Search results for: tetracycline resistance genes.

Authors: Achraf El Allali, John R. Rose

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A number of competing methodologies have been developed to identify genes and classify DNA sequences into coding and non-coding sequences. This classification process is fundamental in gene finding and gene annotation tools and is one of the most challenging tasks in bioinformatics and computational biology. An information theory measure based on mutual information has shown good accuracy in classifying DNA sequences into coding and noncoding. In this paper we describe a species independent iterative approach that distinguishes coding from non-coding sequences using the mutual information measure (MIM). A set of sixty prokaryotes is used to extract universal training data. To facilitate comparisons with the published results of other researchers, a test set of 51 bacterial and archaeal genomes was used to evaluate MIM. These results demonstrate that MIM produces superior results while remaining species independent.

Keywords: Coding Non-coding Classification, Entropy, GeneRecognition, Mutual Information.

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Authors: M. F. Omar, R. A. Salam, R. Abdullah, N. A. Rashid

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Proteins or genes that have similar sequences are likely to perform the same function. One of the most widely used techniques for sequence comparison is sequence alignment. Sequence alignment allows mismatches and insertion/deletion, which represents biological mutations. Sequence alignment is usually performed only on two sequences. Multiple sequence alignment, is a natural extension of two-sequence alignment. In multiple sequence alignment, the emphasis is to find optimal alignment for a group of sequences. Several applicable techniques were observed in this research, from traditional method such as dynamic programming to the extend of widely used stochastic optimization method such as Genetic Algorithms (GAs) and Simulated Annealing. A framework with combination of Genetic Algorithm and Simulated Annealing is presented to solve Multiple Sequence Alignment problem. The Genetic Algorithm phase will try to find new region of solution while Simulated Annealing can be considered as an alignment improver for any near optimal solution produced by GAs.

Keywords: Simulated annealing, genetic algorithm, sequence alignment, multiple sequence alignment.

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Authors: Hossein Ramezani Ali-Akbari

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This paper presents an innovative method to control the rotational speed of a satellite solar panel during its deployment phase. A brushed DC motor has been utilized in the passive spring driven deployment mechanism to reduce the deployment speed. In order to use the DC motor as a damper, its connector terminals have been connected with an external resistance in a closed circuit. It means that, in this approach, there is no external power supply in the circuit. The working principle of this method is based on the back electromotive force (or back EMF) of the DC motor when an external torque (here the torque produced by the torsional springs) is coupled to the DC motor’s shaft. In fact, the DC motor converts to an electric generator and the current flows into the circuit and then produces the back EMF. Based on Lenz’s law, the generated current produced a torque which acts opposite to the applied external torque, and as a result, the deployment speed of the solar panel decreases. The main advantage of this method is to set an intended damping coefficient to the system via changing the external resistance. To produce the sufficient current, a gearbox has been assembled to the DC motor which magnifies the number of turns experienced by the DC motor. The coupled electro-mechanical equations of the system have been derived and solved, then, the obtained results have been presented. A full-scale prototype of the deployment mechanism has been built and tested. The potential application of brushed DC motors as a rotational speed damper has been successfully demonstrated.

Keywords: Back electromotive force, brushed DC motor, rotational speed damper, satellite solar panel deployment mechanism.

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Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

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Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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Authors: JiEun Jeong, Dong Hyun Kim, Bharat Bhusan Patnaik, Se Won Kang, HeeJu Hwang, Yong Hun Jo, Dae-Hyun Seog, YeonSooHan, Yong Seok Lee

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An expressed sequence tag (EST) analysis provideus portions of expressed genes. We have constructed cDNA library and determined randomly sequences from cDNA library clones of T. molitor injected with acholeplasma lysate. We identified the homologous to a galectin gene. As the result of cloning and characterization of novel, we found that the protein has an open reading frame (ORF) of 495 bp, with 164 amino acid residues and molecular weight of 18.5 kDa. To characterize the role of novel Tm-galectin in immune system, we quantified the mRNA level of galectin at different times after treatment with immune elicitors. The galectin mRNA was up-regulated about 7-folds within 18 hrs. This suggests that Tm-galectin is a novel member of animal lectins, and has a role in the process of pathogen recognition. Our study would be helpful for the study on immune defense system and signaling cascade.

Keywords: EST, Innate immunity, Tenebrio molitor, Galectin.

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Authors: Samy A. Selim

Abstract:

The antimicrobial, antiplasmid and cytotoxic activities of marine algae Halimeda opuntia and Sarconema filiforme were investigated. Antimicrobial bioassay against some human pathogenic bacteria and yeast were conducted using disc diffusion method. Halimeda extract exhibited antibacterial activity against six species of microrganisms, with significant inhibition against Staphylococcus aureus. While Sarconema extract was better potent as antifungal against Candida albicans. Comparative antibacterial studies showed that Halimeda extract showed equivalent or better activity as compared with commercial antibiotic when tested against Staphylococcus aureus. Further tests conducted using dilution method showed both extracts as having bacteriostatic mode of action against the tested microorganisms. Methanol extract of two species showed significant cytotoxicity (LC50 <500μg) on brine shrimp. Halimeda opuntia showed highest cytotoxic activity (LC50 =192.3μg). Also, the present investigation was undertaken to investigate the ability of methanolic extract of the algal extracts to cure R-plasmids from certain clinical E. coli isolates. The active fraction of Halimeda and Sarconema could cure plasmids from E. coli at curing efficiencies of approximately 78%. The active fraction mediated plasmid curing resulted in the subsequent loss of antibiotic resistance encoded in the plasmids as revealed by antibiotic resistance profile of cured strains. The screening results confirm the possible use of marine algae Halimeda opuntia and Sarconema filiforme as a source of pharmacological benefits.

Keywords: Antimicrobial, antiplasmid Cytotoxicity, Marine Algae.

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Authors: Mai S. Mabrouk, Nahed H. Solouma, Abou-Bakr M. Youssef, Yasser M. Kadah

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Many digital signal processing, techniques have been used to automatically distinguish protein coding regions (exons) from non-coding regions (introns) in DNA sequences. In this work, we have characterized these sequences according to their nonlinear dynamical features such as moment invariants, correlation dimension, and largest Lyapunov exponent estimates. We have applied our model to a number of real sequences encoded into a time series using EIIP sequence indicators. In order to discriminate between coding and non coding DNA regions, the phase space trajectory was first reconstructed for coding and non-coding regions. Nonlinear dynamical features are extracted from those regions and used to investigate a difference between them. Our results indicate that the nonlinear dynamical characteristics have yielded significant differences between coding (CR) and non-coding regions (NCR) in DNA sequences. Finally, the classifier is tested on real genes where coding and non-coding regions are well known.

Keywords: Gene prediction, nonlinear dynamics, correlation dimension, Lyapunov exponent.

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Authors: Moses, G, Osinubi, K. J.

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A laboratory study on the influence of compactive effort on expansive black cotton specimens treated with up to 8% ordinary Portland cement (OPC) admixed with up to 8% bagasse ash (BA) by dry weight of soil and compacted using the energies of the standard Proctor (SP), West African Standard (WAS) or “intermediate” and modified Proctor (MP) were undertaken. The expansive black cotton soil was classified as A-7-6 (16) or CL using the American Association of Highway and Transportation Officials (AASHTO) and Unified Soil Classification System (USCS), respectively. The 7day unconfined compressive strength (UCS) values of the natural soil for SP, WAS and MP compactive efforts are 286, 401 and 515kN/m2 respectively, while peak values of 1019, 1328 and 1420kN/m2 recorded at 8% OPC/ 6% BA, 8% OPC/ 2% BA and 6% OPC/ 4% BA treatments, respectively were less than the UCS value of 1710kN/m2 conventionally used as criterion for adequate cement stabilization. The soaked California bearing ratio (CBR) values of the OPC/BA stabilized soil increased with higher energy level from 2, 4 and 10% for the natural soil to Peak values of 55, 18 and 8% were recorded at 8% OPC/4% BA 8% OPC/2% BA and 8% OPC/4% BA, treatments when SP, WAS and MP compactive effort were used, respectively. The durability of specimens was determined by immersion in water. Soils treatment at 8% OPC/ 4% BA blend gave a value of 50% resistance to loss in strength value which is acceptable because of the harsh test condition of 7 days soaking period specimens were subjected instead of the 4 days soaking period that specified a minimum resistance to loss in strength of 80%. Finally An optimal blend of is 8% OPC/ 4% BA is recommended for treatment of expansive black cotton soil for use as a sub-base material.

Keywords: Bagasse ash, California bearing ratio, Compaction, Durability, Ordinary Portland cement, Unconfined compressive strength.

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Authors: T. Qasim, B. El Masoud, D. Ailabouni

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This in vitro study focused on investigating the fatigue resistance of veneered zirconia molar crowns with different veneering ceramic thicknesses, simulating the relative wear depths under simulated cyclic loading. A mandibular first molar was prepared and then scanned using computer-aided design/computer-aided manufacturing (CAD/CAM) technology to fabricate 32 zirconia copings of uniform 0.5 mm thickness. The manufactured copings then veneered with 1.5 mm, 1.0 mm, 0.5 mm, and 0.0 mm representing 0%, 33%, 66%, and 100% relative wear of a normal ceramic thickness of 1.5 mm. All samples were thermally aged to 6000 thermo-cycles for 2 minutes with distilled water between 5 ˚C and 55 ˚C. The samples subjected to cyclic fatigue and fracture testing using SD Mechatronik chewing simulator. These samples are loaded up to 1.25x10⁶ cycles or until they fail. During fatigue, testing, extensive cracks were observed in samples with 0.5 mm veneering layer thickness. Veneering layer thickness 1.5-mm group and 1.0-mm group were not different in terms of resisting loads necessary to cause an initial crack or final failure. All ceramic zirconia-based crown restorations with varying occlusal veneering layer thicknesses appeared to be fatigue resistant. Fracture load measurement for all tested groups before and after fatigue loading exceeded the clinical chewing forces in the posterior region. In general, the fracture loads increased after fatigue loading and with the increase in the thickness of the occlusal layering ceramic.

Keywords: All ceramic, dental crowns, relative wear, chewing simulator, cyclic loading, thermally ageing.

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Authors: S. S. Sravanthi, Swati Ghosh Acharyya

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Automotive light weighting is of major prominence in the current times due to its contribution in improved fuel economy and reduced environmental pollution. Various arc welding technologies are being employed in the production of automobile components with reduced weight. The present study is of practical importance since it involves preferential substitution of Zinc coated mild steel with a light weight alloy such as 6061 Aluminium by means of Gas Metal Arc Welding (GMAW) – Brazing technique at different processing parameters. However, the fabricated joints have shown the generation of Al – Fe layer at the interfacial regions which was confirmed by the Scanning Electron Microscope and Energy Dispersion Spectroscopy. These Al-Fe compounds not only affect the mechanical strength, but also predominantly deteriorate the corrosion resistance of the joints. Hence, it is essential to understand the phases formed in this layer and their crystal structure. Micro area X - ray diffraction technique has been exclusively used for this study. Moreover, the crevice corrosion analysis at the joint interfaces was done by exposing the joints to 5 wt.% FeCl₃ solution at regular time intervals as per ASTM G 48-03. The joints have shown a decreased crevice corrosion resistance with increased heat intensity. Inner surfaces of welds have shown severe oxide cracking and a remarkable weight loss when exposed to concentrated FeCl₃. The weight loss was enhanced with decreased filler wire feed rate and increased heat intensity. 

Keywords: Automobiles, welding, corrosion, lap joints, Micro XRD.

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Authors: Orkide Donma, Mustafa M. Donma

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Association between insulin resistance (IR) and hematological parameters has long been a matter of interest. Within this context, body mass index (BMI), red blood cells, white blood cells and platelets were involved in this discussion. Parameters related to platelets associated with IR may be useful indicators for the identification of IR. Platelet indices such as mean platelet volume (MPV), platelet distribution width (PDW) and plateletcrit (PCT) are being questioned for their possible association with IR. The aim of this study was to investigate the association between platelet (PLT) count as well as PLT indices and the surrogate indices used to determine IR in morbid obese (MO) children. A total of 167 children participated in the study. Three groups were constituted. The number of cases was 34, 97 and 36 children in the normal BMI, MO and metabolic syndrome (MetS) groups, respectively. Sex- and age-dependent BMI-based percentile tables prepared by World Health Organization were used for the definition of morbid obesity. MetS criteria were determined. BMI values, homeostatic model assessment for IR (HOMA-IR), alanine transaminase-to-aspartate transaminase ratio (ALT/AST) and diagnostic obesity notation model assessment laboratory (DONMA-lab) index values were computed. PLT count and indices were analyzed using automated hematology analyzer. Data were collected for statistical analysis using SPSS for Windows. Arithmetic mean and standard deviation were calculated. Mean values of PLT-related parameters in both control and study groups were compared by one-way ANOVA followed by Tukey post hoc tests to determine whether a significant difference exists among the groups. The correlation analyses between PLT as well as IR indices were performed. Statistically significant difference was accepted as p-value < 0.05. Increased values were detected for PLT (p < 0.01) and PCT (p > 0.05) in MO group compared to those observed in children with N-BMI. Significant increases for PLT (p < 0.01) and PCT (p < 0.05) were observed in MetS group in comparison with the values obtained in children with N-BMI (p < 0.01). Significantly lower MPV and PDW values were obtained in MO group compared to the control group (p < 0.01). HOMA-IR (p < 0.05), DONMA-lab index (p < 0.001) and ALT/AST (p < 0.001) values in MO and MetS groups were significantly increased compared to the N-BMI group. On the other hand, DONMA-lab index values also differed between MO and MetS groups (p < 0.001). In the MO group, PLT was negatively correlated with MPV and PDW values. These correlations were not observed in the N-BMI group. None of the IR indices exhibited a correlation with PLT and PLT indices in the N-BMI group. HOMA-IR showed significant correlations both with PLT and PCT in the MO group. All of the three IR indices were well-correlated with each other in all groups. These findings point out the missing link between IR and PLT activation. In conclusion, PLT and PCT may be related to IR in addition to their identities as hemostasis markers during morbid obesity. Our findings have suggested that DONMA-lab index appears as the best surrogate marker for IR due to its discriminative feature between morbid obesity and MetS.

Keywords: Children, insulin resistance, metabolic syndrome, plateletcrit, platelet indices.

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Authors: M.C. Zaghdoudi, S. Maalej, J. Mansouri, M.B.H. Sassi

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An experimental study is realized in order to verify the Mini Heat Pipe (MHP) concept for cooling high power dissipation electronic components and determines the potential advantages of constructing mini channels as an integrated part of a flat heat pipe. A Flat Mini Heat Pipe (FMHP) prototype including a capillary structure composed of parallel rectangular microchannels is manufactured and a filling apparatus is developed in order to charge the FMHP. The heat transfer improvement obtained by comparing the heat pipe thermal resistance to the heat conduction thermal resistance of a copper plate having the same dimensions as the tested FMHP is demonstrated for different heat input flux rates. Moreover, the heat transfer in the evaporator and condenser sections are analyzed, and heat transfer laws are proposed. In the theoretical part of this work, a detailed mathematical model of a FMHP with axial microchannels is developed in which the fluid flow is considered along with the heat and mass transfer processes during evaporation and condensation. The model is based on the equations for the mass, momentum and energy conservation, which are written for the evaporator, adiabatic, and condenser zones. The model, which permits to simulate several shapes of microchannels, can predict the maximum heat transfer capacity of FMHP, the optimal fluid mass, and the flow and thermal parameters along the FMHP. The comparison between experimental and model results shows the good ability of the numerical model to predict the axial temperature distribution along the FMHP.

Keywords: Electronics Cooling, Micro Heat Pipe, Mini Heat Pipe, Mini Heat Spreader, Capillary grooves.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias, Zalmiyah Zakaria, Saberi M. Mohamad

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Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology has caused problems in maintaining and processing them. One way to obtain their accessibility is by clustering them into fragmented groups. Clustering the Gene Ontology is a difficult combinatorial problem and can be modeled as a graph partitioning problem. Additionally, deciding the number k of clusters to use is not easily perceived and is a hard algorithmic problem. Therefore, an approach for solving the automatic clustering of the Gene Ontology is proposed by incorporating cohesion-and-coupling metric into a hybrid algorithm consisting of a genetic algorithm and a split-and-merge algorithm. Experimental results and an example of modularized Gene Ontology in RDF/XML format are given to illustrate the effectiveness of the algorithm.

Keywords: Automatic clustering, cohesion-and-coupling metric, gene ontology; genetic algorithm, split-and-merge algorithm.

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Authors: Khaled S. Ragab, Ahmed S. Eisa

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This paper investigates experimentally and analytically the torsion behavior of steel fibered high strength self compacting concrete beams reinforced by GFRP bars. Steel fibered high strength self compacting concrete (SFHSSCC) and GFRP bars became in the recent decades a very important materials in the structural engineering field. The use of GFRP bars to replace steel bars has emerged as one of the many techniques put forward to enhance the corrosion resistance of reinforced concrete structures. High strength concrete and GFRP bars attract designers and architects as it allows improving the durability as well as the esthetics of a construction. One of the trends in SFHSSCC structures is to provide their ductile behavior and additional goal is to limit development and propagation of macro-cracks in the body of SFHSSCC elements. SFHSSCC and GFRP bars are tough, improve the workability, enhance the corrosion resistance of reinforced concrete structures, and demonstrate high residual strengths after appearance of the first crack. Experimental studies were carried out to select effective fiber contents. Three types of volume fraction from hooked shape steel fibers are used in this study, the hooked steel fibers were evaluated in volume fractions ranging between 0.0%, 0.75% and 1.5%. The beams shape is chosen to create the required forces (i.e. torsion and bending moments simultaneously) on the test zone. A total of seven beams were tested, classified into three groups. All beams, have 200cm length, cross section of 10×20cm, longitudinal bottom reinforcement of 3

Keywords: Self compacting concrete, torsion behavior, steel fiber, steel fiber reinforced high strength self compacting concrete (SFRHSCC), GFRP bars.

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Authors: Ali Asghar Saki, Sayed Ali Hosseini Siyar, Abbass Ashoori

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This study was conducted to evaluate the effect of Echinacea purpurea on the expression of cyclooxygenase-2 (COX-2), interleukin-17F (IL-17F) in seven-day-old broiler chickens. Four groups were fed with concentration of 0 g/kg, 5 g/kg, 10 g/kg and 20 g/kg from the root of E. purpurea in the basal diet and two other groups were only fed with the basal diet for 21 days. At the 28^th day, lipopolysaccharide (LPS, 2 mg/kg diet) was injected in four groups and the basal diet group was injected by saline as control. The chickens’ spleen RNA expression was measured for the COX-2 and IL-17F genes by Real-Time PCR. The results have shown that chickens which were fed E. purpurea had a lower COX-2 and IL-17F mRNA expression. The chickens who have received LPS only, lymphocyte was lower than other treatments. Vital organ weights were not significantly different, but body weight loss was recovered by dietary herbs inclusion. The results of this study have shown the positive effect of an anti-inflammatory herb to prevent the undesirable effect of inflammation.

Keywords: Echinacea purpurea, broiler chickens, gene expression, lipopolysaccharide.

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Authors: H. Sakamoto, S. Kurosawa, M. Suzuki, S. Oguri

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In Arabidopsis, several genes encoding proteins with ankyrin repeats and transmembrane domains (AtANKTM) have been identified as mediators of biotic and abiotic stress responses. It has been known that the expression of an AtANKTM gene, At2g24600, is induced in response to abiotic stress and that there are four splicing variants derived from this locus. In this study, by RT-PCR and sequencing analysis, an unknown splicing variant of the At2g24600 transcript was identified. Based on differences in the predicted amino acid sequences, the five splicing variants are divided into three groups. The three predicted proteins are highly homologous, yet have different numbers of ankyrinrepeats and transmembrane domains. It is generally considered that ankyrin repeats mediate protein-protein interaction and that the number oftransmembrane domains affects membrane topology of proteins. The protein variants derived from the At2g24600 locus may have different molecular functions each other.

Keywords: Alternative splicing, ankyrin repeats, transmembrane domains, Arabidopsis.

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Authors: M. Anidha, K. Premalatha

Abstract:

Feature Selection is significant in order to perform constructive classification in the area of cancer diagnosis. However, a large number of features compared to the number of samples makes the task of classification computationally very hard and prone to errors in microarray gene expression datasets. In this paper, we present an innovative method for selecting highly informative gene subsets of gene expression data that effectively classifies the cancer data into tumorous and non-tumorous. The hybrid gene selection technique comprises of combined Mutual Information and Fisher score to select informative genes. The gene selection is validated by classification using Support Vector Machine (SVM) which is a supervised learning algorithm capable of solving complex classification problems. The results obtained from improved Mutual Information and F-Score with SVM as a classifier has produced efficient results.

Keywords: Gene selection, mutual information, Fisher score, classification, SVM.

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Authors: Rio G. L. D'Souza, K. Chandra Sekaran, A. Kandasamy

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The goal of Gene Expression Analysis is to understand the processes that underlie the regulatory networks and pathways controlling inter-cellular and intra-cellular activities. In recent times microarray datasets are extensively used for this purpose. The scope of such analysis has broadened in recent times towards reconstruction of gene networks and other holistic approaches of Systems Biology. Evolutionary methods are proving to be successful in such problems and a number of such methods have been proposed. However all these methods are based on processing of genotypic information. Towards this end, there is a need to develop evolutionary methods that address phenotypic interactions together with genotypic interactions. We present a novel evolutionary approach, called Phenomic algorithm, wherein the focus is on phenotypic interaction. We use the expression profiles of genes to model the interactions between them at the phenotypic level. We apply this algorithm to the yeast sporulation dataset and show that the algorithm can identify gene networks with relative ease.

Keywords: Evolutionary computing, gene expression analysis, gene networks, microarray data analysis, phenomic algorithms.

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Authors: Cha-Hwa Lin, Je-Wei Hu

Abstract:

The conventional GA combined with a local search algorithm, such as the 2-OPT, forms a hybrid genetic algorithm(HGA) for the traveling salesman problem (TSP). However, the geometric properties which are problem specific knowledge can be used to improve the search process of the HGA. Some tour segments (edges) of TSPs are fine while some maybe too long to appear in a short tour. This knowledge could constrain GAs to work out with fine tour segments without considering long tour segments as often. Consequently, a new algorithm is proposed, called intelligent-OPT hybrid genetic algorithm (IOHGA), to improve the GA and the 2-OPT algorithm in order to reduce the search time for the optimal solution. Based on the geometric properties, all the tour segments are assigned 2-level priorities to distinguish between good and bad genes. A simulation study was conducted to evaluate the performance of the IOHGA. The experimental results indicate that in general the IOHGA could obtain near-optimal solutions with less time and better accuracy than the hybrid genetic algorithm with simulated annealing algorithm (HGA(SA)).

Keywords: Traveling salesman problem, hybrid geneticalgorithm, priority selection, 2-OPT.

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Authors: Shou-Chen Lo, Chia-Ching Lin, Chieh-Chen Huang

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To decompose organochlorides by bioremediation, co-culture biohydrogen producer and dehalogenation microorganisms is a useful method. In this study, we combined these two characteristics from a biohydrogen producer, Rhodopseudomonas palustris, and a dehalogenation microorganism, Pseudomonas putida, to enchance halorespiration in R. palustris. The genes encoding cytochrome P450cam system (camC, camA, and camB) from P. putida were expressed in R. palustris with designated expression plasmid. All tested strains were cultured to log phase then presented pentachloroethane (PCA) in media. The vector control strain could degrade PCA about 78% after 16 hours, however, the cytochrome P450cam system expressed strain, CGA-camCAB, could completely degrade PCA in 12 hours. While taking chlorinated aromatic, 3-chlorobenzoate, as sole carbon source or present benzoate as co-substrate, CGA-camCAB presented faster growth rate than vector control strain.

Keywords: cytochrome P450, halorespiration, nitrogen fixation, Rhodopseudomonas palustris CGA009

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Authors: Amit Kumar Bhandary, Prithviraj Gupta, Siddhartha Mukherjee, Mahua Ghosh Chaudhuri, Rajib Dey

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Chromite ores are primarily used for extraction of chromium, which is an expensive metal. For low grade chromite ores (containing less than 40% Cr₂O₃), the chromium extraction is not usually economically viable. India possesses huge quantities of low grade chromite reserves. This deposit can be utilized after proper physical beneficiation. Magnetic separation techniques may be useful after reduction for the beneficiation of low grade chromite ore. The sample collected from the sukinda mines is characterized by XRD which shows predominant phases like maghemite, chromite, silica, magnesia and alumina. The raw ore is crushed and ground to below 75 micrometer size. The microstructure of the ore shows that the chromite grains surrounded by a silicate matrix and porosity observed the exposed side of the chromite ore. However, this ore may be utilized in refractory applications. Chromite ores contain Cr₂O₃, FeO, Al₂O₃ and other oxides like Fe-Cr, Mg-Cr have a high tendency to form spinel compounds, which usually show high refractoriness. Initially, the low grade chromite ore (containing 34.8% Cr₂O₃) was reduced at 1200 ⁰C for 80 minutes with 30% coke fines by weight, before being subjected to magnetic separation. The reduction by coke leads to conversion of higher state of iron oxides converted to lower state of iron oxides. The pre-reduced samples are then characterized by XRD. The magnetically inert mass was then reacted with 20% MgO by weight at 1450 ⁰C for 2 hours. The resultant product was then tested for various refractoriness parameters like apparent porosity, slag resistance etc. The results were satisfactory, indicating that the resultant spinel compounds are suitable for refractory applications for elevated temperature processes.

Keywords: Apparent porosity, beneficiation, low grade chromite, refractory, spinel compounds, slag resistance.

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Authors: M. Maimunah, G. A. Froemming, H. Nawawi, M. I. Nafeeza, O. Effat, M. Y. Rosmadi, M. S. Mohamed Saifulaman

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Atherosclerosis was identified as a chronic inflammatory process resulting from interactions between plasma lipoproteins, cellular components (monocyte, macrophages, T lymphocytes, endothelial cells and smooth muscle cells) and the extracellular matrix of the arterial wall. Several types of genes were known to express during formation of atherosclerosis. This study is carried out to identify unknown differentially expressed gene (DEG) in atherogenesis. Rabbit’s aorta tissues were stained by H&E for histomorphology. GeneFishing™ PCR analysis was performed from total RNA extracted from the aorta tissues. The DNA fragment from DEG was cloned, sequenced and validated by Real-time PCR. Histomorphology showed intimal thickening in the aorta. DEG detected from ACP-41 was identified as cathepsin B gene and showed upregulation at week-8 and week-12 of atherogenesis. Therefore, ACP-based GeneFishing™ PCR facilitated identification of cathepsin B gene which was differentially expressed during development of atherosclerosis.

Keywords: Atherosclerosis, GeneFishing™ PCR, cathepsin B gene.

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Authors: Kritsada Khongnomnan, Wittaya Poomipak, Yong Poovorawan, Sunchai Payungporn

Abstract:

In this study, three subtypes of influenza A viruses (pH1N1, H5N1 and H3N2) which naturally infected human were analyzed by bioinformatic approaches to find candidate human cellular miRNAs targeting viral genomes. There were 76 miRNAs targeting influenza A viruses. Among these candidates, 70 miRNAs were subtypes specifically targeting each subtype of influenza A virus including 21 miRNAs targeted subtype H1N1, 27 miRNAs targeted subtype H5N1 and 22 miRNAs targeted subtype H3N2. The remaining 6 miRNAs target on multiple subtypes of influenza A viruses. Uniquely, hsa-miR-3145 is the only one candidate miRNA targeting PB1 gene of all three subtypes. Obviously, most of the candidate miRNAs are targeting on polymerase complex genes (PB2, PB1 and PA) of influenza A viruses. This study predicted potential human miRNAs targeting on different subtypes of influenza A viruses which might be useful for inhibition of viral replication and for better understanding of the interaction between virus and host cell.

Keywords: Human miRNAs, Influenza A viruses, H1N1, H5N1, H3N2

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Authors: Zhenhuan Zhu, David Mulvaney, Vassilios Chouliaras

Abstract:

A new genetic algorithm, termed the 'optimum individual monogenetic genetic algorithm' (OIMGA), is presented whose properties have been deliberately designed to be well suited to hardware implementation. Specific design criteria were to ensure fast access to the individuals in the population, to keep the required silicon area for hardware implementation to a minimum and to incorporate flexibility in the structure for the targeting of a range of applications. The first two criteria are met by retaining only the current optimum individual, thereby guaranteeing a small memory requirement that can easily be stored in fast on-chip memory. Also, OIMGA can be easily reconfigured to allow the investigation of problems that normally warrant either large GA populations or individuals many genes in length. Local convergence is achieved in OIMGA by retaining elite individuals, while population diversity is ensured by continually searching for the best individuals in fresh regions of the search space. The results given in this paper demonstrate that both the performance of OIMGA and its convergence time are superior to those of a range of existing hardware GA implementations.

Keywords: Genetic algorithms, genetic hardware, machinelearning.

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Authors: Jun Hee Lee, Young Kyu Kim, Seong Jae Hong, Chamroeun Chhorn, Seung Woo Lee

Abstract:

Roller-compacted concrete pavement (RCCP), an environmental friendly pavement of which load carry capacity benefitted from both hydration and aggregate interlock from roller compacting, demonstrated a superb structural performance for a relatively small amount of water and cement content. Even though an excellent structural performance can be secured, it is required to investigate roller-compacted concrete (RCC) under environmental loading and its long-term durability under critical conditions. In order to secure long-term durability, an appropriate internal air-void structure is required for this concrete. In this study, a method for improving the long-term durability of RCCP is suggested by analyzing the internal air-void structure and corresponding durability of RCC. The method of improving the long-term durability involves measurements of air content, air voids, and air-spacing factors in RCC that experiences changes in terms of type of air-entraining agent and its usage amount. This test is conducted according to the testing criteria in ASTM C 457, 672, and KS F 2456. It was found that the freezing-thawing and scaling resistances of RCC without any chemical admixture was quite low. Interestingly, an improvement of freezing-thawing and scaling resistances was observed for RCC with appropriate the air entraining (AE) agent content; Relative dynamic elastic modulus was found to be more than 80% for those mixtures. In RCC with AE agent mixtures, large amount of air was distributed within a range of 2% to 3%, and an air void spacing factor ranging between 200 and 300 μm (close to 250 μm, recommended by PCA) was secured. The long-term durability of RCC has a direct relationship with air-void spacing factor, and thus it can only be secured by ensuring the air void spacing factor through the inclusion of the AE in the mixture.

Keywords: RCCP, durability, air spacing factor, surface scaling resistance test, freezing and thawing resistance test.

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Authors: Zue Chin Chang

Abstract:

RF magnetron sputtering is used on the ceramic targets, each of which contains zinc oxide (ZnO), zinc oxide doped with aluminum (AZO) and zinc oxide doped with gallium (GZO). The XRD analysis showed a preferred orientation along the (002) plane for ZnO, AZO, and GZO films. The AZO film had the best electrical properties; it had the lowest resistivity of 6.6 × 10-4 cm, the best sheet resistance of 2.2 × 10-1 Ω/square, and the highest carrier concentration of 4.3 × 1020 cm-3, as compared to the ZnO and GZO films.

Keywords: Aging, films, Microstructure, Photoelectric Property.

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

Abstract:

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: Gaurav D. Sonawane, Vikas G. Sargade

Abstract:

The present investigation is a study of the effect of advanced Physical Vapor Deposition (PVD) coatings on cutting temperature residual stresses and surface roughness during Duplex Stainless Steel (DSS) 2205 turning. Austenite stabilizers like nickel, manganese, and molybdenum reduced the cost of DSS. Surface Integrity (SI) plays an important role in determining corrosion resistance and fatigue life. Resistance to various types of corrosion makes DSS suitable for applications with critical environments like Heat exchangers, Desalination plants, Seawater pipes and Marine components. However, lower thermal conductivity, poor chip control and non-uniform tool wear make DSS very difficult to machine. Cemented carbide tools (M grade) were used to turn DSS in a dry environment. AlTiN and AlTiCrN coatings were deposited using advanced PVD High Pulse Impulse Magnetron Sputtering (HiPIMS) technique. Experiments were conducted with cutting speed of 100 m/min, 140 m/min and 180 m/min. A constant feed and depth of cut of 0.18 mm/rev and 0.8 mm were used, respectively. AlTiCrN coated tools followed by AlTiN coated tools outperformed uncoated tools due to properties like lower thermal conductivity, higher adhesion strength and hardness. Residual stresses were found to be compressive for all the tools used for dry turning, increasing the fatigue life of the machined component. Higher cutting temperatures were observed for coated tools due to its lower thermal conductivity, which results in very less tool wear than uncoated tools. Surface roughness with uncoated tools was found to be three times higher than coated tools due to lower coefficient of friction of coating used.

Keywords: Cutting temperatures, DSS2205, dry turning, HiPIMS, surface integrity.

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Authors: Berna Istegun, Erkan Celebi

Abstract:

The main objective of this experimental study is to assess the shear strength and the crack behavior of the triplets built of perforated brickwork masonry elements. In order to observe the influence of shear resistance and energy dissipating before and after retrofitting applications by using the reinforcing system, static-cyclic shear tests were employed in the structural mechanics laboratory of Sakarya University. The reinforcing system is composed of hybrid multiaxial seismic fabric consisting of alkali resistant glass and polypropylene fibers. The plaster as bonding material used in the specimen’s retrofitting consists of expanded glass granular. In order to acquire exact measuring data about the failure behavior of the two mortar joints under shear stressing, vertical load-controlled cylinder having force capacity of 50 kN and loading rate of 1.5 mm/min. with an internal inductive displacement transducers is carried out perpendicular to the triplet specimens. In this study, a total of six triplet specimens with textile reinforcement were prepared for these shear bond tests. The three of them were produced as single-sided reinforced triplets with seismic fabric, while the others were strengthened on both sides. In addition, three triplet specimens without retrofitting and plaster were also tested as reference samples. The obtained test results were given in the manner of force-displacement relationships, ductility coefficients and shear strength parameters comparatively. It is concluded that two-side seismic textile applications on masonry elements with relevant plaster have considerably increased the sheer force resistance and the ductility capacity.

Keywords: Triplet shears tests, retrofitting, seismic fabric, perforated brickwork, expanded glass granular.

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Authors: H. Shamoradifar, B. Teimuri, P. Parvaresh, S. Mohammadi

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One of the main characteristics of Heavy Water Moderated Reactors is their high production of plutonium. This article demonstrates the possibility of reduction of plutonium and other actinides in Heavy Water Research Reactor. Among the many ways for reducing plutonium production in a heavy water reactor, in this research, changing the fuel from natural Uranium fuel to Thorium-Uranium mixed fuel was focused. The main fissile nucleus in Thorium-Uranium fuels is U-233 which would be produced after neutron absorption by Th-232, so the Thorium-Uranium fuels have some known advantages compared to the Uranium fuels. Due to this fact, four Thorium-Uranium fuels with different compositions ratios were chosen in our simulations; a) 10% UO₂-90% THO₂ (enriched= 20%); b) 15% UO₂-85% THO₂ (enriched= 10%); c) 30% UO₂-70% THO₂ (enriched= 5%); d) 35% UO₂-65% THO₂ (enriched= 3.7%). The natural Uranium Oxide (UO₂) is considered as the reference fuel, in other words all of the calculated data are compared with the related data from Uranium fuel. Neutronic parameters were calculated and used as the comparison parameters. All calculations were performed by Monte Carol (MCNPX2.6) steady state reaction rate calculation linked to a deterministic depletion calculation (CINDER90). The obtained computational data showed that Thorium-Uranium fuels with four different fissile compositions ratios can satisfy the safety and operating requirements for Heavy Water Research Reactor. Furthermore, Thorium-Uranium fuels have a very good proliferation resistance and consume less fissile material than uranium fuels at the same reactor operation time. Using mixed Thorium-Uranium fuels reduced the long-lived α emitter, high radiotoxic wastes and the radio toxicity level of spent fuel.

Keywords: Burn-up, heavy water reactor, minor actinides, Monte Carlo, proliferation resistance.

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