Search results for: protein residue contact

Authors: Vernie C. Convicto, Henry P. Aringa, Wilson I. Barredo

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This study presents a conformational model of the helical structures of globular protein particularly ferritin in the framework of white noise path integral formulation by using Associated Legendre functions, Bessel and convolution of Bessel and trigonometric functions as modulating functions. The model incorporates chirality features of proteins and their helix-turn-helix sequence structural motif.

Keywords: Globular protein, modulating function, white noise, winding probability.

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Authors: Leong Lee, Cyriac Kandoth, Jennifer L. Leopold, Ronald L. Frank

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Protein 3D structure prediction has always been an important research area in bioinformatics. In particular, the prediction of secondary structure has been a well-studied research topic. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q3 accuracy of various computational prediction algorithms rarely has exceeded 75%. In a previous paper [1], this research team presented a rule-based method called RT-RICO (Relaxed Threshold Rule Induction from Coverings) to predict protein secondary structure. The average Q3 accuracy on the sample datasets using RT-RICO was 80.3%, an improvement over comparable computational methods. Although this demonstrated that RT-RICO might be a promising approach for predicting secondary structure, the algorithm-s computational complexity and program running time limited its use. Herein a parallelized implementation of a slightly modified RT-RICO approach is presented. This new version of the algorithm facilitated the testing of a much larger dataset of 396 protein domains [2]. Parallelized RTRICO achieved a Q3 score of 74.6%, which is higher than the consensus prediction accuracy of 72.9% that was achieved for the same test dataset by a combination of four secondary structure prediction methods [2].

Keywords: data mining, protein secondary structure prediction, parallelization.

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Authors: Elaheh Jooybar, Mohammad J. Abdekhodaie, Marcel Karperien, Pieter J. Dijkstra

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In this study, hyaluronic acid (HA) microgels were developed for the goal of protein delivery. First, a hyaluronic acid-tyramine conjugate (HA-TA) was synthesized with a degree of substitution of 13 TA moieties per 100 disaccharide units. Then, HA-TA microdroplets were produced using a water in oil emulsion method and crosslinked in the presence of horseradish peroxidase (HRP) and hydrogen peroxide (H₂O₂). Loading capacity and the release kinetics of lysozyme and BSA, as model proteins, were investigated. It was shown that lysozyme, a cationic protein, can be incorporated efficiently in the HA microgels, while the loading efficiency for BSA, as a negatively charged protein, is low. The release profile of lysozyme showed a sustained release over a period of one month. The results demonstrated that the HA-TA microgels are a good carrier for spatial delivery of cationic proteins for biomedical applications.

Keywords: Microgel, inverse emulsion, protein delivery, hyaluronic acid, crosslinking.

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Authors: Zarmina Gillani, Nuzhat Huma, Aysha Sameen, Mulazim Hussain Bukhari

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Whey is an excellent food ingredient owing to its high nutritive value and its functional properties. However, composition of whey varies depending on composition of milk, processing conditions, processing method, and its whey protein content. The aim of this study was to prepare a whey powder from raw whey and to determine the influence of different processing temperatures (160 and 180 °C) on the physicochemical, functional properties during storage of 180 days and on whey protein denaturation. Results have shown that temperature significantly (P < 0.05) affects the pH, acidity, non-protein nitrogen (NPN), protein total soluble solids, fat and lactose contents. Significantly (p < 0.05) higher foaming capacity (FC), foam stability (FS), whey protein nitrogen index (WPNI), and a lower turbidity and solubility index (SI) were observed in whey powder processed at 160 °C compared to whey powder processed at 180 °C. During storage of 180 days, slow but progressive changes were noticed on the physicochemical and functional properties of whey powder. Reverse phase-HPLC analysis revealed a significant (P < 0.05) effect of temperature on whey protein contents. Denaturation of β-Lactoglobulin is followed by α-lacalbumin, casein glycomacropeptide (CMP/GMP), and bovine serum albumin (BSA).

Keywords: Whey powder, temperature, denaturation, reverse phase – HPLC.

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Authors: Abinash Tripathy, Girish Muralidharan, Amitava Pramanik, Prosenjit Sen

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Superhydrophobic surfaces are abundant in nature. Several surfaces such as wings of butterfly, legs of water strider, feet of gecko and the lotus leaf show extreme water repellence behaviour. Self-cleaning, stain-free fabrics, spill-resistant protective wears, drag reduction in micro-fluidic devices etc. are few applications of superhydrophobic surfaces. In order to design robust superhydrophobic surface, it is important to understand the interaction of water with superhydrophobic surface textures. In this work, we report a simple coating method for creating large-scale flexible superhydrophobic paper surface. The surface consists of multiple layers of silanized zirconia microparticles decorated with zirconia nanoparticles. Water contact angle as high as 159±1⁰ and contact angle hysteresis less than 8⁰ was observed. Drop impact studies on superhydrophobic paper surface were carried out by impinging water droplet and capturing its dynamics through high speed imaging. During the drop impact, the Weber number was varied from 20 to 80 by altering the impact velocity of the drop and the parameters such as contact time, normalized spread diameter were obtained. In contrast to earlier literature reports, we observed contact time to be dependent on impact velocity on superhydrophobic surface. Total contact time was split into two components as spread time and recoil time. The recoil time was found to be dependent on the impact velocity while the spread time on the surface did not show much variation with the impact velocity. Further, normalized spreading parameter was found to increase with increase in impact velocity.

Keywords: Contact angle, contact angle hysteresis, contact time, superhydrophobic.

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Authors: Marios Poulos, Eirini Maliagani, Minas Paschopoulos, George Bokos

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The purpose of my research proposal is to demonstrate that there is a relationship between EEG and endometrial cancer. The above relationship is based on an Aristotelian Syllogism; since it is known that the 14-3-3 protein is related to the electrical activity of the brain via control of the flow of Na+ and K+ ions and since it is also known that many types of cancer are associated with 14-3-3 protein, it is possible that there is a relationship between EEG and cancer. This research will be carried out by well-defined diagnostic indicators, obtained via the EEG, using signal processing procedures and pattern recognition tools such as neural networks in order to recognize the endometrial cancer type. The current research shall compare the findings from EEG and hysteroscopy performed on women of a wide age range. Moreover, this practice could be expanded to other types of cancer. The implementation of this methodology will be completed with the creation of an ontology. This ontology shall define the concepts existing in this research-s domain and the relationships between them. It will represent the types of relationships between hysteroscopy and EEG findings.

Keywords: Bioinformatics, Protein 14-3-3, EEG, Endometrial cancer, Ontology.

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Authors: S. Balaji, M. Rajaram, Y. Harold Robinson, E. Golden Julie

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Delay Tolerant Networks (DTN) which have sufficient state information include trajectory and contact information, to protect routing efficiency. However, state information is dynamic and hard to obtain without a global and/or long-term collection process. To deal with these problems, the internal social features of each node are introduced in the network to perform the routing process. This type of application is motivated from several human contact networks where people contact each other more frequently if they have more social features in common. Two unique processes were developed for this process; social feature extraction and multipath routing. The routing method then becomes a hypercube–based feature matching process. Furthermore, the effectiveness of multipath routing is evaluated and compared to that of single-path routing.

Keywords: Delay tolerant networks, entropy, human contact networks, hyper cubes, multipath Routing, social features.

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Authors: Xia Chen, Hua-Quan Yang, Shi-Hua Zhou

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Alkali-active sandstone aggregate was ground by vertical and ball mill into particles with residue over 45 μm less than 12%, and investigations have been launched on particles distribution and characterization of ground sandstone powder, fluidity, heat of hydration, strength as well as hydration products morphology of pastes with incorporation of ground sandstone powder. Results indicated that ground alkali-active sandstone powder with residue over 45 μm less than 8% was easily obtainable, and specific surface area was more sensitive to characterize its fineness with extension of grinding length. Incorporation of sandstone powder resulted in higher water demand and lower strength, advanced hydration of C₃A and C₂S within 3days and refined pore structure. Based on its manufacturing, characteristics and influence on properties of pastes, it was concluded that sandstone powder was a good selection for use in concrete as mineral admixture.

Keywords: Concrete, mineral admixture, hydration, structure.

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Authors: Chieh-Yuan Tsai, Chuang-Cheng Chiu

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Biclustering aims at identifying several biclusters that reveal potential local patterns from a microarray matrix. A bicluster is a sub-matrix of the microarray consisting of only a subset of genes co-regulates in a subset of conditions. In this study, we extend the motif of subspace clustering to present a K-biclusters clustering (KBC) algorithm for the microarray biclustering issue. Besides minimizing the dissimilarities between genes and bicluster centers within all biclusters, the objective function of the KBC algorithm additionally takes into account how to minimize the residues within all biclusters based on the mean square residue model. In addition, the objective function also maximizes the entropy of conditions to stimulate more conditions to contribute the identification of biclusters. The KBC algorithm adopts the K-means type clustering process to efficiently make the partition of K biclusters be optimized. A set of experiments on a practical microarray dataset are demonstrated to show the performance of the proposed KBC algorithm.

Keywords: Microarray, Biclustering, Subspace clustering, Meansquare residue model.

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Authors: Meysam Naeimi, Zili Li, Rolf Dollevoet

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A new small–scale test rig developed for rolling contact fatigue (RCF) investigations in wheel–rail material. This paper presents the scaling strategy of the rig based on dimensional analysis and mechanical modelling. The new experimental rig is indeed a spinning frame structure with multiple wheel components over a fixed rail-track ring, capable of simulating continuous wheelrail contact in a laboratory scale. This paper describes the dimensional design of the rig, to derive its overall scaling strategy and to determine the key elements’ specifications. Finite element (FE) modelling is used to simulate the mechanical behavior of the rig with two sample scale factors of 1/5 and 1/7. The results of FE models are compared with the actual railway system to observe the effectiveness of the chosen scales. The mechanical properties of the components and variables of the system are finally determined through the design process.

Keywords: New test rig, rolling contact fatigue, rail, small scale.

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Authors: Patrick Nwabueze Okechukwu, Ima Nirwana Soelaiman, Gabriele Anisah Ruth Froemming, Mohd Yusri Idorus, Norazlina Mohamed

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Supplementation of palm vitamin E has been reported to prevent loss of bone density in ovariectomised female rats. The mechanism by which palm vitamin E exerts these effects is still unknown. We hypothesized that palm vitamin E may act by preventing the protein expression changes. Two dimensional poly acyrilamide gel electrophoresis (2-D PAGE) and PD Quest software genomic solutions Investigator (proteomics) was used to analyze the differential protein expression profile in femoral and humeri bones harvested from three groups of rats; sham-operated rats (SO), ovariectomised rats (Ovx) and ovariectomised rats supplemented for 2 months with palm vitamin E. The results showed that there were over 300 valued spot on each of the groups PVE and OVX as compared to about 200 in SO. Comparison between the differential protein expression between OVX and PVE groups showed that ten spots were down –regulated in OVX but up-regulated in PVE. The ten differential spots were separately named P1-P10. The identification and understanding of the pathway of the differential protein expression among the groups is ongoing and may account for the molecular mechanism through which palm vitamin E exert its anti-osteoporotic effect.

Keywords: Palm vitamin E, ovariectomised, osteoporosis protein expression, 2-d-page.

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Authors: Norlin Pauzi, Ahmad R.M. Yahya, Zairossani Nor, Amirul A. Abdullah

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Strain M was isolated from the latex of Hevea brasiliensis that grow in the rubber farm area of Malaysia Rubber Board. Strain M was tentatively identified as Bacillus sp. Strain M demonstrated high protease production at pH 9, and this was suitable to be applied in rubber processing that was in alkaline conditions. The right and suitable proportion to be used in applying supernatant into the latex was two parts of latex and one part of enzyme. In this proportion, the latex was stable throughout the 72 hours of treatment. The potential of strain M to degrade protein in the natural rubber latex was proven with the reduction of 79.3% nitrogen in 24 hours treatment. Centrifugation process of the latex before undergoing the treatment had increased the protein degradation in latex. Although the centrifugation process did not achieve zero nitrogen content, it had improved the performance of protein denaturing in the natural rubber.

Keywords: Hevea brasiliensis, Bacillus sp., protease, latex.

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Authors: Vita Strazdina, Aleksandrs Jemeljanovs, Vita Sterna

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Not all proteins have the same nutritional value, since protein quality strongly depends on its amino acid composition and digestibility. The meat of game animals could be a high protein source because of its well-balanced essential amino acids composition. Investigations about biochemical composition of game meat such as wild boar (Sus scrofa scrofa), roe deer (Capreolus capreolus) and beaver (Castor fiber) are not very much. Therefore, the aim of the investigation was evaluate protein composition of game meat hunted in Latvia. The biochemical analysis, evaluation of connective tissue and essential amino acids in meat samples were done, the amino acids score were calculate. Results of analysis showed that protein content 20.88-22.05% of all types of meat samples is not different statistically. The content of connective tissue from 1.3% in roe deer till 1.5% in beaver meat allowed classified game animal as high quality meat. The sum of essential amino acids in game meat samples were determined 7.05–8.26g100g-1. Roe deer meat has highest protein content and lowest content of connective tissues among game meat hunted in Latvia. Concluded that amino acid score for limiting amino acids phenylalanine and tyrosine is high and shows high biological value of game meat.

Keywords: Dietic product, game meat, amino acids, scores.

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Authors: C. C. Okafor, E. E. Ugwu

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A comparative study on the feasibility of producing instant high fibre plantain flour for diabetic fufu by blending soy residence with different plantain (Musa spp) varieties (Horn, false Horn and French), all sieved at 60 mesh, mixed in ratio of 60:40 was analyzed for their passing properties using standard analytical method. Results show that VIIIS60 had the highest peak viscosity (303.75 RVU), Trough value (182.08 RVU), final viscosity (284.50 RVU), and lowest in breakdown viscosity (79.58 RVU), set back value (88.17 RVU), peak time (4.36min), pasting temperature (81.18°C) and differed significantly (p <0.05) from other samples. VIS60 had the lowest in peak viscosity (192.25 RVU), Trough value (112.67 RVU), final viscosity (211.92 RVU), but highest in breakdown viscosity (121.61 RVU), peak time (4.66min) pasting temperature (82.35°C), and differed significantly (p <0.05), from other samples. VIIS60 had the medium peak viscosity (236.67 RVU), Trough value (116.58 RVU), Break down viscosity (120:08 RVU), set back viscosity (167.92 RVU), peak time (4.39min), pasting temp (81.44°C) and differed significantly (p <0.05) from other samples. High final viscosity and low set back values of the French variety with soy residue blended at 60 mesh particle size recommends this french variety and fibre composition as optimum for production of instant plantain soy residue flour blend for production of diabetic fufu. 

Keywords: Plantain, soy residue pasting properties particle size.

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Authors: Anna Trusek-Holownia, Andrzej Noworyta

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Using an enzyme of known specificity the hydrolysis of protein was carried out in a controlled manner. The aim was to obtain oligopeptides being the so-called active peptides or their direct precursors. An original way of expression of the protein hydrolysis kinetics was introduced. Peptide bonds contained in the protein were recognized as a diverse-quality substrate for hydrolysis by the applied protease. This assumption was positively verified taking as an example the hydrolysis of albumin by thermolysin. Peptide linkages for this system should be divided into at least four groups. One of them is a group of bonds non-hydrolyzable by this enzyme. These that are broken are hydrolyzed at a rate that differs even by tens of thousands of times. Designated kinetic constants were k'_F = 10991.4 L/g^.h, k'_M = 14.83L/g^.h, k'_S about 10^-1 L/g^.h for fast, medium and slow bonds, respectively. Moreover, a procedure for unfolding of the protein, conducive to the improved susceptibility to enzymatic hydrolysis (approximately three-fold increase in the rate) was proposed.

Keywords: Peptide bond hydrolysis, kinetics, enzyme specificity, biologically active peptides.

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Authors: Xiaoli Shen, Yuehui Chen

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Interactions among proteins are the basis of various life events. So, it is important to recognize and research protein interaction sites. A control set that contains 149 protein molecules were used here. Then 10 features were extracted and 4 sample sets that contained 9 sliding windows were made according to features. These 4 sample sets were calculated by Radial Basis Functional neutral networks which were optimized by Particle Swarm Optimization respectively. Then 4 groups of results were obtained. Finally, these 4 groups of results were integrated by decision fusion (DF) and Genetic Algorithm based Selected Ensemble (GASEN). A better accuracy was got by DF and GASEN. So, the integrated methods were proved to be effective.

Keywords: protein interaction sites, features, sliding windows, radial basis functional neutral networks, genetic algorithm basedselected ensemble.

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Authors: W. Hasan, H. Farhat

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A hybrid quasi-steady thermal lattice Boltzmann model was used to study the combined effects of temperature and contact angle on the movement of slugs and droplets of oil in water (O/W) system flowing between two parallel plates. The model static contact angle due to the deposition of the O/W droplet on a flat surface with simulated hydrophilic characteristic at different fluid temperatures, matched very well the proposed theoretical calculation. Furthermore, the model was used to simulate the dynamic behavior of droplets and slugs deposited on the domain’s upper and lower surfaces, while subjected to parabolic flow conditions. The model accurately simulated the contact angle hysteresis for the dynamic droplets cases. It was also shown that at elevated temperatures the required power to transport the mixture diminished remarkably.

Keywords: Lattice Boltzmann method, Gunstensen model, thermal, contact angle, high viscosity ratio.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

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Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.

Keywords: automatic clustering, bioinformatics tool, gene ontology, protein sequence annotation, semantic similarity search

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Authors: B. R. S. Babu, E. Prasad, P. V. Laveen, A. M. Vinodkumar

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Searching the “Island of stability” is a topic of extreme interest in theoretical as well as experimental modern physics today. This “island of stability” is spanned by superheavy elements (SHE's) that are produced in the laboratory. SHE's are believed to exist primarily due to the “magic” stabilizing effects of nuclear shell structure. SHE synthesis is extremely difficult due to their very low production cross section, often of the order of pico barns or less. Stabilizing effects of shell closures at proton number Z=82 and neutron number N=126 are predicted theoretically. Though stabilizing effects of Z=82 have been experimentally verified, no concluding observations have been made with N=126, so far. We measured and analyzed the total evaporation residue (ER) cross sections for a number of systems with neutron number around 126 to explore possible shell closure effects in ER cross sections, in this work.

Keywords: Superheavy element, fusion evaporation, evaporation reside, compound nucleus.

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Authors: Nannan Zong, Manicka Dhanasekar

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The effect of the discontinuity of the rail ends and the presence of lower modulus insulation material at the gap to the variations of stresses in the insulated rail joint (IRJ) is presented. A three-dimensional wheel – rail contact model in the finite element framework is used for the analysis. It is shown that the maximum stress occurs in the subsurface of the railhead when the wheel contact occurs far away from the rail end and migrates to the railhead surface as the wheel approaches the rail end; under this condition, the interface between the rail ends and the insulation material has suffered significantly increased levels of stress concentration. The ratio of the elastic modulus of the railhead and insulation material is found to alter the levels of stress concentration. Numerical result indicates that a higher elastic modulus insulating material can reduce the stress concentration in the railhead but will generate higher stresses in the insulation material, leading to earlier failure of the insulation material

Keywords: Rail end, material interface, wheel-rail contact, stress, finite element method

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Authors: Thomas Jin-Chee Liu

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The numerical simulation of the crack welding process is reported in this paper. The thermo-electro-structural coupled-field finite element analysis is adopted to investigate the welding process of crack surfaces. In the simulation, the pressure-dependent and temperature-dependent electrical contact conditions are considered. From the results, the crack surfaces can melt and weld together under the compressive load and electric current. The contact pressure effect must be considered in the finite element analysis to obtain more practical results.

Keywords: Crack welding, contact pressure, Joule heating, finite element, coupled-field.

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Authors: Allagui Hatem, Ghodbane Fathi

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The primary objective of this paper is to study the thermal effects of the electric arc on the breaker apparatus contacts for forecasting and improving the contact durability. We will propose a model which takes account of the main influence factors on the erosion contacts. This phenomenon is very complicated because the amount of ejected metal is not necessarily constituted by the whole melted metal bath but this depends on the balance of forces on the contact surface. Consequently, to calculate the metal ejection coefficient, we propose a method which consists in comparing the experimental results with the calculated ones. The proposed model estimates the mass lost by vaporization, by droplets ejection and by the extraction mechanism of liquid or solid metal. In the one-dimensional geometry, to calculate of the contact heating, we used Green’s function which expresses the point source and allows the transition to the surface source. However, for the two- dimensional model we used explicit and implicit numerical methods. The results are similar to those found by Wilson’s experiments.

Keywords: Electric arc, thermal effect, erosion, contact, durability.

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Authors: J. Tengrang, T. Rungrotmongkol, S. Hannongbua

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Every 2-3 years the influenza B virus serves epidemics. Neuraminidase (NA) is an important target for influenza drug design. Although, oseltamivir, an oral neuraminidase drug, has been shown good inhibitory efficiency against wild-type of influenza B virus, the lower susceptibility to the R152K mutation has been reported. Better understanding of oseltamivir efficiency and resistance toward the influenza B NA wild-type and R152K mutant, respectively, could be useful for rational drug design. Here, two complex systems of wild-type and R152K NAs with oseltamivir bound were studied using molecular dynamics (MD) simulations. Based on 5-ns MD simulation, the loss of notable hydrogen bond and decrease in per-residue decomposition energy from the mutated residue K152 contributed to drug compared to those of R152 in wildtype were found to be a primary source of high-level of oseltamivir resistance due to the R152K mutation.

Keywords: Influenza B neuraminidase, Molecular dynamics simulation, Oseltamivir resistance, R152K mutant

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Authors: G. Lavanya Devi, Allam Appa Rao, A. Damodaram, GR Sridhar, G. Jaya Suma

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Cluster analysis divides data into groups that are meaningful, useful, or both. Analysis of biological data is creating a new generation of epidemiologic, prognostic, diagnostic and treatment modalities. Clustering of protein sequences is one of the current research topics in the field of computer science. Linear relation is valuable in rule discovery for a given data, such as if value X goes up 1, value Y will go down 3", etc. The classical linear regression models the linear relation of two sequences perfectly. However, if we need to cluster a large repository of protein sequences into groups where sequences have strong linear relationship with each other, it is prohibitively expensive to compare sequences one by one. In this paper, we propose a new technique named General Regression Model Technique Clustering Algorithm (GRMTCA) to benignly handle the problem of linear sequences clustering. GRMT gives a measure, GR*, to tell the degree of linearity of multiple sequences without having to compare each pair of them.

Keywords: Clustering, General Regression Model, Protein Sequences, Similarity Measure.

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Authors: Farai Nyabadza

Abstract:

The functional response of an infective is the relationship between an infected individual-s infection rate and the abundance of the number of susceptibles that one can potentially be infected. In this paper, we consider defensive attitudes for HIV prevention (primary prevention) while at the same time emphasizing on offensive attitudes that reduce infection for those infected (secondary prevention). We look at how defenses can protect an uninfected individual in the case where high risk groups such as commercial sex workers and those who deliberately go out to look for partners. We propose an infection cycle that begins with a search, then an encounter, a proposal and contact. The infection cycle illustrates the various steps an infected individual goes through to successfully infect a susceptible. For heterogeneous transmission of HIV, there will be no infection unless there is contact. The ability to avoid an encounter, detection, proposal and contact constitute defense.

Keywords: Functional response, Infection cycle, Prevention, Defences, SSS equation.

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Authors: Toan Vu Duc, Son Ha Viet

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This research presents the first comprehensive survey of congener profiles (7 indicator congeners) of polybrominated diphenyl ethers (PBDEs) in sediment samples covering ten sites in CauBay River, Vietnam. Chemical analyses were carried out in gas chromatography–mass spectrometry (GC–MS) for tri- to hepta- brominated congeners. Results pointed out a non-homogenous contamination of the sediment with ∑₇ PBDE values ranging from 8.93 to 25.64ng g⁻¹, reflecting moderate to low contamination closely in conformity to other Asian aquatic environments. The general order of decreasing congener contribution to the total load was: BDE 47 > 99 > 100 > 154, similar to the distribution pattern worldwide. PBDEs had rare risks in the sediment of studied area.  However, due to the propensity of PBDEs to accumulate in various compartments of wildlife and human food webs, evaluation of biological tissues should be undertaken as a high priority. 

Keywords: Residue, Risk assessment, PBDEs, Sediment.

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Authors: Fiona Browne, Huiru Zheng, Haiying Wang, Francisco Azuaje

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Recent years have seen a growing trend towards the integration of multiple information sources to support large-scale prediction of protein-protein interaction (PPI) networks in model organisms. Despite advances in computational approaches, the combination of multiple “omic" datasets representing the same type of data, e.g. different gene expression datasets, has not been rigorously studied. Furthermore, there is a need to further investigate the inference capability of powerful approaches, such as fullyconnected Bayesian networks, in the context of the prediction of PPI networks. This paper addresses these limitations by proposing a Bayesian approach to integrate multiple datasets, some of which encode the same type of “omic" data to support the identification of PPI networks. The case study reported involved the combination of three gene expression datasets relevant to human heart failure (HF). In comparison with two traditional methods, Naive Bayesian and maximum likelihood ratio approaches, the proposed technique can accurately identify known PPI and can be applied to infer potentially novel interactions.

Keywords: Bayesian network, Classification, Data integration, Protein interaction networks.

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Authors: Gry M, Bergström J, Lengquist J, Lindberg J, Drobin K, Schwenk J, Nilsson P, Schuppe-Koistinen I.

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Sensitive and predictive DILI (Drug Induced Liver Injury) biomarkers are needed in drug R&D to improve early detection of hepatotoxicity. The discovery of DILI biomarkers that demonstrate the predictive power to identify individuals at risk to DILI would represent a major advance in the development of personalized healthcare approaches. In this healthy volunteer acetaminophen study (4g/day for 7 days, with 3 monitored nontreatment days before and 4 after), 450 serum samples from 32 subjects were analyzed using protein profiling by antibody suspension bead arrays. Multiparallel protein profiles were generated using a DILI target protein array with 300 antibodies, where the antibodies were selected based on previous literature findings of putative DILI biomarkers and a screening process using pre dose samples from the same cohort. Of the 32 subjects, 16 were found to develop an elevated ALT value (2Xbaseline, responders). Using the plasma profiling approach together with multivariate statistical analysis some novel findings linked to lipid metabolism were found and more important, endogenous protein profiles in baseline samples (prior to treatment) with predictive power for ALT elevations were identified.

Keywords: DILI, Plasma profiling, PLSDA, Randomforest.

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Authors: Shigeyuki Haruyama , Didik Nurhadiyanto, Moch Agus Choiron, Ken Kaminishi

Abstract:

The previous study of new metal gasket that contact width and contact stress an important design parameter for optimizing metal gasket performance. The optimum design based on an elastic and plastic contact stress was founded. However, the influence of flange surface roughness had not been investigated thoroughly. The flange has many kinds of surface roughness. In this study, we conducted a gasket model include a flange surface roughness effect. A finite element method was employed to develop simulation solution. A uniform quadratic mesh used for meshing the gasket material and a gradually quadrilateral mesh used for meshing the flange. The gasket model was simulated by using two simulation stages which is forming and tightening simulation. A simulation result shows that a smoother of surface roughness has higher slope for force per unit length. This mean a squeezed against between flange and gasket will be strong. The slope of force per unit length for gasket 400-MPa mode was higher than the gasket 0-MPa mode.

Keywords: Surface roughness, flange, metal gasket, leakage, simulation.

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Authors: M. F. Sung, Y.D. Kuan, R.J. Shyu, S.M. Lee

Abstract:

Tread design has evolved over the years to achieve the common tread pattern used in current vehicles. However, to meet safety and comfort requirements, tread design considers more than one design factor. Tread design must consider the grip and drainage, and the manner in which to reduce rolling noise, which is one of the main factors considered by manufacturers. The main objective of this study was the application the computational fluid dynamics (CFD) technique to simulate the contact surface of the tire and ground. The results demonstrated an air-Pumping and large pressure drop effect in the process of contact surface. The results also revealed that the pressure can be used to analyze sound pressure level (SPL).

Keywords: Air-pumping, computational fluid dynamics, sound pressure level, tire.

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