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
In earthquake engineering problems, uncertainty exists not only in the seismic excitations but also in the structure's parameters. This study investigates the influence of structural geometry, elastic modulus, mass density, and section dimension uncertainty on the stochastic earthquake response of a multi-story moment resisting frame subjected to random ground motion. The North-south component of the Ali Gharbi earthquake in 2012, Iraq, is selected as ground excitation. Using the power spectral density function (PSD), the two-dimensional finite element model of the moment resisting frame's base motion is modified to account for random ground motion. The probabilistic study of the moment resisting frame structure using stochastic fin
... Show MoreIn this paper will be applied to a probability model of inventories periods of multiple stores of raw materials used in the cement industry, cement factory in Samawah and basic materials are limestone, soil normal, iron soil, fuel oil and gypsum. It was built of this model after the test and determine the distribution of demand during the supply period (waiting period) for each subject and independently of the rest of the material as it is not affected by any of the materials above interrelated in the process of supply, this test has been using the Statistical Package of (SPSS) and then was determining the amount of request optimum seeking in each batch and each substance known volume of economic optimization of
... Show MoreWithin this research, The problem of scheduling jobs on a single machine is the subject of study to minimize the multi-criteria and multi-objective functions. The first problem, minimizing the multi-criteria, which include Total Completion Time, Total Late Work, and Maximum Earliness Time (∑𝐶𝑗, ∑𝑉𝑗, 𝐸𝑚𝑎𝑥), and the second problem, minimizing the multi-objective functions ∑𝐶𝑗 + ∑𝑉𝑗 +𝐸𝑚𝑎𝑥 are the problems at hand in this paper. In this study, a mathematical model is created to address the research problems, and some rules provide efficient (optimal) solutions to these problems. It has also been proven that each optimal solution for ∑𝐶𝑗 + ∑𝑉𝑗 + 𝐸𝑚𝑎𝑥 is an effic
... Show MoreNewly series of 6,6’-((2-(Aryl)dihydropyrimidine-1,3(2H,4H)-diyl)bis(methylene))bis(2-methoxy phenol) (3a-i) were synthesized from cyclization of 6,6’-((propane-1,3-diylbis (azanediyl)) bis(methylene)) bis(2-methoxyphenol) with several aryl aldehyde in the presence of acetic acid. The newly compounds characterized from their IR, NMR and EIMs spectra. The antioxidant capacity of these compounds screened by utilizing DPPH and FRAP assays. Compounds 3g and 3i exhibited significant antioxidant capability in both assays. Docking study for these compounds as a potential inhibitors of gyrase enzyme were carried out. Compound 3g exhibited significant inhibition with binding free energies (DG) higher than novobiocin. compounds 2, 3a, 3b, 3
... Show MoreAir stripping for removal of Trichloroethylene (TCE), Chloroform (CF) and Dichloromethane (DCM) from water were studied in a bubble column (0.073 m inside dia. and 1.08 m height with several sampling ports). The contaminated water was prepared from deionized water and VOCs. The presence of VOCs in feed solution was single, binary or ternary components. They were diluted to the concentrations ranged between 50 mg/l to 250 mg/l. The experiments were carried out in batch experiments which regard the bubble column as stirred tank and only gas was bubbled through stationary liquid. In this case transient measurements of VOC concentration in the liquid phase and the measured concentra
... Show MoreA simple physical technique was used in this study to create stable and cost-effective copper oxide (CuO) nanoparticles from pure copper metal using the pulsed laser ablation technique. The synthesis of crystalline CuO nanoparticles was confirmed by various analytical techniques such as particle concentration measurement using atomic absorption spectrometry (AAS), field emission scanning electron microscopy (FE-SEM), the energy dispersive X-ray (EDX), and X-ray diffraction (XRD) to determine the crystal size and identify of the crystal structure of the prepared particles. The main characteristic diffraction peaks of the three samples were consistent. The corresponding 2θ is also consistent, and the cytotoxicity of the nanoparticles was
... Show MoreThis work presents the use of laser diode in the fiber distributed data interface FDDI networks. FDDI uses optical fiber as a transmission media. This solves the problems resulted from the EMI, and noise. In addition it increases the security of transmission. A network with a ring topology consists of three computers was designed and implemented. The timed token protocol was used to achieve and control the process of communication over the ring. Nonreturn to zero inversion (NRZI) modulation was carried out as a part of the physical (PHY) sublayer. The optical system consists of a laser diode with wavelength of 820 nm and 2.5 mW maximum output power as a source, optical fiber as a channel, and positive intrinsic negative (PIN) photodiode
... Show MoreSilica-based mesoporous materials are a class of porous materials with unique characteristics such as ordered pore structure, large surface area, and large pore volume. This review covers the different types of porous material (zeolite and mesoporous) and the physical properties of mesoporous materials that make them valuable in industry. Mesoporous materials can be divided into two groups: silica-based mesoporous materials and non-silica-based mesoporous materials. The most well-known family of silica-based mesoporous materials is the Mesoporous Molecular Sieves family, which attracts attention because of its beneficial properties. The family includes three members that are differentiated based on their pore arrangement. In this review,
... Show MoreIn this work, the detection of zinc (Zn) ions that cause water pollution is studied using the CSNPs- Linker-alkaloids compound that was prepared by linking extracted alkaloids from Iraqi Catharanthus roseus plant with Chitosan nanoparticles (CSNPs) using maleic anhydride. This compound is characterized by an X-ray diffractometer (XRD) which shows that it has an orthorhombic structure with crystallite size in the nano dimension. Zeta Potential results show that the CSNPs-Linker-alkaloids carried a positive charge of 54.4 mV, which means it possesses high stability. The Fourier transform infrared spectroscopy (FTIR) shows a new distinct band at 1708.93 cm-1 due to C=O esterification. Scanning electron microscope (SEM) image
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