Author: "Murphy T" / Publisher: oxford university press - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Murphy T"' showing total 110 results

Start Over Author "Murphy T" Publisher oxford university press

110 results on '"Murphy T"'

1. An all-sky survey of circular polarization at 200 MHz

Author: Lenc, E., Murphy, T., Lynch, Christene, Kaplan, D., Zhang, S., Lenc, E., Murphy, T., Lynch, Christene, Kaplan, D., and Zhang, S.
Abstract: We present results from the first all-sky radio survey in circular polarization. The survey uses the Murchison Widefield Array (MWA) to cover 30 900 sq deg, over declinations south of +30° and north of -86° centred at 200MHz (over a 169-231MHz band).We achieve a spatial resolution of ~3 arcmin and a typical sensitivity of 3.0mJy PSF-1over most of the survey region. We demonstrate a new leakage mitigation technique that reduces the leakage from total intensity into circular polarization by an order of magnitude. In a blind survey of the imaged region, we detect 14 pulsars in circular polarization above a 6s threshold. We also detect six transient sources associated with artificial satellites. A targeted survey of 2376 pulsars within the surveyed region yielded 33 detections above 4s. Looking specifically at pulsars previously detected at 200 MHz in total intensity, this represents a 35 per cent detection rate. We also conducted a targeted survey of 2400 known flare stars, this resulted in two tentative detections above 4s. A similar targeted search for 1506 known exoplanets in the field yielded no detections above 4s. The success of the survey suggests that similar surveys at longer wavelength bands and of deeper fields are warranted.
Published: 2018

2. A pilot survey for transients and variables with the Australian Square Kilometre Array Pathfinder

Author: Bhandari, S., Bannister, K., Murphy, T., Bell, M., Raja, W., Marvil, J., Hancock, Paul, Whiting, M., Flynn, C., Collier, J., Kaplan, D., Allison, J., Anderson, C., Heywood, I., Hotan, A., Hunstead, R., Lee-Waddell, K., Madrid, J., McConnell, D., Popping, A., Rhee, J., Sadler, E., Voronkov, M., Bhandari, S., Bannister, K., Murphy, T., Bell, M., Raja, W., Marvil, J., Hancock, Paul, Whiting, M., Flynn, C., Collier, J., Kaplan, D., Allison, J., Anderson, C., Heywood, I., Hotan, A., Hunstead, R., Lee-Waddell, K., Madrid, J., McConnell, D., Popping, A., Rhee, J., Sadler, E., and Voronkov, M.
Abstract: We present a pilot search for variable and transient sources at 1.4 GHz with the Australian Square Kilometre Array Pathfinder (ASKAP). The search was performed in a 30 deg2 area centred on the NGC 7232 galaxy group over eight epochs and observed with a near-daily cadence. The search yielded nine potential variable sources, rejecting the null hypothesis that the flux densities of these sources do not change with 99.9 per cent confidence. These nine sources displayed flux density variations with modulation indices m = 0.1 above our flux density limit of ~1.5mJy. They are identified to be compact active galactic nucleus (AGN)/quasars or galaxies hosting an AGN, whose variability is consistent with refractive interstellar scintillation.We also detect a highly variable source with modulation index m > 0.5 over a time interval of a decade between the SydneyUniversity Molonglo Sky Survey (SUMSS) and our latest ASKAP observations. We find the source to be consistent with the properties of long-term variability of a quasar. No transients were detected on time-scales of days and we place an upper limit ?t < 0.01 deg-2 with 95 per cent confidence for non-detections on near-daily time-scales. The future VAST-Wide survey with 36-ASKAP dishes will probe the transient phase space with similar cadence to our pilot survey, but better sensitivity, and will detect and monitor rarer brighter events.
Published: 2018

3. The detectability of radio emission from exoplanets

Author: Lynch, Christene, Murphy, T., Lenc, E., Kaplan, D., Lynch, Christene, Murphy, T., Lenc, E., and Kaplan, D.
Abstract: Like the magnetized planets in our Solar system, magnetized exoplanets should emit strongly at radio wavelengths. Radio emission directly traces the planetary magnetic fields and radio detections can place constraints on the physical parameters of these features. Large comparative studies of predicted radio emission characteristics for the known population of exoplanets help to identify what physical parameters could be the key for producing bright, observable radio emission. Since the last comparative study, many thousands of exoplanets have been discovered. We report new estimates for the radio flux densities and maximum emission frequencies for the current population of known exoplanets orbiting pre-main-sequence and main-sequence stars with spectral types F-M. The set of exoplanets predicted to produce observable radio emission are Hot Jupiters orbiting young stars. The youth of these systems predicts strong stellar magnetic fields and/or dense winds, which are the key for producing bright, observable radio emission. We use a new all-sky circular polarization Murchison Widefield Array survey to place sensitive limits on 200MHz emission from exoplanets, with 3s values ranging from 4.0 to 45.0mJy. Using a targeted Giant Metrewave Radio Telescope observing campaign, we also report a 3s upper limit of 4.5mJy on the radio emission from V830 Tau b, the first Hot Jupiter to be discovered orbiting a pre-main-sequence star. Our limit is the first to be reported for the low-frequency radio emission from this source.
Published: 2018

4. A search for circularly polarized emission from young exoplanets

Author: Lynch, Christene, Murphy, T., Kaplan, D., Ireland, M., Bell, M., Lynch, Christene, Murphy, T., Kaplan, D., Ireland, M., and Bell, M.
Abstract: We report the results of a 154 MHz survey to search for emission from exoplanets located in the Upper Scorpius subgroup of the Sco Cen OB2 Association, the closest substantial region of recent star formation. This survey is different from previous efforts in that it is the first to target exoplanets orbiting Myr-old stars. Young exoplanet systems are expected to be the best candidates for radio detections given the higher magnetic field strengths predicted for young planets as well as the stronger and more dense stellar wind expected for the host stars. The radio emission from exoplanets is expected to be highly circularly polarized therefore we restricted our search to the circular polarization images rather than the total intensity images. We carried out two different search methods using this data. The first method was a targeted search for exoplanet emission using catalogues of known stars and Hot Jupiters within the Upper Scorpius field. The second search method was a blind search for highly circularly polarized sources in the field and for sources identified only in our polarization images. Both the blind and targeted search resulted in non-detections with typical 3σ flux density limits of 4–235 mJy over time-scales of 1.87–1000 min. In particular, we place the first limits on low-frequency emission from the Hot Jupiter systems WASP-17 b and K2-33 b. These are the first results from a larger program to systematically search for low-frequency radio emission from planets orbiting young stars.
Published: 2017

5. A search for long-time-scale, low-frequency radio transients

Author: Murphy, T., Kaplan, D., Croft, S., Lynch, C., Callingham, J., Bannister, K., Bell, M., Hurley-Walker, Natasha, Hancock, Paul, Line, J., Rowlinson, A., Lenc, E., Intema, H., Jagannathan, P., Ekers, Ronald, Tingay, Steven, Yuan, F., Wolf, C., Onken, C., Dwarakanath, K., For, B., Gaensler, B., Hindson, L., Johnston-Hollitt, M., Kapinska, A., McKinley, B., Morgan, J., Offringa, A., Procopio, P., Staveley-Smith, L., Wayth, Randall, Wu, C., Zheng, Q., Murphy, T., Kaplan, D., Croft, S., Lynch, C., Callingham, J., Bannister, K., Bell, M., Hurley-Walker, Natasha, Hancock, Paul, Line, J., Rowlinson, A., Lenc, E., Intema, H., Jagannathan, P., Ekers, Ronald, Tingay, Steven, Yuan, F., Wolf, C., Onken, C., Dwarakanath, K., For, B., Gaensler, B., Hindson, L., Johnston-Hollitt, M., Kapinska, A., McKinley, B., Morgan, J., Offringa, A., Procopio, P., Staveley-Smith, L., Wayth, Randall, Wu, C., and Zheng, Q.
Abstract: We present a search for transient and highly variable sources at low radio frequencies (150-200 MHz) that explores long timescales of 1-3 years. We conducted this search by comparing the TIFR GMRT Sky Survey Alternative Data Release 1 (TGSS ADR1) and the GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey catalogues. To account for the different completeness thresholds in the individual surveys, we searched for compact GLEAM sources above a flux density limit of 100 mJy that were not present in the TGSS ADR1; and also for compact TGSS ADR1 sources above a flux density limit of 200 mJy that had no counterpart in GLEAM. From a total sample of 234 333 GLEAM sources and 275 612 TGSS ADR1 sources in the overlap region between the two surveys, there were 99658 GLEAM sources and 38 978 TGSS ADR sources that passed our flux density cutoff and compactness criteria. Analysis of these sources resulted in three candidate transient sources. Further analysis ruled out two candidates as imaging artefacts. We analyse the third candidate and show it is likely to be real, with a flux density of 182 +/- 26 mJy at 147.5 MHz. This gives a transient surface density of rho = (6.2 +/- 6) x 10-5 deg-2 . We present initial follow-up observations and discuss possible causes for this candidate. The small number of spurious sources from this search demonstrates the high reliability of these two new low-frequency radio catalogues.
Published: 2017

6. GRB 110715A: The peculiar multiwavelength evolution of the first afterglow detected by ALMA

Author: Sánchez-Ramírez, R., Hancock, Paul, Jóhannesson, G., Murphy, T., de Ugarte Postigo, A., Gorosabel, J., Kann, D., Krühler, T., Oates, S., Japelj, J., Thöne, C., Lundgren, A., Perley, D., Malesani, D., de Gregorio Monsalvo, I., Castro-Tirado, A., D'Elia, V., Fynbo, J., Garcia-Appadoo, D., Goldoni, P., Greiner, J., Hu, Y., Jelínek, M., Jeong, S., Kamble, A., Klose, S., Kuin, N., Llorente, A., Martín, S., Nicuesa Guelbenzu, A., Rossi, A., Schady, P., Sparre, M., Sudilovsky, V., Tello, J., Updike, A., Wiersema, K., Zhang, B., Sánchez-Ramírez, R., Hancock, Paul, Jóhannesson, G., Murphy, T., de Ugarte Postigo, A., Gorosabel, J., Kann, D., Krühler, T., Oates, S., Japelj, J., Thöne, C., Lundgren, A., Perley, D., Malesani, D., de Gregorio Monsalvo, I., Castro-Tirado, A., D'Elia, V., Fynbo, J., Garcia-Appadoo, D., Goldoni, P., Greiner, J., Hu, Y., Jelínek, M., Jeong, S., Kamble, A., Klose, S., Kuin, N., Llorente, A., Martín, S., Nicuesa Guelbenzu, A., Rossi, A., Schady, P., Sparre, M., Sudilovsky, V., Tello, J., Updike, A., Wiersema, K., and Zhang, B.
Abstract: We present the extensive follow-up campaign on the afterglowof GRB 110715A at 17 different wavelengths, from X-ray to radio bands, starting 81 s after the burst and extending up to 74 d later.We performed for the first time aGRBafterglowobservationwith theALMAobservatory. We find that the afterglow of GRB 110715A is very bright at optical and radio wavelengths. We use the optical and near-infrared spectroscopy to provide further information about the progenitor's environment and its host galaxy. The spectrum shows weak absorption features at a redshift z = 0.8225, which reveal a host-galaxy environment with low ionization, column density, and dynamical activity. Late deep imaging shows a very faint galaxy, consistent with the spectroscopic results. The broad-band afterglow emission is modelled with synchrotron radiation using a numerical algorithm and we determine the best-fitting parameters using Bayesian inference in order to constrain the physical parameters of the jet and the medium in which the relativistic shock propagates. We fitted our data with a variety of models, including different density profiles and energy injections. Although the general behaviour can be roughly described by thesemodels, none of them are able to fully explain all data points simultaneously. GRB 110715A shows the complexity of reproducing extensive multiwavelength broad-band afterglow observations, and the need of good sampling in wavelength and time and more complex models to accurately constrain the physics of GRB afterglows. © 2016 The Authors. Published by Oxford University Press on behalf of the Royal Astronomical Society.
Published: 2017

7. GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey - I. A low-frequency extragalactic catalogue

Author: Hurley-Walker, Natasha, Callingham, J., Hancock, Paul, Franzen, Thomas, Hindson, L., Kapinska, A., Morgan, J., Offringa, A., Wayth, Randall, Wu, C., Zheng, Q., Murphy, T., Bell, M., Dwarakanath, K., For, B., Gaensler, B., Johnston-Hollitt, M., Lenc, E., Procopio, P., Staveley-Smith, L., Ekers, Ronald, Bowman, J., Briggs, F., Cappallo, R., Deshpande, A., Greenhill, L., Hazelton, B., Kaplan, D., Lonsdale, C., McWhirter, S., Mitchell, D., Morales, M., Morgan, E., Oberoi, D., Ord, S., Prabu, T., Udaya Shankar, N., Srivani, K., Subrahmanyan, R., Tingay, Steven, Webster, R., Williams, A., Williams, C., Hurley-Walker, Natasha, Callingham, J., Hancock, Paul, Franzen, Thomas, Hindson, L., Kapinska, A., Morgan, J., Offringa, A., Wayth, Randall, Wu, C., Zheng, Q., Murphy, T., Bell, M., Dwarakanath, K., For, B., Gaensler, B., Johnston-Hollitt, M., Lenc, E., Procopio, P., Staveley-Smith, L., Ekers, Ronald, Bowman, J., Briggs, F., Cappallo, R., Deshpande, A., Greenhill, L., Hazelton, B., Kaplan, D., Lonsdale, C., McWhirter, S., Mitchell, D., Morales, M., Morgan, E., Oberoi, D., Ord, S., Prabu, T., Udaya Shankar, N., Srivani, K., Subrahmanyan, R., Tingay, Steven, Webster, R., Williams, A., and Williams, C.
Abstract: Using the Murchison Widefield Array (MWA), the low-frequency Square Kilometre Array precursor located in Western Australia, we have completed the GaLactic and Extragalactic All-sky MWA (GLEAM) survey, and present the resulting extragalactic catalogue, utilizing the first year of observations. The catalogue covers 24 831 square degrees, over declinations south of +30° and Galactic latitudes outside 10° of the Galactic plane, excluding some areas such as theMagellanic Clouds. It contains 307 455 radio sources with 20 separate flux density measurements across 72-231 MHz, selected from a time- and frequency-integrated image centred at 200 MHz, with a resolution of ˜2 arcmin. Over the catalogued region, we estimate that the catalogue is 90 per cent complete at 170 mJy, and 50 per cent complete at 55 mJy, and large areas are complete at even lower flux density levels. Its reliability is 99.97 per cent above the detection threshold of 5s, which itself is typically 50 mJy. These observations constitute the widest fractional bandwidth and largest sky area survey at radio frequencies to date, and calibrate the low-frequency flux density scale of the southern sky to better than 10 per cent. This paper presents details of the flagging, imaging, mosaicking and source extraction/characterization, as well as estimates of the completeness and reliability. All source measurements and images are available online. 1 This is the first in a series of publications describing the GLEAM survey results. © 2016 The Authors. Published by Oxford University Press on behalf of the Royal Astronomical Society
Published: 2017

8. Time-domain and spectral properties of pulsars at 154 MHz

Author: Bell, M., Murphy, T., Johnston, S., Kaplan, D., Croft, S., Hancock, P., Callingham, J., Zic, A., Dobie, D., Swiggum, J., Rowlinson, A., Hurley-Walker, N., Offringa, A., Bernardi, G., Bowman, J., Briggs, F., Cappallo, R., Deshpande, A., Gaensler, B., Greenhill, L., Hazelton, B., Johnston-Hollitt, M., Lonsdale, C., McWhirter, S., Mitchell, D., Morales, M., Morgan, E., Oberoi, D., Ord, S., Prabu, T., Udaya Shankar, N., Srivani, K., Subrahmanyan, R., Tingay, Steven, Wayth, Randall, Webster, R., Williams, A., Williams, C., Bell, M., Murphy, T., Johnston, S., Kaplan, D., Croft, S., Hancock, P., Callingham, J., Zic, A., Dobie, D., Swiggum, J., Rowlinson, A., Hurley-Walker, N., Offringa, A., Bernardi, G., Bowman, J., Briggs, F., Cappallo, R., Deshpande, A., Gaensler, B., Greenhill, L., Hazelton, B., Johnston-Hollitt, M., Lonsdale, C., McWhirter, S., Mitchell, D., Morales, M., Morgan, E., Oberoi, D., Ord, S., Prabu, T., Udaya Shankar, N., Srivani, K., Subrahmanyan, R., Tingay, Steven, Wayth, Randall, Webster, R., Williams, A., and Williams, C.
Abstract: We present 154 MHz Murchison Widefield Array imaging observations and variability information for a sample of pulsars. Over the declination range −80° < δ < 10°, we detect 17 known pulsars with mean flux density greater than 0.3 Jy. We explore the variability properties of this sample on time-scales of minutes to years. For three of these pulsars, PSR J0953+0755, PSR J0437−4715, and PSR J0630−2834, we observe interstellar scintillation and variability on time-scales of greater than 2 min. One further pulsar, PSR J0034−0721, showed significant variability, the physical origins of which are difficult to determine. The dynamic spectra for PSR J0953+0755 and PSR J0437−4715 show discrete time and frequency structure consistent with diffractive interstellar scintillation and we present the scintillation bandwidth and time-scales from these observations. The remaining pulsars within our sample were statistically non-variable. We also explore the spectral properties of this sample and find spectral curvature in pulsars PSR J0835−4510, PSR J1752−2806, and PSR J0437−4715.
Published: 2016

9. Gamma-ray bursts from massive Population-III stars: Clues from the radio band

Author: Burlon, D., Murphy, T., Ghirlanda, G., Hancock, Paul, Parry, R., Salvaterra, R., Burlon, D., Murphy, T., Ghirlanda, G., Hancock, Paul, Parry, R., and Salvaterra, R.
Abstract: Current models suggest gamma-ray bursts could be used as a way of probing Population-III stars - the first stars in the early Universe. In this paper, we use numerical simulations to demonstrate that late-time radio observations of gamma-ray burst afterglows could provide a means of identifying bursts that originate from Population-III stars, if these were highly massive, independently from their redshift. We then present the results from a pilot study using the Australia Telescope Compact Array at 17 GHz, designed to test the hypothesis that there may be Population-III gamma-ray bursts amongst the current sample of known events. We observed three candidates plus a control gamma-ray burst, and make no detections with upper limits of 20-40 µJy at 500-1300 d post-explosion.
Published: 2016

10. Radio detections of southern ultracool dwarfs

Author: Lynch, Christene, Murphy, T., Ravi, V., Hobbs, G., Lo, K., Ward, C., Lynch, Christene, Murphy, T., Ravi, V., Hobbs, G., Lo, K., and Ward, C.
Abstract: We report the results of a volume-limited survey using the Australia Telescope Compact Array to search for transient and quiescent radio emission from 15 Southern hemisphere ultracool dwarfs. We detect radio emission from 2MASSW J0004348-404405 increasing the number of radio loud ultracool dwarfs to 22. We also observe radio emission from 2MASS J10481463-3956062 and 2MASSI J0339352-352544, two sources with previous radio detections. The radio emission from the three detected sources shows no variability or flare emission. Modelling this quiescent emission we find that it is consistent with optically thin gyrosynchrotron emission from a magnetosphere with an emitting region radius of (1-2)R*, magnetic field inclination 20°-80°, field strength ~10-200 G, and power-law electron density ~104-108cm-3. Additionally, we place upper limits on four ultracool dwarfs with no previous radio observations. This increases the number of ultracool dwarfs studied at radio frequencies to 222. Analysing general trends of the radio emission for this sample of 15 sources, we find that the radio activity increases for later spectral types and more rapidly rotating objects. Furthermore, comparing the ratio of the radio to X-ray luminosities for these sources, we find 2MASS J10481463-3956062 and 2MASSI J0339352-352544 violate the Güdel-Benz relation by more than two orders of magnitude.
Published: 2016

11. Wide-field broad-band radio imaging with phased array feeds: A pilot multi-epoch continuum survey with ASKAP-BETA

Author: Heywood, I., Bannister, K., Marvil, J., Allison, J., Ball, L., Bell, M., Bock, D., Brothers, M., Bunton, J., Chippendale, A., Cooray, F., Cornwell, T., De Boer, D., Edwards, P., Gough, R., Gupta, N., Harvey-Smith, L., Hay, S., Hotan, A., Indermuehle, B., Jacka, C., Jackson, Carole, Johnston, S., Kimball, A., Koribalski, B., Lenc, E., Macleod, A., McClure-Griffiths, N., McConnell, D., Mirtschin, P., Murphy, T., Neuhold, S., Norris, R., Pearce, S., Popping, A., Qiao, R., Reynolds, J., Sadler, E., Sault, R., Schinckel, A., Serra, P., Shimwell, T., Stevens, J., Tuthill, J., Tzioumis, A., Voronkov, M., Westmeier, T., Whiting, M., Heywood, I., Bannister, K., Marvil, J., Allison, J., Ball, L., Bell, M., Bock, D., Brothers, M., Bunton, J., Chippendale, A., Cooray, F., Cornwell, T., De Boer, D., Edwards, P., Gough, R., Gupta, N., Harvey-Smith, L., Hay, S., Hotan, A., Indermuehle, B., Jacka, C., Jackson, Carole, Johnston, S., Kimball, A., Koribalski, B., Lenc, E., Macleod, A., McClure-Griffiths, N., McConnell, D., Mirtschin, P., Murphy, T., Neuhold, S., Norris, R., Pearce, S., Popping, A., Qiao, R., Reynolds, J., Sadler, E., Sault, R., Schinckel, A., Serra, P., Shimwell, T., Stevens, J., Tuthill, J., Tzioumis, A., Voronkov, M., Westmeier, T., and Whiting, M.
Abstract: The Boolardy Engineering TestArray is a 6×12mdish interferometer and the prototype of the Australian Square Kilometre Array Pathfinder (ASKAP), equipped with the first generation of ASKAP's phased array feed (PAF) receivers. These facilitate rapid wide-area imaging via the deployment of simultaneous multiple beams within an ~30 deg2 field of view. By cycling the array through 12 interleaved pointing positions and using nine digitally formed beams, we effectively mimic a traditional 1 h × 108 pointing survey, covering ~150 deg2 over 711-1015 MHz in 12 h of observing time. Three such observations were executed over the course of a week. We verify the full bandwidth continuum imaging performance and stability of the system via self-consistency checks and comparisons to existing radio data. The combined three epoch image has arcminute resolution and a 1s thermal noise level of 375 µJy beam-1, although the effective noise is a factor of ~3 higher due to residual sidelobe confusion. From this we derive a catalogue of 3722 discrete radio components, using the 35 per cent fractional bandwidth to measure in-band spectral indices for 1037 of them. A search for transient events reveals one significantly variable source within the survey area. The survey covers approximately two-thirds of the Spitzer South Pole Telescope Deep Field. This pilot project demonstrates the viability and potential of using PAFs to rapidly and accurately survey the sky at radio wavelengths.
Published: 2016

12. Radio variability in the phoenix deep survey at 1.4 GHz

Author: Hancock, Paul, Drury, J., Bell, M., Murphy, T., Gaensler, B., Hancock, Paul, Drury, J., Bell, M., Murphy, T., and Gaensler, B.
Abstract: © 2016 The Authors. We use archival data from the Phoenix Deep Survey to investigate the variable radio source population above 1 mJy beam-1 at 1.4 GHz. Given the similarity of this survey to other such surveys we take the opportunity to investigate the conflicting results which have appeared in the literature. Two previous surveys for variability conducted with the Very Large Array (VLA) achieved a sensitivity of 1 mJy beam-1 . However, one survey found an areal density of radio variables on time-scales of decades that is a factor of ~4 times greater than a second survey which was conducted on time-scales of less than a few years. In the Phoenix deep field we measure the density of variable radio sources to be ? = 0.98 deg-2 on time-scales of 6 months to 8 yr. We make use of Wide-field Infrared Survey Explorer infrared cross-ids, and identify all variable sources as an active galactic nucleus of some description.We suggest that the discrepancy between previous VLA results is due to the different time-scales probed by each of the surveys, and that radio variability at 1.4 GHz is greatest on time-scales of 2-5 yr.
Published: 2016

13. Limits on Fast Radio Bursts and other transient sources at 182 MHz using the Murchison Widefield Array

Author: Rowlinson, A., Bell, M., Murphy, T., Trott, C., Hurley-Walker, N., Johnston, S., Tingay, Steven, Kaplan, D., Carbone, D., Hancock, P., Feng, L., Offringa, A., Bernardi, G., Bowman, J., Briggs, F., Cappallo, R., Deshpande, A., Gaensler, B., Greenhill, L., Hazelton, B., Johnston-Hollitt, M., Lonsdale, C., McWhirter, S., Mitchell, D., Morales, M., Morgan, E., Oberoi, D., Ord, S., Prabu, T., Udaya Shankar, N., Srivani, K., Subrahmanyan, R., Wayth, Randall, Webster, R., Williams, A., Williams, C., Rowlinson, A., Bell, M., Murphy, T., Trott, C., Hurley-Walker, N., Johnston, S., Tingay, Steven, Kaplan, D., Carbone, D., Hancock, P., Feng, L., Offringa, A., Bernardi, G., Bowman, J., Briggs, F., Cappallo, R., Deshpande, A., Gaensler, B., Greenhill, L., Hazelton, B., Johnston-Hollitt, M., Lonsdale, C., McWhirter, S., Mitchell, D., Morales, M., Morgan, E., Oberoi, D., Ord, S., Prabu, T., Udaya Shankar, N., Srivani, K., Subrahmanyan, R., Wayth, Randall, Webster, R., Williams, A., and Williams, C.
Abstract: We present a survey for transient and variable sources, on time-scales from 28 s to ~1 yr, using the Murchison Widefield Array (MWA) at 182 MHz. Down to a detection threshold of 0.285 Jy, no transient candidates were identified, making this the most constraining low-frequency survey to date and placing a limit on the surface density of transients of <4.1 × 10-7 deg-2 for the shortest time-scale considered. At these frequencies, emission from Fast Radio Bursts (FRBs) is expected to be detectable in the shortest time-scale images without any corrections for interstellar or intergalactic dispersion. At an FRB limiting flux density of 7980 Jy, we find a rate of <82 FRBs per sky per day for dispersion measures <700 pc cm-3. Assuming a cosmological population of standard candles, our rate limits are consistent with the FRB rates obtained by Thornton et al. if they have a flat spectral slope. Finally, we conduct an initial variability survey of sources in the field with flux densities = 0.5 Jy and identify no sources with significant variability in their light curves. However, we note that substantial further work is required to fully characterize both the short-term and low-level variability within this field.
Published: 2016

14. A pilot ASKAP survey of radio transient events in the region around the intermittent pulsar PSR J1107-5907

Author: Hobbs, G., Heywood, I., Bell, M., Kerr, M., Rowlinson, A., Johnston, S., Shannon, R., Voronkov, M., Ward, C., Banyer, J., Hancock, P., Murphy, T., Allison, J., Amy, S., Ball, L., Bannister, K., Bock, D., Brodrick, D., Brothers, M., Brown, A., Bunton, J., Chapman, J., Chippendale, A., Chung, Y., DeBoer, D., Diamond, P., Edwards, P., Ekers, Ronald, Ferris, R., Forsyth, R., Gough, R., Grancea, A., Gupta, N., Harvey-Smith, L., Hay, S., Hayman, D., Hotan, A., Hoyle, S., Humphreys, B., Indermuehle, B., Jacka, C., Jackson, C., Jackson, S., Jeganathan, K., Joseph, J., Kenda, R., Kiraly, D., Koribalski, B., Leach, M., Lenc, E., MacLeod, A., Mader, S., Marquarding, M., Marvil, J., McClure-Griffiths, N., McConnell, D., Mirtschin, P., Neuhold, S., Ng, A., Norris, R., O'Sullivan, J., Pearce, S., Phillips, C., Popping, A., Qiao, R., Reynolds, J., Roberts, P., Sault, R., Schinckel, A., Serra, P., Shaw, R., Shimwel, T., Storey, M., Sweetnam, A., Tzioumis, A., Westmeier, T., Whitingl, M., Wilson, C., Hobbs, G., Heywood, I., Bell, M., Kerr, M., Rowlinson, A., Johnston, S., Shannon, R., Voronkov, M., Ward, C., Banyer, J., Hancock, P., Murphy, T., Allison, J., Amy, S., Ball, L., Bannister, K., Bock, D., Brodrick, D., Brothers, M., Brown, A., Bunton, J., Chapman, J., Chippendale, A., Chung, Y., DeBoer, D., Diamond, P., Edwards, P., Ekers, Ronald, Ferris, R., Forsyth, R., Gough, R., Grancea, A., Gupta, N., Harvey-Smith, L., Hay, S., Hayman, D., Hotan, A., Hoyle, S., Humphreys, B., Indermuehle, B., Jacka, C., Jackson, C., Jackson, S., Jeganathan, K., Joseph, J., Kenda, R., Kiraly, D., Koribalski, B., Leach, M., Lenc, E., MacLeod, A., Mader, S., Marquarding, M., Marvil, J., McClure-Griffiths, N., McConnell, D., Mirtschin, P., Neuhold, S., Ng, A., Norris, R., O'Sullivan, J., Pearce, S., Phillips, C., Popping, A., Qiao, R., Reynolds, J., Roberts, P., Sault, R., Schinckel, A., Serra, P., Shaw, R., Shimwel, T., Storey, M., Sweetnam, A., Tzioumis, A., Westmeier, T., Whitingl, M., and Wilson, C.
Abstract: We use observations from the Boolardy Engineering Test Array (BETA) of the Australian Square Kilometre Array Pathfinder (ASKAP) telescope to search for transient radio sources in the field around the intermittent pulsar PSR J1107-5907. The pulsar is thought to switch between an "off" state in which no emission is detectable, a weak state and a strong state. We ran three independent transient detection pipelines on two-minute snapshot images from a 13 hour BETA observation in order to 1) study the emission from the pulsar, 2) search for other transient emission from elsewhere in the image and 3) to compare the results from the different transient detection pipelines. The pulsar was easily detected as a transient source and, over the course of the observations, it switched into the strong state three times giving a typical timescale between the strong emission states of 3.7 hours. After the first switch it remained in the strong state for almost 40 minutes. The other strong states lasted less than 4 minutes. The second state change was confirmed using observations with the Parkes radio telescope. No other transient events were found and we place constraints on the surface density of such events on these timescales. The high sensitivity Parkes observations enabled us to detect individual bright pulses during the weak state and to study the strong state over a wide observing band. We conclude by showing that future transient surveys with ASKAP will have the potential to probe the intermittent pulsar population.
Published: 2016

15. The Governance of therapeutic nanoproducts in the European Union - a model for new health technology regulation?

Author: Dorbeck-Jung, Barbel R., Flear, M.L., Farrell, A., Hervey, T.K., Murphy, T., and Faculty of Behavioural, Management and Social Sciences
Subjects: IR-82608, METIS-290800
Published: 2012

16. WSCLEAN: an implementation of a fast, generic wide-field imager for radio astronomy

Author: Offringa, A., McKinley, B., Hurley-Walker, Natasha, Briggs, F., Wayth, Randall, Kaplan, D., Bell, M., Feng, L., Neben, A., Hughes, J., Rhee, J., Murphy, T., Bhat, Ramesh, Bernardi, G., Bowman, J., Cappallo, R., Corey, B., Deshpande, A., Emrich, David, Ewall-Wice, A., Gaensler, B., Goeke, R., Greenhill, L., Hazelton, B., Hindson, L., Johnston-Hollitt, M., Jacobs, D., Kasper, J., Kratzenberg, E., Lenc, E., Lonsdale, C., Lynch, M., McWhirter, S., Mitchell, D., Morales, M., Morgan, E., Kudryavtseva, N., Oberoi, D., Ord, S., Pindor, B., Procopio, P., Prabu, T., Riding, J., Roshi, A., Shankar, N., Srivani, K., Subrahmanyan, R., Tingay, Steven, Waterson, Mark, Webster, R., Whitney, A., Williams, A., Williams, C., Offringa, A., McKinley, B., Hurley-Walker, Natasha, Briggs, F., Wayth, Randall, Kaplan, D., Bell, M., Feng, L., Neben, A., Hughes, J., Rhee, J., Murphy, T., Bhat, Ramesh, Bernardi, G., Bowman, J., Cappallo, R., Corey, B., Deshpande, A., Emrich, David, Ewall-Wice, A., Gaensler, B., Goeke, R., Greenhill, L., Hazelton, B., Hindson, L., Johnston-Hollitt, M., Jacobs, D., Kasper, J., Kratzenberg, E., Lenc, E., Lonsdale, C., Lynch, M., McWhirter, S., Mitchell, D., Morales, M., Morgan, E., Kudryavtseva, N., Oberoi, D., Ord, S., Pindor, B., Procopio, P., Prabu, T., Riding, J., Roshi, A., Shankar, N., Srivani, K., Subrahmanyan, R., Tingay, Steven, Waterson, Mark, Webster, R., Whitney, A., Williams, A., and Williams, C.
Abstract: Astronomical wide-field 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 wide-field interferometric imager that uses the w-stacking algorithm and can make use of the w-snapshot algorithm. The performance dependences 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 polarization 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.
Published: 2014

17. Deep 20-GHz survey of the Chandra Deep Field South and SDSS Stripe 82: source catalogue and spectral properties

Author: Franzen, Thomas, Sadler, E., Chhertri, R., Ekers, Ronald, Mahony, E., Murphy, T., Norris, R., Waldram, E., Whittam, I., Franzen, Thomas, Sadler, E., Chhertri, R., Ekers, Ronald, Mahony, E., Murphy, T., Norris, R., Waldram, E., and Whittam, I.
Abstract: We present a source catalogue and first results from a deep, blind radio survey carried out at 20 GHz with the Australia Telescope Compact Array, with follow-up observations at 5.5, 9 and 18 GHz. The Australia Telescope 20 GHz (AT20G) deep pilot survey covers a total area of 5 deg2 in the Chandra Deep Field South and in Stripe 82 of the Sloan Digital Sky Survey. We estimate the survey to be 90 per cent complete above 2.5 mJy. Of the 85 sources detected, 55 per cent have steep spectra [graphic] and 45 per cent have flat or inverted spectra [graphic]. The steep-spectrum sources tend to have single power-law spectra between 1.4 and 18 GHz, while the spectral indices of the flat- or inverted-spectrum sources tend to steepen with frequency. Among the 18 inverted-spectrum [graphic] sources, 10 have clearly defined peaks in their spectra with [graphic] and [graphic]. On a 3-yr time-scale, at least 10 sources varied by more than 15 per cent at 20 GHz, showing that variability is still common at the low flux densities probed by the AT20G-deep pilot survey. We find a strong and puzzling shift in the typical spectral index of the 15–20-GHz source population when combining data from the AT20G, Ninth Cambridge and Tenth Cambridge surveys: there is a shift towards a steeper-spectrum population when going from ~1 Jy to ~5 mJy, which is followed by a shift back towards a flatter-spectrum population below ~5 mJy. The 5-GHz source-count model by Jackson & Wall, which only includes contributions from FRI and FRII sources, and star-forming galaxies, does not reproduce the observed flattening of the flat-spectrum counts below ~5 mJy. It is therefore possible that another population of sources is contributing to this effect.
Published: 2014

18. Regulating human genetics in a neo-genetic era

Author: Somsen, H. and Murphy, T.
Published: 2009

19. The AT20G view of swift/BAT selected AGN: High-frequency radio waves meet hard X-rays

Author: Burlon, D., Ghirlanda, G., Murphy, T., Chhetri, Rajan, Sadler, E., Ajello, M., Burlon, D., Ghirlanda, G., Murphy, T., Chhetri, Rajan, Sadler, E., and Ajello, M.
Abstract: We cross-matched the 6-year Swift/Burst Alert Telescope (BAT) survey of active galactic nuclei (AGN) with the AT20G radio survey of the southern sky, which is one of the largest high-frequency radio surveys available.With these datawe investigated the possible correlation between the radio and the X-ray emission at the highest radio and X-ray frequencies.We found 37AGNwith a high probability of association (>80 per cent), among which 19 are local Seyfert galaxies (with median redshift z=0.03) and 18 blazars.We found that˜20 per cent of theAGN detected in hard X-rays are also bright radio sources at 20 GHz, but the apparent correlation between the radio and hard X-ray luminosity is completely driven by the different median redshifts of the two subgroups of AGN. When we consider only the local Seyfert sample we find no evidence of a correlation between their 20 GHz and 15-55 keV power. Therefore it appears that at high frequencies the radio-X connection, which had been previously observed at lower frequencies, disappears. The disappearance of the radio-X correlation at high radio and X-ray frequencies could be tested through Very Long Baseline Interferometry and the use of the Nuclear Spectroscopic Telescope Array (NuSTAR) satellite. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.
Published: 2013

20. A survey for transients and variables with the Murchison Widefield Array 32-tile prototype at 154 MHz

Author: Trott, Cathryn, Hurley-Walker, Natasha, Wayth, Randall, Macquart, Jean-Pierre, Arcus, Wayne, Emrich, David, Herne, David, Lynch, Mervyn, Ord, Stephen, Tingay, Steven, Waterson, Mark, Williams, Andrew, Bell, M., Murphy, T., Kaplan, D., Hancock, P., Gaensler, B., Banyer, J., Bannister, K., Barnes, D., Bernardi, G., Bowman, J., Briggs, F., Bunton, J., Cappallo, R., Corey, B., Deshpande, A., deSouza, L., Goeke, R., Greenhill, L., Hazelton, B., Hewitt, J., Johnston-Hollitt, M., Kasper, J., Kincaid, B., Koenig, R., Kratzenberg, E., Lonsdale, C., McWhirter, S., Mitchell, D., Morales, M., Morgan, E., Oberoi, D., Pathikulangara, J., Prabu, T., Remillard, R., Rogers, A., Roshi, A., Salah, J., Sault, R., Udaya Shankar, N., Srivani, K., Stevens, J., Subrahmanyan, R., Webster, R., Whitney, A., Williams, C., Wyithe, J., Trott, Cathryn, Hurley-Walker, Natasha, Wayth, Randall, Macquart, Jean-Pierre, Arcus, Wayne, Emrich, David, Herne, David, Lynch, Mervyn, Ord, Stephen, Tingay, Steven, Waterson, Mark, Williams, Andrew, Bell, M., Murphy, T., Kaplan, D., Hancock, P., Gaensler, B., Banyer, J., Bannister, K., Barnes, D., Bernardi, G., Bowman, J., Briggs, F., Bunton, J., Cappallo, R., Corey, B., Deshpande, A., deSouza, L., Goeke, R., Greenhill, L., Hazelton, B., Hewitt, J., Johnston-Hollitt, M., Kasper, J., Kincaid, B., Koenig, R., Kratzenberg, E., Lonsdale, C., McWhirter, S., Mitchell, D., Morales, M., Morgan, E., Oberoi, D., Pathikulangara, J., Prabu, T., Remillard, R., Rogers, A., Roshi, A., Salah, J., Sault, R., Udaya Shankar, N., Srivani, K., Stevens, J., Subrahmanyan, R., Webster, R., Whitney, A., Williams, C., and Wyithe, J.
Abstract: We present a search for transient and variable radio sources at 154 MHz with the Murchison Widefield Array 32-tile prototype. Fifty-one images were obtained that cover a field of view of 1430 deg2 centred on Hydra A. The observations were obtained over three days in 2010 March and three days in 2011 April and May. The mean cadence of the observations was 26 minutes and there was additional temporal information on day and year timescales. We explore the variability of a sample of 105 low frequency radio sources within the field. Four bright (S > 6 Jy) candidate variable radio sources were identified that displayed low levels of short timescale variability (26 minutes). We conclude that this variability is likely caused by simplifications in the calibration strategy or ionospheric effects. On the timescale of one year we find two sources that show significant variability. We attribute this variability to either refractive scintillation or intrinsic variability. No radio transients were identified and we place an upper limit on the surface density of sources p < 7.5 × 10-5 deg-2 with flux densities > 5.5 Jy, and characteristic timescales of both 26 minutes and one year.
Published: 2013

21. ATPMN: Accurate positions and flux densities at 5 and 8GHz for 8385 sources from the PMN survey

Author: McConnell, D., Sadler, E., Murphy, T., Ekers, Ronald, McConnell, D., Sadler, E., Murphy, T., and Ekers, Ronald
Abstract: We present a source catalogue of 9,040 radio sources resulting from high-resolution observations of 8,385PMN sources with the Australia Telescope Compact Array. The catalogue lists flux density and structural measurements at 4.8 and 8.6 GHz, derived from observations of all PMN sources in the declination range −87° < δ < −38.°5 (exclusive of galactic latitudes |b| < 2°) with flux density S4850 ≥ 70 mJy (50 mJy south of δ = −73°). We assess the quality of the data, which was gathered in 1992–1994, describe the population of catalogued sources, and compare it to samples from complementary catalogues. In particular we find 127 radio sources with probable association with γ-ray sources observed by the orbiting Fermi Large Area Telescope.
Published: 2012

22. Compact continuum source finding for next generation radio surveys

Author: Hancock, Paul, Murphy, T., Gaensler, B., Hopkins, A., Curran, J., Hancock, Paul, Murphy, T., Gaensler, B., Hopkins, A., and Curran, J.
Abstract: We present a detailed analysis of four of the most widely used radio source-finding packagesin radio astronomy, and a program being developed for the Australian Square Kilometer ArrayPathfinder telescope. The four packages: SEXTRACTOR, SFIND, IMSAD and SELAVY are shown to produce source catalogues with high completeness and reliability. In this paper we analyse the small fraction (~1 per cent) of cases in which these packages do not perform well.This small fraction of sources will be of concern for the next generation of radio surveyswhich will produce many thousands of sources on a daily basis, in particular for blind radiotransients surveys. From our analysis we identify the ways in which the underlying sourcefinding algorithms fail. We demonstrate a new source-finding algorithm AEGEAN, based on the application of a Laplacian kernel, which can avoid these problems and can produce complete and reliable source catalogues for the next generation of radio surveys.
Published: 2012

23. The Australia Telescope 20 GHz Survey: the source catalogue

Author: Murphy, T., Sadler, E., Ekers, Ronald, Massardi, M., Hancock, Paul, Mahony, E., Ricci, R., Burke-Spolaor, S., Calabretta, M., Chhetri, R., De Zotti, G., Edwards, P., Ekers, J., Jackson, Carole, Kesteven, M., Lindley, E., Newton-McGee, K., Phillips, C., Roberts, P., Sault, R., Staveley-Smith, L., Subrahmanyan, R., Walker, M., Wilson, W., Murphy, T., Sadler, E., Ekers, Ronald, Massardi, M., Hancock, Paul, Mahony, E., Ricci, R., Burke-Spolaor, S., Calabretta, M., Chhetri, R., De Zotti, G., Edwards, P., Ekers, J., Jackson, Carole, Kesteven, M., Lindley, E., Newton-McGee, K., Phillips, C., Roberts, P., Sault, R., Staveley-Smith, L., Subrahmanyan, R., Walker, M., and Wilson, W.
Abstract: We present the full source catalogue from the Australia Telescope 20 GHz (AT20G) Survey. The AT20G is a blind radio survey carried out at 20 GHz with the Australia Telescope Compact Array (ATCA) from 2004 to 2008, and covers the whole sky south of declination 0?. The AT20G source catalogue presented here is an order of magnitude larger than any previous catalogue of high-frequency radio sources, and includes 5890 sources above a 20 GHz flux-density limit of 40 mJy. All AT20G sources have total intensity and polarization measured at 20 GHz, and most sources south of declination -15? also have near-simultaneous flux-density measurements at 5 and 8 GHz. A total of 1559 sources were detected in polarized total intensity at one or more of the three frequencies.The completeness of the AT20G source catalogue is 91 per cent above 100 mJy beam-1 and 79 per cent above 50 mJy beam-1 in regions south of declination -15?. North of -15?, some observations of sources between 14 and 20 h in right ascension were lost due to bad weather and could not be repeated, so the catalogue completeness is lower in this region. Each detected source was visually inspected as part of our quality control process, and so the reliability of the final catalogue is essentially 100 per cent. We detect a small but significant population of non-thermal sources that are either undetected or have only weak detections in low-frequency catalogues. We introduce the term Ultra-Inverted Spectrum to describe these radio sources, which have a spectral index a(5, 20) >+0.7 and which constitute roughly 1.2 per cent of the AT20G sample.
Published: 2010

24. Wide-field imaging and polarimetry for the biggest and brightest in the 20-GHz southern sky

Author: Burke-Spolaor, S., Ekers, Ronald, Massardi, M., Murphy, T., Partridge, B., Ricci, R., Sadler, E., Burke-Spolaor, S., Ekers, Ronald, Massardi, M., Murphy, T., Partridge, B., Ricci, R., and Sadler, E.
Abstract: We present the wide-field imaging and polarimetry at ? = 20 GHz of seven most extended, bright (Stotal = 0.50 Jy), high-frequency selected radio sources in the southern sky with declinations d < -30°. Accompanying the data are brief reviews of the literature for each source. The results presented here aid in the statistical completeness of the Australia Telescope 20-GHz Survey: the Bright Source Sample. The data are of crucial interest for future cosmic microwave background missions as a collection of information about candidate calibrator sources. We were able to obtain data for seven of the nine sources identified by our selection criteria. We report that Pictor A is thus far the best extragalactic calibrator candidate for the Low Frequency Instrument of the Planck European Space Agency mission due to its high level of integrated polarized flux density (~0.50 ± 0.06 Jy) on a scale of 10 arcmin. Six out of the seven sources have a clearly detected compact radio core in our images, with either a null detection or less than 2 per cent detection of polarized emission from the nuclei. Most sources with detected jets have magnetic field alignments running in a longitudinal configuration, however, PKS 1333-33 exhibits transverse fields and an orthogonal change in field geometry from nucleus to jets. © 2009 RAS.
Published: 2009

25. The Australia Telescope 20-GHz (AT20G) Survey: the Bright Source Sample

Author: Massardi, M., Ekers, Ronald, Murphy, T., Ricci, R., Sadler, E., Burke, S., De Zotti, G., Edwards, P., Hancock, Paul, Jackson, Carole, Kesteven, M., Mahony, E., Phillips, C., Staveley-Smith, L., Subrahmanyan, R., Walker, M., Wilson, W., Massardi, M., Ekers, Ronald, Murphy, T., Ricci, R., Sadler, E., Burke, S., De Zotti, G., Edwards, P., Hancock, Paul, Jackson, Carole, Kesteven, M., Mahony, E., Phillips, C., Staveley-Smith, L., Subrahmanyan, R., Walker, M., and Wilson, W.
Abstract: The Australia Telescope 20-GHz (AT20G) Survey is a blind survey of the whole southern sky at 20 GHz (with follow-up observations at 4.8 and 8.6 GHz) carried out with the Australia Telescope Compact Array from 2004 to 2007. The Bright Source Sample (BSS) is a complete flux-limited subsample of the AT20G Survey catalogue comprising 320 extragalactic (|b| > 1. ? 5) radio sources south of d = -15? withS20 GHz > 0.50 Jy. Of these, 218 have near simultaneous observations at 8 and 5 GHz. In this paper we present an analysis of radio spectral properties in total intensity and polarization, size, optical identifications and redshift distribution of the BSS sources. The analysis of the spectral behaviour shows spectral curvature in most sources with spectral steepening that increases at higher frequencies (the median spectral index a, assuming S ? ?a, decreases from a8.6 4.8 = 0.11 between 4.8 and 8.6 GHz to a20 8.6 = -0.16 between 8.6 and 20 GHz), even if the sample is dominated by flat spectra sources (85 per cent of the sample has a20 8.6 > -0.5). The almost simultaneous spectra in total intensity and polarization allowed us a comparison of the polarized and total intensity spectra: polarized fraction slightly increases with frequency, but the shapes of the spectra have little correlation. Optical identifications provided an estimation of redshift for 186 sources with a median value of 1.20 and 0.13, respectively, for QSO and galaxies.
Published: 2008

26. A leap of faith? Trust in the police among migrants in England and Wales

Author: Bradford, B., Sargeant, E., Murphy, T., Jackson, J., Bradford, B., Sargeant, E., Murphy, T., and Jackson, J.
Abstract: It is often assumed that immigrants in countries such as the United Kingdom will report lower levels of trust in the police. Immigrant communities are thought ‘difficult to police’, and minority groups frequently experience problematic relationships with police. Yet, there has been little empirical investigation of this issue in the United Kingdom. In this paper, data from the Crime Survey of England and Wales are used to explore the relationship between immigration and trust in the police. Results suggest that trust is higher among immigrants than among the UK-born population, although there is important variation by time since arrival and experience of policing. Trust in the police is also higher in neighbourhoods that have more immigrants. The paper concludes with some reflection on the nature of trust in the police.

27. Ileocolic intussusception secondary to Peutz-Jeghers polyp: the need for oncological resection surgery.

Author: Ylli K, Eljack W, Hayes B, and Murphy T
Abstract: In this case report, we detail the management of a woman in her late 30s with ileocolic intussusception, emphasizing the high malignancy risk inherent in adult intussusception cases. Given the patient's acute symptoms and significant family history of ovarian and breast cancers, radical oncological resection was pursued. The surgical intervention comprised a right hemicolectomy and right ovarian cystectomy, with histopathological findings revealing a Peutz-Jeghers polyp and benign thyroid tissue, but no malignancy. This case underscores the imperative for a surgical approach that anticipates the potential for malignancy in adult intussusception, advocating for radical resection as a fundamental strategy, even in the absence of confirmed malignant histopathology, to ensure comprehensive management and alignment with oncological best practices., Competing Interests: None declared., (Published by Oxford University Press and JSCR Publishing Ltd. © The Author(s) 2024.)
Published: 2024
Full Text: View/download PDF

28. The impact of ovarian stimulation on the human endometrial microenvironment.

Author: Chemerinski A, Shen M, Valero-Pacheco N, Zhao Q, Murphy T, George L, Lemenze A, Sherman L, Heller D, Chen X, Wu T, McGovern PG, Morelli SS, Arora R, Beaulieu AM, and Douglas NC
Subjects: Humans, Female, Adult, Cellular Microenvironment, Prospective Studies, Estradiol blood, Embryo Implantation physiology, Progesterone blood, Progesterone metabolism, Pregnancy, Menstrual Cycle, Endometrium metabolism, Ovulation Induction, Transcriptome
Abstract: Study Question: How does ovarian stimulation (OS), which is used to mature multiple oocytes for ART procedures, impact the principal cellular compartments and transcriptome of the human endometrium in the periovulatory and mid-secretory phases?, Summary Answer: During the mid-secretory window of implantation, OS alters the abundance of endometrial immune cells, whereas during the periovulatory period, OS substantially changes the endometrial transcriptome and impacts both endometrial glandular and immune cells., What Is Known Already: Pregnancies conceived in an OS cycle are at risk of complications reflective of abnormal placentation and placental function. OS can alter endometrial gene expression and immune cell populations. How OS impacts the glandular, stromal, immune, and vascular compartments of the endometrium, in the periovulatory period as compared to the window of implantation, is unknown., Study Design, Size, Duration: This prospective cohort study carried out between 2020 and 2022 included 25 subjects undergoing OS and 25 subjects in natural menstrual cycles. Endometrial biopsies were performed in the proliferative, periovulatory, and mid-secretory phases., Participants/materials, Setting, Methods: Blood samples were processed to determine serum estradiol and progesterone levels. Both the endometrial transcriptome and the principal cellular compartments of the endometrium, including glands, stroma, immune, and vasculature, were evaluated by examining endometrial dating, differential gene expression, protein expression, cell populations, and the three-dimensional structure in endometrial tissue. Mann-Whitney U tests, unpaired t-tests or one-way ANOVA and pairwise multiple comparison tests were used to statistically evaluate differences., Main Results and the Role of Chance: In the periovulatory period, OS induced high levels of differential gene expression, glandular-stromal dyssynchrony, and an increase in both glandular epithelial volume and the frequency of endometrial monocytes/macrophages. In the window of implantation during the mid-secretory phase, OS induced changes in endometrial immune cells, with a greater frequency of B cells and a lower frequency of CD4 effector T cells., Large Scale Data: The data underlying this article have been uploaded to the Genome Expression Omnibus/National Center for Biotechnology Information with accession number GSE220044., Limitations, Reasons for Caution: A limited number of subjects were included in this study, although the subjects within each group, natural cycle or OS, were homogenous in their clinical characteristics. The number of subjects utilized was sufficient to identify significant differences; however, with a larger number of subjects and additional power, we may detect additional differences. Another limitation of the study is that proliferative phase biopsies were collected in natural cycles, but not in OS cycles. Given that the OS cycle subjects did not have known endometrial factor infertility, and the comparisons involved subjects who had a similar and robust response to stimulation, the findings are generalizable to women with a normal response to OS., Wider Implications of the Findings: OS substantially altered the periovulatory phase endometrium, with fewer transcriptomic and cell type-specific changes in the mid-secretory phase. Our findings show that after OS, the endometrial microenvironment in the window of implantation possesses many more similarities to that of a natural cycle than does the periovulatory endometrium. Further investigation of the immune compartment and the functional significance of this cellular compartment under OS conditions is warranted., Study Funding/competing Interests: Research reported in this publication was supported by the National Institute of Allergy and Infectious Diseases (R01AI148695 to A.M.B. and N.C.D.), Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD109152 to R.A.), and the March of Dimes (5-FY20-209 to R.A.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or March of Dimes. All authors declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of European Society of Human Reproduction and Embryology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
Published: 2024
Full Text: View/download PDF

29. Cattle, carcass, economic, and estimated emission impacts of feeding finishing steers lubabegron or ractopamine hydrochloride.

Author: McAtee TB, Renter DG, Murphy T, Betts NB, and Depenbusch BE
Abstract: Lubabegron (Experior; Elanco, Greenfield, IN, USA) is the first U.S. Food and Drug Administration approved feed additive for reducing gas emissions from feedlot animals or their waste; it does not have live or carcass performance claims. Our primary objective was to determine the effect of lubabegron on feedlot performance and carcass traits in finishing beef steers compared to ractopamine hydrochloride (Optaflexx; Elanco, Greenfield, IN, USA). A commercial feedlot trial using cross-bred beef steers ( n = 2,117; 373 ± 15 kg initial body weight [BW]) was completed with a randomized complete block design. Treatments consisted of two feed additives: (1) OPT targeted to deliver 300 mg/animal/d of ractopamine hydrochloride for 28 ± 7 d out from harvest and (2) EXP targeted to deliver 36 mg/animal/d of lubabegron 56 ± 7 d out from harvest and a 4-d preslaughter withdrawal period. Twenty 70 to 142 hd pens with 10 pens per treatment were used. Cattle were weighed at arrival processing and at harvest and fed for an average of 167 d. Data were used to calculate production metrics, partial budgets, and estimated greenhouse gas emissions using published methods, and were analyzed using linear mixed models with pen as the experimental unit and block as a random intercept. A statistical significance threshold of α = 0.05 was determined a priori. There was no evidence for statistically significant differences between treatments for initial BW ( P = 0.70), health-related outcomes ( P values ≥ 0.43), or mobility scores (P = 0.09). Cattle-fed EXP had increased final BW, ADG, G:F, and decreased dry matter intake ( P values ≤ 0.01) compared to OPT. Carcasses were 11 ± 1.76 kg (hot carcass weight) heavier in EXP group ( P < 0.01), and differed between treatments for both yield grades (YG) and quality grades distributions (P values ≤ 0.01). Cattle-fed EXP had a shift toward more YG 1 and 2, select and sub-select carcasses compared to OPT, which had as shift toward more YG 3, 4, 5, prime and choice carcasses. With increased beef production and efficiency compared to OPT, the estimated CO 2 equivalent emissions from production were reduced by 6.2% per unit of carcass weight for EXP ( P ≤ 0.01). Estimated net returns/animal shipped were $56.61 ± 9.37 more for EXP than OPT ( P ≤ 0.01). In conclusion, when cattle were fed for the same total number of days, feeding EXP compared to OPT increased net returns, feedlot performance, and efficiency, but resulted in carcass yield and quality characteristics that may impact marketing programs., Competing Interests: One author (NB) is an employee of Elanco Animal Health, but he had no role in the design or implementation of the study; he calculated estimated emissions for de-identified lots (i.e., was masked to treatments). Other authors (DR, BD) have previously received funding from Elanco Animal Health for research or consulting work., (© The Author(s) 2024. Published by Oxford University Press on behalf of the American Society of Animal Science.)
Published: 2024
Full Text: View/download PDF

30. Traumatic brain injury disrupts state-dependent functional cortical connectivity in a mouse model.

Author: Bottom-Tanzer S, Corella S, Meyer J, Sommer M, Bolaños L, Murphy T, Quiñones S, Heiney S, Shtrahman M, Whalen M, Oren R, Higley MJ, Cardin JA, Noubary F, Armbruster M, and Dulla C
Subjects: Humans, Mice, Animals, Adolescent, Disease Models, Animal, Cerebral Cortex diagnostic imaging, Cognition, Brain Injuries, Traumatic complications, Brain Injuries, Traumatic diagnostic imaging, Brain Injuries
Abstract: Traumatic brain injury (TBI) is the leading cause of death in young people and can cause cognitive and motor dysfunction and disruptions in functional connectivity between brain regions. In human TBI patients and rodent models of TBI, functional connectivity is decreased after injury. Recovery of connectivity after TBI is associated with improved cognition and memory, suggesting an important link between connectivity and functional outcome. We examined widespread alterations in functional connectivity following TBI using simultaneous widefield mesoscale GCaMP7c calcium imaging and electrocorticography (ECoG) in mice injured using the controlled cortical impact (CCI) model of TBI. Combining CCI with widefield cortical imaging provides us with unprecedented access to characterize network connectivity changes throughout the entire injured cortex over time. Our data demonstrate that CCI profoundly disrupts functional connectivity immediately after injury, followed by partial recovery over 3 weeks. Examining discrete periods of locomotion and stillness reveals that CCI alters functional connectivity and reduces theta power only during periods of behavioral stillness. Together, these findings demonstrate that TBI causes dynamic, behavioral state-dependent changes in functional connectivity and ECoG activity across the cortex., (© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Published: 2024
Full Text: View/download PDF

31. Diagnostic performance of clinical likelihood models of obstructive coronary artery disease to predict myocardial perfusion defects.

Author: Rasmussen LD, Albertsen LEB, Nissen L, Ejlersen JA, Isaksen C, Murphy T, Søndergaard HM, Kirk J, Brix L, Gormsen LC, Petersen SE, Bøttcher M, and Winther S
Subjects: Humans, Likelihood Functions, Coronary Angiography methods, Tomography, Emission-Computed, Single-Photon methods, Computed Tomography Angiography, Predictive Value of Tests, Coronary Artery Disease epidemiology, Coronary Stenosis diagnosis, Myocardial Perfusion Imaging methods
Abstract: Aims: Clinical likelihood (CL) models are designed based on a reference of coronary stenosis in patients with suspected obstructive coronary artery disease. However, a reference standard for myocardial perfusion defects (MPDs) could be more appropriate. We aimed to investigate the ability of the 2019 European Society of Cardiology pre-test probability (ESC-PTP), the risk-factor-weighted (RF-CL) model, and coronary artery calcium score-weighted (CACS-CL) model to diagnose MPDs., Methods and Results: Symptomatic stable de novo chest pain patients (n = 3374) underwent coronary computed tomography angiography and subsequent myocardial perfusion imaging by single-photon emission computed tomography, positron emission tomography, or cardiac magnetic resonance. For all modalities, MPD was defined as coronary computed tomography angiography with suspected stenosis and stress-perfusion abnormality in ≥2 segments. The ESC-PTP was calculated based on age, sex, and symptom typicality, and the RF-CL and CACS-CL additionally included a number of risk factors and CACS. In total, 219/3374 (6.5%) patients had an MPD. Both the RF-CL and the CACS-CL classified substantially more patients to low CL (<5%) of obstructive coronary artery disease compared with the ESC-PTP (32.5 and 54.1 vs. 12.0%, P < 0.001) with preserved low prevalences of MPD (<2% for all models). Compared with the ESC-PTP [area under the receiver-operating characteristic curve (AUC) 0.74 (0.71-0.78)], the discrimination of having an MPD was higher for the CACS-CL model [AUC 0.88 (0.86-0.91), P < 0.001], while it was similar for the RF-CL model [AUC 0.73 (0.70-0.76), P = 0.32]., Conclusion: Compared with basic CL models, the RF-CL and CACS-CL models improve down classification of patients to a very low-risk group with a low prevalence of MPD., Competing Interests: Conflict of interest: L.D.R. acknowledges support from the Danish Cardiovascular Academy (grant number PD5Y-2023001-DCA), which is funded by the Novo Nordisk Foundation (grant number NNF20SA0067242) and The Danish Heart Foundation. S.W. acknowledges support from the Novo Nordisk Foundation Clinical Emerging Investigator grant (NNF21OC0066981). S.E.P. provides consultancy to Circle Cardiovascular Imaging Inc. M.B. discloses advisory board participation for Novo Nordisk, Astra-Zeneca, Pfizer, Boeringer Ingelheim, Bayer, Sanofi, Novartis, Amgen, CLS-Behring Acarix, and MEDtrace. All other authors declare no conflicts of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of the European Society of Cardiology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Published: 2023
Full Text: View/download PDF

32. Neuroticism personality traits are linked to adverse cardiovascular phenotypes in the UK Biobank.

Author: Mahmood A, Simon J, Cooper J, Murphy T, McCracken C, Quiroz J, Laranjo L, Aung N, Lee AM, Khanji MY, Neubauer S, Raisi-Estabragh Z, Maurovich-Horvat P, and Petersen SE
Subjects: Male, Humans, Female, Middle Aged, Aged, Neuroticism, Magnetic Resonance Imaging, Cine methods, Stroke Volume, Heart Ventricles diagnostic imaging, Personality, United Kingdom, Ventricular Function, Left, Biological Specimen Banks
Abstract: Aims: To evaluate the relationship between neuroticism personality traits and cardiovascular magnetic resonance (CMR) measures of cardiac morphology and function, considering potential differential associations in men and women., Methods and Results: The analysis includes 36 309 UK Biobank participants (average age = 63.9 ± 7.7 years; 47.8% men) with CMR available and neuroticism score assessed by the 12-item Eysenck Personality Questionnaire-Revised Short Form. CMR scans were performed on 1.5 Tesla scanners (MAGNETOM Aera, Siemens Healthcare, Erlangen, Germany) according to pre-defined protocols and analysed using automated pipelines. We considered measures of left ventricular (LV) and right ventricular (RV) structure and function, and indicators of arterial compliance. Multivariable linear regression was used to estimate association of neuroticism score with individual CMR metrics, with adjustment for age, sex, obesity, deprivation, smoking, diabetes, hypertension, hypercholesterolaemia, alcohol use, exercise, and education. Higher neuroticism scores were associated with smaller LV and RV end-diastolic volumes, lower LV mass, greater concentricity (higher LV mass to volume ratio), and higher native T1. Greater neuroticism was also linked to poorer LV and RV function (lower stroke volumes) and greater arterial stiffness. In sex-stratified analyses, the relationships between neuroticism and LV stroke volume, concentricity, and arterial stiffness were attenuated in women. In men, association (with exception of native T1) remained robust., Conclusion: Greater tendency towards neuroticism personality traits is linked to smaller, poorer functioning ventricles with lower LV mass, higher myocardial fibrosis, and higher arterial stiffness. These relationships are independent of traditional vascular risk factors and are more robust in men than women., Competing Interests: Conflict of interest: S.E.P. provides consultancy to Cardiovascular Imaging Inc, Calgary, Alberta, Canada. The remaining authors have no disclosures., (© The Author(s) 2023. Published by Oxford University Press on behalf of the European Society of Cardiology.)
Published: 2023
Full Text: View/download PDF

33. Parsing human rights, promoting health equity: reflections on Colombia's response to Venezuelan migration.

Author: Angeleri S and Murphy T
Subjects: Humans, Venezuela, Colombia, Human Rights, Socioeconomic Factors, Health Equity
Abstract: Over the last 7 years, a multidimensional crisis in Venezuela has resulted in massive emigration. Over 7 million have fled the country, with more than 2.4 million seeking to settle in Colombia. Of these, as of 2021, more than 1 million were undocumented, but the situation has started to change with the implementation of an ambitious migrant regularisation scheme. Regularisation promises access to comprehensive healthcare, full educational opportunities and the formal labour market. Securing these social determinants of health is critical because social inequalities produce health inequalities-that is, systematic health differences that are preventable and thus unjust. Social medicine, social epidemiology and international human rights law agree on this, yet law-focused studies of health equity initiatives remain rare. Aiming to reverse this, we examine Colombia's response to Venezuelan migration, including its recent migrant regularisation initiative, which was introduced in part to comply with the country's obligations under international human rights law. The examination foregrounds what we are calling 'legal literacy', testing the hypothesis that advancing health equity involves asking more and better questions about international human rights law., (© The Author(s) 2023. Published by Oxford University Press.)
Published: 2023
Full Text: View/download PDF

34. Predicting progression to Alzheimer's disease with human hippocampal progenitors exposed to serum.

Author: Maruszak A, Silajdžić E, Lee H, Murphy T, Liu B, Shi L, de Lucia C, Douiri A, Salta E, Nevado AJ, Teunissen CE, Visser PJ, Price J, Zetterberg H, Lovestone S, and Thuret S
Subjects: Adult, Humans, Hippocampus metabolism, Learning, Neurogenesis physiology, Disease Progression, Alzheimer Disease metabolism, Cognitive Dysfunction psychology
Abstract: Adult hippocampal neurogenesis is important for learning and memory and is altered early in Alzheimer's disease. As hippocampal neurogenesis is modulated by the circulatory systemic environment, evaluating a proxy of how hippocampal neurogenesis is affected by the systemic milieu could serve as an early biomarker for Alzheimer's disease progression. Here, we used an in vitro assay to model the impact of systemic environment on hippocampal neurogenesis. A human hippocampal progenitor cell line was treated with longitudinal serum samples from individuals with mild cognitive impairment, who either progressed to Alzheimer's disease or remained cognitively stable. Mild cognitive impairment to Alzheimer's disease progression was characterized most prominently with decreased proliferation, increased cell death and increased neurogenesis. A subset of 'baseline' cellular readouts together with education level were able to predict Alzheimer's disease progression. The assay could provide a powerful platform for early prognosis, monitoring disease progression and further mechanistic studies., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Guarantors of Brain.)
Published: 2023
Full Text: View/download PDF

35. Ventricular tachycardia storm and hypertrophic cardiomyopathy: cardiovascular magnetic resonance guiding management in presence of implantable cardioverter-defibrillator.

Author: Murphy T, Sawhney V, Lowe M, and Khanji MY
Subjects: Humans, Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy, Cardiomyopathy, Hypertrophic complications, Cardiomyopathy, Hypertrophic diagnostic imaging, Cardiomyopathy, Hypertrophic therapy, Defibrillators, Implantable, Tachycardia, Ventricular diagnostic imaging, Tachycardia, Ventricular therapy
Published: 2022
Full Text: View/download PDF

36. Database resources of the national center for biotechnology information.

Author: Sayers EW, Bolton EE, Brister JR, Canese K, Chan J, Comeau DC, Connor R, Funk K, Kelly C, Kim S, Madej T, Marchler-Bauer A, Lanczycki C, Lathrop S, Lu Z, Thibaud-Nissen F, Murphy T, Phan L, Skripchenko Y, Tse T, Wang J, Williams R, Trawick BW, Pruitt KD, and Sherry ST
Subjects: Databases, Chemical, Databases, Nucleic Acid, Databases, Protein, Humans, Internet, National Library of Medicine (U.S.), PubMed, United States, Biotechnology trends, Databases, Genetic trends
Abstract: The National Center for Biotechnology Information (NCBI) produces a variety of online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the most of these databases. Resources receiving significant updates in the past year include PubMed, PMC, Bookshelf, RefSeq, SRA, Virus, dbSNP, dbVar, ClinicalTrials.gov, MMDB, iCn3D and PubChem. These resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov., (Published by Oxford University Press on behalf of Nucleic Acids Research 2021.)
Published: 2022
Full Text: View/download PDF

37. Data Resource Profile: The Opioid Agonist Treatment and Safety (OATS) Study, New South Wales, Australia.

Author: Larney S, Jones N, Fiellin DA, Nielsen S, Hickman M, Dobbins T, Murphy T, Ali R, and Degenhardt L
Subjects: Australia epidemiology, Humans, New South Wales epidemiology, Analgesics, Opioid adverse effects, Opioid-Related Disorders drug therapy, Opioid-Related Disorders epidemiology
Published: 2021
Full Text: View/download PDF

38. A Quantitative Retrospective Exposure Assessment for Former Chrysotile Asbestos Miners and Millers from Baie Verte, NL, Canada.

Author: Giles Murphy T, Bornstein S, Oudyk J, and Demers PA
Subjects: Asbestos, Serpentine, Canada, Humans, Italy, Quebec, Retrospective Studies, Asbestos adverse effects, Mesothelioma chemically induced, Mesothelioma epidemiology, Occupational Diseases chemically induced, Occupational Diseases epidemiology, Occupational Exposure
Abstract: Despite numerous studies of asbestos workers in the epidemiologic literature, there are very few cohort studies of chrysotile asbestos miners/millers that include high-quality retrospective exposure assessments. As part of the creation of the Baie Verte Miners' Registry in 2008, a two-dimensional job exposure matrix (JEM) was developed for estimating asbestos exposures for former chrysotile asbestos miners/millers. Industrial hygiene data collected between 1963 and 1994 were analysed to assess validity for use in a retrospective exposure assessment and epidemiologic study. Registered former employees were divided into 52 exposure groups (EGs) based on job title and department and mean asbestos concentrations were calculated for each EG. The resulting exposure estimates were linked to individual registrants' work histories allowing for the calculation of cumulative asbestos exposure for each registrant. The distribution of exposure for most EGs (82.6%) could be described as fitting a log-normal distribution, although variability within some EGs (55%) exceeded a geometric standard deviation (GSD) of 2.5. Overall, the data used to create EGs in the development of the JEM were deemed to be of adequate quality for estimating cumulative asbestos exposures for the former employees of the Baie Verte asbestos mine/mill. The variability between workers in the same job was often high and is an important factor to be considered when using estimates of cumulative asbestos exposure to adjudicate compensation claims. The exposures experienced in this cohort were comparable to those of other chrysotile asbestos miners/millers cohorts, specifically Italian and Québec cohorts., (© The Author(s) 2020. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.)
Published: 2021
Full Text: View/download PDF

39. Barrett's Registry Collaboration of academic centers in Ireland reveals high progression rate of low-grade dysplasia and low risk from nondysplastic Barrett's esophagus: report of the RIBBON network.

Author: O'Byrne LM, Witherspoon J, Verhage RJJ, O'Brien M, Muldoon C, Ryan C, Buckley M, Murphy T, Reynolds R, Patchett S, Kay E, Azam H, Robb W, Arumugasamy M, Mathuna PM, Leyden J, Gargan S, Doherty G, Sheahan K, Collins C, Nath A, O'Sullivan J, Donohoe CL, Ravi N, O'Toole D, and Reynolds JV
Subjects: Disease Progression, Female, Humans, Ireland epidemiology, Male, Registries, Barrett Esophagus epidemiology, Esophageal Neoplasms epidemiology, Esophageal Neoplasms etiology, Precancerous Conditions epidemiology
Abstract: Barrett's esophagus (BE) is the main pathological precursor of esophageal adenocarcinoma (EAC). Progression to high-grade dysplasia (HGD) or EAC from nondysplastic BE (NDBE), low-grade dysplasia (LGD) and indefinite for dysplasia (IND) varies widely between population-based studies and specialized centers for many reasons, principally the rigor of the biopsy protocol and the accuracy of pathologic definition. In the Republic of Ireland, a multicenter prospective registry and bioresource (RIBBON) was established in 2011 involving six academic medical centers, and this paper represents the first report from this network. A detailed clinical, endoscopic and pathologic database registered 3,557 patients. BE was defined strictly by both endoscopic evidence of Barrett's epithelium and the presence of specialized intestinal metaplasia (SIM). A prospective web-based database was used to gather information with initial and follow-up data abstracted by a data manager at each site. A total of 2,244 patients, 1,925 with no dysplasia, were included with complete follow-up. The median age at diagnosis was 60.5 with a 2.1:1 male to female ratio and a median follow-up time of 2.7 years (IQR 1.19-4.04), and 6609.25 person years. In this time period, 125 (5.57%) progressed to HGD/EAC, with 74 (3.3%) after 1 year of follow-up and 38 (1.69%) developed EAC, with 20 (0.89%) beyond 1 year. The overall incidence of HGD/EAC was 1.89% per year; 1.16% if the first year is excluded. The risk of progression to EAC alone overall was 0.57% per year, 0.31% excluding the first year, and 0.21% in the 1,925 patients who had SIM alone at diagnosis. Low-grade dysplasia (LGD) progressed to HGD/EAC in 31% of patients, a progression rate of 12.96% per year, 6.71% with the first year excluded. In a national collaboration of academic centers in Ireland, the progression rate for NDBE was similar to recent population studies. Almost one in two who progressed was evident within 1 year. Crucially, LGD diagnosed and confirmed by specialist gastrointestinal pathologists represents truly high-risk disease, highlighting the importance of expertise in diagnosis and management, and providing indirect support for ablative therapies in this context., (© The Author(s) 2020. Published by Oxford University Press on behalf of International Society for Diseases of the Esophagus. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Published: 2020
Full Text: View/download PDF

40. Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

Author: Pujar S, O'Leary NA, Farrell CM, Loveland JE, Mudge JM, Wallin C, Girón CG, Diekhans M, Barnes I, Bennett R, Berry AE, Cox E, Davidson C, Goldfarb T, Gonzalez JM, Hunt T, Jackson J, Joardar V, Kay MP, Kodali VK, Martin FJ, McAndrews M, McGarvey KM, Murphy M, Rajput B, Rangwala SH, Riddick LD, Seal RL, Suner MM, Webb D, Zhu S, Aken BL, Bruford EA, Bult CJ, Frankish A, Murphy T, and Pruitt KD
Subjects: Animals, Data Curation methods, Data Curation standards, Guidelines as Topic, Humans, Mice, Molecular Sequence Annotation, National Library of Medicine (U.S.), United States, User-Computer Interface, Consensus Sequence, Databases, Genetic standards, Open Reading Frames
Abstract: The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community., (Published by Oxford University Press on behalf of Nucleic Acids Research 2017.)
Published: 2018
Full Text: View/download PDF

41. Adult neck hemangiolymphangioma: a case and review of its etiology, diagnosis and management.

Author: Murphy T, Ramai D, Lai J, Sullivan K, and Grimes C
Abstract: Vascular anomalies constitute some of the most difficult diagnostic and therapeutic enigmas in the practice of medicine, ranging from an asymptomatic birthmark to life-threatening congestive heart failure. Hemangiolymphangiomas (HLA) are extremely rare vascular malformations of both lymphatic and blood vessels in which 80-90% are diagnosed during the first 2 years of life. Though rare, these vascular malformations have promising clinical outcomes. We report a case of a 28-year-old male who presented with a neck mass of unknown etiology. A computed axial tomography scan revealed a cystic mass, and subsequent aspiration biopsy showed lymphatic fluid. The mass was surgically excised and identified as a 6 × 6 × 3 cm 3 multilocular cystic mass weighing 81 g. Histopathology showed cellular characteristics consistent with HLA. We review the salient clinical and pathophysiologic features of vascular anomalies.
Published: 2017
Full Text: View/download PDF

42. β1-Adrenergic and M2 Muscarinic Autoantibodies and Thyroid Hormone Facilitate Induction of Atrial Fibrillation in Male Rabbits.

Author: Li H, Murphy T, Zhang L, Huang B, Veitla V, Scherlag BJ, Kem DC, and Yu X
Subjects: Adrenergic beta-1 Receptor Agonists blood, Adrenergic beta-1 Receptor Agonists chemistry, Adrenergic beta-1 Receptor Agonists metabolism, Animals, Antigens pharmacology, Antigens therapeutic use, Antigens toxicity, Atrial Fibrillation chemically induced, Atrial Fibrillation immunology, Atrial Fibrillation prevention & control, Autoantibodies analysis, Autoantibodies biosynthesis, Autoantibodies chemistry, Coronary Sinus drug effects, Coronary Sinus immunology, Coronary Sinus physiopathology, Graves Disease blood, Graves Disease immunology, Graves Disease metabolism, Heart Atria drug effects, Heart Atria immunology, Heart Atria physiopathology, Heart Conduction System drug effects, Heart Conduction System immunology, Heart Conduction System physiopathology, Male, Muscarinic Agonists blood, Muscarinic Agonists chemistry, Muscarinic Agonists metabolism, Peptide Fragments pharmacology, Peptide Fragments therapeutic use, Peptide Fragments toxicity, Rabbits, Receptor, Muscarinic M2 agonists, Receptor, Muscarinic M2 chemistry, Receptors, Adrenergic, beta-1 chemistry, Refractory Period, Electrophysiological drug effects, Tachycardia chemically induced, Thyroxine blood, Thyroxine pharmacology, Thyroxine poisoning, Up-Regulation drug effects, Atrial Fibrillation etiology, Disease Models, Animal, Graves Disease physiopathology, Receptor, Muscarinic M2 metabolism, Receptors, Adrenergic, beta-1 metabolism, Tachycardia etiology, Thyroxine metabolism
Abstract: Activating autoantibodies to the β1-adrenergic and M2 muscarinic receptors are present in a very high percentage of patients with Graves' disease and atrial fibrillation (AF). The objective of this study was to develop a reproducible animal model and thereby to examine the impact of these endocrine-like autoantibodies alone and with thyroid hormone on induction of thyroid-associated atrial tachyarrhythmias. Five New Zealand white rabbits were coimmunized with peptides from the second extracellular loops of the β1-adrenergic and M2 muscarinic receptors to produce both sympathomimetic and parasympathomimetic antibodies. A catheter-based electrophysiological study was performed on anesthetized rabbits before and after immunization and subsequent treatment with thyroid hormone. Antibody expression facilitated the induction of sustained sinus, junctional and atrial tachycardias, but not AF. Addition of excessive thyroid hormone resulted in induced sustained AF in all animals. AF induction was blocked acutely by the neutralization of these antibodies with immunogenic peptides despite continued hyperthyroidism. The measured atrial effective refractory period as one parameter of AF propensity shortened significantly after immunization and was acutely reversed by peptide neutralization. No further decrease in the effective refractory period was observed after the addition of thyroid hormone, suggesting other cardiac effects of thyroid hormone may contribute to its role in AF induction. This study demonstrates autonomic autoantibodies and thyroid hormone potentiate the vulnerability of the heart to AF, which can be reversed by decoy peptide therapy. These data help fulfill Witebsky's postulates for an increased autoimmune/endocrine basis for Graves' hyperthyroidism and AF.
Published: 2016
Full Text: View/download PDF

43. Kinship: born and bred (but also facilitated)? A commentary on 'Donor conception: ethical aspects of information sharing' (Nuffield Council on Bioethics, London 2013).

Author: Murphy T and Turkmendag I
Subjects: Access to Information legislation & jurisprudence, Decision Making ethics, Disclosure legislation & jurisprudence, Human Rights legislation & jurisprudence, Humans, Parent-Child Relations legislation & jurisprudence, Privacy legislation & jurisprudence, Reproductive Techniques, Assisted legislation & jurisprudence, Tissue Donors legislation & jurisprudence, United Kingdom, Access to Information ethics, Bioethics, Disclosure ethics, Reproductive Techniques, Assisted ethics, Tissue Donors ethics
Published: 2014
Full Text: View/download PDF

44. Regulatory 'desirables' for new health technologies.

Author: Farrell AM, Devaney S, Hervey TK, and Murphy T
Subjects: Access to Information, Community Participation, European Union, Humans, Nanotechnology legislation & jurisprudence, Risk Assessment, Uncertainty, Biomedical Technology legislation & jurisprudence, Government Regulation
Published: 2013
Full Text: View/download PDF

45. A Western diet increases serotonin availability in rat small intestine.

Author: Bertrand RL, Senadheera S, Markus I, Liu L, Howitt L, Chen H, Murphy TV, Sandow SL, and Bertrand PP
Subjects: Animals, Blood Glucose, Disease Models, Animal, Electrochemistry methods, Gene Expression Regulation, Male, RNA, Messenger genetics, RNA, Messenger metabolism, RNA-Binding Proteins genetics, RNA-Binding Proteins metabolism, Random Allocation, Rats, Rats, Sprague-Dawley, Tryptophan Hydroxylase genetics, Tryptophan Hydroxylase metabolism, Diet, Ileum metabolism, Obesity metabolism, Serotonin metabolism
Abstract: Diet-induced obesity is associated with changes in gastrointestinal function and induction of a mild inflammatory state. Serotonin (5-HT) containing enterochromaffin (EC) cells within the intestine respond to nutrients and are altered by inflammation. Thus, our aim was to characterize the uptake and release of 5-HT from EC cells of the rat ileum in a physiologically relevant model of diet-induced obesity. In chow-fed (CF) and Western diet-fed (WD) rats electrochemical methods were used to measure compression evoked (peak) and steady state (SS) 5-HT levels with fluoxetine used to block the serotonin reuptake transporter (SERT). The levels of mRNA for tryptophan hydroxylase 1 (TPH1) and SERT were determined by quantitative PCR, while EC cell numbers were determined immunohistochemically. In WD rats, the levels of 5-HT were significantly increased (SS: 19.2 ± 3.7 μm; peak: 73.5 ± 14.1 μm) compared with CF rats (SS: 12.3 ± 1.8 μm; peak: 32.2 ± 7.2 μm), while SERT-dependent uptake of 5-HT was reduced (peak WD: 108% of control versus peak CF: 212% control). In WD rats, there was a significant increase in TPH1 mRNA, a decrease in SERT mRNA and protein, and an increase in EC cells. In conclusion, our data show that foods typical of a Western diet are associated with an increased 5-HT availability in the rat ileum. Increased 5-HT availability is driven by the up-regulation of 5-HT synthesis genes, decreased re-uptake of 5-HT, and increased numbers and/or 5-HT content of EC cells which are likely to cause altered intestinal motility and sensation in vivo.
Published: 2011
Full Text: View/download PDF

46. ETV5 regulates sertoli cell chemokines involved in mouse stem/progenitor spermatogonia maintenance.

Author: Simon L, Ekman GC, Garcia T, Carnes K, Zhang Z, Murphy T, Murphy KM, Hess RA, Cooke PS, and Hofmann MC
Subjects: Animals, Blotting, Western, Cell Movement genetics, Cells, Cultured, Chemokine CCL7 genetics, Chemokine CCL7 metabolism, Chemokine CXCL5 genetics, Chemokine CXCL5 metabolism, Chemokines genetics, Chemokines, CC genetics, Chemokines, CC metabolism, DNA-Binding Proteins genetics, Electrophoretic Mobility Shift Assay, Immunohistochemistry, Macrophage Inflammatory Proteins genetics, Macrophage Inflammatory Proteins metabolism, Male, Mice, Mice, Inbred C57BL, Mice, Knockout, Monocyte Chemoattractant Proteins genetics, Monocyte Chemoattractant Proteins metabolism, Polymerase Chain Reaction, Promoter Regions, Genetic genetics, Protein Binding, RNA Interference, Receptors, CCR1 genetics, Receptors, CCR1 metabolism, Testis cytology, Testis metabolism, Transcription Factors genetics, Chemokines metabolism, DNA-Binding Proteins metabolism, Sertoli Cells metabolism, Spermatogonia cytology, Spermatogonia metabolism, Stem Cells cytology, Stem Cells metabolism, Transcription Factors metabolism
Abstract: Spermatogonial stem cells are the only stem cells in the body that transmit genetic information to offspring. Although growth factors responsible for self-renewal of these cells are known, the factors and mechanisms that attract and physically maintain these cells within their microenvironment are poorly understood. Mice with targeted disruption of Ets variant gene 5 (Etv5) show total loss of stem/progenitor spermatogonia following the first wave of spermatogenesis, resulting in a Sertoli cell-only phenotype and aspermia. Microarray analysis of primary Sertoli cells from Etv5 knockout (Etv5(-/-)) versus wild-type (WT) mice revealed significant decreases in expression of several chemokines. Chemotaxis assays demonstrated that migration of stem/progenitor spermatogonia toward Etv5(-/-) Sertoli cells was significantly decreased compared to migration toward WT Sertoli cells. Interestingly, differentiating spermatogonia, spermatocytes, and round spermatids were not chemoattracted by WT Sertoli cells, whereas stem/progenitor spermatogonia showed a high and significant chemotactic index. Rescue assays using recombinant chemokines indicated that C-C-motif ligand 9 (CCL9) facilitates Sertoli cell chemoattraction of stem/progenitor spermatogonia, which express C-C-receptor type 1 (CCR1). In addition, there is protein-DNA interaction between ETV5 and Ccl9, suggesting that ETV5 might be a direct regulator of Ccl9 expression. Taken together, our data show for the first time that Sertoli cells are chemoattractive for stem/progenitor spermatogonia, and that production of specific chemokines is regulated by ETV5. Therefore, changes in chemokine production and consequent decreases in chemoattraction by Etv5(-/-) Sertoli cells helps to explain stem/progenitor spermatogonia loss in Etv5(-/-) mice.
Published: 2010
Full Text: View/download PDF

47. BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum.

Author: Kim HS, Murphy T, Xia J, Caragea D, Park Y, Beeman RW, Lorenzen MD, Butcher S, Manak JR, and Brown SJ
Subjects: Animals, Computational Biology trends, Databases, Protein, Expressed Sequence Tags, Genome, Genomics, Information Storage and Retrieval methods, Internet, Models, Genetic, Protein Structure, Tertiary, Software, Computational Biology methods, Databases, Genetic, Databases, Nucleic Acid, Tribolium genetics
Abstract: BeetleBase (http://www.beetlebase.org) has been updated to provide more comprehensive genomic information for the red flour beetle Tribolium castaneum. The database contains genomic sequence scaffolds mapped to 10 linkage groups (genome assembly release Tcas_3.0), genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The database was reconstructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relatational database using the Chado schema and visualized as tracks in GBrowse. The updated genetic map is visualized using the comparative genetic map viewer CMAP. To enhance the database search capabilities, the BLAST and BLAT search tools have been integrated with the GMOD tools. BeetleBase serves as a long-term repository for Tribolium genomic data, and is compatible with other model organism databases.
Published: 2010
Full Text: View/download PDF

48. digeR: a graphical user interface R package for analyzing 2D-DIGE data.

Author: Fan Y, Murphy TB, and Watson RW
Subjects: Proteomics methods, User-Computer Interface, Computer Graphics, Electrophoresis, Gel, Two-Dimensional methods, Software
Abstract: Unlabelled: 2D Difference In-Gel Electrophoresis (2D-DIGE) or 2D gel technology is being used as a routine proteomics technique for biomarker discovery. Analyzing such high-dimensional data requires multivariate analysis techniques to be applied. In addition, protein post-translational modification (PTM) information from the 2D gel data is usually overlooked. We report on an R package, digeR, with an easy to use graphical user interface for analyzing 2D-DIGE (2D gel) data. It provides a tool for visually looking for potential PTM changes from different biological states and support biomarker discovery through multivariate analysis techniques., Availability: digeR package is freely available from the CRAN: http://cran.r-project.org/web/packages/digeR/index.html.
Published: 2009
Full Text: View/download PDF

49. Is human rights prepared? Risk, rights and public health emergencies.

Author: Murphy T and Whitty N
Subjects: Humans, Security Measures legislation & jurisprudence, Emergencies, Human Rights legislation & jurisprudence, Public Health, Risk
Published: 2009
Full Text: View/download PDF

50. Effects of ETV5 (ets variant gene 5) on testis and body growth, time course of spermatogonial stem cell loss, and fertility in mice.

Author: Schlesser HN, Simon L, Hofmann MC, Murphy KM, Murphy T, Hess RA, and Cooke PS
Subjects: Animals, Cell Death genetics, Female, Growth and Development genetics, Male, Mice, Mice, Knockout, Organ Size genetics, Spermatogenesis genetics, Body Weight genetics, DNA-Binding Proteins genetics, DNA-Binding Proteins physiology, Fertility genetics, Spermatogonia physiology, Stem Cells physiology, Testis growth & development, Transcription Factors genetics, Transcription Factors physiology
Abstract: The transcription factor ets variant gene 5 (ETV5; also known as ERM) is essential for self-renewal of spermatogonial stem cells (SSCs). Mice with targeted disruption of Etv5 (Etv5(-/-)) undergo the first wave of spermatogenesis, but all SSCs are lost during this time, causing a Sertoli cell-only phenotype. This study examined body and testis growth and the time course of SSC loss in Etv5(-/-) mice to understand how loss of ETV5 impacts testicular and somatic development. Body weights were reduced in postnatal Etv5(-/-) males, indicating a role of ETV5 in growth. Testis weights and histology in Etv5(-/-) and wild-type (WT) males were similar at Postnatal Day 4, but testis weights were reduced at d8 and subsequently, indicating that ETV5 impacts postnatal testis growth. SSC density (SSCs per mum(2) of seminiferous tubule), estimated using an antibody against GFRA1, was similar in 4d WT and Etv5(-/-) mice. By 8 and 12d, GFRA1-positive cell density in Etv5(-/-) mice was decreased 17% and 32%, respectively, vs. WT. By 28d, GFRA1-positive cell density in Etv5(-/-) was reduced 95%, and GFRA1-positive cells were absent in 36d Etv5(-/-) males. In contrast to WT, 35- to 56-day-old Etv5(-/-) mice were infertile as assessed by natural breeding, artificial insemination, and in vitro fertilization, although motile sperm were present in epididymides of Etv5(-/-) mice during this time. In summary, initial testis development is normal in Etv5(-/-) mice despite decreased body weight, but SSC loss begins between 4 and 8d of age, indicating that ETV5 has effects beginning in the early neonatal period. Etv5(-/-) mice are infertile even when sperm is produced, indicating that ETV5 loss has other effects besides lack of SSC self-renewal that impair fertility.
Published: 2008
Full Text: View/download PDF

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Region

Database

110 results on '"Murphy T"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources