DSA image registration using non-uniform MRF model and pivotal control points

In order to reduce the motion artifacts in DSA, non-rigid image registration is commonly used before subtracting the mask from the contrast image. Since DSA registration requires a set of spatially non-uniform control points, a conventional MRF model is not very efficient. In this paper, we introduce the concept of pivotal and non-pivotal control points to address this, and propose a non-uniform MRF for DSA registration. We use quad-trees in a novel way to generate the non-uniform grid of control points. Our MRF formulation produces a smooth displacement field and therefore results in better artifact reduction than that of registering the control points independently. We achieve improved computational performance using pivotal control points without compromising on the artifact reduction. We have tested our approach using several clinical data sets, and have presented the results of quantitative analysis, clinical assessment and performance improvement on a GPU. (C) 2013 Elsevier Ltd. All rights reserved.

Taylor series expansion based multidimensional image reconstruction for confocal and 4pi microscopy

We propose and experimentally demonstrate a three-dimensional (3D) image reconstruction methodology based on Taylor series approximation (TSA) in a Bayesian image reconstruction formulation. TSA incorporates the requirement of analyticity in the image domain, and acts as a finite impulse response filter. This technique is validated on images obtained from widefield, confocal laser scanning fluorescence microscopy and two-photon excited 4pi (2PE-4pi) fluorescence microscopy. Studies on simulated 3D objects, mitochondria-tagged yeast cells (labeled with Mitotracker Orange) and mitochondrial networks (tagged with Green fluorescent protein) show a signal-to-background improvement of 40% and resolution enhancement from 360 to 240 nm. This technique can easily be extended to other imaging modalities (single plane illumination microscopy (SPIM), individual molecule localization SPIM, stimulated emission depletion microscopy and its variants).

Stall flutter of NACA 0012 airfoil at low Reynolds numbers

In the present work, we experimentally study and demarcate the stall flutter boundaries of a NACA 0012 airfoil at low Reynolds numbers (Re similar to 10(4)) by measuring the forces and flow fields around the airfoil when it is forced to oscillate. The airfoil is placed at large mean angle of attack (alpha(m)), and is forced to undergo small amplitude pitch oscillations, the amplitude (Delta alpha) and frequency (f) of which are systematically varied. The unsteady loads on the oscillating airfoil are directly measured, and are used to calculate the energy transfer to the airfoil from the flow. These measurements indicate that for large mean angles of attack of the airfoil (alpha(m)), there is positive energy transfer to the airfoil over a range of reduced frequencies (k=pi fc/U), indicating that there is a possibility of airfoil excitation or stall flutter even at these low Re (c=chord length). Outside this range of reduced frequencies, the energy transfer is negative and under these conditions the oscillations would be damped. Particle Image Velocimetry (PIV) measurements of the flow around the oscillating airfoil show that the shear layer separates from the leading edge and forms a leading edge vortex, although it is not very clear and distinct due to the low oscillation amplitudes. On the other hand, the shear layer formed after separation is found to clearly move periodically away from the airfoil suction surface and towards it with a phase lag to the airfoil oscillations. The phase of the shear layer motion with respect to the airfoil motions shows a clear difference between the exciting and the damping case.

Image reconstruction enables high resolution imaging at large penetration depths in fluorescence microscopy

Imaging thick specimen at a large penetration depth is a challenge in biophysics and material science. Refractive index mismatch results in spherical aberration that is responsible for streaking artifacts, while Poissonian nature of photon emission and scattering introduces noise in the acquired three-dimensional image. To overcome these unwanted artifacts, we introduced a two-fold approach: first, point-spread function modeling with correction for spherical aberration and second, employing maximum-likelihood reconstruction technique to eliminate noise. Experimental results on fluorescent nano-beads and fluorescently coated yeast cells (encaged in Agarose gel) shows substantial minimization of artifacts. The noise is substantially suppressed, whereas the side-lobes (generated by streaking effect) drops by 48.6% as compared to raw data at a depth of 150 mu m. Proposed imaging technique can be integrated to sophisticated fluorescence imaging techniques for rendering high resolution beyond 150 mu m mark. (C) 2013 AIP Publishing LLC.

Locating the attacker of wormhole attack by using the honeypot

Mobile Ad hoc Networks (MANETs) having strikingly superior features also come with notable disadvantage and troubles and the most exigent amongst all being security related issues. Such an ringent network dexterously pave approach for the malicious nodes. Hence providing security is a tedious task. For such a dynamic environment, a security system which dynamically observes the attacker's plans and protect the highly sophisticated resources is in high demand. In this paper we present a method of providing security against wormhole attacks to a MANET by learning about the environment dynamically and adapting itself to avoid malicious nodes. We accomplish this with the assistance of Honeypot. Our method predicts the wormhole attack that may take place and protect the resources well-in advance. Also it cleverly deal with the attacker by using previous history and different type of messages to locate the attacker. Several experiments suggest that the system is accurate in handling wormhole attack.

Experimental analysis of composite single-lap joints using digital image correlation and comparison with theoretical models

The demand for energy efficient, low weight structures has boosted the use of composite structures assembled using increased quantities of structural adhesives. Bonded structures may be subjected to severe working environments such as high temperature and moisture due to which the adhesive gets degraded over a period of time. This reduces the strength of a joint and leads to premature failure. Measurement of strains in the adhesive bondline at any point of time during service may be beneficial as an assessment can be made on the integrity of a joint and necessary preventive actions may be taken before failure. This paper presents an experimental approach of measuring peel and shear strains in the adhesive bondline of composite single-lap joints using digital image correlation. Different sets of composite adhesive joints with varied bond quality were prepared and subjected to tensile load during which digital images were taken and processed using digital image correlation software. The measured peel strain at the joint edge showed a rapid increase with the initiation of a crack till failure of the joint. The measured strains were used to compute the corresponding stresses assuming a plane strain condition and the results were compared with stresses predicted using theoretical models, namely linear and nonlinear adhesive beam models. A similar trend in stress distribution was observed. Further comparison of peel and shear strains also exhibited similar trend for both healthy and degraded joints. Maximum peel stress failure criterion was used to predict the failure load of a composite adhesive joint and a comparison was made between predicted and actual failure loads. The predicted failure loads from theoretical models were found to be higher than the actual failure load for all the joints.

An early in-situ stress signature of the AlN-Si pre-growth interface for successful integration of nitrides with (111) Si

The integration of Metal Organic Chemical Vapor Deposition (MOCVD) grown group III-A nitride device stacks on Si (111) substrates is critically dependent on the quality of the first AlN buffer layer grown. A Si surface that is both oxide-free and smooth is a primary requirement for nucleating such layers. A single parameter, the AlN layer growth stress, is shown to be an early (within 50 nm), clear (<0.5 GPa versus > 1GPa), and fail-safe indicator of the pre-growth surface, and the AlN quality required for successful epitaxy. Grain coalescence model for stress generation is used to correlate growth stress, the AlN-Si interface, and crystal quality. (C) 2013 AIP Publishing LLC.

Long ranged structural modulation in the pre-morphotropic phase boundary cubic-like state of the lead-free piezoelectric Na1/2Bi1/2TiO3-BaTiO3

The nature of the pre-morphotropic phase boundary (MPB) cubic-like state in the lead-free piezoelectric ceramics (1-x)Na1/2Bi1/2TiO3-(x)BaTiO3 at x similar to 0.06 has been examined in detail by electric field and temperature dependent neutron diffraction, x-ray diffraction, dielectric and ferroelectric characterization. The superlattice reflections in the neutron diffraction patterns cannot be explained with the tetragonal P4bm and the rhombohedral (R3c) phase coexistence model. The cubic like state is rather a result of long ranged modulated complex octahedral tilt. This modulated structure exhibits anomalously large dielectric dispersion. The modulated structure transforms to a MPB state on poling. The field-stabilized MPB state is destroyed and the modulated structure is restored on heating the poled specimen above the Vogel-Fulcher freezing temperature. The results show the predominant role of competing octahedral tilts in determining the nature of structural and polar states in Na1/2Bi1/2TiO3-based ferroelectrics. (C) 2013 AIP Publishing LLC.

Image deconvolution research: its scope and importance in live cell microscopy

Fluorescence microscopy has become an indispensable tool in cell biology research due its exceptional specificity and ability to visualize subcellular structures with high contrast. It has highest impact when applied in 4D mode, i.e. when applied to record 3D image information as a function of time, since it allows the study of dynamic cellular processes in their native environment. The main issue in 4D fluorescence microscopy is that the phototoxic effect of fluorescence excitation gets accumulated during 4D image acquisition to the extent that normal cell functions are altered. Hence to avoid the alteration of normal cell functioning, it is required to minimize the excitation dose used for individual 2D images constituting a 4D image. Consequently, the noise level becomes very high degrading the resolution. According to the current status of technology, there is a minimum required excitation dose to ensure a resolution that is adequate for biological investigations. This minimum is sufficient to damage light-sensitive cells such as yeast if 4D imaging is performed for an extended period of time, for example, imaging for a complete cell cycle. Nevertheless, our recently developed deconvolution method resolves this conflict forming an enabling technology for visualization of dynamical processes of light-sensitive cells for durations longer than ever without perturbing normal cell functioning. The main goal of this article is to emphasize that there are still possibilities for enabling newer kinds of experiment in cell biology research involving even longer 4D imaging, by only improving deconvolution methods without any new optical technologies.

Sparse Recovery Methods Hold Promise for Diffuse Optical Tomographic Image Reconstruction

The sparse recovery methods utilize the l(p)-normbased regularization in the estimation problem with 0 <= p <= 1. These methods have a better utility when the number of independent measurements are limited in nature, which is a typical case for diffuse optical tomographic image reconstruction problem. These sparse recovery methods, along with an approximation to utilize the l(0)-norm, have been deployed for the reconstruction of diffuse optical images. Their performancewas compared systematically using both numerical and gelatin phantom cases to show that these methods hold promise in improving the reconstructed image quality.

Pre-clinical toxicity & immunobiological evaluation of DNA rabies vaccine & combination rabies vaccine in rhesus monkeys (Macaca mulatta)

Background & objectives: Pre-clinical toxicology evaluation of biotechnology products is a challenge to the toxicologist. The present investigation is an attempt to evaluate the safety profile of the first indigenously developed recombinant DNA anti-rabies vaccine DRV (100 mu g)] and combination rabies vaccine CRV (100 mu g DRV and 1.25 IU of cell culture-derived inactivated rabies virus vaccine)], which are intended for clinical use by intramuscular route in Rhesus monkeys. Methods: As per the regulatory requirements, the study was designed for acute (single dose - 14 days), sub-chronic (repeat dose - 28 days) and chronic (intended clinical dose - 120 days) toxicity tests using three dose levels, viz. therapeutic, average (2x therapeutic dose) and highest dose (10 x therapeutic dose) exposure in monkeys. The selection of the model i.e. monkey was based on affinity and rapid higher antibody response during the efficacy studies. An attempt was made to evaluate all parameters which included physical, physiological, clinical, haematological and histopathological profiles of all target organs, as well as Tiers I, II, III immunotoxicity parameters. Results: In acute toxicity there was no mortality in spite of exposing the monkeys to 10XDRV. In sub chronic and chronic toxicity studies there were no abnormalities in physical, physiological, neurological, clinical parameters, after administration of test compound in intended and 10 times of clinical dosage schedule of DRV and CRV under the experimental conditions. Clinical chemistry, haematology, organ weights and histopathology studies were essentially unremarkable except the presence of residual DNA in femtogram level at site of injection in animal which received 10X DRV in chronic toxicity study. No Observational Adverse Effects Level (NOAEL) of DRV is 1000 ug/dose (10 times of therapeutic dose) if administered on 0, 4, 7, 14, 28th day. Interpretation & conclusions: The information generated by this study not only draws attention to the need for national and international regulatory agencies in formulating guidelines for pre-clinical safety evaluation of biotech products but also facilitates the development of biopharmaceuticals as safe potential therapeutic agents.

RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state

Flaviviral RNA-dependent RNA polymerases (RdRps) initiate replication of the single-stranded RNA genome in the absence of a primer. The template sequence 5'-CU-3' at the 3'-end of the flaviviral genome is highly conserved. Surprisingly, flaviviral RdRps require high concentrations of the second incoming nucleotide GTP to catalyze de novo template-dependent RNA synthesis. We show that GTP stimulates de novo RNA synthesis by RdRp from Japanese encephalitis virus (jRdRp) also. Crystal structures of jRdRp complexed with GTP and ATP provide a basis for specific recognition of GTP. Comparison of the jRdRp(GTP) structure with other viral RdRp-GTP structures shows that GTP binds jRdRp in a novel conformation. Apo-jRdRp structure suggests that the conserved motif F of jRdRp occupies multiple conformations in absence of GTP. Motif F becomes ordered on GTP binding and occludes the nucleotide triphosphate entry tunnel. Mutational analysis of key residues that interact with GTP evinces that the jRdRp(GTP) structure represents a novel pre-initiation state. Also, binding studies show that GTP binding reduces affinity of RdRp for RNA, but the presence of the catalytic Mn2+ ion abolishes this inhibition. Collectively, these observations suggest that the observed pre-initiation state may serve as a check-point to prevent erroneous template-independent RNA synthesis by jRdRp during initiation.

Multi-Temporal Satellite Image Analysis Using Gene Expression Programming

This paper discusses an approach for river mapping and flood evaluation to aid multi-temporal time series analysis of satellite images utilizing pixel spectral information for image classification and region-based segmentation to extract water covered region. Analysis of Moderate Resolution Imaging Spectroradiometer (MODIS) satellite images is applied in two stages: before flood and during flood. For these images the extraction of water region utilizes spectral information for image classification and spatial information for image segmentation. Multi-temporal MODIS images from ``normal'' (non-flood) and flood time-periods are processed in two steps. In the first step, image classifiers such as artificial neural networks and gene expression programming to separate the image pixels into water and non-water groups based on their spectral features. The classified image is then segmented using spatial features of the water pixels to remove the misclassified water region. From the results obtained, we evaluate the performance of the method and conclude that the use of image classification and region-based segmentation is an accurate and reliable for the extraction of water-covered region.

Studies and Evaluation of EIT Image Reconstruction in EIDORS with Simulated Boundary Data

Simulated boundary potential data for Electrical Impedance Tomography (EIT) are generated by a MATLAB based EIT data generator and the resistivity reconstruction is evaluated with Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software (EIDORS). Circular domains containing subdomains as inhomogeneity are defined in MATLAB-based EIT data generator and the boundary data are calculated by a constant current simulation with opposite current injection (OCI) method. The resistivity images reconstructed for different boundary data sets and images are analyzed with image parameters to evaluate the reconstruction.

Nonlinear analysis of a thin pre-twisted and delaminated anisotropic strip

The present work is aimed at the development of an efficient mathematical model to assess the degradation in the stiffness properties of an anisotropic strip due to delamination. In particular, the motive is to capture those nonlinear effects in a strip that arise due to the geometry of the structure, in the presence of delamination. The variational asymptotic method (VAM) is used as a mathematical tool to simplify the original 3D problem to a 1D problem. Further simplification is achieved by modeling the delaminated structure by a sublaminate approach. By VAM, a 2D nonlinear sectional analysis is carried out to determine compact expression for the stiffness terms. The stiffness terms, both linear and nonlinear, are derived as functions of delamination length and location in closed form. In general, the results from the analysis include fully coupled nonlinear 1D stiffness coefficients, 3D strain field, 3D stress field, and in-plane and warping fields. In this work, the utility of the model is demonstrated for a static case, and its capability to capture the trapeze effect in the presence of delamination is investigated and compared with results available in the literature.