Integrated Access to Genomic and Other Bioinformation: An Essential Ingredient of the Drug Discovery Process

Abstract

Due to the high rate of data production and the need of researchers to have rapid access to new data, public databases have become the major medium through which genome mapping and sequencing data as well as macromolecular structural data are published. There are now more than 250 databases of biomolecular, structural, genetic, or phenotypic data, many of which are doubling in size annually. These databases, many of which were created and are maintained by experimentalists for their own research use, provide valuable collections of organized, validated data. However, the very number and diversity of databases now make efficient data resource discovery as important as effective data resource use. Existing autonomous biological databases contain related data which are more valuable when interconnected than when isolated. Political and scientific realities dictate that these databases will be built by different teams, in different locations, for different purposes, and using different data models and supporting DBMSs. As a consequence, connecting the related data they contain is not straightforward. Experience with existing biological databases indicates that it is possible to form useful queries across these databases, but that doing so usually requires expertise in the semantic structure of each source database. Advancing to the next level of integration among biological information resources poses significant technical and sociological challenges.     

Avoiding problems with hydrogen misplacement in reporting crystal structures

Intermolecular hydrogen bonding is an integral part of many crystal structures. Hydrogen bonding sometimes results in one‐, two‐ or three‐dimensional supramolecular assemblies, a common feature of which is positional disorder of H atoms related to space‐group symmetry. Yet some reported structures fail to include all possible donor–acceptor close contacts, or to seek H‐atom electron densities associated with apparent D—H...A trios, while some H‐atom positions violate principles of chemistry or crystal physics. Modern diffraction equipment and sophisticated computing systems provide high‐quality data; thus, failure to characterize and report fully an accurate, complete and physically correct hydrogen‐bonding model should not be acceptable. We illustrate the relevant issues with three published examples in the hope of slowing the proliferation of these problems, with the scientifically desirable goal of improving the accuracy of crystallographic models while also providing improved search keys for information retrieval.     

Search of truncation of (N−1) electron basis containing full connected triple excitations in computing main and satellite ionization potentials via Fock‐space coupled cluster approach

A valence‐universal multireference coupled cluster (VUMRCC) theory, realized via the eigenvalue independent partitioning (EIP) route, has been implemented with full inclusion of triples excitations for computing and analyzing the entire main and several satellite peaks in the ionization potential spectra of several molecules. The EIP‐VUMRCC method, unlike the traditional VUMRCC theory, allows divergence‐free homing‐in to satellite roots which would otherwise have been plagued by intruders, and is thus numerically more robust to obtain more efficient and dependable computational schemes allowing more extensive use of the approach. The computed ionization potentials (IPs) as a result of truncation of the (N−1) electron basis manifold involving virtual functions such as 2h‐p and 3h‐2p by different energy thresholds varying from 5 to 15 a.u. with 1 a.u. intervals as well as thresholds such as 20, 25, and 30 a.u. have been carefully looked into. Cutoff at around 25 a.u. turns out to be an optimal threshold. Molecules such as C₂H₄ and C₂H₂ (X = D,T), and N₂ and CO (X = D,T,Q) with Dunning's cc‐pVXZ bases have been investigated to determine all main and 2h‐p shake‐up and 3h‐2p double shake‐up satellite IPs. We believe that the present work will pave the way to a wider application of the method by providing main and satellite IPs for some problematic N‐electron closed shell systems. © 2013 Wiley Periodicals, Inc.     

Interactions of delta shock waves for the relativistic Chaplygin Euler equations with split delta functions

In this article, we are concerned with the interactions of delta shock waves with contact discontinuities for the relativistic Euler equations for Chaplygin gas by using split delta functions method. The solutions are obtained constructively and globally when the initial data consists of three piecewise constant states. The global structure and large time‐asymptotic behaviors of the solutions are analyzed case by case. During the process of the interaction, the strengths of delta shock waves are computed completely. Moreover, it can be found that the Riemann solutions are stable for such small perturbations with special initial data by letting perturbed parameter ε tends to zero. Copyright © 2014 John Wiley & Sons, Ltd.     

基于多小波统计特征的纹理图像检索

为了研究多小波性能,对多小波系数分布的统计特性进行了研究.多小波在实数域能同时具有正交、对称、短紧支撑和高消失矩等特性,单小波却不具有上述的性质,因此在理论上多小波比单小波具有更多的优势.提出并验证了多小波系数直方图服从于指数族分布;根据多小波的特点研究了其系数分布的一阶、二阶矩(共生矩阵)和系数直方图的统计特性,并应用于纹理特征的提取.通过理论分析和在纹理图像检索的对比实验说明在冗余预滤波方式下,采用二阶统计矩方法时多小波优于单小波.     

文本社会学的语言中介性及其推论实证

文本社会学是奥大利学者皮埃尔.V.齐马在20世纪80年代提出的一种社会学批评理论。这一理论的精义之处就在于:立足于文学作品本身,以“语言”为中介来深入细致地考察文学与社会之间的关系,并将文学的“内部分析”与“外部分析”融于“语言”向“意识形态”的推论过程之中,运用此理论对《白鹿原》和《尘埃落定》进行文本解读,见出它具有思路清晰性、层次明确性和技术可操作性的三大特点,能为当下的文学研究、文化研究提供一种精致而有效的理论范式。     

基于广播影视资料的图像检索技术研究

本文以国家发改委CNGI项目“基于IPv6的广播影视资料P2P内容存取中闾件系统”为背景,研究了基于内容的图像检索技术。通过对常用颜色和纹理特征提取算法的研究,选择了块RGB均值法、改进参考颜色表法和灰度一平滑共生矩阵法对图像进行特征提取,并使用标准的Corel库建立图像特征数据库,分析和比较这几秤算法单独检索和综合检索的效果。实验结果证明,采用多特征的综合检索比采用单特征的检索具有更高的查全率和查准率,因此采用综合特征检索技术,能够更好地实现对广播影视资料的内容检索。     

Remarkably improved cycling stability of 3D porous Cu–Sn anode for lithium-ion full cells by adjusting working voltage range

Numerous studies confirm that three dimensional porous Cu–Sn (3DP Cu–Sn) anode possesses good application prospect in light of its desirable electrochemical performance on lithium ion half cells, but there are a few related systematic researches on lithium ion full cells until now, which is indispensable before its commercialization. Herein, the effects of galvanostatic charge-discharge voltage range on the cycling stability of 3DP Cu–Sn anode for lithium ion full cells are investigated systematically. The results show that the suitable charge-discharge voltage range plays a key role in improving the reversible capacity and cycling stability of the 3DP Cu–Sn||LiCoO₂ full cell, which is closely related to maintaining the electrode structure stable by controlling the amount of Li⁺ extracted and inserted. Especially, in the voltage range of 1.2–3.9 ​V, the full cell exhibits remarkably improved electrochemical properties with the high initial reversible capacity of 2.71 ​mAh cm⁻² and 71.95% capacity retention upon 80 cycles. We believe that this work can provide a significant reference for the practical application of porous Sn-based anodes.     

基于瑞利-索末菲积分的大衍射角衍射光学元件设计方法

针对现有的衍射光学元件设计方法只适用于小角度衍射的情况,本文提出了一种基于瑞利-索末菲衍射积分的设计方法,可以用来设计具有大衍射角的衍射光学元件。先对目标光场进行坐标变换和强度调整,再利用改进的Gerchberg-Saxton算法优化得到衍射光学元件的相位分布。分别采用本文方法和原有的基于夫琅禾费衍射积分的方法设计衍射光学元件实现线条结构光和不同角度方框图形的光场重构,结果表明:原有的设计方法只适用于衍射角全角小于25°的情况,当衍射角大于25°时,重构光场会出现显著的枕形畸变和不均匀的强度分布。而本文方法在小角度和大角度衍射下都能重构出准确的衍射角和较为均匀的强度分布.     

Determining the micro-optical element surfaces profiles using transmission deflectometry with liquids

We propose a method for simultaneously measuring the front and back surface profiles of transparent optical components. The proposed method combines dual wavelength transmission deflectometry with liquids to record distorted phases at different wavelengths, and then numerically reconstructs the three-dimensional phase information to image the front and back surfaces of the lens. We propose a theoretical model to determine the surface information, and the imaging of achromatic lenses is experimentally demonstrated. Unlike conventional transmission deflectometry, our proposed method supports direct observation of the front and back surface profiles of the optical elements. Compared with other techniques such as interferometry, the proposed setup is simpler to align, has lower cost, and does not require coherent illumination. The proposed method can be applied to normal transmission deflectometry for determining the three-dimensional surface profiles of optical components.