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A graph-based multi-sample test for identifying pathways associated with cancer progression
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Cancer is in general not a result of an abnormality of a single gene but a consequence of changes in many genes, it is therefore of great importance to understand the roles of different oncogenic and tumor suppressor pathways in tumorigenesis. In recent years, there have been many computational models developed to study the genetic alterations of different pathways in the evolutionary process of cancer. However, most of the methods are knowledge-based enrichment analyses and inflexible to analyze user-defined pathways or gene sets. In this paper, we develop a nonparametric and data-driven approach to testing for the dynamic changes of pathways over the cancer progression. Our method is based on an expansion and refinement of the pathway being studied, followed by a graph-based multivariate test, which is very easy to implement in practice. The new test is applied to the rich Cancer Genome Atlas data to study the (epi)genetic alterations of 186 KEGG pathways in the development of serous ovarian cancer. To make use of the comprehensive data, we incorporate three data types in the analysis representing gene expression level, copy number and DNA methylation level. Our analysis suggests a list of nine pathways that are closely associated with serous ovarian cancer progression, including cell cycle, ERBB, JAK-STAT signaling and p53 signaling pathways. By pairwise tests, we found that most of the identified pathways contribute only to a particular transition step. For instance, the cell cycle and ERBB pathways play key roles in the early-stage transition, while the ECM receptor and apoptosis pathways contribute to the progression from stage III to stage IV. The proposed computational pipeline is powerful in detecting important pathways and gene sets that drive cancers at certain stage(s). It offers new insights into the understanding of molecular mechanism of cancer initiation and progression. © 2020 Elsevier Ltd

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Publication Date
Tue Aug 27 2024
Journal Name
Algorithms
Multithreading-Based Algorithm for High-Performance Tchebichef Polynomials with Higher Orders
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Tchebichef polynomials (TPs) play a crucial role in various fields of mathematics and applied sciences, including numerical analysis, image and signal processing, and computer vision. This is due to the unique properties of the TPs and their remarkable performance. Nowadays, the demand for high-quality images (2D signals) is increasing and is expected to continue growing. The processing of these signals requires the generation of accurate and fast polynomials. The existing algorithms generate the TPs sequentially, and this is considered as computationally costly for high-order and larger-sized polynomials. To this end, we present a new efficient solution to overcome the limitation of sequential algorithms. The presented algorithm us

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Publication Date
Sun Mar 13 2011
Journal Name
Baghdad Science Journal
Bacteriological and Cytological study For bronchial washes from lung cancer patients
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The study included the collection of 75 bronchial wash samples from patients suspected to have lung cancer. These samples were subjected to a diagnostic cytological study to detect the dominant type of lung cancer. It was noticed that 33 patients proved to have a lung cancer out of 75 (44%) of these, 19 cases (57.6%)were diagnosed having Squamus cell carcinoma,7cases (21.21%) showed Adenocarcinoma ,6 cases (18.18%) were having small cell carcinoma while only one case (3.03%)was large cell carcinoma .Nearly 70% of cases were correlated with smokers .Bacteria were isolated from 53 patients in which 33 isolates were associated with the cancer cases while 20 of them from non infected patients. By using different morphological ,biochemical test

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Publication Date
Tue Apr 27 2021
Journal Name
Frontiers In Pharmacology
The Endocannabinoid Anandamide Attenuates Acute Respiratory Distress Syndrome by Downregulating miRNA that Target Inflammatory Pathways
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Acute respiratory distress syndrome (ARDS) is defined as a type of respiratory failure that is caused by a variety of insults such as pneumonia, sepsis, trauma and certain viral infections. In this study, we investigated the effect of an endocannabinoid, anandamide (AEA), on ARDS induced in the mouse byStaphylococcusEnterotoxin B (SEB). Administration of a single intranasal dose of SEB in mice and treated with exogenous AEA at a dose of 40 mg/kg body weight led to the amelioration of ARDS in mice. Clinically, plethysmography results indicated that there was an improvement in lung function after AEA treatment accompanied by a decrease of inflammatory cell infiltrate. There was also a significant decrease i

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Publication Date
Wed Jun 11 2025
Journal Name
Discover Oncology
The role of non-coding RNAs in the regulation of cell death pathways in melanoma
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Publication Date
Wed Feb 01 2023
Journal Name
Baghdad Science Journal
Breast Cancer MRI Classification Based on Fractional Entropy Image Enhancement and Deep Feature Extraction
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Disease diagnosis with computer-aided methods has been extensively studied and applied in diagnosing and monitoring of several chronic diseases. Early detection and risk assessment of breast diseases based on clinical data is helpful for doctors to make early diagnosis and monitor the disease progression. The purpose of this study is to exploit the Convolutional Neural Network (CNN) in discriminating breast MRI scans into pathological and healthy. In this study, a fully automated and efficient deep features extraction algorithm that exploits the spatial information obtained from both T2W-TSE and STIR MRI sequences to discriminate between pathological and healthy breast MRI scans. The breast MRI scans are preprocessed prior to the feature

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Publication Date
Sun Sep 05 2010
Journal Name
Baghdad Science Journal
The susceptibility test of vaginal yeasts and their relationship with the age in Iraqi women
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This study aims to isolate the pathogenic yeasts from genital tract and investigate their relationship with the age .The results clarified that the most pathogenic yeast isolated from genital tract was Candida albicans , also the results of C.albicanas isolates susceptibility test, to different antifungal revealed that they were sensitive to Miconazole, Ketoconazole and Clotrimazol and were resistant to Nystatin and Grisofulvin. The study of relationship of vaginal infection with the age showed that the incidence of infection with Candida was high among females age group (19-39 years).

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Publication Date
Tue Jun 21 2022
Journal Name
Analytical Science & Technology
The whole wheat effect and refined with E-selectin polymorphism on breast cancer
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Wheat is rich in sources of fiber, oligosaccharides, and resistant starch, simple carbohydrates which may have a protective role against carcinoma. Additionally, Whole wheat/bran as well includes contains phytochemicals such as flavonoids, lignans, folate, phytosterols, phenolic acids, and tocols. The above phytochemicals suitable forms antioxidant and cholesterol-reducing activities. Phytoestrogens are regarded as especially essential in the preventative measures of hormonally dependent malignancies such as breast cancer (BC). In this study lowered BC risk has been associated with whole grain/bran consumption with an odds ratio (OR=0.24 and 95 %CI=0.10-0.56). Wheat/bran appears to have a reliable protective impact against BC. While intake

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Publication Date
Tue Dec 01 2020
Journal Name
Baghdad Science Journal
A Modified Support Vector Machine Classifiers Using Stochastic Gradient Descent with Application to Leukemia Cancer Type Dataset
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Support vector machines (SVMs) are supervised learning models that analyze data for classification or regression. For classification, SVM is widely used by selecting an optimal hyperplane that separates two classes. SVM has very good accuracy and extremally robust comparing with some other classification methods such as logistics linear regression, random forest, k-nearest neighbor and naïve model. However, working with large datasets can cause many problems such as time-consuming and inefficient results. In this paper, the SVM has been modified by using a stochastic Gradient descent process. The modified method, stochastic gradient descent SVM (SGD-SVM), checked by using two simulation datasets. Since the classification of different ca

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Publication Date
Wed Jul 22 2026
Journal Name
Journal Of Engineering
Testing and Commissioning of a Low-Speed Wind Tunnel (LSWT) Test Section
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The calibration of a low-speed wind tunnel (LSWT) test section had been made in the present work. The tunnel was designed and constructed at the Aerodynamics Lab. in the Mechanical Engineering Department/University of Baghdad. The test section design speed is 70 m/s. Frictional loses and uniformity of the flow inside the test section had been tested and calibrated based on the British standards for flow inside ducts and conduits. Pitot-static tube, boundary layer Pitot tube were the main instruments which were used in the present work to measure the flow characteristics with emphasize on the velocity uniformity and boundary layer growth along the walls of the test section. It is found that the maximum calibrated velocity for empty test sect

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Publication Date
Fri Jan 01 2021
Journal Name
Computers, Materials & Continua
A New Hybrid Feature Selection Method Using T-test and Fitness Function
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