An improved algorithm for nucleic acid secondary structure display

An improved algorithm for the display of nucleic acid secondary structures is presented. It is particularly suitable for large sequence segments and it automatically generates an aesthetically pleasing display of the structure with very limited overlap of strands. Structural similarities in different structures are conserved in the display thus greatly aiding structural homology comparisons. Using the algorithm, we illustrate the effect of ribosome translocation on the secondary structure of a rat neuropeptide messenger RNA.     

A secondary and tertiary structure editor for nucleic acids

A major difficulty in the evaluation of secondary and tertiary structures of nucleic acids is the lack of convenient methods for their construction and representation. As a first step in a study of the symbolic representation of biopolymers, we report the development of a structure editor written in Pascal, permitting model construction on the screen of a personal computer. The program calculates energies for helical regions, allows user-defined helices and displays the secondary structure of a nucleic acid based on a user-selected set of helices. Screen and printer outputs can be in the form of a backbone or the letters of the primary sequence. The molecule can then be displayed in a format which simulates its three-dimensional structure. Using appropriate glasses, the molecule can be viewed on the screen in three dimensions. Other options include the manipulation of helices and single-stranded regions which results in changes in the spatial relationship between different regions of the molecule. The editor requires an IBM or compatible PC, 640 kbyte memory and a medium or high resolution graphics card.     

Computational study of protein secondary structure elements: Ramachandran plots revisited

Potential energy surface (PES) were built for nineteen amino acids using density functional theory (PW91 and DFT M062X/6-311**). Examining the energy as a function of the φ/ψ dihedral angles in the allowed regions of the Ramachandran plot, amino acid groups that share common patterns on their PES plots and global minima were identified. These patterns show partial correlation with their structural and pharmacophoric features. Differences between these computational results and the experimentally noted permitted conformations of each amino acid are rationalized on the basis of attractive intra- and inter-molecular non-covalent interactions. The present data are focused on the intrinsic properties of an amino acid – an element which to our knowledge is typically ignored, as larger models are always used for the sake of similarity to real biological polypeptides.     

含伪结的RNA分子二级结构预测

预测含伪结的RNA分子二级结构是生物信息学的一个研究难点。利用多分类支持向量机结合贝叶斯神经网络针对含伪结的RNA分子二级结构进行预测。利用多分类支持向量机进行预测,输出端得到相应碱基的平面伪结结构的E-NSSEL（Extend New Secondary Structure Element Label）类别标签。使用碱基已预测的结果通过贝叶斯神经网络进行修正,并恢复RNA分子二级结构。使用该方法能有效地改善含伪结的RNA分子二级结构的预测效果。     

蛋白质二级结构的协同训练预测方法*

针对蛋白质二级结构机器学习预测方法,忽略氨基酸疏水性特征以及氨基酸之间的长程作用和准确率不高的现状,进行了比较实验分析。采用氨基酸对应的疏水能值替换蛋白质中相应的氨基酸,得到疏水能值的序列实验结果表明,用长的疏水能值序列,训练BP网络,对长程作用起主导的E结构的预测效果好。由于Profile编码特征和疏水能值特征是独立的冗余视图,基于协同训练思想,提出Cotraining算法。该算法的主要步骤是在Profile特征空间训练SVM分类器,在疏水性特征空间训练BP神经网络分类器,协同对氨基酸二级结构进行预测     

多视频摘要技术:方法、应用及挑战

多视频摘要技术近年来受到了国内外学者的广泛关注,它是指通过对视频结构和内容的分析,从多个相关视频文件中提取出有意义的部分,将它们以一定方式进行组合,形成简洁的、能够充分表现语义内容的概要,目的是提供快捷的浏览和查询服务。目前该技术还处于起步阶段,实际的应用系统很少,有关体系结构、技术方法仍需要深入研究,更多的应用方向还有待开拓。在介绍研究意义的基础上,对多视频摘要的研究现状和主要方法进行了归纳、评述,探讨了一些应用方向,指出了目前研究面临的重点问题以及发展趋势。     

Tactile interfaces: technologies,applications and challenges

Tactile interfaces are used to communicate information through the sense of touch, which is an area of growing interest in the research community. Potential applications include virtual training for surgeons, remotely touching materials via the Internet, automotive industry, active interfaces for blind persons, and sensory substitution devices.     

Containerization technologies: taxonomies,applications and challenges

Modern scientific research challenges require new technologies, integrated tools, reusable and complex experiments in distributed computing infrastructures. But above all, computing power for efficient data processing and analyzing. Containers technologies have emerged as a new paradigm to address such intensive scientific applications problems. Their easy deployment in a reasonable amount of time and the few required computational resource make them more suitable. Containers are considered light virtualization solutions. They enable performance isolation and flexible deployment of complex, parallel, and high-performance systems. Moreover, they gained popularity to modernize and migrate scientific applications in computing infrastructure management. Additionally, they reduce computational time processing. In this paper, we first give an overview of virtualization and containerization technologies. We discuss the taxonomies of containerization technologies of the literature, and then we provide a new one that covers and completes those proposed in the literature. We identify the most important application domains of containerization and their technological progress. Furthermore, we discuss the performance metrics used in most containerization techniques. Finally, we point out research gaps in the related aspects of containerization technology that require more research.

     

计算摄像学:核心、方法与应用

针对现有计算机视觉、图形学、信号处理、数字图像处理、应用光学等领域无法通过现有成像模型与装置及计算方法获取足够目标场景信息的难题,计算摄像学研究提出新的成像机制与对应的计算重构方法,在光信号观测领域另辟蹊径,创新性地将视觉信息处理与计算前移至成像过程,从而极大地提高了信息优化计算的自由度,能够在维度、尺度与分辨率上实现质的突破,从而观测到传统成像系统看不清与看不见的场景信息.本文沿着计算摄像学思路、方法与目标三条主线,对国内外研究现状进行分析与综述,期望能够帮助读者更快地了解及进入相关研究.     

蛋白质二级结构预测方法研究

为提高蛋白质二级结构预测精度,提出一种新的网络模型和编码方法。首先利用基因表达式编程（GEP）的全局搜索能力同时进化设计神经网络的结构和连接权;其次,对神经网络输入层编码进行了改进,添加了氨基酸残基所处的疏水环境。用PDBSelect25中的36条蛋白质共6 122个残基进行测试,结果表明提出的网络模型和编码方法能有效提高蛋白质二级结构预测的精度。     

Inferring consensus structure from nucleic acid sequences

This paper presents an unsupervised inference method for determining the higher-order structure from sequence data. The method is general, but in this paper it is applied to nucleic acid sequences in determining the secondary (2-D) and tertiary (3-D) structure of the macromolecule. The method evaluates position - position interdependence of the sequence using an information measure known as expected mutual information. The expected mutual information is calculated for each pair of positions and the chi-square test is used to screen statistically significant position pairs. In the calculation of expected mutual information, an unbiased probability estimator is used to overcome the problem associated with zero observation in conserved sites. A selection criterion based on known structural constraints of the strongest interdependent position pairs is applied yielding position pairs most indicative of secondary and tertiary interactions. The method has been tested using tRNA and 5S rRNA sequences with very good results.     

Projection displays: New technologies,challenges, and applications

The achievable color gamut and light output of projection displays based on light‐emitting diodes (LEDs), phosphor conversion, and lasers are discussed. The color appearance phenomena, colorfulness, and the Helmholtz–Kohlrausch effect are discussed in the context of LED and laser illumination of projection displays, as well as some pitfalls concerning the interpretation of the Helmholtz–Kohlrausch effect. Also the laser speckle phenomenon and the characterization of it are addressed. The importance of both the American National Standards Institute (ANSI) contrast and the sequential contrast of projectors, as well as the discrepancy between measured and perceived contrasts, are explained. Visibility criteria for contouring artifacts are explained and compared with new emerging electro‐optical transfer functions that are more adapted to this issue. Stereoscopic solutions and early prototypes of autostereoscopic multi‐view, super multi‐view projection displays, and electro‐holographic displays are discussed as well as the limiting factors of these systems in the context of display resolution, and LED and laser light sources.     

Computational depth: Concept and applications

We introduce Computational Depth, a measure for the amount of “nonrandom” or “useful” information in a string by considering the difference of various Kolmogorov complexity measures. We investigate three instantiations of Computational Depth:

•$•$

Basic Computational Depth, a clean notion capturing the spirit of Bennett's Logical Depth. We show that a Turing machine M runs in time polynomial on average over the time-bounded universal distribution if and only if for all inputs x, M uses time exponential in the basic computational depth of x.     

蛋白质二级结构预测方法的评价

蛋白质结构预测是后基因组时代的一项重要任务，蛋白质二级结构预测是蛋白质结构预测的关键步骤。现在一般认为，如果蛋白质二级结构的预测准确率达到80％的话，就可以基本准确地预测一个蛋白质分子的三维空间结构。目前蛋白质二级结构预测的方法不断涌现，提供二级结构预测的网站也逐渐增多。为给广大研究工作者在选择使用这些预测方法时提供一种参考，文章采用统一的标准对10种比较重要而且有效的方法进行测试，并在此基础上做出评价和分析，这10种方法是：GORI、PROF、GORⅣ、NNPREDICT、PHDsec、SSpro v 2．0、PSIPRED、PREDATOR、SOPMA和APSSP2。比较结果显示：APSSP2、SSpro v 2．0和PSIPRED方法的预测效果较好，可以作为使用时的首选方案，其中尤其以APSSP2方法的预测效果最佳。     

蛋白质二级结构预测的一种新的编码方式

编码方式是影响蛋白质二级结构预测准确率的重要因素之一。针对单序列蛋白质二级结构预测问题,提出了一种新的综合编码方法。该编码是根据氨基酸出现在每种二级结构中的倾向因子以及氨基酸的疏水性值进行分类,并以二进制形式来表示每类氨基酸的编码方法。在相同的实验条件下,首先用不同的编码方式对数据集CB513进行编码,然后采用支持向量机的方法进行训练建模预测。实验结果显示提出编码的预测准确率比20位正交编码和5位编码分别高出1.48%和10.68%。可见,该编码比较适合非同源或低同源蛋白质结构预测。     

Ultra-reliable and low-latency communications:applications,opportunities and challenges

In the upcoming 5G and beyond systems,ultra-reliable and low latency communication(URLLC)has been considered as the key enabler to support diverse mission-criti...     

Methods for discovering novel motifs in nucleic acid sequences

We describe a computer tool to aid the discovery of new motifs in nucleic acid sequences. A typical use would be to analyse a set of upstream regions from a family of related genes in order to find possible control sequences. The heart of the method is the creation of dictionaries of related subsequences. These dictionaries can then be analysed to look for the commonest or best-defined subsequences, those that occur in the highest number of different sequences, or for those in equivalent positions within the family. We show the application of the method to a set of E. coli promoter sequences.     

基于动态规划的DNA二级结构预测算法

基于DNA分子二级结构的结构稳定性和热力学稳定性,提出一种预测DNA分子二级结构的算法.利用基于矩阵的动态规划算法求解DNA分子最大碱基对匹配的所有二级结构;利用Nearest-Neighbor热力学模型计算所有结构的自由能,自由能在阈值范围内的即为DNA分子可能的二级结构.将实验结果与RNAstructure软件结果进行对比,对比结果表明,该方法具有较高的准确率和覆盖范围.     

结合蛋白质二级结构信息预测蛋白质空间结构中的二硫键*

在蛋白质空间结构预测中,二硫键的确定可以大大减少蛋白质构象的搜索空间。为提高二硫键预测的准确率,对形成二硫键的半胱氨酸及其周围的氨基酸残基在蛋白质二级结构形成上的偏性进行了分析,并提出将蛋白质二级结构信息加入到BP神经网络预测模型的输入编码信息中。研究对象为从SWISS-PROT数据库中选取的252条蛋白质序列,随机均分4组,对预测准确率进行4-交叉验证。各项准确率均比未加入蛋白质二级结构信息前,有明显提高。结果表明,结合蛋白质二级结构信息的编码方式是可行且有效的。