Search results for: sequence diagrams.

Authors: Janet Holland

Abstract:

Eye tracking is a great way to triangulate multiple data sources for deeper, more complete knowledge of how instructional materials are really being used and emotional connections made. Using sensor based biometrics provides a detailed local analysis in real time expanding our ability to collect science based data for a more comprehensive level of understanding, not previously possible, for teaching and learning. The knowledge gained will be used to make future improvements to instructional materials, tools, and interactions. The literature has been examined and a preliminary pilot test was implemented to develop a methodology for research in Instructional Design and Technology. Eye tracking now offers the addition of objective metrics obtained from eye tracking and other biometric data collection with analysis for a fresh perspective.

Keywords: Area of interest, eye tracking, biometrics, fixation, fixation count, fixation sequence, fixation time, gaze points, heat map, saccades, time to first fixation.

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Authors: Irtaza M. Syed, Kaamran Raahemifar

Abstract:

This paper presents a model predictive control (MPC) of a utility interactive (UI) single phase inverter (SPI) for a photovoltaic (PV) system at residential/distribution level. The proposed model uses single-phase phase locked loop (PLL) to synchronize SPI with the grid and performs MPC control in a dq reference frame. SPI model consists of boost converter (BC), maximum power point tracking (MPPT) control, and a full bridge (FB) voltage source inverter (VSI). No PI regulators to tune and carrier and modulating waves are required to produce switching sequence. Instead, the operational model of VSI is used to synthesize sinusoidal current and track the reference. Model is validated using a three kW PV system at the input of UI-SPI in Matlab/Simulink. Implementation and results demonstrate simplicity and accuracy, as well as reliability of the model.

Keywords: Matlab/Simulink, Model Predictive Control, Phase Locked Loop, Single Phase Inverter, Voltage Source Inverter.

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Authors: Majid Forghani, Michael Khachay

Abstract:

In genetics, the impact of neighboring amino acids on a target site is referred as the nearest-neighbor effect or simply neighbor effect. In this paper, a new method called wavelet particle decomposition representing the one-dimensional neighbor effect using wavelet packet decomposition is proposed. The main idea lies in known dependence of wavelet packet sub-bands on location and order of neighboring samples. The method decomposes the value of a signal sample into small values called particles that represent a part of the neighbor effect information. The results have shown that the information obtained from the particle decomposition can be used to create better model variables or features. As an example, the approach has been applied to improve the correlation of test and reference sequence distance with titer in the hemagglutination inhibition assay.

Keywords: Antigenic variants, neighbor effect, wavelet packet, wavelet particle decomposition.

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Authors: S. Kahvecioglu, A. Karamancioglu, A. Yazici

Abstract:

In this paper, a nonlinear model predictive swing-up and stabilizing sliding controller is proposed for an inverted pendulum-cart system. In the swing up phase, the nonlinear model predictive control is formulated as a nonlinear programming problem with energy based objective function. By solving this problem at each sampling instant, a sequence of control inputs that optimize the nonlinear objective function subject to various constraints over a finite horizon are obtained. Then, this control drives the pendulum to a predefined neighborhood of the upper equilibrium point, at where sliding mode based model predictive control is used to stabilize the systems with the specified constraints. It is shown by the simulations that, due to the way of formulating the problem, short horizon lengths are sufficient for attaining the swing up goal.

Keywords: Inverted pendulum, model predictive control, swingup, stabilization.

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Authors: Hu Haibo, Zhao Hong

Abstract:

Gaussian mixture background model is widely used in moving target detection of the image sequences. However, traditional Gaussian mixture background model usually considers the time continuity of the pixels, and establishes background through statistical distribution of pixels without taking into account the pixels- spatial similarity, which will cause noise, imperfection and other problems. This paper proposes a new Gaussian mixture modeling approach, which combines the color and gradient of the spatial information, and integrates the spatial information of the pixel sequences to establish Gaussian mixture background. The experimental results show that the movement background can be extracted accurately and efficiently, and the algorithm is more robust, and can work in real time in tracking applications.

Keywords: Gaussian mixture model, real-time tracking, sequence image, gradient.

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Authors: S.L. Loh, S. Salleh, N.H. Sarmin

Abstract:

A spanning tree of a connected graph is a tree which consists the set of vertices and some or perhaps all of the edges from the connected graph. In this paper, a model for spanning tree transformation of connected graphs into single-row networks, namely Spanning Tree of Connected Graph Modeling (STCGM) will be introduced. Path-Growing Tree-Forming algorithm applied with Vertex-Prioritized is contained in the model to produce the spanning tree from the connected graph. Paths are produced by Path-Growing and they are combined into a spanning tree by Tree-Forming. The spanning tree that is produced from the connected graph is then transformed into single-row network using Tree Sequence Modeling (TSM). Finally, the single-row routing problem is solved using a method called Enhanced Simulated Annealing for Single-Row Routing (ESSR).

Keywords: Graph theory, simulated annealing, single-rowrouting and spanning tree.

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Authors: M. Michael Gromiha, Y. Yabuki, K. Imai, P. Horton, K. Fukui

Abstract:

We have developed a database for membrane protein functions, which has more than 3000 experimental data on functionally important amino acid residues in membrane proteins along with sequence, structure and literature information. Further, we have proposed different methods for identifying membrane proteins based on their functions: (i) discrimination of membrane transport proteins from other globular and membrane proteins and classifying them into channels/pores, electrochemical and active transporters, and (ii) β-signal for the insertion of mitochondrial β-barrel outer membrane proteins and potential targets. Our method showed an accuracy of 82% in discriminating transport proteins and 68% to classify them into three different transporters. In addition, we have identified a motif for targeting β-signal and potential candidates for mitochondrial β-barrel membrane proteins. Our methods can be used as effective tools for genome-wide annotations.

Keywords: Membrane proteins, database, transporters, discrimination, β-signal.

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Authors: Ali Beydoun, Hamzé H. Alaeddine

Abstract:

One of the main challenges in MIMO-OFDM system to achieve the expected performances in terms of data rate and robustness against multi-path fading channels is the channel estimation. Several methods were proposed in the literature based on either least square (LS) or minimum mean squared error (MMSE) estimators. These methods present high implementation complexity as they require the inversion of large matrices. In order to overcome this problem and to reduce the complexity, this paper presents a solution that benefits from the use of the STBC encoder and transforms the channel estimation process into a set of simple linear operations. The proposed method is evaluated via simulation in AWGN-Rayleigh fading channel. Simulation results show a maximum reduction of 6.85% of the bit error rate (BER) compared to the one obtained with the ideal case where the receiver has a perfect knowledge of the channel.

Keywords: Channel estimation, MIMO, OFDM, STBC, CAZAC sequence.

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Authors: M. Kashfi, K. Jahani

Abstract:

Sound attenuation in absorptive silencers has been analyzed in this paper. The structure of such devices is as follows. When the rigid duct of an expansion chamber has been lined by a packed absorptive material under a perforated membrane, incident sound waves will be dissipated by the absorptive liners. This kind of silencer, usually are applicable for medium to high frequency ranges. Several conditions for different absorptive materials, variety in their thicknesses, and different shapes of the expansion chambers have been studied in this paper. Also, graphs of sound attenuation have been compared between empty expansion chamber and duct of silencer with applying liner. Plane waves have been assumed in inlet and outlet regions of the silencer. Presented results that have been achieved by applying finite element method (FEM), have shown the dependence of the sound attenuation spectrum to flow resistivity and the thicknesses of the absorptive materials, and geometries of the cross section (configuration of the silencer). As flow resistivity and thickness of absorptive materials increase, sound attenuation improves. In this paper, diagrams of the transmission loss (TL) for absorptive silencers in five different cross sections (rectangle, circle, ellipse, square, and rounded rectangle as the main geometry) have been presented. Also, TL graphs for silencers using different absorptive material (glass wool, wood fiber, and kind of spongy materials) as liner with three different thicknesses of 5 mm, 15 mm, and 30 mm for glass wool liner have been exhibited. At first, the effect of substances of the absorptive materials with the specific flow resistivity and densities on the TL spectrum, then the effect of the thicknesses of the glass wool, and at last the efficacy of the shape of the cross section of the silencer have been investigated.

Keywords: Transmission loss, absorptive material, flow resistivity, thickness, frequency.

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Authors: Ali Akbar Attari, Ali Asghar Beheshti Shirazi

Abstract:

In this paper, we propose a blind and robust audio watermarking scheme based on spread spectrum in Discrete Wavelet Transform (DWT) domain. Watermarks are embedded in the low-frequency coefficients, which is less audible. The key idea is dividing the audio signal into small frames, and magnitude of the 6^th level of DWT approximation coefficients is modifying based upon the Direct Sequence Spread Spectrum (DSSS) technique. Also, the psychoacoustic model for enhancing in imperceptibility, as well as Savitsky-Golay filter for increasing accuracy in extraction, is used. The experimental results illustrate high robustness against most common attacks, i.e. Gaussian noise addition, Low pass filter, Resampling, Requantizing, MP3 compression, without significant perceptual distortion (ODG is higher than -1). The proposed scheme has about 83 bps data payload.

Keywords: Audio watermarking, spread spectrum, discrete wavelet transform, psychoacoustic, Savitsky-Golay filter.

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Authors: Mattheos K. Protopapas, Elias B. Kosmatopoulos

Abstract:

An iterative algorithm is proposed and tested in Cournot Game models, which is based on the convergence of sequential best responses and the utilization of a genetic algorithm for determining each player-s best response to a given strategy profile of its opponents. An extra outer loop is used, to address the problem of finite accuracy, which is inherent in genetic algorithms, since the set of feasible values in such an algorithm is finite. The algorithm is tested in five Cournot models, three of which have convergent best replies sequence, one with divergent sequential best replies and one with “local NE traps"[14], where classical local search algorithms fail to identify the Nash Equilibrium. After a series of simulations, we conclude that the algorithm proposed converges to the Nash Equilibrium, with any level of accuracy needed, in all but the case where the sequential best replies process diverges.

Keywords: Best response, Cournot oligopoly, genetic algorithms, Nash equilibrium.

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Authors: H. Motameni, M. Norouzi, M. Jahandar, A. Hatami

Abstract:

In this paper a way of hiding text message (Steganography) in the gray image has been presented. In this method tried to find binary value of each character of text message and then in the next stage, tried to find dark places of gray image (black) by converting the original image to binary image for labeling each object of image by considering on 8 connectivity. Then these images have been converted to RGB image in order to find dark places. Because in this way each sequence of gray color turns into RGB color and dark level of grey image is found by this way if the Gary image is very light the histogram must be changed manually to find just dark places. In the final stage each 8 pixels of dark places has been considered as a byte and binary value of each character has been put in low bit of each byte that was created manually by dark places pixels for increasing security of the main way of steganography (LSB).

Keywords: Binary image, labeling, low bit, neighborhood, RGB image, steganography, threshold.

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Authors: Jiadong Liang

Abstract:

This paper presented a video watermarking algorithm based on wavelet chaotic neural network. First, to enhance binary image’s security, the algorithm encrypted it with double chaotic based on Arnold and Logistic map, Then, the host video was divided into some equal frames and distilled the key frame through chaotic sequence which generated by Logistic. Meanwhile, we distilled the low frequency coefficients of luminance component and self-adaptively embedded the processed image watermark into the low frequency coefficients of the wavelet transformed luminance component with the wavelet neural network. The experimental result suggested that the presented algorithm has better invisibility and robustness against noise, Gaussian filter, rotation, frame loss and other attacks.

Keywords: Video watermark, double chaotic encryption, wavelet neural network.

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Authors: Erika Martinez Ramirez, Rene V. Mayorga

Abstract:

The internet is constantly expanding. Identifying web links of interest from web browsers requires users to visit each of the links listed, individually until a satisfactory link is found, therefore those users need to evaluate a considerable amount of links before finding their link of interest; this can be tedious and even unproductive. By incorporating web assistance, web users could be benefited from reduced time searching on relevant websites. In this paper, a rough set approach is presented, which facilitates classification of unlimited available e-vocabulary, to assist web users in reducing search times looking for relevant web sites. This approach includes two methods for identifying relevance data on web links based on the priority and percentage of relevance. As a result of these methods, a list of web sites is generated in priority sequence with an emphasis of the search criteria.

Keywords: Web search, Web Mining, Rough Sets, Web Intelligence, Intelligent Portals, Relevance.

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Authors: M. A. Torkamani, S. Mahmoodzadeh, S. Pourroostaei, C. Lucas

Abstract:

Daily production of information and importance of the sequence of produced data in forecasting future performance of market causes analysis of data behavior to become a problem of analyzing time series. But time series that are very complicated, usually are random and as a result their changes considered being unpredictable. While these series might be products of a deterministic dynamical and nonlinear process (chaotic) and as a result be predictable. Point of Chaotic theory view, complicated systems have only chaotically face and as a result they seem to be unregulated and random, but it is possible that they abide by a specified math formula. In this article, with regard to test of strange attractor and biggest Lyapunov exponent probability of chaos on several foreign exchange rates vs. IRR (Iranian Rial) has been investigated. Results show that data in this market have complex chaotic behavior with big degree of freedom.

Keywords: Chaos, Exchange Rate, Nonlinear Models.

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Authors: Zurinahni Zainol, Rosalina Abdul Salam, Rosni Abdullah, Nur'Aini, Wahidah Husain

Abstract:

The size, complexity and number of databases used for protein information have caused bioinformatics to lag behind in adapting to the need to handle this distributed information. Integrating all the information from different databases into one database is a challenging problem. Our main research is to develop a tool which can be used to access and manipulate protein information from difference databases. In our approach, we have integrated difference databases such as Swiss-prot, PDB, Interpro, and EMBL and transformed these databases in flat file format into relational form using XML and Bioperl. As a result, we showed this tool can search different sizes of protein information stored in relational database and the result can be retrieved faster compared to flat file database. A web based user interface is provided to allow user to access or search for protein information in the local database.

Keywords: Protein sequence database, relational database, integrated database.

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Authors: Chuen-Ching Wang, Yao-Tang Chang, Yu-Chang Hsu

Abstract:

A simple but effective digital watermarking scheme utilizing a context adaptive variable length coding (CAVLC) method is presented for wireless communication system. In the proposed approach, the watermark bits are embedded in the final non-zero quantized coefficient of each DCT block, thereby yielding a potential reduction in the length of the coded block. As a result, the watermarking scheme not only provides the means to check the authenticity and integrity of the video stream, but also improves the compression ratio and therefore reduces both the transmission time and the storage space requirements of the coded video sequence. The results confirm that the proposed scheme enables the detection of malicious tampering attacks and reduces the size of the coded H.264 file. Therefore, the current study is feasible to apply in the video applications of wireless communication such as 3G system

Keywords: 3G, wireless communication, CAVLC, digitalwatermarking, motion compensation

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Authors: Othon Kamariotis

Abstract:

This paper provides a flexible way of controlling Variable-Bit-Rate (VBR) of compressed digital video, applicable to the new H264 video compression standard. The entire video sequence is assessed in advance and the quantisation level is then set such that bit rate (and thus the frame rate) remains within predetermined limits compatible with the bandwidth of the transmission system and the capabilities of the remote end, while at the same time providing constant quality similar to VBR encoding. A process for avoiding buffer starvation by selectively eliminating frames from the encoded output at times when the frame rate is slow (large number of bits per frame) will be also described. Finally, the problem of buffer overflow will be solved by selectively eliminating frames from the received input to the decoder. The decoder detects the omission of the frames and resynchronizes the transmission by monitoring time stamps and repeating frames if necessary.

Keywords: H264, CBR, VBR, Video Streaming, Digital Video, Multimedia, Buffering, Encoding, Decoding, Compression, Video-On-Demand

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Authors: Maciej Paszynski, Leszek Demkowicz, Jason Kurtz

Abstract:

In this paper, a new formulation for acoustics coupled with linear elasticity is presented. The primary objective of the work is to develop a three dimensional hp adaptive finite element method code destinated for modeling of acoustics of human head. The code will have numerous applications e.g. in designing hearing protection devices for individuals working in high noise environments. The presented work is in the preliminary stage. The variational formulation has been implemented and tested on a sequence of meshes with concentric multi-layer spheres, with material data representing the tissue (the brain), skull and the air. Thus, an efficient solver for coupled elasticity/acoustics problems has been developed, and tested on high contrast material data representing the human head.

Keywords: finite element method, acoustics, coupled problems, biomechanics

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Authors: Jae-Min Yu, Hyoung-Ho Doh, Ji-Su Kim, Dong-Ho Lee, Sung-Ho Nam

Abstract:

A reconfigurable manufacturing system (RMS) is an advanced system designed at the outset for rapid changes in its hardware and software components in order to quickly adjust its production capacity and functionally. Among various operational decisions, this study considers the scheduling problem that determines the input sequence and schedule at the same time for a given set of parts. In particular, we consider the practical constraints that the numbers of pallets/fixtures are limited and hence a part can be released into the system only when the fixture required for the part is available. To solve the integrated input sequencing and scheduling problems, we suggest a priority rule based approach in which the two sub-problems are solved using a combination of priority rules. To show the effectiveness of various rule combinations, a simulation experiment was done on the data for a real RMS, and the test results are reported.

Keywords: Reconfigurable manufacturing system, scheduling, priority rules, multiple process plans, pallets/fixtures

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Authors: Jing Lu, Malcolm Keech, Weiru Chen

Abstract:

Web usage mining is an interesting application of data mining which provides insight into customer behaviour on the Internet. An important technique to discover user access and navigation trails is based on sequential patterns mining. One of the key challenges for web access patterns mining is tackling the problem of mining richly structured patterns. This paper proposes a novel model called Web Access Patterns Graph (WAP-Graph) to represent all of the access patterns from web mining graphically. WAP-Graph also motivates the search for new structural relation patterns, i.e. Concurrent Access Patterns (CAP), to identify and predict more complex web page requests. Corresponding CAP mining and modelling methods are proposed and shown to be effective in the search for and representation of concurrency between access patterns on the web. From experiments conducted on large-scale synthetic sequence data as well as real web access data, it is demonstrated that CAP mining provides a powerful method for structural knowledge discovery, which can be visualised through the CAP-Graph model.

Keywords: concurrent access patterns (CAP), CAP mining and modelling, CAP-Graph, web access patterns (WAP), WAP-Graph, Web usage mining.

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Authors: Chyn Liaw, Chun-Wei Tung, Shinn-Jang Ho, Shinn-Ying Ho

Abstract:

The γ-turns play important roles in protein folding and molecular recognition. The prediction and analysis of γ-turn types are important for both protein structure predictions and better understanding the characteristics of different γ-turn types. This study proposed a physicochemical property-based decision tree (PPDT) method to interpretably predict γ-turn types. In addition to the good prediction performance of PPDT, three simple and human interpretable IF-THEN rules are extracted from the decision tree constructed by PPDT. The identified informative physicochemical properties and concise rules provide a simple way for discriminating and understanding γ-turn types.

Keywords: Classification and regression tree (CART), γ-turn, Physicochemical properties, Protein secondary structure.

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Authors: Waqar Shahid Qureshi, Abu-Baqar Nisar Alvi

Abstract:

Vision based tracking problem is solved through a combination of optical flow, MACH filter and log r-θ mapping. Optical flow is used for detecting regions of movement in video frames acquired under variable lighting conditions. The region of movement is segmented and then searched for the target. A template is used for target recognition on the segmented regions for detecting the region of interest. The template is trained offline on a sequence of target images that are created using the MACH filter and log r-θ mapping. The template is applied on areas of movement in successive frames and strong correlation is seen for in-class targets. Correlation peaks above a certain threshold indicate the presence of target and the target is tracked over successive frames.

Keywords: Correlation filters, optical flow, log r-θ mapping.

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Authors: Tahir Majeed, Michael Handschuh, René Meier

Abstract:

Rheumatoid Arthritis patients have swelling and pain in joints of the hand. The regions where the patient feels pain also show increased body temperature. Thermal cameras can be used to detect the rise in temperature of the affected regions. To monitor the progression of Rheumatoid Arthritis, patients must visit the clinic regularly for scanning and examination. After scanning and evaluation, the dosage of the medicine is regulated accordingly. To monitor the disease progression over time, the correlation of the images between different visits must be established. It has been observed that the thermal measurements do not remain the same over time, even within a single scanning, when low-cost thermal cameras are used. In some situations, temperatures can vary as much as 2◦C within the same scanning sequence. In this paper, it has been shown that although the absolute temperature varies over time, the relative difference between different regions remains similar. Results have been computed over four scanning sequences and are presented.

Keywords: Relative thermal difference, rheumatoid arthritis, thermal imaging, thermal sensors.

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Authors: N. Manavizadeh , M. Rabbani , H. Sotudian , F. Jolai

Abstract:

Mixed Model Production is the practice of assembling several distinct and different models of a product on the same assembly line without changeovers and then sequencing those models in a way that smoothes the demand for upstream components. In this paper, we consider an objective function which minimizes total stoppage time and total idle time and it is presented sequence dependent set up time. Many studies have been done on the mixed model assembly lines. But in this paper we specifically focused on reducing the idle times. This is possible through various help policies. For improving the solutions, some cases developed and about 40 tests problem was considered. We use scatter search for optimization and for showing the efficiency of our algorithm, experimental results shows behavior of method. Scatter search and help policies can produce high quality answers, so it has been used in this paper.

Keywords: mixed model assembly lines, Scatter search, help policies, idle time, Stoppage time

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Authors: Florian Mach, Eric Hund, Malte Stonis

Abstract:

The dismantling of disused industrial facilities such as nuclear power plants or refineries is an enormous challenge for the planning and control of the logistic processes. Existing control models do not meet the requirements for a proper dismantling of industrial plants. Therefore, the paper presents an approach for the control of dismantling and post-processing processes (e.g. decontamination) in plant decommissioning. In contrast to existing approaches, the dismantling sequence and depth are selected depending on the capacity utilization of required post-processing processes by also considering individual characteristics of respective dismantling tasks (e.g. decontamination success rate, uncertainties regarding the process times). The results can be used in the dismantling of industrial plants (e.g. nuclear power plants) to reduce dismantling time and costs by avoiding bottlenecks such as capacity constraints.

Keywords: Dismantling management, logistics planning and control models, nuclear power plant dismantling, reverse logistics.

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Authors: Hamad K. Al-Khalid, Ayman M. Alaskari, Samy E. Oraby

Abstract:

Hardness of the widely used structural steel is of vital importance since it may help in the determination of many mechanical properties of a material under loading situations. In order to obtain reliable information for design, properties homogeneity should be validated. In the current study the hardness variation over the different diameters of the same AISI 4140 bar is investigated. Measurements were taken on the two faces of the stock at equally spaced eight sectors and fifteen layers. Statistical and graphical analysis are performed to asses the distribution of hardness measurements over the specified area. Hardness measurements showed some degree of dispersion with about ± 10% of its nominal value provided by manufacturer. Hardness value is found to have a slight decrease trend as the diameter is reduced. However, an opposite behavior is noticed regarding the sequence of the sector indicating a nonuniform distribution over the same area either on the same face or considering the corresponding sector on the other face (cross section) of the same material bar.

Keywords: Hardness; Hardness variation; AISI 4140 steel; Bardiameter; Statistical Analysis.

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Authors: O. Abusaeeda, J. P. O Evans, D. Downes

Abstract:

We demonstrate the synthesis of intermediary views within a sequence of color encoded, materials discriminating, X-ray images that exhibit animated depth in a visual display. During the image acquisition process, the requirement for a linear X-ray detector array is replaced by synthetic image. Scale Invariant Feature Transform, SIFT, in combination with material segmented morphing is employed to produce synthetic imagery. A quantitative analysis of the feature matching performance of the SIFT is presented along with a comparative study of the synthetic imagery. We show that the total number of matches produced by SIFT reduces as the angular separation between the generating views increases. This effect is accompanied by an increase in the total number of synthetic pixel errors. The trends observed are obtained from 15 different luggage items. This programme of research is in collaboration with the UK Home Office and the US Dept. of Homeland Security.

Keywords: X-ray, kinetic depth, view synthesis, KDE

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Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

Abstract:

Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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Authors: S. C. Kattimani

Abstract:

This article deals with the analysis of active constrained layer damping (ACLD) of smart multiferroic or magneto-electro-elastic doubly curved shells. The kinematics of deformations of the multiferroic doubly curved shell is described by a layer-wise shear deformation theory. A three-dimensional finite element model of multiferroic shells has been developed taking into account the electro-elastic and magneto-elastic couplings. A simple velocity feedback control law is employed to incorporate the active damping. Influence of layer stacking sequence and boundary conditions on the response of the multiferroic doubly curved shell has been studied. In addition, for the different orientation of the fibers of the constraining layer, the performance of the ACLD treatment has been studied.

Keywords: Active constrained layer damping, doubly curved shells, magneto-electro-elastic, multiferroic composite, smart structures.

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