Search results for: tetracycline resistance genes.

Authors: Murugan. A., Jerlin Nirmala. F .

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Life is beautiful. But, it is decided by genes, environment and the individual and shattered by the natural and / or the invited problems. Most of the global rural helpless masses are struggling for their survival since; they are neglected in all aspects of life including health. Amidst a countless number of miserable diseases in man, diabetes is becoming a dreaded killer and ramifying the entire globe in a jet speed. Diabetes control continues as a Herculean task to the scientific community and the modern society in the 21st century also. T2DM is not pertaining to any age and it can develop even during the childhood. This multifactorial disease abruptly changes the activities of certain vital biomarkers in the present rural T2DM cases. A remarkable variation in the levels of biomarkers like AST, ALT, GGT, ALP, LDH, HbA1C, C- peptide, fasting sugar, post-prandial sugar, sodium, potassium, BUN, creatinine and insulin show the rampant nature of T2DM in this physically active rural agrarian community.

Keywords: Alanine aminotransferase, Aspartate aminotransferase, Blood urea nitrogen, Glycated haemoglobin, Thyroid stimulating hormone

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Authors: M. Omer Faruk, A. M. A. M. Zonaed Siddiki, M. Fazal Karim, Md. Masuduzzaman, S. Chowdhury, Md. Shafiqul Islam, M. Alamgir Hossain

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The dog tapeworms Echinococcus granulosus develop hydatid cysts in various organs in human and domestic animals worldwide including Bangladesh. The aim of this study was to identify and characterize the genotype of E. granulosus isolated from cattle using 12S rRNA and Cytochrome oxidase 1 (COX 1) genes. A total of 43 hydatid cyst samples were collected from 390 examined cattle samples derived from slaughterhouses. Among them, three cysts were fertile. Genomic DNA was extracted from germinal membrane and/or protoscoleces followed by PCR amplification of mitochondrial 12S rRNA and Cytochrome oxidase 1 gene fragments. The sequence data revealed existence of G1 (64.28%) and possible G3 (21.43%) genotypes for the first time in Bangladesh. The study indicates that common sheep strain G1 is the dominant subtype of E. granulosus in Chittagong region of Bangladesh. This will increase our understanding of the epidemiology of hydatidosis in the southern part of the country and will be useful to plan suitable control measures in the long run.

Keywords: Echinococcus granulosus, molecular characterization, cattle, Bangladesh.

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Authors: Vinod B. Suryawanshi, Ajit D. Kelkar

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Composite materials, due to their unique properties such as high strength to weight ratio, corrosion resistance, and impact resistance have huge potential as structural materials in automotive, construction and transportation applications. However, these properties often come at higher cost owing to complex design methods, difficult manufacturing processes and raw material cost. Traditionally, tapered laminated composite structures are manufactured using autoclave manufacturing process by ply drop off technique. Autoclave manufacturing though very powerful suffers from high capital investment and higher energy consumption. As per the current trends in composite manufacturing, Out of Autoclave (OoA) processes are looked as emerging technologies for manufacturing the structural composite components for aerospace and defense applications. However, there is a need for improvement among these processes to make them reliable and consistent. In this paper, feasibility of using out of autoclave process to manufacture the variable thickness cantilever beam is discussed. The minimum weight design for the composite beam is obtained using constant stress beam concept by tailoring the thickness of the beam. Ply drop off techniques was used to fabricate the variable thickness beam from glass/epoxy prepregs. Experiments were conducted to measure bending stresses along the span of the cantilever beam at different intervals by applying the concentrated load at the free end. Experimental results showed that the stresses in the bean at different intervals were constant. This proves the ability of OoA process to manufacture the constant stress beam. Finite element model for the constant stress beam was developed using commercial finite element simulation software. It was observed that the simulation results agreed very well with the experimental results and thus validated design and manufacturing approach used.

Keywords: Beams, Composites, Constant Stress, Structures.

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Authors: Salma H. Abu Hafsa, A. Mendonca, B. Brehm-Stecher, A. A. Hassan, S. A. Ibrahim

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Enterococci are important inhabitants of the animal intestine and are widely used in probiotic products. A probiotic strain is expected to possess several desirable properties in order to exert beneficial effects. Therefore, the objective of this study was to isolate, characterize and identify Enterococcus sp. from chicken cecal and fecal samples to determine potential probiotic properties. Enterococci were isolated from chicken ceca and feces of thirty three clinically healthy chickens from a local farm. In vitro studies were performed to assess antibacterial activity of the isolated LAB (using agar well diffusion and cell free supernatant broth technique against Salmonella enterica serotype Enteritidis), survival in acidic conditions, resistance to bile salts, and their survival during simulated gastric juice conditions at pH 2.5. Isolates were identified by biochemical carbohydrate fermentation patterns using an API 50 CHL kit and API ZYM kits and by sequenced 16S rDNA. An isolate belonging to E. faecium species exhibited inhibitory effect against S. enteritidis. This isolate producing a clear zone as large as 10.30 mm or greater and was able to grow in the coculture medium and at the same time, inhibited the growth S. enteritidis. In addition, E. faecium exhibited significant resistance under highly acidic conditions at pH 2.5 for 8 h and survived well in bile salt at 0.2% for 24 h and showing ability to survive in the presence of simulated gastric juice at pH 2.5. Based on these results, E. faecium isolate fulfills some of the criteria to be considered as a probiotic strain and therefore, could be used as a feed additive with good potential for controlling S. Enteritidis in chickens. However, in vivo studies are needed to determine the safety of the strain.

Keywords: Acid tolerance, antimicrobial activity, Enterococcus faecium, probiotic.

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Authors: Assyl Bari, Olga Berillo, Saltanat Orazova, Anatoliy Ivashchenko

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Among all microRNAs (miRNAs) in 12 plant species investigated in this study, only miR398 targeted the copper chaperone for superoxide dismutase (CCS). The nucleotide sequences of miRNA binding sites were located in the mRNA protein-coding sequence (CDS) and were highly homologous. These binding sites in CCS mRNA encoded a conservative GDLGTL hexapeptide. The binding sites for miR398 in the CDS of superoxide dismutase 1 mRNA encoded GDLGN pentapeptide. The conservative miR398 binding site located in the CDS of superoxide dismutase 2 mRNA encoded the GDLGNI hexapeptide. The miR398 binding site in the CDS of superoxide dismutase 3 mRNA encoded the GDLGNI or GDLGNV hexapeptide. Gene expression of the entire superoxide dismutase family in the studied plant species was regulated only by miR398. All members of the miR398 family, i.e. miR398a,b,c were connected to one site for each CuZnSOD and chaperone mRNA.

Keywords: MicroRNA, mRNA, plant, superoxide dismutase.

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Authors: Mohd A. Mezher, Maysam F. Abbod

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Genetic Folding (GF) a new class of EA named as is introduced for the first time. It is based on chromosomes composed of floating genes structurally organized in a parent form and separated by dots. Although, the genotype/phenotype system of GF generates a kernel expression, which is the objective function of superior classifier. In this work the question of the satisfying mapping-s rules in evolving populations is addressed by analyzing populations undergoing either Mercer-s or none Mercer-s rule. The results presented here show that populations undergoing Mercer-s rules improve practically models selection of Support Vector Machine (SVM). The experiment is trained multi-classification problem and tested on nonlinear Ionosphere dataset. The target of this paper is to answer the question of evolving Mercer-s rule in SVM addressed using either genetic folding satisfied kernel-s rules or not applied to complicated domains and problems.

Keywords: Genetic Folding, GF, Evolutionary Algorithms, Support Vector Machine, Genetic Algorithm, Genetic Programming, Multi-Classification, Mercer's Rules

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

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Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: Synthetic gene network, network identification, nonlinear modeling, optimization.

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Authors: S. Makal, L. Ozyilmaz, S. Palavaroglu

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Gene, principal unit of inheritance, is an ordered sequence of nucleotides. The genes of eukaryotic organisms include alternating segments of exons and introns. The region of Deoxyribonucleic acid (DNA) within a gene containing instructions for coding a protein is called exon. On the other hand, non-coding regions called introns are another part of DNA that regulates gene expression by removing from the messenger Ribonucleic acid (RNA) in a splicing process. This paper proposes to determine splice junctions that are exon-intron boundaries by analyzing DNA sequences. A splice junction can be either exon-intron (EI) or intron exon (IE). Because of the popularity and compatibility of the artificial neural network (ANN) in genetic fields; various ANN models are applied in this research. Multi-layer Perceptron (MLP), Radial Basis Function (RBF) and Generalized Regression Neural Networks (GRNN) are used to analyze and detect the splice junctions of gene sequences. 10-fold cross validation is used to demonstrate the accuracy of networks. The real performances of these networks are found by applying Receiver Operating Characteristic (ROC) analysis.

Keywords: Gene, neural networks, ROC analysis, splice junctions.

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Authors: Junki Miyamoto, Mariko Kiyomi, Yuuki Nagashio, Takuya Suzuki, Soichi Tanabe

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Anti-allergic effects of royal jelly were evaluated in a human-like mouse model of atopic dermatitis. NC/Nga mice were cutaneously applied with royal jelly for 6 weeks. Royal jelly-treated mice exhibited lower levels of serum total immunoglobulin E in comparison with controls. We found that the treatment decreased (11% to the control) expression of mRNA for aquaporin-3, which is involved in the modulation of epidermal hydration. Microarray analysis revealed more than 10-fold changes in the expression of several genes, such as transglutaminase 2, repetin, and keratins. In normal human epidermal keratinocytes, royal jelly extract suppressed interleukin-8 elevation induced by TNF-α and interferon-γ, suggesting direct anti-inflammatory activity in keratinocytes. Collectively, topical application of royal jelly may be useful for amelioration of lesions and inflammation in atopic dermatitis.

Keywords: Aquaporin 3, immunoglobulin E, NC/Nga, royal jelly.

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Authors: Sang-Ho Baik

Abstract:

D-erythro-cyclohexylserine (D chiral unnatural β-hydroxy amino acid expected for the synthesis of drug for AIDS treatment. To develop a continuous bioconversion system with whole cell biocatalyst of D-threonine aldolase (D genes for the D-erythro-CHS production, D-threonine aldolase gene was amplified from Ensifer arboris 100383 by direct PCR amplication using two degenerated oligonucleotide primers designed based on genomic sequence of Shinorhizobium meliloti Sequence analysis of the cloned DNA fragment revealed one open-reading frame of 1059 bp and 386 amino acids. This putative D-TA gene was cloned into NdeI and EcoRI (pEnsi His-tag sequence or BamHI (pEnsi-DTA[2]) sequence of the pET21(a) vector. The expression level of the cloned gene was extremely overexpressed by E. coli BL21(DE3) transformed with pEnsi-DTA[1] compared to E. coli BL21(DE3) transformed with pEnsi-DTA[2]. When the cells expressing the wild used for D-TA enzyme activity, 12 mM glycine was successfully detected in HPLC analysis. Moreover, the whole cells harbouring the recombinant D-TA was able to synthesize D-erythro of 0.6 mg/ml in a batch reaction.

Keywords: About four key words or phrases in alphabetical order, separated by commas.

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Authors: Guillaume Mullier, Jean François Chatelain

Abstract:

Carbon Fiber Reinforced Plastics (CFRPs) are widely used for advanced applications, in particular in aerospace, automotive and wind energy industries. Once cured to near net shape, CFRP parts need several finishing operations such as trimming, milling or drilling in order to accommodate fastening hardware and meeting the final dimensions. The present research aims to study the effect of the cutting temperature in trimming on the mechanical strength of high performance CFRP laminates used for aeronautics applications. The cutting temperature is of great importance when dealing with trimming of CFRP. Temperatures higher than the glass-transition temperature (Tg) of the resin matrix are highly undesirable: they cause degradation of the matrix in the trimmed edges area, which can severely affect the mechanical performance of the entire component. In this study, a 9.50mm diameter CVD diamond coated carbide tool with six flutes was used to trim 24-plies CFRP laminates. A 300m/min cutting speed and 1140mm/min feed rate were used in the experiments. The tool was heated prior to trimming using a blowtorch, for temperatures ranging from 20°C to 300°C. The temperature at the cutting edge was measured using embedded KType thermocouples. Samples trimmed for different cutting temperatures, below and above Tg, were mechanically tested using three-points bending short-beam loading configurations. New cutting tools as well as worn cutting tools were utilized for the experiments. The experiments with the new tools could not prove any correlation between the length of cut, the cutting temperature and the mechanical performance. Thus mechanical strength was constant, regardless of the cutting temperature. However, for worn tools, producing a cutting temperature rising up to 450°C, thermal damage of the resin was observed. The mechanical tests showed a reduced mean resistance in short beam configuration, while the resistance in three point bending decreases with increase of the cutting temperature.

Keywords: Composites, Trimming, Thermal Damage, Surface Quality.

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Authors: Rameswar Debnath, Haruhisa Takahashi

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An evolutionary method whose selection and recombination operations are based on generalization error-bounds of support vector machine (SVM) can select a subset of potentially informative genes for SVM classifier very efficiently [7]. In this paper, we will use the derivative of error-bound (first-order criteria) to select and recombine gene features in the evolutionary process, and compare the performance of the derivative of error-bound with the error-bound itself (zero-order) in the evolutionary process. We also investigate several error-bounds and their derivatives to compare the performance, and find the best criteria for gene selection and classification. We use 7 cancer-related human gene expression datasets to evaluate the performance of the zero-order and first-order criteria of error-bounds. Though both criteria have the same strategy in theoretically, experimental results demonstrate the best criterion for microarray gene expression data.

Keywords: support vector machine, generalization error-bound, feature selection, evolutionary algorithm, microarray data

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Authors: Shanawaz Patil, Mohamed Haneef, K. S. Narayanaswamy

Abstract:

In the recent years, aluminum metal matrix composites were most widely used, which are finding wide applications in various field such as automobile, aerospace defense etc., due to their outstanding mechanical properties like low density, light weight, exceptional high levels of strength, stiffness, wear resistance, high temperature resistance, low coefficient of thermal expansion and good formability. In the present work, an effort is made to study the effect of heat treatment on mechanical properties of aluminum 7075 alloy reinforced with constant weight percentage of naturally occurring mineral beryl and varying weight percentage of graphene. The hybrid composites are developed with 0.5 wt. %, 1wt.%, 1.5 wt.% and 2 wt.% of graphene and 6 wt.% of beryl  by stir casting liquid metallurgy route. The cast specimens of unreinforced aluminum alloy and hybrid composite samples were prepared for heat treatment process and subjected to solutionizing treatment (T6) at a temperature of 490±5 ^oC for 8 hours in a muffle furnace followed by quenching in boiling water. The microstructure analysis of as cast and heat treated hybrid composite specimens are examined by scanning electron microscope (SEM). The tensile test and hardness test of unreinforced aluminum alloy and hybrid composites are examined. The wear behavior is examined by pin-on disc apparatus. The results of as cast specimens and heat treated specimens were compared. The heat treated Al7075-Beryl-Graphene hybrid composite had better properties and significantly improved the ultimate tensile strength, hardness and reduced wear loss when compared to aluminum alloy and  as cast hybrid composites.

Keywords: Beryl, graphene, heat treatment, mechanical properties.

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Authors: Daisy Biswas, Samar Kanti Bose, M. Mozaffar Hossain

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The development of value added composite products from bamboo with the application of gluing technology can play a vital role in economic development and also in forest resource conservation of any country. In this study, the gluability of Bambusa balcooa and Bambusa vulgaris, two locally grown bamboo species of Bangladesh was assessed. As the culm wall thickness of bamboos decreases from bottom to top, a culm portion of up to 5.4 m and 3.6 m were used from the base of B. balcooa and B. vulgaris, respectively, to get rectangular strips of uniform thickness. The color of the B. vulgaris strips was yellowish brown and that of B. balcooa was reddish brown. The strips were treated in borax-boric, bleaching and carbonization for extending the service life of the laminates. The preservative treatments changed the color of the strips. Borax–boric acid treated strips were reddish brown. When bleached with hydrogen peroxide, the color of the strips turned into whitish yellow. Carbonization produced dark brownish strips having coffee flavor. Chemical constituents for untreated and treated strips were determined. B. vulgaris was more acidic than B. balcooa. Then the treated strips were used to develop three-layered bamboo laminated panel. Urea formaldehyde (UF) and polyvinyl acetate (PVA) were used as binder. The shear strength and abrasive resistance of the panel were evaluated. It was found that the shear strength of the UF-panel was higher than the PVA-panel for all treatments. Between the species, gluability of B. vulgaris was better and in some cases better than hardwood species. The abrasive resistance of B. balcooa is slightly higher than B. vulgaris; however, the latter was preferred as it showed well gluability. The panels could be used as structural panel, floor tiles, flat pack furniture component, and wall panel etc. However, further research on durability and creep behavior of the product in service condition is warranted.

Keywords: Bambusa balcooa, Bambusa vulgaris, polyvinyl acetate, urea formaldehyde.

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Authors: Mohammed W. Abdulrahman

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The thermochemical copper-chlorine (Cu-Cl) cycle is considered as a sustainable and efficient technology for a hydrogen production, when linked with clean-energy systems such as nuclear reactors or solar thermal plants. In the Cu-Cl cycle, water is decomposed thermally into hydrogen and oxygen through a series of intermediate reactions. This paper investigates the thermal scale up analysis of the three phase oxygen production reactor in the Cu-Cl cycle, where the reaction is endothermic and the temperature is about 530 ^oC. The paper focuses on examining the size and number of oxygen reactors required to provide enough heat input for different rates of hydrogen production. The type of the multiphase reactor used in this paper is the continuous stirred tank reactor (CSTR) that is heated by a half pipe jacket. The thermal resistance of each section in the jacketed reactor system is studied to examine its effect on the heat balance of the reactor. It is found that the dominant contribution to the system thermal resistance is from the reactor wall. In the analysis, the Cu-Cl cycle is assumed to be driven by a nuclear reactor where two types of nuclear reactors are examined as the heat source to the oxygen reactor. These types are the CANDU Super Critical Water Reactor (CANDU-SCWR) and High Temperature Gas Reactor (HTGR). It is concluded that a better heat transfer rate has to be provided for CANDU-SCWR by 3-4 times than HTGR. The effect of the reactor aspect ratio is also examined in this paper and is found that increasing the aspect ratio decreases the number of reactors and the rate of decrease in the number of reactors decreases by increasing the aspect ratio. Finally, a comparison between the results of heat balance and existing results of mass balance is performed and is found that the size of the oxygen reactor is dominated by the heat balance rather than the material balance.

Keywords: Clean energy, Cu-Cl cycle, heat transfer, sustainable energy.

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Authors: Yoonsuh Jung

Abstract:

As DNA microarray data contain relatively small sample size compared to the number of genes, high dimensional models are often employed. In high dimensional models, the selection of tuning parameter (or, penalty parameter) is often one of the crucial parts of the modeling. Cross-validation is one of the most common methods for the tuning parameter selection, which selects a parameter value with the smallest cross-validated score. However, selecting a single value as an ‘optimal’ value for the parameter can be very unstable due to the sampling variation since the sample sizes of microarray data are often small. Our approach is to choose multiple candidates of tuning parameter first, then average the candidates with different weights depending on their performance. The additional step of estimating the weights and averaging the candidates rarely increase the computational cost, while it can considerably improve the traditional cross-validation. We show that the selected value from the suggested methods often lead to stable parameter selection as well as improved detection of significant genetic variables compared to the tradition cross-validation via real data and simulated data sets.

Keywords: Cross Validation, Parameter Averaging, Parameter Selection, Regularization Parameter Search.

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Authors: R. Balamurugan, A. M. Natarajan, K. Premalatha

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Microarray gene expression data play a vital in biological processes, gene regulation and disease mechanism. Biclustering in gene expression data is a subset of the genes indicating consistent patterns under the subset of the conditions. Finding a biclustering is an optimization problem. In recent years, swarm intelligence techniques are popular due to the fact that many real-world problems are increasingly large, complex and dynamic. By reasons of the size and complexity of the problems, it is necessary to find an optimization technique whose efficiency is measured by finding the near optimal solution within a reasonable amount of time. In this paper, the algorithmic concepts of the Particle Swarm Optimization (PSO), Shuffled Frog Leaping (SFL) and Cuckoo Search (CS) algorithms have been analyzed for the four benchmark gene expression dataset. The experiment results show that CS outperforms PSO and SFL for 3 datasets and SFL give better performance in one dataset. Also this work determines the biological relevance of the biclusters with Gene Ontology in terms of function, process and component.

Keywords: Particle swarm optimization, Shuffled frog leaping, Cuckoo search, biclustering, gene expression data.

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Authors: Rupinder Bakshi, Geeta Walia, Anita Gupta

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Urinary Tract Infections are considered as one of the most common bacterial infections with an estimated annual global incidence of 150 million. Antimicrobial drug resistance is one of the major threats due to wide spread usage of uncontrolled antibiotics. In this study, a total number of 9149 urine samples were collected from R.H Patiala and processed in the Department of Microbiology G. M. C Patiala (January 2013 to December 2013). Urine samples were inoculated on MacConkey’s and blood agar plates and incubated at 370C for 24 hrs. The organisms were identified by colony characters, Gram’s staining, and biochemical reactions. Antimicrobial susceptibility of the isolates was determined against various antimicrobial agents (Hi – Media Mumbai India) by Kirby Bauer DISK diffusion method on Muller Hinton agar plates. Maximum patients were in the age group of 21-30 yrs followed by 31-40 yrs. Males (34%) are less prone to urinary tract infections than females (66%). Culture was positive in 25% of the samples. Escherichia coli was the most common isolate 60.3% followed by Klebsiella pneumoniae 13.5%, Proteus spp. 9% and Staphylococcus aureus 7.6%. Most of the urinary isolates were sensitive to, carbepenems, Aztreonam, Amikacin, and Piperacillin + Tazobactum. All the isolates showed a good sensitivity towards Nitrofurantoin (82%). ESBL production was found to be 70.6% in Escherichia coli and 29.4% in Klebsiella pneumonia. Susceptibility of ESBL producers to Imipenem, Nitrofurantoin and Amikacin were found to be 100%, 76%, and 75% respectively. Uropathogens are increasingly showing resistance to many antibiotics making empiric management of outpatient UTIs challenging. Ampicillin, Cotrimoxazole and Ciprofloxacin should not be used in empiric treatment. Nitrofurantoin could be used in lower urinary tract infection. Knowledge of uropathogens and their antimicrobial susceptibility pattern in a geographical region will help in appropriate and judicious antibiotic usage in a health care setup.

Keywords: Urinary Tract Infection, UTI, antibiotic susceptibility pattern, ESBL.

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Authors: K. Karuppasamy

Abstract:

In this paper, analysis of an infinite beam resting on multilayer tensionless extensible geosynthetic reinforced granular fill-poor soil system overlying soft soil strata under moving load with constant velocity is presented. The beam is subjected to a concentrated load moving with constant velocity. The upper reinforced granular bed is modeled by a rough membrane embedded in Pasternak shear layer overlying a series of compressible nonlinear winkler springs representing the underlying the very poor soil. The multilayer tensionless extensible geosynthetic layer has been assumed to deform such that at interface the geosynthetic and the soil have some deformation. Nonlinear behaviour of granular fill and the very poor soil has been considered in the analysis by means of hyperbolic constitutive relationships. Governing differential equations of the soil foundation system have been obtained and solved with the help of appropriate boundary conditions. The solution has been obtained by employing finite difference method by means of Gauss-Siedal iterative scheme. Detailed parametric study has been conducted to study the influence of various parameters on the response of soil–foundation system under consideration by means of deflection and bending moment in the beam and tension mobilized in the geosynthetic layer. These parameters include magnitude of applied load, velocity of load, damping, ultimate resistance of poor soil and granular fill layer. Range of values of parameters has been considered as per Indian Railway conditions. This study clearly observed that the comparisons of multilayer tensionless extensible geosynthetic reinforcement with poor foundation soil and magnitude of applied load, relative compressibility of granular fill and ultimate resistance of poor soil has significant influence on the response of soil–foundation system.

Keywords: Infinite beams, multilayer tensionless extensible geosynthetic, granular layer, moving load, nonlinear behavior of poor soil.

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Authors: A. Zahra, G. de Cesare, D. Caputo, A. Nascetti

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PDMS (Polydimethylsiloxane) polymer is a suitable material for biological and MEMS (Microelectromechanical systems) designers, because of its biocompatibility, transparency and high resistance under plasma treatment. PDMS round channel is always been of great interest due to its ability to confine the liquid with membrane type micro valves. In this paper we are presenting a very simple way to form round shapemicrofluidic channel, which is based on reflow of positive photoresist AZ® 40 XT. With this method, it is possible to obtain channel of different height simply by varying the spin coating parameters of photoresist.

Keywords: Lab-on-Chip, PDMS, Reflow, Round microfluidic channel.

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Authors: Goksen Arik, Mihriban Korukluoglu

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Lactic acid bacteria (LAB) and some yeast species are common microorganisms found in dairy products and most of them are responsible for the fermentation of foods. Such cultures are isolated and used as a starter culture in the food industry because of providing standardisation of the final product during the food processing. Choice of starter culture is the most important step for the production of fermented food. Isolated LAB and yeast cultures which have the ability to create a biofilm layer can be preferred as a starter in the food industry. The biofilm formation could be beneficial to extend the period of usage time of microorganisms as a starter. On the other hand, it is an undesirable property in pathogens, since biofilm structure allows a microorganism become more resistant to stress conditions such as antibiotic presence. It is thought that the resistance mechanism could be turned into an advantage by promoting the effective microorganisms which are used in the food industry as starter culture and also which have potential to stimulate the gastrointestinal system. Development of the biofilm layer is observed in some LAB and yeast strains. The resistance could make LAB and yeast strains dominant microflora in the human gastrointestinal system; thus, competition against pathogen microorganisms can be provided more easily. Based on this circumstance, in the study, 10 LAB and 10 yeast strains were isolated from various dairy products, such as cheese, yoghurt, kefir, and cream. Samples were obtained from farmer markets and bazaars in Bursa, Turkey. As a part of this research, all isolated strains were identified and their ability of biofilm formation was detected with two different methods and compared with each other. The first goal of this research was to determine whether isolates have the potential for biofilm production, and the second was to compare the validity of two different methods, which are known as “Tube method” and “96-well plate-based method”. This study may offer an insight into developing a point of view about biofilm formation and its beneficial properties in LAB and yeast cultures used as a starter in the food industry.

Keywords: Biofilm, dairy products, lactic acid bacteria, yeast.

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Authors: A. Sakavičius, A. Lukša, V. Nargelienė, V. Bukauskas, G. Astromskas, A. Šetkus

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We investigate the influence of annealing on the properties of a contact between graphene and metal (Au and Ni), using circular transmission line model (CTLM) contact geometry. Kelvin probe force microscopy (KPFM) and Raman spectroscopy are applied for characterization of the surface and interface properties. Annealing causes a decrease of the metal-graphene contact resistance for both Ni and Au.

Keywords: Graphene, Kelvin force probe microscopy, Raman spectroscopy.

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Authors: Samy A. Selim, Nashwa I. Hagag

Abstract:

Abstract–The objectives of the current study are to determine the prevalence, etiological agents, drug susceptibility pattern and plasmid profile of Acinetobacter baumannii isolates from Hospital-Acquired Infections (HAI) at Community Hospital, Al Jouf Province, Saudi Arabia. A total of 1890 patients had developed infection during hospital admission and were included in the study. Among those who developed nosocomial infections, 15(9.4), 10(2.7) and 118 (12.7) had respiratory tract infection (RTI), blood stream infections (BSI) and urinary tract (UTI) respectively. A total of 268 bacterial isolates were isolated from nosocomial infection. S. aureus was reported in 23.5% for of the total isolates followed by Klebsiella pneumoniae (17.5%), E. coli (17.2%), P. aeruginosa (11.9%), coagulase negative staphylococcus (9%), A. baumannii (7.1%), Enterobacter spp. (3.4%), Citrobacter freundii (3%), Proteus mirabilis (2.6%), and Proteus vulgaris and Enterococcous faecalis (0.7%). Isolated organisms are multi-drug resistant, predominantly Gram-positive pathogens with a high incidence of methicillin-resistant S. aureus, extended spectrum beta lactamase and vancomycin resistant enterococci organisms. The RFLP (Fragment Length Polymorphisms) patterns of plasmid preparations from isolated A. baumannii isolates had altered RFLP patterns, possibly due to the presence of plasmid(s). Five A. baumannii isolates harbored plasmids all of which were not less than 2.71kbp in molecular weight. Hence, it showed that the gene coding for the isolates were located on the plasmid DNA while the remaining isolates which have no plasmid might showed gene coding for antibiotic resistance being located on chromosomal DNA. Nosocomial infections represent a current problem in Community Hospital, Al Jouf Province, Saudi Arabia. Problems associated with SSI include infection with multidrug resistant pathogens which are difficult to treat and are associated with increased mortality.

Keywords: Hospital-Acquired Infections, Acinetobacter baumannii, antibiotic resistance, plasmid profile, RFLP patterns, Al Jouf Province, Saudi Arabia

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Authors: Mbala Mukenga, Edison Muzenda, Kalala Jalama, Reinout Meijboom

Abstract:

TiO2 supported nano-ZnO catalyst was prepared by deposition-precipitation and tested for the trans-esterification reaction of soybean oil to biodiesel. The TiO2 support stabilized the nano-ZnO in a dispersed form with limited crystallite size compared to the unsupported ZnO. The final ZnO dispersion and crystallite size and the material transfer resistance in the catalyst significantly influenced the supported nano-ZnO catalyst performance.

Keywords: nano-ZnO, soybean oil, TiO2, trans-esterification

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Authors: C. Alexandridou, G. N. Angelopoulos, F. A. Coutelieris

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Construction industry in Greece consumes annually more than 25 million tons of natural aggregates originating mainly from quarries. At the same time, more than 2 million tons of construction and demolition waste are deposited every year, usually without control, therefore increasing the environmental impact of this sector. A potential alternative for saving natural resources and minimize landfilling, could be the recycling and re-use of Concrete and Demolition Waste (CDW) in concrete production. Moreover, in order to conform to the European legislation, Greece is obliged to recycle non-hazardous construction and demolition waste to a minimum of 70% by 2020. In this paper characterization of recycled materials - commercially and laboratory produced, coarse and fine, Recycled Concrete Aggregates (RCA) - has been performed. Namely, X-Ray Fluorescence and X-ray diffraction (XRD) analysis were used for chemical and mineralogical analysis respectively. Physical properties such as particle density, water absorption, sand equivalent and resistance to fragmentation were also determined. This study, first time made in Greece, aims at outlining the differences between RCA and natural aggregates and evaluating their possible influence in concrete performance. Results indicate that RCA’s chemical composition is enriched in Si, Al, and alkali oxides compared to natural aggregates. X-ray diffraction (XRD) analyses results indicated the presence of calcite, quartz and minor peaks of mica and feldspars. From all the evaluated physical properties of coarse RCA, only water absorption and resistance to fragmentation seem to have a direct influence on the properties of concrete. Low Sand Equivalent and significantly high water absorption values indicate that fine fractions of RCA cannot be used for concrete production unless further processed. Chemical properties of RCA in terms of water soluble ions are similar to those of natural aggregates. Four different concrete mixtures were produced and examined, replacing natural coarse aggregates with RCA by a ratio of 0%, 25%, 50% and 75% respectively. Results indicate that concrete mixtures containing recycled concrete aggregates have a minor deterioration of their properties (3-9% lower compression strength at 28 days) compared to conventional concrete containing the same cement quantity.

Keywords: Chemical and physical characterization, compressive strength, mineralogical analysis, recycled concrete aggregates, waste management.

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Authors: Yahia I. Mohamed, Ahmed I. Marzouk, Mohamed A. Yacout

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Aim of this work was to study the genetic basis for oil accumulation in olive fruit via tracking DGAT2 (Diacylglycerol acyltransferase type-2) gene in three Egyptian Origen Olive cultivars namely Toffahi, Hamed and Maraki using molecular marker techniques and bioinformatics tools. Results illustrate that, firstly: specific genomic band of Maraki cultivars was identified as DGAT2 (Diacylglycerol acyltransferase type-2) and identical for this gene in Olea europaea with 100% of similarity. Secondly, differential genomic band of Maraki cultivars which produced from RAPD fingerprinting technique reflected predicted distinguished sequence which identified as DGAT2 (Diacylglycerol acyltransferase type-2) in Fragaria vesca subsp. Vesca with 76% of sequential similarity. Third and finally, specific genomic specific band of Hamed cultivars was identified as two fragments, 1- Olea europaea cultivar Koroneiki diacylglycerol acyltransferase type 2 mRNA, complete cds with two matches regions with 99% or 2- Predicted: Fragaria vesca subsp. vesca diacylglycerol O-acyltransferase 2-like (LOC101313050), mRNA with 86 % of similarity.

Keywords: Olea europaea, fingerprinting, Diacylglycerol acyltransferase type- 2 (DGAT2).

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Authors: Titin Andri Wihastuti, Djanggan Sargowo

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NFκB is a transcription factor regulating many function of the vessel wall. In the normal condition , NFκB is revealed diffuse cytoplasmic expressionsuggesting that the system is inactive. The presence of activation NFκB provide a potential pathway for the rapid transcriptional of a variety of genes encoding cytokines, growth factors, adhesion molecules and procoagulatory factors. It is likely to play an important role in chronic inflamatory disease involved atherosclerosis. There are many stimuli with the potential to active NFκB, including hyperlipidemia. We used 24 mice which was divided in 6 groups. The HFD given by et libitum procedure during 2, 4, and 6 months. The parameters in this study were the amount of NFKB activation ,H2O2 as ROS and VCAM-1 as a product of NFKB activation. H2O2 colorimetryc assay performed directly using Anti Rat H2O2 ELISA Kit. The NFKB and VCAM-1 detection obtained from aorta mice, measured by ELISA kit and imunohistochemistry. There was a significant difference activation of H2O2, NFKB and VCAM-1 level at induce HFD after 2, 4 and 6 months. It suggest that HFD induce ROS formation and increase the activation of NFKB as one of atherosclerosis marker that caused by hyperlipidemia as classical atheroschlerosis risk factor.

Keywords: High Fat Diet, NFKB, H2O2, atherosclerosis

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Authors: Niousha Bagheri Khulenjani, Mohammad Saniee Abadeh

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Learning from very big datasets is a significant problem for most present data mining and machine learning algorithms. MicroRNA (miRNA) is one of the important big genomic and non-coding datasets presenting the genome sequences. In this paper, a hybrid method for the classification of the miRNA data is proposed. Due to the variety of cancers and high number of genes, analyzing the miRNA dataset has been a challenging problem for researchers. The number of features corresponding to the number of samples is high and the data suffer from being imbalanced. The feature selection method has been used to select features having more ability to distinguish classes and eliminating obscures features. Afterward, a Convolutional Neural Network (CNN) classifier for classification of cancer types is utilized, which employs a Genetic Algorithm to highlight optimized hyper-parameters of CNN. In order to make the process of classification by CNN faster, Graphics Processing Unit (GPU) is recommended for calculating the mathematic equation in a parallel way. The proposed method is tested on a real-world dataset with 8,129 patients, 29 different types of tumors, and 1,046 miRNA biomarkers, taken from The Cancer Genome Atlas (TCGA) database.

Keywords: Cancer classification, feature selection, deep learning, genetic algorithm.

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Authors: Mohamed A. Mahfouz, M. A. Ismail

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Biclustering is a very useful data mining technique for identifying patterns where different genes are co-related based on a subset of conditions in gene expression analysis. Association rules mining is an efficient approach to achieve biclustering as in BIMODULE algorithm but it is sensitive to the value given to its input parameters and the discretization procedure used in the preprocessing step, also when noise is present, classical association rules miners discover multiple small fragments of the true bicluster, but miss the true bicluster itself. This paper formally presents a generalized noise tolerant bicluster model, termed as μBicluster. An iterative algorithm termed as BIDENS based on the proposed model is introduced that can discover a set of k possibly overlapping biclusters simultaneously. Our model uses a more flexible method to partition the dimensions to preserve meaningful and significant biclusters. The proposed algorithm allows discovering biclusters that hard to be discovered by BIMODULE. Experimental study on yeast, human gene expression data and several artificial datasets shows that our algorithm offers substantial improvements over several previously proposed biclustering algorithms.

Keywords: Machine learning, biclustering, bi-dimensional clustering, gene expression analysis, data mining.

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Authors: C. Kozkurt, A. Fenercioglu, M. Soyaslan

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In this study rack systems that are structural storage units of warehouses have been analyzed as structural with Finite Element Method (FEA). Each cell of discussed rack system storages pallets which have from 800 kg to 1000 kg weights and 0.80x1.15x1.50 m dimensions. Under this load, total deformations and equivalent stresses of structural elements and principal stresses, tensile stresses and shear stresses of connection elements have been analyzed. The results of analyses have been evaluated according to resistance limits of structural and connection elements. Obtained results have been presented as visual and magnitude.

Keywords: warehouse, structural analysis, AS/RS, FEM, FEA

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