Search results for: inter story drift ratio.

Authors: Oluseye Adeniyi Adeleke, Mohd Fadzli Salleh

Abstract:

Cooperative communication provides transmit diversity, even when, due to size constraints, mobile units cannot accommodate multiple antennas. A versatile cooperation method called coded cooperation has been developed, in which cooperation is implemented through channel coding with a view to controlling the errors inherent in wireless communication. In this work we evaluate the performance of coded cooperation in flat Rayleigh fading environment using a concept known as the pair wise error probability (PEP). We derive the PEP for a flat fading scenario in coded cooperation and then compare with the signal-to-noise ratio of the users in the network. Results show that an increase in the SNR leads to a decrease in the PEP. We also carried out simulations to validate the result.

Keywords: Channel state information, coded cooperation, cooperative systems, pairwise-error-probability, Reed-Solomon codes.

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Authors: Mustafa Abdalla, Khaled A. Madi, Rajab Farhat

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An array antenna system with innovative signal processing can improve the resolution of a source direction of arrival (DoA) estimation. High resolution techniques take the advantage of array antenna structures to better process the incoming waves. They also have the capability to identify the direction of multiple targets. This paper investigates performance of the DOA estimation algorithm namely; Capon and MUSIC on the uniform linear array (ULA). The simulation results show that in Capon and MUSIC algorithm the resolution of the DOA techniques improves as number of snapshots, number of array elements, signal-to-noise ratio and separation angle between the two sources θ increases.

Keywords: Antenna array, Capon, MUSIC, Direction-of-arrival estimation, signal processing, uniform linear arrays.

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Authors: M. J. Go, H. S. Shin, D. W. Kim, D. Chang, S. B. Han, J. M. Hur, B. R. Chung, J. K. Choi, J. Fan

Abstract:

This study developed a high efficient and combined biological and chemical filter treatment process. This process used PAC (Powder Activated Carbon), Alum and attached growth treatment process. The system removals of total nitrogen and total phosphorus ratio of two were as high as 70% and 73%, moreover, the effluent water was suitable to urban and agricultural water. Also the advantages of this process are not only occupies small place but is simple, economic and easy operating. Besides, our developed process can keep stable process efficiency even in relative low load level. Therefore, this study judges that use of the high efficient and combined biological and chemical filter treatment process, it is expected that the effluent water in this system can be reused as urban and agricultural water.

Keywords: biological and chemical filter treatment, wastewaterreuse, PAC, Alum

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Authors: Panos D. Kotsas, Tony Dodd

Abstract:

The purpose of this work is to present a method for rigid registration of medical images using 1D binary projections when a part of one of the two images is missing. We use 1D binary projections and we adjust the projection limits according to the reduced image in order to perform accurate registration. We use the variance of the weighted ratio as a registration function which we have shown is able to register 2D and 3D images more accurately and robustly than mutual information methods. The function is computed explicitly for n=5 Chebyshev points in a [-9,+9] interval and it is approximated using Chebyshev polynomials for all other points. The images used are MR scans of the head. We find that the method is able to register the two images with average accuracy 0.3degrees for rotations and 0.2 pixels for translations for a y dimension of 156 with initial dimension 256. For y dimension 128/256 the accuracy decreases to 0.7 degrees for rotations and 0.6 pixels for translations.

Keywords: binary projections, image registration, reduceddimension images.

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Authors: Wahiba Mohguen, Raïs El’hadi Bekka

Abstract:

This paper presents a denoising method called EMD-Custom that was based on Empirical Mode Decomposition (EMD) and the modified Customized Thresholding Function (Custom) algorithms. EMD was applied to decompose adaptively a noisy signal into intrinsic mode functions (IMFs). Then, all the noisy IMFs got threshold by applying the presented thresholding function to suppress noise and to improve the signal to noise ratio (SNR). The method was tested on simulated data and real ECG signal, and the results were compared to the EMD-Based signal denoising methods using the soft and hard thresholding. The results showed the superior performance of the proposed EMD-Custom denoising over the traditional approach. The performances were evaluated in terms of SNR in dB, and Mean Square Error (MSE).

Keywords: Customized thresholding, ECG signal, EMD, hard thresholding, Soft-thresholding.

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Authors: Mario Mastriani, Juliana Gambini

Abstract:

In this work, we present a comparison between two techniques of image compression. In the first case, the image is divided in blocks which are collected according to zig-zag scan. In the second one, we apply the Fast Cosine Transform to the image, and then the transformed image is divided in blocks which are collected according to zig-zag scan too. Later, in both cases, the Karhunen-Loève transform is applied to mentioned blocks. On the other hand, we present three new metrics based on eigenvalues for a better comparative evaluation of the techniques. Simulations show that the combined version is the best, with minor Mean Absolute Error (MAE) and Mean Squared Error (MSE), higher Peak Signal to Noise Ratio (PSNR) and better image quality. Finally, new technique was far superior to JPEG and JPEG2000.

Keywords: Fast Cosine Transform, image compression, JPEG, JPEG2000, Karhunen-Loève Transform, zig-zag scan.

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Authors: Muhammad Tahir, Muhammad H. Sayyad, Dil N. Khan, Fazal Wahab

Abstract:

Herein, the organic semiconductor methyl orange (MO), is investigated for the first time for its electronic applications. For this purpose, Al/MO/n-Si heterojunction is fabricated through economical cheap and simple “drop casting” technique. The currentvoltage (I-V) measurements of the device are made at room temperature under dark conditions. The I-V characteristics of Al/MO/n-Si junction exhibits asymmetrical and rectifying behavior that confirms the formation of diode. The diode parameters such as rectification ratio (RR), turn on voltage (Vturn on), reverse saturation current (I0), ideality factor (n), barrier height ( b f ), series resistance (Rs) and shunt resistance (Rsh) are determined from I-V curves using Schottky equations. These values of these parameters are also extracted and verified by applying Cheung’s functions. The conduction mechanisms are explained from the forward bias I-V characteristics using the power law.

Keywords: Electrical properties, Organic/inorganic heterojunction diode, Methyl Orange, Cheungs Functions

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Authors: Mostafa Raki, Mahdi Hamzehei

Abstract:

Equilibrium and stability equations of a thin rectangular plate with length a, width b, and thickness h(x)=C1x+C2, made of functionally graded materials under thermal loads are derived based on the first order shear deformation theory. It is assumed that the material properties vary as a power form of thickness coordinate variable z. The derived equilibrium and buckling equations are then solved analytically for a plate with simply supported boundary conditions. One type of thermal loading, uniform temperature rise and gradient through the thickness are considered, and the buckling temperatures are derived. The influences of the plate aspect ratio, the relative thickness, the gradient index and the transverse shear on buckling temperature difference are all discussed.

Keywords: Stability of plate, thermal buckling, rectangularplate, functionally graded material, first order shear deformationtheory.

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Authors: Tayeb Aissaoui, Inas M. AlNashef

Abstract:

In recent years, green solvents named deep eutectic solvents (DESs) have been found to possess significant properties and to be applicable in several technologies. Choline chloride (ChCl) mixed with urea at a ratio of 1:2 and 80 °C was the first discovered DES. In this article, chemical structure and combination mechanism of ChCl: urea based DES were investigated. Moreover, the implementation of this DES in water removal from natural gas was reported. Dehydration of natural gas by ChCl:urea shows significant absorption efficiency compared to triethylene glycol. All above operations were retrieved from COSMOthermX software. This article confirms the potential application of DESs in gas industry.

Keywords: COSMO-RS, deep eutectic solvents, dehydration, natural gas, structure, organic salt.

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Authors: Young-Kwan Choi, Gang-Wook Shin, Sung-Taek Hong

Abstract:

Water supply system consumes large amount of power load during water treatment and transportation of purified water. Many energy conserving high efficiency materials such as DC motor and LED light have recently been introduced to water supply system for energy conservation. This paper performed empirical analysis on BLDC and AC motors and comparatively analyzed the change in power according to DC power supply ratio in order to conserve energy of a next-generation water treatment system called vertical water treatment system. In addition, a DC distribution system linked with photovoltaic generation was simulated to analyze the energy conserving effect of DC load.

Keywords: Vertical Water Treatment System, DC Power Supply, Energy Efficiency, BLDC.

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Authors: Yin Yin Pey, Leok Poh Chua, Wei Long Siauw

Abstract:

Linear stochastic estimation and quadratic stochastic estimation techniques were applied to estimate the entire velocity flow-field of an open cavity with a length to depth ratio of 2. The estimations were done through the use of instantaneous velocity magnitude as estimators. These measurements were obtained by Particle Image Velocimetry. The predicted flow was compared against the original flow-field in terms of the Reynolds stresses and turbulent kinetic energy. Quadratic stochastic estimation proved to be more superior than linear stochastic estimation in resolving the shear layer flow. When the velocity fluctuations were scaled up in the quadratic estimate, both the time-averaged quantities and the instantaneous cavity flow can be predicted to a rather accurate extent.

Keywords: Open cavity, Particle Image Velocimetry, Stochastic estimation, Turbulent kinetic energy.

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Authors: M. M. Doustdar, M. Mojtahedpoor

Abstract:

The effects of flame-holder position, the ratio of flame holder diameter to combustion chamber diameter and injection angle on fuel propulsive droplets sizing and effective mass fraction have been studied by a cold flow. We named the mass of fuel vapor inside the flammability limit as the effective mass fraction. An empty cylinder as well as a flame-holder which are a simulator for duct combustion has been considered. The airflow comes into the cylinder from one side and injection operation will be done by four nozzles which are located on the entrance of cylinder. To fulfill the calculations a modified version of KIVA-3V code which is a transient, three-dimensional, multiphase, multi component code for the analysis of chemically reacting flows with sprays, is used.

Keywords: KIVA-3V, flame-holder, duct combustion, effective mass fraction, mean diameter of droplets.

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Authors: S. A. Naeini, M. Ghorbani Tochaee

Abstract:

The aim of this study is to assess the influence of plastic fines content on sand-clay mixtures on maximum shear modulus and liquefaction resistance using a series of resonant column tests. A high plasticity clay called bentonite was added to 161 Firoozkooh sand at the percentages of 10, 15, 20, 25, 30 and 35 by dry weight. The resonant column tests were performed on the remolded specimens at constant confining pressure of 100 KPa and then the values of G_max and liquefaction resistance were investigated. The maximum shear modulus and cyclic resistance ratio (CRR) are examined in terms of fines content. Based on the results, the maximum shear modulus and liquefaction resistance tend to decrease within the increment of fine contents.

Keywords: Gmax, liquefaction, plastic fines, resonant column, sand-clay mixtures, bentonite.

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Authors: Eleni Ioannou, Pascal Nucara, Keith Pullen

Abstract:

The subject of this paper is the investigation of the best efficiency design of a compressor diffuser applied in new lightweight, ultra efficient micro-gas turbine engines for vehicles. The Computational Fluid Dynamics (CFD) results are obtained utilizing steady state simulations for a wedge and an ”oval” type pipe diffuser in an effort to identify the beneficial effects of the pipe diffuser design. The basic flow features are presented with particular focus on the optimization of the pipe diffuser leading to higher efficiencies for the compressor stage. The optimised pipe diffuser is designed to exploit the 3D freedom enabled by Selective Laser Melting, hence purposely involves an investigation of geometric characteristics that do not follow the traditional diffuser concept.

Keywords: CFD, centrifugal compressor, micro-gas turbine, pipe diffuser, SLM, wedge diffuser.

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Authors: Sunitha S. L., V. Udayashankara

Abstract:

Hearing impairment is the number one chronic disability affecting many people in the world. Background noise is particularly damaging to speech intelligibility for people with hearing loss especially for sensorineural loss patients. Several investigations on speech intelligibility have demonstrated sensorineural loss patients need 5-15 dB higher SNR than the normal hearing subjects. This paper describes Discrete Hartley Transform Power Normalized Least Mean Square algorithm (DHT-LMS) to improve the SNR and to reduce the convergence rate of the Least Means Square (LMS) for sensorineural loss patients. The DHT transforms n real numbers to n real numbers, and has the convenient property of being its own inverse. It can be effectively used for noise cancellation with less convergence time. The simulated result shows the superior characteristics by improving the SNR at least 9 dB for input SNR with zero dB and faster convergence rate (eigenvalue ratio 12) compare to time domain method and DFT-LMS.

Keywords: Hearing Impairment, DHT-LMS, Convergence rate, SNR improvement.

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Authors: Kotaro Miura, Makoto Sakamoto, Yuji Tanabe

Abstract:

We focus on internal stress and displacement of an elastic axisymmetric contact problem for indentation of a layer-substrate body. An elastic layer is assumed to be perfectly bonded to an elastic semi-infinite substrate. The elastic layer is smoothly indented with a flat-ended cylindrical indenter. The analytical and exact solutions were obtained by solving an infinite system of simultaneous equations using the method to express a normal contact stress at the upper surface of the elastic layer as an appropriate series. This paper presented the numerical results of internal stress and displacement distributions for hard-coating system with constant values of Poisson’s ratio and the thickness of elastic layer.

Keywords: Indentation, contact problem, stress distribution, coating materials, layer-substrate body.

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Authors: Elham Farahmand, Fatimah Ibrahim, Samira Hosseini, Ivan Djordjevic, Leo. H. Koole

Abstract:

Compositions of different molar ratios of polymethylmethacrylate-co-methacrylic acid (PMMA-co-MAA) were synthesized via free-radical polymerization. Polymer coated surfaces have been produced on silicon wafers. Coated samples were analyzed by atomic force microscopy (AFM). The results have shown that the roughness of the surfaces have increased by increasing the molar ratio of monomer methacrylic acid (MAA). This study reveals that the gradual increase in surface roughness is due to the fact that carboxylic functional groups have been generated by MAA segments. Such surfaces can be desirable platforms for fabrication of the biosensors for detection of the viruses and diseases.

Keywords: Polymethylmethacrylate-co-methacrylic acid (PMMA-co-MAA), Polymeric material, Atomic Force Microscopy, roughness, carboxylic functional groups.

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Authors: Shinji Oouchi, Hajime Nomura, Kung-Da Wu, Yong-Run Chen, Jui-Pin Hung

Abstract:

This paper presents the variation of the dynamic characteristics of a spindle with the change of bearing preload. The correlations between the variation of bearing preload and fundamental modal parameters were first examined by conducting vibration tests on physical spindle units. Experimental measurements show that the dynamic compliance and damping ratio associated with the dominating modes were affected to vary with variation of the bearing preload. When the bearing preload was slightly deviated from a standard value, the modal frequency and damping ability also vary to different extent, which further enable the spindle to perform with different compliance. For the spindle used in this study, a standard preload value set on bearings would enable the spindle to behave a higher stiffness as compared with others with a preload variation. This characteristic can be served as a reference to examine the variation of bearing preload of spindle in assemblage or operation.

Keywords: Dynamic compliance, Bearing preload, Modal damping.

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Authors: Achuthsankar S. Nair, J. S. Jayasudha

Abstract:

The ever increasing use of World Wide Web in the existing network, results in poor performance. Several techniques have been developed for reducing web traffic by compressing the size of the file, saving the web pages at the client side, changing the burst nature of traffic into constant rate etc. No single method was adequate enough to access the document instantly through the Internet. In this paper, adaptive hybrid algorithms are developed for reducing web traffic. Intelligent agents are used for monitoring the web traffic. Depending upon the bandwidth usage, user-s preferences, server and browser capabilities, intelligent agents use the best techniques to achieve maximum traffic reduction. Web caching, compression, filtering, optimization of HTML tags, and traffic dispersion are incorporated into this adaptive selection. Using this new hybrid technique, latency is reduced to 20 – 60 % and cache hit ratio is increased 40 – 82 %.

Keywords: Bandwidth, Congestion, Intelligent Agents, Prefetching, Web Caching.

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Authors: V. Sudha, D. Sriram Kumar

Abstract:

In this paper, we present a low complexity hybrid scheme using conventional selective mapping (C-SLM) and clipping algorithms to reduce the high peak-to-average power ratio (PAPR) of orthogonal frequency division multiplexing (OFDM) signal. In the proposed scheme, the input data sequence (X) is divided into two sub-blocks, then clipping algorithm is applied to the first sub-block, whereas C-SLM algorithm is applied to the second sub-block in order to reduce both computational complexity and PAPR. The resultant time domain OFDM signal is obtained by combining the output of two sub-blocks. The simulation results show that the proposed hybrid scheme provides 0.45 dB PAPR reduction gain at CCDF value of 10-2 and 52% of computational complexity reduction when compared to C-SLM scheme at the expense of slight degradation in bit error rate (BER) performance.

Keywords: CCDF, Clipping, OFDM, PAPR, SLM.

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Authors: Mehrdad Nouri Khajavi, Sajjad Ahoui Ghazvin, Ghader Rezazadeh, Mohammad Fathalilou

Abstract:

In this paper static and dynamic response of a varactor of a micro-phase shifter to DC, step DC and AC voltages have been studied. By presenting a mathematical modeling Galerkin-based step by step linearization method (SSLM) and Galerkin-based reduced order model have been used to solve the governing static and dynamic equations, respectively. The calculated static and dynamic pull-in voltages have been validated by previous experimental and theoretical results and a good agreement has been achieved. Then the frequency response and phase diagram of the system has been studied. It has been shown that applying the DC voltage shifts down the phase diagram and frequency response. Also increasing the damping ratio shifts up the phase diagram.

Keywords: MEMS, Phase Shifter, Pull-in Voltage, PhaseDiagram

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Authors: Esam Jassim

Abstract:

Supersonic nozzles are commonly used to purify natural gas in gas processing technology. As an innovated technology, it is employed to overcome the deficit of the traditional method, related to gas dynamics, thermodynamics and fluid dynamics theory. An indoor test rig is built to study the dehumidification process of moisture fluid. Humid air was chosen for the study. The working fluid was circulating in an open loop, which had provision for filtering, metering, and humidifying. A stainless steel supersonic separator is constructed together with the C-D nozzle system. The result shows that dehumidification enhances as NPR increases. This is due to the high intensity in the turbulence caused by the shock formation in the divergent section. Such disturbance strengthens the centrifugal force, pushing more particles toward the near-wall region. In return return, the pressure recovery factor, defined as the ratio of the outlet static pressure of the fluid to its inlet value, decreases with NPR.

Keywords: Supersonic nozzle, dehumidification, particle separation, geometry.

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Authors: J. K. Choi , D. W. Kim, H. S. Shin, H. J. Yeon, B. K. Kim, Yeon. Fan, D. Chang, S. B. Han, J.M. Hur, B. R. Jung, S. M. Park

Abstract:

The purpose of this research was develop a biological nutrient removal (BNR) system which has low energy consumption, sludge production, and land usage. These indicate that BNR system could be a alternative of future wastewater treatment in ubiquitous city(U-city). Organics and nitrogen compounds could be removed by this system so that secondary or tertiary stages of wastewater treatment satisfy their standards. This system was composed of oxic and anoxic filter filed with PVDC and POM media. Anoxic/oxic filter system operated under empty bed contact time of 4 hours by increasing recirculation ratio from 0 to 100 %. The system removals of total nitrogen and COD were 76.3% and 93%, respectively. To be observed internal behavior in this system SCOD, NH3-N, and NO3-N were conducted and removal shows range of 25~100%, 59~99%, and 70~100%, respectively.

Keywords: BNR, nitrification, denitrification, organics removal, anoxic, oxic, advanced treatment.

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Authors: Robert Prucek, Aleš Panáček, Jan Filip, Libor Kvítek, Radek Zbořil

Abstract:

The preparation of Cu nanoparticles (NPs) through the reduction of copper ions by sodium borohydride in the presence of sodium polyacrylate with a molecular weight of 1200 is reported. Cu NPs were synthesized at a concentration of copper salt equal to 2.5, 5, and 10 mM, and at a molar ratio of copper ions and monomeric unit of polyacrylate equal to 1:2. The as-prepared Cu NPs have diameters of about 2.5–3 nm for copper concentrations of 2.5 and 5 mM, and 6 nm for copper concentration of 10 mM. Depending on the copper salt concentration and concentration of additionally added polyacrylate to Cu particle dispersion, primarily formed NPs grow through the process of aggregation and/or coalescence into clusters and/or particles with a diameter between 20–100 nm. The amount of additionally added sodium polyacrylate influences the stability of Cu particles against air oxidation. The catalytic efficiency of the prepared Cu particles for the reduction of 4-nitrophenol is discussed.

Keywords: Copper, nanoparticles, sodium polyacrylate, catalyst, 4-nitrophenol.

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Authors: Gábor Szládek, Balázs Héder, János Bitó

Abstract:

In a BFWA (Broadband Fixed Wireless Access Network) the evolved SINR (Signal to Interference plus Noise Ratio) is relevant influenced by the applied duplex method. The TDD (Time Division Duplex), especially adaptive TDD method has some advantage contrary to FDD (Frequency Division Duplex), for example the spectrum efficiency and flexibility. However these methods are suffering several new interference situations that can-t occur in a FDD system. This leads to reduced SINR in the covered area what could cause some connection outages. Therefore, countermeasure techniques against interference are necessary to apply in TDD systems. Synchronization is one way to handling the interference. In this paper the TDD systems – applying different system synchronization degree - will be compared by the evolved SINR at different locations of the BFWA service area and the percentage of the covered area by the system.

Keywords: Adaptive TDD, BFWA networks, duplex methods, intra system interferences.

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Authors: Yi-Ping Fang, Yi-Ting Wong

Abstract:

Transcription factor p53 has a powerful tumor suppressing function that is associated with many cancers. However, p53 of the molecular weight was higher make the limitation across to skin or cell membrane. Thymidine dinucleotide (pTT), an oligonucleotide, can activate the p53 transcription factor. pTT is a hydrophilic and negative charge oligonucleotide, which delivery in to cell membrane need an appropriate carrier. The aim of this study was to improve the bioavailability of the nucleotide fragment, thymidine dinucleotide (pTT), using elasic liposome carriers to deliver the drug into the skin. The study demonstrate that dioleoylphosphocholine (DOPC) incorporated with sodium cholate at molar ratio 1:1 can archived the particle size about 220 nm. This elastic liposome could penetration through skin from stratum corneum to whole epidermis by confocal laser scanning microscopy (CLSM). Moreover, we observed the the slight increase in generation of p53 by western blot.

Keywords: Elastic liposome, Tymidine dinucleotide, p53, Topical delivery

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Authors: Sangjun Park, Sangbae Jeong, Moonsung Han, Minsoo hahn

Abstract:

In this paper, a target signal detection method using multiple signal classification (MUSIC) algorithm is proposed. The MUSIC algorithm is a subspace-based direction of arrival (DOA) estimation method. The algorithm detects the DOAs of multiple sources using the inverse of the eigenvalue-weighted eigen spectra. To apply the algorithm to target signal detection for GSC-based beamforming, we utilize its spectral response for the target DOA in noisy conditions. For evaluation of the algorithm, the performance of the proposed target signal detection method is compared with that of the normalized cross-correlation (NCC), the fixed beamforming, and the power ratio method. Experimental results show that the proposed algorithm significantly outperforms the conventional ones in receiver operating characteristics(ROC) curves.

Keywords: Beamforming, direction of arrival, multiple signal classification, target signal detection.

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Authors: Sana Ktata, Kaïs Ouni, Noureddine Ellouze

Abstract:

Electrocardiogram (ECG) data compression algorithm is needed that will reduce the amount of data to be transmitted, stored and analyzed, but without losing the clinical information content. A wavelet ECG data codec based on the Set Partitioning In Hierarchical Trees (SPIHT) compression algorithm is proposed in this paper. The SPIHT algorithm has achieved notable success in still image coding. We modified the algorithm for the one-dimensional (1-D) case and applied it to compression of ECG data. By this compression method, small percent root mean square difference (PRD) and high compression ratio with low implementation complexity are achieved. Experiments on selected records from the MIT-BIH arrhythmia database revealed that the proposed codec is significantly more efficient in compression and in computation than previously proposed ECG compression schemes. Compression ratios of up to 48:1 for ECG signals lead to acceptable results for visual inspection.

Keywords: Discrete Wavelet Transform, ECG compression, SPIHT.

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Authors: Tae Yun Chung, Jungho Moon, Tae Kwon Ha

Abstract:

Al/Cu clad sheet has been fabricated by using differential speed rolling (DSR) process, which caused severe shear deformation between Al and Cu plate to easily bond to each other. Rolling was carried out at 100 and 150oC with speed ratios from 1.4 to 2.2, in which the total thickness reduction was in the range between 14 and 46%. Interfacial microstructure and mechanical properties of Al/Cu clad were investigated by scanning electron microscope equipped with energy dispersive X-ray detector, and tension tests. The DSR process was very effective to provide a good interface for atoms diffusion during subsequent annealing. The strength of bonding was higher with the increasing speed ratio. Post heat treatment enhanced the mechanical properties of clad sheet by forming intermetallic compounds in the interface area. 

Keywords: Aluminum/Copper clad sheet, Differential speed rolling, Interface microstructure, Annealing, Tensile test.

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Authors: Maria E. Manioudaki, Panayiota Poirazi

Abstract:

Yeast cells live in a constantly changing environment that requires the continuous adaptation of their genomic program in order to sustain their homeostasis, survive and proliferate. Due to the advancement of high throughput technologies, there is currently a large amount of data such as gene expression, gene deletion and protein-protein interactions for S. Cerevisiae under various environmental conditions. Mining these datasets requires efficient computational methods capable of integrating different types of data, identifying inter-relations between different components and inferring functional groups or 'modules' that shape intracellular processes. This study uses computational methods to delineate some of the mechanisms used by yeast cells to respond to environmental changes. The GRAM algorithm is first used to integrate gene expression data and ChIP-chip data in order to find modules of coexpressed and co-regulated genes as well as the transcription factors (TFs) that regulate these modules. Since transcription factors are themselves transcriptionally regulated, a three-layer regulatory cascade consisting of the TF-regulators, the TFs and the regulated modules is subsequently considered. This three-layer cascade is then modeled quantitatively using artificial neural networks (ANNs) where the input layer corresponds to the expression of the up-stream transcription factors (TF-regulators) and the output layer corresponds to the expression of genes within each module. This work shows that (a) the expression of at least 33 genes over time and for different stress conditions is well predicted by the expression of the top layer transcription factors, including cases in which the effect of up-stream regulators is shifted in time and (b) identifies at least 6 novel regulatory interactions that were not previously associated with stress-induced changes in gene expression. These findings suggest that the combination of gene expression and protein-DNA interaction data with artificial neural networks can successfully model biological pathways and capture quantitative dependencies between distant regulators and downstream genes.

Keywords: gene modules, artificial neural networks, yeast, stress

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