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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
Thu Nov 18 2021
Journal Name
Frontiers In Public Health
Dentists' Practices and Attitudes Toward Using Personal Protection Equipment and Associated Drawbacks and Cost Implications During the COVID-19 Pandemic
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Objectives: During the COVID-19 pandemic, dentists have had to work under stressful conditions due to the nature of their work. Personal protection equipment (PPE) has become mandatory for work in the dentistry field. This study aimed to examine dentists' practices and attitudes regarding the use of PPE and the associated drawbacks and cost implications during the pandemic.

Methods: A questionnaire-based survey was used and was divided into five sections dedicated to collect demographic variables and to examine the dentists' practices, attitudes toward PPE, drawbacks, and cost of using PPE. Mann-Whitney U and Kruskal-Wallis tests were used to compare different sections of

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Publication Date
Mon Jan 15 2018
Journal Name
Iraqi Journal Of Laser
Effect of 410 nm Diode Laser Irradiation on the Growth of Burn Wounds-associated Bacteria, Pseudomonas Aeruginosa and Staphylococcus Aureus
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The effect of 410nm with 100 mW output power and one centimetre spot size (0.128 W/cm2 power density) Diode laser irradiation at different exposure times on the growth of Gram-negative Pseudomonas aeruginosa and Gram-positive Staphylococcus aureus was evaluated. Seventy swap samples were collected from burn and infected wounds of 35 patients admitted to the burn-wound unit in Al-Yarmouk Teaching Hospital in Baghdad during the period from December 2014 to February 2015. These bacteria were isolated and identified depending on their growth on selective media, cultural characteristics, Gram stain morphology and biochemical tests and finally were confirmed by Vitek 2 compact system test .Susceptibility of bacterial isolates to 15antibiotics

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Publication Date
Thu Dec 20 2018
Journal Name
Frontiers In Immunology
Resveratrol Attenuates Allergic Asthma and Associated Inflammation in the Lungs Through Regulation of miRNA-34a That Targets FoxP3 in Mice
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Asthma is a chronic inflammatory disease of airways mediated by T-helper 2 (Th2) cells involving complex signaling pathways. Although resveratrol has previously been shown to attenuate allergic asthma, the role of miRNA in this process has not been studied. We investigated the effect of resveratrol on ovalbumin-induced experimental allergic asthma in mice. To that end, BALB/c mice were immunized with ovalbumin (OVA) intraperitoneally followed by oral gavage of vehicle (OVA-veh) or resveratrol (100 mg/kg body) (OVA-res). On day 7, the experimental groups received intranasal challenge of OVA followed by 7 days of additional oral gavage of vehicle or resveratrol. At day 15, all mice were euthanized and bronchioalveolar fluid (BALF), se

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Publication Date
Fri Mar 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Balancing the Multi Assembly line Using Ranked Positional Weight and COMSOAL Algorithms: Case Study at the Sewing line Factory (7) /the General Company for Leather Industries (GCLI/ Baghdad)
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      The problem of multi assembly line balancing appears as one of the most prominent and complex type of problem. The research problem of this dissertation is concerned with choosing the suitable method that includes the nature of the processes of the multi assembly type of the sewing line at factory no. (7). The State Company for Leather Manufacturing. The sewing line currently suffers from idle times at work stations which resulted in low production levels that do not meet the production plans. The authors have devised a flexible simulation model which uses the uniform distribution to generate task time for each shoe type produced by the factory. The simulation of the multi assembly line was based on assigni

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Publication Date
Wed Mar 29 2023
Journal Name
Journal Of Robotics
Real-Time SLAM Mobile Robot and Navigation Based on Cloud-Based Implementation
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This study investigates the feasibility of a mobile robot navigating and discovering its location in unknown environments, followed by the creation of maps of these navigated environments for future use. First, a real mobile robot named TurtleBot3 Burger was used to achieve the simultaneous localization and mapping (SLAM) technique for a complex environment with 12 obstacles of different sizes based on the Rviz library, which is built on the robot operating system (ROS) booted in Linux. It is possible to control the robot and perform this process remotely by using an Amazon Elastic Compute Cloud (Amazon EC2) instance service. Then, the map to the Amazon Simple Storage Service (Amazon S3) cloud was uploaded. This provides a database

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Publication Date
Tue Dec 07 2021
Journal Name
2021 14th International Conference On Developments In Esystems Engineering (dese)
Content Based Image Retrieval Based on Feature Fusion and Support Vector Machine
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Publication Date
Tue Sep 01 2020
Journal Name
Clinical Plasma Medicine
Breast cancer treatment using cold atmospheric plasma generated by the FE-DBD scheme
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Background Cold atmospheric plasma (CAP) is widely used in the cancer therapy field. This type of plasma is very close to room temperature. This paper illustrates the effects of CAP on breast cancer tissues both in vivo and in vitro. Methods The mouse mammary adenocarcinoma cell line AN3 was used for the in vivo study, and the MCF7, AMJ13, AMN3, and HBL cell lines were used for the in vitro study. A floating electrode-dielectric barrier discharge (FE-DBD) system was used. The cold plasma produced by the device was tested against breast cancer cells. Results The induced cytotoxicity percentages were 61.7%, 68% and 58.07% for the MCF7, AMN3, and AMJ13 cell lines, respectively, whereas the normal breast tissue HBL cell line exhibited very li

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Publication Date
Mon Jun 01 2020
Journal Name
P J M H S
The influence of Breast Cancer Molecular Subtypes on Metastatic pattern in Iraqi patients
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Publication Date
Mon Jul 01 2024
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Immunohistochemical Expression and Histopathological Role of CD47 in Colorectal Cancer in Iraqi Patients
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Background: Bowel cancer is the most prevalent digestive system cancer and is the 4th largest cause of cancer-related death worldwide. In Iraq, colon and rectal cancer (CRC) is the 6th most common malignancy in males and the 5th in females. This cancer is sluggish in growth, which gives a window of opportunity to screen for both precursor lesions and early cancer. The Cluster of Differentiation 47 (CD47) protein is a type of transmembrane glycoproteins found on nearly all human cells, including non-hematopoietic and hematopoietic cells. CD47 promotes CRC growth by triggering angiogenesis and apoptosis of tumor cell. Objectives: To evaluate the immunohistochemical expression of (CD47) in various colorectal samples from Iraqi patients

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Publication Date
Fri Apr 30 2021
Journal Name
Al-kindy College Medical Journal
The Expression of Epstein-Barr virus in Breast cancer in relation to age
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Background: Breast cancer is the most common
malignancy affecting females worldwide. The association
of Epstein-Barr virus (EBV) with this cancer is a longstanding
interest to this field.
Aim: to investigate the presence of EBV in breast tumor
tissue in relation to age.
Patients and Methods: Paraffin-embedded tissue blocks
from 45 female patients with breast tumors (ranged in age
from 28 to 85 years) were retrieved. The cases were
grouped into two categories: group (A): included 30 cases
with breast carcinoma and group (B): included 15 cases
with benign breast diseases as a control group .The
expression of EBV protein was examined
immunohistochemically.
Results: Twelve (40%) of the 30 breast canc

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