果蝇体极性基因网络的稳定性分析

果蝇的全基因组的序列测定早已完成,但是,对于基因之间是如何相互调控以实现复杂的生物功能,还需要深入的研究.认识并解析复杂的基因调控网络的构成和动力学机制,已成为现代生命科学中的前沿课题之一.在本文中,我们重点研究了果蝇的胚胎发育过程中图式形成的体极性基因网络调控.这一调控是通过相邻细胞中的基因网络的相互影响而达成的.本文主要考察这种基因网络调控对于初始条件的稳定性,以此说明生物胚胎发育对于初始条件的相对稳定性.我们发现该调控系统对于特定位置的干扰有极好的稳定性,对于整个系统的小干扰有良好的稳定性.     

基于相关反馈的视频检索算法

针对信息检索中如何提高检索的精度问题,提出了一个基于相关反馈的视频检索算法。利用信号在神经网络中来回传递实现自动相关反馈,提高了检索精度,且最大限度地减少了相关反馈中人的参与,最后检索的结果是与查询最接近的一段视频片段。给出了神经网络的构造和具体的检索算法,并与基于关键帧的视频检索方法进行了比较。实验结果表明,用该算法检索的准确度比用基于关键帧的视频检索方法平均提高6%以上。     

考虑网络韧性的三级轴辐式物流网络模型及算法研究

为了实现城市物流运作的集约化，并尽可能降低因突发事件导致的物流供需中断，以物流节点定位和通道布局为落脚点，研究了三级轴辐式物流网络的多目标规划。考虑轴辐式网络的结构约束、多级节点间的连通关系限制，以多级轴辐点选址、轴辐点间的连通关系及强度为决策变量，以网络建设成本最小和网络韧性度最大为目标函数，构建三级轴辐式物流网络模型。结合模型的特点设计了具有双层结构的遗传算法，其中外层为三段编码结构的小生境Pareto遗传算法，用于求解多目标规划，内层为0-1编码的遗传算法，用于求解网络韧性度。以某区域14个节点城市作为案例，验证模型及算法的有效性，并将优化结果与两类传统的单目标物流网络进行了比较。研究结果表明：双层遗传算法能够有效求解三级轴辐式物流网络规划模型；选取案例计算得到的Pareto最优解参与比较分析，优化结果与传统三级轴辐式物流网络相比，网络韧性度提高了6倍，但网络建设成本也随之增加；与单纯以韧性度最大化为优化目标的物流网络相比，网络建设成本降低了7倍，网络韧性度也随之降低。可见提出的双目标三级轴辐式物流网络模型实现了网络建设成本和网络韧性度间的均衡，对于追求具备一定抗毁性能的轴辐式物流网络规划人员，具有参考和应用价值。     

Evidence for dynamically organized modularity in the yeast protein-protein interaction network

In apparently scale-free protein-protein interaction networks, or 'interactome' networks, most proteins interact with few partners, whereas a small but significant proportion of proteins, the 'hubs', interact with many partners. Both biological and non-biological scale-free networks are particularly resistant to random node removal but are extremely sensitive to the targeted removal of hubs. A link between the potential scale-free topology of interactome networks and genetic robustness seems to exist, because knockouts of yeast genes encoding hubs are approximately threefold more likely to confer lethality than those of non-hubs. Here we investigate how hubs might contribute to robustness and other cellular properties for protein-protein interactions dynamically regulated both in time and in space. We uncovered two types of hub: 'party' hubs, which interact with most of their partners simultaneously, and 'date' hubs, which bind their different partners at different times or locations. Both in silico studies of network connectivity and genetic interactions described in vivo support a model of organized modularity in which date hubs organize the proteome, connecting biological processes--or modules--to each other, whereas party hubs function inside modules.     

Genetic background of phenotypic variation

A noteworthy feature of the living world is its bewildering variability. A key issue in several biological disciplines is the achievement of an understanding of the hereditary basis of this variability. Two opposing, but not necessarily irreconcilable conceptions attempt to explain the underlying mechanism. The gene function paradigm postulates that phenotypic variance is generated by the polymorphism in the coding sequences of genes. However, comparisons of a great number of homologous gene and protein sequences have revealed that they predominantly remained functionally conserved even across distantly related phylogenic taxa. Alternatively, the gene regulation paradigm assumes that differences in the cis-regulatory region of genes do account for phenotype variation within species. An extension of this latter concept is that phenotypic variability is generated by the polymorphism in the overall gene expression profiles of gene networks. In other words, the activity of a particular gene is a system property determined both by the cis-regulatory sequences of the given genes and by the other genes of a gene network, whose expressions vary among individuals, too. Novel proponents of gene function paradigm claim that functional genetic variance within the coding sequences of regulatory genes is critical for the generation of morphological polymorphism. Note, however, that these developmental genes play direct regulatory roles in the control of gene expression.     

基于深度学习的汽车轮毂缺陷自动分割技术

针对建立轮毂无损检测智能化平台的需要,本文提出一种基于深度学习算法的轮毂缺陷自动分割方法,利用卷积神经网络的结构和径向基函数神经网络的非线性特点,构造一种深度学习网络结构来模拟人类的视觉感知。本文依据汽车轮毂X射线图像,利用U-Net网络来训练轮毂缺陷分割模型,并在感兴趣区域的基础上模拟人脑层次感知系统,该层次感知系统能识别感兴趣区域的灰度像素,通过深度学习分层网络和卷积神经网络,逐层提取缺陷区域的内在特征,从而实现轮毂缺陷的自动分割。实验表明本方法针对复杂轮毂缺陷的识别率达到90%以上,且识别时间开销大约5ms/张,优于传统方法。可见该方法能够满足轮毂缺陷自动分割的需求,具有潜在的应用前景。     

基因调控网络的父节点筛选贝叶斯建模方法

在构建基因调控网络的方法中,贝叶斯网络模型可以直观地表达基因间的调控关系,但在结构学习时的复杂度极高,使得网络建模效率较低且规模有限.因此,本文提出一种基于父节点筛选的贝叶斯网络(parent node screening based Bayesian network, PS-BN)建模方法.PS-BN方法将关联模型与贝叶斯网络模型相结合,在充分利用贝叶斯网络模型结构学习搜索策略的前提下,先基于父节点筛选方法去除部分冗余信息,以达到缩减搜索空间的目的.实验结果表明,与传统的贝叶斯网络模型方法相比,PS-BN方法极大提升了基因调控网络构建效率,同时准确率有所提高.     

Investigation of gene expression profiles in coronary heart disease and functional analysis of target gene

The research outlined here includes constitution of the differential gene expression profile by means of oligonucleotide gene microarray and functional analysis of the target gene for coronary heart disease (CHD). In a microarray screening experiment, the predominance of inflammation- and immune-related genes is presented in the expression profile of 107 differential genes based on the analysis of gene ontology and gene pathway. IL-8, an inflammatory factor, is identified as one of the genes that were markedly up-regulated in CHD. The plasma level of IL-8 is significantly raised in patients with CHD (n = 30) compared with healthy controls (n = 40), which underscores the clinical relevance of the in vitro finding. The further functional analysis shows that IL-8 affects platelet aggregation percentage, expression of CD62p and platelet aggregation morphology in 12 healthy volunteers to some extent. These findings suggest the relevance of inflammation and immune responses to CHD at the DNA level. Moreover, IL-8 may be involved in the pathogenesis of CHD through the pathway of platelet activation. Supported by the National Natural Science Foundation of China (Grant No. 90409021)     

Statistical properties of Chinese semantic networks

Almost all language networks in word and syntactic levels are small-world and scale-free. This raises the questions of whether a language network in deeper semantic or cognitive level also has the similar properties. To answer the question, we built up a Chinese semantic network based on a treebank with semantic role （argument structure） annotation and investigated its global statistical properties. The results show that although semantic network is also small-world and scale-free, it is different from syntactic network in hierarchical structure and K-Nearest-Neighbor correlation.     

基于表达谱分析筛选肾母细胞瘤关键基因

为探究肾母细胞瘤(Nephroblastoma)发生的关键基因,并筛选出潜在的治疗靶点及生物标志,采用由GEO数据库获取的基因芯片GSE11151和GSE53224,经归一化处理后,通过GO和KEGG分析筛选出差异基因,并通过构建蛋白互作网络获得其中的关键基因.总计获得差异基因404个,其中上调基因385个,下调基因19个.PMCH、CCR5、CCR7、RGS1和KNG1作为关键基因,涉及趋化因子信号通路、G蛋白偶联信号通路,参与肿瘤微环境的形成.这5个关键基因在肾母细胞瘤的发生中有着重要作用,并可能作为潜在治疗靶点及生物标志.     

基于生物信息学方法分析GABRD基因在结肠癌中的表达及预后情况

采用生物信息学方法探讨GABRD基因在结肠癌样本中的表达及预后情况。通过UCSC XENA下载33种肿瘤类型和正常组织的RNA序列数据和相关临床数据,使用R软件分析GABRD基因在结肠癌样本中的表达,并筛选共表达基因,对其进行富集分析;分析GABRD基因对结肠癌患者生存及预后的影响,并建立预后列线图;构建GABRD基因的蛋白质-蛋白质相互作用(protein-proteininteraction, PPI)网络并筛选关键模块及枢纽基因,验证枢纽基因的生存及临床诊断价值。结果表明：GABRD基因在结肠癌样本中高表达并影响患者生存,筛选得到369个共表达基因,基因本体论(gene ontology, GO)功能富集发现其主要参与G蛋白偶联等生物学过程,京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)通路富集显示其主要参与AMPK等信号通路;构建出由51个节点和523个连接组成的PPI网络,筛选枢纽基因5个,其中2个显著影响生存,5个具有临床诊断价值。综上,GABRD基因在结肠癌样本中高表达,影响结肠癌患者生存及预后,可能...     

抽样对复杂网络生长机制的影响

运用基于机器学习理论开发的网络机制辨识方法，对不同抽样方案得到的抽样网络生长机制进行识别，将结果与完全网络比较,以分析抽样对网络机制的影响.研究表明，不同抽样方案对网络生长机制具有不可忽视的影响.在抽样绩效方面，中枢链式抽样具有较好的网络机制保持能力；而对比网络结构特征与网络机制，中枢抽样和链式抽样对网络机制的影响更显著.此外，各抽样方案对网络机制的影响随网络类型的不同有一定差异，这表明在实践中有必要根据网络类型选择恰当的抽样方法.     

基于网络药理学与分子对接探索人参-五味子配伍治疗特发性肺间质纤维化的分子机制

基于网络药理学与分子对接方法,探讨中药人参-五味子配伍治疗特发性肺间质纤维化(idiopathic pulmonary fibrosis,IPF)的潜在分子机制.通过GeneCards、CTD、GEO等数据库预测IPF疾病靶标基因,从TCMSP平台筛选人参-五味子有效活性成分及其治疗靶标,构建中药-活性成分-靶标基因调...     

区域创新网络行为主体间信任机制研究——以江苏省高新技术开发区和大学科技园区为实证

在经济全球化、市场竞争日益加剧的背景下,创新网络行为主体要适应环境的变化,就必须在保证各自独立的前提下相互依赖,这就要求创新网络行为主体相互信任、真诚相待、信守承诺,这是维持创新网络长久生存并促进创新网络行为主体共同发展的基础。研究归纳出创新网络主体间的6种信任建立机制,以东南大学科技园和南京-鼓楼大学科技园中的创新主体为实证对象,探讨了信任建立机制以及网络成员特性对信任关系建立的影响。     

Probabilistic Analysis on Connectivity for Sensor Grids with Unreliable Nodes

0 IntroductionWireless sensor networks consist of manynodes , each containing application-specificsensors ,a wirelesstransceiver ,anda si mple proces-sor[1-4]. Sensor networks have extensive applica-tions . A large number of research results can beseenin Refs .[5-7] .This paper mainly concerns with sensor net-works that are inherently unreliable. We consider anetwork with mn nodes ,arranged in a grid over asquare region of areaA. This model was presentedin[8 ,9].Each nodeis a sensor ,and can…     

Differential expression analysis and regulatory network reconstruction for genes associated with muscle growth and adipose deposition in obese and lean pigs

During the growth and development of skeletal muscle cells and adipose cells, the regulatory mechanism of micro-effect polygenes determines porcine meat quality, carcass characteristics and other relative quantitative traits. Obese and lean type pig breeds show obvious differences in muscle growth and adipose deposition; however, the molecular mechanism underlying this phenotypic variation remains unknown. We used pathway-focused oligo microarray studies to examine the expression changes of 140 genes associated with muscle growth and adipose deposition in longissimus dorsi muscle at six growth stages （birth, 1, 2, 3, 4 and 5 months） of Landrace （a leaner, Western breed） and Taihu pigs （a fatty, indigenous, Chinese breed）. Variance analysis （ANOVA） revealed that differences in the expression of 18 genes in Landrace pigs and three genes in Taihu pigs were very significant （FDR-adjusted permutation, P 〈 0.01） and differences for 22 genes in Landrace pigs and seven genes in Taihu pigs were significant （FDR-adjusted permutation, P 〈 0.05） among six growth stages. Clustering analysis revealed a high level of significance （FDR-adjusted, P 〈 0.01） for four gene expression patterns, in which genes that strongly up-regulated were mainly associated with the positive regulation of myofiber formation and fatty acid biogenesis and genes that strongly down-regulated were mainly associated with the inhibition of cell proliferation and positive regulation of fatty acid β-oxidation. Based on a dynamic Bayesian network （DBN） model, gene regulatory networks （GRNs） were reconstructed from time-series data for each pig breed. These two GRNs initially revealed the distinct differences in physiological and biochemical aspects of muscle growth and adipose deposition between the two pig breeds; from these results, some potential key genes could be identified. Quantitative real-time RT-PCR （QRT-PCR） was used to verify the microarray data for five modulated genes, and a good correlation between     

基于网络拓扑相似性预测潜在致病基因

相关疾病基因的发现和预测是人类基因组研究的重要目标.近些年,一些研究者通过基于网络结构的方法来解决这个难题.然而,大多数方法在推理过程中仅使用了局部的网络信息,并且仅限于推理单一基因的关联.并且这些方法很少考虑到疾病-基因关联网络的网络拓扑性.笔者提出一种改进的基于二部图网络结构推理(improved network-based inference)的计算方法.该方法基于已知的疾病-基因网络拓扑相似性来发现更多潜在致病基因.文中使用的是OMIM数据库中的203种疾病的数据,通过留一交叉验证法验证实验,并获得了88.9%的AUC值.与文中提到的另外两种方法相比,该文方法能够有效地预测潜在致病基因.     

基于动态博弈的补贴模式对机场群航线网络结构的影响研究

为探讨不同补贴模式对机场群航线网络结构的影响，本文构建了关于机场、航空公司和乘客之间的动态博弈模型，通过逆向归纳法得到了纳什均衡条件. 研究结果发现：（1）不同的补贴模式对多机场航线网络结构产生重要影响，低补贴模式促使机场群倾向于形成点对点航线网络结构，反之，在高补贴模式下机场群易于形成枢纽辐射航线网络； （2）在较低的空铁联运总运营成本环境下，补贴竞争使得航空公司倾向于选择系统内的大型机场作为枢纽机场；反之，如果空铁联运总运营成本相对较高，补贴竞争使得航空公司倾向于选择小机场作为枢纽节点； （3）随航班固定成本和空铁联运总运营成本的增大，大型机场作为枢纽节点的概率逐渐减少，而小机场被选为枢纽节点的概率将逐渐增大. 随着机场群内大型机场腹地服务人口比例的增大，航空公司选择点对点航线网络的概率在减小. 研究结论能够为民航管理部门科学制定和应用航线补贴政策提供决策依据.