| 1. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 2. |
- Blunden, Jessica, et al.
(författare)
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State of the climate in 2013
- 2014
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Ingår i: Bulletin of the American Meteorological Society. - 0003-0007. ; 95
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Tidskriftsartikel (refereegranskat)abstract
- © 2014, American Meteorological Society. All rights reserved. In 2013, the vast majority of the monitored climate variables reported here maintained trends established in recent decades. ENSO was in a neutral state during the entire year, remaining mostly on the cool side of neutral with modest impacts on regional weather patterns around the world. This follows several years dominated by the effects of either La Niña or El Niño events. According to several independent analyses, 2013 was again among the 10 warmest years on record at the global scale, both at the Earth’s surface and through the troposphere. Some regions in the Southern Hemisphere had record or near-record high temperatures for the year. Australia observed its hottest year on record, while Argentina and New Zealand reported their second and third hottest years, respectively. In Antarctica, Amundsen-Scott South Pole Station reported its highest annual temperature since records began in 1957. At the opposite pole, the Arctic observed its seventh warmest year since records began in the early 20th century. At 20-m depth, record high temperatures were measured at some permafrost stations on the North Slope of Alaska and in the Brooks Range. In the Northern Hemisphere extratropics, anomalous meridional atmospheric circulation occurred throughout much of the year, leading to marked regional extremes of both temperature and precipitation. Cold temperature anomalies during winter across Eurasia were followed by warm spring temperature anomalies, which were linked to a new record low Eurasian snow cover extent in May. Minimum sea ice extent in the Arctic was the sixth lowest since satellite observations began in 1979. Including 2013, all seven lowest extents on record have occurred in the past seven years. Antarctica, on the other hand, had above-average sea ice extent throughout 2013, with 116 days of new daily high extent records, including a new daily maximum sea ice area of 19.57 million km2 reached on 1 October. ENSO-neutral conditions in the eastern central Pacific Ocean and a negative Pacific decadal oscillation pattern in the North Pacific had the largest impacts on the global sea surface temperature in 2013. The North Pacific reached a historic high temperature in 2013 and on balance the globally-averaged sea surface temperature was among the 10 highest on record. Overall, the salt content in nearsurface ocean waters increased while in intermediate waters it decreased. Global mean sea level continued to rise during 2013, on pace with a trend of 3.2 mm yr-1 over the past two decades. A portion of this trend (0.5 mm yr-1) has been attributed to natural variability associated with the Pacific decadal oscillation as well as to ongoing contributions from the melting of glaciers and ice sheets and ocean warming. Global tropical cyclone frequency during 2013 was slightly above average with a total of 94 storms, although the North Atlantic Basin had its quietest hurricane season since 1994. In the Western North Pacific Basin, Super Typhoon Haiyan, the deadliest tropical cyclone of 2013, had 1-minute sustained winds estimated to be 170 kt (87.5 m s-1) on 7 November, the highest wind speed ever assigned to a tropical cyclone. High storm surge was also associated with Haiyan as it made landfall over the central Philippines, an area where sea level is currently at historic highs, increasing by 200 mm since 1970. In the atmosphere, carbon dioxide, methane, and nitrous oxide all continued to increase in 2013. As in previous years, each of these major greenhouse gases once again reached historic high concentrations. In the Arctic, carbon dioxide and methane increased at the same rate as the global increase. These increases are likely due to export from lower latitudes rather than a consequence of increases in Arctic sources, such as thawing permafrost. At Mauna Loa, Hawaii, for the first time since measurements began in 1958, the daily average mixing ratio of carbon dioxide exceeded 400 ppm on 9 May. The state of these variables, along with dozens of others, and the 2013 climate conditions of regions around the world are discussed in further detail in this 24th edition of the State of the Climate series.
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| 3. |
- Abramowski, A., et al.
(författare)
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Constraints on axionlike particles with HESS from the irregularity of the PKS 2155-304 energy spectrum
- 2013
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Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; 88:10, s. 102003-
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Tidskriftsartikel (refereegranskat)abstract
- Axionlike particles (ALPs) are hypothetical light (sub-eV) bosons predicted in some extensions of the Standard Model of particle physics. In astrophysical environments comprising high-energy gamma rays and turbulent magnetic fields, the existence of ALPs can modify the energy spectrum of the gamma rays for a sufficiently large coupling between ALPs and photons. This modification would take the form of an irregular behavior of the energy spectrum in a limited energy range. Data from the H. E. S. S. observations of the distant BL Lac object PKS 2155 - 304 (z = 0.116) are used to derive upper limits at the 95% C. L. on the strength of the ALP coupling to photons, g(gamma a) < 2.1 x 10(-11) GeV-1 for an ALP mass between 15 and 60 neV. The results depend on assumptions on the magnetic field around the source, which are chosen conservatively. The derived constraints apply to both light pseudoscalar and scalar bosons that couple to the electromagnetic field.
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| 4. |
- Abramowski, A., et al.
(författare)
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Constraints on the gamma-ray emission from the cluster-scale AGN outburst in the Hydra A galaxy cluster
- 2012
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 545, s. A103-
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Tidskriftsartikel (refereegranskat)abstract
- Context. In some galaxy clusters, powerful active galactic nuclei (AGN) have blown bubbles with cluster scale extent into the ambient medium. The main pressure support of these bubbles is not known to date, but cosmic rays are a viable possibility. For such a scenario copious gamma-ray emission is expected as a tracer of cosmic rays from these systems. Aims. Hydra A, the closest galaxy cluster hosting a cluster scale AGN outburst, located at a redshift of 0.0538, is investigated for being a gamma-ray emitter with the High Energy Stereoscopic System (H.E.S.S.) array and the Fermi Large Area Telescope (Fermi-LAT). Methods. Data obtained in 20.2 h of dedicated H. E. S. S. observations and 38 months of Fermi-LAT data, gathered by its usual all-sky scanning mode, have been analyzed to search for a gamma-ray signal. Results. No signal has been found in either data set. Upper limits on the gamma-ray flux are derived and are compared to models. These are the first limits on gamma-ray emission ever presented for galaxy clusters hosting cluster scale AGN outbursts. Conclusions. The non-detection of Hydra A in gamma-rays has important implications on the particle populations and physical conditions inside the bubbles in this system. For the case of bubbles mainly supported by hadronic cosmic rays, the most favorable scenario, which involves full mixing between cosmic rays and embedding medium, can be excluded. However, hadronic cosmic rays still remain a viable pressure support agent to sustain the bubbles against the thermal pressure of the ambient medium. The largest population of highly-energetic electrons, which are relevant for inverse-Compton gamma-ray production is found in the youngest inner lobes of Hydra A. The limit on the inverse-Compton gamma-ray flux excludes a magnetic field below half of the equipartition value of 16 mu G in the inner lobes.
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| 5. |
- Abramowski, A., et al.
(författare)
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Diffuse Galactic gamma-ray emission with HESS
- 2014
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Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:12, s. Article ID: 122007-
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Tidskriftsartikel (refereegranskat)abstract
- Diffuse gamma-ray emission is the most prominent observable signature of celestial cosmic-ray interactions at high energies. While already being investigated at GeVenergies over several decades, assessments of diffuse gamma-ray emission at TeVenergies remain sparse. After completion of the systematic survey of the inner Galaxy, the H.E.S.S. experiment is in a prime position to observe large-scale diffuse emission at TeVenergies. Data of the H.E.S.S. Galactic Plane Survey are investigated in regions off known gamma-ray sources. Corresponding gamma-ray flux measurements were made over an extensive grid of celestial locations. Longitudinal and latitudinal profiles of the observed gamma-ray fluxes show characteristic excess emission not attributable to known gamma-ray sources. For the first time large-scale gamma-ray emission along the Galactic plane using imaging atmospheric Cherenkov telescopes has been observed. While the background subtraction technique limits the ability to recover modest variation on the scale of the H.E.S.S. field of view or larger, which is characteristic of the inverse Compton scatter-induced Galactic diffuse emission, contributions of neutral pion decay as well as emission from unresolved gamma-ray sources can be recovered in the observed signal to a large fraction. Calculations show that the minimum gamma-ray emission from pi(0) decay represents a significant contribution to the total signal. This detection is interpreted as a mix of diffuse Galactic gamma-ray emission and unresolved sources.
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| 6. |
- Abramowski, A., et al.
(författare)
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Discovery of gamma-ray emission from the extragalactic pulsar wind nebula N 157B with HESS
- 2012
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 545, s. Article ID: L2-
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Tidskriftsartikel (refereegranskat)abstract
- We present the significant detection of the first extragalactic pulsar wind nebula (PWN) detected in gamma rays, N 157B, located in the large Magellanic Cloud (LMC). Pulsars with high spin-down luminosity are found to power energised nebulae that emit gamma rays up to energies of several tens of TeV. N 157B is associated with PSR J0537-6910, which is the pulsar with the highest known spin-down luminosity. The High Energy Stereoscopic System telescope array observed this nebula on a yearly basis from 2004 to 2009 with a dead-time corrected exposure of 46 h. The gamma-ray spectrum between 600 GeV and 12 TeV is well-described by a pure power-law with a photon index of 2.8 +/- 0.2(stat) +/- 0.3(syst) and a normalisation at 1 TeV of (8.2 +/- 0.8(stat) +/- 2.5(syst)) x 10(-13) cm(-2) s(-1) TeV-1. A leptonic multi-wavelength model shows that an energy of about 4 x 10(49) erg is stored in electrons and positrons. The apparent efficiency, which is the ratio of the TeV gamma-ray luminosity to the pulsar's spin-down luminosity, 0.08% +/- 0.01%, is comparable to those of PWNe found in the Milky Way. The detection of a PWN at such a large distance is possible due to the pulsar's favourable spin-down luminosity and a bright infrared photon-field serving as an inverse-Compton-scattering target for accelerated leptons. By applying a calorimetric technique to these observations, the pulsar's birth period is estimated to be shorter than 10 ms.
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| 7. |
- Abramowski, A., et al.
(författare)
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Discovery of high and very high-energy emission from the BL Lacertae object SHBL J001355.9-185406
- 2013
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 554, s. A72-
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Tidskriftsartikel (refereegranskat)abstract
- The detection of the high-frequency peaked BL Lac object (HBL) SHBL J001355.9-185406 (z = 0.095) at high (HE; 100 MeV < E < 300 GeV) and very high-energy (VHE; E > 100 GeV) with the Fermi Large Area Telescope (LAT) and the High Energy Stereoscopic System (H.E.S.S.) is reported. Dedicated observations were performed with the H. E. S. S. telescopes, leading to a detection at the 5.5 sigma significance level. The measured flux above 310 GeV is (8.3 +/- 1.7(stat) +/- 1.7(sys)) x 10(-13) photons cm(-2) s(-1) (about 0.6% of that of the Crab Nebula), and the power-law spectrum has a photon index of Gamma = 3.4 +/- 0.5(stat) +/- 0.2(sys). Using 3.5 years of publicly available Fermi-LAT data, a faint counterpart has been detected in the LAT data at the 5.5 sigma significance level, with an integrated flux above 300 MeV of (9.3 +/- 3.4(stat) +/- 0.8(sys)) x 10(-10) photons cm(-2) s(-1) and a photon index of Gamma = 1.96 +/- 0.20(stat) +/- 0.08(sys). X-ray observations with Swift-XRT allow the synchrotron peak energy in vF(v) representation to be located at similar to 1.0 keV. The broadband spectral energy distribution is modelled with a one-zone synchrotron self-Compton (SSC) model and the optical data by a black-body emission describing the thermal emission of the host galaxy. The derived parameters are typical of HBLs detected at VHE, with a particle-dominated jet.
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| 8. |
- Abramowski, A., et al.
(författare)
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Discovery of TeV gamma-ray emission from PKS 0447-439 and derivation of an upper limit on its redshift
- 2013
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 552, s. A118-
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Tidskriftsartikel (refereegranskat)abstract
- Very high-energy gamma-ray emission from PKS 0447-439 was detected with the H. E. S. S. Cherenkov telescope array in December 2009. This blazar is one of the brightest extragalactic objects in the Fermi bright source list and has a hard spectrum in the MeV to GeV range. In the TeV range, a photon index of 3.89 +/- 0.37 (stat) +/- 0.22 (sys) and a flux normalisation at 1 TeV, phi(1) (TeV) = (3.5 +/- 1.1(stat) +/- 0.9(sys)) x 10(-13) cm(-2) s(-1) TeV-1 were found. The detection with H. E. S. S. triggered observations in the X-ray band with the Swift and RXTE telescopes. Simultaneous UV and optical data from Swift UVOT and data from the optical telescopes ATOM and ROTSE are also available. The spectrum and light curve measured with H. E. S. S. are presented and compared to the multi-wavelength data at lower energies. A rapid flare is seen in the Swift XRT and RXTE data, together with a flux variation in the UV band, at a time scale of the order of one day. A firm upper limit of z < 0.59 on the redshift of PKS 0447-439 is derived from the combined Fermi-LAT and H. E. S. S. data, given the assumptions that there is no upturn in the intrinsic spectrum above the Fermi-LAT energy range and that absorption on the extragalactic background light (EBL) is not weaker than the lower limit provided by current models. The spectral energy distribution is well described by a simple one-zone synchrotron self-Compton scenario, if the redshift of the source is less than z less than or similar to 0.4.
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| 9. |
- Abramowski, A., et al.
(författare)
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Discovery of the Hard Spectrum VHE γ-Ray Source HESS J1641–463
- 2014
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Ingår i: Astrophysical Journal Letters. - 2041-8205 .- 2041-8213. ; 794:1, s. Article ID: L1-
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Tidskriftsartikel (refereegranskat)abstract
- This Letter reports the discovery of a remarkably hard spectrum source, HESS J1641-463, by the High Energy Stereoscopic System (H.E.S.S.) in the very high energy (VHE) domain. HESS J1641-463 remained unnoticed by the usual analysis techniques due to confusion with the bright nearby source HESS J1640-465. It emerged at a significance level of 8.5 standard deviations after restricting the analysis to events with energies above 4 TeV. It shows a moderate flux level of phi(E > 1TeV) = (3.64 +/- 0.44(stat)+/- 0.73(sys)) x 10(-13) cm(-2) s(-1), corresponding to 1.8% of the Crab Nebula flux above the same energy, and a hard spectrum with a photon index of Gamma = 2.07 +/- 0.11(stat)+/- 0.20(sys). It is a point-like source, although an extension up to a Gaussian width of sigma = 3 arcmin cannot be discounted due to uncertainties in the H.E.S.S. point-spread function. The VHE gamma-ray flux of HESS J1641-463 is found to be constant over the observed period when checking time binnings from the year-by-year to the 28 minute exposure timescales. HESS J1641-463 is positionally coincident with the radio supernova remnant SNR G338.5+0.1. No X-ray candidate stands out as a clear association; however, Chandra and XMM-Newton data reveal some potential weak counterparts. Various VHE gamma-ray production scenarios are discussed. If the emission from HESS J1641-463 is produced by cosmic ray protons colliding with the ambient gas, then their spectrum must extend close to 1 PeV. This object may represent a source population contributing significantly to the galactic cosmic ray flux around the knee.
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| 10. |
- Abramowski, A., et al.
(författare)
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Discovery of very high energy gamma-ray emission from the BL Lacertae object PKS0301-243 with HESS
- 2013
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 559, s. A136-
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Tidskriftsartikel (refereegranskat)abstract
- The active galactic nucleus PKS 0301-243 (z = 0.266) is a high-synchrotron-peaked BL Lac object that is detected at high energies (HE, 100 MeV < E < 100 GeV) by Fermi/LAT. This paper reports on the discovery of PKS 0301-243 at very high energies (E > 100 GeV) by the High Energy Stereoscopic System (H.E.S.S.) from observations between September 2009 and December 2011 for a total live time of 34.9 h. Gamma rays above 200 GeV are detected at a significance of 9.4 sigma. A hint of variability at the 2.5 sigma level is found. An integral flux I(E > 200GeV) = (3.3 +/- 1.1(stat) +/- 0.7(syst)) x 10(-12) ph cm(-2) s(-1) and a photon index Gamma = 4.6 +/- 0.7(stat) +/- 0.2(syst) are measured. Multi-wavelength light curves in HE, X-ray and optical bands show strong variability, and a minimal variability timescale of eight days is estimated from the optical light curve. A single-zone leptonic synchrotron self-Compton scenario satisfactorily reproduces the multi-wavelength data. In this model, the emitting region is out of equipartition and the jet is particle dominated. Because of its high redshift compared to other sources observed at TeV energies, the very high energy emission from PKS 0301-243 is attenuated by the extragalactic background light (EBL) and the measured spectrum is used to derive an upper limit on the opacity of the EBL.
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