Pressurized H-2 rf Cavities in Ionizing Beams and Magnetic Fields

A major technological challenge in building a muon cooling channel is operating rf cavities in multitesla external magnetic fields. We report the first proof-of-principle experiment of a high pressure gas-filled rf cavity for use with intense ionizing beams and strong external magnetic fields. rf power consumption by beam-induced plasma is investigated with hydrogen and deuterium gases with pressures between 20 and 100 atm and peak rf gradients between 5 and 50 MV/m. The low pressure case agrees well with an analytical model based on electron and ion mobilities. Varying concentrations of oxygen gas are investigated to remove free electrons from the cavity and reduce the rf power consumption. Measurements of the electron attachment time to oxygen and rate of ion-ion recombination are also made. Additionally, we demonstrate the operation of the gas-filled rf cavity in a solenoidal field of up to 3 T, finding no major magnetic field dependence. All these results indicate that a high pressure gas-filled cavity is a viable technology for muon ionization cooling.open1

Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains

<p>Abstract</p> <p>Background</p> <p>Many plant genomes are resistant to whole-genome assembly due to an abundance of repetitive sequence, leading to the development of gene-rich sequencing techniques. Two such techniques are hypomethylated partial restriction (HMPR) and methylation spanning linker libraries (MSLL). These libraries differ from other gene-rich datasets in having larger insert sizes, and the MSLL clones are designed to provide reads localized to "epigenetic boundaries" where methylation begins or ends.</p> <p>Results</p> <p>A large-scale study in maize generated 40,299 HMPR sequences and 80,723 MSLL sequences, including MSLL clones exceeding 100 kb. The paired end reads of MSLL and HMPR clones were shown to be effective in linking existing gene-rich sequences into scaffolds. In addition, it was shown that the MSLL clones can be used for anchoring these scaffolds to a BAC-based physical map. The MSLL end reads effectively identified epigenetic boundaries, as indicated by their preferential alignment to regions upstream and downstream from annotated genes. The ability to precisely map long stretches of fully methylated DNA sequence is a unique outcome of MSLL analysis, and was also shown to provide evidence for errors in gene identification. MSLL clones were observed to be significantly more repeat-rich in their interiors than in their end reads, confirming the correlation between methylation and retroelement content. Both MSLL and HMPR reads were found to be substantially gene-enriched, with the <it>Sal</it>I MSLL libraries being the most highly enriched (31% align to an EST contig), while the HMPR clones exhibited exceptional depletion of repetitive DNA (to ~11%). These two techniques were compared with other gene-enrichment methods, and shown to be complementary.</p> <p>Conclusion</p> <p>MSLL technology provides an unparalleled approach for mapping the epigenetic status of repetitive blocks and for identifying sequences mis-identified as genes. Although the types and natures of epigenetic boundaries are barely understood at this time, MSLL technology flags both approximate boundaries and methylated genes that deserve additional investigation. MSLL and HMPR sequences provide a valuable resource for maize genome annotation, and are a uniquely valuable complement to any plant genome sequencing project. In order to make these results fully accessible to the community, a web display was developed that shows the alignment of MSLL, HMPR, and other gene-rich sequences to the BACs; this display is continually updated with the latest ESTs and BAC sequences.</p

Gradient critical phenomena in the Ising quantum chain: surface behaviour

We consider the influence of a power-law deviation from the critical coupling such that the system is critical at its surface. We develop a scaling theory showing that such a perturbation introduces a new length scale which governs the scaling behaviour of the density profiles as well as the finite-size behaviour of the surface properties. Exact results are obtained for the Ising quantum chain when the perturbation varies linearly whereas the quadratic perturbation is mainly studied numerically. The scaling theory is well confirmed in both cases

The European Photon Imaging Camera on XMM-Newton: The MOS Cameras

The EPIC focal plane imaging spectrometers on XMM-Newton use CCDs to record the images and spectra of celestial X-ray sources focused by the three X-ray mirrors. There is one camera at the focus of each mirror; two of the cameras contain seven MOS CCDs, while the third uses twelve PN CCDs, defining a circular field of view of 30 arcmin diameter in each case. The CCDs were specially developed for EPIC, and combine high quality imaging with spectral resolution close to the Fano limit. A filter wheel carrying three kinds of X-ray transparent light blocking filter, a fully closed, and a fully open position, is fitted to each EPIC instrument. The CCDs are cooled passively and are under full closed loop thermal control. A radio-active source is fitted for internal calibration. Data are processed on-board to save telemetry by removing cosmic ray tracks, and generating X-ray event files; a variety of different instrument modes are available to increase the dynamic range of the instrument and to enable fast timing. The instruments were calibrated using laboratory X-ray beams, and synchrotron generated monochromatic X-ray beams before launch; in-orbit calibration makes use of a variety of celestial X-ray targets. The current calibration is better than 10% over the entire energy range of 0.2 to 10 keV. All three instruments survived launch and are performing nominally in orbit. In particular full field-of-view coverage is available, all electronic modes work, and the energy resolution is close to pre-launch values. Radiation damage is well within pre-launch predictions and does not yet impact on the energy resolution. The scientific results from EPIC amply fulfil pre-launch expectations.Comment: 9 pages, 11 figures, accepted for publication in the A&A Special Issue on XMM-Newto

MKID Exoplanet Camera for Subaru SCExAO

We present the MKID Exoplanet Camera (MEC), a z through J band (800–1400 nm) integral field spectrograph located behind The Subaru Coronagraphic Extreme Adaptive Optics (SCExAO) at the Subaru Telescope on Maunakea that utilizes Microwave Kinetic Inductance Detectors (MKIDs) as the enabling technology for high contrast imaging. MEC is the first permanently deployed near-infrared MKID instrument and is designed to operate both as an IFU, and as a focal plane wavefront sensor in a multi-kHz feedback loop with SCExAO. The read noise free, fast time domain information attainable by MKIDs allows for the direct probing of fast speckle fluctuations that currently limit the performance of most high contrast imaging systems on the ground and will help MEC achieve its ultimate goal of reaching contrasts of 10⁻⁷ at 2 λ/D. Here we outline the instrument details of MEC including the hardware, firmware, and data reduction and analysis pipeline. We then discuss MEC's current on-sky performance and end with future upgrades and plans

The MKID Exoplanet Camera for Subaru SCExAO

We present the MKID Exoplanet Camera (MEC), a z through J band (800 - 1400 nm) integral field spectrograph located behind The Subaru Coronagraphic Extreme Adaptive Optics (SCExAO) at the Subaru Telescope on Maunakea that utilizes Microwave Kinetic Inductance Detectors (MKIDs) as the enabling technology for high contrast imaging. MEC is the first permanently deployed near-infrared MKID instrument and is designed to operate both as an IFU, and as a focal plane wavefront sensor in a multi-kHz feedback loop with SCExAO. The read noise free, fast time domain information attainable by MKIDs allows for the direct probing of fast speckle fluctuations that currently limit the performance of most high contrast imaging systems on the ground and will help MEC achieve its ultimate goal of reaching contrasts of $10^{-7}$ at 2$\lambda / D$. Here we outline the instrument details of MEC including the hardware, firmware, and data reduction and analysis pipeline. We then discuss MEC's current on-sky performance and end with future upgrades and plans.Comment: To be published in Publications of the Astronomical Society of the Pacifi

Radio and submillimetre observations of wind structure in zeta Pup

We present radio and submillimetre observations of the O4I(n)f star zeta Pup, and discuss structure in the outer region of its wind (~ 10-100 R*). The properties of bremsstrahlung, the dominant emission process at these wavelengths, make it sensitive to structure and allow us to study how the amount of structure changes in the wind by comparing the fluxes at different wavelengths. To look for variability, we acquired 3.6 and 6 cm observations with the Australia Telescope Compact Array (ATCA). We supplemented these with archive observations from the NRAO Very Large Array (VLA). We did not find variability at more than the +- 20 % level. The long integration time does allow an accurate determination of the fluxes at 3.6 and 6 cm. Converting these fluxes into a mass loss rate, we find Mdot = 3.5 x 10^{-6} Msun/yr. This value confirms the significant discrepancy with the mass loss rate derived from the Halpha profile, making zeta Pup an exception to the usually good agreement between Halpha and radio mass loss rates. We also observed zeta Pup at 850 mum with the James Clerk Maxwell Telescope (JCMT) and at 20 cm with the VLA. A smooth wind model shows that the millimetre fluxes are too high compared to the radio fluxes. While recombination of helium in the outer wind cannot be discounted as an explanation, the wealth of evidence for structure strongly suggests this as the explanation for the discrepancy. Model calculations show that the structure needs to be present in the inner ~ 70 R* of the wind, but that it decays significantly, or maybe even disappears, beyond that radius.Comment: 13 pages, 8 figures, to be published in Astronomy and Astrophysic

The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications

Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals. Results: We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes. Conclusion: Because the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently evolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as previously suggested