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
Arabic text categorization for pattern recognitions is challenging. We propose for the first time a novel holistic method based on clustering for classifying Arabic writer. The categorization is accomplished stage-wise. Firstly, these document images are sectioned into lines, words, and characters. Secondly, their structural and statistical features are obtained from sectioned portions. Thirdly, F-Measure is used to evaluate the performance of the extracted features and their combination in different linkage methods for each distance measures and different numbers of groups. Finally, experiments are conducted on the standard KHATT dataset of Arabic handwritten text comprised of varying samples from 1000 writers. The results in the generatio
... Show MoreThe quality of Global Navigation Satellite Systems (GNSS) networks are considerably influenced by the configuration of the observed baselines. Where, this study aims to find an optimal configuration for GNSS baselines in terms of the number and distribution of baselines to improve the quality criteria of the GNSS networks. First order design problem (FOD) was applied in this research to optimize GNSS network baselines configuration, and based on sequential adjustment method to solve its objective functions.
FOD for optimum precision (FOD-p) was the proposed model which based on the design criteria of A-optimality and E-optimality. These design criteria were selected as objective functions of precision, whic
... Show MoreIn this paper, we implement and examine a Simulink model with electroencephalography (EEG) to control many actuators based on brain waves. This will be in great demand since it will be useful for certain individuals who are unable to access some control units that need direct contact with humans. In the beginning, ten volunteers of a wide range of (20-66) participated in this study, and the statistical measurements were first calculated for all eight channels. Then the number of channels was reduced by half according to the activation of brain regions within the utilized protocol and the processing time also decreased. Consequently, four of the participants (three males and one female) were chosen to examine the Simulink model duri
... Show MoreToday with increase using social media, a lot of researchers have interested in topic extraction from Twitter. Twitter is an unstructured short text and messy that it is critical to find topics from tweets. While topic modeling algorithms such as Latent Semantic Analysis (LSA) and Latent Dirichlet Allocation (LDA) are originally designed to derive topics from large documents such as articles, and books. They are often less efficient when applied to short text content like Twitter. Luckily, Twitter has many features that represent the interaction between users. Tweets have rich user-generated hashtags as keywords. In this paper, we exploit the hashtags feature to improve topics learned
This paper deals with the design and implementation of an ECG system. The proposed system gives a new concept of ECG signal manipulation, storing, and editing. It consists mainly of hardware circuits and the related software. The hardware includes the circuits of ECG signals capturing, and system interfaces. The software is written using Visual Basic languages, to perform the task of identification of the ECG signal. The main advantage of the system is to provide a reported ECG recording on a personal computer, so that it can be stored and processed at any time as required. This system was tested for different ECG signals, some of them are abnormal and the other is normal, and the results show that the system has a good quality of diagno
... Show MoreImage retrieval is used in searching for images from images database. In this paper, content – based image retrieval (CBIR) using four feature extraction techniques has been achieved. The four techniques are colored histogram features technique, properties features technique, gray level co- occurrence matrix (GLCM) statistical features technique and hybrid technique. The features are extracted from the data base images and query (test) images in order to find the similarity measure. The similarity-based matching is very important in CBIR, so, three types of similarity measure are used, normalized Mahalanobis distance, Euclidean distance and Manhattan distance. A comparison between them has been implemented. From the results, it is conclud
... Show MoreIris research is focused on developing techniques for identifying and locating relevant biometric features, accurate segmentation and efficient computation while lending themselves to compression methods. Most iris segmentation methods are based on complex modelling of traits and characteristics which, in turn, reduce the effectiveness of the system being used as a real time system. This paper introduces a novel parameterized technique for iris segmentation. The method is based on a number of steps starting from converting grayscale eye image to a bit plane representation, selection of the most significant bit planes followed by a parameterization of the iris location resulting in an accurate segmentation of the iris from the origin
... Show MoreIn recent years, there has been expanding development in the vehicular part and the number of vehicles moving on the road in all the sections of the country. Vehicle number plate identification based on image processing is a dynamic area of this work; this technique is used for security purposes such as tracking of stolen cars and access control to restricted areas. The License Plate Recognition System (LPRS) exploits a digital camera to capture vehicle plate numbers is used as input to the proposed recognition system. Basically, the developing system is consist of three phases, vehicle license plate localization, character segmentation, and character recognition, the License Plate (LP) detection is presented using canny
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