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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
Sun Jan 01 2017
Journal Name
Iec2017 Proceedings Book
Improving TF-IDF with Singular Value Decomposition (SVD) for Feature Extraction on Twitter
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Publication Date
Wed Oct 18 2023
Journal Name
Iraqi National Journal Of Nursing Specialties
Assessment of Quality of Life for Patients with Permanent Pacemaker in Baghdad City
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Objectives: To determine the (QoL) for patients with permanent pacemaker and to find-out the relationship between
these patients’ (QoL) and their sociodemographic characteristics such as age, gender, level of education, and
occupation.
Methodology: ٨ purposive non-probability” sample of (62) patient with permanent pacemaker was involved in this
study. The developed questionnaire consists of (4) parts which include !.demographic data form, 2.disease-related
information form, 3.socioeconomic data form, and 4.Permanent pacemaker patient’s quality of life questionnaire data
form. The validity and reliability of the questionnaire were determined through the application of a pilot study. ٨
descriptive statistical a

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Publication Date
Wed May 01 2013
Journal Name
Ieee Journal Of Biomedical And Health Informatics
Classification of Finger Movements for the Dexterous Hand Prosthesis Control With Surface Electromyography
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Publication Date
Wed Oct 09 2024
Journal Name
Engineering, Technology & Applied Science Research
Improving Pre-trained CNN-LSTM Models for Image Captioning with Hyper-Parameter Optimization
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The issue of image captioning, which comprises automatic text generation to understand an image’s visual information, has become feasible with the developments in object recognition and image classification. Deep learning has received much interest from the scientific community and can be very useful in real-world applications. The proposed image captioning approach involves the use of Convolution Neural Network (CNN) pre-trained models combined with Long Short Term Memory (LSTM) to generate image captions. The process includes two stages. The first stage entails training the CNN-LSTM models using baseline hyper-parameters and the second stage encompasses training CNN-LSTM models by optimizing and adjusting the hyper-parameters of

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Publication Date
Sun Oct 30 2022
Journal Name
Egyptian Journal Of Hospital Medicine
Antibiofilm Activity of Conocarpus erectus Leaves Extract and Assessment Its Effect on pelA and algD Genes on Multi-drug Resistant Pseudomonas aeruginosa
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Due to its various resistance mechanisms, Pseudomonas aeruginosa is the most prevalent opportunistic infection that kills hospitalized patients. Thus, therapeutic options become limited. Objective: The study aimed to estimate the antibiofilm effectiveness of Conocarpus erectus leaf extracts against MDR P. aeruginosa isolates and examines pelA and algD gene expression. Subjects and Methods: One hundred-fifty clinical samples were collected from five Baghdad hospitals between September 2021 and January 2022. Samples were grown on different mediums. Despite cetrimide agar's ability to detect P. aeruginosa, only 83 isolates developed at 42°C. VITEK 2 compact system identification followed. This study examined 83 of P. aeruginosa isolates for r

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Publication Date
Fri Nov 28 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Thickness of Buccal Bone at Various Sites of the Mandible and Its Clinical Significance in MonocorticalScrews Placement Using Multi-Slice Computed Tomography
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Background:Open reduction and internal fixation (ORIF) of using miniplates and screws is the treatment of choice of mandibular fractures. It is important to know both: the region where the bone providesafirm anchorage, andthe topography of the dental apices and inferior alveolar nerve to avoiddamaging them when inserting the screw. The aim of this study is to determine the thickness of buccal cortical plate and that of buccal bone at the parasymphysis and mandibular body, thereby determining the area that provide afirm anchorage and the maximum length of mono-cortical screws that can be safely placed in these regions without injuring the tooth roots or mandibular nerve. Materials and Methods:The sample of the present study was 110 Iraqi sub

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Publication Date
Fri Nov 28 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Diagnosis and localization of the maxillary impacted canines by using dental multi-slice computed tomography 3D view and reconstructed panoramic 2D view
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Background: Diagnosis and treatment planning can be difficult with conventional radiographic methods as the orthodontic-surgical management of impacted canines requires accurate diagnosis and precise localization of the impacted canine and the surrounding structures. This study was aimed to localize and evaluate weather there is any differences in the diagnostic information provided by multi-slice computed tomography three dimensional volumetric CT images and two dimensional reconstructed panorama images (derived from CT) in subjects with impacted maxillary canines. Materials and Methods: Thirty patients including 24 female and 6 male with mean age of 18 years with suspected unilaterally or bilaterally impacted maxillary canines were evalu

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Publication Date
Mon May 07 2018
Journal Name
Human And Ecological Risk Assessment: An International Journal
Multi-biomarker responses after exposure to organophosphates chlorpyrifos in the freshwater mussels <i>Unio tigridis</i> and snails <i>Viviparous benglensis</i>
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Publication Date
Fri Jan 01 2016
Journal Name
Ieee Access
Towards an Applicability of Current Network Forensics for Cloud Networks: A SWOT Analysis
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In recent years, the migration of the computational workload to computational clouds has attracted intruders to target and exploit cloud networks internally and externally. The investigation of such hazardous network attacks in the cloud network requires comprehensive network forensics methods (NFM) to identify the source of the attack. However, cloud computing lacks NFM to identify the network attacks that affect various cloud resources by disseminating through cloud networks. In this paper, the study is motivated by the need to find the applicability of current (C-NFMs) for cloud networks of the cloud computing. The applicability is evaluated based on strengths, weaknesses, opportunities, and threats (SWOT) to outlook the cloud network. T

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Publication Date
Tue Jan 01 2013
Journal Name
Iraqi Journal Of Physics
A comparison between PCA and some enhancement filters for denoising astronomical images
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This paper includes a comparison between denoising techniques by using statistical approach, principal component analysis with local pixel grouping (PCA-LPG), this procedure is iterated second time to further improve the denoising performance, and other enhancement filters were used. Like adaptive Wiener low pass-filter to a grayscale image that has been degraded by constant power additive noise, based on statistics estimated from a local neighborhood of each pixel. Performs Median filter of the input noisy image, each output pixel contains the Median value in the M-by-N neighborhood around the corresponding pixel in the input image, Gaussian low pass-filter and Order-statistic filter also be used. Experimental results shows LPG-PCA method

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