Search results for: gene modules

Authors: Assyl Bari, Olga Berillo, Saltanat Orazova, Anatoliy Ivashchenko

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Among all microRNAs (miRNAs) in 12 plant species investigated in this study, only miR398 targeted the copper chaperone for superoxide dismutase (CCS). The nucleotide sequences of miRNA binding sites were located in the mRNA protein-coding sequence (CDS) and were highly homologous. These binding sites in CCS mRNA encoded a conservative GDLGTL hexapeptide. The binding sites for miR398 in the CDS of superoxide dismutase 1 mRNA encoded GDLGN pentapeptide. The conservative miR398 binding site located in the CDS of superoxide dismutase 2 mRNA encoded the GDLGNI hexapeptide. The miR398 binding site in the CDS of superoxide dismutase 3 mRNA encoded the GDLGNI or GDLGNV hexapeptide. Gene expression of the entire superoxide dismutase family in the studied plant species was regulated only by miR398. All members of the miR398 family, i.e. miR398a,b,c were connected to one site for each CuZnSOD and chaperone mRNA.

Keywords: MicroRNA, mRNA, plant, superoxide dismutase.

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Authors: T. Costa, D. Narvaez, K. Melo, M. Villalva

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Installation of micro-generators based on renewable energy in power distribution system has increased in recent years, with the main renewable sources being solar and wind. Due to the intermittent nature of renewable energy sources, such micro-generators produce time-varying energy which does not correspond at certain times of the day to the peak energy consumption of end users. For this reason, the use of energy storage units next to the grid contributes to the proper leveling of the buses’ voltage level according to Brazilian energy quality standards. In this work, the effect of the addition of a photovoltaic solar generator and a store of energy in the busbar voltages of an electric system is analyzed. The consumption profile is defined as the average hourly use of appliances in a common residence, and the generation profile is defined as a function of the solar irradiation available in a locality. The power summation method is validated with analytical calculation and is used to calculate the modules and angles of the voltages in the buses of an electrical system based on the IEEE standard, at each hour of the day and with defined load and generation profiles. The results show that bus 5 presents the worst voltage level at the power consumption peaks and stabilizes at the appropriate range with the inclusion of the energy storage during the night time period. Solar generator maintains improvement of the voltage level during the period when it receives solar irradiation, having peaks of production during the 12 pm (without exceeding the appropriate maximum levels of tension).

Keywords: Energy storage, power distribution system, solar generator, voltage level.

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Authors: Hock Chuan, Lim

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This paper presents an approach for identifying interactive effects using Network Science (NS) supported by Social Network Analysis (SNA) techniques. Based on general observations that learning processes and behaviors are shaped by the social relationships and influenced by learning environment, the central idea was to understand both the human and non-human interactive effects for a blended learning mode of delivery of computer science modules. Important findings include (a) the importance of non-human nodes to influence the centrality and transfer; (b) the degree of non-human and human connectivity impacts learning. This project reveals that the NS pattern and connectivity as measured by node relationships offer alternative approach for hypothesis generation and design of qualitative data collection. An iterative process further reinforces the analysis, whereas the experimental simulation option itself is an interesting alternative option, a hybrid combination of both experimental simulation and qualitative data collection presents itself as a promising and viable means to study complex scenario such as blended learning delivery mode. The primary value of this paper lies in the design of the approach for studying interactive effects of human (social nodes) and non-human (learning/study environment, Information and Communication Technologies (ICT) infrastructures nodes) components. In conclusion, this project adds to the understanding and the use of SNA to model and study interactive effects in blended social learning.

Keywords: Blended learning, network science, social learning, social network analysis, study environment.

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Authors: Chao-Linag Hsieh, Zheng-Wei Ye, Chen-Kang Huang, Yeun-Chung Lee, Chih-Hong Sun, Tzai-Hung Wen, Jehn-Yih Juang, Joe-Air Jiang

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Air pollution and climate warming become more and more intensified in many areas, especially in urban areas. Environmental parameters are critical information to air pollution and weather monitoring. Thus, it is necessary to develop a suitable air pollution and weather monitoring system for urban areas. In this study, a vehicle monitoring system (VMS) based on the IoT technique is developed. Cars are selected as the research tool because it can reach a greater number of streets to collect data. The VMS can monitor different environmental parameters, including ambient temperature and humidity, and air quality parameters, including PM2.5, NO₂, CO, and O₃. The VMS can provide other information, including GPS signals and the vibration information through driving a car on the street. Different sensor modules are used to measure the parameters and collect the measured data and transmit them to a cloud server through the LoRa protocol. A user interface is used to show the sensing data storing at the cloud server. To examine the performance of the system, a researcher drove a Nissan x-trail 1998 to the area close to the Da’an District office in Taipei to collect monitoring data. The collected data are instantly shown on the user interface. The four kinds of information are provided by the interface: GPS positions, weather parameters, vehicle information, and air quality information. With the VMS, users can obtain the information regarding air quality and weather conditions when they drive their car to an urban area. Also, government agencies can make decisions on traffic planning based on the information provided by the proposed VMS.

Keywords: Vehicle, monitoring system, LoRa, smart city.

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Authors: Ali Anaissi, Paul J. Kennedy, Madhu Goyal

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Analysis and visualization of microarraydata is veryassistantfor biologists and clinicians in the field of diagnosis and treatment of patients. It allows Clinicians to better understand the structure of microarray and facilitates understanding gene expression in cells. However, microarray dataset is a complex data set and has thousands of features and a very small number of observations. This very high dimensional data set often contains some noise, non-useful information and a small number of relevant features for disease or genotype. This paper proposes a non-linear dimensionality reduction algorithm Local Principal Component (LPC) which aims to maps high dimensional data to a lower dimensional space. The reduced data represents the most important variables underlying the original data. Experimental results and comparisons are presented to show the quality of the proposed algorithm. Moreover, experiments also show how this algorithm reduces high dimensional data whilst preserving the neighbourhoods of the points in the low dimensional space as in the high dimensional space.

Keywords: Linear Dimension Reduction, Non-Linear Dimension Reduction, Principal Component Analysis, Biologists.

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Authors: Henrik L. Funke, Lars Ulke-Winter, Sandra Gelbrich, Lothar Kroll

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This work reports about an approach for an automatic adaptation of concrete formulations based on genetic algorithms (GA) to optimize a wide range of different fit-functions. In order to achieve the goal, a method was developed which provides a numerical description of a fibre reinforced concrete (FRC) mixture regarding the production technology and the property spectrum of the concrete. In a first step, the FRC mixture with seven fixed components was characterized by varying amounts of the components. For that purpose, ten concrete mixtures were prepared and tested. The testing procedure comprised flow spread, compressive and bending tensile strength. The analysis and approximation of the determined data was carried out by GAs. The aim was to obtain a closed mathematical expression which best describes the given seven-point cloud of FRC by applying a Gene Expression Programming with Free Coefficients (GEP-FC) strategy. The seven-parametric FRC-mixtures model which is generated according to this method correlated well with the measured data. The developed procedure can be used for concrete mixtures finding closed mathematical expressions, which are based on the measured data.

Keywords: Concrete design, fibre reinforced concrete, genetic algorithms, GEP-FC.

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Authors: Chia-Chi Chang, Chuan-Bi Lin, Chia-Min Chan

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Most ZigBee sensor networks to date make use of nodes with limited processing, communication, and energy capabilities. Energy consumption is of great importance in wireless sensor applications as their nodes are commonly battery-driven. Once ZigBee nodes are deployed outdoors, limited power may make a sensor network useless before its purpose is complete. At present, there are two strategies for long node and network lifetime. The first strategy is saving energy as much as possible. The energy consumption will be minimized through switching the node from active mode to sleep mode and routing protocol with ultra-low energy consumption. The second strategy is to evaluate the energy consumption of sensor applications as accurately as possible. Erroneous energy model may render a ZigBee sensor network useless before changing batteries.

In this paper, we present a ZigBee wireless sensor node with four key modules: a processing and radio unit, an energy harvesting unit, an energy storage unit, and a sensor unit. The processing unit uses CC2530 for controlling the sensor, carrying out routing protocol, and performing wireless communication with other nodes. The harvesting unit uses a 2W solar panel to provide lasting energy for the node. The storage unit consists of a rechargeable 1200 mAh Li-ion battery and a battery charger using a constant-current/constant-voltage algorithm. Our solution to extend node lifetime is implemented. Finally, a long-term sensor network test is used to exhibit the functionality of the solar powered system.

Keywords: ZigBee, Li-ion battery, solar panel, CC2530.

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Authors: Delly C. Lestari, Linosefa, Ardiana Kusumaningrum, Andi Yasmon, Anis Karuniawati

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The objective of this study is to determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) harboring mecA genes from screening isolates among intensive care unit (ICU) patients. All MRSA screening isolates from ICU’s patients of Cipto Mangunkusumo Hospital during 2011 and 2014 were included in this study. Identification and susceptibility test was performed using Vitek2 system (Biomereux®). PCR was conducted to characterize the SCCmec of S. aureus harboring the mecA gene on each isolate. Patient’s history of illness was traced through medical record. 24 isolates from 327 screening isolates were MRSA positive (7.3%). From PCR, we found 17 (70.8%) isolates carrying SCCmec type I, 3 (12.5%) isolates carrying SCCmec type III, and 2 (8.3%) isolates carrying SCCmec type IV. In conclusion, SCCmec type I is the most prevalent MRSA colonization among ICU patients in Cipto Mangunkusumo Hospital.

Keywords: MRSA, mecA genes, ICU, colonization.

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Authors: Cheng-Hong Yang, Yu-Huei Cheng, Hsueh-Wei Chang, Li-Yeh Chuang

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Before performing polymerase chain reactions (PCR), a feasible primer set is required. Many primer design methods have been proposed for design a feasible primer set. However, the majority of these methods require a relatively long time to obtain an optimal solution since large quantities of template DNA need to be analyzed. Furthermore, the designed primer sets usually do not provide a specific PCR product. In recent years, evolutionary computation has been applied to PCR primer design and yielded promising results. In this paper, a particle swarm optimization (PSO) algorithm is proposed to solve primer design problems associated with providing a specific product for PCR experiments. A test set of the gene CYP1A1, associated with a heightened lung cancer risk was analyzed and the comparison of accuracy and running time with the genetic algorithm (GA) and memetic algorithm (MA) was performed. A comparison of results indicated that the proposed PSO method for primer design finds optimal or near-optimal primer sets and effective PCR products in a relatively short time.

Keywords: polymerase chain reaction (PCR), primer design, evolutionary computation, particle swarm optimization (PSO).

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Authors: Chien-Hung Huang, Chia-Wei Weng, Chang-Chih Chiang, Shih-Hua Wu, Chih-Hsien Huang, Ka-Lok Ng

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MicroRNAs (miRNAs) are a class of non-coding RNAs that hybridize to mRNAs and induce either translation repression or mRNA cleavage. Recently, it has been reported that miRNAs could possibly play an important role in human diseases. By integrating miRNA target genes, cancer genes, miRNA and mRNA expression profiles information, a database is developed to link miRNAs to cancer target genes. The database provides experimentally verified human miRNA target genes information, including oncogenes and tumor suppressor genes. In addition, fragile sites information for miRNAs, and the strength of the correlation of miRNA and its target mRNA expression level for nine tissue types are computed, which serve as an indicator for suggesting miRNAs could play a role in human cancer. The database is freely accessible at http://ppi.bioinfo.asia.edu.tw/mirna_target/index.html.

Keywords: MicroRNA, miRNA expression profile, mRNAexpression profile, cancer genes, oncogene, tumor suppressor gene

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Authors: Hanina M. N., Hairul Shahril M., Ismatul Nurul Asyikin I., Abdul Jalil A. K., Salina M. R., Maryam M. R., Rosfarizan M.

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The extracellular proteins secreted by bacteria may be increased in stressful surroundings, such as in the presence of antibiotics. It appears that many antibiotics, when used at low concentrations, have in common the ability to activate or repress gene transcription, which is distinct from their inhibitory effect. There have been comparatively few studies on the potential of antibiotics as a specific chemical signal that can trigger a variety of biological functions. Therefore, this study was carried out to determine the effect of Streptomycin Sulfate in regulating extracellular proteins secreted by Bacillus subtilis ATCC21332. Results of Microdilution assay showed that the Minimum Inhibition Concentration (MIC) of Streptomycin Sulfate on B. subtilis ATCC21332 was 2.5 mg/ml. The bacteria cells were then exposed to Streptomycin Sulfate at concentration of 0.01 MIC before being further incubated for 48h to 72 h. The extracellular proteins secreted were then isolated and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Proteins profile revealed that three additional bands with approximate sizes of 30 kDa, 22 kDa and 23 kDa were appeared for the treated bacteria with Streptomycin Sulfate. Thus, B. subtilis ATCC21332 in stressful condition with the presence of Streptomycin Sulfate at low concentration could induce the extracellular proteins secretion.

Keywords: Bacillus subtilis ATCC21332, Streptomycin Sulfate, extracellular proteins.

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Authors: Jafar Ahmadi, Alireza Pour-Aboughadareh

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Wheat is the first and the most important grain of the world and its bakery property is due to glutenin and gliadin qualities. Wheat seed proteins were divided into four groups according to solubility including albumin, globulin, glutenin and prolamin or gliadin. Gliadins are major components of the storage proteins in wheat endosperm. It seems that little information is available about gliadin genes in Iranian wild relatives of wheat. Thus, the aim of this study was the evaluation of the wheat wild relatives collected from different origins of Zagros Mountains in Iran, in terms of coding gliadin genes using specific primers. For this, forty accessions of Triticum boeoticum and Triticum urartu were selected for this study. For each accession, genomic DNA was extracted and PCRs were performed in total volumes of 15 μl. The amplification products were separated on 1.5% agarose gels. In results, for Gli-2A locus three allelic variants were detected by Gli-2As primer pairs. The sizes of PCR products for these alleles were 210, 490 and 700 bp. Only five (13%) and two accessions (5%) produced 700 and 490 bp fragments when their DNA was amplified with the Gli.As.2 primer pairs. However, 93% of the accessions carried allele 210 bp, and only 8% did not any product for this marker. Therefore, these germplasm could be used as rich gene pool to broaden the genetic base of bread wheat.

Keywords: Diploied wheat, gliadin, Triticum boeoticum, Triticum urartu.

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Authors: Fabio Fabris, Alex A. Freitas

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Hierarchical classification is a special type of classification task where the class labels are organised into a hierarchy, with more generic class labels being ancestors of more specific ones. Meta-learning for classification-algorithm recommendation consists of recommending to the user a classification algorithm, from a pool of candidate algorithms, for a dataset, based on the past performance of the candidate algorithms in other datasets. Meta-learning is normally used in conventional, non-hierarchical classification. By contrast, this paper proposes a meta-learning approach for more challenging task of hierarchical classification, and evaluates it in a large number of bioinformatics datasets. Hierarchical classification is especially relevant for bioinformatics problems, as protein and gene functions tend to be organised into a hierarchy of class labels. This work proposes meta-learning approach for recommending the best hierarchical classification algorithm to a hierarchical classification dataset. This work’s contributions are: 1) proposing an algorithm for splitting hierarchical datasets into new datasets to increase the number of meta-instances, 2) proposing meta-features for hierarchical classification, and 3) interpreting decision-tree meta-models for hierarchical classification algorithm recommendation.

Keywords: Algorithm recommendation, meta-learning, bioinformatics, hierarchical classification.

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Authors: Patsaraporn Somboonsak, Mud-Armeen Munlin

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In April 2009, a new variant of Influenza A virus subtype H1N1 emerged in Mexico and spread all over the world. The influenza has three subtypes in human (H1N1, H1N2 and H3N2) Types B and C influenza tend to be associated with local or regional epidemics. Preliminary genetic characterization of the influenza viruses has identified them as swine influenza A (H1N1) viruses. Nucleotide sequence analysis of the Haemagglutinin (HA) and Neuraminidase (NA) are similar to each other and the majority of their genes of swine influenza viruses, two genes coding for the neuraminidase (NA) and matrix (M) proteins are similar to corresponding genes of swine influenza. Sequence similarity between the 2009 A (H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Nucleic acid sequence Maximum Likelihood (MCL) and DNA Empirical base frequencies, Phylogenetic relationship amongst the HA genes of H1N1 virus isolated in Genbank having high nucleotide sequence homology. In this paper we used 16 HA nucleotide sequences from NCBI for computing sequence relationships similarity of swine influenza A virus using the following method MCL the result is 28%, 36.64% for Optimal tree with the sum of branch length, 35.62% for Interior branch phylogeny Neighber – Join Tree, 1.85% for the overall transition/transversion, and 8.28% for Overall mean distance.

Keywords: Sequence DNA, Relationship of swine, Swineinfluenza, Sequence Similarity

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Authors: N. Tsvetkova, R. Harizanov A. Ivanova, I. Rainova, N. Yancheva-Petrova, D. Strashimirov, R. Enikova, M. Videnova, E. Kaneva, I. Kaftandjiev, V. Levterova, I. Simeonovski, N. Yanev, G. Hinkov

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The Pneumocystis jirovecii (P. jirovecii) and protozoan of the genera Acanthamoeba, Cryptosporidium, and Toxoplasma gondii are opportunistic pathogens that can cause life-threatening infections in immunocompromised patients. Aim of the study was to evaluate the coinfection rate with opportunistic protozoal agents among Bulgarian patients diagnosed with P. jirovecii pneumonia. 38 pulmonary samples were collected from 38 patients (28 HIV-infected) with P. jirovecii infection. P. jirovecii DNA was detected by real-time PCR targeting the large mitochondrial subunit ribosomal RNA gene. Acanthamoeba was determined by genus-specific conventional PCR assay. Real-time PCR for the detection of a Toxoplasma gondii and Cryptosporidium DNA fragment was used. Pneumocystis DNA was detected in all 38 specimens; 28 (73.7%) were from HIV-infected patients. Three (10,7%) of them were coinfected with T. gondii and 1 (3.6%) with Cryptosporidium. In the group of non-HIV-infected (n = 10), Cryptosporidium DNA was detected in an infant (10%). Acanthamoeba DNA was not found in the tested samples. The current study showed a relatively low rate of coinfections of Cryptosporidium spp./T. gondii and P. jirovecii in the Bulgarian patients studied.

Keywords: Coinfection, opportunistic protozoal agents, Pneumocystis jirovecii, pulmonary infections.

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Authors: Guyue Zhu, Liangping Hong

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Chinese overall urban design faces a large number of problems such as the neglect of urban characteristics, generalization of content, and difficulty in implementation. Focusing on these issues, this paper proposes the main points of shaping urban characteristics in overall urban design: focuses on core problems in city function and scale, landscape pattern, historical culture, social resources and modern city style and digs the urban characteristic genes. Then, we put forward “core problem location and characteristic gene enhancement” as a kind of overall urban design technical method. Firstly, based on the main problems in urban space as a whole, for the operability goal, the method extracts the key genes and integrates into the multi-dimension system in a targeted manner. Secondly, hierarchical management and guidance system is established which may be in line with administrative management. Finally, by converting the results, action plan is drawn up that can be dynamically implemented. Based on the above idea and method, a practical exploration has been performed in the case of Xiangyang central city.

Keywords: City characteristics, overall urban design, planning implementation, Xiangyang central city.

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Authors: Billel Kenidra, Mohamed Benmohammed

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Data mining technique used in the field of clustering is a subject of active research and assists in biological pattern recognition and extraction of new knowledge from raw data. Clustering means the act of partitioning an unlabeled dataset into groups of similar objects. Each group, called a cluster, consists of objects that are similar between themselves and dissimilar to objects of other groups. Several clustering methods are based on partitional clustering. This category attempts to directly decompose the dataset into a set of disjoint clusters leading to an integer number of clusters that optimizes a given criterion function. The criterion function may emphasize a local or a global structure of the data, and its optimization is an iterative relocation procedure. The K-Means algorithm is one of the most widely used partitional clustering techniques. Since K-Means is extremely sensitive to the initial choice of centers and a poor choice of centers may lead to a local optimum that is quite inferior to the global optimum, we propose a strategy to initiate K-Means centers. The improved K-Means algorithm is compared with the original K-Means, and the results prove how the efficiency has been significantly improved.

Keywords: Microarray data mining, biological pattern recognition, partitional clustering, k-means algorithm, centroid initialization.

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Authors: Saif Obaid Alkaabi, Nabil Ayad

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Governments constantly seek to offer faster, more secure, efficient and effective services for their citizens. Recent changes and developments to communication services and technologies, mainly due the Internet, have led to immense improvements in the way governments of advanced countries carry out their interior operations Therefore, advances in e-government services have been broadly adopted and used in various developed countries, as well as being adapted to developing countries. The implementation of advances depends on the utilization of the most innovative structures of data techniques, mainly in web dependent applications, to enhance the main functions of governments. These functions, in turn, have spread to mobile and wireless techniques, generating a new advanced direction called m-government. This paper discusses a selection of available m-government applications and several business modules and frameworks in various fields. Practically, the m-government models, techniques and methods have become the improved version of e-government. M-government offers the potential for applications which will work better, providing citizens with services utilizing mobile communication and data models incorporating several government entities. Developing countries can benefit greatly from this innovation due to the fact that a large percentage of their population is young and can adapt to new technology and to the fact that mobile computing devices are more affordable. The use of models of mobile transactions encourages effective participation through the use of mobile portals by businesses, various organizations, and individual citizens. Although the application of m-government has great potential, it does have major limitations. The limitations include: the implementation of wireless networks and relative communications, the encouragement of mobile diffusion, the administration of complicated tasks concerning the protection of security (including the ability to offer privacy for information), and the management of the legal issues concerning mobile applications and the utilization of services.

Keywords: E-government, m-government, system dependability, system security, trust.

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Authors: Tzyy Rong Jinn, Nguyen Tiep Khac, Tzong Yuan Wu

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Highly pathogenic avian influenza (HPAI) H5N1 viruses have created demand for a cost-effective vaccine to prevent a pandemic of the disease. Here, we report that Trichoplusia ni (T. ni) larvae can act as a cost-effective bioreactor to produce recombinant HA5 (rH5HA) proteins as an potential effective vaccine for chickens. To facilitate the recombinant virus identification, virus titer determination and access the infected larvae, we employed the internal ribosome entry site (IRES) derived from Perina nuda virus (PnV, belongs to insect picorna like Iflavirus genus) to construct a bi-cistronic baculovirus expression vector that can express the rH5HA protein and enhanced green fluorescent protein (EGFP) simultaneously. Western blot analysis revealed that the 70 kDa rH5HA protein and partially cleaved products (40 kDa H5HA1) were generated in T. ni larvae infected with recombinant baculovirus carrying the H5HA gene. These data suggest that the baculovirus-larvae recombinant protein expression system could be a cost-effective platform for H5N1 vaccine production.

Keywords: Avian Influenza, baculovirus, hemagglutinin, Trichoplusia ni larvae

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Authors: Carmen Maria Moraru, Iuliana Stefan, Ovidiu Balteanu, Ciprian Bucur, Liviu Stefan, Anisia Bornea, Ioan Stefanescu

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The implementation of the new software and hardware-s technologies for tritium processing nuclear plants, and especially those with an experimental character or of new technology developments shows a coefficient of complexity due to issues raised by the implementation of the performing instrumentation and equipment into a unitary monitoring system of the nuclear technological process of tritium removal. Keeping the system-s flexibility is a demand of the nuclear experimental plants for which the change of configuration, process and parameters is something usual. The big amount of data that needs to be processed stored and accessed for real time simulation and optimization demands the achievement of the virtual technologic platform where the data acquiring, control and analysis systems of the technological process can be integrated with a developed technological monitoring system. Thus, integrated computing and monitoring systems needed for the supervising of the technological process will be executed, to be continued with the execution of optimization system, by choosing new and performed methods corresponding to the technological processes within the tritium removal processing nuclear plants. The developing software applications is executed with the support of the program packages dedicated to industrial processes and they will include acquisition and monitoring sub-modules, named “virtually" as well as the storage sub-module of the process data later required for the software of optimization and simulation of the technological process for tritium removal. The system plays and important role in the environment protection and durable development through new technologies, that is – the reduction of and fight against industrial accidents in the case of tritium processing nuclear plants. Research for monitoring optimisation of nuclear processes is also a major driving force for economic and social development.

Keywords: Monitoring system, process simulation.

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Authors: Yongquan Zhao, Bo Huang

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Spatial, Temporal, and Spectral Resolution (STSR) are three key characteristics of Earth observation satellite sensors; however, any single satellite sensor cannot provide Earth observations with high STSR simultaneously because of the hardware technology limitations of satellite sensors. On the other hand, a conflicting circumstance is that the demand for high STSR has been growing with the remote sensing application development. Although image fusion technology provides a feasible means to overcome the limitations of the current Earth observation data, the current fusion technologies cannot enhance all STSR simultaneously and provide high enough resolution improvement level. This study proposes a Hybrid Spatial-Temporal-Spectral image Fusion Model (HSTSFM) to generate synthetic satellite data with high STSR simultaneously, which blends the high spatial resolution from the panchromatic image of Landsat-8 Operational Land Imager (OLI), the high temporal resolution from the multi-spectral image of Moderate Resolution Imaging Spectroradiometer (MODIS), and the high spectral resolution from the hyper-spectral image of Hyperion to produce high STSR images. The proposed HSTSFM contains three fusion modules: (1) spatial-spectral image fusion; (2) spatial-temporal image fusion; (3) temporal-spectral image fusion. A set of test data with both phenological and land cover type changes in Beijing suburb area, China is adopted to demonstrate the performance of the proposed method. The experimental results indicate that HSTSFM can produce fused image that has good spatial and spectral fidelity to the reference image, which means it has the potential to generate synthetic data to support the studies that require high STSR satellite imagery.

Keywords: Hybrid spatial-temporal-spectral fusion, high resolution synthetic imagery, least square regression, sparse representation, spectral transformation.

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Authors: Miguel García-Ferrús, Ana González, María A. Ferrús

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The most demanded organic foods worldwide are those that are consumed fresh, such as fruits and vegetables. However, there is a knowledge gap about some aspects of organic food microbiological quality and safety. Organic fruits and vegetables are more exposed to pathogenic microorganisms due to surface contact with natural fertilizers such as animal manure, wastes and vermicompost used during farming. Therefore, the objective of this work was to study the contamination of organic fresh green leafy vegetables by two emergent pathogens, Arcobacter spp. and Helicobacter pylori. For this purpose, a total of 24 vegetable samples, 13 lettuce and 11 spinach were acquired from 10 different ecological supermarkets and greengroceries and analyzed by culture and PCR. Arcobacter spp. was detected in five samples (20%) by PCR, four spinach and one lettuce. One spinach sample was found to be also positive by culture. For H. pylori, the H. pylori VacA gene-specific band was detected in 12 vegetable samples (50%), 10 lettuces and two spinach. Isolation in the selective medium did not yield any positive result, possibly because of low contamination levels together with the presence of the organism in its viable but non-culturable form. Results showed significant levels of H. pylori and Arcobacter contamination in organic vegetables that are generally consumed raw, which seems to confirm that these foods can act as transmission vehicles to humans.

Keywords: Arcobacter spp., Helicobacter pylori, organic vegetables, Polymerase Chain Reaction, PCR.

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Authors: Hai Xu, Yiwei Wang, Xi Bao, Bihua Deng, Pengcheng Li, Yu Lu

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T7 phage could be used as a perfect vector for peptides expression and haptens presentation. T7-3GnRH recombinant phage was constructed by inserting three copies of Gonadotrophin Releasing Hormone (GnRH) gene into the multiple cloning site of T7 Select 415-1b phage genome. The positive T7-3GnRH phage was selected by using polymerase chain reaction amplification, and the p10B-3GnRH fusion protein was verified by SDS-PAGE and Western-blotting assay. T7-3GnRH vaccine was made and immunized with 10¹⁰ pfu in 0.2 ml per dose in mice. Blood samples were collected at an interval in weeks, and anti-GnRH antibody and testosterone concentrations were detected by ELISA and radioimmunoassay, respectively. The results show that T7-3GnRH phage particles confer a high immunogenicity to the GnRH-derived epitope. Moreover, the T7-3GnRH vaccine induced higher level of anti-GnRH antibody than ImproVac^®. However, the testosterone concentrations in both immunized groups were at a similar level, and the testis developments were significantly inhibited compared to controls. These findings demonstrated that the anti-GnRH antibody could neutralize the endogenous GnRH to down regulate testosterone level and limit testis development, highlighting the potential value of T7-3GnRH in the immunocastration vaccine research.

Keywords: Gonadotrophin releasing hormone, GnRH, immunocastration, T7 phage, phage vaccine.

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Authors: A. Nour Eddine, D. Chalet, L. Aixala, P. Chessé, X. Faure, N. Hatat

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Thermal power technology such as the TEG (Thermo-Electric Generator) arouses significant attention worldwide for waste heat recovery. Despite the potential benefits of marine application due to the permanent heat sink from sea water, no significant studies on this application were to be found. In this study, a test rig has been designed and built to test the performance of the TEG on engine operating points. The TEG device is built from commercially available materials for the sake of possible economical application. Two types of commercial TEM (thermo electric module) have been studied separately on the test rig. The engine data were extracted from a commercial Diesel engine since it shares the same principle in terms of engine efficiency and exhaust with the marine Diesel engine. An open circuit water cooling system is used to replicate the sea water cold source. The characterization tests showed that the silicium-germanium alloys TEM proved a remarkable reliability on all engine operating points, with no significant deterioration of performance even under sever variation in the hot source conditions. The performance of the bismuth-telluride alloys was 100% better than the first type of TEM but it showed a deterioration in power generation when the air temperature exceeds 300 °C. The temperature distribution on the heat exchange surfaces revealed no useful combination of these two types of TEM with this tube length, since the surface temperature difference between both ends is no more than 10 °C. This study exposed the perspective of use of TEG technology for marine engine exhaust heat recovery. Although the results suggested non-sufficient power generation from the low cost commercial TEM used, it provides valuable information about TEG device optimization, including the design of heat exchanger and the types of thermo-electric materials.

Keywords: Internal combustion engine application, Seebeck, thermo-electricity, waste heat recovery.

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Authors: Mark Kaahwa, Chang Zhu, Moses Muhumuza

Abstract:

This study investigates the satisfaction of distance education university students (DEUS) with the use of audio media as a medium of instruction. Studying students’ satisfaction is vital because it shows whether learners are comfortable with a certain instructional strategy or not. Although previous studies have investigated the use of audio media, the satisfaction of students with an instructional strategy that combines radio teaching and podcasts as an independent teaching strategy has not been fully investigated. In this study, all lectures were delivered through the radio and students had no direct contact with their instructors. No modules or any other material in form of text were given to the students. They instead, revised the taught content by listening to podcasts saved on their mobile electronic gadgets. Prior to data collection, DEUS received orientation through workshops on how to use audio media in distance education. To achieve objectives of the study, a survey, naturalistic observations and face-to-face interviews were used to collect data from a sample of 211 undergraduate and graduate students. Findings indicate that there was no statistically significant difference in the levels of satisfaction between male and female students. The results from post hoc analysis show that there is a statistically significant difference in the levels of satisfaction regarding the use of audio media between diploma and graduate students. Diploma students are more satisfied compared to their graduate counterparts. T-test results reveal that there was no statistically significant difference in the general satisfaction with audio media between rural and urban-based students. And ANOVA results indicate that there is no statistically significant difference in the levels of satisfaction with the use of audio media across age groups. Furthermore, results from observations and interviews reveal that DEUS found learning using audio media a pleasurable medium of instruction. This is an indication that audio media can be considered as an instructional strategy on its own merit.

Keywords: Audio media, distance education, distance education university students, medium of instruction, satisfaction.

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Authors: A. Gruzdz, A. Ihnatowicz, J. Siddiqi, B. Akhgar

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MATCH project [1] entitle the development of an automatic diagnosis system that aims to support treatment of colon cancer diseases by discovering mutations that occurs to tumour suppressor genes (TSGs) and contributes to the development of cancerous tumours. The constitution of the system is based on a) colon cancer clinical data and b) biological information that will be derived by data mining techniques from genomic and proteomic sources The core mining module will consist of the popular, well tested hybrid feature extraction methods, and new combined algorithms, designed especially for the project. Elements of rough sets, evolutionary computing, cluster analysis, self-organization maps and association rules will be used to discover the annotations between genes, and their influence on tumours [2]-[11]. The methods used to process the data have to address their high complexity, potential inconsistency and problems of dealing with the missing values. They must integrate all the useful information necessary to solve the expert's question. For this purpose, the system has to learn from data, or be able to interactively specify by a domain specialist, the part of the knowledge structure it needs to answer a given query. The program should also take into account the importance/rank of the particular parts of data it analyses, and adjusts the used algorithms accordingly.

Keywords: Bioinformatics, gene expression, ontology, selforganizingmaps.

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Authors: M. Kaomek, J. R. Ketudat-Cairns

Abstract:

The cDNA encoding the 326 amino acids of a Class I basic chitinase gene from Leucaena leucocephala de Wit (KB3, Genbank accession: AAM49597) was cloned under the control of CaMV35S promoter in pCAMBIA 1300 and transferred to Koshihikari. Calli of Koshihikari rice was transformed with agrobacterium with this construct expressing the chitinase and β- glucouronidase (GUS). The frequencies of calli 90 % has been obtained from rice seedlings cultured on NB medium. The high regeneration frequencies, 74% was obtained from calli cultured on regeneration medium containing 4 mg/l BAP, and 7 g/l phytagel at 25°C. Various factors were studied in order to establish a procedure for the transformation of Koshihikari Agrobacterium tumefaciens. Supplementation of 50 mM acetosyringone to the medium during coculivation was important to enhance the frequency to transient transformation. The 4 week-old scutellum-derived calli were excellent starting materials. Selection medium based on NB medium supplement with 40 mg/l hygromycin and 400 mg/l cefotaxime were an optimized medium for selection of transformed rice calli. The percentage of transformation 70 was obtained. Recombinant calli and regenerated rice plants were checked the expression of chitinase and gus by PCR, northern blot gel, southern blot gel, and gus assay. Chitinase and gus were expressed in all parts of recombinant rice. The rice line expressing the KB3 chiitnase was more resistant to the blast fungus Fusarium monoliforme than control line.

Keywords: chitinase, Leucaena leucocephala de Wit, Koshihikari, transgenic rice.

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Authors: Isam A. Mohamed Ahmed, Jiro Arima, Tsuyoshi Ichiyanagi, Emi Sakuno, Nobuhiro Mori

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The aim of this study was to screen for microorganism that able to utilize 3-N-trimethylamino-1-propanol (homocholine) as a sole source of carbon and nitrogen. The aerobic degradation of homocholine has been found by a gram-positive Rhodococcus sp. bacterium isolated from soil. The isolate was identified as Rhodococcus sp. strain A4 based on the phenotypic features, physiologic and biochemical characteristics, and phylogenetic analysis. The cells of the isolated strain grown on both basal-TMAP and nutrient agar medium displayed elementary branching mycelia fragmented into irregular rod and coccoid elements. Comparative 16S rDNA sequencing studies indicated that the strain A4 falls into the Rhodococcus erythropolis subclade and forms a monophyletic group with the type-strains of R. opacus, and R. wratislaviensis. Metabolites analysis by capillary electrophoresis, fast atom bombardment-mass spectrometry, and gas chromatography- mass spectrometry, showed trimethylamine (TMA) as the major metabolite beside β-alanine betaine and trimethylaminopropionaldehyde. Therefore, the possible degradation pathway of trimethylamino propanol in the isolated strain is through consequence oxidation of alcohol group (-OH) to aldehyde (-CHO) and acid (-COOH), and thereafter the cleavage of β-alanine betaine C-N bonds yielded trimethylamine and alkyl chain.

Keywords: Homocholine, 3-N-trimethylamino-1-propanol, Quaternary ammonium compounds, 16S rDNA gene sequence.

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Authors: Hanina M. N., Hairul Shahril M., Mohd Fazrullah Innsan M. F., Ismatul Nurul Asyikin I., Abdul Jalil A. K, Salina M. R., Ahmad I.B.

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Proteins levels produced by bacteria may be increased in stressful surroundings, such as in the presence of antibiotics. It appears that many antimicrobial agents or antibiotics, when used at low concentrations, have in common the ability to activate or repress gene transcription, which is distinct from their inhibitory effect. There have been comparatively few studies on the potential of antibiotics or natural compounds in nature as a specific chemical signal that can trigger a variety of biological functions. Therefore, this study was focusing on the effect of essential oils from Cymbopogon flexuosus and C. nardus in regulating proteins production by Bacillus subtilis ATCC 21332. The Minimum Inhibition Concentrations (MICs) of both essential oils on B. subtilis were determined by using microdilution assay, resulting 0.2% and 1.56% for each C. flexuosus and C. nardus subsequently. The bacteria were further exposed to each essential oils at concentration of 0.01XMIC for 2 days. The proteins were then isolated and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Protein profile showed that a band with approximate size of 250 kD was appeared for the treated bacteria with essential oils. Thus, Bacillus subtilis ATCC 21332 in stressful condition with the presence of essential oils at low concentration could induce the protein production.

Keywords: Bacillus subtilis ATCC 21332, Cymbopogon essential oils, protein

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Authors: Ratnakar Tripathi, Rajnikant Mishra

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The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.

Keywords: Interacting Proteins, Pax6, PIP, STRING

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