Search results for: Model organism genome
7311 Exons and Introns Classification in Human and Other Organisms
Authors: Benjamin Y. M. Kwan, Jennifer Y. Y. Kwan, Hon Keung Kwan
Abstract:In the paper, the relative performances on spectral classification of short exon and intron sequences of the human and eleven model organisms is studied. In the simulations, all combinations of sixteen one-sequence numerical representations, four threshold values, and four window lengths are considered. Sequences of 150-base length are chosen and for each organism, a total of 16,000 sequences are used for training and testing. Results indicate that an appropriate combination of one-sequence numerical representation, threshold value, and window length is essential for arriving at top spectral classification results. For fixed-length sequences, the precisions on exon and intron classification obtained for different organisms are not the same because of their genomic differences. In general, precision increases as sequence length increases.
Keywords: Exons and introns classification, Human genome, Model organism genome, Spectral analysisProcedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1927
7310 Evolutionary Distance in the Yeast Genome
Authors: Somayyeh Azizi, Saeed Kaboli, Atsushi Yagi
Abstract:Whole genome duplication (WGD) increased the number of yeast Saccharomyces cerevisiae chromosomes from 8 to 16. In spite of retention the number of chromosomes in the genome of this organism after WGD to date, chromosomal rearrangement events have caused an evolutionary distance between current genome and its ancestor. Studies under evolutionary-based approaches on eukaryotic genomes have shown that the rearrangement distance is an approximable problem. In the case of S. cerevisiae, we describe that rearrangement distance is accessible by using dedoubled adjacency graph drawn for 55 large paired chromosomal regions originated from WGD. Then, we provide a program extracted from a C program database to draw a dedoubled genome adjacency graph for S. cerevisiae. From a bioinformatical perspective, using the duplicated blocks of current genome in S. cerevisiae, we infer that genomic organization of eukaryotes has the potential to provide valuable detailed information about their ancestrygenome.
Keywords: Whole-genome duplication, Evolution, Double-cutand- join operation, Yeast.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1399
7309 Research on Online Consumption of College Students in China with Stimulate-Organism-Reaction Driven Model
Authors: Wei Lu
With the development of information technology in China, network consumption is becoming more and more popular. As a special group, college students have a high degree of education and distinct opinions and personalities. In the future, the key groups of network consumption have gradually become the focus groups of network consumption. Studying college students’ online consumption behavior has important theoretical significance and practical value. Based on the Stimulus-Organism-Response (SOR) driving model and the structural equation model, this paper establishes the influencing factors model of College students’ online consumption behavior, evaluates and amends the model by using SPSS and AMOS software, analyses and determines the positive factors of marketing college students’ consumption, and provides an effective basis for guiding and promoting college student consumption.
Keywords: College students, online consumption, stimulus-organism-response driving model, structural equation model.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 415
7308 Modified Genome-Scale Metabolic Model of Escherichia coli by Adding Hyaluronic Acid Biosynthesis-Related Enzymes (GLMU2 and HYAD) from Pasteurella multocida
Authors: P. Pasomboon, P. Chumnanpuen, T. E-kobon
Abstract:Hyaluronic acid (HA) consists of linear heteropolysaccharides repeat of D-glucuronic acid and N-acetyl-D-glucosamine. HA has various useful properties to maintain skin elasticity and moisture, reduce inflammation, and lubricate the movement of various body parts without causing immunogenic allergy. HA can be found in several animal tissues as well as in the capsule component of some bacteria including Pasteurella multocida. This study aimed to modify a genome-scale metabolic model of Escherichia coli using computational simulation and flux analysis methods to predict HA productivity under different carbon sources and nitrogen supplement by the addition of two enzymes (GLMU2 and HYAD) from P. multocida to improve the HA production under the specified amount of carbon sources and nitrogen supplements. Result revealed that threonine and aspartate supplement raised the HA production by 12.186%. Our analyses proposed the genome-scale metabolic model is useful for improving the HA production and narrows the number of conditions to be tested further.
Keywords: Pasteurella multocida, Escherichia coli, hyaluronic acid, genome-scale metabolic model, bioinformatics.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 409
7307 Computing the Similarity and the Diversity in the Species Based on Cronobacter Genome
Authors: E. Al Daoud
The purpose of computing the similarity and the diversity in the species is to trace the process of evolution and to find the relationship between the species and discover the unique, the special, the common and the universal proteins. The proteins of the whole genome of 40 species are compared with the cronobacter genome which is used as reference genome. More than 3 billion pairwise alignments are performed using blastp. Several findings are introduced in this study, for example, we found 172 proteins in cronobacter genome which have insignificant hits in other species, 116 significant proteins in the all tested species with very high score value and 129 common proteins in the plants but have insignificant hits in mammals, birds, fishes, and insects.
Keywords: Genome, species, blastp, conserved genes, cronobacter.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 640
7306 Analysis and Classification of Hiv-1 Sub- Type Viruses by AR Model through Artificial Neural Networks
Authors: O. Yavuz, L. Ozyilmaz
Abstract:HIV-1 genome is highly heterogeneous. Due to this variation, features of HIV-I genome is in a wide range. For this reason, the ability to infection of the virus changes depending on different chemokine receptors. From this point of view, R5 HIV viruses use CCR5 coreceptor while X4 viruses use CXCR5 and R5X4 viruses can utilize both coreceptors. Recently, in Bioinformatics, R5X4 viruses have been studied to classify by using the experiments on HIV-1 genome. In this study, R5X4 type of HIV viruses were classified using Auto Regressive (AR) model through Artificial Neural Networks (ANNs). The statistical data of R5X4, R5 and X4 viruses was analyzed by using signal processing methods and ANNs. Accessible residues of these virus sequences were obtained and modeled by AR model since the dimension of residues is large and different from each other. Finally the pre-processed data was used to evolve various ANN structures for determining R5X4 viruses. Furthermore ROC analysis was applied to ANNs to show their real performances. The results indicate that R5X4 viruses successfully classified with high sensitivity and specificity values training and testing ROC analysis for RBF, which gives the best performance among ANN structures.
Keywords: Auto-Regressive Model, HIV, Neural Networks, ROC Analysis.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1080
7305 Reconstruction of a Genome-Scale Metabolic Model to Simulate Uncoupled Growth of Zymomonas mobilis
Authors: Maryam Saeidi, Ehsan Motamedian, Seyed Abbas Shojaosadati
Abstract:Zymomonas mobilis is known as an example of the uncoupled growth phenomenon. This microorganism also has a unique metabolism that degrades glucose by the Entner–Doudoroff (ED) pathway. In this paper, a genome-scale metabolic model including 434 genes, 757 reactions and 691 metabolites was reconstructed to simulate uncoupled growth and study its effect on flux distribution in the central metabolism. The model properly predicted that ATPase was activated in experimental growth yields of Z. mobilis. Flux distribution obtained from model indicates that the major carbon flux passed through ED pathway that resulted in the production of ethanol. Small amounts of carbon source were entered into pentose phosphate pathway and TCA cycle to produce biomass precursors. Predicted flux distribution was in good agreement with experimental data. The model results also indicated that Z. mobilis metabolism is able to produce biomass with maximum growth yield of 123.7 g (mol glucose)-1 if ATP synthase is coupled with growth and produces 82 mmol ATP gDCW-1h-1. Coupling the growth and energy reduced ethanol secretion and changed the flux distribution to produce biomass precursors.
Keywords: Genome-scale metabolic model, Zymomonas mobilis, uncoupled growth, flux distribution, ATP dissipation.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1021
7304 An Improved Ant Colony Algorithm for Genome Rearrangements
Authors: Essam Al Daoud
Genome rearrangement is an important area in computational biology and bioinformatics. The basic problem in genome rearrangements is to compute the edit distance, i.e., the minimum number of operations needed to transform one genome into another. Unfortunately, unsigned genome rearrangement problem is NP-hard. In this study an improved ant colony optimization algorithm to approximate the edit distance is proposed. The main idea is to convert the unsigned permutation to signed permutation and evaluate the ants by using Kaplan algorithm. Two new operations are added to the standard ant colony algorithm: Replacing the worst ants by re-sampling the ants from a new probability distribution and applying the crossover operations on the best ants. The proposed algorithm is tested and compared with the improved breakpoint reversal sort algorithm by using three datasets. The results indicate that the proposed algorithm achieves better accuracy ratio than the previous methods.
Keywords: Ant colony algorithm, Edit distance, Genome breakpoint, Genome rearrangement, Reversal sort.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1789
7303 The Role and Importance of Genome Sequencing in Prediction of Cancer Risk
Authors: M. Sadeghi, H. Pezeshk, R. Tusserkani, A. Sharifi Zarchi, A. Malekpour, M. Foroughmand, S. Goliaei, M. Totonchi, N. Ansari–Pour
The role and relative importance of intrinsic and extrinsic factors in the development of complex diseases such as cancer still remains a controversial issue. Determining the amount of variation explained by these factors needs experimental data and statistical models. These models are nevertheless based on the occurrence and accumulation of random mutational events during stem cell division, thus rendering cancer development a stochastic outcome. We demonstrate that not only individual genome sequencing is uninformative in determining cancer risk, but also assigning a unique genome sequence to any given individual (healthy or affected) is not meaningful. Current whole-genome sequencing approaches are therefore unlikely to realize the promise of personalized medicine. In conclusion, since genome sequence differs from cell to cell and changes over time, it seems that determining the risk factor of complex diseases based on genome sequence is somewhat unrealistic, and therefore, the resulting data are likely to be inherently uninformative.
Keywords: Cancer risk, extrinsic factors, genome sequencing, intrinsic factors.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 983
7302 Symbiotic Organism Search (SOS) for Solving the Capacitated Vehicle Routing Problem
Authors: Ruskartina Eki, Vincent F. Yu, Santosa Budi, A. A. N. Perwira Redi
Abstract:This paper introduces symbiotic organism search (SOS) for solving capacitated vehicle routing problem (CVRP). SOS is a new approach in metaheuristics fields and never been used to solve discrete problems. A sophisticated decoding method to deal with a discrete problem setting in CVRP is applied using the basic symbiotic organism search (SOS) framework. The performance of the algorithm was evaluated on a set of benchmark instances and compared results with best known solution. The computational results show that the proposed algorithm can produce good solution as a preliminary testing. These results indicated that the proposed SOS can be applied as an alternative to solve the capacitated vehicle routing problem.
Keywords: Symbiotic organism search, vehicle routing problem, metaheuristics, Solution Representation.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2894
7301 Optimal Multilayer Perceptron Structure For Classification of HIV Sub-Type Viruses
Authors: Zeyneb Kurt, Oguzhan Yavuz
Abstract:The feature of HIV genome is in a wide range because of it is highly heterogeneous. Hence, the infection ability of the virus changes related with different chemokine receptors. From this point, R5 and X4 HIV viruses use CCR5 and CXCR5 coreceptors respectively while R5X4 viruses can utilize both coreceptors. Recently, in Bioinformatics, R5X4 viruses have been studied to classify by using the coreceptors of HIV genome. The aim of this study is to develop the optimal Multilayer Perceptron (MLP) for high classification accuracy of HIV sub-type viruses. To accomplish this purpose, the unit number in hidden layer was incremented one by one, from one to a particular number. The statistical data of R5X4, R5 and X4 viruses was preprocessed by the signal processing methods. Accessible residues of these virus sequences were extracted and modeled by Auto-Regressive Model (AR) due to the dimension of residues is large and different from each other. Finally the pre-processed dataset was used to evolve MLP with various number of hidden units to determine R5X4 viruses. Furthermore, ROC analysis was used to figure out the optimal MLP structure.
Keywords: Multilayer Perceptron, Auto-Regressive Model, HIV, ROC AnalysisProcedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1317
7300 Pathogen Removal Under the Influence of Iron
Authors: Umapriya.R., S.Shrihari
Abstract:Drinking water is one of the most valuable resources available to mankind. The presence of pathogens in drinking water is highly undesirable. Because of the Lateritic soil, the iron concentrations were high in ground water. High concentration of iron and other trace elements could restrict bacterial growth and modify their metabolic pattern as well. The bacterial growth rate reduced in the presence of iron in water. This paper presents the results of a controlled laboratory study conducted to assess the inhibition of micro-organism (pathogen) in well waters in the presence of dissolved iron concentrations. Synthetic samples were studied in the laboratory and the results compared with field samples. Predictive model for microbial inhibition in the presence of iron is presented. It was seen that the bore wells, open wells and the field results varied, probably due to the nature of micro-organism utilizing the iron in well waters.
Keywords: Disinfection, Disinfectant, Iron, Laterite.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1757
7299 SIMGraph: Simplifying Contig Graph to Improve de Novo Genome Assembly Using Next-generation Sequencing Data
Authors: Chien-Ju Li, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu , Darby Tien-Hao Chang
De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.
Keywords: Contig graph, NGS, de novo assembly, scaffold.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1631
7298 Sorting Primitives and Genome Rearrangementin Bioinformatics: A Unified Perspective
Authors: Swapnoneel Roy, Minhazur Rahman, Ashok Kumar Thakur
Abstract:Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and proteinprotein interactions, and the modeling of evolution. Various global rearrangements of permutations, such as reversals and transpositions,have recently become of interest because of their applications in computational molecular biology. A reversal is an operation that reverses the order of a substring of a permutation. A transposition is an operation that swaps two adjacent substrings of a permutation. The problem of determining the smallest number of reversals required to transform a given permutation into the identity permutation is called sorting by reversals. Similar problems can be defined for transpositions and other global rearrangements. In this work we perform a study about some genome rearrangement primitives. We show how a genome is modelled by a permutation, introduce some of the existing primitives and the lower and upper bounds on them. We then provide a comparison of the introduced primitives.
Keywords: Sorting Primitives, Genome Rearrangements, Transpositions, Block Interchanges, Strip Exchanges.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2015
7297 From Primer Generation to Chromosome Identification: A Primer Generation Genotyping Method for Bacterial Identification and Typing
Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari
A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.
Keywords: Bacteria chromosome, bacterial identification, sequence, primer generation.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 919
7296 Effect of Adaptation Gain on system Performance for Model Reference Adaptive Control Scheme using MIT Rule
Authors: Pankaj Swarnkar, Shailendra Jain, R.K Nema
Abstract:Adaptive control involves modifying the control law used by the controller to cope with the fact that the parameters of the system being controlled change drastically due to change in environmental conditions or in system itself. This technique is based on the fundamental characteristic of adaptation of living organism. The adaptive control process is one that continuously and automatically measures the dynamic behavior of plant, compares it with the desired output and uses the difference to vary adjustable system parameters or to generate an actuating signal in such a way so that optimal performance can be maintained regardless of system changes. This paper deals with application of model reference adaptive control scheme in first order system. The rule which is used for this application is MIT rule. This paper also shows the effect of adaptation gain on the system performance. Simulation is done in MATLAB and results are discussed in detail.
Keywords: Adaptive control system, Adaptation gain, MIT rule, Model reference adaptive control.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2039
7295 Error-Robust Nature of Genome Profiling Applied for Clustering of Species Demonstrated by Computer Simulation
Authors: Shamim Ahmed Koichi Nishigaki
Genome profiling (GP), a genotype based technology, which exploits random PCR and temperature gradient gel electrophoresis, has been successful in identification/classification of organisms. In this technology, spiddos (Species identification dots) and PaSS (Pattern similarity score) were employed for measuring the closeness (or distance) between genomes. Based on the closeness (PaSS), we can buildup phylogenetic trees of the organisms. We noticed that the topology of the tree is rather robust against the experimental fluctuation conveyed by spiddos. This fact was confirmed quantitatively in this study by computer-simulation, providing the limit of the reliability of this highly powerful methodology. As a result, we could demonstrate the effectiveness of the GP approach for identification/classification of organisms.
Keywords: Fluctuation, Genome profiling (GP), Pattern similarity score (PaSS), Robustness, Spiddos-shift.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1417
7294 A Simple Epidemiological Model for Typhoid with Saturated Incidence Rate and Treatment Effect
Authors: Steady Mushayabasa
Typhoid fever is a communicable disease, found only in man and occurs due to systemic infection mainly by Salmonella typhi organism. The disease is endemic in many developing countries and remains a substantial public health problem despite recent progress in water and sanitation coverage. Globally, it is estimated that typhoid causes over 16 million cases of illness each year, resulting in over 600,000 deaths. A mathematical model for assessing the impact of educational campaigns on controlling the transmission dynamics of typhoid in the community, has been formulated and analyzed. The reproductive number has been computed. Stability of the model steady-states has been examined. The impact of educational campaigns on controlling the transmission dynamics of typhoid has been discussed through the basic reproductive number and numerical simulations. At its best the study suggests that targeted education campaigns, which are effective at stopping transmission of typhoid more than 40% of the time, will be highly effective at controlling the disease in the community.
Keywords: Mathematical model, Typhoid, saturated incidence rate, treatment, reproductive number, sensitivity analysis.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3342
7293 Application of Whole Genome Amplification Technique for Genotype Analysis of Bovine Embryos
Authors: S. Moghaddaszadeh-Ahrabi, S. Farajnia, Gh. Rahimi-Mianji, A. Nejati-Javaremi
Abstract:In recent years, there has been an increasing interest toward the use of bovine genotyped embryos for commercial embryo transfer programs. Biopsy of a few cells in morulla stage is essential for preimplantation genetic diagnosis (PGD). Low amount of DNA have limited performing the several molecular analyses within PGD analyses. Whole genome amplification (WGA) promises to eliminate this problem. We evaluated the possibility and performance of an improved primer extension preamplification (I-PEP) method with a range of starting bovine genomic DNA from 1-8 cells into the WGA reaction. We optimized a short and simple I-PEP (ssI-PEP) procedure (~3h). This optimized WGA method was assessed by 6 loci specific polymerase chain reactions (PCRs), included restriction fragments length polymorphism (RFLP). Optimized WGA procedure possesses enough sensitivity for molecular genetic analyses through the few input cells. This is a new era for generating characterized bovine embryos in preimplantation stage.
Keywords: Whole genome amplification (WGA), Genotyping, Bovine, Preimplantation genetic diagnosis (PGD)Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1477
7292 Integration of Microarray Data into a Genome-Scale Metabolic Model to Study Flux Distribution after Gene Knockout
Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati
Abstract:Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.
Keywords: Metabolic network, gene knockout, flux balance analysis, microarray data, integration.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 885
7291 A Survey of Model Comparison Strategies and Techniques in Model Driven Engineering
Authors: Junaid Rashid, Waqar Mehmood, Muhammad Wasif Nisar
Abstract:This survey paper shows the recent state of model comparison as it’s applies to Model Driven engineering. In Model Driven Engineering to calculate the difference between the models is a very important and challenging task. There are number of tasks involved in model differencing that firstly starts with identifying and matching the elements of the model. In this paper, we discuss how model matching is accomplished, the strategies, techniques and the types of the model. We also discuss the future direction. We found out that many of the latest model comparison strategies are geared near enabling Meta model and similarity based matching. Therefore model versioning is the most dominant application of the model comparison. Recently to work on comparison for versioning has begun to deteriorate, giving way to different applications. Ultimately there is wide change among the tools in the measure of client exertion needed to perform model comparisons, as some require more push to encourage more sweeping statement and expressive force.
Keywords: Model comparison, model clone detection, model versioning, EMF Model, model diff.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1955
7290 On Reversal and Transposition Medians
Authors: Martin Bader
Abstract:During the last years, the genomes of more and more species have been sequenced, providing data for phylogenetic recon- struction based on genome rearrangement measures. A main task in all phylogenetic reconstruction algorithms is to solve the median of three problem. Although this problem is NP-hard even for the sim- plest distance measures, there are exact algorithms for the breakpoint median and the reversal median that are fast enough for practical use. In this paper, this approach is extended to the transposition median as well as to the weighted reversal and transposition median. Although there is no exact polynomial algorithm known even for the pairwise distances, we will show that it is in most cases possible to solve these problems exactly within reasonable time by using a branch and bound algorithm.
Keywords: Comparative genomics, genome rearrangements, me-dian, reversals, transpositions.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1556
7289 Blood Elements Activation in Hemodialysis – Animal Model Studies
Authors: Karolina Grzeszczuk-Kuć, Jolanta Bujok, Tomasz Walski, Małgorzata Komorowska
Haemodialysis (HD) is a procedure saving patient lives around the world, unfortunately it brings numerous complications. Oxidative stress is one of the major factors which lead to erythrocytes destruction during extracorporeal circulation. Repeated HD procedures destroy blood elements and the organism is not able to keep up with their production. 30 HD procedures on healthy sheep were performed to evaluate effects of such treatment. Oxidative stress study was performed together with an analysis of basic blood parameters and empirical assessment of dialyzer condition after the procedure. A reversible decline in absolute leukocyte count, during first 30 min of HD, was observed. Blood clots were formed in the area of the blood inlet and outlet of the dialyzer. Our results are consistent with outcomes presented throughout the literature specifically with respect to the effects observed in humans and will provide a basis to evaluate methods for blood protection during haemodialysis.
Keywords: Animal model, blood components, haemodialysis, leukocytes, oxidative stress, sheep.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2232
7288 A New Method for Rapid DNA Extraction from Artemia (Branchiopoda, Crustacea)
Authors: R. Manaffar, R. Maleki, S. Zare, N. Agh, S. Soltanian, B. Sehatnia, P. Sorgeloos, P. Bossier, G. Van Stappen
Abstract:Artemia is one of the most conspicuous invertebrates associated with aquaculture. It can be considered as a model organism, offering numerous advantages for comprehensive and multidisciplinary studies using morphologic or molecular methods. Since DNA extraction is an important step of any molecular experiment, a new and a rapid method of DNA extraction from adult Artemia was described in this study. Besides, the efficiency of this technique was compared with two widely used alternative techniques, namely Chelex® 100 resin and SDS-chloroform methods. Data analysis revealed that the new method is the easiest and the most cost effective method among the other methods which allows a quick and efficient extraction of DNA from the adult animal.
Keywords: APD, Artemia, DNA extraction, MolecularexperimentsProcedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3051
7287 Proteins Length and their Phenotypic Potential
Authors: Tom Snir, Eitan Rubin
Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.
Keywords: Systems Biology, Protein LengthProcedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1669
7286 Concurrent Approach to Data Parallel Model using Java
Authors: Bala Dhandayuthapani Veerasamy
Abstract:Parallel programming models exist as an abstraction of hardware and memory architectures. There are several parallel programming models in commonly use; they are shared memory model, thread model, message passing model, data parallel model, hybrid model, Flynn-s models, embarrassingly parallel computations model, pipelined computations model. These models are not specific to a particular type of machine or memory architecture. This paper expresses the model program for concurrent approach to data parallel model through java programming.
Keywords: Concurrent, Data Parallel, JDK, Parallel, ThreadProcedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1798
7285 An Integrated Biotechnology Database of the National Agricultural Information Center in Korea
Authors: Chang Kug Kim, Dong Suk Park, Young Joo Seol, Jang Ho Hahn
Abstract:The National Agricultural Biotechnology Information Center (NABIC) plays a leading role in the biotechnology information database for agricultural plants in Korea. Since 2002, we have concentrated on functional genomics of major crops, building an integrated biotechnology database for agro-biotech information that focuses on bioinformatics of major agricultural resources such as rice, Chinese cabbage, and microorganisms. In the NABIC, integration-based biotechnology database provides useful information through a user-friendly web interface that allows analysis of genome infrastructure, multiple plants, microbial resources, and living modified organisms.
Keywords: biotechnology, database, genome informationProcedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2389
7284 A Generalised Relational Data Model
Authors: Georgia Garani
Abstract:A generalised relational data model is formalised for the representation of data with nested structure of arbitrary depth. A recursive algebra for the proposed model is presented. All the operations are formally defined. The proposed model is proved to be a superset of the conventional relational model (CRM). The functionality and validity of the model is shown by a prototype implementation that has been undertaken in the functional programming language Miranda.
Keywords: nested relations, recursive algebra, recursive nested operations, relational data model.Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1329
7283 Behavior Model Mapping and Transformation using Model-Driven Architecture
Authors: Mohammed Abdalla Osman Mukhtar, Azween Abdullah, Alan Giffin Downe
Model mapping and transformation are important processes in high level system abstractions, and form the cornerstone of model-driven architecture (MDA) techniques. Considerable research in this field has devoted attention to static system abstraction, despite the fact that most systems are dynamic with high frequency changes in behavior. In this paper we provide an overview of work that has been done with regard to behavior model mapping and transformation, based on: (1) the completeness of the platform independent model (PIM); (2) semantics of behavioral models; (3) languages supporting behavior model transformation processes; and (4) an evaluation of model composition to effect the best approach to describing large systems with high complexity.
Keywords: MDA; PIM, PSM, QVT, Model TransformationProcedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1603
7282 Text Retrieval Relevance Feedback Techniques for Bag of Words Model in CBIR
Authors: Nhu Van NGUYEN, Jean-Marc OGIER, Salvatore TABBONE, Alain BOUCHER
Abstract:The state-of-the-art Bag of Words model in Content- Based Image Retrieval has been used for years but the relevance feedback strategies for this model are not fully investigated. Inspired from text retrieval, the Bag of Words model has the ability to use the wealth of knowledge and practices available in text retrieval. We study and experiment the relevance feedback model in text retrieval for adapting it to image retrieval. The experiments show that the techniques from text retrieval give good results for image retrieval and that further improvements is possible.
Keywords: Relevance feedback, bag of words model, probabilistic model, vector space model, image retrievalProcedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1970