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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
Mon Sep 29 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An Extrafollicular Cystic Adenomatoid Odontogenic Tumor of the Mandible Associated with Clear Cell Calcifying Epithelial Odontogenic Tumor: A Rare Case Report
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Background: The adenomatoid odontogenic tumor is a relatively rare benign epithelial odontogenic tumor. It contains both epithelial and mesenchymal components. Few cases presented as an extrafollicular lesion or involve the mandible or associated with other odontogenic lesions. This paper represents a rare case of an extrafollicular AOT. Case presentation: A 24-year-old female had a painless swelling on the right side of the lower jaw since one-month duration. Intraorally there was a well defined fluctuant-blue swelling in the right alveolar premolar region measuring 1×2 cm obliterating the right lower buccal vestibule. Grade II mobility in the vital 44 and 45 teeth were observed. Panoramic radiographs showed a well-defined pear shaped

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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
Thu Jan 07 2016
Journal Name
Ibn Al-haitham Jour. For Pure & Appl. Sci.
Determination of Some Trace Element Levels in Iraqi Male patients with Colorectal Cancer
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Alterations of trace element concentrations adversely affect biological processes and could promote carcinogenesis. Trace element deficiency or excess is implicated in the development or progression of some cancers like colorectal cancer. The aim of the present study was to compare the serum copper (Cu) and zinc (Zn) concentrations in patients with colorectal cancer from Iraqi male patient with those of healthy subjects. During the period of March 2015 until august 2015, a total of 25 patients with metastatic colon cancer and 20 healthy volunteers were enrolled from the Al-Kadhimia Teaching Hospital after the diagnosis using a histopathological examination for the malignant tumor; their age was between (38-60) years. Higher levels o

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Publication Date
Wed Sep 11 2024
Journal Name
International Journal Of Multidisciplinary Science And Advanced Technology
Superbugs (Multi Drug Resistant Bacteria to antibiotics): A Review
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Publication Date
Wed Jan 01 2020
Journal Name
Construction Research Congress
Exploratory Study of Potential Negative Safety Outcomes Associated with UAV-Assisted Construction Management
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Publication Date
Wed Jun 02 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Identification of microflora associated with dust falling on Karbala province and seasonal distribution
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Publication Date
Sun Jan 01 2017
Journal Name
International Journal Of Medical Research & Health Sciences
Clinical and Radiographical Assessment of Alveolar Bone Loss Associated with Overhang Amalgam Filling
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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
identification of fungi and their toxins associated with imported rice grain to iraq
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The study included the investigation of fungi ringed and inventory and Aflatoxins in rice and recorded average temperatures and humidity 22.75 degree Celsius and 13.2% respectively were obtained 1356 isolation innate possible diagnosis 15 species inherent in rice imported back to 8 races represented races b Fusarium , Cladosporium, Aspergillus and Alternaria

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Publication Date
Wed Mar 23 2011
Journal Name
Journal Of Baghdad College Of Dentistry
Factors associated with parotid gland enlargement among poorly controlled Type II Diabetes Mellitus
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Background: Microscopic examination of parotid gland reveals hypertrophy of the aciner cells sometimes two to three times greater than normal size of PG, in cases associated with longstanding diabetes. This study was designed to determine the effects of duration, fasting plasma glucose and glycosylated hemoglobin on parotid gland enlargement among poorly controlled type 2 diabetes mellitus. Subjects, Materials, and Method: This study was conducted on 36 parotid glands of 18 with type 2 DM , at age range ( 40-60) years, all of them were selected from subjects attending (Endocrine clinic for diabetic patients) in Baghdad Teaching Hospital. , pg was measured with ultrasonography in both longitudinal and horizontal plane. Results: the rate of e

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Publication Date
Tue Dec 05 2023
Journal Name
Baghdad Science Journal
Antifungal Potential of Cladosporium sp. (Endophytic fungi) Associated with Olea europaea L. Leaves
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In the leaves of Olea europaea L. Olive trees an endophytic fungus was discovered. Cladosporium sp. was identified to be the fungus based on its morphological characteristics and nuclear ribosomal DNA ITS sequence analysis and was registered in NCBI as the Cladosporium genus has been registered under the number (0P939922.1) The species was not specified, and it was considered of unknown species after comparing it to global isolates. In comparison to olive leaf extract, Cladosporium sp. including total flavonoid, total phenolic, total terpenoid, and total saponins, Which were 121.9%, 198.1%, 89.13%, and 29.87 % respectively compared to its content in olive leaf extract, which was 61.54 %, 67.88 % , 17.1

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