An extended Shine-Dalgarno sequence in mRNA functionally bypasses a vital defect in initiator tRNA

Initiator tRNAs are special in their direct binding to the ribosomal P-site due to the hallmark occurrence of the three consecutive G-C base pairs (3GC pairs) in their anticodon stems. How the 3GC pairs function in this role, has remained unsolved. We show that mutations in either the mRNA or 16S rRNA leading to extended interaction between the Shine-Dalgarno (SD) and anti-SD sequences compensate for the vital need of the 3GC pairs in tRNA(fMet) for its function in Escherichia coli. In vivo, the 3GC mutant tRNA(fMet) occurred less abundantly in 70S ribosomes but normally on 30S subunits. However, the extended SD:anti-SD interaction increased its occurrence in 70S ribosomes. We propose that the 3GC pairs play a critical role in tRNA(fMet) retention in ribosome during the conformational changes that mark the transition of 30S preinitiation complex into elongation competent 70S complex. Furthermore, treating cells with kasugamycin, decreasing ribosome recycling factor (RRF) activity or increasing initiation factor 2 (IF2) levels enhanced initiation with the 3GC mutant tRNA(fMet), suggesting that the 70S mode of initiation is less dependent on the 3GC pairs in tRNA(fMet).

Improved tuning of the extended concentric tube resonator for wide-band transmission loss

Transmission loss (TL) of a simple expansion chamber (SEC) consists of periodic domes with sharp troughs. This limits practical application of the SEC in the variable-speed automobile exhaust systems. Three-fourths of the troughs of the SEC can be lifted by appropriate tuning of the extended inlet/outlet lengths. However, such mufflers suffer from high back pressure and generation of aerodynamic noise due to free shear layers at the area discontinuities. Therefore, a perforate bridge is made between the extended inlet and outlet. It is shown that the TL curve of a concentric tube resonator (CTR) can also be lifted in a similar way by proper tuning of the extended unperforated lengths. Differential lengths have to be used to correct the inlet/outlet lengths in order to account for the perforate inertance. The resonance peak frequencies calculated by means of the 1-D analysis are compared with those of the 3-D FEM, and appropriate differential lengths are calculated. It is shown how different geometric characteristics of the muffler and mean flow affect the differential lengths. A general correlation is obtained for the differential lengths by considering seven relevant geometric and environmental parameters in a comprehensive parametric study. The resulting expressions would help in design of extended-tube CTR for wide-band TL. (C) 2014 Institute of Noise Control Engineering.

A smart approach to achieve an exceptionally high loading of metal nanoparticles supported by functionalized extended frameworks for efficient catalysis

The problem associated with metal nanoparticle (NP) agglomeration when trying to achieve a high loading amount has been solved by a new method of functionalization of MOFs' pores with terminal alkyne moieties. The alkynophilicity of the Au3+ ions has been utilized successfully for an exceptionally high loading (similar to 50 wt%) of Au-NPs on supported functionalized MOFs.

Ultrasound-modulated optical tomography: direct recovery of elasticity distribution from experimentally measured intensity autocorrelation

Based on an ultrasound-modulated optical tomography experiment, a direct, quantitative recovery of Young's modulus (E) is achieved from the modulation depth (M) in the intensity autocorrelation. The number of detector locations is limited to two in orthogonal directions, reducing the complexity of the data gathering step whilst ensuring against an impoverishment of the measurement, by employing ultrasound frequency as a parameter to vary during data collection. The M and E are related via two partial differential equations. The first one connects M to the amplitude of vibration of the scattering centers in the focal volume and the other, this amplitude to E. A (composite) sensitivity matrix is arrived at mapping the variation of M with that of E and used in a (barely regularized) Gauss-Newton algorithm to iteratively recover E. The reconstruction results showing the variation of E are presented. (C) 2015 Optical Society of America

Structural characterization of folded and extended conformations in peptides containing gamma amino acids with proteinogenic side chains: crystal structures of gamma(n), (alpha gamma)(n) and gamma gamma delta gamma sequences

The crystal structures of nine peptides containing gamma(4)Val and gamma(4)Leu are described. The short sequences Boc-gamma(4)(R)Val](2)-OMe 1, Boc-gamma(4)(R)Val](3)-NHMe 2 and Boc-gamma(4)(S)Val-gamma(4)(R)Val-OMe 3 adopt extended apolar, sheet like structures. The tetrapeptide Boc-gamma(4)(R)Val](4)-OMe 4 adopts an extended conformation, in contrast to the folded C-14 helical structure determined previously for Boc-gamma(4)(R)Leu](4)-OMe. The hybrid alpha gamma sequence Boc-Ala-gamma(4)(R)Leu](2)-OMe 5 adopts an S-shaped structure devoid of intramolecular hydrogen bonds, with both alpha residues adopting local helical conformations. In sharp contrast, the tetrapeptides Boc-Aib-gamma(4)(S)Leu](2)-OMe 6 and Boc-Leu-gamma(4)(R)Leu](2)-OMe 7 adopt folded structures stabilized by two successive C-12 hydrogen bonds. gamma(4)Val residues have also been incorporated into the strand segments of a crystalline octapeptide, Boc-Leu-gamma(4)(R)Val-Val-(D)Pro-Gly-Leu-gamma(4)(R)Val-Val-OMe 8. The gamma gamma delta gamma tetrapeptide containing gamma(4)Val and delta(5)Leu residues adopts an extended sheet like structure. The hydrogen bonding pattern at gamma residues corresponds to an apolar sheet, while a polar sheet is observed at the lone delta residue. The transition between folded and extended structures at gamma residues involves a change of the torsion angle from the gauche to the trans conformation about the C-beta-C-alpha bond.

High Quality Photometric Reconstruction using a Depth Camera

In this paper we present a depth-guided photometric 3D reconstruction method that works solely with a depth camera like the Kinect. Existing methods that fuse depth with normal estimates use an external RGB camera to obtain photometric information and treat the depth camera as a black box that provides a low quality depth estimate. Our contribution to such methods are two fold. Firstly, instead of using an extra RGB camera, we use the infra-red (IR) camera of the depth camera system itself to directly obtain high resolution photometric information. We believe that ours is the first method to use an IR depth camera system in this manner. Secondly, photometric methods applied to complex objects result in numerous holes in the reconstructed surface due to shadows and self-occlusions. To mitigate this problem, we develop a simple and effective multiview reconstruction approach that fuses depth and normal information from multiple viewpoints to build a complete, consistent and accurate 3D surface representation. We demonstrate the efficacy of our method to generate high quality 3D surface reconstructions for some complex 3D figurines.

Tungsten-based nanomaterials (WO3 & Bi2WO6): Modifications related to charge carrier transfer mechanisms and photocatalytic applications

Heterogeneous photocatalysis is an ideal green energy technology for the purification of wastewater. Although titania dominates as the reference photocatalyst, its wide band gap is a bottleneck for extended utility. Thus, search for non-TiO2 based nanomaterials has become an active area of research in recent years. In this regard, visible light absorbing polycrystalline WO3 (2.4-2.8 eV) and Bi2WO6 (2.8 eV) with versatile structure-electronic properties has gained considerable interest to promote the photocatalytic reactions. These materials are also explored in selective functional group transformation in organic reactions, because of low reduction and oxidation potential of WO3 CB and Bi2WO6 VB, respectively. In this focused review, various strategies such as foreign ion doping, noble metal deposition and heterostructuring with other semiconductors designed for efficient photocatalysis is discussed. These modifications not only extend the optical response to longer wavelengths, but also prolong the life-time of the charge carriers and strengthen the photocatalyst stability. The changes in the surface-bulk properties and the charge carrier transfer dynamics associated with each modification correlating to the high activity are emphasized. The presence of oxidizing agents, surface modification with Cu2+ ions and synthesis of exposed facets to promote the degradation rate is highlighted. In depth study on these nanomaterials is likely to sustain interest in wastewater remediation and envisaged to signify in various green energy applications. (C) 2015 Elsevier B.V. All rights reserved.

Part I: Physical Insights Into the Two-Stage Breakdown Characteristics of STI-Type Drain-Extended pMOS Device

In this paper, we study breakdown characteristics in shallow-trench isolation (STI)-type drain-extended MOSFETs (DeMOS) fabricated using a low-power 65-nm triple-well CMOS process with a thin gate oxide. Experimental data of p-type STI-DeMOS device showed distinct two-stage behavior in breakdown characteristics in both OFF-and ON-states, unlike the n-type device, causing a reduction in the breakdown voltage and safe operating area. The first-stage breakdown occurs due to punchthrough in the vertical structure formed by p-well, deep n-well, and p-substrate, whereas the second-stage breakdown occurs due to avalanche breakdown of lateral n-well/p-well junction. The breakdown characteristics are also compared with the STI-DeNMOS device structure. Using the experimental results and advanced TCAD simulations, a complete understanding of breakdown mechanisms is provided in this paper for STI-DeMOS devices in advanced CMOS processes.

Constraints based analysis of extended cybernetic models

The cybernetic modeling framework provides an interesting approach to model the regulatory phenomena occurring in microorganisms. In the present work, we adopt a constraints based approach to analyze the nonlinear behavior of the extended equations of the cybernetic model. We first show that the cybernetic model exhibits linear growth behavior under the constraint of no resource allocation for the induction of the key enzyme. We then quantify the maximum achievable specific growth rate of microorganisms on mixtures of substitutable substrates under various kinds of regulation and show its use in gaining an understanding of the regulatory strategies of microorganisms. Finally, we show that Saccharomyces cerevisiae exhibits suboptimal dynamic growth with a long diauxic lag phase when growing on a mixture of glucose and galactose and discuss on its potential to achieve optimal growth with a significantly reduced diauxic lag period. The analysis carried out in the present study illustrates the utility of adopting a constraints based approach to understand the dynamic growth strategies of microorganisms. (C) 2015 Elsevier Ireland Ltd. All rights reserved.

An Exponential Lower Bound for Homogeneous Depth Four Arithmetic Formulas

We show here a 2(Omega(root d.log N)) size lower bound for homogeneous depth four arithmetic formulas. That is, we give an explicit family of polynomials of degree d on N variables (with N = d(3) in our case) with 0, 1-coefficients such that for any representation of a polynomial f in this family of the form f = Sigma(i) Pi(j) Q(ij), where the Q(ij)'s are homogeneous polynomials (recall that a polynomial is said to be homogeneous if all its monomials have the same degree), it must hold that Sigma(i,j) (Number of monomials of Q(ij)) >= 2(Omega(root d.log N)). The above mentioned family, which we refer to as the Nisan-Wigderson design-based family of polynomials, is in the complexity class VNP. Our work builds on the recent lower bound results 1], 2], 3], 4], 5] and yields an improved quantitative bound as compared to the quasi-polynomial lower bound of 6] and the N-Omega(log log (N)) lower bound in the independent work of 7].

The role of intra- and inter-site exchange correlations in the extended Falicov-Kimball model on a triangular lattice

Ground state magnetic properties of the spin-dependent Falicov-Kimball model (FKM) are studied by incorporating the intrasite exchange correlation J (between itinerant d- and localized f-electrons) and intersite (superexchange) correlation J (between localized f-electrons) on a triangular lattice for two different fillings. Numerical diagonalization and Monte-Carlo techniques are used to determine the ground state magnetic properties. Transitions from antiferromagnetic to ferromagnetic and again to re-entrant antiferromagnetic phase is observed in a wide range of parameter space. The magnetic moments of d- and f-electrons are observed to depend strongly on the value off, J and also on the total number of d-electrons (N-d). (C) 2015 Elsevier Ltd. All rights reserved.

General Relationship Between Contact Stiffness, Contact Depth, and Mechanical Properties for Indentation in Linear Viscoelastic Solids Using Axisymmetric Indenters of Arbitrary Profiles

We derive a relationship between the initial unloading slope, contact depth, and the instantaneous relaxation modulus for indentation in linear viscoelastic solids by a rigid indenter with an arbitrary axisymmetric smooth profile. Although the same expression is well known for indentation in elastic and in elastic-plastic solids, we show that it is also true for indentation in linear viscoelastic solids, provided that the unloading rate is sufficiently fast. Furthermore, the same expression holds true for both fast loading and unloading. These results should provide a sound basis for using the relationship for determining properties of viscoelastic solids using indentation techniques.

Depth dependence of nanohardness in a CuAlNi single crystal shape memory alloy

Instrumented nanoindentation was employed to study the depth dependence of nanohardness in a CuAlNi single crystal shape memory alloy that exhibits shape memory effect (SME). A Berkovich indenter and a cube comer indenter were used in this study, and the

Modification of Bertrand's theorem and extended Runge-Lenz vector

It is shown that for a particle with suitable angular moments in the screened Coulomb potential or isotropic harmonic potential, there still exist closed orbits rather than ellipse, characterized by the conserved aphelion and perihelion vectors, i.e. extended Runge-Lenz vector, which implies a higher dynamical symmetry than the geometrical symmetry O-3. The closeness of a planar orbit implies the radial and angular motional frequencies are commensurable.