Search results for: transcription factor binding site.

Authors: H. Elsawy, A. Jeltsch

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EcoDam is an adenine-N6 DNA methyltransferase that methylates the GATC sites in the Escherichia coli genome. DNA-adenine methylation is not present in higher eukaryotes including humans. These observations raise the possibility that dam inhibitors may be used as anti-microbial agents. Polyphosphate (Poly(P)) is an important metabolite and signaling molecule in prokaryotes and eukaryotes. Here, by using gel retardation experiments to investigate the competition of DNA binding by EcoDam in the presence of polyphosphate, we found that Poly (P) strongly interferes with DNA binding by EcoDam, while same concentration of monophosphate does not. In addition, we demonstrated that Poly (P) binding inhibits the activity of EcoDam and our results suggest that Poly (P) led to strong inhibition of the EcoDam catalytic activity, while monophosphate had only moderate effect.

Keywords: Antibacterial drugs, EcoDam inhibitors, Polyphosphate.

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Authors: Shaila Ahmed, Raghu Prasad Rao Metpally, Sreedhara Sangadala, Boojala Vijay B Reddy

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Bone growth factors, such as Bone Morphogenic Protein-2 (BMP-2) have been approved by the FDA to replace grafting for some surgical interventions, but the high dose requirement limits its use in patients. Noggin, an extracellular protein, blocks the effect of BMP-2 by binding to BMP. Preventing the BMP-2/noggin interaction will help increase the free concentration of BMP-2 and therefore should enhance its efficacy to induce bone formation. The work presented here involves computational design of novel small molecule inhibitory agents of BMP-2/noggin interaction, based on our current understanding of BMP-2, and its known putative ligands (receptors and antagonists). A successful acquisition of such an inhibitory agent of BMP-2/noggin interaction would allow clinicians to reduce the dose required of BMP-2 protein in clinical applications to promote osteogenesis. The available crystal structures of the BMPs, its receptors, and the binding partner noggin were analyzed to identify the critical residues involved in their interaction. In presenting this study, LUDI de novo design method was utilized to perform virtual screening of a large number of compounds from a commercially available library against the binding sites of noggin to identify the lead chemical compounds that could potentially block BMP-noggin interaction with a high specificity.

Keywords: Transforming growth factor-beta, Bone morphogenic proteins, Noggin, LUDI de novo design method, CAP small molecules.

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Authors: G. V. Novikov, V. S. Sivozhelezov, S. S. Kolesnikov, K. V. Shaitan

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The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus receptor’s constitutive activity directly results from its conformational dynamics. On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behavior.

Keywords: Seven-transmembrane receptors, constitutive activity, activation, x-ray crystallography, principal component analysis, molecular dynamics simulation.

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Authors: Yin-Yann Chen

Abstract:

As the gradual increase of the enterprise scale, the firms may possess many manufacturing plants located in different places geographically. This change will result in the multi-site production planning problems under the environment of multiple plants or production resources. Our research proposes the structural framework to analyze the multi-site planning problems. The analytical framework is composed of six elements: multi-site conceptual model, product structure (bill of manufacturing), production strategy, manufacturing capability and characteristics, production planning constraints, and key performance indicators. As well as the discussion of these six ingredients, we also review related literatures in this paper to match our analytical framework. Finally we take a real-world practical example of a TFT-LCD manufacturer in Taiwan to explain our proposed analytical framework for the multi-site production planning problems.

Keywords: Multi-Site, Production Planning, Supply Chain, TFT-LCD.

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Authors: I GD Yudha Partama, A. Kanno, Y. Akamatsu, R. Inui, M. Goto, M. Sekine

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The aerial photogrammetry of shallow water bottoms has the potential to be an efficient high-resolution survey technique for shallow water topography, thanks to the advent of convenient UAV and automatic image processing techniques Structure-from-Motion (SfM) and Multi-View Stereo (MVS)). However, it suffers from the systematic overestimation of the bottom elevation, due to the light refraction at the air-water interface. In this study, we present an empirical method to correct for the effect of refraction after the usual SfM-MVS processing, using common software. The presented method utilizes the empirical relation between the measured true depth and the estimated apparent depth to generate an empirical correction factor. Furthermore, this correction factor was utilized to convert the apparent water depth into a refraction-corrected (real-scale) water depth. To examine its effectiveness, we applied the method to two river sites, and compared the RMS errors in the corrected bottom elevations with those obtained by three existing methods. The result shows that the presented method is more effective than the two existing methods: The method without applying correction factor and the method utilizes the refractive index of water (1.34) as correction factor. In comparison with the remaining existing method, which used the additive terms (offset) after calculating correction factor, the presented method performs well in Site 2 and worse in Site 1. However, we found this linear regression method to be unstable when the training data used for calibration are limited. It also suffers from a large negative bias in the correction factor when the apparent water depth estimated is affected by noise, according to our numerical experiment. Overall, the good accuracy of refraction correction method depends on various factors such as the locations, image acquisition, and GPS measurement conditions. The most effective method can be selected by using statistical selection (e.g. leave-one-out cross validation).

Keywords: Bottom elevation, multi-view stereo, river, structure-from-motion.

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Authors: Zs. Csanádi, A. Szabó Nagy, J. Szabó, J. Erdős

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The main objective of this study was to assess the annual concentration and seasonal variation of benzo(a)pyrene (BaP) associated with PM10 in an urban site of Győr and in a rural site of Sarród in the sampling period of 2008–2012. A total of 280 PM10 aerosol samples were collected in each sampling site and analyzed for BaP by gas chromatography method. The BaP concentrations ranged from undetected to 8 ng/m3 with the mean value of 1.01 ng/m3 in the sampling site of Győr, and from undetected to 4.07 ng/m3 with the mean value of 0.52 ng/m3 in the sampling site of Sarród, respectively. Relatively higher concentrations of BaP were detected in samples collected in both sampling sites in the heating seasons compared with non-heating periods. The annual mean BaP concentrations were comparable with the published data of different other Hungarian sites.

Keywords: Air quality, benzo(a)pyrene, PAHs, polycyclic aromatic hydrocarbons.

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Authors: Alan Luo, Hunter N. B. Moseley

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Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for X-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across X-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: Biomacromolecular structure, coenzyme, electron density discrepancy analysis, X-ray crystallography.

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Authors: Sizhong Zhou

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Let a and b be nonnegative integers with 2 ≤ a < b, and let G be a Hamiltonian graph of order n with n ≥ (a+b−4)(a+b−2) b−2 . An [a, b]-factor F of G is called a Hamiltonian [a, b]-factor if F contains a Hamiltonian cycle. In this paper, it is proved that G has a Hamiltonian [a, b]-factor if |NG(X)| > (a−1)n+|X|−1 a+b−3 for every nonempty independent subset X of V (G) and δ(G) > (a−1)n+a+b−4 a+b−3 .

Keywords: graph, minimum degree, neighborhood, [a, b]-factor, Hamiltonian [a, b]-factor.

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Authors: Shirong Li, Xueping Xiang

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Construction site safety in China has aroused comprehensive concern all over the world. It is imperative to investigate the main causes of poor construction site safety. This paper divides all the causes into four aspects, namely the factors of workers, object, environment and management and sets up the accident causes element system based on Delphi Method. This is followed by the application of structural equation modeling to examine the importance of each aspect of causes from the standpoints of different roles related to the construction respectively. The results indicate that all the four aspects of factors are in need of improvement, and different roles have different ideas considering the priority of those factors. The paper has instructive significance for the practitioners to take measures to improve construction site safety in China accordingly.

Keywords: construction site safety, Delphi Method, structuralequation modeling, different perspective.

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Authors: Titin Andri Wihastuti, Djanggan Sargowo

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NFκB is a transcription factor regulating many function of the vessel wall. In the normal condition , NFκB is revealed diffuse cytoplasmic expressionsuggesting that the system is inactive. The presence of activation NFκB provide a potential pathway for the rapid transcriptional of a variety of genes encoding cytokines, growth factors, adhesion molecules and procoagulatory factors. It is likely to play an important role in chronic inflamatory disease involved atherosclerosis. There are many stimuli with the potential to active NFκB, including hyperlipidemia. We used 24 mice which was divided in 6 groups. The HFD given by et libitum procedure during 2, 4, and 6 months. The parameters in this study were the amount of NFKB activation ,H2O2 as ROS and VCAM-1 as a product of NFKB activation. H2O2 colorimetryc assay performed directly using Anti Rat H2O2 ELISA Kit. The NFKB and VCAM-1 detection obtained from aorta mice, measured by ELISA kit and imunohistochemistry. There was a significant difference activation of H2O2, NFKB and VCAM-1 level at induce HFD after 2, 4 and 6 months. It suggest that HFD induce ROS formation and increase the activation of NFKB as one of atherosclerosis marker that caused by hyperlipidemia as classical atheroschlerosis risk factor.

Keywords: High Fat Diet, NFKB, H2O2, atherosclerosis

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Authors: Keun Woo Lee, Minky Son, Chanin Park, Ayoung Baek

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Certain tRNA synthetases have developed highly accurate molecular machinery to discriminate their cognate amino acids. Those aaRSs achieve their goal via editing reaction in the Connective Polypeptide 1 (CP1). Recently mutagenesis studies have revealed the critical importance of residues in the CP1 domain for editing activity and X-ray structures have shown binding mode of noncognate amino acids in the editing domain. To pursue molecular mechanism for amino acid discrimination, molecular modeling studies were performed. Our results suggest that aaRS bind the noncognate amino acid more tightly than the cognate one. Finally, by comparing binding conformations of the amino acids in three systems, the amino acid binding mode was elucidated and a discrimination mechanism proposed. The results strongly reveal that the conserved threonines are responsible for amino acid discrimination. This is achieved through side chain interactions between T252 and T247/T248 as well as between those threonines and the incoming amino acids.

Keywords: Amino acid discrimination, Binding free energy Leucyl-tRNAsynthetase, Molecular dynamics.

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Authors: Hai-Ying Liu, Yi-Hao Chen, Shu-Yin Pang, Feng-Hua Wang, Xiao-Fang Peng, Li-Yuan Yang, Zheng-Rong Chen, Yi Chen, Bing Zhu

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Objective: Biliary atresia (BA) is characterized by progressive liver fibrosis. Epithelial-mesenchymal transition (EMT) has been implicated as a key mechanism in the pathogenesis of organ fibrosis. MiR-200a has been shown to repress EMT. We aim to explore the role of miR-200a in the fibrogenesis of BA. Methods: We obtained the plasma samples and liver samples from patients with BA or controls to examine the role of miR-200a. Histological liver fibrosis was assessed using the Ishak fibrosis scores. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was performed to detect the expression of miR-200a in plasma. We also evaluated the expression of miR-200a in liver tissues using tyramide signal amplification fluorescence in situ hybridization (TSA-FISH). The expression of EMT related proteins zinc finger E-box-binding homeobox 1 (ZEB1), E-cadherin and α-smooth muscle actin (α-SMA) in the liver sections were detected by immunohistochemical staining. Results: We found that the expression of miR-200a was both elevated in the plasma and liver tissues from BA patients compared with the controls. The hepatic expression of ZEB1 and α-SMA were markedly increased in the liver sections from BA patients compared to the controls, whereas E-cadherin was downregulated in the BA group. Simultaneously, we noted that the hepatic expression of miR-200a, E-cadherin and α-SMA were upregulated with the progression of liver fibrosis in the BA group, while ZEB1 was downregulated with the progression of liver fibrosis in BA patients. Conclusion: These findings suggest EMT has a critical effect on the fibrotic process of BA, and the interaction between miR-200a and ZEB1 may regulate EMT and eventually influence liver fibrogenesis of BA.

Keywords: Biliary atresia, liver fibrosis, MicroRNA, epithelial-mesenchymal transition, zinc finger e-box-binding homeobox 1.

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Authors: Sizhong Zhou, Bingyuan Pu

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Let G be a Hamiltonian graph. A factor F of G is called a Hamiltonian factor if F contains a Hamiltonian cycle. In this paper, two sufficient conditions are given, which are two neighborhood conditions for a Hamiltonian graph G to have a Hamiltonian factor.

Keywords: graph, neighborhood, factor, Hamiltonian factor.

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Authors: Erika Pigliapoco, Valerio Freschi, Alessandro Bogliolo

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This work presents a new phonetic transcription system based on a tree of hierarchical pronunciation rules expressed as context-specific grapheme-phoneme correspondences. The tree is automatically inferred from a phonetic dictionary by incrementally analyzing deeper context levels, eventually representing a minimum set of exhaustive rules that pronounce without errors all the words in the training dictionary and that can be applied to out-of-vocabulary words. The proposed approach improves upon existing rule-tree-based techniques in that it makes use of graphemes, rather than letters, as elementary orthographic units. A new linear algorithm for the segmentation of a word in graphemes is introduced to enable outof- vocabulary grapheme-based phonetic transcription. Exhaustive rule trees provide a canonical representation of the pronunciation rules of a language that can be used not only to pronounce out-of-vocabulary words, but also to analyze and compare the pronunciation rules inferred from different dictionaries. The proposed approach has been implemented in C and tested on Oxford British English and Basic English. Experimental results show that grapheme-based rule trees represent phonetically sound rules and provide better performance than letter-based rule trees.

Keywords: Automatic phonetic transcription, pronunciation rules, hierarchical tree inference.

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Authors: Pedro Gutemberg de Alcântara Segundinho, José Antonio Matthiesen, Marcelo Rodrigo Carreira

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Timber-concrete structures were recently introduced in Brazil as a viable option for bridge construction on side roads. Binding between timber and concrete is fundamentally important to assure the rigidity and performance of this structural system. The objective of this study was to assess the structural performance of a timber-concrete bridge prototype with width of 170cm and span of 400cm, whose binding among timber beams and concrete slabs was made with metal pins, obtained from CA 50 construction steel bars of 12.5mm diameter. It was possible to conclude, from the results obtained experimentally in laboratory, that the timber-concrete bridge prototype showed a good structural performance. This structural system provides an economical, rapid implementation solution, which may be used on side roads, favoring regional integration and agricultural production flow.

Keywords: Binding, bridge prototype, timber and concrete

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Authors: Chang-Guk Sun, Jin-Soo Shin

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In this study, an inland metropolitan area, Gwangju, in Korea was selected to assess the amplification potential of earthquake motion and provide the information for regional seismic countermeasure. A geographic information system-based expert system was implemented for reliably predicting the spatial geotechnical layers in the entire region of interesting by building a geo-knowledge database. Particularly, the database consists of the existing boring data gathered from the prior geotechnical projects and the surface geo-knowledge data acquired from the site visit. For practical application of the geo-knowledge database to estimate the earthquake hazard potential related to site amplification effects at the study area, seismic zoning maps on geotechnical parameters, such as the bedrock depth and the site period, were created within GIS framework. In addition, seismic zonation of site classification was also performed to determine the site amplification coefficients for seismic design at any site in the study area. KeywordsEarthquake hazard, geo-knowledge, geographic information system, seismic zonation, site period.

Keywords: Earthquake hazard, geo-knowledge, geographic information system, seismic zonation, site period.

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

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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: James D. Clark, Bernard H. Stark

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The paper presents a modelling methodology for small scale multi-source renewable energy systems. Using historical site-specific weather data, the relationships of cost, availability and energy form are visualised as a function of the sizing of photovoltaic arrays, wind turbines, and battery capacity. The specific dependency of each site on its own particular weather patterns show that unique solutions exist for each site. It is shown that in certain cases the capital component cost can be halved if the desired theoretical demand availability is reduced from 100% to 99%.

Keywords: Energy Analysis, Forecasting, Distributed powergeneration.

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Authors: B. Chouhan, A. Denesyuk, J. Heino, M. S. Johnson, K. Denessiouk

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Integrins are a large family of multidomain α/β cell signaling receptors. Some integrins contain an additional inserted I domain, whose earliest expression appears to be with the chordates, since they are observed in the urochordates Ciona intestinalis (vase tunicate) and Halocynthia roretzi (sea pineapple), but not in integrins of earlier diverging species. The domain-s presence is viewed as a hallmark of integrins of higher metazoans, however in vertebrates, there are clearly three structurally-different classes: integrins without I domains, and two groups of integrins with I domains but separable by the presence or absence of an additional αC helix. For example, the αI domains in collagen-binding integrins from Osteichthyes (bony fish) and all higher vertebrates contain the specific αC helix, whereas the αI domains in non-collagen binding integrins from vertebrates and the αI domains from earlier diverging urochordate integrins, i.e. tunicates, do not. Unfortunately, within the early chordates, there is an evolutionary gap due to extinctions between the tunicates and cartilaginous fish. This, coupled with a knowledge gap due to the lack of complete genomic data from surviving species, means that the origin of collagen-binding αC-containing αI domains remains unknown. Here, we analyzed two available genomes from Callorhinchus milii (ghost shark/elephant shark; Chondrichthyes – cartilaginous fish) and Petromyzon marinus (sea lamprey; Agnathostomata), and several available Expression Sequence Tags from two Chondrichthyes species: Raja erinacea (little skate) and Squalus acanthias (dogfish shark); and Eptatretus burgeri (inshore hagfish; Agnathostomata), which evolutionary reside between the urochordates and osteichthyes. In P. marinus, we observed several fragments coding for the αC-containing αI domain, allowing us to shed more light on the evolution of the collagen-binding integrins.

Keywords: Integrin αI domain, integrin evolution, collagen binding, structure, αC helix

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Authors: Simon Brown, Raewyn Tuffery

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Candida albicans ATCC 10231 had low endogenous activity of the alternative oxidase compared with that of C. albicans ATCC 10261. In C. albicans ATCC 10231 the endogenous activity declined as the cultures aged. Alternative oxidase activity could be induced in C. albicans ATCC 10231 by treatment with cyanide, but the induction of this activity required the presence of oxygen which could be replaced, at least in part, with high concentrations of potassium ferricyanide. We infer from this that the expression of the gene encoding the alternative oxidase is under the control of a redoxsensitive transcription factor.

Keywords: alternative oxidase, Candida albicans, enzymeinduction, oxygen, redox potential.

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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: A. K. Abd El-Aleem, W. F. Abd El-wahed, N. A. Ismail, F. A. Torkey

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This study suggests a model of a new set of evaluation criteria that will be used to measure the efficiency of real-world E-commerce websites. Evaluation criteria include design, usability and performance for websites, the Data Envelopment Analysis (DEA) technique has been used to measure the websites efficiency. An efficient Web site is defined as a site that generates the most outputs, using the smallest amount of inputs. Inputs refer to measurements representing the amount of effort required to build, maintain and perform the site. Output is amount of traffic the site generates. These outputs are measured as the average number of daily hits and the average number of daily unique visitors.

Keywords: Data Envelopment Analysis, E-commerce, Efficiency.

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Authors: Ma. Rosario Concepcion O. Ang, Luis Caezar Ian K. Panganiban, Charmyne B. Mamador, Oliver Dan G. De Luna, Michael D. Bausas, Joselito P. Cruz

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PhilSHORE is a multi-site, multi-device and multicriteria decision support tool designed to support the development of tidal current energy in the Philippines. Its platform is based on Geographic Information Systems (GIS) which allows for the collection, storage, processing, analyses and display of geospatial data. Combining GIS tools with open source web development applications, PhilSHORE becomes a webGIS-based marine spatial planning tool. To date, PhilSHORE displays output maps and graphs of power and energy density, site suitability and site-device analysis. It enables stakeholders and the public easy access to the results of tidal current energy resource assessments and site suitability analyses. Results of the initial development show that PhilSHORE is a promising decision support tool for ORE project developments.

Keywords: GIS, Site Suitability Analysis, Tidal Current Energy Resource Assessment, WebGIS.

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Authors: F. Iscan, C. Yagci

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Rapid population growth, urbanization and industrialization are known as the most important factors of environment problems. Elimination and management of solid wastes are also within the most important environment problems. One of the main problems in solid waste management is the selection of the best site for elimination of solid wastes. Lately, Geographical Information System (GIS) has been used for easing selection of landfill area. GIS has the ability of imitating necessary economic, environmental and political limitations. They play an important role for the site selection of landfill area as a decision support tool. In this study; map layers will be studied for minimum effect of environmental, social and cultural factors and maximum effect for engineering/economic factors for site selection of landfill areas and using GIS for a decision support mechanism in solid waste landfill areas site selection will be presented in Aksaray/Turkey city, Güzelyurt district practice.

Keywords: GIS, landfill, solid waste, spatial analysis.

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Authors: Yen-Cheng Chen, Fu-Chen Yang

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IETF defines mobility support in IPv6, i.e. MIPv6, to allow nodes to remain reachable while moving around in the IPv6 internet. When a node moves and visits a foreign network, it is still reachable through the indirect packet forwarding from its home network. This triangular routing feature provides node mobility but increases the communication latency between nodes. This deficiency can be overcome by using a Binding Update (BU) scheme, which let nodes keep up-to-date IP addresses and communicate with each other through direct IP routing. To further protect the security of BU, a Return Routability (RR) procedure was developed. However, it has been found that RR procedure is vulnerable to many attacks. In this paper, we will propose a lightweight RR procedure based on geometric computing. In consideration of the inherent limitation of computing resources in mobile node, the proposed scheme is developed to minimize the cost of computations and to eliminate the overhead of state maintenance during binding updates. Compared with other CGA-based BU schemes, our scheme is more efficient and doesn-t need nonce tables in nodes.

Keywords: Mobile IPv6, Binding update, Geometric computing.

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Authors: Göksu Gözen Citak

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The process of constructing a scale measuring the attitudes of youth toward violence on televisions is reported. A 30-item draft attitude scale was applied to a working group of 232 students attending the Faculty of Educational Sciences at Ankara University between the years 2005-2006. To introduce the construct validity and dimensionality of the scale, exploratory and confirmatory factor analysis was applied to the data. Results of the exploratory factor analysis showed that the scale had three factors that accounted for 58,44% (22,46% for the first, 22,15% for the second and 13,83% for the third factor) of the common variance. It is determined that the first factor considered issues related individual effects of violence on televisions, the second factor concerned issues related social effects of violence on televisions and the third factor concerned issues related violence on television programs. Results of the confirmatory factor analysis showed that all the items under each factor are fitting the concerning factors structure. An alpha reliability of 0,90 was estimated for the whole scale. It is concluded that the scale is valid and reliable.

Keywords: Attitudes toward violence, confirmatory factor analysis, constructing attitude scale, exploratory factor analysis, violence on televisions.

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Authors: R. Testoni, R. Levizzari, M. De Salve

Abstract:

Radioactive waste management is fundamental to safeguard population and environment by radiological risks. Environmental assessment of a site, where nuclear activities are located, allows understanding the hydro geological system and the radionuclides transport in groundwater and subsoil. Use of dedicated software is the basis of transport phenomena investigation and for dynamic scenarios prediction; this permits to understand the evolution of accidental contamination events, but at the same time the potentiality of the software itself can be verified. The aim of this paper is to perform a numerical analysis by means of HYDRUS 1D code, so as to evaluate radionuclides transport in a nuclear site in Piedmont region (Italy). In particular, the behavior in vadose zone was investigated. An iterative assessment process was performed for risk assessment of radioactive contamination. The analysis therein developed considers the following aspects: i) hydro geological site characterization; ii) individuation of the main intrinsic and external site factors influencing water flow and radionuclides transport phenomena; iii) software potential for radionuclides leakage simulation purposes.

Keywords: HYDRUS 1D, radionuclides transport phenomena, site characterization.

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Authors: I. Blazkova, A. Moulick, V. Milosavljevic, P. Kopel, M. Vaculovicova, V. Adam, R. Kizek

Abstract:

Doxorubicin (DOX) is an anthracycline drug used to treat many cancer diseases. Similarly to other cytostatic drugs, DOX has serious side effects; the biggest obstacle is the cardiotoxicity. With the aim of lowering the negative side effects and to target the DOX into the tumor tissue, the different nanoparticles (NPs) are studied. The aim of this work was to synthetized different NPs and conjugated them with DOX and determine the binding capacity of the NPs. For this experiment, carbon nanotubes (CNTs), graphene oxide (GO), fullerene (FUL) and liposomes (LIP) were used. The highest binding capacity was observed in GO (85%). Subsequently the toxicity of NPs and NPs-DOX conjugates was analyzed in in vivo system (chicken embryos). Some NPs (GO) can increase the toxicity of DOX, whereas other NPs (LIP, CNTs) decrease DOX toxicity.

Keywords: Chicken embryos, Doxorubicin, Nanotransporters, Toxicity

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Authors: V.R Gannapathy, S.K Subramaniam, A.B Mohamad Diah, M.K Suaidi, A.H Hamidon

Abstract:

The picture of a perfect road construction site is the one that utilizes conventional vertical road signs and a flagman to optimize the traffic flow with minimum hazel to the public. Former research has been carried out by Department of Occupational Safety and Health (DOSH) and Ministry of Works to further enhance smoothness in traffic operations and particularly in safety issues within work zones. This paper highlights on hazardous zones in a certain road construction or road maintenance site. Most cases show that the flagman falls into high risk of fatal accidents within work zone. Various measures have been taken by both the authorities and contractors to overcome such miseries, yet it-s impossible to eliminate the usage of a flagman since it is considered the best practice. With the implementation of new technologies in automating the traffic flow in road construction site, it is possible to eliminate the usage of a flagman. The intelligent traffic light system is designed to solve problems which contribute hazardous at road construction site and to be inline with the road safety regulation which is taken into granted.

Keywords: Intelligent Traffic Light, Critical Zones, Safety Regulation, Flagman

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Authors: Seyed Abolhasan Naeini, Saeideh Mohammadi

Abstract:

Site response has a profound effect on earthquake damages. Seismic interaction of urban tunnels with surface structures could also affect seismic site response. Here, we use FLAC 2D to investigate the interaction of a single tunnel and twin tunnels-surface structures on the site response. Soil stratification and properties are selected based on Line. No 7 of the Tehran subway. The effect of surface structure is considered in two ways: Equivalent surcharge and geometrical modeling of the structure. Comparison of the results shows that consideration of the structure geometry is vital in dynamic analysis and leads to the changes in the magnitude of displacements, accelerations and response spectrum. Therefore it is necessary for the surface structures to be wholly modeled and not just considered as a surcharge in dynamic analysis. The use of twin tunnel also leads to the reduction of dynamic residual settlement.

Keywords: Superstructure, tunnel, site response, surcharge, interaction.

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