An information-theoretical measure of taxonomic diversity

Traditional diversity indices are computed from the abundances of species present and are insensitive to taxonomic differences between species. However, a community in which most species belong to the same genus is intuitively less diverse than another community with a similar number of species distributed more evenly between genera. In this paper, we propose an information-theoretical measure of taxonomic diversity that reflects both the abundances and taxonomic distinctness of the species. Unlike previous measures of taxonomic diversity, such as Rao's quadratic entropy, in this new measure the analyzed taxonomic properties are associated with the single species instead of species pairs.     

中国三种常见蒿属植物潜在地理分布及其主导气候因子

裂叶蒿(Artemisia tanacetifolia)、大籽蒿(Artemisia sieversiana)和艾(Artemisia argyi)是我国常见的蒿属(Artemisia)植物,其分布区域遍布全国.本文利用MaxEnt模型预测3种蒿属植物在当前气候条件以及未来两种气候情景下的潜在分布区.采用受试者工作特征...     

scGET: Predicting Cell Fate Transition During Early Embryonic Development by Single-cell Graph Entropy

During early embryonic development, cell fate commitment represents a critical transition or"tipping point"of embryonic differentiation, at which there is a drastic and qualitative shift of the cell populations. In this study, we presented a computational approach, scGET, to explore the gene–gene associations based on single-cell RNA sequencing (scRNA-seq) data for critical transition prediction. Specifically, by transforming the gene expression data to the local network entropy, the single-cell graph entropy (SGE) value quantitatively characterizes the stability and criticality of gene regu-latory networks among cell populations and thus can be employed to detect the critical signal of cell fate or lineage commitment at the single-cell level. Being applied to five scRNA-seq datasets of embryonic differentiation, scGET accurately predicts all the impending cell fate transitions. After identifying the"dark genes"that are non-differentially expressed genes but sensitive to the SGE value, the underlying signaling mechanisms were revealed, suggesting that the synergy of dark genes and their downstream targets may play a key role in various cell development processes. The application in all five datasets demonstrates the effectiveness of scGET in analyzing scRNA-seq data from a network perspective and its potential to track the dynamics of cell differentiation. The source code of scGET is accessible at https://github.com/zhongjiayuna/scGET_Project.     

气候变化背景下基于MaxEnt模型的刺梨潜在适生区分布预测

为阐明气候变化背景下刺梨(Rosa roxburghii)在中国的潜在适生区分布,该研究基于刺梨的自然分布数据及当代(1960～1990)、未来(21世纪50年代及70年代)气候因子数据,采用最大熵(MaxEnt)模型模拟了当前和未来气候情景下刺梨在中国的潜在适生区,并确定影响其地理分布的主要气候因子.结果表明:(1)...     

基于熵权模糊物元模型的我国省域森林生态安全研究

近年来随着经济社会的快速发展,森林资源锐减和生态环境恶化等问题日益威胁到人们的生产生活,在建设生态文明的背景下研究我国省域森林生态安全状况,是关系国计民生和可持续发展的重要议题。在整理现有生态安全研究体系的基础上,独创性地提出森林生态安全压力-承压模型,应用SPSS、EXCEL等软件,通过主成分分析、熵权法和物元分析等手段对2014年我国31个省级行政单位的森林生态安全水平进行实证研究。结果表明:在压力方面,19个省级行政单位承受了较大森林生态安全压力;在承压方面,12个省级行政单位的承压能力较强;在综合评价方面,14个省级行政单位的森林生态安全水平较高。在深入探讨分析评价结果的同时,为提高我国森林生态安全水平提出对策和建议。     

Reinterpreting maximum entropy in ecology: a null hypothesis constrained by ecological mechanism

Simplified mechanistic models in ecology have been criticised for the fact that a good fit to data does not imply the mechanism is true: pattern does not equal process. In parallel, the maximum entropy principle (MaxEnt) has been applied in ecology to make predictions constrained by just a handful of state variables, like total abundance or species richness. But an outstanding question remains: what principle tells us which state variables to constrain? Here we attempt to solve both problems simultaneously, by translating a given set of mechanisms into the state variables to be used in MaxEnt, and then using this MaxEnt theory as a null model against which to compare mechanistic predictions. In particular, we identify the sufficient statistics needed to parametrise a given mechanistic model from data and use them as MaxEnt constraints. Our approach isolates exactly what mechanism is telling us over and above the state variables alone.     

Solute complexation degree with human serum albumin: biochromatographic approach

A mathematical model was developed for the study of the D,L-dansylamino acid retention mechanism in reversed-phase liquid chromatography using a C18 column as a stationary phase and human serum albumin (HSA) as an eluent modifier. The solute retention factor is dependent on the HSA concentration in the eluent as well as the binding constant of the guest-HSA complex. A determination of the degree of complexation n(c) (the percent of the complexed guest) could be carried out. Different Van 't Hoff plot shapes of the degree of complexation were observed with different eluent pH, confirming a change in the solute complexation mechanism for physiological pH (between 7-7.5). Enthalpy-entropy compensation was also analysed in relation to this mathematical model to confirm the solute complexation behavior with HSA. These results finally confirmed that at physiological pH and temperature (approximately 35 degrees C) values the HSA was in a favorable structural conformation for its binding with a great majority of drugs.     

基于灰熵关联的平均住院日影响因素研究

目的:分析医疗指标与平均住院日的关联程度,为医院有效缩短平均住院日提供参考依据。方法:建立基于灰熵优化的加权灰色关联度模型,对影响平均住院日的医疗指标进行重要程度的分析。结果:根据关联程度分析,可知影响平均住院日的医疗指标重要程度依次为开放床位数、床位周转次数、治疗有效率、床位使用率、年门诊量、住院手术人次和出院人数。结论:基于灰熵优化的加权灰色关联分析方法可以有效分析医疗指标对平均住院日的影响程度,提高医疗服务质量。     

Free‐energy function based on an all‐atom model for proteins

We have developed a free‐energy function based on an all‐atom model for proteins. It comprises two components, the hydration entropy (HE) and the total dehydration penalty (TDP). Upon a transition to a more compact structure, the number of accessible configurations arising from the translational displacement of water molecules in the system increases, leading to a water‐entropy gain. To fully account for this effect, the HE is calculated using a statistical‐mechanical theory applied to a molecular model for water. The TDP corresponds to the sum of the hydration energy and the protein intramolecular energy when a fully extended structure, which possesses the maximum number of hydrogen bonds with water molecules and no intramolecular hydrogen bonds, is chosen as the standard one. When a donor and an acceptor (e.g., N and O, respectively) are buried in the interior after the break of hydrogen bonds with water molecules, if they form an intramolecular hydrogen bond, no penalty is imposed. When a donor or an acceptor is buried with no intramolecular hydrogen bond formed, an energetic penalty is imposed. We examine all the donors and acceptors for backbone‐backbone, backbone‐side chain, and side chain‐side chain intramolecular hydrogen bonds and calculate the TDP. Our free‐energy function has been tested for three different decoy sets. It is better than any other physics‐based or knowledge‐based potential function in terms of the accuracy in discriminating the native fold from misfolded decoys and the achievement of high Z‐scores. Proteins 2009. © 2009 Wiley‐Liss, Inc.