Search results for: Biological sequence

Authors: Chizoba Chinweze, Gwen Abiola-Oloke, Chike Jideani

Abstract:

There is an urgent need to conserve the biological diversity of the Nigerian Environment for the future and present generation in the face of current energy resources development. This paper gives an in-depth analysis of the impact of oil and gas activities on the biological diversity of the Nigerian Niger Delta area and its consequences on the sustainable development of the host communities as it relates to their social, economic and environmental issues, particularly on the womenfolk who are the key managers of environmental resources. Also reviewed is the frustration of these communities that is reflected in unending conflicts.

Keywords: Biodiversity, energy resources, sustainable development, and women issues.

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Authors: P. Sowa

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The article reviews the current state of large-scale studies about the impact of electromagnetic field on natural environment. The scenario of investigations – simulation of natural conditions at the workplace, taking into consideration the influence both low and high frequency electromagnetic fields is shown.The biological effects of low and high frequency electromagnetic fields are below presented. Results of investigation with animals are shown. The norms and regulations concerning the levels of electromagnetic field intensity are reviewed.

Keywords: Electromagnetic field and environment, biological effects of electric field on human body, simulation of natural condition at workplace

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Authors: Kozak K, M. Kozak, K. Stapor

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The k-nearest neighbors (knn) is a simple but effective method of classification. In this paper we present an extended version of this technique for chemical compounds used in High Throughput Screening, where the distances of the nearest neighbors can be taken into account. Our algorithm uses kernel weight functions as guidance for the process of defining activity in screening data. Proposed kernel weight function aims to combine properties of graphical structure and molecule descriptors of screening compounds. We apply the modified knn method on several experimental data from biological screens. The experimental results confirm the effectiveness of the proposed method.

Keywords: biological screening, kernel methods, KNN, QSAR

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Authors: Pablo Barrera, Jose M. Canas, Vicente Matellan

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This paper addresses the problem of determining the current 3D location of a moving object and robustly tracking it from a sequence of camera images. The approach presented here uses a particle filter and does not perform any explicit triangulation. Only the color of the object to be tracked is required, but not any precisemotion model. The observation model we have developed avoids the color filtering of the entire image. That and the Monte Carlotechniques inside the particle filter provide real time performance.Experiments with two real cameras are presented and lessons learned are commented. The approach scales easily to more than two cameras and new sensor cues.

Keywords: Monte Carlo sampling, multiple view, particle filters, visual tracking.

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Authors: N. Reehana, A. Parveez Ahamed, D. Mubarak Ali, A. Suresh, R. Arvind Kumar, N. Thajuddin

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Cyanobacteria play a vital role in the production of phycobiliproteins that includes phycocyanin and phycoerythrin pigments. Phycocyanin and related phycobiliproteins have wide variety of application that is used in the food, biotechnology and cosmetic industry because of their color, fluorescent and antioxidant properties. The present study is focused to understand the pigment at molecular level in the Cyanobacteria Oscillatoria terebriformis NTRI05 and Oscillatoria foreaui NTRI06. After extraction of genomic DNA, the amplification of C-Phycocyanin gene was done with the suitable primer PCβF and PCαR and the sequencing was performed. Structural and Phylogenetic analysis was attained using the sequence to develop a molecular model.

Keywords: Cyanobacteria, C-Phycocyanin gene, Phylogenetic analysis, Structural analysis.

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Authors: Azizeh Chalak, Niloufar Nasri

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Students' academic achievement, along with the effects of different variables, has been a serious concern of educators since long ago. This study was an attempt to investigate the interplay of Locus of Control (LOC), academic achievement and biological variables among Iranian online EFL Learners. The participants of the study included 100 students of different age groups and genders studying English online at Iran Language Institute (ILI), Isfahan, Iran. The instrument used was Trice Academic LOC questionnaire which identifies orientations of internality or externality. The participants' Grade Point Averages (GPAs) were used as the measure of their academic achievement. A series of independent samples ttests were performed on the data. The results of the study showed that (a) there were no significant differences between male and female participants in LOC orientation, (b) there was no relationship between LOC and academic achievement among internal males and females, (c) external females were better achievers than external males, (d) and the age had no significant relationship with LOC and academic achievement. It can be concluded that the social, cultural patterns of genders have changed. This study might help sociologists and psychologists as well as applied linguists in that they reflect the recent social changes and their effects on the LOC and their consequent implications in teaching languages.

Keywords: Academic achievement, biological variables, Iranian online EFL learners, locus of control.

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Authors: Yu-Jen Chang, Shih-Chieh Chen, Yu-Wei Kuo

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In this study, we are interested in the economic lot scheduling problem (ELSP) that considers manufacturing of the serviceable products and remanufacturing of the reworked products. In this paper, we formulate a mathematical model for the ELSP with reworks using the basic period approach. In order to solve this problem, we propose a search algorithm to find the cyclic multiplier ki of each product that can be cyclically produced for every ki basic periods. This research also uses two heuristics to search for the optimal production sequence of all lots and the optimal time length of the basic period so as to minimize the average total cost. This research uses a numerical example to show the effectiveness of our approach.

Keywords: Economic lot, reworks, inventory, basic period.

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Authors: David Jones, Richard McWilliam, Alan Purvis

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Morphogenesis is the process that underpins the selforganised development and regeneration of biological systems. The ability to mimick morphogenesis in artificial systems has great potential for many engineering applications, including production of biological tissue, design of robust electronic systems and the co-ordination of parallel computing. Previous attempts to mimick these complex dynamics within artificial systems have relied upon the use of evolutionary algorithms that have limited their size and complexity. This paper will present some insight into the underlying dynamics of morphogenesis, then show how to, without the assistance of evolutionary algorithms, design cellular architectures that converge to complex patterns.

Keywords: Morphogenesis, regeneration, robustness, convergence, cellular automata.

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Authors: Toktam Zoughi, Reza Boostani

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Determining depth of anesthesia is a challenging problem in the context of biomedical signal processing. Various methods have been suggested to determine a quantitative index as depth of anesthesia, but most of these methods suffer from high sensitivity during the surgery. A novel method based on energy scattering of samples in the wavelet domain is suggested to represent the basic content of electroencephalogram (EEG) signal. In this method, first EEG signal is decomposed into different sub-bands, then samples are squared and energy of samples sequence is constructed through each scale and time, which is normalized and finally entropy of the resulted sequences is suggested as a reliable index. Empirical Results showed that applying the proposed method to the EEG signals can classify the awake, moderate and deep anesthesia states similar to BIS.

Keywords: Depth of anesthesia, EEG, BIS, Wavelet transforms.

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Authors: Paula Verdugo-Hernández, Patricio Cumsille

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We analyze a first-class on the convergence of real number sequences, named hereafter sequences, to foster exploration and discovery of concepts through graphical representations before engaging students in proving. The main goal was to differentiate between sequences and continuous functions-of-a-real-variable and better understand concepts at an initial stage. We applied the analytic frame of Mathematical Working Spaces, which we expect to contribute to extending to sequences since, as far as we know, it has only developed for other objects, and which is relevant to analyze how mathematical work is built systematically by connecting the epistemological and cognitive perspectives, and involving the semiotic, instrumental, and discursive dimensions.

Keywords: Convergence, graphical representations, Mathematical Working Spaces, paradigms of real analysis, real number sequences.

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Authors: Afef Salhi, Ameni Yengui Jammaoussi

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This paper presents a implementation of an object tracking system in a video sequence. This object tracking is an important task in many vision applications. The main steps in video analysis are two: detection of interesting moving objects and tracking of such objects from frame to frame. In a similar vein, most tracking algorithms use pre-specified methods for preprocessing. In our work, we have implemented several object tracking algorithms (Meanshift, Camshift, Kalman filter) with different preprocessing methods. Then, we have evaluated the performance of these algorithms for different video sequences. The obtained results have shown good performances according to the degree of applicability and evaluation criteria.

Keywords: Tracking, meanshift, camshift, Kalman filter, evaluation.

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Authors: Hamed Alipour-Banaei, Farhad Mehdizadeh

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We report the design and characterization of ultra high quality factor filter based on one-dimensional photonic-crystal Thue- Morse sequence structure. The behavior of aperiodic array of photonic crystal structure is numerically investigated and we show that by changing the angle of incident wave, desired wavelengths could be tuned and a tunable filter is realized. Also it is shown that high quality factor filter be achieved in the telecommunication window around 1550 nm, with a device based on Thue-Morse structure. Simulation results show that the proposed structure has a quality factor more than 100000 and it is suitable for DWDM communication applications.

Keywords: Thue-Morse, filter, quality factor.

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Authors: A. A. Shafie, Fadhlan Hafiz, M. H. Ali

Abstract:

Motion detection is very important in image processing. One way of detecting motion is using optical flow. Optical flow cannot be computed locally, since only one independent measurement is available from the image sequence at a point, while the flow velocity has two components. A second constraint is needed. The method used for finding the optical flow in this project is assuming that the apparent velocity of the brightness pattern varies smoothly almost everywhere in the image. This technique is later used in developing software for motion detection which has the capability to carry out four types of motion detection. The motion detection software presented in this project also can highlight motion region, count motion level as well as counting object numbers. Many objects such as vehicles and human from video streams can be recognized by applying optical flow technique.

Keywords: Background modeling, Motion detection, Optical flow, Velocity smoothness constant, motion trajectories.

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Authors: Gholamreza Habibi

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In order to study seed yield and seed yield components in bean under reduced irrigation condition and assessment drought tolerance of genotypes, 15 lines of White beans were evaluated in two separate RCB design with 3 replications under stress and non stress conditions. Analysis of variance showed that there were significant differences among varieties in terms of traits under study, indicating the existence of genetic variation among varieties. The results indicate that drought stress reduced seed yield, number of seed per plant, biological yield and number of pod in White been. In non stress condition, yield was highly correlated with the biological yield, whereas in stress condition it was highly correlated with harvest index. Results of stepwise regression showed that, selection can we done based on, biological yield, harvest index, number of seed per pod, seed length, 100 seed weight. Result of path analysis showed that the highest direct effect, being positive, was related to biological yield in non stress and to harvest index in stress conditions. Factor analysis were accomplished in stress and nonstress condition a, there were 4 factors that explained more than 76 percent of total variations. We used several selection indices such as Stress Susceptibility Index ( SSI ), Geometric Mean Productivity ( GMP ), Mean Productivity ( MP ), Stress Tolerance Index ( STI ) and Tolerance Index ( TOL ) to study drought tolerance of genotypes, we found that the best Stress Index for selection tolerance genotypes were STI, GMP and MP were the greatest correlations between these Indices and seed yield under stress and non stress conditions. In classification of genotypes base on phenotypic characteristics, using cluster analysis ( UPGMA ), all allels classified in 5 separate groups in stress and non stress conditions.

Keywords: Cluster analysis, factor analysis, path analysis, selection index, White bean

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Authors: Adnan Al-Smadi

Abstract:

One of the primary uses of higher order statistics in signal processing has been for detecting and estimation of non- Gaussian signals in Gaussian noise of unknown covariance. This is motivated by the ability of higher order statistics to suppress additive Gaussian noise. In this paper, several methods to test for non- Gaussianity of a given process are presented. These methods include histogram plot, kurtosis test, and hypothesis testing using cumulants and bispectrum of the available sequence. The hypothesis testing is performed by constructing a statistic to test whether the bispectrum of the given signal is non-zero. A zero bispectrum is not a proof of Gaussianity. Hence, other tests such as the kurtosis test should be employed. Examples are given to demonstrate the performance of the presented methods.

Keywords: Non-Gaussian, bispectrum, kurtosis, hypothesistesting, histogram.

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Authors: D.J. Brink, N.G. van der Berg, L.C. Prinsloo, A. Botha

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In this work we study the reflection of circularly polarised light from a nano-structured biological material found in the exocuticle of scarabus beetles. This material is made of a stack of ultra-thin (~5 nm) uniaxial layers arranged in a left-handed helicoidal stack, which resonantly reflects circularly polarized light. A chirp in the layer thickness combined with a finite absorption coefficient produce a broad smooth reflectance spectrum. By comparing model calculations and electron microscopy with measured spectra we can explain our observations and quantify most relevant structural parameters.

Keywords: Chiral reflectors, circularly polarised light, helicoidal structures, nano photonics.

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Authors: H. Nasiraghdam, A. Jalilian

Abstract:

DSTATCOM is one of the equipments for voltage sag mitigation in power systems. In this paper a new control method for balanced and unbalanced voltage sag mitigation using DSTATCOM is proposed. The control system has two loops in order to regulate compensator current and load voltage. Delayed signal cancellation has been used for sequence separation. The compensator should protect sensitive loads against different types of voltage sag. Performance of the proposed method is investigated under different types of voltage sags for linear and nonlinear loads. Simulation results show appropriate operation of the proposed control system.

Keywords: Custom power, power quality, voltage sagmitigation, current vector control.

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Authors: R. Croitoru, L. A. M. van den Broek, A. E. Frissen, C. M. Davidescu, F. Peter, C. G. Boeriu

Abstract:

Commercially available lipases (Candida antarctica lipase B, Novozyme 435, Thermomyces lanuginosus lipase, and Lipozyme TL IM), as well as sol-gel immobilized lipases, have been screened for their ability to acylate regioselectively xylitol, sorbitol, and mannitol with a phenolic ester in a binary mixture of t-butanol and dimethylsulfoxide. HPLC and MALDI-TOF MS analysis revealed the exclusive formation of monoesters for all studied sugar alcohols. The lipases immobilized by the sol-gel entrapment method proved to be efficient catalysts, leading to high conversions (up to 60%) in the investigated acylation reactions. From a sequence of silane precursors with different nonhydrolyzable groups in their structure, the presence of octyl and i-butyl group was most beneficial for the catalytic activity of sol-gel entrapped lipases in the studied process.

Keywords: Lipase, phenolic ester, specificity, sugar alcohol, transesterification.

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Authors: Rasmus Engholm, Eva B. Vedel Jensen, Henrik Karstoft

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In this paper we present a noise reduction filter for video processing. It is based on the recently proposed two dimensional steering kernel, extended to three dimensions and further augmented to suit the spatial-temporal domain of video processing. Two alternative filters are proposed - the time symmetric kernel and the time asymmetric kernel. The first reduces the noise on single sequences, but to handle the problems at scene shift the asymmetric kernel is introduced. The performance of both are tested on simulated data and on a real video sequence together with the existing steering kernel. The proposed kernels improves the Rooted Mean Squared Error (RMSE) compared to the original steering kernel method on video material.

Keywords: Adaptive image filtering, noise reduction, kernel methods, video processing.

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Authors: Alexandra Oliveros, Miguel Sotaquirá

Abstract:

DNA microarray technology is widely used by geneticists to diagnose or treat diseases through gene expression. This technology is based on the hybridization of a tissue-s DNA sequence into a substrate and the further analysis of the image formed by the thousands of genes in the DNA as green, red or yellow spots. The process of DNA microarray image analysis involves finding the location of the spots and the quantification of the expression level of these. In this paper, a tool to perform DNA microarray image analysis is presented, including a spot addressing method based on the image projections, the spot segmentation through contour based segmentation and the extraction of relevant information due to gene expression.

Keywords: Contour segmentation, DNA microarrays, edge detection, image processing, segmentation, spot addressing.

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Authors: Ahmad Rabanimotlagh

Abstract:

In this paper an ant colony optimization algorithm is developed to solve the permutation flow shop scheduling problem. In the permutation flow shop scheduling problem which has been vastly studied in the literature, there are a set of m machines and a set of n jobs. All the jobs are processed on all the machines and the sequence of jobs being processed is the same on all the machines. Here this problem is optimized considering two criteria, makespan and total flow time. Then the results are compared with the ones obtained by previously developed algorithms. Finally it is visible that our proposed approach performs best among all other algorithms in the literature.

Keywords: Scheduling, Flow shop, Ant colony optimization, Makespan, Flow time

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Authors: A. AlKalbany, H. Al hassan, M. Saeb

Abstract:

The “PYRAMIDS" Block Cipher is a symmetric encryption algorithm of a 64, 128, 256-bit length, that accepts a variable key length of 128, 192, 256 bits. The algorithm is an iterated cipher consisting of repeated applications of a simple round transformation with different operations and different sequence in each round. The algorithm was previously software implemented in Cµ code. In this paper, a hardware implementation of the algorithm, using Field Programmable Gate Arrays (FPGA), is presented. In this work, we discuss the algorithm, the implemented micro-architecture, and the simulation and implementation results. Moreover, we present a detailed comparison with other implemented standard algorithms. In addition, we include the floor plan as well as the circuit diagrams of the various micro-architecture modules.

Keywords: FPGA, VHDL, micro-architecture, encryption, cryptography, algorithm, data communication security.

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Authors: P. Thongmuang, Y. Sudjaroen

Abstract:

The methanolic extracts from seeds of tamarind (Tamarindus indica) was prepared by Soxhlet apparatus extraction and evaluated for total phenolic content by Folin-Ciocalteu method. Then, methanolic extract was screened biological activities (In vitro) for anti-melanogenic activity by tyrosinase inhibition test, antiinflammation activity by cyclooxygenase 1 (COX-1) and cyclooxygenase 2 (COX-2) inhibition test, and cytotoxic screening test with Vero cells. The results showed that total phenolic content, which contained in extract, was contained 27.72 mg of gallic acid equivalent per g of dry weight. The ability to inhibit tyrosinase enzyme, which exerted by Tamarind seed extracts (1 mg/ml) was 52.13 ± 0.42 %. The extract was not possessed inhibitory effect to COX-1 and COX-2 enzymes and cytotoxic effect to Vero cells. The finding is concludes that tested seed extract was possessed antimelanogenic activity with non-toxic effects. However, there was not exhibited anti-inflammatory activity. Further studies include the use of advance biological models to confirm this biological activity, as well as, the isolation and characterization of the purified compounds that it was contained.

Keywords: Tamarindus indica, anti-melanogenic, antiinflammatotion, cytotoxicity, seed, phenolic compounds.

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Authors: Yayun Hsu, Henry Horng-Shing Lu

Abstract:

This paper proposes a data-driven, biology-inspired neural segmentation method of 3D drosophila Brainbow images. We use Bayesian Sequential Partitioning algorithm for probabilistic modeling, which can be used to detect somas and to eliminate crosstalk effects. This work attempts to develop an automatic methodology for neuron image segmentation, which nowadays still lacks a complete solution due to the complexity of the image. The proposed method does not need any predetermined, risk-prone thresholds, since biological information is inherently included inside the image processing procedure. Therefore, it is less sensitive to variations in neuron morphology; meanwhile, its flexibility would be beneficial for tracing the intertwining structure of neurons.

Keywords: Brainbow, 3D imaging, image segmentation, neuron morphology, biological data mining, non-parametric learning.

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Authors: Changjin Xu

Abstract:

In this paper, applying frequency domain approach, a delayed predator-prey fishery model with prey reserve is investigated. By choosing the delay τ as a bifurcation parameter, It is found that Hopf bifurcation occurs as the bifurcation parameter τ passes a sequence of critical values. That is, a family of periodic solutions bifurcate from the equilibrium when the bifurcation parameter exceeds a critical value. The length of delay which preserves the stability of the positive equilibrium is calculated. Some numerical simulations are included to justify the theoretical analysis results. Finally, main conclusions are given.

Keywords: Predator-prey model, stability, Hopf bifurcation, frequency domain, Nyquist criterion.

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Authors: Tudor Barbu

Abstract:

An automatic moment-based texture segmentation approach is proposed in this paper. First, we describe the related work in this computer vision domain. Our texture feature extraction, the first part of the texture recognition process, produces a set of moment-based feature vectors. For each image pixel, a texture feature vector is computed as a sequence of area moments. Then, an automatic pixel classification approach is proposed. The feature vectors are clustered using an unsupervised classification algorithm, the optimal number of clusters being determined using a measure based on validation indexes. From the resulted pixel classes one determines easily the desired texture regions of the image.

Keywords: Image segmentation, moment-based texture analysis, automatic classification, validity indexes.

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Authors: C. Porkodi, R. Arumuganathan

Abstract:

In this paper a Public Key Cryptosystem is proposed using the number theoretic transforms (NTT) over a ring of integer modulo a composite number. The key agreement is similar to ElGamal public key algorithm. The security of the system is based on solution of multivariate linear congruence equations and discrete logarithm problem. In the proposed cryptosystem only fixed numbers of multiplications are carried out (constant complexity) and hence the encryption and decryption can be done easily. At the same time, it is very difficult to attack the cryptosystem, since the cipher text is a sequence of integers which are interrelated. The system provides authentication also. Using Mathematica version 5.0 the proposed algorithm is justified with a numerical example.

Keywords: Cryptography, decryption, discrete logarithm problem encryption, Integer Factorization problem, Key agreement, Number Theoretic Transform.

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Authors: Boukerch Haroun, Luo Qing Sheng, Li Hua Shi, Boukraa Sebti

Abstract:

In this paper we present the design and the implementation of a target tracking system where the target is set to be a moving person in a video sequence. The system can be applied easily as a vision system for mobile robot. The system is composed of two major parts the first is the detection of the person in the video frame using the SVM learning machine based on the “HOG” descriptors. The second part is the tracking of a moving person it’s done by using a combination of the Kalman filter and a modified version of the Camshift tracking algorithm by adding the target motion feature to the color feature, the experimental results had shown that the new algorithm had overcame the traditional Camshift algorithm in robustness and in case of occlusion.

Keywords: Camshift Algorithm, Computer Vision, Kalman Filter, Object tracking.

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Authors: H. Rong, X. C. Yin, J. Yang, Y. N. Shen

Abstract:

Based on Rayleigh beam theory, the sub-impacts of a free-free beam struck horizontally by a round-nosed rigid mass is simulated by the finite difference method and the impact-separation conditions. In order to obtain the sub-impact force, a uniaxial compression elastic-plastic contact model is employed to analyze the local deformation field on contact zone. It is found that the horizontal impact is a complicated process including the elastic plastic sub-impacts in sequence. There are two sub-zones of sub-impact. In addition, it found that the elastic energy of the free-free beam is more suitable for the Poisson collision hypothesis to explain compression and recovery processes.

Keywords: beam, sub-impact, elastic-plastic deformation, finite difference method.

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Authors: Seung Pil Pack

Abstract:

Deaminated lesions were produced via nitrosative oxidation of natural nucleobases; uracul (Ura, U) from cytosine (Cyt, C), hypoxanthine (Hyp, H) from adenine (Ade, A), and xanthine (Xan, X) and oxanine (Oxa, O) from guanine (Gua, G). Such damaged nucleobases may induce mutagenic problems, so that much attentions and efforts have been poured on the revealing of their mechanisms in vivo or in vitro. In this study, we employed these deaminated lesions as useful probes for analysis of DNA-binding/recognizing proteins or enzymes. Since the pyrimidine lesions such as Hyp, Oxa and Xan are employed as analogues of guanine, their comparative uses are informative for analyzing the role of Gua in DNA sequence in DNA-protein interaction. Several DNA oligomers containing such Hyp, Oxa or Xan substituted for Gua were designed to reveal the molecular interaction between DNA and protein. From this approach, we have got useful information to understand the molecular mechanisms of the DNA-recognizing enzymes, which have not ever been observed using conventional DNA oligomer composed of just natural nucleobases.

Keywords: Deaminated lesion, DNA-protein interaction, DNA-recognizing enzymes

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