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Caracterização de circuitos pecuários com base em redes de movimentação de animais 基于动物移动网络的牲畜回路特征
Pub Date : 2012-10-05 DOI: 10.11606/T.10.2012.tde-24042014-075742
G. Filho, Jos e
A network is a set of nodes that are linked together by a set of edges. Networks can represent any set of objects that have relations among themselves. Communities are sets of nodes that are related in an important way, probably sharing common properties and/or playing similar roles within a network. When network analysis is applied to study the livestock movement patterns, the epidemiological units of interest (farm premises, counties, states, countries, etc.) are represented as nodes, and animal movements between the nodes are represented as the edges of a network. Unraveling a network structure, and hence the trade preferences and pathways, could be very useful to a researcher or a decision-maker. We implemented a community detection algorithm to find livestock communities that is consistent with the definition of a livestock production zone, assuming that a community is a group of farm premises in which an animal is more likely to stay during its life time than expected by chance. We applied this algorithm to the network of within animal movements made inside the State of Mato Grosso, for the year of 2007. This database holds information about 87,899 premises and 521,431 movements throughout the year, totalizing 15,844,779 animals moved. The community detection algorithm achieved a network partition that shows a clear geographical and commercial pattern, two crucial features to preventive veterinary medicine applications, and also has a meaningful interpretation in trade networks where links emerge from the choice of trader nodes.
网络是由一组边连接在一起的一组节点。网络可以表示彼此之间有关系的任何一组对象。社区是一组节点,它们以一种重要的方式相互关联,可能在网络中共享共同的属性和/或扮演相似的角色。当网络分析应用于研究牲畜运动模式时,感兴趣的流行病学单位(农场、县、州、国家等)被表示为节点,节点之间的动物运动被表示为网络的边缘。揭示一个网络结构,从而揭示贸易偏好和途径,对研究人员或决策者可能非常有用。我们实施了一种社区检测算法,以寻找符合牲畜生产区定义的牲畜社区,假设社区是一组农场场所,其中动物在其一生中比偶然预期更有可能留在其中。我们将这个算法应用到2007年马托格罗索州内部动物运动的网络中。该数据库保存了全年87,899个场所和521,431次移动的信息,总共移动了15,844,779只动物。社区检测算法实现了网络分区,显示了明确的地理和商业模式,这是预防兽药应用的两个关键特征,并且在贸易网络中也有意义的解释,其中链接来自贸易商节点的选择。
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引用次数: 1
Iterative Approximate Solutions of Kinetic Equations for Reversible Enzyme Reactions 可逆酶反应动力学方程的迭代近似解
Pub Date : 2012-08-03 DOI: 10.4236/NS.2013.56091
S. Khoshnaw
We study kinetic models of reversible enzyme reactions and compare two techniques for analytic approximate solutions of the model. Analytic approximate solutions of non-linear reaction equations for reversible enzyme reactions are calculated using the Homotopy Perturbation Method (HPM) and the Simple Iteration Method (SIM). The results of the approximations are similar. The Matlab programs are included in appendices.
我们研究了可逆酶反应的动力学模型,并比较了两种方法对该模型的解析近似解。采用同伦摄动法和简单迭代法计算了可逆酶反应非线性方程的解析近似解。近似的结果是相似的。Matlab程序包含在附录中。
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引用次数: 9
Ising Models for Inferring Network Structure From Spike Data 从峰值数据推断网络结构的Ising模型
Pub Date : 2011-06-09 DOI: 10.1201/B14756-31
J. Hertz, Y. Roudi, J. Tyrcha
Now that spike trains from many neurons can be recorded simultaneously, there is a need for methods to decode these data to learn about the networks that these neurons are part of. One approach to this problem is to adjust the parameters of a simple model network to make its spike trains resemble the data as much as possible. The connections in the model network can then give us an idea of how the real neurons that generated the data are connected and how they influence each other. In this chapter we describe how to do this for the simplest kind of model: an Ising network. We derive algorithms for finding the best model connection strengths for fitting a given data set, as well as faster approximate algorithms based on mean field theory. We test the performance of these algorithms on data from model networks and experiments.
既然可以同时记录来自许多神经元的尖峰序列,那么就需要一种方法来解码这些数据,以了解这些神经元所处的网络。解决这个问题的一种方法是调整一个简单模型网络的参数,使其峰值列车尽可能地与数据相似。模型网络中的连接可以让我们了解生成数据的真实神经元是如何连接的,以及它们是如何相互影响的。在这一章中,我们将描述如何对最简单的一种模型:一个伊辛网络做到这一点。我们推导了用于寻找拟合给定数据集的最佳模型连接强度的算法,以及基于平均场理论的更快的近似算法。我们在模型网络和实验数据上测试了这些算法的性能。
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引用次数: 24
Errors in Length-weight Parameters at FishBase.org 在FishBase.org中的长度-权重参数错误
Pub Date : 2011-04-27 DOI: 10.1038/NPRE.2011.5927.1
Simeon Cole-Fletcher, Lucas Marin-Salcedo, A. Rana, M. Courtney
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引用次数: 13
Stochastic Modeling in Systems Biology 系统生物学中的随机建模
Pub Date : 2011-04-23 DOI: 10.1166/JAMA.2012.1007
J. Lei
Many cellular behaviors are regulated by gene regulation networks, kinetics of which is one of the main subjects in the study of systems biology. Because of the low number molecules in these reacting systems, stochastic effects are significant. In recent years, stochasticity in modeling the kinetics of gene regulation networks have been drawing the attention of many researchers. This paper is a self contained review trying to provide an overview of stochastic modeling. I will introduce the derivation of the main equations in modeling the biochemical systems with intrinsic noise (chemical master equation, Fokker-Plan equation, reaction rate equation, chemical Langevin equation), and will discuss the relations between these formulations. The mathematical formulations for systems with fluctuations in kinetic parameters are also discussed. Finally, I will introduce the exact stochastic simulation algorithm and the approximate explicit tau-leaping method for making numerical simulations.
许多细胞行为受基因调控网络的调控,其动力学是系统生物学研究的主要课题之一。由于这些反应体系中的分子数很少,因此随机效应很重要。近年来,基因调控网络动力学建模的随机性受到了许多研究者的关注。本文是一篇自成一体的综述,试图提供随机建模的概述。我将介绍具有本征噪声的生化系统建模的主要方程(化学主方程、福克-计划方程、反应速率方程、化学朗之万方程)的推导,并讨论这些公式之间的关系。讨论了动力学参数波动系统的数学表达式。最后,我将介绍精确随机模拟算法和近似显式tau跳跃法进行数值模拟。
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引用次数: 30
Monte-Carlo Simulation of a Multi-Dimensional Switch-Like Model of Stem Cell Differentiation 干细胞分化多维开关模型的蒙特卡罗模拟
Pub Date : 2011-02-28 DOI: 10.5772/15474
M. Andrecut
The process controlling the diferentiation of stem, or progenitor, cells into one specific functional direction is called lineage specification. An important characteristic of this process is the multi-lineage priming, which requires the simultaneous expression of lineage-specific genes. Prior to commitment to a certain lineage, it has been observed that these genes exhibit intermediate values of their expression levels. Multi-lineage differentiation has been reported for various progenitor cells, and it has been explained through the bifurcation of a metastable state. During the differentiation process the dynamics of the core regulatory network follows a bifurcation, where the metastable state, corresponding to the progenitor cell, is destabilized and the system is forced to choose between the possible developmental alternatives. While this approach gives a reasonable interpretation of the cell fate decision process, it fails to explain the multi-lineage priming characteristic. Here, we describe a new multi-dimensional switch-like model that captures both the process of cell fate decision and the phenomenon of multi-lineage priming. We show that in the symmetrical interaction case, the system exhibits a new type of degenerate bifurcation, characterized by a critical hyperplane, containing an infinite number of critical steady states. This critical hyperplane may be interpreted as the support for the multi-lineage priming states of the progenitor. Also, the cell fate decision (the multi-stability and switching behavior) can be explained by a symmetry breaking in the parameter space of this critical hyperplane. These analytical results are confirmed by Monte-Carlo simulations of the corresponding chemical master equations.
控制干细胞或祖细胞向特定功能方向分化的过程称为谱系规范。这个过程的一个重要特征是多谱系启动,这需要谱系特异性基因的同时表达。在承诺到某个谱系之前,已经观察到这些基因表现出其表达水平的中间值。多种祖细胞的多系分化已被报道,并已通过亚稳态的分叉来解释。在分化过程中,核心调控网络的动力学遵循一个分支,其中亚稳态(对应于祖细胞)被破坏,系统被迫在可能的发育选择中做出选择。虽然这种方法给出了细胞命运决定过程的合理解释,但它无法解释多谱系启动特征。在这里,我们描述了一个新的多维开关模型,该模型捕获了细胞命运决定过程和多谱系启动现象。我们证明了在对称相互作用情况下,系统表现出一种新型的简并分岔,其特征是一个包含无限个临界稳态的临界超平面。这个临界超平面可以解释为支持多谱系启动状态的祖先。此外,细胞命运的决定(多稳定性和切换行为)可以用临界超平面参数空间中的对称性破缺来解释。这些分析结果通过相应的化学主方程的蒙特卡罗模拟得到了证实。
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引用次数: 6
Sparse Partitioning: Nonlinear regression with binary or tertiary predictors, with application to association studies 稀疏分割:二元或三级预测因子的非线性回归,应用于关联研究
Pub Date : 2011-01-04 DOI: 10.1214/10-AOAS411
D. Speed, Simon Tavar'e
This paper presents Sparse Partitioning, a Bayesian method for identifying predictors that either individually or in combination with others affect a response variable. The method is designed for regression problems involving binary or tertiary predictors and allows the number of predictors to exceed the size of the sample, two properties which make it well suited for association studies. Sparse Partitioning differs from other regression methods by placing no restrictions on how the predictors may influence the response. To compensate for this generality, Sparse Partitioning implements a novel way of exploring the model space. It searches for high posterior probability partitions of the predictor set, where each partition defines groups of predictors that jointly influence the response. The result is a robust method that requires no prior knowledge of the true predictor--response relationship. Testing on simulated data suggests Sparse Partitioning will typically match the performance of an existing method on a data set which obeys the existing method's model assumptions. When these assumptions are violated, Sparse Partitioning will generally offer superior performance.
本文提出了稀疏分区,一种贝叶斯方法,用于识别单独或与其他因素联合影响响应变量的预测因子。该方法是为涉及二元或三级预测因子的回归问题而设计的,并且允许预测因子的数量超过样本的大小,这两个特性使其非常适合关联研究。稀疏分区与其他回归方法的不同之处在于,它不限制预测因子如何影响响应。为了弥补这种通用性,稀疏分区实现了一种探索模型空间的新方法。它搜索预测集的高后验概率分区,其中每个分区定义共同影响响应的预测器组。结果是一个健壮的方法,不需要真正的预测-响应关系的先验知识。在模拟数据上的测试表明,稀疏分区通常会在遵循现有方法模型假设的数据集上匹配现有方法的性能。当这些假设被违反时,稀疏分区通常会提供更好的性能。
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引用次数: 4
Non-extensive radiobiology Non-extensive放射生物学
Pub Date : 2010-06-17 DOI: 10.1063/1.3573620
O. Sotolongo-Grau, Daniel Rodr'iguez-P'erez, J. Antoranz, O. Sotolongo-Costa
The expression of survival factors for radiation damaged cells is based on probabilistic assumptions and experimentally fitted for each tumor, radiation and conditions. Here we show how the simplest of these radiobiological models can be derived from the maximum entropy principle of the classical Boltzmann-Gibbs expression. We extend this derivation using the Tsallis entropy and a cutoff hypothesis, motivated by clinical observations. A generalization of the exponential, the logarithm and the product to a non-extensive framework, provides a simple formula for the survival fraction corresponding to the application of several radiation doses on a living tissue. The obtained expression shows a remarkable agreement with the experimental data found in the literature, also providing a new interpretation of some of the parameters introduced anew. It is also shown how the presented formalism may has direct application in radiotherapy treatment optimization through the definition of the potential effect difference, simply calculated between the tumour and the surrounding tissue.
辐射损伤细胞存活因子的表达基于概率假设,并对每种肿瘤、辐射和条件进行实验拟合。在这里,我们展示了如何从经典玻尔兹曼-吉布斯表达式的最大熵原理中推导出这些最简单的放射生物学模型。我们使用Tsallis熵和截断假设来扩展这个推导,这是由临床观察激发的。将指数、对数和乘积推广到一个不广泛的框架,就提供了一个简单的公式,计算在活组织上施加若干辐射剂量所对应的生存分数。所得表达式与文献中的实验数据非常吻合,并对新引入的一些参数提供了新的解释。通过定义肿瘤和周围组织之间简单计算的潜在效应差异,也显示了所提出的形式如何直接应用于放疗治疗的优化。
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引用次数: 4
Gains in Power from Structured Two-Sample Tests of Means on Graphs 图上均值的结构化双样本检验的功率增益
Pub Date : 2010-06-03 DOI: 10.1214/11-AOAS528
Laurent Jacob, P. Neuvial, S. Dudoit
We consider multivariate two-sample tests of means, where the location shift between the two populations is expected to be related to a known graph structure. An important application of such tests is the detection of differentially expressed genes between two patient populations, as shifts in expression levels are expected to be coherent with the structure of graphs reflecting gene properties such as biological process, molecular function, regulation, or metabolism. For a fixed graph of interest, we demonstrate that accounting for graph structure can yield more powerful tests under the assumption of smooth distribution shift on the graph. We also investigate the identification of non-homogeneous subgraphs of a given large graph, which poses both computational and multiple testing problems. The relevance and benefits of the proposed approach are illustrated on synthetic data and on breast cancer gene expression data analyzed in context of KEGG pathways.
我们考虑多变量双样本均值检验,其中两个总体之间的位置转移预计与已知的图结构相关。这种测试的一个重要应用是检测两个患者群体之间的差异表达基因,因为预计表达水平的变化与反映基因特性(如生物过程、分子功能、调节或代谢)的图形结构一致。对于一个固定的感兴趣的图,我们证明了在图上平滑分布移动的假设下,考虑图结构可以产生更强大的检验。我们还研究了给定大图的非齐次子图的识别,这将带来计算和多重测试问题。在合成数据和KEGG通路背景下分析的乳腺癌基因表达数据上说明了所提出方法的相关性和益处。
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引用次数: 35
Making it Possible: Constructing a Reliable Mechanism from a Finite Trajectory 使其成为可能:从有限轨迹构建可靠的机构
Pub Date : 2009-12-20 DOI: 10.1002/9781118131374.CH13
O. Flomenbom
Deducing an underlying multi-substate on-off kinetic scheme (KS) from the statistical properties of a two-state trajectory is the aim from many experiments in biophysics and chemistry, such as, ion channel recordings, enzymatic activity and structural dynamics of bio-molecules. Doing so is almost always impossible, as the mapping of a KS into a two-state trajectory leads to the loss of information about the KS (almost always). Here, we present the optimal way to solve this problem. It is based on unique forms of reduced dimensions (RD). RD forms are on-off networks with connections only between substates of different states, where the connections can have multi-exponential waiting time probability density functions (WT-PDFs). A RD form has the simplest toplogy that can reproduce a given data. In theory, only a single RD form can be constructed from the full data (hence its uniqueness), still this task is not easy when dealing with finite data. For doing so, a toolbox made of known statistical methods in data analysis and new statistical methods and numerical algorithms develped for this problem is presented. Our toolbox is self-contained: it builds a mechanism based only on the information it extracts from the data. The implementation of the toolbox on the data is fast. The toolbox is automated and is available for academic research upon electronic request.
从两态轨迹的统计特性中推断出潜在的多亚态开关动力学方案(KS)是生物物理和化学中许多实验的目标,例如离子通道记录、酶活性和生物分子结构动力学。这样做几乎总是不可能的,因为将KS映射到双态轨迹会导致有关KS的信息丢失(几乎总是)。在此,我们提出了解决这一问题的最优方法。它基于独特的降维形式(RD)。RD形式是只在不同状态的子状态之间有连接的开断网络,这种连接可以具有多指数等待时间概率密度函数(wt - pdf)。RD表单具有可以重现给定数据的最简单拓扑。理论上,从完整的数据中只能构造一个RD表单(因此它的唯一性),但是在处理有限的数据时,这个任务并不容易。为此,提出了一个由数据分析中已知的统计方法和为此问题开发的新的统计方法和数值算法组成的工具箱。我们的工具箱是自包含的:它仅基于从数据中提取的信息构建机制。工具箱对数据的实现速度很快。该工具箱是自动化的,可用于电子要求的学术研究。
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引用次数: 2
期刊
arXiv: Quantitative Methods
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