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pLoc_Deep-mVirus: A CNN Model for Predicting Subcellular Localization of Virus Proteins by Deep Learning

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Natural Science 2020年第6期12卷 388-399页

作者： yutao shao Kuo-Chen Chou Computer Science Jingdezhen Ceramic Institute Jingdezhen China Gordon Life Science Institute Boston MA USA

The recent worldwide spreading of pneumonia-causing virus, such as Coronavirus, COVID-19, and H1N1, has been endangering the life of human beings all around the world. In order to really understand the biological process within a cell level and provide useful clues to develop antiviral drugs, information of virus protein subcellular localization is vitally important. In view of this, a CNN based virus protein subcellular localization predictor called “pLoc_Deep-mVirus” was developed. The predictor is particularly useful in dealing with the multi-sites systems in which some proteins may simultaneously occur in two or more different organelles that are the current focus of pharmaceutical industry. The global absolute true rate achieved by the new predictor is over 97% and its local accuracy is over 98%. Both are transcending other existing state-of-the-art predictors significantly. It has not escaped our notice that the deep-learning treatment can be used to deal with many other biological systems as well. To maximize the convenience for most experimental scientists, a user-friendly web-server for the new predictor has been established at http://***/pLoc_Deep-mVirus/.

关键词： Coronavirus Virus Proteins Multi-Label System Deep Learning Five-Steps Rule PseAAC

pLoc_Deep-mEuk: Predict Subcellular Localization of Eukaryotic Proteins by Deep Learning

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Natural Science 2020年第6期12卷 400-428页

作者： yutao shao Kuo-Chen Chou Computer Science Jingdezhen Ceramic Institute Jingdezhen China Gordon Life Science Institute Boston MA USA

Recently, the life of worldwide human beings has been endangering by the spreading of pneu- monia-causing virus, such as Coronavirus, COVID-19, and H1N1. To develop effective drugs against Coronavirus, knowledge of protein subcellular localization is prerequisite. In 2019, a predictor called “pLoc_bal-mEuk” was developed for identifying the subcellular localization of eukaryotic proteins. Its predicted results are significantly better than its counterparts, particularly for those proteins that may simultaneously occur or move between two or more subcellular location site

关键词： Coronavirus Multi-Label System Eukaryotic Proteins Deep Learning Five-Steps Rule PseAAC

Topologically Correct Intersection Curves of Two Trimmed Quadrics with Tolerance Control

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Journal of Systems Science & Complexity 2024年第5期37卷 2207-2239页

作者： shao Wenbing CHEN Falai Department of Mathematics University of Science and Technology of China

Surface/surface intersection is a fundamental problem in Compute Aided Design and Geometric Modeling since it is essential to solid modeling, numerically controlled machining, feature recognition, computer animation, etc. In practical applications, quadric surfaces, which are the most basic type of surfaces, are typically bounded surfaces trimmed by a sequence of planes. In this paper,a robust algorithm is proposed for computing the intersection curve segments of two trimmed quadrics based on the parametric representation of the intersection curves of two quadrics. The proposed algorithm guarantees correct topology and ensures that the approximation errors of the end points of the intersection curve segments are less than a given tolerance. The error control is based on an effective solution to a set of polynomial inequality system using the root isolation technique. Some examples are presented to validate the robustness and effectiveness of the proposed algorithm.

关键词： Polynomial inequality system root isolation surface/surface intersection tolerance control trimmed quadrics

Pseudoeffective thresholds and cohomology of twisted symmetric tensor fields on irreducible Hermitian symmetric spaces

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Science China Mathematics 2024年第11期67卷 2433-2452页

作者： Feng shao Institute of Mathematics Academy of Mathematics and Systems ScienceChinese Academy of Sciences School of Mathematical Sciences University of Chinese Academy of Sciences

Let X be an irreducible Hermitian symmetric space of compact type(IHSS for short).In this paper,we give the irreducible decomposition of *** a by-product,we give a cohomological characterization of the rank of ***,we introduce pseudoeffective thresholds to measure the bigness of tangent bundles of smooth complex projective varieties precisely and calculate them for irreducible Hermitian symmetric spaces of compact type.

关键词： tangent bundle pseudoeffective threshold irreducible Hermitian symmetric space of compact type (IHSS) multiplicity free action

Homogeneous void nucleation in the presence of supersaturated vacancies and interstitials

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Journal of Materiomics 2024年第5期10卷 1147-1159页

作者： Lin shao Accelerator Laboratory Department of Nuclear EngineeringTexas A&M UniversityCollege StationTX77843USA

Homogeneous void nucleation in metals containing arbitrary vacancies and interstitials has been reexamined,with corrections made to the original work by Katz and *** void size distributions derived previously missed an exponential modification function with void size as the *** a result,void nucleation under a given vacancy supersaturation ratio is underestimated by orders of *** second improvement arises from the accuracy in calculating the vacancy arrival rate to a *** present work proposes establishing a direct relationship between the vacancy arrival rate and the available self-diffusion *** these corrections and improvements,void nucleation in pure Fe is calculated as an example,and an analytic fitting formula is *** required vacancy supersaturation ratio and interstitial-to-vacancy flux ratio for void nucleation calculations can be easily obtained from an analytical solution of rate theory calculations,in which dislocation density and displacements per atom(dpa)rate are adjustable ***,the nucleation rate calculation can be incorporated into rate theory calculations considering evolving dislocation densities,which leads to time-dependent void nucleation.

关键词： Void nucleation Voids Irradiation Swelling Defects

Analysis of spatial distribution characteristics and driving factors of ethnicminority villages in China using geospatial technology and statistical models

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Journal of Mountain Science 2024年第8期21卷 2770-2789页

作者： shao Dandan ZOH Kyungjin Interdisciplinary Program in Landscape Architecture Graduate School of Environmental StudiesSeoul National UniversitySeoul 08826Korea Graduate School of Environmental Studies Seoul National UniversitySeoul 08826Korea

This study aims to reveal the spatial structural characteristics of 1,652 Ethnic-Minority Villages(EMV)in China and to analyze the mechanisms driving their spatial *** are a special type of settlement space that preserve a large number of historical traces of the ethnic culture of ancient *** are important carriers of China’s excellent traditional culture and are key to the implementation of rural revitalization *** this study,1652 EMV in China were selected as the research *** Nearest Neighbor Index,kernel density,and spatial autocorrelation index were employed to reveal the spatial structural characteristics of minority *** network models,spatial lag models,and geographical detectors were used to analyze the formation mechanism of spatial heterogeneity in *** results indicate that:(1)EMV exhibit significant spatial differentiation characterized by“single-core with multiple surrounding sub-centers,”“polarization between east and west,”“decreasing quantity from southwest to east coast to northeast to northwest,”and“large dispersion with small agglomeration.”(2)EMV are mainly distributed in areas rich in intangible cultural heritage,with high vegetation coverage and low altitude,far from central cities,and having limited arable land and an underdeveloped economy and transportation,particularly in shaded or riverbank areas.(3)Distance from the nearest river(X3),distance from central cities(X8),national intangible cultural heritage(X9),and NDVI(X10)were the main driving factors affecting the spatial distribution of EMV,whereas elevation(X1)and GDP(X5)had the weakest *** EMV are a relatively unique territorial spatial unit,the identification of their spatial heterogeneity characteristics not only deepens the research content of settlement geography,but also involves the assessment,protection,and development of Minority Villages,which is of great significance for the inheritance and utilization of excellent

关键词： Ethnic-Minority Villages Spatial structure Settlement geography Neural network model Spatial econometric model GeoDetector

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Fear and delay effects on a food chain system with two kinds of different functional responses

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International Journal of Biomathematics 2024年第3期17卷 89-122页

作者： Yuanfu shao College of Science Guilin University of Technology GuilinGuangci 541004P.R.China

For food chain system with three populations,direct predation is the basic interaction between *** species often have different predation functional responses,so a food chain system with Holling-II response for middle predator and Beddinton-DeAngelis response for top predator is *** from direct predation,predator population can significantly impact the survival of prey population by inducing the prey's fear,but the impact often possesses a time *** paper is concentrated to explore how the fear and time delay affect the system stability and the species *** use of Lyapunov functional method and bifurcation theory,the positiveness and boundedness of solutions,local and global behavior of species,the system stability around the equilibrium states and various kinds of bifurcation are ***,some simulations are carried out to validate the main findings and the critical values of the bifurcation parameters of fear and conversion rate are *** is observed that fear and delay can not only stabilize,but also destabilize the system,which depends on the magnitude of the fear and *** system varies from unstable to stable due to the continuous increase of the prey's fear by middle *** fear induced by top predator or small delay of the prey's fear can stabilize the system,while they are sufficiently large,the system stability is to be ***,the conversion rate can also change the stability and even make the species to be *** rich dynamics like multiple stabilities and various types of bistability behaviors are also exhibited,which results in the convergence of the species from one stable equilibrium to another.

关键词： Fear functional response equilibrium bifurcation analysis bi-stability

高粱赤霉素信号途径关键基因的鉴定及qPCR引物筛选

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分子植物育种 2022年第6期20卷 1883-1889页

作者：郭磊高琳邵玉涛内蒙古科技大学生命科学与技术学院包头014010

赤霉素(GA)在植物响应生物和非生物胁迫过程中扮演着重要角色。为了探究GA在高粱响应蚜虫胁迫过程中的作用,本研究采用激素外施实验,证实GA参与了高粱的抗蚜反应;在此基础上,利用NCBI数据库查找已报道参与GA合成、代谢及Della蛋白合成... 详细信息

赤霉素(GA)在植物响应生物和非生物胁迫过程中扮演着重要角色。为了探究GA在高粱响应蚜虫胁迫过程中的作用,本研究采用激素外施实验,证实GA参与了高粱的抗蚜反应;在此基础上,利用NCBI数据库查找已报道参与GA合成、代谢及Della蛋白合成相关基因在高粱中的同源基因,并设计特异引物,采用PCR和qPCR的方法验证引物的特异性。通过PCR技术共筛选出7对引物,大小符合预期,且条带单一,进一步采用qPCR技术验证,最终筛选到5个基因的5对引物,扩增曲线光滑,呈现单峰,且Ct值较小,特异性良好。研究结果为下一步研究这些基因的表达模式变化,揭示GA信号途径在高粱抗蚜反应中的作用提供理论依据。

关键词：高粱(Sorghum bicolor) 赤霉素荧光定量PCR

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Layered double hydroxides functionalization toward rechargeable batteries Author links open overlay panel

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Particuology 2024年第8期91卷 138-154页

作者： Jianxiong Gao Bowen Jin Mingfei shao State Key Laboratory of Chemical Resource Engineering Beijing University of Chemical TechnologyBeijing100029China Renewable Energy Research Institute Quzhou Institute for Innovation in Resource Chemical EngineeringQuzhou324000China

Layered double hydroxides(LDHs),known as typical two-dimensional materials with unique physicochemical properties,are regarded as promising candidates in energy storage ***,some inherent defects,such as poor conductivity and limited active sites,hinder the further development of ***,various functionalization strategies(e.g.,intercalation of guest molecules;metal ions doping and defect introduction of host layer;exfoliation to monolayer;hybridization with functional materials;construction of hierarchical structure;interface engineering and phase transformation)have been used to modify the characteristics of LDHs,which provides guidance for designing novel *** this review,we discuss how these strategies improve the properties of LDH-based materials,which are expected to possess high electronic and ionic conductivity,high specific surface area and high mechanical and chemical stability ***,the application of LDH-based materials in advanced energy conversion and storage techniques,including metal-ions batteries,lithium-sulfur batteries and metal-air batteries,have been comprehensively summarized.

关键词： Layered double hydroxide Functionalization strategy Rechargeable battery