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A graph-based multi-sample test for identifying pathways associated with cancer progression
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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

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Publication Date
Fri Mar 31 2023
Journal Name
Wasit Journal Of Computer And Mathematics Science
Security In Wireless Sensor Networks Based On Lightweight Algorithms : An Effective Survey
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At the level of both individuals and companies, Wireless Sensor Networks (WSNs) get a wide range of applications and uses. Sensors are used in a wide range of industries, including agriculture, transportation, health, and many more. Many technologies, such as wireless communication protocols, the Internet of Things, cloud computing, mobile computing, and other emerging technologies, are connected to the usage of sensors. In many circumstances, this contact necessitates the transmission of crucial data, necessitating the need to protect that data from potential threats. However, as the WSN components often have constrained computation and power capabilities, protecting the communication in WSNs comes at a significant performance pena

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Publication Date
Mon Sep 03 2012
Journal Name
The International Archives Of The Photogrammetry, Remote Sensing And Spatial Information Sciences
CALIBRATION OF FULL-WAVEFORM ALS DATA BASED ON ROBUST INCIDENCE ANGLE ESTIMATION
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Abstract. Full-waveform airborne laser scanning data has shown its potential to enhance available segmentation and classification approaches through the additional information it can provide. However, this additional information is unable to directly provide a valid physical representation of surface features due to many variables affecting the backscattered energy during travel between the sensor and the target. Effectively, this delivers a mis-match between signals from overlapping flightlines. Therefore direct use of this information is not recommended without the adoption of a comprehensive radiometric calibration strategy that accounts for all these effects. This paper presents a practical and reliable radiometric calibration r

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Publication Date
Tue Sep 21 2021
Journal Name
Journal Of Healthcare Engineering
Complexity and Entropy Analysis to Improve Gender Identification from Emotional-Based EEGs
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Investigating gender differences based on emotional changes becomes essential to understand various human behaviors in our daily life. Ten students from the University of Vienna have been recruited by recording the electroencephalogram (EEG) dataset while watching four short emotional video clips (anger, happiness, sadness, and neutral) of audiovisual stimuli. In this study, conventional filter and wavelet (WT) denoising techniques were applied as a preprocessing stage and Hurst exponent

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Publication Date
Sat Apr 01 2023
Journal Name
Journal Of Engineering
Proposed Face Detection Classification Model Based on Amazon Web Services Cloud (AWS)
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One of the most important features of the Amazon Web Services (AWS) cloud is that the program can be run and accessed from any location. You can access and monitor the result of the program from any location, saving many images and allowing for faster computation. This work proposes a face detection classification model based on AWS cloud aiming to classify the faces into two classes: a non-permission class, and a permission class, by training the real data set collected from our cameras. The proposed Convolutional Neural Network (CNN) cloud-based system was used to share computational resources for Artificial Neural Networks (ANN) to reduce redundant computation. The test system uses Internet of Things (IoT) services through our ca

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Publication Date
Thu Apr 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Groundwater Quality Study Based on the Existence of Escherichia coli as Bioindicator
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Abstract<p>The research aim was to observe the distribution pattern of <italic>Escherichia coli</italic> as groundwater pollution indicator in the most populous area, Matraman Sub-District Area in Jakarta, Indonesia (106°49’35” EL and 06°10’37” SL) consists of six (6) Urban Villages. The existence of <italic>Escherichia coli</italic> was measured with Most Probable Number (MPN) method as mentioned in Indonesian Standard Number 01-2332.1-2006. This research was also measure pollution parameter of Dissolved Oxygen (DO) and pH, and topography analyses used as well to determine groundwater flow direction. Groundwater sampling was conducted in several housings that have </p> ... Show More
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Publication Date
Thu Jun 01 2023
Journal Name
Advances In Mechanical Engineering
3D-shape formation of blood vessels based on computer aided design system
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This paper proposes and tests a computerized approach for constructing a 3D model of blood vessels from angiogram images. The approach is divided into two steps, image features extraction and solid model formation. In the first step, image morphological operations and post-processing techniques are used for extracting geometrical entities from the angiogram image. These entities are the middle curve and outer edges of the blood vessel, which are then passed to a computer-aided graphical system for the second phase of processing. The system has embedded programming capabilities and pre-programmed libraries for automating a sequence of events that are exploited to create a solid model of the blood vessel. The gradient of the middle c

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Publication Date
Mon Aug 01 2022
Journal Name
Journal Of Molecular Liquids
Study to amino acid-based inhibitors as an effective anti-corrosion material
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The inhibitory behavior of L-Cysteine (Cys) and its derivatives towards iron corrosion through density functional theory (DFT) was investigated. The current research study undertakes a rigorous evaluation of global as well as local reactivity descriptors of the Cys in protonated as well as neutral forms and the changes in reactivity after the combination of Cys into di- and tripeptides. The inhibitory effect of di- and tri-peptides increases since, in the molecular structure, the number of reaction centers increase. We computed the adsorption energies (Eads) and low energy complexes with most stability for the adsorption of small peptides and Cys amino acids onto the surfaces of Fe (1 1 1). We found that the adsorption of tri-peptides onto

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Publication Date
Sun Dec 31 2023
Journal Name
Iraqi Journal Of Information And Communication Technology
EEG Signal Classification Based on Orthogonal Polynomials, Sparse Filter and SVM Classifier
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This work implements an Electroencephalogram (EEG) signal classifier. The implemented method uses Orthogonal Polynomials (OP) to convert the EEG signal samples to moments. A Sparse Filter (SF) reduces the number of converted moments to increase the classification accuracy. A Support Vector Machine (SVM) is used to classify the reduced moments between two classes. The proposed method’s performance is tested and compared with two methods by using two datasets. The datasets are divided into 80% for training and 20% for testing, with 5 -fold used for cross-validation. The results show that this method overcomes the accuracy of other methods. The proposed method’s best accuracy is 95.6% and 99.5%, respectively. Finally, from the results, it

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Publication Date
Sun Jun 20 2021
Journal Name
Baghdad Science Journal
Arabic Speech Classification Method Based on Padding and Deep Learning Neural Network
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Deep learning convolution neural network has been widely used to recognize or classify voice. Various techniques have been used together with convolution neural network to prepare voice data before the training process in developing the classification model. However, not all model can produce good classification accuracy as there are many types of voice or speech. Classification of Arabic alphabet pronunciation is a one of the types of voice and accurate pronunciation is required in the learning of the Qur’an reading. Thus, the technique to process the pronunciation and training of the processed data requires specific approach. To overcome this issue, a method based on padding and deep learning convolution neural network is proposed to

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Publication Date
Mon Aug 31 2015
Journal Name
Journal Of Theoretical And Applied Information Technology
EXAM QUESTIONS CLASSIFICATION BASED ON BLOOM’S TAXONOMY COGNITIVE LEVEL USING CLASSIFIERS COMBINATION
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