predForm-Site: Formylation site prediction by incorporating multiple features and resolving data imbalance

Formylation is one of the newly discovered post-translational modifications in lysine residue which is responsible for different kinds of diseases. In this work, a novel predictor, named predForm-Site, has been developed to predict formylation sites with higher accuracy. We have integrated multiple sequence features for developing a more informative representation of formylation sites. Moreover, decision function of the underlying classifier have been optimized on skewed formylation dataset during prediction model training for prediction quality improvement. On the dataset used by LFPred and Formator predictor, predForm-Site achieved 99.5% sensitivity, 99.8% specificity and 99.8% overall accuracy with AUC of 0.999 in the jackknife test. In the independent test, it has also achieved more than 97% sensitivity and 99% specificity. Similarly, in benchmarking with recent method CKSAAP_FormSite, the proposed predictor significantly outperformed in all the measures, particularly sensitivity by around 20%, specificity by nearly 30% and overall accuracy by more than 22%. These experimental results show that the proposed predForm-Site can be used as a complementary tool for the fast exploration of formylation sites. For convenience of the scientific community, predForm-Site has been deployed as an online tool, accessible at http://103.99.176.239:8080/predForm-Site.     

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。     

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.     

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.     

Exponential stability of discrete-time systems with slowly time-varying delays

Slowly time-varying delays are seldom, but do need to be, considered in the context of discrete-time systems. This paper addresses the exponential stability issue of discrete-time systems with slowly time-varying delays. The basic idea is to transform, by utilizing the switching transformation approach, the original system with slowly time-varying delays into an equivalent switched system with special switching signal. Different types of delays correspond to different types of switching signals, and the stability issue of the original system is converted into that of a switched system. It is the first time that the method of switched homogeneous polynomial Lyapunov function is applied to general delayed systems. Some sufficient exponential stability conditions for the original system are proposed in several situations. It is numerically shown that the conservativeness of the proposed conditions reduces as the degree of the switched homogeneous polynomial Lyapunov function increases.     

Impulsive systems with hybrid delayed impulses: Input-to-state stability

This paper investigates input-to-state stability (ISS) and integral-input-to-state stability (iISS) of nonlinear impulsive systems with hybrid delayed impulses. Based on Lyapunov method, some sufficient conditions ensuring ISS and iISS of impulsive systems are obtained, where the time derivative of Lyapunov function is indefinite, and the hybrid effects of delayed impulses are also fully considered. It is shown that the impulsive system is ISS provided that the combined action of time delay existing in impulses, continuous dynamic, and the cumulative strength of hybrid impulses satisfies some conditions, even if the hybrid delayed impulses play a destabilizing effect on ISS. Examples and their simulations are presented to illustrate the applicability of the proposed results.     

Standard pseudo-Hermitian structure on manifolds and seifert fibration

A strictly pseudoconvex pseudo-Hermitian manifoldM admits a canonical Lorentz metric as well as a canonical Riemannian metric. Using these metrics, we can define a curvaturelike function onM. AsM supports a contact form, there exists a characteristic vector field dual to the contact structure. If induces a local one-parameter group ofCR transformations, then a strictly pseudoconvex pseudo-Hermitian manifoldM is said to be a standard pseudo-Hermitian manifold. We study topological and geometric properties of standard pseudo-Hermitian manifolds of positive curvature or of nonpositive curvature . By the definition, standard pseudo-Hermitian manifolds are calledK-contact manifolds by Sasaki. In particular, standard pseudo-Hermitian manifolds of constant curvature turn out to be Sasakian space forms. It is well known that a conformally flat manifold contains a class of Riemannian manifolds of constant curvature. A sphericalCR manifold is aCR manifold whose Chern-Moser curvature form vanishes (equivalently, Weyl pseudo-conformal curvature tensor vanishes). In contrast, it is emphasized that a sphericalCR manifold contains a class of standard pseudo-Hermitian manifolds of constant curvature (i.e., Sasakian space forms). We shall classify those compact Sasakian space forms. When 0, standard pseudo-Hermitian closed aspherical manifolds are shown to be Seifert fiber spaces. We consider a deformation of standard pseudo-Hermitian structure preserving a sphericalCR structure.Dedicated to Professor Sasao Seiya for his sixtieth birthday     

An algebraic approach to the vector ε-algorithm

The vector -algorithm is obtained from the scalar -algorithm by taking the pseudo-inverse of a vector instead of the inverse of a scalar. Thus the vector -algorithm is known only through its rules contrarily to the scalar -algorithm and some other extrapolation algorithms.The aim of this paper is to provide an algebraic approach to the vector -algorithm.     

基于支持向量机的羰基化合物红外光谱研究

设计了一个4层分等级分类系统，通过支持向量机技术对羰基化合物的红外光谱成功地进行了信息分类和提取，并与人工神经网络进行比较，结果表明：支持向量机对羰基类化合物红外光谱分类效果优于人工神经网络；另外详细探讨了表征酰胺类化合物的特征光谱峰片段对识圳伯仲叔酰胺的影响，证明了酰胺的N-H伸缩振动峰对识别伯仲叔酰胺贡献最大，为构建红外光谱智能解析系统提供了定量依据。