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| 3. |
- Romagnoni, A, et al.
(författare)
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Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
- 2019
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1, s. 10351-
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Tidskriftsartikel (refereegranskat)abstract
- Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers.
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- Craddock, Nick, et al.
(författare)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Tidskriftsartikel (refereegranskat)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 5. |
- Amiri, M., et al.
(författare)
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Periodic activity from a fast radio burst source
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 582:7812, s. 351-355
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Tidskriftsartikel (refereegranskat)abstract
- Fast radio bursts (FRBs) are bright, millisecond-duration radio transients originating from sources at extragalactic distances1, the origin of which is unknown. Some FRB sources emit repeat bursts, ruling out cataclysmic origins for those events2–4. Despite searches for periodicity in repeat burst arrival times on timescales from milliseconds to many days2,5–7, these bursts have hitherto been observed to appear sporadically and—although clustered8—without a regular pattern. Here we report observations of a 16.35 ± 0.15 day periodicity (or possibly a higher-frequency alias of that periodicity) from the repeating FRB 180916.J0158+65 detected by the Canadian Hydrogen Intensity Mapping Experiment Fast Radio Burst Project4,9. In 38 bursts recorded from 16 September 2018 to 4 February 2020 utc, we find that all bursts arrive in a five-day phase window, and 50 per cent of the bursts arrive in a 0.6-day phase window. Our results suggest a mechanism for periodic modulation either of the burst emission itself or through external amplification or absorption, and disfavour models invoking purely sporadic processes.
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- Tobie, G., et al.
(författare)
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Science goals and mission concept for the future exploration of Titan and Enceladus
- 2014
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Ingår i: Planetary and Space Science. - : Elsevier BV. - 0032-0633 .- 1873-5088. ; 104, s. 59-77
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Tidskriftsartikel (refereegranskat)abstract
- Saturn's moons, Titan and Enceladus, are two of the Solar System's most enigmatic bodies and are prime targets for future space exploration. Titan provides an analogue for many processes relevant to the Earth, more generally to outer Solar System bodies, and a growing host of newly discovered icy exoplanets. Processes represented include atmospheric dynamics, complex organic chemistry, meteorological cycles (with methane as a working fluid), astrobiology, surface liquids and lakes, geology, fluvial and aeolian erosion, and interactions with an external plasma environment. In addition, exploring Enceladus over multiple targeted flybys will give us a unique opportunity to further study the most active icy moon in our Solar System as revealed by Cassini and to analyse in situ its active plume with highly capable instrumentation addressing its complex chemistry and dynamics. Enceladus' plume likely represents the most accessible samples from an extra-terrestrial liquid water environment in the Solar system, which has far reaching implications for many areas of planetary and biological science. Titan with its massive atmosphere and Enceladus with its active plume are prime planetary objects in the Outer Solar System to perform in situ investigations. In the present paper, we describe the science goals and key measurements to be performed by a future exploration mission involving a Saturn-Titan orbiter and a Titan balloon, which was proposed to ESA in response to the call for definition of the science themes of the next Large-class mission in 2013. The mission scenario is built around three complementary science goals: (A) Titan as an Earth-like system; (B) Enceladus as an active cryovolcanic moon; and (C) Chemistry of Titan and Enceladus - clues for the origin of life. The proposed measurements would provide a step change in our understanding of planetary processes and evolution, with many orders of magnitude improvement in temporal, spatial, and chemical resolution over that which is possible with Cassini-Huygens. This mission concept builds upon the successes of Cassini-Huygens and takes advantage of previous mission heritage in both remote sensing and in situ measurement technologies. (C) 2014 Elsevier Ltd. All rights reserved.
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| 8. |
- Marcote, B., et al.
(författare)
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A repeating fast radio burst source localized to a nearby spiral galaxy
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 577:7789, s. 190-194
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Tidskriftsartikel (refereegranskat)abstract
- Fast radio bursts (FRBs) are brief, bright, extragalactic radio flashes1,2. Their physical origin remains unknown, but dozens of possible models have been postulated3. Some FRB sources exhibit repeat bursts4–7. Although over a hundred FRB sources have been discovered8, only four have been localized and associated with a host galaxy9–12, and just one of these four is known to emit repeating FRBs9. The properties of the host galaxies, and the local environments of FRBs, could provide important clues about their physical origins. The first known repeating FRB, however, was localized to a low-metallicity, irregular dwarf galaxy, and the apparently non-repeating sources were localized to higher-metallicity, massive elliptical or star-forming galaxies, suggesting that perhaps the repeating and apparently non-repeating sources could have distinct physical origins. Here we report the precise localization of a second repeating FRB source6, FRB 180916.J0158+65, to a star-forming region in a nearby (redshift 0.0337 ± 0.0002) massive spiral galaxy, whose properties and proximity distinguish it from all known hosts. The lack of both a comparably luminous persistent radio counterpart and a high Faraday rotation measure6 further distinguish the local environment of FRB 180916.J0158+65 from that of the single previously localized repeating FRB source, FRB 121102. This suggests that repeating FRBs may have a wide range of luminosities, and originate from diverse host galaxies and local environments.
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| 9. |
- Nimmo, K., et al.
(författare)
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A burst storm from the repeating FRB 20200120E in an M81 globular cluster
- 2023
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Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 520:2, s. 2281-2305
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Tidskriftsartikel (refereegranskat)abstract
- The repeating fast radio burst (FRB) source FRB 20200120E is exceptional because of its proximity and association with a globular cluster. Here we report 60 bursts detected with the Effelsberg telescope at 1.4 GHz. We observe large variations in the burst rate, and report the first FRB 20200120E 'burst storm', where the source suddenly became active and 53 bursts (fluence ≥0.04 Jy ms) occurred within only 40 min. We find no strict periodicity in the burst arrival times, nor any evidence for periodicity in the source's activity between observations. The burst storm shows a steep energy distribution (power-law index α = 2.39 ± 0.12) and a bimodal wait-time distribution, with log-normal means of 0.94+0.07−0.06 s and 23.61+3.06−2.71 s. We attribute these wait-time distribution peaks to a characteristic event time-scale and pseudo-Poisson burst rate, respectively. The secondary wait-time peak at ∼1 s is ∼50 × longer than the ∼24 ms time-scale seen for both FRB 20121102A and FRB 20201124A - potentially indicating a larger emission region, or slower burst propagation. FRB 20200120E shows order-of-magnitude lower burst durations and luminosities compared with FRB 20121102A and FRB 20201124A. Lastly, in contrast to FRB 20121102A, which has observed dispersion measure (DM) variations of ΔDM > 1 pc cm−3 on month-to-year time-scales, we determine that FRB 20200120E's DM has remained stable (ΔDM < 0.15 pc cm−3) over >10 months. Overall, the observational characteristics of FRB 20200120E deviate quantitatively from other active repeaters, but it is unclear whether it is qualitatively a different type of source.
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| 10. |
- Scholz, P., et al.
(författare)
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Simultaneous X-Ray and Radio Observations of the Repeating Fast Radio Burst FRB similar to 180916.J0158+65
- 2020
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 901:2
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Tidskriftsartikel (refereegranskat)abstract
- We report on simultaneous radio and X-ray observations of the repeating fast radio burst source FRB 180916.J0158+65 using the Canadian Hydrogen Intensity Mapping Experiment (CHIME), Effelsberg, and Deep Space Network (DSS-14 and DSS-63) radio telescopes and the Chandra X-ray Observatory. During 33 ks of Chandra observations, we detect no radio bursts in overlapping Effelsberg or Deep Space Network observations and a single burst during CHIME/FRB source transits. We detect no X-ray events in excess of the background during the Chandra observations. These non-detections imply a 5 sigma limit of <5 x 10(-10)erg cm(-2)for the 0.5-10 keV fluence of prompt emission at the time of the radio burst and 1.3 x 10(-9)erg cm(-2)at any time during the Chandra observations. Given the host-galaxy redshift of FRB 180916.J0158+65 (z similar to 0.034), these correspond to energy limits of <1.6 x 10(45)erg and <4 x 10(45)erg, respectively. We also place a 5 sigma limit of <8 x 10(-15)erg s(-1) cm(-2)on the 0.5-10 keV absorbed flux of a persistent source at the location of FRB 180916.J0158+65. This corresponds to a luminosity limit of <2 x 10(40)erg s(-1). Using an archival set of radio bursts from FRB 180916.J0158+65, we search for prompt gamma-ray emission in Fermi/GBM data but find no significant gamma-ray bursts, thereby placing a limit of 9 x 10(-9)erg cm(-2)on the 10-100 keV fluence. We also search Fermi/LAT data for periodic modulation of the gamma-ray brightness at the 16.35 days period of radio burst activity and detect no significant modulation. We compare these deep limits to the predictions of various fast radio burst models, but conclude that similar X-ray constraints on a closer fast radio burst source would be needed to strongly constrain theory.
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