| 1. |
- Brownstein, Catherine A., et al.
(author)
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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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In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Journal article (peer-reviewed)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. |
- Abbasi, R., et al.
(author)
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Constraints on high-energy neutrino emission from SN 2008D
- 2011
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 527:4, s. A28-
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Journal article (peer-reviewed)abstract
- SN 2008D, a core collapse supernova at a distance of 27 Mpc, was serendipitously discovered by the Swift satellite through an associated X-ray flash. Core collapse supernovae have been observed in association with long gamma-ray bursts and X-ray flashes and a physical connection is widely assumed. This connection could imply that some core collapse supernovae possess mildly relativistic jets in which high-energy neutrinos are produced through proton-proton collisions. The predicted neutrino spectra would be detectable by Cherenkov neutrino detectors like IceCube. A search for a neutrino signal in temporal and spatial correlation with the observed X-ray flash of SN 2008D was conducted using data taken in 2007-2008 with 22 strings of the IceCube detector. Events were selected based on a boosted decision tree classifier trained with simulated signal and experimental background data. The classifier was optimized to the position and a "soft jet" neutrino spectrum assumed for SN 2008D. Using three search windows placed around the X-ray peak, emission time scales from 100-10 000 s were probed. No events passing the cuts were observed in agreement with the signal expectation of 0.13 events. Upper limits on the muon neutrino flux from core collapse supernovae were derived for different emission time scales and the principal model parameters were constrained. While no meaningful limits can be given in the case of an isotropic neutrino emission, the parameter space for a jetted emission can be constrained. Future analyses with the full 86 string IceCube detector could detect up to similar to 100 events for a core-collapse supernova at 10 Mpc according to the soft jet model.
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| 3. |
- Abbasi, R., et al.
(author)
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Constraints on the extremely-high energy cosmic neutrino flux with the IceCube 2008-2009 data
- 2011
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In: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 1550-7998 .- 1550-2368. ; 83:9, s. 092003-
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Journal article (peer-reviewed)abstract
- We report on a search for extremely-high energy neutrinos with energies greater than 10(6) GeV using the data taken with the IceCube detector at the South Pole. The data was collected between April 2008 and May 2009 with the half-completed IceCube array. The absence of signal candidate events in the sample of 333.5 days of live time significantly improves model-independent limits from previous searches and allows to place a limit on the diffuse flux of cosmic neutrinos with an E-2 spectrum in the energy range 2.0 x 10(6) - 6.3 x 10(9) GeV to a level of E-2 phi <= 3.6 x 10(-8) GeV cm(-2) sec(-1) sr(-1).
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| 4. |
- Abbasi, R., et al.
(author)
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First search for atmospheric and extraterrestrial neutrino-induced cascades with the IceCube detector
- 2011
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 84:7, s. 072001-
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Journal article (peer-reviewed)abstract
- We report on the first search for atmospheric and for diffuse astrophysical neutrino-induced showers (cascades) in the IceCube detector using 257 days of data collected in the year 2007-2008 with 22 strings active. A total of 14 events with energies above 16 TeV remained after event selections in the diffuse analysis, with an expected total background contribution of 8.3 +/- 3.6. At 90% confidence we set an upper limit of E(2)Phi(90%CL) < 3.6 x 10(-7) GeV.cm(-2).s(-1).sr(-1) on the diffuse flux of neutrinos of all flavors in the energy range between 24 TeV and 6.6 PeV assuming that Phi proportional to E(-2) and the flavor composition of the nu(e):nu(mu):nu(tau) flux is 1:1:1 at the Earth. The atmospheric neutrino analysis was optimized for lower energies. A total of 12 events were observed with energies above 5 TeV. The observed number of events is consistent with the expected background, within the uncertainties.
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| 5. |
- Abbasi, R., et al.
(author)
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First search for extremely high energy cosmogenic neutrinos with the IceCube Neutrino Observatory
- 2010
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In: Physical review. D, Particles, fields, gravitation, and cosmology. - 1550-7998. ; 82:7, s. 072003-
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Journal article (peer-reviewed)abstract
- We report on the results of the search for extremely-high energy neutrinos with energies above 10(7) GeV obtained with the partially (similar to 30%) constructed IceCube in 2007. From the absence of signal events in the sample of 242.1 days of effective live time, we derive a 90% C.L. model independent differential upper limit based on the number of signal events per energy decade at E-2 phi(ve+v mu+v tau) similar or equal to 1.4 x 10(-6) GeV cm(-2) sec(-1) sr(-1) for neutrinos in the energy range from 3 x 10(7) to 3 x 10(9) GeV.
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| 6. |
- Abbasi, R., et al.
(author)
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Limits on Neutrino Emission from Gamma-Ray Bursts with the 40 String IceCube Detector
- 2011
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 106:14, s. 141101-
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Journal article (peer-reviewed)abstract
- IceCube has become the first neutrino telescope with a sensitivity below the TeV neutrino flux predicted from gamma-ray bursts if gamma-ray bursts are responsible for the observed cosmic-ray flux above 10(18) eV. Two separate analyses using the half-complete IceCube detector, one a dedicated search for neutrinos from p gamma interactions in the prompt phase of the gamma-ray burst fireball and the other a generic search for any neutrino emission from these sources over a wide range of energies and emission times, produced no evidence for neutrino emission, excluding prevailing models at 90% confidence.
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| 7. |
- Abbasi, R., et al.
(author)
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Measurement of the anisotropy of cosmic-ray arrival directions with icecube
- 2010
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In: The Astrophysical Journal Letters. - 2041-8205. ; 718, s. L194-L198
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Journal article (peer-reviewed)abstract
- We report the first observation of an anisotropy in the arrival direction of cosmic rays with energies in the multi-TeV region in the Southern sky using data from the IceCube detector. Between 2007 June and 2008 March, the partially deployed IceCube detector was operated in a configuration with 1320 digital optical sensors distributed over 22 strings at depths between 1450 and 2450 m inside the Antarctic ice. IceCube is a neutrino detector, but the data are dominated by a large background of cosmic-ray muons. Therefore, the background data are suitable for high-statistics studies of cosmic rays in the southern sky. The data include 4.3 billion muons produced by downward-going cosmic-ray interactions in the atmosphere; these events were reconstructed with a median angular resolution of 3 degrees and a median energy of similar to 20 TeV. Their arrival direction distribution exhibits an anisotropy in right ascension with a first-harmonic amplitude of (6.4 +/- 0.2 stat. +/- 0.8 syst.) x 10(-4).
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| 8. |
- Abbasi, R., et al.
(author)
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Measurement of the atmospheric neutrino energy spectrum from 100 GeV to 400 TeV with IceCube
- 2011
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In: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 1550-7998 .- 1550-2368. ; 83:1, s. 012001-
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Journal article (peer-reviewed)abstract
- A measurement of the atmospheric muon neutrino energy spectrum from 100 GeV to 400 TeV was performed using a data sample of about 18 000 up-going atmospheric muon neutrino events in IceCube. Boosted decision trees were used for event selection to reject misreconstructed atmospheric muons and obtain a sample of up-going muon neutrino events. Background contamination in the final event sample is less than 1%. This is the first measurement of atmospheric neutrinos up to 400 TeV, and is fundamental to understanding the impact of this neutrino background on astrophysical neutrino observations with IceCube. The measured spectrum is consistent with predictions for the atmospheric nu(mu) + (nu) over bar (mu) flux.
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| 9. |
- Abbasi, R., et al.
(author)
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Search for a Lorentz-violating sidereal signal with atmospheric neutrinos in IceCube
- 2010
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In: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 1550-7998. ; 82, s. 112003-
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Journal article (peer-reviewed)abstract
- A search for sidereal modulation in the flux of atmospheric muon neutrinos in IceCube was performed. Such a signal could be an indication of Lorentz-violating physics. Neutrino oscillation models, derivable from extensions to the standard model, allow for neutrino oscillations that depend on the neutrino's direction of propagation. No such direction-dependent variation was found. A discrete Fourier transform method was used to constrain the Lorentz and CPT-violating coefficients in one of these models. Because of the unique high energy reach of IceCube, it was possible to improve constraints on certain Lorentz-violating oscillations by 3 orders of magnitude with respect to limits set by other experiments.
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| 10. |
- Abbasi, R., et al.
(author)
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Search for dark matter from the Galactic halo with the IceCube Neutrino Telescope
- 2011
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 84:2, s. 022004-
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Journal article (peer-reviewed)abstract
- Self-annihilating or decaying dark matter in the Galactic halo might produce high energy neutrinos detectable with neutrino telescopes. We have conducted a search for such a signal using 276 days of data from the IceCube 22-string configuration detector acquired during 2007 and 2008. The effect of halo model choice in the extracted limit is reduced by performing a search that considers the outer halo region and not the Galactic Center. We constrain any large-scale neutrino anisotropy and are able to set a limit on the dark matter self-annihilation cross section of h similar or equal to 10(-22) cm(3) s(-1) for weakly interacting massive particle masses above 1 TeV, assuming a monochromatic neutrino line spectrum.
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