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/.

Moderate intensity static magnetic field has bactericidal effect on E. coli and S. epidermidis on sintered hydroxyapatite

The application of electromagnetic field in the context of bacteria associated infections on biomaterial surfaces has not been extensively explored. In this work, we applied a moderate intensity static magnetic field (100 mT) to understand the adhesion and growth behavior of both gram positive (S. epidermidis) and gram negative bacteria (E. coli) and also to investigate bactericidal/bacteriostatic property of the applied electromagnetic field. An in-house built magnetometer was used to apply static homogeneous magnetic field during a planned set of in vitro experiments. Both the sintered hydroxyapatite (HA) and the control samples seeded with bacteria were exposed to the magnetic field (100 mT) for different timescale during their log phase growth. Quantitative analysis of the SEM images confirms the effect of electromagnetic field on suppressing bacterial growth. Furthermore, cell integrity and inner membrane permeabilization assays were performed to understand the origin of such effect. The results of these assays were statistically analyzed to reveal the bactericidal effect of magnetic field, indicating cell membrane damage. Under the investigated culture conditions, the bactericidal effect was found to be less effective for S. Epidermidis than E. coli. (c) 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 2012:100B:12061217, 2012.

Static analysis for checking data format compatibility of programs

Large software systems are developed by composing multiple programs. If the programs manip-ulate and exchange complex data, such as network packets or files, it is essential to establish that they follow compatible data formats. Most of the complexity of data formats is associated with the headers. In this paper, we address compatibility of programs operating over headers of network packets, files, images, etc. As format specifications are rarely available, we infer the format associated with headers by a program as a set of guarded layouts. In terms of these formats, we define and check compatibility of (a) producer-consumer programs and (b) different versions of producer (or consumer) programs. A compatible producer-consumer pair is free of type mismatches and logical incompatibilities such as the consumer rejecting valid outputs gen-erated by the producer. A backward compatible producer (resp. consumer) is guaranteed to be compatible with consumers (resp. producers) that were compatible with its older version. With our prototype tool, we identified 5 known bugs and 1 potential bug in (a) sender-receiver modules of Linux network drivers of 3 vendors and (b) different versions of a TIFF image library.

A Vision-Based Micro-Newton Static Force Sensor Using a Displacement-Amplifying Compliant Mechanism (DaCM)

A micro-newton static force sensor is presented here as a packaged product. The sensor, which is based on the mechanics of deformable objects, consists of a compliant mechanism that amplifies the displacement caused by the force that is to be measured. The output displacement, captured using a digital microscope and analyzed using image processing techniques, is used to calculate the force using precalibrated force-displacement curve. Images are scanned in real time at a frequency of 15 frames per second and sampled at around half the scanning frequency. The sensor was built, packaged, calibrated, and tested. It has simulated and measured stiffness values of 2.60N/m and 2.57N/m, respectively. The smallest force it can reliably measure in the presence of noise is about 2 mu N over a range of 1.4mN. The off-the-shelf digital microscope aside, all of its other components are purely mechanical; they are inexpensive and can be easily made using simple machines. Another highlight of the sensor is that its movable and delicate components are easily replaceable. The sensor can be used in aqueous environment as it does not use electric, magnetic, thermal, or any other fields. Currently, it can only measure static forces or forces that vary at less than 1Hz because its response time and bandwidth are limited by the speed of imaging with a camera. With a universal serial bus (USB) connection of its digital microscope, custom-developed graphical user interface (GUI), and related software, the sensor is fully developed as a readily usable product.

Static analysis of infinite laminated cylindrical shell panel

This paper presents an approximate three-dimensional elasticity solution for an infinitely long, cross-ply laminated circular cylindrical shell panel with simply supported boundary conditions, subjected to an arbitrary discontinuous transverse loading. The solution is based on the principal assumption that the ratio of the thickness of the lamina to its middle surface radius is negligible compared to unity. The validity of this assumption and the range of application of this approximate solution have been established through a comparison with an exact solution. Results of classical and first-order shear deformation shell theories have been compared with the results of the present solution to bring out the accuracy of these theories. It is also shown that for very shallow shell panels the definition of a thin shell should be based on the ratio of thickness to chord width rather than the ratio of thickness to mean radius.

A Network Model of Static Foam Drainage

On the basis of a more realistic tetrakaidecahedral structure of foam bubbles, a network model of static foam drainage has been developed. The model considers the foam to be made up of films and Plateau borders. The films drain into the adjacent Plateau borders, which in turn form a network through which the liquid moves from the foam to the liquid pool. From the structure, a unit flow cell was found, which constitutes the foam when stacked together both horizontally and vertically. Symmetry in the unit flow cell indicates that the flow analysis of a part of it can be employed to obtain the drainage for the whole foam. Material balance equations have been written for each segment of this subsection, ensuring connectivity, and solved with the appropriate boundary and initial conditions. The calculated rates of drainage, when compared with the available experimental results, indicate that the model predicts the experimental results well.

Model Predictive Static Programming: A Computationally Efficient Technique For Suboptimal Control Design

Combining the philosophies of nonlinear model predictive control and approximate dynamic programming, a new suboptimal control design technique is presented in this paper, named as model predictive static programming (MPSP), which is applicable for finite-horizon nonlinear problems with terminal constraints. This technique is computationally efficient, and hence, can possibly be implemented online. The effectiveness of the proposed method is demonstrated by designing an ascent phase guidance scheme for a ballistic missile propelled by solid motors. A comparison study with a conventional gradient method shows that the MPSP solution is quite close to the optimal solution.

CCD: Connected Component Descriptor for Robust Mosaicing of Camera-Captured Document Images

We propose a robust method for mosaicing of document images using features derived from connected components. Each connected component is described using the Angular Radial Tran. form (ART). To ensure geometric consistency during feature matching, the ART coefficients of a connected component are augmented with those of its two nearest neighbors. The proposed method addresses two critical issues often encountered in correspondence matching: (i) The stability of features and (ii) Robustness against false matches due to the multiple instances of characters in a document image. The use of connected components guarantees a stable localization across images. The augmented features ensure a successful correspondence matching even in the presence of multiple similar regions within the page. We illustrate the effectiveness of the proposed method on camera captured document images exhibiting large variations in viewpoint, illumination and scale.

Quasi-static and dynamic strain sensing using carbon nanotube/epoxy nanocomposite thin films

Thin films are developed by dispersing carbon black nanoparticles and carbon nanotubes (CNTs) in an epoxy polymer. The films show a large variation in electrical resistance when subjected to quasi-static and dynamic mechanical loading. This phenomenon is attributed to the change in the band-gap of the CNTs due to the applied strain, and also to the change in the volume fraction of the constituent phases in the percolation network. Under quasi-static loading, the films show a nonlinear response. This nonlinearity in the response of the films is primarily attributed to the pre-yield softening of the epoxy polymer. The electrical resistance of the films is found to be strongly dependent on the magnitude and frequency of the applied dynamic strain, induced by a piezoelectric substrate. Interestingly, the resistance variation is found to be a linear function of frequency and dynamic strain. Samples with a small concentration of just 0.57% of CNT show a sensitivity as high as 2.5% MPa-1 for static mechanical loading. A mathematical model based on Bruggeman's effective medium theory is developed to better understand the experimental results. Dynamic mechanical loading experiments reveal a sensitivity as high as 0.007% Hz(-1) at a constant small-amplitude vibration and up to 0.13%/mu-strain at 0-500 Hz vibration. Potential applications of such thin films include highly sensitive strain sensors, accelerometers, artificial neural networks, artificial skin and polymer electronics.

A Proposal for Concurrent Estimation of Static and Dynamic Nonlinearity of ADC

Despite great advances in very large scale integrated-circuit design and manufacturing, performance of even the best available high-speed, high-resolution analog-to-digital converter (ADC) is known to deteriorate while acquiring fast-rising, high-frequency, and nonrepetitive waveforms. Waveform digitizers (ADCs) used in high-voltage impulse recordings and measurements are invariably subjected to such waveforms. Errors resulting from a lowered ADC performance can be unacceptably high, especially when higher accuracies have to be achieved (e.g., when part of a reference measuring system). Static and dynamic nonlinearities (estimated independently) are vital indices for evaluating performance and suitability of ADCs to be used in such environments. Typically, the estimation of static nonlinearity involves 10-12 h of time or more (for a 12-b ADC) and the acquisition of millions of samples at high input frequencies for dynamic characterization. ADCs with even higher resolution and faster sampling speeds will soon become available. So, there is a need to reduce testing time for evaluating these parameters. This paper proposes a novel and time-efficient method for the simultaneous estimation of static and dynamic nonlinearity from a single test. This is achieved by conceiving a test signal, comprised of a high-frequency sinusoid (which addresses dynamic assessment) modulated by a low-frequency ramp (relevant to the static part). Details of implementation and results on two digitizers are presented and compared with nonlinearities determined by the existing standardized approaches. Good agreement in results and time savings achievable indicates its suitability.

A Proposal for Concurrent Estimation of Static and Dynamic Nonlinearity of ADC

Despite great advances in very large scale integrated-circuit design and manufacturing, performance of even the best available high-speed, high-resolution analog-to-digital converter (ADC) is known to deteriorate while acquiring fast-rising, high-frequency, and nonrepetitive waveforms. Waveform digitizers (ADCs) used in high-voltage impulse recordings and measurements are invariably subjected to such waveforms. Errors resulting from a lowered ADC performance can be unacceptably high, especially when higher accuracies have to be achieved (e.g., when part of a reference measuring system). Static and dynamic nonlinearities (estimated independently) are vital indices for evaluating performance and suitability of ADCs to be used in such environments. Typically, the estimation of static nonlinearity involves 10-12 h of time or more (for a 12-b ADC) and the acquisition of millions of samples at high input frequencies for dynamic characterization. ADCs with even higher resolution and faster sampling speeds will soon become available. So, there is a need to reduce testing time for evaluating these parameters. This paper proposes a novel and time-efficient method for the simultaneous estimation of static and dynamic nonlinearity from a single test. This is achieved by conceiving a test signal, comprised of a high-frequency sinusoid (which addresses dynamic assessment) modulated by a low-frequency ramp (relevant to the static part). Details of implementation and results on two digitizers are presented and compared with nonlinearities determined by the existing standardized approaches. Good agreement in results and time savings achievable indicates its suitability.

An algorithm for optimum control of static VAR compensators to meet phase-wise unbalanced reactive power demands

The operation of thyristor-controlled static VAR compensators (SVCs) at various conduction angles can be used advantageously to meet the unablanced reactive power demands in a system. However, such operation introduces harmonic currents into the AC system. This paper presents an algorithm to evaluate an optimum combination of the phase-wise reactive power generations from SVC and balanced reactive power supply from the AC system, based on the defined performance indices, namely, the telephone influence factor (TIF), the total harmonic current factor (IT) and the distortion factor (D). Results of the studies conducted on a typical distribution system are presented and discussed.

Efficient implementations of a pseudodynamical stochastic filtering strategy for static elastography

A computationally efficient pseudodynamical filtering setup is established for elasticity imaging (i.e., reconstruction of shear modulus distribution) in soft-tissue organs given statically recorded and partially measured displacement data. Unlike a regularized quasi-Newton method (QNM) that needs inversion of ill-conditioned matrices, the authors explore pseudodynamic extended and ensemble Kalman filters (PD-EKF and PD-EnKF) that use a parsimonious representation of states and bypass explicit regularization by recursion over pseudotime. Numerical experiments with QNM and the two filters suggest that the PD-EnKF is the most robust performer as it exhibits no sensitivity to process noise covariance and yields good reconstruction even with small ensemble sizes.

Simple technique for noise reduction in images retrieved from crystalline storage media

Now that crystals are being considered suitable for high density optical information storage, it is important to reduce the noise levels of retrieved images. The paper describes a simple technique to bring this about.