Search results for: Error Detection and Correction

Authors: G. Ghodrati Amiri, M. Khorasani, Razavian Ameri, M.Mohamadi Dehcheshmeh, S.Fathi

Abstract:

Many studies have been conducted for derivation of attenuation relationships worldwide, however few relationships have been developed to use for the seismic region of Iranian plateau and only few of these studies have been conducted for derivation of attenuation relationships for parameters such as uniform duration. Uniform duration is the total time during which the acceleration is larger than a given threshold value (default is 5% of PGA). In this study, the database was same as that used previously by Ghodrati Amiri et al. (2007) with same correction methods for earthquake records in Iran. However in this study, records from earthquakes with MS< 4.0 were excluded from this database, each record has individually filtered afterward, and therefore the dataset has been expanded. These new set of attenuation relationships for Iran are derived based on tectonic conditions with soil classification into rock and soil. Earthquake parameters were chosen to be hypocentral distance and magnitude in order to make it easier to use the relationships for seismic hazard analysis. Tehran is the capital city of Iran wit ha large number of important structures. In this study, a probabilistic approach has been utilized for seismic hazard assessment of this city. The resulting uniform duration against return period diagrams are suggested to be used in any projects in the area.

Keywords: Attenuation Relationships, Iran, Probabilistic Seismic Hazard Analysis, Tehran, Uniform Duration

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Authors: Chao Yuan, Bao Guang Tian

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A relative efficiency is defined as Ridge Estimate in the general linear model. The relative efficiency is based on the Mean square error. In this paper, we put forward a parameter of Ridge Estimate and discussions are made on the relative efficiency between the ridge estimation and the General Ridge Estimate. Eventually, this paper proves that the estimation is better than the general ridge estimate, which is based on the MSE.

Keywords: Ridge estimate, generalized ridge estimate, MSE, relative efficiency.

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Authors: Olaf Hallan Graven, Dag Andreas Hals Samuelsen

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An implementation of a design for a game based virtual learning environment is described. The game is developed for a course in analogue electronics, and the topic is the design of a power supply. This task can be solved in a number of different ways, with certain constraints, giving the students a certain amount of freedom, although the game is designed not to facilitate trial-and error approach. The use of storytelling and a virtual gaming environment provides the student with the learning material in a MMORPG environment. The game is tested on a group of second year electrical engineering students with good results.

Keywords: analogue electronics, e-learning, computer games for learning, virtual reality

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Authors: Samah Jawad Jabari

Abstract:

Water is the most important and valuable resource not only for human life but also for all living things on the planet. The water supply utilities should fulfill the water requirement quantitatively and qualitatively. Drinking water systems are exposed to both natural (hurricanes and flood) and manmade hazards (risks) that are common in Palestine. Non-Revenue Water (NRW) is a manmade risk which remains a major concern in Palestine, as the NRW levels are estimated to be at a high level. In this research, Hebron city water distribution network was taken as a case study to estimate and audit the NRW levels. The research also investigated the state of the existing water distribution system in the study area by investigating the water losses and obtained more information on NRW prevention and management practices. Data and information have been collected from the Palestinian Water Authority (PWA) and Hebron Municipality (HM) archive. In addition to that, a questionnaire has been designed and administered by the researcher in order to collect the necessary data for water auditing. The questionnaire also assessed the views of stakeholder in PWA and HM (staff) on the current status of the NRW in the Hebron water distribution system. The important result obtained by this research shows that NRW in Hebron city was high and in excess of 30%. The main factors that contribute to NRW were the inaccuracies in billing volumes, unauthorized consumption, and the method of estimating consumptions through faulty meters. Policy for NRW reduction is available in Palestine; however, it is clear that the number of qualified staff available to carry out the activities related to leak detection is low, and that there is a lack of appropriate technologies to reduce water losses and undertake sufficient system maintenance, which needs to be improved to enhance the performance of the network and decrease the level of NRW losses.

Keywords: Non-revenue water, water auditing, leak detection, water meters.

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Authors: Said Elkassimi, Said Safi, B. Manaut

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This paper presented a study of three algorithms, the equalization algorithm to equalize the transmission channel with ZF and MMSE criteria, application of channel Bran A, and adaptive filtering algorithms LMS and RLS to estimate the parameters of the equalizer filter, i.e. move to the channel estimation and therefore reflect the temporal variations of the channel, and reduce the error in the transmitted signal. So far the performance of the algorithm equalizer with ZF and MMSE criteria both in the case without noise, a comparison of performance of the LMS and RLS algorithm.

Keywords: Adaptive filtering second equalizer, LMS, RLS Bran A, Proakis (B) MMSE, ZF.

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Authors: Zixin Liu, Shu Lü, Shouming Zhong, Mao Ye

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This paper studies the pth moment exponential synchronization of a class of stochastic neural networks with mixed delays. Based on Lyapunov stability theory, by establishing a new integrodifferential inequality with mixed delays, several sufficient conditions have been derived to ensure the pth moment exponential stability for the error system. The criteria extend and improve some earlier results. One numerical example is presented to illustrate the validity of the main results.

Keywords: pth Moment Exponential synchronization, Stochastic, Neural networks, Mixed time delays

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Authors: Yan Wang, Yasushi Asami, Yukio Sadahiro

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In urban area, several landmarks may affect housing price and rents, and hedonic analysis should employ distance variables corresponding to each landmarks. Unfortunately, the effects of distances to landmarks on housing prices are generally not consistent with the true price. These distance variables may cause magnitude error in regression, pointing a problem of spatial multicollinearity. In this paper, we provided some approaches for getting the samples with less bias and method on locating the specific sampling area to avoid the multicollinerity problem in two specific landmarks case.

Keywords: Landmarks, hedonic regression, distance variables, collinearity, multicollinerity.

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Authors: Mahmoud Zarrini, Sanaz Torkaman

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In this paper, we have proposed a numerical method for solving fuzzy Fredholm integral equation of the second kind. In this method a combination of orthonormal Bernstein and Block-Pulse functions are used. In most cases, the proposed method leads to the exact solution. The advantages of this method are shown by an example and calculate the error analysis.

Keywords: Fuzzy Fredholm Integral Equation, Bernstein, Block-Pulse, Orthonormal.

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Authors: Keunhong Chae, Seokho Yoon

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This paper proposes a cooperative Alamouti space time transmission scheme with low relay complexity for the cooperative communication systems. In the proposed scheme, the source node combines the data symbols to construct the Alamouti-coded form at the destination node, while the conventional scheme performs the corresponding operations at the relay nodes. In simulation results, it is shown that the proposed scheme achieves the second order cooperative diversity while maintaining the same bit error rate (BER) performance as that of the conventional scheme.

Keywords: Space-time transmission, cooperative communication system, MIMO.

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Authors: M. Zahid Hossain, M. Ashraful Amin

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The algorithms of convex hull have been extensively studied in literature, principally because of their wide range of applications in different areas. This article presents an efficient algorithm to construct approximate convex hull from a set of n points in the plane in O(n + k) time, where k is the approximation error control parameter. The proposed algorithm is suitable for applications preferred to reduce the computation time in exchange of accuracy level such as animation and interaction in computer graphics where rapid and real-time graphics rendering is indispensable.

Keywords: Convex hull, Approximation algorithm, Computational geometry, Linear time.

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Authors: André C. Silva, Mariana R. Barros, Elenice M. S. Silva, Douglas. Y. Marinho, Diego F. Lopes, Débora N. Sousa, Raphael S. Tomáz

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Modern agriculture requires productivity, efficiency and quality. Therefore, there is need for agricultural limestone implementation that provides adequate amounts of calcium and magnesium carbonates in order to correct soil acidity. During the limestone process, fine particles (with average size under 400#) are generated. These particles do not have economic value in agricultural and metallurgical sectors due their size. When limestone is used for agriculture purposes, these fine particles can be easily transported by wind generated air pollution. Therefore, briquetting, a mineral processing technique, was used to mitigate this problem resulting in an agglomerated product suitable for agriculture use. Briquetting uses compressive pressure to agglomerate fine particles. It can be aided by agglutination agents, allowing adjustments in shape, size and mechanical parameters of the mass. Briquettes can generate extra profits for mineral industry, presenting as a distinct product for agriculture, and can reduce the environmental liabilities of the fine particles storage or disposition. The produced limestone briquettes were subjected to shatter and water action resistance tests. The results show that after six minutes completely submerged in water, the briquettes where fully diluted, a highly favorable result considering its use for soil acidity correction.

Keywords: Agglomeration, briquetting, limestone, agriculture.

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Authors: Mohammed H. Nafie, Ahmed F. Shalash

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With the advent of DSL services, high data rates are now available over phone lines, yet higher rates are in demand. In this paper, we optimize the transmit filters that can be used over wireline channels. Results showing the bit error rates when optimized filters are used, and with a decision feedback equalizer (DFE) employed in the receiver, are given. We then show that significantly higher throughput can be achieved by modeling the channel as a multiple input multiple output (MIMO) channel. A receiver that employs a MIMO-DFE that deals jointly with several users is proposed and shown to provide significant improvement over the conventional DFE.

Keywords: DFE, MIMO Channels, Receiver Architectures, Transmit Filters.

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Authors: A. U. Haque, W. Asrar, A. A. Omar, E. Sulaeman, J. S. Mohamed Ali

Abstract:

Due to the interference effects, the intrinsic aerodynamic parameters obtained from the individual component testing are always fundamentally different than those obtained for complete model testing. Consideration and limitation for such testing need to be taken into account in any design work related to the component buildup method. In this paper, the scaled model of a straight rectangular canard of a hybrid buoyant aircraft is tested at 50 m/s in IIUM-LSWT (Low Speed Wind Tunnel). Model and its attachment with the balance are kept rigid to have results free from the aeroelastic distortion. Based on the velocity profile of the test section’s floor; the height of the model is kept equal to the corresponding boundary layer displacement. Balance measurements provide valuable but limited information of overall aerodynamic behavior of the model. Zero lift coefficient is obtained at -2.2o and the corresponding drag coefficient was found to be less than that at zero angle of attack. As a part of the validation of low fidelity tool, plot of lift coefficient plot was verified by the experimental data and except the value of zero lift coefficients, the overall trend has under predicted the lift coefficient. Based on this comparative study, a correction factor of 1.36 is proposed for lift curve slope obtained from the panel method.

Keywords: Wind tunnel testing, boundary layer displacement, lift curve slope, canard, aerodynamics.

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Authors: Le Thanh Ha, Hye-Soo Kim, Chun-Su Park, Seung-Won Jung, Sung-Jea Ko

Abstract:

Flexible macroblock ordering (FMO), adopted in the H.264 standard, allows to partition all macroblocks (MBs) in a frame into separate groups of MBs called Slice Groups (SGs). FMO can not only support error-resilience, but also control the size of video packets for different network types. However, it is well-known that the number of bits required for encoding the frame is increased by adopting FMO. In this paper, we propose a novel algorithm that can reduce the bitrate overhead caused by utilizing FMO. In the proposed algorithm, all MBs are grouped in SGs based on the similarity of the transform coefficients. Experimental results show that our algorithm can reduce the bitrate as compared with conventional FMO.

Keywords: Data Partition, Entropy Coding, Greedy Algorithm, H.264/AVC, Slice Group.

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Authors: S. GhaffariTooran, H. Abolghasemi, H. Bahmanyar, M. Esmaeili, A. Safari

Abstract:

Using plug flow model in conjunction with experimental solute concentration profiles, overall volumetric mass transfer coefficient based on continuous phase (Koca), in a packed liquid-liquid extraction column has been optimized. Number of 12 experiments has been done using standard system of water/acid acetic/toluene in a 6 cm diameter, 120 cm height column. Thorough consideration of influencing parameters we intended to correlate dimensionless parameters in term of overall Sherwood number which has an acceptable average error of about 15.8%.

Keywords: Packed column, mass transfer coefficient, solvent extraction, Sherwood number.

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Authors: Eda Gök

Abstract:

Peridynamics is a new modeling concept of non-local interactions for solid structures. The formulations of Peridynamic (PD) theory are based on integral equations rather than differential equations. Through, undefined equations of associated problems are avoided. PD theory might be defined as continuum version of molecular dynamics. The medium is usually modeled with mass particles bonded together. Particles interact with each other directly across finite distances through central forces named as bonds. The main assumption of this theory is that the body is composed of material points which interact with other material points within a finite distance. Although, PD theory developed for discontinuities, it gives good results for structures which have no discontinuities. In this paper, displacement control of the isotropic plate under the effect of tensile and bending loading has been investigated by means of PD theory. A MATLAB code is generated to create PD bonds and corresponding surface correction factors. Using generated MATLAB code the geometry of the specimen is generated, and the code is implemented in Finite Element Software. The results obtained from non-local continuum theory are compared with the Finite Element Analysis results and analytical solution. The results show good agreement.

Keywords: Flexural loading, non-local continuum mechanics, Peridynamic theory, solid structures, tensile loading.

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Authors: M. A. Koroma, C. Zhan, A. F. Kamara, A. B. Sesay

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In this work we adopt a combination of Laplace transform and the decomposition method to find numerical solutions of a system of multi-pantograph equations. The procedure leads to a rapid convergence of the series to the exact solution after computing a few terms. The effectiveness of the method is demonstrated in some examples by obtaining the exact solution and in others by computing the absolute error which decreases as the number of terms of the series increases.

Keywords: Laplace decomposition, pantograph equations, exact solution, numerical solution, approximate solution.

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Authors: Abeer Aljohani

Abstract:

The COVID-19 virus spread has been one of the extreme pandemics across the globe. It is also referred as corona virus which is a contagious disease that continuously mutates into numerous variants. Currently, the B.1.1.529 variant labeled as Omicron is detected in South Africa. The huge spread of COVID-19 disease has affected several lives and has surged exceptional pressure on the healthcare systems worldwide. Also, everyday life and the global economy have been at stake. Numerous COVID-19 cases have produced a huge burden on hospitals as well as health workers. To reduce this burden, this paper predicts COVID-19 disease based on the symptoms and medical history of the patient. As machine learning is a widely accepted area and gives promising results for healthcare, this research presents an architecture for COVID-19 detection using ML techniques integrated with feature dimensionality reduction. This paper uses a standard University of California Irvine (UCI) dataset for predicting COVID-19 disease. This dataset comprises symptoms of 5434 patients. This paper also compares several supervised ML techniques on the presented architecture. The architecture has also utilized 10-fold cross validation process for generalization and Principal Component Analysis (PCA) technique for feature reduction. Standard parameters are used to evaluate the proposed architecture including F1-Score, precision, accuracy, recall, Receiver Operating Characteristic (ROC) and Area under Curve (AUC). The results depict that Decision tree, Random Forest and neural networks outperform all other state-of-the-art ML techniques. This result can be used to effectively identify COVID-19 infection cases.

Keywords: Supervised machine learning, COVID-19 prediction, healthcare analytics, Random Forest, Neural Network.

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Authors: Naci Büyükkaracığan

Abstract:

Hydroclimatic observation values ​​are used in the planning of the project of water resources. Climate variables are the first of the values ​​used in planning projects. At the same time, the climate system is a complex and interactive system involving the atmosphere, land surfaces, snow and bubbles, the oceans and other water structures. The amount and distribution of precipitation, which is an important climate parameter, is a limiting environmental factor for dispersed living things. Trend analysis is applied to the detection of the presence of a pattern or trend in the data set. Many trends work in different parts of the world are usually made for the determination of climate change. The detection and attribution of past trends and variability in climatic variables is essential for explaining potential future alteration resulting from anthropogenic activities. Parametric and non-parametric tests are used for determining the trends in climatic variables. In this study, trend tests were applied to annual total precipitation data obtained in period of 1972 and 2012, in the Konya Basin. Non-parametric trend tests, (Sen’s T, Spearman’s Rho, Mann-Kendal, Sen’s T trend, Wald-Wolfowitz) and parametric test (mean square) were applied to annual total precipitations of 15 stations for trend analysis. The linear slopes (change per unit time) of trends are calculated by using a non-parametric estimator developed by Sen. The beginning of trends is determined by using the Mann-Kendall rank correlation test. In addition, homogeneities in precipitation trends are tested by using a method developed by Van Belle and Hughes. As a result of tests, negative linear slopes were found in annual total precipitations in Konya.

Keywords: Trend analysis, precipitation, hydroclimatology, Konya, Turkey.

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Authors: Nadia El Alami El Hassani, Soukaina Motia, Benachir Bouchikhi, Nezha El Bari

Abstract:

Doxycycline (DXy) is a cycline antibiotic, most frequently prescribed to treat bacterial infections in veterinary medicine. However, its broad antimicrobial activity and low cost, lead to an intensive use, which can seriously affect human health. Therefore, its spread in the food products has to be monitored. The scope of this work was to synthetize a sensitive and very selective molecularly imprinted polymer (MIP) for DXy detection in honey samples. Firstly, the synthesis of this biosensor was performed by casting a layer of carboxylate polyvinyl chloride (PVC-COOH) on the working surface of a gold screen-printed electrode (Au-SPE) in order to bind covalently the analyte under mild conditions. Secondly, DXy as a template molecule was bounded to the activated carboxylic groups, and the formation of MIP was performed by a biocompatible polymer by the mean of polyacrylamide matrix. Then, DXy was detected by measurements of differential pulse voltammetry (DPV). A non-imprinted polymer (NIP) prepared in the same conditions and without the use of template molecule was also performed. We have noticed that the elaborated biosensor exhibits a high sensitivity and a linear behavior between the regenerated current and the logarithmic concentrations of DXy from 0.1 pg.mL⁻¹ to 1000 pg.mL⁻¹. This technic was successfully applied to determine DXy residues in honey samples with a limit of detection (LOD) of 0.1 pg.mL⁻¹ and an excellent selectivity when compared to the results of oxytetracycline (OXy) as analogous interfering compound. The proposed method is cheap, sensitive, selective, simple, and is applied successfully to detect DXy in honey with the recoveries of 87% and 95%. Considering these advantages, this system provides a further perspective for food quality control in industrial fields.

Keywords: Electrochemical sensor, molecular imprinted polymer, doxycycline, food control.

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Authors: Partha Sarathi Majee, S. Bhattacharyya

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Migration of a core-shell soft particle under the influence of an external electric field in an electrolyte solution is studied numerically. The soft particle is coated with a positively charged polyelectrolyte layer (PEL) and the rigid core is having a uniform surface charge density. The Darcy-Brinkman extended Navier-Stokes equations are solved for the motion of the ionized fluid, the non-linear Nernst-Planck equations for the ion transport and the Poisson equation for the electric potential. A pressure correction based iterative algorithm is adopted for numerical computations. The effects of convection on double layer polarization (DLP) and diffusion dominated counter ions penetration are investigated for a wide range of Debye layer thickness, PEL fixed surface charge density, and permeability of the PEL. Our results show that when the Debye layer is in order of the particle size, the DLP effect is significant and produces a reduction in electrophoretic mobility. However, the double layer polarization effect is negligible for a thin Debye layer or low permeable cases. The point of zero mobility and the existence of mobility reversal depending on the electrolyte concentration are also presented.

Keywords: Debye length, double layer polarization, electrophoresis, mobility reversal, soft particle.

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Authors: Shu-Xin Miao

Abstract:

In this paper, the Gaussian type quadrature rules for fuzzy functions are discussed. The errors representation and convergence theorems are given. Moreover, four kinds of Gaussian type quadrature rules with error terms for approximate of fuzzy integrals are presented. The present paper complements the theoretical results of the paper by T. Allahviranloo and M. Otadi [T. Allahviranloo, M. Otadi, Gaussian quadratures for approximate of fuzzy integrals, Applied Mathematics and Computation 170 (2005) 874-885]. The obtained results are illustrated by solving some numerical examples.

Keywords: Guassian quadrature rules, fuzzy number, fuzzy integral, fuzzy solution.

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Authors: Juliana Panova

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Severe symptoms, such as dissociation, depersonalization, self-mutilation, suicidal ideations and gestures, are the main reasons for a person to be diagnosed with Borderline Personality Disorder (BPD) and admitted to an inpatient Psychiatric Hospital. However, these symptoms are also indicators of a severe traumatic history as indicated by the extensive research on the topic. Unfortunately patients with such clinical presentation often are treated repeatedly only for their symptomatic behavior, while the main cause for their suffering, the trauma itself, is usually left unaddressed therapeutically. All of the highly structured, replicable, and manualized treatments lack the recognition of the uniqueness of the person and fail to respect his/her rights to experience and react in an idiosyncratic manner. Thus the communicative and adaptive meaning of such symptomatic behavior is missed. Only its pathological side is recognized and subjected to correction and stigmatization, and the message that the person is damaged goods that needs fixing is conveyed once again. However, this time the message would be even more convincing for the victim, because it is sent by mental health providers, who have the credibility to make such a judgment. The result is a revolving door of very expensive hospitalizations for only a temporary and patchy fix. In this way the patients, once victims of abuse and hardship are left invalidated and thus their re-victimization is perpetuated in their search for understanding and help. Keywordsborderline personality disorder (BPD), complex PTSD, integrative treatment of trauma, re-victimization of trauma victims.

Keywords: borderline personality disorder (BPD), complex PTSD, integrative treatment of trauma, re-victimization of trauma victims.

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Authors: Adekitan I. Aderibigbe, Fakolujo A. Olaosebikan

Abstract:

The parameters of a two-layer soil can be determined by processing resistivity data obtained from resistivity measurements carried out on the soil of interest. The processing usually entails applying the resistivity data as inputs to an optimisation function. This paper proposes an algorithm which utilises the square error as an optimisation function. Resistivity data from previous works were applied to test the accuracy of the new algorithm developed and the result obtained conforms significantly to results from previous works.

 

Keywords: Algorithm, earthing, resistivity, two-layer soil-model.

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Authors: A. Ghanbari Mardasi, N. Wu, C. Wu

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In this study, a spatial wavelet-based crack localization technique for a thick beam is presented. Wavelet scale in spatial wavelet transformation is optimized to enhance crack detection sensitivity. A windowing function is also employed to erase the edge effect of the wavelet transformation, which enables the method to detect and localize cracks near the beam/measurement boundaries. Theoretical model and vibration analysis considering the crack effect are first proposed and performed in MATLAB based on the Timoshenko beam model. Gabor wavelet family is applied to the beam vibration mode shapes derived from the theoretical beam model to magnify the crack effect so as to locate the crack. Relative wavelet coefficient is obtained for sensitivity analysis by comparing the coefficient values at different positions of the beam with the lowest value in the intact area of the beam. Afterward, the optimal wavelet scale corresponding to the highest relative wavelet coefficient at the crack position is obtained for each vibration mode, through numerical simulations. The same procedure is performed for cracks with different sizes and positions in order to find the optimal scale range for the Gabor wavelet family. Finally, Hanning window is applied to different vibration mode shapes in order to overcome the edge effect problem of wavelet transformation and its effect on the localization of crack close to the measurement boundaries. Comparison of the wavelet coefficients distribution of windowed and initial mode shapes demonstrates that window function eases the identification of the cracks close to the boundaries.

Keywords: Edge effect, scale optimization, small crack locating, spatial wavelet.

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Authors: C. Ardil

Abstract:

A mathematical model and an effective numerical method for calculating the temperature field of the profile part of convection cooled blades have been developed. The theoretical substantiation of the method is proved by corresponding theorems. To this end, convergent quadrature processes were developed and error estimates were obtained in terms of the Zygmund continuity moduli.The boundary conditions for heat exchange are determined from the solution of the corresponding integral equations and empirical relations.The reliability of the developed methods is confirmed by the calculation-experimental studies of the thermohydraulic characteristics of the nozzle apparatus of the first stage of a gas turbine.

Keywords: Integral methods, determination of temperature fields, cooled blades, gas turbines.

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Authors: A. M. Pashaev, R. A. Sadihov, A. S. Samedov, C. Ardil

Abstract:

A mathematical model and a numerical method for computing the temperature field of the profile part of convectionally cooled blades are developed. The theoretical substantiation of the method is proved by corresponding theorems. To this end, convergent quadrature processes were developed and error estimates were obtained in terms of the Zygmund continuity moduli. The boundary conditions for heat exchange are determined from the solution of the corresponding integral equations and empirical relations. The reliability of the developed methods is confirmed by calculation and experimental studies of the thermohydraulic characteristics of the nozzle apparatus of the first stage of the gas turbine.

Keywords: Aviation gas turbine, temperature field, cooled blades, numerical modeling.

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Authors: K. A. D. N. K Wimalawarne

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In this paper we introduce a novel kernel classifier based on a iterative shrinkage algorithm developed for compressive sensing. We have adopted Bregman iteration with soft and hard shrinkage functions and generalized hinge loss for solving l1 norm minimization problem for classification. Our experimental results with face recognition and digit classification using SVM as the benchmark have shown that our method has a close error rate compared to SVM but do not perform better than SVM. We have found that the soft shrinkage method give more accuracy and in some situations more sparseness than hard shrinkage methods.

Keywords: Compressive sensing, Bregman iteration, Generalisedhinge loss, sparse, kernels, shrinkage functions

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Authors: Kaewkarn Phuangsombat, Arthit Phuangsombat, Anupun Terdwongworakul

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Hard seeds will not grow and can cause mold in sprouting process. Thus, the hard seeds need to be separated from the normal seeds. Near infrared hyperspectral imaging in a range of 900 to 1700 nm was implemented to develop a model by partial least squares discriminant analysis to discriminate the hard seeds from the normal seeds. The orientation of the seeds was also studied to compare the performance of the models. The model based on hilum-up orientation achieved the best result giving the coefficient of determination of 0.98, and root mean square error of prediction of 0.07 with classification accuracy was equal to 100%.

Keywords: Mung bean, near infrared, germinatability, hard seed.

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Authors: Alan Luo, Hunter N. B. Moseley

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Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for X-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across X-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: Biomacromolecular structure, coenzyme, electron density discrepancy analysis, X-ray crystallography.

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