Biology subjects

Golabi, F.

Publications and source records attributed to Golabi, F..

3 recordsLinked to original sources

bioRxiv2022

Novel Mathematical Model Based on Cellular Automata for Study of Alzheimer's Disease Progress

In recent years, extensive research has been done for the prediction, treatment, and recognition of Alzheimers disease (AD). Among these scientific works, mathematical modeling of AD is an efficient way to study the influence of various parameters such as drugs on AD progression. This paper proposes a novel model based on Cellular Automata (CA), a powerful collection of colored cells, for the investigation of AD progress. In our model, the synapses of each neuron have been considered as square cells located around the central cell. The key parameter for the progression of AD in our model is the amount of amyloid-{beta} (A{beta}), which is calculated by differential rate equations of the Puri-Li model. Based on the proposed model in this article, we introduce a new definition of AD Rate for a M x L-neuron network, which can be expanded for the whole space of the hippocampus. To better illustrate the mechanism of this model, we simulate a 3x3 neuron network and discuss the obtained results. Our numerical results show that the variations of some parameters have a great effect on AD progress. For instance, it is obtained that AD Rate is more sensitive to astroglia variations, in comparison to microglia variations. The presented model can improve the scientist's insight into the progress of AD, which will assist them to effectively consider the influence of various parameters on AD.

neuroscience↗

bioRxiv2022

FMSClusterFinder: A new tool for detection and identification of clusters of sequential motifs with varying characteristics inside genomic sequences

This paper describes FMSClusterFinder, a new tool and algorithm for identification and detection of clusters of sequential blocks inside the DNA and RNA subject sequences. Gene expression and genomic groups performance is under the control of functional elements cooperating with each other as clusters. The functional motifs or blocks are often comparably short, degenerate and are located within varying distances from each other. Since functional motifs mostly act in relation to each other as clusters, finding such clusters of blocks is an effective approach to identify functional groups and their function and structure, which represents the need for development of new corresponding tools. The presented web application finds clusters of sequential blocks, with even altering sequences and located in varying distances from each other inside the subject sequences, simultaneously. Additionally, the blocks could be searched with user defined constant or varying characteristics such as: a) different levels of similarity, b) varying minimum number of blocks required to build up the query cluster, c) different types of sequence (degenerate or standard) and d) one or multiple alternative sequences for each block. FMSClusterFinder is available freely at http://fmsclusterfinder.fmsbiog.com.

bioinformatics↗

bioRxiv2022

Evaluation of Various Drugs' Influence on Alzheimer's Disease Progress Using a New Analytical Model Based on Cellular Automata

This article aims to introduce and propose a novel mathematical model for the study of Alzheimers disease (AD) progress. The presented model is based on Cellular Automata for better representation of AD progression. The differential equations of the Puri-Li model are utilized to calculate the number of Amyloid-{beta} molecules. Also, a new definition for AD rate is presented in this study. Moreover, other useful factors such as Critical Rate (CR) and Warning Rate (WR) are defined to determine the status of AD progression. To get exact insight into the neuron-to-neuron communications, the model is obtained for a 3x3 neuron system to investigate the influence of drug injection on the reduction of AR, CR, and WR factors. It is shown that using drugs can decrease AR and CR factors and also enhance the WR. The presented study can be utilized for the investigation of various factors in the control and treatment of AD progression.

systems biology↗