Design and development of Fiber Bragg Grating sensing plate for plantar strain measurement and postural stability analysis

This paper describes an ab initio design and development of a novel Fiber Bragg Grating (FBG) sensor based strain sensing plate for the measurement of plantar strain distribution in human foot. The primary aim of this work is to study the feasibility of usage of FBG sensors in the measurement of plantar strain in the foot; in particular, to spatially resolve the strain distribution in the foot at different regions such as fore-foot, mid-foot and hind-foot. This study also provides a method to quantify and compare relative postural stability of different subjects under test; in addition, traditional accelerometers have been used to record the movements of center of gravity (second lumbar vertebra) of the subject and the results obtained have been compared against the outcome of the postural stability studies undertaken using the developed FBG plantar strain sensing plate. (C) 2013 Elsevier Ltd. All rights reserved.

mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet

The increasing number of available protein structures requires efficient tools for multiple structure comparison. Indeed, multiple structural alignments are essential for the analysis of function, evolution and architecture of protein structures. For this purpose, we proposed a new web server called multiple Protein Block Alignment (mulPBA). This server implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles. This sequence-like' representation enables the use of powerful sequence alignment methods for primary structure comparison, followed by an iterative refinement of the structural superposition. This approach yields alignments superior to most of the rigid-body alignment methods and highly comparable with the flexible structure comparison approaches. We implement this method in a web server designed to do multiple structure superimpositions from a set of structures given by the user. Outputs are given as both sequence alignment and superposed 3D structures visualized directly by static images generated by PyMol or through a Jmol applet allowing dynamic interaction. Multiple global quality measures are given. Relatedness between structures is indicated by a distance dendogram. Superimposed structures in PDB format can be also downloaded, and the results are quickly obtained. mulPBA server can be accessed at www.dsimb.inserm.fr/dsimb_tools/mulpba/.

Elliptical tracers in two-dimensional, homogeneous, isotropic fluid turbulence: The statistics of alignment, rotation, and nematic order

We study the statistical properties of orientation and rotation dynamics of elliptical tracer particles in two-dimensional, homogeneous, and isotropic turbulence by direct numerical simulations. We consider both the cases in which the turbulent flow is generated by forcing at large and intermediate length scales. We show that the two cases are qualitatively different. For large-scale forcing, the spatial distribution of particle orientations forms large-scale structures, which are absent for intermediate-scale forcing. The alignment with the local directions of the flow is much weaker in the latter case than in the former. For intermediate-scale forcing, the statistics of rotation rates depends weakly on the Reynolds number and on the aspect ratio of particles. In contrast with what is observed in three-dimensional turbulence, in two dimensions the mean-square rotation rate increases as the aspect ratio increases.

The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.

Interference Alignment With Diversity for the 2 x 2 X-Network With Four Antennas

A transmission scheme based on the Alamouti code, which we call the Li-Jafarkhani-Jafar (LJJ) scheme, was recently proposed for the 2 x 2 X-network i.e., two-transmitter (Tx) two-receiver X-network] with two antennas at each node. This scheme was claimed to achieve a sum degrees of freedom (DoF) of 8/3 and also a diversity gain of two when fixed finite constellations are employed at each Tx. Furthermore, each Tx required the knowledge of only its own channel unlike the Jafar-Shamai scheme which required global CSIT to achieve the maximum possible sum DoF of 8/3. In this paper, we extend the LJJ scheme to the 2 x 2 X-network with four antennas at each node. The proposed scheme also assumes only local channel knowledge at each Tx. We prove that the proposed scheme achieves the maximum possible sum DoF of 16/3. In addition, we also prove that, using any fixed finite constellation with appropriate rotation at each Tx, the proposed scheme achieves a diversity gain of at least four.

Precoding-Based Network Alignment Using Transform Approach for Acyclic Networks With Delay

The algebraic formulation for linear network coding in acyclic networks with the links having integer delay is well known. Based on this formulation, for a given set of connections over an arbitrary acyclic network with integer delay assumed for the links, the output symbols at the sink nodes, at any given time instant, is a F(p)m-linear combination of the input symbols across different generations, where F(p)m denotes the field over which the network operates (p is prime and m is a positive integer). We use finite-field discrete Fourier transform to convert the output symbols at the sink nodes, at any given time instant, into a F(p)m-linear combination of the input symbols generated during the same generation without making use of memory at the intermediate nodes. We call this as transforming the acyclic network with delay into n-instantaneous networks (n is sufficiently large). We show that under certain conditions, there exists a network code satisfying sink demands in the usual (nontransform) approach if and only if there exists a network code satisfying sink demands in the transform approach. When the zero-interference conditions are not satisfied, we propose three precoding-based network alignment (PBNA) schemes for three-source three-destination multiple unicast network with delays (3-S 3-D MUN-D) termed as PBNA using transform approach and time-invariant local encoding coefficients (LECs), PBNA using time-varying LECs, and PBNA using transform approach and block time-varying LECs. We derive sets of necessary and sufficient conditions under which throughputs close to n' + 1/2n' + 1, n'/2n' + 1, and n'/2n' + 1 are achieved for the three source-destination pairs in a 3-S 3-D MUN-D employing PBNA using transform approach and time-invariant LECs, and PBNA using transform approach and block time-varying LECs, where n' is a positive integer. For PBNA using time-varying LECs, we obtain a sufficient condition under which a throughput demand of n(1)/n, n(2)/n, and n(3)/n can be met for the three source-destination pairs in a 3-S 3-D MUN-D, where n(1), n(2), and n(3) are positive integers less than or equal to the positive integer n. This condition is also necessary when n(1) + n(3) = n(1) + n(2) = n where n(1) >= n(2) >= n(3).

Membrane-based deformable mirror: intrinsic aberrations and alignment issues

A deformable mirror (DM) is an important component of an adaptive optics system. It is known that an on-axis spherical/parabolic optical component, placed at an angle to the incident beam introduces defocus as well as astigmatism in the image plane. Although the former can be compensated by changing the focal plane position, the latter cannot be removed by mere optical realignment. Since the DM is to be used to compensate a turbulence-induced curvature term in addition to other aberrations, it is necessary to determine the aberrations induced by such (curved DM surface) an optical element when placed at an angle (other than 0 deg) of incidence in the optical path. To this effect, we estimate to a first order the aberrations introduced by a DM as a function of the incidence angle and deformation of the DM surface. We record images using a simple setup in which the incident beam is reflected by a 37 channel micro-machined membrane deformable mirror for various angles of incidence. It is observed that astigmatism is a dominant aberration, which was determined by measuring the difference between the tangential and sagittal focal planes. We justify our results on the basis of theoretical simulations and discuss the feasibility of using such a system for adaptive optics considering a trade-off between wavefront correction and astigmatism due to deformation. (C) 2015 Optical Society of America

Carbon nanotube alignment via electrohydrodynamic patterning of nanocomposites

Electrohydrodynamic (EHD) pattern formation in carbon nanotube-polymer composite films yields well-defined patterns on the micrometer scale along with the alignment of carbon nanotubes (CNTs) within these patterns. Conductive pathways in nanotube networks formed during EHD patterning of nanocomposite films results in a substantial increase in the composites' conductivity at loadings exceeding the percolation threshold. The degree of nanotube alignment can be tuned by adjusting the EHD parameters and the degree of alignment is mirrored by the conductivity across the film. Using etching techniques or by embedding relatively long nanotubes, patterned surfaces decorated by CNT brushes were generated. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.