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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 01 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Assessment of Factors That Contribute to Bladder Cancer
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Abstract Objective: The study aimed to assess the factors contributes of patient with bladder cancer and to find out the relationship between the factors of bladder cancer with certain variable. Methodology: A descriptive study to assessment of factors that contribute to bladder cancer that was carried out Al-Karama teaching hospital, Al-Kendy teaching hospital, Specialty Surgery teaching hospital and Al-Yarmok teaching hospital for the period of November 2003 to August 2004. A purposive (non-probability) sample of (100) patients with bladder cancer. An assessment from was constructed for the purpose of the st

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Publication Date
Fri Nov 26 2021
Journal Name
Nanomaterials
Solidification Enhancement in a Multi-Tube Latent Heat Storage System for Efficient and Economical Production: Effect of Number, Position and Temperature of the Tubes
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Thermal energy storage is an important component in energy units to decrease the gap between energy supply and demand. Free convection and the locations of the tubes carrying the heat-transfer fluid (HTF) have a significant influence on both the energy discharging potential and the buoyancy effect during the solidification mode. In the present study, the impact of the tube position was examined during the discharging process. Liquid-fraction evolution and energy removal rate with thermo-fluid contour profiles were used to examine the performance of the unit. Heat exchanger tubes are proposed with different numbers and positions in the unit for various cases including uniform and non-uniform tubes distribution. The results show that

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Publication Date
Sun Mar 31 2024
Journal Name
Acta Microbiologica Bulgarica
Human Papillomavirus Genotyping among Women and its Relationship with Cervical Cancer in Diyala Province
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The study aimed to identify Human Papillomavirus (HPV) and its genotypes prevalent among Iraqi women. They collected 89 cervical swab samples from diagnosed patients at Baghdad Teaching Hospital's Early Detection Clinic. Using PCR technique on 19 samples, they found HPV16 (57.89%) and HPV6 (10.52%) genotypes, while HPV-11, 18, and 45 were absent. HPV 16 and HPV 6 were common in cervical cancer among Iraqi women. Sequencing revealed nucleic acid variants in HPV-6 (124A>C) and HPV-16 (225G>T) E6 genes, resulting in silent effects on the encoded protein. These changes didn't alter amino acid residues (p.74I= and p.L117=). Phylogenetic analysis showed substantial distances between their samples and other viral types, indicating di

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Publication Date
Fri Apr 29 2022
Journal Name
Iraqi Journal Of Agricultural Sciences
RECURRENT OF TMPRSS2 GENETIC POLYMORPHISM AND ITS ROLE IN IRAQI PATIENTS WITH PROSTATE CANCER
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The role of transmembrane protease serine 2(TMPRSS2) in prostate carcinogenesis relies on overexpression of ETS transcription factors. The aim of this article was to investigate the association of TMPRSS2 polymorphism (rs12329760 (C\T)) with prostate cancer (PCa) in sample of Iraqi patients. One hundred and two individuals were involved in this study for the period from February – 2019 to February – 2020. The sample type was formalin fixed paraffin embedded tissue samples (FFPE), which involved  fifty-six samples of pre-diagnosed patients with prostate cancer, aged between 48 and 86 years, and forty-six samples were found to be controls (healthy group) dependent on Prostate Gland integrity, which is the same age as in a group o

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Publication Date
Tue Nov 01 2011
Journal Name
Advanced Materials Research
Experimental Test of Magneto-Rheological Directional Control Valve
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Directional control valve is the main part in hydraulic system which has complex construction, such as moving spool to control the direction of actuator for required speed. Utilizing MR fluid properties, direct interface can be realized between magnetic field and fluid power without the need for moving parts like spool in directional control valves. This paper dedicates the experimental test of four ways, three position MR directional control valve. The experimental methods were done by connecting the MR directional control valve with hydraulic actuators. The experiment was conducted to show the principle work of the valve functionally and performance test for valve was done. The valve works proportionally to control the direction a

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Publication Date
Fri Feb 28 2020
Journal Name
Iraqi Journal Of Agricultural Sciences (ijas)
PHYTOTOXICITY TEST OF KEROSENE-CONTAMINATED SOIL USING BARLEY
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This study was aimed to determine a phytotoxicity experiment with kerosene as a model of a total petroleum hydrocarbon (TPHs) as Kerosene pollutant at different concentrations (1% and 6%) with aeration rate (0 and 1 L/min) and retention time (7, 14, 21, 28 and 42 days), was carried out in a subsurface flow system (SSF) on the Barley wetland. It was noted that greatest elimination 95.7% recorded at 1% kerosene levels and aeration rate 1L / min after a period of 42 days of exposure; whereas it was 47% in the control test without plants. Furthermore, the percent of elimination efficiencies of hydrocarbons from the soil was ranged between 34.155%-95.7% for all TPHs (Kerosene) concentrations at aeration rate (0 and 1 L/min). The Barley c

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Publication Date
Mon Jul 14 2025
Journal Name
European Journal Of Clinical Microbiology & Infectious Diseases
Vibriosis-Associated Acute Kidney Injury: Incidence and Outcome
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Abstract<p><bold>Purpose: </bold>Vibriosis, caused by <italic>Vibrio cholerae</italic>, is an intestinal infection characterized by profuse watery diarrhea, leading to significant fluid loss. This study aimed to assess the clinical features, outcomes, and severity of cholera among hospitalized patients and its association with acute kidney injury (AKI). <bold>Methods</bold>: A prospective cohort study was conducted on 70 patients with confirmed <italic>V. cholerae</italic> infection at Baghdad Teaching Hospital, Medical City, during the cholera outbreak in Iraq (June–October 2022). Patients were recruited from the emergency department and medical quarantine ward. Diagnosis was based on clinical features and confir</p> ... Show More
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Publication Date
Sun Feb 28 2021
Journal Name
Journal Of Economics And Administrative Sciences
Using jack knife to estimation logistic regression model for Breast cancer disease
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It is considered as one of the statistical methods used to describe and estimate the relationship between randomness (Y) and explanatory variables (X). The second is the homogeneity of the variance, in which the dependent variable is a binary response takes two values  (One when a specific event occurred and zero when that event did not happen) such as (injured and uninjured, married and unmarried) and that a large number of explanatory variables led to the emergence of the problem of linear multiplicity that makes the estimates inaccurate, and the method of greatest possibility and the method of declination of the letter was used in estimating A double-response logistic regression model by adopting the Jackna

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Publication Date
Mon Mar 23 2020
Journal Name
International Journal Of Nanoscience
Gold Nanoparticles Synthesis Using Environmentally Friendly Approach for Inhibition Human Breast Cancer
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In this study, gold nanoparticles were synthesized in a single step biosynthetic method using aqueous leaves extract of thymus vulgaris L. It acts as a reducing and capping agent. The characterizations of nanoparticles were carried out using UV-Visible spectra, X-ray diffraction (XRD) and FTIR. The surface plasmon resonance of the as-prepared gold nanoparticles (GNPs) showed the surface plasmon resonance centered at 550[Formula: see text]nm. The XRD pattern showed that the strong four intense peaks indicated the crystalline nature and the face centered cubic structure of the gold nanoparticles. The average crystallite size of the AuNPs was 14.93[Formula: see text]nm. Field emission scanning electron microscope (FESEM) was used to s

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Publication Date
Sun Feb 28 2021
Journal Name
Journal Of Economics And Administrative Sciences
Using jack knife to estimation logistic regression model for Breast cancer disease
...Show More Authors

 

It is considered as one of the statistical methods used to describe and estimate the relationship between randomness (Y) and explanatory variables (X). The second is the homogeneity of the variance, in which the dependent variable is a binary response takes two values  (One when a specific event occurred and zero when that event did not happen) such as (injured and uninjured, married and unmarried) and that a large number of explanatory variables led to the emergence of the problem of linear multiplicity that makes the estimates inaccurate, and the method of greatest possibility and the method of declination of the letter was used in estimating A double-response logistic regression model by adopting the Jackna

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