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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 Oct 25 2023
Journal Name
Journal Of Optics
Integrated gallium phosphide-waveguide polarization rotator based on rotating a horizontal slot by 45 degree for 700 nm wavelength
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Abstract<p>Polarization manipulation elements operating at visible wavelengths represent a critical component of quantum communication sub-systems, equivalent to their telecom wavelength counterparts. The method proposed involves rotating the optic axis of the polarized input light by an angle of 45 degree, thereby converting the fundamental transverse electric (TE<sub>0</sub>) mode to the fundamental transverse magnetic (TM<sub>0</sub>) mode. This paper outlines an integrated gallium phosphide-waveguide polarization rotator, which relies on the rotation of a horizontal slot by 45 degree at a wavelength of 700 nm. This will ultimately lead to the conception of a mode hybridization phenomeno</p> ... Show More
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Publication Date
Thu Aug 01 2019
Journal Name
Nanomedicine: Nanotechnology, Biology And Medicine
Listeria innocua Dps as a nanoplatform for bioluminescence based photodynamic therapy utilizing Gaussia princeps luciferase and zinc protoporphyrin IX
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Publication Date
Wed Oct 25 2023
Journal Name
Journal Of Optics
Integrated gallium phosphide-waveguide polarization rotator based on rotating a horizontal slot by 45 degree for 700 nm wavelength
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Polarization manipulation elements operating at visible wavelengths represent a critical component of quantum communication sub-systems, equivalent to their telecom wavelength counterparts. The method proposed involves rotating the optic axis of the polarized input light by an angle of 45 degree, thereby converting the fundamental transverse electric (TE0) mode to the fundamental transverse magnetic (TM0) mode. This paper outlines an integrated gallium phosphide-waveguide polarization rotator, which relies on the rotation of a horizontal slot by 45 degree at a wavelength of 700 nm. This will ultimately lead to the conception of a mode hybridization phenomenon in the waveguide. The simulation results demonstrate a polarization co

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Publication Date
Sun Oct 01 2023
Journal Name
Applied Sciences
Multiobjective Optimization of Stereolithography for Dental Bridge Based on a Simple Shape Model Using Taguchi and Response Surface Methods
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Stereolithography (SLA) has become an essential photocuring 3D printing process for producing parts of complex shapes from photosensitive resin exposed to UV light. The selection of the best printing parameters for good accuracy and surface quality can be further complicated by the geometric complexity of the models. This work introduces multiobjective optimization of SLA printing of 3D dental bridges based on simple CAD objects. The effect of the best combination of a low-cost resin 3D printer’s machine parameter settings, namely normal exposure time, bottom exposure time and bottom layers for less dimensional deviation and surface roughness, was studied. A multiobjective optimization method was utilized, combining the Taguchi me

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Publication Date
Fri Feb 08 2019
Journal Name
Iraqi Journal Of Laser
Random Number Generation for Quantum Key Distribution Systems Based on Shot-Noise Fluctuations in a P-I-N Photodiode
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A simple setup of random number generator is proposed. The random number generation is based on the shot-noise fluctuations in a p-i-n photodiode. These fluctuations that are defined as shot noise are based on a stationary random process whose statistical properties reflect Poisson statistics associated with photon streams. It has its origin in the quantum nature of light and it is related to vacuum fluctuations. Two photodiodes were used and their shot noise fluctuations were subtracted. The difference was applied to a comparator to obtain the random sequence.

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Publication Date
Mon Aug 25 2025
Journal Name
مجلة كلية التربية
A Multi-modal Critical Discourse Analysis of Selected English Political Cartoons تحليل خطاب نقدي متعدد الوسائط لرسوم كاريكاتورية سياسية إنجليزية مختارة
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This study analyses six political cartoons selected based on their relevance to current Iraqi political issues, specifically the period between 2005 and 2015, from American online newspapers (calgecartooms.com). The selection criteria included the cartoons' satirical elements, visual rhetoric, and their ability to engage with themes such as power dynamics, social issues, and public opinion. It sheds light on how these cartoons can function as mediators of meanings between the cartoonists and the readers. The data is examined using multimodal discourse analysis (MDA), which combines language study with the analysis of other visual elements, like colors, gestures, and images, to understand meaning (O’Halloran et al., 2011). The Visual Socia

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Publication Date
Mon Jan 01 2018
Journal Name
Current Research In Microbiology And Biotechnology
Serodiagnosis of Human Cytomegalovirus in Iraqi Breast cancer and fibroadenoma patients
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Human cytomegalovirus (HCMV) has a worldwide distribution and extremely common infections. The presence of HCMV genome and antigens has been detected in many kinds of human cancers especially breast cancer. In Iraq, the incidence of breast cancer generally exceeds any other type of malignancies among Iraqi population. The study was performed in the period between October 2016 and June 2017 in Central public health laboratory/Baghdad. It involve samples from 90 women including 60 breast cancer patients, 20 benign tumor patients, and 10 normal breast tissues. A blood sample was obtained from each woman included in this study. Anti-HCMV IgG antibody was presented in 9/10 (90%) of normal women, benign breast tumor patients 19/20 (95%) and malig

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Publication Date
Tue Mar 15 2022
Journal Name
Gene Reports
Genotyping of Human Cytomegalovirus Glycoprotein N in Iraqi Breast cancer Patients
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Human Cytomegalovirus (HCMV) is an enveloped ubiquitous ds-DNA virus that has been implicated in several types of malignancies. The current work was conducted in the period extending from (November 2018 to the end of October 2019) and aimed to assess the frequency of glycoprotein N (gN) genotypes of HCMV. A total number of 91serum and plasma specimens were collected to fulfill this purpose from females (71 breast cancer patients, and a control group of 20 females) attending Al-Amal hospital for cancer management and Baghdad teaching hospital. The molecular part of this data was achieved through both PCR and Multiplex PCR for detection of HCMV gN (UL73) entire gene as well as for genotyping. gN was detected in 36/71 (50.7%) of breast cancer

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Publication Date
Sun Jul 01 2018
Journal Name
2018 2nd International Conference On Imaging, Signal Processing And Communication (icispc)
Analogy-based Common-Sense Knowledge for Opinion-Target Identification and Aggregation
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The development of Web 2.0 has improved people's ability to share their opinions. These opinions serve as an important piece of knowledge for other reviewers. To figure out what the opinions is all about, an automatic system of analysis is needed. Aspect-based sentiment analysis is the most important research topic conducted to extract reviewers-opinions about certain attribute, for instance opinion-target (aspect). In aspect-based tasks, the identification of the implicit aspect such as aspects implicitly implied in a review, is the most challenging task to accomplish. However, this paper strives to identify the implicit aspects based on hierarchical algorithm incorporated with common-sense knowledge by means of dimensionality reduction.

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Publication Date
Tue Apr 30 2024
Journal Name
Iraqi Journal Of Science
Detection of Anti-cancer Activity of Silver Nanoparticles Synthesized using Aqueous Mushroom Extract of Pleurotus ostreatus on MCF-7 Human Breast Cancer Cell Line
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     In this research, silver nanoparticles (AgNPs) were manufactured using aqueous extract of mushroom Pleurotus ostreatus. Anticancer potential of AgNPs was investigated versus human breast cancer cell line (MCF-7). Cytotoxic response was assessed by MTT assay. AgNPs showed inhibition effect at the following concentrations 12.5, 25, 50, 100 and 200 µg/ml versus MCF-7 cell line, and all treatments had a positive result. The MCF-7 cells were inhibited up to 85.14 % at the concentration 200 μg/ml of AgNPs which reduced cells viability to 14.86%, while 12.5 μg/ml of AgNPs caused 24.23% cells inhibition with reduction of cells viability to 75.77%.

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