Search results for: biological method

Authors: S. N. Hosseini, S. M. H. Karimian

Abstract:

A new conserving approach in the context of Immersed Boundary Method (IBM) is presented to simulate one dimensional, incompressible flow in a moving boundary problem. The method employs control volume scheme to simulate the flow field. The concept of ghost node is used at the boundaries to conserve the mass and momentum equations. The Present method implements the conservation laws in all cells including boundary control volumes. Application of the method is studied in a test case with moving boundary. Comparison between the results of this new method and a sharp interface (Image Point Method) IBM algorithm shows a well distinguished improvement in both pressure and velocity fields of the present method. Fluctuations in pressure field are fully resolved in this proposed method. This approach expands the IBM capability to simulate flow field for variety of problems by implementing conservation laws in a fully Cartesian grid compared to other conserving methods.

Keywords: Immersed Boundary Method, conservation of mass and momentum laws, moving boundary, boundary condition.

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Authors: Muhammad Azam, Micheal Olaolu Arowolo, Fei He, Mihail Popescu, Dong Xu

Abstract:

The number of biological papers is growing quickly, which means that the number of biological pathway figures in those papers is also increasing quickly. Each pathway figure shows extensive biological information, like the names of genes and how the genes are related. However, manually annotating pathway figures takes a lot of time and work. Even though using advanced image understanding models could speed up the process of curation, these models still need to be made more accurate. To improve gene name recognition from pathway figures, we applied a Siamese network to map image segments to a library of pictures containing known genes in a similar way to person recognition from photos in many photo applications. We used a triple loss function and a triplet spatial pyramid pooling network by combining the triplet convolution neural network and the spatial pyramid pooling (TSPP-Net). We compared VGG19 and VGG16 as the Siamese network model. VGG16 achieved better performance with an accuracy of 93%, which is much higher than Optical Character Recognition (OCR) results.

Keywords: Biological pathway, image understanding, gene name recognition, object detection, Siamese network, Visual Geometry Group.

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Authors: Wei Zhang, Hong Yu, Xian-ping Zhao, Da-da Wang, Fei Xue

Abstract:

For lack of the visualization of the ultrasonic detection method of partial discharge (PD), the ultrasonic detection technology combined with the X-ray visual detection method (UXV) is proposed. The method can conduct qualitative analysis accurately and conduct reliable positioning diagnosis to the internal insulation defects of GIS, and while it could make up the blindness of the X-ray visual detection method and improve the detection rate. In this paper, an experimental model of GIS is used as the trial platform, a variety of insulation defects are set inside the GIS cavity. With the proposed method, the ultrasonic method is used to conduct the preliminary detection, and then the X-ray visual detection is used to locate and diagnose precisely. Therefore, the proposed UXV technology is feasible and practical.

Keywords: GIS, ultrasonic, visual detection, X-ray

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Authors: M. Zarebnia, R. Parvaz

Abstract:

In this paper the Kuramoto-Sivashinsky equation is solved numerically by collocation method. The solution is approximated as a linear combination of septic B-spline functions. Applying the Von-Neumann stability analysis technique, we show that the method is unconditionally stable. The method is applied on some test examples, and the numerical results have been compared with the exact solutions. The global relative error and L∞ in the solutions show the efficiency of the method computationally.

Keywords: Kuramoto-Sivashinsky equation, Septic B-spline, Collocation method, Finite difference.

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Authors: Yanan Yang, Zhigang Wang, Xiang Chen

Abstract:

This paper presents the use of Legendre pseudospectral method for the optimization of finite-thrust orbital transfer for spacecrafts. In order to get an accurate solution, the System-s dynamics equations were normalized through a dimensionless method. The Legendre pseudospectral method is based on interpolating functions on Legendre-Gauss-Lobatto (LGL) quadrature nodes. This is used to transform the optimal control problem into a constrained parameter optimization problem. The developed novel optimization algorithm can be used to solve similar optimization problems of spacecraft finite-thrust orbital transfer. The results of a numerical simulation verified the validity of the proposed optimization method. The simulation results reveal that pseudospectral optimization method is a promising method for real-time trajectory optimization and provides good accuracy and fast convergence.

Keywords: Finite-thrust, Orbital transfer, Legendre pseudospectral method

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Authors: Hailong Zhu, Zhaoxiang Li, Kejun Zhuang

Abstract:

By means of Contractor Iteration Method, we solve and visualize the Lane-Emden(-Fowler) equation Δu + up = 0, in Ω, u = 0, on ∂Ω. It is shown that the present method converges quadratically as Newton’s method and the computation of Contractor Iteration Method is cheaper than the Newton’s method.

Keywords: Positive solutions, newton's method, contractor iteration method, Eigenpairs.

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Authors: Osamu Igawa, Hiroshi Kouchiwa, Yuji Ito

Abstract:

In recent years, a reconstruction project for sewer  pipelines has been progressing in Japan with the aim of renewing old  sewer culverts. However, it is difficult to secure a sufficient base area  for shafts in an urban area because many streets are narrow with a  complex layout. As a result, construction in such urban areas is  generally very demanding.  In urban areas, there is a strong requirement for a safe, reliable and  economical construction method that does not disturb the public’s  daily life and urban activities. With this in mind, we developed a new  construction method called the “shield switching type micro-tunneling  method,” which integrates the micro-tunneling method and shield  method.  In this method, pipeline is constructed first for sections that are  gently curved or straight using the economical micro-tunneling  method, and then the method is switched to the shield method for  sections with a sharp curve or a series of curves without establishing  an intermediate shaft.  This paper provides the information, features and construction  examples of this newly developed method.

 

Keywords: Micro-tunneling method, Secondary lining applied RC segment, Sharp curve, Shield method, Switching type.

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Authors: Shigeaki Sakurai, Ryohei Orihara

Abstract:

This paper proposes a new method for analyzing textual data. The method deals with items of textual data, where each item is described based on various viewpoints. The method acquires 2- class classification models of the viewpoints by applying an inductive learning method to items with multiple viewpoints. The method infers whether the viewpoints are assigned to the new items or not by using the models. The method extracts expressions from the new items classified into the viewpoints and extracts characteristic expressions corresponding to the viewpoints by comparing the frequency of expressions among the viewpoints. This paper also applies the method to questionnaire data given by guests at a hotel and verifies its effect through numerical experiments.

Keywords: Text mining, Multiple viewpoints, Differential analysis, Questionnaire data

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Authors: Mohamed E. Khalifa

Abstract:

The chemistry of sulphone hydrazide has gained increase interest in both synthetic organic chemistry and biological fields and has considerable value. The therapeutic importance of these compounds is the attractive force to continue research in such a point. The present review covers the literature up to date for the synthesis, reactions and applications of such compounds.

Keywords: Sulphone hydrazide compounds, Reactions, Synthesis, Biological activities.

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Authors: A. Raminfard, S. M. Shahrtash

Abstract:

In this paper, a new efficient method for load balancing in low voltage distribution systems is presented. The proposed method introduces an improved Leap-frog method for optimization. The proposed objective function includes the difference between three phase currents, as well as two other terms to provide the integer property of the variables; where the latter are the status of the connection of loads to different phases. Afterwards, a new algorithm is supplemented to undertake the integer values for the load connection status. Finally, the method is applied to different parts of Tabriz low voltage network, where the results have shown the good performance of the proposed method.

Keywords: Load balancing, improved leap-frog method, optimization algorithm, low voltage distribution systems.

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Authors: Changqing Yang, Jianhua Hou, Beibo Qin

Abstract:

A numerical method for Riccati equation is presented in this work. The method is based on the replacement of unknown functions through a truncated series of hybrid of block-pulse functions and Chebyshev polynomials. The operational matrices of derivative and product of hybrid functions are presented. These matrices together with the tau method are then utilized to transform the differential equation into a system of algebraic equations. Corresponding numerical examples are presented to demonstrate the accuracy of the proposed method.

Keywords: Hybrid functions, Riccati differential equation, Blockpulse, Chebyshev polynomials, Tau method, operational matrix.

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Authors: Lina Yan, Shiheng Wang, Ke Wang

Abstract:

A preconditioned Jacobi (PJ) method is provided for solving fuzzy linear systems whose coefficient matrices are crisp Mmatrices and the right-hand side columns are arbitrary fuzzy number vectors. The iterative algorithm is given for the preconditioned Jacobi method. The convergence is analyzed with convergence theorems. Numerical examples are given to illustrate the procedure and show the effectiveness and efficiency of the method.

Keywords: preconditioning, M-matrix, Jacobi method, fuzzy linear system (FLS).

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Authors: H. N. Agiza, M. A. Sohaly, M. A. Elfouly

Abstract:

Parkinson's disease (PD) is a heterogeneous disorder with common age of onset, symptoms, and progression levels. In this paper we will solve analytically the PD model as a non-linear delay differential equation using the steps method. The step method transforms a system of delay differential equations (DDEs) into systems of ordinary differential equations (ODEs). On some numerical examples, the analytical solution will be difficult. So we will approximate the analytical solution using Picard method and Taylor method to ODEs.

Keywords: Parkinson's disease, Step method, delay differential equation, simulation.

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Authors: Haruo Okabayashi

Abstract:

Human biological signals (pulse wave and brain wave, etc.) have a rhythm which shows fluctuations. This study investigates the relationship between fluctuations of biological signals which are shown by a finger plethysmogram (i.e., finger pulse wave) in conversation and anthropophobic tendency, and identifies whether the fluctuation could be an index of mental health. 32 college students participated in the experiment. The finger plethysmogram of each subject was measured in the following conversation situations: Fun memory talking/listening situation and regrettable memory talking/ listening situation for three minutes each. Lyspect 3.5 was used to collect the data of the finger plethysmogram. Since Lyspect calculates the Lyapunov spectrum, it is possible to obtain the largest Lyapunov exponent (LLE). LLE is an indicator of the fluctuation and shows the degree to which a measure is going away from close proximity to the track in a dynamical system. Before the finger plethysmogram experiment, each participant took the psychological test questionnaire “Anthropophobic Scale.” The scale measures the social phobia trend close to the consciousness of social phobia. It is revealed that there is a remarkable relationship between the fluctuation of the finger plethysmography and anthropophobic tendency scale in talking about a regrettable story in conversation: The participants (N=15) who have a low anthropophobic tendency show significantly more fluctuation of finger pulse waves than the participants (N=17) who have a high anthropophobic tendency (F (1, 31) =5.66, p<0.05). That is, the participants who have a low anthropophobic tendency make conversation flexibly using large fluctuation of biological signal; on the other hand, the participants who have a high anthropophobic tendency constrain a conversation because of small fluctuation. Therefore, fluctuation is not an error but an important drive to make better relationships with others and go towards the development of interaction. In considering mental health, the fluctuation of biological signals would be an important indicator.

Keywords: Anthropophobic tendency, finger plethymogram, fluctuation of biological signal, LLE.

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Authors: Jafar Biazar, Behzad Ghanbari

Abstract:

In this paper, we are concerned with the further study for system of nonlinear equations. Since systems with inaccurate function values or problems with high computational cost arise frequently in science and engineering, recently such systems have attracted researcher-s interest. In this work we present a new method which is independent of function evolutions and has a quadratic convergence. This method can be viewed as a extension of some recent methods for solving mentioned systems of nonlinear equations. Numerical results of applying this method to some test problems show the efficiently and reliability of method.

Keywords: System of nonlinear equations.

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Authors: A. Soltani, M. Karimi Demneh

Abstract:

In this paper, modeling of an acoustic enclosed vehicle cabin has been carried out by using boundary element method. Also, the second purpose of this study is analyzing of linear wave equation in an acoustic field. The resultants of this modeling consist of natural frequencies that have been compared with resultants derived from finite element method. By using numerical method (boundary element method) and after solution of wave equation inside an acoustic enclosed cabin, this method has been progressed to simulate noise inside a simple vehicle cabin.

Keywords: Boundary element method, natural frequency, noise, vehicle cabin.

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Authors: A. Ghaffari, A. S. Mostafavi

Abstract:

Complex assemblies of interacting proteins carry out most of the interesting jobs in a cell, such as metabolism, DNA synthesis, mitosis and cell division. These physiological properties play out as a subtle molecular dance, choreographed by underlying regulatory networks that control the activities of cyclin-dependent kinases (CDK). The network can be modeled by a set of nonlinear differential equations and its behavior predicted by numerical simulation. In this paper, an innovative approach has been proposed that uses genetic algorithms to mine a set of behavior data output by a biological system in order to determine the kinetic parameters of the system. In our approach, the machine learning method is integrated with the framework of existent biological information in a wiring diagram so that its findings are expressed in a form of system dynamic behavior. By numerical simulations it has been illustrated that the model is consistent with experiments and successfully shown that such application of genetic algorithms will highly improve the performance of mathematical model of the cell division cycle to simulate such a complicated bio-system.

Keywords: Cell cycle, Cyclin-dependent kinase, Fission yeast, Genetic algorithms, Mathematical modeling, Wiring diagram

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Authors: B. S. Raghavendra, D. Narayana Dutt

Abstract:

In this paper, we have developed a method to compute fractal dimension (FD) of discrete time signals, in the time domain, by modifying the box-counting method. The size of the box is dependent on the sampling frequency of the signal. The number of boxes required to completely cover the signal are obtained at multiple time resolutions. The time resolutions are made coarse by decimating the signal. The loglog plot of total number of boxes required to cover the curve versus size of the box used appears to be a straight line, whose slope is taken as an estimate of FD of the signal. The results are provided to demonstrate the performance of the proposed method using parametric fractal signals. The estimation accuracy of the method is compared with that of Katz, Sevcik, and Higuchi methods. In addition, some properties of the FD are discussed.

Keywords: Box-counting, Fractal dimension, Higuchi method, Katz method, Parametric fractal signals, Sevcik method.

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Authors: Yiqin Lin, Liang Bao, Qinghua Wu, Liping Zhou

Abstract:

In this paper, we propose a direct method based on the real Schur factorization for solving the projected Sylvester equation with relatively small size. The algebraic formula of the solution of the projected continuous-time Sylvester equation is presented. The computational cost of the direct method is estimated. Numerical experiments show that this direct method has high accuracy.

Keywords: Projected Sylvester equation, Schur factorization, Spectral projection, Direct method.

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Authors: S. J. Hosseini Ghoncheh, M. Paripour

Abstract:

In this paper the Huang-s method for solving a m×n fuzzy linear system when, m≤ n, is considered. The method in detail is discussed and illustrated by solving some numerical examples.

Keywords: Fuzzy number, fuzzy linear systems, Huang's method.

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Authors: M. Zarebnia, R. Parvaz

Abstract:

In this paper, numerical solutions of the nonlinear Benjamin-Bona-Mahony-Burgers (BBMB) equation are obtained by a method based on collocation of cubic B-splines. Applying the Von-Neumann stability analysis, the proposed method is shown to be unconditionally stable. The method is applied on some test examples, and the numerical results have been compared with the exact solutions. The L∞ and L2 in the solutions show the efficiency of the method computationally.

Keywords: Benjamin-Bona-Mahony-Burgers equation, Cubic Bspline, Collocation method, Finite difference.

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Authors: H. Taghvafard, G. H. Erjaee

Abstract:

A method for solving linear and non-linear Goursat problem is given by using the two-dimensional differential transform method. The approximate solution of this problem is calculated in the form of a series with easily computable terms and also the exact solutions can be achieved by the known forms of the series solutions. The method can easily be applied to many linear and non-linear problems and is capable of reducing the size of computational work. Several examples are given to demonstrate the reliability and the performance of the presented method.

Keywords: Quadrature, Spline interpolation, Trapezoidal rule, Numericalintegration, Error analysis.

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Authors: Sumachaya Harnsukworapanich, Tetsuo Ichimori

Abstract:

The apportionment method is used by many countries, to calculate the distribution of seats in political bodies. For example, this method is used in the United States (U.S.) to distribute house seats proportionally based on the population of the electoral district. Famous apportionment methods include the divisor methods called the Adams Method, Dean Method, Hill Method, Jefferson Method and Webster Method. Sometimes the results from the implementation of these divisor methods are unfair and include errors. Therefore, it is important to examine the optimization of this method by using a bias measurement to figure out precise and fair results. In this research we investigate the bias of divisor methods in the U.S. Houses of Representatives toward large and small states by applying the Stolarsky Mean Method. We compare the bias of the apportionment method by using two famous bias measurements: the Balinski and Young measurement and the Ernst measurement. Both measurements have a formula for large and small states. The Third measurement however, which was created by the researchers, did not factor in the element of large and small states into the formula. All three measurements are compared and the results show that our measurement produces similar results to the other two famous measurements.

Keywords: Apportionment, Bias, Divisor, Fair, Simulation

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Authors: Mokhtar Ghobadi, Saeed Khosravi, Danial Kahrizi, Firooz Shirvani

Abstract:

The objective of this experiment was to study of water relations and chlorophyll in different wheat genotypes and their correlations with grain and biological yields. 21 genotypes of bread wheat were compared in a field experiment as randomized complete blocks design with four replications. The results showed that relative water deficit, relative water loss, excised leaf water retention, cell membrane stability, chlorophyll-a, chlorophyll-b, total chlorophyll, grain yield and biological yield were different significantly among wheat genotypes, but SPAD-chlorophyll index, relative water content and chlorophyll florescence were not. Significant correlations were not observed among above mentioned water relations and chlorophyll characteristics with grain yield, but there was a positive and significant correlation between biological yield and grain yield.

Keywords: Wheat, water relations, chlorophyll, yield

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Authors: Zhenyu Zhao, Lei You

Abstract:

The numerical analytic continuation of a function f(z) = f(x + iy) on a strip is discussed in this paper. The data are only given approximately on the real axis. The periodicity of given data is assumed. A truncated Fourier spectral method has been introduced to deal with the ill-posedness of the problem. The theoretic results show that the discrepancy principle can work well for this problem. Some numerical results are also given to show the efficiency of the method.

Keywords: Analytic continuation, ill-posed problem, regularization method Fourier spectral method, the discrepancy principle.

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Authors: Khosrow Maleknejad, Asyieh Ebrahimzadeh

Abstract:

In this paper, the numerical solution of optimal control problem (OCP) for systems governed by Volterra integro-differential (VID) equation is considered. The method is developed by means of the Legendre wavelet approximation and collocation method. The properties of Legendre wavelet together with Gaussian integration method are utilized to reduce the problem to the solution of nonlinear programming one. Some numerical examples are given to confirm the accuracy and ease of implementation of the method.

Keywords: Collocation method, Legendre wavelet, optimal control, Volterra integro-differential equation.

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Authors: V. Ghadamyari, F. Samadi, F. Kowsary

Abstract:

An inverse geometry problem is solved to predict an unknown irregular boundary profile. The aim is to minimize the objective function, which is the difference between real and computed temperatures, using three different versions of Conjugate Gradient Method. The gradient of the objective function, considered necessary in this method, obtained as a result of solving the adjoint equation. The abilities of three versions of Conjugate Gradient Method in predicting the boundary profile are compared using a numerical algorithm based on the method. The predicted shapes show that due to its convergence rate and accuracy of predicted values, the Powell-Beale version of the method is more effective than the Fletcher-Reeves and Polak –Ribiere versions.

Keywords: Boundary elements, Conjugate Gradient Method, Inverse Geometry Problem, Sensitivity equation.

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Authors: Shigeaki Sakurai, Youichi Kitahata, Ryohei Orihara

Abstract:

This paper proposes a method that discovers sequential patterns corresponding to user-s interests from sequential data. This method expresses the interests as constraint patterns. The constraint patterns can define relationships among attributes of the items composing the data. The method recursively decomposes the constraint patterns into constraint subpatterns. The method evaluates the constraint subpatterns in order to efficiently discover sequential patterns satisfying the constraint patterns. Also, this paper applies the method to the sequential data composed of stock price indexes and verifies its effectiveness through comparing it with a method without using the constraint patterns.

Keywords: Sequential pattern mining, Constraint pattern, Attribute constraint, Stock price indexes

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Authors: N. Behidj-Benyounes, S. Bennaamane, F. Zohra Bissaad, N. Chebouti, H. Mohandkaci, N. Abdalaziz, S. Iddou

Abstract:

In this study, we are interested in a species of the family of Asteraceae (Tagetes erecta). This family is considered as a source of antimicrobial extracts with strong capacity. The extraction of the flavonoids is carried out by the method of liquid/liquid with the use of successive solvents. Afterwards, we evaluated the biological activity of the flavonoids on five pathogenic bacterial stocks such as Escherichia coli, Bacillus subtilis, Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus and two stocks of yeasts to knowing Candida albicans) and Saccharomyces cerevisiae, by employing the method of the aromatogramme starting from a solid disc. The result of the antimicrobial activity shows an action and a variable degree of sensitivity according to bacterial stocks tested. It will be noted that the flavonoids have an inhibiting effect on E. coli, B. subtilis, K. pneumoniae and S. aureus. But a resistance with respect to the extract by P. aeruginosa, C. albicans and S. cerevisiae is to be mentioned.

Keywords: Antimicrobial activity, flavonoids, microbial strains, Tagetes erecta L.

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Authors: Chintanu K. Sarmah, Sandhya Samarasinghe, Don Kulasiri, Daniel Catchpoole

Abstract:

Gene expression profiling is rapidly evolving into a powerful technique for investigating tumor malignancies. The researchers are overwhelmed with the microarray-based platforms and methods that confer them the freedom to conduct large-scale gene expression profiling measurements. Simultaneously, investigations into cross-platform integration methods have started gaining momentum due to their underlying potential to help comprehend a myriad of broad biological issues in tumor diagnosis, prognosis, and therapy. However, comparing results from different platforms remains to be a challenging task as various inherent technical differences exist between the microarray platforms. In this paper, we explain a simple ratio-transformation method, which can provide some common ground for cDNA and Affymetrix platform towards cross-platform integration. The method is based on the characteristic data attributes of Affymetrix- and cDNA- platform. In the work, we considered seven childhood leukemia patients and their gene expression levels in either platform. With a dataset of 822 differentially expressed genes from both these platforms, we carried out a specific ratio-treatment to Affymetrix data, which subsequently showed an improvement in the relationship with the cDNA data.

Keywords: Gene expression profiling, microarray, cDNA, Affymetrix, childhood leukaemia.

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