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Finite State Automata Generator for DNA Motif Template as Preparation Step for Motif Mining

There are many tools and S/W systems to generate finite state automata, FSA, due to its importance in modeling and simulation and its wide variety of applications. However, no appropriate tool that can generate finite state automata, FSA, for DNA motif template due to the huge size of the motif template. In addition to the optional paths in the motif structure which are represented by the gap. These reasons lead to the unavailability of the specifications of the automata to be generated. This absence of specifications makes the generating process very difficult. This paper presents a novel algorithm to construct FSAs for DNA motif templates. This research is the first research presents the problem of generating FSAs for DNA motif templates and offers novel algorithm to accomplish this. It is tested using many simple and compound motif templates of different sizes and various numbers of gaps that have unlimited ranges of intervals. The motifs sizes are up to 2M Bases. The motif templates include up to 2000 gaps and the interval of a gap is [1,100] up to [1, 1000000]. All of these cases were processed successfully.

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Publication Date
Wed Dec 30 2020
Journal Name
Iraqi Journal Of Science
DNA Encoding for Misuse Intrusion Detection System based on UNSW-NB15 Data Set

Recent researches showed that DNA encoding and pattern matching can be used for the intrusion-detection system (IDS), with results of high rate of attack detection. The evaluation of these intrusion detection systems is based on datasets that are generated decades ago. However, numerous studies outlined that these datasets neither inclusively reflect the network traffic, nor the modern low footprint attacks, and do not cover the current network threat environment. In this paper, a new DNA encoding for misuse IDS based on UNSW-NB15 dataset is proposed. The proposed system is performed by building a DNA encoding for all values of 49 attributes. Then attack keys (based on attack signatures) are extracted and, finally, Raita algorithm is app

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Publication Date
Mon Apr 06 2020
Journal Name
Journal Of Techniques
Finite Element Modeling Of Saint-Venant Equations For Shatt-Al Hilla

Shatt Al-Hilla was considered one of the important branches of Euphrates River that supplies irrigation water to millions of dunams of planted areas. It is important to control the velocity and water level along the river to maintain the required level for easily diverting water to the branches located along the river. So, in this research, a numerical model was developed to simulate the gradually varied unsteady flow in Shatt AL-Hilla. The present study aims to solve the continuity and momentum (Saint-Venant) equations numerically to predict the hydraulic characteristics in the river using Galerkin finite element method. A computer program was designed and built using the programming language FORTRAN-77. Fifty kilometers was consid

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Publication Date
Sun Jan 01 2017
Journal Name
Optics & Laser Technology
Finite element thermal analysis for PMMA/st.st.304 laser direct joining

This work is concerned with building a three-dimensional (3D) ab-initio models that is capable of predicting the thermal distribution of laser direct joining processes between Polymethylmethacrylate (PMMA) and stainless steel 304(st.st.304). ANSYS® simulation based on finite element analysis (FEA) was implemented for materials joining in two modes; laser transmission joining (LTJ) and conduction joining (CJ). ANSYS® simulator was used to explore the thermal environment of the joints during joining (heating time) and after joining (cooling time). For both modes, the investigation is carried out when the laser spot is at the middle of the joint width, at 15 mm from the commencement point (joint edge) at traveling time of 3.75 s. Process par

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Publication Date
Tue Feb 01 2022
Journal Name
Baghdad Science Journal
Numerical Solution for Linear State Space Systems using Haar Wavelets Method

In this research, Haar wavelets method has been utilized to approximate a numerical solution for Linear state space systems. The solution technique is used Haar wavelet functions and Haar wavelet operational matrix with the operation to transform the state space system into a system of linear algebraic equations which can be resolved by MATLAB over an interval from 0 to . The exactness of the state variables can be enhanced by increasing the Haar wavelet resolution. The method has been applied for different examples and the simulation results have been illustrated in graphics and compared with the exact solution.

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Publication Date
Sat Nov 10 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Effect of Long Term Exposure to Sodium Nitrite on Gene Responsible for DNA Repair

Objective: The aim of this study is to detect the effect of continuous exposure to Sodium Nitrite on 8-oxoguanine
DNA glycosylase (OGG1) gene which responsible on DNA repairs. DNA repair play a major role in maintaining
genomic stability when DNA exposure to damage. Genomic stability is very important for keeping body cells
healthy and to prevent many types of tumor development. Many genes are responsible for this job; one of them is
OGG1 gene.
Methodology: In current study two groups of mice were chronically exposed to sodium nitrite for six months and
eighteen months while third group was used as a control. Then sizes of OGG1 were estimated.
Results: The results exhibited in the unexposed (control) mice had two dif

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Publication Date
Mon Dec 20 2021
Journal Name
Baghdad Science Journal
Numerical Analysis of Least-Squares Group Finite Element Method for Coupled Burgers' Problem

In this paper, a least squares group finite element method for solving coupled Burgers' problem in   2-D is presented. A fully discrete formulation of least squares finite element method is analyzed, the backward-Euler scheme for the time variable is considered, the discretization with respect to space variable is applied as biquadratic quadrangular elements with nine nodes for each element. The continuity, ellipticity, stability condition and error estimate of least squares group finite element method are proved.  The theoretical results  show that the error estimate of this method is . The numerical results are compared with the exact solution and other available literature when the convection-dominated case to illustrate the effic

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Publication Date
Tue Feb 28 2023
Journal Name
Iraqi Journal Of Science
A Secure Private Key Recovery Based on DNA Bio-Cryptography for Blockchain

     The existence of the Internet, networking, and cloud computing support a wide range of new technologies. Blockchain is one of these technologies; this increases the interest of researchers who are concerned with providing a safe environment for the circulation of important information via the Internet. Maintaining solidity and integrity of a blockchain’s transactions is an important issue, which must always be borne in mind. Transactions in blockchain are based on use of public and private keys asymmetric cryptography. This work proposes usage of users’ DNA as a supporting technology for storing and recovering their keys in case those keys are lost — as an effective bio-cryptographic recovery method. The RSA private key is

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Publication Date
Tue Mar 26 2024
Journal Name
World Electric Vehicle Journal
Fast Finite-Time Composite Controller for Vehicle Steer-by-Wire Systems with Communication Delays

The modern steer-by-wire (SBW) systems represent a revolutionary departure from traditional automotive designs, replacing mechanical linkages with electronic control mechanisms. However, the integration of such cutting-edge technologies is not without its challenges, and one critical aspect that demands thorough consideration is the presence of nonlinear dynamics and communication network time delays. Therefore, to handle the tracking error caused by the challenge of time delays and to overcome the parameter uncertainties and external perturbations, a robust fast finite-time composite controller (FFTCC) is proposed for improving the performance and safety of the SBW systems in the present article. By lumping the uncertainties, parameter var

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Publication Date
Tue May 30 2023
Journal Name
Iraqi Journal Of Science
Application of Data Mining and Imputation Algorithms for Missing Value Handling: A Study Case Car Evaluation Dataset

     Data mining is a data analysis process using software to find certain patterns or rules in a large amount of data, which is expected to provide knowledge to support decisions. However, missing value in data mining often leads to a loss of information. The purpose of this study is to improve the performance of data classification with missing values, ​​precisely and accurately. The test method is carried out using the Car Evaluation dataset from the UCI Machine Learning Repository. RStudio and RapidMiner tools were used for testing the algorithm. This study will result in a data analysis of the tested parameters to measure the performance of the algorithm. Using test variations: performance at C5.0, C4.5, and k-NN at 0% missi

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Publication Date
Sat Mar 31 2018
Journal Name
Journal Of Engineering
Potential of Microalgae Cultivation in Dairy Wastewater as a Step in Low-Cost Biofuel Production

The present study addresses adopting the organic and nutritious materials in dairy wastewater as media for cultivation of microalgae, which represent an important source of renewable energy. This study was carried out through cultivation of three types of microalgae; Chlorella sp., Synechococcus, and Anabaena. The results shows the success the cultivation of the Synechococcus and  Chlorella Sp, while the Anabaena microalgae were in low-growth level. The highest growth was in the Synechococcus farm, followed by Chlorella and Anabaena. However, the growth of Synechococcus required 10 days to achieve this increase that re

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