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A New Approach to DNA, RNA, and Protein Motifs Templates Visualization and Analysis via Compilation Technique
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Motifs template is the input for many bioinformatics systems such codons finding, transcription, transaction, sequential pattern miner, and bioinformatics databases analysis. The size of motifs arranged from one base up to several Mega bases, therefore, the typing errors increase according to the size of motifs. In addition, when the structures motifs are submitted to bioinformatics systems, the specifications of motifs components are required, i.e. the simple motifs, gaps, and the lower bound and upper bound of each gap. The motifs can be of DNA, RNA, or Protein. In this research, a motif parser and visualization module is designed depending on a proposed a context free grammar, CFG, and colors human recognition system. GFC describes the motif structure to parse the motifs, detect, debug the errors, and analyze the motifs template to its components. Many experiments are accomplished using motifs templates of various sizes arranged from 10 Kbase to 10 Mbase, various numbers of gaps arranged from 15 gaps to 15000 gaps, and different numbers of errors arranged from 100 errors to 1820 errors. The proposed systems, in all these experiments, exhibited linear behavior in parsing phase and visualization phase that indicates its scalability to motifs template sizes.

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Publication Date
Mon May 01 2017
Journal Name
Journal Of Stored Products Research
Detection and prediction of Sitophilus oryzae infestations in triticale via visible and near-infrared spectral signatures
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Triticale is a hybrid of wheat and rye grown for use as animal feed. In Florida, due to its soft coat, triticale is highly vulnerable to Sitophilus oryzae L. (rice weevil) and there is interest in development of methods to detect early-instar larvae so that infestations can be targeted before they become economically damaging. The objective of this study was to develop prediction models of the infestation degree for triticale seed infested with rice weevils of different growth stages. Spectral signatures were tested as a method to detect rice weevils in triticale seed. Groups of seeds at 11 different levels (degrees) of infestation, 0–62%, were obtained by combining different ratios of infested and uninfested seeds. A spectrophotometer wa

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Publication Date
Mon Aug 21 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
New techniques to estimate the solution of autonomous system
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This research aims to solve the nonlinear model formulated in a system of differential equations with an initial value problem (IVP) represented in COVID-19 mathematical epidemiology model as an application using new approach: Approximate Shrunken are proposed to solve such model under investigation, which combines classic numerical method and numerical simulation techniques in an effective statistical form which is shrunken estimation formula. Two numerical simulation methods are used firstly to solve this model: Mean Monte Carlo Runge-Kutta and Mean Latin Hypercube Runge-Kutta Methods. Then two approximate simulation methods are proposed to solve the current study. The results of the proposed approximate shrunken methods and the numerical

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of Engineering
New Correlation To Calculate Absolute Permeability From Gas Permeameter
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In this study, two correlations are developed to calculate absolute rocks permeability from core samples tested by Gas Permeameter Apparatus. The first correlation can be applied if K g≤100, the second correlation can be applied if Kg>100. Sixty core samples having different permeabilities to give a wide range of values that necessary to achieve a correlation.

 

The developed correlation is easily applied and a quick method to avoid repeating the test at different pressure values. Only one pressure test is required to reach absolu

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Publication Date
Sun Jul 03 2022
Journal Name
International Journal Of Health Sciences
effects of toxoplasmosis infection on the levels of IL-18 and anti-ds-DNA antibodies in SLE patients
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The present study was set to demonstrate the prevalence of toxoplasmosis infection and its effects on patients with systemic  lupus erythematosus (SLE) through determining their serum levels of anti-dsDNA and IL-18 antibodies. For this purpose, the sera from 132 SLE and/or toxoplasmosis patients and 30 healthy women, were collected. The study sample was divided into four groups of SLE, toxoplasmosis, SLE coinfected with toxoplasmosis, and healthy control. Anti-Toxoplasma IgG antibodies were examined for all the samples using ELISA kit. The results showed a high mean level of anti-Toxoplasma IgG among SLE patients coinfected with toxoplasmosis (104.8792±12.31585pg/ml) in comparison to that in toxoplasmosis patients (91.1705±12.577

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Publication Date
Sun Mar 17 2019
Journal Name
Baghdad Science Journal
DNA Methylation Patterns of Interferon Gamma Gene Promoter and Serum Level in Pulmonary Tuberculosis: Their Role in Prognosis
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Tuberculosis (TB) still remains an important medical problem due to high levels of morbidity and mortality worldwide. A series of innate immune mechanisms that create a cytokine network control the pathogenesis of tuberculosis and this response has the capacity to modify the host genomic DNA structure through epigenetic mechanisms such as DNA methylation which could constantly alter the local gene expression pattern that can modulate the metabolism of the tissues and the immune-response. Interferon-gamma (IFN-γ) is an important pro-inflammatory cytokine regulator of the innate immune response to TB. This study aims to determine DNA methylation patterns of INF-γ gene promoter and measure serum IFN- γ level in newly diagnosed TB patient

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Publication Date
Sat Jun 19 2021
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
The Pharmacological Effects of Kappa Carrageenan on Different Human Cell Lines and Genomic DNA: An in vitro study
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Carrageenan extract is a compound of sulfated polyglycan that is taken out from red seaweeds. Being hydrocolloid in nature, carrageenan has gelling, emulsifying and thickening properties allowing it to be commonly used in the oral healthcare products and cosmetics. Due to its bioactive compounds, carrageenan has been shown to have antimicrobial, antiviral, and antitumor properties. The purpose of this work is to study the probable use of carrageenan on the diseases that are related to oral cavity and on the genomic DNA in in vitro experimental model

In this study, the effects of k-carrageenan on four different cell lines related to the cancer and normal cells which cultured on selective media were done. Moreover, the eff

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Publication Date
Wed Jun 11 2008
Journal Name
Journal Of Al-nahrain University
ANALYSIS OF A MOLECULAR DYNAMICS SIMULATION OF THE ACETYLCHOLINESTERASE ENZYME AND ITS COMPLEX WITH (AXILLARIDINE-A) INHIBITOR
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Molecular dynamics (MD) simulations were carried out in order to investigate the binding mode of axillaridine-A at the active site of human acetylcholinesterase (AChE) enzyme. 2.0 nanosecond of MD simulations was made for the protein and the complex to dynamically explore the active site and the behavior of the ligand at the peripheral AChE binding site. These calculations for the enzyme alone showed that the active site of AChE is located at the bottom of a deep and narrow cavity whose surface is lined with rings of aromatic residues and Tyr72 is almost perpendicular to the Trp286 ring and forms a stable - interaction. The size of the active site of the complex decreases with time due to increase the interaction. Axillaridine-A forms

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Publication Date
Thu Jun 05 2014
Journal Name
Arabian Journal Of Geosciences
Applying the cluster analysis technique in logfacies determination for Mishrif Formation, Amara oil field, South Eastern Iraq
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Publication Date
Mon Sep 30 2024
Journal Name
Iraqi Journal Of Science
Anticancer, Antioxidant and Antimicrobial Evaluation of Cr (III) and Rh(III) Complexes Derived from A New Mannich Base
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The Mannich base ligand was synthesized in an ethanol medium through a condensation reaction of 2-mercaptobenzimidazole and ciprofloxacin at room temperature. Subsequently, several metal complexes of this ligand were prepared. To characterize both the base ligand and the metal complexes, various techniques were employed, including elemental analysis, FT-IR spectroscopy, UV-Vis spectroscopy, molar conductivity measurements, magnetic moment determination, and melting point analysis. The results were shown that the metal complexes formed have the formula [Cr(L)2Cl2] Cl.H2O and [Rh(L)2(H2O)2] Cl3.H2O, where L= mannich base ligand. Based on spectroscopic analytical, coordination with metal ions involves the 'N' donor atom of mannich base

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Publication Date
Sat Jun 01 2024
Journal Name
Results In Engineering
Electrochemical preparation and characterization of a new configuration SnO2 anode and its application for treating petroleum refinery wastewater
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