This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the PoissonBoltzmann equation.In this model,an interior spherical cavity ...This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the PoissonBoltzmann equation.In this model,an interior spherical cavity will contain the solute and some explicit solvent molecules,and an intermediate buffer layer and an exterior layer contain the bulk solvent.A special dielectric permittivity profile is used to achieve a continuous dielectric transition from the interior cavity to the exterior layer.The selection of this special profile using a harmonic interpolation allows an analytical solution of the model by generalizing the classical Kirkwood series expansion.Discrete image charges are used to speed up calculations for the electrostatic potential within the interior and buffer layer regions.Semi-analytical and least squares methods are used to construct an accurate discrete image approximation for the reaction field due to solvent with or without salt effects.In particular,the image charges obtained by the least squares method provide accurate approximations to the reaction field independent of the ionic concentration of the solvent.Numerical results are presented to validate the accuracy and effectiveness of the image charge methods.展开更多
Background： Information about competition responses is mainly available for monospecific stands or mixed stands with a small number of species. Studies on complex multi-species and highly structured forest ecosystems...Background： Information about competition responses is mainly available for monospecific stands or mixed stands with a small number of species. Studies on complex multi-species and highly structured forest ecosystems are scarce. Accordingly, the objective of this study was to quantify competition effects and analyse competition responses in a species-diverse afrotemperate forest in South Africa, based on an observational study with mapped tree positions and long-term diameter increment records. Methods： The sensitivity to competition was analysed for individual species and involved the calculation of the slope of the linear relation between the value of a competition index （CI） and diameter growth as a measure of sensitivity. In a next step different competition indices were combined and tree diameters were grouped in three classes as surrogates for canopy status and ontogenetic stage. Results： Five competition indices were found to be effective in showing sensitivity to competition for a number of canopy and sub-canopy species. Significant linear regressions were fitted for 18 of a total of 25 species. Species reactions varied significantly in their sensitivity to the different CIs. The indices were classified as belonging to two groups, those that responded more to local crowding and those that are more sensitive to overtopping, which revealed species-specific sensitivities to both factors. The analysis based on diameter classes revealed that species clearly changed their sensitivity to crowding or overtopping depending on diameter. Canopy and sub-canopy species showed distinct differences in their reactions. Conclusions： The application of multiple CIs brought novel insights relating to the dynamics of afrotemperate forests. The response patterns to different competition indices that focus on crowding and overtopping are varied and tree diameter dependent, indicating that oversimplified assumptions are not warranted in the interpretation of Cl- growth relations.展开更多
为探究生境面积大小对Janzen-Connell (JC)效应中密度和距离制约的影响以及驱动机制,为生境破碎化背景下植物多样性的维持机制提供科学依据,本研究在Web of Science数据库中收集并筛选出1970-2019年全球50个森林地点作为数据基础,采用...为探究生境面积大小对Janzen-Connell (JC)效应中密度和距离制约的影响以及驱动机制,为生境破碎化背景下植物多样性的维持机制提供科学依据,本研究在Web of Science数据库中收集并筛选出1970-2019年全球50个森林地点作为数据基础,采用荟萃分析法分析密度和距离制约实验中不同类型驱动者的效应值大小,并采用分段回归和非分段回归分别模拟分析密度和距离制约效应值与生境面积的关系。结果表明,在67项研究的161项实验中,病原菌和无脊椎动物的效应值大小在距离制约实验中显著小于0(存在JC效应),而在密度制约实验中不显著。相反地,脊椎动物的效应值大小仅在密度制约实验中显著小于0。虽然只有距离制约效应值随生境面积的减少呈先增大后减小的趋势,但密度制约趋势线的拟合转折点在距离制约之前,表明生境面积减少会先影响密度制约。本研究阐明了密度和距离制约的主要驱动者分别是密度型驱动者(脊椎动物)和距离型驱动者(病原菌和无脊椎动物),而密度制约比距离制约对生境面积的减少有更为敏感的表现,可能是这两种驱动者对生境面积的需求不同所导致的。因此,在不同生境面积的片段中关注不同类型的驱动者有利于生物多样性的维持。展开更多
当前的位置预测方法大多没有考虑到用户行为信息,由于用户的访问时间、行为模式等能够在很大程度上反映所处位置,因此在对位置潜在向量进行预训练时有必要使用该信息。进行位置预测时,采样粒度较细的序列长度较长,难以捕获长距离依赖。...当前的位置预测方法大多没有考虑到用户行为信息,由于用户的访问时间、行为模式等能够在很大程度上反映所处位置,因此在对位置潜在向量进行预训练时有必要使用该信息。进行位置预测时,采样粒度较细的序列长度较长,难以捕获长距离依赖。针对这2个问题,提出了基于用户行为和上下文语义的分层时空长短期记忆网络(Hierarchical Spatiotemporal Long Short-Term Memory Based on User Behavior and Contextual Semantics,CHST-LSTM)模型。该模型通过Transformer编码层处理轨迹数据,将用户相关行为信息考虑在内,融合位置的上下文语义信息,通过预训练得到位置的嵌入表征。根据用户的行为状态分割轨迹阶段,采用编码器-解码器方式对ST-LSTM进行分段分层扩展,利用BiLSTM对全局信息建模,同时处理轨迹的长短期变化,解决长序列的长距离依赖问题。对外卖员用户群体的真实移动轨迹数据进行分析和实验,通过聚类发现其特有的工作模式,在预训练时加入工作模式信息与到访时间信息,得到位置的特征向量并用于预测模型。结果表明CHST-LSTM模型在预测用户下一位置时精度更高。展开更多
基金The authors would like to thank the financial support provided by the National Institutes of Health(Grant No.1R01GM083600-02)Z.Xu is also partially supported by the Charlotte Research Institute through a Duke Postdoctoral FellowshipW.Cai and Z.Xu are also partially supported by the Department of Energy(Grant No.DEFG0205ER25678).
文摘This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the PoissonBoltzmann equation.In this model,an interior spherical cavity will contain the solute and some explicit solvent molecules,and an intermediate buffer layer and an exterior layer contain the bulk solvent.A special dielectric permittivity profile is used to achieve a continuous dielectric transition from the interior cavity to the exterior layer.The selection of this special profile using a harmonic interpolation allows an analytical solution of the model by generalizing the classical Kirkwood series expansion.Discrete image charges are used to speed up calculations for the electrostatic potential within the interior and buffer layer regions.Semi-analytical and least squares methods are used to construct an accurate discrete image approximation for the reaction field due to solvent with or without salt effects.In particular,the image charges obtained by the least squares method provide accurate approximations to the reaction field independent of the ionic concentration of the solvent.Numerical results are presented to validate the accuracy and effectiveness of the image charge methods.
基金support (data,scientific input) by South African National ParksFunding for this study was contributed by three projects,financed by the South African Department of Science and Technology through the National Research Foundation:i) the 'Green Landscapes' Project within the Global Change, Sustainability and Society Research Programme of the National Research Foundation(NRF) of South Africa,ⅱ)+1 种基金the EU Marie Curie Project "Climate Fit Forests" and ⅲ)the Project 'impact of drought on mortality,ingrowth and diameter increment in the afro-temperate forests of the Southern Cape, South Africa' funded by the NRF/DST Centre of Excellence of Tree Health and Biotechnology(CTHB) in Pretoria
文摘Background： Information about competition responses is mainly available for monospecific stands or mixed stands with a small number of species. Studies on complex multi-species and highly structured forest ecosystems are scarce. Accordingly, the objective of this study was to quantify competition effects and analyse competition responses in a species-diverse afrotemperate forest in South Africa, based on an observational study with mapped tree positions and long-term diameter increment records. Methods： The sensitivity to competition was analysed for individual species and involved the calculation of the slope of the linear relation between the value of a competition index （CI） and diameter growth as a measure of sensitivity. In a next step different competition indices were combined and tree diameters were grouped in three classes as surrogates for canopy status and ontogenetic stage. Results： Five competition indices were found to be effective in showing sensitivity to competition for a number of canopy and sub-canopy species. Significant linear regressions were fitted for 18 of a total of 25 species. Species reactions varied significantly in their sensitivity to the different CIs. The indices were classified as belonging to two groups, those that responded more to local crowding and those that are more sensitive to overtopping, which revealed species-specific sensitivities to both factors. The analysis based on diameter classes revealed that species clearly changed their sensitivity to crowding or overtopping depending on diameter. Canopy and sub-canopy species showed distinct differences in their reactions. Conclusions： The application of multiple CIs brought novel insights relating to the dynamics of afrotemperate forests. The response patterns to different competition indices that focus on crowding and overtopping are varied and tree diameter dependent, indicating that oversimplified assumptions are not warranted in the interpretation of Cl- growth relations.
文摘为探究生境面积大小对Janzen-Connell (JC)效应中密度和距离制约的影响以及驱动机制,为生境破碎化背景下植物多样性的维持机制提供科学依据,本研究在Web of Science数据库中收集并筛选出1970-2019年全球50个森林地点作为数据基础,采用荟萃分析法分析密度和距离制约实验中不同类型驱动者的效应值大小,并采用分段回归和非分段回归分别模拟分析密度和距离制约效应值与生境面积的关系。结果表明,在67项研究的161项实验中,病原菌和无脊椎动物的效应值大小在距离制约实验中显著小于0(存在JC效应),而在密度制约实验中不显著。相反地,脊椎动物的效应值大小仅在密度制约实验中显著小于0。虽然只有距离制约效应值随生境面积的减少呈先增大后减小的趋势,但密度制约趋势线的拟合转折点在距离制约之前,表明生境面积减少会先影响密度制约。本研究阐明了密度和距离制约的主要驱动者分别是密度型驱动者(脊椎动物)和距离型驱动者(病原菌和无脊椎动物),而密度制约比距离制约对生境面积的减少有更为敏感的表现,可能是这两种驱动者对生境面积的需求不同所导致的。因此,在不同生境面积的片段中关注不同类型的驱动者有利于生物多样性的维持。
文摘当前的位置预测方法大多没有考虑到用户行为信息,由于用户的访问时间、行为模式等能够在很大程度上反映所处位置,因此在对位置潜在向量进行预训练时有必要使用该信息。进行位置预测时,采样粒度较细的序列长度较长,难以捕获长距离依赖。针对这2个问题,提出了基于用户行为和上下文语义的分层时空长短期记忆网络(Hierarchical Spatiotemporal Long Short-Term Memory Based on User Behavior and Contextual Semantics,CHST-LSTM)模型。该模型通过Transformer编码层处理轨迹数据,将用户相关行为信息考虑在内,融合位置的上下文语义信息,通过预训练得到位置的嵌入表征。根据用户的行为状态分割轨迹阶段,采用编码器-解码器方式对ST-LSTM进行分段分层扩展,利用BiLSTM对全局信息建模,同时处理轨迹的长短期变化,解决长序列的长距离依赖问题。对外卖员用户群体的真实移动轨迹数据进行分析和实验,通过聚类发现其特有的工作模式,在预训练时加入工作模式信息与到访时间信息,得到位置的特征向量并用于预测模型。结果表明CHST-LSTM模型在预测用户下一位置时精度更高。
