Abstract: Statistical analysis of electrophysiological recordings
obtained under, e.g. tactile, stimulation frequently suggests participation
in the network dynamics of experimentally unobserved “hidden"
neurons. Such interneurons making synapses to experimentally
recorded neurons may strongly alter their dynamical responses to
the stimuli. We propose a mathematical method that formalizes this
possibility and provides an algorithm for inferring on the presence
and dynamics of hidden neurons based on fitting of the experimental
data to spike trains generated by the network model. The model
makes use of Integrate and Fire neurons “chemically" coupled
through exponentially decaying synaptic currents. We test the method
on simulated data and also provide an example of its application to
the experimental recording from the Dorsal Column Nuclei neurons
of the rat under tactile stimulation of a hind limb.
Abstract: The counting process of cell colonies is always a long
and laborious process that is dependent on the judgment and ability
of the operator. The judgment of the operator in counting can vary in
relation to fatigue. Moreover, since this activity is time consuming it
can limit the usable number of dishes for each experiment. For these
purposes, it is necessary that an automatic system of cell colony
counting is used. This article introduces a new automatic system of
counting based on the elaboration of the digital images of cellular
colonies grown on petri dishes. This system is mainly based on the
algorithms of region-growing for the recognition of the regions of
interest (ROI) in the image and a Sanger neural net for the
characterization of such regions. The better final classification is
supplied from a Feed-Forward Neural Net (FF-NN) and confronted
with the K-Nearest Neighbour (K-NN) and a Linear Discriminative
Function (LDF). The preliminary results are shown.
Abstract: Cluster analysis divides data into groups that are
meaningful, useful, or both. Analysis of biological data is creating a
new generation of epidemiologic, prognostic, diagnostic and
treatment modalities. Clustering of protein sequences is one of the
current research topics in the field of computer science. Linear
relation is valuable in rule discovery for a given data, such as if value
X goes up 1, value Y will go down 3", etc. The classical linear
regression models the linear relation of two sequences perfectly.
However, if we need to cluster a large repository of protein sequences
into groups where sequences have strong linear relationship with
each other, it is prohibitively expensive to compare sequences one by
one. In this paper, we propose a new technique named General
Regression Model Technique Clustering Algorithm (GRMTCA) to
benignly handle the problem of linear sequences clustering. GRMT
gives a measure, GR*, to tell the degree of linearity of multiple
sequences without having to compare each pair of them.
Abstract: The drug discovery process starts with protein
identification because proteins are responsible for many functions
required for maintenance of life. Protein identification further needs
determination of protein function. Proposed method develops a
classifier for human protein function prediction. The model uses
decision tree for classification process. The protein function is
predicted on the basis of matched sequence derived features per each
protein function. The research work includes the development of a
tool which determines sequence derived features by analyzing
different parameters. The other sequence derived features are
determined using various web based tools.
Abstract: The emergence of information technology has
resulted in an ever-increasing demand to use computers for the
efficient management and dissemination of information. Keeping in
view the strong need of farmers to collect important and updated
information for interactive, flexible and quick decision-making, a
model of Decision Support System for Farm Management is
developed. The paper discusses the use of Internet technology for the
farmers to take decisions. A model is developed for the farmers to
access online interactive and flexible information for their farm
management. The workflow of the model is presented highlighting
the information transfer between different modules.
Abstract: Reactiondiffusion systems are mathematical models that describe how the concentration of one or more substances distributed in space changes under the influence of local chemical reactions in which the substances are converted into each other, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear parabolic partial differential equations, whose general form is ÔêétX(x, t) = DΔX(x, t), where X(x, t) is the state vector, D is the matrix of the diffusion coefficients and Δ is the Laplace operator. If the solute move in an homogeneous system in thermal equilibrium, the diffusion coefficients are constants that do not depend on the local concentration of solvent and of solutes and on local temperature of the medium. In this paper a new stochastic reaction-diffusion model in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces of solvent and solute is presented. Such a model provides a more realistic description of the molecular kinetics in non-homogenoeus and highly structured media as the intra- and inter-cellular spaces. The movement of a molecule A from a region i to a region j of the space is described as a first order reaction Ai k- → Aj , where the rate constant k depends on the diffusion coefficient. Representing the diffusional motion as a chemical reaction allows to assimilate a reaction-diffusion system to a pure reaction system and to simulate it with Gillespie-inspired stochastic simulation algorithms. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the specific speed of reaction and diffusion events. Redi is the software tool, developed to implement the model of reaction-diffusion kinetics and dynamics. It is a free software, that can be downloaded from http://www.cosbi.eu. To demonstrate the validity of the new reaction-diffusion model, the simulation results of the chaperone-assisted protein folding in cytoplasm obtained with Redi are reported. This case study is redrawing the attention of the scientific community due to current interests on protein aggregation as a potential cause for neurodegenerative diseases.