质心法:受类别驱动的RNA二级结构预测方法

RNA二级结构预测问题是计算分子生物学中的一个重要问题.目前的RNA二级结构预测模型和算法都是把待测结构RNA的一级序列作为输入,仅根据输入的序列预测其二级结构.这样做丢失了待测RNA的类别信息,进而无法利用同类别RNA二级结构的保守性.在实际的生物学研究中,对于关心二级结构的RNA,其类别往往是已知的.本文提出一种新的RNA二级结构预测思路:结合类别信息、根据已知的近似形状细化RNA的二级结构.这种方法尤其适用于长度较短、保守性好的非编码RNA.该方法的一个关键问题是如何将一个序列按照近似的形状进行折叠.为此本文首次提出了茎区的"质心"和"质心距"的概念,并且给出了一个结合了Hopfield网络和类别信息的RNA二级结构预测算法.实验表明本文提出的方法在所测试ncRNA分子上效果好于目前的方法.     

基于免疫与神经网络的 RNA 二级结构预测

RNA二级结构预测是生物信息学领域的一个热点问题，通过计算机仿真模拟和数学建模计算来“预测”这些结构信息，具有较好的参考价值以及可信度，并能够节省大量的时间与成本。本文通过改进传统的RNA二级结构预测算法，提出了混沌Hopfield神经网络算法算法。算法以茎区作为神经元，同时采用相似距离函数、对神经元的初始值进行优化，在获得初步结果后，通过使用混沌函数优化结果，使得其跳出局部最优解，提高了全局搜索能力，能简单、快速规范的获得最优解。仿真结果表明，本算法能够有效的对RNA二级结构进行预测，有较好的的预测效果。     

基于进化神经网络的RNA二级结构预测方法

本文提出了一种基于进化神经网络预测RNA二级结构的方法.该方法利用进化算法优化了神经网络结构和权值,改善了传统BP人工神经网络容易陷入局部最优等缺陷.实验结果表明该算法能够获得一个最优结构和权值的神经网络,利用该网络去预测不带伪结的RNA二级结构能获得理想的效果,敏感性和相关系数都有所提升,证明了该改进算法的可行性.     

SARS病毒RNA二级结构及RNAi作用靶位的计算机预测

该研究使用两个基于不同算法的RNA二级结构预测软件RNAstructure 3．71和RNAdraw V1．1b2，通过对SARS冠状病毒BJ01和TOR02株的基因组序列的二级结构进行计算机初步模拟，得到可能用于RNAi作用药物设计的6个结构．     

RNA二级结构预测的神经网络方法

针对利用经典的随机上下文无关文法(SCFG)等模型对RNA(R ibonucle ic ac id)二级结构进行预测时,存在计算复杂性问题,该文给出了RNA二级结构的“新二级结构单元标签”(N SSEL)表示,相应提出了一种新的RNA二级结构预测的神经网络方法。这种二级结构的N SSEL表示格式很容易转换成常用的CT格式。基于tRNA数据集的实验表明,在完全相同的训练与测试数据集下,该方法,较之性能最好的B JK与BK 2等SCFG模型,其预测精度与相关系数都有所提高,证明了所提方法的可行性与有效性。由于神经网络启发式方法不存在计算时间复杂性问题,因此可望将此法用于预测SCFG等算法难以处理的大于1 000个碱基的长RNA序列的折叠问题。     

基于茎区的神经网络方法预测RNA二级结构

RNA二级结构预测是生物信息学的一个重要研究内容.作为预测方法之一的神经网络已被广泛应用于蛋白质结构预测,但在RNA二级结构的应用甚少.本文改进传统预测RNA二级结构的Hopfield神经网络.算法以茎作为网络神经元,通过与相似结构茎区的比对,初始化神经元,并据此修改网络的激励系数.实验把改进后算法与改进前2种算法、M...     

基于改进适应度函数的RNA结构预测

RNA二级结构预测是生物信息学的重要研究内容。本文提出了一个新的启发式算法进行带假节的RNA结构预测。本文首先通过对RNA序列的若干特征和RNA二级结构进行相关性分析,从中选择跟RNA结构有较大相关性的特征,然后依据遗传算法、综合自由能、被选择茎区的条数以及被选择茎区的平均长度等特征来构造打分函数预测RNA的结构。本文对该方法进行了测试,结果表明本文所采用的从特征分析中得出的打分函数以及通过启发式算法来叠加茎的方法是有效的,在对tRNA以及5SrRNA等序列的预测上相比单纯的自由能最小方法有更高的准确性。并且该方法进一步推广到预测含假结的RNA的二级结构时也有较好的结果。     

RNA二级结构预测的计算语言学方法

RNA是一类重要的生物大分子,计算语言学方法把RNA序列看成是具有一定语法规则的语句,通过这些语法规划来分析RNA序列中存在的碱基配对关系,也就是它的语义,从而得到该序列的二级结构,本文阐述了该类方法预测RNA二级结构的原理及实现。     

RNA二级结构点括号图与CT文件表示法的相互转换算法研究

由于RNA二级结构表示方法对其功能和相似性的研究具有关键性作用,通过对现有RNA二级结构的各种表示方法进行讨论,重点介绍了点括号图表示法和二级结构平面图文本（CT文件）表示法,给出二者之间的相互转换算法,并通过实例验证了该转换算法准确、有效,可为研究RNA二级结构的相似性提供有效的数据支持.     

一个预测RNA二级结构的回溯算法

本文讨论了一个预测RNA二级结构的回溯算法。该算法根据极大基配对的原则按字典顺序产生所有可能的二级结构。它的时间复杂性是O(n~2),空间复杂性是O(n)。     

An Index mechanism for multi-scale view in spatial databases

There are numerous geometric objects stored in the spatial databases. An importance function in a spatial database is that users can browse the geometric objects as a map efficiently. Thus the spatial database should display the geometric objects users concern about swiftly onto the display window. This process includes two operations:retrieve data from database and then draw them onto screen. Accordingly, to improve the efficiency, we should try to reduce time of both retrieving object and displaying them. The former can be achieved with the aid of spatial index such as R-tree, the latter require to simplify the objects. Simplification means that objects are shown with sufficient but not with unnecessary detail which depend on the scale of browse. So the major problem is how to retrieve data at different detail level efficiently. This paper introduces the implementation of a multi-scale index in the spatial database SISP (Spatial Information Shared Platform) which is generalized from R-tree. The difference between the generalization and the R-tree lies on two facets: One is that every node and geometric object in the generalization is assigned with a importance value which denote the importance of them, and every vertex in the objects are assigned with a importance value,too. The importance value can be use to decide which data should be retrieve from disk in a query. The other difference is that geometric objects in the generalization are divided into one or more sub-blocks, and vertexes are total ordered by their importance value. With the help of the generalized R-tree, one can easily retrieve data at different detail levels.Some experiments are performed on real-life data to evaluate the performance of solutions that separately use normal spatial index and multi-scale spatial index. The results show that the solution using multi-scale index in SISP is satisfying.     

Characterization of Ordovician carbonate reservoirs, southeastern Saskatchewan, Canada

The discovery of the prolific Ordovician Red River reservoirs in 1995 in southeastern Saskatchewan was the catalyst for extensive exploration activity which resulted in the discovery of more than 15 new Red River pools. The best yields of Red River production to date have been from dolomite reservoirs. Understanding the processes of dolomitization is, therefore, crucial for the prediction of the connectivity, spatial distribution and heterogeneity of dolomite reservoirs.The Red River reservoirs in the Midale area consist of 3～4 thin dolomitized zones, with a total thickness of about 20 m, which occur at the top of the Yeoman Formation. Two types of replacement dolomite were recognized in the Red River reservoir: dolomitized burrow infills and dolomitized host matrix. The spatial distribution of dolomite suggests that burrowing organisms played an important role in facilitating the fluid flow in the backfilled sediments. This resulted in penecontemporaneous dolomitization of burrow infills by normal seawater. The dolomite in the host matrix is interpreted as having occurred at shallow burial by evaporitic seawater during precipitation of Lake Almar anhydrite that immediately overlies the Yeoman Formation. However, the low δ18O values of dolomited burrow infills (-5.9‰～ -7.8‰, PDB) and matrix dolomites (-6.6‰～ -8.1‰, avg. -7.4‰ PDB) compared to the estimated values for the late Ordovician marine dolomite could be attributed to modification and alteration of dolomite at higher temperatures during deeper burial, which could also be responsible for its 87Sr/86Sr ratios (0.7084～0.7088) that are higher than suggested for the late Ordovician seawaters (0.7078～0.7080). The trace amounts of saddle dolomite cement in the Red River carbonates are probably related to "cannibalization" of earlier replacement dolomite during the chemical compaction.     

A computer generator for randomly layered structures

AcomputergeneratorforrandomlylayeredstructuresYUJia shun1,2,HEZhen hua2(1.TheInstituteofGeologicalandNuclearSciences,NewZealand;2.StateKeyLaboratoryofOilandGasReservoirGeologyandExploitation,ChengduUniversityofTechnology,China)Abstract:Analgorithmisintrod…     

Perspherical Approaches for Electrons in Atoms and Charged Excitons in Quantum Wells

Instead of following Fock’s expansion,we solve the Schrodinger equation for some quantum mechanical manybody systems such as electrons in atoms and charged excitons in quantum wells in a similar way in hyperspherical coordinates by expanding the wave functions into orthonormal complete basis sets of the hyperspherical hannonics(HHs)of hyperangles and generalized Laguerre polynomials(GLPs)of the hyperradius.This leads the equation to     

Advances in broadband wireless communications under high-mobility scenarios

Future mobile communication systems aim at providing very high data transmission rates, even in high-mobility scenarios such as high-speed wheel-track trains, maglev trains, highway vehicles, airplanes, guided missiles or spacecraft. A particularly important commercial application is the strong and increasing worldwide demand for high- speed broadband wireless communications （up to 574.8 km/ h test speeds or 380 km/h commercial speeds） in railways, providing data, voice and video services for applications such as onboard entertainment services to passengers, train control, train dispatch, train sensor status handling and sur- veillance. In such high-mobility scenarios, there are a number of communication challenges, including fast hand- over, location updating, high-speed channel modeling, estimation and equalization, anti-Doppler spreading tech- niques, fast power control, and dedicated network architec- ture. Because signal transmission in very high-speed scenarios will inevitably experience serious deterioration, it is imperative to develop key broadband mobile communi- cation techniques for such high-speed vehicles.     

Wuhan University Journal of Natural Sciences TOTAL CONTENTS

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海南岛地体及其毗邻陆缘晚中生代—新生代古地磁研究和构造演化

本文叙述了对海南岛及其毗邻大陆边缘白垩纪到第四纪地层岩石进行古地磁研究的全部工作过程。通过分析岩石中剩余磁矢量的磁偏角及磁倾角的变化,提出海南岛白垩纪以来经历的构造演化模式如下:早期伴随顺时针旋转而向南迁移,后期伴随逆时针转动并向北运移。联系该地区及邻区的地质、地球物理资料,对海南岛上述的构造地体运动提出以下认识:北部湾内早期有一拉张作用,主要是该作用使湾内地壳显著伸长减薄,形成北部湾盆地。从而导致了海南岛的早期构造运动,而海南岛后期的构造运动则主要是受南海海底扩张的影响。海南地体运动规律的阐明对于了解北部湾油气盆地的形成演化有重要的理论和实际意义。     

Scale-based spatial data model for GIS

Being the primary media of geographical information and the elementary objects manipulated, almost all of maps adopt the layer-based model to represent geographic information in the existent GIS. However, it is difficult to extend the map represented in layer-based model. Furthermore, in Web-Based GIS, It is slow to transmit the spatial data for map viewing. In this paper, for solving the questions above, we have proposed a new method for representing the spatial data. That is scale-based model. In this model we represent maps in three levels: scale-view, block, and spatial object, and organize the maps in a set of map layers, named Scale-View, which associates some given scales.Lastly, a prototype Web-Based GIS using the proposed spatial data representation is described briefly.     

Exciton Seebeck in Molecular Systems

Various applications relevant to the exciton dynamics,such as the organic solar cell,the large-area organic light-emitting diodes and the thermoelectricity,are operating under temperature gradient.The potential abnormal behavior of the exicton dynamics driven by the temperature difference may affect the efficiency and performance of the corresponding devices.In the above situations,the exciton dynamics under temperature difference is mixed with     

Achieving Unusual States of Matter Under High Pressure

The elongation method,originally proposed by Imamura was further developed for many years in our group.As a method towards O(N)with high efficiency and high accuracy for any dimensional systems.This treatment designed for one-dimensional(ID)polymers is now available for three-dimensional(3D)systems,but geometry optimization is now possible only for 1D-systems.As an approach toward post-Hartree-Fock,it was also extended to