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
Background/Objectives: Early and accurate discrimination of neurological conditions, dementia, stroke and healthy aging, remains a critical clinical challenge. Electroencephalography (EEG) is a non-invasive measure of brain dynamics and entropy-based features obtained from multichannel EEG have shown strong discriminative ability. However, existing deep learning approaches do not sufficiently address the combined challenges of small clinical cohorts and high-dimensional entropy feature spaces. In this study, a novel architecture is proposed for multi-class neurological EEG classification under extreme small-sample conditions. Methods: A novel dual-branch Channel-wise Transformer and Attention-Branch Network (EEG-ChTABNet) are pr to
... Show MoreIntroduction: Carrier-based gutta-percha is an effective method of root canal obturation creating a 3-dimensional filling; however, retrieval of the plastic carrier is relatively difficult, particularly with smaller sizes. The purpose of this study was to develop composite carriers consisting of polyethylene (PE), hydroxyapatite (HA), and strontium oxide (SrO) for carrier-based root canal obturation. Methods: Composite fibers of HA, PE, and SrO were fabricated in the shape of a carrier for delivering gutta-percha (GP) using a melt-extrusion process. The fibers were characterized using infrared spectroscopy and the thermal properties determined using differential scanning calorimetry. The elastic modulus and tensile strength tests were dete
... Show MoreTchebichef polynomials (TPs) play a crucial role in various fields of mathematics and applied sciences, including numerical analysis, image and signal processing, and computer vision. This is due to the unique properties of the TPs and their remarkable performance. Nowadays, the demand for high-quality images (2D signals) is increasing and is expected to continue growing. The processing of these signals requires the generation of accurate and fast polynomials. The existing algorithms generate the TPs sequentially, and this is considered as computationally costly for high-order and larger-sized polynomials. To this end, we present a new efficient solution to overcome the limitation of sequential algorithms. The presented algorithm us
... Show MoreThis study aims to isolate the pathogenic yeasts from genital tract and investigate their relationship with the age .The results clarified that the most pathogenic yeast isolated from genital tract was Candida albicans , also the results of C.albicanas isolates susceptibility test, to different antifungal revealed that they were sensitive to Miconazole, Ketoconazole and Clotrimazol and were resistant to Nystatin and Grisofulvin. The study of relationship of vaginal infection with the age showed that the incidence of infection with Candida was high among females age group (19-39 years).
Wheat is rich in sources of fiber, oligosaccharides, and resistant starch, simple carbohydrates which may have a protective role against carcinoma. Additionally, Whole wheat/bran as well includes contains phytochemicals such as flavonoids, lignans, folate, phytosterols, phenolic acids, and tocols. The above phytochemicals suitable forms antioxidant and cholesterol-reducing activities. Phytoestrogens are regarded as especially essential in the preventative measures of hormonally dependent malignancies such as breast cancer (BC). In this study lowered BC risk has been associated with whole grain/bran consumption with an odds ratio (OR=0.24 and 95 %CI=0.10-0.56). Wheat/bran appears to have a reliable protective impact against BC. While intake
... Show MoreThe calibration of a low-speed wind tunnel (LSWT) test section had been made in the present work. The tunnel was designed and constructed at the Aerodynamics Lab. in the Mechanical Engineering Department/University of Baghdad. The test section design speed is 70 m/s. Frictional loses and uniformity of the flow inside the test section had been tested and calibrated based on the British standards for flow inside ducts and conduits. Pitot-static tube, boundary layer Pitot tube were the main instruments which were used in the present work to measure the flow characteristics with emphasize on the velocity uniformity and boundary layer growth along the walls of the test section. It is found that the maximum calibrated velocity for empty test sect
... Show MoreDisease diagnosis with computer-aided methods has been extensively studied and applied in diagnosing and monitoring of several chronic diseases. Early detection and risk assessment of breast diseases based on clinical data is helpful for doctors to make early diagnosis and monitor the disease progression. The purpose of this study is to exploit the Convolutional Neural Network (CNN) in discriminating breast MRI scans into pathological and healthy. In this study, a fully automated and efficient deep features extraction algorithm that exploits the spatial information obtained from both T2W-TSE and STIR MRI sequences to discriminate between pathological and healthy breast MRI scans. The breast MRI scans are preprocessed prior to the feature
... Show MoreSupport vector machines (SVMs) are supervised learning models that analyze data for classification or regression. For classification, SVM is widely used by selecting an optimal hyperplane that separates two classes. SVM has very good accuracy and extremally robust comparing with some other classification methods such as logistics linear regression, random forest, k-nearest neighbor and naïve model. However, working with large datasets can cause many problems such as time-consuming and inefficient results. In this paper, the SVM has been modified by using a stochastic Gradient descent process. The modified method, stochastic gradient descent SVM (SGD-SVM), checked by using two simulation datasets. Since the classification of different ca
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