BarraCUDA - a fast short read sequence aligner using graphics processing units.

BACKGROUND: With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. FINDINGS: Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. CONCLUSIONS: BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology.BarraCUDA is currently available from http://seqbarracuda.sf.net.

Polarization multiplexed write-once-read-many optical data storage in bacteriorhodopsin films

In polymeric films of bacteriorhodopsin (BR) a photoconversion product, which was named the F620 state, was observed on excitation of the film with 532 nm nanosecond laser pulses. This photoproduct shows a strong nonlinear absorption. Such BR films can be used for write-once-read-many (WORM) optical data storage. We demonstrate that a photoproduct similar or even identical to that obtained with nanosecond pulses is generated on excitation with 532 mn femtosecond pulses. This photoproduct also shows strong anisotropic absorption, which facilitates polarization storage of data. The product is thermally stable and is irretrievable to the initial B state either by photochemical reaction or through a thermal pathway. The experimental results indicate that the product is formed by a two-photon absorption process. Optical WORM storage is demonstrated by use of two polarization states, but more polarization states may be used. The combination of polarization data multiplexing and extremely short recording time in the femtosecond range enables very high data volumes to be stored within a very short time. (c) 2005 Optical Society of America.

应变异质结外延材料的缓冲层厚度与Frank-Read源的关系研究

基于能量最小近似模型,研究了应变异质结外延材料中,产生Frank-Read源以释放失配应力所需GeSi合金缓冲层的厚度。对Ge_xSi_(1-x)/Si进行了具体计算,其结果表明:产生Frank-Read源时缓冲层厚度要比临界厚度大得多,L_(min)=1300A是钉扎点间的最小距离。计算结果与LeGoues等的实验结果相符。就作者所知,计算产生Frank-Read源时GeSi合金缓冲层厚度的工作,以前未见报道。

Realization of write-once-read-many-times memory devices based on poly(N-vinylcarbazole) by thermally annealing

A nonvolatile write-once-read-many-time (WORM-time) memory device based on poly(N-vinylcarbazole) (PVK) films was realized by thermally annealing. The device can be fabricated using a simple spin coat method. It was found that the control of PVK film surface morphology by thermally annealing plays an important role in achieving the WORM memory properties. The memory device showed an ON/OFF current ratio as high as 10(4) and the retention time was over 2000 s without degradation.

The morphology control of pentacene for write-once-read-many-times memory devices

We realized write-once-read-many-times (WORM) memory devices based on pentacene and demonstrated that the morphology control of the vacuum deposited pentacene thin film is greatly important for achieving the unique nonvolatile memory properties. The resulted memory devices show a high ON/OFF current ratio (10(4)), long retention time (over 12 h), and good storage stability (over 240 h). The reduction of the barrier height caused by a large interface dipole and the damage of the interface dipole under a critical bias voltage have been used to explain the transition processes.

Write-Once Read-Many-Times Memory Based on a Single Layer of Pentacene

We realized an organic electrical memory device with a simple structure based on single-layer pentacene film embedded between Al and ITO electrodes. The optimization of the thickness and deposition rate of pentacene resulted in a reliable device with an on/off current ratio as high as nearly 10(6), which was two orders of magnitude higher than previous results, and the storage time was more than 576 h. The current transition process is attributed to the formation and damage of the Interface dipole at different electric fields, in which the current conduction showed a transition from ohmic conductive current to Fowler-Nordheim tunneling current. After the transition from ON- to OFF-state, the device tended to remain in the OFF-State even when the applied voltage was removed, which indicated that the device was very promising for write-once read-many-times memory.

I Cannot Tell: Edward Thomas's Uncertainties

Poster, Jeremy, 'I Cannot Tell: Edward Thomas's Uncertainties', In: 'Branch-Lines: Edward Thomas and Contemporary Poetry', Guy Cuthbertson & Lucy Newlyn (eds), (London: Enitharmon Press), pp.264, 2007 RAE2008

Writing Home : Martin Walser's Ein fliehendes Pferd as Anti-Tourist Literature

Wilkinson, Jane, 'Writing Home: Martin Walser's Ein fliehendes Pferd as Anti-Tourist Literature', Journal of Tourism and Cultural Change (2006) 4(3) pp.001-017 RAE2008

Memoirs and sermons of Wm. J. Armstrong / edited by Hollis Read.

http://www.archive.org/details/memoirsandsermon00armsiala

Islam and missions : being papers read at the Second Missionary Conference on behalf of the Mohammedan World at Lucknow, January 23-28, 1911 / edited by E.M. Wherry, S.M. Zwemer, C.G. Mylrea.

http://www.archive.org/details/islamandmissions012033mbp

By canoe and dog-train among the Cree and Salteaux Indians / by Egerton Ryerson Young ; with an introduction by Mark Guy Pearse.

http://www.archive.org/details/bycanoedogtraina00younrich

Christology in the Epistle to the Hebrews: Martin Luther's Reception of John Chrysostom

Throughout the history of the Church, the Epistle to the Hebrews has been one of the most puzzling letters in the Canon, particularly regarding the implications of understanding the person of Jesus Christ. John Chrysostom, an important patristic writer, is acknowledged to have made significant contributions to the exegesis of this letter. Chrysostom's thought became the norm for traditional thinking and interpretation of this letter in the Middle Ages. Martin Luther's reception of Chrysostom's Homilies on Hebrews presents a unique interpretation that some scholars may describe as the "Reformation Discovery" on Hebrews. In tracing Luther's reception and appropriation of Chrysostom's exegesis of the letter to the Hebrews, there is a noticeable and significant shift in Christological interpretation. Whether or not these modifications were necessary is a matter of debate; however, they do reflect Luther's contextual and existential questions regarding faith, Christ and knowledge of God, which is evident in his Lectures on Hebrews.

Nurturing Change: Lilly Martin Spencer's Images of Children

This dissertation is the first full-length study to concentrate on American genre painter Lilly Martin Spencer's images of children, which constituted nearly one half of her saleable production during the height of her artistic career from 1848 to 1869. At this time, many young parents received advice regarding child rearing through books and other publications, having moved away from their families of origin in search of employment. These literatures, which gained in popularity from the 1830s onward, focused on spiritual, emotional, and disciplinary matters. My study considers four major themes from the period's writing on child nurture that changed over time, including depravity and innocence, parent/child bonding, standards of behavior and moral rectitude, and children's influence on adults. It demonstrates how Spencer's paintings, prints, and drawings featuring children supported and challenged these evolving ideologies, helping to shed light not only on the artist's reception of child-rearing advice, but also on its possible impact on her middle-class audience, to whom she closely catered. In four chapters, I investigate Spencer's images of sleeping children as visual equivalents of contemporary consolation literature during a time of high infant and child mortality rates; her paintings of parent/child interaction as promoting separation from mothers and emotional bonding with fathers; her prints of mischievous children as both considering changing ideals about children's behavior and comforting Anglo-American citizens afraid of what they saw as threatening minority groups; and her pictures with Civil War and Reconstruction subject matter as contending with the popular concept of the moral utility of children. By framing my interpretations of Spencer's output around key issues in the period's dynamic child-nurture literature, I advance new comprehensive readings of many of her most well-known paintings, including Domestic Happiness, Fi, Fo, Fum!, and The Pic Nic or the Fourth of July. I also consider work often overlooked by other art historians, but which received acclaim in Spencer's own time, including the lithographs of children made after her designs, and the allegorical painting Truth Unveiling Falsehood. Significantly, I provide the first in-depth analysis of a newly rediscovered Reconstruction-era painting, The Home of the Red, White, and Blue.

Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.