Adaptive evolution of a novel avian-origin influenza A/H7N9 virus

In China, the recent outbreak of novel influenza A/H7N9 virus has been assumed to be severe, and it may possibly turn brutal in the near future. In order to develop highly protective vaccines and drugs for the A/H7N9 virus, it is critical to find out the selection pressure of each amino acid site. In the present study, six different statistical methods consisting of four independent codon-based maximum likelihood (CML) methods, one hierarchical Bayesian (HB) method and one branch-site (BS) method, were employed to determine if each amino acid site of A/H7N9 virus is under natural selection pressure. Functions for both positively and negatively selected sites were inferred by annotating these sites with experimentally verified amino acid sites. Comprehensively, the single amino acid site 627 of PB2 protein was inferred as positively selected and it function was identified as a T-cell epitope (TCE). Among the 26 negatively selected amino acid sites of PB2, PB1, PA, HA, NP, NA, M1 and NS2 proteins, only 16 amino acid sites were identified to be involved in TCEs. In addition, 7 amino acid sites including, 608 and 609 of PA, 480 of NP, and 24, 25, 109 and 205 of M1, were identified to be involved in both B-cell epitopes (BCEs) and TCEs. Conversely, the function of positions 62 of PA, and, 43 and 113 of HA was unknown. In conclusion, the seven amino acid sites engaged in both BCEs and TCEs were identified as highly suitable targets, as these sites will be predicted to play a principal role in inducing strong humoral and cellular immune responses against A/H7N9 virus. (C) 2014 Elsevier Inc. All rights reserved.

Finite Element Analysis of Stress Evolution in Al-Si Alloy

A 2D multi-particle model is carried out to understand the effect of microstructural variations and loading conditions on the stress evolution in Al-Si alloy under compression. A total of six parameters are varied to create 26 idealized microstructures: particle size, shape, orientation, matrix temper, strain rate, and temperature. The effect of these parameters is investigated to understand the fracture of Si particles and the yielding of Al matrix. The Si particles are modeled as a linear elastic solid and the Al matrix is modeled as an elasto-plastic solid. The results of the study demonstrate that the increase in particle size decreases the yield strength of the alloy. The particles with high aspect ratio and oriented at 0A degrees and 90A degrees to the loading axis show higher stress values. This implies that the particle shape and orientation are dominant factors in controlling particle fracture. The heat treatment of the alloy is found to increase the stress levels of both particles and matrix. Stress calculations also show that higher particle fracture and matrix yielding is expected at higher strain rate deformation. Particle fracture decreases with increase in temperature and the Al matrix plays an important role in controlling the properties of the alloy at higher temperatures. Further, this strain rate and temperature dependence is more pronounced in the heat-treated microstructure. These predictions are consistent with the experimentally observed Si particle fracture in real microstructure.

Evolution of deformation texture and magnetic properties in a nanocrystalline nickel-20 wt% cobalt alloy

The evolution of crystallographic texture in a nanocrystalline nickel-20 wt% cobalt alloy has been investigated for deformation up to large strains. The effect of texture on magnetic properties has been evaluated. The material shows characteristic copper-type texture at large strain levels. Microstructural examinations indicate that the evolution of texture is assisted by deformation-induced grain growth. The values of saturation magnetization and coercivity have been correlated with the crystallographic texture and grain size. (C) 2014 Elsevier B.V. All rights reserved.

Texture Evolution in Nanocrystalline Nickel: Critical Role of Strain Path

The effect of strain path change during rolling on the evolution of deformation texture has been studied for nanocrystalline (nc) nickel. An orthogonal change in strain path, as imparted by alternating rolling and transverse directions, leads to a texture with a strong Bs {110}aOE (c) 112 > component. The microstructural features, after large deformation, show distinct grain morphology for the cross-rolled material. Crystal plasticity simulations, based on viscoplastic self-consistent model, indicate that slip involving partial dislocation plays a vital role in accommodating plastic deformation during the initial stages of rolling. The brass-type texture evolved after cross rolling to large strains is attributed to change in strain path.

Transverse single spin asymmetry in e plus p up arrow -> e plus J/psi plus X and Q(2) evolution of Sivers function-II

We present estimates of single spin asymmetry in the electroproduction of J/psi taking into account the transverse momentum-dependent (TMD) evolution of the gluon Sivers function. We estimate single spin asymmetry for JLab, HERMES, COMPASS and eRHIC energies using the color evaporation model of J/psi. We have calculated the asymmetry using recent parameters extracted by Echevarria et al. using the Collins-Soper-Sterman approach to TMD evolution. These recent TMD evolution fits are based on the evolution kernel in which the perturbative part is resummed up to next-to-leading logarithmic accuracy. We have also estimated the asymmetry by using parameters which had been obtained by a fit by Anselmino et al., using both an exact numerical and an approximate analytical solution of the TMD evolution equations. We find that the variation among the different estimates obtained using TMD evolution is much smaller than between these on one hand and the estimates obtained using DGLAP evolution on the other. Even though the use of TMD evolution causes an overall reduction in asymmetries compared to the ones obtained without it, they remain sizable. Overall, upon use of TMD evolution, predictions for asymmetries stabilize.

Evolution of Aromatic beta-Glucoside Utilization by Successive Mutational Steps in Escherichia coli

The bglA gene of Escherichia coli encodes phospho-beta-glucosidase A capable of hydrolyzing the plant-derived aromatic beta-glucoside arbutin. We report that the sequential accumulation of mutations in bglA can confer the ability to hydrolyze the related aromatic beta-glucosides esculin and salicin in two steps. In the first step, esculin hydrolysis is achieved through the acquisition of a four-nucleotide insertion within the promoter of the bglA gene, resulting in enhanced steady-state levels of the bglA transcript. In the second step, hydrolysis of salicin is achieved through the acquisition of a point mutation within the bglA structural gene close to the active site without the loss of the original catabolic activity against arbutin. These studies underscore the ability of microorganisms to evolve additional metabolic capabilities by mutational modification of preexisting genetic systems under selection pressure, thereby expanding their repertoire of utilizable substrates.

Morphological Evolution in Air-Stable Metallic Iron Nanostructures and Their Magnetic Study

Iron nanostructures with morphology ranging from discrete nanoparticles to nearly monodisperse hierarchical nanostructures have been successfully synthesized using solvated metal atom dispersion (SMAD) method. Such a morphological evolution was realized by tuning the molar ratio of ligand to metal. Surface energy minimization in confluence with strong magnetic interactions and ligand-based stabilization results in the formation of nanospheres of iron. The as-prepared amorphous iron nanostructures exhibit remarkably high coercivity in comparison to the discrete nanoparticles and bulk counterpart. Annealing the as-prepared amorphous Fe nanostructures under anaerobic conditions affords air-stable carbon-encapsulated Fe(0) and Fe3C nanostructures with retention of the morphology. The resulting nanostructures were thoroughly analyzed by powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA), transmission electron microscopy (TEM), and Raman spectroscopy. TGA brought out that Fe3C nanostructures are more robust toward oxidation than those of a-Fe. Finally, detailed magnetic studies were carried out by superconducting quantum interference device (SQUID) magnetometer and it was found that the magnetic properties remain conserved even upon exposure of the annealed samples to ambient conditions for months.

Study of Microstructure Evolution during Semi-Solid Processing of an In-Situ Al Alloy Composite

In the present work, effect of pouring temperature (650 degrees C, 655 degrees C, and 660 degrees C) on semi-solid microstructure evolution of in-situ magnesium silicide (Mg2Si) reinforced aluminum (Al) alloy composite has been studied. The shear force exerted by the cooling slope during gravity driven flow of the melt facilitates the formation of near spherical primary Mg2Si and primary Al grains. Shear driven melt flow along the cooling slope and grain fragmentation have been identified as the responsible mechanisms for refinement of primary Mg2Si and Al grains with improved sphericity. Results show that, while flowing down the cooling slope, morphology of primary Mg2Si and primary Al transformed gradually from coarse dendritic to mixture of near spherical particles, rosettes, and degenerated dendrites. In terms of minimum grain size and maximum sphericity, 650 degrees C has been identified as the ideal pouring temperature for the cooling slope semi-solid processing of present Al alloy composite. Formation of spheroidal grains with homogeneous distribution of reinforcing phase (Mg2Si) improves the isotropic property of the said composite, which is desirable in most of the engineering applications.

The cold mode: a phenomenological model for the evolution of density perturbations in the intracluster medium

Cool cluster cores are in global thermal equilibrium but are locally thermally unstable. We study a non-linear phenomenological model for the evolution of density perturbations in the intracluster medium (ICM) due to local thermal instability and gravity. We have analysed and extended a model for the evolution of an overdense blob in the ICM. We find two regimes in which the overdense blobs can cool to thermally stable low temperatures. One for large t(cool)/t(ff) (t(cool) is the cooling time and t(ff) is the free-fall time), where a large initial overdensity is required for thermal runaway to occur; this is the regime which was previously analysed in detail. We discover a second regime for t(cool)/t(ff) less than or similar to 1 (in agreement with Cartesian simulations of local thermal instability in an external gravitational field), where runaway cooling happens for arbitrarily small amplitudes. Numerical simulations have shown that cold gas condenses out more easily in a spherical geometry. We extend the analysis to include geometrical compression in weakly stratified atmospheres such as the ICM. With a single parameter, analogous to the mixing length, we are able to reproduce the results from numerical simulations; namely, small density perturbations lead to the condensation of extended cold filaments only if t(cool)/t(ff) less than or similar to 10.

The Evolution of Animal Welfare and the 3Rs in Brazil, China, and India

Increasingly, scientific collaborations and contracts cross country borders. The need for assurance that the quality of animal welfare and the caliber of animal research conducted are equivalent among research partners around the globe is of concern to the scientific and laboratory animal medicine communities, the general public, and other key stakeholders. Therefore, global harmonization of animal care and use standards and practices, with the welfare of the animals as a cornerstone, is essential. In the evolving global landscape of enhanced attention to animal welfare, a widely accepted path to achieving this goal is the successful integration of the 3Rs in animal care and use programs. Currently, awareness of the 3Rs, their implementation, and the resulting animal care and use standards and practices vary across countries. This variability has direct effects on the animals used in research and potentially the data generated and may also have secondary effects on the country's ability to be viewed as a global research partner. Here we review the status of implementation of the 3Rs worldwide and focus on 3 countries-Brazil, China and India-with increasing economic influence and an increasing footprint in the biomedical research enterprise.

Microstructure and Crystallographic Texture Evolution During the Friction-Stir Processing of a Precipitation-Hardenable Aluminum Alloy

Friction-stir processing (FSP) has been proven as a successful method for the grain refinement of high-strength aluminum alloys. The most important attributes of this process are the fine-grain microstructure and characteristic texture, which impart suitable properties in the as-processed material. In the current work, FSP of the precipitation-hardenable aluminum alloy 2219 has been carried out and the consequent evolution of microstructure and texture has been studied. The as-processed materials were characterized using electron back-scattered diffraction, x-ray diffraction, and electron probe microanalysis. Onion-ring formation was observed in the nugget zone, which has been found to be related to the precipitation response and crystallographic texture of the alloy. Texture development in the alloy has been attributed to the combined effect of shear deformation and dynamic recrystallization. The texture was found heterogeneous even within the nugget zone. A microtexture analysis revealed the dominance of shear texture components, with C component at the top of nugget zone and the B and A(2)* components in the middle and bottom. The bulk texture measurement in the nugget zone revealed a dominant C component. The development of a weaker texture along with the presence of some large particles in the nugget zone indicates particle-stimulated nucleation as the dominant nucleation mechanism during FSP. Grain growth follows the Burke and Turnbull mechanism and geometrical coalescence.

Analysis of Microstructure and Texture Evolution in Mg-3Al-1Zn Alloy Processed Through Groove Rolling

The mechanism of grain refinement in a AZ31 Mg alloy subjected to hot groove rolling is investigated up to large strain (epsilon(t) similar to 2.5). The alloy shows enhanced yield strength without compromising ductility. The change in strain path during rolling has resulted in significant weakening of basal texture. The microstructure analyses show that dynamic recrystallization (DRX) contributed significantly to grain refinement and hence to the observed mechanical properties. The combined effects of DRX and texture evolution on mechanical properties have been addressed.

Texture evolution during hot deformation of Moly-TZM

Moly-TZM was deformed at constant strain rate of 1.0 s(-1) to investigate the high strain rate deformation behaviour by microstructural and stress response change within a temperature range of 1400-1700 degrees C. To correlate the deformation behaviour with orientational change, recrystallization and recovery of the material, the microstructural investigation was undertaken using scanning electron microscopy (SEM) of electron back scattered diffraction (EBSD). Depending on the grain size and orientation spread recrystallized grains were identified and texture was calculated. Change in grain boundary characteristics with increasing temperature was determined by the misorientation angle distribution for the deformed and recrystallized grains. Subgrain coalescence and increase in subgrain size with increasing temperature was observed, indicating recrystallization not only occurred from the nucleation of the dislocation free grains in grain boundaries but also from the subgrain rotation and merging of the subgrains by annihilation of the low angle grain boundaries. Detailed studies on the evolution of texture of recrystallized grains showed continuous increase in <001> fiber texture in recrystallised grains, in contrast to a mixed fiber <001> +<111> for the deformed grains.

Role of stacking fault energy on texture evolution revisited

Three materials, pure aluminium, Al-4 wt.% Mg, alpha-brass have been chosen to understand the evolution of texture and microstructure during rolling. Pure Al develops a strong copper-type rolling texture and the deformation is entirely slip dominated. In Al-4Mg alloy, texture is copper-type throughout the deformation. The advent of Cu-type shear bands in the later stages of deformation has a negligible effect on the final texture. alpha-brass shows a characteristic brass-type texture from the early stages of rolling. Extensive twinning in the intermediate stages of deformation (epsilon(t) similar to 0.5) causes significant texture reorientation towards alpha-fiber. Beyond 40% reduction, deformation is dominated by Bs-type shear bands, and the banding coincides with the evolution of <111>parallel to ND components. The crystallites within the bands preferentially show <110>parallel to ND components. The absence of the Cu component throughout the deformation process indicates that, for the evolution of brass-type texture, the presence of Cu component is not a necessary condition. The final rolling texture is a synergistic effect of deformation twinning and shear banding.

Evolution of texture and its influence on the failure of components in some aluminium alloys

This paper describes the evolution of crystallographic texture in three of the most important high strength aluminium alloys, viz., AA2219, AA7075 and AFNOR7020 in the cold rolled and artificially aged condition. Bulk texture results were obtained by plotting pole figures from X-ray diffraction results followed by Orientation Distribution Function (ODF) analysis and micro-textures were measured using EBSD. The results indicate that the deformation texture components Cu, Bs and S, which were also present in the starting materials, strengthen with increase in amount of deformation. On the other hand, recrystallization texture components Goss and Cube weaken. The Bs component is stronger in the deformation texture. This is attributed to the shear banding. In-service applications indicate that the as-processed AFNOR7020 alloy fails more frequently compared to the other high strength Al alloys used in the aerospace industry. Detailed study of deformation texture revealed that strong Brass (Bs) component could be associated to shear banding, which in turn could explain the frequent failures in AFNOR7020 alloy. The alloying elements in this alloy that could possibly influence the stacking fault energy of the material could be accounted for the strong Bs component in the texture.