Mapping Post-translational Modifications of Mammalian Testicular Specific Histone Variant TH2B in Tetraploid and Haploid Germ Cells and Their Implications on the Dynamics of Nucleosome Structure

Histones regulate a variety of chromatin templated events by their post-translational modifications (PTMs). Although there are extensive reports on the PTMs of canonical histones, the information on the histone variants remains very scanty. Here, we report the identification of different PTMs, such as acetylation, methylation, and phosphorylation of a major mammalian histone variant TH2B. Our mass spectrometric analysis has led to the identification of both conserved and unique modifications across tetraploid spermatocytes and haploid spermatids. We have also computationally derived the 3-dimensional model of a TH2B containing nucleosome in order to study the spatial orientation of the PTMs identified and their effect on nucleosome stability and DNA binding potential. From our nucleosome model, it is evident that substititution of specific amino acid residues in TH2B results in both differential histone-DNA and histone-histone contacts. Furthermore, we have also observed that acetylation on the N-terminal tail of TH2B weakens the interactions with the DNA. These results provide direct evidence that, similar to somatic H2B, the testis specific histone TH2B also undergoes multiple PTMs, suggesting the possibility of chromatin regulation by such covalent modifications in mammalian male germ cells.

An iterative framework for sparse signal reconstruction algorithms

It has been shown that iterative re-weighted strategies will often improve the performance of many sparse reconstruction algorithms. However, these strategies are algorithm dependent and cannot be easily extended for an arbitrary sparse reconstruction algorithm. In this paper, we propose a general iterative framework and a novel algorithm which iteratively enhance the performance of any given arbitrary sparse reconstruction algorithm. We theoretically analyze the proposed method using restricted isometry property and derive sufficient conditions for convergence and performance improvement. We also evaluate the performance of the proposed method using numerical experiments with both synthetic and real-world data. (C) 2014 Elsevier B.V. All rights reserved.

Multispectral Bayesian reconstruction technique for real-time two color fluorescence microscopy

We have developed a real-time imaging method for two-color wide-field fluorescence microscopy using a combined approach that integrates multi-spectral imaging and Bayesian image reconstruction technique. To enable simultaneous observation of two dyes (primary and secondary), we exploit their spectral properties that allow parallel recording in both the channels. The key advantage of this technique is the use of a single wavelength of light to excite both the primary dye and the secondary dye. The primary and secondary dyes respectively give rise to fluorescence and bleed-through signal, which after normalization were merged to obtain two-color 3D images. To realize real-time imaging, we employed maximum likelihood (ML) and maximum a posteriori (MAP) techniques on a high-performance computing platform (GPU). The results show two-fold improvement in contrast while the signal-to-background ratio (SBR) is improved by a factor of 4. We report a speed boost of 52 and 350 for 2D and 3D images respectively. Using this system, we have studied the real-time protein aggregation in yeast cells and HeLa cells that exhibits dot-like protein distribution. The proposed technique has the ability to temporally resolve rapidly occurring biological events.

Post-failure Analysis and Fractography of In-plane Tension-Tested Tufted Carbon Fabric-Reinforced Epoxy Composite Laminates

Tufted and plain unidirectional carbon fabric-reinforced epoxy composite laminates were fabricated by vacuum-enhanced resin infusion technology and subjected to in-plane tensile tests with a view to study the changes in mechanical properties and failure responses. Owing to the presence of tufts in the laminates, both the tensile strength and modulus decrease by similar to 38 and similar to 20%, respectively, vis-A -vis the values recorded for plain composites. The fracture features point to the fact that though both the composites fail in brittle manner, they, however, exhibit differing fiber pull out lengths. Further, it was noticed that for the tufted ones, crack originates in the vicinity of tuft thread, spreads through the composite in a brittle manner, and results in a display of shorter fiber pull out lengths. These observations and other results are discussed in this paper.

B-Spline potential function for maximum a-posteriori image reconstruction in fluorescence microscopy

An iterative image reconstruction technique employing B-Spline potential function in a Bayesian framework is proposed for fluorescence microscopy images. B-splines are piecewise polynomials with smooth transition, compact support and are the shortest polynomial splines. Incorporation of the B-spline potential function in the maximum-a-posteriori reconstruction technique resulted in improved contrast, enhanced resolution and substantial background reduction. The proposed technique is validated on simulated data as well as on the images acquired from fluorescence microscopes (widefield, confocal laser scanning fluorescence and super-resolution 4Pi microscopy). A comparative study of the proposed technique with the state-of-art maximum likelihood (ML) and maximum-a-posteriori (MAP) with quadratic potential function shows its superiority over the others. B-Spline MAP technique can find applications in several imaging modalities of fluorescence microscopy like selective plane illumination microscopy, localization microscopy and STED. (C) 2015 Author(s).

Third post-Newtonian gravitational waveforms for compact binary systems in general orbits: Instantaneous terms

We compute the instantaneous contributions to the spherical harmonic modes of gravitational waveforms from compact binary systems in general orbits up to the third post-Newtonian (PN) order. We further extend these results for compact binaries in quasielliptical orbits using the 3PN quasi-Keplerian representation of the conserved dynamics of compact binaries in eccentric orbits. Using the multipolar post-Minkowskian formalism, starting from the different mass and current-type multipole moments, we compute the spin-weighted spherical harmonic decomposition of the instantaneous part of the gravitational waveform. These are terms which are functions of the retarded time and do not depend on the history of the binary evolution. Together with the hereditary part, which depends on the binary's dynamical history, these waveforms form the basis for construction of accurate templates for the detection of gravitational wave signals from binaries moving in quasielliptical orbits.

Real-time maximum a-posteriori image reconstruction for fluorescence microscopy

Rapid reconstruction of multidimensional image is crucial for enabling real-time 3D fluorescence imaging. This becomes a key factor for imaging rapidly occurring events in the cellular environment. To facilitate real-time imaging, we have developed a graphics processing unit (GPU) based real-time maximum a-posteriori (MAP) image reconstruction system. The parallel processing capability of GPU device that consists of a large number of tiny processing cores and the adaptability of image reconstruction algorithm to parallel processing (that employ multiple independent computing modules called threads) results in high temporal resolution. Moreover, the proposed quadratic potential based MAP algorithm effectively deconvolves the images as well as suppresses the noise. The multi-node multi-threaded GPU and the Compute Unified Device Architecture (CUDA) efficiently execute the iterative image reconstruction algorithm that is similar to 200-fold faster (for large dataset) when compared to existing CPU based systems. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Reconstruction of the Disassembly Pathway of an Icosahedral Viral Capsid and Shape Determination of Two Successive Intermediates

Viral capsids derived from an icosahedral plant virus widely used in physical and nanotechnological investigations were fully dissociated into dimers by a rapid change of pH. The process was probed in vitro at high spatiotemporal resolution by time-resolved small-angle X-ray scattering using a high brilliance synchrotron source. A powerful custom-made global fitting algorithm allowed us to reconstruct the most likely pathway parametrized by a set of stoichiometric coefficients and to determine the shape of two successive intermediates by ab initio calculations. None of these two unexpected intermediates was previously identified in self-assembly experiments, which suggests that the disassembly pathway is not a mirror image of the assembly pathway. These findings shed new light on the mechanisms and the reversibility of the assembly/disassembly of natural and synthetic virus-based systems. They also demonstrate that both the structure and dynamics of an increasing number of intermediate species become accessible to experiments.

Optimum Parameter Selection in Sparse Reconstruction of Frequency-Domain Optical-Coherence Tomography Signals

For a multilayered specimen, the back-scattered signal in frequency-domain optical-coherence tomography (FDOCT) is expressible as a sum of cosines, each corresponding to a change of refractive index in the specimen. Each of the cosines represent a peak in the reconstructed tomogram. We consider a truncated cosine series representation of the signal, with the constraint that the coefficients in the basis expansion be sparse. An l(2) (sum of squared errors) data error is considered with an l(1) (summation of absolute values) constraint on the coefficients. The optimization problem is solved using Weiszfeld's iteratively reweighted least squares (IRLS) algorithm. On real FDOCT data, improved results are obtained over the standard reconstruction technique with lower levels of background measurement noise and artifacts due to a strong l(1) penalty. The previous sparse tomogram reconstruction techniques in the literature proposed collecting sparse samples, necessitating a change in the data capturing process conventionally used in FDOCT. The IRLS-based method proposed in this paper does not suffer from this drawback.

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.

Event-triggered Sampling and Reconstruction of Sparse Real-valued Trigonometric Polynomials

We propose data acquisition from continuous-time signals belonging to the class of real-valued trigonometric polynomials using an event-triggered sampling paradigm. The sampling schemes proposed are: level crossing (LC), close to extrema LC, and extrema sampling. Analysis of robustness of these schemes to jitter, and bandpass additive gaussian noise is presented. In general these sampling schemes will result in non-uniformly spaced sample instants. We address the issue of signal reconstruction from the acquired data-set by imposing structure of sparsity on the signal model to circumvent the problem of gap and density constraints. The recovery performance is contrasted amongst the various schemes and with random sampling scheme. In the proposed approach, both sampling and reconstruction are non-linear operations, and in contrast to random sampling methodologies proposed in compressive sensing these techniques may be implemented in practice with low-power circuitry.

Prior image based temporally constrained reconstruction algorithm for magnetic resonance guided high intensity focused ultrasound

Purpose: A prior image based temporally constrained reconstruction ( PITCR) algorithm was developed for obtaining accurate temperature maps having better volume coverage, and spatial, and temporal resolution than other algorithms for highly undersampled data in magnetic resonance (MR) thermometry. Methods: The proposed PITCR approach is an algorithm that gives weight to the prior image and performs accurate reconstruction in a dynamic imaging environment. The PITCR method is compared with the temporally constrained reconstruction (TCR) algorithm using pork muscle data. Results: The PITCR method provides superior performance compared to the TCR approach with highly undersampled data. The proposed approach is computationally expensive compared to the TCR approach, but this could be overcome by the advantage of reconstructing with fewer measurements. In the case of reconstruction of temperature maps from 16% of fully sampled data, the PITCR approach was 1.57x slower compared to the TCR approach, while the root mean square error using PITCR is 0.784 compared to 2.815 with the TCR scheme. Conclusions: The PITCR approach is able to perform more accurate reconstructions of temperature maps compared to the TCR approach with highly undersampled data in MR guided high intensity focused ultrasound. (C) 2015 American Association of Physicists in Medicine.

Dictionary-Learning-Based Post-Filter for HMM-Based Speech Synthesis

Oversmoothing of speech parameter trajectories is one of the causes for quality degradation of HMM-based speech synthesis. Various methods have been proposed to overcome this effect, the most recent ones being global variance (GV) and modulation-spectrum-based post-filter (MSPF). However, there is still a significant quality gap between natural and synthesized speech. In this paper, we propose a two-fold post-filtering technique to alleviate to a certain extent the oversmoothing of spectral and excitation parameter trajectories of HMM-based speech synthesis. For the spectral parameters, we propose a sparse coding-based post-filter to match the trajectories of synthetic speech to that of natural speech, and for the excitation trajectory, we introduce a perceptually motivated post-filter. Experimental evaluations show quality improvement compared with existing methods.

Study on Post Foundation of Highway Medium Guardrail

目前高速公路中央分隔带波形梁护栏立柱的实际设置中,普遍存在着由于分隔带地基强度低于压实路基,护栏立柱承载能力偏低,护栏的防护性能达不到设计要求的问题。对粘性土地基中立柱的受力情况进行了分析,并对地基为压实土与回填土两种情况进行了对比,给出了中央分隔带中立柱地基的加固方案。

Experimental Study of the Earthquake Recurrence Period and the Trend of Post-Seismic Development

In order to study the earthquake recurrence and the characteristics of earthquake series, rupture tests of rock samples and plexiglass samples were made. On rock samples, a number of acoustic emission (AE) and strain measuring points were deployed; the load was one side direct shear. The variation characteristics of AE and strain at different detecting points around the extra large fracture were observed and studied. On plexiglass samples, a series of inclined cracks were prefabricated by a small-scale compressive testing machine. The samples were then loaded on a shockproof platen, when the samples were loaded, the stress intensity factor (SIF) was determined by the laser interferometric technique and shadow optical method of caustics. The fracture conditions such as material toughness around the extra large fracture were also studied. From those experimental results and the theory of fracture mechanics, the earthquake recurrence period and the trend of post-seismic development were studied.