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Mining residue contacts in proteins using local structure predictions 利用局部结构预测挖掘蛋白质中的残馀接触
Mohammed J. Zaki, Shanrong Jin, C. Bystroff
In this paper, we develop data mining techniques to predict 3D contact potentials among protein residues (or amino acids) based on the hierarchical nucleation-propagation model of protein folding. We apply a hybrid approach, using a hidden Markov model (HMM) to extract folding initiation sites, and then apply association mining to discover contact potentials. The new hybrid approach achieves accuracy results better than those reported previously.
在本文中,我们基于蛋白质折叠的分层成核-传播模型开发了数据挖掘技术来预测蛋白质残基(或氨基酸)之间的三维接触电位。我们采用了一种混合方法,使用隐马尔可夫模型(HMM)提取折叠起始位点,然后使用关联挖掘来发现接触电位。新的混合方法比以前报道的方法获得了更好的精度结果。
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引用次数: 57
Achieving interoperability of genome databases through intelligent Web mediators 通过智能Web中介实现基因组数据库的互操作性
H. Jamil
Resolving the tension between the flexibilities offered by a database query language and the so-called "user friendliness" supported by a form-based or menu-driven database query interface is undoubtedly a daunting task. However, researchers believe that the flexibilities offered by a declarative query language should be fully exploited to harvest genetic solutions within the wealth of information offered by genomics and proteomics. Additionally, the need to query databases at different abstraction levels, in a set-based fashion, and to process the queries efficiently by resolving the structural and semantic disparities among the genomic databases in a user-transparent way has never been more evident than in recent years. Inspired by such needs, we have developed an SQL3-compliant database query language called the Genomic Query Language (GQL) for manipulating globally distributed genomic databases that are publicly accessible. GQL, an SQL-like language, is given a source-independent syntax and exploits a high-level global view of the underlying databases. The uniqueness of this language relies heavily on the supporting interface through which all communications take place and the interoperability of databases behind firewalls is realized. In this paper, we describe how the Web-based interface we have built for GQL makes it possible to understand the scheme of any participating database, assimilates the syntactic and semantic information into the global view, and responds to user queries. The interface is autonomous for many genomic databases and is also fully self-maintainable.
解决数据库查询语言提供的灵活性与基于表单或菜单驱动的数据库查询接口所支持的所谓“用户友好性”之间的紧张关系无疑是一项艰巨的任务。然而,研究人员认为,应该充分利用声明性查询语言提供的灵活性,从基因组学和蛋白质组学提供的丰富信息中获取遗传解决方案。此外,近年来,以基于集合的方式在不同抽象层次上查询数据库,并通过以用户透明的方式解决基因组数据库之间的结构和语义差异来有效地处理查询的需求从未像现在这样明显。受这些需求的启发,我们开发了一种符合sql3的数据库查询语言,称为基因组查询语言(Genomic query language, GQL),用于操作可公开访问的全球分布式基因组数据库。GQL是一种类似sql的语言,具有独立于源的语法,并利用底层数据库的高级全局视图。这种语言的独特性在很大程度上依赖于支持接口,所有通信都通过该接口进行,防火墙后面的数据库的互操作性也通过该接口实现。在本文中,我们描述了我们为GQL构建的基于web的接口如何能够理解任何参与数据库的方案,将语法和语义信息吸收到全局视图中,并响应用户查询。该接口对于许多基因组数据库来说是自治的,并且完全可以自我维护。
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引用次数: 9
Phylogenetic tree reconstruction using self-adaptive genetic algorithm 基于自适应遗传算法的系统发育树重建
A. Skourikhine
We have developed a self-adaptive genetic algorithm (GA) for a maximum-likelihood reconstruction of phylogenetic trees using nucleotide sequence data. It resulted in a faster reconstruction of the trees with less computing power and automatic self-adjustment of settings of the optimization algorithm parameters. We focused on the use of GAs with self-adaptive control parameters and GA integration with phylogenetic tree representations. The developed technique is applicable to any nucleotide sequences inferring evolutionary relationships between organisms.
我们开发了一种自适应遗传算法(GA),用于使用核苷酸序列数据进行系统发育树的最大似然重建。该方法可以在较小的计算能力下实现更快的树重建,并可以自动调整优化算法参数的设置。我们着重于使用具有自适应控制参数的遗传算法和具有系统发育树表示的遗传算法集成。所开发的技术适用于推断生物体之间进化关系的任何核苷酸序列。
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引用次数: 17
Hierarchical control for artificial hearts 人工心脏的层次控制
J. Boston, J. Antaki, M. Simaan
This paper describes a hierarchical control structure to regulate the operation of turbo-hydrodynamic heart assist devices. The goal of the controller is to provide performance that satisfies as many clinical constraints as possible, consistent with the amount and validity of hemodynamic measurements available. Local control algorithms built into the devices maintain pump speed at a reference value, and the primary problem addressed by the hierarchical controller is to determine the desired reference. At the top of the hierarchy is a supervisor that maintains a model of the pump and the patient and continuously evaluates the available estimates of hemodynamic variables, reliability of the patient model, past history of the patient, and validity of the information available. Depending on this evaluation, the supervisor uses either heuristic criteria or a multi-objective optimization algorithm to determine the reference speed. It also evaluates the operating status of the device.
本文介绍了一种调节涡轮流体动力心脏辅助装置运行的分层控制结构。控制器的目标是提供满足尽可能多的临床限制的性能,与可用的血流动力学测量的数量和有效性一致。内置在设备中的本地控制算法将泵转速保持在参考值,分层控制器解决的主要问题是确定所需的参考值。在层级的顶端是一个主管,负责维护泵和患者的模型,并持续评估血液动力学变量的可用估计、患者模型的可靠性、患者过去的病史和可用信息的有效性。根据这一评估,监督者使用启发式标准或多目标优化算法来确定参考速度。它还评估设备的运行状态。
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引用次数: 4
Pencil beam scanning: a dynamical approach to proton therapy 铅笔束扫描:质子治疗的动态方法
R. Sepulchre, M. Gérard, B. Marchand, D. Prieels
Pencil Beam Scanning is a dynamic beam delivery system developed at IBA s.a. for proton therapy. The radiation field necessary to reach in a fast and robust way a prescribed 3D dose distribution is obtained by accurately controlling both the extraction of the beam from a 235 MeV accelerator and the motion of the beam spot thanks to scanning magnets. Compared to existing beam delivery systems, the hardware of the PBS system is considerably simplified while offering the possibility of accurate delivery and short treatment time. The simplification in hardware is compensated for by advanced actuation, which is the topic of the present paper.
铅笔束扫描是一种动态光束传输系统开发的IBA s.a.质子治疗。通过精确控制235mev加速器的光束提取和扫描磁体的光束点运动,可以获得快速而可靠地达到规定的三维剂量分布所需的辐射场。与现有的光束输送系统相比,PBS系统的硬件大大简化,同时提供了准确输送和短治疗时间的可能性。硬件上的简化通过先进的驱动来弥补,这是本文的主题。
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引用次数: 1
Gene mapping by haplotype pattern mining 单倍型模式挖掘的基因定位
Hannu (TT) Toivonen, P. Onkamo, Kari Vasko, V. Ollikainen, P. Sevon, H. Mannila, J. Kere
Genetic markers are being increasingly utilized in gene mapping. The discovery of associations between markers and patient phenotypes - such as a disease status - enables the identification of potential disease gene loci. The rationale is that, in diseases with a reasonable genetic contribution, diseased individuals are more likely to have associated marker alleles near the disease susceptibility gene than control individuals. We describe a new gene mapping method-haplotype pattern mining (HPM) - that is based on discovering recurrent marker patterns. We define a class of useful haplotype patterns in genetic case-control data, give an algorithm for finding disease-associated haplotypes, and show how to use them to identify disease susceptibility loci. Experimental studies show that the method has good localization power in data sets with large degrees of phenocopies and with lots of missing and erroneous data. We also demonstrate how the method can be used to discover several genes simultaneously.
遗传标记在基因定位中的应用越来越广泛。发现标记物与患者表型(如疾病状态)之间的关联,可以识别潜在的疾病基因位点。其基本原理是,在具有合理遗传贡献的疾病中,患病个体比对照个体更有可能在疾病易感基因附近拥有相关的标记等位基因。我们描述了一种新的基因定位方法-单倍型模式挖掘(HPM) -这是基于发现复发标记模式。我们在遗传病例对照数据中定义了一类有用的单倍型模式,给出了一种寻找疾病相关单倍型的算法,并展示了如何使用它们来识别疾病易感位点。实验研究表明,该方法在表型程度大、缺失数据多、错误数据多的数据集中具有良好的定位能力。我们还演示了如何使用该方法同时发现几个基因。
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引用次数: 14
Feedback analysis of calcium homeostasis and parturient paresis 钙稳态与分娩轻瘫的反馈分析
H. El-Samad, M. Khammash
In the technological and engineering sciences feedback control methods have been studied and applied extensively to man-made systems. Recently, there has been an increasing interest as to the applicability of feedback and control theory to the life sciences. In a previous paper (H. El-Samad et al., "Calcium homeostasis: a feedback control point of view," Proceedings of the 2000 American Control Conference, Chicago, Il, June 2000), the applicability of control theory to the analysis of calcium homeostasis was investigated. A mathematical model for this homeostatic mechanism was derived. Here, the authors provide an overview of this model, and then use it to study a pathological condition of the calcium regulatory mechanism in dairy cows. The clinical condition studied is referred to as parturient paresis (milk fever) and is the result of severe hypocalcemia at the time of parturition. The authors show that their mathematical feedback model for calcium homeostasis exhibits dynamic behavior that can correspond to milk fever. They then present a rigorous mathematical result that guarantees the presence of milk fever-like dynamics for a range of model parameters.
在技术和工程科学中,反馈控制方法得到了广泛的研究和应用。最近,人们对反馈和控制理论在生命科学中的适用性越来越感兴趣。在之前的一篇论文中(H. El-Samad et al.,“钙稳态:反馈控制点”,2000年美国控制会议论文集,芝加哥,伊利诺伊州,2000年6月),研究了控制论对钙稳态分析的适用性。推导了这种自稳态机制的数学模型。本文将对该模型进行概述,并利用该模型研究奶牛病理状态下钙的调节机制。所研究的临床状况被称为分娩轻瘫(乳热),是分娩时严重低钙血症的结果。作者表明,他们的钙稳态数学反馈模型显示出与牛奶热相对应的动态行为。然后,他们提出了一个严格的数学结果,以保证在一系列模型参数中存在类似牛奶热的动力学。
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引用次数: 0
A schema-based approach to building a bioinformatics database federation 基于模式的生物信息学数据库联盟构建方法
G. Kemp, N. Angelopoulos, P. Gray
Developments in our ability to integrate and analyse the data held in existing heterogeneous data resources can lead to an increase in our understanding of biological function at all levels. However, supporting ad-hoc queries across multiple data resources and correlating the data retrieved from these is still difficult. To address this, we are building a mediator based on the functional data model database, P/FDM, which integrates access to heterogeneous, distributed biological databases, while making use of existing search engines and indexes, without infringing on the autonomy of the underlying databases. Central to our design philosophy is the use of schemas. We have adopted a federated architecture with a five-level schema, arising from the use of the ANSI-SPARC three-level schema to describe both the existing autonomous data resources and the mediator itself. We describe the use of mapping functions and list comprehensions in query splitting, producing execution plans, code generation and result fusion. We give an example of cross-database querying involving data held locally in P/FDM systems and external data in the Sequence Retrieval System (SRS).
我们整合和分析现有异构数据资源中持有的数据的能力的发展可以增加我们对各级生物功能的理解。但是,支持跨多个数据资源的特别查询和关联从这些数据资源检索到的数据仍然很困难。为了解决这个问题,我们正在构建一个基于功能数据模型数据库P/FDM的中介,它集成了对异构、分布式生物数据库的访问,同时利用现有的搜索引擎和索引,而不侵犯底层数据库的自主权。我们设计理念的核心是模式的使用。我们采用了一个具有五层模式的联邦体系结构,这源于使用ANSI-SPARC三层模式来描述现有的自治数据资源和中介本身。我们描述了映射函数和列表推导在查询拆分、生成执行计划、代码生成和结果融合中的使用。我们给出了一个跨数据库查询的例子,涉及到P/FDM系统中本地保存的数据和序列检索系统(SRS)中的外部数据。
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引用次数: 30
Futuristic combinatorial analog computing systems: the DNA synchro solution 未来组合模拟计算系统:DNA同步解决方案
E. Hibbs
This paper discusses a combinatorial analog method of attacking the overall challenge in scientific computation - to accurately and quickly performs several types of multidimensional digital and analog computations. The paper presents a challenge to break the historical binary-driven computational paradigm. The resultant recommendation is for an electromagnetic DNA computing synchro using the intrinsic quantum properties of DNA.
本文讨论了一种组合模拟方法来应对科学计算中的整体挑战——准确、快速地进行几种多维数字和模拟计算。本文提出了打破历史上二进制驱动的计算范式的挑战。由此产生的建议是使用DNA固有的量子特性的电磁DNA计算同步器。
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引用次数: 0
A digital retina-like low level vision processor 一种类似视网膜的数字低电平视觉处理器
J. S. Mertoguno, N. Bourbakis
Presents the basic design and the simulation of a low level multi-layer vision processor that emulates to some degree the functional behavior of a human retina. This retina-like multi-layer processor is the lower part of an autonomous self-organized vision system, called Kydon, which could be used on visually impaired people with a damaged visual cerebral cortex. The retina-like processor consists of four major layers, where each is an array processor that performs a certain set of low level vision tasks, such as smoothing and light adaptation, edge detection, segmentation, line recognition and region-graph generation. At each layer the array processor is a 2-D array of kxm hexagonal identical autonomous cells that simultaneously execute certain tasks. Thus, in this paper the hardware design and the entire simulation of the retina-like processor with illustrative examples are provided.
介绍了一种低级多层视觉处理器的基本设计和仿真,该处理器在一定程度上模拟了人类视网膜的功能行为。这个类似视网膜的多层处理器是一个自主自组织视觉系统的下部,被称为Kydon,它可以用于大脑视觉皮层受损的视力受损的人。类视网膜处理器由四层组成,每层都是一个阵列处理器,执行一定的低级视觉任务,如平滑和光适应、边缘检测、分割、线识别和区域图生成。在每一层,阵列处理器是一个由kxm六边形相同的自主单元组成的二维阵列,这些单元同时执行某些任务。因此,本文给出了类视网膜处理器的硬件设计和整体仿真,并给出了实例说明。
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引用次数: 6
期刊
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering
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