to the materials data mining(MDM)process is provided using case studies.Both qualitative and quantitative methods in machine learning can be adopted in the MDM process to accomplish different tasks in materials discovery,design,and optimization.State-of-the-art techniques in data mining-aided materials discovery and optimization are demonstrated by reviewing the controllable synthesis of dendritic Co_(3)O_(4) superstructures,materials design of layered double hydroxide,battery materials discovery,and thermoelectric materials design.The results of the case studies indicate that MDM is a powerful approach for use in materials discovery and innovation,and will play an important role in the development of the Materials Genome Initiative and Materials Informatics. | Wencong Lu Ruijuan Xiao Jiong Yang Hong Li Wenqing Zhang | 2017 | Journal of Materiomics2017，3，3： | 11 |
| 4 | MiR156 regulates anthocyanin biosynthesis through SPL targets and other microRNAs in poplar显示文摘Anthocyanins biosynthesized from the flavonoid pathway are types of pigments that are involved in the protection of poplar from biotic and abiotic stresses.Previous researchers studying anthocyanin-related transcription factors and structural genes in poplar have made significant discoveries.However,little is known about the regulatory role of microRNAs in anthocyanin biosynthesis in poplar.Here,we overexpressed miR156 in poplar to study the comprehensive effects of the miR156-SPL module on the biosynthesis of anthocyanins.Small RNA sequencing analysis revealed 228 microRNAs differentially expressed in transgenic poplar plants with dramatically increased miR156 levels.Furthermore,integrated microRNAomic and transcriptomic analysis suggested that two microRNAs,miR160h,and miR858,have the potential to affect anthocyanin accumulation in poplar by regulating auxin response factors and MYB transcription factors,respectively.Additionally,the accumulation of miR160h and miR858 displayed a positive correlation with miR156 levels,suggesting a possible interaction between the miR156-SPL module and these microRNAs in poplar.Last,metabolomics analysis revealed that the levels of anthocyanins,flavones,and flavonols were substantially elevated in transgenic poplar plants overexpressing miR156 compared with the wild type,whereas the total lignin content was reduced in the transgenic plants.Taken together,our results indicate that miR156 can fine tune the anthocyanin biosynthetic pathway via multiple factors,including microRNAs,transcription factors,and the levels of structural genes,in poplar.This provides additional clues for understanding the complex regulatory network of anthocyanin biosynthesis in woody plants. | Yamei Wang Wenwen Liu Xinwei Wang Ruijuan Yang Zhenying Wu HanWang LeiWang Zhubing Hu Siyi Guo Hailing Zhang Jinxing Lin Chunxiang Fu | 2020 | Horticulture Research2020，7，1： | 9 |
| 5 | 5-Hydroxymethylome in Circulating Cell-free DNA as A Potential Biomarker for Non-small-cell Lung Cancer显示文摘Non-small-cell lung cancer(NSCLC), the most common type of lung cancer accounting for 85% of the cases, is often diagnosed at advanced stages owing to the lack of efficient early diagnostic tools. 5-Hydroxymethylcytosine(5 hmC) signatures in circulating cell-free DNA(cfDNA) that carries the cancer-specific epigenetic patterns may represent the valuable biomarkers for discriminating tumor and healthy individuals, and thus could be potentially useful for NSCLC diagnosis. Here,we employed a sensitive and reliable method to map genome-wide 5 hmC in the cfDNA of Chinese NSCLC patients and detected a significant 5 hmC gain in both the gene bodies and promoter regions in the blood samples from tumor patients compared with healthy controls. Specifically, we identified six potential biomarkers from 66 patients and 67 healthy controls(mean decrease accuracy>3.2, P < 3.68E-19) using machine-learning-based tumor classifiers with high accuracy. Thus,the unique signature of 5 hmC in tumor patient's cfDNA identified in our study may provide valuable information in facilitating the development of new diagnostic and therapeutic modalities for NSCLC. | Ji Zhang Xiao Han Chunchun Gao Yurong Xing Zheng Qi Ruijuan Liu Yueqin Wang Xiaojian Zhang Yun-Gui Yang Xiangnan Li Baofa Sun Xin Tian | 2018 | Genomics, Proteomics & Bioinformatics2018，16，3： | 7 |
| 6 | Different Expression Analysis in Fruit Softening and Ethylene Biosynthetic Pathways in Peaches of Different Flesh Textures显示文摘The aim of our study was to assess differences in the expression of genes involved in fruit softening and ethylene biosynthetic pathways under different temperature storage conditions. Different peach cultivars of ‘Xiacui' and ‘Yumyeong', which are stonyhard, ‘Yinhualu', which is softmelting, ‘Hujing Milu', which is hard-melting, and ‘Baby Gold 6', which is non-melting at 80% ripening, were collected as test materials. The results showed that only slight ethylene production was detected after harvesting of ‘Yumyeong' and ‘Xiacui' under either a room temperature(25 °C) or low temperature(4 °C). The fruit firmness of stonyhard cultivars was retained at a high level under room temperature over time, whereas a low temperature induced ‘Yumyeong' fruit to soften. Quantitative real-time PCR results indicated that the PpACS1 gene was highly expressed in soft-melting, hard-melting and non-melting cultivars; however, expression was extremely low in stonyhard peaches. PpACS2 or PpACS3, however,was not detected in all five cultivars. Interestingly, cold treatment significantly decreased firmness along with endo-PG expression obviously upregulated in ‘Yumyeong', but not in ‘Xiacui' peaches. In conclusion, this study revealed that fruit softening of peaches with different flesh textures was closely related to ethylene biosynthesis during the storage period, which was controlled via regulating relevant gene expression levels under different storage temperatures. | YANG Yong MA Ruijuan ZHANG Binbin SONG Zhizhong ZHANG Chunhua GUO Shaolei YU Mingliang | 2016 | Horticultural Plant Journal2016，2，2： | 7 |
| 7 | Distributed accelerated optimization algorithms:Insights from an ODE显示文摘In this paper, we consider the distributed optimization problem, where the goal is to minimize the global objective function formed by a sum of agents' local smooth and strongly convex objective functions, over undirected connected graphs. Several distributed accelerated algorithms have been proposed for solving such a problem in the existing literature. In this paper, we provide insights for understanding these existing distributed algorithms from an ordinary differential equation(ODE) point of view. More specifically, we first derive an equivalent second-order ODE, which is the exact limit of these existing algorithms by taking the small step-size. Moreover, focusing on the quadratic objective functions, we show that the solution of the resulting ODE exponentially converges to the unique global optimal solution. The theoretical results are validated and illustrated by numerical simulations. | CHEN RuiJuan YANG Tao CHAI Tian You | 2020 | Science China(Technological Sciences)2020，63，9： | 2 |
| 8 | Corrosion formation and phase transformation of nickel-iron hydroxide nanosheets array for efficient water oxidation显示文摘Designing earth-abundant electrocatalysts with high performance towards water oxidation is highly decisive for the sustainable energy technologies. This study develops a facile natural corrosion approach to fabricate nickel-iron hydroxides for water oxidation. The resulted electrode demonstrates an outstanding activity and stability with an overpotential of 275 mV to deliver 10 mA·cm^(−2). Experimental and theoretical results suggest the corrosion-induced formation of hydroxides and their transformation to oxyhydroxides would account for this excellent performance. This work not only provides an interesting corrosion approach for the fabrication of excellent water oxidation electrode, but also bridges traditional corrosion engineering and novel materials fabrication, which would offer some insights in the innovative principles for nanomaterials and energy technologies. | Lanqian Gong Huan Yang Hongming Wang Ruijuan Qi Junlei Wang Shenghua Chen Bo You Zehua Dong Hongfang Liu Bao Yu Xia | 2021 | Nano Research2021，14，12： | 2 |
| 9 | Balancing benefits of strength,plasticity and glass-forming ability in Co-based metallic glasses显示文摘Development of advanced metals materials with ultrahigh strength,large plasticity and high thermostability is one of the most attractive aims for materials researchers.Co-based bulk metallic glasses(BMGs)with the highest strength(up to 6 GPa)and special strength(up to 650 Nm/g)among all of metals materials so far we known have received extensive attentions.In this paper,a family of Co-Ta-B-Si BMGs with high glass-transition temperature(above 870 K),large compressive plasticity(up to 6.4%)and high strength(above 5.5 GPa),and high glass-forming ability(the critical diameter,Dc:up to 4 mm)was developed by accurately tuning metalloid element contents of Si and B in the parental alloy of Co_(55)Ta_(10)B_(35).The changes of glass formation and plasticity caused by the adjustment of the constituent metalloid elements were evaluated by the combination of experimental and calculated results.The reason for the significant improvement of plastic deformation is revealed by the analysis of the self-organization behaviors of high-density shear bands. | Yimeng Zhao Xuan Li Xiaobin Liu Jiazi Bi Yang Wu Ruijuan Xiao Ran Li Tao Zhang | 2021 | Journal of Materials Science & Technology2021，，27： | 1 |
| 10 | Rings over which polynomial rings are semicommutative 显示文摘 | YANG Gang DU Ruijuan | 2009 | Vietnam J of Math2009，37，4： | 1 |
| 11 | DeceFL:a principled fully decentralized federated learning framework显示文摘Traditional machine learning relies on a centralized data pipeline for model training in various applications;however,data are inherently fragmented.Such a decentralized nature of databases presents the serious challenge for collaboration:sending all decentralized datasets to a central server raises serious privacy concerns.Although there has been a joint effort in tackling such a critical issue by proposing privacy-preserving machine learning frameworks,such as federated learning,most state-of-the-art frameworks are built still in a centralized way,in which a central client is needed for collecting and distributing model information(instead of data itself)from every other client,leading to high communication burden and high vulnerability when there exists a failure at or an attack on the central client.Here we propose a principled decentralized federated learning algorithm(DeceFL),which does not require a central client and relies only on local information transmission between clients and their neighbors,representing a fully decentralized learning framework.It has been further proven that every client reaches the global minimum with zero performance gap and achieves the same convergence rate O(1=T)(where T is the number of iterations in gradient descent)as centralized federated learning when the loss function is smooth and strongly convex.Finally,the proposed algorithm has been applied to a number of applications to illustrate its effectiveness for both convex and nonconvex loss functions,time-invariant and time-varying topologies,as well as IID and Non-IID of datasets,demonstrating its applicability to a wide range of real-world medical and industrial applications. | Ye Yuan Jun Liu Dou Jin Zuogong Yue Tao Yang Ruijuan Chen Maolin Wang Chuan Sun Lei Xu Feng Hua Yuqi Guo Xiuchuan Tang Xin He Xinlei Yi Dong Li Guanghui Wen Wenwu Yu Hai-Tao Zhang Tianyou Chai Shaochun Sui Han Ding | 2023 | National Science Open2023，2，1： | 1 |
| 12 | Cluster based hierarchical resource searching model in P2P network显示文摘For the problem of large network load generated by the Gnutella resource-searching model in Peer to Peer (P2P) network, a improved model to decrease the network expense is proposed, which establishes a cluster in P2P network, auto-organizes logical layers, and applies a hybrid mechanism of directional searching and flooding. The performance analysis and simulation results show that the proposed hierarchical searching model has availably reduced the generated message load and that its searching-response time performance is as fairly good as that of the Gnutella model. | Yang Ruijuan Liu Jian Tian Jingwen | 2007 | Journal of Systems Engineering and Electronics2007，18，1： | 1 |
| 13 | Localized-domains staging structure and evolution in lithiated graphite显示文摘Intercalation provides to the host materials a means for controlled variation of many physical/chemical properties and dominates the reactions in metal‐ion batteries.Of particular interest is the graphite intercalation compounds with intriguing staging structures,which however are still unclear,especially in their nanostructure and dynamic transition mechanism.Herein,the nature of the staging structure and evolution of the lithium(Li)‐intercalated graphite was revealed by cryogenic‐transmission electron microscopy and other methods at the nanoscale.The intercalated Li‐ions distribute unevenly,generating local stress and dislocations in the graphitic structure.Each staging compound is found macroscopically ordered but microscopically inhomogeneous,exhibiting a localized‐domains structural model.Our findings uncover the correlation between the long‐range ordered structure and short‐range domains,refresh the insights on the staging structure and transition of Li‐intercalated/deintercalated graphite,and provide effective ways to enhance the reaction kinetic in rechargeable batteries by defect engineering. | Suting Weng Siyuan Wu Zepeng Liu Gaojing Yang Xiaozhi Liu Xiao Zhang Chu Zhang Qiuyan Liu Yao Huang Yejing Li Mehmet NAteş Dong Su Lin Gu Hong Li Liquan Chen Ruijuan Xiao Zhaoxiang Wang Xuefeng Wang | 2023 | Carbon Energy2023，5，1： | 1 |
| 14 | Overexpression of PvWOX3a in switchgrass promotes stem development and increases plant height显示文摘Switchgrass(Panicum virgatum L.)is an important perennial,noninvasive,tall ornamental grass that adds color and texture to gardens and landscapes.Moreover,switchgrass has been considered a forage and bioenergy crop because of its vigorous growth,low-input requirements,and broad geography.Here,we identified PvWOX3a from switchgrass,which encodes a WUSCHEL-related homeobox transcription factor.Transgenic overexpression of PvWOX3a in switchgrass increased stem length,internode diameter,and leaf blade length and width,all of which contributed to a 95%average increase in dry weight biomass compared with control plants.Yeast one-hybrid and transient dual-luciferase assays showed that PvWOX3a can repress the expression of gibberellin 2-oxidase and cytokinin oxidase/dehydrogenase through apparently direct interaction with their promoter sequences.These results suggested that overexpression of PvWOX3a could increase gibberellin and cytokinin levels in transgenic switchgrass plants,which promotes cell division,elongation,and vascular bundle development.We also overexpressed PvWOX3a in a transgenic miR156-overexpressing switchgrass line that characteristically exhibited more tillers,thinner internodes,and narrower leaf blades.Double transgenic switchgrass plants displayed significant increases in internode length and diameter,leaf blade width,and plant height but retained a tiller number comparable to that of plants expressing miR156 alone.Ultimately,the double transgenic switchgrass plants produced 174%more dry-weight biomass and 162%more solubilized sugars on average than control plants.These findings indicated that PvWOX3a is a viable potential genetic target for engineering improved shoot architecture and biomass yield of horticulture,fodder,and biofuel crops. | Ruijuan Yang Zhenying Wu Chen Bai Zhichao Sun Mengqi Wang Yuzhu Huo Hailing Zhang Yamei Wang Huapeng Zhou Shaojun Dai Wenwen Liu Chunxiang Fu | 2021 | Horticulture Research2021，8，1： | 1 |
| 15 | Hierarchical micro-nanostructures from polyoxometalates and polydopamine:Characterization,electrochemical and intrinsic peroxidase-like properties显示文摘Hybrid composite materials with hierarchical structures have attracted continuing attention for their enhanced features and various applications.The new hybrid composites XW_(9)@PDA(XW_(9) means Na_(8)H[α-PW_(9)O_(34)],Na_(10)[α-SiW_(9)O_(34)]and Na_(10)[α-GeW_(9)O_(34)];PDA means polydopamine)have been synthesized for potential sensing applications.The effect of polyoxometalates on the formation of the hybrid composites was investigated.Scanning electron microscopy(SEM)supported the obtained XW_(9)@PDA were hierarchical microsphere.By monitoring the reaction of classical peroxidase substrate o-phenylenediamine(OPD)to form yellow 2,3-diaminophenazine(DAB)in the presence of H_(2)O_(2),the peroxidase-like activity of XW_(9)@PDA was calculated.The results showed that XW_(9)@PDA still keep the peroxidase-like activity and have 505.98%,208.58%and 582.78%enhancement in intrinsic catalytic activity for PW_(9)@PDA,SiW_(9)@PDA and GeW_(9)@PDA.Among the three composites,PW_(9)@PDA showed the highest peroxidase-like activity.Therefore,PW_(9)@PDA was applicable to the colorimetric and electrochemical sensing for H_(2)O_(2). | Ruijuan Lv Xinming Zhang Ruimeng Sun Lixia Chen Yang Zhang Rongtian Sheng Ting Du Yuhan Li Yanfei Qi | 2022 | Particuology2022，20，5： | 1 |
| 16 | Design,Synthesis and Bioactivity Study of Marine Alkaloid Neobacillamide-A Derivatives显示文摘The Janus kinases(JAKs)are a family of intracellular tyrosine kinases that play an essential role in many basic biological processes,such as apoptosis and inflammation.Thus any dysfunction of the proteins in this pathway may lead to a variety of diseases,including cancer and diseases that affect the immune system,such as severe combined immune deficient(SCID).Marine biological resources have become an important source in new drug research and development due to their diversity,complexity and speciality.In this study,Marine alkaloid Neobacillamide A was isolated from the greedy and stubborn sponge symbiotic Bacillus atrophicus C89 in the South China Sea.Totally 24 novel marine alkaloid Neobacillamide A derivatives were designed and synthesized,which were evaluated for their inhibitory activity against JAK/STAT signaling pathway and their cytotoxicity to A549 cells.Compounds 13c,13o,14d,14g and 14h showed potent JAK/STAT inhibition capability(concentration of 25μmol L^(-1),all inhibitory potencies were above 60%),especially compound 14g exhibited superior JAK/STAT inhibition effect(89.70%inhibition).In addition,all these compounds with a concentration of 25μmol L^(-1)displayed weak or no cytotoxicity to A549 cells,which means that these Neobacillamide A derivatives with JAK/STAT inhibition capability may have potential anti-inflammatory function. | WANG Jiali LI Maowei ZHANG Xiao ZHANG Zhijin LIU Yang LIU Lu YIN Ruijuan JIANG Tao | 2023 | Journal of Ocean University of China2023，22，3： | 0 |
| 17 | A recombineering system for Bacillus subtilis based on the native phage recombinase pair YqaJ/YqaK显示文摘Bacillus subtilis plays an important role in fundamental and applied research,and it has been widely used as a cell factory for the production of enzymes,antimicrobial materials,and chemicals for agriculture,medicine,and industry.However,genetic manipulation tools for B.subtilis have low efficiency.In this work,our goal was to develop a simple recombineering system for B.subtilis.We showed that genome editing can be achieved in B.subtiliis 1A751 through co-expression of YqaJ/YqaK,a native phage recombinase pair found in B.sub-tilis 168,and the competence master regulator ComK using a double-stranded DNA substrate with short ho-mology arms(100 bp)and a phosphorothioate modification at the 5′-end.Efficient gene knockouts and large DNA insertions were achieved using this new recombineering system in B.subtilis 1A751.As far as we know,this is the first recombineering system using the native phage recombinase pair YqaJ/YqaK in B.subtilis.In conclusion,this new recombineering system provides a simple and fast tool for genetic manipulation of B.sub-tilis,and it will promote studies of genome function,construction of production strains,and genome mining in B.subtilis. | Qingshu Liu Ruijuan Li Hongbo Shi Runyu Yang Qiyao Shen Qingwen Cui Xiuling Wang Aiying Li Youming Zhang Jun Fu | 2023 | Engineering Microbiology2023，3，3： | 0 |
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