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
The objective of image fusion is to merge multiple sources of images together in such a way that the final representation contains higher amount of useful information than any input one.. In this paper, a weighted average fusion method is proposed. It depends on using weights that are extracted from source images using counterlet transform. The extraction method is done by making the approximated transformed coefficients equal to zero, then taking the inverse counterlet transform to get the details of the images to be fused. The performance of the proposed algorithm has been verified on several grey scale and color test images, and compared with some present methods.
... Show MoreMost Internet of Vehicles (IoV) applications are delay-sensitive and require resources for data storage and tasks processing, which is very difficult to afford by vehicles. Such tasks are often offloaded to more powerful entities, like cloud and fog servers. Fog computing is decentralized infrastructure located between data source and cloud, supplies several benefits that make it a non-frivolous extension of the cloud. The high volume data which is generated by vehicles’ sensors and also the limited computation capabilities of vehicles have imposed several challenges on VANETs systems. Therefore, VANETs is integrated with fog computing to form a paradigm namely Vehicular Fog Computing (VFC) which provide low-latency services to mo
... Show MoreIn high-dimensional semiparametric regression, balancing accuracy and interpretability often requires combining dimension reduction with variable selection. This study intro- duces two novel methods for dimension reduction in additive partial linear models: (i) minimum average variance estimation (MAVE) combined with the adaptive least abso- lute shrinkage and selection operator (MAVE-ALASSO) and (ii) MAVE with smoothly clipped absolute deviation (MAVE-SCAD). These methods leverage the flexibility of MAVE for sufficient dimension reduction while incorporating adaptive penalties to en- sure sparse and interpretable models. The performance of both methods is evaluated through simulations using the mean squared error and variable selection cri
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XML is being incorporated into the foundation of E-business data applications. This paper addresses the problem of the freeform information that stored in any organization and how XML with using this new approach will make the operation of the search very efficient and time consuming. This paper introduces new solution and methodology that has been developed to capture and manage such unstructured freeform information (multi information) depending on the use of XML schema technologies, neural network idea and object oriented relational database, in order to provide a practical solution for efficiently management multi freeform information system.
This dissertation depends on study of the topological structure in graph theory as well as introduce some concerning concepts, and generalization them into new topological spaces constructed using elements of graph. Thus, it is required presenting some theorems, propositions, and corollaries that are available in resources and proof which are not available. Moreover, studying some relationships between many concepts and examining their equivalence property like locally connectedness, convexity, intervals, and compactness. In addition, introducing the concepts of weaker separation axioms in α-topological spaces than the standard once like, α-feebly Hausdorff, α-feebly regular, and α-feebly normal and studying their properties. Furthermor
... Show MoreThe study aimed at identifying the strategic gaps in the actual reality of the management of public organizations investigated to determine the strategy used based on the study model. The study relied on the variable of the general organization strategy in its dimensions (the general organization strategy, the organization's political strategy and the defense strategy of the organization) The sample of the study was (General Directorate of Traffic, Civil Status Directorate and Civil Defense Directorate), formations affiliated to the Ministry of the Interior, for the importance of the activity carried out by these public organizations by providing them In order to translate the answers into a quantitative expression in the analysi
... Show MoreThe accurate identification of internal and external pressures in thick-walled hyperelastic vessels is a challenging inverse problem with significant implications for structural health monitoring, biomedical devices, and soft robotics. Conventional analytical and numerical approaches address the forward problem effectively but offer limited means for recovering unknown load conditions from observable deformations. In this study, we introduce a Graph-FEM/ML framework that couples high-fidelity finite element simulations with machine learning models to infer normalized internal and external pressures from measurable boundary deformations. A dataset of 1386 valid samples was generated through Latin Hypercube Sampling of geometric and l
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