Search results for: integration test
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 3509

Search results for: integration test

1739 Solving the Quadratic Assignment Problems by a Genetic Algorithm with a New Replacement Strategy

Authors: Yongzhong Wu, Ping Ji

Abstract:

This paper proposes a genetic algorithm based on a new replacement strategy to solve the quadratic assignment problems, which are NP-hard. The new replacement strategy aims to improve the performance of the genetic algorithm through well balancing the convergence of the searching process and the diversity of the population. In order to test the performance of the algorithm, the instances in QAPLIB, a quadratic assignment problem library, are tried and the results are compared with those reported in the literature. The performance of the genetic algorithm is promising. The significance is that this genetic algorithm is generic. It does not rely on problem-specific genetic operators, and may be easily applied to various types of combinatorial problems.

Keywords: Quadratic assignment problem, Genetic algorithm, Replacement strategy, QAPLIB.

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1738 GPU-Based Volume Rendering for Medical Imagery

Authors: Hadjira Bentoumi, Pascal Gautron, Kadi Bouatouch

Abstract:

We present a method for fast volume rendering using graphics hardware (GPU). To our knowledge, it is the first implementation on the GPU. Based on the Shear-Warp algorithm, our GPU-based method provides real-time frame rates and outperforms the CPU-based implementation. When the number of slices is not sufficient, we add in-between slices computed by interpolation. This improves then the quality of the rendered images. We have also implemented the ray marching algorithm on the GPU. The results generated by the three algorithms (CPU-based and GPU-based Shear- Warp, GPU-based Ray Marching) for two test models has proved that the ray marching algorithm outperforms the shear-warp methods in terms of speed up and image quality.

Keywords: Volume rendering, graphics processors

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1737 Evaluation of Linear and Geometrically Nonlinear Static and Dynamic Analysis of Thin Shells by Flat Shell Finite Elements

Authors: Djamel Boutagouga, Kamel Djeghaba

Abstract:

The choice of finite element to use in order to predict nonlinear static or dynamic response of complex structures becomes an important factor. Then, the main goal of this research work is to focus a study on the effect of the in-plane rotational degrees of freedom in linear and geometrically non linear static and dynamic analysis of thin shell structures by flat shell finite elements. In this purpose: First, simple triangular and quadrilateral flat shell finite elements are implemented in an incremental formulation based on the updated lagrangian corotational description for geometrically nonlinear analysis. The triangular element is a combination of DKT and CST elements, while the quadrilateral is a combination of DKQ and the bilinear quadrilateral membrane element. In both elements, the sixth degree of freedom is handled via introducing fictitious stiffness. Secondly, in the same code, the sixth degrees of freedom in these elements is handled differently where the in-plane rotational d.o.f is considered as an effective d.o.f in the in-plane filed interpolation. Our goal is to compare resulting shell elements. Third, the analysis is enlarged to dynamic linear analysis by direct integration using Newmark-s implicit method. Finally, the linear dynamic analysis is extended to geometrically nonlinear dynamic analysis where Newmark-s method is used to integrate equations of motion and the Newton-Raphson method is employed for iterating within each time step increment until equilibrium is achieved. The obtained results demonstrate the effectiveness and robustness of the interpolation of the in-plane rotational d.o.f. and present deficiencies of using fictitious stiffness in dynamic linear and nonlinear analysis.

Keywords: Flat shell, dynamic analysis, nonlinear, Newmark, drilling rotation.

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1736 Voltage Stability Proximity Index Determined by LES Algorithm

Authors: Benalia Nadia, Bensiali Nadia, Mekki Mounira

Abstract:

In this paper, we propose an easily computable proximity index for predicting voltage collapse of a load bus using only measured values of the bus voltage and power; Using these measurements a polynomial of fourth order is obtained by using LES estimation algorithms. The sum of the absolute values of the polynomial coefficient gives an idea of the critical bus. We demonstrate the applicability of our proposed method on 6 bus test system. The results obtained verify its applicability, as well as its accuracy and the simplicity. From this indicator, it is allowed to predict the voltage instability or the proximity of a collapse. Results obtained by the PV curve are compared with corresponding values by QV curves and are observed to be in close agreement.

Keywords: least square method, Voltage Collapse, Voltage Stability, PV curve

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1735 A New Approach for Assertions Processing during Assertion-Based Software Testing

Authors: Ali M. Alakeel

Abstract:

Assertion-Based software testing has been shown to be a promising tool for generating test cases that reveal program faults. Because the number of assertions may be very large for industry-size programs, one of the main concerns to the applicability of assertion-based testing is the amount of search time required to explore a large number of assertions. This paper presents a new approach for assertions exploration during the process of Assertion- Based software testing. Our initial exterminations with the proposed approach show that the performance of Assertion-Based testing may be improved, therefore, making this approach more efficient when applied on programs with large number of assertions.

Keywords: Software testing, assertion-based testing, program assertions.

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1734 Intrinsic Kinetics of Methanol Dehydration over Al2O3 Catalyst

Authors: Liang Zhang, Hai-Tao Zhang, W ei-Yong Ying, Ding-Ye Fang

Abstract:

Dehydration of methanol to dimethyl ether (DME) over a commercial Al2O3 catalyst was studied in an isothermal integral fixed bed reactor. The experiments were performed on the temperature interval 513-613 K, liquid hourly space velocity (LHSV) of 0.9-2.1h-1, pressures between 0.1 and 1.0 MPa. The effect of different operation conditions on the dehydration of methanol was investigated in a laboratory scale experiment. A new intrinsic kinetics equation based on the mechanism of Langmuir-Hinshelwood dissociation adsorption was developed for the dehydration reaction by fitting the expressions to the experimental data. An activation energy of 67.21 kJ/mol was obtained for the catalyst with the best performance. Statistic test showed that this new intrinsic kinetics equation was acceptable.

Keywords: catalyst, dimethyl ether, intrinsic kinetics, methanol

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1733 Real-Time Physics Simulation Packages: An Evaluation Study

Authors: J.Zouhair, D.Ellison

Abstract:

This paper includes a review of three physics simulation packages that can be used to provide researchers with a virtual ground for modeling, implementing and simulating complex models, as well as testing their control methods with less cost and time of development. The inverted pendulum model was used as a test bed for comparing ODE, DANCE and Webots, while Linear State Feedback was used to control its behavior. The packages were compared with respect to model creation, solving systems of differential equation, data storage, setting system variables, control the experiment and ease of use. The purpose of this paper is to give an overview about our experience with these environments and to demonstrate some of the benefits and drawbacks involved in practice for each package.

Keywords: DANCE, Inverted Pendulum, ODE, Simulation Packages, Webots.

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1732 Synchronization of 0.1 Hz Oscillations in Heart Rate and Blood Pressure: Application to Treatment of Myocardial Infarction Patients

Authors: M. D. Prokhorov, A. R. Kiselev, A. S. Karavaev, O. M. Posnenkova, V. I. Gridnev, V. I. Ponomarenko

Abstract:

Synchronization between 0.1 Hz oscillations in heart rate and blood pressure is studied and its change during vertical tilt is evaluated in 37 myocardial infarction patients. Two groups of patients are identified with decreased and increased, respectively, synchronization of the studied oscillations as a response to a tilt test. It is shown that assessment of synchronization of 0.1 Hz oscillations as a response to vertical tilt can be used as a guideline for selecting optimal dose of beta-blocker treatment in post-myocardial infarction patients.

Keywords: Cardiovascular system, heart rate variability, synchronization.

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1731 On the Modeling and State Estimation for Dynamic Power System

Authors: A. Thabet, M. Boutayeb, M. N. Abdelkrim

Abstract:

This paper investigates a method for the state estimation of nonlinear systems described by a class of differential-algebraic equation (DAE) models using the extended Kalman filter. The method involves the use of a transformation from a DAE to ordinary differential equation (ODE). A relevant dynamic power system model using decoupled techniques will be proposed. The estimation technique consists of a state estimator based on the EKF technique as well as the local stability analysis. High performances are illustrated through a simulation study applied on IEEE 13 buses test system.

Keywords: Power system, Dynamic decoupled model, Extended Kalman Filter, Convergence analysis, Time computing.

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1730 A New Heuristic Algorithm for the Classical Symmetric Traveling Salesman Problem

Authors: S. B. Liu, K. M. Ng, H. L. Ong

Abstract:

This paper presents a new heuristic algorithm for the classical symmetric traveling salesman problem (TSP). The idea of the algorithm is to cut a TSP tour into overlapped blocks and then each block is improved separately. It is conjectured that the chance of improving a good solution by moving a node to a position far away from its original one is small. By doing intensive search in each block, it is possible to further improve a TSP tour that cannot be improved by other local search methods. To test the performance of the proposed algorithm, computational experiments are carried out based on benchmark problem instances. The computational results show that algorithm proposed in this paper is efficient for solving the TSPs.

Keywords: Local search, overlapped neighborhood, travelingsalesman problem.

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1729 Sensor Fusion Based Discrete Kalman Filter for Outdoor Robot Navigation

Authors: Mbaitiga Zacharie

Abstract:

The objective of the presented work is to implement the Kalman Filter into an application that reduces the influence of the environmental changes over the robot expected to navigate over a terrain of varying friction properties. The Discrete Kalman Filter is used to estimate the robot position, project the estimated current state ahead at time through time update and adjust the projected estimated state by an actual measurement at that time via the measurement update using the data coming from the infrared sensors, ultrasonic sensors and the visual sensor respectively. The navigation test has been performed in a real world environment and has been found to be robust.

Keywords: Kalman filter, sensors fusion, robot navigation.

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1728 A Comparative Study of Web-pages Classification Methods using Fuzzy Operators Applied to Arabic Web-pages

Authors: Ahmad T. Al-Taani, Noor Aldeen K. Al-Awad

Abstract:

In this study, a fuzzy similarity approach for Arabic web pages classification is presented. The approach uses a fuzzy term-category relation by manipulating membership degree for the training data and the degree value for a test web page. Six measures are used and compared in this study. These measures include: Einstein, Algebraic, Hamacher, MinMax, Special case fuzzy and Bounded Difference approaches. These measures are applied and compared using 50 different Arabic web-pages. Einstein measure was gave best performance among the other measures. An analysis of these measures and concluding remarks are drawn in this study.

Keywords: Text classification, HTML, web pages, machine learning, fuzzy logic, Arabic web pages.

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1727 Customer Satisfaction on Reliability Dimension of Service Quality in Indian Higher Education

Authors: Rajasekhar Mamilla, Janardhana G., Anjan Babu G.

Abstract:

The present research study analyses the students’ satisfaction with university performance regarding the reliability dimension, ability of professors and staff to perform the promised services with quality to students in the post-graduate courses offered by Sri Venkateswara University in India. The research is done with the notion that the student compares the perceived performance with prior expectations. Customer satisfaction is seen as the outcome of this comparison. The sample respondents were administered with schedule based on stratified random technique for this study. Statistical techniques such as factor analysis, t-test and correlation analysis were used to accomplish the respective objectives of the study.

Keywords: Satisfaction, Reliability, Service Quality.

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1726 Radio Frequency Identification Encryption via Modified Two Dimensional Logistic Map

Authors: Hongmin Deng, Qionghua Wang

Abstract:

A modified two dimensional (2D) logistic map based on cross feedback control is proposed. This 2D map exhibits more random chaotic dynamical properties than the classic one dimensional (1D) logistic map in the statistical characteristics analysis. So it is utilized as the pseudo-random (PN) sequence generator, where the obtained real-valued PN sequence is quantized at first, then applied to radio frequency identification (RFID) communication system in this paper. This system is experimentally validated on a cortex-M0 development board, which shows the effectiveness in key generation, the size of key space and security. At last, further cryptanalysis is studied through the test suite in the National Institute of Standards and Technology (NIST).

Keywords: Chaos encryption, logistic map, pseudo-random sequence, RFID.

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1725 The Exploitation of Balancing an Inverted Pendulum System Using Sliding Mode Control

Authors: Sheren H. Salah, Ahmed Y. Ben Sasi

Abstract:

The inverted pendulum system is a classic control problem that is used in universities around the world. It is a suitable process to test prototype controllers due to its high non-linearities and lack of stability. The inverted pendulum represents a challenging control problem, which continually moves toward an uncontrolled state. This paper presents the possibility of balancing an inverted pendulum system using sliding mode control (SMC). The goal is to determine which control strategy delivers better performance with respect to pendulum’s angle and cart's position. Therefore, proportional-integral-derivative (PID) is used for comparison. Results have proven SMC control produced better response compared to PID control in both normal and noisy systems.

Keywords: Inverted pendulum (IP) proportional-integralderivative (PID), sliding mode control (SMC).

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1724 Modeling and Validation of Microspheres Generation in the Modified T-Junction Device

Authors: Lei Lei, Hongbo Zhang, Donald J. Bergstrom, Bing Zhang, K. Y. Song, W. J. Zhang

Abstract:

This paper presents a model for a modified T-junction device for microspheres generation. The numerical model is developed using a commercial software package: COMSOL Multiphysics. In order to test the accuracy of the numerical model, multiple variables, such as the flow rate of cross-flow, fluid properties, structure, and geometry of the microdevice are applied. The results from the model are compared with the experimental results in the diameter of the microsphere generated. The comparison shows a good agreement. Therefore the model is useful in further optimization of the device and feedback control of microsphere generation if any.

Keywords: CFD modeling, validation, microsphere generation, modified T-junction.

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1723 Biofungicide Trichodex WP

Authors: Snezana Rajkovic, Miroslava Markovic, Radoslav Rajkovic, Ljubinko Rakonjac

Abstract:

Grey mold on grape is caused by the fungus Botrytis cinerea Pers. Trichodex WP, a new biofungicide, that contains fungal spores of Trichoderma harzianum Rifai, was used for biological control of Grey mold on grape. The efficacy of Trichodex WP has been reported from many experiments. Experiments were carried out in the locality – Banatski Karlovac, on grapevine species – talijanski rizling. The trials were set according to instructions of methods PP1/152(2) and PP1/17(3) , according to a fully randomized block design. Phytotoxicity was estimated by PP methods 1/135(2), the intensity of infection according to Towsend Heuberger , the efficiency by Abbott, the analysis of variance with Duncan test and PP/181(2). Application of Trichodex WP is limited to the first two treatments. Other treatments are performed with the fungicides based on a.i. procymidone, vinclozoline and iprodione.

Keywords: Biofungicides, efficacy, grey mold, Trichodex WP.

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1722 Comparison of SVC and STATCOM in Static Voltage Stability Margin Enhancement

Authors: Mehrdad Ahmadi Kamarposhti, Mostafa Alinezhad

Abstract:

One of the major causes of voltage instability is the reactive power limit of the system. Improving the system's reactive power handling capacity via Flexible AC transmission System (FACTS) devices is a remedy for prevention of voltage instability and hence voltage collapse. In this paper, the effects of SVC and STATCOM in Static Voltage Stability Margin Enhancement will be studied. AC and DC representations of SVC and STATCOM are used in the continuation power flow process in static voltage stability study. The IEEE-14 bus system is simulated to test the increasing loadability. It is found that these controllers significantly increase the loadability margin of power systems.

Keywords: SVC, STATCOM, Voltage Collapse, Maximum Loading Point.

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1721 Simulation Based Performance Comparison of Different Control Methods of ZSI Feeding Industrial Drives

Authors: Parag Nihawan, Ravinder Singh Bhatia, Dinesh Kumar Jain

Abstract:

Industrial drives are source of serious power quality problems. In this, two typical industrial drives have been dealt with, namely, FOC induction motor drives and DTC induction motor drive. The Z-source inverter is an emerging topology of power electronic converters which is capable of buck boost characteristics. The performances of different control methods based Z-source inverters feeding these industrial drives have been investigated, in this work. The test systems have been modeled and simulated in MATLAB/SIMULINK. The results obtained after carrying out these simulations have been used to draw the conclusions.

Keywords: Z-Source Inverter, total harmonic distortion, direct torque control, field orientation control.

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1720 A Development of Personalized Edutainment Contents through Storytelling

Authors: Min Kyeong Cha, Ju Yeon Mun, Seong Baeg Kim

Abstract:

Recently, ‘play of learning’ becomes important and is  emphasized as a useful learning tool. Therefore, interest in  edutainment contents is growing. Storytelling is considered first as a  method that improves the transmission of information and learner's  interest when planning edutainment contents. In this study, we  designed edutainment contents in the form of an adventure game that  applies the storytelling method. This content provides questions and  items constituted dynamically and reorganized learning contents  through analysis of test results. It allows learners to solve various  questions through effective iterative learning. As a result, the learners  can reach mastery learning.

 

Keywords: Storytelling, edutainment, mastery learning, computer operating principle.

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1719 Statistical Analysis of Interferon-γ for the Effectiveness of an Anti-Tuberculous Treatment

Authors: Shishen Xie, Yingda L. Xie

Abstract:

Tuberculosis (TB) is a potentially serious infectious disease that remains a health concern. The Interferon Gamma Release Assay (IGRA) is a blood test to find out if an individual is tuberculous positive or negative. This study applies statistical analysis to the clinical data of interferon-gamma levels of seventy-three subjects who diagnosed pulmonary TB in an anti-tuberculous treatment. Data analysis is performed to determine if there is a significant decline in interferon-gamma levels for the subjects during a period of six months, and to infer if the anti-tuberculous treatment is effective.

Keywords: Data analysis, interferon gamma release assay, statistical methods, tuberculosis infection.

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1718 The Effects of Quality of Web-Based Applications on Competitive Advantage: An Empirical Study in Commercial Banks in Jordan

Authors: Faisal Asad Aburub

Abstract:

Many organizations are investing in web applications and technologies in order to be competitive, some of them could not achieve its goals. The quality of web-based applications could play an important role for organizations to be competitive. So the aim of this study is to investigate the impact of quality of web-based applications to achieve a competitive advantage. A new model has been developed. An empirical investigation was performed on a banking sector in Jordan to test the new model. The results show that impact of web-based applications on competitive advantage is significant. Finally, further work is planned to validate and evaluate the proposed model using several domains.

Keywords: Competitive advantage, web-based applications, empirical investigation.

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1717 Genetic Algorithm Application in a Dynamic PCB Assembly with Carryover Sequence- Dependent Setups

Authors: M. T. Yazdani Sabouni, Rasaratnam Logendran

Abstract:

We consider a typical problem in the assembly of printed circuit boards (PCBs) in a two-machine flow shop system to simultaneously minimize the weighted sum of weighted tardiness and weighted flow time. The investigated problem is a group scheduling problem in which PCBs are assembled in groups and the interest is to find the best sequence of groups as well as the boards within each group to minimize the objective function value. The type of setup operation between any two board groups is characterized as carryover sequence-dependent setup time, which exactly matches with the real application of this problem. As a technical constraint, all of the boards must be kitted before the assembly operation starts (kitting operation) and by kitting staff. The main idea developed in this paper is to completely eliminate the role of kitting staff by assigning the task of kitting to the machine operator during the time he is idle which is referred to as integration of internal (machine) and external (kitting) setup times. Performing the kitting operation, which is a preparation process of the next set of boards while the other boards are currently being assembled, results in the boards to continuously enter the system or have dynamic arrival times. Consequently, a dynamic PCB assembly system is introduced for the first time in the assembly of PCBs, which also has characteristics similar to that of just-in-time manufacturing. The problem investigated is computationally very complex, meaning that finding the optimal solutions especially when the problem size gets larger is impossible. Thus, a heuristic based on Genetic Algorithm (GA) is employed. An example problem on the application of the GA developed is demonstrated and also numerical results of applying the GA on solving several instances are provided.

Keywords: Genetic algorithm, Dynamic PCB assembly, Carryover sequence-dependent setup times, Multi-objective.

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1716 Identification of Risks Associated with Process Automation Systems

Authors: J. K. Visser, H. T. Malan

Abstract:

A need exists to identify the sources of risks associated with the process automation systems within petrochemical companies or similar energy related industries. These companies use many different process automation technologies in its value chain. A crucial part of the process automation system is the information technology component featuring in the supervisory control layer. The ever-changing technology within the process automation layers and the rate at which it advances pose a risk to safe and predictable automation system performance. The age of the automation equipment also provides challenges to the operations and maintenance managers of the plant due to obsolescence and unavailability of spare parts. The main objective of this research was to determine the risk sources associated with the equipment that is part of the process automation systems. A secondary objective was to establish whether technology managers and technicians were aware of the risks and share the same viewpoint on the importance of the risks associated with automation systems. A conceptual model for risk sources of automation systems was formulated from models and frameworks in literature. This model comprised six categories of risk which forms the basis for identifying specific risks. This model was used to develop a questionnaire that was sent to 172 instrument technicians and technology managers in the company to obtain primary data. 75 completed and useful responses were received. These responses were analyzed statistically to determine the highest risk sources and to determine whether there was difference in opinion between technology managers and technicians. The most important risks that were revealed in this study are: 1) the lack of skilled technicians, 2) integration capability of third-party system software, 3) reliability of the process automation hardware, 4) excessive costs pertaining to performing maintenance and migrations on process automation systems, and 5) requirements of having third-party communication interfacing compatibility as well as real-time communication networks.

Keywords: Distributed control system, identification of risks, information technology, process automation system.

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1715 GPS and Discrete Kalman Filter for Indoor Robot Navigation

Authors: Mbaitiga Zacharie

Abstract:

This paper discusses the implementation of the Kalman Filter along with the Global Positioning System (GPS) for indoor robot navigation. Two dimensional coordinates is used for the map building, and refers to the global coordinate which is attached to the reference landmark for position and direction information the robot gets. The Discrete Kalman Filter is used to estimate the robot position, project the estimated current state ahead in time through time update and adjust the projected estimated state by an actual measurement at that time via the measurement update. The navigation test has been performed and has been found to be robust.

Keywords: Global positioning System, kalman filter, robot navigation.

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1714 Development of Multimedia Learning Application for Mastery Learning Style: A Graduated Difficulty Strategy

Authors: Nur Azlina Mohamed Mokmin, Mona Masood

Abstract:

Guided by the theory of learning styles, this study is based on the development of a multimedia learning application for students with mastery learning style. The learning material was developed by applying a graduated difficulty learning strategy. Algebra was chosen as the learning topic for this application. The effectiveness of this application in helping students learn is measured by giving a pre- and post-test. The result shows that students who learn using the learning material that matches their preferred learning style perform better than the students with a non-personalized learning material.

Keywords: Algebraic Fractions, Graduated Difficulty, Mastery Learning Style, Multimedia.

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1713 Can EEG Test Helps in Identifying Brain Tumor?

Authors: M. Sharanreddy, P. K. Kulkarni

Abstract:

Brain tumor is inherently serious and life-threatening disease. Brain tumor builds the intracranial pressure in the brain, by shifting the brain or pushing against the skull, and also damaging nerves and healthy brain tissues. This intracranial pressure affects and interferes with normal brain functionality, which results in generation of abnormal electrical activities from brain. With recent development in the medical engineering and instruments, EEG instruments are able to record the brain electric activities with high accuracy, which establishes EEG as a primary tool for diagnosing the brain abnormalities. Research scholars and general physicians, often face difficulty in understanding EEG patterns. This paper presents the EEG patterns associated with brain tumor by combing medicine theory and neurologist experience. Paper also explains the pros-cons of the EEG based brain tumor identification.

Keywords: Brain tumor, Electroencephalogram (EEG).

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1712 Application of Neural Network for Contingency Ranking Based on Combination of Severity Indices

Authors: S. Jadid, S. Jalilzadeh

Abstract:

In this paper, an improved technique for contingency ranking using artificial neural network (ANN) is presented. The proposed approach is based on multi-layer perceptrons trained by backpropagation to contingency analysis. Severity indices in dynamic stability assessment are presented. These indices are based on the concept of coherency and three dot products of the system variables. It is well known that some indices work better than others for a particular power system. This paper along with test results using several different systems, demonstrates that combination of indices with ANN provides better ranking than a single index. The presented results are obtained through the use of power system simulation (PSS/E) and MATLAB 6.5 software.

Keywords: composite indices, transient stability, neural network.

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1711 Simulation of Multiphase Flows Using a Modified Upwind-Splitting Scheme

Authors: David J. Robbins, R. Stewart Cant, Lynn F. Gladden

Abstract:

A robust AUSM+ upwind discretisation scheme has been developed to simulate multiphase flow using consistent spatial discretisation schemes and a modified low-Mach number diffusion term. The impact of the selection of an interfacial pressure model has also been investigated. Three representative test cases have been simulated to evaluate the accuracy of the commonly-used stiffenedgas equation of state with respect to the IAPWS-IF97 equation of state for water. The algorithm demonstrates a combination of robustness and accuracy over a range of flow conditions, with the stiffened-gas equation tending to overestimate liquid temperature and density profiles.

Keywords: Multiphase flow, AUSM+ scheme, liquid EOS, low Mach number models

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1710 Full-genomic Network Inference for Non-model organisms: A Case Study for the Fungal Pathogen Candida albicans

Authors: Jörg Linde, Ekaterina Buyko, Robert Altwasser, Udo Hahn, Reinhard Guthke

Abstract:

Reverse engineering of full-genomic interaction networks based on compendia of expression data has been successfully applied for a number of model organisms. This study adapts these approaches for an important non-model organism: The major human fungal pathogen Candida albicans. During the infection process, the pathogen can adapt to a wide range of environmental niches and reversibly changes its growth form. Given the importance of these processes, it is important to know how they are regulated. This study presents a reverse engineering strategy able to infer fullgenomic interaction networks for C. albicans based on a linear regression, utilizing the sparseness criterion (LASSO). To overcome the limited amount of expression data and small number of known interactions, we utilize different prior-knowledge sources guiding the network inference to a knowledge driven solution. Since, no database of known interactions for C. albicans exists, we use a textmining system which utilizes full-text research papers to identify known regulatory interactions. By comparing with these known regulatory interactions, we find an optimal value for global modelling parameters weighting the influence of the sparseness criterion and the prior-knowledge. Furthermore, we show that soft integration of prior-knowledge additionally improves the performance. Finally, we compare the performance of our approach to state of the art network inference approaches.

Keywords: Pathogen, network inference, text-mining, Candida albicans, LASSO, mutual information, reverse engineering, linear regression, modelling.

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