| 1. |
- Richards, Stephen, et al.
(författare)
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
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Tidskriftsartikel (refereegranskat)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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| 2. |
- Aad, G., et al.
(författare)
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Commissioning of the ATLAS Muon Spectrometer with cosmic rays
- 2010
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 70:3, s. 875-916
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Tidskriftsartikel (refereegranskat)abstract
- The ATLAS detector at the Large Hadron Collider has collected several hundred million cosmic ray events during 2008 and 2009. These data were used to commission the Muon Spectrometer and to study the performance of the trigger and tracking chambers, their alignment, the detector control system, the data acquisition and the analysis programs. We present the performance in the relevant parameters that determine the quality of the muon measurement. We discuss the single element efficiency, resolution and noise rates, the calibration method of the detector response and of the alignment system, the track reconstruction efficiency and the momentum measurement. The results show that the detector is close to the design performance and that the Muon Spectrometer is ready to detect muons produced in high energy proton-proton collisions.
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| 3. |
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| 4. |
- Aad, G., et al.
(författare)
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Readiness of the ATLAS Tile Calorimeter for LHC collisions
- 2010
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 70:4, s. 1193-1236
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Tidskriftsartikel (refereegranskat)abstract
- The Tile hadronic calorimeter of the ATLAS detector has undergone extensive testing in the experimental hall since its installation in late 2005. The readout, control and calibration systems have been fully operational since 2007 and the detector has successfully collected data from the LHC single beams in 2008 and first collisions in 2009. This paper gives an overview of the Tile Calorimeter performance as measured using random triggers, calibration data, data from cosmic ray muons and single beam data. The detector operation status, noise characteristics and performance of the calibration systems are presented, as well as the validation of the timing and energy calibration carried out with minimum ionising cosmic ray muons data. The calibration systems' precision is well below the design value of 1%. The determination of the global energy scale was performed with an uncertainty of 4%.
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| 5. |
- Aad, G., et al.
(författare)
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Studies of the performance of the ATLAS detector using cosmic-ray muons
- 2011
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 71:3
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Tidskriftsartikel (refereegranskat)abstract
- Muons from cosmic-ray interactions in the atmosphere provide a high-statistics source of particles that can be used to study the performance and calibration of the ATLAS detector. Cosmic-ray muons can penetrate to the cavern and deposit energy in all detector subsystems. Such events have played an important role in the commissioning of the detector since the start of the installation phase in 2005 and were particularly important for understanding the detector performance in the time prior to the arrival of the first LHC beams. Global cosmic-ray runs were undertaken in both 2008 and 2009 and these data have been used through to the early phases of collision data-taking as a tool for calibration, alignment and detector monitoring. These large datasets have also been used for detector performance studies, including investigations that rely on the combined performance of different subsystems. This paper presents the results of performance studies related to combined tracking, lepton identification and the reconstruction of jets and missing transverse energy. Results are compared to expectations based on a cosmic-ray event generator and a full simulation of the detector response.
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| 6. |
- Aad, G., et al.
(författare)
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The ATLAS Inner Detector commissioning and calibration
- 2010
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 70:3, s. 787-821
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Tidskriftsartikel (refereegranskat)abstract
- The ATLAS Inner Detector is a composite tracking system consisting of silicon pixels, silicon strips and straw tubes in a 2 T magnetic field. Its installation was completed in August 2008 and the detector took part in data-taking with single LHC beams and cosmic rays. The initial detector operation, hardware commissioning and in-situ calibrations are described. Tracking performance has been measured with 7.6 million cosmic-ray events, collected using a tracking trigger and reconstructed with modular pattern-recognition and fitting software. The intrinsic hit efficiency and tracking trigger efficiencies are close to 100%. Lorentz angle measurements for both electrons and holes, specific energy-loss calibration and transition radiation turn-on measurements have been performed. Different alignment techniques have been used to reconstruct the detector geometry. After the initial alignment, a transverse impact parameter resolution of 22.1 +/- 0.9 mu m and a relative momentum resolution sigma (p) /p=(4.83 +/- 0.16)x10(-4) GeV(-1)xp (T) have been measured for high momentum tracks.
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| 7. |
- Aad, G., et al.
(författare)
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The ATLAS Simulation Infrastructure
- 2010
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 70:3, s. 823-874
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Tidskriftsartikel (refereegranskat)abstract
- The simulation software for the ATLAS Experiment at the Large Hadron Collider is being used for large-scale production of events on the LHC Computing Grid. This simulation requires many components, from the generators that simulate particle collisions, through packages simulating the response of the various detectors and triggers. All of these components come together under the ATLAS simulation infrastructure. In this paper, that infrastructure is discussed, including that supporting the detector description, interfacing the event generation, and combining the GEANT4 simulation of the response of the individual detectors. Also described are the tools allowing the software validation, performance testing, and the validation of the simulated output against known physics processes.
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| 8. |
- Orton, Glenn S., et al.
(författare)
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Mid-infrared spectroscopy of Uranus from the Spitzer Infrared Spectrometer : 1. Determination of the mean temperature structure of the upper troposphere and stratosphere
- 2014
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Ingår i: Icarus. - : Elsevier BV. - 0019-1035 .- 1090-2643. ; 243, s. 494-513
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Tidskriftsartikel (refereegranskat)abstract
- On 2007 December 16-17, spectra were acquired of the disk of Uranus by the Spitzer Infrared Spectrometer (IRS), ten days after the planet's equinox, when its equator was close to the sub-Earth point. This spectrum provides the highest-resolution broad-band spectrum ever obtained for Uranus from space, allowing a determination of the disk-averaged temperature and molecule composition to a greater degree of accuracy than ever before. The temperature profiles derived from the Voyager radio occultation experiment by Lindal et al. (Lindal, G.F., Lyons, J.R., Sweetnam, D.N., Eshleman, V.R., Hinson, D.P. [1987]. J. Geophys. Res. 92, 14987-15001) and revisions suggested by Sromovsky et al. (Sromovsky, L.A., Fry, P.A., Kim, J.H. [2011]. Icarus 215, 292-312) that match these data best are those that assume a high abundance of methane in the deep atmosphere. However, none of these model profiles provides a satisfactory fit over the full spectral range sampled. This result could be the result of spatial differences between global and low-latitudinal regions, changes in time, missing continuum opacity sources such as stratospheric hazes or unknown tropospheric constituents, or undiagnosed systematic problems with either the Voyager radio-occultation or the Spitzer IRS data sets. The spectrum is compatible with the stratospheric temperatures derived from the Voyager ultraviolet occultations measurements by Herbert et al. (Herbert, F. et al. [1987]. J. Geophys. Res. 92, 15093-15109), but it is incompatible with the hot stratospheric temperatures derived from the same data by Stevens et al. (Stevens, M.H., Strobel, D.F., Herbert, F.H. [1993]. Icarus 101, 45-63). Thermospheric temperatures determined from the analysis of the observed H2 quadrupole emission features are colder than those derived by Herbert et al. at pressures less than ~1μbar. Extrapolation of the nominal model spectrum to far-infrared through millimeter wavelengths shows that the spectrum arising solely from H2 collision-induced absorption is too warm to reproduce observations between wavelengths of 0.8 and 3.3mm. Adding an additional absorber such as H2S provides a reasonable match to the spectrum, although a unique identification of the responsible absorber is not yet possible with available data. An immediate practical use for the spectrum resulting from this model is to establish a high-precision continuum flux model for use as an absolute radiometric standard for future astronomical observations.
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| 9. |
- Orton, Glenn S., et al.
(författare)
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Mid-infrared spectroscopy of Uranus from the Spitzer infrared spectrometer : 2. Determination of the mean composition of the upper troposphere and stratosphere
- 2014
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Ingår i: Icarus. - : Elsevier BV. - 0019-1035 .- 1090-2643. ; 243, s. 471-493
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Tidskriftsartikel (refereegranskat)abstract
- Mid-infrared spectral observations Uranus acquired with the Infrared Spectrometer (IRS) on the Spitzer Space Telescope are used to determine the abundances of C2H2, C2H6, CH3C2H, C4H2, CO2, and tentatively CH3 on Uranus at the time of the 2007 equinox. For vertically uniform eddy diffusion coefficients in the range 2200-2600cm2s-1, photochemical models that reproduce the observed methane emission also predict C2H6 profiles that compare well with emission in the 11.6-12.5μm wavelength region, where the υ9 band of C2H6 is prominent. Our nominal model with a uniform eddy diffusion coefficient Kzz=2430cm2s-1 and a CH4 tropopause mole fraction of 1.6×10-5 provides a good fit to other hydrocarbon emission features, such as those of C2H2 and C4H2, but the model profile for CH3C2H must be scaled by a factor of 0.43, suggesting that improvements are needed in the chemical reaction mechanism for C3Hx species. The nominal model is consistent with a CH3D/CH4 ratio of 3.0±0.2×10-4. From the best-fit scaling of these photochemical-model profiles, we derive column abundances above the 10-mbar level of 4.5+01.1/-0.8×1019molecule-cm-2 for CH4, 6.2±1.0×1016molecule-cm-2 for C2H2 (with a value 24% higher from a different longitudinal sampling), 3.1±0.3×1016molecule-cm-2 for C2H6, 8.6±2.6×1013molecule-cm-2 for CH3C2H, 1.8±0.3×1013molecule-cm-2 for C4H2, and 1.7±0.4×1013molecule-cm-2 for CO2 on Uranus. A model with Kzz increasing with altitude fits the observed spectrum and requires CH4 and C2H6 column abundances that are 54% and 45% higher than their respective values in the nominal model, but the other hydrocarbons and CO2 are within 14% of their values in the nominal model. Systematic uncertainties arising from errors in the temperature profile are estimated very conservatively by assuming an unrealistic "alternative" temperature profile that is nonetheless consistent with the observations; for this profile the column abundance of CH4 is over four times higher than in the nominal model, but the column abundances of the hydrocarbons and CO2 differ from their value in the nominal model by less than 22%. The CH3D/CH4 ratio is the same in both the nominal model with its uniform Kzz as in the vertically variable Kzz model, and it is 10% lower with the "alternative" temperature profile than the nominal model. There is no compelling evidence for temporal variations in global-average hydrocarbon abundances over the decade between Infrared Space Observatory and Spitzer observations, but we cannot preclude a possible large increase in the C2H2 abundance since the Voyager era. Our results have implications with respect to the influx rate of exogenic oxygen species and the production rate of stratospheric hazes on Uranus, as well as the C4H2 vapor pressure over C4H2 ice at low temperatures.
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| 10. |
- Aad, G., et al.
(författare)
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- 2011
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swepub:Mat__t (refereegranskat)
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