SEARCH · Search PubMed

Results for “Networks”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,405 records · Page 78Linked to original sources

PubMed2006

Inferring biomolecular regulatory networks from phase portraits of time-series expression profiles.

Reverse engineering of biomolecular regulatory networks such as gene regulatory networks, protein interaction networks, and metabolic networks has received an increasing attention as more high-throughput time-series measurements become available. In spite of various approaches developed from this motivation, it still remains as a challenging subject to develop a new reverse engineering scheme that can effectively uncover the functional interaction structure of a biomolecular network from given time-series expression profiles (TSEPs). We propose a new reverse engineering scheme that makes use of phase portraits constructed by projection of every two TSEPs into respective phase planes. We introduce two measures of a slope index (SI) and a winding index (WI) to quantify the interaction properties embedded in the phase portrait. Based on the SI and WI, we can reconstruct the functional interaction network in a very efficient and systematic way with better inference results compared to previous approaches. By using the SI, we can also estimate the time-lag accompanied with the interaction between molecular components of a network.

Animals↗

PubMed2006

Perceptions and attitudes of land managers in multi-tenure reserve networks and the implications for conservation.

Multi-tenure reserve networks aim to connect areas managed for biodiversity conservation across public and private land and address the impacts of fragmentation on both biotic and social systems. The operation and function of Australian multi-tenure reserve networks as perceived by their land managers was investigated. Overall, the conservation of natural assets was the most frequently reported primary reason for involvement in a network. The perceived aims of the respective networks largely reflected the response identified for involvement and management. Over 88% of managers considered their involvement in multi-tenure reserve networks to be a positive or very positive experience. A lack of resources and time for management were considered major limitations of these networks. The majority (80%) of private land managers within networks were willing to be included in a national reserve system of conservation lands. As the Australian National Reserve System currently incorporates mostly public land, these findings have important and potentially positive implications for a greater role for protected private land.

Agriculture↗

PubMed2006

Study of hypothermia on cultured neuronal networks using multi-electrode arrays.

Efficient and safe use of hypothermia during various neuro-medical procedures requires sound understanding of low temperature effects on the neuronal network's activity. In this report, we introduce the use of cultivated dissociated neuronal networks on temperature controlled multi-electrode arrays (MEAs) as a simple methodology for studying the long-term effects of hypothermia. The networks exhibit spontaneous activity in the form of synchronized bursting events (SBEs), followed by long intervals of sporadic firing. Through the use of our correlation method, these SBEs can be clustered into sub-groups of similar spatio-temporal patterns. Application of hypothermia to the network resulted in a reduction in the SBE rate, the spike intensity and an increase in inter-neuronal correlations. Within 2h following the cessation of hypothermia, the cultured network returned to its initial spatio-temporal SBE structure. These results suggest that the network survived cold exposure and demonstrate the feasibility of long-term continuous neural network recording during hypothermic conditions.

Action Potentials↗

PubMed2005

Design of a network with state stability.

Designing a network with given functions or reconstruct a network based on its dynamical behavior is an important problem in the study of complex systems. In this paper, we put forward certain principles in constructing a network with state stability. We show that a necessary and sufficient condition to design networks with a global fixed point is that active nodes inhibit inactive nodes, while the latter activate the former directly or indirectly. We also designed networks based on basic modules, where each basic module consists a sub-network, they communicate through the inhibition link from each activator in lower module to the inhibitor of upper module. We found that long activation links, i.e. indirect activation links are important to the formation of convergence trajectory. We believe that these principles may help us to understand the topology of biological networks.

Animals↗

PubMed2006

Cryopreservation of adherent neuronal networks.

Neuronal networks have been widely used for neurophysiology, drug discovery and toxicity testing. An essential prerequisite for future widespread application of neuronal networks is the development of efficient cryopreservation protocols to facilitate their storage and transportation. Here is the first report on cryopreservation of mammalian adherent neuronal networks. Dissociated spinal cord cells were attached to a poly-d-lysine/laminin surface and allowed to form neuronal networks. Adherent neuronal networks were embedded in a thin film of collagen gel and loaded with trehalose prior to transfer to a freezing medium containing DMSO, FBS and culture medium. This was followed by a slow rate of cooling to -80 degrees C for 24 h and then storage for up to 2 months in liquid nitrogen at -196 degrees C. The three components: DMSO, collagen gel entrapment and trehalose loading combined provided the highest post-thaw viability, relative to individual or two component protocols. The post-thaw cells with this protocol demonstrated similar neuronal and astrocytic markers and morphological structure as those detected in unfrozen cells. Fluorescent dye FM1-43 staining revealed active recycling of synaptic vesicles upon depolarizing stimulation in the post-thaw neuronal networks. These results suggest that a combination of DMSO, collagen gel entrapment and trehalose loading can significantly improve conventional slow-cooling methods in cryopreservation of adherent neuronal networks.

Animals↗

PubMed2005

Parallel networks operating across attentional deployment and motion processing: a multi-seed partial least squares fMRI study.

Anticipatory deployment of attention may operate through networks of brain areas that modulate the representations of to-be-attended items in advance of their occurrence through top-down control. Luks and Simpson (2004) (Luks, T.L., Simpson, G.V., 2004. Preparatory deployment of attention to motion activates higher order motion-processing brain regions. NeuroImage 22, 1515-1522) found activations in both control areas and sensory areas during anticipatory deployment of attention to visual motion in the absence of stimuli. In the present follow-up analysis, we tested which network activity during anticipatory deployment of attention is functionally connected with task-related network activity during subsequent selective processing of motion stimuli. Following a cue (anticipatory phase), participants monitored a sequence of complex motion stimuli for a target motion pattern (task phase). We analyzed fMR signal using a partial least squares analysis with previously identified cue- and motion-related voxels as seed regions. The method identified two networks that covaried with the activity of seed regions during the cue and motion-stimulus-processing phases of the task. We suggest that the first network, involving ventral intraparietal sulcus, superior parietal lobule and motor areas, is related to anticipatory and sustained visuomotor attention. Operating in parallel to this visuomotor attention network, there is a second network, involving visual occipital areas, frontal areas as well as angular and supramarginal gyri, that may underlie anticipatory and sustained visual attention processes.

Adult↗

PubMed2006

Multiple brain networks for visual self-recognition with different sensitivity for motion and body part.

Multiple brain networks may support visual self-recognition. It has been hypothesized that the left ventral occipito-temporal cortex processes one's own face as a symbol, and the right parieto-frontal network processes self-image in association with motion-action contingency. Using functional magnetic resonance imaging, we first tested these hypotheses based on the prediction that these networks preferentially respond to a static self-face and to moving one's whole body, respectively. Brain activation specifically related to self-image during familiarity judgment was compared across four stimulus conditions comprising a two factorial design: factor Motion contrasted picture (Picture) and movie (Movie), and factor Body part a face (Face) and whole body (Body). Second, we attempted to segregate self-specific networks using a principal component analysis (PCA), assuming an independent pattern of inter-subject variability in activation over the four stimulus conditions in each network. The bilateral ventral occipito-temporal and the right parietal and frontal cortices exhibited self-specific activation. The left ventral occipito-temporal cortex exhibited greater self-specific activation for Face than for Body, in Picture, consistent with the prediction for this region. The activation profiles of the right parietal and frontal cortices did not show preference for Movie Body predicted by the assumed roles of these regions. The PCA extracted two cortical networks, one with its peaks in the right posterior, and another in frontal cortices; their possible roles in visuo-spatial and conceptual self-representations, respectively, were suggested by previous findings. The results thus supported and provided evidence of multiple brain networks for visual self-recognition.

Adolescent↗

PubMed2006

Developmental neural networks in children performing a Categorical N-Back Task.

The prefrontal and temporal networks subserving object working memory tasks in adults have been reported as immature in young children; yet children are adequately capable of performing such tasks. We investigated the basis of this apparent contradiction using a complex object working memory task, a Categorical n-back (CN-BT). We examined whether the neural networks engaged by the CN-BT in children consist of the same brain regions as those in adults, but with a different magnitude of activation, or whether the networks are qualitatively different. Event-related fMRI was used to study differences in brain activation between healthy children ages 6 and 10 years, and young adults (20-28 years). Performance accuracy and RTs in 10-year-olds and adults were comparable, but the performance in 6-year-olds was lower. In adults, the CN-BT was highly effective in engaging the bilateral (L>R) ventral prefrontal cortex, the bilateral fusiform gyrus, posterior cingulate and precuneus, thus suggesting an involvement of the ventral visual stream, with related feature extraction and semantic labeling strategies. In children, the brain networks were distinctly different. They involved the premotor and parietal cortex, anterior insula, caudate/putamen, and the cerebellum, thus suggesting a predominant involvement of the visual dorsal and sensory-motor pathways, with related visual-spatial and action cognitive strategies. The findings indicate engagement of developmental networks in children reflecting task-effective brain activation. The age-related pattern of fMRI activation suggests a working hypothesis of a developmental shift from reliance on the dorsal visual stream and premotor/striatal/cerebellar networks in young children to reliance on the ventral prefrontal and inferior temporal networks in adults.

Adult↗

PubMed2004

Structure and evolution of transcriptional regulatory networks.

The regulatory interactions between transcription factors and their target genes can be conceptualised as a directed graph. At a global level, these regulatory networks display a scale-free topology, indicating the presence of regulatory hubs. At a local level, substructures such as motifs and modules can be discerned in these networks. Despite the general organisational similarity of networks across the phylogenetic spectrum, there are interesting qualitative differences among the network components, such as the transcription factors. Although the DNA-binding domains of the transcription factors encoded by a given organism are drawn from a small set of ancient conserved superfamilies, their relative abundance often shows dramatic variation among different phylogenetic groups. Large portions of these networks appear to have evolved through extensive duplication of transcription factors and targets, often with inheritance of regulatory interactions from the ancestral gene. Interactions are conserved to varying degrees among genomes. Insights from the structure and evolution of these networks can be translated into predictions and used for engineering of the regulatory networks of different organisms.

Amino Acid Motifs↗

PubMed2005

Development of a multiple objective planning theory and system for sustainable air quality monitoring networks.

Air quality monitoring data are important bases for air quality management strategies planning and performance assessment. Therefore, the environmental protection authorities need to plan the air quality monitoring network effectively. However, in Taiwan, the national Environmental Protection Administration (EPA) and some county environmental protection bureaus (EPB) separately installed their own monitoring stations. This study developed an integrated methodology and computer system for planning air quality monitoring networks. The environmental, social, and economic objectives and sub-objectives, and their weights were identified using system analysis and multiple objective planning, based on the principles of sustainable development. A multiple objective optimization model and procedure for sustainable air quality monitoring networks planning are developed in this study. According to the procedure, a multiple objective planning system for sustainable air quality monitoring networks (MOPSSAQMN) is developed using computer software based on the modified bounded implicit enumeration algorithm with the constraint arrangement method. The air quality monitoring network of Taoyuan County, in northern Taiwan, was used as a case study to demonstrate the proposed method. Two satisfactory alternatives based on different conditions were generated using MOPSSAQMN. The compared results show that this study generated better alternatives than the current monitoring network. An installation schedule for the alternative was proposed, and its first step is now being implemented by the EPB of Taoyuan County Government. The procedure and computer system developed in this study can be used to assist the competent authorities to devise good and different alternatives for air quality monitoring networks planning.

Air Pollutants↗

PubMed2005

Being around and knowing the players: networks of influence in health policy.

The accumulation and use of power is crucial to the health policy process. This paper examines the power of the medical profession in the health policy arena, by analysing which actors are perceived as influential, and how influence is structured in health policy. It combines an analysis of policy networks and social networks, to examine positional and personal influence in health policy in the state of Victoria, Australia. In the sub-graph of the influence network examined here, those most widely regarded as influential are academics, medically qualified and male. Positional actors (the top politician, political advisor and bureaucrat in health and the top nursing official) form part of a core group within this network structure. A second central group consists of medical influentials working in academia, research institutes and health-related NGOs. In this network locale overall, medical academics appear to combine positional and personal influence, and play significant intermediary roles across the network. While many claim that the medical profession has lost power in health policy and politics, this analysis yields few signs that the power of medicine to shape the health policy process has been greatly diminished in Victoria. Medical expertise is a potent embedded resource connecting actors through ties of association, making it difficult for actors with other resources and different knowledge to be considered influential. The network concepts and analytical techniques used here provide a novel means for uncovering different types of influence in health policy.

Administrative Personnel↗

PubMed2004

Likelihood-based inference for stochastic models of sexual network formation.

Sexually-transmitted diseases (STDs) constitute a major public health concern. Mathematical models for the transmission dynamics of STDs indicate that heterogeneity in sexual activity level allow them to persist even when the typical behavior of the population would not support endemicity. This insight focuses attention on the distribution of sexual activity level in a population. In this paper, we develop several stochastic process models for the formation of sexual partnership networks. Using likelihood-based model selection procedures, we assess the fit of the different models to three large distributions of sexual partner counts: (1) Rakai, Uganda, (2) Sweden, and (3) the USA. Five of the six single-sex networks were fit best by the negative binomial model. The American women's network was best fit by a power-law model, the Yule. For most networks, several competing models fit approximately equally well. These results suggest three conclusions: (1) no single unitary process clearly underlies the formation of these sexual networks, (2) behavioral heterogeneity plays an essential role in network structure, (3) substantial model uncertainty exists for sexual network degree distributions. Behavioral research focused on the mechanisms of partnership formation will play an essential role in specifying the best model for empirical degree distributions. We discuss the limitations of inferences from such data, and the utility of degree-based epidemiological models more generally.

Databases as Topic↗

PubMed2004

A Boolean algorithm for reconstructing the structure of regulatory networks.

Advances in transcriptional analysis offer great opportunities to delineate the structure and hierarchy of regulatory networks in biochemical systems. We present an approach based on Boolean analysis to reconstruct a set of parsimonious networks from gene disruption and over expression data. Our algorithms, Causal Predictor (CP) and Relaxed Causal Predictor (RCP) distinguish the direct and indirect causality relations from the non-causal interactions, thus significantly reducing the number of miss-predicted edges. The algorithms also yield substantially fewer plausible networks. This greatly reduces the number of experiments required to deduce a unique network from the plausible network structures. Computational simulations are presented to substantiate these results. The algorithms are also applied to reconstruct the entire network of galactose utilization pathway in Saccharomyces cerevisiae. These algorithms will greatly facilitate the elucidation of regulatory networks using large scale gene expression profile data.

Algorithms↗

PubMed2006

Translating DNA data tables into quasi-median networks for parsimony analysis and error detection.

Every DNA data table can be turned into a quasi-median network that faithfully represents the data. We show that for (weighted) condensed data tables the associated network harbors all most parsimonious reconstructions for any tree that connects the sampled haplotypes. Structural features of this network can be computed directly from the data table. The key principle repeatedly used is that the quasi-median network is uniquely determined by the sub-tables for pairs of characters. The translation of a table into a network enhances the understanding of the properties of the data in regard to homoplasy and potential artifacts. The total number of nodes of such a network measures the complexity of the data. In particular, networks that display the results of filter analyses by which hotspot mutations are removed help to detect data idiosyncrasies and thus pinpoint sequencing problems. A pertinent example drawn from human mtDNA illustrates these points.

Animals↗

PubMed2001

Mechanics and multiple-particle tracking microheterogeneity of alpha-actinin-cross-linked actin filament networks.

Cell morphology is controlled by the actin cytoskeleton organization and mechanical properties, which are regulated by the available contents in actin and actin regulatory proteins. Using rheometry and the recently developed multiple-particle tracking method, we compare the mechanical properties and microheterogeneity of actin filament networks containing the F-actin cross-linking protein alpha-actinin. The elasticity of F-actin/alpha-actinin networks increases with actin concentration more rapidly for a fixed molar ratio of actin to alpha-actinin than in the absence of alpha-actinin, for networks of fixed alpha-actinin concentration and of fixed actin concentration, but more slowly than theoretically predicted for a homogeneous cross-linked semiflexible polymer network. These rheological measurements are complemented by multiple-particle tracking of fluorescent microspheres imbedded in the networks. The distribution of the mean squared displacements of these microspheres becomes progressively more asymmetric and wider for increasing concentration in alpha-actinin and, to a lesser extent, for increasing actin concentration, which suggests that F-actin networks become progressively heterogeneous for increasing protein content. This may explain the slower-than-predicted rise in elasticity of F-actin/alpha-actinin networks. Together these in vitro results suggest that actin and alpha-actinin provides the cell with an unsuspected range of regulatory pathways to modulate its cytoskeleton's micromechanics and local organization in vivo.

Actin Cytoskeleton↗

PubMed2002

Pore network modelling of the behaviour of a solute in chromatography media: transient and steady-state diffusion properties.

A pore network model is presented, that is a geometrical simplification of a porous medium. The network consists of pore chambers interconnected by pore throats. A recursive algorithm for the simulation of mercury intrusion porosimetry in the network is presented. Calculations indicate that it is possible to fit simulated mercury intrusion data to experimental data, and thereby obtain parameters of the pore size distribution and pore topology (pore connectivity). A time-dependent material balance equation for diffusion on the pore level is set up and solved for the pore network. By calculating the concentration evolution in the network, the transient diffusivity and the steady-state diffusivity are found. When the network is well connected, those two diffusivities are equal, but for poorly-connected networks they differ. For migrating solutes that are non-negligibly small compared to the pore throats, considerable differences between the transient and steady-state diffusivities were found.

Chromatography↗

PubMed2003

Experimental study of the immiscible displacement of shear-thinning fluids in pore networks.

The pore scale mechanisms and network scale transient pattern of the immiscible displacement of a shear-thinning nonwetting oil phase (NWP) by a Newtonian wetting aqueous phase (WP) are investigated. Visualization imbibition experiments are performed on transparent glass-etched pore networks at a constant unfavorable viscosity ratio and varying values of the capillary number (Ca), and equilibrium contact angle (theta(e)). Dispersions of ozokerite in paraffin oil are used as the shear-thinning NWP, and aqueous solutions of PEG colored with methylene blue are used as the Newtonian WP. At high Ca values, the tip splitting and lateral spreading of WP viscous fingers are suppressed; at intermediate Ca values, the primary viscous fingers expand laterally with the growth of smaller capillary fingers; at low Ca values, network spanning clusters of capillary fingers separated by hydraulically conductive noninvaded zones of NWP arise. The spatial distribution of the mobility of shear-thinning NWP over the pore network is very broad. Pore network regions of low NWP mobility are invaded through a precursor advancement/swelling mechanism even at relatively high Ca and theta(e) values; this mechanism leads to irregular interfacial configurations and retention of a substantial amount of NWP along pore walls; it becomes the dominant mechanism in displacements performed at low Ca and theta(e) values. The residual NWP saturation increases and the end WP relative permeability decreases as Ca increases and both become more sensitive to this parameter as the shear-thinning behavior strengthens. The shear-thinning NWP is primarily entrapped in individual pores of the network rather than in clusters of pores bypassed by the WP. At relatively high flow rates, the amplitude of the variations of pressure drop, caused by fluid redistribution in the pore network, increase with shear-thinning strengthening, whereas at low flow rates, the motion of stable and unstable menisci in pores is reflected in strong pressure drop fluctuations.

Journal Article↗

PubMed2005

[Spatio-temporal dynamics of neuronal networks in partial epilepsy].

INTRODUCTION: The anatomo-functional organization of partial drug-resistant epilepsies is the subject of much current research aiming at better understanding these pathologies and improving their treatment. The work carried out by our team on the study of intracerebral recording falls within this category of research. The objectives are to identify the neural networks involved in the generation of paroxysmal activity and to understand their spatio-temporal dynamics, in order to be able in the long term to propose targeted therapeutic approaches likely to "control" these networks. STATE OF ART: The traditional concept of epileptic "focus" must nowadays be replaced by a more complex model taking into account potential interactions within the neural networks involved in the seizure. Indeed, during partial seizures, involved cerebral structures are the site of characteristic oscillations which may be synchronized or on the contrary transiently desynchronized. These epileptic rhythms may disturb the physiological rhythms underlying normal cognitive processes; these cognitive processes may thus be impaired in partial epilepsy, even those remote from the site of origin of the discharge. In this article we describe a model of organization of human partial seizures, through characterization of the relationships ("synchrony") between intracerebral signals recorded in the involved structures. We propose that seizures are generated in an initial network of highly epileptogenic brain structures (epileptogenic zone network, EZN) whose activity is synchronized; this activity is then transiently desynchronized with the appearance of fast oscillations. During a second ictal phase, other cortical and subcortical structures are the seat of slower rhythmic modifications that are synchronized (propagation network, PN). The emergence of a particular clinical semiology in the course of the seizure depends on these phenomena which can in certain cases "mimic" a normal cerebral process or on the contrary provoke a major rupture in normal cerebral functioning. CONCLUSIONS: These studies contribute to improvement in our knowledge of the neural networks involved in partial epilepsies. In the future, this type of research may contribute to the development of specific treatments that target certain pathophysiological mechanisms involved in seizure generation.

Brain↗