1. |
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2. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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3. |
- Abbasi, R., et al.
(författare)
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Acceptance Tests of more than 10 000 Photomultiplier Tubes for the multi-PMT Digital Optical Modules of the IceCube Upgrade
- 2024
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 19:7
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Tidskriftsartikel (refereegranskat)abstract
- More than 10 000 photomultiplier tubes (PMTs) with a diameter of 80 mm will be installed in multi-PMT Digital Optical Modules (mDOMs) of the IceCube Upgrade. These have been tested and pre-calibrated at two sites. A throughput of more than 1000 PMTs per week with both sites was achieved with a modular design of the testing facilities and highly automated testing procedures. The testing facilities can easily be adapted to other PMTs, such that they can, e.g., be re-used for testing the PMTs for IceCube-Gen2. Single photoelectron response, high voltage dependence, time resolution, prepulse, late pulse, afterpulse probabilities, and dark rates were measured for each PMT. We describe the design of the testing facilities, the testing procedures, and the results of the acceptance tests.
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4. |
- Abbasi, R., et al.
(författare)
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Characterization of the astrophysical diffuse neutrino flux using starting track events in IceCube
- 2024
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Ingår i: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 2470-0010 .- 2470-0029. ; 110:2
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Tidskriftsartikel (refereegranskat)abstract
- A measurement of the diffuse astrophysical neutrino spectrum is presented using IceCube data collected from 2011-2022 (10.3 years). We developed novel detection techniques to search for events with a contained vertex and exiting track induced by muon neutrinos undergoing a charged-current interaction. Searching for these starting track events allows us to not only more effectively reject atmospheric muons but also atmospheric neutrino backgrounds in the southern sky, opening a new window to the sub-100 TeV astrophysical neutrino sky. The event selection is constructed using a dynamic starting track veto and machine learning algorithms. We use this data to measure the astrophysical diffuse flux as a single power law flux (SPL) with a best-fit spectral index of γ=2.58-0.09+0.10 and per-flavor normalization of φper-flavorAstro=1.68-0.22+0.19×10-18×GeV-1 cm-2 s-1 sr-1 (at 100 TeV). The sensitive energy range for this dataset is 3-550 TeV under the SPL assumption. This data was also used to measure the flux under a broken power law, however we did not find any evidence of a low energy cutoff.
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5. |
- Abbasi, R., et al.
(författare)
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Improved modeling of in-ice particle showers for IceCube event reconstruction
- 2024
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 19:6
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Tidskriftsartikel (refereegranskat)abstract
- The IceCube Neutrino Observatory relies on an array of photomultiplier tubes to detect Cherenkov light produced by charged particles in the South Pole ice. IceCube data analyses depend on an in-depth characterization of the glacial ice, and on novel approaches in event reconstruction that utilize fast approximations of photoelectron yields. Here, a more accurate model is derived for event reconstruction that better captures our current knowledge of ice optical properties. When evaluated on a Monte Carlo simulation set, the median angular resolution for in-ice particle showers improves by over a factor of three compared to a reconstruction based on a simplified model of the ice. The most substantial improvement is obtained when including effects of birefringence due to the polycrystalline structure of the ice. When evaluated on data classified as particle showers in the high-energy starting events sample, a significantly improved description of the events is observed.
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6. |
- Abbasi, R., et al.
(författare)
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Citizen science for IceCube: Name that Neutrino
- 2024
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Ingår i: European Physical Journal Plus. - 2190-5444. ; 139:6
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Tidskriftsartikel (refereegranskat)abstract
- Name that Neutrino is a citizen science project where volunteers aid in classification of events for the IceCube Neutrino Observatory, an immense particle detector at the geographic South Pole. From March 2023 to September 2023, volunteers did classifications of videos produced from simulated data of both neutrino signal and background interactions. Name that Neutrino obtained more than 128,000 classifications by over 1800 registered volunteers that were compared to results obtained by a deep neural network machine-learning algorithm. Possible improvements for both Name that Neutrino and the deep neural network are discussed.
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7. |
- Abbasi, R., et al.
(författare)
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Search for decoherence from quantum gravity with atmospheric neutrinos
- 2024
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Ingår i: Nature Physics. - 1745-2481 .- 1745-2473. ; 20:6, s. 913-920
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Tidskriftsartikel (refereegranskat)abstract
- Neutrino oscillations at the highest energies and longest baselines can be used to study the structure of spacetime and test the fundamental principles of quantum mechanics. If the metric of spacetime has a quantum mechanical description, its fluctuations at the Planck scale are expected to introduce non-unitary effects that are inconsistent with the standard unitary time evolution of quantum mechanics. Neutrinos interacting with such fluctuations would lose their quantum coherence, deviating from the expected oscillatory flavour composition at long distances and high energies. Here we use atmospheric neutrinos detected by the IceCube South Pole Neutrino Observatory in the energy range of 0.5-10.0 TeV to search for coherence loss in neutrino propagation. We find no evidence of anomalous neutrino decoherence and determine limits on neutrino-quantum gravity interactions. The constraint on the effective decoherence strength parameter within an energy-independent decoherence model improves on previous limits by a factor of 30. For decoherence effects scaling as E2, our limits are advanced by more than six orders of magnitude beyond past measurements compared with the state of the art. Interactions of atmospheric neutrinos with quantum-gravity-induced fluctuations of the metric of spacetime would lead to decoherence. The IceCube Collaboration constrains such interactions with atmospheric neutrinos.
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8. |
- Abbasi, R., et al.
(författare)
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Search for Continuous and Transient Neutrino Emission Associated with IceCube's Highest-energy Tracks: An 11 yr Analysis
- 2024
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Ingår i: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 964:1
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Tidskriftsartikel (refereegranskat)abstract
- IceCube alert events are neutrinos with a moderate-to-high probability of having astrophysical origin. In this study, we analyze 11 yr of IceCube data and investigate 122 alert events and a selection of high-energy tracks detected between 2009 and the end of 2021. This high-energy event selection (alert events + high-energy tracks) has an average probability of >= 0.5 of being of astrophysical origin. We search for additional continuous and transient neutrino emission within the high-energy events' error regions. We find no evidence for significant continuous neutrino emission from any of the alert event directions. The only locally significant neutrino emission is the transient emission associated with the blazar TXS 0506+056, with a local significance of 3 sigma, which confirms previous IceCube studies. When correcting for 122 test positions, the global p-value is 0.156 and compatible with the background hypothesis. We constrain the total continuous flux emitted from all 122 test positions at 100 TeV to be below 1.2 x 10-15 (TeV cm2 s)-1 at 90% confidence assuming an E -2 spectrum. This corresponds to 4.5% of IceCube's astrophysical diffuse flux. Overall, we find no indication that alert events in general are linked to lower-energetic continuous or transient neutrino emission.
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9. |
- Abbasi, R., et al.
(författare)
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Search for 10-1000 GeV Neutrinos from Gamma-Ray Bursts with IceCube
- 2024
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Ingår i: Astrophysical Journal. - : Institute of Physics (IOP). - 1538-4357 .- 0004-637X. ; 964:2
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Tidskriftsartikel (refereegranskat)abstract
- We present the results of a search for 10-1000 GeV neutrinos from 2268 gamma-ray bursts (GRBs) over 8 yr of IceCube-DeepCore data. This work probes burst physics below the photosphere where electromagnetic radiation cannot escape. Neutrinos of tens of giga electronvolts are predicted in sub-photospheric collision of free-streaming neutrons with bulk-jet protons. In a first analysis, we searched for the most significant neutrino-GRB coincidence using six overlapping time windows centered on the prompt phase of each GRB. In a second analysis, we conducted a search for a group of GRBs, each individually too weak to be detectable, but potentially significant when combined. No evidence of neutrino emission is found for either analysis. The most significant neutrino coincidence is for Fermi-GBM GRB bn 140807500, with a p-value of 0.097 corrected for all trials. The binomial test used to search for a group of GRBs had a p-value of 0.65 after all trial corrections. The binomial test found a group consisting only of GRB bn 140807500 and no additional GRBs. The neutrino limits of this work complement those obtained by IceCube at tera electronvolt to peta electronvolt energies. We compare our findings for the large set of GRBs as well as GRB 221009A to the sub-photospheric neutron-proton collision model and find that GRB 221009A provides the most constraining limit on baryon loading. For a jet Lorentz factor of 300 (800), the baryon loading on GRB 221009A is lower than 3.85 (2.13) at a 90% confidence level.
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10. |
- Abbasi, R., et al.
(författare)
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Measurement of atmospheric neutrino mixing with improved IceCube DeepCore calibration and data processing
- 2023
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 108:1
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Tidskriftsartikel (refereegranskat)abstract
- We describe a new data sample of IceCube DeepCore and report on the latest measurement of atmospheric neutrino oscillations obtained with data recorded between 2011-2019. The sample includes significant improvements in data calibration, detector simulation, and data processing, and the analysis benefits from a sophisticated treatment of systematic uncertainties, with significantly greater level of detail since our last study. By measuring the relative fluxes of neutrino flavors as a function of their reconstructed energies and arrival directions we constrain the atmospheric neutrino mixing parameters to be sin2θ23=0.51±0.05 and Δm322=2.41±0.07×10-3 eV2, assuming a normal mass ordering. The errors include both statistical and systematic uncertainties. The resulting 40% reduction in the error of both parameters with respect to our previous result makes this the most precise measurement of oscillation parameters using atmospheric neutrinos. Our results are also compatible and complementary to those obtained using neutrino beams from accelerators, which are obtained at lower neutrino energies and are subject to different sources of uncertainties.
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11. |
- Abbasi, R., et al.
(författare)
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Limits on Neutrino Emission from GRB 221009A from MeV to PeV Using the IceCube Neutrino Observatory
- 2023
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Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 946:1
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Tidskriftsartikel (refereegranskat)abstract
- Gamma-ray bursts (GRBs) have long been considered a possible source of high-energy neutrinos. While no correlations have yet been detected between high-energy neutrinos and GRBs, the recent observation of GRB 221009A-the brightest GRB observed by Fermi-GBM to date and the first one to be observed above an energy of 10 TeV-provides a unique opportunity to test for hadronic emission. In this paper, we leverage the wide energy range of the IceCube Neutrino Observatory to search for neutrinos from GRB 221009A. We find no significant deviation from background expectation across event samples ranging from MeV to PeV energies, placing stringent upper limits on the neutrino emission from this source.
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12. |
- Abbasi, R., et al.
(författare)
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Observation of seasonal variations of the flux of high-energy atmospheric neutrinos with IceCube
- 2023
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Ingår i: European Physical Journal C. - : Springer. - 1434-6044 .- 1434-6052. ; 83:9
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Tidskriftsartikel (refereegranskat)abstract
- Atmospheric muon neutrinos are produced by meson decays in cosmic-ray-induced air showers. The flux depends on meteorological quantities such as the air temperature, which affects the density of air. Competition between decay and re-interaction of those mesons in the first particle production generations gives rise to a higher neutrino flux when the air density in the stratosphere is lower, corresponding to a higher temperature. A measurement of a temperature dependence of the atmospheric νμ flux provides a novel method for constraining hadronic interaction models of air showers. It is particularly sensitive to the production of kaons. Studying this temperature dependence for the first time requires a large sample of high-energy neutrinos as well as a detailed understanding of atmospheric properties. We report the significant (>10σ) observation of a correlation between the rate of more than 260,000 neutrinos, detected by IceCube between 2012 and 2018, and atmospheric temperatures of the stratosphere, measured by the Atmospheric Infrared Sounder (AIRS) instrument aboard NASA’s AQUA satellite. For the observed 10 % seasonal change of effective atmospheric temperature we measure a 3.5(3) % change in the muon neutrino flux. This observed correlation deviates by about 2-3 standard deviations from the expected correlation of 4.3 % as obtained from theoretical predictions under the assumption of various hadronic interaction models.
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13. |
- Abbasi, R., et al.
(författare)
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Search for Galactic Core-collapse Supernovae in a Decade of Data Taken with the IceCube Neutrino Observatory
- 2024
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Ingår i: Astrophysical Journal. - : Institute of Physics Publishing (IOPP). - 1538-4357 .- 0004-637X. ; 961:1
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Tidskriftsartikel (refereegranskat)abstract
- The IceCube Neutrino Observatory has been continuously taking data to search for O(0.5–10) s long neutrino bursts since 2007. Even if a Galactic core-collapse supernova is optically obscured or collapses to a black hole instead of exploding, it will be detectable via the O(10) MeV neutrino burst emitted during the collapse. We discuss a search for such events covering the time between 2008 April 17 and 2019 December 31. Considering the average data taking and analysis uptime of 91.7% after all selection cuts, this is equivalent to 10.735 yr of continuous data taking. In order to test the most conservative neutrino production scenario, the selection cuts were optimized for a model based on an 8.8 solar mass progenitor collapsing to an O–Ne–Mg core. Conservative assumptions on the effects of neutrino oscillations in the exploding star were made. The final selection cut was set to ensure that the probability to detect such a supernova within the Milky Way exceeds 99%. No such neutrino burst was found in the data after performing a blind analysis. Hence, a 90% C.L. upper limit on the rate of core-collapse supernovae out to distances of ≈25 kpc was determined to be 0.23 yr−1. For the more distant Magellanic Clouds, only high neutrino luminosity supernovae will be detectable by IceCube, unless external information on the burst time is available. We determined a model-independent limit by parameterizing the dependence on the neutrino luminosity and the energy spectrum.
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14. |
- Abbasi, R., et al.
(författare)
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A Search for IceCube Sub-TeV Neutrinos Correlated with Gravitational-wave Events Detected By LIGO/Virgo
- 2023
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Ingår i: Astrophysical Journal. - : Institute of Physics Publishing (IOPP). - 1538-4357 .- 0004-637X. ; 959:2
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Tidskriftsartikel (refereegranskat)abstract
- The LIGO/Virgo collaboration published the catalogs GWTC-1, GWTC-2.1, and GWTC-3 containing candidate gravitational-wave (GW) events detected during its runs O1, O2, and O3. These GW events can be possible sites of neutrino emission. In this paper, we present a search for neutrino counterparts of 90 GW candidates using IceCube DeepCore, the low-energy infill array of the IceCube Neutrino Observatory. The search is conducted using an unbinned maximum likelihood method, within a time window of 1000 s, and uses the spatial and timing information from the GW events. The neutrinos used for the search have energies ranging from a few GeV to several tens of TeV. We do not find any significant emission of neutrinos, and place upper limits on the flux and the isotropic-equivalent energy emitted in low-energy neutrinos. We also conduct a binomial test to search for source populations potentially contributing to neutrino emission. We report a nondetection of a significant neutrino-source population with this test.
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15. |
- Abbasi, R., et al.
(författare)
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IceCat-1: The IceCube Event Catalog of Alert Tracks
- 2023
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Ingår i: Astrophysical Journal, Supplement Series. - : IOP Publishing Ltd. - 1538-4365 .- 0067-0049. ; 269:1
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Tidskriftsartikel (refereegranskat)abstract
- We present a catalog of likely astrophysical neutrino track-like events from the IceCube Neutrino Observatory. IceCube began reporting likely astrophysical neutrinos in 2016, and this system was updated in 2019. The catalog presented here includes events that were reported in real time since 2019, as well as events identified in archival data samples starting from 2011. We report 275 neutrino events from two selection channels as the first entries in the catalog, the IceCube Event Catalog of Alert Tracks, which will see ongoing extensions with additional alerts. The Gold and Bronze alert channels respectively provide neutrino candidates with a 50% and 30% probability of being astrophysical, on average assuming an astrophysical neutrino power-law energy spectral index of 2.19. For each neutrino alert, we provide the reconstructed energy, direction, false-alarm rate, probability of being astrophysical in origin, and likelihood contours describing the spatial uncertainty in the alert's reconstructed location. We also investigate a directional correlation of these neutrino events with gamma-ray and X-ray catalogs, including 4FGL, 3HWC, TeVCat, and Swift-BAT.
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16. |
- Abbasi, R., et al.
(författare)
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Search for neutrino lines from dark matter annihilation and decay with IceCube
- 2023
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Ingår i: Physical Review D. - : American Physical Society. - 2470-0010 .- 2470-0029. ; 108:10
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Tidskriftsartikel (refereegranskat)abstract
- Dark matter particles in the Galactic Center and halo can annihilate or decay into a pair of neutrinos producing a monochromatic flux of neutrinos. The spectral feature of this signal is unique and it is not expected from any astrophysical production mechanism. Its observation would constitute a dark matter smoking gun signal. We performed the first dedicated search with a neutrino telescope for such signal, by looking at both the angular and energy information of the neutrino events. To this end, a total of five years of IceCube's DeepCore data has been used to test dark matter masses ranging from 10 GeV to 40 TeV. No significant neutrino excess was found and upper limits on the annihilation cross section, as well as lower limits on the dark matter lifetime, were set. The limits reached are of the order of 10-24 cm3/s for an annihilation and up to 1027 s for decaying dark matter. Using the same data sample we also derive limits for dark matter annihilation or decay into a pair of Standard Model charged particles.
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17. |
- Aartsen, M. G., et al.
(författare)
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Cosmic ray spectrum and composition from PeV to EeV using 3 years of data from IceTop and IceCube
- 2019
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Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 100:8
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Tidskriftsartikel (refereegranskat)abstract
- We report on measurements of the all-particle cosmic ray energy spectrum and composition in the PeV to EeV energy range using 3 years of data from the IceCube Neutrino Observatory. The IceTop detector measures cosmic ray induced air showers on the surface of the ice, from which the energy spectrum of cosmic rays is determined by making additional assumptions about the mass composition. A separate measurement is performed when IceTop data are analyzed in coincidence with the high-energy muon energy loss information from the deep in-ice IceCube detector. In this measurement, both the spectrum and the mass composition of the primary cosmic rays are simultaneously reconstructed using a neural network trained on observables from both detectors. The performance and relative advantages of these two distinct analyses are discussed, including the systematic uncertainties and the dependence on the hadronic interaction models, and both all-particle spectra as well as individual spectra for elemental groups are presented.
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18. |
- Kankare, E., et al.
(författare)
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Search for transient optical counterparts to high-energy IceCube neutrinos with Pan-STARRS1
- 2019
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 626
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Tidskriftsartikel (refereegranskat)abstract
- In order to identify the sources of the observed diffuse high-energy neutrino flux, it is crucial to discover their electromagnetic counterparts. To increase the sensitivity of detecting counterparts of transient or variable sources by telescopes with a limited field of view, IceCube began releasing alerts for single high-energy (E-v > 60 TeV) neutrino detections with sky localisation regions of order 1 degrees radius in 2016. We used Pan-STARRS1 to follow-up five of these alerts during 2016-2017 to search for any optical transients that may be related to the neutrinos. Typically 10-20 faint m(ip1) less than or similar to 22.5 mag) extragalactic transients are found within the Pan-STARRS1 footprints and are generally consistent with being unrelated field supernovae (SNe) and AGN. We looked for unusual properties of the detected transients, such as temporal coincidence of explosion epoch with the IceCube timestamp, or other peculiar light curve and physical properties. We found only one transient that had properties worthy of a specific follow-up. In the Pan-STARRS1 imaging for IceCube-160427A (probability to be of astrophysical origin of similar to 50%), we found a SN PS16cgx, located at 10.0' from the nominal IceCube direction. Spectroscopic observations of PS16cgx showed that it was an H-poor SN at redshift z = 0.2895 +/- 0.0001. The spectra and light curve resemble some high-energy Type Ic SNe, raising the possibility of a jet driven SN with an explosion epoch temporally coincident with the neutrino detection. However, distinguishing Type Ia and Type Ic SNe at this redshift is notoriously difficult. Based on all available data we conclude that the transient is more likely to be a Type Ia with relatively weak Sin absorption and a fairly normal rest-frame r-band light curve. If, as predicted, there is no high-energy neutrino emission from Type Ia SNe, then PS16cgx must be a random coincidence, and unrelated to the IceCube-160427A. We find no other plausible optical transient for any of the five IceCube events observed down to a 5 sigma limiting magnitude of mip1 approximate to 22 mag, between 1 day and 25 days after detection.
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19. |
- Aartsen, M. G., et al.
(författare)
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Measurement of atmospheric tau neutrino appearance with IceCube DeepCore
- 2019
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Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 99:3
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Tidskriftsartikel (refereegranskat)abstract
- We present a measurement of atmospheric tau neutrino appearance from oscillations with three years of data from the DeepCore subarray of the IceCube Neutrino Observatory. This analysis uses atmospheric neutrinos from the full sky with reconstructed energies between 5.6 and 56 GeV to search for a statistical excess of cascadelike neutrino events which are the signature of nu(tau) interactions. For CC thorn NC (CC-only) interactions, we measure the tau neutrino normalization to be 0.73(-0.24)(+0.30) (0.57(-0.30)(+0.36)) and exclude the absence of tau neutrino oscillations at a significance of 3.2 sigma (2.0 sigma) These results are consistent with, and of similar precision to, a confirmatory IceCube analysis also presented, as well as measurements performed by other experiments.
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20. |
- Garrappa, S., et al.
(författare)
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Investigation of Two Fermi-LAT Gamma-Ray Blazars Coincident with High-energy Neutrinos Detected by IceCube
- 2019
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 880:2
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Tidskriftsartikel (refereegranskat)abstract
- After the identification of the gamma-ray blazar TXS 0506+056 as the first compelling IceCube neutrino source candidate, we perform a systematic analysis of all high-energy neutrino events satisfying the IceCube realtime trigger criteria. We find one additional known gamma-ray source, the blazar GB6 J1040+0617, in spatial coincidence with a neutrino in this sample. The chance probability of this coincidence is 30% after trial correction. For the first time, we present a systematic study of the gamma-ray flux, spectral and optical variability, and multiwavelength behavior of GB6 J1040+0617 and compare it to TXS 0506+056. We find that TXS 0506+056 shows strong flux variability in the Fermi-Large Area Telescope gamma-ray band, being in an active state around the arrival of IceCube-170922A, but in a low state during the archival IceCube neutrino flare in 2014/15. In both cases the spectral shape is statistically compatible (<= 2 sigma) with the average spectrum showing no indication of a significant relative increase of a high-energy component. While the association of GB6 J1040+0617 with the neutrino is consistent with background expectations, the source appears to be a plausible neutrino source candidate based on its energetics and multiwavelength features, namely a bright optical flare and modestly increased gamma-ray activity. Finding one or two neutrinos originating from gamma-ray blazars in the given sample of high-energy neutrinos is consistent with previously derived limits of neutrino emission from gamma-ray blazars, indicating the sources of the majority of cosmic high-energy neutrinos remain unknown.
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21. |
- Aartsen, M. G., et al.
(författare)
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Development of an analysis to probe the neutrino mass ordering with atmospheric neutrinos using three years of IceCube DeepCore data IceCube Collaboration
- 2020
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Ingår i: European Physical Journal C. - : SPRINGER. - 1434-6044 .- 1434-6052. ; 80:1
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Tidskriftsartikel (refereegranskat)abstract
- The Neutrino Mass Ordering (NMO) remains one of the outstanding questions in the field of neutrino physics. One strategy to measure the NMO is to observe matter effects in the oscillation pattern of atmospheric neutrinos above similar to 1GeV, as proposed for several next-generation neutrino experiments. Moreover, the existing IceCube DeepCore detector can already explore this type of measurement. We present the development and application of two independent analyses to search for the signature of the NMO with three years of DeepCore data. These analyses include a full treatment of systematic uncertainties and a statistically-rigorous method to determine the significance for the NMO from a fit to the data. Both analyses show that the dataset is fully compatible with both mass orderings. For the more sensitive analysis, we observe a preference for normal ordering with a p-value of pIO=15.3% and CLs=53.3% for the inverted ordering hypothesis, while the experimental results from both analyses are consistent within their uncertainties. Since the result is independent of the value of delta CP and obtained from energies E nu greater than or similar to 5GeV, it is complementary to recent results from long-baseline experiments. These analyses set the groundwork for the future of this measurement with more capable detectors, such as the IceCube Upgrade and the proposed PINGU detector.
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22. |
- Aartsen, M. G., et al.
(författare)
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Neutrinos below 100 TeV from the southern sky employing refined veto techniques to IceCube data
- 2020
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Ingår i: Astroparticle physics. - : ELSEVIER. - 0927-6505 .- 1873-2852. ; 116
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Tidskriftsartikel (refereegranskat)abstract
- Many Galactic sources of gamma rays, such as supernova remnants, are expected to produce neutrinos with a typical energy cutoff well below 100 TeV. For the IceCube Neutrino Observatory located at the South Pole, the southern sky, containing the inner part of the Galactic plane and the Galactic Center, is a particularly challenging region at these energies, because of the large background of atmospheric muons. In this paper, we present recent advancements in data selection strategies for track-like muon neutrino events with energies below 100 TeV from the southern sky. The strategies utilize the outer detector regions as veto and features of the signal pattern to reduce the background of atmospheric muons to a level which, for the first time, allows IceCube searching for point-like sources of neutrinos in the southern sky at energies between 100 GeV and several TeV in the muon neutrino charged current channel. No significant clustering of neutrinos above background expectation was observed in four years of data recorded with the completed IceCube detector. Upper limits on the neutrino flux for a number of spectral hypotheses are reported for a list of astrophysical objects in the southern hemisphere.
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26. |
- Fresard, Laure, et al.
(författare)
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Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
- 2019
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Ingår i: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919
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Tidskriftsartikel (refereegranskat)abstract
- It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
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27. |
- Brahm, R., et al.
(författare)
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HATS-43b, HATS-44b, HATS-45b, and HATS-46b : Four Short-period Transiting Giant Planets in the Neptune-Jupiter Mass Range
- 2018
-
Ingår i: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 155:3
-
Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of four short-period extrasolar planets transiting moderately bright stars from photometric measurements of the HATSouth network coupled to additional spectroscopic and photometric follow-up observations. While the planet masses range from 0.26 to 0.90 M-J, the radii are all approximately a Jupiter radii, resulting in a wide range of bulk densities. The orbital period of the planets ranges from 2.7 days to 4.7 days, with HATS-43b having an orbit that appears to be marginally non-circular (e = 0.173 +/- 0.089). HATS-44 is notable for having a high metallicity ([Fe/H]= 0.320 +/- 0.071). The host stars spectral types range from late F to early K, and all of them are moderately bright (13.3 < V < 14.4), allowing the execution of future detailed follow-up observations. HATS-43b and HATS-46b, with expected transmission signals of 2350 ppm and 1500 ppm, respectively, are particularly well suited targets for atmospheric characterization via transmission spectroscopy.
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28. |
- Burisch, J., et al.
(författare)
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Health care and patients' education in a European inflammatory bowel disease inception cohort : an ECCO-EpiCom study
- 2014
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Ingår i: Journal of Crohn's & Colitis. - : Oxford University Press (OUP). - 1873-9946 .- 1876-4479. ; 8:8, s. 811-818
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Tidskriftsartikel (refereegranskat)abstract
- Background and Aims: The EpiCom study and inception cohort was initiated in 2010 in 31 centers from 14 Western and 8 Eastern European countries, covering a 10.1 million person background population. Our aim was to investigate whether there is a difference between Eastern and Western Europe in health care and education of patients with inflammatory bowel disease (IBD).Methods: A quality of care (QoC) questionnaire was developed in the EpiCom group consisting of 16 questions covering 5 items: time interval between the onset of symptoms and diagnosis, information, education, empathy and access to health care providers.Results: Of 1,515 patients, 947 (217 east/730 west) answered the QoC questionnaire. Only 23% of all patients had knowledge about IBD before diagnosis. In Eastern Europe, significantly more patients searched out information about IBD themselves (77% vs. 68%, p < 0.05), the main source was the Internet (92% vs. 88% p = 0.23). In Western Europe, significantly more patients were educated by nurses (19% vs. 1%, p < 0.05), while in Eastern Europe, gastroenterologists were easier to contact (80% vs. 68%, p < 0.05).Conclusion: Health care differed significantly between Eastern and Western Europe in all items, but satisfaction rates were high in both geographic regions. Because of the low awareness and the rising incidence of IBD, general information should be the focus of patient organizations and medical societies. In Western Europe IBD nurses play a very important role in reducing the burden of patient management. (c) 2014 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.
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29. |
- Burisch, J., et al.
(författare)
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Health-related quality of life improves during one year of medical and surgical treatment in a European population-based inception cohort of patients with Inflammatory Bowel Disease : An ECCO-EpiCom study
- 2014
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Ingår i: Journal of Crohn's & Colitis. - Oxford, United Kingdom : Oxford University Press. - 1873-9946 .- 1876-4479. ; 8:9, s. 1030-1042
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Tidskriftsartikel (refereegranskat)abstract
- Background & Aims: Health-related quality of life (HRQoL) is impaired in patients with Inflammatory Bowel Disease (IBD). The aim was prospectively to assess and validate the pattern of HRQoL in an unselected, population-based inception cohort of IBD patients from Eastern and Western Europe.Methods: The EpiCom inception cohort consists of 1560 IBD patients from 31 European centres covering a background population of approximately 10.1 million. Patients answered the disease specific Short Inflammatory Bowel Disease Questionnaire (SIBDQ) and generic Short Form 12 (SF-12) questionnaire at diagnosis and after one year of follow-up.Results: In total, 1079 patients were included in this study. Crohn's disease (CD) patients mean SIBDQ scores improved from 45.3 to 55.3 in Eastern Europe and from 44.9 to 53.6 in Western Europe. SIBDQ scores for ulcerative colitis (UC) patients improved from 44.9 to 57.4 and from 48.8 to 55.7, respectively. UC patients needing surgery or biologicals had lower SIBDQ scores before and after compared to the rest, while biological therapy improved SIBDQ scores in CD. CD and UC patients in both regions improved all SF-12 scores. Only Eastern European UC patients achieved SF-12 summary scores equal to or above the normal population.Conclusion: Medical and surgical treatment improved HRQoL during the first year of disease. The majority of IBD patients in both Eastern and Western Europe reported a positive perception of disease-specific but not generic HRQoL. Biological therapy improved HRQoL in CD patients, while UC patients in need of surgery or biological therapy experienced lower perceptions of HRQoL than the rest.
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30. |
- Lazar, J., et al.
(författare)
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Human-computer interaction and international public policymaking : A framework for understanding and taking future actions
- 2015
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Ingår i: Foundations and Trends in Human-Computer Interaction. - : Now Publishers Inc.. - 1551-3955 .- 1551-3963. ; 9:2, s. 69-149
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Tidskriftsartikel (refereegranskat)abstract
- This monograph lays out a discussion framework for understanding the role of human-computer interaction (HCI) in public policymaking. We take an international view, discussing potential areas for research and application, and their potential for impact. Little has been written about the intersection of HCI and public policy; existing reports typically focus on one specific policy issue or incident. To date, there has been no overarching view of the areas of existing impact and potential impact. We have begun that analysis and argue here that such a global view is needed. Our aims are to provide a solid foundation for discussion, cooperation and collaborative interaction, and to outline future programs of activity. The five sections of this report provide relevant background along with a preliminary version of what we expect to be an evolving framework. Sections 1 and 2 provides an introduction to HCI and public policy. Section 3 discusses how HCI already informs public policy, with representative examples. Section 4 discusses how public policy influences HCI and provides representative public policy areas relevant to HCI, where HCI could have even more impact in the future: (i) laws, regulations, and guidelines for HCI research, (ii) HCI research assessments, (iii) research funding, (iv) laws for interface design - accessibility and language, (v) data privacy laws and regulations, (vi) intellectual property, and (vii) laws and regulations in specific sectors. There is a striking difference between where the HCI community has had impact (Section 3) and the many areas of potential involvement (Section 4). Section 5 a framework for action by the HCI community in public policy internationally. This monograph summarizes the observations and recommendations from a daylong workshop at the CHI 2013 conference in Paris, France. The workshop invited the community's perspectives regarding the intersection of governmental policies, international and domestic standards, recent HCI research discoveries, and emergent considerations and challenges. It also incorporates contributions made after the workshop by workshop participants and by individuals who were unable to participate in the workshop but whose work and interests were highly related and relevant.
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31. |
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32. |
- Burisch, J., et al.
(författare)
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Environmental factors in a population-based inception cohort of inflammatory bowel disease patients in Europe : An ECCO-EpiCom study
- 2014
-
Ingår i: Journal of Crohn's & Colitis. - : Oxford University Press. - 1873-9946 .- 1876-4479. ; 8:7, s. 607-616
-
Tidskriftsartikel (refereegranskat)abstract
- Background and Aims: The incidence of inflammatory bowel disease (IBD) is increasing in Eastern Europe possibly due to changes in environmental factors towards a more "westernised" standard of Living. The aim of this study was to investigate differences in exposure to environmental factors prior to diagnosis in Eastern and Western European IBD patients.Methods: The EpiCom cohort is a population-based, prospective inception cohort of 1560 unselected IBD patients from 31 European countries covering a background population of 10.1 million. At the time of diagnosis patients were asked to complete an 87-item questionnaire concerning environmental factors.Results: A total of 1182 patients (76%) answered the questionnaire, 444 (38%) had Crohn's disease (CD), 627 (53%) ulcerative colitis (UC), and 111 (9%) IBD unclassified. No geographic differences regarding smoking status, caffeine intake, use of oral contraceptives, or number of first-degree relatives with IBD were found. Sugar intake was higher in CD and UC patients from Eastern Europe than in Western Europe while fibre intake was lower (p < 0.01). Daily consumption of fast food as well as appendectomy before the age of 20 was more frequent in Eastern European than in Western European UC patients (p < 0.01). Eastern European CD and UC patients had received more vaccinations and experienced fewer childhood infections than Western European patients (p < 0.01).Conclusions: In this European population-based inception cohort of unselected IBD patients, Eastern and Western European patients differed in environmental factors prior to diagnosis. Eastern European patients exhibited higher occurrences of suspected risk factors for IBD included in the Western lifestyle. (C) 2013 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.
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33. |
- Amgad, M, et al.
(författare)
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Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group
- 2020
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Ingår i: NPJ breast cancer. - : Springer Science and Business Media LLC. - 2374-4677. ; 6:1, s. 16-
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Tidskriftsartikel (refereegranskat)abstract
- Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring.
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34. |
- Burisch, J., et al.
(författare)
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East-West gradient in the incidence of inflammatory bowel disease in Europe: the ECCO-EpiCom inception cohort
- 2014
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Ingår i: Gut. - : BMJ Publishing Group. - 0017-5749 .- 1468-3288. ; 63:4, s. 588-597
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Tidskriftsartikel (refereegranskat)abstract
- Objective The incidence of inflammatory bowel disease (IBD) is increasing in Eastern Europe. The reasons for these changes remain unknown. The aim of this study was to investigate whether an East–West gradient in the incidence of IBD in Europe exists.Design A prospective, uniformly diagnosed, population based inception cohort of IBD patients in 31 centres from 14 Western and eight Eastern European countries covering a total background population of approximately 10.1 million people was created. One-third of the centres had previous experience with inception cohorts. Patients were entered into a low cost, web based epidemiological database, making participation possible regardless of socioeconomic status and prior experience.Results 1515 patients aged 15 years or older were included, of whom 535 (35%) were diagnosed with Crohn's disease (CD), 813 (54%) with ulcerative colitis (UC) and 167 (11%) with IBD unclassified (IBDU). The overall incidence rate ratios in all Western European centres were 1.9 (95% CI 1.5 to 2.4) for CD and 2.1 (95% CI 1.8 to 2.6) for UC compared with Eastern European centres. The median crude annual incidence rates per 100 000 in 2010 for CD were 6.5 (range 0–10.7) in Western European centres and 3.1 (range 0.4–11.5) in Eastern European centres, for UC 10.8 (range 2.9–31.5) and 4.1 (range 2.4–10.3), respectively, and for IBDU 1.9 (range 0–39.4) and 0 (range 0–1.2), respectively. In Western Europe, 92% of CD, 78% of UC and 74% of IBDU patients had a colonoscopy performed as the diagnostic procedure compared with 90%, 100% and 96%, respectively, in Eastern Europe. 8% of CD and 1% of UC patients in both regions underwent surgery within the first 3 months of the onset of disease. 7% of CD patients and 3% of UC patients from Western Europe received biological treatment as rescue therapy. Of all European CD patients, 20% received only 5-aminosalicylates as induction therapy.Conclusions An East–West gradient in IBD incidence exists in Europe. Among this inception cohort—including indolent and aggressive cases—international guidelines for diagnosis and initial treatment are not being followed uniformly by physicians.
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35. |
- Henning, Th., et al.
(författare)
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HATS-50b through HATS-53b : Four Transiting Hot Jupiters Orbiting G-type Stars Discovered by the HATSouth Survey
- 2018
-
Ingår i: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 155:2
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Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of four close-in transiting exoplanets (HATS-50b through HATS-53b), discovered using the HATSouth three-continent network of homogeneous and automated telescopes. These new exoplanets belong to the class of hot Jupiters and orbit G-type dwarf stars, with brightness in the range V = 12.5-14.0 mag. While HATS-53 has many physical characteristics similar to the Sun, the other three stars appear to be metal-rich ([Fe/H]= 0.2-0.3), larger, and more massive. Three of the new exoplanets, namely HATS-50b, HATS-51b, and HATS-53b, have low density (HATS-50b: 0.39 +/- 0.10 M-J, 1.130 +/- 0.075 R-J; HATS-51b: 0.768 +/- 0.045 M-J, 1.41 +/- 0.19 R-J; HATS-53b: 0.595 +/- 0.089 M-J, 1.340 +/- 0.056 R-J) and similar orbital periods (3.8297 days, 3.3489 days, 3.8538 days, respectively). Instead, HATS-52b is more dense (mass 2.24. +/- 0.15 M-J and radius 1.382 +/- 0.086 R-J) and has a shorter orbital period (1.3667 days). It also receives an intensive radiation from its parent star and, consequently, presents a high equilibrium temperature (T-eq = 1834 +/- 73 K). HATS-50 shows a marginal additional transit feature consistent with an ultra-short-period hot super Neptune (upper mass limit 0.16 M-J), which will be able to be confirmed with TESS photometry.
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36. |
- de Val-Borro, M., et al.
(författare)
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HATS-31B THROUGH HATS-35B : FIVE TRANSITING HOT JUPITERS DISCOVERED BY THE HATSOUTH SURVEY
- 2016
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Ingår i: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 152:6
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Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of five new transiting hot-Jupiter planets discovered by the HATSouth survey, HATS-31b through HATS-35b. These planets orbit moderately bright stars with V magnitudes within the range of 11.9-14.4 mag while the planets span a range of masses of. 0.88-1.22 M-J. and have somewhat inflated radii between 1.23 and 1.64 R-J. These planets can be classified as typical hot Jupiters, with HATS-31b and HATS-35b being moderately inflated gas giant planets with radii of 1.64 +/- 0.22 R-J and 1.464(-0.044)(+0.069) R-J, respectively, that can be used to constrain inflation mechanisms. All five systems present a higher Bayesian evidence for a fixed-circular-orbit model than for an eccentric orbit. The orbital periods range from 1.8209993 +/- 0.0000016 day for HATS-35b) to 3.377960 +/- 0.000012 day for HATS-31b. Additionally, HATS-35b orbits a relatively young F star with an age of 2.13 +/- 0.51 Gyr. We discuss the analysis to derive the properties of these systems and compare them in the context of the sample of well-characterized transiting hot Jupiters known to date.
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37. |
- Hangen, E, et al.
(författare)
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A brain-specific isoform of mitochondrial apoptosis-inducing factor: AIF2.
- 2010
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Ingår i: Cell death and differentiation. - : Springer Science and Business Media LLC. - 1476-5403 .- 1350-9047. ; 17:7, s. 1155-66
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Tidskriftsartikel (refereegranskat)abstract
- Apoptosis-inducing factor (AIF) has important supportive as well as potentially lethal roles in neurons. Under normal physiological conditions, AIF is a vital redox-active mitochondrial enzyme, whereas in pathological situations, it translocates from mitochondria to the nuclei of injured neurons and mediates apoptotic chromatin condensation and cell death. In this study, we reveal the existence of a brain-specific isoform of AIF, AIF2, whose expression increases as neuronal precursor cells differentiate. AIF2 arises from the utilization of the alternative exon 2b, yet uses the same remaining 15 exons as the ubiquitous AIF1 isoform. AIF1 and AIF2 are similarly imported to mitochondria in which they anchor to the inner membrane facing the intermembrane space. However, the mitochondrial inner membrane sorting signal encoded in the exon 2b of AIF2 is more hydrophobic than that of AIF1, indicating a stronger membrane anchorage of AIF2 than AIF1. AIF2 is more difficult to be desorbed from mitochondria than AIF1 on exposure to non-ionic detergents or basic pH. Furthermore, AIF2 dimerizes with AIF1, thereby preventing its release from mitochondria. Conversely, it is conceivable that a neuron-specific AIF isoform, AIF2, may have been 'designed' to be retained in mitochondria and to minimize its potential neurotoxic activity.Cell Death and Differentiation advance online publication, 29 January 2010; doi:10.1038/cdd.2009.211.
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38. |
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39. |
- Abolhassani, H, et al.
(författare)
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Care of patients with inborn errors of immunity in thirty J Project countries between 2004 and 2021
- 2022
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Ingår i: Frontiers in immunology. - : Frontiers Media SA. - 1664-3224. ; 13, s. 1032358-
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Tidskriftsartikel (refereegranskat)abstract
- The J Project (JP) physician education and clinical research collaboration program was started in 2004 and includes by now 32 countries mostly in Eastern and Central Europe (ECE). Until the end of 2021, 344 inborn errors of immunity (IEI)-focused meetings were organized by the JP to raise awareness and facilitate the diagnosis and treatment of patients with IEI.ResultsIn this study, meeting profiles and major diagnostic and treatment parameters were studied. JP center leaders reported patients’ data from 30 countries representing a total population of 506 567 565. Two countries reported patients from JP centers (Konya, Turkey and Cairo University, Egypt). Diagnostic criteria were based on the 2020 update of classification by the IUIS Expert Committee on IEI. The number of JP meetings increased from 6 per year in 2004 and 2005 to 44 and 63 in 2020 and 2021, respectively. The cumulative number of meetings per country varied from 1 to 59 in various countries reflecting partly but not entirely the population of the respective countries. Altogether, 24,879 patients were reported giving an average prevalence of 4.9. Most of the patients had predominantly antibody deficiency (46,32%) followed by patients with combined immunodeficiencies (14.3%). The percentages of patients with bone marrow failure and phenocopies of IEI were less than 1 each. The number of patients was remarkably higher that those reported to the ESID Registry in 13 countries. Immunoglobulin (IgG) substitution was provided to 7,572 patients (5,693 intravenously) and 1,480 patients received hematopoietic stem cell therapy (HSCT). Searching for basic diagnostic parameters revealed the availability of immunochemistry and flow cytometry in 27 and 28 countries, respectively, and targeted gene sequencing and new generation sequencing was available in 21 and 18 countries. The number of IEI centers and experts in the field were 260 and 690, respectively. We found high correlation between the number of IEI centers and patients treated with intravenous IgG (IVIG) (correlation coefficient, cc, 0,916) and with those who were treated with HSCT (cc, 0,905). Similar correlation was found when the number of experts was compared with those treated with HSCT. However, the number of patients treated with subcutaneous Ig (SCIG) only slightly correlated with the number of experts (cc, 0,489) and no correlation was found between the number of centers and patients on SCIG (cc, 0,174).Conclusions1) this is the first study describing major diagnostic and treatment parameters of IEI care in countries of the JP; 2) the data suggest that the JP had tremendous impact on the development of IEI care in ECE; 3) our data help to define major future targets of JP activity in various countries; 4) we suggest that the number of IEI centers and IEI experts closely correlate to the most important treatment parameters; 5) we propose that specialist education among medical professionals plays pivotal role in increasing levels of diagnostics and adequate care of this vulnerable and still highly neglected patient population; 6) this study also provides the basis for further analysis of more specific aspects of IEI care including genetic diagnostics, disease specific prevalence, newborn screening and professional collaboration in JP countries.
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40. |
- Bento, J., et al.
(författare)
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HATS-22b, HATS-23b and HATS-24b : three new transiting super-Jupiters from the HATSouth project
- 2017
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 468:1, s. 835-848
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Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of three moderately high-mass transiting hot Jupiters from the HATSouth survey: HATS-22b, HATS-23b and HATS-24b. These planets add to the number of known planets in the similar to 2MJ regime. HATS-22b is a 2.74 +/- 0.11MJ mass and 0.953(-0.029)(+0.048) R-J radius planet orbiting a V = 13.455 +/- 0.040 sub-solar mass (M-* = 0.759 +/- 0.019M(circle dot); R-* = 0.759 +/- 0.019 R-circle dot) K-dwarf host star on an eccentric (e = 0.079 +/- 0.026) orbit. This planet's high planet-to-stellar mass ratio is further evidence that migration mechanisms for hot Jupiters may rely on exciting orbital eccentricities that bring the planets closer to their parent stars followed by tidal circularization. HATS-23b is a 1.478 +/- 0.080M(J) mass and 1.69 +/- 0.24 R-J radius planet on a grazing orbit around a V = 13.901 +/- 0.010 G-dwarf with properties very similar to those of the Sun (M* = 1.115 +/- 0.054; R-* = 1.145 +/- 0.070). HATS24b orbits a moderately bright V = 12.830 +/- 0.010 F-dwarf star (M-* = 1.218 +/- 0.036M circle dot; R-* = 1.194(-0.041)(+0.066) R circle dot). This planet has a mass of 2.39+0.21 -0.12MJ and an inflated radius of 1.516(-0.065)(+0.085) R-J.
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41. |
- Benton, S., et al.
(författare)
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Impact of Next-generation Sequencing on Interobserver Agreement and Diagnosis of Spitzoid Neoplasms
- 2021
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Ingår i: American Journal of Surgical Pathology. - : Ovid Technologies (Wolters Kluwer Health). - 0147-5185 .- 1532-0979. ; 45:12, s. 1597-1605
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Tidskriftsartikel (refereegranskat)abstract
- Atypical Spitzoid melanocytic tumors are diagnostically challenging. Many studies have suggested various genomic markers to improve classification and prognostication. We aimed to assess whether next-generation sequencing studies using the Tempus xO assay assessing mutations in 1711 cancer-related genes and performing whole transcriptome mRNA sequencing for structural alterations could improve diagnostic agreement and accuracy in assessing neoplasms with Spitzoid histologic features. Twenty expert pathologists were asked to review 70 consultation level cases with Spitzoid features, once with limited clinical information and again with additional genomic information. There was an improvement in overall agreement with additional genomic information. Most significantly, there was increase in agreement of the diagnosis of conventional melanoma from moderate (kappa=0.470, SE=0.0105) to substantial (kappa=0.645, SE=0.0143) as measured by an average Cohen kappa. Clinical follow-up was available in all 70 cases which substantiated that the improved agreement was clinically significant. Among 3 patients with distant metastatic disease, there was a highly significant increase in diagnostic recognition of the cases as conventional melanoma with genomics (P<0.005). In one case, none of 20 pathologists recognized a tumor with BRAF and TERT promoter mutations associated with fatal outcome as a conventional melanoma when only limited clinical information was provided, whereas 60% of pathologists correctly diagnosed this case when genomic information was also available. There was also a significant improvement in agreement of which lesions should be classified in the Spitz category/WHO Pathway from an average Cohen kappa of 0.360 (SE=0.00921) to 0.607 (SE=0.0232) with genomics.
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42. |
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43. |
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44. |
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45. |
- Baker, Brett J., et al.
(författare)
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Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea
- 2016
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Ingår i: Nature Microbiology. - 2058-5276. ; 1:3
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Tidskriftsartikel (refereegranskat)abstract
- The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes(1). Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface(2-4), the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63-90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H-2 oxidation (or H-2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.
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46. |
- Barbosa, S., et al.
(författare)
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Workshop on Engaging the Human-Computer Interaction Community with Public Policymaking Internationally : Extended Abstract
- 2013
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Ingår i: Proceeding CHI EA '13 CHI '13 Extended Abstracts on Human Factors in Computing Systems. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450318990 ; , s. 3279-3282
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Konferensbidrag (refereegranskat)abstract
- There is an increasing interest in the intersection of human-computer interaction and public policy. This day-long workshop will examine successes and challenges related to public policy and human computer interaction, in order to provide a forum to create a baseline of examples and to start the process of writing a white paper on the topic.
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47. |
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48. |
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49. |
- Hatos, Andras, et al.
(författare)
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DisProt : intrinsic protein disorder annotation in 2020
- 2020
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:D1, s. D269-D276
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Tidskriftsartikel (refereegranskat)abstract
- The Database of Protein Disorder (DisProt, URL:https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome.
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50. |
- Lee, WJ, et al.
(författare)
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Identifying and Assessing Interesting Subgroups in a Heterogeneous Population
- 2015
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Ingår i: BioMed research international. - : Hindawi Limited. - 2314-6141 .- 2314-6133. ; 2015, s. 462549-
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Tidskriftsartikel (refereegranskat)abstract
- Biological heterogeneity is common in many diseases and it is often the reason for therapeutic failures. Thus, there is great interest in classifying a disease into subtypes that have clinical significance in terms of prognosis or therapy response. One of the most popular methods to uncover unrecognized subtypes is cluster analysis. However, classical clustering methods such ask-means clustering or hierarchical clustering are not guaranteed to produce clinically interesting subtypes. This could be because the main statistical variability—the basis of cluster generation—is dominated by genes not associated with the clinical phenotype of interest. Furthermore, a strong prognostic factor might be relevant for a certain subgroup but not for the whole population; thus an analysis of the whole sample may not reveal this prognostic factor. To address these problems we investigate methods to identify and assess clinically interesting subgroups in a heterogeneous population. The identification step uses a clustering algorithm and to assess significance we use a false discovery rate- (FDR-) based measure. Under the heterogeneity condition the standard FDR estimate is shown to overestimate the true FDR value, but this is remedied by an improved FDR estimation procedure. As illustrations, two real data examples from gene expression studies of lung cancer are provided.
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