Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

Metabolic changes in rat prefrontal cortex and hippocampus induced by chronic morphine treatment studied ex vivo by high resolution H-1 NMR spectroscopy

Ex vivo H-1 NMR spectroscopy was used to measure changes in the concentrations of cerebral metabolites in the prefrontal cortex (PFC) and hippocampus of rats subjected to repeated morphine treatment known to cause tolerance/dependence. The results show th

Restoration of images and 3D data to higher resolution by deconvolution with sparsity regularization

Image convolution is conventionally approximated by the LTI discrete model. It is well recognized that the higher the sampling rate, the better is the approximation. However sometimes images or 3D data are only available at a lower sampling rate due to physical constraints of the imaging system. In this paper, we model the under-sampled observation as the result of combining convolution and subsampling. Because the wavelet coefficients of piecewise smooth images tend to be sparse and well modelled by tree-like structures, we propose the L0 reweighted-L2 minimization (L0RL2 ) algorithm to solve this problem. This promotes model-based sparsity by minimizing the reweighted L2 norm, which approximates the L0 norm, and by enforcing a tree model over the weights. We test the algorithm on 3 examples: a simple ring, the cameraman image and a 3D microscope dataset; and show that good results can be obtained. © 2010 IEEE.

A microfluidic device for high density hydrodynamic cell trapping, growth and super-resolution imaging

Super-Resolution imaging techniques such as Fluorescent Photo-Activation Localisation Microscopy (FPALM) have created a powerful new toolkit for investigating living cells, however a simple platform for growing, trapping, holding and controlling the cells is needed before the approach can become truly widespread. We present a microfluidic device formed in polydimethylsiloxane (PDMS) with a fluidic design which traps cells in a high-density array of wells and holds them very still throughout the life cycle, using hydrodynamic forces only. The device meets or exceeds all the necessary criteria for FPALM imaging of Schizosaccharomyces pombe and is designed to remain flexible, robust and easy to use. © 2011 IEEE.

A unifying resolution-independent formulation for early vision

We present a model for early vision tasks such as denoising, super-resolution, deblurring, and demosaicing. The model provides a resolution-independent representation of discrete images which admits a truly rotationally invariant prior. The model generalizes several existing approaches: variational methods, finite element methods, and discrete random fields. The primary contribution is a novel energy functional which has not previously been written down, which combines the discrete measurements from pixels with a continuous-domain world viewed through continous-domain point-spread functions. The value of the functional is that simple priors (such as total variation and generalizations) on the continous-domain world become realistic priors on the sampled images. We show that despite its apparent complexity, optimization of this model depends on just a few computational primitives, which although tedious to derive, can now be reused in many domains. We define a set of optimization algorithms which greatly overcome the apparent complexity of this model, and make possible its practical application. New experimental results include infinite-resolution upsampling, and a method for obtaining subpixel superpixels. © 2012 IEEE.

Carbon nanotubes: carbon nanotube based high resolution holograms (adv. Mater. 44/2012).

By using carbon nanotubes as the smallest possible scattering element, light can be diffracted in a highly controlled manner to produce a 2D image, as reported by Haider Butt and co-workers on page OP331. An array of carbon nanotubes is elegantly patterned to produce a high resolution hologram. In response to incident light on the hologram, a high contrast and wide field of view "CAMBRIDGE" image is produced.

High-resolution γ-ray spectroscopy: A versatile tool for nuclear β-decay studies at TRIUMF-ISAC

High-resolution γ-ray spectroscopy is essential to fully exploit the unique, high-quality beams available at the next generation of radioactive ion beam facilities such as the TRIUMF isotope separator and accelerator (ISAC). The 8π spectrometer, which consists of 20 Compton-suppressed HPGe detectors, has recently been reconfigured for a vigorous research programme in weak interaction and nuclear structure physics. With the addition of a variety of ancillary detectors it has become the world's most powerful device dedicated to β-decay studies. This paper provides a brief overview of the apparatus and highlights from recent experiments. © 2005 IOP Publishing Ltd.

Carbon nanotube based high resolution holograms.

Carbon nanotubes are used as the smallest possible scattering element for diffracting light in a highly controlled manner to produce a 2D image. An array of carbon nanotubes is elegantly patterned to produce a high resolution hologram. In response to incident light on the hologram, a high contrast and wide field of view CAMBRIDGE image is produced.

A high-resolution atlas and statistical model of the human heart from multislice CT

Atlases and statistical models play important roles in the personalization and simulation of cardiac physiology. For the study of the heart, however, the construction of comprehensive atlases and spatio-temporal models is faced with a number of challenges, in particular the need to handle large and highly variable image datasets, the multi-region nature of the heart, and the presence of complex as well as small cardiovascular structures. In this paper, we present a detailed atlas and spatio-temporal statistical model of the human heart based on a large population of 3D+time multi-slice computed tomography sequences, and the framework for its construction. It uses spatial normalization based on nonrigid image registration to synthesize a population mean image and establish the spatial relationships between the mean and the subjects in the population. Temporal image registration is then applied to resolve each subject-specific cardiac motion and the resulting transformations are used to warp a surface mesh representation of the atlas to fit the images of the remaining cardiac phases in each subject. Subsequently, we demonstrate the construction of a spatio-temporal statistical model of shape such that the inter-subject and dynamic sources of variation are suitably separated. The framework is applied to a 3D+time data set of 138 subjects. The data is drawn from a variety of pathologies, which benefits its generalization to new subjects and physiological studies. The obtained level of detail and the extendability of the atlas present an advantage over most cardiac models published previously. © 1982-2012 IEEE.

Airfoil flow and noise computation using monotonically integrated large eddy simulation and acoustic analogy: Effect of the grid resolution.

A new scalable Monotonically Integrated Large Eddy Simulation (MILES) method based on the Compact Accurately Boundary-Adjusting high-REsolution Technique (CABARET) has been applied for the simulation of unsteady flow around NACA0012 airfoil at Re = 400,000 and M = 0.058. The flow solution is coupled with the Ffowcs Williams-Hawkings formulation for far-field noise prediction. The computational modeling results are presented for several computational grid resolutions: 8, 16, and 32 million grid cells and compared with the experimental data available.