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Isolation and characterization of a novel Linear-plasmid phage from the sediment of the Mariana Trench

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Virologica Sinica 2022年第2期37卷 311-313页

作者： Yali Hao Siyuan Wang Mujie Zhang Qingxue Tang Canxing Meng Liping Wang Qilian Fan Yaxian Yan Xiang Xiao Huahua Jian State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic&Developmental SciencesSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China Key Laboratory of Marine Genetic Resources Third Institute of OceanographyMinistry of Natural ResourcesXiamen361005China Shanghai Key Laboratory of Veterinary Biotechnology School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai200240China Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Zhuhai519082China

Dear Editor,Temperate bacteriophages are widely distributed in bacteria isolated from different natural environments(Howard-Varona et al.,2017).The phages normally lead to lysogenic infection and merge their genetic components into the bacterial chromosome.Among the temperate phages,Linear plasmid phages are atypical because of their capability to reside in host cells as Linear ds DNA with covalently closed ends,rather than being integrated in host genomes in the form of prophages(Ravin et al.,2000;Ravin,2011).

关键词： Trench Linear characterization

Monte Carlo sampling for error propagation in Linear regression and applications in isochron geochronology

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Science Bulletin 2019年第3期64卷 189-197页

作者： Yang Li Shuang Zhang Richard Hobbs Camila Caiado Adam D.Sproson David Selby Alan D.Rooney State Key Laboratory of Lithospheric Evolution Institute of Geology and Geophysics Chinese Academy of Sciences Department of Earth Sciences Durham University Department of Geology and Geophysics Yale University Department of Mathematical Sciences Durham University Atmosphere and Ocean Research Institute The University of Tokyo

Geochronology is essential for understanding Earth's history. The availability of precise and accurate isotopic data is increasing; hence it is crucial to develop transparent and accessible data reduction techniques and tools to transform raw mass spectrometry data into robust chronological data. Here we present a Monte Carlo sampling approach to fully propagate uncertainties from Linear regressions for isochron dating. Our new approach makes no prior assumption about the causes of variability in the derived chronological results and propagates uncertainties from both experimental measurements(analytical uncertainties) and underlying assumptions(model uncertainties) into the final age determination.Using synthetic examples, we find that although the estimates of the slope and y-intercept(hence age and initial isotopic ratios) are comparable between the Monte Carlo method and the benchmark‘‘Isoplot" algorithm, uncertainties from the later could be underestimated by up to 60%, which are likely due to an incomplete propagation of model uncertainties. An additional advantage of the new method is its ability to integrate with geological information to yield refined chronological constraints. The new method presented here is specifically designed to fully propagate errors in geochronological applications involves Linear regressions such as Rb-Sr, Sm-Nd, Re-Os, Pt-Os, Lu-Hf, U-Pb(with discordant points),Pb-Pb and Ar-Ar.

关键词： Linear regression Isochron Geochronology Uncertainty propagation Monte Carlo Isoplot

Adaptive Linear Quadratic Regulator for Continuous-Time Systems With Uncertain Dynamics

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IEEE/CAA Journal of Automatica Sinica 2020年第3期7卷 833-841页

作者： Sumit Kumar Jha Shubhendu Bhasin IEEE Department of Electronics and Communication Engineering Motilal Nehru National Institute of Technology AllahabadPrayagraj-211004India Department of Electrical Engineering Indian Institute of Technology DelhiNew Delhi-110016India

In this paper, adaptive Linear quadratic regulator(LQR) is proposed for continuous-time systems with uncertain dynamics. The dynamic state-feedback controller uses inputoutput data along the system trajectory to continuously adapt and converge to the optimal controller. The result differs from previous results in that the adaptive optimal controller is designed without the knowledge of the system dynamics and an initial stabilizing policy. Further, the controller is updated continuously using input-output data, as opposed to the commonly used switched/intermittent updates which can potentially lead to stability issues. An online state derivative estimator facilitates the design of a model-free controller. Gradient-based update laws are developed for online estimation of the optimal gain. Uniform exponential stability of the closed-loop system is established using the Lyapunov-based analysis, and a simulation example is provided to validate the theoretical contribution.

关键词： Adaptive optimal control continuous policy update Linear quadratic regulator uncertain system dynamics

Identification of heavy metal-contaminated Tegillarca granosa using laser-induced breakdown spectroscopy and Linear regression for classification

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Plasma Science and Technology 2020年第8期22卷 151-159页

作者：谢忠好孟留伟冯西安陈孝敬陈熙袁雷鸣石文黄光造衣铭 School of Marine Science and Technology Northwestern Polytechnical UniversityXi'an 710072People's Republic of China College of Physical and Electronic Information Engineering Wenzhou UniversityWenzhou 325035People's Republic of China Research and Development Department Hangzhou Goodhere Biotechnology Co.LtdHangzhou 311100People's Republic of China Research and Development Department Hangzhou Weizan Technology Co.LtdHangzhou 311100People's Republic of China

Tegillarca granosa(T.granosa)is susceptible to heavy metals,which may pose a threat to consumer health.Thus,healthy and polluted T.granosa should be distinguished quickly.This study aimed to rapidly identify heavy metal pollution by using laser-induced breakdown spectroscopy(LIBS)coupled with Linear regression classification(LRC).Five types of T.granosa were studied,namely,Cd-,Zn-,Pb-contaminated,mixed contaminated,and control samples.Threshold method was applied to extract the significant variables from LIBS spectra.Then,LRC was used to classify the different types of T.granosa.Other classification models and feature selection methods were used for comparison.LRC was the best model,achieving an accuracy of 90.67%.Results indicated that LIBS combined with LRC is effective and feasible for T.granosa heavy metal detection.

关键词： shellfish laser-induced breakdown spectrometry heavy metal Linear regression classification

Robust Admissibility and Stabilization of Uncertain Singular Fractional-Order Linear Time-Invariant Systems

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IEEE/CAA Journal of Automatica Sinica 2019年第3期6卷 685-692页

作者： Saliha Marir Mohammed Chadli IEEE University Mohamed Boudiaf USTO University of Picardie Jules Verne

This paper addresses the robust admissibility problem in singular fractional-order continuous time systems. It is based on new admissibility conditions of singular fractional-order systems expressed in a set of strict Linear matrix inequalities(LMIs). Then, a static output feedback controller is designed for the uncertain closed-loop system to be admissible. Numerical examples are given to illustrate the proposed methods.

关键词： Control fractional-order systems Linear matrix inequalities (LMIs) output feedback control robust admissibility singular systems uncertain systems

Stability and Robust Stability of Switched Positive Linear Systems With All Modes Unstable

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IEEE/CAA Journal of Automatica Sinica 2019年第1期6卷 167-176页

作者： Shaoxia Feng Juan Wang Jun Zhao Shanxi Institute of Mechanical and Electrical Engineering the College of Information Scienceand Engineering Northeastern University the Faculty of Information and Control Engineering Shenyang Jianzhu University the State Key Laboratory of Synthetical Automationfor Process Industries (Northeastern University) the Collegeof Information Science and Engineering Northeastern University

This paper is concerned with the stability and robust stability of switched positive Linear systems(SPLSs) whose subsystems are all unstable. By means of the mode-dependent dwell time approach and a class of discretized co-positive Lyapunov functions, some stability conditions of switched positive Linear systems with all modes unstable are derived in both the continuous-time and the discrete-time cases, respectively. The copositive Lyapunov functions constructed in this paper are timevarying during the dwell time and time-invariant afterwards. In addition, the above approach is extended to the switched interval positive systems. A numerical example is proposed to illustrate our approach.

关键词： Discretized co-positive Lyapunov functions mode-dependent dwell time robust stability switched positive Linear systems (SPLSs) unstable subsystem

Quadratic Stabilization of Switched Uncertain Linear Systems: A Convex Combination Approach

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IEEE/CAA Journal of Automatica Sinica 2019年第5期6卷 1116-1126页

作者： Yufang Chang Guisheng Zhai Bo Fu Lianglin Xiong the School of Electrical and Electronic Engineering Hubei University of TechnologyWuhan 430068China the Department of Mathematical Sciences Shibaura Institute of TechnologySaitama 337-8570Japan the School of Mathematics and Computer Science Yunnan Minzu UniversityKunming 650500China

We consider quadratic stabilization for a class of switched systems which are composed of a finite set of continuoustime Linear subsystems with norm bounded uncertainties. Under the assumption that there is no single quadratically stable subsystem, if a convex combination of subsystems is quadratically stable, then we propose a state-dependent switching law, based on the convex combination of subsystems, such that the entire switched Linear system is quadratically stable. When the state information is not available, we extend the discussion to designing an outputdependent switching law by constructing a robust Luenberger observer for each subsystem.

关键词： Convex combination limear matrix inequalities (LMIs) norm bounded uncertainties output-dependent switching, quadratic stabilization state-dependent switching switched uncertain Linear systems(SULS)

Direct position determination using single moving rotating Linear array: Noncoherent and coherent processing

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Chinese Journal of Aeronautics 2020年第2期33卷 688-700页

作者： Guizhou WU Min ZHANG Chaoxin HE Fucheng GUO State Key Laboratory of Complex Electromagnetic Environment Effects on Electronics and Information System National University of Defense TechnologyChangsha 410073China

To improve the resolution and accuracy of Direct Position Determination(DPD),this paper investigates the problem of positioning multiple emitters directly with a single moving Rotating Linear Array(RLA).Firstly,the geometry of the RLA is formulated and analysed.According to its geometry,the intercepted noncoherent signals in multiple interception intervals are modeled.Correspondingly,the Multiple SIgnal Classification(MUSIC)based noncoherent DPD approach is proposed.Secondly,the synchronous coherent pulse signals are individually considered and formulated.And the coherent DPD approach which aims for localizing this special type of signal is presented by stacking all array responses at different interception intervals.Besides,we also derive the constrained Cramer-Rao Lower Bound(CRLB)expression for both noncoherent and coherent DPD with RLA under the constraint that the altitudes of the emitters are known.At last,computer simulations are included to examine the performance of the proposed approach.The results demonstrate that the localization accuracy and resolution of DPD with single moving Linear array can be significantly improved by the array rotation.In addition,coherent DPD with RLA further improves the resolution and increases the maximum emitter number that can be localized compared with the noncoherent DPD with RLA.

关键词： Coherent signal processing Constrained Cramer-Rao lower bound Direct position determination Multiple signal classification Resolution Rotating Linear array

CIRCexplorer3:A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression

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Genomics, Proteomics & Bioinformatics 2019年第5期17卷 511-521页

作者： Xu-Kai Ma Meng-Ran Wang Chu-Xiao Liu Rui Dong Gordon G.Carmichael Ling-Ling Chen Li Yang CAS Key Laboratory of Computational Biology CAS-MPG Partner Institute for Computational BiologyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China State Key Laboratory of Molecular Biology CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China Department of Genetics and Genome Sciences University of Connecticut Health CenterFarmingtonCT 06030USA School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China

Sequences of circular RNAs(circ RNAs)produced from back-splicing of exon(s)completely overlap with those from cognate Linear RNAs transcribed from the same gene loci with the exception of their back-splicing junction(BSJ)sites.Therefore,examination of global circ RNA expression from RNA-seq datasets generally relies on the detection of RNA-seq fragments spanning BSJ sites,which is different from the quantification of Linear RNA expression by normalized RNA-seq fragments mapped to whole gene bodies.Thus,direct comparison of circular and Linear RNA expression from the same gene loci in a genome-wide manner has remained challenging.Here,we update the previously-reported CIRCexplorer pipeline to version 3 for circular and Linear RNA expression analysis from ribosomal-RNA depleted RNA-seq(CIRCexplorer3-CLEAR).A new quantitation parameter,fragments per billion mapped bases(FPB),is applied to evaluate circular and Linear RNA expression individually by fragments mapped to circ RNA-specific BSJ sites or to Linear RNA-specific splicing junction(SJ)sites.Comparison of circular and Linear RNA expression levels is directly achieved by dividing FPBcircby FPBLinearto generate a CIRCscore,which indicates the relative circ RNA expression level using Linear RNA expression level as the background.Highlyexpressed circ RNAs with low cognate Linear RNA expression background can be readily identified by CIRCexplorer3-CLEAR for further investigation.CIRCexplorer3-CLEAR is publically available at https://***/Yang Lab/CLEAR.

关键词： Circular RNA Back-splicing Linear RNA Pre-mRNA splicing Ribo-RNA-seq