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.     

The frequency of CFVD speed report for highway traffic

The control signals of cellular networks have been used to infer the traffic conditions of the road network. In particular, consecutive handover events are being used to estimate the traffic speed. During traffic congestion, consecutive handover events may be rare because vehicles move slowly, and thus very few or no speed reports would be generated from the congested area.However, the traffic speed report rate during traffic congestion has not been investigated in the literature. In this paper, we present an analytic model to estimate the speed report rate from cellular network signaling in steady traffic conditions, that is, the traffic speed and flow are assumed constant. Real field trial data were used to validate our analytic model. In addition, computer simulations were conducted to study how speed reports are generated in dynamic traffic conditions when traffic speed and flow change rapidly. Our study indicates that in a typical cell of length 1.5 km with a typical expected call holding time of 1 min, no speed report was generated from a congested three‐lane highway. Our study demonstrates that the lack of speed reports from consecutive handover events during rush hours indicates severe traffic congestion, and new methods that can estimate traffic speed from cellular network data during severe traffic congestion need to be developed. Copyright © 2013 John Wiley & Sons, Ltd.     

基于CNN的键盘电磁信息泄漏识别检测方法

针对键盘电磁信息安全问题,分析了PS/2键盘的工作原理以及信号特征,提出一种基于深度学习的检测方法。该方法针对键盘设备的电磁泄漏信号特征,对卷积神经网络(CNN)结构进行了适应性调整;结合改进的梯度加权类激活映射方法,实现了对键盘电磁信息的智能识别和精准定位。对4个按键的电磁信号进行测试,分类准确率达到了98%;在噪声环境下的分类准确率也达到了81%。将梯度加权类激活映射方法及其改进方法对键盘电磁信息的定位效果进行了对比,实验结果证明改进后的方法定位效果更佳。     

基于视觉辐条图案识别方法的蓝宝石引晶机制研究

工业生产蓝宝石晶体过程中,引晶步骤有着至关重要的地位。引晶必须在温度梯度较小,温度分布趋于稳定的条件下进行。目前,工业生产蓝宝石主要依靠人工经验操控籽晶杆实现引晶操作,但是人工引晶操作的准确性不高会导致成品品质不佳、资源浪费。为此,本文提出一种基于蓝宝石视觉辐条图案识别方法来检测蓝宝石熔体状态自由液面状态,从而实现一种高效率引晶的机制。此方法利用经典骨架化算法细化辐条图案,Harris算子实现特征信息的提取,提取的特征信息放入运动轨迹模型中判断熔体稳定性,分析液面温度分布稳定性从而实现引晶。结果表明,此算法具有有效性,蓝宝石晶体引晶效率大大提高,生产出的成品良率也有提升,可有效指导蓝宝石的工业生产。     

信息融合系统效能灰色评估模型与算法

根据信息融合系统效能评估的需求,建立了基于层次结构的信息融合系统效能评估指标体系,并运用灰色理论方法讨论了效能评估模型和评估算法．通过仿真举例,结果表明该算法简单方便．模型及算法有效可行,评价结果具有客观性．     

基于像全息技术的资料存储

文中利用像全息技术,对二维文字资料作了全息存储,并对实验结果进行了分析,不仅 提高了存诸质量,而且为今后的全息显示打下了基础。     

Gaussian states as minimum uncertainty states

In bosonic fields, Gaussian states, which consist of a rather wide family of states including coherent states, squeezed states, thermal states, etc., have many classical-like features, and are usually defined from the mathematical perspective in terms of characteristic functions. It is well known that some special Gaussian states, such as coherent states, are minimum uncertainty states for the conventional Heisenberg uncertainty relation involving canonical pair of position and momentum observables. A natural question arises as whether all Gaussian states can be characterized as minimum uncertainty states. In this work, we show that indeed Gaussian states coincide with minimum uncertainty states for an information-theoretic refinement of the conventional uncertainty relation established in Luo (2005) [40]. This characterization puts Gaussian states on a novel basis of physical significance.     

Channel-Supermodular Entropies: Order Theory and an Application to Query Anonymization

This work introduces channel-supermodular entropies, a subset of quasi-concave entropies. Channel-supermodularity is a property shared by some of the most commonly used entropies in the literature, including Arimoto–Rényi conditional entropies (which include Shannon and min-entropy as special cases), k-tries entropies, and guessing entropy. Based on channel-supermodularity, new preorders for channels that strictly include degradedness and inclusion (or Shannon ordering) are defined, and these preorders are shown to provide a sufficient condition for the more-capable and capacity ordering, not only for Shannon entropy but also regarding analogous concepts for other entropy measures. The theory developed is then applied in the context of query anonymization. We introduce a greedy algorithm based on channel-supermodularity for query anonymization and prove its optimality, in terms of information leakage, for all symmetric channel-supermodular entropies.