Amino acid interaction preferences in helical membrane proteins

Membrane proteins are involved in a number of important biological functions. Yet, they are poorly understood from the structure and folding point of view. The external environment being drastically different from that of globular proteins, the intra-protein interactions in membrane proteins are also expected to be different. Hence, statistical potentials representing the features of inter-residue interactions based exclusively on the structures of membrane proteins are much needed. Currently, a reasonable number of structures are available, making it possible to undertake such an analysis on membrane proteins. In this study we have examined the inter-residue interaction propensities of amino acids in the membrane spanning regions of the alpha-helical membrane (HM) proteins. Recently we have shown that valuable information can be obtained on globular proteins by the evaluation of the pair-wise interactions of amino acids by classifying them into different structural environments, based on factors such as the secondary structure or the number of contacts that a residue can make. Here we have explored the possible ways of classifying the intra-protein environment of HM proteins and have developed scoring functions based on different classification schemes. On evaluation of different schemes, we find that the scheme which classifies amino acids to different intra-contact environment is the most promising one. Based on this classification scheme, we also redefine the hydrophobicity scale of amino acids in HM proteins.     

Application of evolutionary optimization techniques for finding the optimal set of concentric circular antenna array

In this paper the maximum sidelobe level (SLL) reductions, optimal beam patterns and optimal beam widths of various designs of three-ring planar concentric circular antenna arrays (PCCAA) are examined using three different classes of evolutionary optimization techniques to finally determine the global optimal three-ring PCCAA design and then establish some sort of ranking among the techniques. Apart from physical construction of a PCCAA, one may broadly classify its design into two major categories: uniformly excited arrays and non-uniformly excited arrays. The present paper assumes non-uniform excitations and uniform spacing of excitation elements in each three-ring PCCAA design and a design goal of maximizing SLL reduction associated with optimal beam patterns and beam widths. The design problem is modeled as an optimization problem for each PCCAA design and solved using different evolutionary optimization techniques to determine an optimum set of normalized excitation weights for PCCAA elements, which, when incorporated, results in a radiation pattern with optimal (maximum) SLL reduction. Among the various PCCAA designs, one which yields the global minimum SLL with global minimum first null beamwidth is the global optimal design. In this work the three-ring PCCAA containing (N₁ = 4, N₂ = 6, N₃ = 8) elements proves to be such global optimal design. The optimization techniques employed are real coded GA (RGA), canonical PSO (CPSO), craziness based PSO (CRPSO), evolutionary programming (BEP), hybrid evolutionary programming (HEP). While ranking the techniques after 30 total runs for each design, HEP, CRPSO, RGA, CPSO, BGA hold the first five ranks in order of optimization capability. HEP yields global minimum SLL (?32.86 dB) and global minimum BWFN (77.0°) for the optimal design. BEP often changes the rank from second to fifth depending on the design set. Further, when compared to a uniformly excited PCCAA having equal number of elements and same radii a reduction of major lobe beamwidth is also observed in the optimal non-uniformly excited case.     

Divergence of Intracellular Trafficking of Sphingosine Kinase 1 and Sphingosine-1-Phosphate Receptor 3 in MCF-7 Breast Cancer Cells and MCF-7-Derived Stem Cell-Enriched Mammospheres

Breast cancer MCF-7 cell-line-derived mammospheres were shown to be enriched in cells with a CD44+/CD24– surface profile, consistent with breast cancer stem cells (BCSC). These BCSC were previously reported to express key sphingolipid signaling effectors, including pro-oncogenic sphingosine kinase 1 (SphK1) and sphingosine-1-phosphate receptor 3 (S1P3). In this study, we explored intracellular trafficking and localization of SphK1 and S1P3 in parental MCF-7 cells, and MCF-7 derived BCSC-enriched mammospheres treated with growth- or apoptosis-stimulating agents. Intracellular trafficking and localization were assessed using confocal microscopy and cell fractionation, while CD44+/CD24- marker status was confirmed by flow cytometry. Mammospheres expressed significantly higher levels of S1P3 compared to parental MCF-7 cells (p < 0.01). Growth-promoting agents (S1P and estrogen) induced SphK1 and S1P3 translocation from cytoplasm to nuclei, which may facilitate the involvement of SphK1 and S1P3 in gene regulation. In contrast, pro-apoptotic cytokine tumor necrosis factor α (TNFα)-treated MCF-7 cells demonstrated increased apoptosis and no nuclear localization of SphK1 and S1P3, suggesting that TNFα can inhibit nuclear translocation of SphK1 and S1P3. TNFα inhibited mammosphere formation and induced S1P3 internalization and degradation. No nuclear translocation of S1P3 was detected in TNFα-stimulated mammospheres. Notably, SphK1 and S1P3 expression and localization were highly heterogenous in mammospheres, suggesting the potential for a large variety of responses. The findings provide further insights into the understanding of sphingolipid signaling and intracellular trafficking in BCs. Our data indicates that the inhibition of SphK1 and S1P3 nuclear translocation represents a novel method to prevent BCSCs proliferation.     

Prediction of the hydraulic diffusivity from pore size distribution of concrete

A model is presented in this work through which variation of hydraulic diffusivity of concrete with relative water content can be obtained from pore size distribution as an input. The specific water capacity and hydraulic conductivity of concrete are expressed in terms of pore size characteristics, considering laminar flow due to capillary suction through tortuous elliptic tubes, oriented equally in three orthogonal directions. Hydraulic diffusivity being the ratio of hydraulic conductivity and specific water capacity is thus expressed in terms of pore size characteristics. The input pore size distributions have been determined experimentally for normal strength concrete mixes through mercury intrusion porosimetry. Using the model the variation of hydraulic diffusivity with relative water content is determined for three cases viz. 1) ideal continuous wetting, 2) ideal continuous drying and 3) random access of pores by water. These results are then compared with an experimentally obtained variation.     

Buckling of laminated sandwich plates subjected to partial edge compression

The buckling characteristics of sandwich plates having laminated stiff layers are studied for different types of partial edge loadings using a refined plate theory. With this plate theory, the through thickness variation of transverse shear stresses is represented by piecewise parabolic functions where the continuity of these stresses is satisfied at the layer interfaces by taking jumps in the transverse shear strains at the interfaces. The transverse shear stresses free condition at the plate top and bottom surfaces is also satisfied. It is quite interesting to note that this plate model having all these refined features requires unknown parameters only at the reference plane. To have a generality in the present analysis, finite element technique is adopted and it is carried out with newly developed triangular element, as existing finite elements cannot accommodate this plate model. So far, no solution exists in the literature for the problem of sandwich plate subjected to partial edge loading. The present analysis is first validated for the case of an isotropic plate subjected to partial edge compression and then it is extended to analyze sandwich plates. Few results are presented.     

A hybrid deep learning model by combining convolutional neural network and recurrent neural network to detect forest fire

Multimedia Tools and Applications - Forest fire poses a serious threat to wildlife, environment, and all mankind. This threat has prompted the development of various intelligent and computer vision...     

Characterization of Oxide Dispersed AlCoCrFe High Entropy Alloy Synthesized by Mechanical Alloying and Spark Plasma Sintering

The present study deals with phase evolution of oxide dispersed AlCoCrFe high entropy alloy during mechanical alloying and spark plasma sintering. Mechanical alloying of AlCoCrFe resulted in a single BCC phase. However, ordering of BCC phase with evolution of chromium carbide and sigma phase were observed after spark plasma sintering. High hardness of 1,050 ± 20 HV₁ and 1,070 ± 20 HV₁ was observed for AlCoCrFe high entropy alloy without and with oxide dispersion, respectively. Significant contribution from solid solution strengthening effect in high entropy alloys appears to have overwhelmed the effect of oxide dispersion on hardness.     

Slurry Erosion Mechanism of Hydroturbine Steel: Effect of Operating Parameters

Performance of hydropower plant is severely affected by the presence of sand particles in river water. Degree of degradation significantly depends on the level of operating parameters (velocity, impingement angle, concentration, particle size and shape), which is further related to erosion mechanism. In this investigation, the effect of some of these operating parameters on erosion mechanism of generally used hydroturbine steel, CA6NM (13Cr4Ni), is reported. Morphology and variation in the martensite and austenite phases of the eroded surfaces were investigated using SEM and XRD. It was observed that velocity and impingement angle affect the erosion mechanism of CA6NM steel. Erosion mechanism was also significantly affected by the radial distance from the impact zone. Primary mechanism responsible for the removal of material at normal impingement angle was the formation and removal of platelets. At acute impingement angle, ploughing was observed to be one of the prime mechanisms responsible for the loss of the material. Other than these two well-known erosion mechanisms, the presence of another two erosion mechanisms was also observed. Models have been proposed for these unfamiliar erosion mechanisms. Interaction amongst different operating parameters was studied using line and contour plots. It was observed that the interaction between velocity and concentration was most significant. Using the experimental results, a statistical model based on regression approach was developed. Validity of this statistical model was checked using the experimental results from the literature and present study.     

Wide null control of symmetric linear antenna array using novel particle swarm optimization

In this article, the method of nullifying the radiation pattern of a symmetric linear antenna array in a particular direction is propounded using an evolutionary swarm intelligence technique, Novel particle swarm optimization (NPSO). Particle swarm optimization with constriction factor approach (PSOCFA) is also adopted to compare the NPSO based results. Single or multiple wide nulls are achieved by optimum perturbations of elements current amplitude weights to have symmetric nulls about the main beam. Different numerical examples are presented to illustrate the capability of NPSO for pattern synthesis with a prescribed wide nulls locations and depths. Further, the peak Sidelobe Levels are also reduces when compared to a uniformly excited array having equal number of elements. © 2011 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2011.