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PubMed2005

Gene duplication and the properties of biological networks.

Patterns of network connection of members of multigene families were examined for two biological networks: a genetic network from the yeast Saccharomyces cerevisiae and a protein-protein interaction network from Caenorhabditis elegans. In both networks, genes belonging to gene families represented by a single member in the genome ("singletons") were disproportionately represented among the nodes having large numbers of connections. Of 68 single-member yeast families with 25 or more network connections, 28 (44.4%) were located in duplicated genomic segments believed to have originated from an ancient polyploidization event; thus, each of these 28 loci was thus presumably duplicated along with the genomic segment to which it belongs, but one of the two duplicates has subsequently been deleted. Nodes connected to major "hubs" with a large number of connections, tended to be relatively sparsely interconnected among themselves. Furthermore, duplicated genes, even those arising from recent duplication, rarely shared many network connections, suggesting that network connections are remarkably labile over evolutionary time. These factors serve to explain well-known general properties of biological networks, including their scale-free and modular nature.

Animals↗
PubMed2006

Pair-level approximations to the spatio-temporal dynamics of epidemics on asymmetric contact networks.

The process of infection during an epidemic can be envisaged as being transmitted via a network of routes represented by a contact network. Most differential equation models of epidemics are mean-field models. These contain none of the underlying spatial structure of the contact network. By extending the mean-field models to pair-level, some of the spatial structure can be contained in the model. Some networks of transmission such as river or transportation networks are clearly asymmetric, whereas others such as airborne infection can be regarded as symmetric. Pair-level models have been developed to describe symmetric contact networks. Here we report on work to develop a pair-level model that is also applicable to asymmetric contact networks. The procedure for closing the model at the level of pairs is discussed in detail. The model is compared against stochastic simulations of epidemics on asymmetric contact networks and against the predictions of the symmetric model on the same networks.

Communicable Diseases↗
PubMed2002

[Correlation between ICG angiography verified networks in uveal melanomas and rate of tumor regression after brachytherapy].

INTRODUCTION: The post-irradiation regression rate of uveal melanomas is a prognostically significant factor for the development of metastases. Other predictive factors for metastases are histological networks which are imagable with confocal ICG angiography. The purpose of this study was to evaluate a possible connection of networks in the ICGA and tumor regression rates. METHODS: We compared the post-irradiation regression rates (as %) in 20 patients 1 year after brachytherapy with networks identified in pre-treatment indocyanine green angiography (ICGA). The ICG angiography was performed before irradiation, 10 patients were irradiated with Ru-106 and 10 were irradiated with Id-125. RESULTS: The mean preoperative maximum apical height was 5.2 mm [SD: 1.5 mm; Ru106 group: 5.7 mm (SD: 1.0 mm); Id-125 group: 5.0 mm (SD: 1.9 mm)]. In 11 patients (55%) (Ru-106: 5; Id-125: 6) we found networks in the preoperative ICG. The mean regression rate in tumors with networks was 51.3% (SD: 14.7%) and 28.0% (SD: 16.4%) in the group without networks. The difference between both groups was statistically significant (p = 0.003, Mann-Whitney test). No statistically significant difference in the regression rates was found between the two groups of brachytherapy Ru-106 and Id-125 (p = 0.165, Mann-Whitney test). DISCUSSION: Highly proliferative tumors are known to be more sensitive to irradiation. This may be one reason why tumors with a rapid post-irradiation regression are the more aggressive ones with regard to later development of metastases. Histopathological networks are also known to be a strong indication of more aggressive, metastasizing tumors. These networks are also imagable in ICG angiography. Our observation emphasizes a connection between networks in ICG angiography and regression rates of uveal melanomas after brachytherapy.

Adult↗
PubMed2004

Edge vulnerability in neural and metabolic networks.

Biological networks, such as cellular metabolic pathways or networks of corticocortical connections in the brain, are intricately organized, yet remarkably robust toward structural damage. Whereas many studies have investigated specific aspects of robustness, such as molecular mechanisms of repair, this article focuses more generally on how local structural features in networks may give rise to their global stability. In many networks the failure of single connections may be more likely than the extinction of entire nodes, yet no analysis of edge importance (edge vulnerability) has been provided so far for biological networks. We tested several measures for identifying vulnerable edges and compared their prediction performance in biological and artificial networks. Among the tested measures, edge frequency in all shortest paths of a network yielded a particularly high correlation with vulnerability and identified intercluster connections in biological but not in random and scale-free benchmark networks. We discuss different local and global network patterns and the edge vulnerability resulting from them.

Animals↗
PubMed1993

Effects of Poloxamer 188 on fibrin network structure, whole blood clot premeability and fibrinolysis.

The effects of Poloxamer 188 (0-5 mg/ml) on the permeability, turbidity, compaction, and fibrinolysis of fibrin network developed in human plasma, and on the permeability and fibrinolysis of network developed in whole blood were examined. Poloxamer 188 was found to increase network permeability and compaction in plasma. In networks in plasma, effects on the fibre mass-length ratio from turbidity and fibrinolysis with recombinant tissue plasminogen activator were small. Poloxamer did not alter the fibrinolysis with streptokinase. The increase in fibrin network permeability at low poloxamer concentrations was not attributable to an increase in fibre thickness, but results from alterations in the arrangement of fibrin fibres. Poloxamer also significantly increased the permeability of networks developed in whole blood. Studies with the platelet inhibitor cytochalasin B demonstrated that this effect in whole blood networks was partly from facilitation of platelet induced clot retraction. Poloxamer was not found to affect streptokinase induced fibrinolysis of whole blood networks. The effects of poloxamer support the hypothesis that depletion flocculation of fibrin intermediaries by soluble macromolecules is a significant determinant of network permeability. The therapeutic use of poloxamer will result in altered fibrin function in particular its permeability and mechanical stability. These alterations may contribute to its described antithrombotic and rheological effects.

Blood Coagulation↗
PubMed1996

A Decomposition Principle for Complexity Reduction of Artificial Neural Networks.

A decomposition principle is developed for systematic determination of the dimensionality and the connections of Hopfield-type associative memory networks. Given a set of high dimensional prototype vectors of given memory objects, we develop decomposition algorithms to extract a set of lower dimensional key features of the pattern vectors. Every key feature can be used to build an associative memory with the lowest complexity, and more than one key feature can be simultaneously used to build networks with higher recognition accuracy. In the latter case, we further propose a "decomposed neural network" based on a new encoding scheme to reduce the network complexity. In contrast to the original Hopfield network, the decomposed networks not only increase the network's storage capacity, but also reduce the network's connection complexity from quadratic to linear growth with the network dimension. Both theoretical analysis and simulation results demonstrate that the proposed principle is powerful. Copyright 1996 Elsevier Science Ltd

Journal Article↗
PubMed2006

Transient electrical coupling regulates formation of neuronal networks.

Electrical synapses are abundant before and during developmental windows of intense chemical synapse formation, and might therefore contribute to the establishment of neuronal networks. Transient electrical coupling develops and is then eliminated between regenerating Helisoma motoneurons 110 and 19 during a period of 48-72 h in vivo and in vitro following nerve injury. An inverse relationship exists between electrical coupling and chemical synaptic transmission at these synapses, such that the decline in electrical coupling is coincident with the emergence of cholinergic synaptic transmission. In this study, we have generated two- and three-cell neuronal networks to test whether predicted synaptogenic capabilities were affected by previous synaptic interactions. Electrophysiological analyses demonstrated that synapses formed in three-cell neuronal networks were not those predicted based on synaptogenic outcomes in two-cell networks. Thus, new electrical and chemical synapse formation within a neuronal network is dependent on existing connectivity of that network. In addition, new contacts formed with established networks have little impact on these existing connections. These results suggest that network-dependent mechanisms, particularly those mediated by gap junctional coupling, regulate synapse formation within simple neural networks.

Acetylcholine↗
PubMed2006

Aging cellular networks: chaperones as major participants.

We increasingly rely on the network approach to understand the complexity of cellular functions. Chaperones (heat shock proteins) are key "networkers", which sequester and repair damaged proteins. In order to link the network approach and chaperones with the aging process, we first summarize the properties of aging networks suggesting a "weak link theory of aging". This theory suggests that age-related random damage primarily affects the overwhelming majority of the low affinity, transient interactions (weak links) in cellular networks leading to increased noise, destabilization and diversity. These processes may be further amplified by age-specific network remodelling and by the sequestration of weakly linked cellular proteins to protein aggregates of aging cells. Chaperones are weakly linked hubs (i.e., network elements with a large number of connections) and inter-modular bridge elements of protein-protein interaction, signalling and mitochondrial networks. As aging proceeds, the increased overload of damaged proteins is an especially important element contributing to cellular disintegration and destabilization. Additionally, chaperone overload may contribute to the increase of "noise" in aging cells, which leads to an increased stochastic resonance resulting in a deficient discrimination between signals and noise. Chaperone- and other multi-target therapies, which restore the missing weak links in aging cellular networks, may emerge as important anti-aging interventions.

Aged↗
PubMed2006

Simulation and analysis of solute transport in 2D fracture/pipe networks: the SOLFRAC program.

The Time Domain Random Walk (TDRW) method has been recently developed by Delay and Bodin [Delay, F. and Bodin, J., 2001. Time domain random walk method to simulate transport by advection-dispersion and matrix diffusion in fracture networks. Geophys. Res. Lett., 28(21): 4051-4054.] and Bodin et al. [Bodin, J., Porel, G. and Delay, F., 2003c. Simulation of solute transport in discrete fracture networks using the time domain random walk method. Earth Planet. Sci. Lett., 6566: 1-8.] for simulating solute transport in discrete fracture networks. It is assumed that the fracture network can reasonably be represented by a network of interconnected one-dimensional pipes (i.e. flow channels). Processes accounted for are: (1) advection and hydrodynamic dispersion in the channels, (2) matrix diffusion, (3) diffusion into stagnant zones within the fracture planes, (4) sorption reactions onto the fracture walls and in the matrix, (5) linear decay, and (6) mass sharing at fracture intersections. The TDRW method is handy and very efficient in terms of computation costs since it allows for the one-step calculation of the particle residence time in each bond of the network. This method has been programmed in C++, and efforts have been made to develop an efficient and user-friendly software, called SOLFRAC. This program is freely downloadable at the URL (labo.univ-poitiers.fr/hydrasa/intranet/telechargement.htm). It calculates solute transport into 2D pipe networks, while considering different types of injections and different concepts of local dispersion within each flow channel. Post-simulation analyses are also available, such as the mean velocity or the macroscopic dispersion at the scale of the entire network. The program may be used to evaluate how a given transport mechanism influences the macroscopic transport behaviour of fracture networks. It may also be used, as is the case, e.g., with analytical solutions, to interpret laboratory or field tracer test experiments performed in single fractures.

Computer Simulation↗
PubMed2006

The growth and form of tunnelling networks in ants.

Many biological networks grow under strong spatial constraints, where the large-scale structure emerges from the extension, the branching and intersection of growing parts of the network. One example is provided by ant tunnelling networks, which represent the most common nest architecture in ants. Our goal was to understand how these network structures emerge from the tunnel growth dynamics. We used a standardized two-dimensional set-up shaped as a disk and studied the characteristics of tunnel growth in terms of initiation, propagation and termination of new digging sites and found that they can be described with simple probabilistic laws. We show that a model based on these simple laws and for which parameters were measured from the sand disks experiments can account for the emergence of several topological properties that were observed in experimental networks. In particular, the model accurately reproduced an allometric relation between the number of edges and the number of nodes, as well as an invariance of the node degree distribution. The model was then used to make predictions about the resulting networks' topology when the geometry of the sand substrate was shaped as a square. Experiments aimed at testing the model's predictions showed that the predictions were indeed validated. Both in the model and in the experiments, there was a similar trend for the node degree distribution tail to be steeper in the square sand patch than in the disk sand patch, while other characteristics such as the meshedness (i.e. how densely the network is internally connected) remained constant. Because network growth based on branching/fusion events is widespread in biological systems, this general model might provide useful insights for the study of other systems and, more generally, the evolution of spatial networks in biological systems.

Animals↗
PubMed2006

Analyzing and shaping human attentional networks.

In this paper we outline a conception of attentional networks arising from imaging studies as connections between activated brain areas carrying out localized mental operations. We consider both the areas of functional activation (nodes) and the structural (DTI) and functional connections (DCM) between them in real time (EEG, frequency analysis) as important tools in analyzing the network. The efficiency of network function involves the time course of activation of nodes and their connectivity to other areas of the network. We outline landmarks in the development of brain networks underlying executive attention from infancy and childhood. We use individual differences in network efficiency to examine genetic alleles that are related to performance. We consider how animal studies might be used to determine the genes that influence network development. Finally we indicate how training may aid in enhancing attentional networks. Our goal is to show the wide range of methods that can be used to suggest and analyze models of network function in the study of attention.

Attention↗
PubMed2005

Selective impairment of attentional networks of orienting and executive control in schizophrenia.

BACKGROUND: Difficulty attending is a common deficit of schizophrenic patients. However, it is not known whether this is a global attentional deficit or relates to a specific attentional network. METHOD: This study used the attention network test to compare schizophrenic patients (N=77) with controls (N=53) on the efficiency of three anatomically defined attentional networks: alerting, orienting, and executive control. RESULTS: Schizophrenic patients showed a large and highly significant deficit in the executive network and a smaller but significant deficit in the orienting network as well as in overall RT and accuracy. There was no deficit in the alerting network. CONCLUSION: These results suggest some specificity in the attentional networks influenced by the disorder. The executive attention network has been shown in normal subjects to activate the anterior cingulate and lateral prefrontal areas. Previous data using neuroimaging with schizophrenic patients has shown abnormal control by the anterior cingulate. Our findings support this previous research by indicating that the major attentional deficit in schizophrenic patients is in a network that includes the anterior cingulate.

Adult↗
PubMed2005

Network thinking in ecology and evolution.

Although pairwise interactions have always had a key role in ecology and evolutionary biology, the recent increase in the amount and availability of biological data has placed a new focus on the complex networks embedded in biological systems. The increased availability of computational tools to store and retrieve biological data has facilitated wide access to these data, not just by biologists but also by specialists from the social sciences, computer science, physics and mathematics. This fusion of interests has led to a burst of research on the properties and consequences of network structure in biological systems. Although traditional measures of network structure and function have started us off on the right foot, an important next step is to create biologically realistic models of network formation, evolution, and function. Here, we review recent applications of network thinking to the evolution of networks at the gene and protein level and to the dynamics and stability of communities. These studies have provided new insights into the organization and function of biological systems by applying existing techniques of network analysis. The current challenge is to recognize the commonalities in evolutionary and ecological applications of network thinking to create a predictive science of biological networks.

Journal Article↗
PubMed2005

Dynamics and plasticity in developing neuronal networks in vitro.

When dissociated cortical tissue is brought into culture, neurons readily grow out by forming axonal and dendritic arborizations and synaptic connections. These developing neuronal networks in vitro display spontaneous firing activity from about the end of the first week in vitro. When cultured on multielectrode arrays firing activity can be recorded from many neurons simultaneously over long periods of time. These experimental approaches provide valuable data for studying firing dynamics in neuronal networks in relation to an ongoing development of neurons and synaptic connectivity in the network. This chapter summarizes recent findings on the characteristics and developmental changes in the spontaneous firing dynamics. These changes include long-lasting transient periods of increased firing at individual sites on a time scale of days to weeks, and an age-specific repetitive pattern of synchronous network firing (network bursts) on a time scale of seconds. Especially the spatio-temporal organization of firing within network bursts showed great stability over many hours. In addition, a progressive day-to-day evolution was observed, with an initial broadening of the burst firing rate profile during the 3rd week in vitro (WIV) and a pattern of abrupt onset and precise spike timing from the 5th WIV onwards. These developmental changes are discussed in the light of structural changes in the network and activity-dependent plasticity mechanisms. Preliminary findings are presented on the pattern of spike sequences within network burst, as well as the effect of external stimulation on the spatio-temporal organization within network bursts.

Animals↗
PubMed2005

Genes and experience shape brain networks of conscious control.

One aspect of consciousness involves voluntary control over thoughts and feelings, often called will. Progress in neuroimaging and in sequencing the human genome makes it possible to think about voluntary control in terms of a specific neural network that includes midline and lateral frontal areas. A number of cognitive tasks involving conflict as well as the control of emotions have been shown to activate these brain areas. Studies have traced the development of this network in the ability to regulate cognition and emotion from about 2.5 to 7 years of age. Individual differences in this network have been related to parental reports of the ability of children to regulate their behavior, to delay reward and to develop a conscience. In adolescents these individual differences predict the propensity for antisocial behavior. Differences in specific genes are related to individual efficiency in performance of the network, and by neuroimaging, to the strength of its activation of this network. Future animal studies may make it possible to learn in detail how genes influence the common pattern of development of self-regulation made possible by this network. Moreover, a number of neurological and psychiatric pathologies involving difficulties in awareness and volition show deficits in parts of this network. We are now studying whether specific training experiences can influence the development of this network in 4-year-old children and if so, for whom it is most effective. Voluntary control is also important for the regulation of conscious input from the sensory environment. It seems likely that the same network involved in self-regulation is also crucial for focal attention to the sensory world.

Brain↗
PubMed2003

Use of mammography screening among older Samoan women in Los Angeles county: a diffusion network approach.

Minority migrant populations, such as older Samoan women, are likely to underuse preventive health services, including mammography screening. The purpose of this paper is to explore how informal (lay peers from churches) and formal (health care providers) health communication networks influence mammography screening use among older Samoan women. To do so, we apply diffusion of innovation theory and network analysis to understand how interpersonal networks may affect mammography use in this urban-dwelling, migrant population. The data come from a survey of 260 Samoan women, aged 50 years or older, who attended 39 randomly sampled Samoan churches in Los Angeles County (USA) between 1996 and 1997. Retrospective data, based over a 20-year period from this sample's year of first use of mammography screening, suggest that interpersonal networks may have accounted for the dramatic increase in the rate of adoption within the past 5 years of the survey. Using this information, we categorized women into mutually exclusive stages of mammography use and regressed these stages of mammography use on formal (had a provider referral) and informal (level of connectedness with peers in churches) health communication networks. The results indicated that being well-connected within women's informal, church-based health communication networks increased the likelihood of being in the decision (planned to have) and implementation and confirmation (had a recent mammogram) stages, but having a provider referral for a mammogram (formal networks) only increased the likelihood of being in the latter stages compared to women in the knowledge and persuasion stages. Formal and informal health communication networks influence recent use of mammography screening, but informal networks, in and of themselves, are also influential on future intention to use mammography screening.

Aged↗
PubMedDate not supplied

Genetic network identification by high density, multiplexed reversed transcriptional (HD-MRT) analysis in steroidogenic axis model cell lines.

Transcriptional network analysis in steroidogenic axis cell lines requires an understanding of cellular network composition and complexity. Previous studies have shown that absence of transcriptional network components in a cell line compromises that cell line's functional capacity for transcriptional regulation. Our goal was to analyze qualitatively steroidogenic axis-derived cell lines' expression of a putative transcriptional network involved in human and mouse development. To pursue this analysis we used Northern blots and a high density-multiplexed reverse transcription-polymerase chain reaction (HD-MRT-PCR) approach. Our results revealed that, while some members of this putative network were universally expressed, only a minority of the non-constitutive targeted transcripts were present in any single line. Based on our data and previously published results for contextual expression of these transcription factors, a model was constructed possessing the topology suggestive of a scale-free network: certain network members were highly connected nodes and would represent critical sites of vulnerability. The importance of these highly connected nodes for network function is supported by the severe phenotypes exhibited by human patients and animal models when these genes are mutated. We conclude that knowledge of network composition in specific cell lines is essential for their use as models to investigate functional interactions within selected subnetworks.

Alternative Splicing↗
PubMedDate not supplied

Structure and properties of triolein-based polyurethane networks.

Polyurethane networks based on vegetable oils have very heterogeneous composition, and it is difficult to find a close correlation between their structure and properties. To establish benchmark structure-properties relationships, we have prepared model polyurethane networks based on triolein and 4,4'-diphenylmethane diisocyanate (MDI). Cross-linking in the middle of fatty acid chains leaves significant parts of the triglyceride as dangling chains. To examine their effect on properties, we have synthesized another polyurethane network using triolein without dangling chains (removed by metathesis). The structure of polyols was studied in detail since it affects the structure of polyurethane networks. The network structure was analyzed from swelling and mechanical measurements and by applying network and rubber elasticity theories. The cross-linking density in both networks was found to be close to theoretical. The triolein-based model network displayed modulus (around 6 MPa), tensile strength (8.7 MPa), and elongation at break (136%), characteristic of hard rubbers. Glass transition temperatures of the networks from triolein and its metathesis analogue were 25 and 31.5 degrees C, respectively.

Molecular Structure↗