Search results for: Binding update

Authors: Sizhong Zhou, Yang Xu

Abstract:

A graph G is fractional k-covered if for each edge e of G, there exists a fractional k-factor h, such that h(e) = 1. If k = 2, then a fractional k-covered graph is called a fractional 2-covered graph. The binding number bind(G) is defined as follows, bind(G) = min{|NG(X)| |X| : ├ÿ = X Ôèå V (G),NG(X) = V (G)}. In this paper, it is proved that G is fractional 2-covered if δ(G) ≥ 4 and bind(G) > 5 3 .

Keywords: graph, binding number, fractional k-factor, fractional k-covered graph.

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Authors: S. Farokhzad, M. Reza Salehnamadi

Abstract:

Grid environments include aggregation of geographical distributed resources. Grid is put forward in three types of computational, data and storage. This paper presents a research on data grid. Data grid is used for covering and securing accessibility to data from among many heterogeneous sources. Users are not worry on the place where data is located in it, provided that, they should get access to the data. Metadata is used for getting access to data in data grid. Presently, application metadata catalogue and SRB middle-ware package are used in data grids for management of metadata. At this paper, possibility of updating, streamlining and searching is provided simultaneously and rapidly through classified table of preserving metadata and conversion of each table to numerous tables. Meanwhile, with regard to the specific application, the most appropriate and best division is set and determined. Concurrency of implementation of some of requests and execution of pipeline is adaptability as a result of this technique.

Keywords: Grids, data grid, metadata, update.

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

Abstract:

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: H. Ghanbarpour Asl, S. H. Pourtakdoust

Abstract:

Extended Kalman Filter (EKF) is probably the most widely used estimation algorithm for nonlinear systems. However, not only it has difficulties arising from linearization but also many times it becomes numerically unstable because of computer round off errors that occur in the process of its implementation. To overcome linearization limitations, the unscented transformation (UT) was developed as a method to propagate mean and covariance information through nonlinear transformations. Kalman filter that uses UT for calculation of the first two statistical moments is called Unscented Kalman Filter (UKF). Square-root form of UKF (SRUKF) developed by Rudolph van der Merwe and Eric Wan to achieve numerical stability and guarantee positive semi-definiteness of the Kalman filter covariances. This paper develops another implementation of SR-UKF for sequential update measurement equation, and also derives a new UD covariance factorization filter for the implementation of UKF. This filter is equivalent to UKF but is computationally more efficient.

Keywords: Unscented Kalman filter, Square-root unscentedKalman filter, UD covariance factorization, Target tracking.

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Authors: S. Ashrafpour, T. Tohidi Moghadam, B. Ranjbar

Abstract:

Identifying the nature of protein-nanoparticle interactions and favored binding sites is an important issue in functional characterization of biomolecules and their physiological responses. Herein, interaction of silver nanoparticles with lysozyme as a model protein has been monitored via fluorescence spectroscopy. Formation of complex between the biomolecule and silver nanoparticles (AgNPs) induced a steady state reduction in the fluorescence intensity of protein at different concentrations of nanoparticles. Tryptophan fluorescence quenching spectra suggested that silver nanoparticles act as a foreign quencher, approaching the protein via this residue. Analysis of the Stern-Volmer plot showed quenching constant of 3.73 μM−1. Moreover, a single binding site in lysozyme is suggested to play role during interaction with AgNPs, having low affinity of binding compared to gold nanoparticles. Unfolding studies of lysozyme showed that complex of lysozyme- AgNPs has not undergone structural perturbations compared to the bare protein. Results of this effort will pave the way for utilization of sensitive spectroscopic techniques for rational design of nanobiomaterials in biomedical applications.

Keywords: Nanocarrier, Nanoparticles, Surface Plasmon Resonance, Quenching Fluorescence.

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Authors: Mansour Tarafdar, Mohammad Saniee Abade

Abstract:

This paper investigates the problem of sampling from transactional data streams. We introduce CFISDS as a content based sampling algorithm that works on a landmark window model of data streams and preserve more informed sample in sample space. This algorithm that work based on closed frequent itemset mining tasks, first initiate a concept lattice using initial data, then update lattice structure using an incremental mechanism.Incremental mechanism insert, update and delete nodes in/from concept lattice in batch manner. Presented algorithm extracts the final samples on demand of user. Experimental results show the accuracy of CFISDS on synthetic and real datasets, despite on CFISDS algorithm is not faster than exist sampling algorithms such as Z and DSS.

Keywords: Sampling, data streams, closed frequent item set mining.

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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: A. Żebrowska, A. Kochańska-Dziurowicz, A. Stanjek-Cichoracka

Abstract:

We investigated the response of testosterone (T), growth hormone (GH), cortisol (C), steroid hormone binding globulin (SHBG), insulin-like growth factor (IGF-1), insulin-like growth factor binding protein-3 (IGFBP-3), and some anaboliccatabolic indexes, i.e.: T/C, T/SHBG, and IGF-1/IGFBP-3 to maximal exercise in endurance-trained athletes (TREN) and untrained subjects (CG). The baseline concentration of IGF-1 was higher in athletes (TREN) when compared to the CG (p<0.05). The GH concentration and GH/IGF-1 ratio increased after exercise in all subjects compared to respective values at rest. The resting IGF- 1/IGFBP-3 ratio was significantly higher in athletes. The maximal exercise test induced an increase in post-exercise T/SHGB ratio in athletes compared to CG (p<0.05). These results indicate that elevation of baseline serum IGF-1/IGFBP-3 and T/SHGB ratio after exercise might suggest that free fractions of these hormones may act as a potent stimulant of muscle hypertrophy in trained endurance athletes.

Keywords: anabolic hormones, endurance training, exercise, growth factors

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Authors: Perapong Vichitkraivin, Orachat Chitsobhuk

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In this paper, an improvement of PDLZW implementation with a new dictionary updating technique is proposed. A unique dictionary is partitioned into hierarchical variable word-width dictionaries. This allows us to search through dictionaries in parallel. Moreover, the barrel shifter is adopted for loading a new input string into the shift register in order to achieve a faster speed. However, the original PDLZW uses a simple FIFO update strategy, which is not efficient. Therefore, a new window based updating technique is implemented to better classify the difference in how often each particular address in the window is referred. The freezing policy is applied to the address most often referred, which would not be updated until all the other addresses in the window have the same priority. This guarantees that the more often referred addresses would not be updated until their time comes. This updating policy leads to an improvement on the compression efficiency of the proposed algorithm while still keep the architecture low complexity and easy to implement.

Keywords: lossless data compression, LZW algorithm, PDLZW algorithm, WSC and dictionary update.

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Authors: K. Diwakar, N. Vasudevan, C. Senthilpari

Abstract:

This paper presents MOSFET based analog to digital converter which is simple in design, has high resolution, and conversion rate better than dual slope ADC. It has no DAC which will limit the performance, no error in conversion, can operate for wide range of inputs and never become unstable. One of the industrial applications, where the proposed high resolution MOSFET ADC can be used is, for the positioning of control valves in a multi channel data acquisition and control system (DACS), using stepper motors as actuators of control valves. It is observed that in a DACS having ten control valves, 0.02% of positional accuracy of control valves can be achieved with the data update period of 250ms and with stepper motors of maximum pulse rate 20 Kpulses per sec. and minimum pulse width of 2.5 μsec. The reported accuracy so far by other authors is 0.2%, with update period of 255 ms and with 8 bit DAC. The accuracy in the proposed configuration is limited by the available precision stepper motor and not by the MOSFET based ADC.

Keywords: MOSFET based ADC, Actuators, Positional accuracy, Stepper Motors.

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Authors: Chunshien Li, Jhao-Wun Hu, Tai-Wei Chiang, Tsunghan Wu

Abstract:

Time series forecasting is an important and widely popular topic in the research of system modeling. This paper describes how to use the hybrid PSO-RLSE neuro-fuzzy learning approach to the problem of time series forecasting. The PSO algorithm is used to update the premise parameters of the proposed prediction system, and the RLSE is used to update the consequence parameters. Thanks to the hybrid learning (HL) approach for the neuro-fuzzy system, the prediction performance is excellent and the speed of learning convergence is much faster than other compared approaches. In the experiments, we use the well-known Mackey-Glass chaos time series. According to the experimental results, the prediction performance and accuracy in time series forecasting by the proposed approach is much better than other compared approaches, as shown in Table IV. Excellent prediction performance by the proposed approach has been observed.

Keywords: forecasting, hybrid learning (HL), Neuro-FuzzySystem (NFS), particle swarm optimization (PSO), recursiveleast-squares estimator (RLSE), time series

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Authors: Wei Yan, Wei Dong

Abstract:

Facing the understanding problem of update and preservation of urban history space under background of rapid Chinese urbanization, so at first there is a need to dig the philosophic principles of “antithesis” and “unification” which are contained in the traditional Chinese literature known as “antithesis” and do the job of planning translation by personal understanding in order to form understanding and value systems of dialectical urban history space under the foundation of “antithesis”. Then we could put forward a “context” concept for urban history space under the foregoing basis. After that, we will take the update and preservation of Ningbo Tianyi Pavilion’s historical district as an example to discuss problems related to understanding of urban history area under the basis of Chinese tradition culture, improvement of value system, construction of urban trait space and Chinese “localization” of planning theory.

Keywords: Antithesis, traditional values, City renewal and conservation, the “context” of city history space.

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Authors: A. Amar, O. Hemeda

Abstract:

A study of the structure of the nucleus with the analogy by solid-state physics has been developed. We have used binding energy to calculate R (a parameter that is proportional to the radius of the nucleus) for deuteron, alpha, and ⁸Be. The calculated parameter r calculated from solid state physics produces a probe for calculation the nuclear radii. ⁸Be has special attention as it is radioactive nucleus and the latest nucleus to be calculated from crystalline model approach. The distribution of nucleons inside the nucleus is taken to be tetrahedral for ¹⁶O. The model has failed to expect the radius of ⁹Be which is an impression about the modification should be done on the model at near future. A comparison between our calculations and those from literature has been made, and a good agreement has been obtained.

Keywords: The structure of the nucleus, binding energy, crystalline model approach, nuclear radii, tetrahedral for 16O.

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Authors: Z. Zainuddin, W. D. Wan Rosli, R. Lanouette, S. Sathasivam

Abstract:

This paper reports work done to improve the modeling of complex processes when only small experimental data sets are available. Neural networks are used to capture the nonlinear underlying phenomena contained in the data set and to partly eliminate the burden of having to specify completely the structure of the model. Two different types of neural networks were used for the application of pulping problem. A three layer feed forward neural networks, using the Preconditioned Conjugate Gradient (PCG) methods were used in this investigation. Preconditioning is a method to improve convergence by lowering the condition number and increasing the eigenvalues clustering. The idea is to solve the modified odified problem M-1 Ax= M-1b where M is a positive-definite preconditioner that is closely related to A. We mainly focused on Preconditioned Conjugate Gradient- based training methods which originated from optimization theory, namely Preconditioned Conjugate Gradient with Fletcher-Reeves Update (PCGF), Preconditioned Conjugate Gradient with Polak-Ribiere Update (PCGP) and Preconditioned Conjugate Gradient with Powell-Beale Restarts (PCGB). The behavior of the PCG methods in the simulations proved to be robust against phenomenon such as oscillations due to large step size.

Keywords: Convergence, pulping modeling, neural networks, preconditioned conjugate gradient.

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Authors: Ibrahim Gomaa, Hoda M. O. Mokhtar

Abstract:

Although most of the existing skyline queries algorithms focused basically on querying static points through static databases; with the expanding number of sensors, wireless communications and mobile applications, the demand for continuous skyline queries has increased. Unlike traditional skyline queries which only consider static attributes, continuous skyline queries include dynamic attributes, as well as the static ones. However, as skyline queries computation is based on checking the domination of skyline points over all dimensions, considering both the static and dynamic attributes without separation is required. In this paper, we present an efficient algorithm for computing continuous skyline queries without discriminating between static and dynamic attributes. Our algorithm in brief proceeds as follows: First, it excludes the points which will not be in the initial skyline result; this pruning phase reduces the required number of comparisons. Second, the association between the spatial positions of data points is examined; this phase gives an idea of where changes in the result might occur and consequently enables us to efficiently update the skyline result (continuous update) rather than computing the skyline from scratch. Finally, experimental evaluation is provided which demonstrates the accuracy, performance and efficiency of our algorithm over other existing approaches.

Keywords: Continuous query processing, dynamic database, moving object, skyline queries.

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Authors: Dhananjay C. Joshi, Jung-Hsin Lin

Abstract:

Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.

Keywords: protein-protein docking, protein-protein interaction, molecular mechanics energetics, Poisson-Boltzmann calculations

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Authors: W. D. Wan Rosli, Z. Zainuddin, R. Lanouette, S. Sathasivam

Abstract:

This paper reports work done to improve the modeling of complex processes when only small experimental data sets are available. Neural networks are used to capture the nonlinear underlying phenomena contained in the data set and to partly eliminate the burden of having to specify completely the structure of the model. Two different types of neural networks were used for the application of Pulping of Sugar Maple problem. A three layer feed forward neural networks, using the Preconditioned Conjugate Gradient (PCG) methods were used in this investigation. Preconditioning is a method to improve convergence by lowering the condition number and increasing the eigenvalues clustering. The idea is to solve the modified problem where M is a positive-definite preconditioner that is closely related to A. We mainly focused on Preconditioned Conjugate Gradient- based training methods which originated from optimization theory, namely Preconditioned Conjugate Gradient with Fletcher-Reeves Update (PCGF), Preconditioned Conjugate Gradient with Polak-Ribiere Update (PCGP) and Preconditioned Conjugate Gradient with Powell-Beale Restarts (PCGB). The behavior of the PCG methods in the simulations proved to be robust against phenomenon such as oscillations due to large step size.

Keywords: Convergence, Modeling, Neural Networks, Preconditioned Conjugate Gradient.

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

Abstract:

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: W. Wiyaratn, A. Watanapa

Abstract:

This study was aimed to study the probability about the production of fiberboard made of durian rind through latex with phenolic resin as binding agent. The durian rind underwent the boiling process with NaOH [7], [8] and then the fiber from durian rind was formed into fiberboard through heat press. This means that durian rind could be used as replacement for plywood in plywood industry by using durian fiber as composite material with adhesive substance. This research would study the probability about the production of fiberboard made of durian rind through latex with phenolic resin as binding agent. At first, durian rind was split, exposed to light, boiled and steamed in order to gain durian fiber. Then, fiberboard was tested with the density of 600 Kg/m3 and 800 Kg/m3. in order to find a suitable ratio of durian fiber and latex. Afterwards, mechanical properties were tested according to the standards of ASTM and JIS A5905-1994. After the suitable ratio was known, the test results would be compared with medium density fiberboard (MDF) and other related research studies. According to the results, fiberboard made of durian rind through latex with phenolic resin at the density of 800 Kg/m3 at ratio of 1:1, the moisture was measured to be 5.05% with specific gravity (ASTM D 2395-07a) of 0.81, density (JIS A 5905-1994) of 0.88 g/m3, tensile strength, hardness (ASTM D2240), flexibility or elongation at break yielded similar values as the ones by medium density fiberboard (MDF).

Keywords: Durian rind, latex, phenolic resin, medium density fiberboard

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Authors: Kakali Bhadra

Abstract:

Harmalol administration caused remarkable reduction in proliferation of HepG₂ cells with GI₅₀ of 14.2 mM, without showing much cytotoxicity in embryonic liver cell line, WRL-68. Data from circular dichroism and differential scanning calorimetric analysis of harmalol-CT DNA complex shows conformational changes with prominent CD perturbation and stabilization of CT DNA by 8 ^oC. Binding constant and stoichiometry was also calculated using the above biophysical techniques. Further, dose dependent apoptotic induction ability of harmalol was studied in HepG₂ cells using different biochemical assays. Generation of ROS, DNA damage, changes in cellular external and ultramorphology, alteration of membrane, formation of comet tail, decreased mitochondrial membrane potential and a significant increase in Sub G_o/G₁ population made the cancer cell, HepG₂, prone to apoptosis. Up regulation of p53 and caspase 3 further indicated the apoptotic role of harmalol.

Keywords: Apoptosis, beta carboline alkaloid, comet assay, cytotoxicity, ROS.

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Authors: Youngsuck Ji, Youngjoon Han, Hernsoo Hahn

Abstract:

In this paper, we proposed the robust mobile object detection method for light effect in the night street image block based updating reference background model using block state analysis. Experiment image is acquired sequence color video from steady camera. When suddenly appeared artificial illumination, reference background model update this information such as street light, sign light. Generally natural illumination is change by temporal, but artificial illumination is suddenly appearance. So in this paper for exactly detect artificial illumination have 2 state process. First process is compare difference between current image and reference background by block based, it can know changed blocks. Second process is difference between current image-s edge map and reference background image-s edge map, it possible to estimate illumination at any block. This information is possible to exactly detect object, artificial illumination and it was generating reference background more clearly. Block is classified by block-state analysis. Block-state has a 4 state (i.e. transient, stationary, background, artificial illumination). Fig. 1 is show characteristic of block-state respectively [1]. Experimental results show that the presented approach works well in the presence of illumination variance.

Keywords: Block-state, Edge component, Reference backgroundi, Artificial illumination.

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Authors: Musammat F. Nahar, Anna Roujeinikova

Abstract:

Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.

Keywords: Helicobacter pylori, molecular chaperone DnaK, pyrrhocoricin, structural biology.

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Authors: M. Jahangiri Lahkani, Gh. Ghassemi, N. Sohrabi, N. Rasooli

Abstract:

Geometry optimizations of metal complexes of Salen(bis(Salicylidene)1,2-ethylenediamine) were carried out at HF and DFT methods employing Lanl2DZ basis set. In this work structural, energies, bond lengths and other physical properties between Mn2+,Cu2+ and Ni2+ ions coordinated by salen–type ligands are examined. All calculations were performed using Gaussian 98W program series. To investigate local aromaticities, NICS were calculated at all centers of rings. The higher the band gap indicating a higher global aromaticity. The possible binding energies have been evaluated. We have evaluated Frequencies and Zero-point energy with freq calculation. The NICS(Nucleous Independent Chemical Shift) Results show Ni(II) complexes are antiaromatic and aromaticites of Mn(II) complexes are larger than Cu(II) complexes. The energy Results show Cu(II) complexes are stability than Mn(II) and Ni(II) complexes.

Keywords: Frequency Calculation, Hartree-Fock (HF), Nucleous Independent Chemical Shift (NICS), Salen(bis(Salicylidene)1, 2-ethylenediamine).

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Authors: Aiman Elragig, Hanan Dreiwi, Dung Ly, Idriss Elmabrook

Abstract:

This paper highlights a new approach to look at online principle components analysis (OPCA). Given a data matrix X ∈ R,^m x n we characterise the online updates of its covariance as a matrix perturbation problem. Up to the principle components, it turns out that online updates of the batch PCA can be captured by symmetric matrix perturbation of the batch covariance matrix. We have shown that as n→ n0 >> 1, the batch covariance and its update become almost similar. Finally, utilize our new setup of online updates to find a bound on the angle distance of the principle components of X and its update.

Keywords: Online data updates, covariance matrix, online principle component analysis (OPCA), matrix perturbation.

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Authors: Mahasen M. Abdel-Mageed, H. S. Zaghloul

Abstract:

Annihilations, phase shifts, scattering lengths and elastic cross sections of low energy positrons scattering from magnesium atoms were studied using the least-squares variational method (LSVM). The possibility of positron binding to the magnesium atoms is investigated. A trial wave function is suggested to represent e+-Mg elastic scattering and scattering parameters were derived to estimate the binding energy and annihilation rates. The trial function is taken to depend on several adjustable parameters, and is improved iteratively by increasing the number of terms. The present results have the same behavior as reported semi-empirical, theoretical and experimental results. Especially, the estimated positive scattering length supports the possibility of positronmagnesium bound state system that was confirmed in previous experimental and theoretical work.

Keywords: Bound wave function, Positron Annihilation, scattering phase shift, scattering length.

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Authors: D. Bhaskar, N. R. Wadehra, M. Gulati, A. Narula, R. Vishnu, G. Katyal

Abstract:

With drug resistance becoming widespread in Plasmodium falciparum infections, the development of the alternative drugs is the desired strategy for prevention and cure of malaria. Three drug targets were selected to screen promising drug molecules from the GSK library of 13469 molecules. Using an in silico structure-based drug designing approach, the differences in binding energies of the substrate and inhibitor were exploited between target sites of parasite and human to design a drug molecule against Plasmodium. The docking studies have shown several promising molecules from GSK library with more effective binding as compared to the already known inhibitors for the drug targets. Though stronger interaction has been shown by several molecules as compared to the reference, few molecules have shown the potential as drug candidates though in vitro studies are required to validate the results. In case of thymidylate synthase-dihydrofolatereductase (TS-DHFR), three compounds have shown promise for future studies as potential drugs.

Keywords: Drug resistance, Drug targets, In silico studies, Plasmodium falciparum.

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Authors: A. Meeprasert, W. Khuntawee, S. Hannongbua, T. Rungrotmongkol

Abstract:

Viral influenza A subtypes H5N1 and pandemic H1N1 (pH1N1) have worldwide emerged and transmitted. The most common anti-influenza drug for treatment of both seasonal and pandemic influenza viruses is oseltamivir that nowadays becomes resistance to influenza neuraminidase. The novel long-acting drug, laninamivir, was discovered for treatment of the patients infected with influenza B and influenza A viruses. In the present study, laninamivir complexed with wild-type strain of both H5N1 and pH1N1 viruses were comparatively determined the structures and drug-target interactions by means of molecular dynamics (MD) simulations. The results show that the hydrogen bonding interactions formed between laninamivir and its binding residues are likely similar for the two systems. Additionally, the presence of intermolecular interactions from laninamivir to the residues in the binding pocket is established through their side chains in accordance with hydrogen bond interactions.

Keywords: Laninamivir, neuraminidase, H5N1, pandemic H1N1, wild-type, MD simulation

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Authors: Maryam Nejat Dehkordi, Per Lincoln, Hassan Momtaz

Abstract:

Interaction of Schiff base complexes of Iron and Manganese: Iron [N, N’ Bis (5- (triphenyl phosphonium methyl) salicylidene) -1, 2 ethanediamine) chloride, [Fe Salen]Cl; Manganese [N, N’ Bis (5- (triphenyl phosphonium methyl) salicylidene) -1, 2 ethanediamine) acetate, were investigated by spectroscopic and isothermal titration calorimetry techniques (ITC). The absorbance spectra of complexes have shown hyper and hypochromism in the presence of DNA that is indication of interaction of complexes with DNA. The linear dichroism (LD) measurements confirmed the bending of DNA in the presence of complexes. Furthermore, Isothermal titration calorimetry experiments approved that complexes bound to DNA on the base of both electrostatic and hydrophobic interactions. More, ITC profile exhibits the existence of two binding phases for the complexes. Antibacterial activity of ligand and complexes were tested in vitro to evaluate their activity against the gram positive and negative bacteria.

Keywords: Schiff base complexes, Linear dichroism (LD), Isothermal titration calorimetry (ITC).

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Authors: Sarka Keprdova, Jiri Bydzovsky

Abstract:

This article describes to what extent the addition of energy by-products into the structures of the technical hemp filling materials influence their properties. The article focuses on the changes in physical-mechanical and thermal technical properties of materials after the addition of ash or FBC ash or slag in the binding component of material. Technical hemp filling materials are made of technical hemp shives bonded by the mixture of cement and dry hydrate lime. They are applicable as fillers of vertical or horizontal structures or roofs. The research used eight types of energy by-products of power or heating plants in the Czech Republic. Secondary energy products were dispensed in three different percentage ratios as a replacement of cement in the binding component. Density, compressive strength and determination of the coefficient of thermal conductivity after 28, 60 and 90 days of curing in a laboratory environment were determined and subsequently evaluated on the specimens produced.

Keywords: Ash, binder, cement, energy by-product, FBC ash (fluidized bed combustion ash), filling materials, shives, slag, technical hemp.

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Authors: Aytekin A.O., Morimura S.

Abstract:

Chitosan is a biopolymer composed of glucosamine and N-acetyl glucosamine. Solubility and viscosity pose problems in some applications. These problems can be overcome with unique modifications. In this study, firstly, chitosan was modified by caffeic acid and thioglycolic acid, separately. Then, growing effects of these modified polymers was observed in U937 cell line. Caffeic acid is a phenolic compound and its modifications act carcinogenic inhibitors in drugs. Thiolated chitosans are commonly being used for drugdelivery systems in various routes, because of enhancing mucoadhesiveness property. U937 cell line was used model cell for leukaemia. Modifications were achieved by 1 – 15 % binding range. Increasing binding ratios showed higher radical-scavenging activity and reducing cell growth, in compared to native chitosan. Caffeic acid modifications showed higher radical-scavenging activity than thiolated chitosans at the same concentrations. Caffeic acid and thioglycolic acid modifications inhibited growth of U937, effectively.

Keywords: Chitosan, U937 cell, caffeic acid, thioglycolic acid

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