A combination of modified particle swarm optimization algorithm and support vector machine for gene selection and tumor classification

In the analysis of gene expression profiles, the number of tissue samples with genes expression levels available is usually small compared with the number of genes. This can lead either to possible overfitting or even to a complete failure in analysis of microarray data. The selection of genes that are really indicative of the tissue classification concerned is becoming one of the key steps in microarray studies. In the present paper, we have combined the modified discrete particle swarm optimization (PSO) and support vector machines (SVM) for tumor classification. The modified discrete PSO is applied to select genes, while SVM is used as the classifier or the evaluator. The proposed approach is used to the microarray data of 22 normal and 40 colon tumor tissues and showed good prediction performance. It has been demonstrated that the modified PSO is a useful tool for gene selection and mining high dimension data.     

一维〔M（tmp）〕_2ReO_4（M＝Ni、Cu、Pd）聚合物的能带结构

用紧束缚ＥＨＴ晶体轨道方法对一维〔Ｍ（ｔｍｐ）〕_２ＲｅＯ_４（Ｍ＝Ｎｉ、Ｃｕ、Ｐｄ）聚合物进行了能带计算，利用键向量近似方法对能带的结构及组成进行了讨论。结果表明，该类型聚合物具有不同的导电机理，并进一步研究了环平面间的成键性质及转角改变对聚合物导电性能的影响。     

多组分体系同时定性定量测定的逐步回归分析法

阐述了逐步回归分析法用于多组分体系同时定性定量分析的原理、实验及数据处理方法。分析了硝基酚类人工样、未知样及合成样。该法可用于仅知可能含有的组分范围的样品分析。     

Complexation of well-controlled low-molecular weight polyelectrolytes with antisense oligonucleotides

The influences of polymer-related properties such as molecular weight, charge density, counter ion, and hydrophilic block on the complexation of polyelectrolytes and a fluorescein-labeled oligonucleotide (ON) were investigated. A series of well-defined and well-controlled 2-(N,N-dimethylamino)ethyl methacrylate (DMAEMA) polymers and block copolymers were prepared using living anionic and radical polymerization methods. Fluorescence measurement was used to reveal the effects of polymer molecular weight, charge density, and counter ion type on the complexation. PolyDMAEMA samples having double molecular weights of the chosen oligonucleotide gave the optimal complexation performance. Kinetic studies showed that high-molecular weight/high-charge density polymer samples produced very stable complexes. The fully charged polyDMAEMA displayed the strongest binding with the ON. These complexes were therefore less sensitive to the changes in the environment. PolyDMAEMA–DMSQ samples had slightly higher complexation ability than polyDMAEMA–MCQ (DMSQ: dimethylsulfate quat; MCQ: methylchloride quat). Both poly(DMAEMA-b-HEMA) and poly(DMAEMA–MCQ-b-PEG) block copolymers showed good complexation ability and steric stability [HEMA: 2-hydroxyethyl methacrylate; PEG: poly(ethylene glycol)]. PEG, but not HEMA block, enhanced the effectiveness of polyDMAEMA–MCQ binding with the ON.     

Refining adsorption parameters of n-butyl alcohol at the interface of mercury electrode with aqueous NaF and Na2SO4 solutions by correcting the adsorbate concentration

As an adjunct to the regression analysis of differential capacitance curves, which allows refining the adsorption parameters, a program, which takes into account possible errors in volume concentrations of organic substances, is developed. Using this procedure, the earlier data on the differential capacitance of a mercury electrode in aqueous solutions of normal butanol (1-BuOH) containing either 0.1 M NaF or 0.05 and 0.5 M Na₂SO₄ as the supporting electrolyte are analyzed. This allows obtaining the most accurate values of adsorption parameters for the systems mentioned above within the framework of the model of two parallel capacitors and the Frumkin isotherm. It is shown that, when a linear dependence of the intermolecular interaction parameter on the electrode potential is taken into account, the standard deviation of experimental capacitance values from those calculated using the mentioned model is 6.8–8.8%, which points to very high accuracy of this phenomenological model.     

Estimation of parameters characterizing the adsorption of sodium,potassium, and rubidium cryptates at the mercury electrode/solution interface

The adsorption of complexes formed by sodium, potassium, and rubidium cations with macrobicyclic ligand (kryptofix 222 with C₁₈H₃₆N₂O₆ composition) is studied as a function of the ligand concentration on a stationary mercury drop in 0.1 M solutions of corresponding sulfates and chlorides by using the differential capacitance technique. Based on the model of two parallel capacitors supplemented by the Frumkin isotherm, the adsorption parameters of studied cryptates are estimated by using the regression analysis technique. Differential capacitance curves calculated with the parameters found are compared with experimental data. The comparison of the found adsorption parameters makes it possible to reveal the effects of the nature of included cations and specifically adsorbed supporting-electrolyte anions on the adsorption behavior of cryptates under study.__________Translated from Elektrokhimiya, Vol. 41, No. 4, 2005, pp. 475–481.Original Russian Text Copyright © 2005 by Stenina, Sviridova.     

Mathematical studies of Kekulé structures

The perfect matching vector and forcing and the Kekulé-vector of cata-benzenoids are defined. Two theorems are given which set the sufficient and necessary conditions for HKZ-vector (Harary et al. J Math Chem 6:295, 1991) and Kekulé-vector in cata-benzenoids. Additional two theorems are obtained which give sharp bounds for the modules of HKZ- and Kekulé vectors. Dedicated to Professor Tadeusz Marek Krygowski on the happy occasion of his 70th birthday.     

基于SVR和k-近邻群的组合预测在QSAR中的应用

为提高定量构效关系(QSAR)研究的预测精度,发展了一种新的基于支持向量机回归(SVR)非线性筛选分子结构描述符、基于k-近邻群的非线性组合预测方法.首先以均方误差(MSE)最小为原则,以留一法通过多轮末尾淘汰实施分子结构描述符的非线性SVR汰选并给出最优核函数和相应保留描述符;其次基于待测样本与训练样本保留描述符向量的欧氏距离,以不同k-近邻群子模型双重留一法预测值反映样本集的异质性;然后基于MSE最小,以留一法通过多轮末尾淘汰实施近邻群子模型的非线性SVR汰选并给出最优核函数和相应保留子模型;最后基于保留子模型以双重留一法实施组合预测.以取代苯胺和苯酚类化合物对大型溞的QSAR实例验证表明:新方法在所有参比模型中预测精度最高,且能更精细地反映描述符与化合物毒性间的非线性关系,具结构风险最小、非线性、适于小样本,能有效克服过拟合、维数灾和局极小,非线性筛选描述符和子模型,非线性组合预测,自动选择最优核函数及其相应参数,泛化推广能力优异、预测精度高等诸多优点,在QSAR研究中有广泛应用前景.     

Simultaneous measurement of glucose and glutamine in aqueous solutions by near infrared spectroscopy

A method is described for measuring the concentrations of both glucose and glutamine in binary mixtures from near infrared (NIR) absorption spectra. Spectra are collected over the range from 5000–4000/cm (2.0–2.5μm) with a 1-mm optical path length. Glucose absorbance features at 4710, 4400, and 4300/cm and glutamine features at 4700, 4580, and 4390/cm provide the analytical information required for the measurement. Multivariate calibration models are generated by using partial least squares (PLS) regression alone and PLS regression combined with a preprocessing digital Fourier filtering step. The ideal number of PLS factors and spectral range are identified separately for each analyte. In addition, the optimum Fourier filter parameters are established for both compounds. The best overall analytical performance is obtained by combining Fourier filtering and PLS regression. Glucose measurements are established over the concentration range from 1.66–59.91 mM, with a standard error of prediction (SEP) of 0.32 mM and a mean percent error of 1.84%. Glutamine can be measured over the concentration range from 1.10–30.65 mM with a SEP of 0.75 mM and a mean percent error of 6.67%. These results demonstrate the analytical utility of NIR spectroscopy for monitoring glucose and glutamine levels in mammalian and insect cell cultures.     

Adsorption parameters of cyclobutane carboxylic acid at the interface of a mercury electrode with aqueous solutions of 0.4 M Na2SO4 + 0.1 M H2SO4

Based on the results of the regression analysis of differential capacitance curves of a mercury electrode in solutions of cyclobutane carboxylic acid (CBCA) at 25, 50, and 75°C, the adsorption parameters that enter into both the Frumkin isotherm and the model of two parallel capacitors are estimated. The free energies of adsorption found from the analysis of the temperature dependence of these parameters are incorrect due to the partial blowing out of CBCA during the deaeration of the solutions. The corresponding adsorption parameters are corrected under the assumption that the hydrophobic effect associated with the increase in the liquid-water entropy at the removal from it of CBCA molecules is the same as for n-valeric acid. The physical meaning of the squeezing-out effect is revised.