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
The solution casting method was used to prepare a polyvinylpyrrolidone (PVP)/Multi-walled carbon nanotubes (MWCNTs) nanocomposite with Graphene (Gr). Field Effect Scanning Electron Microscope (FESEM) and Fourier Transformer Infrared (FTIR) were used to characterize the surface morphology and optical properties of samples. FESEM images revealed a uniform distribution of graphene within the PVP-MWCNT nanocomposite. The FTIR spectra confirmed the nanocomposite information is successful with apperaring the presence of primary distinct peaks belonging to vibration groups that describe the prepared samples.. Furthermore, found that the DC electrical conductivity of the prepared nanocomposites increases with increasing MWCNT concentratio
... Show MoreA recently reported Nile red (NR) dye conjugated with benzothiadiazole species paves the way for the development of novel organic-based sensitizers used in solar cells whose structures are susceptible to modifications. Thus, six novel NR structures were derived from two previously developed structures in laboratories. In this study, density functional theory (DFT) calculations and time-dependent DFT (TD-DFT) were used to determine the optoelectronic properties of the NR-derived moieties such as absorption spectra. Various linkers were investigated in an attempt to understand the impact of π-linkers on the optoelectronic properties. According to the findings, the presence of furan species led to the planarity of the molecule and a reduction
... Show MoreBackground: Breast Cancer is the most common malignancy among the Iraqi population; the majority of cases are still diagnosed at advanced stages with poor prospects of cure. Early detection through promoting public awareness is one of the promising tools in its control. Objectives: To evaluate the baseline needs for breast cancer awareness in Iraq through exploring level of knowledge, beliefs and behavior towards the disease and highlighting barriers to screening among a sample of Iraqi women complaining of breast cancer. Methodology: Two-hundred samples were enrolled in this study; gathered from the National
The Machine learning methods, which are one of the most important branches of promising artificial intelligence, have great importance in all sciences such as engineering, medical, and also recently involved widely in statistical sciences and its various branches, including analysis of survival, as it can be considered a new branch used to estimate the survival and was parallel with parametric, nonparametric and semi-parametric methods that are widely used to estimate survival in statistical research. In this paper, the estimate of survival based on medical images of patients with breast cancer who receive their treatment in Iraqi hospitals was discussed. Three algorithms for feature extraction were explained: The first principal compone
... Show MoreToday’s academics have a major hurdle in solving combinatorial problems in the actual world. It is nevertheless possible to use optimization techniques to find, design, and solve a genuine optimal solution to a particular problem, despite the limitations of the applied approach. A surge in interest in population-based optimization methodologies has spawned a plethora of new and improved approaches to a wide range of engineering problems. Optimizing test suites is a combinatorial testing challenge that has been demonstrated to be an extremely difficult combinatorial optimization limitation of the research. The authors have proposed an almost infallible method for selecting combinatorial test cases. It uses a hybrid whale–gray wol
... Show MoreRutting has a significant impact on the pavements' performance. Rutting depth is often used as a parameter to assess the quality of pavements. The Asphalt Institute (AI) design method prescribes a maximum allowable rutting depth of 13mm, whereas the AASHTO design method stipulates a critical serviceability index of 2.5 which is equivalent to an average rutting depth of 15mm. In this research, static and repeated compression tests were performed to evaluate the permanent strain based on (1) the relationship between mix properties (asphalt content and type), and (2) testing temperature. The results indicated that the accumulated plastic strain was higher during the repeated load test than that during the static load tests. Notably, temperatur
... Show MoreCD40 is a type 1 transmembrane protein composed of 277 amino acids, and it belongs to the tumor necrosis factor receptor (TNFR) superfamily. It is expressed in a variety of cell types, including normal B cells, macrophages, dendritic cells, and endothelial cells, as a costimulatory molecule. This study aims to summarize the CD40 polymorphism effect and its susceptibility to immune-related disorders. The CD40 gene polymorphisms showed a significant association with different immune-related disorders and act as a risk factor for increased susceptibility to these diseases.
Analyzing the size of the interrelationships between the main economic sectors in the Iraqi economy is an important necessity to know the impact of each sector on other economic sectors on the basis of the interrelationships and reciprocity between them, and what these relationships have achieved in terms of enhancing development and increasing the gross domestic product. To achieve the objectives of the study, we relied on mathematical (quantitative) analysis using user-product tables. Issued by the Ministry of Planning / Central Bureau of Statistics and Research (Directorate of National Accounts) for the economic sectors that make up the Iraqi economy. The study conc
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