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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
Wed Aug 30 2023
Journal Name
Al-kindy College Medical Journal
‘Peacock tail’ Clipping Technique for a Giant Middle Cerebral Artery Aneurysm: A Technical Note
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Background: Giant middle cerebral artery (MCA) aneurysms are surgically challenging lesions. Because of the complexity and variability of these aneurysms, a customized surgical technique is often needed for each case. In this article, we present a modified clip reconstruction technique of a ruptured complex giant partially thrombosed middle cerebral artery aneurysm.

Case description: The aneurysm was exposed using the pterional approach. Following proximal control, the aneurysm sac was decompressed. Then, we applied permanent clips to reconstruct the aneurysm neck. The configuration of the aneurysm mandated a tailored clipping pattern to account for resi

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Publication Date
Thu Feb 29 2024
Journal Name
International Journal Of Safety And Security Engineering
Urban Safety is a Tool for Containing Slums to Reach a Sustainable Urban Structure
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Many cities suffer from the large spread of slums, especially the cities of the Middle East. The purpose of the paper is to study the reality of informal housing in Al-Barrakia and the most important problems that it suffers from. The paper also seeks to study the presence or absence of a correlation between urban safety indicators and urban containment indicators as one of the methods of developing and planning cities. This can be achieved through sustainable urban management. The slums are a source of many urban problems that threaten the security and safety of the residents and represent a focus for the concentration of crimes and drugs. The paper seeks to answer the following question: How can urban safety be improved through urban cont

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Publication Date
Mon Aug 18 2025
Journal Name
Journal Of Genetic And Environment Conservation
Ultrasound application as a new green technology for preservation of table eggs: A review
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In recent years, there has been a significant increase in research demonstrating the new and diverse uses of non-thermal food processing technologies, including more efficient mixing and blending processes, faster energy and mass transfer, lower temperature and selective extraction, reduced thermal and concentration gradients, reduced equipment size, faster response to extraction control, faster start-up, increased production, and a reduction in the number of steps in preparation and processing. Applications of ultrasound technology have indicated that this technology has a promising and significant future in the food industry and preservation, and there is a wide scope for its use due to the higher purity of final products and the

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Publication Date
Wed Dec 15 2021
Journal Name
Arab World English Journal
Reading Difficulties in English as a Second Language in Grade Five at a Saint Patrick’s High School for Boys, Hyderabad- India
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Reading is one of the essential components of the English language. Countries that use English as a second language (ESL) sometimes have difficulties in reading and comprehension. According to many researches, mother tongue has proved some interferences with learning a second language. This study investigated the results of reading difficulties of young second language learners in terms of accuracy, comprehension, and rate using the Neale Analysis of Reading Ability test. The study was carried out in one of the High Schools for Boys in Hyderabad, India and included Grade five, aged 10-12 years. In order to understand the reading difficulties of English as a second language, a qualitative approach was employed. Interview, reading tes

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Publication Date
Sat Jun 08 2024
Journal Name
Karbala International Journal Of Modern Science
Designing of Human Serum Albumin Nanoparticles for Drug Delivery: a Potential Use of Anticancer Treatment
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Human serum albumin (HSA) nanoparticles have been widely used as versatile drug delivery systems for improving the efficiency and pharmaceutical properties of drugs. The present study aimed to design HSA nanoparticle encapsulated with the hydrophobic anticancer pyridine derivative (2-((2-([1,1'-biphenyl]-4-yl)imidazo[1,2-a]pyrimidin-3-yl)methylene)hydrazine-1-carbothioamide (BIPHC)). The synthesis of HSA-BIPHC nanoparticles was achieved using a desolvation process. Atomic force microscopy (AFM) analysis showed the average size of HSA-BIPHC nanoparticles was 80.21 nm. The percentages of entrapment efficacy, loading capacity and production yield were 98.11%, 9.77% and 91.29%, respectively. An In vitro release study revealed that HSA-BIPHC nan

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Publication Date
Mon Nov 06 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
Effect of hunting cooperation and fear in a food chain model with intraspecific competition
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Taking into account the significance of food chains in the environment, it demonstrates the interdependence of all living things and has economic implications for people. Hunting cooperation, fear, and intraspecific competition are all included in a food chain model that has been developed and researched. The study tries to comprehend how these elements affect the behavior of species along the food chain. We first examined the suggested model's solution properties before calculating every potential equilibrium point and examining the stability and bifurcation nearby. We have identified the factors that guarantee the global stability of the positive equilibrium point using the geometric approach. Additionally, the circumstances that would gu

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Publication Date
Thu Nov 21 2019
Journal Name
Al-kindy College Medical Journal
Magnetic Resonance Venography Findings In A Group Of Patients With Multiple Sclerosis
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Background: Multiple sclerosis is a chronic heterogeneous demyelinating axonal and inflammatory disease involving the Central Nervous System [CNS] white matter with a possibility of gray matter involvement in which the insulating covers of nerve cells in the brain and spinal cord are damaged. This damage disrupts the ability of parts of the nervous system to communicate, resulting in a wide range of signs and symptoms. Cerebral venous insufficiency theory was raised as a possible etiology for the disease at 2008 by Zamboni an Italian cardiothoracic surgeon. This theory was defeated by Multiple Sclerosis[ MS] researchers and scientists who thought that the disease is an autoimmune rather than vascular.

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Publication Date
Mon Sep 23 2019
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Buckling analysis of reinforced composite plates with a multiwall carbon nanotube (MWCNT)
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Publication Date
Thu Nov 17 2016
Journal Name
International Journal Of Computer Applications
Colour Recognizing Robot Arm Equipped with a CMOS Camera and an FPGA
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In this paper a system is designed on an FPGA using a Nios II soft-core processor, to detect the colour of a specific surface and moving a robot arm accordingly. The surface being detected is bounded by a starting mark and an ending mark, to define the region of interest. The surface is also divided into sections as rows and columns and each section can have any colour. Such a system has so many uses like for example warehouses or even in stores where their storing areas can be divided to sections and each section is coloured and a robot arm collects objects from these sections according to the section’s colour also the robot arm can organize objects in sections according to the section’s colour.

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Publication Date
Fri Sep 29 2023
Journal Name
International Journal Of Applied Mechanics And Engineering
Fuzzy logic control of active suspension system equipped with a hydraulic actuator
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In this paper, the Active Suspension System (ASS) of road vehicles was investigated. In addition to the conventional stiffness and damper, the proposed ASS includes a fuzzy controller, a hydraulic actuator, and an LVDT position sensor. Furthermore, this paper presents a nonlinear model describing the operation of the hydraulic actuator as a part of the suspension system. Additionally, the detailed steps of the fuzzy controller design for such a system are introduced. A MATLAB/Simulink model was constructed to study the proposed ASS at different profiles of road irregularities. The results have shown that the proposed ASS has superior performance compared to the conventional Passive Suspension System (PSS), where the body displacemen

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