Search results for: gene regulation

Authors: Kritsada Khongnomnan, Wittaya Poomipak, Yong Poovorawan, Sunchai Payungporn

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In this study, three subtypes of influenza A viruses (pH1N1, H5N1 and H3N2) which naturally infected human were analyzed by bioinformatic approaches to find candidate human cellular miRNAs targeting viral genomes. There were 76 miRNAs targeting influenza A viruses. Among these candidates, 70 miRNAs were subtypes specifically targeting each subtype of influenza A virus including 21 miRNAs targeted subtype H1N1, 27 miRNAs targeted subtype H5N1 and 22 miRNAs targeted subtype H3N2. The remaining 6 miRNAs target on multiple subtypes of influenza A viruses. Uniquely, hsa-miR-3145 is the only one candidate miRNA targeting PB1 gene of all three subtypes. Obviously, most of the candidate miRNAs are targeting on polymerase complex genes (PB2, PB1 and PA) of influenza A viruses. This study predicted potential human miRNAs targeting on different subtypes of influenza A viruses which might be useful for inhibition of viral replication and for better understanding of the interaction between virus and host cell.

Keywords: Human miRNAs, Influenza A viruses, H1N1, H5N1, H3N2

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Authors: Zeinep A. Berkimbayeva, Almagul T. Mansharipova, Elmira M. Khussainova, Leyla B. Djansugurova

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It is believed that DNA damaging toxic metabolites contributes to the development of different pathological conditions. To prevent harmful influence of toxic agents, cells developed number of protecting mechanisms, such as enzymatic reaction of detoxification of reactive metabolites and repair of DNA damage. The aim of the study was to examine the association between polymorphism of GSTT1/GSTM1 and XRCC1/3 genes and coronary artery disease (CAD) incidence. To examine a polymorphism of these genes in CAD susceptibility in patients and controls, PCR based genotyping assay was performed. For GST genes, frequency of GSTM1 null genotype among CAD affected group was significantly increased than in control group (P<0.001). Frequencies of the GSTT1 null and positive alleles are almost equal in both groups (P>0.1). We found that neither XRCC1 Arg399Gln nor XRCC3 Thr241Met were associated with CAD risk. Obtained data suggests that GSTM1 null genotype carriers are more susceptible to CAD development.

Keywords: Cardiovascular disease, DNA reparation, gene polymorphism, risk factors, xenobiotic detoxification.

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Authors: N. B. Dhayanithi, T. T. Ajith Kumar, T. Balasubramanian

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Present study summarizes the control of Vibrio alginolyticus infection in hatchery reared Clownfish, Amphiprion sebae with the extract of the mangrove plant, Avicennia marina. Fishes with visible symptoms of hemorrhagic spots were chosen and the genomic DNA of the causative bacterium was isolated and sequenced based on 16S rDNA gene. The in vitro assay revealed that a fraction of A. marina leaf extract elucidated with ethyl acetate: methanol (6:4) showed a high activity (28 mm) at 125 μg/ml concentrations. About 4 % of the fraction fed along with live V. alginolyticus was significantly decreased the cumulative mortality (P<0.05) in the experimental groups than the control group. The responsible fraction was investigated by gas chromatography - mass spectroscopy and found the presence of active compounds. This is the first research in India to control vibriosis infection in marine ornamental fish with mangrove leaf extract.

Keywords: Amphiprion seabe, Avicennia marina, Gas Chromatography - Mass Spectroscopy, Vibrio alginolyticus

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.

Keywords: Alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance.

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Authors: Jeng-Wen Lin, Simon Chien-Yuan Chen

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Based on assumptions of neo-classical economics and rational choice / public choice theory, this paper investigates the regulation of industrial land use in Taiwan by homeowners associations (HOAs) as opposed to traditional government administration. The comparison, which applies the transaction cost theory and a polynomial regression analysis, manifested that HOAs are superior to conventional government administration in terms of transaction costs and overall efficiency. A case study that compares Taiwan-s commonhold industrial park, NangKang Software Park, to traditional government counterparts using limited data on the costs and returns was analyzed. This empirical study on the relative efficiency of governmental and private institutions justified the important theoretical proposition. Numerical results prove the efficiency of the established model.

Keywords: Homeowners Associations, Institutional Efficiency, Polynomial Regression, Transaction Cost.

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.

Keywords: Alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance.

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Authors: JiEun Jeong, Se-Won Kang, Hee-Ju Hwang, Sung-Hwa Chae, Sang-Haeng Choi, Hong-SeogPark, YeonSoo Han, Bok-Reul Lee, Dae-Hyun Seog, Yong Seok Lee

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Tofurther advance research on immune-related genes from T. molitor, we constructed acDNA library and analyzed expressed sequence taq (EST) sequences from 1,056 clones. After removing vector sequence and quality checkingthrough thePhred program (trim_alt 0.05 (P-score>20), 1039 sequences were generated. The average length of insert was 792 bp. In addition, we identified 162 clusters, 167 contigs and 391 contigs after clustering and assembling process using a TGICL package. EST sequences were searchedagainst NCBI nr database by local BLAST (blastx, EKeywords: EST, Innate immunity, Tenebriomolitor

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Authors: Ben Hamed M., Sbita L

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This paper presents a new method for the implementation of a direct rotor flux control (DRFOC) of induction motor (IM) drives. It is based on the rotor flux components regulation. The d and q axis rotor flux components feed proportional integral (PI) controllers. The outputs of which are the target stator voltages (vdsref and vqsref). While, the synchronous speed is depicted at the output of rotor speed controller. In order to accomplish variable speed operation, conventional PI like controller is commonly used. These controllers provide limited good performances over a wide range of operations even under ideal field oriented conditions. An alternate approach is to use the so called fuzzy logic controller. The overall investigated system is implemented using dSpace system based on digital signal processor (DSP). Simulation and experimental results have been presented for a one kw IM drives to confirm the validity of the proposed algorithms.

Keywords: DRFOC, fuzzy logic, variable speed drives, control, IM and real time.

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Authors: P. O. Angienda, B. O. Aketch, E. N. Waindi

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Juvenile Nile tilapia subjected to heat treatment at temperatures ranging from 260C to 370C showed positive correlation (P<0.01) between treatment temperatures and resultant sex ratios, while, survival rate of the fry showed a negative correlation against temperature (P<0.01). The optimal temperature for both sex shift towards males and survival rates was 36±0.5°C, producing male percentage of 86.31 and a fry survival of 65.25. To determine the genetic basis of temperature sex-determination in Nile tilapia, we employed three microsatellite markers (Abur36, Abur100 and UNH846). Abur36 predicted the sex of 95% of the heat induced individuals, suggesting that the locus influence sex ratio and its interaction with temperature result in male biased sex ratio. This locus could turn out to be the major sex determining gene operating in Nile tilapia. These markers could be used in marker-assisted selection to select genotypes that give a higher percentage of males for commercial production.

Keywords: Heat treatment, Microsatellite, Nile tilapia, sex-determination.

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Authors: A. R. Abdul Syukor, A. W. Zularisam, Z. Ideris, M. S. Mohd Ismid, H. M. Nakmal, S. Sulaiman, A. H. Hasmanie, M. R. Siti Norsita, M. Nasrullah

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In this study, the effectiveness of an integrated aquatic plants in phytogreen zone was studied and statistical analysis for the promotional integrated phytogreen system approached was discussed. It was found that's the effectiveness of using aquatic plant such as Typha angustifolia sp., Lepironia articulata sp., Limnocharis flava sp., Monochoria vaginalis sp., Pistia stratiotes sp., and Eichhornia crassipes sp., in the conventional oxidation pond process in order to comply the standard A according to Malaysia Environmental Quality Act 1974 (Act 127); Environmental Quality (Sewage) Regulation 2009 for effluent discharge into inland water near the residential area was successfully shown. It was concluded that the integrated phtogreen system developed in this study has great potential for refurbishment wastewater in conventional oxidation pond.

Keywords: Phytoremediation, integrated phytogreen system, sewage treatment plant, oxidation pond, aquatic plants.

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Authors: He YuanYan

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In recent years, China has implemented the reform of land and space planning. As an important public policy, land and space planning plays a vital role in the construction and development of cities. Land and space planning throughout the country is in full swing, but there are still many disputes from all walks of life. The content, scope, and specific implementation process of land and space planning are also ambiguous, leading to the integration of multiple regulation problems such as unclear authority, unclear responsibilities, and poor planning results during the implementation of land and space planning. Therefore, it is necessary to sort out the development and evolution of domestic and foreign land space planning, clarify the problems and cruxes from the current situation of China's land space planning, and sort out the obstacles and countermeasures to the implementation of this policy, so as to deepen the understanding of the connotation of land space planning. It is of great practical significance for all planners to correctly understand and clarify the specific contents and methods of land space planning and to smoothly promote the implementation of land space planning at all levels.

Keywords: Territorial spatial planning, public policy, land space, overall planning.

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Authors: D. He, Y. Pang, G. Lodewijks

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Belt conveyors play an important role in continuous dry bulk material transport, especially at the mining industry. Speed control is expected to reduce the energy consumption of belt conveyors. Transient operation is the operation of increasing or decreasing conveyor speed for speed control. According to literature review, current research rarely takes the conveyor dynamics in transient operation into account. However, in belt conveyor speed control, the conveyor dynamic behaviors are significantly important since the poor dynamics might result in risks. In this paper, the potential risks in transient operation will be analyzed. An existing finite element model will be applied to build a conveyor model, and simulations will be carried out to analyze the conveyor dynamics. In order to realize the soft speed regulation, Harrison’s sinusoid acceleration profile will be applied, and Lodewijks estimator will be built to approximate the required acceleration time. A long inclined belt conveyor will be studied with two major simulations. The conveyor dynamics will be given.

Keywords: Belt conveyor, speed control, transient operation, dynamics

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Authors: Ali Dehghani, Mojtaba Hakimzadeh, Amir Habibi, Navid Mehdizadeh Afroozi

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In this paper an isolated wind-diesel hybrid power system has been considered for reactive power control study having an induction generator for wind power conversion and synchronous alternator with automatic voltage regulator (AVR) for diesel unit is presented. The dynamic voltage stability evaluation is dependent on small signal analysis considering a Static VAR Compensator (SVC) and IEEE type -I excitation system. It's shown that the variable reactive power source like SVC is crucial to meet the varying demand of reactive power by induction generator and load and to acquire an excellent voltage regulation of the system with minimum fluctuations. Integral square error (ISE) criterion can be used to evaluate the optimum setting of gain parameters. Finally the dynamic responses of the power systems considered with optimum gain setting will also be presented.

Keywords: SVC, Small Signal Stability, Reactive Power, Control, Hybrid System.

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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: Aline Alves Bandeira, Maria Cecília de Paula Silva

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The existing legal gap regarding thes treatment and final disposal of industrial effluents in Brazil promotes legal uncertainty. The government has not structured itself to guarantee environmental protection. The current legal system and public policies must guarantee the protection of bodies of water and an effective treatment of industrial effluents. This is because economic progress, eco-efficiency and industrial ecology are inseparable. The lack of protection for the water bodies weakens environmental protection, with abuses by companies that do not give due treatment to their effluents, or fail to present the water balance of their factories. It is considered necessary to enact a specific law on industrial effluents related to a National Industrial Effluent Policy, because it is the location of the largest Integrated Industrial Complex in the Southern Hemisphere. The regulation of this subject cannot be limited by decrees of the local Executive Branch, allowing the inspection of the industrial activity or enterprise to be affected fundamentally by environmental self-control, or by private institutions.

Keywords: Effluent policy, environmental law, environmental management, industrial effluents.

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Authors: Elangeshwaran Pathmanathan, Rosdiazli Ibrahim, Vijanth Sagayan Asirvadam

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This paper aims to develop a NOx emission model of an acid gas incinerator using Nelder-Mead least squares support vector regression (LS-SVR). Malaysia DOE is actively imposing the Clean Air Regulation to mandate the installation of analytical instrumentation known as Continuous Emission Monitoring System (CEMS) to report emission level online to DOE . As a hardware based analyzer, CEMS is expensive, maintenance intensive and often unreliable. Therefore, software predictive technique is often preferred and considered as a feasible alternative to replace the CEMS for regulatory compliance. The LS-SVR model is built based on the emissions from an acid gas incinerator that operates in a LNG Complex. Simulated Annealing (SA) is first used to determine the initial hyperparameters which are then further optimized based on the performance of the model using Nelder-Mead simplex algorithm. The LS-SVR model is shown to outperform a benchmark model based on backpropagation neural networks (BPNN) in both training and testing data.

Keywords: artificial neural networks, industrial pollution, predictive algorithms, support vector machines

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Authors: Alan Vaško, Juraj Belan, Lenka Hurtalová, Eva Tillová

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The aim of this study is to evaluate the influence of raw material composition on the microstructure, mechanical and fatigue properties and micromechanisms of failure of nodular cast iron. In order to evaluate the influence of charge composition, the structural analysis, mechanical and fatigue tests and microfractographic analysis were carried out on specimens of ten melts with different charge compositions. The basic charge of individual melts was formed by different ratio of pig iron and steel scrap and by different additive for regulation of chemical composition (silicon carbide or ferrosilicon). The results show differences in mechanical and fatigue properties, which are connected with the microstructure. SiC additive positively influences microstructure. Consequently, mechanical and fatigue properties of nodular cast iron are improved, especially in the melts with higher ratio of steel scrap in the charge.

Keywords: Nodular cast iron, silicon carbide, microstructure, mechanical properties.

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Authors: Simin Sadeghi-Saeb

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Metacognitive strategies consistently play important roles in reading comprehension. The metacognitive strategies involve the active monitoring and consequent regulation and orchestration of the cognitive processes in relation to the cognitive objects or data on which they bear. In this paper, the effect of instruction in using metacognitive strategies on reading academic materials, type of metacognitive strategies were mostly used by college university students before and after the instruction and the level they use those strategies before and after the instruction were studied. For these aims, 50 female college students were chosen. Then, they were divided randomly into two groups, experimental and control groups. At first session, students in both groups took the standard TOFEL exam. After the pre-test had been administered, the instruction began. After treatment, a post-test was taken. It is useful to state that after pre-test and post-test the same questionnaire was handed to the students of experimental group. The results of this research show that the instruction of metacognitive strategies has positive effect on the students' scores in reading comprehension tests. Furthermore, it showed that before and after the instruction, the students' usage of metacognitive strategies changed. Also, it demonstrated that the instruction affected the students' level of metacognitive strategies' usage.

Keywords: EFL students, English reading comprehension, instruction, metacognitive strategies.

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Authors: Reza Sedaghati, Mojtaba Hakimzadeh, Mohammad Hasan Raouf, Mostafa Mirzadeh

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Nowadays the growth of distributed generation within the bulk power system is feasible by using the optimal control of the transmission lines power flow. Static Synchronous Compensators (STATCOM) is effective for improving voltage stability but it can only exchange reactive power with the power grid. The integration of Superconducting Magnetic Energy Storage (SMES) with a STATCOM can extend the traditional STATCOM capabilities to four-quadrant bulk power system power flow control and providing exchange both the active and reactive power related to the STATCOM with the ac network. This paper shows how the SMES system can be connected to the ac system via the DC bus of a STATCOM and also analyzes how the integration of STATCOM and SMES allows the bus voltage regulation and power oscillation damping (POD) to be achieved simultaneously. The dynamic performance of the integrated STATCOM-SMES is evaluated through simulation by using PSCAD/EMTDC software and the compensation effectiveness of this integrated compensator is shown.

Keywords: STATCOM-SMES compensator, Power Oscillation Damping (POD), stabilizing, signal, voltage.

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Authors: R. Govender, D. Naidoo, E. M. Buys

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The importance of ensuring safe meat handling and processing practices has been demonstrated in global reports on food safety scares and related illness and deaths. This necessitated stricter meat safety control strategies. Today, many countries have regulated towards preventative and systematic control over safe meat processing at abattoirs utilizing the Hazard Analysis Critical Control Point (HACCP) principles. HACCP systems have been reported as effective in managing food safety risks, if correctly implemented. South Africa has regulated the Hygiene Management System (HMS) based on HACCP principles applicable to abattoirs. Regulators utilise the Hygiene Assessment System (HAS) to audit compliance at abattoirs. These systems were benchmarked from the United Kingdom (UK). Little research has been done them since inception as of 2004. This paper presents a review of the two systems, its implementation and comparison with HACCP. Recommendations are made for future research to demonstrate the utility of the HMS and HAS in assuring safe meat to consumers.

Keywords: Abattoir, co-regulation, food safety, HACCP, meat hygiene.

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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: Seung-Kyung Kye, Sang-Seung Lee, Dooyong Cho, Sun-Kyu Park

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Although many studies on the assembly technology of the bridge construction have dealt mostly with on the pier, girder or the deck of the bridge, studies on the prefabricated barrier have rarely been performed. For understanding structural characteristics and application of the concrete barrier in the modular bridge, which is an assembly of structure members, static loading test was performed. Structural performances as a road barrier of the three methods, conventional cast-in-place(ST), vertical bolt connection(BVC) and horizontal bolt connection(BHC) were evaluated and compared through the analyses of load-displacement curves, strain curves of the steel, concrete strain curves and the visual appearances of crack patterns. The vertical bolt connection(BVC) method demonstrated comparable performance as an alternative to conventional cast-in-place(ST) while providing all the advantages of prefabricated technology. Necessities for the future improvement in nuts enforcement as well as legal standard and regulation are also addressed.

Keywords: Modular Bridge, Concrete Barrier, Bolt Connection

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Authors: Andreas Körtge, Susanne Stählke, Regina Lange, Mario Birkholz, Mirko Fraschke, Katrin Schulz, Barbara Nebe, Patrick Elter

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A major challenge in biomaterials research is the regulation of protein adsorption which is a key factor for controlling the subsequent cell adhesion at implant surfaces. The aim of the present study was to control the adsorption of fibronectin (FN) and the attachment of MG-63 osteoblasts with an electronic nanostructure. Shallow doping line lattices with a period of 260 nm were produced for this purpose by implantation of phosphorous in silicon wafers. Protein coverage was determined after incubating the substrate with FN by means of an immunostaining procedure and the measurement of the fluorescence intensity with a TECAN analyzer. We observed an increased amount of adsorbed FN on the nanostructure compared to control substrates. MG-63 osteoblasts were cultivated for 24h on FN-incubated substrates and their morphology was assessed by SEM. Preferred orientation and elongation of the cells in direction of the doping lattice lines was observed on FN-coated nanostructures.

Keywords: Cell adhesion, electronic nanostructures, doping lattice, fibronectin, MG-63 osteoblasts, protein adsorption.

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Authors: E. Hlavacova, J. Chrenova, Z. Rausova, M. Vlcek, A. Penesova, L. Dedik

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En bloc assumes modeling all phases of the orthostatic test with the only one mathematical model, which allows the complex parametric view of orthostatic response. The work presents the implementation of a mathematical model for processing of the measurements of systolic, diastolic blood pressure and heart rate performed on volunteers during orthostatic test. The original assumption of model hypothesis that every postural change means only one Stressor, did not complying with the measurements of physiological circulation factor-time profiles. Results of the identification support the hypothesis that second postural change of orthostatic test causes induced Stressors, with the observation of a physiological regulation mechanism. Maximal demonstrations are on the heart rate and diastolic blood pressure-time profile, minimal are for the measurements of the systolic blood pressure. Presented study gives a new view on orthostatic test with impact on clinical practice.

Keywords: En bloc modeling, physiological circulatory factor, postural change, stressor

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Authors: S. Venkateshwarlu, B. P. Muni, A. D. Rajkumar, J. Praveen

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Custom power is a technology driven product and service solution which embraces a family devices such as Dynamic Voltage Restorer (DVR), Distributed Shunt Compensator (DSTATCOM), Solid State Breaker (SSB) etc which will provide power quality functions at distribution voltages. The rapid response of these devices enables them to operate in real time, providing continuous and dynamic control of the supply including voltage and reactive power regulation, harmonic reduction and elimination of voltage dips. This paper presents the benefits of multilevel inverters when they are used for DPC based custom power devices. Power flow control mechanism, salient features, advantages and disadvantages of direct power control (DPC) using lookup table, SVM, predictive voltage vector and hybrid DPC strategies are discussed in this paper. Simulation results of three level inverter based STATCOM, harmonic analysis of multi level inverters are presented at the end.

Keywords: DPC, DPC-SVM, Dynamic voltage restorer, DSTATCOM, Multilevel inverter, PWM Converter, PDPC, VF-DPC.

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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: 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: Mikko Mäkelä, Risto Pöykiö, Gary Watkins, Hannu Nurmesniemi, Olli Dahl

Abstract:

Trace element speciation of an integrated soil amendment matrix was studied with a modified BCR sequential extraction procedure. The analysis included pseudo-total concentration determinations according to USEPA 3051A and relevant physicochemical properties by standardized methods. Based on the results, the soil amendment matrix possessed neutralization capacity comparable to commercial fertilizers. Additionally, the pseudo-total concentrations of all trace elements included in the Finnish regulation for agricultural fertilizers were lower than the respective statutory limit values. According to chemical speciation, the lability of trace elements increased in the following order: Hg < Cr < Co < Cu < As < Zn < Ni < Pb < Cd < V < Mo < Ba. The validity of the BCR approach as a tool for chemical speciation was confirmed by the additional acid digestion phase. Recovery of trace elements during the procedure assured the validity of the approach and indicated good quality of the analytical work.

Keywords: BCR, bioavailability, trace element, industrialresidue, sequential extraction

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