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
STAG proteins, which are part of the cohesin complex and encoded by the STAG genes, are known as Irr1/Scc3 in yeast and as SA/STAG/stromalin in mammals. There are more variants as there are alternate splice sites, maybe three open reading frames (ORFs) code for three main proteins, including: SA1 (STAG1), SA2 (STAG2) and SA3 (STAG3). The cohesin protein complex has various essential roles in eukaryotic cell biology. This study compared the expression of the STAG1 gene in four different breast cancer cell lines, including: MCF-7, T-47D, MDA-MB-468, and MDA-MB-231 and normal breast tissue. RNA was extracted from these cell lines and mRNA was converted to cDNA, and then expression of the STAG1 gene was quantified by three sets of specific prim
... Show MoreIt is well known that the spread of cancer or tumor growth increases in polluted environments. In this paper, the dynamic behavior of the cancer model in the polluted environment is studied taking into consideration the delay in clearance of the environment from their contamination. The set of differential equations that simulates this epidemic model is formulated. The existence, uniqueness, and the bound of the solution are discussed. The local and global stability conditions of disease-free and endemic equilibrium points are investigated. The occurrence of the Hopf bifurcation around the endemic equilibrium point is proved. The stability and direction of the periodic dynamics are studied. Finally, the paper is ended with a numerical simul
... Show MoreBackground: Recurrent aphthous stomatitis (RAS) is one of the most common oral mucosa diseases characterized by recurrent, shallow, round or oval painful oral ulcers surrounded by inflammatory erythematous halos, the condition is chronic and self-limiting in immunocompetent patients. Aim of the study: to investigate the serum vitamin D levels in Iraqi female patients with RAS and the relationship between vitamin D levels and the severity of RAS. In this cross sectional study 30 female patients with idiopathic RAS, and 30 age and sex matched healthy controls were included, the severity of RAS is assessed by the number of oral aphthous ulcers in each attack and the frequency of attacks. Serum 25(OH) D levels were determined by the Enzy
... Show MoreFifty one patients with serologically confirmed brucellosis and 70 healthy controls were phenotyped for HLA-A, -B, -DR and -DQ antigens by using standard microlympho-cytotoxicity method, and lymphocytes defined by their CD markers (CD3, CD4, CD8 and CD19). The results revealed a significant (Pc = 0.001) increased frequency of HLA-DR8 (41.18 vs. 10.0%) in the patients . A significant increased percentage of CD8+ lymphocytes was also increased in the patients (25.15 vs. 22.0%; P = 0.006), while CD3+ lymphocytes were significantly decreased (75.1 vs. 79.4%; P = 0.02).
Background: The aim of the present study is to evaluate the esthetic smile in sample of Iraqi adults and to assess the gender differences. Materials and Methods: 100 persons (50malesand 50 females had class I normal dental and skeletal selected for this study.Clinical examination and digital photograph with posed smile were performed for each individual. Six linear soft tissue parameters in each photograph using AutoCAD program 2011. Five visual and four quantitative evaluations of the smile were studied for eachsubject. The smile arch and index, buccal corridor spaces (BCSs) were studied.Descriptive statistics of the measurements were calculated. Independent student’s ttestswere used to evaluate the gender differences. Statistics: Desc
... Show MoreBackground: Tubal ligation, recognized as a surgical intervention that ensures permanent contraception, has established itself as an option for women seeking a definitive solution for family planning. Objective: To assess the psychosexual implications of tubal ligation in a sample of women in Baghdad, Iraq. Methods: A prospective cohort study was conducted in a teaching hospital for 2 years, from the first of January 2022 to the end of December 2023, in which 203 women who underwent tubal ligation were included. Results: In the present study, we found that 158 (77.8%) had no depression, mild depression presented in 27 (13.3%), and moderate depression in only 15 (7.4%). While 163 (80.3%) of women did not suffer from anxiety, 32 (15.8
... Show MoreBackground: Immediate postpartum contraceptive and post abortion contraception methods are effective safe methods and are becoming a standard practice in many countries, yet it is not widely used in Iraq.
Aims: this study: is designed to assess the attitude and willingness of women to immediate contraception after giving birth or abortion and their satisfaction to previous use.
Methods and Material: Four hundred thirty-four women were surveyed in the labor word immediately after giving birth/ abortion. Their knowledge, attitude and contraception use were assessed according to the response they reported to a given questionnaire.
Results: women were not sure abo
... Show MoreUtilizing phase change materials in thermal energy storage systems is commonly considered as an alternative solution for the effective use of energy. This study presents numerical simulations of the charging process for a multitube latent heat thermal energy storage system. A thermal energy storage model, consisting of five tubes of heat transfer fluids, was investigated using Rubitherm phase change material (RT35) as the. The locations of the tubes were optimized by applying the Taguchi method. The thermal behavior of the unit was evaluated by considering the liquid fraction graphs, streamlines, and isotherm contours. The numerical model was first verified compared with existed experimental data from the literature. The outcomes re
... Show MoreThe study objectives were to (1) describe the characteristics of the pharmacy professionals and (2) explore the association between job satisfaction and factors, such as work control, work stress, workload and organization and professional commitments.
This study was a cross-sectional design. The survey items were mainly adapted from the US National Pharmacist Workforce Survey. An electronic (Qualtrics) questionnaire was posted on pharmacist social media in several A