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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
Mon Jan 11 2021
Journal Name
2nd International Conference In Physical Science & Advanced Materials
Comparing the optical parameters for thin CAZTSe films prepared with various Ag ratios and annealing temperatures
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􀀑􀀃Pure Cu (CZTSe) and Ag dopant CZTSe (CAZTSe) thin films with Ag content of 0.1 and 0.2 were fabricated on coring glass substrate at R.T with thickness of 800nm by thermal evaporation method. Comparison between the optical characteristics of pure Cu and Ag alloying thin films was done by measuring and analyzing the absorbance and transmittance spectra in the range of (400-1100)nm. Also, the effect of annealing temperature at 373K and 473K on these characteristics was studied. The results indicated that all films had high absorbance and low transmittance in visible region, and the direct bang gap of films decreases with increasing Ag content and annealing temperature. Optical parameters like extinction coefficientrefractive index, and

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Publication Date
Thu Feb 11 2016
Journal Name
Journal Of Materials Science: Materials In Electronics
Electrochemical deposition of CdSe-sensitized TiO2 nanotube arrays with enhanced photoelectrochemical performance for solar cell application
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Publication Date
Tue Dec 05 2023
Journal Name
Baghdad Science Journal
AlexNet Convolutional Neural Network Architecture with Cosine and Hamming Similarity/Distance Measures for Fingerprint Biometric Matching
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In information security, fingerprint verification is one of the most common recent approaches for verifying human identity through a distinctive pattern. The verification process works by comparing a pair of fingerprint templates and identifying the similarity/matching among them. Several research studies have utilized different techniques for the matching process such as fuzzy vault and image filtering approaches. Yet, these approaches are still suffering from the imprecise articulation of the biometrics’ interesting patterns. The emergence of deep learning architectures such as the Convolutional Neural Network (CNN) has been extensively used for image processing and object detection tasks and showed an outstanding performance compare

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Publication Date
Sun Sep 01 2019
Journal Name
Gazi University Journal Of Science
Reliable Iterative Methods for Solving Convective Straight and Radial Fins with Temperature-Dependent Thermal Conductivity Problems
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In our article, three iterative methods are performed to solve the nonlinear differential equations that represent the straight and radial fins affected by thermal conductivity. The iterative methods are the Daftardar-Jafari method namely (DJM), Temimi-Ansari method namely (TAM) and Banach contraction method namely (BCM) to get the approximate solutions. For comparison purposes, the numerical solutions were further achieved by using the fourth Runge-Kutta (RK4) method, Euler method and previous analytical methods that available in the literature. Moreover, the convergence of the proposed methods was discussed and proved. In addition, the maximum error remainder values are also evaluated which indicates that the propo

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Publication Date
Wed Oct 17 2018
Journal Name
Journal Of Economics And Administrative Sciences
The Use Of Some Parametric And Non parametric Methods For Analysis Of Factorial Experiments With Application
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In this search, we examined the factorial experiments and the study of the significance of the main effects, the interaction of the factors and their simple effects by the F test (ANOVA) for analyze the data of the factorial experience. It is also known that the analysis of variance requires several assumptions to achieve them, Therefore, in case of violation of one of these conditions we conduct a transform to the data in order to match or achieve the conditions of analysis of variance, but it was noted that these transfers do not produce accurate results, so we resort to tests or non-parametric methods that work as a solution or alternative to the parametric tests , these method

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Publication Date
Sat Dec 01 2012
Journal Name
Iraqi Journal Of Physics
The transition rates for 232Th using the two component particle-hole state density with different corrections
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The particle-hole state densities have been calculated for 232Th in
the case of incident neutron with  ,  1 Z Z T T T T and   2 Z T T .
The finite well depth, surface effect, isospin and Pauli correction are
considered in the calculation of the state densities and then the
transition rates. The isospin correction function ( ) iso f has been
examined for different exciton configurations and at different
excitation energies up to 100 MeV. The present results are indicated
that the included corrections have more affected on transition rates
behavior for        , , and    above 30MeV excitation energy

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Publication Date
Fri Sep 30 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Laboratory Testing and Evaluating of Shale Interaction with Mud for Tanuma Shale formation in Southern Iraq
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   Rock failure during drilling is an important problem to be solved in petroleum technology. one of the most causes of rock failure is shale chemical interaction with drilling fluids. This interaction is changing the shale strength as well as its pore pressure relatively near the wellbore wall. In several oilfields in southern Iraq, drilling through the Tanuma formation is known as the most challenging operation due to its unstable behavior. Understanding the chemical reactions between shale and drilling fluid is determined by examining the features of shale and its behavior with drilling mud. Chemical interactions must be mitigated by the selection of suitable drilling mud with effective chemical additives. This study is describing t

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Publication Date
Thu Nov 11 2021
Journal Name
Nano Express
Near-infrared PbS quantum dots functionalized with affibodies and ZnPP for targeted imaging and therapeutic applications
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Abstract<p>We report a new theranostic device based on lead sulfide quantum dots (PbS QDs) with optical emission in the near infrared wavelength range decorated with affibodies (small 6.5 kDa protein-based antibody replacements) specific to the cancer biomarker human epidermal growth factor receptor 2 (HER2), and zinc(II) protoporphyrin IX (ZnPP) to combine imaging, targeting and therapy within one nanostructure. Colloidal PbS QDs were synthesized in aqueous solution with a nanocrystal diameter of ∼5 nm and photoluminescence emission in the near infrared wavelength range. The Z<sub>HER2:432</sub> affibody, mutated through the introduction of two cysteine residues at the C-terminus (</p> ... Show More
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Publication Date
Sat Jun 01 2024
Journal Name
Results In Engineering
Stability analysis for the phytoplankton-zooplankton model with depletion of dissolved oxygen and strong Allee effects
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Publication Date
Tue Feb 01 2022
Journal Name
Baghdad Science Journal
Flow Injection Analysis with Turbidity Detection for the Quantitative Determination of Mebeverine Hydrochloride in Pharmaceutical Formulations
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The main objective of this paper is to develop and validate flow injection method, a precise, accurate, simple, economic, low cost and specific turbidimetric method for the quantitative determination of mebeverine hydrochloride (MbH) in pharmaceutical preparations.  A homemade NAG Dual & Solo (0-180º) analyser which contains two identical detections units (cell 1 and 2) was applied for turbidity measurements. The developed method was optimized for different chemical and physical parameters such as perception reagent concentrations, aqueous salts solutions, flow rate, the intensity of the sources light, sample volume, mixing coil and purge time. The correlation coefficients (r) of the developed method were 0.9980 and 0.9986 for

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