Search results for: Protein sequence annotation

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: 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: S. Banerjee, A. Apte Deshpande, N. Mandi, S. Padmanabhan

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We report a novel fusion tag for expressing recombinant proteins in E. coli. The fusion tag is the C-terminus part of the human GMCSF gene comprising 45 amino acids, which aid in over expression of otherwise non expressible genes. Expression of hIFN a2b with this fusion tag also escapes the requirement of rare codons for expression. This is also a first report of a small fusion tag of human origin having affinity to heparin sepharose column facilitating the purification of fusion protein.

Keywords: fusion tag, bacterial expression, rare codons, human GMCSF

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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: Hanaa M. M. El-Khayat, Hoda Abdel-Hamid, Kadria M. A. Mahmoud, Hanan S. Gaber, Hoda, M. A. Abu Taleb, Hassan E. Flefel

Abstract:

Snails are considered as suitable diagnostic organisms for heavy metal–contaminated sites. Biomphalaria alexandrina snails are used in this work as pollution bioindicators after exposure to chemical mixtures consisted of heavy metals (HM); zinc (Zn), copper (Cu) and lead (Pb); and persistent organic pollutants; Decabromodiphenyl ether 98% (D) and Aroclor 1254 (A). The impacts of these tested chemicals, individual and mixtures, on liver and kidney functions, antioxidant enzymes, complete blood picture, and tissue histology were studied. Results showed that Cu was proved to be the highly toxic against snails than Zn and Pb where LC₅₀ values were 1.362, 213.198 and 277.396 ppm, respectively. Also, B. alexandrina snails exposed to the mixture of HM (¼ LC₅ Cu, Pb and Zn) showed the highest bioaccumulation of Cu and Zn in their whole tissue, the most significant increase in AST, ALT & ALP activities and the highest significant levels of total protein, albumin and globulin. Results showed significant alterations in CAT activity in snail tissue extracts while snail samples exposed to most experimental tests showed significant increase in GST activity. Snail samples that exposed to HM mixtures showed a significant decrease in total hemocytes count while snail samples that exposed to mixtures containing A & D showed a significant increase in total hemocytes and Hyalinocytes. Histopathological alterations in snail samples exposed to individual HM and their mixtures for 4 weeks showed degeneration, edema, hyper trophy and vaculation in head-foot muscle, degeneration and necrotic changes in the digestive gland and accumulation in most tested organs. Also, the hermaphrodite gland showed mature ova with irregular shape and reduction in sperm number. In conclusion, the resulted damage and alterations in B. alexandrina studied parameters can be used as bioindicators to the presence of pollutants in its habitats.

Keywords: Biomphalaria, Zn, Cu, Pb, AST, ALT, ALP, total protein albumin, globulin, CAT and Histopathology.

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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: 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: Congo Tak Shing Ching, Hong-Sheng Chen, Tai-Ping Sun, Hsiu-Li Shieh

Abstract:

Nuclear matrix protein 22 (NMP22) is a FDA approved biomarker for bladder cancer. The objective of this study is to develop a simple NMP22 immumosensor (NMP22-IMS) for accurate measurement of NMP22. The NMP22-IMS was constructed with NMP22 antibody immobilized on screen-printed carbon electrodes. The construction procedures and antibody immobilization are simple. Results showed that the NMP22-IMS has an excellent (r2³0.95) response range (20 – 100 ng/mL). In conclusion, a simple and reliable NMP22-IMS was developed, capable of precisely determining urine NMP22 level.

Keywords: Bladder Cancer, Immunosensor, Impedance, NMP22

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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: Antonella Bandiera

Abstract:

A new sythetic gene coding for a Human Elastin-Like Polypeptide was constructed and expressed. The recombinant product was tested as coating agent to realize a surface suitable for cell growth. Coatings showed peculiar features and different human cell lines were seeded and cultured. All cell lines tested showed to adhere and proliferate on this substrate that has been shown also to exert a specific effect on cells, depending on cell type.

Keywords: elastin, recombinant protein, coating, cell adhesion.

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Authors: Aravind Mohan Krishnan

Abstract:

This paper identifies a research gap in the literature on tourism entrepreneurship in Malawi, Africa, and investigates how entrepreneurs from the Malawian tourism sector discover and exploit business opportunities. In particular, the importance of prior experience and business networks in the opportunity development process is debated. Another area of empirical research examined here is the opportunity recognition-venture creation sequence. While Malawi presents fruitful business opportunities, exploiting these opportunities into fully realized business ideas is a real challenge due to the country’s difficult business environment and poor promotional and marketing efforts. The study concludes by calling for further research in Sub-Saharan Africa in order to develop our understanding of entrepreneurship in this (African) context.

Keywords: Tourism, entrepreneurship, Malawi, business opportunities.

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Authors: P. Vit, J. Uddin, V. Zuccato, F. Maza, E. Schievano

Abstract:

Honeys are produced by Apis mellifera and stingless bees (Meliponini) in Ecuador. We studied honey produced in beeswax combs by Apis mellifera, and honey produced in pots by Geotrigona and Scaptotrigona bees. Chloroform extracts of honey were obtained for fast NMR spectra. The 1D spectra were acquired at 298 K, with a 600 MHz NMR Bruker instrument, using a modified double pulsed field gradient spin echoes (DPFGSE) sequence. Signals of 1H NMR spectra were integrated and used as inputs for PCA, PLS-DA analysis, and labelled sets of classes were successfully identified, enhancing the separation between the three groups of honey according to the entomological origin: A. mellifera, Geotrigona and Scaptotrigona. This procedure is therefore recommended for authenticity test of honey in Ecuador.

Keywords: Apis mellifera, honey, 1H NMR, entomological origin, Meliponini.

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Authors: Nyah C. Temaneh, F. A. Phiri, E. Ruhunga

Abstract:

Most of the well known methods for generating Gaussian variables require at least one standard uniform distributed value, for each Gaussian variable generated. The length of the random number generator therefore, limits the number of independent Gaussian distributed variables that can be generated meanwhile the statistical solution of complex systems requires a large number of random numbers for their statistical analysis. We propose an alternative simple method of generating almost infinite number of Gaussian distributed variables using a limited number of standard uniform distributed random numbers.

Keywords: Gaussian variable, statistical analysis, simulation ofCommunication Network, Random numbers.

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Authors: Ghulam Zakria, Zailin Guan , Yasser Riaz Awan, Wan Lizhi

Abstract:

There are many real world problems in which parameters like the arrival time of new jobs, failure of resources, and completion time of jobs change continuously. This paper tackles the problem of scheduling jobs with random due dates on multiple identical machines in a stochastic environment. First to assign jobs to different machine centers LPT scheduling methods have been used, after that the particular sequence of jobs to be processed on the machine have been found using simple stochastic techniques. The performance parameter under consideration has been the maximum lateness concerning the stochastic due dates which are independent and exponentially distributed. At the end a relevant problem has been solved using the techniques in the paper..

Keywords: Quantity Production Flow Shop, LPT Scheduling, Stochastic Scheduling, Maximum Lateness, Random Due Dates

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Authors: Alireza Rezaei, Fatemeh Baharifard, Kourosh Parand

Abstract:

In this paper we improve the quasilinearization method by barycentric Lagrange interpolation because of its numerical stability and computation speed to achieve a stable semi analytical solution. Then we applied the improved method for solving the Fin problem which is a nonlinear equation that occurs in the heat transferring. In the quasilinearization approach the nonlinear differential equation is treated by approximating the nonlinear terms by a sequence of linear expressions. The modified QLM is iterative but not perturbative and gives stable semi analytical solutions to nonlinear problems without depending on the existence of a smallness parameter. Comparison with some numerical solutions shows that the present solution is applicable.

Keywords: Quasilinearization method, Barycentric lagrange interpolation, nonlinear ODE, fin problem, heat transfer.

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Authors: Emad T. Khalaf, Norrozila Sulaiman

Abstract:

Many researchers are working on information hiding techniques using different ideas and areas to hide their secrete data. This paper introduces a robust technique of hiding secret data in image based on LSB insertion and RSA encryption technique. The key of the proposed technique is to encrypt the secret data. Then the encrypted data will be converted into a bit stream and divided it into number of segments. However, the cover image will also be divided into the same number of segments. Each segment of data will be compared with each segment of image to find the best match segment, in order to create a new random sequence of segments to be inserted then in a cover image. Experimental results show that the proposed technique has a high security level and produced better stego-image quality.

Keywords: steganography; LSB Matching; RSA Encryption; data segments

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Authors: Ming-Ta Yang, Jin-Lung Guan, Jhy-Cherng Gu

Abstract:

The purpose of this paper is to solve the problem of protecting aerial lines from high impedance faults (HIFs) in distribution systems. This investigation successfully applies 3I0 zero sequence current to solve HIF problems. The feature extraction system based on discrete wavelet transform (DWT) and the feature identification technique found on statistical confidence are then applied to discriminate effectively between the HIFs and the switch operations. Based on continuous wavelet transform (CWT) pattern recognition of HIFs is proposed, also. Staged fault testing results demonstrate that the proposed wavelet based algorithm is feasible performance well.

Keywords: Continuous wavelet transform, discrete wavelet transform, high impedance faults, statistical confidence.

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Authors: Bezuidt O., Lima-Mendez G., Reva O. N.

Abstract:

SeqWord Gene Island Sniffer, a new program for the identification of mobile genetic elements in sequences of bacterial chromosomes is presented. This program is based on the analysis of oligonucleotide usage variations in DNA sequences. 3,518 mobile genetic elements were identified in 637 bacterial genomes and further analyzed by sequence similarity and the functionality of encoded proteins. The results of this study are stored in an open database http://anjie.bi.up.ac.za/geidb/geidbhome. php). The developed computer program and the database provide the information valuable for further investigation of the distribution of mobile genetic elements and virulence factors among bacteria. The program is available for download at www.bi.up.ac.za/SeqWord/sniffer/index.html.

Keywords: mobile genetic elements, virulence, bacterial genomes

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Authors: Motonobu Hattori, Rina Suzuki

Abstract:

In neural networks, when new patters are learned by a network, they radically interfere with previously stored patterns. This drawback is called catastrophic forgetting. We have already proposed a biologically inspired dual-network memory model which can much reduce this forgetting for static patterns. In this model, information is first stored in the hippocampal network, and thereafter, it is transferred to the neocortical network using pseudopatterns. Because temporal sequence learning is more important than static pattern learning in the real world, in this study, we improve our conventional  dual-network memory model so that it can deal with temporal sequences without catastrophic forgetting. The computer simulation results show the effectiveness of the proposed dual-network memory model.  

Keywords: Catastrophic forgetting, dual-network, temporal sequences.

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Authors: H. K. Hwang, Zekeriya Aliyazicioglu, Solomon Wu, Hung Lu, Nick Wilkins, Daniel Kerr

Abstract:

Multiple-input multiple-output (MIMO) radar has received increasing attention in recent years. MIMO radar has many advantages over conventional phased array radar such as target detection,resolution enhancement, and interference suppression. In this paper, the results are presented from a simulation study of MIMO uniformly-spaced linear array (ULA) antennas. The performance is investigated under varied parameters, including varied array size, pseudo random (PN) sequence length, number of snapshots, and signal to noise ratio (SNR). The results of MIMO are compared to a traditional array antenna.

Keywords: Multiple-input multiple-output (MIMO) radar, phased array antenna, target detection, radar signal processing.

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Authors: Farag Azzedin, Ali Rizvi

Abstract:

In any trust model, the two information sources that a peer relies on to predict trustworthiness of another peer are direct experience as well as reputation. These two vital components evolve over time. Trust evolution is an important issue, where the objective is to observe a sequence of past values of a trust parameter and determine the future estimates. Unfortunately, trust evolution algorithms received little attention and the proposed algorithms in the literature do not comply with the conditions and the nature of trust. This paper contributes to this important problem in the following ways: (a) presents an algorithm that manages and models trust evolution in a P2P environment, (b) devises new mechanisms for effectively maintaining trust values based on the conditions that influence trust evolution , and (c) introduces a new methodology for incorporating trust-nurture incentives into the trust evolution algorithm. Simulation experiments are carried out to evaluate our trust evolution algorithm.

Keywords: P2P, Trust, Reputation, Incentives.

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Authors: Parvinder Singh Sandhu, Sumeet Kaur Sehra, Karmjit Kaur

Abstract:

Phylogenetic tree is a graphical representation of the evolutionary relationship among three or more genes or organisms. These trees show relatedness of data sets, species or genes divergence time and nature of their common ancestors. Quality of a phylogenetic tree requires parsimony criterion. Various approaches have been proposed for constructing most parsimonious trees. This paper is concerned about calculating and optimizing the changes of state that are needed called Small Parsimony Algorithms. This paper has proposed enhanced small parsimony algorithm to give better score based on number of evolutionary changes needed to produce the observed sequence changes tree and also give the ancestor of the given input.

Keywords: Phylogenetic Analysis, Small Parsimony, EnhancedFitch Algorithm, Enhanced Sakoff Algorithm.

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Authors: W. Suksombat, P. Suksombat, R. Mirattanaphrai

Abstract:

The effects of commercial or bovine yeasts on the performance and blood variables of broiler chickens intoxicated with aflatoxin were investigated in broilers. Four hundred eighty broilers (Arbor Acres; 3-wk-old) were randomly assigned to 4 groups. Each group (120 broiler chickens) was further randomly divided into 6 replicates of 20 chickens. The treatments were control diet without additives (treatment 1), 250 ppb AFB1 (treatment 2), commercial yeast, Saccharomyces cerevisiae, (CY 2.5 x 107 CFU/g) + 250 ppb AFB1 (treatment 3) and bovine yeast, Saccharomyces cerevisiae, (BY 2.5 x 107 CFU/g + 250 ppb AFB1 (treatment 4). Complete randomized design (CRD) was used in the experiment. Feed consumption and body weight were recorded at every five-day period. On day 42, carcass compositions were determined from 30 birds per treatment. While chicks were sacrificed, 3-4 ml blood sample was taken and stored frozen at (-20°C) for serum chemical analysis to determine effects of consumption of diets on blood chemistry (total protein, albumin, glucose, urea, cholesterol and triglycerides). There were no significant differences in ADFI among the treatments(P>0.05). However, BWG, FCR and mortality were highly significantly different (P<0.01) between treatments. ADG was significantly reduced (P<0.05) by aflatoxin but was unaffected by aflatoxin supplemented with either commercial or bovine yeasts (P>0.05). In terms of carcass portions, percentage of carcass was unaffected by the treatments, however, percentages of drumstick were reduced by aflatoxin and aflatoxin supplemented commercial yeast. Abdominal fat was significantly reduced (P<0.01) when commercial or bovine yeasts were added to the aflatoxin contaminated diets. Percentage of liver were significantly increased by aflatoxin contamination but were unaffected when yeasts were added to the diets. Blood chemical parameters, i.e. albumin, blood urea nitrogen and glucose were unaffected the treatments, while total protein, cholesterol and triglycerides were significantly decreased by aflatoxin. When yeasts were supplemented, such effect was not differed from the control. It is clearly indicated in the present study that supplementation of either commercial or bovine yeasts had beneficial effects on performance of broiler chickens intoxicated with aflatoxins.

Keywords: Aflatoxin, Commercial yeast, Bovine yeast, Growth performance, Blood chemical parameters, Broilers

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