Computational framework to integrate the effect of antigen recognition on disease epidemiology outcome: multi-scale approach

Human Leukocyte Antigen (HLA) plays an important role, in presenting foreign pathogens to our immune system, there by eliciting early immune responses. HLA genes are highly polymorphic, giving rise to diverse antigen presentation capability. An important factor contributing to enormous variations in individual responses to diseases is differences in their HLA profiles. The heterogeneity in allele specific disease responses decides the overall disease epidemiological outcome. Here we propose an agent based computational framework, capable of incorporating allele specific information, to analyze disease epidemiology. This framework assumes a SIR model to estimate average disease transmission and recovery rate. Using epitope prediction tool, it performs sequence based epitope detection for a given the pathogenic genome and derives an allele specific disease susceptibility index depending on the epitope detection efficiency. The allele specific disease transmission rate, that follows, is then fed to the agent based epidemiology model, to analyze the disease outcome. The methodology presented here has a potential use in understanding how a disease spreads and effective measures to control the disease.

Effect of High-Pressure Torsion on Texture, Microstructure, and Raman Spectroscopy: Case Study of Fe- and Te-Substituted CoSb3

Fe0.05Co0.95Sb2.875Te0.125, a double-element-substituted skutterudite, was prepared by induction melting, annealing, and hot pressing (HP). The hot-pressed sample was subjected to high-pressure torsion (HPT) with 4 GPa pressure at 673 K. X-ray diffraction was performed before and after HPT processing of the sample; the skutterudite phase was observed as a main phase, but an additional impurity phase (CoSb2) was observed in the HPT-processed sample. Surface morphology was determined by high-resolution scanning electron microscopy. In the HP sample, coarse grains with sizes in the range of approximately 100 nm to 300 nm were obtained. They changed to fine grains with a reduction in grain size to 75 nm to 125 nm after HPT due to severe plastic deformation. Crystallographic texture, as measured by x-ray diffraction, indicated strengthening of (112), (102) poles and weakening of the (123) pole of the HPT-processed sample. Raman-active vibrational modes showed a peak position shift towards the lower energy side, indicating softening of the modes after HPT. The distortion of the rectangular Sb-Sb rings leads to broadening of Sb-Sb vibrational modes due to local strain fluctuation. In the HPT process, a significant effect on the shorter Sb-Sb bond was observed as compared with the longer Sb-Sb bond.

The importance of crystallographic texture in the use of titanium as an orthopedic biomaterial

Crystallographic texture is perceived to play an important role in controlling material properties. However, the influence of texture in modulating the properties of biomedical materials has not been well investigated. In this work, commercially pure titanium (cp-Ti) was processed through six different routes to generate a variety of textures. The effect of texture on mechanical properties, corrosion behavior, cell proliferation and osteogenesis was characterized for potential use in orthopedic applications. The presence of closely packed, low-energy crystallographic planes at the material surface was influenced by the volume fraction of the components in the overall texture, thereby influencing surface energy and corrosion behavior. Texture modulated osteoblast proliferation through variations in surface water wettability. It also affected mineralization by possibly influencing the coherency between the substrate and calcium phosphate deposits. This study demonstrates that crystallographic texture can be an important tool in improving the properties of biomaterials to achieve the enhanced performance of biomedical implants.

New insights into the development of microstructure and deformation texture in nickel-60 wt.% cobalt alloy

The present study investigates the critical role of deformation twinning and Bs-type shear bands in the evolution of deformation texture in a low stacking fault energy Ni-60Co alloy up to very large rolling strain (epsilon(t) approximate to 4). The alloy develops a strong brass-type rolling texture, and its formation is initiated at the early stages of deformation. Extensive twinning is observed at the intermediate stages of deformation, which causes significant texture reorientation towards alpha-fiber. A pseudo-in-situ electron back-scattered diffraction technique adopted to capture orientation changes within individual grains during the early stages suggests that twinning should be subsequently aided by crystallographic slip to attain alpha-fiber (< 1 1 0 >parallel to ND) orientations. Beyond 40% reduction, deformation is dominated by Bs-type shear bands, and the banding coincides with the evolution of < 1 1 1 >parallel to ND components. The volume fraction of shear bands is significant at higher strains, and crystallites within the bands preferentially show < 1 1 0 >parallel to ND components. The absence of the Cu {1 1 2}< 1 1 1 > component in the initial texture, and subsequently during rolling, indicates that, for the evolution of a brass-type texture, the presence of the Cu component is not a necessary condition. The final rolling texture is a synergistic effect of deformation twinning and shear banding. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Combinatorial effect of rolling and carbonaceous nanoparticles on the evolution of crystallographic texture and structural properties of ultra high molecular weight polyethylene

Ultra high molecular weight polyethylene (PE) is a structural polymer widely used in biomedical implants. The mechanical properties of PE can be improved either by controlled crystalline orientation (texture) or by the addition of reinforcing agents. However, the combinatorial effect has not received much attention. The objective of this study was to characterize the structure and mechanical properties of PE composites incorporating multiwall carbon nanotubes (MWCNT) and reduced graphene oxide (RGO) subjected to hot rolling. The wide angle X-ray diffraction studies revealed that mechanical deformation resulted in a mixture of orthorhombic and monoclinic crystals. Furthermore, the presence of nanoparticles resulted in lower crystallinity in PE with smaller crystallite size, more so in RGO than in MWCNT composites. Rolling strengthened the texture of both orthorhombic and the monoclinic phases in PE. Presence of RGO weakened the texture of both phases of PE after rolling whereas MWCNT only mildly weakened the texture. This resulted in a reduction in the elastic modulus of RGO composites whereas moduli of neat polymer and the MWCNT composite increased after rolling. This study provides new insight into the role of nanoparticles in texture evolution during polymer processing with implications for processing of structural polymer composites.

The interaction of N-trifluoroacetylgalactosamine and its derivatives with winged bean (Psophocarpus tetragonolobus) basic agglutinin reveals differential mechanism of their recognition: a fluorine-19 nuclear magnetic resonance study

Here, we show the binding results of a leguminosae lectin, winged bean basic agglutinin (WBA I) to N-trifluoroacetylgalactosamine (NTFAGalN), methyl-alpha-N-trifluoroacetylgalactosamine (Me alpha NTFAGalN) and methyl-beta-tifluoroacetylgalactosamine (Me beta NTFAGalN) using (19) F NMR spectroscopy. No chemical shift difference between the free and bound states for NTFAGalN and Me beta NTFAGalN, and 0.01-ppm chemical shift change for Me alpha NTFAGalN, demonstrate that the Me alpha NTFAGalN has a sufficiently long residence time on the protein binding site as compared to Me beta NTFAGalN and the free anomers of NTFAGalN. The sugar anomers were found in slow exchange with the binding site of agglutinin. Consequently, we obtained their binding parameters to the protein using line shape analyses. Aforementioned analyses of the activation parameters for the interactions of these saccharides indicate that the binding of alpha and beta anomers of NTFAGalN and Me alpha NTFAGalN is controlled enthalpically, while that of Me beta NTFAGalN is controlled entropically. This asserts the sterically constrained nature of the interaction of the Me beta NTFAGalN with WBA I. These studies thus highlight a significant role of the conformation of the monosaccharide ligands for their recognition by WBA I.

The control of crystallographic texture in the use of magnesium as a resorbable biomaterial

Magnesium and its alloys are an emerging class of resorbable materials for orthopedic and cardiovascular applications. The typical strategy underlying the development of these materials involves the control of material processing routes and the addition of alloying elements. Crystallographic texture is known to control bulk mechanical as well as surface properties. However, its role in determining the properties of magnesium for implant materials has not been well studied. In this work, an extruded rod of pure magnesium was cut in multiple directions to generate samples with different textures. It was found that texture significantly affected the strength and ductility of magnesium. Corrosion rates in Hank's solution decreased with the increased presence of low energy basal planes at the surface. In vitro cell studies revealed that changes in texture did not induce cytotoxicity. Thus, the control of texture in magnesium based implants could be used to tailor the mechanical properties and the resorption rates without compromising cytocompatibility. This study elucidates the importance of texture in the use of magnesium as a resorbable biomaterial.

Influence of crystallographic texture and microstructure on elastic modulus of steels

In this paper the effects of crystallographic texture and microstructure on the elastic modulus of different grades of steel have been collected from the available literature and put in one place. It is expected that this will help researchers in their understanding of both the fundamental and the practical aspects of the different grades of steel used for various purposes.

Texture discriminability in monkey inferotemporal cortex predicts human texture perception

Shape and texture are both important properties of visual objects, but texture is relatively less understood. Here, we characterized neuronal responses to discrete textures in monkey inferotemporal (IT) cortex and asked whether they can explain classic findings in human texture perception. We focused on three classic findings on texture discrimination: 1) it can be easy or hard depending on the constituent elements; 2) it can have asymmetries, and 3) it is reduced for textures with randomly oriented elements. We recorded neuronal activity from monkey inferotemporal (IT) cortex and measured texture perception in humans for a variety of textures. Our main findings are as follows: 1) IT neurons show congruent selectivity for textures across array size; 2) textures that were easy for humans to discriminate also elicited distinct patterns of neuronal activity in monkey IT; 3) texture pairs with asymmetries in humans also exhibited asymmetric variation in firing rate across monkey IT; and 4) neuronal responses to randomly oriented textures were explained by an average of responses to homogeneous textures, which rendered them less discriminable. The reduction in discriminability of monkey IT neurons predicted the reduced discriminability in humans during texture discrimination. Taken together, our results suggest that texture perception in humans is likely based on neuronal representations similar to those in monkey IT.

Influence of Surface Texture and Roughness of Softer and Harder Counter Materials on Friction During Sliding

Surface texture influences friction during sliding contact conditions. In the present investigation, the effect of surface texture and roughness of softer and harder counter materials on friction during sliding was analyzed using an inclined scratch testing system. In the experiments, two test configurations, namely (a) steel balls against aluminum alloy flats of different surface textures and (b) aluminum alloy pins against steel flats of different surface textures, are utilized. The surface textures were classified into unidirectionally ground, 8-ground, and randomly polished. For a given texture, the roughness of the flat surfaces was varied using grinding or polishing methods. Optical profilometer and scanning electron microscope were used to characterize the contact surfaces before and after the experiments. Experimental results showed that the surface textures of both harder and softer materials are important in controlling the frictional behavior. The softer material surface textures showed larger variations in friction between ground and polished surfaces. However, the harder material surface textures demonstrated a better control over friction among the ground surfaces. Although the effect of roughness on friction was less significant when compared to textures, the harder material roughness showed better correlations when compared to the softer material roughness.

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.

Effect of extrusion ratio on the microstructure, texture and mechanical properties of (Mg/AZ91)(m)-SiCp composite

Cast Mg/SiCp and AZ91/SiCp composites were successfully hot extruded vis-a-vis cast and unreinforced Mg and AZ91 alloy up to low (R=15:1) and high (R=54:1) extrusion ratios at 350 degrees C. Significant matrix grain refinement was noticed after extrusion due to dynamic recrystallization; the degree of refinement being relatively higher for the two composites. The AZ91 based materials (AZ91 and AZ91/SiCp) exhibited comparatively finer grain size both in cast condition and after extrusion due to strong pinning effect from alloying elements as well as Mg17Al12 intermetallic phase. Compositional analyses eliminated the possibility of any interfacial reaction between matrix (Mg/AZ91) and second phase reinforcement (SiCp) in case of the composites. Texture evolution shows the formation of < 10 (1) over bar0 >parallel to ED texture fibre for all the materials after extrusion irrespective of SiCp addition or alloying which is primarily due to the deformation of the matrix phase. Micro-hardness did not significantly increased on extrusion in comparison to the respective cast materials for both composites and unreinforced alloys. Dynamic mechanical analysis, however, confirmed that the damping properties were affected by the extrusion ratio and to a lesser extent, due to the presence of second phase at room temperature as well as at higher temperature (300 degrees C). (C) 2014 Elsevier B.V. All rights reserved.

Manipulating Crystallographic Texture of Sn Coatings by Optimization of Electrodeposition Process Conditions to Suppress Growth of Whiskers

The effects of two major electrodeposition process conditions, electrolyte bath temperature and current density, on the microstructure and crystallographic texture of pure tin coatings on brass and, ultimately, on the extent of whisker formation have been examined. The grain size of the deposited coatings increased with increasing electrolyte bath temperature and current density, which significantly affected the dominant texture: (211) or (420) was the dominant texture at low current densities whereas, depending on deposition temperature, (200) or (220) became the dominant texture at high current densities. After deposition, coatings were subjected to different environmental conditions, for example isothermal aging (room temperature, 50A degrees C, or 150A degrees C) for up to 90 days and thermal cycling between -25A degrees C and 85A degrees C for 100 cycles, and whisker growth was studied. The Sn coatings with low Miller index planes, for example (200) and (220), and with moderate aging temperature were more prone to whiskering than coating with high Miller index planes, for example (420), and high aging temperature. A processing route involving the optimum combination of current density and deposition temperature is proposed for suppressing whisker growth.