Search results for: protein interaction sites

Authors: M. Rahimnejad, B. Vahidi, B. Ebrahimi Hoseinzadeh, F. Yazdian, P. Motamed Fath, R. Jamjah

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In this study, we developed and simulated nano-drug delivery systems efficacy in compare to free drug prescription. Computational models can be utilized to accelerate experimental steps and control the experiments high cost. Molecular dynamics simulation (MDS), in particular NAMD was utilized to better understand the anti-cancer drug interaction with cell membrane model. Paclitaxel (PTX) and dipalmitoylphosphatidylcholine (DPPC) were selected for the drug molecule and as a natural phospholipid nanocarrier, respectively. This work focused on two important interaction parameters between molecules in terms of center of mass (COM) and van der Waals interaction energy. Furthermore, we compared the simulation results of the PTX interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane. The molecular dynamic analysis resulted in low energy between the nanocarrier and the cell membrane as well as significant decrease of COM amount in the nanocarrier and the cell membrane system during the interaction. Thus, the drug vehicle showed notably better interaction with the cell membrane in compared to free drug interaction with the cell membrane.

Keywords: Anti-cancer drug, center of Mass, interaction energy, molecular dynamics simulation, nanocarrier.

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Authors: Nichole Haag, Kimberly Velk, Tyler McCune, Chun Wu

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Methicillin/multiple-resistant Staphylococcus aureus (MRSA) are infectious bacteria that are resistant to common antibiotics. A previous in silico study in our group has identified a hypothetical protein SAV1226 as one of the potential drug targets. In this study, we reported the bioinformatics characterization, as well as cloning, expression, purification and kinetic assays of hypothetical protein SAV1226 from methicillin/vancomycin-resistant Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis revealed a low degree of structural similarity with known proteins. Kinetic assays demonstrated that hypothetical protein SAV1226 is neither a domain of an ATP dependent dihydroxyacetone kinase nor of a phosphotransferase system (PTS) dihydroxyacetone kinase, suggesting that the function of hypothetical protein SAV1226 might be misannotated on public databases such as UniProt and InterProScan 5.

Keywords: Dihydroxyacetone kinase, essential genes, Methicillin-resistant Staphylococcus aureus, drug target.

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Authors: Olga A. Berillo, Gaukhar K. Baidildinova, Аnatoliy Т. Ivashchenko

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Tumour suppressors are key participants in the prevention of cancer. Regulation of their expression through miRNAs is important for comprehensive translation inhibition of tumour suppressors and elucidation of carcinogenesis mechanisms. We studies the possibility of 1521 miRNAs to bind with 873 mRNAs of human tumour suppressors using RNAHybrid 2.1 and ERNAhybrid programmes. Only 978 miRNAs were found to be translational regulators of 812 mRNAs, and 61 mRNAs did not have any miRNA binding sites. Additionally, 45.9% of all miRNA binding sites were located in coding sequences (CDSs), 33.8% were located in 3' untranslated region (UTR), and 20.3% were located in the 5'UTR. MiRNAs binding with more than 50 target mRNAs and mRNAs binding with several miRNAs were selected. Hsa-miR-5096 had 15 perfectly complementary binding sites with mRNAs of 14 tumour suppressors. These newly indentified miRNA binding sites can be used in the development of medicines (anti-sense therapies) for cancer treatment.

Keywords: Exonic miRNA, intergenic miRNA, intronic miRNA, tumor suppressor.

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Authors: Sivapan Choo-In, Chaisri Tharasawatpipat, Srisuwan Kaseamsawat, Tatsanawalai Utarasakul

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The research aims to study the quality of surface water for consumer in Samut Songkram province. Water sample were collected from 217 sampling sites conclude 72 sampling sites in Amphawa, 67 sampling sites in Bangkhonthee and 65 sampling sites in Muang. Water sample were collected in December 2011 for winter, March 2012 for summer and August 2012 for rainy season. From the investigation of surface water quality in Mae Klong River, main and tributaries canals in Samut Songkram province, we found that water quality meet the type III of surface water quality standard issued by the National Environmental Quality Act B.E. 1992. Seasonal variations of pH, Temperature, nitrate, lead and cadmium have statistical differences between 3 seasons.

Keywords: Samut Songkram Province, Surface water quality.

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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: Raif Parlakkaya, Huseyin Cetin, Duygu Irdiren

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By the development of World Wide Web, the usage rate of Internet has rapidly grown globally; and provided a basis for the emergence of electronic business. As well as other sectors, the banking sector has adopted the use of internet with the developments in information and communication technologies. Due to the public disclosure and transparency principle of Corporate Governance, the importance of information disclosure of banks on their web sites has increased significantly. For the purpose of this study, a Bank Disclosure Attribute Index (BDAI) in Turkey has been constructed through classifying the information disclosure on banks’ web sites into general, financial, investors and corporate governance attributes. All 47 banks in Turkish Banking System have been evaluated according to the index with the aim of providing a comparison between banks. By Chi Square Test, Pearson Correlation, T-Test, and ANOVA statistical tools, it has been concluded that the majority of banks in Turkey have shared information on their web sites adequately with respect to their total index score. Although there is a positive correlation between various types of information on banks’ web sites, there is no uniformity among them. Also, no significant difference between various types of information disclosure and bank types has been observed. Compared with the total index score averages of the five largest banks in Turkey, there are some banks that need to improve the content of their web sites.

Keywords: Banking sector, public disclosure, Turkey, web site evaluation.

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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: Huynh Quyet Thang, Le Hai Quan

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Interaction Model plays an important role in Modelbased Intelligent Interface Agent Architecture for developing Intelligent User Interface. In this paper we are presenting some improvements in the algorithms for development interaction model of interface agent including: the action segmentation algorithm, the action pair selection algorithm, the final action pair selection algorithm, the interaction graph construction algorithm and the probability calculation algorithm. The analysis of the algorithms also presented. At the end of this paper, we introduce an experimental program called “Personal Transfer System".

Keywords: interface agent, interaction model, user model.

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Authors: A. Maitarad, P. Maitarad

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In order to find the particular interaction energy between cylcloguanil and the amino acids surrounding the pocket of wild type and quadruple mutant type PfDHFR enzymes, the MP2 method with basis set 6-31G(d,p) level of calculations was performed. The obtained interaction energies found that Asp54 has the strongest interaction energy to both wild type and mutant type of - 12.439 and -11.250 kcal/mol, respectively and three amino acids; Asp54, Ile164 and Ile14 formed the H-bonding with cycloguanil drug. Importantly, the mutation at Ser108Asn was the key important of cycloguanil resistant with showing repulsive interaction energy.

Keywords: Cycloguanil, DHFR, malaria disease, interactionenergy, quantum calculations

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Authors: Parvaneh Vafa, Rahim Naseri, Meysam Moradi

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In order to study the effect of drought stress on grain yield, yield components and associated traits of durum wheat cultivars, an experiment was done as split plot arrangement using randomized complete block design with three replications in Ilam province, Iran in 2009-2010 cropping season. Different levels of irrigation (Full irrigation, drought stress at stem elongation, Flowering and grain formation stages) were considered as a main plot and three durum wheat cultivars (Yavaros, Seimareh and Karkheh) were assigned as a sub plot. The results showed that drought stress was significant on grain yield, spike.m-2, grain. Spike-1, 1000-grain weight, biological yield, harvest index and protein content. Drought stress at all stages caused a loss in grain yield and its components. Full irrigation had the highest grain yield and yield components. Drought stress at stem elongation, flowering and grain formation stages caused a reduction in spike.m-2, grain.spike-1 and 1000-grain weight, respectively. Protein content was significantly affected by drought stress. The highest protein content was obtained from drought stress at grain formation stage. Cultivars had an influence on grain yield and yield components. Yavaros and Seimareh cultivars had the highest and lowest grain yield, respectively. Interaction effect between drought stress and cultivar had a significant effect on grain and yield components. Full irrigation and Yavaros cultivar had the highest grain yield and drought stress at grain formation stage and Seimareh cultivar had the lowest grain yield, respectively.

Keywords: Durum wheat, Drought stress, Grain yield.

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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: Ikumapayi Catherine Mayowa

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The well been of human beings on construction site is very important, many man power had been lost through accidents which kills or make workers physically unfit to carry out construction activities, these in turn have multiple effects on the whole economy. Thus it is necessary to put all safety items and regulations in place before construction activities can commence. This study was carried out in Ondo state of Nigeria to known and analyse the state of health and safety of construction workers in the state. The study was done using first hand observation method, 50 construction project sites were visited in 10 major towns of Ondo state, questionnaires were distributed and the results were analysed. The result show that construction workers are being exposed to a lot of construction site hazards due to lack of inadequate safety programmes and nonprovision of appropriate safety materials for workers on site. From the data gotten for each site visited and the statistical analysis, it can be concluded that occurrence of accident on construction sites depends significantly on the available safety facilities on the sites. The result of the regression statistics show that the level of significant of the dependence of occurrence of accident on the availability of safety items on site is 0.0362 which is less than 0.05 maximum significant level required. Therefore a vital way of sustaining our building strategy is by given a detail attention to provision of adequate health and safety items on construction sites which will reduce the occurrence of accident, loss of man power and death of skilled workers among others.

Keywords: Construction sites, health, safety, welfare.

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Authors: Kholoud H. Al-Zedjali, Abir S. Al-Harrasi, Ali H. Al-Badi

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Recently there has been a dramatic proliferation in the number of social networking sites (SNSs) users; however, little is published about what motivates college students to use SNSs in education. The main goal of this research is to explore the college students’ motives for using SNSs in education. A conceptual framework has therefore been developed to identify the main factors that influence/motivate students to use social networking sites for learning purposes. To achieve the research objectives a quantitative method was used to collect data. A questionnaire has been distributed amongst college students. The results reveal that social influence, perceived enjoyment, institute regulation, perceived usefulness, ranking up-lift, attractiveness, communication tools, free of charge, sharing material and course nature all play an important role in the motivation of college students to use SNSs for learning purposes.

Keywords: Social networking sites (SNSs), education, college students.

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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: Hong Ding, Fatiha Benslimane, Isra Marei, Chris R. Triggle

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Hyperglycaemia is a key factor that contributes to the development of diabetes-related microvascular disease and a major risk factor for endothelial dysfunction. In the current study, we have explored glucose-induced abnormal intracellular calcium (Ca2+ i) homeostasis in mouse microvessel endothelial cells (MMECs) in high glucose (HG) (40mmol/L) versus control (low glucose, LG) (11 mmol/L). We demonstrated that the exposure of MMECs to HG for 3 days did not change basal Ca2+ i, however, there was a significant increase of acetylcholine-induced Ca2+ entry. Western blots illustrated that exposure to HG also increased STIM1 (Stromal Interaction Molecule 1), but not Orai1 (the pore forming subunit), protein expression levels. Although the link between HG-induced changes in STIM1 expression, enhanced Ca2+ entry and endothelial dysfunction requires further study, the current data are suggestive that targeting these pathways may reduce the impact of HG on endothelial function.

Keywords: store-operated calcium entry, hyperglycaemia, STIM1, endothelial dysfunction

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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: Dilip Singh Sisodia, Shrish Verma

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In this paper we are presenting some spamming techniques their behaviour and possible solutions. We have analyzed how Spammers enters into online social networking sites (OSNSs) to target them and diverse techniques used by them for this purpose. Spamming is very common issue in present era of Internet especially through Online Social Networking Sites (like Facebook, Twitter, and Google+ etc.). Spam messages keep wasting Internet bandwidth and the storage space of servers. On social networking sites; spammers often disguise themselves by creating fake accounts and hijacking user’s accounts for personal gains. They behave like normal user and they continue to change their spamming strategy. Following spamming techniques are discussed in this paper like clickjacking, social engineered attacks, cross site scripting, URL shortening, and drive by download. We have used elgg framework for demonstration of some of spamming threats and respective implementation of solutions.

Keywords: Online social networking sites, spam attacks, Internet, clickjacking/likejacking, drive-by-download, URL shortening, cross site scripting, socially engineered attacks, elgg framework.

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Authors: Yu-Min Wang

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This study attempts to validate the consumer-oriented criteria list, developed by Wang et al. (2010), for selecting online travel shopping sites. Based on a sample of 985 respondents, confirmatory factor analysis was employed to test the factor structure and assess the reliability and validity of the list. The results support the list developed by Wang et al. (2010) and claim the list can be further used to analyze, explain, and understand consumer behaviors about online travel shopping.

Keywords: Online travel agency, online travel shopping sites, confirmatory analysis.

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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: Almas Tayebi, Tayeb Saki Nejad, Alireza Shoukofar

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The trial in the city, located 170 kilometers from the Iranian city of Ahvaz was Omidiyeh. The main factor in this project includes 4 levels in control (without hormones), use of hormones in the seed, vegetative and flowering stage respectively. And sub-plots included 3 varieties of vetch in three levels, with local names, was the jewel in the study of light and Auxin in the vegetative and reproductive different times in different varieties of vetch was investigated. This test has been taken in the plots in a randomized complete block with four replications. In order to study the effects of the hormone Auxin in the growth stages (seed, vegetative and flowering) to control (no hormone Auxin) on three local varieties of vetch, the essence of light and plant height, number of pods per plant, seed number The pods, seeds per plant, grain weight, grain yield, plant dry weight and protein content were measured. Among the vetch varieties for plant height, number of pods per plant, a seed per plant, grain weight, grain yield, and plant dry weight and protein levels of 1 percent of plant and seed number per pod per plant at 5% level of There was no significant difference. Interactions for grain yield per plant, grain yield and protein levels of 1 percent and the number of seeds per pod and seed weight are significant differences in levels 5 and plant height and plant dry weight of the interaction were INFLUENCE There was no significant difference in them.

Keywords: Auxin hormones, various periods of growth, production components, vetch

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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: Ahmed El Azab, Amira M. Idrees, Mahmoud A. Mahmoud, Hesham Hefny

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Social networking sites such as Twitter and Facebook attracts over 500 million users across the world, for those users, their social life, even their practical life, has become interrelated. Their interaction with social networking has affected their life forever. Accordingly, social networking sites have become among the main channels that are responsible for vast dissemination of different kinds of information during real time events. This popularity in Social networking has led to different problems including the possibility of exposing incorrect information to their users through fake accounts which results to the spread of malicious content during life events. This situation can result to a huge damage in the real world to the society in general including citizens, business entities, and others. In this paper, we present a classification method for detecting the fake accounts on Twitter. The study determines the minimized set of the main factors that influence the detection of the fake accounts on Twitter, and then the determined factors are applied using different classification techniques. A comparison of the results of these techniques has been performed and the most accurate algorithm is selected according to the accuracy of the results. The study has been compared with different recent researches in the same area; this comparison has proved the accuracy of the proposed study. We claim that this study can be continuously applied on Twitter social network to automatically detect the fake accounts; moreover, the study can be applied on different social network sites such as Facebook with minor changes according to the nature of the social network which are discussed in this paper.

Keywords: Fake accounts detection, classification algorithms, twitter accounts analysis, features based techniques.

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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: R. K. Apalowo, D. Chronopoulos

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A Finite Element (FE) based scheme is presented for quantifying guided wave interaction with Localised Nonlinear Structural Damage (LNSD) within structures of arbitrary layering and geometric complexity. The through-thickness mode-shape of the structure is obtained through a wave and finite element method. This is applied in a time domain FE simulation in order to generate time harmonic excitation for a specific wave mode. Interaction of the wave with LNSD within the system is computed through an element activation and deactivation iteration. The scheme is validated against experimental measurements and a WFE-FE methodology for calculating wave interaction with damage. Case studies for guided wave interaction with crack and delamination are presented to verify the robustness of the proposed method in classifying and identifying damage.

Keywords: Layered Structures, nonlinear ultrasound, wave interaction with nonlinear damage, wave finite element, finite element.

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Authors: Kuan-Liang Liu, Eric Lee, Jung-Jyh Lee, Jyh-Ping Hsu

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The electrical interaction between two axisymmetric spheroidal particles in an electrolyte solution is examined numerically. A Galerkin finite element method combined with a Newton-Raphson iteration scheme is proposed to evaluate the spatial variation in the electrical potential, and the result obtained used to estimate the interaction energy between two particles. We show that if the surface charge density is fixed, the potential gradient is larger at a point, which has a larger curvature, and if surface potential is fixed, surface charge density is proportional to the curvature. Also, if the total interaction energy against closest surface-to-surface curve exhibits a primary maximum, the maximum follows the order (oblate-oblate) > (sphere-sphere)>(oblate-prolate)>(prolate-prolate), and if the curve has a secondary minimum, the absolute value of the minimum follows the same order.

Keywords: interaction energy, interaction force, Poisson-Boltzmann equation, spheroid.

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Authors: A. Jawahar

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In this paper, the dependence of soliton pulses with respect to phase in a 10Gbps, single channel, dispersion uncompensated telecommunication system was studied. The characteristic feature of periodic soliton interaction was noted at the Interaction point (I=6202.5Km) in one collision length of L=12405.1 Km. The interaction point is located for 10Gbps system with an initial relative spacing (qo) of soliton as 5.28 using Perturbation theory. It is shown that, when two in-phase solitons are launched, they interact at the point I=6202.5 Km, but the interaction could be restricted with introduction of different phase initially. When the phase of the input solitons increases, the deviation of soliton pulses at the ‘I’ also increases. We have successfully demonstrated this effect in a telecommunication set-up in terms of Quality factor (Q), where the Q=0 for in-phase soliton. The Q was noted to be 125.9, 38.63, 47.53, 59.60, 161.37, and 78.04 for different phases such as 10o, 20o, 30o, 45o, 60o and 90o degrees respectively at Interaction point (I).

Keywords: Soliton interaction, Initial relative spacing, phase, Perturbation theory and telecommunication system.

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Authors: Waleed Maqableh, Ahmad Al-Hamad, Manjit Sidhu

Abstract:

Augmented reality (AR) technology has the capability to provide many benefits in the field of education as a modern technology which aided learning and improved the learning experience. This paper evaluates AR based application with multiple markers interaction technique (touch-to-print) which is designed for analyzing the kinematics of 4BL mechanism in mechanical engineering. The application is termed as AR-4BL-MAST and it allows the users to touch the symbols on a paper in natural way of interaction. The evaluation of this application was performed with mechanical engineering students and human–computer interaction (HCI) experts to test its effectiveness as a tangible user interface application where the statistical results show its ability as an interaction technique, and it gives the users more freedom in interaction with the virtual mechanical objects.

Keywords: Augmented reality, engineering, four-bar linkage, Multimedia, user interface, visualization.

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Authors: Vinicius Binotte, Guilherme Baldo, Christiane Goulart, Carlos Valadão, Eliete Caldeira, Teodiano Bastos

Abstract:

Socially assistive robotic has become increasingly active and it is present in therapies of people affected for several neurobehavioral conditions, such as Autism Spectrum Disorder (ASD). In fact, robots have played a significant role for positive interaction with children with ASD, by stimulating their social and cognitive skills. This work introduces a mobile socially-assistive robot, which was built for interaction with children with ASD, using non-linear control techniques for this interaction.

Keywords: Socially assistive robotics, mobile robot, autonomous control, autism.

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