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Tightening up the structure, lighting up the pathway:application of molecular constraints and light to manipulate protein folding, self-assembly and function

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Science China Chemistry 2014年第12期57卷 1615-1624页

作者： mARKIEWICZ Beatrice N. CULIK Robert m. gai Feng Department of Chemistry University of Pennsylvania Department of Biochemistry and Biophysics University of Pennsylvania

Chemical cross-linking provides an effective avenue to reduce the conformational entropy of polypeptide chains and hence has become a popular method to induce or force structural formation in peptides and ***,other types of molecular constraints,especially photoresponsive linkers and functional groups,have also found increased use in a wide variety of ***,we provide a concise review of using various forms of molecular strategies to constrain proteins,thereby stabilizing their native states,gaining insight into their folding mechanisms,and/or providing a handle to trigger a conformational process of interest with *** applications discussed here cover a wide range of topics,ranging from delineating the details of the protein folding energy landscape to controlling protein assembly and function.

关键词： protein folding aggregation self-assembly cross-linker phototrigger light-activation

Asymtotics of Dantzig Selector for a General Single-Index model

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Journal of Systems Science & Complexity 2016年第4期29卷 1123-1144页

作者： FAN yan gai yujie ZHU Lixing School of Business Information Shanghai University of International Business and Economics Shanghai 201620 China School of statistics and mathematics Central University of Finance and Economics Beijing 100081 China Baptist University of Hong Kong China

As two popularly used variable selection methods, the Dantzig selector and the LASSO have been proved asymptotically equivalent in some scenarios. However, it is not the case in general for linear models, as disclosed in gai, Zhu and Lin's paper in 2013. In this paper, it is further shown that generally the asymptotic equivalence is not true either for a general single-index model with random design of predictors. To achieve this goal, the authors systematically investigate necessary and sufficient conditions for the consistent model selection of the Dantzig selector. An adaptive Dantzig selector is also recommended for the cases where those conditions are not satisfied. Also, different from existing methods for linear models, no distributional assumption on error term is needed with a trade-off that more stringent condition on the predictor vector is assumed. A small scale simulation is conducted to examine the performances of the Dantzig selector and the adaptive Dantzig selector.

关键词： Adaptive Dantzig Selector Dantzig selector general single-index model model selection consistency.

Density fluctuations in intermediate-energy heavy-ion collisions

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Nuclear Science and Techniques 2022年第5期33卷 1-7页

作者： Cong Liu Xian-gai Deng yu-Gang ma Shanghai Institute of Applied Physics Chinese Academy of SciencesShanghai 201800China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of Nuclear Physics and Ion-beam Application(mOE) Institute of Modern PhysicsFudan UniversityShanghai 200433China Shanghai Research Center for Theoretical Nuclear Physics NSFC and Fudan UniversityShanghai 200438China

Within the framework of the isospin-dependent quantum molecular dynamics model,we simulate^(129)Xe+^(119)Sn collisions in an incident energy range of 20 to 190meV/nucleon and discuss the liquid-gas phase transition with density *** comparison,we also extract the effective Fisher parameter τ_(eff),multiplicity of intermediate-mass fragments(ImFs),and information *** is found that the Fisher parameter and maximum information entropy of collisions have peak values at E_(beam)=50-80 meV/*** addition,the maximum multiplicity of ImFs has a plateau around 70 meV/*** higher-order density moments in a larger central region of[-5,5]^(3) fm^(3) in the collision system,a maximum plateau also appears as function of beam energy at energies exceeding 70 meV/*** observables,which are consistent with each other,indicate a liquid-gas phase transition around 70 meV/nucleon for the^(129)Xe+^(119)Sn system.

关键词： Heavy-ioncollisions Liquid-gasphase transition IQmD Density moment Intermediatemass fragment Informationentropy Fisher-lawparameter

Transposable elements play an important role during cotton genome evolution and fiber cell development

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Science China(Life Sciences) 2016年第2期59卷 112-121页

作者： Kun Wang gai Huang yuxian Zhu College of Life Sciences Wuhan University Wuhan 430072 China Institute for Advanced Studies Wuhan University Wuhan 430072 China State Key Laboratory of Protein and Plant Gene Research College of Life Sciences Peking University Beijing 100871 China

Transposable elements(TEs)usually occupy largest fractions of plant genome and are also the most variable part of the *** traditionally it is hallmarked as"junk and selfish DNA",today more and more evidence points out TE’s participation in gene regulations including gene mutation,duplication,movement and novel gene creation via genetic and epigenetic *** recently sequenced genomes of diploid cottons Gossypium arboreum(AA)and Gossypium raimondii(DD)together with their allotetraploid progeny Gossypium hirsutum(At At Dt Dt)provides a unique opportunity to compare genome variations in the Gossypium genus and to analyze the functions of TEs during its *** accounted for 57%,68.5%and67.2%,respectively in DD,AA and At At Dt Dt *** 1,694 mb A-genome was found to harbor more LTR(long terminal repeat)-type retrotransposons that made cardinal contributions to the twofold increase in its genome size after evolution from the 775.2 mb *** the 2,173 mb At At Dt Dt genome showed similar TE content to the A-genome,the total numbers of LTR-gypsy and LTR-copia type TEs varied significantly between these two *** their roles on rewiring gene regulatory networks,we believe that TEs may somehow be involved in cotton fiber cell ***,the insertion or deletion of different TEs in the upstream region of two important transcription factor genes in At or Dt subgenomes resulted in qualitative differences in target gene *** suggest that our findings may open a window for improving cotton agronomic traits by editing TE activities.

关键词： transposable elements Gossypium genus genome evolution fiber development

A malvaceae-specific miRNA targeting the newly duplicated GaZIP1L to regulate Zn^(2+)ion transporter capacity in cotton ovules

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Science China(Life Sciences) 2021年第3期64卷 339-351页

作者： Xingpeng Wen gai Huang Chenyu Li yuxian Zhu Institute for Advanced Studies Wuhan UniversityWuhan 430072China State Key Laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China

microRNAs(miRNAs)play critical roles in regulating gene expression in plants,yet their functions underlying cultivated diploid Gossypium arboreum cotton ovule development are largely ***,we acquired small RNA profiles from *** ovules and fibers collected at different growth stages,and identified 46 novel miRNAs that accounted for 23.7%of all miRNAs in *** reported in the latest plant sRNA *** analysis of 84(including 38 conserved)differentially expressed *** miRNAs,we detected 215 putative protein-coding genes in 26 biological processes as their potential targets.A malvaceae-specific novel miRNA named gar-miRN44 was found to likely regulate cotton ovule growth by targeting to a newly duplicated Zn^(2+)ion transporter gene *** cotton ovule development,gar-miRN44 transcript level decreased sharply after 10 to 15 days post-anthesis(DPA),while that of the GaZIP1L increased significantly,with a concomitant increase of Zn^(2+)ion concentration in late ovule developmental *** dynamics simulation and ion absorption analysis showed that GaZIP1L has stronger Zn2+ion binding ability than the original GaZIP1,indicating that the newly evolved GaZIP1L may be more suitable for maintaining high Zn2+ion transport capacity that is likely required for cotton ovule growth via enhanced cellulose synthase *** systematic miRNA profiling in *** and characterization of gar-miRN44 not only contribute to the understanding of miRNA function in cotton,but also provide potential targets for plant breeding.

关键词： gar-miRN44 malvaceae GaZIP1L Zn^(2+)ion transport cotton ovule development

Sustainable plant disease control: biotic information flow and behavior manipulation

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Science China(Life Sciences) 2019年第12期62卷 1710-1713页

作者： yuying Xia gai Huang yuxian Zhu Institute for Advanced Studies Wuhan UniversityWuhan 430072China State Key Laboratory of Protein and Plant Gene Research College of Life SciencesPeking UniversityBeijing 100871China

Crop pests and diseases are a major threat to agricultural production *** utilize massive quantities of chemical pesticides,herbicides,and fungicides for secure crop *** the extensive use of pesticides and other chemicals,serious problems regarding human and animal poisoning,agricultural product pollution,and ecological and environmental damage can no longer be ignored(Toju et al.,2018).Therefore,there is an urgent need to develop new strategies and technologies by employing basic research on information flow and cross-talk among crops,insects,and pathogenic microorganisms for sustainable *** recent years,great progress has been made in understanding the relationship between plants and other organisms to ensure the safety of food production in China and worldwide.

关键词： Sustainable pesticides utilize

Effects of Sealing Flow Supply Configuration with Holes on Sealing Effectiveness of Turbine Rim Seal

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Journal of Thermal Science 2023年第1期32卷 366-386页

作者： gai Zepeng ZHU Pengfei HU Jianping LIU Zhenxia yIN Hang School of Power and Energy Northwestern Polytechnical UniversityXi'an 710072China

This paper proposes a new-designed rim seal configuration with sealing holes based on the conventional radial rim seal,and presents a numerical comparison of the sealing performance between the conventional sealing flow supply configuration and the new sealing flow supply configuration with holes at different sealing flow *** sealing effectiveness and unsteady flow yields at the rim seal are numerically simulated by using the URANS method and SST turbulent model from ANSyS *** influence of the new sealing flow supply configuration on the sealing effectiveness at different sealing flow rates is *** effectiveness of different sealing flow rates in the conventional rim seal is also *** to the conventional rim seal,the increase in the sealing flow rate reduces the degree of gas ingestion induced by the effect of mainstream ingress at the rim clearance,while the unsteady flow characteristics are enhanced,and the number and amplitude of the low-frequency signals *** position of the Kelvin-Helmholtz instabilities vortex structures is left by the increased sealing flow rate,and its strength is *** with the conventional rim seal configuration,the new sealing flow supply configuration with holes could reduce the sealing efficiency by 5.06%at most at sealing flow distribution m_(1):m_(2)=3:1 when Cw=2000,and improve the sealing efficiency by 11.71%at most at sealing flow distribution m_(1):m_(2)=1:1 when Cw=*** shows that the lateral jet from the holes induces a larger-scale Kelvin-Helmholtz vortex structure at Cw=2000,thus the sealing efficiency in the wheel space is also ***,the size of the Kelvin-Helmholtz vortex structures is significantly suppressed by the new sealing flow supply configuration at Cw=7500,which is beneficial to improving the sealing effectiveness of the conventional rim seal.

关键词： secondary air system rim seal ingestion and seal unsteady flow discrete sealing holes

Approximation Algorithm for the Balanced 2-Correlation Clustering Problem

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Tsinghua Science and Technology 2022年第5期27卷 777-784页

作者： Sai Ji Dachuan Xu Donglei Du Ling gai Zhongrui Zhao Department of Operations Research and Information Engineering Beijing University of TechnologyBeijing 100124China Beijing Institute for Scientific and Engineering Computing Beijing University of TechnologyBeijing 100124China Faculty of Business Administration University of New BrunswickFrederictonNB E3B 5A3Canada Glorious Sun School of Business and management Donghua UniversityShanghai 200051China

The Correlation Clustering Problem(CorCP) is a significant clustering problem based on the similarity of *** has significant applications in different fields,such as machine learning,biology,and data mining,and many different problems in other *** this paper,the Balanced 2-CorCP(B2-CorCP) is introduced and examined,and a new interesting variant of the CorCP is *** goal of this clustering problem is to partition the vertex set into two clusters with equal size,such that the number of disagreements is *** first present a polynomial time algorithm for the B2-CorCP on m-positive edge dominant graphs(m≥ 3).Then,we provide a series of numerical experiments,and the results show the effectiveness of our algorithm.

关键词： balanced clustering k-correlation clustering positive edge dominant graphs approximation algorithm

Spatial variations in daily average CO_2 concentrations above wetland surface of Xianghai National Nature Reserve, China

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Journal of Environmental Sciences 2005年第1期17卷 54-58页

作者： BAIJun-hong OUyANGHua WANGQing-gai ZHOUCai-ping XUXiao-feng InstituteofGeographicalSciencesandNaturalResourcesResearch ChineseAcademyofSciencesBeijing100101China

Horizontal and vertical variations of daily average CO 2 concentration above the wetland surface were studied in Xianghai National Nature Reserve of China in August, 2000 The primary purpose was to study spatial distribution characteristics of CO 2 concentration on the four levels of height(0 1 m, 0 6 m, 1 2 m and 2 m) and compare the differences of CO 2 concentration under different land covers. Results showed that daily average CO 2 concentration above wetland surface in Xianghai National Natural Reserve was lower than that above other wetlands in northeast China as well as the worldwide average, suggesting that Xianghai wetland absorbed CO 2 in August and acted as “sink” of CO 2 The horizontal variations on the four levels of height along the latitude were distinct, and had the changing tendency of “decreasing after increasing” with the increase of height. The areas with obvious variations were consistent on different levels of height, and those with the highest variations appeared above surface of shore, sloping field, Typha wetland and Phragmites wetland; the vertical variations were greatly different, with the higher variations in Phragmites wetland and Typha wetland, and the lands near the shore and the sloping field with the lower variations. Spatial variations of daily average CO 2 concentrations above wetland surface were affected by surface qualities and land covers.

关键词： wetland surface daily average CO_2 concentration sink horizontal variation vertical variation