The putative role of some conserved water molecules in the structure and function of human transthyretin

Human transthyretin (hTTR) is a multifunctional protein that is involved in several neurodegenerative diseases. Besides the transportation of thyroxin and vitamin A, it is also involved in the proteolysis of apolipoprotein A1 and A beta peptide. Extensive analyses of 32 high-resolution X-ray and neutron diffraction structures of hTTR followed by molecular-dynamics simulation studies using a set of 15 selected structures affirmed the presence of 44 conserved water molecules in its dimeric structure. They are found to play several important roles in the structure and function of the protein. Eight water molecules stabilize the dimeric structure through an extensive hydrogen-bonding network. The absence of some of these water molecules in highly acidic conditions (pH <= 4.0) severely affects the interfacial hydrogen-bond network, which may destabilize the native tetrameric structure, leading to its dissociation. Three pairs of conserved water molecules contribute to maintaining the geometry of the ligand-binding cavities. Some other water molecules control the orientation and dynamics of different structural elements of hTTR. This systematic study of the location, absence, networking and interactions of the conserved water molecules may shed some light on various structural and functional aspects of the protein. The present study may also provide some rational clues about the conserved water-mediated architecture and stability of hTTR.

Joint Bilateral Filtering based Non-local Means Image Denoising

This paper proposes a denoising algorithm which performs non-local means bilateral filtering. As existing literature suggests, non-local means (NLM) is one of the widely used denoising techniques, but has a critical drawback of smoothing of edges. In order to improve this, we perform fast and efficient NLM using Approximate Nearest Neighbour Fields and improve the edge content in denoising by formulating a joint-bilateral filter. Using the proposed joint bilateral, we are able to denoise smooth regions using the NLM approach and efficient edge reconstruction is obtained from the bilateral filter. Furthermore, to avoid tedious parameter selection, we carry out a noise estimation before performing joint bilateral filtering. The proposed approach is observed to perform well on high noise images.

Protein Structure and Function: Looking through the Network of Side-Chain Interactions

Network theory has become an excellent method of choice through which biological data are smoothly integrated to gain insights into complex biological problems. Understanding protein structure, folding, and function has been an important problem, which is being extensively investigated by the network approach. Since the sequence uniquely determines the structure, this review focuses on the networks of non-covalently connected amino acid side chains in proteins. Questions in structural biology are addressed within the framework of such a formalism. While general applications are mentioned in this review, challenging problems which have demanded the attention of scientific community for a long time, such as allostery and protein folding, are considered in greater detail. Our aim has been to explore these important problems through the eyes of networks. Various methods of constructing protein structure networks (PSN) are consolidated. They include the methods based on geometry, edges weighted by different schemes, and also bipartite network of protein-nucleic acid complexes. A number of network metrics that elegantly capture the general features as well as specific features related to phenomena, such as allostery and protein model validation, are described. Additionally, an integration of network theory with ensembles of equilibrium structures of a single protein or that of a large number of structures from the data bank has been presented to perceive complex phenomena from network perspective. Finally, we discuss briefly the capabilities, limitations, and the scope for further explorations of protein structure networks.

Dissecting pi-helices: sequence, structure and function

A new procedure for the identification of regular secondary structures using a C-alpha trace has identified 659 pi-helices in 3582 protein chains, solved at high resolution. Taking advantage of this significantly expanded database of pi-helices, we have analysed the functional and structural roles of helices and determined the position-wise amino acid propensity within and around them. These helices range from 5 to 18 residues in length with the average twist and rise being 85.2 +/- 7.2 and 1.28 +/- 0.31 angstrom, respectively. A total of 546 (similar to 83%) out of 659 pi-helices occur in conjunction with alpha-helices, with 101 pi-helices being interspersed between two alpha-helices. The majority of interspersed pi-helices were found to be conserved across a large number of structures within a protein family and produce a significant bend in the overall helical segment as well as local distortions in the neighbouring a-helices. The presence of a pi-helical fragment leads to appropriate orientation of the constituent residues, so as to facilitate favourable interactions and also help in proper folding of the protein chain. In addition to intra helical 6 -> 1 N H center dot center dot center dot O hydrogen bonds, pi-helices are also stabilized by several other non-bonded interactions. pi-Helices show distinct positional residue preferences, which are different from those of a-helices.

Mutations in the nucleotide binding and hydrolysis domains of Helicobacter pylori MutS2 lead to altered biochemical activities and inactivation of its in vivo function

Background: Helicobacter pylori MutS2 (HpMutS2), an inhibitor of recombination during transformation is a non-specific nuclease with two catalytic sites, both of which are essential for its anti-recombinase activity. Although HpMutS2 belongs to a highly conserved family of ABC transporter ATPases, the role of its ATP binding and hydrolysis activities remains elusive. Results: To explore the putative role of ATP binding and hydrolysis activities of HpMutS2 we specifically generated point mutations in the nucleotide-binding Walker-A (HpMutS2-G338R) and hydrolysis Walker-B (HpMutS2-E413A) domains of the protein. Compared to wild-type protein, HpMutS2-G338R exhibited similar to 2.5-fold lower affinity for both ATP and ADP while ATP hydrolysis was reduced by similar to 3-fold. Nucleotide binding efficiencies of HpMutS2-E413A were not significantly altered; however the ATP hydrolysis was reduced by similar to 10-fold. Although mutations in the Walker-A and Walker-B motifs of HpMutS2 only partially reduced its ability to bind and hydrolyze ATP, we demonstrate that these mutants not only exhibited alterations in the conformation, DNA binding and nuclease activities of the protein but failed to complement the hyper-recombinant phenotype displayed by mutS2-disrupted strain of H. pylori. In addition, we show that the nucleotide cofactor modulates the conformation, DNA binding and nuclease activities of HpMutS2. Conclusions: These data describe a strong crosstalk between the ATPase, DNA binding, and nuclease activities of HpMutS2. Furthermore these data show that both, ATP binding and hydrolysis activities of HpMutS2 are essential for the in vivo anti-recombinase function of the protein.

Quasi-geostrophic dynamics in the presence of moisture gradients

The derivation of a quasi-geostrophic system from the rotating shallow-water equations on a midlatitude -plane coupled with moisture is presented. Condensation is prescribed to occur whenever the moisture at a point exceeds a prescribed saturation value. It is seen that a slow condensation time-scale is required to obtain a consistent set of equations at leading order. Further, since the advecting wind fields are geostrophic, changes in moisture (and hence precipitation) occur only via non-divergent mechanisms. Following observations, a saturation profile with gradients in the zonal and meridional directions is prescribed. A purely meridional gradient has the effect of slowing down the dry Rossby waves, through a reduction in the equivalent gradient' of the background potential vorticity. A large-scale unstable moist mode results on the inclusion of a zonal gradient by itself, or in conjunction with a meridional moisture gradient. For gradients that are are representative of the atmosphere, the most unstable moist mode propagates zonally in the direction of increasing moisture, matures over an intraseasonal time-scale and has small phase speed.

Reply to Discussion on ``Bearing capacity of circular footings over rock mass by using axisymmetric quasi lower bound finite element limit analysis'' Comput. Geotech. 70 (2015) 138-149]

A discussion has been provided for the comments raised by the discusser (Clausen, 2015)1] on the article recently published by the authors (Chakraborty and Kumar, 2015). The effect of exponent alpha for values of GSI approximately smaller than 30 becomes more critical. On the other hand, for greater values of GSI, the results obtained by the authors earlier remain primarily independent of alpha and can be easily used. (C) 2015 Elsevier Ltd. All rights reserved.

Spatio-temporal Map Formation Based on a Potential Function

We revisit the problem of temporal self organization using activity diffusion based on the neural gas (NGAS) algorithm. Using a potential function formulation motivated by a spatio-temporal metric, we derive an adaptation rule for dynamic vector quantization of data. Simulations results show that our algorithm learns the input distribution and time correlation much faster compared to the static neural gas method over the same data sequence under similar training conditions.

On Fast Bilateral Filtering Using Fourier Kernels

It was demonstrated in earlier work that, by approximating its range kernel using shiftable functions, the nonlinear bilateral filter can be computed using a series of fast convolutions. Previous approaches based on shiftable approximation have, however, been restricted to Gaussian range kernels. In this work, we propose a novel approximation that can be applied to any range kernel, provided it has a pointwise-convergent Fourier series. More specifically, we propose to approximate the Gaussian range kernel of the bilateral filter using a Fourier basis, where the coefficients of the basis are obtained by solving a series of least-squares problems. The coefficients can be efficiently computed using a recursive form of the QR decomposition. By controlling the cardinality of the Fourier basis, we can obtain a good tradeoff between the run-time and the filtering accuracy. In particular, we are able to guarantee subpixel accuracy for the overall filtering, which is not provided by the most existing methods for fast bilateral filtering. We present simulation results to demonstrate the speed and accuracy of the proposed algorithm.

On the Geometrically Dependent Quasi-Saturation and g(m) Reduction in Advanced DeMOS Transistors

This paper reveals an early quasi-saturation (QS) effect attributed to the geometrical parameters in shallow trench isolation-type drain-extended MOS (STI-DeMOS) transistors in advanced CMOS technologies. The quasi-saturation effect leads to serious g(m) reduction in STI-DeMOS. This paper investigates the nonlinear resistive behavior of the drain-extended region and its impact on the particular behavior of the STI-DeMOS transistor. In difference to vertical DMOS or lateral DMOS structures, STI-DeMOS exhibits three distinct regions of the drain extension. A complete understanding of the physics in these regions and their impact on the QS behavior are developed in this paper. An optimization strategy is shown for an improved g(m) device in a state-of-the-art 28-nm CMOS technology node.

Theoretical insights on the electro-thermal transport properties of monolayer MoS2 with line defects

Two dimensional (2D) materials demonstrate several novel electrical, mechanical, and thermal properties which are quite distinctive to those of their bulk form. Among many others, one important potential application of the 2D material is its use in the field of energy harvesting. Owing to that, here we present a detailed study on electrical as well as thermal transport of monolayer MoS2, in quasi ballistic regime. Besides the perfect monolayer in its pristine form, we also consider various line defects which have been experimentally observed in mechanically exfoliated MoS2 samples. For calculating various parameters related to the electrical transmission, we employ the non-equilibrium Green's function-density functional theory combination. However, to obtain the phonon transmission, we take help of the parametrized Stillinger-Weber potential which can accurately delineate the inter-atomic interactions for the monolayer MoS2. Due to the presence of line defects, we observed significant reductions in both the charge carrier and the phonon transmissions through a monolayer MoS2 flake. Moreover, we also report a comparative analysis showing the temperature dependency of the thermoelectric figure of merit values, as obtained for the perfect as well as the other defective 2D samples. (C) 2016 AIP Publishing LLC.

IMAGE DENOISING USING OPTIMALLY WEIGHTED BILATERAL FILTERS: A SURE AND FAST APPROACH

The bilateral filter is known to be quite effective in denoising images corrupted with small dosages of additive Gaussian noise. The denoising performance of the filter, however, is known to degrade quickly with the increase in noise level. Several adaptations of the filter have been proposed in the literature to address this shortcoming, but often at a substantial computational overhead. In this paper, we report a simple pre-processing step that can substantially improve the denoising performance of the bilateral filter, at almost no additional cost. The modified filter is designed to be robust at large noise levels, and often tends to perform poorly below a certain noise threshold. To get the best of the original and the modified filter, we propose to combine them in a weighted fashion, where the weights are chosen to minimize (a surrogate of) the oracle mean-squared-error (MSE). The optimally-weighted filter is thus guaranteed to perform better than either of the component filters in terms of the MSE, at all noise levels. We also provide a fast algorithm for the weighted filtering. Visual and quantitative denoising results on standard test images are reported which demonstrate that the improvement over the original filter is significant both visually and in terms of PSNR. Moreover, the denoising performance of the optimally-weighted bilateral filter is competitive with the computation-intensive non-local means filter.

FAST AND ACCURATE BILATERAL FILTERING USING GAUSS-POLYNOMIAL DECOMPOSITION

The bilateral filter is a versatile non-linear filter that has found diverse applications in image processing, computer vision, computer graphics, and computational photography. A common form of the filter is the Gaussian bilateral filter in which both the spatial and range kernels are Gaussian. A direct implementation of this filter requires O(sigma(2)) operations per pixel, where sigma is the standard deviation of the spatial Gaussian. In this paper, we propose an accurate approximation algorithm that can cut down the computational complexity to O(1) per pixel for any arbitrary sigma (constant-time implementation). This is based on the observation that the range kernel operates via the translations of a fixed Gaussian over the range space, and that these translated Gaussians can be accurately approximated using the so-called Gauss-polynomials. The overall algorithm emerging from this approximation involves a series of spatial Gaussian filtering, which can be efficiently implemented (in parallel) using separability and recursion. We present some preliminary results to demonstrate that the proposed algorithm compares favorably with some of the existing fast algorithms in terms of speed and accuracy.

An New Area Function for Sharp indenter Tips in Nanoindentation

A new area function is introduced and applied to a Berkovich tip in order to characterize the contact projected area between an indenter and indented material. The function can be related directly to tip-rounding, thereby having obviously physical meaning. Nanoindentation experiments are performed on a commercial Nano Indenter XPsystem. The other two area functions introduced by Oliver and Pharr and by Thurn and Cook respectively are involved in this paper for comparison. By comparison from experimental results among different area functions, the indenter tip described by the proposed area function here is very close to the experimental indenter.

Component Assembling Model and Its Application to Quasi-Brittle Damage

Potential energy can be approximated by ‘‘pair-functional’’ potentials which is composed of pair potentials and embedding energy. Pair potentials are grouped according to discrete directions of atomic bonds such that each group is represented by an orientational component. Meanwhile, another kind of component, the volumetric one is derived from embedding energy. Damage and fracture are the changing and breaking of atomic bonds at the most fundamental level and have been reflected by the changing of these components’ properties. Therefore, material is treated as a component assembly, and its constitutive equations are formed by means of assembling these two kinds of components’ response functions. This material model is referred to as the component assembling model. Theoretical analysis and numerical computing indicate that the proposed model has the capacity of reproducing some results satisfactorily, with the advantages of physical explicitness and intrinsic induced anisotropy, etc.