Solitons in a generalized space- and time-variable coefficients nonlinear Schrödinger equation with higher-order terms

We introduce an approach that combines a similarity method with several transformations to find analytical solitary wave solutions for a generalized space- and time-variable coefficients of nonlinear Schrödinger equation with higher-order terms with consideration of varying dispersion, higher nonlinearities, gain/loss and external potential. One of these transformations is constructed in such a way that allows study of the width of localized solutions. Solitary-like wave solutions for front, bright and dark are given. The precise expressions of the soliton?s width, peak, and the trajectory of its mass center and the external potential which are symbol of dynamic behavior of these solutions, are investigated analytically. In addition, the dynamical behavior of moving, periodic, quasi-periodic of breathing, and resonant are discussed. Stability of the obtained solutions is analyzed both analytically and numerically.     

Exploring structure–selectivity relationships of biogenic amine GPCR antagonists using similarity searching and dynamic compound mapping

We design and analyze compound selectivity sets of antagonists with differential selectivity against seven biogenic amine G-protein coupled receptors. The selectivity sets consist of a total of 267 antagonists and contain a spectrum of in part closely related molecular scaffolds. Each set represents a different selectivity profile. Using these com- pound sets, a systematic computational analysis of structure-selectivity relationships is carried out with different 2D similarity methods including fingerprints, recursive partitioning, clustering, and dynamic compound mapping. Screening calculations are performed in a background database containing nearly four million molecules. Fingerprint searching and compound mapping are found to enrich target-selective antagonists over family-selective ones. Dynamic compound mapping effectively discriminates database compounds from GPCR antagonists and consistently retains target-selective antagonists during the final dimension extension levels. Furthermore, the widely used MACCS key fingerprint displays a strong tendency to distinguish between target- and family-selective GPCR antagonists. Taken together, the results indicate that different types of 2D similarity methods are capable of distinguishing closely related molecules having different selectivity. The reported compound benchmark system is made freely available in order to enable selectivity-oriented analyses using other computational approaches.     

基于不完整描述样本的制冷系统故障诊断研究

制冷系统故障信息样本中的部分特征缺失时,已有的故障诊断模型无法使用这些样本。为解决该问题,提出了一种新颖的故障诊断策略。该诊断策略可通过以下步骤实现:(1)在部分问题描述与历史数据库的相互作用及领域知识的基础上,产生了用于特征转换的相似转换矩阵;(2)将不完整描述样本中的未知特征转变为与其相关的已知特征,形成检索目标;(3)通过计算和比较检索目标与数据库中样本间的相似度,得到最佳案例,将该案例中的相应值赋予未知特征;(4)运用已有的故障诊断模型及再生的完整描述样本,对制冷系统进行故障诊断。利用实验数据对该诊断策略进行验证,取得了满意的结果。     

基于均值距离测度的医学图像配准

针对互信息测度在配准医学图像时易陷入局部极值、速度慢的缺点,提出了基于均值不等式的均值距离测度.首先根据均值不等式推导出5种均值距离测度：方根-算术均值距离(SAM)、方根-几何均值距离(SGM)、方根-调和均值距离(SHM)、算术-几何均值距离(AGM)、算术-调和均值距离(AHM).然后通过人体脑部CT/MR和MR-T1/PD图像的刚体配准实验,从函数曲线、配准精度、计算时间和收敛性能方面,对互信息与5种均值距离信息测度进行了比较与分析.实验结果表明,在不损失配准精度的前提下,AHM和SAM测度可以获得更快的配准速度,对噪声有很强的鲁棒性.     

Similar,or dissimilar,that is the question. How different are methods for comparison of compounds similarity?

Comparison of compounds similarity is one of the main strategies of virtual screening protocols. Both similarity and dissimilarity concepts are of great importance during the search for new active compounds. Similarity is important due to the assumption that underlies the process of searching for new drug candidates: structurally similar compounds should induce similar biological response. On the other hand, we are also interested in dissimilarity, as we usually aim to find structurally novel ligands. In the study, we compared several approaches of evaluating compound similarity. Various representations and metrics were applied and we indicated the rate of variation of the results that can occur when shifting from one strategy to another. We compared both general similarity of datasets using different approaches, as well as examined the changes in the set of nearest neighbors when changing one compound representation into another, and the influence of representation/metric settings on the clustering outcome. We hope that the study will be of great help during the preparation of virtual screening experiments, stressing the need for careful selection of the way, the compound similarity is assessed. The differences in the results that can be obtained via the application of particular strategy can significantly influence the outcome of comparison studies; therefore, its settings should be carefully selected beforerunning the comparison.     

A Construction of Subsets of the Reals which have a Similarity Decomposition

We construct a subset of the set R of real numbers of cardinality |R| which has a similarity decomposition, and which has an ordertype < that of R. Seymour Ginsburg had posed the question whether there exist sets with another ordertype than that of R which also have a similarity decomposition.      

Characterizing vibrational motion beyond internal coordinates

We present a procedure for the decomposition of the normal modes of a composite system, including its rotations and translations, into those of fragments. The method permits—by the cross-contraction of dyads of mass-weighted displacement vectors, without recourse to valence coordinates—the direct comparison of nuclear motions of structurally similar but otherwise arbitrary fragments of molecules, and it leads to a quantitative definition of the similarity and the overlap of nuclear motions. We illustrate its usefulness by the quantification of the mixing of the normal modes of formic acid monomers upon the formation of a dimer, by the comparison of the overlap of the intermolecular normal vibrations of the water dimer computed with different ab initio schemes, and by the comparison of similarity and overlap of vibrations of (4S,7R)-galaxolide and (4S)-4-methylisochromane. The approach is expected to become a standard tool in vibrational analysis.     

A computational model for predicting fusion peptide of retroviruses

As a pivotal domain within envelope protein, fusion peptide (FP) plays a crucial role in pathogenicity and therapeutic intervention. Taken into account the limited FP annotations in NCBI database and absence of FP prediction software, it is urgent and desirable to develop a bioinformatics tool to predict new putative FPs (np-FPs) in retroviruses. In this work, a sequence-based FP model was proposed by combining Hidden Markov Method with similarity comparison. The classification accuracies are 91.97% and 92.31% corresponding to 10-fold and leave-one-out cross-validation. After scanning sequences without FP annotations, this model discovered 53,946 np-FPs. The statistical results on FPs or np-FPs reveal that FP is a conserved and hydrophobic domain. The FP software programmed for windows environment is available at https://sourceforge.net/projects/fptool/files/?source=navbar.     

一种识别病毒和蠕虫的算法

对现有的恶意软件检测算法进行研究之后发现,某些检测算法只能检测一种恶意软件,并且部分传统的检测算法在检测恶意程序时漏检率偏高。针对目前现有的检测算法缺乏综合性检测能力的短板,在此文中提出了一种新的检测算法,该检测算法具有一定的综合检测能力。新算法的思路如下：第一步区分某种软件是恶意软件还是非恶意软件,如果是恶意软件则提取其特征码,然后使用决策树根据恶意软件的特征码对恶意软件进行识别和分类,如果存在特征码不能识别的恶意软件,那么再根据病毒和蠕虫的特征使用相似性计算算法对未知的恶意软件进行相似性计算,最后使用决策系统对相似性算法计算的结果进行决策,该恶意软件是病毒还是蠕虫。将相似性计算算法,决策树和决策系统在检测恶意软件算法中进行应用是本文的创新之处。