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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 2023
Journal Name
Aip Conference Proceedings
Sliding mode control based on high-order extended state observer for flexible joint robot under time-varying disturbance
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Abstract. In this paper, a high order extended state observer (HOESO) based a sliding mode control (SMC) is proposed for a flexible joint robot (FJR) system in the presence of time varying external disturbance. A composite controller is integrated the merits of both HOESO and SMC to enhance the tracking performance of FJR system under the time varying and fast lumped disturbance. First, the HOESO estimator is constructed based on only one measured state to precisely estimate unknown system states and lumped disturbance with its high order derivatives in the FJR system. Second, the SMC scheme is designed based on such accurate estimations to govern the nominal FJR system by well compensating the estimation errors in the states and the lumped

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Publication Date
Wed Dec 22 2021
Journal Name
Antibiotics
Classic vs. Novel Antibacterial Approaches for Eradicating Dental Biofilm as Adjunct to Periodontal Debridement: An Evidence-Based Overview
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Periodontitis is a multifactorial chronic inflammatory disease that affects tooth-supporting soft/hard tissues of the dentition. The dental plaque biofilm is considered as a primary etiological factor in susceptible patients; however, other factors contribute to progression, such as diabetes and smoking. Current management utilizes mechanical biofilm removal as the gold standard of treatment. Antibacterial agents might be indicated in certain conditions as an adjunct to this mechanical approach. However, in view of the growing concern about bacterial resistance, alternative approaches have been investigated. Currently, a range of antimicrobial agents and protocols have been used in clinical management, but these remain largely non-v

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Publication Date
Tue Jun 01 2021
Journal Name
Food Chemistry
Development of cellulose Nanofiber-based substrates for rapid detection of ferbam in kale by Surface-enhanced Raman spectroscopy
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Publication Date
Wed Dec 01 2021
Journal Name
Baghdad Science Journal
Improvement of the Fault Tolerance in IoT Based Positioning Systems by Applying for Redundancy in the Controller Layer
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In recent years, the positioning applications of Internet-of-Things (IoT) based systems have grown increasingly popular, and are found to be useful in tracking the daily activities of children, the elderly and vehicle tracking. It can be argued that the data obtained from GPS based systems may contain error, hence taking these factors into account, the proposed method for this study is based on the application of IoT-based positioning and the replacement of using IoT instead of GPS.  This cannot, however, be a reason for not using the GPS, and in order to enhance the reliability, a parallel combination of the modern system and traditional methods simultaneously can be applied. Although GPS signals can only be accessed in open spaces, GP

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Publication Date
Tue Sep 08 2020
Journal Name
Baghdad Science Journal
Modified BFGS Update (H-Version) Based on the Determinant Property of Inverse of Hessian Matrix for Unconstrained Optimization
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The study presents the modification of the Broyden-Flecher-Goldfarb-Shanno (BFGS) update (H-Version) based on the determinant property of inverse of Hessian matrix (second derivative of the objective function), via updating of the vector s ( the difference between the next solution and the current solution), such that the determinant of the next inverse of Hessian matrix is equal to the determinant of the current inverse of Hessian matrix at every iteration. Moreover, the sequence of inverse of Hessian matrix generated by the method would never  approach a near-singular matrix, such that the program would never break before the minimum value of the objective function is obtained. Moreover, the new modification of BFGS update (H-vers

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Publication Date
Mon Dec 05 2022
Journal Name
Baghdad Science Journal
K-Nearest Neighbor Method with Principal Component Analysis for Functional Nonparametric Regression
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This paper proposed a new  method to study functional non-parametric regression data analysis with conditional expectation in the case that the covariates  are functional and the Principal Component Analysis was utilized to de-correlate the multivariate response variables. It  utilized the formula of the Nadaraya Watson estimator (K-Nearest Neighbour (KNN)) for prediction with different types of the semi-metrics, (which are based on Second Derivative and Functional Principal Component Analysis (FPCA))  for measureing the closeness between curves.  Root Mean Square Errors is used for the  implementation of this model which is then compared to the independent response method. R program is used for analysing data. Then, when  the cov

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Publication Date
Wed Jan 30 2019
Journal Name
Journal Of The College Of Education For Women
Peripheral Perception And its Relation With The Need for Cognition for The University Students
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The most important topic for psychologist generally is factor of education and it's active tools because learning needs active perception for stimulus that recived by the educator and give it avalue and meaning , Need for cognition is
very important in the various daily fields of life , especially in learning and teaching and the academy work , it help with shifting the learning level for people , and icreas the intense and challenge between them
The research endeavored to achieve the following aim :
1- Measuring the level of peripheral perception for the university student .
2- Measuring the level of need for cognition for the university student .
3- Measuring the level of peripheral perception for the university student

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
Thinking Styles And Its Relationship With The Need for Cognitive for Students of University
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This study aims to recognize the most common thinking styles and level of the need for cognitive university students , the relation between thinking styles and the need for cognitive, and there are differences according to gender .The sample consists of (250) males and females university students for the academic year (2013-2014), and the researcher uses two scales;" thinking styles scale (Harison &Bramson, 1986), and the need for cognitive scale" (Cacioppo, Petty & Kao , 1996).
The results show that there is difference in the range of the prevalence of the thinking styles among university students , the scientific thinking style is the most common , the students have got the arrange level of the need for cognitive , and there

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Publication Date
Mon May 27 2019
Journal Name
Al-khwarizmi Engineering Journal
Prediction of Process Parameters That Affecting on Surface Roughness in Multi-Point Forming Process Using ANOVA Algorithm
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Multipoint forming process is an engineering concept which means that the working surface of the punch and die is produced as hemispherical ends of individual active elements (called pins), where each pin can be independently, vertically displaced using a geometrically reconfigurable die. Several different products can be made without changing tools saved precious production time. Also, the manufacturing of very expensive rigid dies is reduced, and a lot of expenses are saved. But the most important aspects of using such types of equipment are the flexibility of the tooling. This paper presents an experimental investigation of the effect of three main parameters which are blank holder, rubber thickness and forming speed th

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Publication Date
Thu Feb 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The technique of converting multi-choice mathematical programming into linear mathematical programming to find the optimal solution
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The study deals with the issue of multi-choice linear mathematical programming. The right side of the constraints will be multi-choice. However, the issue of multi-purpose mathematical programming can not be solved directly through linear or nonlinear techniques. The idea is to transform this matter into a normal linear problem and solve it In this research, a simple technique is introduced that enables us to deal with this issue as regular linear programming. The idea is to introduce a number of binary variables And its use to create a linear combination gives one parameter was used multiple. As well as the options of linear programming model to maximize profits to the General Company for Plastic Industries product irrigation sy

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