813 results on '"Wren, J"'
Search Results
2. Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis
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Wren, Jonathan, Wren, J ( Jonathan ), Balázs, Zsolt; https://orcid.org/0000-0003-3537-7441, Gitchev, Todor; https://orcid.org/0000-0002-7470-0646, Ivanković, Ivna, Krauthammer, Michael, Wren, Jonathan, Wren, J ( Jonathan ), Balázs, Zsolt; https://orcid.org/0000-0003-3537-7441, Gitchev, Todor; https://orcid.org/0000-0002-7470-0646, Ivanković, Ivna, and Krauthammer, Michael
- Abstract
Method development for the analysis of cell-free DNA (cfDNA) sequencing data is impeded by limited data sharing due to the strict control of sensitive genomic data. An existing solution for facilitating data sharing removes nucleotide-level information from raw cfDNA sequencing data, keeping alignment coordinates only. This simplified format can be publicly shared and would, theoretically, suffice for common functional analyses of cfDNA data. However, current bioinformatics software requires nucleotide-level information and cannot process the simplified format. We present Fragmentstein, a command-line tool for converting non-sensitive cfDNA-fragmentation data into alignment mapping (BAM) files. Fragmentstein complements fragment coordinates with sequence information from a reference genome to reconstruct BAM files. We demonstrate the utility of Fragmentstein by showing the feasibility of copy number variant (CNV), nucleosome occupancy, and fragment length analyses from non-sensitive fragmentation data. Availability and implementatio: Implemented in bash, Fragmentstein is available at https://github.com/uzh-dqbm-cmi/fragmentstein, licensed under GNU GPLv3.
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- 2024
3. The Bright Optical flash and Afterglow from the Gamma-Ray Burst GRB 130427A
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Vestrand, W. T., Wren, J., Panaitescu, A., Wozniak, P., Davis, H., Palmer, D., Vianello, G., Omodei, N., Xiong, S., Briggs, M., Elphick, M., and Rosing, W.
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Astrophysics - High Energy Astrophysical Phenomena - Abstract
The optical light that is generated simultaneously with the x-rays and gamma-rays during a gamma-ray burst (GRB) provides clues about the nature of the explosions that occur as massive stars collapse to form black holes. We report on the bright optical flash and fading afterglow from the powerful burst GRB 130427A and present a comparison with the properties of the gamma-ray emission that show correlation of the optical and >100 MeV photon flux light curves during the first 7,000 seconds. We attribute this correlation to co-generation in an external shock. The simultaneous, multi-color, optical observations are best explained at early times by reverse shock emission generated in the relativistic burst ejecta as it collides with surrounding material and at late times by a forward shock traversing the circumburst environment. The link between optical afterglow and >100 MeV emission suggests that nearby early peaked afterglows will be the best candidates for studying GRB emission at GeV/TeV energies., Comment: Main text and supplementary materials that will appear in Science
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- 2013
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4. SDWFS-MT-1: A Self-Obscured Luminous Supernova at z~0.2
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Kozlowski, Szymon, Kochanek, C. S., Stern, D., Prieto, J. L., Stanek, K. Z., Thompson, T. A., Assef, R. J., Drake, A. J., Szczygiel, D. M., Wozniak, P. R., Nugent, P., Ashby, M. L. N., Beshore, E., Brown, M. J. I., Dey, Arjun, Griffith, R., Harrison, F., Jannuzi, B. T., Larson, S., Madsen, K., Pilecki, B., Pojmanski, G., Skowron, J., Vestrand, W. T., and Wren, J. A.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
We report the discovery of a six-month-long mid-infrared transient, SDWFS-MT-1 (aka SN 2007va), in the Spitzer Deep, Wide-Field Survey of the NOAO Deep Wide-Field Survey Bootes field. The transient, located in a z=0.19 low luminosity (M_[4.5]~-18.6 mag, L/L_MilkyWay~0.01) metal-poor (12+log(O/H)~7.8) irregular galaxy, peaked at a mid-infrared absolute magnitude of M_[4.5]~-24.2 in the 4.5 micron Spitzer/IRAC band and emitted a total energy of at least 10^51 ergs. The optical emission was likely fainter than the mid-infrared, although our constraints on the optical emission are poor because the transient peaked when the source was "behind" the Sun. The Spitzer data are consistent with emission by a modified black body with a temperature of ~1350 K. We rule out a number of scenarios for the origin of the transient such as a Galactic star, AGN activity, GRB, tidal disruption of a star by a black hole and gravitational lensing. The most plausible scenario is a supernova exploding inside a massive, optically thick circumstellar medium, composed of multiple shells of previously ejected material. If the proposed scenario is correct, then a significant fraction (~10%) of the most luminous supernova may be self-enshrouded by dust not only before but also after the supernova occurs. The spectral energy distribution of the progenitor of such a supernova would be a slightly cooler version of eta Carina, peaking at 20-30 microns., Comment: 26 pages, 5 figures, 1 table, accepted for publication in ApJ
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- 2010
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5. GRB 081008: from burst to afterglow and the transition phase in between
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Yuan, F., Schady, P., Racusin, J. L., Willingale, R., Kruhler, T., O'Brien, P. T., Greiner, J., Oates, S. R., Rykoff, E. S., Aharonian, F., Akerlof, C. W., Ashley, M. C. B., Barthelmy, S. D., Filgas, R., Flewelling, H. A., Gehrels, N., Gogus, E., Guver, T., Horns, D., Kiziloglu, U., Krimm, H. A., McKay, T. A., Ozel, M. E., Pandey, S. B., Phillips, A., Quimby, R. M., Rowell, G., Rujopakarn, W., Schaefer, B. E., Vestrand, W. T., Wheeler, J. C., Wren, J., and Zheng, W.
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Astrophysics - High Energy Astrophysical Phenomena - Abstract
We present a multi-wavelength study of GRB 081008, at redshift 1.967, by Swift, ROTSE-III and GROND. Compared to other Swift GRBs, GRB 081008 has a typical gamma-ray isotropic equivalent energy output (10^53 erg) during the prompt phase, and displayed two temporally separated clusters of pulses. The early X-ray emission seen by the Swift/XRT was dominated by the softening tail of the prompt emission, producing multiple flares during and after the Swift/BAT detections. Optical observations that started shortly after the first active phase of gamma-ray emission showed two consecutive peaks. We interpret the first optical peak as the onset of the afterglow associated with the early burst activities. A second optical peak, coincident with the later gamma-ray pulses, imposes a small modification to the otherwise smooth lightcurve and thus suggests a minimal contribution from a probable internal component. We suggest the early optical variability may be from continuous energy injection into the forward shock front by later shells producing the second epoch of burst activities. These early observations thus provide a potential probe for the transition from prompt to the afterglow phase. The later lightcurve of GRB 081008 displays a smooth steepening in all optical bands and X-ray. The temporal break is consistent with being achromatic at the observed wavelengths. Our broad energy coverage shortly after the break constrains a spectral break within optical. However, the evolution of the break frequency is not observed. We discuss the plausible interpretations of this behavior., Comment: 16 pages, 4 figures, accepted for publication in ApJ
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- 2010
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6. Looking Into the Fireball: ROTSE-III and Swift Observations of Early GRB Afterglows
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Rykoff, E. S., Aharonian, F., Akerlof, C. W., Ashley, M. C. B., Barthelmy, S. D., Flewelling, H. A., Gehrels, N., Gogus, E., Guver, T., Kiziloglu, U., Krimm, H. A., McKay, T. A., Ozel, M., Phillips, A., Quimby, R. M., Rowell, G., Rujopakarn, W., Schaefer, B. E., Smith, D. A., Vestrand, W. T., Wheeler, J. C., Wren, J., Yuan, F., and Yost, S. A.
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Astrophysics - High Energy Astrophysical Phenomena ,Astrophysics - Cosmology and Extragalactic Astrophysics - Abstract
We report on a complete set of early optical afterglows of gamma-ray bursts (GRBs) obtained with the ROTSE-III telescope network from March 2005 through June 2007. This set is comprised of 12 afterglows with early optical and Swift/XRT observations, with a median ROTSE-III response time of 45 s after the start of gamma-ray emission (8 s after the GCN notice time). These afterglows span four orders of magnitude in optical luminosity, and the contemporaneous X-ray detections allow multi-wavelength spectral analysis. Excluding X-ray flares, the broadband synchrotron spectra show that the optical and X-ray emission originate in a common region, consistent with predictions of the external forward shock in the fireball model. However, the fireball model is inadequate to predict the temporal decay indices of the early afterglows, even after accounting for possible long-duration continuous energy injection. We find that the optical afterglow is a clean tracer of the forward shock, and we use the peak time of the forward shock to estimate the initial bulk Lorentz factor of the GRB outflow, and find 100
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- 2009
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7. Gamma-Ray Burst at the extreme: 'the naked-eye burst' GRB 080319B
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Wozniak, P. R., Vestrand, W. T., Panaitescu, A. D., Wren, J. A., Davis, H. R., and White, R. R.
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Astrophysics - Abstract
On 19 March 2008, the northern sky was the stage of a spectacular optical transient that for a few seconds remained visible to the naked eye. The transient was associated with GRB 080319B, a gamma-ray burst at a luminosity distance of about 6 Gpc (standard cosmology), making it the most luminous optical object ever recorded by human kind. We present comprehensive sky monitoring and multi-color optical follow-up observations of GRB 080319B collected by the RAPTOR telescope network covering the development of the explosion and the afterglow before, during, and after the burst. The extremely bright prompt optical emission revealed features that are normally not detectable. The optical and gamma-ray variability during the explosion are correlated, but the optical flux is much greater than can be reconciled with single emission mechanism and a flat gamma-ray spectrum. This extreme optical behavior is best understood as synchrotron self-Compton model (SSC). After a gradual onset of the gamma-ray emission, there is an abrupt rise of the prompt optical flux suggesting that variable self-absorption dominates the early optical light curve. Our simultaneous multi-color optical light curves following the flash show spectral evolution consistent with a rapidly decaying red component due to large angle emission and the emergence of a blue forward shock component from interaction with the surrounding environment. While providing little support for the reverse shock that dominates the early afterglow, these observations strengthen the case for the universal role of the SSC mechanism in generating gamma-ray bursts., Comment: accepted for publication in ApJ
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- 2008
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8. The Dark Side of ROTSE-III Prompt GRB Observations
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Yost, S. A., Aharonian, F., Akerlof, C. W., Ashley, M. C. B., Barthelmy, S., Gehrels, N., Gogus, E., Guver, T., Horns, D., Kiziloglu, U., Krimm, H. A., McKay, T. A., Ozel, M., Phillips, A., Quimby, R. M., Rowell, G., Rujopakarn, W., Rykoff, E. S., Schaefer, B. E., Smith, D. A., Swan, H. F., Vestrand, W. T., Wheeler, J. C., Wren, J., and Yuan, F.
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Astrophysics - Abstract
We present several cases of optical observations during gamma-ray bursts (GRBs) which resulted in prompt limits but no detection of optical emission. These limits constrain the prompt optical flux densities and the optical brightness relative to the gamma-ray emission. The derived constraints fall within the range of properties observed in GRBs with prompt optical detections, though at the faint end of optical/gamma flux ratios. The presently accessible prompt optical limits do not require a different set of intrinsic or environmental GRB properties, relative to the events with prompt optical detections., Comment: ApJ accepted. 20 pages in draft manuscript form, which includes 6 pages of tables and 2 figures
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- 2007
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9. Detection of GRB 060927 at z = 5.47: Implications for the Use of Gamma-Ray Bursts as Probes of the End of the Dark Ages
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Ruiz-Velasco, A. E., Swan, H., Troja, E., Malesani, D., Fynbo, J. P. U., Starling, R. L. C., Xu, D., Aharonian, F., Akerlof, C., Andersen, M. I., Ashley, M. C. B., Barthelmy, S. D., Bersier, D., Cerón, J. M. Castro, Castro-Tirado, A. J., Gehrels, N., Göğüş, E., Gorosabel, J., Guidorzi, C., Güver, T., Hjorth, J., Horns, D., Huang, K. Y., Jakobsson, P., Jensen, B. L., Kızıloģlu, Ü., Kouveliotou, C., Krimm, H. A., Ledoux, C., Levan, A. J., Marsh, T., McKay, T., Melandri, A., Milvang-Jensen, B., Mundell, C. G., O'Brien, P. T., Özel, M., Phillips, A., Quimby, R., Rowell, G., Rujopakarn, W., Rykoff, E. S., Schaefer, B. E., Sollerman, J., Tanvir, N. R., Thöne, C. C., Urata, Y., Vestrand, W. T., Vreeswijk, P. M., Watson, D., Wheeler, J. C., Wijers, R. A. M. J., Wren, J., Yost, S. A., Yuan, F., Zhai, M., and Zheng, W. K.
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Astrophysics - Abstract
We report on follow-up observations of the GRB 060927 using the ROTSE-IIIa telescope and a suite of larger aperture ground-based telescopes. An optical afterglow was detected 20 s after the burst, the earliest rest-frame detection of optical emission from any GRB. Spectroscopy performed with the VLT about 13 hours after the trigger shows a continuum break at lambda ~ 8070 A produced by neutral hydrogen absorption at z~5.6. We also detect an absorption line at 8158 A which we interpret as SiII at z=5.467. Hence, GRB 060927 is the second most distant GRB with a spectroscopically measured redshift. The shape of the red wing of the spectral break can be fitted by a damped Lyalpha profile with a column density with log(N_HI/cm^-2) ~ 22.5. We discuss the implications of this work for the use of GRBs as probes of the end of the dark ages and draw three main conclusions: i) GRB afterglows originating from z>6 should be relatively easy to detect from the ground, but rapid NIR monitoring is necessary to ensure that they are found; ii) The presence of large HI column densities in some GRBs host galaxies at z>5 makes the use of GRBs to probe the reionization epoch via spectroscopy of the red damping wing challenging; iii) GRBs appear crucial to locate typical star-forming galaxies at z>5 and therefore the type of galaxies responsible for the reionization of the universe., Comment: 15 pages, 6 figures, 2 tables, accepted for publication in ApJ, uses emulateapj
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- 2007
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10. The Troublesome Broadband Evolution of GRB 061126: Does a Grey Burst Imply Grey Dust?
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Perley, D. A., Bloom, J. S., Butler, N. R., Pollack, L. K., Holtzman, J., Blake, C. H., Kocevski, D., Vestrand, W. T., Li, W., Foley, R. J., Bellm, E., Chen, H. -W., Prochaska, J. X., Starr, D., Filippenko, A. V., Falco, E. E., Szentgyorgyi, A. H., Wren, J., Wozniak, P. R., White, R., and Pergande, J.
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Astrophysics - Abstract
We report on observations of a gamma-ray burst (GRB 061126) with an extremely bright (R ~ 12 mag at peak) early-time optical afterglow. The optical afterglow is already fading as a power law 22 seconds after the trigger, with no detectable prompt contribution in our first exposure, which was coincident with a large prompt-emission gamma-ray pulse. The optical--infrared photometric spectral energy distribution is an excellent fit to a power law, but it exhibits a moderate red-to-blue evolution in the spectral index at about 500 s after the burst. This color change is contemporaneous with a switch from a relatively fast decay to slower decay. The rapidly decaying early afterglow is broadly consistent with synchrotron emission from a reverse shock, but a bright forward-shock component predicted by the intermediate- to late-time X-ray observations under the assumptions of standard afterglow models is not observed. Indeed, despite its remarkable early-time brightness, this burst would qualify as a dark burst at later times on the basis of its nearly flat optical-to-X-ray spectral index. Our photometric spectral energy distribution provides no evidence of host-galaxy extinction, requiring either large quantities of grey dust in the host system (at redshift 1.1588 +/- 0.0006, based upon our late-time Keck spectroscopy) or separate physical origins for the X-ray and optical afterglows., Comment: Revised version submitted to ApJ. Contains significantly expanded discussion, an additional figure, and numerous other changes
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- 2007
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11. Exploring Broadband GRB Behavior During gamma-ray Emission
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Yost, S. A., Swan, H. F., Rykoff, E. S., Aharonian, F., Akerlof, C. W., Alday, A., Ashley, M. C. B., Barthelmy, S., Burrows, D., Depoy, D. L., Dufour, R. J., Eastman, J. D., Forgey, R. D., Gehrels, N., Göğüş, E., Güver, T., Halpern, J. P., Hardin, L. C., Horns, D., Kızıloǧlu, U., Krimm, H. A., Lepine, S., Liang, E. P., Marshall, J. L., McKay, T. A., Mineo, T., Mirabal, N., Özel, M., Phillips, A., Prieto, J. L., Quimby, R. M., Romano, P., Rowell, G., Rujopakarn, W., Schaefer, B. E., Silverman, J. M., Siverd, R., Skinner, M., Smith, D. A., Smith, I. A., Tonnesen, S., Troja, E., Vestrand, W. T., Wheeler, J. C., Wren, J., Yuan, F., and Zhang, B.
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Astrophysics - Abstract
The robotic ROTSE-III telescope network detected prompt optical emission contemporaneous with the gamma-ray emission of Swift events GRB051109A and GRB051111. Both datasets have continuous coverage at high signal-to-noise levels from the prompt phase onwards, thus the early observations are readily compared to the Swift XRT and BAT high energy detections. In both cases, the optical afterglow is established, declining steadily during the prompt emission. For GRB051111, there is evidence of an excess optical component during the prompt emission. The component is consistent with the flux spectrally extrapolated from the gamma-rays, using the gamma-ray spectral index. A compilation of spectral information from previous prompt detections shows that such a component is unusual. The existence of two prompt optical components - one connected to the high-energy emission, the other to separate afterglow flux, as indicated in GRB051111 - is not compatible with a simple ``external-external'' shock model for the GRB and its afterglow., Comment: ApJ accepted. 32 pages (in preprint form), 5 tables, 5 figures
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- 2006
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12. Energy input and response from prompt and early optical afterglow emission in gamma-ray bursts
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Vestrand, W. T., Wren, J. A., Wozniak, P. R., Aptekar, R., Golentskii, S., Palshin, V., Sakamoto, T., White, R. R., Evans, S., Casperson, D., and Fenimore, E.
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Astrophysics - Abstract
The taxonomy of optical emission detected during the critical first few minutes after the onset of a gamma-ray burst (GRB) defines two broad classes: prompt optical emission correlated with prompt gamma-ray emission, and early optical afterglow emission uncorrelated with the gamma-ray emission. The standard theoretical interpretation attributes prompt emission to internal shocks in the ultra-relativistic outflow generated by the internal engine; early afterglow emission is attributed to shocks generated by interaction with the surrounding medium. Here we report on observations of a bright GRB that, for the first time, clearly show the temporal relationship and relative strength of the two optical components. The observations indicate that early afterglow emission can be understood as reverberation of the energy input measured by prompt emission. Measurements of the early afterglow reverberations therefore probe the structure of the environment around the burst, whereas the subsequent response to late-time impulsive energy releases reveals how earlier flaring episodes have altered the jet and environment parameters. Many GRBs are generated by the death of massive stars that were born and died before the Universe was ten per cent of its current age, so GRB afterglow reverberations provide clues about the environments around some of the first stars., Comment: 13 pages, 4 figures, 1 table. Note: This paper has been accepted for publication in Nature, but is embargoed for discussion in the popular press until formal publication in Nature
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- 2006
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13. RAPTOR observations of delayed explosive activity in the high-redshift gamma-ray burst GRB 060206
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Wozniak, P. R., Vestrand, W. T., Wren, J. A., White, R. R., Evans, S. M., and Casperson, D.
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Astrophysics - Abstract
The RAPid Telescopes for Optical Response (RAPTOR) system at Los Alamos National Laboratory observed GRB 060206 starting 48.1 minutes after gamma-ray emission triggered the Burst Alert Telescope (BAT) on-board the Swift satellite. The afterglow light curve measured by RAPTOR shows a spectacular re-brightening by ~1 mag about 1 h after the trigger and peaks at R ~ 16.4 mag. Shortly after the onset of the explosive re-brightening the OT doubled its flux on a time-scale of about 4 minutes. The total R-band fluence received from GRB 060206 during this episode is 2.3e-9 erg/cm2. In the rest frame of the burst (z = 4.045) this yields an isotropic equivalent energy release of ~0.7e50 erg in just a narrow UV band 130 +/- 22 nm. We discuss the implications of RAPTOR observations for untriggered searches for fast optical transients and studies of GRB environments at high redshift., Comment: Submitted to ApJ Letters
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- 2006
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14. The Anomalous Early Afterglow of GRB 050801
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Rykoff, E. S., Mangano, V., Yost, S. A., Sari, R., Aharonian, F., Akerlof, C. W., Ashley, M. C. B., Barthelmy, S. D., Burrows, D. N., Gehrels, N., Gogus, E., Horns, D., Kiziloglu, U., Krimm, H. A., McKay, T. A., Ozel, M., Phillips, A., Quimby, R. M., Rowell, G., Rujopakarn, W., Schaefer, B. E., Smith, D. A., Swan, H. F., Vestrand, W. T., Wheeler, J. C., Wren, J., and Yuan, F.
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Astrophysics - Abstract
The ROTSE-IIIc telescope at the H.E.S.S. site, Namibia, obtained the earliest detection of optical emission from a Gamma-Ray Burst (GRB), beginning only 21.8 s from the onset of Swift GRB 050801. The optical lightcurve does not fade or brighten significantly over the first ~250 s, after which there is an achromatic break and the lightcurve declines in typical power-law fashion. The Swift/XRT also obtained early observations starting at 69 s after the burst onset. The X-ray lightcurve shows the same features as the optical lightcurve. These correlated variations in the early optical and X-ray emission imply a common origin in space and time. This behavior is difficult to reconcile with the standard models of early afterglow emission., Comment: 5 pages, 1 figure. Accepted for publication in ApJ Letters
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- 2006
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15. Early-Time Observations of the GRB 050319 Optical Transient
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Quimby, R. M., Rykoff, E. S., Yost, S. A., Aharonian, F., Akerlof, C. W., Alatalo, K., Ashley, M. C. B., Goegues, E., Guever, T., Horns, D., Kehoe, R. L., Kiziloglu, Ue., McKay, T. A., Oezel, M., Phillips, A., Schaefer, B. E., Smith, D. A., Swan, H. F., Vestrand, W. T., Wheeler, J. C., and Wren, J.
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Astrophysics - Abstract
We present the unfiltered ROTSE-III light curve of the optical transient associated with GRB 050319 beginning 4 s after the cessation of gamma-ray activity. We fit a power-law function to the data using the revised trigger time given by Chincarini et al. (2005), and a smoothly broken power-law to the data using the original trigger disseminated through the GCN notices. Including the RAPTOR data from Wozniak et al. (2005), the best fit power-law indices are alpha=-0.854 (+/- 0.014) for the single power-law and alpha_1=-0.364 (+/- 0.020), alpha_2= -0.881 (+/- 0.030), with a break at t_b = 418 (+/- 30) s for the smoothly broken fit. We discuss the fit results with emphasis placed on the importance of knowing the true start time of the optical transient for this multi-peaked burst. As Swift continues to provide prompt GRB locations, it becomes more important to answer the question, "when does the afterglow begin" to correctly interpret the light curves., Comment: 14 pages including 2 figures; Accepted for publication in ApJ
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- 2005
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16. Optical Lightcurve & Cooling Break of GRB 050502A
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Yost, S. A., Alatalo, K., Rykoff, E. S., Aharonian, F., Akerlof, C. W., Ashley, M. C. B., Blake, C. H., Bloom, J. S., Boettcher, M., Falco, E. E., Gogus, E., Guver, T., Halpern, J. P., Horns, D., Joshi, M., Kiziloglu, U., McKay, T. A., Mirabal, N., Ozel, M., Phillips, A., Quimby, R. M., Rujopakarn, W., Schaefer, B. E., Shields, J. C., Skrutskie, M., Smith, D. A., Starr, D. L., Swan, H. F., Szentgyorgi, A., Vestrand, W. T., Wheeler, J. C., and Wren, J.
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Astrophysics - Abstract
We present lightcurves of the afterglow of GRB050502A, including very early data at t-t_{GRB} < 60s. The lightcurve is composed of unfiltered ROTSE-IIIb optical observations from 44s to 6h post-burst, R-band MDM observations from 1.6 to 8.4h post-burst, and PAIRITEL J H K_s observations from 0.6 to 2.6h post-burst. The optical lightcurve is fit by a broken power law, where t^{alpha} steepens from alpha = -1.13 +- 0.02 to alpha = -1.44 +- 0.02 at \~5700s. This steepening is consistent with the evolution expected for the passage of the cooling frequency nu_c through the optical band. Even in our earliest observation at 44s post-burst, there is no evidence that the optical flux is brighter than a backward extrapolation of the later power law would suggest. The observed decay indices and spectral index are consistent with either an ISM or a Wind fireball model, but slightly favor the ISM interpretation. The expected spectral index in the ISM interpretation is consistent within 1 sigma with the observed spectral index beta = -0.8 +- 0.1; the Wind interpretation would imply a slightly (~2 sigma) shallower spectral index than observed. A small amount of dust extinction at the source redshift could steepen an intrinsic spectrum sufficiently to account for the observed value of beta. In this picture, the early optical decay, with the peak at or below 4.7e14 Hz at 44s, requires very small electron and magnetic energy partitions from the fireball., Comment: 22 pages, including 3 tables and 1 figure, Accepted by ApJ
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- 2005
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17. Prompt Optical Detection of GRB 050401 with ROTSE-IIIa
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Rykoff, E. S., Yost, S. A., Krimm, H. A., Aharonian, F., Akerlof, C. W., Alatalo, K., Ashley, M. C. B., Barthelmy, S. D., Gehrels, N., Guver, T., Horns, D., Kiziloglu, U., McKay, T. A., Ozel, M., Phillips, A., Quimby, R. M., Rujopakarn, W., Schaefer, B. E., Smith, D. A., Swan, H. F., Vestrand, W. T., Wheeler, J. C., and Wren, J.
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Astrophysics - Abstract
The ROTSE-IIIa telescope at Siding Spring Observatory, Australia, detected prompt optical emission from Swift GRB 050401. In this letter, we present observations of the early optical afterglow, first detected by the ROTSE-IIIa telescope 33 s after the start of gamma-ray emission, contemporaneous with the brightest peak of this emission. This GRB was neither exceptionally long nor bright. This is the first prompt optical detection of a GRB of typical duration and luminosity. We find that the early afterglow decay does not deviate significantly from the power-law decay observable at later times, and is uncorrelated with the prompt gamma-ray emission. We compare this detection with the other two GRBs with prompt observations, GRB 990123 and GRB 041219a. All three bursts exhibit quite different behavior at early times., Comment: 4 pages, 3 figures. Accepted for publication in ApJ Letters
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- 2005
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18. A Search for Untriggered GRB Afterglows with ROTSE-III
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Rykoff, E. S., Aharonian, F., Akerlof, C. W., Alatalo, K., Ashley, M. C. B., Guver, T., Horns, D., Kehoe, R. L., Kiziloglu, U., McKay, T. A., Ozel, M., Phillips, A., Quimby, R. M., Schaefer, B. E., Smith, D. A., Swan, H. F., Vestrand, W. T., Wheeler, J. C., Wren, J., and Yost, S. A.
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Astrophysics - Abstract
We present the results of a search for untriggered gamma-ray burst (GRB) afterglows with the Robotic Optical Transient Search Experiment-III (ROTSE-III) telescope array. This search covers observations from September 2003 to March 2005. We have an effective coverage of 1.74 deg^2 yr for rapidly fading transients that remain brighter than ~ 17.5 magnitude for more than 30 minutes. This search is the first large area survey to be able to detect typical untriggered GRB afterglows. Our background rate is very low and purely astrophysical. We have found 4 previously unknown cataclysmic variables (CVs) and 1 new flare star. We have not detected any candidate afterglow events or other unidentified transients. We can place an upper limit on the rate of fading optical transients with quiescent counterparts dimmer than ~ 20th magnitude at a rate of less than 1.9 deg^-2 yr-1 with 95% confidence. This places limits on the optical characteristics of off-axis (orphan) GRB afterglows. As a byproduct of this search, we have an effective ~ 52 deg^2 yr of coverage for very slowly decaying transients, such as CVs. This implies an overall rate of outbursts from high galactic latitude CVs of 0.1 deg^2 yr^-1., Comment: Seven pages, five figures, uses emulateapj class file. Accepted to Astrophysical Journal
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- 2005
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19. RAPTOR observations of the early optical afterglow from GRB 050319
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Wozniak, P. R., Vestrand, W. T., Wren, J. A., White, R. R., Evans, S. M., and Casperson, D.
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Astrophysics - Abstract
The RAPid Telescopes for Optical Response (RAPTOR) system at Los Alamos National Laboratory observed GRB 050319 starting 25.4 seconds after gamma-ray emission triggered the Burst Alert Telescope (BAT) on-board the Swift satellite. Our well sampled light curve of the early optical afterglow is composed of 32 points (derived from 70 exposures) that measure the flux decay during the first hour after the GRB. The GRB 050319 light curve measured by RAPTOR can be described as a relatively gradual flux decline (power-law index alpha = -0.37) with a transition, at about 400 s after the GRB, to a faster flux decay (alpha = -0.91). The addition of other available measurements to the RAPTOR light curve suggests that another emission component emerged after 10^4 s. We hypothesize that the early afterglow emission is powered by extended energy injection or delayed reverse shock emission followed by the emergence of forward shock emission., Comment: Accepted for publication in ApJ Letters. To see a short movie of fading GRB 050319 go to http://www.raptor.lanl.gov/images/GRB050319/grb050319_movie_annotated.gif
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- 2005
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20. A Link between Prompt Optical and Prompt Gamma-Ray Emission in Gamma-Ray Bursts
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Vestrand, W. T., Wozniak, P. R., Wren, J. A., Fenimore, E. E., Sakamoto, T., White, R. R., Casperson, D., Davis, H., Evans, S., Galassi, M., McGowan, K. E., Schier, J. A., Asa, J. W., Barthelmy, S. D., Cummings, J. R., Gehrels, N., Hullinger, D., Krimm, H. A., Markwardt, C. B., McLean, K., Palmer, D., Parsons, A., and Tueller, J.
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Astrophysics - Abstract
The prompt optical emission that arrives with gamma-rays from a cosmic gamma-ray burst (GRB) is a signature of the engine powering the burst, the properties of the ultra-relativistic ejecta of the explosion, and the ejecta's interactions with the surroundings. Until now, only GRB 990123 had been detected at optical wavelengths during the burst phase. Its prompt optical emission was variable and uncorrelated with the prompt gamma-ray emission, suggesting that the optical emission was generated by a reverse shock arising from the ejecta's collision with the surrounding material. Here we report prompt optical emission from GRB 041219a. It is variable and correlated with the prompt gamma-rays, indicating a common origin for the optical light and the gamma-rays. Within the context of the standard fireball model of GRBs, we attribute this new optical component to internal shocks driven into the burst ejecta by variations of the inner engine. The correlated optical emission is a direct probe of the jet isolated from the medium. The timing of the uncorrelated optical emission is strongly dependent on the nature of the medium., Comment: 9 pages, 4 figures. Note: This paper has been accepted for publication in Nature, but is embargoed for discussion in the popular press until formal publication in Nature. Resubmit - Added table comparing Swift and RAPTOR data
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- 2005
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21. TALON - The Telescope Alert Operation Network System: Intelligent Linking of Distributed Autonomous Robotic Telescopes
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White, R. R., Wren, J., Davis, H., Galassi, M., Starr, D., Vestrand, W. T., and Wozniak, P.
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Astrophysics - Abstract
The internet has brought about great change in the astronomical community, but this interconnectivity is just starting to be exploited for use in instrumentation. Utilizing the internet for communicating between distributed astronomical systems is still in its infancy, but it already shows great potential. Here we present an example of a distributed network of telescopes that performs more efficiently in synchronous operation than as individual instruments. RAPid Telescopes for Optical Response (RAPTOR) is a system of telescopes at LANL that has intelligent intercommunication, combined with wide-field optics, temporal monitoring software, and deep-field follow-up capability all working in closed-loop real-time operation. The Telescope ALert Operations Network (TALON) is a network server that allows intercommunication of alert triggers from external and internal resources and controls the distribution of these to each of the telescopes on the network. TALON is designed to grow, allowing any number of telescopes to be linked together and communicate. Coupled with an intelligent alert client at each telescope, it can analyze and respond to each distributed TALON alert based on the telescopes needs and schedule., Comment: Presentation at SPIE 2004, Glasgow, Scotland (UK)
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- 2004
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22. Northern Sky Variability Survey (NSVS): Public data release
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Wozniak, P. R., Vestrand, W. T., Akerlof, C. W., Balsano, R., Bloch, J., Casperson, D., Fletcher, S., Gisler, G., Kehoe, R., Kinemuchi, K., Lee, B. C., Marshall, S., McGowan, K. E., McKay, T. A., Rykoff, E. S., Smith, D. A., Szymanski, J., and Wren, J.
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Astrophysics - Abstract
The Northern Sky Variability Survey (NSVS) is a temporal record of the sky over the optical magnitude range from 8 to 15.5. It was conducted in the course of the first generation Robotic Optical Transient Search Experiment (ROTSE-I) using a robotic system of four co-mounted unfiltered telephoto lenses equipped with CCD cameras. The survey was conducted from Los Alamos, NM, and primarily covers the entire northern sky. Some data in southern fields between declinations 0 and -38 deg is also available, although with fewer epochs and noticeably lesser quality. The NSVS contains light curves for approximately 14 million objects. With a one year baseline and typically 100-500 measurements per object, the NSVS is the most extensive record of stellar variability across the bright sky available today. In a median field, bright unsaturated stars attain a point to point photometric scatter of ~0.02 mag and position errors within 2 arcsec. At Galactic latitudes |b| < 20 deg the data quality is limited by severe blending due to ~14 arcsec pixel size. We present basic characteristics of the data set and describe data collection, analysis, and distribution. All NSVS photometric measurements are available for on-line public access from the Sky Database for Objects in Time-Domain (SkyDOT; http://skydot.lanl.gov) at LANL. Copies of the full survey photometry may also be requested on tape., Comment: accepted for publication in Astronomical Journal
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- 2004
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23. The Early Optical Afterglow of GRB 030418 and Progenitor Mass Loss
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Rykoff, E. S., Smith, D. A., Price, P. A., Akerlof, C. W., Ashley, M. C. B., Bizyaev, D., Garradd, G. J., McKay, T. A., McNaught, R. H., Phillips, A., Quimby, R., Schaefer, B., Schmidt, B., Vestrand, W. T., Wheeler, J. C., and Wren, J.
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Astrophysics - Abstract
The ROTSE-IIIa telescope and the SSO-40 inch telescope, both located at Siding Spring Observatory, imaged the early time afterglow of GRB 030418. In this report we present observations of the early afterglow, first detected by the ROTSE-IIIa telescope 211 s after the start of the burst, and only 76 s after the end of the gamma-ray activity. We detect optical emission that rises for ~600 s, slowly varies around R=17.3 mag for ~1400 s, and then fades as a power law of index alpha=-1.36. Additionally, the ROTSE-IIIb telescope, located at McDonald Observatory, imaged the early time afterglow of GRB 030723. The behavior of this light curve was qualitatively similar to that of GRB 030418, but two magnitudes dimmer. These two afterglows are dissimilar to other afterglows such as GRB 990123 and GRB 021211. We investigate whether the early afterglow can be attributed to a synchrotron break in a cooling synchrotron spectrum as it passes through the optical band, but find this model is unable to accurately describe the early light curve. We present a simple model for gamma-ray burst emission emerging from a wind medium surrounding a massive progenitor star. This model provides an effective description of the data, and suggests that the rise of the afterglow can be ascribed to extinction in the local circumburst environment. In this interpretation, these events provide further evidence for the connection between gamma-ray bursts and the collapse of massive stars., Comment: Five pages, four figures, uses emulateapj class file. Accepted to Astrophysical Journal Letters
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- 2003
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24. ROTSE-III Observations of the Early Afterglow From GRB 030329
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Smith, D. A., Rykoff, E. S., Akerlof, C. W., Ashley, M. C. B., Bizyaev, D., McKay, T. A., Mukadum, A., Phillips, A., Quimby, R., Schaefer, B., Sullivan, D., Swan, H. F., Vestrand, W. T., Wheeler, J. C., and Wren, J.
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Astrophysics - Abstract
Using two identical telescopes at widely separated longitudes, the ROTSE-III network observed decaying emission from the remarkably bright afterglow of GRB 030329. In this report we present observations covering 56% of the period from 1.5-47 hours after the burst. We find that the light curve is piecewise consistent with a powerlaw decay. When the ROTSE-III data are combined with data reported by other groups, there is evidence for five breaks within the first 20 hours after the burst. Between two of those breaks, observations from 15.9-17.1 h after the burst at 1-s time resolution with McDonald Observatory's 2.1-m telescope reveal no evidence for fluctuations or deviations from a simple power law. Multiple breaks may indicate complex structure in the jet. There are also two unambiguous episodes at 23 and 45 hours after the burst where the intensity becomes consistent with a constant for several hours, perhaps indicating multiple injections of energy into the GRB/afterglow system., Comment: Four pages, two figures, uses emulateapj class file. Accepted to Astrophysical Journal Letters
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- 2003
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25. SkyDOT (Sky Database for Objects in the Time Domain): A Virtual Observatory for Variability Studies at LANL
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Wozniak, P., Borozdin, K., Galassi, M., Priedhorsky, W., Starr, D., Vestrand, W. T., White, R., and Wren, J.
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Astrophysics - Abstract
The mining of Virtual Observatories (VOs) is becoming a powerful new method for discovery in astronomy. Here we report on the development of SkyDOT (Sky Database for Objects in the Time domain), a new Virtual Observatory, which is dedicated to the study of sky variability. The site will confederate a number of massive variability surveys and enable exploration of the time domain in astronomy. We discuss the architecture of the database and the functionality of the user interface. An important aspect of SkyDOT is that it is continuously updated in near real time so that users can access new observations in a timely manner. The site will also utilize high level machine learning tools that will allow sophisticated mining of the archive. Another key feature is the real time data stream provided by RAPTOR (RAPid Telescopes for Optical Response), a new sky monitoring experiment under construction at Los Alamos National Laboratory (LANL)., Comment: to appear in SPIE proceedings vol. 4846, 11 pages, 5 figures
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- 2002
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26. The ROTSE-III Robotic Telescope System
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Akerlof, C. W., Ashley, M. C. B., Casperson, D. E., Epps, H. W., Kehoe, R. L., Marshall, S. L., McGowan, K. E., McKay, T. A., Phillips, M. A., Rykoff, E. S., Schier, J. A., Smith, D. A., Vestrand, W. T., Wozniak, P. R., and Wren, J. A.
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Astrophysics - Abstract
The observation of a prompt optical flash from GRB990123 convincingly demonstrated the value of autonomous robotic telescope systems. Pursuing a program of rapid follow-up observations of gamma-ray bursts, the Robotic Optical Transient Search Experiment (ROTSE) has developed a next-generation instrument, ROTSE-III, that will continue the search for fast optical transients. The entire system was designed as an economical robotic facility to be installed at remote sites throughout the world. There are seven major system components: optics, optical tube assembly, CCD camera, telescope mount, enclosure, environmental sensing & protection and data acquisition. Each is described in turn in the hope that the techniques developed here will be useful in similar contexts elsewhere., Comment: 19 pages, including 4 figures. To be published in PASP in January, 2003. PASP Number IP02-110
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- 2002
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27. A Distributed Control System for Rapid Astronomical Transient Detection
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Wren, J., Borozdin, K., Brumby, S., Casperson, D., Galassi, M., McGowan, K., Starr, D., Vestrand, W. T., White, R., and Wozniak, P.
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Astrophysics - Abstract
The Rapid Telescope for Optical Response (RAPTOR) program consists of a network of robotic telescopes dedicated to the search for fast optical transients. The pilot project is composed of three observatories separated by approximately 38 kilometers located near Los Alamos, New Mexico. Each of these observatories is composed of a telescope, mount, enclosure, and weather station, all operating robotically to perform individual or coordinated transient searches. The telescopes employ rapidly slewing mounts capable of slewing a 250 pound load 180 degrees in under 2 seconds with arcsecond precision. Each telescope consists of wide-field cameras for transient detection and a narrow-field camera with greater resolution and sensitivity. The telescopes work together by employing a closed-loop system for transient detection and follow-up. Using the combined data from simultaneous observations, transient alerts are generated and distributed via the Internet. Each RAPTOR telescope also has the capability of rapidly responding to external transient alerts received over the Internet from a variety of ground-based and satellite sources. Each observatory may be controlled directly, remotely, or robotically while providing state-of-health and observational results to the client and the other RAPTOR observatories. We discuss the design and implementation of the spatially distributed RAPTOR system., Comment: To appear in SPIE proceedings vol. 4845
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- 2002
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28. The RAPTOR Experiment: A System for Monitoring the Optical Sky in Real Time
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Vestrand, W. T., Borozdin, K., Brumby, S., Casperson, D., Fenimore, E., Galassi, M., McGowan, K., Perkins, S., Priedhorsky, W., Starr, D., White, R., Wozniak, P., and Wren, J.
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Astrophysics - Abstract
The Rapid Telescopes for Optical Response (RAPTOR) experiment is a spatially distributed system of autonomous robotic telescopes that is designed to monitor the sky for optical transients. The core of the system is composed of two telescope arrays, separated by 38 kilometers, that stereoscopically view the same 1500 square-degree field with a wide-field imaging array and a central 4 square-degree field with a more sensitive narrow-field "fovea" imager. Coupled to each telescope array is a real-time data analysis pipeline that is designed to identify interesting transients on timescales of seconds and, when a celestial transient is identified, to command the rapidly slewing robotic mounts to point the narrow-field ``fovea'' imagers at the transient. The two narrow-field telescopes then image the transient with higher spatial resolution and at a faster cadence to gather light curve information. Each "fovea" camera also images the transient through a different filter to provide color information. This stereoscopic monitoring array is supplemented by a rapidly slewing telescope with a low resolution spectrograph for follow-up observations of transients and a sky patrol telescope that nightly monitors about 10,000 square-degrees for variations, with timescales of a day or longer, to a depth about 100 times fainter. In addition to searching for fast transients, we will use the data stream from RAPTOR as a real-time sentinel for recognizing important variations in known sources. Altogether, the RAPTOR project aims to construct a new type of system for discovery in optical astronomy--one that explores the time domain by "mining the sky in real time"., Comment: 11 pages, To appear in the Proceedings of the SPIE, Volume 4845
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- 2002
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29. The ROTSE-IIIa Telescope System
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Smith, D. A., Akerlof, C., Ashley, M. C. B., Casperson, D., Gisler, G., Kehoe, R., Marshall, S., McGowan, K., McKay, T., Phillips, M. A., Rykoff, E., Vestrand, W. T., Wozniak, P., and Wren, J.
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Astrophysics - Abstract
We report on the current operating status of the ROTSE-IIIa telescope, currently undergoing testing at Los Alamos National Laboratories in New Mexico. It will be shipped to Siding Spring Observatory, Australia, in first quarter 2002. ROTSE-IIIa has been in automated observing mode since early October, 2001, after completing several weeks of calibration and check-out observations. Calibrated lists of objects in ROTSE-IIIa sky patrol data are produced routinely in an automated pipeline, and we are currently automating analysis procedures to compile these lists, eliminate false detections, and automatically identify transient and variable objects. The manual application of these procedures has already led to the detection of a nova that rose over six magnitudes in two days to a maximum detected brightness of m_R~13.9 and then faded two magnitudes in two weeks. We also readily identify variable stars, includings those suspected to be variables from the Sloan Digital Sky Survey. We report on our system to allow public monitoring of the telescope operational status in real time over the WWW., Comment: 3 pages, 4 figures, submitted for publication in the proceedings of ``Gamma-Ray Burst and Afterglow Astronomy 2001: A Workshop Celebrating the First Year of the HETE Mission''
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- 2002
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30. SDSS J124602.54+011318.8: A Highly Luminous Optical Transient at z=0.385
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Berk, D. E. Vanden, Lee, B. C., Wilhite, B. C., Beacom, J. F., Lamb, D. Q., Annis, J., Abazajian, K., McKay, T. A., Kron, R. G., Kent, S., Hurley, K., Kehoe, R., Wren, J., Henden, A., York, D. G., and Schneider, D. P.
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Astrophysics - Abstract
We report the discovery of a highly luminous optical transient (OT), SDSS J124602.54+011318.8, associated with a galaxy at a redshift of 0.385. In this paper we consider the possibility that the OT may be a GRB afterglow. Three sets of images and two sets of spectra were obtained as part of the normal operations of the Sloan Digital Sky Survey (SDSS). In the first two image sets, observed two nights apart, the object appears as a point source at $r^{*}\approx 17$. The third image set, observed about 410 days later, shows an extended source which is more than 2.5 magnitudes fainter. The spectra were observed about 400 and 670 days after the first two image sets, and both show an apparently normal galaxy at a redshift of 0.385. Associating the OT with the galaxy, the absolute magnitude was $M_{r^*}=-24.8$, which is over 4 magnitudes brighter than the most luminous supernova ever measured. The spectral energy distributions of the galaxy-subtracted OT derived from the first two image sets are well-fit by single power-laws with indices of $\beta_{\nu}=-0.92$ and -1.29 respectively, similar to most GRB afterglows. Based upon the luminosity of the OT, non-detections in contemporaneous ROTSE-I images, and the change in spectral slope, the OT, if an afterglow, was likely discovered early during a ``plateau'' or slowly-fading phase. The discovery of a GRB afterglow at this stage of the SDSS is consistent with expectations, but only if the optical emission is much less strongly beamed than the gamma-rays. We emphasize that other explanations for the OT cannot be ruled out; a recent follow-up study by [galyam02] provides strong evidence that this source is in fact an unusual AGN., Comment: Updated version to appear in ApJ
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- 2001
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31. Observations of the Optical Counterpart to XTE J1118+480 During Outburst by the ROTSE-I Telescope
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Wren, J., Akerlof, C., Balsano, R., Bloch, J., Borozdin, K., Casperson, D., Gisler, G., Kehoe, R., Lee, B. C., Marshall, S., McKay, T., Priedhorsky, W., Rykoff, E., Smith, D., Trudolyubov, S., and Vestrand, W. T.
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Astrophysics - Abstract
The X-ray nova XTE J1118+480 exhibited two outbursts in the early part of 2000. As detected by the Rossi X-ray Timing Explorer (RXTE), the first outburst began in early January and the second began in early March. Routine imaging of the northern sky by the Robotic Optical Transient Search Experiment (ROTSE) shows the optical counterpart to XTE J1118+480 during both outbursts. These data include over 60 epochs from January to June 2000. A search of the ROTSE data archives reveal no previous optical outbursts of this source in selected data between April 1998 and January 2000. While the X-ray to optical flux ratio of XTE J1118+480 was low during both outbursts, we suggest that they were full X-ray novae and not mini-outbursts based on comparison with similar sources. The ROTSE measurements taken during the March 2000 outburst also indicate a rapid rise in the optical flux that preceded the X-ray emission measured by the RXTE by approximately 10 days. Using these results, we estimate a pre-outburst accretion disk inner truncation radius of 1.2 x 10^4 Schwarzschild radii., Comment: 9 pages, 1 table, 2 figures
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- 2001
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32. Rapid Optical Followup Observations of SGR Events with ROTSE-I
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ROTSE Collaboration, Akerlof, C., Balsano, R., Barthelmy, S., Bloch, J., Butterworth, P., Casperson, D., Cline, T., Fletcher, S., Gisler, G., Hills, J., Kehoe, R., Lee, B., Marshall, S., McKay, T., Pawl, A., Priedhorsky, W., Seldomridge, N., Szymanski, J., and Wren, J.
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Astrophysics - Abstract
In order to observe nearly simultaneous emission from Gamma-ray Bursts (GRBs), the Robotic Optical Transient Search Experiment (ROTSE) receives triggers via the GRB Coordinates Network (GCN). Since beginning operations in March, 1998, ROTSE has also taken useful data for 10 SGR events: 8 from SGR 1900+14 and 2 from SGR 1806-20. We have searched for new or variable sources in the error regions of these SGRs and no optical counterparts were observed. Limits are in the range m_ROTSE ~ 12.5 - 15.5 during the period 20 seconds to 1 hour after the observed SGR events., Comment: 16 pages, 6 figures, accepted for publication in the Astrophysical Journal
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- 2000
33. ROTSE All Sky Surveys for Variable Stars I: Test Fields
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ROTSE Collaboration, Akerlof, C., Amrose, S., Balsano, R., Bloch, J., Casperson, D., Fletcher, S., Gisler, G., Hills, J., Kehoe, R., Lee, B., Marshall, S., McKay, T., Pawl, A., Schaefer, J., Szymanski, J., and Wren, J.
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Astrophysics - Abstract
The ROTSE-I experiment has generated CCD photometry for the entire Northern sky in two epochs nightly since March 1998. These sky patrol data are a powerful resource for studies of astrophysical transients. As a demonstration project, we present first results of a search for periodic variable stars derived from ROTSE-I observations. Variable identification, period determination, and type classification are conducted via automatic algorithms. In a set of nine ROTSE-I sky patrol fields covering about 2000 square degrees we identify 1781 periodic variable stars with mean magnitudes between m_v=10.0 and m_v=15.5. About 90% of these objects are newly identified as variable. Examples of many familiar types are presented. All classifications for this study have been manually confirmed. The selection criteria for this analysis have been conservatively defined, and are known to be biased against some variable classes. This preliminary study includes only 5.6% of the total ROTSE-I sky coverage, suggesting that the full ROTSE-I variable catalog will include more than 32,000 periodic variable stars., Comment: Accepted for publication in AJ 4/00. LaTeX manuscript. (28 pages, 11 postscript figures and 1 gif)
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- 2000
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34. Observation of contemporaneous optical radiation from a gamma-ray burst
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Akerlof, C., Balsano, R., Barthelmy, S., Bloch, J., Butterworth, P., Casperson, D., Cline, T., Fletcher, S., Frontera, F., Gisler, G., Heise, J., Hills, J., Kehoe, R., Lee, B., Marshall, S., McKay, T., Miller, R., Piro, L., Priedhorsky, W., Szymanski, J., and Wren, J.
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Astrophysics - Abstract
The origin of gamma-ray bursts (GRBs) has been enigmatic since their discovery. The situation improved dramatically in 1997, when the rapid availability of precise coordinates for the bursts allowed the detection of faint optical and radio afterglows - optical spectra thus obtained have demonstrated conclusively that the bursts occur at cosmological distances. But, despite efforts by several groups, optical detection has not hitherto been achieved during the brief duration of a burst. Here we report the detection of bright optical emission from GRB990123 while the burst was still in progress. Our observations begin 22 seconds after the onset of the burst and show an increase in brightness by a factor of 14 during the first 25 seconds; the brightness then declines by a factor of 100, at which point (700 seconds after the burst onset) it falls below our detection threshold. The redshift of this burst, approximately 1.6, implies a peak optical luminosity of 5 times 10^{49} erg per second. Optical emission from gamma-ray bursts has been generally thought to take place at the shock fronts generated by interaction of the primary energy source with the surrounding medium, where the gamma-rays might also be produced. The lack of a significant change in the gamma-ray light curve when the optical emission develops suggests that the gamma-rays are not produced at the shock front, but closer to the site of the original explosion., Comment: 10 pages, 2 figures. Accepted for publication in Nature. For additional information see http://www.umich.edu/~rotse/
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- 1999
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35. enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways
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Wren, Jonathan, Wren, J ( Jonathan ), Zhang, Kunyang; https://orcid.org/0009-0008-4588-9487, Fenner, Kathrin; https://orcid.org/0000-0001-6068-8220, Wren, Jonathan, Wren, J ( Jonathan ), Zhang, Kunyang; https://orcid.org/0009-0008-4588-9487, and Fenner, Kathrin; https://orcid.org/0000-0001-6068-8220
- Abstract
Transformation products (TPs) of man-made chemicals, formed through microbially mediated transformation in the environment, can have serious adverse environmental effects, yet the analytical identification of TPs is challenging. Rule-based prediction tools are successful in predicting TPs, especially in environmental chemistry applications that typically have to rely on small datasets, by imparting the existing knowledge on enzyme-mediated biotransformation reactions. However, the rules extracted from biotransformation reaction databases usually face the issue of being over/under-generalized and are not flexible to be updated with new reactions. We developed an automatic rule extraction tool called enviRule. It clusters biotransformation reactions into different groups based on the similarities of reaction fingerprints, and then automatically extracts and generalizes rules for each reaction group in SMARTS format. It optimizes the genericity of automatic rules against the downstream TP prediction task. Models trained with automatic rules outperformed the models trained with manually curated rules by 30% in the area under curve (AUC) scores. Moreover, automatic rules can be easily updated with new reactions, highlighting enviRule’s strengths for both automatic extraction of optimized reactions rules and automated updating thereof.
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- 2023
36. Conclusion : Leadership and the Liberal Arts: Moving Forward
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Wren, J. Thomas, Riggio, Ronald E., Genovese, Michael A., Wren, J. Thomas, editor, Riggio, Ronald E., editor, and Genovese, Michael A., editor
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- 2009
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37. Introduction
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Wren, J. Thomas, Riggio, Ronald E., Genovese, Michael A., Wren, J. Thomas, editor, Riggio, Ronald E., editor, and Genovese, Michael A., editor
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- 2009
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38. Reinventing the Liberal Arts through Leadership
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Wren, J. Thomas, Wren, J. Thomas, editor, Riggio, Ronald E., editor, and Genovese, Michael A., editor
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- 2009
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39. Introduction
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Goethals, George R., Wren, J. Thomas, Goethals, George R., editor, and Wren, J. Thomas, editor
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- 2009
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40. Conclusion
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Wren, J. Thomas, Price, Terry L., Price, Terry L., editor, and Wren, J. Thomas, editor
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- 2007
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41. Introduction
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Price, Terry L., Wren, J. Thomas, Price, Terry L., editor, and Wren, J. Thomas, editor
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- 2007
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42. Long-term (180-day) outcomes in critically ill patients with COVID-19 in the REMAP-CAP randomized clinical trial
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Florescu, S, Stanciu, D, Zaharia, M, Kosa, A, Codreanu, D, Kidwai, A, Masood, S, Kaye, C, Coutts, A, MacKay, L, Summers, C, Polgarova, P, Farahi, N, Fox, E, McWilliam, S, Hawcutt, D, Rad, L, O’Malley, L, Whitbread, J, Jones, D, Dore, R, Saunderson, P, Kelsall, O, Cowley, N, Wild, L, Thrush, J, Wood, H, Austin, K, Bélteczki, J, Magyar, I, Fazekas, Á, Kovács, S, Szőke, V, Donnelly, A, Kelly, M, Smyth, N, O’Kane, S, McClintock, D, Warnock, M, Campbell, R, McCallion, E, Azaiz, A, Charron, C, Godement, M, Geri, G, Vieillard-Baron, A, Johnson, P, McKenna, S, Hanley, J, Currie, A, Allen, B, McGoldrick, C, McMaster, M, Mani, A, Mathew, M, Kandeepan, R, Vignesh, C, TV, B, Ramakrishnan, N, James, A, Elvira, E, Jayakumar, D, Pratheema, R, Babu, S, Ebenezer, R, Krishnaoorthy, S, Ranganathan, L, Ganesan, M, Shree, M, Guilder, E, Butler, M, Cowdrey, K-A, Robertson, M, Ali, F, McMahon, E, Duffy, E, Chen, Y, Simmonds, C, McConnochie, R, O’Connor, C, El-Khawas, K, Richardson, A, Hill, D, Commons, R, Abdelkharim, H, Saxena, M, Muteithia, M, Dobell-Brown, K, Jha, R, Kalogirou, M, Ellis, C, Krishnamurthy, V, O’Connor, A, Thurairatnam, S, Mukherjee, D, Kaliappan, A, Vertue, M, Nicholson, A, Riches, J, Maloney, G, Kittridge, L, Solesbury, A, Ramos, A, Collins, D, Brickell, K, Reid, L, Smyth, M, Breen, P, Spain, S, Curley, G, McEvoy, N, Geoghegan, P, Clarke, J, Silversides, J, McGuigan, P, Ward, K, O’Neill, A, Finn, S, Wright, C, Green, J, Collins, É, Knott, C, Smith, J, Boschert, C, Slieker, K, Ewalds, E, Sanders, A, Wittenberg, W, Geurts, H, Poojara, L, Sara, T, Nand, K, Reeve, B, Dechert, W, Phillips, B, Oritz-Ruiz de Gordoa, L, Affleck, J, Shaikh, A, Murray, A, Ramanan, M, Frakking, T, Pinnell, J, Robinson, M, Gledhill, L, Wood, T, Sanghavi, R, Bhonagiri, D, Ford, M, Parikh, HG, Avard, B, Nourse, M, McDonald, B, Edmunds, N, Hoiting, O, Peters, M, Rengers, E, Evers, M, Prinssen, A, Morgan, M, Cole, J, Hill, H, Davies, M, Williams, A, Thomas, E, Davies, R, Wise, M, Grimm, P, Soukup, J, Wetzold, R, Löbel, M, Starke, L, Lellouche, F, Lizotte, P, Declerq, P, Antoine, M, Stephanie, G, Jean-Pierre, E, François, B, Marion, B, Philippe, R, Pourcine, F, Monchi, M, Luis, D, Mercier, R, Sagnier, A, Verrier, N, Caplin, C, Richecoeu, J, Combaux, D, Siami, S, Aparicio, C, Vautier, S, Jeblaoui, A, Lemaire-Brunel, D, D'Aragon, F, Carbonneau, E, Leblond, J, Plantefeve, G, Leparco, C, Contou, D, Fartoukh, M, Courtin, L, Labbe, V, Voiriot, G, Salhi, S, Chassé, M, Carrier, F, Boumahni, D, Benettaib, F, Ghamraoui, A, Sement, A, Gachet, A, Hanisch, A, Haffiane, A, Boivin, A-H, Barreau, A, Guerineau, E, Poupblanc, S, Egreteau, P, Lefevre, M, Bocher, S, Le Loup, G, Le Guen, L, Carn, V, Bertel, M, Antcliffe, D, Templeton, M, Rojo, R, Coghlan, P, Smee, J, Barker, G, Finn, A, Kreb, G, Hoff, U, Hinrichs, C, Nee, J, Mackay, E, Cort, J, Whileman, A, Spencer, T, Spittle, N, Beavis, S, Padmakumar, A, Dale, K, Hawes, J, Moakes, E, Gascoyne, R, Pritchard, K, Stevenson, L, Cooke, J, Nemeth-Roszpopa, K, Gauli, B, Bastola, S, Muller, G, Nay, M-A, Kamel, T, Benzekri, D, Jacquier, S, Runge, I, Mathonnet, A, Barbier, F, Bretagnol, A, Carter, J, Van Der Heyden, K, Mehrtens, J, Morris, A, Morgan, S, Burke, T, Mercier, E, Chartier, D, Salmon, C, Dequin, P-F, Garot, D, Bellemare, D, Cloutier, È, Daher, R, Costerousse, O, Boulanger, M-C, Couillard-Chénard, É, Lauzier, F, Francoeur, C, Francois, B, Gay, A, Anne-Laure, F, Ramali, M, HC, O, Ghosh, A, Osagie, R, Arachchige, M, Hartley, M, Cheung, W, Wong, H, Seigne, P, Eustace, J, O'Callaghan, A-M, O'Brien, F, Bamford, P, Reid, A, Cawley, K, Faulkner, M, Pickering, C, Raj, A, Tsinaslanidis, G, Khade, R, Agha, G, Sekiwala, R, Smith, T, Brewer, C, Gregory, J, Limb, J, Cowton, A, O’Brien, J, Postlethwaite, K, Malakouti, S, Music, E, Ricketts, D, King, A, Clermont, G, Bart, R, Mayr, F, Schoenling, A, Andreae, M, Shetty, V, Brant, E, Malley, B, Donadee, C, Sackrowitz, R, Weissman, A, Yealy, D, Barton, D, Talia, N, Nikitas, N, Wells, C, Lankester, L, McMillan, H, Van den Oever, H, Kruisdijk-Gerritsen, A, Haidar, G, Bain, W, Barbash, I, Fitzpatrick, M, Franz, C, Kitsios, G, Moghbeli, K, Rosborough, B, Shah, F, Suber, T, Pulletz, M, Williams, P, Birch, J, Wiseman, S, Horton, S, Alegria, A, Turki, S, Elsefi, T, Crisp, N, Allen, L, Truman, N, Smith, M, Chukkambotla, S, Goddard, W, Duberley, S, Khan, M, Kazi, A, Simpson, J, Duke, G, Chan, P, Carter, B, Hunter, S, Voigt, I, Schueler, R, Blank, E, Hüning, V, Steffen, M, Goralski, P, Litton, E, Regli, A, Pellicano, S, Palermo, A, Eroglu, E, Bihari, S, Laver, RD, Jin, X, Brown, J, McIntyre, J, French, C, Bates, S, Towns, M, Yang, Y, McGain, F, McCullagh, I, Cairns, T, Hanson, H, Patel, B, Clement, I, Evetts, G, Touma, O, Holland, S, Hodge, C, Taylor, H, Alderman, M, Barnes, N, Da Rocha, J, Smith, C, Brooks, N, Weerasinghe, T, Sinclair, J-A, Abusamra, Y, Doherty, R, Cudlipp, J, Singh, R, Yu, H, Daebis, A, Ng, C, Kendrick, S, Saran, A, Makky, A, Greener, D, Rowe-Leete, L, Edwards, A, Bland, Y, Dolman, R, Foster, T, Laffey, J, McNicholas, B, Scully, M, Casey, S, Kernan, M, Brennan, A, Rangan, R, Tully, R, Corbett, S, McCarthy, A, Duffy, O, Burke, D, Linnett, V, Sanderson, A, Ritzema, J, Wild, H, Lucas, R, Marriott, Y, Andric, Z, Cviljevic, S, Br, R, Zapalac, M, Mirković, G, Khare, D, Pinder, M, Gopinath, A, Kannan, T, Dean, S, Vanmali, P, Depuydt, P, De Waele, J, De Bus, L, Fierens, J, Bracke, S, Vermassen, J, Vermeiren, D, Pugh, R, Lean, R, Qiu, X, Scanlan, J, Evans, A, Davies, G, Lewis, J, Plesnikova, Y, Khoud, A, Coetzee, S, Puxty, K, Cathcart, S, Rimmer, D, Bagot, C, Scott, K, Martin, L, Yusuff, H, Isgro, G, Brightling, C, Bourne, M, Craner, M, Boyles, R, Alexander, B, Roberts, T, Nelli, A, Rosenstein-Sisson, R, Speyer, R, Pech, Y, McCullough, J, Tallott, M, Vazquez-Grande, G, Marten, N, Liu, T, Siddiqui, A, Khanal, S, Amatya, S, Szakmany, T, Cherian, S, Williams, G, James, C, Waters, A, Prout, R, Stedman, R, Davies, L, Pegler, S, Kyeremeh, L, Moorhouse, L, Arbane, G, Marotti, M, Bociek, A, Campos, S, Van Nieuwkoop, K, Ottens, T, Visser, Y, Van den Berg, L, Van der Kraan-Donker, A, Brett, S, Arias, S, Hall, R, Paneru, H, Koirala, S, Paudel, P, Wilson, M, Vaara, S, Pettilä, L, Heinonen, J, Pettilä, V, Jain, S, Gupta, A, Holbrook, C, Antoine, P, Meziani, F, Allam, H, Cattelan, J, Clere-Jehl, R, Helms, J, Kummerlen, C, Merdji, H, Monnier, A, Rahmani, H, Studer, A, Schneider, F, Castelain, V, Morel, G, L’Hotellier, S, Ochin, E, Vanjak, C, Rouge, P, Bendjemar, L, Albert, M, Serri, K, Cavayas, A, Duplaix, M, Williams, V, Catorze, NJTADS, Pereira, TNAL, Ferreira, RMC, Bastos, JMPS, Batista, TMO, Badie, J, Berdaguer, F, Malfroy, S, Mezher, C, Bourgoin, C, Moneger, G, Bouvier, E, Muñoz-Bermúdez, R, Marin-Corral, J, Degracia, A, Gómez, F, López, M, Aceto, R, Aghemo, A, Badalamenti, S, Brunetta, E, Cecconi, M, Ciccarelli, M, Constantini, E, Greco, M, Folci, M, Selmi, C, Voza, A, Henning, J, Bonner, S, Hugill, K, Cirstea, E, Wilkinson, D, Jones, J, Altomy, M, Karlikowski, M, Sutherland, H, Wilhelmsen, E, Woods, J, North, J, Pletz, M, Hagel, S, Ankert, J, Kolanos, S, Bloos, F, Simons, K, Van Zuylen, T, Bouman, A, Kumar, N, Panwar, R, Poulter, A-L, Sunkara, K, Szigligeti, G, Leszkoven, J, Rochwerg, B, Karachi, T, Oczkowski, S, Centofanti, J, Millen, T, Sundaran, D, Hollos, L, Turns, M, Walsh, J, Al Qasim, E, Alswaidan, L, Hegazy, M, Arishi, H, Al Amri, A, AlQahtani, S, Naidu, B, Tlayjeh, H, Hussain, S, Al Enezi, F, Abdukahil, SA, Hopkins, P, Noble, H, O’Reilly, K, Mehta, R, Wong, O, Makanju, E, Rao, D, Sikondari, N, Saha, S, Corcoran, E, Pappa, E, Cockrell, M, Donegan, C, Balaie, M, Nickoleit-Bitzenberger, D, Schaaf, B, Meermeier, W, Prebeg, K, Azzaui, H, Hower, M, Brieger, K-G, Elender, C, Sabelhaus, T, Riepe, A, Akamp, C, Kremling, J, Klein, D, Landsiedel-Mechenbier, E, Laha, S, Verlander, M, Jha, A, Megarbane, B, Voicu, S, Deye, N, Malissin, I, Sutterlin, L, Mrad, A, Lehalleur, A, Naim, G, Nguyen, P, Ekhérian, J-M, Boué, Y, Sidéris, G, Vodovar, D, Guérin, E, Grant, C, Brain, M, Mineall, S, Paramasivam, E, Wilby, E, Ogg, B, Howcroft, C, Aspinwall, A, Charlton, S, Gould, R, Mistry, D, Awan, S, Bedford, C, Carr-Wilkinson, J, Hall, A, Gardiner-Hill, C, Maloney, C, Brunskill, N, Watchorn, O, Hardy, C, Qureshi, H, Flint, N, Nicholson, S, Southin, S, Ghattaoraya, A, Harding, D, O’Halloran, S, Collins, A, Smith, E, Trues, E, Borgatta, B, Turner-Bone, I, Reddy, A, Wilding, L, Wilson, C, Surti, Z, Aneman, A, Miller, J, White, H, Estensen, K, Morrison, L, Sutton, J, Cooper, M, Warnapura, L, Agno, R, Sathianathan, P, Shaw, D, Ijaz, N, Spong, A, Sabaretnam, S, Burns, D, Lang, E, Tate, M, Fischer, R, Biradar, V, Soar, N, Golden, D, Davey, M, Seaman, R, Osborne, A, Bannard-Smith, J, Clark, R, Birchall, K, Henry, J, Pomeroy, F, Quayle, R, Wylie, K, Sukuraman, A, John, M, Sibin, S, Leditschke, A, Finnis, M, Jongebloed, K, Khwaja, K, Campisi, J, Van Vonderen, M, Pietersma, M, Vrolijk, L, Kampschreur, L, Van Gulik, L, Makowski, A, Misztal, B, Haider, S, Liao, A, Squires, R, Oborska, A, Kayani, A, Kalchko-Veyssal, S, Prabakaran, R, Hadebe, B, KalchkoVeyssal, S, Williams, T, Song, R, Morpeth, S, Lai, V, Habraken, H, Stewart, R, Mwaura, E, Mew, L, Wren, L, Willams, F, Sutherland, S-B, Rebello, R, Shehabi, Y, Al-Bassam, W, Hulley, A, Kadam, U, Sathianathan, K, Innes, R, Doble, P, Graham, L, Shovelton, C, Dean, T, Salahuddin, N, Aryal, D, Koirala, K, Rai, N, Luitel, S, Seppelt, I, Whitehead, C, Lowrey, J, Gresham, R, Masters, K, Hamlyn, V, Hawkins, N, Roynon-Reed, A, Cutler, S, Lewis, S, Lazaro, J, Newman, T, Aravindan, L, Asghar, A, Bartholomew, J, Bayne, M, Beddows, S, Birch, C, Brend, M, Byrne, R, Campbell, D, Campbell, H, Chambers, E, Clinton, A, Collins, J, Crawshaw, S, Dawson, LA, Donaldson, K, Drake, C, Dyas, S, Ellis, Y, Gilmour, K, Goodwin, J, Halden, S, Hall, AS, Hanson, J, Harper, H, Harrison, S, Hayes, A, Hodgson, H, Hurford, S-A, Jackson, S, Levett, C, Lock, S, Lockett, T, Logan, M, Lomme, K, Luo, J, Marsh, E, Mguni, N, Monaghan, H, Murphy, S, Muzengi, N, Naz, M, O'Kell, E, Oliver, A, O'Reilly, J, Pearson, K, Porter, D, Potter, A, Rook, C, Rounds, C, Sheffield, J, Shirley, K, Siewersk, C, Skinner, T, Speight, H, Sutu, M, Unsworth, A, Van’t Hoff, W, Walker, S, Williams, H, Williamson, D, Williamson, JD, Duan, E, Tsang, J, Patterson, L, Austin, P, Chapman, S, Cabrelli, L, Fletcher, S, Nortje, J, Fottrell-Gould, D, Randell, G, Stammers, K, Healey, G, Pinto, M, Borrill, Z, Duncan, T, Ustianowski, A, Uriel, A, Eltayeb, A, Alfonso, J, Hey, S, Shaw, J, Fox, C, Lindergard, G, Charles, B, Blackledge, B, Connolly, K, Harris, J, Cuesta, J, Xavier, K, Purohit, D, Elhassan, M, Haldeos, A, Vincent, R, Abdelrazik, M, Jenkins, S, Ganesan, A, Kumar, R, Carter, D, Bakthavatsalam, D, Frater, A, Saleem, M, Everitt, R, Hacking, D, Zaman, M, Elmahi, E, Jones, A, Hall, K, Phillips, M, Terrill, L, Mills, G, Raithatha, A, Bauchmuller, K, Ryalls, K, Harrington, K, Bowler, H, Sall, J, Bourne, R, Gross, J, Massey, N, Adebambo, O, Long, M, Tony, K, Juffermans, N, Koopmans, M, Dujardin, R, Alderink, B, Rowland, M, Hutton, P, Bashyal, A, Davidson, N, Hird, C, Chhablani, M, Phalod, G, Kirkby, A, Archer, S, Netherton, K, Reschreiter, H, Camsooksai, J, Patch, S, Humphrey, C, Flynn, G, Harrington, C, Kruger, P, Walsham, J, Meyer, J, Harward, M, Jones, C, Sathe, S, Roche, L, Davies, E, Skinner, D, Gaylard, J, Newman, J, Pogson, D, Rose, S, Daly, Z, Brimfield, L, Nown, A, Parekh, D, Bergin, C, Bates, M, McGhee, C, Lynch, D, Bhandal, K, Tsakiridou, K, Bamford, A, Cooper, L, Whitehouse, T, Veenith, T, Forster, E, O'Connell, M, Sim, M, Hay, S, Henderson, S, Nygren, M, Valentine, E, Katary, A, Bell, G, Wilcox, L, Mataliotakis, M, Smith, P, Ali, M, Isguzar, A, Phull, M-K, Zaidi, A, Pogreban, T, Rosaroso, L, Harvey, D, Lowe, B, Meredith, M, Ryan, L, Schouten, J, Pickkers, P, Roovers, N, Klop-Riehl, M, Van der Eng, H, Sloots-Cuppen, S, Preijers, L, Van Oosten, N, Moine, P, Heming, N, Maxime, V, Bossard, I, Nicholier, T, Clair, B, Orlikowski, D, Bounab, R, Abdeladim, L, Baker, S, Duroux, M, Ratcliffe, M, Sy, E, Mailman, J, Lee, S, Gupta, C, Kassir, S, López, R, Rodríguez-Gómez, J, Cárcel, S, Carmona, R, De la Fuente, C, Rodriguez, M, Jan Hassing, R, Greven, F, Huijbens, D, Roebers, L, Verheij, H, Miles, H, Attokaran, A, Buehner, U, Williams, E, Chapman, M, O’Connor, S, Glasby, K, Rivett, J, Brown, N, Kutsogiannis, D, Thompson, P, Rooney, K, Rodden, N, Thomson, N, McGlynn, D, Abel, L, Gemmell, L, Sundaram, R, Hornsby, J, Walden, A, Keating, L, Frise, M, Rai, S, Bartley, S, Schuster-Bruce, M, Pitts, S, Miln, R, Purandare, L, Vamplew, L, Dempster, D, Gummadi, M, Dormand, N, Wang, S, Spivey, M, Bean, S, Burt, K, Moore, L, Hammonds, F, Richards, C, Campbell, L, Smyth, K, Day, C, Zitter, L, Benyon, S, Singh, J, Lynch, C, Mikusek, J, Deacon, B, Turner, K, Baker, E, Hickey, J, Champanerkar, S, Aitken, L, LewisProsser, L, Ahmad, N, Wiles, M, Willson, J, Grecu, I, Martin, J, Wrey Brown, C, Arias, A-M, Bevan, E, Westlake, S, Craven, T, Hope, D, Singleton, J, Clark, S, McCulloch, C, Biddie, S, Welters, I, Hamilton, D, Williams, K, Waugh, V, Mulla, S, Waite, A, Roman, J, Martinez, M, Johnston, B, Puthucheary, Z, Martin, T, Santos, F, Uddin, R, Fernandez, M, Seidu, F, Somerville, A, Pakats, M-L, Begum, S, Shahid, T, Presneill, J, Barge, D, Byrne, K, Janin, P, Yarad, E, Bass, F, Hammond, N, Vuylsteke, A, Chan, C, Victor, S, Waterson, S, McNamara, R, Boardman, M, Gattas, D, Buhr, H, Coles, J, Matsa, R, Gellamucho, M, Creagh-Brown, B, Marriot, C, Salberg, A, Zouita, L, Stone, S, Michalak, N, Donlon, S, Mtuwa, S, Mayangao, I, Verula, J, Burda, D, Harris, C, Jones, E, Bradley, P, Tarr, E, Harden, L, Piercy, C, Nolan, J, Kerslake, I, Cook, T, Simpson, T, Dalton, J, Demetriou, C, Mitchard, S, Ramos, L, White, K, Johnson, T, Headdon, W, Spencer, S, White, A, Howie, L, Reay, M, Watts, A, Traverse, E, Jennings, S, Anumakonda, V, Tuckwell, C, Harrow, K, Matthews, J, McGarry, K, Moore, V, Smith, L, Summerfield, A, Dark, P, Harvey, A, Doonan, R, McMorrow, L, Knowles, K, Pendlebury, J, Perez, J, Marsden, T, Taylor, M, Michael, A, Collis, M, Claxton, A, Habeichi, W, Horner, D, Slaughter, M, Thomas, V, Proudfoot, N, Keatley, C, Donnison, P, Casey, R, Irving, B, Matimba-Mupaya, W, Reed, C, Anthony, A, Trim, F, Cambalova, L, Robertson, D, Wilson, A, Hulme, J, Kannan, S, Kinney, F, Senya, H, Ratnam, V, Gill, M, Kirk, J, Shelton, S, Schweikert, S, Wibrow, B, Anstey, M, Rauniyar, R, Khoso, N, Asif, N, Taqdees, H, Frey, C, Scano, R, McKee, M, Murphy, P, Thomas, M, Worner, R, Faulkner, B, Gendall, E, Hayes, K, Blakemore, H, Borislavova, B, Deshpande, K, Van Haren, F, Konecny, P, Inskip, D, Tung, R, Hayes, L, Murphy, L, Neill, A, Reidy, B, O’Dwyer, M, Ryan, D, Ainscough, K, Hamilton-Davies, C, Mfuko, C, Abbass, H, Mandadapu, V, Leaver, S, Patel, K, Farnell-Ward, S, Saluzzio, R, Rawlins, S, Sicat, C, De Keulenaer, B, Ferrier, J, Fysh, E, Davda, A, Mevavala, B, Cook, D, Clarke, F, Banach, D, Fernández de Pinedo Artaraz, Z, Cabreros, L, Latham, V, Kruisselbrink, R, Brochard, L, Burns, K, Sandhu, G, Khalid, I, White, I, Croft, M, Holland, N, Pereira, R, Nair, P, Buscher, H, Reynolds, C, Newman, S, Santamaria, J, Barbazza, L, Homes, J, Smith, R, Zaki, A, Johnson, D, Garrard, H, Juhaz, V, Brown, L, Pemberton, A, Roy, A, Rostron, A, Woods, L, Cornell, S, Fowler, R, Adhikari, N, Kamra, M, Marinoff, N, Garrett, P, Murray, L, Brailsford, J, Fennessy, G, Mulder, J, Morgan, R, Pillai, S, Harford, R, Ivatt, H, Evans, D, Richards, S, Roberts, E, Bowen, J, Ainsworth, J, Kuitunen, A, Karlsson, S, Vahtera, A, Kiiski, H, Ristimäki, S, Albrett, J, Jackson, C, Kirkham, S, Tamme, K, Reinhard, V, Ellervee, A, Põldots, L, Rennit, P, Svitškar, N, Browne, T, Grimwade, K, Goodson, J, Keet, O, Callender, O, Udy, A, McCracken, P, Young, M, Board, J, Martin, E, Kasipandian, V, Patel, A, Allibone, S, Mary-Genetu, R, English, S, Watpool, I, Porteous, R, Miezitis, S, McIntyre, L, Brady, K, Vale, C, Shekar, K, Lavana, J, Parmar, D, Peake, S, Kurenda, C, Hormis, A, Walker, R, Collier, D, Kimpton, S, Oakley, S, Bhagani, S, De Neef, M, Garcia, S, Maharajh, A, Nandani, A, Dobson, J, Fernando, G, Eastgate, C, Gomez, K, Abdi, Z, Tatham, K, Jhanji, S, Black, E, Dela Rosa, A, Howle, R, Baikady, R, Drummond, A, Dearden, J, Philbin, J, Munt, S, Gopal, S, Pooni, J-S, Ganguly, S, Smallwood, A, Metherell, S, Naeem, A, Fagan, L, Ryan, E, Mariappa, V, Foulds, A, Revill, A, Bhattarai, B, De Jonge, E, Wigbers, J, Del Prado, M, Cremer, O, Mulier, J, Peters, A, Romberg, B, Schutgens, R, Troeman, D, Van Opdorp, M, Besten, H, Brakké, K, Barber, R, Hilldrith, A, Kluge, S, Nierhaus, A, Jarczak, D, Roedl, K, Kochanek, M, Rueß-Paterno, G, Mc-Kenzie, J, Eichenauer, D, Shimabukuro-Vornhagen, A, Wilcox, E, Del Sorbo, L, Abdelhady, H, Romagnuolo, T, Simpson, S, Maiden, M, Horton, M, Trickey, J, Krajinovic, V, Kutleša, M, Kotarski, V, Brohi, F, Jagannathan, V, Clark, M, Purvis, S, Wetherill, B, Brajković, A, Babel, J, Sever, H, Dragija, L, Kušan, I, Dushianthan, A, Cusack, R, De Courcy-Golder, K, Salmon, K, Burnish, R, Smith, S, Ruiz, W, Duke, Z, Johns, M, Male, M, Gladas, K, Virdee, S, Swabe, J, Tomlinson, H, Rohde, G, Grünewaldt, A, Bojunga, J, Petros, S, Kunz, K, Schütze, B, Weismann, D, Frey, A, Drayss, M, Goebeler, ME, Flor, T, Fragner, G, Wahl, N, Totzke, J, Sayehli, C, Hakak, S, Altaf, W, O'Sullivan, M, Murphy, A, Walsh, L, Rega La Valle, A, Bewley, J, Sweet, K, Grimmer, L, Johnson, R, Wyatt, R, Morgan, K, Varghese, S, Willis, J, Stratton, E, Kyle, L, Putensen, D, Drury, K, Skorko, A, Bremmer, P, Ward, G, Bassford, C, Sligl, W, Baig, N, Rewa, O, Bagshaw, S, Basile, K, Stavor, D, Burbee, D, McNamara, A, Wunderley, R, Bensen, N, Adams, P, Vita, T, Buhay, M, Scholl, D, Gilliam, M, Winters, J, Doherty, K, Berryman, E, Ghaffari, M, Marroquin, O, Quinn, K, Garrard, W, Kalchthaler, K, Beard, G, Skrtich, A, Bagavathy, K, Drapola, D, Bryan-Morris, K, Arnold, J, Reynolds, B, Hussain, M, Dunsavage, J, Saiyed, S, Hernandez, E, Goldman, J, Brown, C, Comp, S, Raczek, J, Morris, J, Vargas Jr., J, Weiss, D, Hensley, J, Kochert, E, Wnuk, C, Nemeth, C, Mowery, B, Hutchinson, C, Winters, L, McAdams, D, Walker, G, Minnier, T, Wisniewski, M, Mayak, K, McCreary, E, Bariola, R, Viehman, A, Daley, J, Lopus, A, Schmidhofer, M, Ambrosino, R, Keen, S, Toffalo, S, Stambaugh, M, Trimmer, K, Perri, R, Casali, S, Medva, R, Massar, B, Beyerl, A, Burkey, J, Keeler, S, Lowery, M, Oncea, L, Daugherty, J, Sevilla, C, Woelke, A, Dice, J, Weber, L, Roth, J, Ferringer, C, Beer, D, Fesz, J, Carpio, L, Colin, G, Zinzoni, V, Maquigneau, N, Henri-Lagarrigue, M, Pouplet, C, Reill, L, Distler, M, Maselli, A, Martynoga, R, Trask, K, Butler, A, Attwood, B, Parsons, P, Campbell, B, Smith, A, Page, V, Zhao, X, Oza, D, Abrahamson, G, Sheath, B, Young, P, Young, C, Lesona, E, Navarra, L, Cruz, R, Delaney, K, Aguilar-Dano, A, Gojanovic, M, Rhodes, J, Anderson, T, Morris, S, Nayyar, V, Bowen, D, Kong, J, Joy, J, Fuchs, R, Lambert, B, Tai, C, Thomas, A, Keen, A, Tierney, C, Omer, N, Bacon, G, Tridente, A, Shuker, K, Anders, J, Greer, S, Scott, P, Millington, A, Buchanan, P, Binnie, A, Powell, E, McMillan, A, Luk, T, Aref, N, Denmade, C, Sadera, G, Jacob, R, Hughes, D, Sterba, M, Geng, W, Digby, S, Southern, D, Reddy, H, Hulse, S, Campbell, A, Garton, M, Watkins, C, Smuts, S, Quinn, A, Simpson, B, McMillan, C, Finch, C, Hill, C, Cooper, J, Budd, J, Small, C, O’Leary, R, Collins, E, Holland, A, Alexander, P, Felton, T, Ferguson, S, Sellers, K, Ward, L, Yates, D, Birkinshaw, I, Kell, K, Scott, Z, Pearson, H, Hashmi, M, Hassan, N, Panjwani, A, Umrani, Z, Shaikh, M, Ain, Q, Kanwal, D, Van Bree, S, Bouw-Ruiter, M, Osinga, M, Van Zanten, A, McEldrew, R, Rashan, S, Singh, V, Azergui, N, Bari, S, Beltran, M, Brugman, C, Groeneveld, E, Jafarzadeh, M, Keijzer-Timmers, N, Kester, E, Koelink, M, Kwakkenbos-Craanen, M, Okundaye, C, Parker, L, Peters, S, Post, S, Rietveld, I, Scheepstra-Beukers, I, Schreuder, G, Smit, A, Brillinger, N, Markgraf, R, Eichinger, F, Doran, P, Anjum, A, Best-Lane, J, Barton, F, Miller, L, Richards-Belle, A, Saull, M, Sprinckmoller, S, Wiley, D, Darnell, R, Au, C, Lindstrum, K, Cheng, A, Forbes, A, Heritier, S, Trapani, T, Cuthbertson, B, Manoharan, V, Dondrop, A, Tolppa, T, Ehrmann, S, Hullegie, S, Povoa, P, Beasley, R, Daneman, N, McGloughlin, S, Paterson, D, Venkatesh, B, De Jong, M, Uyeki, T, Baillie, K, Netea, M, Orr, K, Patanwala, A, Tong, S, Cooper, N, Galea, J, Leavis, H, Ogungbenro, K, Patawala, A, Rademaker, E, Youngstein, T, Carrier, M, Fergusson, D, Hunt, B, Kumar, A, Laffan, M, Lother, S, Middeldorp, S, Stanworth, S, De Man, A, Masse, M-H, Abraham, J, Arnold, D, Begin, P, Charlewood, R, Chasse, M, Coyne, M, Daly, J, Gosbell, I, Harvala-Simmonds, H, MacLennan, S, McDyer, J, Menon, D, Pridee, N, Roberts, D, Thomas, H, Tinmouth, A, Triulzi, D, Walsh, T, Wood, E, Calfee, C, O’Kane, C, Shyamsundar, M, Sinha, P, Thompson, T, Young, I, Burrell, A, Ferguson, N, Hodgson, C, Orford, N, Phua, J, Baron, R, Epelman, S, Frankfurter, C, Gommans, F, Kim, E, Leaf, D, Vaduganathan, M, Van Kimmenade, R, Sanil, A, Van Beurden, M, Effelaar, E, Schotsman, J, Boyd, C, Harland, C, Shearer, A, Wren, J, Attanayaka, U, Darshana, S, Ishani, P, Udayanga, I, Higgins, AM, Berry, LR, Lorenzi, E, Murthy, S, McQuilten, Z, Mouncey, PR, Al-Beidh, F, Annane, D, Arabi, YM, Beane, A, Van Bentum-Puijk, W, Bhimani, Z, Bonten, MJM, Bradbury, CA, Brunkhorst, FM, Buzgau, A, Buxton, M, Charles, WN, Cove, M, Detry, MA, Estcourt, LJ, Fagbodun, EO, Fitzgerald, M, Girard, TD, Goligher, EC, Goossens, H, Haniffa, R, Hills, T, Horvat, CM, Huang, DT, Ichihara, N, Lamontagne, F, Marshall, JC, McAuley, DF, McGlothlin, A, McGuinness, SP, McVerry, BJ, Neal, MD, Nichol, AD, Parke, RL, Parker, JC, Parry-Billings, K, Peters, SEC, Reyes, LF, Rowan, KM, Saito, H, Santos, MS, Saunders, CT, Serpa-Neto, A, Seymour, CW, Shankar-Hari, M, Stronach, LM, Turgeon, AF, Turner, AM, Van de Veerdonk, FL, Zarychanski, R, Green, C, Lewis, RJ, Angus, DC, McArthur, CJ, Berry, S, Derde, LPG, Gordon, AC, Webb, SA, Lawler, PR, Comm REMAP-CAP Investigators, Apollo - University of Cambridge Repository, Intensive Care Medicine, Université de Versailles Saint-Quentin-en-Yvelines - UFR Sciences de la santé Simone Veil (UVSQ Santé), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Hôpital Raymond Poincaré [Garches], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Pittsburgh Foundation, PF, Amgen, Health Research Board, HRB: CTN 2014-012, Horizon 2020 Framework Programme, H2020: 101003589, Translational Breast Cancer Research Consortium, TBCRC, Canadian Institutes of Health Research, IRSC: 158584, Heart and Stroke Foundation of Canada, HSF, National Institute for Health and Care Research, NIHR, European Commission, EC, National Health and Medical Research Council, NHMRC: 1101719, APP194811, CS-2016-16-011, GNT2008447, RP-2015-06-18, Office of Health and Medical Research, OHMR, Health Research Council of New Zealand, HRC: 16/631, Eisai, Ministère des Affaires Sociales et de la Santé: PHRC-20-0147, Université Pierre et Marie Curie, UPMC, NIHR Imperial Biomedical Research Centre, BRC, Minderoo Foundation, Funding/Support : The Platform for European Preparedness Against (Re-) emerging Epidemics (PREPARE) consortium by the European Union, FP7-HEALTH-2013-INNOVATION-1 (#602525), the Rapid European COVID-19 Emergency Research response (RECOVER) consortium by the European Union’s Horizon 2020 research and innovation programme (#101003589), the Australian National Health and Medical Research Council (#APP1101719), the Australian Medical Research Future Fund (#APP2002132), the Health Research Council of New Zealand (#16/631), the Canadian Institutes of Health Research Strategy for Patient-Oriented Research Innovative Clinical Trials Program Grant (#158584) and the Canadian Institute of Health Research COVID-19 Rapid Research Funding (#447335), the UK National Institute for Health Research (NIHR) and the NIHR Imperial Biomedical Research Centre, the Health Research Board of Ireland (CTN 2014-012), the UPMC Learning While Doing Program, the Translational Breast Cancer Research Consortium, the French Ministry of Health (PHRC-20-0147), the Wellcome Trust Innovations Project (215522), the Minderoo Foundation, the EU Programme Emergency Support Instrument, the NHS Blood and Transplant Research and Development Programme, the Translational Breast Cancer Research Consortium, the NSW Office of Health and Medical Research, Amgen, Eisai, and the Pittsburgh Foundation. Dr Higgins is funded by an NHMRC Emerging Leadership Fellowship (GNT2008447). Dr McQuilten is funded by an NHMRC Emerging Leadership Fellowship (APP194811). Dr Gordon is funded by an NIHR Research Professorship (RP-2015-06-18) and Dr Shankar-Hari by an NIHR Clinician Scientist Fellowship (CS-2016-16-011). Dr Turgeon is the Chairholder of the Canada Research Chair in Critical Care Neurology and Trauma. Dr Lawler is supported by a career award from the Heart and Stroke Foundation of Canada., and European Project: 602525,EC:FP7:HEALTH,FP7-HEALTH-2013-INNOVATION-1,PREPARE(2014)
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Adult ,Male ,corticosteroid ,[SDV]Life Sciences [q-bio] ,Critical Illness ,lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4] ,antiplatelet ,Lopinavir ,Adaptive platform trial randomized controlled trial intensive care, pneumonia COVID-19 antiplatelet immunoglobulin antiviral corticosteroid immune modulation anticoagulation ,All institutes and research themes of the Radboud University Medical Center ,Adrenal Cortex Hormones ,Humans ,anticoagulation ,intensive care, pneumonia ,COVID-19 Serotherapy ,Original Investigation ,Medicine(all) ,immune modulation ,Ritonavir ,SARS-CoV-2 ,COVID-19 ,Anticoagulants ,Bayes Theorem ,General Medicine ,Middle Aged ,antiviral ,Receptors, Interleukin-6 ,Adaptive platform trial ,randomized controlled trial ,Female ,Human medicine ,immunoglobulin ,Follow-Up Studies ,Hydroxychloroquine - Abstract
ImportanceThe longer-term effects of therapies for the treatment of critically ill patients with COVID-19 are unknown.ObjectiveTo determine the effect of multiple interventions for critically ill adults with COVID-19 on longer-term outcomes.Design, Setting, and ParticipantsPrespecified secondary analysis of an ongoing adaptive platform trial (REMAP-CAP) testing interventions within multiple therapeutic domains in which 4869 critically ill adult patients with COVID-19 were enrolled between March 9, 2020, and June 22, 2021, from 197 sites in 14 countries. The final 180-day follow-up was completed on March 2, 2022.InterventionsPatients were randomized to receive 1 or more interventions within 6 treatment domains: immune modulators (n = 2274), convalescent plasma (n = 2011), antiplatelet therapy (n = 1557), anticoagulation (n = 1033), antivirals (n = 726), and corticosteroids (n = 401).Main Outcomes and MeasuresThe main outcome was survival through day 180, analyzed using a bayesian piecewise exponential model. A hazard ratio (HR) less than 1 represented improved survival (superiority), while an HR greater than 1 represented worsened survival (harm); futility was represented by a relative improvement less than 20% in outcome, shown by an HR greater than 0.83.ResultsAmong 4869 randomized patients (mean age, 59.3 years; 1537 [32.1%] women), 4107 (84.3%) had known vital status and 2590 (63.1%) were alive at day 180. IL-6 receptor antagonists had a greater than 99.9% probability of improving 6-month survival (adjusted HR, 0.74 [95% credible interval {CrI}, 0.61-0.90]) and antiplatelet agents had a 95% probability of improving 6-month survival (adjusted HR, 0.85 [95% CrI, 0.71-1.03]) compared with the control, while the probability of trial-defined statistical futility (HR >0.83) was high for therapeutic anticoagulation (99.9%; HR, 1.13 [95% CrI, 0.93-1.42]), convalescent plasma (99.2%; HR, 0.99 [95% CrI, 0.86-1.14]), and lopinavir-ritonavir (96.6%; HR, 1.06 [95% CrI, 0.82-1.38]) and the probabilities of harm from hydroxychloroquine (96.9%; HR, 1.51 [95% CrI, 0.98-2.29]) and the combination of lopinavir-ritonavir and hydroxychloroquine (96.8%; HR, 1.61 [95% CrI, 0.97-2.67]) were high. The corticosteroid domain was stopped early prior to reaching a predefined statistical trigger; there was a 57.1% to 61.6% probability of improving 6-month survival across varying hydrocortisone dosing strategies.Conclusions and RelevanceAmong critically ill patients with COVID-19 randomized to receive 1 or more therapeutic interventions, treatment with an IL-6 receptor antagonist had a greater than 99.9% probability of improved 180-day mortality compared with patients randomized to the control, and treatment with an antiplatelet had a 95.0% probability of improved 180-day mortality compared with patients randomized to the control. Overall, when considered with previously reported short-term results, the findings indicate that initial in-hospital treatment effects were consistent for most therapies through 6 months.
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- 2023
43. The molecular structures and the relationships between the calculated molecular and observed bulk phase properties of phosphonium-based ionic liquids
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Morco, Ryan P., Musa, Ahmed Y., and Wren, J. Clara
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- 2014
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44. The Bright Optical Flash and Afterglow from the Gamma-Ray Burst GRB 130427A
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Vestrand, W. T., Wren, J. A., Panaitescu, A., Wozniak, P. R., Davis, H., Palmer, D. M., Vianello, G., Omodei, N., Xiong, S., Briggs, M. S., Elphick, M., Paciesas, W., and Rosing, W.
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- 2014
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45. dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning
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Wren, J, Cao, H, Zhang, Y, Baumbach, J, Burton, PR, Dwyer, D, Koutsouleris, N, Matschinske, J, Marcon, Y, Rajan, S, Rieg, T, Ryser-Welch, P, Spaeth, J, Herrmann, C, Schwarz, E, Wren, J, Cao, H, Zhang, Y, Baumbach, J, Burton, PR, Dwyer, D, Koutsouleris, N, Matschinske, J, Marcon, Y, Rajan, S, Rieg, T, Ryser-Welch, P, Spaeth, J, Herrmann, C, and Schwarz, E
- Abstract
MOTIVATION: In multi-cohort machine learning studies, it is critical to differentiate between effects that are reproducible across cohorts and those that are cohort-specific. Multi-task learning (MTL) is a machine learning approach that facilitates this differentiation through the simultaneous learning of prediction tasks across cohorts. Since multi-cohort data can often not be combined into a single storage solution, there would be the substantial utility of an MTL application for geographically distributed data sources. RESULTS: Here, we describe the development of 'dsMTL', a computational framework for privacy-preserving, distributed multi-task machine learning that includes three supervised and one unsupervised algorithms. First, we derive the theoretical properties of these methods and the relevant machine learning workflows to ensure the validity of the software implementation. Second, we implement dsMTL as a library for the R programming language, building on the DataSHIELD platform that supports the federated analysis of sensitive individual-level data. Third, we demonstrate the applicability of dsMTL for comorbidity modeling in distributed data. We show that comorbidity modeling using dsMTL outperformed conventional, federated machine learning, as well as the aggregation of multiple models built on the distributed datasets individually. The application of dsMTL was computationally efficient and highly scalable when applied to moderate-size (n < 500), real expression data given the actual network latency. AVAILABILITY AND IMPLEMENTATION: dsMTL is freely available at https://github.com/transbioZI/dsMTLBase (server-side package) and https://github.com/transbioZI/dsMTLClient (client-side package). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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- 2022
46. Activation of the JAK/STAT pathway in Behcet’s disease
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Tulunay, A, Dozmorov, M G, Ture-Ozdemir, F, Yilmaz, V, Eksioglu-Demiralp, E, Alibaz-Oner, F, Ozen, G, Wren, J D, Saruhan-Direskeneli, G, Sawalha, A H, and Direskeneli, H
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- 2015
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47. POS0098 LINC01871, IMPLICATED IN SJÖGREN’S DISEASE PATHOGENESIS, IS REGULATED BY INTERFERON-G AND CALCINEURIN SIGNALING
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Joachims, M. L., primary, Khatri, B., additional, Li, C., additional, Tessneer, K. L., additional, Ice, J., additional, Stolarczyk, A. M., additional, Means, N., additional, Grundahl, K., additional, Glenn, S., additional, Kelly, J., additional, Lewis, D., additional, Radfar, L., additional, Stone, D., additional, Guthridge, J., additional, James, J. A., additional, Scofield, R. H., additional, Wiley, G. B., additional, Wren, J., additional, Gaffney, P. M., additional, Montgomery, C., additional, Sivils, K., additional, Rasmussen, A., additional, Farris, A. D., additional, Adrianto, I., additional, and Lessard, C., additional
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- 2022
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48. Hypoxia Tolerance in Animals: Biology and Application *
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Gorr, T. A., Wichmann, D., Hu, J., Hermes‐Lima, M., Welker, A. F., Terwilliger, N., Wren, J. F., Viney, M., Morris, S., Nilsson, G. E., Deten, A., Soliz, J., and Gassmann, M.
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- 2010
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49. Effect of gamma irradiation on gas-ionic liquid and water-ionic liquid interfacial stability
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Howett, Susan E., Joseph, Jiju M., Noël, James J., and Wren, J. Clara
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- 2011
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50. The effect of interfacial mass transfer on steady-state water radiolysis
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Yakabuskie, Pamela A., Joseph, Jiju M., and Clara Wren, J.
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- 2010
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