基于Gene Ontology的表达谱与基因功能相似性的相关性研究

聚类是芯片数据分析中被广泛使用的方法。未知基因的功能通常通过其与已知基因在不同生物状态下具有表达相似性来进行预测。然而，还未有人就这种通过表达相似性来进行功能注释的方法的可靠性进行评估。本文利用Gene Ontology对表达相似性和基因功能相似性的相关关系进行了全面的研究。研究表明，尽管表达谱的相似性和基因功能相似性之间有一定的依赖关系，但相关性较弱。在Gene Ontology的三大类中，相对生物过程和分子功能，基因表达谱的相似性更有助于细胞组分的注释。本文的研究结果对于基因功能的预测有一定的指导意义。     

Thermotropic gelation of ovalbumin 1. Viscoelastic properties of gels as a function of heating conditions and protein concentration at various pH values

A study has been undertaken of stress relaxation in ovalbumin thermotropic gels with a concentration of 8–20%, depending on time and temperature of heating (respectively, 20–60 min, 70°–110°C), at pH 2.5–10.0. In all instances, the dependence of the initial gel elasticity modulus on heating has a single maximum. Gelation conditions corresponding to this maximum are considered optimal. Optimal gelation time is 30 min, regardless of pH. On the other hand, the optimal heating temperature depends on pH. To the right and left of the isoelectric point of protein (2.5pH<4.0 and 5.5G) of gels on heating conditions, pH and protein concentration (X ₁,X ₂,X ₃,X ₄), as well as on time of relaxation (t) may be generally described asG(X ₁,X ₁,X ₁,X ₁,t)=G _e(X ₁,X ₂,X ₃,X ₄)f(t), whereG _e is the equilibrium value of the elasticity modulus, and f(t) the relaxation function. Thus, a change in the parameters only affects the value of the equilibrium elasticity modulus, and exerts no effect on the relaxation time spectrum. For this reason, all the relaxation curves obtained may be transformed into two normalized relaxation functions:f(t)=f(t)/f(1)=G(X ₁,X ₂,X ₃,X ₄,t)/G(X ₁,X ₂,X ₃,X ₄, 1)Each of these normalized functions corresponds to one of the homologous groups. Rheological similarity of gels in each homologous group evidently points to their structural similarity. Invariance of the gel relaxationproperties with regard to protein concentration, leads to a concentration dependence of the equilibrium modulus at various pH values. These dependences are curvilinear on a double logarithmic scale. The slope of the curve exceeds 2 in the entire concentration interval studied. In other words, the dependences obtained cannot be described by the usual law of squares. On the other hand, they adequately match Hermans theoretical relation for a network formed by random association of identical polyfunctional particles without cyclization. This simple model evidently gives a true picture of the major regularities of thermotropic gelation for ovalbumin. An agreement between this theory and experiment was achieved for a protein concentration ofC ^*=6.0±1.0% at the gel point regardless of pH. Invariance of gelpoint position with regards to pH demands further confirmation.List of symbols T _h,t _h heating temperature and time - T _h ^* ,t _h ^* optimal heating temperature and time - C protein concentration - C ^* protein concentration in gel-point - G relaxation modulus - G _e equilibrium modulus - f(t) relaxation function - t time of relaxation - f(t) normalized relaxation function - fT _A (t), f _B (t) normalized relaxation functions of groups A and B - G ₁ T _h,t _h-reduced modulus - G ₂ T _h,t _h, pH-reduced modulus - G ₃ C-reduced modulus - b ₁ T _h, t_h reduction parameter of modulus - b ₂ pH reduction parameter of modulus - b ₃ C reduction parameter of modulus - W_g gel-fraction     

Calculating the knowledge-based similarity of functional groups using crystallographic data

A knowledge-based method for calculating the similarity of functional groups is described and validated. The method is based on experimental information derived from small molecule crystal structures. These data are used in the form of scatterplots that show the likelihood of a non-bonded interaction being formed between functional group A (the `central group') and functional group B (the `contact group' or `probe'). The scatterplots are converted into three-dimensional maps that show the propensity of the probe at different positions around the central group. Here we describe how to calculate the similarity of a pair of central groups based on these maps. The similarity method is validated using bioisosteric functional group pairs identified in the Bioster database and Relibase. The Bioster database is a critical compilation of thousands of bioisosteric molecule pairs, including drugs, enzyme inhibitors and agrochemicals. Relibase is an object-oriented database containing structural data about protein-ligand interactions. The distributions of the similarities of the bioisosteric functional group pairs are compared with similarities for all the possible pairs in IsoStar, and are found to be significantly different. Enrichment factors are also calculated showing the similarity method is statistically significantly better than random in predicting bioisosteric functional group pairs.     

云南两高辐合背景下低涡强降水过程对比分析

基于气象观测和欧洲中期天气预报中心第五代大气再分析资料（ERA5）,选取2018—2020年发生在云南的3次两高压辐合区（以下简称两高辐合）背景下低涡连续性强降水过程进行对比分析,探究其环流形势、动热力因子及水汽辐合的相似性和差异性.结果显示：(1)夏半年西太平洋副热带高压（以下简称西太副高）西伸时,云南常受两高辐合影响,当辐合区中有低涡生成,易发生连续性强降水,且强降水落区并不完全分布在整个狭长的两高辐合区内.(2)两高辐合区低涡降水具有相似的雨带分布和移动特征,但雨带的集中程度、分布范围、小时雨强和总雨量存在差异.强降水开始时,落区偏东,随着西太副高西伸及东北引导气流的引导,低涡向南向西移动,强降水落区也随之向南向西移动.低涡在某一地区徘徊导致降水集中在该区域,且西太副高西伸较强时,两高辐合形势更强,低涡降水大雨及以上量级雨带也更窄.(3)低涡造成的降水主要分布在低涡中心及低涡切变附近,且降水发生在低层暖湿的环境中,低层及中高层有冷空气侵入时,小时雨强的极端性更强,降水落区也相对偏北.两高辐合区低涡降水落区与水汽辐合区对应较好,水汽辐合强度较弱时,对应的总降水量较小.     

基于三支决策的密度敏感谱聚类

将三支决策与密度敏感谱聚类结合,提出了一种基于三支决策的密度敏感谱聚类算法。该算法通过在密度敏感谱聚类的聚类过程引入容差参数得到每个类的上界,然后通过扰动分析算法从上界中分离出核心域,上界和核心域的差值被认定为该类的边界域。聚类结果用核心域和边界域来表示每个类簇,可以更全面地展示数据的结构信息。与传统的硬聚类算法在UCI数据集的实验结果相比较,本文使用核心域计算聚类的评价指标DBI、AS和ACC都有所提升,较好地解决了不确定性对象的聚类问题。     

The matching of electrostatic extrema: A useful method in drug design? A study of phosphodiesterase III inhibitors

Summary Ligands which bind to a specific protein binding site are often expected to have a similar electrostatic environment which complements that of the binding site. One method of assessing molecular electrostatic similarity is to examine the possible overlay of the maxima and minima in the electrostatic potential outside the molecules and thereby match the regions where strong electrostatic interactions, including hydrogen bonds, with the residues of the binding site may be possible. This approach is validated with accurate calculations of the electrostatic potential, derived from a distributed multipole analysis of an ab initio charge density of the molecule, so that the effects of lone pair and -electron density are correctly included. We have applied this method to the phosphodiesterase (PDE) III substrate adenosine-3,5-cyclic monophosphate (cAMP) and a range of nonspecific and specific PDE III inhibitors. Despite the structural variation between cAMP and the inhibitors, it is possible to match three or four extrema to produce relative orientations in which the inhibitors are sufficiently sterically and electrostatically similar to the natural substrate to account for their affinity for PDE III. This matching of extrema is more apparent using the accurate electrostatic models than it was when this approach was first applied, using semiempirical point charge models. These results reinforce the hypothesis of electrostatic similarity and give weight to the technique of extrema matching as a useful tool in drug design.     

Characterization of the organization in shear layers via the Proper Orthogonal Decomposition

Experiments are performed in an incompressible plane turbulent mixing layer, using various hot wire rake configurations. From these experiments, the Proper Orthogonal Decomposition is applied for kernels where the space-time correlation tensor is evaluated over different spatial meshes and velocity components configurations. The resulting decompositions are then discussed in terms of characterization of the organization of the flow for various scalar or vectorial approaches of the POD. An incrtial range law is evidenced. The instantaneous contribution of the first modes of the POD to the organization of the flow is analyzed. A dynamical behavior for the organization of the flow is observed from the correlation between the first two modes contribution.     

Some remarks on the operator of Foias and Williams

In this paper we study the Foias-Williams operator

where , and is a Hankel operator with symbol . We exhibit a relationship between the similarity of to a contraction and the rate of decay of , the absolute values of the Fourier coefficients of the symbol .

     

坐标动量几率相关分布的辛普森法研究

用辛普森法研究了不同体系的粒子在动量空间和坐标空间的几率分布的相关性及坐标和动量的分布宽度之积与宽度内所含几率的关系。