Contrasting high-resolution characteristic shock-capturing methods in aeroacoustic test problems

Two shock-capturing methods are considered. One is based on a standard conservative Roe scheme with van Leer's MUSCL variable extrapolation method applied to characteristic variables and a Runge-Kutta time stepping scheme. The other is based on the novel CABARET space-time scheme, which uses two sets of staggered variables, one for the conservation step and the other for characteristic splitting into local Riemann invariants. The methods are compared in a range of 2-D inviscid compressible flow test cases. Copyright © 2008 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

Self-aligned high-resolution printed polymer transistors

A process to fabricate solution-processable thin-film transistors (TFTs) with a one-step self-aligned definition of the dimensions in all functional layers is demonstrated. The TFT-channel, semiconductor materials, and effective gate dimention of different layers are determined by a one-step imprint process and the subsequent pattern transfer without the need for multiple patterning and mask alignment. The process is compatible with fabrication of large-scale circuits. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fabrication and testing of a high resolution extensometer based on resonant MEMS strain sensors

A novel type of linear extensometer with exceptionally high resolution of 4 nm based on MEMS resonant strain sensors bonded on steel and operating in a vacuum package is presented. The tool is implemented by means of a steel thin bar that can be pre-stressed in tension within two fixing anchors. The extension of the bar is detected by using two vacuum-packaged resonant MEMS double- ended tuning fork (DETF) sensors bonded on the bar with epoxy glue, one of which is utilized for temperature compensation. Both sensors are driven by a closed loop self-oscillating transresistance amplifier feedback scheme implemented on a PCB (Printed Circuit Board). On the same board, a microcontroller-based frequency measurement circuit is also implemented, which is able to count the square wave fronts of the MEMS oscillator output with a resolution of 20 nsec. The system provides a frequency noise of 0.2 Hz corresponding to an extension resolution of 4 nm for the extensometer. Nearly perfect temperature compensation of the frequency output is achieved in the temperature range 20-35 C using the reference sensor. © 2011 IEEE.

Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.

Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only approximately 5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation.

Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation

Background: Despite the small number of ursid species, bear phylogeny has long been a focus of study due to their conservation value, as all bear genera have been classified as endangered at either the species or subspecies level. The Ursidae family repre

Predicting the performance of an office under climate change: A study of metrics, sensitivity and zonal resolution

Climate change is expected to have significant impact on the future thermal performance of buildings. Building simulation and sensitivity analysis can be employed to predict these impacts, guiding interventions to adapt buildings to future conditions. This article explores the use of simulation to study the impact of climate change on a theoretical office building in the UK, employing a probabilistic approach. The work studies (1) appropriate performance metrics and underlying modelling assumptions, (2) sensitivity of computational results to identify key design parameters and (3) the impact of zonal resolution. The conclusions highlight the importance of assumptions in the field of electricity conversion factors, proper management of internal heat gains, and the need to use an appropriately detailed zonal resolution. © 2010 Elsevier B.V. All rights reserved.

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis(1) and human(2), demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

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.