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1.
It is basic question in biology and other fields to identify the characteristic properties that on one hand are shared by
structures from a particular realm, like gene regulation, protein–protein interaction or neural networks or foodwebs, and
that on the other hand distinguish them from other structures.
We introduce and apply a general method, based on the spectrum of the normalized
graph Laplacian, that yields representations, the spectral plots, that allow us
to find and visualize such properties systematically. We present such
visualizations for a wide range of biological networks and compare them with
those for networks derived from theoretical schemes. The differences that we find
are quite striking and suggest that the search for universal properties of
biological networks should be complemented by an understanding of more specific
features of biological organization principles at different scales.
相似文献
Jürgen JostEmail: |
2.
A key point in the analysis of dynamical models of biological systems is to handle systems of relatively high dimensions.
In the present paper we propose a method to hierarchically organize a certain type of piecewise affine (PWA) differential
systems. This specific class of systems has been extensively studied for the past few years, as it provides a good framework
to model gene regulatory networks. The method, shown on several examples, allows a qualitative analysis of the asymptotic
behavior of a PWA system, decomposing it into several smaller subsystems. This technique, based on the well-known strongly
connected components decomposition, is not new. However, its adaptation to the non-smooth PWA differential equations turns
out to be quite relevant because of the strong discrete structure underlying these equations. Its biological relevance is
shown on a 7-dimensional PWA system modeling the gene network responsible for the carbon starvation response in Escherichia coli.
相似文献
Laurent Tournier (Corresponding author)Email: |
Jean-Luc GouzéEmail: |
3.
The paper introduces a novel computational approach to brain dynamics modeling that integrates dynamic gene–protein regulatory
networks with a neural network model. Interaction of genes and proteins in neurons affects the dynamics of the whole neural
network. Through tuning the gene–protein interaction network and the initial gene/protein expression values, different states
of the neural network dynamics can be achieved. A generic computational neurogenetic model is introduced that implements this
approach. It is illustrated by means of a simple neurogenetic model of a spiking neural network of the generation of local
field potential. Our approach allows for investigation of how deleted or mutated genes can alter the dynamics of a model neural
network. We conclude with the proposal how to extend this approach to model cognitive neurodynamics.
相似文献
Nikola KasabovEmail: |
4.
Srdjan Ostojic Nicolas Brunel Vincent Hakim 《Journal of computational neuroscience》2009,26(3):369-392
We investigate how synchrony can be generated or induced in networks of electrically coupled integrate-and-fire neurons subject
to noisy and heterogeneous inputs. Using analytical tools, we find that in a network under constant external inputs, synchrony
can appear via a Hopf bifurcation from the asynchronous state to an oscillatory state. In a homogeneous net work, in the oscillatory
state all neurons fire in synchrony, while in a heterogeneous network synchrony is looser, many neurons skipping cycles of
the oscillation. If the transmission of action potentials via the electrical synapses is effectively excitatory, the Hopf
bifurcation is supercritical, while effectively inhibitory transmission due to pronounced hyperpolarization leads to a subcritical
bifurcation. In the latter case, the network exhibits bistability between an asynchronous state and an oscillatory state where
all the neurons fire in synchrony. Finally we show that for time-varying external inputs, electrical coupling enhances the
synchronization in an asynchronous network via a resonance at the firing-rate frequency.
相似文献
Srdjan OstojicEmail: |
5.
The numerical simulation of spiking neural networks requires particular attention. On the one hand, time-stepping methods
are generic but they are prone to numerical errors and need specific treatments to deal with the discontinuities of integrate-and-fire
models. On the other hand, event-driven methods are more precise but they are restricted to a limited class of neuron models.
We present here a voltage-stepping scheme that combines the advantages of these two approaches and consists of a discretization
of the voltage state-space. The numerical simulation is reduced to a local event-driven method that induces an implicit activity-dependent time discretization (time-steps automatically increase when
the neuron is slowly varying). We show analytically that such a scheme leads to a high-order algorithm so that it accurately
approximates the neuronal dynamics. The voltage-stepping method is generic and can be used to simulate any kind of neuron
models. We illustrate it on nonlinear integrate-and-fire models and show that it outperforms time-stepping schemes of Runge-Kutta
type in terms of simulation time and accuracy.
相似文献
D. MartinezEmail: |
6.
Terry Harmer 《Cluster computing》2007,10(3):277-285
Gridcast is an R&D project investigating grid ideas and technologies in the broadcasting technical infrastructure. In this
paper I discuss the business and technical issues in building infrastructures to support broadcasters and outline the structure
of the Gridcast grid-based service oriented architecture for broadcasting playout support.
相似文献
Terry HarmerEmail: |
7.
Javier Plaza Rosa Pérez Antonio Plaza Pablo Martínez David Valencia 《Cluster computing》2008,11(1):17-32
The wealth spatial and spectral information available from last-generation Earth observation instruments has introduced extremely
high computational requirements in many applications. Most currently available parallel techniques treat remotely sensed data
not as images, but as unordered listings of spectral measurements with no spatial arrangement. In thematic classification
applications, however, the integration of spatial and spectral information can be greatly beneficial. Although such integrated
approaches can be efficiently mapped in homogeneous commodity clusters, low-cost heterogeneous networks of computers (HNOCs)
have soon become a standard tool of choice for dealing with the massive amount of image data produced by Earth observation
missions. In this paper, we develop a new morphological/neural algorithm for parallel classification of high-dimensional (hyperspectral)
remotely sensed image data sets. The algorithm’s accuracy and parallel performance is tested in a variety of homogeneous and
heterogeneous computing platforms, using two networks of workstations distributed among different locations, and also a massively
parallel Beowulf cluster at NASA’s Goddard Space Flight Center in Maryland.
相似文献
Javier PlazaEmail: |
8.
9.
10.
Dispersed information diffusion with level and schema-based coordination in mobile peer to peer networks 总被引:1,自引:0,他引:1
Several open ended issues for high resource availability in mobile peer to peer networks have been examined in the recent
past. Different approaches were conducted for supporting information distribution and availability, through guided or unguided
packet diffusion. The majority of the recently proposed approaches try to benefit from the spatial characteristics of the
dynamically varying topologies. In this work a directed information diffusion scheme is examined using a level and schema-based
coordination, applied in mobile peer to peer networks. The prioritization degree of any requested advert is modeled and enables
directed prioritized diffusions to end mobile users that are traversing a certain geographic region (location based advertisements).
The proposed method is robust in disseminating redundant messages to users while maintaining connectivity through Gradual
Energy Tree-based (GET) configuration. Simulation is performed for the examination and performance evaluation of the proposed
scheme, taking into account the modeled prioritization as well as the diffusion accuracy by using the Hierarchical and Non-hierarchical
GET configuration.
相似文献
Helen D. KaratzaEmail: |
11.
12.
Sub-Antarctic Marion Island has had a permanent research station for 50 years and the islands Wandering Albatrosses have been intensively studied for 20 years. The reactions of breeding birds to approaches by a human on foot were recorded. Three response variables were calculated: intensity of vocal reaction (IVR), intensity of non-vocal reaction (INR) and overall response index (ORI). At 5 m from the nest, twice as many birds stood and/or vocalised as at 15 m. Nearest neighbour distance, age and gender did not explain individual variability of responses. Study colony birds had higher IVR scores than non-study colony birds; birds at colonies closest to the station had the highest ORI scores. A better breeding record was associated with lower IVR and ORI scores, but a causative relationship remains to be demonstrated. A minimum viewing distance of 25 m is recommended for breeding Wandering Albatrosses.
相似文献
Marienne S. de VilliersEmail: Fax: +27-21-6503434 |
John CooperEmail: |
Peter G. RyanEmail: |
13.
Roger Sansom 《Biology & philosophy》2009,24(4):441-459
One current version of the internalism/externalism debate in evolutionary theory focuses on the relative importance of developmental
constraints in evolutionary explanation. The received view of developmental constraints sees them as an internalist concept
that tend to be shared across related species as opposed to selective pressures that are not. Thus, to the extent that constraints
can explain anything, they can better explain similarity across species, while natural selection is better able to explain
their differences. I challenge both of these aspects of the received view and propose a hierarchical view of constraints.
相似文献
Roger SansomEmail: |
14.
The Cauchy problem for one-dimensional spiking neuron models 总被引:1,自引:1,他引:0
Romain Brette 《Cognitive neurodynamics》2008,2(1):21-27
I consider spiking neuron models defined by a one-dimensional differential equation and a reset—i.e., neuron models of the
integrate-and-fire type. I address the question of the existence and uniqueness of a solution on for a given initial condition. It turns out that the reset introduces a countable and ordered set of backward solutions for
a given initial condition. I discuss the implications of these mathematical results in terms of neural coding and spike timing
precision.
相似文献
Romain BretteEmail: |
15.
16.
The influence of sodium and potassium dynamics on excitability,seizures, and the stability of persistent states: II. Network and glial dynamics 总被引:1,自引:1,他引:0
Ghanim Ullah John R. Cressman Jr. Ernest Barreto Steven J. Schiff 《Journal of computational neuroscience》2009,26(2):171-183
In these companion papers, we study how the interrelated dynamics of sodium and potassium affect the excitability of neurons,
the occurrence of seizures, and the stability of persistent states of activity. We seek to study these dynamics with respect
to the following compartments: neurons, glia, and extracellular space. We are particularly interested in the slower time-scale
dynamics that determine overall excitability, and set the stage for transient episodes of persistent oscillations, working
memory, or seizures. In this second of two companion papers, we present an ionic current network model composed of populations
of Hodgkin–Huxley type excitatory and inhibitory neurons embedded within extracellular space and glia, in order to investigate
the role of micro-environmental ionic dynamics on the stability of persistent activity. We show that these networks reproduce
seizure-like activity if glial cells fail to maintain the proper micro-environmental conditions surrounding neurons, and produce
several experimentally testable predictions. Our work suggests that the stability of persistent states to perturbation is
set by glial activity, and that how the response to such perturbations decays or grows may be a critical factor in a variety
of disparate transient phenomena such as working memory, burst firing in neonatal brain or spinal cord, up states, seizures,
and cortical oscillations.
相似文献
Ghanim UllahEmail: |
17.
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19.
Peter Godfrey-Smith 《Biology & philosophy》2007,22(3):429-437
Jablonka and Lamb's claim that evolutionary biology is undergoing a ‘revolution’ is queried. But the very concept of revolutionary
change has uncertain application to a field organized in the manner of contemporary biology. The explanatory primacy of sequence
properties is also discussed.
相似文献
Peter Godfrey-SmithEmail: |
20.
Catherine Driscoll 《Biology & philosophy》2008,23(1):101-113
This paper tries to explain how individuals manage adaptive individual choice (i.e., the decision to acquire a fitter than
average behavior or idea rapidly and tractably) in cultural evolution, despite the fact that acquiring fitness information
is very difficult. I argue that the means of solving this problem suggested in the cultural evolution literature largely are
various types of decision rules employing representations of fitness correlated properties or states of affairs. I argue that
the problem of adaptive individual choice is best solved where some of these learning rule representations are socially transmitted
and some are biologically transmitted.
相似文献
Catherine DriscollEmail: |