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.     

Channel capacities via p-summing norms

In this paper we show how the metric theory of tensor products developed by Grothendieck perfectly fits in the study of channel capacities, a central topic in Shannon's information theory. Furthermore, in the last years Shannon's theory has been fully generalized to the quantum setting, and revealed qualitatively new phenomena in comparison. In this paper we consider the classical capacity of quantum channels with restricted assisted entanglement. These capacities include the classical capacity and the unlimited entanglement-assisted classical capacity of a quantum channel. Our approach to restricted capacities is based on tools from functional analysis, and in particular the notion of p  -summing maps going back to Grothendieck's work. Pisier's noncommutative vector-valued _Lp$L_p$ spaces allow us to establish the new connection between functional analysis and information theory in the quantum setting.     

关于艺校图书馆信息服务创新的思考

艺校教学内容的特殊性,对其图书馆信息服务的内容和方式提出了独特的要求。因此,艺校图书馆需要在创新信息服务的基础上增强工作的针对性。分析了艺校学生信息需求的特点,探讨了艺校图书馆信息服务创新的原则,提出了艺校图书馆信息服务创新的途径。     

高校图书馆大规模馆藏精准迁移模式探讨--以华北电力大学图书馆为例

书库藏书迁移的运作主要在于精心准备和周密筹划。详细介绍了华北电力大学图书馆利用汇文文献信息服务系统的强大分析功能并结合Excel软件的使用技巧,实现大规模馆藏迁移精准排架工作的经验。     

泊松分布下信息安全事件概率计算模型

从信息安全事件的概率分布规律出发,根据泊松分布的基本特征,通过数学证明了信息安全事件发生频数服从泊松分布,并采用国家互联网应急中心(CNCERT/CC)统计数据验证了这一理论结果.在此基础上,基于贝叶斯定理,建立了泊松分布下的信息安全事件概率计算模型.根据泊松分布的概率质量函数,计算了信息安全事件发生频数的先验概率分布;通过构建似然函数调整先验概率分布,得到信息安全事件发生频数后验概率分布;最后,采用CNCERT/CC统计数据验证了该模型的可行性和有效性.     

基于新浪微博的社交网络演化模型

随着在线社交网络的高速发展和影响力日渐扩大, 研究其演化发展规律已经成为非常重要的课题.通过抓取新浪微博的数据, 将用户划分为意见领袖和普通用户, 并建立了一个定量的两层演化模型. 在此基础上, 分析了意见领袖和普通用户之间社交影响力的差异, 研究了网络内部病毒传播机制和外部媒体因素对在线社交网络演化过程的影响, 并利用抓取的实际数据验证了模型的准确性. 研究结果对进一步探寻在线社交网络结构、社会价值观对在线信息传播的影响均有积极意义.     

Interpretation of TOF-SIMS data based on information entropy of spectra

Time-of-flight secondary ion mass spectrometry (TOF-SIMS), when used for the analysis of complex material samples, typically provides data that are complicated and challenging to understand. Therefore, additional data analysis techniques, such as multivariate analysis, are often required to facilitate the interpretation of TOF-SIMS data. In this study, a new method based on the information entropy (Shannon entropy) is proposed as an indicator of the outline characteristics of an unknown sample, such as changes in the material within the sample and mixing conditions. The Shannon entropy values are calculated using the relative intensity of every secondary ion normalized to the total ion count and reflect the diversity of secondary ions in the spectrum. Mixed samples containing two organic electroluminescence materials of different ratios, multilayers of Irganox 1010, and other organic materials were employed to evaluate the utility of Shannon entropy in the analysis of TOF-SIMS data. The findings demonstrate that the Shannon entropy of a spectrum indicates differences in materials and changes in the conditions of a material in a sample without the need for peak identification or the knowledge of specific peaks corresponding to the materials in the sample.     

Wavelet subspace decomposition of thermal infrared images for defect detection in artworks

Health of ancient artworks must be routinely monitored for their adequate preservation. Faults in these artworks may develop over time and must be identified as precisely as possible. The classical acoustic testing techniques, being invasive, risk causing permanent damage during periodic inspections. Infrared thermometry offers a promising solution to map faults in artworks. It involves heating the artwork and recording its thermal response using infrared camera. A novel strategy based on pseudo-random binary excitation principle is used in this work to suppress the risks associated with prolonged heating. The objective of this work is to develop an automatic scheme for detecting faults in the captured images. An efficient scheme based on wavelet based subspace decomposition is developed which favors identification of, the otherwise invisible, weaker faults. Two major problems addressed in this work are the selection of the optimal wavelet basis and the subspace level selection. A novel criterion based on regional mutual information is proposed for the latter. The approach is successfully tested on a laboratory based sample as well as real artworks. A new contrast enhancement metric is developed to demonstrate the quantitative efficiency of the algorithm. The algorithm is successfully deployed for both laboratory based and real artworks.