Thermotoga martima嗜热木聚糖酶化学修饰结果与其结构特性关系研究

应用化学修饰的实验方法,结合蛋白质结构信息的计算来研究酶蛋白中氨基酸残基化学修饰与结构信息之间的关系。以Thermotoga maritima嗜热木聚糖酶为对象,采用PDB数据库中的1VBR为模板计算其序列中色氨酸、谷氨酸、天冬氨酸的溶剂可及性、氢键、盐桥数等结构特性,并与该酶化学修饰的实验结果相对比。结果表明酶活性中心3个色氨酸中,可及性大的Trp802与Trp602两个残基对酶的活性影响较大;序列中谷氨酸与天冬氨酸的氢键、盐桥数较多,修饰其对酶的热稳定性有很大影响。此结果有助于深入了解蛋白质中与化学修饰有关的结构特性,并为基于蛋白质结构的酶蛋白改性奠定了基础。     

环糊精葡葡萄糖基转移酶热稳定性的研究

环糊精葡萄糖基转移酶(CGTase;EC 2.4.1.19)是一种重要的环糊精生产工业用酶,该转移酶能进行环化、偶合、歧化、水解4种反应.环糊精广泛的用于食品、医药、化妆品、农业和化学工业等生产领域,为了提高环糊精的产量,需要CGTase具有更高的热稳定性.合理的设计耐热蛋白已经成为研究热点.在本文中,首次使用分子动力学模拟研究CGTase热稳定性,以补充实验上不易获得的原子能级和时间相关的信息.使用同源建模方法构建环糊精葡糖基转移酶及其突变体的三维结构,研究氨基酸的突变对CGTase酶耐热性的影响,用CHARMM能量计算CGTase及其突变体的能量与酶蛋白热稳定性之间的关系.证明:氨基酸残基经过突变,突变型比野生型含带电残基更多.相应的,在蛋白天然结构中突变型CGTase中,盐桥数量增加了10%.这些电荷之间、非极性残基之间的非共价键作用力的增强,提高了突变体的刚性,降低了突变体蛋白质分子的总能量,最后增加突变体蛋白质的耐热性.     

引入序列信息的残基相互作用网络比对算法

残基相互作用网络比对,对于研究蛋白质结构与功能的关系具有重要意义.在基于网络拓扑信息进行网络比对的MAGNA算法基础上,将蛋白质的序列信息（即残基匹配度）引入到其优化函数中,确定拓扑信息和序列信息对比对的影响程度,提出适合于残基相互作用网络比对的SI-MAGNA算法.实验结果表明,SI-MAGNA算法比现有的基于网络拓扑信息的经典比对方法（GRAAL、MI-GRAAL、MAGNA和CytoGEDEVO）具有更高的边正确性（edge correctness,简称EC）.最后,使用SI-MAGNA算法对来自不同耐热温度的生物的同源蛋白质进行网络比对和分析,探索蛋白质结构对其热稳定性的影响.     

以分子动力学模拟探究苹果酸脱氢酶的嗜极机制

为了研究嗜热酶、嗜冷酶在极端温度下维持稳定性和活性的机制,本文通过分子动力学模拟的方法,从原子尺度上分析了嗜热苹果酸脱氢酶及其同源嗜冷酶的分子动力学特性。数据显示嗜热酶所形成的盐桥和氢键明显多于嗜冷酶。通过比较均方根偏差、回旋半径、氨基酸残基的柔性等值,发现嗜热酶的结构较非嗜热酶更具刚性。盐桥、氢键数目的不同和整体结构的刚柔性,很可能会是嗜热、嗜冷酶在极端温度下能维持结构稳定的主要原因。     

基于卷积长短时记忆神经网络的蛋白质二级结构预测

鉴于不同类型氨基酸的相互作用对蛋白质结构预测的影响不同,文中融合卷积神经网络和长短时记忆神经网络模型,提出卷积长短时记忆神经网络,并应用到蛋白质8类二级结构的预测中.首先基于氨基酸序列的类别信息和氨基酸结构的进化信息表示蛋白质序列,并采用卷积提取氨基酸残基之间的局部相关特征,然后利用双向长短时记忆神经网络提取蛋白质序列内部残基之间的远程相互作用,最后将提取的蛋白质的局部相关特征和远程相互作用用于蛋白质8类二级结构的预测.实验表明,相比基准方法,文中模型提高8类二级结构预测的精度,并具有良好的可扩展性.     

嗜冷嗜盐菌Halorubrum lacusprofundi中蛋白质稳定性机制的探讨

研究嗜冷嗜盐菌H.lacusprofundi中蛋白质在不同结构区域的特点,对了解其稳定的结构基础及设计新型嗜冷嗜盐蛋白具有重要意义。通过对991对同源嗜冷嗜盐菌和嗜温嗜盐菌的序列及高级结构信息进行统计学对比分析,结果表明:嗜冷嗜盐菌和嗜温嗜盐菌氨基酸组成中亮氨酸、天冬酰胺、含硫氨基酸、带电氨基酸差异显著;苏氨酸差异很显著;丙氨酸、甘氨酸、谷氨酰胺、小分子氨基酸差异极显著。其中苯丙氨酸、甘氨酸、天冬酰胺、中性氨基酸在嗜冷嗜盐菌蛋白的含量较高,亮氨酸、苏氨酸、谷氨酰胺、含硫氨基酸、小分子氨基酸在嗜温嗜盐菌中的含量较高。嗜冷嗜盐蛋白含有更多的中性氨基酸、小分子氨基酸和非极性氨基酸,从而降低蛋白质中氢键等非共价键的相互作用,提高蛋白质结构的柔韧性和可变性。     

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。     

利用序列和组合图卷积网络预测蛋白质功能

蛋白质功能的准确预测有利于推进生物医学发展,高通量测序技术的快速发展加快了蛋白质序列的提取速度,从而产生了大量未注释的蛋白质,并且新测序序列缺乏结构等生物信息,针对该问题提出了基于序列和组合图卷积网络的蛋白质功能预测模型(Protein Function Prediction using Sequences and Combined Graph Convolutional Networks, PFP-SCGCN).首先通过深度学习方法捕获蛋白质序列的多维特征信息,再通过多序列比对从蛋白质序列中提取进化耦合信息和氨基酸残基群落,然后利用进化耦合信息和氨基酸残基群落生成序列氨基酸之间两种不同连接程度的邻接矩阵,将这两种邻接矩阵与序列特征信息一起输入给组合图卷积网络进行信息融合,最后通过多个全连接层获得蛋白质功能类别信息.本文还通过分析PFP-SCGCN的特定网络层识别蛋白质功能位点,可帮助人们推测出新序列中的重要氨基酸.模型结果表明,PFP-SCGCN模型的功能预测准确率远高于对比方法,具有较好的鲁棒性,并且可以较准确的识别功能位点.     

基于贝叶斯方法的蛋白质界面残基预测

蛋白质界面残基预测是蛋白质相互作用研究中的一项基本工作,在生物制药及蛋白质功能研究方面有着重要的应用.以蛋白质中的氨基酸残基为研究对象,使用残基的溶剂可及表面积及残基的序列谱为特征集,构建了基于贝叶斯方法的蛋白质界面残基预测器.方法有效地结合了蛋白质残基特征集的条件独立性假设及贝叶斯方法在处理不确定性数据方面的优点,通过对含77个蛋白质的数据集进行实验,结果比其它方法获得了6%的准确率的提高,三维可视化的结果也表明分类器预测的有效性.     

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。     

Only connect: teaching, technology and telesis

Abstract This paper describes an approach to the design of interactive multimedia materials being developed in a European Community project. The developmental process is seen as a dialogue between technologists and teachers. This dialogue is often problematic because of the differences in training, experience and culture between them. Conditions needed for fruitful dialogue are described and the generic model for learning design used in the project is explained.     

European Community policy and the market

Abstract This paper starts with some reflections on the policy considerations and priorities which are shaping European Commission (EC) research programmes. Then it attempts to position the current projects which seek to capitalise on information and communications technologies for learning in relation to these priorities and the apparent realities of the marketplace. It concludes that while there are grounds to be optimistic about the contribution EC programmes can make to the efficiency and standard of education and training, they are still too technology driven.     

一种自适应子融合集成多分类器方法

融合集成方法已经广泛应用在模式识别领域,然而一些基分类器实时性能稳定性较差,导致多分类器融合性能差,针对上述问题本文提出了一种新的基于多分类器的子融合集成分类器系统。该方法考虑在度量层融合层次之上通过对各类基多分类器进行动态选择,票数最多的类别作为融合系统中对特征向量识别的类别,构成一种新的自适应子融合集成分类器方法。实验表明,该方法比传统的分类器以及分类融合方法识别准确率明显更高,具有更好的鲁棒性。     

Avoiding semantic and temporal gaps in developing software intensive systems

Development of software intensive systems (systems) in practice involves a series of self-contained phases for the lifecycle of a system. Semantic and temporal gaps, which occur among phases and among developer disciplines within and across phases, hinder the ongoing development of a system because of the interdependencies among phases and among disciplines. Such gaps are magnified among systems that are developed at different times by different development teams, which may limit reuse of artifacts of systems development and interoperability among the systems. This article discusses such gaps and a systems development process for avoiding them.     

Designing economic np control charts: A programmed simulation approach

This paper presents control charts models and the necessary simulation software for the location of economic values of the control parameters. The simulation program is written in FORTRAN, requires only 10K of main storage, and can run on most mini and micro computers. Two models are presented - one describes the process when it is operating at full capacity and the other when the process is operating under capacity. The models allow the product quality to deteriorate to a further level before an existing out-of-control state is detected, and they can also be used in situations where no prior knowledge exists of the out-of-control causes and the resulting proportion defectives.     

The development of robot art

Going through a few examples of robot artists who are recognized worldwide, we try to analyze the deepest meaning of what is called “robot art” and the related art field definition. We also try to highlight its well-marked borders, such as kinetic sculptures, kinetic art, cyber art, and cyberpunk. A brief excursion into the importance of the context, the message, and its semiotics is also provided, case by case, together with a few hints on the history of this discipline in the light of an artistic perspective. Therefore, the aim of this article is to try to summarize the main characteristics that might classify robot art as a unique and innovative discipline, and to track down some of the principles by which a robotic artifact can or cannot be considered an art piece in terms of social, cultural, and strictly artistic interest. This work was presented in part at the 13th International Symposium on Artificial Life and Robotics, Oita, Japan, January 31–February 2, 2008     

Explanation and prediction: an architecture for default and abductive reasoning

Although there are many arguments that logic is an appropriate tool for artificial intelligence, there has been a perceived problem with the monotonicity of classical logic. This paper elaborates on the idea that reasoning should be viewed as theory formation where logic tells us the consequences of our assumptions. The two activities of predicting what is expected to be true and explaining observations are considered in a simple theory formation framework. Properties of each activity are discussed, along with a number of proposals as to what should be predicted or accepted as reasonable explanations. An architecture is proposed to combine explanation and prediction into one coherent framework. Algorithms used to implement the system as well as examples from a running implementation are given.     

Three Process Perspectives: Organizations, Teams, and People

This paper provides the author's personal views and perspectives on software process improvement. Starting with his first work on technology assessment in IBM over 20 years ago, Watts Humphrey describes the process improvement work he has been directly involved in. This includes the development of the early process assessment methods, the original design of the CMM, and the introduction of the Personal Software Process (PSP)^SM and Team Software Process (TSP){^SM}. In addition to describing the original motivation for this work, the author also reviews many of the problems he and his associates encountered and why they solved them the way they did. He also comments on the outstanding issues and likely directions for future work. Finally, this work has built on the experiences and contributions of many people. Mr. Humphrey only describes work that he was personally involved in and he names many of the key contributors. However, so many people have been involved in this work that a full list of the important participants would be impractical.     

基于复小波噪声方差显著修正的SAR图像去噪

提出了一种基于复小波域统计建模与噪声方差估计显著性修正相结合的合成孔径雷达(Synthetic Aperture Radar,SAR)图像斑点噪声滤波方法。该方法首先通过对数变换将乘性噪声模型转化为加性噪声模型,然后对变换后的图像进行双树复小波变换(Dualtree Complex Wavelet Transform,DCWT),并对复数小波系数的统计分布进行建模。在此先验分布的基础上,通过运用贝叶斯估计方法从含噪系数中恢复原始系数,达到滤除噪声的目的。实验结果表明该方法在去除噪声的同时保留了图像的细节信息,取得了很好的降噪效果。     

基于QTE的蒙古文显示机制研究与实现

蒙古语言是中国蒙古族使用的通用语言,由于蒙古文区别于其他文字的书写方式和其自身变形机制等特点,在很多通用的文字处理引擎中都不被支持。在嵌入式产品开发与应用领域中Linux加QTE已经成为流行方式。该文给出了一种在QTE环境上实现基于标准Unicode的蒙古文点阵显示和变形算法, 并自定义了支持蒙古文的QTE组件,扩展了QTE功能,为在Linux加QTE方式的嵌入式体系结构中处理蒙古文提供了一种解决方法。