Search results for: gene pair ranking.

Authors: Maria E. Manioudaki, Panayiota Poirazi

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Yeast cells live in a constantly changing environment that requires the continuous adaptation of their genomic program in order to sustain their homeostasis, survive and proliferate. Due to the advancement of high throughput technologies, there is currently a large amount of data such as gene expression, gene deletion and protein-protein interactions for S. Cerevisiae under various environmental conditions. Mining these datasets requires efficient computational methods capable of integrating different types of data, identifying inter-relations between different components and inferring functional groups or 'modules' that shape intracellular processes. This study uses computational methods to delineate some of the mechanisms used by yeast cells to respond to environmental changes. The GRAM algorithm is first used to integrate gene expression data and ChIP-chip data in order to find modules of coexpressed and co-regulated genes as well as the transcription factors (TFs) that regulate these modules. Since transcription factors are themselves transcriptionally regulated, a three-layer regulatory cascade consisting of the TF-regulators, the TFs and the regulated modules is subsequently considered. This three-layer cascade is then modeled quantitatively using artificial neural networks (ANNs) where the input layer corresponds to the expression of the up-stream transcription factors (TF-regulators) and the output layer corresponds to the expression of genes within each module. This work shows that (a) the expression of at least 33 genes over time and for different stress conditions is well predicted by the expression of the top layer transcription factors, including cases in which the effect of up-stream regulators is shifted in time and (b) identifies at least 6 novel regulatory interactions that were not previously associated with stress-induced changes in gene expression. These findings suggest that the combination of gene expression and protein-DNA interaction data with artificial neural networks can successfully model biological pathways and capture quantitative dependencies between distant regulators and downstream genes.

Keywords: gene modules, artificial neural networks, yeast, stress

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Authors: Khalid Abd, Kazem Abhary, Romeo Marian

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Multiple criteria decision making (MCDM) is an approach to ranking the solutions and finding the best one when two or more solutions are provided. In this study, MCDM approach is proposed to select the most suitable scheduling rule of robotic flexible assembly cells (RFACs). Two MCDM approaches, Analytic Hierarchy Process (AHP) and Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) are proposed for solving the scheduling rule selection problem. The AHP method is employed to determine the weights of the evaluation criteria, while the TOPSIS method is employed to obtain final ranking order of scheduling rules. Four criteria are used to evaluate the scheduling rules. Also, four scheduling policies of RFAC are examined to choose the most appropriate one for this purpose. A numerical example illustrates applications of the suggested methodology. The results show that the methodology is practical and works in RFAC settings.

Keywords: AHP, TOPSIS, Scheduling rules selection

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Authors: D. Vainauska, S. Kozireva, A. Karpovs, M. Chistyakovs, M. Baryshev

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Liposomal magnetofection is a simple, highly efficient technology for cell transfection, demonstrating better outcome than a number of other common gene delivery methods. However, aggregate complexes distribution over the cell surface is non-uniform due to the gradient of the permanent magnetic field. The aim of this study was to estimate the efficiency of liposomal magnetofection for prostate carcinoma PC3 cell line using newly designed device, “DynaFECTOR", ensuring magnetofection in a dynamic gradient magnetic field. Liposomal magnetofection in a dynamic gradient magnetic field demonstrated the highest transfection efficiency for PC3 cells – it increased for 21% in comparison with liposomal magnetofection and for 42% in comparison with lipofection alone. The optimal incubation time under dynamic magnetic field for PC3 cell line was 5 minutes and the optimal rotation frequency of magnets – 5 rpm. The new approach also revealed lower cytotoxic effect to cells than liposomal magnetofection.

Keywords: Dynamic gradient magnetic field, gene delivery, liposomal magnetofection, prostate cancer cell line

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Authors: Tokuei Sako, Paul-Antoine Hervieux

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The energy-level structure of a pair of electron and positron confined in a quasi-one-dimensional nano-scale potential well has been investigated focusing on its trend in the small limit of confinement strength ω, namely, the Wigner molecular regime. An anisotropic Gaussian-type basis functions supplemented by high angular momentum functions as large as l = 19 has been used to obtain reliable full configuration interaction (FCI) wave functions. The resultant energy spectrum shows a band structure characterized by ω for the large ω regime whereas for the small ω regime it shows an energy-level pattern dominated by excitation into the in-phase motion of the two particles. The observed trend has been rationalized on the basis of the nodal patterns of the FCI wave functions. 

Keywords: Confined systems, positron, wave function, Wigner molecule, quantum dots.

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Authors: Bhaskar M., Venkataramani B.

Abstract:

In the literature, surfing technique has been proposed for single ended wave-pipelined serial interconnects to increase the data transfer rate. In this paper a novel surfing technique is proposed for differential wave-pipelined serial interconnects, which uses a 'Controllable inverter pair' for surfing. To evaluate the efficiency of this technique, a transceiver with transmitter, receiver, delay locked loop (DLL) along with 40mm metal 4 interconnects using the proposed surfing technique is implemented in UMC 180nm technology and their performances are studied through post layout simulations. From the study, it is observed that the proposed scheme permits 1.875 times higher data transmission rate compared to the single ended scheme whose maximum data transfer rate is 1.33 GB/s. The proposed scheme has the ability to receive the correct data even with stuck-at-faults in the complementary line.

Keywords: Controllable inverter pair, differential interconnect, serial link, surfing, wave pipelining.

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Authors: M. Omer Faruk, A. M. A. M. Zonaed Siddiki, M. Fazal Karim, Md. Masuduzzaman, S. Chowdhury, Md. Shafiqul Islam, M. Alamgir Hossain

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The dog tapeworms Echinococcus granulosus develop hydatid cysts in various organs in human and domestic animals worldwide including Bangladesh. The aim of this study was to identify and characterize the genotype of E. granulosus isolated from cattle using 12S rRNA and Cytochrome oxidase 1 (COX 1) genes. A total of 43 hydatid cyst samples were collected from 390 examined cattle samples derived from slaughterhouses. Among them, three cysts were fertile. Genomic DNA was extracted from germinal membrane and/or protoscoleces followed by PCR amplification of mitochondrial 12S rRNA and Cytochrome oxidase 1 gene fragments. The sequence data revealed existence of G1 (64.28%) and possible G3 (21.43%) genotypes for the first time in Bangladesh. The study indicates that common sheep strain G1 is the dominant subtype of E. granulosus in Chittagong region of Bangladesh. This will increase our understanding of the epidemiology of hydatidosis in the southern part of the country and will be useful to plan suitable control measures in the long run.

Keywords: Echinococcus granulosus, molecular characterization, cattle, Bangladesh.

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Authors: Abdulkadir Abu Lawal

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For the dearth of reliable cardinal numerical data, the linked phenomena in productivity indices such as operational costs and company turnovers, etc. could not be investigated. This would not give us insight to the root of productivity problems at unique sites. So, ordinal ranking by professionals who were most directly involved with construction sites was applied for Kendall’s concordance. Responses gathered from independent architects, builders/engineers, and quantity surveyors were herein analyzed. They were responses based on factors that affect sites productivity, and these factors were categorized as head office factors, resource management effectiveness factors, motivational factors, and training/skill development factors. It was found that productivity is low and has to be improved in order to facilitate Nigerian efforts in bridging its infrastructure deficit. The significance of this work is underlined with the Kendall’s coefficient of concordance of 0.78, while remedial measures must be emphasized to stimulate better productivity. Further detailed study can be undertaken by using Fuzzy logic analysis on wider Delphi survey.

Keywords: Factors, Kendall’s coefficient of concordance, magnitude of agreement, percentage magnitude of dichotomy, ranking variables.

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Authors: Ines Hamdi, Mohamed Ben Ahmed

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The understanding of the system level of biological behavior and phenomenon variously needs some elements such as gene sequence, protein structure, gene functions and metabolic pathways. Challenging problems are representing, learning and reasoning about these biochemical reactions, gene and protein structure, genotype and relation between the phenotype, and expression system on those interactions. The goal of our work is to understand the behaviors of the interactions networks and to model their evolution in time and in space. We propose in this study an ontological meta-model for the knowledge representation of the genetic regulatory networks. Ontology in artificial intelligence means the fundamental categories and relations that provide a framework for knowledge models. Domain ontology's are now commonly used to enable heterogeneous information resources, such as knowledge-based systems, to communicate with each other. The interest of our model is to represent the spatial, temporal and spatio-temporal knowledge. We validated our propositions in the genetic regulatory network of the Aarbidosis thaliana flower

Keywords: Ontological model, spatio-temporal modeling, Genetic Regulatory Networks (GRNs), knowledge representation.

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Authors: P.S. Prakash, S. Selvan

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IP networks are evolving from data communication infrastructure into many real-time applications such as video conferencing, IP telephony and require stringent Quality of Service (QoS) requirements. A rudimentary issue in QoS routing is to find a path between a source-destination pair that satisfies two or more endto- end constraints and termed to be NP hard or complete. In this context, we present an algorithm Multi Constraint Path Problem Version 3 (MCPv3), where all constraints are approximated and return a feasible path in much quicker time. We present another algorithm namely Delay Coerced Multi Constrained Routing (DCMCR) where coerce one constraint and approximate the remaining constraints. Our algorithm returns a feasible path, if exists, in polynomial time between a source-destination pair whose first weight satisfied by the first constraint and every other weight is bounded by remaining constraints by a predefined approximation factor (a). We present our experimental results with different topologies and network conditions.

Keywords: Routing, Quality-of-Service (QoS), additive constraints, shortest path, delay coercion.

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Authors: Alexander Kaplunovsky, Vladimir Khailenko, Alexander Bolshoy, Shara Atambayeva, AnatoliyIvashchenko

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Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from the RNA transcripts before translation into a protein. The exon-intron structures of different eukaryotic species are quite different from each other, and the evolution of such structures raises many questions. We try to address some of these questions using statistical analysis of whole genomes. We go through all the protein-coding genes in a genome and study correlations between the net length of all the exons in a gene, the number of the exons, and the average length of an exon. We also take average values of these features for each chromosome and study correlations between those averages on the chromosomal level. Our data show universal features of exon-intron structures common to animals, plants, and protists (specifically, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Cryptococcus neoformans, Homo sapiens, Mus musculus, Oryza sativa, and Plasmodium falciparum). We have verified linear correlation between the number of exons in a gene and the length of a protein coded by the gene, while the protein length increases in proportion to the number of exons. On the other hand, the average length of an exon always decreases with the number of exons. Finally, chromosome clustering based on average chromosome properties and parameters of linear regression between the number of exons in a gene and the net length of those exons demonstrates that these average chromosome properties are genome-specific features.

Keywords: Comparative genomics, exon-intron structure, eukaryotic clustering, linear regression.

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Authors: Sang-Ho Baik

Abstract:

D-erythro-cyclohexylserine (D chiral unnatural β-hydroxy amino acid expected for the synthesis of drug for AIDS treatment. To develop a continuous bioconversion system with whole cell biocatalyst of D-threonine aldolase (D genes for the D-erythro-CHS production, D-threonine aldolase gene was amplified from Ensifer arboris 100383 by direct PCR amplication using two degenerated oligonucleotide primers designed based on genomic sequence of Shinorhizobium meliloti Sequence analysis of the cloned DNA fragment revealed one open-reading frame of 1059 bp and 386 amino acids. This putative D-TA gene was cloned into NdeI and EcoRI (pEnsi His-tag sequence or BamHI (pEnsi-DTA[2]) sequence of the pET21(a) vector. The expression level of the cloned gene was extremely overexpressed by E. coli BL21(DE3) transformed with pEnsi-DTA[1] compared to E. coli BL21(DE3) transformed with pEnsi-DTA[2]. When the cells expressing the wild used for D-TA enzyme activity, 12 mM glycine was successfully detected in HPLC analysis. Moreover, the whole cells harbouring the recombinant D-TA was able to synthesize D-erythro of 0.6 mg/ml in a batch reaction.

Keywords: About four key words or phrases in alphabetical order, separated by commas.

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Authors: C. Ardil

Abstract:

This article presents a new approach to uncertainty, vagueness, and imprecision analysis for ranking alternatives with fuzzy data for decision making using the Technique for Order Preference by Similarity to Ideal Solution (TOPSIS). In the proposed approach, fuzzy decision information related to the aircraft selection problem is taken into account in ranking the alternatives and selecting the best one. The basic procedural step is to transform the fuzzy decision matrices into matrices of alternatives evaluated according to all decision criteria. A numerical example illustrates the proposed approach for the military combat aircraft selection problem.

Keywords: trapezoidal fuzzy numbers, multiple criteria decision making analysis, decision making, aircraft selection, MCDMA, fuzzy TOPSIS

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Authors: Huihai Wu, Xiaohui Liu

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Using Dynamic Bayesian Networks (DBN) to model genetic regulatory networks from gene expression data is one of the major paradigms for inferring the interactions among genes. Averaging a collection of models for predicting network is desired, rather than relying on a single high scoring model. In this paper, two kinds of model searching approaches are compared, which are Greedy hill-climbing Search with Restarts (GSR) and Markov Chain Monte Carlo (MCMC) methods. The GSR is preferred in many papers, but there is no such comparison study about which one is better for DBN models. Different types of experiments have been carried out to try to give a benchmark test to these approaches. Our experimental results demonstrated that on average the MCMC methods outperform the GSR in accuracy of predicted network, and having the comparable performance in time efficiency. By proposing the different variations of MCMC and employing simulated annealing strategy, the MCMC methods become more efficient and stable. Apart from comparisons between these approaches, another objective of this study is to investigate the feasibility of using DBN modeling approaches for inferring gene networks from few snapshots of high dimensional gene profiles. Through synthetic data experiments as well as systematic data experiments, the experimental results revealed how the performances of these approaches can be influenced as the target gene network varies in the network size, data size, as well as system complexity.

Keywords: Genetic regulatory network, Dynamic Bayesian network, GSR, MCMC.

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Authors: Ahmed N. Shmroukh, Ahmed Hamza H. Ali, Ali K. Abel-Rahman

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Adsorption refrigeration working pair is a vital and is the main component in the adsorption refrigeration machine. Therefore the development key is laying on the adsorption pair that leads to the improvement of the adsorption refrigeration machine. In this study the state-of-the-art in the application of the adsorption refrigeration working pairs in both classical and modern adsorption pairs are presented, compared and summarized. It is found that the maximum adsorption capacity for the classical working pairs was 0.259kg/kg for activated carbon/methanol and that for the modern working pairs was 2kg/kg for maxsorb III/R-134a. The study concluded that, the performances of the adsorption working pairs of adsorption cooling systems are still need further investigations as well as developing adsorption pairs having higher sorption capacity with low or no impact on environmental, to build compact, efficient, reliable and long life performance adsorption chillier. Also, future researches need to be focused on designing the adsorption system that provide efficient heating and cooling for the adsorbent materials through distributing the adsorbent material over heat exchanger surface, to allow good heat and mass transfer between the adsorbent and the refrigerant.

Keywords: Adsorption, Adsorbent/Adsorbate Pairs, Refrigeration.

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Authors: A. Molee, N. Duanghaklang, P. Mernkrathoke

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The objective was to determine the single gene and interaction effect of composite genotype of beta-kappa casein and DGAT1 gene on milk yield (MY) and milk composition, content of milk fat (%FAT), milk protein (%PRO), solid not fat (%SNF), and total solid (%TS) in crossbred Holstein cows. Two hundred and thirty- one cows were genotyped with PCR-RFLP for DGAT1 and composite genotype data of beta-kappa casein from previous work were used. Two model, (1), and (2), was used to estimate single gene effect, and interaction effect on the traits, respectively. The significance of interaction effects on all traits were detected. Most traits have consistent pattern of significant when model (1), and (2) were compared, except the effect of composite genotype of betakappa casein on %FAT, and the effect of DGAT1 on MY, which the significant difference was detected in only model (1).The results suggested that when the optimum of all traits was necessary, interaction effect should be concerned.

Keywords: composite genotype of beta-kappa casein, DGAT1gene, Milk composition, Milk yield

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Authors: C. Kridtayopas, W. Danvilai, P. Sopannarath, A. Kayan, W. Loongyai

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Both Betong chicken (KU Line) and Thai Native chickens were the high quality of the meat and low carcass fat compared to broiler chickens. The objective of this study was to determine the growth performance, carcass characteristic, meat quality and association of polymorphism in the ApoVLDL-II gene with fat accumulation in the female broiler, Thai Native and Betong (KU line) chickens at 4-14 weeks. The chickens were used and reared under the same environment and management (100 chicks per breed). The results showed that body weight (BW) of broiler chickens was significantly higher than Thai Native and Betong (KU line) chickens (P < 0.01) through all the experiment. At 4-8 weeks of age, feed conversion ratio (FCR) of broiler chickens was significantly better than Thai Native and Betong (KU line) chickens (P < 0.01), then increased at week 8-14. The percentage of breast, abdominal fat and subcutaneous fat of broiler chickens was significantly greater than Thai Native and Betong (KU line) chickens (P < 0.01). However, Thai Native chickens showed the highest percentage of liver (P < 0.01) when compared to other breeds. In addition, the percentage of wing of Thai Native and Betong (KU line) chickens were significantly (P < 0.01) higher than broiler chickens. Meat quality was also determined and found that, pH of breast meat left from slaughter 45 minutes (pH45) and 24 hours (pH24) of broiler was significantly higher than Thai Native and Betong (KU line) (P < 0.01) whereas the percentage of drip loss, thawing loss, cooking loss and shear force was not significantly different between breeds. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was used to genotype the polymorphism in the ApoVLDL-II gene in the broiler, Thai Native and Betong (KU line) chickens. The results found that, the polymorphism in the ApoVLDL-II gene at VLDL6 loci was not associated with fat accumulation in those studied population.

Keywords: ApoVLDL-II Gene, Betong (KU line) chickens, broiler chickens, carcass characteristic, growth performance, meat quality, Thai Native Chickens.

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Authors: Ekaterina Y. Lukianova-Hleb, Dmitri O. Lapotko

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Cell processing techniques for gene and cell therapies use several separate procedures for gene transfer and cell separation or elimination, because no current technology can offer simultaneous multi-functional processing of specific cell sub-sets in heterogeneous cell systems. Using our novel on-demand nonstationary intracellular events instead of permanent materials, plasmonic nanobubbles, generated with a short laser pulse only in target cells, we achieved simultaneous multifunctional cell-specific processing with the rate up to 50 million cells per minute.

Keywords: Delivery, cell separation, graft, laser, plasmonic nanobubble, cell therapy, gold nanoparticle.

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Authors: C. Ardil

Abstract:

Using the aid of Hausdorff distance function and Minkowski distance function, this study proposes a novel method for selecting combat aircraft for Air Force. In order to do this, the proximity measure method was developed with determinate fuzzy degrees based on the relationship between attributes and combat aircraft alternatives. The combat aircraft selection attributes were identified as payloadability, maneuverability, speedability, stealthability, and survivability. Determinate fuzzy data from the combat aircraft attributes was then aggregated using the determinate fuzzy weighted arithmetic average operator. For the selection of combat aircraft, correlation analysis of the ranking order patterns of options was also examined. A numerical example from military aviation is used to demonstrate the applicability and effectiveness of the proposed method.

Keywords: Combat aircraft selection, multiple criteria decision making, fuzzy sets, determinate fuzzy sets, intuitionistic fuzzy sets, proximity measure method, Hausdorff distance function, Minkowski distance function, PMM, MCDM

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Authors: Atnaf Tiruneh Mulugeta, Mohammed Ali Hussein, Zelleke Habtamu

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Thirty six genotypes (8 parents and 28 F1 diallel crosses) were grown in randomized complete block design during 2006 at Mandura, North western Ethiopia. The experiment was executed to study the inheritance of two primary yield component traits: number of seeds per pod and 1000 seed weight. Statistical significant difference was observed between genotypes, parents, and crosses for these traits. The mean square due to GCA was significant for the two traits. However, SCA mean square was significant only for number of seeds per pod. Thus both additive and non-additive types of gene actions were important in the inheritance of number of seeds per pod. Significant b1 component was obtained for this trait. The b2 and b3 components, however, were not significant, suggesting the absence of gene asymmetry. From Wr/Vr graph, inheritance of seeds per pod was governed by partial dominance with additive gene action.

Keywords: Diallel crosses, General combining ability, Phaseolus vulgaris L., Specific combining ability

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Authors: R. Majidzadeh Heravi, M. Sankian, H. Kermanshahi, M. R. Nassiri, A. Heravi Moussavi, S. A. Lari, A. R. Varasteh

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The use of probiotics engineered to express specific enzymes has been the subject of considerable attention in poultry industry because of increased nutrient availability and reduced cost of enzyme supplementation. Phytase enzyme is commonly added to poultry feed to improve digestibility and availability of phosphorus from plant sources. To construct a probiotic with potential of phytate degradation, phytase gene (appA) from E. coli was cloned and transformed into two probiotic bacteria Lactobacillus salivarius and Lactococcus lactis. L. salivarous showed plasmid instability, unable to express the gene. The expression of appA gene in L. lactis was analyzed by detecting specific RNA and zymography assay. Phytase enzyme was isolated from cellular extracts of recombinant L. lactis, showing a 46 kDa band upon the SDS-PAGE analysis. Zymogram also confirmed the phytase activity of the 46 kDa band corresponding to the enzyme. An enzyme activity of 4.9U/ml was obtained in cell extracts of L. lactis. The growth of native and recombinant L. lactis was similar in the presence of two concentrations of ox bile.

Keywords: Lactobacillus salivarus, Lactococcus lactis, recombinant, phytase, poultry.

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

Abstract:

Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence, and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, Brassinosteroids, Phylogenetic analysis, Transcription factor.

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Authors: RajPal Garg, Kapil Sharma, Rajive Kumar, R. K. Garg

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This paper presents a computational methodology based on matrix operations for a computer based solution to the problem of performance analysis of software reliability models (SRMs). A set of seven comparison criteria have been formulated to rank various non-homogenous Poisson process software reliability models proposed during the past 30 years to estimate software reliability measures such as the number of remaining faults, software failure rate, and software reliability. Selection of optimal SRM for use in a particular case has been an area of interest for researchers in the field of software reliability. Tools and techniques for software reliability model selection found in the literature cannot be used with high level of confidence as they use a limited number of model selection criteria. A real data set of middle size software project from published papers has been used for demonstration of matrix method. The result of this study will be a ranking of SRMs based on the Permanent value of the criteria matrix formed for each model based on the comparison criteria. The software reliability model with highest value of the Permanent is ranked at number – 1 and so on.

Keywords: Matrix method, Model ranking, Model selection, Model selection criteria, Software reliability models.

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Authors: Zullina H. Shaari, Amzairi Amar, Abdul Mutalib Embong, Hezlina Hashim

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University websites are considered as one of the brand primary touch points for multiple stakeholders, but most of them did not have great designs to create favorable impressions. Some of the elements that web designers should carefully consider are the appearance, the content, the functionality, usability and search engine optimization. However, priority should be placed on website simplicity and negative space. In terms of content, previous research suggests that universities should include reputation, learning environment, graduate career prospects, image destination, cultural integration, and virtual tour on their websites. The study examines how top 200 world ranking science and technology-based universities present their brands online and whether the websites capture the content dimensions. Content analysis of the websites revealed that the top ranking universities captured these dimensions at varying degree. Besides, the UK-based university had better priority on website simplicity and negative space compared to the Malaysian-based university.

Keywords: Science and technology programs, top-ranked universities, online brands, university websites.

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Authors: C. Ardil

Abstract:

Multiplicative multiple criteria decision making analysis (MCDMA) method is a systematic decision support system to aid decision makers reach appropriate decisions. The application of multiplicative MCDMA in the military aircraft selection problem is significant for proper decision making process, which is the decisive factor in minimizing expenditures and increasing defense capability and capacity. Nine military fighter aircraft alternatives were evaluated by ten decision criteria to solve the decision making problem. In this study, multiplicative MCDMA model aims to evaluate and select an appropriate military fighter aircraft for the Air Force fleet planning. The ranking results of multiplicative MCDMA model were compared with the ranking results of additive MCDMA, logarithmic MCDMA, and regrettive MCDMA models under the L₂ norm data normalization technique to substantiate the robustness of the proposed method. The final ranking results indicate the military fighter aircraft Su-57 as the best available solution.

Keywords: Aircraft Selection, Military Fighter Aircraft Selection, Air Force Fleet Planning, Multiplicative MCDMA, Additive MCDMA, Logarithmic MCDMA, Regrettive MCDMA, Mean Weight, Multiple Criteria Decision Making Analysis, Sensitivity Analysis

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Authors: Dana Gabriková, Martin Mistrík, Jarmila Bernasovská, Iveta Tóthová, Jana Kisková

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The Roma (Gypsies) is a transnational minority with a high degree of consanguineous marriages. Similar to other genetically isolated founder populations, the Roma harbor a number of unique or rare genetic disorders. This paper discusses about a rare form of Charcot-Marie-Tooth disease – type 4G (CMT4G), also called Hereditary Motor and Sensory Neuropathy type Russe, an autosomal recessive disease caused by mutation private to Roma characterized by abnormally increased density of non-myelinated axons. CMT4G was originally found in Bulgarian Roma and in 2009 two putative causative mutations in the HK1 gene were identified. Since then, several cases were reported in Roma families mainly from Bulgaria and Spain. Here we present a Slovak Roma family in which CMT4G was diagnosed on the basis of clinical examination and genetic testing. This case is a further proof of the role of the HK1 gene in pathogenesis of the disease. It confirms that mutation in the HK1 gene is a common cause of autosomal recessive CMT disease in Roma and should be considered as a common part of a diagnostic procedure.

Keywords: Gypsies, HK1, HSMN-Russe, rare disease.

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Authors: Wiriya Loongyai, Kiettisak Promphet, Nilubol Kangsukul, Ratchawat Noppha

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Polymerase chain reaction (PCR) assay and conventional microbiological methods were used to detect bacterial contamination of egg shells and egg content in different commercial housing systems, open house system and evaporative cooling system. A PCR assay was developed for direct detection using a set of primers specific for the invasion by A gene (invA) of Salmonella spp. PCR detected the presence of Salmonella in 2 samples of shell egg from the evaporative cooling system, while conventional cultural methods detected no Salmonella from the same samples.

Keywords: egg content, egg shell, invA gene, PCR, Salmonellaspp.

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Authors: Imen Dhaou

Abstract:

This study examines conditional Value at Risk by applying the GJR-EVT-Copula model, and finds the optimal portfolio for eight Dow Jones Islamic-conventional pairs. Our methodology consists of modeling the data by a bivariate GJR-GARCH model in which we extract the filtered residuals and then apply the Peak over threshold model (POT) to fit the residual tails in order to model marginal distributions. After that, we use pair-copula to find the optimal portfolio risk dependence structure. Finally, with Monte Carlo simulations, we estimate the Value at Risk (VaR) and the conditional Value at Risk (CVaR). The empirical results show the VaR and CVaR values for an equally weighted portfolio of Dow Jones Islamic-conventional pairs. In sum, we found that the optimal investment focuses on Islamic-conventional US Market index pairs because of high investment proportion; however, all other index pairs have low investment proportion. These results deliver some real repercussions for portfolio managers and policymakers concerning to optimal asset allocations, portfolio risk management and the diversification advantages of these markets.

Keywords: CVaR, Dow Jones Islamic index, GJR-GARCH-EVT-pair copula, portfolio optimization.

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Authors: Archana Panchapakesan Iyer, Taha Abdullah Kumosani

Abstract:

Many high-risk pathogens that cause disease in humans are transmitted through various food items. Food-borne disease constitutes a major public health problem. Assessment of the quality and safety of foods is important in human health. Rapid and easy detection of pathogenic organisms will facilitate precautionary measures to maintain healthy food. The Polymerase Chain Reaction (PCR) is a handy tool for rapid detection of low numbers of bacteria. We have designed gene specific primers for most common food borne pathogens such as Staphylococci, Salmonella and E.coli. Bacteria were isolated from food samples of various food outlets and identified using gene specific PCRs. We identified Staphylococci, Salmonella and E.coli O157 using gene specific primers by rapid and direct PCR technique in various food samples. This study helps us in getting a complete picture of the various pathogens that threaten to cause and spread food borne diseases and it would also enable establishment of a routine procedure and methodology for rapid identification of food borne bacteria using the rapid technique of direct PCR. This study will also enable us to judge the efficiency of present food safety steps taken by food manufacturers and exporters.

Keywords: food borne pathogens, PCR, food safety, rapiddetection.

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Authors: Hao He, Shaoqian Li

Abstract:

In this paper, we study the cooperative communications where multiple cognitive radio (CR) transmit-receive pairs competitive maximize their own throughputs. In CR networks, the influences of primary users and the spectrum availability are usually different among CR users. Due to the existence of multiple relay nodes and the different spectrum availability, each CR transmit-receive pair should not only select the relay node but also choose the appropriate channel. For this distributed problem, we propose a game theoretic framework to formulate this problem and we apply a regret-matching learning algorithm which is leading to correlated equilibrium. We further formulate a modified regret-matching learning algorithm which is fully distributed and only use the local information of each CR transmit-receive pair. This modified algorithm is more practical and suitable for the cooperative communications in CR network. Simulation results show the algorithm convergence and the modified learning algorithm can achieve comparable performance to the original regretmatching learning algorithm.

Keywords: cognitive radio, cooperative communication, relay selection, channel choice, regret-matching learning, correlated equilibrium.

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Authors: Fabian Horn, Reinhard Guthke

Abstract:

In molecular biology, microarray technology is widely and successfully utilized to efficiently measure gene activity. If working with less studied organisms, methods to design custom-made microarray probes are available. One design criterion is to select probes with minimal melting temperature variances thus ensuring similar hybridization properties. If the microarray application focuses on the investigation of metabolic pathways, it is not necessary to cover the whole genome. It is more efficient to cover each metabolic pathway with a limited number of genes. Firstly, an approach is presented which minimizes the overall melting temperature variance of selected probes for all genes of interest. Secondly, the approach is extended to include the additional constraints of covering all pathways with a limited number of genes while minimizing the overall variance. The new optimization problem is solved by a bottom-up programming approach which reduces the complexity to make it computationally feasible. The new method is exemplary applied for the selection of microarray probes in order to cover all fungal secondary metabolite gene clusters for Aspergillus terreus.

Keywords: bottom-up approach, gene clusters, melting temperature, metabolic pathway, microarray probe design, probe selection

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