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Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method

Abadia E. | Zhang J. | Vultos T.D. | Ritacco V. | Kremer K. | Aktas E. | Matsumoto T.

Article | 2010 | Infection, Genetics and Evolution10 ( 7 ) , pp.1066 - 1074

We developed a new multiplexed-PCR assay to accurately classify Mycobacterium tuberculosis complex (MTC) isolates at the sublineage level by single nucleotide polymorphisms (SNPs). This method relies on 7 SNPs located in different genes of the MTC strains (recC, rec0, recR, ligB, ligC, alkA, and mgtC). Most of these genes are involved in replication, repair and recombination (3R) functions of M. tuberculosis strains, four of the mutations are synonymous, and thus neutral. Genes were chosen as a first empirical approach to assess the congruence between spoligotyping-based phylogeographical classification and SNP typing.This scheme ef . . .ficiently classifies most of MTC phylogeographical groups: (1) confirming and identifying new sublineage-specific SNPs, (2) unraveling phylogenetical relationships between spoligotyping-defined MTC sublineages, (3) appropriately assigning sublineages to some spoligotypes and reassigning sublineages to other mis-labeled spoligotype signatures. This study opens the way to a more meaningful taxonomic, evolutionary and epidemiological classification. It also allows evaluation of spoligotype-signature significance towards a more comprehensive understanding of the evolutionary mechanisms of the clustered regularly interspaced short palindromic repeat (CRISPR) locus in MTC. © 2010 Elsevier B.V Daha fazlası Daha az

Discarding lifetime investigation of a rotation resistant rope subjected to bending over sheave fatigue

Onur Y.A. | İmrak C.E. | Onur T.Ö.

Article | 2019 | Measurement: Journal of the International Measurement Confederation142 , pp.163 - 169

In this paper, theoretical and experimental studies are conducted to exhibit the discarding fatigue lifetime of a rotation resistant rope exposed to alternate bending over sheave (BoS) fatigue. Experimental studies are fulfilled to determine discarding lifetimes of a rotation resistant rope exposed to BoS fatigue. Multiple linear regression analysis is performed and novel theoretical discarding lifetime prediction formula is determined by using the least square method. Furthermore, discarding lifetimes of rotation resistant ropes exposed to BoS fatigue is predicted by using artificial neural network (ANN). There is a vigorous correl . . .ation among the results acquired by regression model, ANN and experimental data. © 2019 Elsevier Lt Daha fazlası Daha az

Liquid–liquid extraction of neodymium ions from aqueous solutions of NdCl3 by phosphonium-based ionic liquids

Panigrahi M. | Grabda M. | Kozak D. | Dorai A. | Shibata E. | Kawamura J. | Nakamura T.

Article | 2016 | Separation and Purification Technology171 , pp.263 - 269

A protocol for the recovery of rare earth elements based on the dissolution of an aqueous solution of a rare earth metal chloride in an ionic liquid (IL) followed by stripping of the dissolved metal ions into an aqueous phase is proposed. The use of ILs is a departure from the traditional strategies employed for extraction. Liquid–liquid extraction of neodymium (Nd) ions from an aqueous solution of NdCl3 with and without hydrochloric acid (HCl) was carried out using phosphonium-based ILs, namely trihexyl(tetradecyl)phosphonium benzoate [T66614][BA] and trihexyl(tetradecyl)phosphonium bis(trifluoromethylsulfonyl)imide [T66614][TFSA]. . . . The extraction was also conducted using a mixture of the aforementioned ILs and toluene. The efficiency of the extraction decreased with increasing concentrations of Nd in the aqueous solution. Furthermore, increasing the concentration of HCl in the aqueous phase decreased the percentage of extracted Nd ions. It indicates that the extraction followed a neutral or ion-pair extraction type of mechanism. Stripping of Nd ions from the metal-loaded organic phase using different acids revealed that HCl and HNO3 were the most effective stripping agents for complete re-extraction of the metal ions. Trihexyl(tetradecyl)phosphonium-based IL with a benzoate counter anion was more effective for Nd extraction than the congener with the bis(trifluoromethylsulfonyl)imide anion. © 2016 Elsevier B.V Daha fazlası Daha az

Compositional fingerprints of chromian spinel from the refractory chrome ores of Metalleion, Othris (Greece): Implications for metallogeny and deformation of chromitites within a “hot” oceanic fault zone

Kapsiotis A. | Rassios A.E. | Uysal I. | Grieco G. | Akmaz R.M. | Saka S. | Bussolesi M.

Article | 2018 | Journal of Geochemical Exploration185 , pp.14 - 32

The chrome ores of the retired Metalleion mine of the Othris ophiolite are hosted in a small volume of a pervasively serpentinized, tabular harzburgite body. These ores have been studied to determine their geological mode of occurrence, mineralogy and chromian spinel (Cr-spinel) chemistry. The ores consist of massive chromitite (85–95% modal Cr-spinel) with mylonitic fabric in imbricate-shaped pods. Chromian spinel displays a limited range in Cr# [Cr/(Cr + Al) × 100 = 53–63] and Mg# [Mg/(Mg + Fe 2 + ) × 100 = 59–73] and low TiO 2 content (? 0.11 wt%). Minor- (Ti, Ni, V, Mn and Zn) and trace-element (Sc, Co and Ga) concentrations do . . .not show any significant variations from Cr-spinel cores to boundaries and were not considerably modified by post-magmatic processes. However, Cr-spinel compositions show slight enrichments in Zn and V, and depletions in Ti and Sc when compared to the composition of chromite from the East Pacific Rise mid-ocean ridge (MOR) basalts. The composition of Cr-spinel from the Metalleion chromitites is quite anomalous on a global perspective as these ores are not clearly associated to a suprasubduction zone (SSZ) or MOR chemistry. Field data indicate that the Metalleion chromitites lack remnant dunite envelopes due to prolonged shearing within the deforming harzburgite host and are constrained in location to a ductile-brittle shear zone that correlates with the transforming direction of the Domokos oceanic fault. Compositional data indicate that chromitites equilibrated with ambient harzburgite via a melt-peridotite interaction process followed by melt mixing. Geochemical calculations demonstrate that the parental magmas of the Metalleion chromitites had intermediate affinity between typical mid-ocean ridge basalts (MORB), island arc tholeiites (IAT) and boninites. We conclude that these melts originated within a hydrated and oxidized mantle wedge beneath an infant forearc basin connected by a transform fault to an active MOR. © 201 Daha fazlası Daha az

Structural, thermal and magnetic characterization of nanocrystalline Co65Ti25W5B5 powders prepared by mechanical alloying

Avar B.

Article | 2016 | Journal of Non-Crystalline Solids432 , pp.246 - 253

In this work, nanocrystalline Co65Ti25W5B5 (at.%) powders were prepared by mechanical alloying (MA) of the elemental powder mixture under argon gas atmosphere. The powders were milled during different periods (2.5, 5, 10, 20 and 30 h) using a planetary ball-mill (Retsch PM100 CM) at 400 rpm. The structural, morphological, thermal and magnetic properties of the nanocrystalline Co65Ti25W5B5 powders were studied by means of X-ray diffraction (XRD), scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM/EDX), differential thermal analysis (DTA) and vibrating sample magnetometer (VSM) techniques. Because of its high . . .melting point, hardness and low solubility in the alloy components, a small amount of tungsten remained in the amorphous matrix during MA. By using the Williamson-Hall method, the crystallite size and lattice strain of the tungsten phase were calculated as about 25 nm and 0.48% respectively, for 30 h of milling. The DTA curves of the milled powders demonstrated an exothermic peak at about 600 °C, indicating the crystallization of the amorphous phase. The apparent mean activation energy, 303.5 ± 7 kJ/mol for 20 h milled powders was determined by Kissenger and Ozawa methods. The saturation magnetization (Ms), the coercivity (Hc) and the remanence-to-saturation ratio (Mr/Ms), values were of about 66 emu/g, 11 Oe and 0.012 respectively, after 30 h of milling. © 2015 Elsevier B.V Daha fazlası Daha az

Structural insights of RmXyn10A – A prebiotic-producing GH10 xylanase with a non-conserved aglycone binding region

Aronsson A. | Güler F. | Petoukhov M.V. | Crennell S.J. | Svergun D.I. | Linares-Pastén J.A. | Nordberg Karlsson E.

Article | 2018 | Biochimica et Biophysica Acta - Proteins and Proteomics1866 ( 2 ) , pp.292 - 306

Hydrolysis of arabinoxylan (AX) by glycoside hydrolase family 10 (GH10) xylanases produces xylo- and arabinoxylo-oligosaccharides ((A)XOS) which have shown prebiotic effects. The thermostable GH10 xylanase RmXyn10A has shown great potential to produce (A)XOS. In this study, the structure of RmXyn10A was investigated, the catalytic module by homology modelling and site-directed mutagenesis and the arrangement of its five domains by small-angle X-ray scattering (SAXS). Substrate specificity was explored in silico by manual docking and molecular dynamic simulations. It has been shown in the literature that the glycone subsites of GH10 . . .xylanases are well conserved and our results suggest that RmXyn10A is no exception. The aglycone subsites are less investigated, and the modelled structure of RmXyn10A suggests that loop ß6?6 in the aglycone part of the active site contains a non-conserved ?-helix, which blocks the otherwise conserved space of subsite +2. This structural feature has only been observed for one other GH10 xylanase. In RmXyn10A, docking revealed two alternative binding regions, one on either side of the ?-helix. However, only one was able to accommodate arabinose-substitutions and the mutation study suggests that the same region is responsible for binding XOS. Several non-conserved structural features are most likely to be responsible for providing affinity for arabinose-substitutions in subsites +1 and +2. The SAXS rigid model of the modular arrangement of RmXyn10A displays the catalytic module close to the cell-anchoring domain while the carbohydrate binding modules are further away, likely explaining the observed lack of contribution of the CBMs to activity. © 2017 The Author Daha fazlası Daha az

Structural and mechanical properties of hypereutectic AlSiFe powders and a new method for determination of sintering temperature

Ergen S. | Yılmaz F. | Gul S. | Kolemen U. | Kilicaslan M.F. | Uzun O.

Article | 2018 | Advanced Powder Technology29 ( 3 ) , pp.563 - 572

In this study, the effect of Si amount on the microstructure, crystal structure and some mechanical properties of Al-(20,25,30 wt%)Si–5Fe powder mixtures produced by high energy ball milling method was investigated by determining the sintering temperature. In the X-ray diffraction analysis, no inter-metallic phases were found except for the Al, Si and Fe phases of the powder mixtures. The X-ray diffraction patterns were analyzed by the Rietveld method to determine amounts of the Al, Si and Fe elements in the powder mixtures. From the scanning electron microscopy analysis, it is seen that as the amount of Si increases, there is a mar . . .ked decrease in the grain size of powders. In the micro-indentation tests performed at room temperature, the hardness and elastic modulus values of the pelletized powders were found to increase with the amount of Si. It was also found that the Al-20Si-5Fe powder mixture with the lowest Si content had the highest damping capability. The high temperature micro-indentation tests showed that the resulting Al-(20,25,30 wt%) Si-5 Fe powder mixtures started to consolidation at 200 °C and completed the consolidation at 400 °C. This method can be used as an alternative method in the determination of the sintering temperature of materials. © 201 Daha fazlası Daha az

Investigation of power quality disturbances by using 2D discrete orthonormal S-transform, machine learning and multi-objective evolutionary algorithms

Karasu S. | Saraç Z.

Article | 2019 | Swarm and Evolutionary Computation44 , pp.1060 - 1072

The aim of this paper is to investigate the power quality analysis by using 2D discrete orthonormal S-transform, machine learning and multi-objective evolutionary algorithms. The fact that PQ signals are one-dimensional (1D) signals due to their nature leads to the search for feature extraction approaches based on 1D signal processing methods. Due to the electric network is getting more and more complicated day by day, it is necessary to determine effectively the disturbances events. In the proposed method, extraction of a new feature based on two-dimensional (2D) signal processing by 2D Fast Discrete Orthonormal Stockwell Transform . . . (2D-FDOST) method and determination of the most suitable feature group by Non-dominated Sorting Genetic Algorithm II (NSGA-II) method are performed. Eleven different PQ events are synthetically produced based on mathematical modelling. 1D signals are transformed into 2D signals with equal row and column numbers. Statistical and image-based features are created on the amplitude and phase matrices obtained by 2D-FDOST method from 2D signals. The NSGA-II method, which is one of the multi-objective evolutionary optimization methods, is used to convert a large number of feature vectors into a small number of useful feature groups. NSGA-II produces the optimal solution for two different fitness functions that calculate the number of features and classifier performance. By using different machine learning classifiers for selected features, a model classifying PQ disturbances with high performance and robust structure against noisy situations is created. © 2018 Elsevier B.V Daha fazlası Daha az

Protic ionic liquids as effective agents for pretreatment of cotton stalks at high biomass loading

Semerci I. | Güler F.

Article | 2018 | Industrial Crops and Products125 , pp.588 - 595

This work demonstrated the performances of different protic ionic liquids (PILs) with respect to their effects on the pretreatment of cotton stalks at a relatively high biomass loading. Among the investigated PILs, 1-butylimidazolium hydrogen sulfate (HBIMHSO4) employed in the presence of 20% (w/w) water at 15% biomass loading and 120 °C for four hours resulted in significant structural changes in the biomass. The lignin content of the cotton stalks was reduced by 35% and the cellulose content increased from 36% to 55% through HBIMHSO4 pretreatment. Enzymatic hydrolysis of the biomass was enhanced almost 5-fold despite an increase i . . .n the biomass crystallinity. Morphological changes in the cotton stalks observed through SEM analysis verified the differences in the composition and enzymatic accessibility of the biomass samples subjected to PIL pretreatment. The results successfully revealed the potential of the PIL, HBIMHSO4 for the valorization of cotton stalks, as a significant industrial crop waste, for the first time in the literature. © 2018 Elsevier B.V Daha fazlası Daha az

Efficiency of glucose oxidase immobilized on tannin modified NiFe2O4 nanoparticles on decolorization of dye in the Fenton and photo-biocatalytic processes

Atacan K. | Güy N. | Çakar S. | Özacar M.

Article | 2019 | Journal of Photochemistry and Photobiology A: Chemistry382 , pp.588 - 595

Immobilized enzymes are significantly studied both environmental and textile industries. In this work, glucose oxidase was immobilized on the tannin coated NiFe2O4 magnetic nanoparticles for decolorization of indigo carmin. The as-synthesized all magnetic nanoparticles were characterized by X-ray diffraction, Fourier transform infrared spectroscopy, UV–vis spectroscopy, Thermogravimetric analysis, Vibrating sample magnetometer and Scanning electron microscopy. The activity of the free and immobilized glucose oxidase in various temperature and pH values was investigated. Finally, the produced immobilized glucose oxidase was applied f . . .or decolorization of indigo carmine due to production of H2O2. The decolorization yields of indigo carmine are 98.6% and 37.6% of the glucose oxidase immobilized on tannin modified NiFe2O4 in presence of the both of UV-light and iron(II)chloride for 90 min, respectively. The results exude that the obtained photocatalysts exhibit excellent both photocatalytic efficiency and easy separation from dye solution by an external magnet. © 2019 Elsevier B.V Daha fazlası Daha az

Adsorption of methylene blue from aqueous solutions by activated carbon prepared from hazelnut husk using zinc chloride

Karaçetin G. | Sivrikaya S. | Imamo?lu M.

Article | 2014 | Journal of Analytical and Applied Pyrolysis110 ( 1 ) , pp.270 - 276

In this study, activated carbon prepared from hazelnut husk (HHAC) using zinc chloride as chemical activating agent was characterized by FT-IR spectroscopy, BET surface area, Boehm titration, SEM and elemental analyses. During adsorption from aqueous solution of methylene blue (MB) studied by the batch method, effects of many variables, including solution pH, agitation time, temperature and initial concentration were investigated. It was established that MB adsorption reached equilibrium at 120 min at pH 7.0 as the appropriate value and is more compatible with Langmuir adsorption isotherm with respect to Freundlich. MB adsorption ca . . .pacity of HHAC was found to be 476.2 mg g-1 and MB adsorption kinetics corresponds well with pseudo second order model. Thermodynamic studies revealed that MB adsorption is a spontaneous and endothermic process. © 2014 Elsevier B.V. All rights reserved Daha fazlası Daha az

Assessment of DNA damage in welders using comet and micronucleus assays

Aksu İ. | Anlar H.G. | Taner G. | Bacanlı M. | İritaş S. | Tutkun E. | Basaran N.

Article | 2019 | Mutation Research - Genetic Toxicology and Environmental Mutagenesis843 , pp.40 - 45

Welding technology is widely used in pressurized containers, thermal power plants, refineries, chemical facilities and steel structures. Welders are exposed to a number of hazardous compounds such as ultraviolet (UV) radiation, electromagnetic fields, toxic metals and polycyclic aromatic hydrocarbons (PAHs). In the present study, 48 welders and an equal number of control subjects were evaluated for DNA damage in the whole blood and isolated lymphocytes using the comet assay. The genotoxic damage in buccal epithelial cells of subjects was determined by micronucleus (MN) assay. Metal(loids) such as Cr, Mn, Ni, Cu, As, Cd and Pb levels . . . in blood samples were evaluated by using Inductively Coupled Plasma–Mass Spectrometer (ICP-MS). Results of this study showed that DNA damage in blood, isolated lymphocytes, and buccal epithelial cells were significantly higher in workers compared to the controls. Also, these workers had remarkably higher blood Cr, Cu, Cd, Ni and Pb levels. These results showed that occupational exposure to welding fumes may cause genotoxic damage that can lead to important health problems in the workers. More extensive epidemiological studies should be performed that enable the assessment of health risk in welding industry. © 2018 Elsevier B.V Daha fazlası Daha az

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