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 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.
Most 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 MoreSickle cell disease (SCD) is a hereditary ailment that can cause severe pain and suffering to people who are affected. However, with continued investment in research and treatment options, we can make progress towards improving the lives of those with SCD. Over 40% of patients experience painful vaso-occlusive crises (VOCs), so we must work towards finding solutions and providing support for those living with this condition, These episodes, a hallmark of SCD, significantly contribute to morbidity, mortality, and a diminished quality of life, while also incurring substantial healthcare costs. Chronic pain particularly affects older adolescents and adults with SCD, with over half reporting daily discomfort. Opioid-based analgesics, though sti
... Show MoreThe debate on the methodology of media and communication research is no longer subject to the logic of the contradiction between the quantitative and the qualitative approach, nor the logic of the comparison between them. The nature of the topics presented for research, the problems they raise, the goals to be achieved from the research, and the epistemological positioning of researchers are among the critical factors that dictate the appropriate approach or methodological approaches to conduct their research. This positioning means the implicit philosophical principles upon which any researcher relies and which determine the path he/ she takes to produce scientifically approved knowledge. The method of the researcher's access to the phe
... Show MoreToday, the prediction system and survival rate became an important request. A previous paper constructed a scoring system to predict breast cancer mortality at 5 to 10 years by using age, personal history of breast cancer, grade, TNM stage and multicentricity as prognostic factors in Spain population. This paper highlights the improvement of survival prediction by using fuzzy logic, through upgrading the scoring system to make it more accurate and efficient in cases of unknown factors, age groups, and in the way of how to calculate the final score. By using Matlab as a simulator, the result shows a wide variation in the possibility of values for calculating the risk percentage instead of only 16. Additionally, the accuracy will be calculate
... Show MoreA cross-sectional study was conducted on 80 type 2 diabetic patients aged 20-60 years in Baghdad and 20 non diabetic persons as controls. Laboratory assessment of glucose related parameters; Fasting blood sugar (FBS), Glycated hemoglobin (HbA1c), Insulin and Insulin resistance (IR), renal function test; Blood urea, serum creatinine, Calcium (Ca) and Phosphorus (P), Calcium regulating hormones; Parathyroid hormone (PTH), calcitonin and vitamin D, cytokines, Adiponectin and Tumor necrosis factor (TNF-α) and comparison these parameters between patients and controls. The results: a high significant (p˂0.01) increase in FBG level in the patients (211.34 ± 11.20 mg/dl) as compared with control (85.89 ± 3.07 mg/dl). A high significant (p˂0.01
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