Search results for: Razib M. Othman

Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

Abstract:

Gene Ontology terms have been actively used to annotate various protein sets. SWISS-PROT, TrEMBL, and InterPro are protein databases that are annotated according to the Gene Ontology terms. However, direct implementation of the Gene Ontology terms for annotation of anonymous protein sequences is not easy, especially for species not commonly represented in biological databases. UTMGO is developed as a tool that allows the user to quickly and easily search for a group of semantically related Gene Ontology terms. The applicability of the UTMGO is demonstrated by applying it to annotation of anonymous protein sequence. The extended UTMGO uses the Gene Ontology terms together with protein sequences associated with the terms to perform the annotation task. GOPET, GOtcha, GoFigure, and JAFA are used to compare the performance of the extended UTMGO.

Keywords: Anonymous protein sequence, Gene Ontology, Protein sequence annotation, Protein sequence alignment

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

Predicting protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been applied to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. Although it is easy to get a dataset of interacting proteins as positive examples, there are no experimentally confirmed non-interacting proteins to be considered as negative examples. Therefore, in this paper we solve this problem as a one-class classification problem using one-class support vector machines (SVM). Using only positive examples (interacting protein pairs) in training phase, the one-class SVM achieves accuracy of about 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with comparable accuracy to the binary classifiers that use artificially constructed negative examples.

Keywords: Bioinformatics, Protein-protein interactions, One-Class Support Vector Machines

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

The protein domain structure has been widely used as the most informative sequence feature to computationally predict protein-protein interactions. However, in a recent study, a research group has reported a very high accuracy of 94% using hydrophobicity feature. Therefore, in this study we compare and verify the usefulness of protein domain structure and hydrophobicity properties as the sequence features. Using the Support Vector Machines (SVM) as the learning system, our results indicate that both features achieved accuracy of nearly 80%. Furthermore, domains structure had receiver operating characteristic (ROC) score of 0.8480 with running time of 34 seconds, while hydrophobicity had ROC score of 0.8159 with running time of 20,571 seconds (5.7 hours). These results indicate that protein-protein interaction can be predicted from domain structure with reliable accuracy and acceptable running time.

Keywords: Bioinformatics, protein-protein interactions, support vector machines, protein features.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias, Zalmiyah Zakaria, Saberi M. Mohamad

Abstract:

Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology has caused problems in maintaining and processing them. One way to obtain their accessibility is by clustering them into fragmented groups. Clustering the Gene Ontology is a difficult combinatorial problem and can be modeled as a graph partitioning problem. Additionally, deciding the number k of clusters to use is not easily perceived and is a hard algorithmic problem. Therefore, an approach for solving the automatic clustering of the Gene Ontology is proposed by incorporating cohesion-and-coupling metric into a hybrid algorithm consisting of a genetic algorithm and a split-and-merge algorithm. Experimental results and an example of modularized Gene Ontology in RDF/XML format are given to illustrate the effectiveness of the algorithm.

Keywords: Automatic clustering, cohesion-and-coupling metric, gene ontology; genetic algorithm, split-and-merge algorithm.

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Authors: Muhammad Faisal Zafar, Dzulkifli Mohamad, Razib M. Othman

Abstract:

On-line handwritten scripts are usually dealt with pen tip traces from pen-down to pen-up positions. Time evaluation of the pen coordinates is also considered along with trajectory information. However, the data obtained needs a lot of preprocessing including filtering, smoothing, slant removing and size normalization before recognition process. Instead of doing such lengthy preprocessing, this paper presents a simple approach to extract the useful character information. This work evaluates the use of the counter- propagation neural network (CPN) and presents feature extraction mechanism in full detail to work with on-line handwriting recognition. The obtained recognition rates were 60% to 94% using the CPN for different sets of character samples. This paper also describes a performance study in which a recognition mechanism with multiple thresholds is evaluated for counter-propagation architecture. The results indicate that the application of multiple thresholds has significant effect on recognition mechanism. The method is applicable for off-line character recognition as well. The technique is tested for upper-case English alphabets for a number of different styles from different peoples.

Keywords: On-line character recognition, character digitization, counter-propagation neural networks, extreme coordinates.

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

Understanding proteins functions is a major goal in the post-genomic era. Proteins usually work in context of other proteins and rarely function alone. Therefore, it is highly relevant to study the interaction partners of a protein in order to understand its function. Machine learning techniques have been widely applied to predict protein-protein interactions. Kernel functions play an important role for a successful machine learning technique. Choosing the appropriate kernel function can lead to a better accuracy in a binary classifier such as the support vector machines. In this paper, we describe a Bayesian kernel for the support vector machine to predict protein-protein interactions. The use of Bayesian kernel can improve the classifier performance by incorporating the probability characteristic of the available experimental protein-protein interactions data that were compiled from different sources. In addition, the probabilistic output from the Bayesian kernel can assist biologists to conduct more research on the highly predicted interactions. The results show that the accuracy of the classifier has been improved using the Bayesian kernel compared to the standard SVM kernels. These results imply that protein-protein interaction can be predicted using Bayesian kernel with better accuracy compared to the standard SVM kernels.

Keywords: Bioinformatics, Protein-protein interactions, Bayesian Kernel, Support Vector Machines.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias, Hany T. Alashwal, Rohayanti Hassan, FarhanMohamed

Abstract:

The most important property of the Gene Ontology is the terms. These control vocabularies are defined to provide consistent descriptions of gene products that are shareable and computationally accessible by humans, software agent, or other machine-readable meta-data. Each term is associated with information such as definition, synonyms, database references, amino acid sequences, and relationships to other terms. This information has made the Gene Ontology broadly applied in microarray and proteomic analysis. However, the process of searching the terms is still carried out using traditional approach which is based on keyword matching. The weaknesses of this approach are: ignoring semantic relationships between terms, and highly depending on a specialist to find similar terms. Therefore, this study combines semantic similarity measure and genetic algorithm to perform a better retrieval process for searching semantically similar terms. The semantic similarity measure is used to compute similitude strength between two terms. Then, the genetic algorithm is employed to perform batch retrievals and to handle the situation of the large search space of the Gene Ontology graph. The computational results are presented to show the effectiveness of the proposed algorithm.

Keywords: Gene Ontology, Semantic similarity measure, Genetic algorithm, Ontology search

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

Abstract:

Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.

Keywords: automatic clustering, bioinformatics tool, gene ontology, protein sequence annotation, semantic similarity search

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Authors: Roshayani Arshad, Suaini Othman, Rohana Othman

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This study examines the effect of Islamic Corporate Social Responsibility disclosure and on corporate reputation as well as performance. These relationships are examined based on content analysis of of annual reports of 17 Islamic banks in Malaysia for 2008, 2009 and 2010. Results of this study provide evidence that CSR activities communicated in corporate annual reports are significantly positively related with corporate reputation as well as firm performance. These results indicate that CSR activities and disclosure from Islamic perspectives are equally important business strategies in creating continuous superior performance for organisations. In addition, it also highlights that organisations need to develop a stakeholder orientation particularly in an environment of increasing pressure from jurisdictions dominated by Islamic stakeholders on organisations engaging in Islamic products to increase their social responsibilities from the Islamic perspectives.

Keywords: Islamic Corporate Social Responsibility, Corporate Reputation, Firm Performance, Islamic Banks

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Authors: Maslinawati Mohamad, Intan Waheedah Othman, Arun Mohamed

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This paper discusses the issues and challenges concerning the issues of accountability and regulation systems of cooperative movement in Malaysia.

Keywords: Cooperative movement, compliance, transparency, issues.

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Authors: Maslinawati Mohamad, Intan Waheedah Othman

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This paper studies the reputation and transparency of cooperative movement in Malaysia.

Keywords: Cooperative movement, reputation, transparency, web presence.

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Authors: Othman O. Khalifa, Sheroz khan, Mohamad Zaid, Muhamad Nawawi

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This paper mainly about the study on one of the widely used error correcting codes that is Low parity check Codes (LDPC). In this paper, the Regular LDPC code has been discussed The LDPC codes explained in this paper is about the Regular Binary LDPC codes or the Gallager.

Keywords: LDPC, channel coding.

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Authors: Othman Maklouf, Ahmed Adwaib

Abstract:

This paper introduces a comparative study between the main GPS\INS coupling schemes, this will include the loosely coupled and tightly coupled configurations, several types of situations and operational conditions, in which the data fusion process is done using Kalman filtering. This will include the importance of sensors calibration as well as the alignment of the strap down inertial navigation system. The limitations of the inertial navigation systems are investigated.

Keywords: GPS, INS, Kalman Filter.

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Authors: Noraini Othman, Aizzat Mohd Nasurdin

Abstract:

The purpose of this study was to investigate the relationship between hope and resilience with work engagement. A total of 422 staff nurses working in three public hospitals in Peninsular Malaysia participated in this study. Statistical results using regression analysis revealed that hope and resilience were positively related to work engagement. Possible reasons for these findings, as well as their implications and future research directions are discussed.

Keywords: hope, nurses, resilience, work engagement

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Authors: Fariba Haghbin, Othman Bin Ibrahim, Mohammad Reza Attarzadeh Niaki

Abstract:

With the development of virtual communities, there is an increase in the number of members in Virtual Communities (VCs). Many join VCs with the objective of sharing their knowledge and seeking knowledge from others. Despite the eagerness of sharing knowledge and receiving knowledge through VCs, there is no standard of assessing ones knowledge sharing capabilities and prospects of knowledge sharing. This paper developed a vector space model to assess the knowledge sharing prospect of VC users.

Keywords: Knowledge sharing network, Virtual community, knowledge relationship, Vector Space Model.

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Authors: Mazin Z. Othman, Maan M. Shaker, Mohammed F. Abdullah

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This study introduces a new method for detecting, sorting, and localizing spikes from multiunit EEG recordings. The method combines the wavelet transform, which localizes distinctive spike features, with Super-Paramagnetic Clustering (SPC) algorithm, which allows automatic classification of the data without assumptions such as low variance or Gaussian distributions. Moreover, the method is capable of setting amplitude thresholds for spike detection. The method makes use of several real EEG data sets, and accordingly the spikes are detected, clustered and their times were detected.

Keywords: EEG time localizations, EEG spike detection, superparamagnetic algorithm, wavelet transform.

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Authors: M. Shuhaimi-Othman, Y. Nadzifah, A.K. Ahmad

Abstract:

Two freshwater fishes, Rasbora sumatrana (Cyprinidae) and Poecilia reticulata (guppy) (Poeciliidae) were exposed for a four-day period in the laboratory condition to a range of copper (Cu) and cadmium (Cd) concentrations. Mortality was assessed and median lethal concentrations (LC50) were calculated. LC50 increased with decrease in mean exposure times for both metals. For R. sumatrana, LC50s for 24, 48, 72 and 96 hours for Cu were 54.2, 30.3, 18.9 and 5.6 μg/L and for Cd 1440.2, 459.3, 392.3 and 101.6 μg/L respectively. For P. reticulata, LC50s for 24, 48, 72 and 96 hours for Cu were 348.9, 145.4, 61.3 and 37.9 μg/L and for Cd 8205.6, 2827.1, 405.8 and 168.1 μg/L, respectively. Results indicated that the Cu was more toxic than Cd to both fishes (Cu>Cd) and R. sumatrana was more sensitive than P. reticulata to the metals.

Keywords: Acute, heavy metals, LT50, toxicity

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Authors: M. Z. Othman

Abstract:

The aim of this study was to investigate the effectiveness of anaerobic digestion for the treatment of wool scouring wastes. The experiments design comprised three ratios of waste (W) to seed(S) (W:S) of 25:75, 50:50 and 75:25, corresponding to 1.9. 1.7 and 1.5g tCOD/g TS, respectively, with or without chemicals addition. NH4Cl was added to the reactors as a source for nitrogen to achieve C:N:P of 420:14:3. A cationic flocculent was added at 0.5 and 0.75% to enhance flocculation of sludge. The results showed that the reactors that received W:S at a ratio of 25:75 produced the largest volume of biogas. The final soluble COD (sCOD) was below the limits for discharge to the sewer system.

Keywords: Anaerobic digestion, wool processing waste, organicloading, biogas.

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Authors: Mazin Z. Othman

Abstract:

This paper presents the idea of a rough controller with application to control the overhead traveling crane system. The structure of such a controller is based on a suggested concept of a fuzzy logic controller. A measure of fuzziness in rough sets is introduced. A comparison between fuzzy logic controller and rough controller has been demonstrated. The results of a simulation comparing the performance of both controllers are shown. From these results we infer that the performance of the proposed rough controller is satisfactory.

Keywords: Accuracy measure, Fuzzy Logic Controller (FLC), Overhead Traveling Crane (OTC), Rough Set Theory (RST), Roughness measure

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Authors: Intan Waheedah Othman, Maslinawati Mohamad, Azizah Abdullah

Abstract:

Cooperative organizations in Malaysia are going through a phase of rapid growth. They are seen by the government as another crucial vehicle to drive and boost up the country-s economical development and growth. Hence, the issue of cooperative governance is of great importance. Unlike literatures on corporate governance for public listed companies-, literatures on governance for social enterprises, in particular the cooperative organizations are still at the early stage in Malaysia and very scant in number. This paper will look into current practices as well as issues and challenges related to cooperative governance. The need for a better solution towards forming best practices of cooperative governance framework appears imperative in deterring cases of mismanagement and fraud.

Keywords: Cooperative, Governance, Issues, Malaysia.

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Authors: Nabilah Filzah Mohd Radzuan, Zalinda Othman, Azuraliza Abu Bakar, Abdul Razak Hamdan

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Uncertain data is believed to be an important issue in building up a prediction model. The main objective in the time series uncertainty analysis is to formulate uncertain data in order to gain knowledge and fit low dimensional model prior to a prediction task. This paper discusses the performance of a number of techniques in dealing with uncertain data specifically those which solve uncertain data condition by minimizing the loss of compression properties.

Keywords: Compression properties, uncertainty, uncertain time series, mining technique, weather prediction.

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Authors: Sin Yin Teh, Abdul Rahman Othman, Michael Boon Chong Khoo

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In this paper, the concepts of dichotomous logistic regression (DLR) with leave-one-out (L-O-O) were discussed. To illustrate this, the L-O-O was run to determine the importance of the simulation conditions for robust test of spread procedures with good Type I error rates. The resultant model was then evaluated. The discussions included 1) assessment of the accuracy of the model, and 2) parameter estimates. These were presented and illustrated by modeling the relationship between the dichotomous dependent variable (Type I error rates) with a set of independent variables (the simulation conditions). The base SAS software containing PROC LOGISTIC and DATA step functions can be making used to do the DLR analysis.

Keywords: Dichotomous logistic regression, leave-one-out, testof spread.

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Authors: K.H.Khairul Anuar, K.I.Othman, F.Ishak, Z.B.Ibrahim, Z.Majid

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Solving Ordinary Differential Equations (ODEs) by using Partitioning Block Intervalwise (PBI) technique is our aim in this paper. The PBI technique is based on Block Adams Method and Backward Differentiation Formula (BDF). Block Adams Method only use the simple iteration for solving while BDF requires Newtonlike iteration involving Jacobian matrix of ODEs which consumes a considerable amount of computational effort. Therefore, PBI is developed in order to reduce the cost of iteration within acceptable maximum error

Keywords: Adam Block Method, BDF, Ordinary Differential Equations, Partitioning Block Intervalwise

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Authors: Othman Maklouf, Abdurazag Ghila, Ahmed Abdulla

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This paper introduces a low cost INS/GPS algorithm for land vehicle navigation application. The data fusion process is done with an extended Kalman filter in cascade configuration mode. In order to perform numerical simulations, MATLAB software has been developed. Loosely coupled configuration is considered. The results obtained in this work demonstrate that a low-cost INS/GPS navigation system is partially capable of meeting the performance requirements for land vehicle navigation. The relative effectiveness of the kalman filter implementation in integrated GPS/INS navigation algorithm is highlighted. The paper also provides experimental results; field test using a car is carried out.

Keywords: GPS, INS, IMU, Kalman filter.

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Authors: Zarina Bibi Ibrahim, Mohamed Suleiman, Khairil Iskandar Othman

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In this paper, a direct method based on variable step size Block Backward Differentiation Formula which is referred as BBDF2 for solving second order Ordinary Differential Equations (ODEs) is developed. The advantages of the BBDF2 method over the corresponding sequential variable step variable order Backward Differentiation Formula (BDFVS) when used to solve the same problem as a first order system are pointed out. Numerical results are given to validate the method.

Keywords: Backward Differentiation Formula, block, secondorder.

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Authors: Othman O. Khalifa, Abdulrazzag Aburas, A. Al Bagul, Meftah Hrairi, Muhammad Shahril bin Shahbuddin, Harman bin Mat Kasa

Abstract:

Cellular communication is being widely used by all over the world. The users of handsets are increasing due to the request from marketing sector. The important aspect that has to be touch in this paper is about the security system of cellular communication. It is important to provide users with a secure channel for communication. A brief description of the new GSM cellular network architecture will be provided. Limitations of cellular networks, their security issues and the different types of attacks will be discussed. The paper will go over some new security mechanisms that have been proposed by researchers. Overall, this paper clarifies the security system or services of cellular communication using GSM. Three Malaysian Communication Companies were taken as Case study in this paper.

Keywords: GSM, Security systems, SIM CARD, IMSI, Authentication.

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Authors: Hayder Natiq Jasem, Zuriati Ahmad Zukarnain, Mohamed Othman, Shamala Subramaniam

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Congestion control is one of the fundamental issues in computer networks. Without proper congestion control mechanisms there is the possibility of inefficient utilization of resources, ultimately leading to network collapse. Hence congestion control is an effort to adapt the performance of a network to changes in the traffic load without adversely affecting users perceived utilities. AIMD (Additive Increase Multiplicative Decrease) is the best algorithm among the set of liner algorithms because it reflects good efficiency as well as good fairness. Our control model is based on the assumption of the original AIMD algorithm; we show that both efficiency and fairness of AIMD can be improved. We call our approach is New AIMD. We present experimental results with TCP that match the expectation of our theoretical analysis.

Keywords: Congestion control, Efficiency, Fairness, TCP, AIMD.

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Authors: N. M. Nusi, M. Othman, M. Suleiman, F. Ismail, N. Alias

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In this paper, an alternating implicit block method for solving two dimensional scalar wave equation is presented. The new method consist of two stages for each time step implemented in alternating directions which are very simple in computation. To increase the speed of computation, a group of adjacent points is computed simultaneously. It is shown that the presented method increase the maximum time step size and more accurate than the conventional finite difference time domain (FDTD) method and other existing method of natural ordering.

Keywords: FDTD, Scalar wave equation, alternating direction implicit (ADI), alternating group explicit (AGE), asymmetric approximation.

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Authors: MohammadReza HeidariNezhad, Zuriati Ahmad Zukarnain, Nur Izura Udzir, Mohamed Othman

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In this paper, we propose APO, a new packet scheduling scheme with Quality of Service (QoS) support for hybrid of real and non-real time services in HSDPA networks. The APO scheduling algorithm is based on the effective channel anticipation model. In contrast to the traditional schemes, the proposed method is implemented based on a cyclic non-work-conserving discipline. Simulation results indicated that proposed scheme has good capability to maximize the channel usage efficiency in compared to another exist scheduling methods. Simulation results demonstrate the effectiveness of the proposed algorithm.

Keywords: Scheduling Algorithm, Quality of Service, HSDPA.

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Authors: Basman Elhadidi, Islam Elqatary, Osama Mohamady, Hesham Othman

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An active slat is developed to increase the lift and delay the separation for a DU96-W180 airfoil. The active slat is a fixed slat that can be closed, fully opened or intermittently opened by a rotating vane depending on the need. Experimental results show that the active slat has reduced the mean pressure and increased the mean velocity on the suction side of the airfoil for all positive angles of attack, indicating an increase of lift. The experimental data and numerical simulations also show that the direction of actuator vane rotation can influence the mixing of the flow streams on the suction side and hence influence the aerodynamic performance.

Keywords: Active slat, flow control.

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