Search results for: Protein molecular formula

Authors: S. Petrovska, D. Jonkus, D. Smiltiņa

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κ-casein is one of milk proteins which are very important for milk processing. Genotypes of κ-casein affect milk yield, fat, and protein content. The main factors which affect local Latvian dairy breed milk yield and composition are analyzed in research. Data were collected from 88 Latvian brown and 82 Latvian blue cows in 2015. AA genotype was 0.557 in Latvian brown and 0.232 in Latvian blue breed. BB genotype was 0.034 in Latvian brown and 0.207 in Latvian blue breed. Highest milk yield was observed in Latvian brown (5131.2 ± 172.01 kg), significantly high fat content and fat yield also was in Latvian brown (p < 0.05). Significant differences between κ-casein genotypes were not found in Latvian brown, but highest milk yield (5057 ± 130.23 kg), protein content (3.42 ± 0.03%), and protein yield (171.9 ± 4.34 kg) were with AB genotype. Significantly high fat content was observed in Latvian blue breed with BB genotype (4.29 ± 0.17%) compared with AA genotypes (3.42 ± 0.19). Similar tendency was found in protein content – 3.27 ± 0.16% with BB genotype and 2.59 ± 0.16% with AA genotype (p < 0.05). Milk yield increases by increasing parity. We did not obtain major tendency of changes of milk fat and protein content according parity.

Keywords: κ-casein, polymorphism, dairy cows, milk productivity.

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Authors: Haitao Yang, Jianming Lv, Fei Xu, Xintong Wang, Yilin Huang, Lanting Xia, Xuewu Zhu

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Given a fixed fund, purchasing fewer hosts of higher capability or inversely more of lower capability is a must-be-made trade-off in practices for building a Hadoop big data platform. An exploratory study is presented for a Housing Big Data Platform project (HBDP), where typical big data computing is with SQL queries of aggregate, join, and space-time condition selections executed upon massive data from more than 10 million housing units. In HBDP, an empirical formula was introduced to predict the performance of host clusters potential for the intended typical big data computing, and it was shaped via a regression approach. With this empirical formula, it is easy to suggest an optimal cluster configuration. The investigation was based on a typical Hadoop computing ecosystem HDFS+Hive+Spark. A proper metric was raised to measure the performance of Hadoop clusters in HBDP, which was tested and compared with its predicted counterpart, on executing three kinds of typical SQL query tasks. Tests were conducted with respect to factors of CPU benchmark, memory size, virtual host division, and the number of element physical host in cluster. The research has been applied to practical cluster procurement for housing big data computing.

Keywords: Hadoop platform planning, optimal cluster scheme at fixed-fund, performance empirical formula, typical SQL query tasks.

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Authors: A.R. Pazoki, A. H. Shirani Rad, D. Habibi, F. Paknejad, S. Kobraee, N. Hadayat

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In the other to Study of drought stress and Selenium spraying effect on superoxide dismotase (SOD) activity of rapeseed (Brassica napus L.) cultivars in Shahr-e-Rey region, an experiment carried out in Split factorial design in the basis of randomized complete blocks with 4 replications in 2006. Irrigation in two levels: Normal irrigation and irrigation with drought stress when the soil electrical conductivity reached to 60 as main factor and rapeseed cultivars in 3 levels Zarfam, Okapi, Opera and selenium spraying at the beginning of flowering stage in 3 levels: 0, 16 and 21 g/ha as sub factor. The results showed that the simple and interaction effect of irrigation, selenium and cultivars on SOD activity had significant difference. In this case Zarfam cultivar with 2010 u.mg-1 protein and Opera with 1454 u.mg-1 protein produced maximum and minimum amounts of SOD activitiy. Interaction effect of irrigation and variety showed that, normal irrigation in Opera with 1115 u.mg-1 protein and drought stress in Zarfam with 2784 u.mg-1 protein conducted to and minimum and maximum amounts of SOD activity. Interaction effect of irrigation, cultivar and selenium on SOD indicated that drought stress condition and 21 gr/ha selenium spraying in Zarfam variety with 3146 u.mg-1 protein gained to highest activities of SOD.

Keywords: Drought stress, Rapeseed, Selenium, Superoxide dismutase.

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Authors: Salem El-tohami Ashoor

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A novel new vanadium (IV) complexes incorporating the chelating diamido cyclopentadienyl {ArN(CH₂)₃NAr)}^2-((ηⁿ-Cp)Cp)} (Ar = 2,6-Prⁱ₂C₆H₃)(Cp = C₅H₅ and n = 1,2,3,4 and 5) have been studied with calculation of the properties of species involved in various of cyclopentadienyl reaction. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP (Becke) (Lee–Yang–Parr) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions.

The optimised of [V(ArN(CH₂)₃NAr)₂Cl(η⁵-Cp)] (Ar = 2,6-Prⁱ₂C₆H₃ and Cp= C₅H₅) was found to be thermally more stable than others of vanadium cyclopentadienyl. In the meantime the complex [V(ArN(CH₂)₃NAr)₂Cl(η¹-Cp)] (Ar = 2,6-Prⁱ₂C₆H₃ and Cp= C₅H₅) which is showed a low thermal stability in case of the just one carbon of cyclopentadienyl can be insertion with vanadium metal centre. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: Vanadium(IV) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO.

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Authors: Kittipong Tripetch

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This paper proposes a study of input impedance of 2 types of CMOS active inductors. It derives 2 input impedance formulas. The first formula is the input impedance of the grounded active inductor. The second formula is the input impedance of the floating active inductor. After that, these formulas can be used to simulate magnitude and phase response of input impedance as a function of current consumption with MATLAB. Common mode rejection ratio (CMRR) of the fully differential bandpass amplifier is derived based on superposition principle. CMRR as a function of input frequency is plotted as a function of current consumption. 

Keywords: Grounded active inductor, floating active inductor, Fully differential bandpass amplifier.

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Authors: Shaiemaa, A. Momen, Dalia, A.M. Salem, Emad, M.S. Barakat, Mohamed, S. Salama

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The present study has been conducted to characterize the prophenoloxidase (PPO) system of the desert locust, Schistocerca gregaria following injection of Bacillus thuringiensis kurstaki (Bt). The bulk of PPO system was associated with haemocytes and a little amount was found in plasma. This system was activated by different activators such as laminarin, lipopolysaccharide (LPS) and trypsin suggesting that the stimulatory mechanism may involve an enzyme cascade of one or more associated molecules. These activators did not activate all the molecules of the cascade. Presence of phenoloxidase activity (PO) coincides with the appearance of protein band with molecular weight (MW) 70.154 KD (Kilo Dalton).

Keywords: Schistocerca gregaria, haemolymph, proteins, prophenoloxidase system, phenoloxidase

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Authors: Radhika Jain, Sangeeta Goomer

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In the present study an attempt has been made to re-engineer traditional wadi into wholesome ready-to-use cereal-pulse-based chunks rich in protein quality and fibre content. Chunks were made using extrusion-dehydration combination. Two formulations i.e., whole green gram dhal with instant oats and washed green gram dhal with whole oats were formulated. These chunks are versatile in nature as they can be easily incorporated in day-to-day home-made preparations such as pulao, potato curry and kadhi. Cereal-pulse ratio was calculated using NDpCal%. Limiting amino acids such as lysine, tryptophan, methionine, cysteine and threonine were calculated for maximum amino acid profile in cereal-pulse combination. Time-temperature combination for extrusion at 130^oC and dehydration at 65^oC for 7 hours and 15 minutes were standardized to obtain maximum protein and fibre content. Proximate analysis such as moisture, fat and ash content were analyzed. Protein content of formulation was 62.10% and 68.50% respectively. Fibre content of formulations was 2.99% and 2.45%, respectively. Using a 5-point hedonic scale, consumer preference trials of 102 consumers were conducted and analyzed. Evaluation of chunks prepared in potato curry, kadi and pulao showed preferences for colour 82%, 87%, 86%, texture and consistency 80%, 81%, 88%, flavour and aroma 74%, 82%, 86%, after taste 70%, 75%, 86% and overall acceptability 77%, 75%, 88% respectively. High temperature inactivates antinutritional compounds such as trypsin inhibitors, lectins, saponins etc. Hence, availability of protein content was increased. Developed products were palatable and easy to prepare.

Keywords: Extrusion, NDpCal%, protein quality, wadi.

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Authors: Nirmal Kumar, Rita N. Kumar, Anubhuti Bora, Manmeet Kaur Amb

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The whole-cell protein-profiling technique was evaluated for studying differences in banding pattern of three different species of Cyanobacteria i.e. Anabaena fertilissima, Aulosira fertilissima and Westiellopsis prolifica under the influence of four different pesticides-2,4-D (Ethyl Ester of 2,4-Dichloro Phenoxy Acetic Acid), Pencycuron (N-[(4-chlorophenyl)methyl]-Ncyclopentyl- N'–phenylurea), Endosulfan (6,7,8,9,10,10hexachloro- 1,5,5a,6,9,9a-hexahydro-6,9-methano-2,4,3-benzodioxathiepine-3- oxide) and Tebuconazole (1-(4-Chlorophenyl)-4,4-dimethyl-3-(1,2,4- triazol-1-ylmethyl)pentan-3-ol). Whole-cell extracts were obtained by sonication treatment (Sonifier cell disruptor -Branson Digital Sonifier S-450D, USA) and were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). SDS-PAGE analyses of the total protein profile of Anabaena fertilissima, Aulosira fertilissima and Westiellopsis prolifica showed a linear decrease in the protein content with increasing pesticide stress when administered to different concentrations of 2, 4-D, Pencycuron, Endosulfan and Tebuconazole. The results indicate that different stressors exert specific effects on cyanobacterial protein synthesis.

Keywords: Cyanobacteria, pesticide, SDS-PAGE

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Authors: Alexander Kaplunovsky, Vladimir Khailenko, Alexander Bolshoy, Shara Atambayeva, AnatoliyIvashchenko

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Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from the RNA transcripts before translation into a protein. The exon-intron structures of different eukaryotic species are quite different from each other, and the evolution of such structures raises many questions. We try to address some of these questions using statistical analysis of whole genomes. We go through all the protein-coding genes in a genome and study correlations between the net length of all the exons in a gene, the number of the exons, and the average length of an exon. We also take average values of these features for each chromosome and study correlations between those averages on the chromosomal level. Our data show universal features of exon-intron structures common to animals, plants, and protists (specifically, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Cryptococcus neoformans, Homo sapiens, Mus musculus, Oryza sativa, and Plasmodium falciparum). We have verified linear correlation between the number of exons in a gene and the length of a protein coded by the gene, while the protein length increases in proportion to the number of exons. On the other hand, the average length of an exon always decreases with the number of exons. Finally, chromosome clustering based on average chromosome properties and parameters of linear regression between the number of exons in a gene and the net length of those exons demonstrates that these average chromosome properties are genome-specific features.

Keywords: Comparative genomics, exon-intron structure, eukaryotic clustering, linear regression.

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Authors: Walter Hussak

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We present an operator for a propositional linear temporal logic over infinite schedules of iterated transactions, which, when applied to a formula, asserts that any schedule satisfying the formula is serializable. The resulting logic is suitable for specifying and verifying consistency properties of concurrent transaction management systems, that can be defined in terms of serializability, as well as other general safety and liveness properties. A strict form of serializability is used requiring that, whenever the read and write steps of a transaction occurrence precede the read and write steps of another transaction occurrence in a schedule, the first transaction must precede the second transaction in an equivalent serial schedule. This work improves on previous work in providing a propositional temporal logic with a serializability operator that is of the same PSPACE complete computational complexity as standard propositional linear temporal logic without a serializability operator.

Keywords: Temporal logic, iterated transactions, serializability.

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Authors: S. Kulsri, M. Jaroensutasinee, K. Jaroensutasinee

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We developed a method based on quasi-molecular modelling to simulate the fall of water drops on horizontally smooth and rough surfaces. Each quasi-molecule was a group of particles that interacted in a fashion entirely analogous to classical Newtonian molecular interactions. When a falling water droplet was simulated at low impact velocity on both smooth and rough surfaces, the droplets moved periodically (i.e. the droplets moved up and down for a certain period, finally they stopped moving and reached a steady state), spreading and recoiling without splash or break-up. Spreading rates of falling water droplets increased rapidly as time increased until the spreading rate reached its steady state at time t ~ 0.25 s for rough surface and t ~ 0.40 s for smooth surface. The droplet height above both surfaces decreased as time increased, remained constant after the droplet diameter attained a maximum value and reached its steady state at time t ~ 0.4 s. However, rough surface had higher spreading rates of falling water droplets and lower height on the surface than smooth one.

Keywords: Quasi-molecular modelling, particle modelling, molecular aggregate approach.

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Authors: Tzyy Rong Jinn, Nguyen Tiep Khac, Tzong Yuan Wu

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Highly pathogenic avian influenza (HPAI) H5N1 viruses have created demand for a cost-effective vaccine to prevent a pandemic of the disease. Here, we report that Trichoplusia ni (T. ni) larvae can act as a cost-effective bioreactor to produce recombinant HA5 (rH5HA) proteins as an potential effective vaccine for chickens. To facilitate the recombinant virus identification, virus titer determination and access the infected larvae, we employed the internal ribosome entry site (IRES) derived from Perina nuda virus (PnV, belongs to insect picorna like Iflavirus genus) to construct a bi-cistronic baculovirus expression vector that can express the rH5HA protein and enhanced green fluorescent protein (EGFP) simultaneously. Western blot analysis revealed that the 70 kDa rH5HA protein and partially cleaved products (40 kDa H5HA1) were generated in T. ni larvae infected with recombinant baculovirus carrying the H5HA gene. These data suggest that the baculovirus-larvae recombinant protein expression system could be a cost-effective platform for H5N1 vaccine production.

Keywords: Avian Influenza, baculovirus, hemagglutinin, Trichoplusia ni larvae

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Authors: Bahareh Hajirostamloo

Abstract:

Cow milk, is a product of the mammary gland and soymilk is a beverage made from soybeans; it is the liquid that remains after soybeans are soaked. In this research effort, we compared nutritional parameters of this two kind milk such as total fat, fiber, protein, minerals (Ca, Fe and P), fatty acids, carbohydrate, lactose, water, total solids, ash, pH, acidity and calories content in one cup (245 g). Results showed soymilk contains 4.67 grams of fat, 0.52 of fatty acids, 3.18 of fiber, 6.73 of protein, 4.43 of carbohydrate, 0.00 of lactose, 228.51 of water, 10.40 of total solids and 0.66 of ash, also 9.80 milligrams of Ca, 1.42 of Fe, and 120.05 of P, 79 Kcal of calories, pH=6.74 and acidity was 0.24%. Cow milk contains 8.15 grams of fat, 5.07 of fatty acids, 0.00 of fiber, 8.02 of protein, 11.37 of carbohydrate, ´Çá4.27 of lactose, 214.69 of water, 12.90 of total solids, 1.75 of ash, 290.36 milligrams of Ca, 0.12 of Fe, and 226.92 of P, 150 Kcal of calories, pH=6.90 and acidity was 0.21% . Soy milk is one of plant-based complete proteins and cow milk is a rich source of nutrients as well. Cow milk is containing near twice as much fat as and ten times more fatty acids do soymilk. Cow milk contains greater amounts of mineral (except Fe) it contain more than three hundred times the amount of Ca and nearly twice the amount of P as does soymilk but soymilk contains more Fe (ten time more) than does cow milk. Cow milk and soy milk contain nearly identical amounts of protein and water and fiber is a big plus, dairy has none. Although what we choose to drink is really a mater of personal preference and our health objectives but looking at the comparison, soy looks like healthier choices.

Keywords: Soymilk, cow milk, nutritional, comparison.

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Authors: A. Niknejad, G. H. Liaghat, A. H. Behravesh, H. Moslemi Naeini

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In this paper, a theoretical formula is presented to predict the instantaneous folding force of the first fold creation in a square column under axial loading. Calculations are based on analysis of “Basic Folding Mechanism" introduced by Wierzbicki and Abramowicz. For this purpose, the sum of dissipated energy rate under bending around horizontal and inclined hinge lines and dissipated energy rate under extensional deformations are equated to the work rate of the external force on the structure. Final formula obtained in this research, reasonably predicts the instantaneous folding force of the first fold creation versus folding distance and folding angle and also predicts the instantaneous folding force instead of the average value. Finally, according to the calculated theoretical relation, instantaneous folding force of the first fold creation in a square column was sketched versus folding distance and was compared to the experimental results which showed a good correlation.

Keywords: Instantaneous force, Folding force, Honeycomb, Square column.

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Authors: N. Reehana, A. Parveez Ahamed, D. Mubarak Ali, A. Suresh, R. Arvind Kumar, N. Thajuddin

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Cyanobacteria play a vital role in the production of phycobiliproteins that includes phycocyanin and phycoerythrin pigments. Phycocyanin and related phycobiliproteins have wide variety of application that is used in the food, biotechnology and cosmetic industry because of their color, fluorescent and antioxidant properties. The present study is focused to understand the pigment at molecular level in the Cyanobacteria Oscillatoria terebriformis NTRI05 and Oscillatoria foreaui NTRI06. After extraction of genomic DNA, the amplification of C-Phycocyanin gene was done with the suitable primer PCβF and PCαR and the sequencing was performed. Structural and Phylogenetic analysis was attained using the sequence to develop a molecular model.

Keywords: Cyanobacteria, C-Phycocyanin gene, Phylogenetic analysis, Structural analysis.

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Authors: Noha A. Mohammed, Isam A. Mohamed Ahmed, Elfadil E. Babiker

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The present study was carried out to evaluate the nutritional value of sorghum flour during processing of injera (unleavened thick bread). The proximate composition of sorghum flour before and after fermentation and that of injera was determined. Compared to the raw flour and fermented one, injera had low protein (11.55%), ash (1.57%) and fat (2.40%) contents but high in fiber content. Moreover, injera was found to have significantly (P ≤ 0.05) higher energy (389.08 Kcal/100g) compared to raw and fermented sorghum flour. Injera contained lower levels of anti-nutritional factors (polyphenols, phytate and tannins) compared to raw and fermented sorghum. Also it was found to be rich in Ca (4.75mg/100g), Fe (3.95 mg/100g), and Cu (0.7 mg/100g) compared to that of raw and fermented flour. Moreover, both the extractable minerals and protein digestibility were high for injera due to low amount of anti-nutrients. Injera was found to contain an appreciable amount of amino acids except arginine and tyrosine.

Keywords: Cooking, Fermentation, Malt, Protein fractions, Sorghum.

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Authors: M. Azizur Rahman, Tamotsu Oomori

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Calcite aCalcite and aragonite are the two common polymorphs of CaCO3 observed as biominerals. It is universal that the sea water contents a high Mg2+ (50mM) relative to Ca2+ (10mM). In vivo crystallization, Mg2+ inhibits calcite formation. For this reason, stony corals skeleton may be formed only aragonite crystals in the biocalcification. It is special in case of soft corals of which formed only calcite crystal; however, this interesting phenomenon, still uncharacterized in the marine environment, has been explored in this study using newly purified cell-free proteins isolated from the endoskeletal sclerites of soft coral. By recording the decline of pH in vitro, the control of CaCO3 nucleation and crystal growth by the cellfree proteins was revealed. Using Atomic Force Microscope, here we find that these endoskeletal cell-free proteins significantly design the morphological shape in the molecular-scale kinetics of crystal formation and those proteins act as surfactants to promote ion attachment at calcite steps.nd aragonite are the two common polymorphs of CaCO3 observed as biominerals. It is universal that the sea water contents a high Mg2+ (50mM) relative to Ca2+ (10mM). In vivo crystallization, Mg2+ inhibits calcite formation. For this reason, stony corals skeleton may be formed only aragonite crystals in the biocalcification. It is special in case of soft corals of which formed only calcite crystal; however, this interesting phenomenon, still uncharacterized in the marine environment, has been explored in this study using newly purified cell-free proteins isolated from the endoskeletal sclerites of soft coral. By recording the decline of pH in vitro, the control of CaCO3 nucleation and crystal growth by the cell-free proteins was revealed. Using Atomic Force Microscope, here we find that these endoskeletal cell-free proteins significantly design the morphological shape in the molecular-scale kinetics of crystal formation and those proteins act as surfactants to promote ion attachment at calcite steps. KeywordsBiomineralization, Calcite, Cell-free protein, Soft coral

Keywords: Biomineralization, Calcite, Cell-free protein, Soft coral

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Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

Abstract:

Model updating method has received increasing attention in damage detection structures based on measured modal parameters. Therefore, a probability-based damage detection (PBDD) procedure based on a model updating procedure is presented in this paper, in which a one-stage model-based damage identification technique based on the dynamic features of a structure is investigated. The presented framework uses a finite element updating method with a Monte Carlo simulation that considers the uncertainty caused by measurement noise. Enhanced ideal gas molecular movement (EIGMM) is used as the main algorithm for model updating. Ideal gas molecular movement (IGMM) is a multiagent algorithm based on the ideal gas molecular movement. Ideal gas molecules disperse rapidly in different directions and cover all the space inside. This is embedded in the high speed of molecules, collisions between them and with the surrounding barriers. In IGMM algorithm to accomplish the optimal solutions, the initial population of gas molecules is randomly generated and the governing equations related to the velocity of gas molecules and collisions between those are utilized. In this paper, an enhanced version of IGMM, which removes unchanged variables after specified iterations, is developed. The proposed method is implemented on two numerical examples in the field of structural damage detection. The results show that the proposed method can perform well and competitive in PBDD of structures.

Keywords: Enhanced ideal gas molecular movement, ideal gas molecular movement, model updating method, probability-based damage detection, uncertainty quantification.

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Authors: Yanhua Jin, Won Suk Lee

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The two-dimensional gel electrophoresis method (2-DE) is widely used in Proteomics to separate thousands of proteins in a sample. By comparing the protein expression levels of proteins in a normal sample with those in a diseased one, it is possible to identify a meaningful set of marker proteins for the targeted disease. The major shortcomings of this approach involve inherent noises and irregular geometric distortions of spots observed in 2-DE images. Various experimental conditions can be the major causes of these problems. In the protein analysis of samples, these problems eventually lead to incorrect conclusions. In order to minimize the influence of these problems, this paper proposes a partition based pair extension method that performs spot-matching on a set of gel images multiple times and segregates more reliable mapping results which can improve the accuracy of gel image analysis. The improved accuracy of the proposed method is analyzed through various experiments on real 2-DE images of human liver tissues.

Keywords: Proteomics, spot-matching, two-dimensionalelectrophoresis.

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Authors: Rizkita R. Esyanti, Iriawati, Olga Mardisadora

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Vetiver oil is secondary metabolite that accumulates in Vetiveria zizanioides roots.  The aim of this study was to obtain best type of root culture which produce high amount of vetiver oil, and was similar to metabolites produce from its mother plant.  Protein analysis was also conducted to detect protein, related to putative enzymes, which have a role in terpenoids synthesis in the root culture. The results showed that root culture derived from crown explant produced the best root growth.   The root culture produced primary and lateral roots, ca. 40 branches.  The vetiver oil produced from root culture was analyzed by using GC-MS., and the highest content of terpenoids from roots of crown explant attained 19.024%.  The result of SDS PAGE showed proteins which were ±61 kD and ± 68 kD, each might be related to putative monoterpene synthase and sesquiterpenes complex, respectively. 

Keywords: Protein, Root culture, Terpenoids, Vetiver oil.

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Authors: Chia-Ta Tsai, Wen-Lin Huang, Shinn-Jang Ho, Li-Sun Shu, Shinn-Ying Ho

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Prediction of bacterial virulent protein sequences can give assistance to identification and characterization of novel virulence-associated factors and discover drug/vaccine targets against proteins indispensable to pathogenicity. Gene Ontology (GO) annotation which describes functions of genes and gene products as a controlled vocabulary of terms has been shown effectively for a variety of tasks such as gene expression study, GO annotation prediction, protein subcellular localization, etc. In this study, we propose a sequence-based method Virulent-GO by mining informative GO terms as features for predicting bacterial virulent proteins. Each protein in the datasets used by the existing method VirulentPred is annotated by using BLAST to obtain its homologies with known accession numbers for retrieving GO terms. After investigating various popular classifiers using the same five-fold cross-validation scheme, Virulent-GO using the single kind of GO term features with an accuracy of 82.5% is slightly better than VirulentPred with 81.8% using five kinds of sequence-based features. For the evaluation of independent test, Virulent-GO also yields better results (82.0%) than VirulentPred (80.7%). When evaluating single kind of feature with SVM, the GO term feature performs much well, compared with each of the five kinds of features.

Keywords: Bacterial virulence factors, GO terms, prediction, protein sequence.

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Authors: David L. Azevedo, Jordan Del Nero

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In this paper we study a system composed by carbon nanotube (CNT) and bundle of carbon nanotube (BuCNT) interacting with a specific fatty acid as molecular probe. Full system is represented by open nanotube (or nanotubes) and the linoleic acid (LA) relaxing due the interaction with CNT and BuCNT. The LA has in his form an asymmetric shape with COOH termination provoking a close BuCNT interaction mainly by van der Waals force field. The simulations were performed by classical molecular dynamics with standard parameterizations. Our results show that these BuCNT and CNT are dynamically stable and it shows a preferential interaction position with LA resulting in three features: (i) when the LA is interacting with CNT and BuCNT (including both termination, CH2 or COOH), the LA is repelled; (ii) when the LA terminated with CH2 is closer to open extremity of BuCNT, the LA is also repelled by the interaction between them; and (iii) when the LA terminated with COOH is closer to open extremity of BuCNT, the LA is encapsulated by the BuCNT. These simulations are part of a more extensive work on searching efficient selective molecular devices and could be useful to reach this goal.

Keywords: Carbon Nanotube, Linoleic Acid, MolecularDynamics.

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Authors: Sajjad Seifoori

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Impact behavior of striker on graphene sheet and carbon nanotube is investigated based on molecular dynamics (MD) simulations. A MD simulation is conducted to obtain the maximum dynamic deflections of a square and rectangular single-layered graphene sheets (SLGSs) with various values of side-length and striker parameter. Effect of (i) chirality, (ii) graphene side-length and nanotube length, (iii) striker mass on the maximum dynamic deflections of graphene and nanotube are investigated. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (Length/Diameter).

Keywords: Impact, molecular dynamic, graphene, nanotube.

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Authors: E. Marei, A. Hammad, S. Ismail, A. El-Gindy

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This study aims to investigate the ability of different formula of mixed bacteria as a biological treatments of wastewater after primary treatment as a bio-treatment and bio-removal and bio-adsorbent of different heavy metals in natural circumstances. The wastewater was collected from Sarpium forest site-Ismailia Governorate, Egypt. These treatments were mixture of free cells and mixture of immobilized cells of different bacteria. These different formulas of mixed bacteria were prepared under Lab. condition. The obtained data indicated that, as a result of wastewater bio-treatment, the removal rate was found to be 76.92 and 76.70% for biological oxygen demand, 79.78 and 71.07% for chemical oxygen demand, 32.45 and 36.84 % for ammonia nitrogen as well as 91.67 and 50.0% for phosphate after 24 and 28 hrs with mixed free cells and mixed immobilized cells, respectively. Moreover, the bio-removals of different heavy metals were found to reach 90.0 and 50. 0% for Cu ion, 98.0 and 98.5% for Fe ion, 97.0 and 99.3% for Mn ion, 90.0 and 90.0% Pb, 80.0% and 75.0% for Zn ion after 24 and 28 hrs with mixed free cells and mixed immobilized cells, respectively. The results indicated that 13.86 and 17.43% of removal efficiency and reduction of total dissolved solids were achieved after 24 and 28 hrs with mixed free cells and mixed immobilized cells, respectively.

Keywords: Biological desalination, bio-sorption heavy metals, free cell bacteria, immobilized bacteria, wastewater bio-treatment.

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Authors: Sihana Ahmeti Lika, Merita Dauti, Ledjan Malaj

Abstract:

The objective of this study is to analyze the prophylactic usage of low molecular weight heparin (LMWH) along pregnancy and the correlation between their usage and month/week of pregnancy, in the Department of Gynecology and Obstetrics, at Clinical Hospital in Tetovo. A retrospective study was undertaken during 01 January – 31 December 2012. Over of one year, the total number of patients was 4636. Among the 1447 (32.21%) pregnant women, 298 (20.59%) of them were prescribed LMWH. The majority of patients given LMWH, 119 (39.93%) were diagnosed hypercoagulable. The age group with the highest attendance was 25- 35, 141 patients (47.32%). For 195 (65.44%) patients, this was their first pregnancy. Earliest stage of using LMWH was the second month of pregnancy 4 (1.34%) cases. The most common patients were 70 women along the seventh month (23.49%), followed by 68 in the ninth month of pregnancy (22.81%). Women in the 28th gestational week, were found to be the most affected, a total of 55 (78.57%) were in that week. Clexane 2000 and Fraxiparine 0.3 were the most common for which low molecular weight heparin was prescribed. The number of patients which received Clexane 2000 was 84 (28.19%), followed by those with Fraxiparine 0.3 81 (27.18%). The administration of LMWH is associated with long hospitalization (median 14,6 days).

Keywords: Hypercoagulable state, low molecular weight heparin, month of pregnancy, pregnant women.

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Authors: Srikanta Bose, Sudip K. Mazumder

Abstract:

We report here, the results of molecular dynamics simulation of p-doped (Ga-face)GaN over n-doped (Siface)( 0001)4H-SiC hetero-epitaxial material system with one-layer each of Ga-flux and (Al-face)AlN, as the interface materials, in the form of, the total Density of States (DOS). It is found that the total DOS at the Fermi-level for the heavily p-doped (Ga-face)GaN and ndoped (Si-face)4H-SiC hetero-epitaxial system, with one layer of (Al-face)AlN as the interface material, is comparatively higher than that of the various cases studied, indicating that there could be good vertical conduction across the (Ga-face)GaN over (Si-face)(0001)4HSiC hetero-epitaxial material system.

Keywords: Molecular dynamics, GaN, 4H-SiC, hetero-epitaxy.

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Authors: Sanwu Wang, Hongli Dang, Wenhua Xue, Darwin Shields, Xin Liu, Friederike C. Jentoft, Daniel E. Resasco

Abstract:

The bonding configuration and the heat of adsorption of a furfural molecule on the Pd(111) surface were determined by ab initio density-functional-theory calculations. The dynamics of pure liquid water, the liquid-solid interface formed by liquid water and the Pd(111) surface, as well as furfural at the water-Pd interface, were investigated by ab initio molecular dynamics simulations at finite temperatures. Calculations and simulations suggest that the bonding configurations at the water-Pd interface promote decarbonylation of furfural.

Keywords: Ab initio molecular dynamics simulations, bio-fuels, density functional theory, liquid-solid interfaces.

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Authors: Hanina M. N., Hairul Shahril M., Mohd Fazrullah Innsan M. F., Ismatul Nurul Asyikin I., Abdul Jalil A. K, Salina M. R., Ahmad I.B.

Abstract:

Proteins levels produced by bacteria may be increased in stressful surroundings, such as in the presence of antibiotics. It appears that many antimicrobial agents or antibiotics, when used at low concentrations, have in common the ability to activate or repress gene transcription, which is distinct from their inhibitory effect. There have been comparatively few studies on the potential of antibiotics or natural compounds in nature as a specific chemical signal that can trigger a variety of biological functions. Therefore, this study was focusing on the effect of essential oils from Cymbopogon flexuosus and C. nardus in regulating proteins production by Bacillus subtilis ATCC 21332. The Minimum Inhibition Concentrations (MICs) of both essential oils on B. subtilis were determined by using microdilution assay, resulting 0.2% and 1.56% for each C. flexuosus and C. nardus subsequently. The bacteria were further exposed to each essential oils at concentration of 0.01XMIC for 2 days. The proteins were then isolated and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Protein profile showed that a band with approximate size of 250 kD was appeared for the treated bacteria with essential oils. Thus, Bacillus subtilis ATCC 21332 in stressful condition with the presence of essential oils at low concentration could induce the protein production.

Keywords: Bacillus subtilis ATCC 21332, Cymbopogon essential oils, protein

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Authors: Uun Yanuhar

Abstract:

The purpose of research was to know the role of immunogenic protein of 49 kDa from V.alginolyticus which capable to initiate molecule expression of MHC Class II in receptor of Cromileptes altivelis. The method used was in vivo experimental research through testing of immunogenic protein 49 kDa from V.alginolyticus at Cromileptes altivelis (size of 250 - 300 grams) using 3 times booster by injecting an immunogenic protein in a intramuscular manner. Response of expressed MHC molecule was shown using immunocytochemistry method and SEM. Results indicated that adhesin V.alginolyticus 49 kDa which have immunogenic character could trigger expression of MHC class II on receptor of grouper and has been proven by staining using immunocytochemistry and SEM with labeling using antibody anti MHC (anti mouse). This visible expression based on binding between epitopes antigen and antibody anti MHC in the receptor. Using immunocytochemistry, intracellular response of MHC to in vivo induction of immunogenic adhesin from V.alginolyticus was shown.

Keywords: C.altivelis, immunogenic, MHC, V.alginolyticus.

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Authors: Sirilak Namwong , Wonnop Visessanguan, Soottawat Benjakul, Somboon Tanasupawat

Abstract:

The halophilic proteinase showed a maximal activity at 50°C and pH 9~10, in 20% NaCl and was highly stabilized by NaCl. It was able to hydrolyse natural actomyosin (NAM), collagen and anchovy protein. For NAM hydrolysis, the myosin heavy chain was completely digested by halophilic proteinase as evidenced by the lowest band intensity remaining, but partially hydrolysed actin. The SR5-3 proteinase was also capable hydrolyzing two major components of collagen, β- and α-compounds, effectively. The degree of hydrolysis (DH) of the halophilic proteinase and commercial proteinases (Novozyme, Neutrase, chymotrypsin and Flavourzyme) on the anchovy protein, were compared, and it was found that the proteinase showed a greater degree of hydrolysis towards anchovy protein than that from commercial proteinases. DH of halophilic proteinase was sharply enhanced according to the increase in the concentration of enzyme from 0.035 U to 0.105 U. The results warranting that the acceleration of the production of fish sauce with higher quality, may be achieved by adding of the halophilic proteinase from this bacterium.

Keywords: Halophilic proteinase, Halobacillus sp. SR5-3, anchovy (Spolephorus spp.) proteins, fish sauce

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