Hierarchical clustering of the genetic connectivity matrix reveals the network topology of gene action on brain microstructure: An N=531 twin study

Genetic correlation (rg) analysis determines how much of the correlation between two measures is due to common genetic influences. In an analysis of 4 Tesla diffusion tensor images (DTI) from 531 healthy young adult twins and their siblings, we generalized the concept of genetic correlation to determine common genetic influences on white matter integrity, measured by fractional anisotropy (FA), at all points of the brain, yielding an NxN genetic correlation matrix rg(x,y) between FA values at all pairs of voxels in the brain. With hierarchical clustering, we identified brain regions with relatively homogeneous genetic determinants, to boost the power to identify causal single nucleotide polymorphisms (SNP). We applied genome-wide association (GWA) to assess associations between 529,497 SNPs and FA in clusters defined by hubs of the clustered genetic correlation matrix. We identified a network of genes, with a scale-free topology, that influences white matter integrity over multiple brain regions.

Heritability of brain network topology in 853 twins and siblings

Anatomical brain networks change throughout life and with diseases. Genetic analysis of these networks may help identify processes giving rise to heritable brain disorders, but we do not yet know which network measures are promising for genetic analyses. Many factors affect the downstream results, such as the tractography algorithm used to define structural connectivity. We tested nine different tractography algorithms and four normalization methods to compute brain networks for 853 young healthy adults (twins and their siblings). We fitted genetic structural equation models to all nine network measures, after a normalization step to increase network consistency across tractography algorithms. Probabilistic tractography algorithms with global optimization (such as Probtrackx and Hough) yielded higher heritability statistics than 'greedy' algorithms (such as FACT) which process small neighborhoods at each step. Some global network measures (probtrackx-derived GLOB and ST) showed significant genetic effects, making them attractive targets for genome-wide association studies.

Electrical switching and thermal studies on Ge22Te78-xIx chalcohalide glasses: The effect of iodine on network-topology

Investigations on the electrical switching behavior and thermal studies using Alternating Differential Scanning Calorimetry have been undertaken on bulk, melt-quenched Ge22Te78-,Is (3 <= x <= 10) chalcohalide glasses. All the glasses studied have been found to exhibit memory-type electrical switching. The threshold voltages of Ge22Te78-I-x(x) glasses have been found to increase with the addition of iodine and the composition dependence of threshold voltages of Ge22Te78-xIx glasses exhibits a cusp at 5 at.% of iodine. Also, the variation with composition of the glass transition temperature (Tg) of Ge22Te78-I-x(x) glasses, exhibits a broad hump around this composition. Based on the present results, the composition x = 5 has been identified as the inverse rigidity percolation threshold at which Ge22Te78-I-x(x) glassy system exhibits a change from a stressed rigid amorphous solid to a flexible polymeric glass. Further, a sharp minimum is seen in the composition dependence of non-reversing enthalpy (Delta H-nr) of Ge22Te78-I-x(x) glasses at x = 5, which is suggestive of a thermally reversing window at this composition. (C) 2007 Elsevier Ltd. All rights reserved.

Sufficient conditions for formation of a network topology by self-interested agents

Networks such as organizational network of a global company play an important role in a variety of knowledge management and information diffusion tasks. The nodes in these networks correspond to individuals who are self-interested. The topology of these networks often plays a crucial role in deciding the ease and speed with which certain tasks can be accomplished using these networks. Consequently, growing a stable network having a certain topology is of interest. Motivated by this, we study the following important problem: given a certain desired network topology, under what conditions would best response (link addition/deletion) strategies played by self-interested agents lead to formation of a pairwise stable network with only that topology. We study this interesting reverse engineering problem by proposing a natural model of recursive network formation. In this model, nodes enter the network sequentially and the utility of a node captures principal determinants of network formation, namely (1) benefits from immediate neighbors, (2) costs of maintaining links with immediate neighbors, (3) benefits from indirect neighbors, (4) bridging benefits, and (5) network entry fee. Based on this model, we analyze relevant network topologies such as star graph, complete graph, bipartite Turan graph, and multiple stars with interconnected centers, and derive a set of sufficient conditions under which these topologies emerge as pairwise stable networks. We also study the social welfare properties of the above topologies.

Influence of network topology and data collection on network inference.

We recently developed an approach for testing the accuracy of network inference algorithms by applying them to biologically realistic simulations with known network topology. Here, we seek to determine the degree to which the network topology and data sampling regime influence the ability of our Bayesian network inference algorithm, NETWORKINFERENCE, to recover gene regulatory networks. NETWORKINFERENCE performed well at recovering feedback loops and multiple targets of a regulator with small amounts of data, but required more data to recover multiple regulators of a gene. When collecting the same number of data samples at different intervals from the system, the best recovery was produced by sampling intervals long enough such that sampling covered propagation of regulation through the network but not so long such that intervals missed internal dynamics. These results further elucidate the possibilities and limitations of network inference based on biological data.

Network Topology, Higher Orders of Stability and Efficiency

Stable networks of order r where r is a natural number refer to those networks that are immune to coalitional deviation of size r or less. In this paper, we introduce stability of a finite order and examine its relation with efficient networks under anonymous and component additive value functions and the component-wise egalitarian allocation rule. In particular, we examine shapes of networks or network architectures that would resolve the conflict between stability and efficiency in the sense that if stable networks assume those shapes they would be efficient and if efficient networks assume those shapes, they would be stable with minimal further restrictions on value functions.

Internet of Things. A proposed secured network topology

The myriad of technologies and protocols working at different layers pose significant security challenges in the upcoming Internet of Things (IoT) paradigm. Security features and needs vary from application to application and it is layer specific. In addition, security has to consider the constraints imposed by energy limited sensor nodes and consider the specific target application in order to provide security at different layers. This paper analyses current standardization efforts and protocols. It proposes a generic secured network topology for IoT and describes the relevant security challenges. Some exploitation examples are also provided.

Availability analysis of GMPLS connections based on physical network topology

This paper presents a study of connection availability in GMPLS over optical transport networks (OTN) taking into account different network topologies. Two basic path protection schemes are considered and compared with the no protection case. The selected topologies are heterogeneous in geographic coverage, network diameter, link lengths, and average node degree. Connection availability is also computed considering the reliability data of physical components and a well-known network availability model. Results show several correspondences between suitable path protection algorithms and several network topology characteristics

Chaotic synchronization in general network topology for scene segmentation

Chaotic synchronization has been discovered to be an important property of neural activities, which in turn has encouraged many researchers to develop chaotic neural networks for scene and data analysis. In this paper, we study the synchronization role of coupled chaotic oscillators in networks of general topology. Specifically, a rigorous proof is presented to show that a large number of oscillators with arbitrary geometrical connections can be synchronized by providing a sufficiently strong coupling strength. Moreover, the results presented in this paper not only are valid to a wide class of chaotic oscillators, but also cover the parameter mismatch case. Finally, we show how the obtained result can be applied to construct an oscillatory network for scene segmentation.

In silico network topology-based prediction of gene essentiality

The identification of genes essential for survival is important for the understanding of the minimal requirements for cellular life and for drug design. As experimental studies with the purpose of building a catalog of essential genes for a given organism are time-consuming and laborious, a computational approach which could predict gene essentiality with high accuracy would be of great value. We present here a novel computational approach, called NTPGE (Network Topology-based Prediction of Gene Essentiality), that relies on the network topology features of a gene to estimate its essentiality. The first step of NTPGE is to construct the integrated molecular network for a given organism comprising protein physical, metabolic and transcriptional regulation interactions. The second step consists in training a decision-tree-based machine-learning algorithm on known essential and non-essential genes of the organism of interest, considering as learning attributes the network topology information for each of these genes. Finally, the decision-tree classifier generated is applied to the set of genes of this organism to estimate essentiality for each gene. We applied the NTPGE approach for discovering the essential genes in Escherichia coli and then assessed its performance. (C) 2007 Elsevier B.V. All rights reserved.

Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A 2D coordination polymer with brick-wall network topology based on the [Cu(NCS)(2)(pn)] monomer

The new complex [Cu(NCS)(2)(pn)] (1) (pn = 1,3-propanediamine) has been synthesized and characterized by elemental analysis, infrared and electronic spectroscopy. Single crystal X-ray diffraction studies revealed that complex 1 is made up of neutral [Cu(NCS)(2)(pn)] units which are connected by mu-1,3,3-thiocyanato groups to yield a 2D metal-organic framework with a brick-wall network topology. Intermolecular hydrogen bonds of the type NH...SCN and NH...NCS are also responsible for the stabilization of the crystal structure. (c) 2007 Elsevier B.V. All rights reserved.

Prediction of Oncogenic Interactions and Cancer-Related Signaling Networks Based on Network Topology

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)