Search results for: optimization of the grid of collection

Authors: K. Sivasubramanian, K. B. Jayanthi

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Floorplanning plays a vital role in the physical design process of Very Large Scale Integrated (VLSI) chips. It is an essential design step to estimate the chip area prior to the optimized placement of digital blocks and their interconnections. Since VLSI floorplanning is an NP-hard problem, many optimization techniques were adopted in the literature. In this work, a music-inspired Harmony Search (HS) algorithm is used for the fixed die outline constrained floorplanning, with the aim of reducing the total chip area. HS draws inspiration from the musical improvisation process of searching for a perfect state of harmony. Initially, B*-tree is used to generate the primary floorplan for the given rectangular hard modules and then HS algorithm is applied to obtain an optimal solution for the efficient floorplan. The experimental results of the HS algorithm are obtained for the MCNC benchmark circuits.

Keywords: Floor planning, harmony search, non-slicing floorplan, very large scale integrated circuits.

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Authors: Norazah Mohd Suki, Norbayah Mohd Suki

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Online shopping enables consumers to search for information and purchase products or services through direct interaction with online store. This study aims to examine the effect of Internet marketing environment, product characteristics, familiarity and confidence, and promotional offers on consumer online shopping behavior. 200 questionnaires were distributed to the respondents, who are students and staff at a public university in the Federal Territory of Labuan, Malaysia, following simple random sampling as a means of data collection. Multiple regression analysis was used as a statistical measure to determine the strength of the relationship between one dependent variable and a series of other independent variables. Results revealed that familiarity and confidence was found to greatly influence consumer online shopping behavior followed by promotional offers. A clear understanding of consumer online shopping behavior can help marketing managers predict the online shopping rate and evaluate the future growth of online commerce.

Keywords: Internet Marketing Environment, Product Characteristics, Multiple Regression Analysis, Malaysia.

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Authors: Hatem. Elmeddeb, Noureddine, Hamdi, Ammar. Bouallègue

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In this paper, a joint source-channel coding (JSCC) scheme for time-varying channels is presented. The proposed scheme uses hierarchical framework for both source encoder and transmission via QAM modulation. Hierarchical joint source channel codes with hierarchical QAM constellations are designed to track the channel variations which yields to a higher throughput by adapting certain parameters of the receiver to the channel variation. We consider the problem of still image transmission over time-varying channels with channel state information (CSI) available at 1) receiver only and 2) both transmitter and receiver being informed about the state of the channel. We describe an algorithm that optimizes hierarchical source codebooks by minimizing the distortion due to source quantizer and channel impairments. Simulation results, based on image representation, show that, the proposed hierarchical system outperforms the conventional schemes based on a single-modulator and channel optimized source coding.

Keywords: Channel-optimized VQ (COVQ), joint optimization, QAM, hierarchical systems.

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Authors: Pavan K. Rallabandi, Kailash C. Patidar

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In this paper, we present an optimization technique or a learning algorithm using the hybrid architecture by combining the most popular sequence recognition models such as Recurrent Neural Networks (RNNs) and Hidden Markov models (HMMs). In order to improve the sequence/pattern recognition/classification performance by applying a hybrid/neural symbolic approach, a gradient descent learning algorithm is developed using the Real Time Recurrent Learning of Recurrent Neural Network for processing the knowledge represented in trained Hidden Markov Models. The developed hybrid algorithm is implemented on automata theory as a sample test beds and the performance of the designed algorithm is demonstrated and evaluated on learning the deterministic finite state automata.

Keywords: Hybrid systems, Hidden Markov Models, Recurrent neural networks, Deterministic finite state automata.

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Authors: Gayadhar Panda, P. K. Rautraya

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In this paper, an investigation into the use of modified Genetic Algorithm optimized SSSC based controller to aid damping of low frequency inter-area oscillations in power systems is presented. Controller design is formulated as a nonlinear constrained optimization problem and modified Genetic Algorithm (MGA) is employed to search for the optimal controller parameters. For evaluation of effectiveness and robustness of proposed controllers, the performance was tested on multi-machine system subjected to different disturbances, loading conditions and system parameter variations. Simulation results are presented to show the fine performance of the proposed SSSC controller in damping the critical modes without significantly deteriorating the damping characteristics of other modes in multi-machine power system.

Keywords: SSSC, FACTS, Controller Design, Damping of Oscillations, Multi-machine system, Modified Genetic Algorithm (MGA).

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Authors: Chunshien Li, Jhao-Wun Hu, Tai-Wei Chiang, Tsunghan Wu

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Time series forecasting is an important and widely popular topic in the research of system modeling. This paper describes how to use the hybrid PSO-RLSE neuro-fuzzy learning approach to the problem of time series forecasting. The PSO algorithm is used to update the premise parameters of the proposed prediction system, and the RLSE is used to update the consequence parameters. Thanks to the hybrid learning (HL) approach for the neuro-fuzzy system, the prediction performance is excellent and the speed of learning convergence is much faster than other compared approaches. In the experiments, we use the well-known Mackey-Glass chaos time series. According to the experimental results, the prediction performance and accuracy in time series forecasting by the proposed approach is much better than other compared approaches, as shown in Table IV. Excellent prediction performance by the proposed approach has been observed.

Keywords: forecasting, hybrid learning (HL), Neuro-FuzzySystem (NFS), particle swarm optimization (PSO), recursiveleast-squares estimator (RLSE), time series

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Authors: Rossella Arcucci, Luisa D’Amore, Simone Celestino, Giuseppe Scotti, Giuliano Laccetti

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This work is the first dowel in a rather wide research activity in collaboration with Euro Mediterranean Center for Climate Changes, aimed at introducing scalable approaches in Ocean Circulation Models. We discuss designing and implementation of a parallel algorithm for solving the Variational Data Assimilation (DA) problem on Graphics Processing Units (GPUs). The algorithm is based on the fully scalable 3DVar DA model, previously proposed by the authors, which uses a Domain Decomposition approach (we refer to this model as the DD-DA model). We proceed with an incremental porting process consisting of 3 distinct stages: requirements and source code analysis, incremental development of CUDA kernels, testing and optimization. Experiments confirm the theoretic performance analysis based on the so-called scale up factor demonstrating that the DD-DA model can be suitably mapped on GPU architectures.

Keywords: Data Assimilation, Parallel Algorithm, GPU architectures, Ocean Models.

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Authors: Henri Champliaud, Zhengkun Feng, Ngan Van Lê, Javad Gholipour

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In this article, a method is presented to effectively estimate the deformed shape of a thick plate due to line heating. The method uses a fifth order spline interpolation, with up to C3 continuity at specific points to compute the shape of the deformed geometry. First and second order derivatives over a surface are the resulting parameters of a given heating line on a plate. These parameters are determined through experiments and/or finite element simulations. Very accurate kriging models are fitted to real or virtual surfaces to build-up a database of maps. Maps of first and second order derivatives are then applied on numerical plate models to evaluate their evolving shapes through a sequence of heating lines. Adding an optimization process to this approach would allow determining the trajectories of heating lines needed to shape complex geometries, such as Francis turbine blades.

Keywords: Deformation, kriging, fifth order spline interpolation, first, second and third order derivatives, C3 continuity, line heating, plate forming, thermal forming.

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Authors: Shweta Kumari, Parmjit S. Panesar, Manab B. Bera

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The hydrolysis of lactose using β-galactosidase is one of the most promising biotechnological applications, which has wide range of potential applications in food processing industries. However, due to intracellular location of the yeast enzyme, and expensive extraction methods, the industrial applications of enzymatic hydrolysis processes are being hampered. The use of permeabilization technique can help to overcome the problems associated with enzyme extraction and purification of yeast cells and to develop the economically viable process for the utilization of whole cell biocatalysts in food industries. In the present investigation, standardization of permeabilization process of novel yeast isolate was carried out using a statistical model approach known as Response Surface Methodology (RSM) to achieve maximal b-galactosidase activity. The optimum operating conditions for permeabilization process for optimal β-galactosidase activity obtained by RSM were 1:1 ratio of toluene (25%, v/v) and ethanol (50%, v/v), 25.0 ^oC temperature and treatment time of 12 min, which displayed enzyme activity of 1.71 IU /mg DW.

Keywords: β-galactosidase, optimization, permeabilization, response surface methodology, yeast.

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Authors: K. Manikandan, T. Viruthagiri

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Studies on Simultaneous Saccharification and Fermentation (SSF) of corn flour, a major agricultural product as the substrate using starch digesting glucoamylase enzyme derived from Aspergillus niger and non starch digesting and sugar fermenting Saccharomyces cerevisiae in a batch fermentation. Experiments based on Central Composite Design (CCD) were conducted to study the effect of substrate concentration, pH, temperature, enzyme concentration on Ethanol Concentration and the above parameters were optimized using Response Surface Methodology (RSM). The optimum values of substrate concentration, pH, temperature and enzyme concentration were found to be 160 g/l, 5.5, 30°C and 50 IU respectively. The effect of inoculums age on ethanol concentration was also investigated. The corn flour solution equivalent to 16% initial starch concentration gave the highest ethanol concentration of 63.04 g/l after 48 h of fermentation at optimum conditions of pH and temperature. Monod model and Logistic model were used for growth kinetics and Leudeking – Piret model was used for product formation kinetics.

Keywords: Simultaneous Saccharification and Fermentation(SSF), Corn Starch, Ethanol, Logisitic Model.

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Authors: Gonzalo Rubio, Eusebio Valero, Sven Lanzan

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The design of a modern aircraft is based on three pillars: theoretical results, experimental test and computational simulations. As a results of this, Computational Fluid Dynamic (CFD) solvers are widely used in the aeronautical field. These solvers require the correct selection of many parameters in order to obtain successful results. Besides, the computational time spent in the simulation depends on the proper choice of these parameters. In this paper we create an expert system capable of making an accurate prediction of the number of iterations and time required for the convergence of a computational fluid dynamic (CFD) solver. Artificial neural network (ANN) has been used to design the expert system. It is shown that the developed expert system is capable of making an accurate prediction the number of iterations and time required for the convergence of a CFD solver.

Keywords: Artificial Neural Network, Computational Fluid Dynamics, Optimization

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Authors: Sungho Lee, Goonjae Lee, Chaeyeon Lim, Sunkuk Kim

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Foundation of tower crane serves to ensure stability against vertical and horizontal forces. If foundation stress is not sufficient, tower crane may be subject to overturning, shearing or foundation settlement. Therefore, engineering review of stable support is a highly critical part of foundation design. However, there are not many professionals who can conduct engineering review of tower crane foundation and, if any, they have information only on a small number of cranes in which they have hands-on experience. It is also customary to rely on empirical knowledge and tower crane renter-s recommendations rather than designing foundation on the basis of engineering knowledge. Therefore, a foundation design automation system considering not only lifting conditions but also overturning risk, shearing and vertical force may facilitate production of foolproof foundation design for experts and enable even non-experts to utilize professional knowledge that only experts can access now. This study proposes Automatic Design Algorithm for the Tower Crane Foundations considering load and horizontal force.

Keywords: Tower Crane, Automatic Design, Foundations, Optimization Algorithm, Stability

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Authors: Ethar H. Khalil, Bahaa I. Kazem

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In this work a software simulation model has been proposed for two driven wheels mobile robot path planning; that can navigate in dynamic environment with static distributed obstacles. The work involves utilizing Bezier curve method in a proposed N order matrix form; for engineering the mobile robot path. The Bezier curve drawbacks in this field have been diagnosed. Two directions: Up and Right function has been proposed; Probability Recursive Function (PRF) to overcome those drawbacks. PRF functionality has been developed through a proposed; obstacle detection function, optimization function which has the capability of prediction the optimum path without comparison between all feasible paths, and N order Bezier curve function that ensures the drawing of the obtained path. The simulation results that have been taken showed; the mobile robot travels successfully from starting point and reaching its goal point. All obstacles that are located in its way have been avoided. This navigation is being done successfully using the proposed PRF techniques.

Keywords: Mobile robot, path planning, Bezier curve.

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Authors: Chansopheak Seang, Afia David Kouadri, Eric Ragneau

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Three dimensional analysis of thermal model in laser full penetration welding, Nd:YAG, by transparent mode DP600 alloy steel 1.25mm of thickness and gap of 0.1mm. Three models studied the influence of thermal dependent temperature properties, thermal independent temperature and the effect of peak value of specific heat at phase transformation temperature, AC1, on the transient temperature. Another seven models studied the influence of discretization, meshes on the temperature distribution in weld plate. It is shown that for the effects of thermal properties, the errors less 4% of maximum temperature in FZ and HAZ have identified. The minimum value of discretization are at least one third increment per radius for temporal discretization and the spatial discretization requires two elements per radius and four elements through thickness of the assembled plate, which therefore represent the minimum requirements of modeling for the laser welding in order to get minimum errors less than 5% compared to the fine mesh.

Keywords: FEA, welding, discretization, ABAQUS user subroutine DFLUX

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Authors: Ingu Kim, Shangmun Shin, Yongsun Choi, Nguyen Manh Thang, Edwin R. Ramos, Won-Joo Hwang

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Project selection problems on management information system (MIS) are often considered a multi-criteria decision-making (MCDM) for a solving method. These problems contain two aspects, such as interdependencies among criteria and candidate projects and qualitative and quantitative factors of projects. However, most existing methods reported in literature consider these aspects separately even though these two aspects are simultaneously incorporated. For this reason, we proposed a hybrid method using analytic network process (ANP) and fuzzy logic in order to represent both aspects. We then propose a goal programming model to conduct an optimization for the project selection problems interpreted by a hybrid concept. Finally, a numerical example is conducted as verification purposes.

Keywords: Analytic Network Process (ANP), Multi-Criteria Decision-Making (MCDM), Fuzzy Logic, Information System Project Selection, Goal Programming.

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Authors: M. Anwar, M. G. Rasul, M. M. K. Khan

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The benefits of rooftop greenery systems (such as energy savings, reduction of greenhouse gas emission for mitigating climate change and maintaining sustainable development, indoor temperature control etc.) in buildings are well recognized, however there remains very little research conducted for quantifying the benefits in subtropical climates such as in Australia. This study mainly focuses on measuring/determining temperature profile and air conditioning energy savings by implementing rooftop greenery systems in subtropical Central Queensland in Australia. An experimental set-up was installed at Rockhampton campus of Central Queensland University, where two standard shipping containers (6m x 2.4m x 2.4m) were converted into small offices, one with green roof and one without. These were used for temperature, humidity and energy consumption data collection. The study found that an energy savings of up to 11.70% and temperature difference of up to 4°C can be achieved in March in subtropical Central Queensland climate in Australia. It is expected that more energy can be saved in peak summer days (December/February) as temperature difference between green roof and non-green roof is higher in December- February.

Keywords: Extensive green roof, Rooftop greenery system, Subtropical climate, Shipping container.

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Authors: Yu T. Tsai, Jin H. Huang

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In this paper, the specific sound Transmission Loss (TL) of the Laminated Composite Plate (LCP) with different material properties in each layer is investigated. The numerical method to obtain the TL of the LCP is proposed by using elastic plate theory. The transfer matrix approach is novelty presented for computational efficiency in solving the numerous layers of dynamic stiffness matrix (D-matrix) of the LCP. Besides the numerical simulations for calculating the TL of the LCP, the material properties inverse method is presented for the design of a laminated composite plate analogous to a metallic plate with a specified TL. As a result, it demonstrates that the proposed computational algorithm exhibits high efficiency with a small number of iterations for achieving the goal. This method can be effectively employed to design and develop tailor-made materials for various applications.

Keywords: Sound transmission loss, laminated composite plate, transfer matrix approach, inverse problem, elastic plate theory, material properties.

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Authors: Giulio Nisoli, Jonas Brüngger, Karin Hostettler, Nicole Stoller, Katrin Fischer

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Technical operators in the railway domain are experts responsible for the supervisory control of the railway power grid as well as of the railway tunnels. The technical systems used to master these demanding tasks are constantly increasing in their degree of automation. It becomes therefore difficult for technical operators to maintain the control over the technical systems and the processes of their job. In particular, the operators must have the necessary experience and knowledge in dealing with a malfunction situation or unexpected event. For this reason, it is of growing importance that the skills relevant for the execution of the job are maintained and further developed beyond the basic training they receive, where they are educated in respect of technical knowledge and the work with guidelines. Training methods aimed at improving the cognitive skills needed by technical operators are still missing and must be developed. Goals of the present study were to identify which are the relevant cognitive skills of technical operators in the railway domain and to define which topics should be addressed by the training of these skills. Observational interviews were conducted in order to identify the main tasks and the organization of the work of technical operators as well as the technical systems used for the execution of their job. Based on this analysis, the most demanding tasks of technical operators could be identified and described. The cognitive skills involved in the execution of these tasks are those, which need to be trained. In order to identify and analyze these cognitive skills a cognitive task analysis (CTA) was developed. CTA specifically aims at identifying the cognitive skills that employees implement when performing their own tasks. The identified cognitive skills of technical operators were summarized and grouped in training topics. For every training topic, specific goals were defined. The goals regard the three main categories; knowledge, skills and attitude to be trained in every training topic. Based on the results of this study, it is possible to develop specific training methods to train the relevant cognitive skills of the technical operators.

Keywords: Cognitive skills, cognitive task analysis, technical operators in the railway domain, training topics.

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Authors: Marco Actis Grande, Somlak Wannarumon

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This paper proposes the numerical simulation of the investment casting of gold jewelry. It aims to study the behavior of fluid flow during mould filling and solidification and to optimize the process parameters, which lead to predict and control casting defects such as gas porosity and shrinkage porosity. A finite difference method, computer simulation software FLOW-3D was used to simulate the jewelry casting process. The simplified model was designed for both numerical simulation and real casting production. A set of sensor acquisitions were allocated on the different positions of the wax tree of the model to detect filling times, while a set of thermocouples were allocated to detect the temperature during casting and cooling. Those detected data were applied to validate the results of the numerical simulation to the results of the real casting. The resulting comparisons signify that the numerical simulation can be used as an effective tool in investment-casting-process optimization and casting-defect prediction.

Keywords: Computer fluid dynamic, Investment casting, Jewelry, Mould filling, Simulation.

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Authors: M. Pandi, K. Premalatha

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A DNA microarray technology is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increase the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. It is handled by clustering which reveals the natural structures and identifying the interesting patterns in the underlying data. In this paper, gene based clustering in gene expression data is proposed using Cuckoo Search with Differential Evolution (CS-DE). The experiment results are analyzed with gene expression benchmark datasets. The results show that CS-DE outperforms CS in benchmark datasets. To find the validation of the clustering results, this work is tested with one internal and one external cluster validation indexes.

Keywords: DNA, Microarray, genomics, Cuckoo Search, Differential Evolution, Gene expression data, Clustering.

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Authors: Marc C. Robini, Pierre-Jean Viverge, Yuemin Zhu, Jianhua Luo

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The standard approach to image reconstruction is to stabilize the problem by including an edge-preserving roughness penalty in addition to faithfulness to the data. However, this methodology produces noisy object boundaries and creates a staircase effect. The existing attempts to favor the formation of smooth contour lines take the edge field explicitly into account; they either are computationally expensive or produce disappointing results. In this paper, we propose to incorporate the smoothness of the edge field in an implicit way by means of an additional penalty term defined in the wavelet domain. We also derive an efficient half-quadratic algorithm to solve the resulting optimization problem, including the case when the data fidelity term is non-quadratic and the cost function is nonconvex. Numerical experiments show that our technique preserves edge sharpness while smoothing contour lines; it produces visually pleasing reconstructions which are quantitatively better than those obtained without wavelet-domain constraints.

Keywords:

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Authors: S. Logeswari, K. Premalatha

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Search is the most obvious application of information retrieval. The variety of widely obtainable biomedical data is enormous and is expanding fast. This expansion makes the existing techniques are not enough to extract the most interesting patterns from the collection as per the user requirement. Recent researches are concentrating more on semantic based searching than the traditional term based searches. Algorithms for semantic searches are implemented based on the relations exist between the words of the documents. Ontologies are used as domain knowledge for identifying the semantic relations as well as to structure the data for effective information retrieval. Annotation of data with concepts of ontology is one of the wide-ranging practices for clustering the documents. In this paper, indexing based on concept and annotation are proposed for clustering the biomedical documents. Fuzzy c-means (FCM) clustering algorithm is used to cluster the documents. The performances of the proposed methods are analyzed with traditional term based clustering for PubMed articles in five different diseases communities. The experimental results show that the proposed methods outperform the term based fuzzy clustering.

Keywords: MeSH Ontology, Concept Indexing, Annotation, semantic relations, Fuzzy c-means.

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Authors: Davide Pierattoni, Ivan Macor, Pier Luca Montessoro

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In the recent years multimedia traffic and in particular VoIP services are growing dramatically. We present a new algorithm to control the resource utilization and to optimize the voice codec selection during SIP call setup on behalf of the traffic condition estimated on the network path. The most suitable methodologies and the tools that perform realtime evaluation of the available bandwidth on a network path have been integrated with our proposed algorithm: this selects the best codec for a VoIP call in function of the instantaneous available bandwidth on the path. The algorithm does not require any explicit feedback from the network, and this makes it easily deployable over the Internet. We have also performed intensive tests on real network scenarios with a software prototype, verifying the algorithm efficiency with different network topologies and traffic patterns between two SIP PBXs. The promising results obtained during the experimental validation of the algorithm are now the basis for the extension towards a larger set of multimedia services and the integration of our methodology with existing PBX appliances.

Keywords: Integrated voice-data communication, computernetwork performance, resource optimization.

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Authors: M. P. Sebastian

Abstract:

Health for all is considered as a sign of well-being and inclusive growth. New healthcare technologies are contributing to the quality of human lives by promoting health education and awareness, leading to the prevention, early diagnosis and treatment of the symptoms of diseases. Healthcare technologies have now migrated from the medical and institutionalized settings to the home and everyday life. This paper explores these new technologies and investigates how they contribute to health education and awareness, promoting the objective of high-value health system for all. The methodology used for the research is literature review. The paper also discusses the opportunities and challenges with futuristic healthcare technologies. The combined advances in genomics medicine, wearables and the IoT with enhanced data collection in electronic health record (EHR) systems, environmental sensors, and mobile device applications can contribute in a big way to high-value health system for all. The promise by these technologies includes reduced total cost of healthcare, reduced incidence of medical diagnosis errors, and reduced treatment variability. The major barriers to adoption include concerns with security, privacy, and integrity of healthcare data, regulation and compliance issues, service reliability, interoperability and portability of data, and user friendliness and convenience of these technologies.

Keywords: Bigdata, education, healthcare, ICT, patients, technologies.

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Authors: Nurul-Akidah M. Yusak, Rahmah Mohamed, Noor Zuhaira Abd Aziz

Abstract:

The introduction of degradable plastic materials into agricultural sectors has represented a promising alternative to promote green agriculture and environmental friendly of modern farming practices. Major challenges of developing degradable agricultural films are to identify the most feasible types of degradation mechanisms, composition of degradable polymers and related processing techniques. The incorrect choice of degradable mechanisms to be applied during the degradation process will cause premature losses of mechanical performance and strength. In order to achieve controlled process of agricultural film degradation, the compositions of degradable agricultural film also important in order to stimulate degradation reaction at required interval of time and to achieve sustainability of the modern agricultural practices. A set of photodegradable polyethylene based agricultural film was developed and produced, following the selective optimization of processing parameters of the agricultural film manufacturing system. Example of agricultural films application for oil palm seedlings cultivation is presented.

Keywords: Photodegradable polyethylene, plasticulture, processing schemes.

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Authors: Sallama Athab, Hala Bahjat, Zhang Yinghui

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Background detection is essential in video analyses; optimization is often needed in order to achieve real time calculation. Information gathered by dual cameras placed in the front and rear part of an Autonomous Vehicle (AV) is integrated for background detection. In this paper, real time calculation is achieved on the proposed technique by using Priority Regions (PR) and Parallel Processing together where each frame is divided into regions then and each region process is processed in parallel. PR division depends upon driver view limitations. A background detection system is built on the Temporal Difference (TD) and Gaussian Filtering (GF). Temporal Difference and Gaussian Filtering with multi threshold and sigma (weight) value are be based on PR characteristics. The experiment result is prepared on real scene. Comparison of the speed and accuracy with traditional background detection techniques, the effectiveness of PR and parallel processing are also discussed in this paper.

Keywords: Autonomous Vehicle, Background Detection, Dual Camera, Gaussian Filtering, Parallel Processing.

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Authors: Dhananjay C. Joshi, Jung-Hsin Lin

Abstract:

Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.

Keywords: protein-protein docking, protein-protein interaction, molecular mechanics energetics, Poisson-Boltzmann calculations

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Authors: Setareh Shekarsaraei, Marjan Moridi, Nasser L. Hadipour

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In this study, nuclear magnetic resonance spectroscopy and nuclear quadrupole resonance spectroscopy parameters of 14N (Nitrogen in imidazole ring) in N–H…O hydrogen bonding for Histidine hydrochloride monohydrate were calculated via density functional theory. We considered a five-molecule model system of Histidine hydrochloride monohydrate. Also we examined the trends of environmental effect on hydrogen bonds as well as cooperativity. The functional used in this research is M06-2X which is a good functional and the obtained results has shown good agreement with experimental data. This functional was applied to calculate the NMR and NQR parameters. Some correlations among NBO parameters, NMR and NQR parameters have been studied which have shown the existence of strong correlations among them. Furthermore, the geometry optimization has been performed using M062X/6-31++G(d,p) method. In addition, in order to study cooperativity and changes in structural parameters, along with increase in cluster size, natural bond orbitals have been employed.

Keywords: Hydrogen bonding, Density Functional Theory (DFT), Natural bond Orbitals (NBO), cooperativity effects.

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Authors: Seongjun Kim, Sanghoon Shim, Jinwooung Kim, Jaehwan Jung, Sung-Ah Kim

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As the development of information and communication technology, the convergence of machine learning of the ICT area and design is attempted. In this way, it is possible to grasp the correlation between various design elements, which was difficult to grasp, and to reflect this in the design result. In architecture, there is an attempt to predict the performance, which is difficult to grasp in the past, by finding the correlation among multiple factors mainly through machine learning. In architectural design area, some attempts to predict the performance affected by various factors have been tried. With machine learning, it is possible to quickly predict performance. The aim of this study is to propose a model that predicts performance according to the block arrangement of apartment housing through machine learning and the design alternative which satisfies the performance such as the daylight hours in the most similar form to the alternative proposed by the designer. Through this study, a designer can proceed with the design considering various design alternatives and accurate performances quickly from the early design stage.

Keywords: Apartment housing, machine learning, multi-objective optimization, performance prediction.

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Authors: Rozilawati Binti Dollah, Masaki Aono

Abstract:

Classifying biomedical literature is a difficult and challenging task, especially when a large number of biomedical articles should be organized into a hierarchical structure. In this paper, we present an approach for classifying a collection of biomedical text abstracts downloaded from Medline database with the help of ontology alignment. To accomplish our goal, we construct two types of hierarchies, the OHSUMED disease hierarchy and the Medline abstract disease hierarchies from the OHSUMED dataset and the Medline abstracts, respectively. Then, we enrich the OHSUMED disease hierarchy before adapting it to ontology alignment process for finding probable concepts or categories. Subsequently, we compute the cosine similarity between the vector in probable concepts (in the “enriched" OHSUMED disease hierarchy) and the vector in Medline abstract disease hierarchies. Finally, we assign category to the new Medline abstracts based on the similarity score. The results obtained from the experiments show the performance of our proposed approach for hierarchical classification is slightly better than the performance of the multi-class flat classification.

Keywords: Biomedical literature, hierarchical text classification, ontology alignment, text mining.

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