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
Abstract
In this paper, fatigue damage accumulation were studied using many methods i.e.Corton-Dalon (CD),Corton-Dalon-Marsh(CDM), new non-linear model and experimental method. The prediction of fatigue lifetimes based on the two classical methods, Corton-Dalon (CD)andCorton-Dalon-Marsh (CDM), are uneconomic and non-conservative respectively. However satisfactory predictions were obtained by applying the proposed non-linear model (present model) for medium carbon steel compared with experimental work. Many shortcomings of the two classical methods are related to their inability to take into account the surface treatment effect as shot peening. It is clear that the new model shows that a much better and cons
... Show MoreThis work involved the successful synthesis of three new Schiff base complexes, including Ni(II), Mn(II), and Cu(II) complexes. The Schiff base ligand was created by reacting the malonyldihydrazide molecule with naphthaldehyde, and the final step involved reacting the ligand with the corresponding metallic chloride yielding pure target complexes. FTIR, 1 H NMR, 13 C NMR, mass, and UV/Vis spectroscopies were used to comprehensively characterize the produced complexes. These substances have been employed in this study to photo-stabilize polystyrene (PS) and lessen the photo-degradation of its polymeric chains. Several methods, including FTIR, weight loss, viscosity average molecular weight, light and atomic force microscopy, and energy disper
... Show MoreA concept of indoor solar illumination is described and simulated. The solar illumination system is composed of a tracking primary reflector, a selective secondary reflector, a visible light guide and a scattering solid glass tube fixture. Each part of the solar illumination system is optically suited and compatible with other parts to realize high efficiency. The simulation is conducted for Baghdad city for a library hall. Two major days over a year are chosen to investigate the illumination system for acceptable visible light level for reading hall. The two days are: summer solstice day and winter solstice day at 8:00 AM and 12:00 PM for each. Research results showed that the design of the solar system is achieved on the base of minimu
... Show MoreThe performance of a solar assisted desiccant cooling system for a meeting-hall located in the College of Engineering/University of Baghdad was evaluated theoretically. The system was composed of four components; a solar air heater, a desiccant dehumidifier, a heat exchanger and an evaporative cooler. A computer simulation was developed by using MATLAB to assess the effect of various design and operating conditions on the performance of the system and its components. The actual weather data on recommended days were used to assess the load variation and the system performance during those days. The radiant time series method (RTS) was used to evaluate the hourly variation of the cooling load. Four operation modes were employed for perform
... Show MoreThe provision of safe water for people is a human right; historically, a major number of people depend on groundwater as a source of water for their needs, such as agricultural, industrial or human activities. Water resources have recently been affected by organic and/or inorganic contaminants as a result of population growth and increased anthropogenic activity, soil leaching and pollution. Water resource remediation has become a serious environmental concern, since it has a direct impact on many aspects of people’s lives. For decades, the pump-and-treat method has been considered the predominant treatment process for the remediation of contaminated groundwater with organic and inorganic contaminants. On the other side, this tech
... Show MoreIn data transmission a change in single bit in the received data may lead to miss understanding or a disaster. Each bit in the sent information has high priority especially with information such as the address of the receiver. The importance of error detection with each single change is a key issue in data transmission field.
The ordinary single parity detection method can detect odd number of errors efficiently, but fails with even number of errors. Other detection methods such as two-dimensional and checksum showed better results and failed to cope with the increasing number of errors.
Two novel methods were suggested to detect the binary bit change errors when transmitting data in a noisy media.Those methods were: 2D-Checksum me