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Overlapping Structure Detection in Protein-Protein Interaction Networks Using a Modified Version of Particle Swarm Optimization
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In today's world, the science of bioinformatics is developing rapidly, especially with regard to the analysis and study of biological networks. Scientists have used various nature-inspired algorithms to find protein complexes in protein-protein interaction (PPI) networks. These networks help scientists guess the molecular function of unknown proteins and show how cells work regularly. It is very common in PPI networks for a protein to participate in multiple functions and belong to many complexes, and as a result, complexes may overlap in the PPI networks. However, developing an efficient and reliable method to address the problem of detecting overlapping protein complexes remains a challenge since it is considered a complex and hard optimization problem. One of the main difficulties in identifying overlapping protein complexes is the accuracy of the partitioning results. In order to accurately identify the overlapping structure of protein complexes, this paper has proposed an overlapping complex detection algorithm termed OCDPSO-Net, which is based on PSO-Net (a well-known modified version of the particle swarm optimization algorithm). The framework of the OCDPSO-Net method consists of three main steps, including an initialization strategy, a movement strategy for each particle, and enhancing search ability in order to expand the solution space. The proposed algorithm has employed the partition density concept for measuring the partitioning quality in PPI network complexes and tried to optimize the value of this quantity by applying the line graph concept of the original graph representing the protein interaction network. The OCDPSO-Net algorithm is applied to a Collins PPI network and the obtained results are compared with different state-of-the-art algorithms in terms of precision ( ), recall ( ), and F-measure ( ). Experimental results confirm that the proposed algorithm has good clustering performance and has outperformed most of the existing recent overlapping algorithms. .

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Publication Date
Fri Mar 21 2014
Journal Name
International Journal Of Antennas And Propagation
Development of a Compact Wide-Slot Antenna for Early Stage Breast Cancer Detection Featuring Circular Array Full-View Geometry
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A novel planar type antenna printed on a high permittivity Rogers’ substrate is proposed for early stage microwave breast cancer detection. The design is based on a p-shaped wide-slot structure with microstrip feeding circuit to eliminate losses of transmission. The design parameters are optimized resulting in a good reflection coefficient at −10 dB from 4.5 to 10.9 GHz. Imaging result using inhomogeneous breast phantom indicates that the proposed antenna is capable of detecting a 5 mm size cancerous tumor embedded inside the fibroglandular region with dielectric contrast between the target and the surrounding materials ranging from 1.7 : 1 to 3.6 : 1.

Publication Date
Sun Jun 07 2015
Journal Name
Baghdad Science Journal
Serum Vascular Endothelial Growth Factor VEGF and Interlukin-8 As a Novel Biomarkers For Early Detection of Ovarian Tumors
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Epithelial ovarian cancer is the leading cause of cancer deaths from gynecological malignancies. Angiogenesis is considered essential for tumor growth and the development of metastases. VEGF and IL?8 are potent angiostimulatory molecules and their expression has been demonstrated in many solid tumors, including ovarian cancer.VEGF and IL-8 concentrations were measured by ELISA test (HumanVEGF,IL-8). Bioassay ELISA/ US Biological / USA).The median VEGF and IL-8 levels were significantly higher in the sera of ovarian cancer patients than in those with benign tumors and in healthy controls.Pretreatment VEGF and IL-8 serum levels might be regarded as an additional tool in the differentiation of ovarian tumors.

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Publication Date
Thu Dec 01 2016
Journal Name
International Journal Of Vlsi Design & Communication Systems (vlsics)
SIMULTANEOUS OPTIMIZATION OF STANDBY AND ACTIVE ENERGY FOR SUB THRESHOLD CIRCUITS
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Increased downscaling of CMOS circuits with respect to feature size and threshold voltage has a result of dramatically increasing in leakage current. So, leakage power reduction is an important design issue for active and standby modes as long as the technology scaling increased. In this paper, a simultaneous active and standby energy optimization methodology is proposed for 22 nm sub-threshold CMOS circuits. In the first phase, we investigate the dual threshold voltage design for active energy per cycle minimization. A slack based genetic algorithm is proposed to find the optimal reverse body bias assignment to set of noncritical paths gates to ensure low active energy per cycle with the maximum allowable frequency at the optimal supply vo

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Publication Date
Thu Oct 01 2015
Journal Name
Iraqi Journal Of Science
optimization of pectinase production from pesudomonas sp. isolated from iraqi soi
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Publication Date
Tue Jan 01 2013
Journal Name
Communications And Network
Link and Cost Optimization of FTTH Network Implementation through GPON Technology
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Publication Date
Mon May 21 2007
Journal Name
Journal Of Planner And Development
Determination of levels of interaction between urban land use and the adoption of spatial analysis techniques (study area, Najaf City)
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the student of the structure of the city and its constituent elements will clearly sense the invisible relationships that underlie the different forms of urban activity, which in turn are defined by the generality of the urban patterns in that city, which will vary clearly according to the location in the city. These relations will be embodied in their true form in the interactions between the different uses of the earth, and the change that will result from their regularity in the form of entities in independent groups, which may share with each other a component of it.
Therefore, the process of controlling the functional interactions between the uses of the urban land and the awareness of t

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Publication Date
Mon Feb 10 2025
Journal Name
Journal Of Optics
Implementing quantum key distribution based on coincidence detection captured from two different single photon detection modules
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Quantum key distribution (QKD) provides unconditional security in theory. However, practical QKD systems face challenges in maximizing the secure key rate and extending transmission distances. In this paper, we introduce a comparative study of the BB84 protocol using coincidence detection with two different quantum channels: a free space and underwater quantum channels. A simulated seawater was used as an example for underwater quantum channel. Different single photon detection modules were used on Bob’s side to capture the coincidence counts. Results showed that increasing the mean photon number generally leads to a higher rate of coincidence detection and therefore higher possibility of increasing the secure key rate. The secure key rat

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Publication Date
Sat Mar 30 2024
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Optimization of Separator Size and Operating Pressure for Three-phase Separators in the West Qurna1 Oil Field
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An optimization study was conducted to determine the optimal operating pressure for the oil and gas separation vessels in the West Qurna 1 oil field. The ASPEN HYSYS software was employed as an effective tool to analyze the optimal pressure for the second and third-stage separators while maintaining a constant operating pressure for the first stage. The analysis involved 10 cases for each separation stage, revealing that the operating pressure of 3.0 Kg/cm2 and 0.7 Kg/cm2 for the second and third stages, respectively, yielded the optimum oil recovery to the flow tank. These pressure set points were selected based on serval factors including API gravity, oil formation volume factor, and gas-oil ratio from the flow tank.    To impro

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Publication Date
Sun Sep 01 2019
Journal Name
Baghdad Science Journal
Symmetric and Positive Definite Broyden Update for Unconstrained Optimization
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Broyden update is one of the one-rank updates which solves the unconstrained optimization problem but this update does not guarantee the positive definite and the symmetric property of Hessian matrix.

In this paper the guarantee of positive definite and symmetric property for the Hessian matrix will be established by updating the vector  which represents the difference between the next gradient and the current gradient of the objective function assumed to be twice continuous and differentiable .Numerical results are reported to compare the proposed method with the Broyden method under standard problems.

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Publication Date
Thu Sep 05 2019
Journal Name
Journal Of Al-qadisiyah For Computer Science And Mathematics
Strongly (E,F)-convexity with applications to optimization problems
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In this paper, a new class of nonconvex sets and functions called strongly -convex sets and strongly -convex functions are introduced. This class is considered as a natural extension of strongly -convex sets and functions introduced in the literature. Some basic and differentiability properties related to strongly -convex functions are discussed. As an application to optimization problems, some optimality properties of constrained optimization problems are proved. In these optimization problems, either the objective function or the inequality constraints functions are strongly -convex. 

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