The Arecibo HII Region Discovery Survey

We report the detection of radio recombination line emission (RRL) using the Arecibo Observatory at X-band (9GHz, 3cm) from 37 previously unknown HII regions in the Galactic zone 66 deg. > l > 31 deg. and |b| < 1 deg. This Arecibo HII Region Discovery Survey (Arecibo HRDS) is a continuation of the Green Bank Telescope (GBT) HRDS. The targets for the Arecibo HRDS have spatially coincident 24 micron and 20 cm emission of a similar angular morphology and extent. To take advantage of Arecibo's sensitivity and small beam size, sources in this sample are fainter, smaller in angle, or in more crowded fields compared to those of the GBT HRDS. These Arecibo nebulae are some of the faintest HII regions ever detected in RRL emission. Our detection rate is 58%, which is low compared to the 95% detection rate for GBT HRDS targets. We derive kinematic distances to 23 of the Arecibo HRDS detections. Four nebulae have negative LSR velocities and are thus unambiguously in the outer Galaxy. The remaining sources are at the tangent point distance or farther. We identify a large, diffuse HII region complex that has an associated HI and 13CO shell. The ~90 pc diameter of the G52L nebula in this complex may be the largest Galactic HII region known, and yet it has escaped previous detection.Comment: Accepted to ApJ Data can be found here: http://go.nrao.edu/hrd

Unexpected Accumulation of ncm\u3csup\u3e5\u3c/sup\u3eU and ncm\u3csup\u3e5\u3c/sup\u3es\u3csup\u3e2\u3c/sup\u3eU in a \u3cem\u3etrm9\u3c/em\u3e Mutant Suggests an Additional Step in the Synthesis of mcm\u3csup\u3e5\u3c/sup\u3eU and mcm\u3csup\u3e5\u3c/sup\u3es\u3csup\u3e2\u3c/sup\u3eU

Background Transfer RNAs are synthesized as a primary transcript that is processed to produce a mature tRNA. As part of the maturation process, a subset of the nucleosides are modified. Modifications in the anticodon region often modulate the decoding ability of the tRNA. At position 34, the majority of yeast cytosolic tRNA species that have a uridine are modified to 5-carbamoylmethyluridine (ncm5U), 5-carbamoylmethyl-2′-O-methyluridine (ncm5Um), 5-methoxycarbonylmethyl-uridine (mcm5U) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U). The formation of mcm5 and ncm5 side chains involves a complex pathway, where the last step in formation of mcm5 is a methyl esterification of cm5 dependent on the Trm9 and Trm112 proteins. Methodology and Principal Findings Both Trm9 and Trm112 are required for the last step in formation of mcm5 side chains at wobble uridines. By co-expressing a histidine-tagged Trm9p together with a native Trm112p in E. coli, these two proteins purified as a complex. The presence of Trm112p dramatically improves the methyltransferase activity of Trm9p in vitro. Single tRNA species that normally contain mcm5U or mcm5s2U nucleosides were isolated from trm9Δ or trm112Δ mutants and the presence of modified nucleosides was analyzed by HPLC. In both mutants, mcm5U and mcm5s2U nucleosides are absent in tRNAs and the major intermediates accumulating were ncm5U and ncm5s2U, not the expected cm5U and cm5s2U. Conclusions Trm9p and Trm112p function together at the final step in formation of mcm5U in tRNA by using the intermediate cm5U as a substrate. In tRNA isolated from trm9Δ and trm112Δ strains, ncm5U and ncm5s2U nucleosides accumulate, questioning the order of nucleoside intermediate formation of the mcm5 side chain. We propose two alternative explanations for this observation. One is that the intermediate cm5U is generated from ncm5U by a yet unknown mechanism and the other is that cm5U is formed before ncm5U and mcm5U

Development and validation of 'AutoRIF': Software for the automated analysis of radiation-induced foci

Copyright @ 2012 McVean et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.This article has been made available through the Brunel Open Access Publishing Fund.Background: The quantification of radiation-induced foci (RIF) to investigate the induction and subsequent repair of DNA double strands breaks is now commonplace. Over the last decade systems specific for the automatic quantification of RIF have been developed for this purpose, however to ask more mechanistic questions on the spatio-temporal aspects of RIF, an automated RIF analysis platform that also quantifies RIF size/volume and relative three-dimensional (3D) distribution of RIF within individual nuclei, is required. Results: A java-based image analysis system has been developed (AutoRIF) that quantifies the number, size/volume and relative nuclear locations of RIF within 3D nuclear volumes. Our approach identifies nuclei using the dynamic Otsu threshold and RIF by enhanced Laplacian filtering and maximum entropy thresholding steps and, has an application ‘batch optimisation’ process to ensure reproducible quantification of RIF. AutoRIF was validated by comparing output against manual quantification of the same 2D and 3D image stacks with results showing excellent concordance over a whole range of sample time points (and therefore range of total RIF/nucleus) after low-LET radiation exposure. Conclusions: This high-throughput automated RIF analysis system generates data with greater depth of information and reproducibility than that which can be achieved manually and may contribute toward the standardisation of RIF analysis. In particular, AutoRIF is a powerful tool for studying spatio-temporal relationships of RIF using a range of DNA damage response markers and can be run independently of other software, enabling most personal computers to perform image analysis. Future considerations for AutoRIF will likely include more complex algorithms that enable multiplex analysis for increasing combinations of cellular markers.This article is made available through the Brunel Open Access Publishing Fund

Schema Independent Relational Learning

Learning novel concepts and relations from relational databases is an important problem with many applications in database systems and machine learning. Relational learning algorithms learn the definition of a new relation in terms of existing relations in the database. Nevertheless, the same data set may be represented under different schemas for various reasons, such as efficiency, data quality, and usability. Unfortunately, the output of current relational learning algorithms tends to vary quite substantially over the choice of schema, both in terms of learning accuracy and efficiency. This variation complicates their off-the-shelf application. In this paper, we introduce and formalize the property of schema independence of relational learning algorithms, and study both the theoretical and empirical dependence of existing algorithms on the common class of (de) composition schema transformations. We study both sample-based learning algorithms, which learn from sets of labeled examples, and query-based algorithms, which learn by asking queries to an oracle. We prove that current relational learning algorithms are generally not schema independent. For query-based learning algorithms we show that the (de) composition transformations influence their query complexity. We propose Castor, a sample-based relational learning algorithm that achieves schema independence by leveraging data dependencies. We support the theoretical results with an empirical study that demonstrates the schema dependence/independence of several algorithms on existing benchmark and real-world datasets under (de) compositions

Untangling the Recombination Line Emission from HII Regions with Multiple Velocity Components

HII regions are the ionized spheres surrounding high-mass stars. They are ideal targets for tracing Galactic structure because they are predominantly found in spiral arms and have high luminosities at infrared and radio wavelengths. In the Green Bank Telescope HII Region Discovery Survey (GBT HRDS) we found that >30% of first Galactic quadrant HII regions have multiple hydrogen radio recombination line (RRL) velocities, which makes determining their Galactic locations and physical properties impossible. Here we make additional GBT RRL observations to determine the discrete HII region velocity for all 117 multiple-velocity sources within 18deg. < l < 65deg. The multiple-velocity sources are concentrated in the zone 22deg. < l < 32deg., coinciding with the largest regions of massive star formation, which implies that the diffuse emission is caused by leaked ionizing photons. We combine our observations with analyses of the electron temperature, molecular gas, and carbon recombination lines to determine the source velocities for 103 discrete H II regions (88% of the sample). With the source velocities known, we resolve the kinematic distance ambiguity for 47 regions, and thus determine their heliocentric distances.Comment: 44 pages, 5 figures, 16 pages of tables; Accepted by ApJ

Catalytic combustion for the automotive gas turbine engine

Fuel injectors to provide a premixed prevaporized fuel-air mixture are studied. An evaluation of commercial catalysts was performed as part of a program leading to the demonstration of a low emissions combustor for an automotive gas turbine engine. At an inlet temperature of 800 K, a pressure of 500,000 Pa and a velocity of 20 m/s a multiple-jet injector produced less than + or - 10 percent variation in Jet-A fuel-air ratio and 100 percent varporization with less than 0.5 percent pressure drop. Fifteen catalytic reactors were tested with propane fuel at an inlet temperature of 800 K, a pressure of 300,000 Pa and inlet velocities of 10 to 25 m/s. Seven of the reactors had less than 2 percent pressure drop while meeting emissions goals of 13.6 gCO/kg fuel and 1.64 gHC/kg fuel at the velocities and exit temperatures required for operation in an automotive gas turbine engine. NO sub x emissions at all conditions were less than 0.5 ppm. All tests were performed with steady state conditions

Non-destructive spatial heterodyne imaging of cold atoms

We demonstrate a new method for non-destructive imaging of laser-cooled atoms. This spatial heterodyne technique forms a phase image by interfering a strong carrier laser beam with a weak probe beam that passes through the cold atom cloud. The figure of merit equals or exceeds that of phase-contrast imaging, and the technique can be used over a wider range of spatial scales. We show images of a dark spot MOT taken with imaging fluences as low as 61 pJ/cm^2 at a detuning of 11 linewidths, resulting in 0.0004 photons scattered per atom.Comment: text+3 figures, submitted to Optics Letter