Evaluation of a Droplet Digital Polymerase Chain Reaction Format for DNA Copy Number Quantification

ABSTRACT: Droplet digital polymerase chain reaction (ddPCR) is a new technology that was recently commercialized to enable the precise quantification of target nucleic acids in a sample. ddPCR measures absolute quantities by counting nucleic acid molecules encapsulated in discrete, volumetrically defined, water-in-oil droplet partitions. This novel ddPCR format offers a simple workflow capable of generating highly stable partitioning of DNA molecules. In this study, we assessed key performance parameters of the ddPCR system. A linear ddPCR response to DNA concentration was obtained from 0.16 % through to 99.6 % saturation in a 20,000 droplet assay corresponding to more than 4 orders of magnitude of target DNA copy number per ddPCR. Analysis of simplex and duplex assays targeting two distinct loci in the Lambda DNA genome using the ddPCR platform agreed, within their expanded uncertainties, with values obtained using a lower density microfluidic chamber based digital PCR (cdPCR). A relative expanded uncertainty under 5 % was achieved for copy number concentration using ddPCR. This level of uncertainty is much lower than values typically observed for quantification of specific DNA target sequences using currently commercially available real-time and digital cdPCR technologies

Imaging ancient and mummified specimens: dual-energy CT with effective atomic number imaging of two ancient Egyptian cat mummies

In mummified animals and humans, soft tissues like skin and muscle become more dense over time due to dehydration. At the same time, bone becomes less dense as marrow is replaced by air. This is a problem for the radiological examination of ancient specimens, as currently used methods such as single-energy CT and MRI rely on density and water content to produce tissue contrast in an image. Dual energy CT with effective atomic number imaging overcomes this problem, as the elemental constituents and consequently effective atomic number of a specimen remain relatively constant over time. This case study of two ancient Egyptian cat mummies demonstrates that effective atomic number imaging can differentiate desiccated soft tissues from low-density bone in ancient remains. Effective atomic number imaging has the potential for superior tissue contrast resolution when compared to single energy CT and can be used to provide new paleoradiological perspectives.James M. Bewes, Antony Morphett, F. Donald Pate, Maciej Henneberg, Andrew J. Low, Lars Kruse, Barry Craig, Aphrodite Hindson, Eleanor Adam

The Spectral Energy Distribution of Powerful Starburst Galaxies I : Modelling the Radio Continuum

This article has been accepted for publication in Monthly Notices of the Royal Astronomical Society. © 2018 The Author(s). Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.We have acquired radio-continuum data between 70MHz and 48 GHz for a sample of 19 southern starburst galaxies at moderate redshifts (0.067 < z < 0.227) with the aim of separating synchrotron and free-free emission components. Using a Bayesian framework, we find the radio continuum is rarely characterized well by a single power law, instead often exhibiting lowfrequency turnovers below 500 MHz, steepening at mid to high frequencies, and a flattening at high frequencies where free-free emission begins to dominate over the synchrotron emission. These higher order curvature components may be attributed to free-free absorption across multiple regions of star formation with varying optical depths. The decomposed synchrotron and free-free emission components in our sample of galaxies form strong correlations with the total-infrared bolometric luminosities. Finally, we find that without accounting for free-free absorption with turnovers between 90 and 500MHz the radio continuum at low frequency (v < 200 MHz) could be overestimated by upwards of a factor of 12 if a simple power-law extrapolation is used from higher frequencies. The mean synchrotron spectral index of our sample is constrained to be α = -1.06, which is steeper than the canonical value of -0.8 for normal galaxies. We suggest this may be caused by an intrinsically steeper cosmic ray distribution.Peer reviewe

The Spectral Energy Distribution of Powerful Starburst Galaxies I: Modelling the Radio Continuum

We have acquired radio continuum data between 70\,MHz and 48\,GHz for a sample of 19 southern starburst galaxies at moderate redshifts ($0.067 < z < 0.227$) with the aim of separating synchrotron and free-free emission components. Using a Bayesian framework we find the radio continuum is rarely characterised well by a single power law, instead often exhibiting low frequency turnovers below 500\,MHz, steepening at mid-to-high frequencies, and a flattening at high frequencies where free-free emission begins to dominate over the synchrotron emission. These higher order curvature components may be attributed to free-free absorption across multiple regions of star formation with varying optical depths. The decomposed synchrotron and free-free emission components in our sample of galaxies form strong correlations with the total-infrared bolometric luminosities. Finally, we find that without accounting for free-free absorption with turnovers between 90 to 500\,MHz the radio-continuum at low frequency ($\nu < 200$\,MHz) could be overestimated by upwards of a factor of twelve if a simple power law extrapolation is used from higher frequencies. The mean synchrotron spectral index of our sample is constrained to be $\alpha=-1.06$, which is steeper then the canonical value of $-0.8$ for normal galaxies. We suggest this may be caused by an intrinsically steeper cosmic ray distribution

Calibration and Stokes Imaging with Full Embedded Element Primary Beam Model for the Murchison Widefield Array

15 pages, 11 figures. Accepted for publication in PASA. © Astronomical Society of Australia 2017The Murchison Widefield Array (MWA), located in Western Australia, is one of the low-frequency precursors of the international Square Kilometre Array (SKA) project. In addition to pursuing its own ambitious science program, it is also a testbed for wide range of future SKA activities ranging from hardware, software to data analysis. The key science programs for the MWA and SKA require very high dynamic ranges, which challenges calibration and imaging systems. Correct calibration of the instrument and accurate measurements of source flux densities and polarisations require precise characterisation of the telescope's primary beam. Recent results from the MWA GaLactic Extragalactic All-sky MWA (GLEAM) survey show that the previously implemented Average Embedded Element (AEE) model still leaves residual polarisations errors of up to 10-20 % in Stokes Q. We present a new simulation-based Full Embedded Element (FEE) model which is the most rigorous realisation yet of the MWA's primary beam model. It enables efficient calculation of the MWA beam response in arbitrary directions without necessity of spatial interpolation. In the new model, every dipole in the MWA tile (4 x 4 bow-tie dipoles) is simulated separately, taking into account all mutual coupling, ground screen and soil effects, and therefore accounts for the different properties of the individual dipoles within a tile. We have applied the FEE beam model to GLEAM observations at 200 - 231 MHz and used false Stokes parameter leakage as a metric to compare the models. We have determined that the FEE model reduced the magnitude and declination-dependent behaviour of false polarisation in Stokes Q and V while retaining low levels of false polarisation in Stokes U.Peer reviewedFinal Accepted Versio

Murchison Widefield Array and XMM-Newton observations of the Galactic supernova remnant G5.9+3.1

In this paper we discuss the radio continuum and X-ray properties of the so-far poorly studied Galactic supernova remnant (SNR) G5.9+3.1. We present the radio spectral energy distribution (SED) of the Galactic SNR G5.9+3.1 obtained with the Murchison Widefield Array (MWA). Combining these new observations with the surveys at other radio continuum frequencies, we discuss the integrated radio continuum spectrum of this particular remnant. We have also analyzed an archival XMM-Newton observation, which represents the first detection of X-ray emission from this remnant. The SNR SED is very well explained by a simple power-law relation. The synchrotron radio spectral index of G5.9+3.1, is estimated to be 0.42$\pm$0.03 and the integrated flux density at 1GHz to be around 2.7Jy. Furthermore, we propose that the identified point radio source, located centrally inside the SNR shell, is most probably a compact remnant of the supernova explosion. The shell-like X-ray morphology of G5.9+3.1 as revealed by XMM-Newton broadly matches the spatial distribution of the radio emission, where the radio-bright eastern and western rims are also readily detected in the X-ray while the radio-weak northern and southern rims are weak or absent in the X-ray. Extracted MOS1+MOS2+PN spectra from the whole SNR as well as the north, east, and west rims of the SNR are fit successfully with an optically thin thermal plasma model in collisional ionization equilibrium with a column density N_H~0.80x$10^{22}$ cm$^{-2}$ and fitted temperatures spanning the range kT~0.14-0.23keV for all of the regions. The derived electron number densities n_e for the whole SNR and the rims are also roughly comparable (ranging from ~$0.20f^{-1/2}$ cm$^{-3}$ to ~$0.40f^{-1/2}$ cm$^{-3}$, where f is the volume filling factor). We also estimate the swept-up mass of the X-ray emitting plasma associated with G5.9+3.1 to be ~$46f^{-1/2}M_{\odot}$.Comment: Accepted for publication in A&

Nurses\u27 Alumnae Association Bulletin, June 1970

Alumnae President\u27s Message Congratulations Alumni Association Portrait of Samuel D. Gross Officers and Chairmen of Committees Financial Report Progress of Jefferson 1969-1970 School of Nursing Annual Report School of Practical Nursing Report Emergency Department Patient Services Department Annual Luncheon Pictures Committee Reports Progress of the Alumnae Association Crossword Puzzle Missing Graduates Resume of Alumnae Meetings Minutes Class News Student Nurses Section Crossword Puzzle Answers Notice

WSClean : an implementation of a fast, generic wide-field imager for radio astronomy

This article has been accepted for publication in Monthly Notices of the Royal Astronomical Society. © 2014 The Authors. Published by Oxford University Press on behalf of the Royal Astronomical Society.Astronomical widefield imaging of interferometric radio data is computationally expensive, especially for the large data volumes created by modern non-coplanar many-element arrays. We present a new widefield interferometric imager that uses the w-stacking algorithm and can make use of the w-snapshot algorithm. The performance dependencies of CASA's w-projection and our new imager are analysed and analytical functions are derived that describe the required computing cost for both imagers. On data from the Murchison Widefield Array, we find our new method to be an order of magnitude faster than w-projection, as well as being capable of full-sky imaging at full resolution and with correct polarisation correction. We predict the computing costs for several other arrays and estimate that our imager is a factor of 2-12 faster, depending on the array configuration. We estimate the computing cost for imaging the low-frequency Square-Kilometre Array observations to be 60 PetaFLOPS with current techniques. We find that combining w-stacking with the w-snapshot algorithm does not significantly improve computing requirements over pure w-stacking. The source code of our new imager is publicly released.Peer reviewedFinal Published versio

GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey II: Galactic plane 345° &lt; l &lt; 67°, 180° &lt; l &lt; 240°

This work makes available a further of the GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey, covering half of the accessible galactic plane, across 20 frequency bands sampling 72-231 MHz, with resolution . Unlike previous GLEAM data releases, we used multi-scale uc(CLEAN) to better deconvolve large-scale galactic structure. For the galactic longitude ranges , , we provide a compact source catalogue of 22 037 components selected from a 60-MHz bandwidth image centred at 200 MHz, with RMS noise and position accuracy better than 2 arcsec. The catalogue has a completeness of 50% at , and a reliability of 99.86%. It covers galactic latitudes towards the galactic centre and for other regions, and is available from Vizier; images covering for all longitudes are made available on the GLEAM Virtual Observatory (VO).server and SkyView

High-energy sources at low radio frequency : the Murchison Widefield Array view of Fermi blazars

This is the accepted version of the following article: Giroletti, M. et al., A&A, 588 (2016) A141, which has been published in final form at DOI: http://dx.doi.org/10.1051/0004-6361/201527817. This article may be used for non-commercial purposes in accordance with the EDP Sciences self-archiving policies.Low-frequency radio arrays are opening a new window for the study of the sky, both to study new phenomena and to better characterize known source classes. Being flat-spectrum sources, blazars are so far poorly studied at low radio frequencies. We characterize the spectral properties of the blazar population at low radio frequency compare the radio and high-energy properties of the gamma-ray blazar population, and search for radio counterparts of unidentified gamma-ray sources. We cross-correlated the 6,100 deg^2 Murchison Widefield Array Commissioning Survey catalogue with the Roma blazar catalogue, the third catalogue of active galactic nuclei detected by Fermi-LAT, and the unidentified members of the entire third catalogue of gamma-ray sources detected by \fermilat. When available, we also added high-frequency radio data from the Australia Telescope 20 GHz catalogue. We find low-frequency counterparts for 186 out of 517 (36%) blazars, 79 out of 174 (45%) gamma-ray blazars, and 8 out of 73 (11%) gamma-ray blazar candidates. The mean low-frequency (120--180 MHz) blazar spectral index is $\langle \alpha_\mathrm{low} \rangle=0.57\pm0.02$: blazar spectra are flatter than the rest of the population of low-frequency sources, but are steeper than at $\sim$GHz frequencies. Low-frequency radio flux density and gamma-ray energy flux display a mildly significant and broadly scattered correlation. Ten unidentified gamma-ray sources have a (probably fortuitous) positional match with low radio frequency sources. Low-frequency radio astronomy provides important information about sources with a flat radio spectrum and high energy. However, the relatively low sensitivity of the present surveys still misses a significant fraction of these objects. Upcoming deeper surveys, such as the GaLactic and Extragalactic All-Sky MWA (GLEAM) survey, will provide further insight into this population.Peer reviewedFinal Published versio