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Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing

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NATURE COMMUNICATIONS 2023年第1期14卷 7803页

作者： Chen, Ningbo Xia, Xiaoting Hanif, Quratulain zhang, Fengwei Dang, Ruihua Huang, Bizhi Lyu, Yang Luo, Xiaoyu zhang, Hucai Yan, Huixuan Wang, Shikang Wang, fuwen Chen, Jialei Guan, Xiwen Liu, Yangkai Li, Shuang Jin, Liangliang Wang, Pengfei Sun, Luyang zhang, Jicai Liu, Jianyong Qu, Kaixing Cao, Yanhong Sun, Junli Liao, Yuying Xiao, Zhengzhong Cai, Ming Mu, Lan Siddiki, Amam Zonaed Asif, Muhammad Mansoor, Shahid Babar, Masroor Ellahi Hussain, Tanveer Silva, Gamamada Liyanage Lalanie Pradeepa Gorkhali, Neena Amatya Terefe, Endashaw Belay, Gurja Tijjani, Abdulfatai Zegeye, Tsadkan Gebre, Mebrate Genet Ma, Yun Wang, Yu Huang, Yongzhen Lan, Xianyong Chen, Hong Migliore, Nicola Rambaldi Colombo, Giulia Semino, Ornella Achilli, Alessandro Sinding, Mikkel-Holger S. Lenstra, Johannes A. Cheng, Haijian Lu, Wenfa Hanotte, Olivier Han, Jianlin Jiang, Yu Lei, Chuzhao Northwest A&F University Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi Province College of Animal Science and Technology Yangling China (GRID:grid.144022.1) (ISNI:0000 0004 1760 4150) National Institute for Biotechnology and Genetic Engineering Faisalabad Pakistan (GRID:grid.419397.1) (ISNI:0000 0004 0447 0237) Chinese Academy of Agricultural Sciences (CAAS) CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources Institute of Animal Science Beijing China (GRID:grid.410727.7) (ISNI:0000 0001 0526 1937) Yunnan Academy of Grassland and Animal Science Kunming China (GRID:grid.506866.b) Yunnan University Institute for Ecological Research and Pollution Control of Plateau Lakes School of Ecology and Environment Science Kunming China (GRID:grid.440773.3) (ISNI:0000 0000 9342 2456) Chuxiong Normal University Academy of Science and Technology Chuxiong China (GRID:grid.469523.f) (ISNI:0000 0000 9870 4997) Guangxi Vocational University of Agriculture Nanning China (GRID:grid.469523.f) Guangxi Key Laboratory of Veterinary Biotechnology Guangxi Veterinary Research Institute Nanning China (GRID:grid.418337.a) Guangxi Vocational University of Agriculture Nanning China (GRID:grid.418337.a) Southwest Forestry University College of Landscape and Horticulture Kunming China (GRID:grid.412720.2) (ISNI:0000 0004 1761 2943) Chattogram Veterinary and Animal Sciences University (CVASU) Genomics Research Group Department of Pathology and Parasitology Faculty of Veterinary Medicine Chattogram Bangladesh (GRID:grid.442958.6) National Institute for Biotechnology and Genetic Engineering Faisalabad Pakistan (GRID:grid.419397.1) (ISNI:0000 0004 0447 0237) The University of Agriculture Dera Ismail Khan Pakistan (GRID:grid.412298.4) (ISNI:0000 0000 8577 8102) Virtual University of Pakistan Department of Molecular Biology Islamabad Pakistan (GRID:grid.444943.a) (ISNI:0000 0004 0609 0887) University of Peradeniya Department of Animal Science Peradeniya Sri Lanka (GRID

Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle.

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Recent selection and introgression facilitated high-altitude adaptation in cattle

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Science Bulletin 2024年第21期69卷 3415-3424页

作者： Yang Lyu fuwen Wang Haijian Cheng Jing Han Ruihua Dang Xiaoting Xia Hui Wang Jincheng Zhong Johannes A.Lenstra Hucai zhang Jianlin Han David E.MacHugh Ivica Medugorac Maulik Upadhyay Alexander SLeonard He Ding Xiaorui Yang Ming-Shan Wang Suolang Quji Basang Zhuzha Pubu Quzhen Silang Wangmu Nima Cangjue Da Wa Weidong Ma Jianyong Liu Jicai zhang Bizhi Huang Xingshan Qi Fuqiang Li Yongzhen Huang Yun Ma Yu Wang Yuanpeng Gao Wenfa Lu Chuzhao Lei Ningbo Chen Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China Key Laboratory of Animal Production Product Qualityand SecurityMinistry of EducationCollege of Animal Science and TechnologyJilin Agricultural UniversityChangchun 130118China Institute of Animal Science and Veterinary Medicine Shandong Academy of Agricultural SciencesShandong Key Lab of Animal Disease Control and BreedingJinan 250000China College of Veterinary Medicine Northwest A&F UniversityYangling 712100China Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengdu 610000China Faculty of Veterinary Medicine Utrecht UniversityUtrecht 3584 CMThe Netherlands Institute for Ecological Research and Pollution Control of Plateau Lakes School of Ecology and Environmental ScienceYunnan UniversityKunming 650500China Southwest United Graduate School Kunming 650500China Yazhouwan National Laboratory Sanya 572024China CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources Institute of Animal ScienceChinese Academy of Agriculture Sciences(CAAS)Beijing 100000China Animal Genomics Laboratory UCD School of Agriculture and Food ScienceUniversity College DublinDublin D04 V1W8Ireland UCD Conway Institute of Biomolecular and Biomedical Research University College DublinDublin D04 V1W8Ireland Population Genomics Group Department of Veterinary SciencesLMU MunichMartinsried 82152Germany Animal Genomics ETH ZurichUniversitaetstrasse 2Zurich 8006Switzerland State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Institute of Animal Husbandry and Veterinary Science Xizang Autonomous Region Academy of Agricultural and Animal Husbandry SciencesLhasa 850000China Shigatse City Kan

During the past 3000 years,cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia,ultraviolet(UV)radiation,and extreme *** genetic mechanism underlying this rapid adaptation is not yet well ***,we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations,including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 *** genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine *** found that recently selected genes in Tibetan cattle were related to body size(HMGA2 and NCAPG)and energy expenditure(DUOXA2).We identiﬁed signals of sympatric introgression from yak into Tibetan cattle at different altitudes,covering 0.64%–3.26%of their genomes,which included introgressed genes responsible for hypoxia response(EGLN1),cold adaptation(LRP11),DNA damage repair(LATS1),and UV radiation resistance(GNPAT).We observed that introgressed yak alleles were associated with noncoding variants,including those in present *** Tibetan cattle,three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1,suggesting that these genomic variants enhance hypoxia *** together,our results indicated complex adaptation processes in Tibetan cattle,where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.

关键词： Tibetan cattle Introgression High-altitude adaptation Noncoding variant Cis-regulation

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Distributed event-triggered H∞ state estimation for T-S fuzzy systems over filtering networks

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JOURNAL OF THE FRANKLIN INSTITUTE-ENGINEERING AND APPLIED MATHEMATICS 2017年第9期354卷 3760-3779页

作者： Yan, Huaicheng Xu, Xiaoli zhang, Hao Yang, fuwen East China Univ Sci & Technol Sch Informat Sci & Engn Minist Educ Key Lab Adv Control & Optimizat Chem Proc Shanghai 200237 Peoples R China Tongji Univ Dept Control Sci & Engn Shanghai 200092 Peoples R China Griffith Univ Sch Engn Gold Coast Qld 4222 Australia

This paper is concerned with the problem of distributed event-triggered H-infinity filtering over sensor networks for a class of discrete-time nonlinear system modeled by a set of linear Takagi Sugeno(T-S) fuzzy models. In the filtering network, every individual filter receives the measurement information from the nonlinear plant, meanwhile, each filter can exchange the information with the other filters. Event-triggered communication scheme is applied to determine whether or not the current instant information should be transmitted to the quantizer. Distributed fuzzy filters are designed to guarantee the H-infinity disturbance attenuation level for the error estimation of the filtering network. Finally, a simulation example is provided to illustrate the effectiveness of the proposed filter design approach. (C) 2016 The Franklin Institute. Published by Elsevier Ltd. All rights reserved.

关键词： FUZZY systems PROBLEM solving DISCRETE-time systems OBSERVABILITY (Control theory) FUZZY control systems INFORMATION measurement

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Suppressing Exciton-Vibration Coupling to Prolong Exciton Lifetime of Nonfullerene Acceptors Enables High-Efficiency Organic Solar Cells

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Angewandte Chemie 2024年第8期136卷

作者： Yufan Zhu Dr. Dan He Chong Wang Xiao Han Zesheng Liu Ke Wang Prof. Jianqi zhang Dr. Xingxing Shen Dr. Jie Li Prof. Yuze Lin Prof. Chunru Wang Prof. Yuehui He Prof. fuwen Zhao State Key Laboratory of Powder Metallurgy Central South University Changsha 410083 P. R. China College of Chemistry and Chemical Engineering Central South University Changsha 410083 P. R. China University of Chinese Academy of Sciences Beijing 100190 P. R. China Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Organic Solids and Laboratory of Molecular Nanostructure and Nanotechnology Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 P. R. China College of Chemical Engineering Hebei Normal University of Science & Technology Qinhuangdao 066004 P. R. China

The limited exciton lifetime ( τ , generally <1 ns) leads to short exciton diffusion length ( L D ) of organic semiconductors, which is the bottleneck issue impeding the further improvement of power conversion efficiencies (PCEs) for organic solar cells (OSCs). However, efficient strategies to prolong intrinsic τ are rare and vague. Herein, we propose a facile method to efficiently reduce vibrational frequency of molecular skeleton and suppress exciton-vibration coupling to decrease non-radiative decay rate and thus prolong τ via deuterating nonfullerene acceptors. The τ remarkably increases from 0.90 ns (non-deuterated L8-BO) to 1.35 ns (deuterated L8-BO-D), which is the record for organic photovoltaic materials. Besides, the inhibited molecular vibration improves molecular planarity of L8-BO-D for enhanced exciton diffusion coefficient. Consequently, the L D increases from 7.9 nm (L8-BO) to 10.7 nm (L8-BO-D). The prolonged L D of L8-BO-D enables PM6 : L8-BO-D-based bulk heterojunction OSCs to acquire higher PCEs of 18.5 % with more efficient exciton dissociation and weaker charge carrier recombination than PM6 : L8-BO-based counterparts. Moreover, benefiting from the prolonged L D , D18/L8-BO-D-based pseudo-planar heterojunction OSCs achieve an impressive PCE of 19.3 %, which is among the highest values. This work provides an efficient strategy to increase the τ and thus L D of organic semiconductors, boosting PCEs of OSCs.

关键词： Deuteration Exciton Diffusion Length Exciton Lifetime Exciton-Vibration Coupling Organic Solar Cells

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大学生日常行为评分管理系统的研究与设计

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信息与电脑 2019年第14期31卷 113-115页

作者：谢辅雯张凯飞赣南师范大学科技学院

学生的日常行为是学生道德行为的主要部分,学生的日常行为表现能反映学生的品德水平。大学生日常行为管理是学生综合素质教育管理的重要组成部分。笔者在充分考虑赣南师范大学科技学院学生日常行为管理体系的基础上,针对当前学生日常行... 详细信息

学生的日常行为是学生道德行为的主要部分,学生的日常行为表现能反映学生的品德水平。大学生日常行为管理是学生综合素质教育管理的重要组成部分。笔者在充分考虑赣南师范大学科技学院学生日常行为管理体系的基础上,针对当前学生日常行为管理现状及存在的问题,设计开发一个符合学生日常行为管理的大学生日常行为评分管理系统。

关键词：大学生日常行为评分管理系统

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Quantitative proteomics analysis reveals alterations of lysine acetylation in mouse testis in response to heat shock and X-ray exposure

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BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018年第3期1866卷 464-472页

作者： Xie, Chengmei Shen, Hongyan zhang, Hui Yan, Jinting Liu, Yang Yao, fuwen Wang, Xi Cheng, Zhongyi Tang, Tie-Shan Guo, Caixia Univ Chinese Acad Sci Chinese Acad Sci Beijing Inst Genom CAS Key Lab Genom & Precis Med Beijing 100101 Peoples R China Univ Chinese Acad Sci Chinese Acad Sci Inst Zool State Key Lab Membrane Biol Beijing 100101 Peoples R China PTM Biolab Hangzhou 310018 Zhejiang Peoples R China

Environmental stresses are important factors causing male infertility which attracts broad attention. Protein acetylation is a pivotal post-translational modification and modulates diverse physiological processes including spermatogenesis. In this study, we employed quantitative proteomic techniques and bioinformatics tools to analyze the alterations of acetylome profile of mouse testis after heat shock and X-irradiation. Overall, we identified 1139 lysine acetylation sites in 587 proteins in which 1020 lysine acetylation sites were quantified. The Gene Ontology analysis showed that the major acetylated protein groups were involved in generation of precursor metabolites and metabolic processes, and were localized predominantly in cytosolic and mitochondrial. Compared to the control group, 36 sites of 28 acetylated proteins have changed after heat shock, and 49 sites of 43 acetylated proteins for X-ray exposure. Some of the differentially acetylated proteins have been reported to be associated with the progression of spermatogenesis and male fertility. We observed the up regulated acetylation level change on testis specific histone 2B and heat shock protein upon heat treatment and a sharp decline of acetylation level on histone H2AX under X-ray treatment, suggesting their roles in male germ cells. Notably, the acetylation level on K279 of histone acetyltransferase (Kat7) was down-regulated in both heat and X-ray treatments, indicating that K279 may be a key acetylated site and affect its functions in spermatogenesis. Our results reveal that protein acetylation might add another layer of complexity to the regulation for spermatogenesis, and further functional studies of these proteins will help us elucidate the mechanisms of abnormal spermatogenesis.

关键词： Mouse testis Spermatogenesis Heat shock X-irradiation Acetylome Lysine acetylation motif

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Mitochondrial genome of a 22,000-year-old giant panda from southern China reveals a new panda lineage

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CURRENT BIOLOGY 2018年第12期28卷 R693-R694页

作者： Ko, Albert Min-Shan zhang, Yingqi Yang, Melinda A. Hu, Yibo Cao, Peng Feng, Xiaotian zhang, Lizhao Wei, fuwen Fu, Qiaomei Chinese Acad Sci Inst Vertebrate Paleontol & Paleoanthropol Key Lab Vertebrate Evolut & Human Origins Beijing 100044 Peoples R China Chinese Acad Sci Ctr Excellence Life & Paleoenvironm Beijing 100044 Peoples R China Chinese Acad Sci Ctr Excellence Anim Evolut & Genet Kunming 650223 Yunnan Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China Chinese Acad Sci Inst Zool Key Lab Anim Ecol & Conservat Biol Beijing Peoples R China

Present-day giant pandas (Ailuropoda melanoleuca) are estimated to have diverged from their closest relatives, all other bears, ∼20 million years ago, based on molecular data [1]. With fewer than 2,500 individuals living today [2], it is unclear how well genetic data from extant and historical giant pandas [3] reflect the past [3]. To date, there has been no complete mitochondrial DNA (mtDNA) sequenced from an ancient giant panda. Here, we use ancient DNA capture techniques [4] to sequence the complete mitochondrial genome of a ∼22,000-year-old giant panda specimen (radiocarbon date of 21,910-21,495 cal BP with ± 2σ at 95.4% probability; *** Beta-473743) from the Cizhutuo Cave, in Leye County, Guangxi Province, China (Figure 1A). Its date and location in Guangxi, where no wild giant pandas live today, as well as the difficulty of DNA preservation in a hot and humid region, place it as a unique specimen to learn about ancient giant pandas from the last glacial maximum. We find that the mtDNA lineage of the Cizhutuo panda coalesced with present-day pandas ∼183 thousand years ago (kya, 95% HPD, 227-144 kya), earlier than the time to the most recent common ancestor (TMRCA) of mtDNA lineages shared by present-day pandas (∼72 kya, 95% HPD, 94-55 kya, Supplemental Information). Furthermore, the Cizhutuo panda possessed 18 non-synonymous mutations across six mitochondrial genes. Our results show that the Cizhutuo mtDNA lineage underwent a distinct history from that of present-day populations.◆ (Copyright © 2018 Elsevier Ltd. All rights reserved.)

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Event-Based Distributed H∞ Filtering Networks of 2-DOF Quarter-Car Suspension Systems

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IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS 2017年第1期13卷 312-321页

作者： zhang, Hao Hong, Qianqian Yan, Huaicheng Yang, fuwen Guo, Ge Tongji Univ Dept Control Sci & Engn Shanghai 200092 Peoples R China East China Univ Sci & Technol Key Lab Adv Control & Optimizat Chem Proc Minist Educ Shanghai 200237 Peoples R China East China Univ Sci & Technol Sch Informat Sci & Engn Shanghai 200237 Peoples R China Griffith Univ Sch Engn Gold Coast Qld 4222 Australia Dalian Maritime Univ Sch Informat Sci & Technol Dalian 116026 Peoples R China

This paper is concerned with the problem of vertical attitude estimation of a two-degree-of-freedom quarter-car suspension system by designing a distributed filtering network, where several distributed filters estimate vehicle heave motion cooperatively under consideration of external disturbance, network channel noises, and measurement error. The sampled data are transmitted through wireless networks. In order to reduce network traffic load and save communication resources, a novel periodic event-triggered sampling scheme is proposed, under which data are transmitted only when the proposed triggering condition is violated. Codesign of event-triggered and distributed filters is derived to guarantee well H-infinity robustness to the system noises considered above. Finally, the experiments are given to show the effectiveness of the proposed filtering system.

关键词： Event-based distributed filtering periodic event-triggered sampling position and velocity estimation spring-mass systems two-degree-of-freedom quarter-car suspension systems (2DOF-QSS)

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基于实际风场载荷的齿轮箱DOE强度失效研究

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机械设计与制造工程 2025年第4期54卷 20-26页

作者：许恒雷廖唯良冯宇王富文张明明刘卫东秦明鲁能新能源(集团)有限公司北京100020 哈尔滨工业大学(深圳)机电工程与自动化学院广东深圳518055 中国长江三峡集团有限公司科学技术研究院北京100038

为解决目前齿轮箱强度校核及失效分析中无法明确各因素对失效形成的“贡献度”及无法高效开展失效优化的问题,引入统计学分析原理,提出基于试验设计(DOE)技术的强度失效分析方法,利用甘肃某风电场的实测数据开展故障齿轮箱的失效分析与... 详细信息

为解决目前齿轮箱强度校核及失效分析中无法明确各因素对失效形成的“贡献度”及无法高效开展失效优化的问题,引入统计学分析原理,提出基于试验设计(DOE)技术的强度失效分析方法,利用甘肃某风电场的实测数据开展故障齿轮箱的失效分析与强度校核计算。根据宏观形貌归纳失效形式,基于失效形式的初步判断构建风力机齿轮箱解析模型,开展相应的强度计算,以实际损伤情况验证强度校核结果;在获取失效解析模型的基础上分析了齿轮箱失效的影响因子,基于薄弱环节建立了影响因子与不同失效形式的响应变量多元回归数学模型,明确了因子在各种失效中的影响显著性规律,为后续开展风电齿轮箱失效分析及优化提供了理论依据。

关键词：风力机齿轮箱强度校核失效分析试验设计方法

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Matching mechanism for networked control systems with multirate sampling

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IET CONTROL THEORY AND APPLICATIONS 2017年第16期11卷 2848-2857页

作者： Jia, Xin-Chun Ma, Weiwei Yang, fuwen zhang, Dawei Shanxi Univ Sch Math Sci Taiyuan 030006 Shanxi Peoples R China Griffith Univ Griffith Sch Engn Southport Qld 4222 Australia

This study deals with the observer-based controller design problem for a class of networked control systems with multirate sampling. A matching mechanism is proposed to synchronise the sampled data between the plant and an observer, and computes the corresponding error. Using the error, the multirate observer is developed to estimate the state of the system in real time. A state feedback controller based on the observer is utilised to control the system. Different from discrete-time modelling methods, the resulting closed-loop system is modelled as a continuous-time system with multiple sawtooth input-delays. Inspired by Wirtinger's inequality, a new Lyapunov-Krasovskii functional is constructed to analyse efficiently the closed-loop system in the presence of time-varying network-induced delays. Then sufficient conditions for H-infinity performance analysis and the observer-based controller design are presented. Finally, two illustrative examples show the effectiveness of the proposed method.

关键词： networked control systems observers control system synthesis state feedback closed loop systems Lyapunov methods time-varying systems multivariable control systems matching mechanism networked control systems multirate sampling observer based controller design problem sampled data multirate observer state feedback controller discrete-time modelling methods closed-loop system continuous-time system multiple sawtooth input-delays Lyapunov-Krasovskii functional time-varying network-induced delays

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