Low-resistance Ni-based Schottky diodes on freestanding n-GaN

Schottky diodes formed on a low doped (5 x 10(16) cm(-3)) n-type GaN epilayer grown on a n(+) freestanding GaN substrate were studied. The temperature dependent electrical characteristics of Ni contacts on the as-grown material are compared with an aqueous, potassium hydroxide (KOH) treated surface. In both cases the diodes are dominated by thermionic emission in forward bias, with low idealities (1.04 at room temperature) which decrease with increasing temperature, reaching 1.03 at 413 K. The Schottky barrier height is 0.79 +/- 0.05 eV for the as-grown surface compared with 0.85 +/- 0.05 eV for the KOH treated surface at room temperature. This is consistent with an inhomogeneous barrier distribution. The specific on-state resistance of the diodes is 0.57 m Omega cm(2) The KOH treatment reduces the room temperature reverse leakage current density at -30 V to 1 x 10(-5) A cm(-2) compared to 6 x 10(-2) A cm(-2) for the as-grown samples. (C) 2007 American Institute of Physics. (DOI:10.1063/1.2799739

Ultrasmall radio frequency driven microhollow cathode discharge

We have operated 25-100 mu m diameter radio frequency microhollow cathode discharges stably, for many hours, in neon and in argon. Electrical and spectroscopic measurements were used to explore three possible electron heating modes and obtain detail regarding the electron energy distribution. Analysis points to the possibility of pendular electron heating at low voltages. (c) 2008 American Institute of Physics

Nonlinear vertical oscillations of a particle in a sheath of a rf discharge

A new simple method to measure the spatial distribution of the electric field in the plasma sheath is proposed. The method is based on the experimental investigation of vertical oscillations of a single particle in the sheath of a low-pressure radio-frequency discharge. It is shown that the oscillations become strongly nonlinear and secondary harmonics are generated as the amplitude increases. The theory of anharmonic oscillations provides a good qualitative description of the data and gives estimates for the first two anharmonic terms in an expansion of the sheath potential around the particle equilibrium.Comment: 11 pages, 4 figure

Biomechanical comparison of the pullout properties of external skeletal fixation pins in the tibiae of intact and ovariectomised ewes.

The pin-bone interface is the least stable component of the external skeletal fixator. Concerns exist regarding the ability to obtain adequate implant purchase in poor quality bone. Consequently, reduced bone quality has been viewed as a contra-indication for the use of external skeletal fixators. The aim of this study was to investigate the holding power of two different fixator pin designs in bone from entire and ovariectomised sheep. Thirty-two aged ewes were divided into two groups. Group 1 were controls, and Group 2 were ovariectomised (OVX). The ewes were sacrificed 12 months post-ovariectomy and five pairs of tibiae were harvested from each group. The holding power of cortical and cancellous fixator pins was assessed at five standardised locations on each tibia. An increase in mean cortical thickness was noted in the OVX group. The holding power of cancellous fixator pins was superior to that of cortical pins, irrespective of whether or not ovariectomy had been performed. Cancellous pins had an increased holding power in post ovariectomy bone compared to control bone. Cortical pin performance was not affected by ovariectomy. There was a lack of correlation between the incidence of insertional fractures of the far cortex and implant holding power. The results raise questions over the effectiveness of ovariectomy in establishing osteopaenic bone suitable for assessing implant performance, hence further investigations are warranted

Regulation of phenylacetic acid uptake is σ54 dependent in Pseudomonas putida CA-3

<p>Abstract</p> <p>Background</p> <p>Styrene is a toxic and potentially carcinogenic alkenylbenzene used extensively in the polymer processing industry. Significant quantities of contaminated liquid waste are generated annually as a consequence. However, styrene is not a true xenobiotic and microbial pathways for its aerobic assimilation, via an intermediate, phenylacetic acid, have been identified in a diverse range of environmental isolates. The potential for microbial bioremediation of styrene waste has received considerable research attention over the last number of years. As a result the structure, organisation and encoded function of the genes responsible for styrene and phenylacetic acid sensing, uptake and catabolism have been elucidated. However, a limited understanding persists in relation to host specific regulatory molecules which may impart additional control over these pathways. In this study the styrene degrader <it>Pseudomonas putida </it>CA-3 was subjected to random mini-Tn<it>5 </it>mutagenesis and mutants screened for altered styrene/phenylacetic acid utilisation profiles potentially linked to non-catabolon encoded regulatory influences.</p> <p>Results</p> <p>One mutant, D7, capable of growth on styrene, but not on phenylacetic acid, harboured a Tn<it>5 </it>insertion in the <it>rpoN </it>gene encoding σ54. Complementation of the D7 mutant with the wild type <it>rpoN </it>gene restored the ability of this strain to utilise phenylacetic acid as a sole carbon source. Subsequent RT-PCR analyses revealed that a phenylacetate permease, PaaL, was expressed in wild type <it>P. putida </it>CA-3 cells utilising styrene or phenylacetic acid, but could not be detected in the disrupted D7 mutant. Expression of plasmid borne <it>paaL </it>in mutant D7 was found to fully restore the phenylacetic acid utilisation capacity of the strain to wild type levels. Bioinformatic analysis of the <it>paaL </it>promoter from <it>P. putida </it>CA-3 revealed two σ⁵⁴consensus binding sites in a non-archetypal configuration, with the transcriptional start site being resolved by primer extension analysis. Comparative analyses of genomes encoding phenylacetyl CoA, (PACoA), catabolic operons identified a common association among styrene degradation linked PACoA catabolons in <it>Pseudomonas </it>species studied to date.</p> <p>Conclusions</p> <p>In summary, this is the first study to report RpoN dependent transcriptional activation of the PACoA catabolon <it>paaL </it>gene, encoding a transport protein essential for phenylacetic acid utilisation in <it>P. putida </it>CA-3. Bioinformatic analysis is provided to suggest this regulatory link may be common among styrene degrading <it>Pseudomonads</it>.</p

Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data

Background: MicroRNAs (miRNAs) are short, non-coding RNA regulators of protein coding genes. miRNAs play a very important role in diverse biological processes and various diseases. Many algorithms are able to predict miRNA genes and their targets, but their transcription regulation is still under investigation. It is generally believed that intragenic miRNAs (located in introns or exons of protein coding genes) are co-transcribed with their host genes and most intergenic miRNAs transcribed from their own RNA polymerase II (Pol II) promoter. However, the length of the primary transcripts and promoter organization is currently unknown. Methodology: We performed Pol II chromatin immunoprecipitation (ChIP)-chip using a custom array surrounding regions of known miRNA genes. To identify the true core transcription start sites of the miRNA genes we developed a new tool (CPPP). We showed that miRNA genes can be transcribed from promoters located several kilobases away and that their promoters share the same general features as those of protein coding genes. Finally, we found evidence that as many as 26% of the intragenic miRNAs may be transcribed from their own unique promoters. Conclusion: miRNA promoters have similar features to those of protein coding genes, but miRNA transcript organization is more complex. © 2009 Corcoran et al

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions. To reliably characterize such condition-specific regulatory binding we introduce MultiGPS, an integrated machine learning approach for the analysis of multiple related ChIP-seq experiments. MultiGPS is based on a generalized Expectation Maximization framework that shares information across multiple experiments for binding event discovery. We demonstrate that our framework enables the simultaneous modeling of sparse condition-specific binding changes, sequence dependence, and replicate-specific noise sources. MultiGPS encourages consistency in reported binding event locations across multiple-condition ChIP-seq datasets and provides accurate estimation of ChIP enrichment levels at each event. MultiGPS's multi-experiment modeling approach thus provides a reliable platform for detecting differential binding enrichment across experimental conditions. We demonstrate the advantages of MultiGPS with an analysis of Cdx2 binding in three distinct developmental contexts. By accurately characterizing condition-specific Cdx2 binding, MultiGPS enables novel insight into the mechanistic basis of Cdx2 site selectivity. Specifically, the condition-specific Cdx2 sites characterized by MultiGPS are highly associated with pre-existing genomic context, suggesting that such sites are pre-determined by cell-specific regulatory architecture. However, MultiGPS-defined condition-independent sites are not predicted by pre-existing regulatory signals, suggesting that Cdx2 can bind to a subset of locations regardless of genomic environment. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2–5.National Science Foundation (U.S.) (Graduate Research Fellowship under Grant 0645960)National Institutes of Health (U.S.) (grant P01 NS055923)Pennsylvania State University. Center for Eukaryotic Gene Regulatio

The radio/gamma-ray connection in Active Galactic Nuclei in the era of the Fermi Large Area Telescope

We present a detailed statistical analysis of the correlation between radio and gamma-ray emission of the Active Galactic Nuclei (AGN) detected by Fermi during its first year of operation, with the largest datasets ever used for this purpose. We use both archival interferometric 8.4 GHz data (from the VLA and ATCA, for the full sample of 599 sources) and concurrent single-dish 15 GHz measurements from the Owens Valley Radio Observatory (OVRO, for a sub sample of 199 objects). Our unprecedentedly large sample permits us to assess with high accuracy the statistical significance of the correlation, using a surrogate-data method designed to simultaneously account for common-distance bias and the effect of a limited dynamical range in the observed quantities. We find that the statistical significance of a positive correlation between the cm radio and the broad band (E>100 MeV) gamma-ray energy flux is very high for the whole AGN sample, with a probability <1e-7 for the correlation appearing by chance. Using the OVRO data, we find that concurrent data improve the significance of the correlation from 1.6e-6 to 9.0e-8. Our large sample size allows us to study the dependence of correlation strength and significance on specific source types and gamma-ray energy band. We find that the correlation is very significant (chance probability <1e-7) for both FSRQs and BL Lacs separately; a dependence of the correlation strength on the considered gamma-ray energy band is also present, but additional data will be necessary to constrain its significance.Comment: Accepted for publications by ApJ. Contact authors: M. Giroletti, V. Pavlidou, A. Reime

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

Hox genes controlling motor neuron subtype identity are expressed in rostrocaudal patterns that are spatially and temporally collinear with their chromosomal organization. Here we demonstrate that Hox chromatin is subdivided into discrete domains that are controlled by rostrocaudal patterning signals that trigger rapid, domain-wide clearance of repressive histone H3 Lys27 trimethylation (H3K27me3) polycomb modifications. Treatment of differentiating mouse neural progenitors with retinoic acid leads to activation and binding of retinoic acid receptors (RARs) to the Hox1–Hox5 chromatin domains, which is followed by a rapid domain-wide removal of H3K27me3 and acquisition of cervical spinal identity. Wnt and fibroblast growth factor (FGF) signals induce expression of the Cdx2 transcription factor that binds and clears H3K27me3 from the Hox1–Hox9 chromatin domains, leading to specification of brachial or thoracic spinal identity. We propose that rapid clearance of repressive modifications in response to transient patterning signals encodes global rostrocaudal neural identity and that maintenance of these chromatin domains ensures the transmission of positional identity to postmitotic motor neurons later in development.Leona M. and Harry B. Helmsley Charitable TrustNational Institutes of Health (U.S.) (Grant P01 NS055923)Smith Family Foundatio