On the validity of the counterpoise correction for the basis set superposition error including the fragment relaxation terms

It is demonstrated that relatively large geometrical changes make Emsley et al.'s assumption (J Am Chem Soc (1978) 100:3303) on the counterpoise correction for the basis set superposition error including the fragment relaxation terms unacceptable. Received: 23 September 1997 / Accepted: 31 October 1997     

基于稳定同位素标记与质谱分析的蛋白质定量算法研究进展

蛋白质定量研究已成为蛋白质组学的热点,它是疾病相关生物标志物发现的重要途径.基于稳定同位素标记的质谱分析技术是蛋白质定量最常用的方法之一.随着实验方法的发展和改进,定量数据处理方法也在不断更新与完善.一般来说,定量数据处理包括四步:搜库鉴定、图谱定量信息提取与计算、肽段丰度比计算和蛋白质丰度比计算及差异显著性分析,其中后三步是数据处理的核心.目前,后三步中每步都有多种可选算法,这些算法一般都是针对特定实验技术而提出的,缺乏深入的工作对它们进行系统比较和优化.为此,在总结目前主要实验技术方法的基础上,论述了定量算法的现状和存在问题,并针对一些问题提出了可行的解决办法.     

Urinary exposure marker discovery for toxicants using ultra-high pressure liquid chromatography coupled with Orbitrap high resolution mass spectrometry and three untargeted metabolomics approaches

Human biomonitoring is the assessment of actual internal contamination of chemicals by measuring exposure markers, chemicals or their metabolites, in human urine, blood, serum, and other body fluids. However, the metabolism of chemicals within an organism is extremely complex. Therefore, the identification of metabolites is often difficult and laborious. Several untargeted metabolomics methods have been developed to perform objective searching/filtering of accurate-mass-based LC-MS data to facilitate metabolite identification. In this study, three metabolomics data processing approaches were used for chemical exposure marker discovery in urine with an LTQ-Orbitrap high-resolution mass spectrometry (HRMS) dataset; di-isononyl phthalate (DINP) was used as an example. The data processing techniques included the SMAIT, mass defect filtering (MDF), and XCMS Online. Sixteen, 83, and 139 probable DINP metabolite signals were obtained using the SMAIT, MDF, and XCMS procedures, respectively. Fourteen probable metabolite signals mined simultaneously by the three metabolomics approaches were confirmed as DINP metabolites by structural information provided by LC-MS/MS. Among them, 13 probable metabolite signals were validated as exposure-related markers in a rat model. Six (m/z 319.155, 361.127, 373.126, 389.157, 437.112 and 443.130) of the 13 exposure-related DINP metabolite signals have not previously been reported in the literature. Our data indicate that SMAIT provided an efficient method to discover effectively and systematically urinary exposure markers of toxicant. The DINP metabolism information can provide valuable information for further investigations of DINP toxicity, toxicokinetics, exposure assessment, and human health effects.     

Stability of Conjugated Carbon Nanocones

We use interlacing techniques to prove that carbon nanocones who have a Fries Kekulé structure have closed Hückel shells, and that this result can be extended to all conjugated cones where each edge belongs to a hexagonal face and the configuration of the non-hexagonal faces are consistent with a Fries Kekulé structure. Cones with Fries Kekulé structure or substructure are topical—not only from a valence bond theoretical point of view—since a previous ab initioanalysis favored cones where the pentagons at the tip are configured as in a Fries Kekulé structure. The question of interdependence will therefore be addressed.     

A Comparison of Three Heuristic Algorithms for Molecular Docking

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遗传光度法用于地质样品中多组分同时测定

将遗传算法（ＧＡ）用于地质样品中１５个稀土元素同时测定,分析结果与ＩＣＰ法进行了比较,大多数组分浓度的相对误差小于１０％,个别小于１６．２％,初步验证,遗传算法可以摆脱对校准模型的依赖。文中还讨论了变异概率,交配概率,种群数大小等因素的影响。     

Extended connectivity in chemical graphs

The true nature of the extended connectivity, used in Morgan algorithm for the canonical numerotation of points in chemical graphs, is discussed. An alternative method for its calculation based on the number of walks is described and shown to yield results identical to Morgan's method.     

四元数矩阵方程的复转化及保结构算法

给出四元数矩阵复表示运算定义及其相关性质,并运用复表示运算的保结构特性,讨论了四元数矩阵Moore-Penrose逆计算以及两类四元数矩阵方程AXB=C和AX-XB=C的数值求解方法.数值算例检验了所给算法的可行性.     

Collocation by singular splines

Splines determined by the kernel of the differential operator are known to be useful to solve the singular boundary value problems of the form . One of the most successful methods is the collocation method based on special Chebyshev splines. We investigate the construction of the associated B-splines based on knot-insertion algorithms for their evaluation, and their application in collocation at generalized Gaussian points. Specially, we show how to obtain these points as eigenvalues of a symmetric tridiagonal matrix of order k. This research was supported by Grant 037-1193086-2771, by the Ministry of science, education and sports of the Republic of Croatia.     

A stable manifold MCMC method for high dimensions

We combine two important recent advancements of MCMC algorithms: first, methods utilizing the intrinsic manifold structure of the parameter space; then, algorithms effective for targets in infinite-dimensions with the critical property that their mixing time is robust to mesh refinement.