WSN中基于任播的新型分层路由算法

传感器网络已成为一种重要、新型的信息获取和处理技术,路由协议作为其中的一种支撑技术占有重要地位.文章在简要介绍并分析现有的路由算法的基础上,提出了一种新型的基于任播的分层路由算法;算法在节能、灵活性、容错性、QOS、延迟及负载平衡等方面都有一定程度的提高;最后,展望了Anycast协议在传感器网络中的应用前景.     

SLEACH： Secure Low.Energy Adaptive Clustering Hierarchy Protocol for Wireless Sensor Networks

LEACH (Low-Energy Adaptive Clustering Hierarchy) protocol is a basic clustering-based routing protocol of sensor networks. In this paper, we present the design of SLEACH, a secure extension for the LEACH protocol. We divide SLEACH into four phases and fit inexpensive cryptographic operations to each part of the protocol functionality to create an efficient, practical protocol. Then we give security analyses of SLEACH. Our security analyses show that our scheme is robust against any external attacker or compromised nodes in the sensor network     

Summing up the noise in gene networks

Random fluctuations in genetic networks are inevitable as chemical reactions are probabilistic and many genes, RNAs and proteins are present in low numbers per cell. Such 'noise' affects all life processes and has recently been measured using green fluorescent protein (GFP). Two studies show that negative feedback suppresses noise, and three others identify the sources of noise in gene expression. Here I critically analyse these studies and present a simple equation that unifies and extends both the mathematical and biological perspectives.     

Lateral gene transfer and the nature of bacterial innovation

Unlike eukaryotes, which evolve principally through the modification of existing genetic information, bacteria have obtained a significant proportion of their genetic diversity through the acquisition of sequences from distantly related organisms. Horizontal gene transfer produces extremely dynamic genomes in which substantial amounts of DNA are introduced into and deleted from the chromosome. These lateral transfers have effectively changed the ecological and pathogenic character of bacterial species.     

Expression of a bacterial modification methylase gene in yeast

Methylation of specific cytosines in the DNA is generally believed to play some role in the regulation of gene expression in eukaryotes. However, some eukaryotes, such as Drosophila and yeast (S. Hattman, personal communication) seem not to contain 5-methylcytosine in their DNA. It would be interesting to test, how gene expression in such organisms would respond to the methylation of specific cytosines in the genome. As a first step towards this goal, we have introduced the gene encoding the Bacillus sphaericus R modification methylase, which methylates the internal cytosine within the recognition sequence 5'-GGCC, into yeast cells. Southern-type hybridization to DNAs isolated from the transformed yeast clones revealed that the yeast plasmid carrying the prokaryotic methylase gene, as well as the two chromosomal genes tested (his3 and leu2) were methylated, whereas the bulk of the yeast DNA remained largely unmethylated. This indicates that the Bacillus sphaericus modification methylase was expressed in yeast but it modified only certain parts of the yeast DNA.     

Emerging properties of animal gene regulatory networks

Gene regulatory networks (GRNs) provide system level explanations of developmental and physiological functions in the terms of the genomic regulatory code. Depending on their developmental functions, GRNs differ in their degree of hierarchy, and also in the types of modular sub-circuit of which they are composed, although there is a commonly employed sub-circuit repertoire. Mathematical modelling of some types of GRN sub-circuit has deepened biological understanding of the functions they mediate. The structural organization of various kinds of GRN reflects their roles in the life process, and causally illuminates both developmental and evolutionary process.     

共有基因模块构建大规模基因调控网络

目的 提出一种利用共有基因模块构建大规模基因调控网络算法(Common Gene Mod-ules Network,CGMN),有效降低传统基因调控网络构建基因节点规模较大的基因调控网络(包含几百个,甚至几千个基因节点)时时间复杂度过大的缺陷.方法 CGMN算法从基因表达数据出发,采用6种常用聚类算法把基因表达模式相似的基因聚类成功能模块,找出6种聚类方法的共有模块,并将其作为功能模块基因节点,采用局部贝叶斯网络(Local Bayesian Network,LBN)算法构建功能模块基因-基因调控网络.结果 与结论 大规模细胞周期基因表达数据集上仿真实验结果表明,搜索共有模块压缩基因节点数目策略,能够有效降低大规模基因调控网络重构时间复杂度,且验证了CGMN算法构建大规模基因调控网络的有效性.     

Stable expression of the bacterial neor gene in Leishmania enriettii

Molecular genetic studies in parasitic protozoa have been hindered by the lack of methods for the introduction and expression of modified or foreign genes in these organisms. Two recent reports described the transient expression of the bacterial chloramphenicol acetyl transferase (CAT) gene under the control of parasite-specific sequences. We now describe the stable expression of a selectable marker, the gene for neomycin resistance (neor) in Leishmania enriettii. A chimaeric gene containing the neor gene inserted between two alpha-tubulin intergenic sequences was introduced into the cells and drug-resistant L. enriettii were observed which stably expressed the neor gene. One goal of this work was to analyse the sequences necessary for trans-splicing of messenger RNA, as trypanosomatids have a novel process of RNA trans-splicing, described initially in Trypanosome brucei and subsequently in several other trypanosomatids, including L. enriettii. Many trypanosomatid genes are arranged in tandem arrays and the intergenic sequences contain both the splice acceptor site for the addition of the spliced leader sequence and a putative polyadenylation site. Messenger RNA isolated from several different neor L. enrietti lines contained the spliced leader sequence joined to the neor gene at the position of the splice acceptor site in the alpha-tubulin intergenic sequence. The neor mRNA was also polyadenylated. Plasmid DNA is present within the drug-resistant organisms and appears to be extrachromosomal. The development of these methods allows the functional analysis of sequences necessary for trans-splicing.     

Sexual reproduction selects for robustness and negative epistasis in artificial gene networks

The mutational deterministic hypothesis for the origin and maintenance of sexual reproduction posits that sex enhances the ability of natural selection to purge deleterious mutations after recombination brings them together into single genomes. This explanation requires negative epistasis, a type of genetic interaction where mutations are more harmful in combination than expected from their separate effects. The conceptual appeal of the mutational deterministic hypothesis has been offset by our inability to identify the mechanistic and evolutionary bases of negative epistasis. Here we show that negative epistasis can evolve as a consequence of sexual reproduction itself. Using an artificial gene network model, we find that recombination between gene networks imposes selection for genetic robustness, and that negative epistasis evolves as a by-product of this selection. Our results suggest that sexual reproduction selects for conditions that favour its own maintenance, a case of evolution forging its own path.     

Mapping and characterization of two relevance networks from SNP and gene levels

Variations of gene expression and DNA sequence are genetically associated. The goal of this study was to build genetic networks to map from SNPs to gene expressions and to characterize the two different kinds of networks. We employed mutual information to evaluate the strength of SNP–SNP and gene–gene associations based on SNPs identity by descent (IBD) data and differences of gene expressions. We applied the approach to one dataset of Genetics of Gene Expression in Humans, and discovered that both the SNP relevance network and the gene relevance network approximated the scale-free topology. We also found that 12.09% of SNP–SNP interactions matched 24.49% of gene–gene interactions, which was consistent with that of the previous studies. Finally, we identified 49 hub SNPs and 115 hub genes in their relevance networks, in which 27 hub SNPs were associated with 25 hub genes.     

动词的类义及其层级——动词类义系列研究之一

从中文信息处理的角度提出了动词类义的概念 ,讨论了动词类义的层级问题 ,并且谈到了动词类义研究的实践意义。动词类义的提出将为中文信息处理技术注入新的活力 ,有望解决一些现行技术中的瓶颈问题。     

基于动态Bayesian网络的基因调控网络建模

为了精确建模与推断基因调控网络,提出一种基于动态Bayesian网络的多数据融合方法(SP-DBN).该方法利用结构期望最大算法进行未知结构学习,基于粒子滤波方法完成参数学习,可有效处理数据缺失与噪声问题,更好地捕捉数据中固有的动态特性,并通过其先验结构,在基因表达数据的基础上,自然地融合转录因子绑定位点等多数据源信息.基于酿酒酵母的真实数据,实验结果表明: 对于仅采用基因表达数据的情况, SP-DBN的敏感度与特异度分别提高到19%和95%;融入绑定位点数据后, SP-DBN的敏感度可从19%进一步提升至20%, 而特异度则仍保持在95%的水平.     

由基因调控网络数据分析揭示振荡斑图的功能结构

自然和社会系统的许多实际问题都可以用复杂网络动力学来描述,特别是生物网络和社会网络的应用最为广泛.人们已经积累了各种网络行为的大量数据,如何提出合理的物理思想和有效的数学方法来分析这些数据、从中提取有用的信息;从这些信息出发,理解在许多实际过程中由复杂的网络拓扑结构产生的简单动力学关系,并辨识支持各种网络动力学行为的自组织结构,是一个重要的课题.本文综述了其中一种研究方法.以生物学基因调控网络(Gene Regulatory Network,GRN)为研究对象,提出了一种功能权重(Functional Weight,FW)计算方法.通过FW方法定量计算在GRN的振荡动力学中不同调控作用(称为作用边)的重要性.进一步研究发现在各种GRN中这种FW的分布普遍极不均匀,绝大部分作用边具有很小权重(弱作用边),只有少数边具有大的权重(强作用边).而这些强作用边构成的子网络比原网络简单得不可比拟,但它们揭示了网络节点之间的相互作用关系并控制着整个网络的动力学行为.由这些强作用边构成的网络,我们可以辨识GRN的功能骨架和振荡核心子网络.振荡核心起到网络振荡源的作用,而振荡骨架则成为网络中信号传播的主要路径.FW方法可以广泛应用到不同尺寸、不同调控规则(AND,OR等形式)和不同动力学行为(周期振荡、混沌动力学和暂态过程)的GRNs,并且由FW分析出发我们可以对GRN动力学进行有效调控.     

Neutrino mass hierarchy and lepton flavor mixing

In the standard model of particle physics there are three species of neutrinos whose masses were originally assumed to be zero. But the discovery of solar and atmospheric neutrino oscillations indicates that neutrinos are massive and lepton flavors are mixed. In this brief review we first give an overview of our current knowledge about the neutrino mass spectrum and lepton flavor mixing angles, and then comment on the seesaw mechanisms which allow us to understand the origin of tiny neutrino masses. We pay particular attention to the nearly tri-bi-maximal neutrino mixing pattern and the Friedberg-Lee symmetry to derive it. A relatively promising possibility of detecting hot and warm neutrino dark matter in the Universe will also be discussed.     

动词的类义及其层级--动词类义系列研究之一

从中文信息处理的角度提出了动词类义的概念，讨论了动词类义的层级问题，并且谈到了动词类义研究的实践意义。动词类义的提出将为中文信息处理技术注入新的活力，有望解决一些现行技术中的瓶颈问题。