| 1. |
- 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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| 2. |
- Chauvin, G., et al.
(författare)
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Discovery of a warm, dusty giant planet around HIP 65426
- 2017
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 605
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Tidskriftsartikel (refereegranskat)abstract
- Aims. The SHINE program is a high-contrast near-infrared survey of 600 young, nearby stars aimed at searching for and characterizing new planetary systems using VLT/SPHERE's unprecedented high-contrast and high-angular-resolution imaging capabilities. It is also intended to place statistical constraints on the rate, mass and orbital distributions of the giant planet population at large orbits as a function of the stellar host mass and age to test planet-formation theories.Methods. We used the IRDIS dual-band imager and the IFS integral field spectrograph of SPHERE to acquire high-contrast coronagraphic differential near-infrared images and spectra of the young A2 star HIP 65426. It is a member of the similar to 17 Myr old Lower Centaurus-Crux association. Results. At a separation of 830 mas (92 au projected) from the star, we detect a faint red companion. Multi-epoch observations confirm that it shares common proper motion with HIP 65426. Spectro-photometric measurements extracted with IFS and IRDIS between 0.95 and 2.2 mu m indicate a warm, dusty atmosphere characteristic of young low-surface-gravity L5-L7 dwarfs. Hot-start evolutionary models predict a luminosity consistent with a 6-12 M-Jup, T-eff = 1300-1600K and R = 1.5 +/- 0.1 R-Jup giant planet. Finally, the comparison with Exo-REM and PHOENIX BT-Settl synthetic atmosphere models gives consistent effective temperatures but with slightly higher surface gravity solutions of log(g) = 4.0-5.0 with smaller radii (1.0-1.3 R-Jup).Conclusions. Given its physical and spectral properties, HIP 65426 b occupies a rather unique placement in terms of age, mass, and spectral-type among the currently known imaged planets. It represents a particularly interesting case to study the presence of clouds as a function of particle size, composition, and location in the atmosphere, to search for signatures of non-equilibrium chemistry, and finally to test the theory of planet formation and evolution.
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| 3. |
- Cheetham, A., et al.
(författare)
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Discovery of a brown dwarf companion to the star HIP 64892
- 2018
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 615
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Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of a bright, brown dwarf companion to the star HIP 64892, imaged with VLT/SPHERE during the SHINE exoplanet survey. The host is a B9.5V member of the Lower-Centaurus-Crux subgroup of the Scorpius Centaurus OB association. The measured angular separation of the companion (1.2705 +/- 0.0023) corresponds to a projected distance of 159 +/- 12AU. We observed the target with the dual-band imaging and long-slit spectroscopy modes of the IRDIS imager to obtain its spectral energy distribution (SED) and astrometry. In addition, we reprocessed archival NACO L-band data, from which we also recover the companion. Its SED is consistent with a young (<30 Myr), low surface gravity object with a spectral type of M9 gamma +/- 1. From comparison with the BT-Settl atmospheric models we estimate an effective temperature of T-eff = 2600 +/- 100 K, and comparison of the companion photometry to the COND evolutionary models yields a mass of similar to 29-37 M-J at the estimated age of 16(-7)(+15) Myr for the system. The star HIP 64892 is a rare example of an extreme-mass ratio system (q similar to 0.01) and will be useful for testing models relating to the formation and evolution of such low-mass objects.
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| 4. |
- Keppler, M., et al.
(författare)
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Discovery of a planetary-mass companion within the gap of the transition disk around PDS 70
- 2018
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 617
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Tidskriftsartikel (refereegranskat)abstract
- Context. Young circumstellar disks are the birthplaces of planets. Their study is of prime interest to understand the physical and chemical conditions under which planet formation takes place. Only very few detections of planet candidates within these disks exist, and most of them are currently suspected to be disk features.Aims. In this context, the transition disk around the young star PDS 70 is of particular interest, due to its large gap identified in previous observations, indicative of ongoing planet formation. We aim to search for the presence of an embedded young planet and search for disk structures that may be the result of disk-planet interactions and other evolutionary processes.Methods. We analyse new and archival near-infrared images of the transition disk PDS 70 obtained with the VLT/SPHERE, VLT/NaCo, and Gemini/NICI instruments in polarimetric differential imaging and angular differential imaging modes.Results. We detect a point source within the gap of the disk at about 195 mas (similar to 22 au) projected separation. The detection is confirmed at five different epochs, in three filter bands and using different instruments. The astrometry results in an object of bound nature, with high significance. The comparison of the measured magnitudes and colours to evolutionary tracks suggests that the detection is a companion of planetary mass. The luminosity of the detected object is consistent with that of an L-type dwarf, but its IR colours are redder, possibly indicating the presence of warm surrounding material. Further, we confirm the detection of a large gap of similar to 54 au in size within the disk in our scattered light images, and detect a signal from an inner disk component. We find that its spatial extent is very likely smaller than similar to 17 au in radius, and its position angle is consistent with that of the outer disk. The images of the outer disk show evidence of a complex azimuthal brightness distribution which is different at different wavelengths and may in part be explained by Rayleigh scattering from very small grains.Conclusions. The detection of a young protoplanet within the gap of the transition disk around PDS 70 opens the door to a so far observationally unexplored parameter space of planetary formation and evolution. Future observations of this system at different wavelengths and continuing astrometry will allow us to test theoretical predictions regarding planet-disk interactions, planetary atmospheres, and evolutionary models.
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| 5. |
- Lagrange, A. -M., et al.
(författare)
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Post-conjunction detection of beta Pictoris b with VLT/SPHERE
- 2019
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 621
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Tidskriftsartikel (refereegranskat)abstract
- Context. With an orbital distance comparable to that of Saturn in the solar system, beta Pictoris b is the closest (semi-major axis similar or equal to 9 au) exoplanet that has been imaged to orbit a star. Thus it offers unique opportunities for detailed studies of its orbital, physical, and atmospheric properties, and of disk-planet interactions. With the exception of the discovery observations in 2003 with NaCo at the Very Large Telescope (VLT), all following astrometric measurements relative to beta Pictoris have been obtained in the southwestern part of the orbit, which severely limits the determination of the planet's orbital parameters.Aims. We aimed at further constraining beta Pictoris b orbital properties using more data, and, in particular, data taken in the northeastern part of the orbit.Methods. We used SPHERE at the VLT to precisely monitor the orbital motion of beta beta Pictoris b since first light of the instrument in 2014.Results. We were able to monitor the planet until November 2016, when its angular separation became too small (125 mas, i.e., 1.6 au) and prevented further detection. We redetected beta Pictoris b on the northeast side of the disk at a separation of 139 mas and a PA of 30 degrees in September 2018. The planetary orbit is now well constrained. With a semi-major axis (sma) of a = 9.0 +/- 0.5 au (1 sigma), it definitely excludes previously reported possible long orbital periods, and excludes beta Pictoris b as the origin of photometric variations that took place in 1981. We also refine the eccentricity and inclination of the planet. From an instrumental point of view, these data demonstrate that it is possible to detect, if they exist, young massive Jupiters that orbit at less than 2 au from a star that is 20 pc away.
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| 6. |
- Mesal, D., et al.
(författare)
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Exploring the R CrA environment with SPHERE Discovery of a new stellar companion
- 2019
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 624
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Tidskriftsartikel (refereegranskat)abstract
- Aims. R Coronae Australis (R CrA) is the brightest star of the Coronet nebula of the Corona Australis (CrA) star forming region. This star is very red in color, probably due to dust absorption, and is strongly variable. High-contrast instruments allow for an unprecedented direct exploration of the immediate circumstellar environment of this star. Methods. We observed R CrA with the near-infrared (NIR) channels (IFS and IRDIS) of SPHERE at the Very Large Telescope (VET). In this paper, we used four different epochs, three of which are from open time observations while one is from SPHERE guaranteed time. The data were reduced using the data reduction and handling pipeline and the SPHERE Data Center. We implemented custom IDL routines on the reduced data with the aim to subtract the speckle halo. We have also obtained pupil-tracking H-band (1.45-1.85 mu m) observations with the VLT/SINFONI NIR medium-resolution (R similar to 3000) spectrograph. Results. A companion was found at a separation of 0.156 '' from the star in the first epoch and increasing to 0.184 '' in the final epoch. Furthermore, several extended structures were found around the star, the most noteworthy of which is a very bright jet-like structure northeast from the star. The astrometric measurements of the companion in the four epochs confirm that it is gravitationally bound to the star. The SPHERE photometry and SINFONI spectrum, once corrected for extinction, point toward a spectral type object that is early M with a mass between 0.3 and 0.55 M-circle dot. The astrometric analyis provides constraints on the orbit paramenters: e similar to 0.4, semimajor axis at 27-28 au, inclination of similar to 70 degrees, and a period larger than 30 yr. We were also able to put constraints of few M (jup) on the mass of possible other companions down to separations of few tens of au.
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| 7. |
- Momozawa, Y, et al.
(författare)
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IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes
- 2018
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9:1, s. 2427-
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Tidskriftsartikel (refereegranskat)abstract
- GWAS have identified >200 risk loci for Inflammatory Bowel Disease (IBD). The majority of disease associations are known to be driven by regulatory variants. To identify the putative causative genes that are perturbed by these variants, we generate a large transcriptome data set (nine disease-relevant cell types) and identify 23,650 cis-eQTL. We show that these are determined by ∼9720 regulatory modules, of which ∼3000 operate in multiple tissues and ∼970 on multiple genes. We identify regulatory modules that drive the disease association for 63 of the 200 risk loci, and show that these are enriched in multigenic modules. Based on these analyses, we resequence 45 of the corresponding 100 candidate genes in 6600 Crohn disease (CD) cases and 5500 controls, and show with burden tests that they include likely causative genes. Our analyses indicate that ≥10-fold larger sample sizes will be required to demonstrate the causality of individual genes using this approach.
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| 8. |
- Rigliaco, E., et al.
(författare)
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Investigating the nature of the extended structure around the Herbig star RCrA using integral field and high-resolution spectroscopy
- 2019
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 632
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Tidskriftsartikel (refereegranskat)abstract
- Context. We present a detailed analysis of the extended structure detected around the young and close-by Herbig Ae/Be star R CrA. This is a young triple system with an intermediate mass central binary whose separation is of the order of a few tens of the radii of the individual components, and an M-star companion at about 30 au.Aims. Our aim is to understand the nature of the extended structure by means of combining integral-field and high-resolution spectroscopy.Methods. We conducted the analysis based on FEROS archival optical spectroscopy data and adaptive optics images and integral-field spectra obtained with SINFONI and SPHERE at the VLT.Results. The observations reveal a complex extended structure that is composed of at least two components: a non-uniform wide cavity whose walls are detected in continuum emission up to 400 au, and a collimated wiggling-jet detected in the emission lines of helium and hydrogen. Moreover, the presence of [Fe II] emission projected close to the cavity walls suggests the presence of a slower moving wind, most likely a disk wind. The multiple components of the optical forbidden lines also indicate the presence of a high-velocity jet co-existing with a slow wind. We constructed a geometrical model of the collimated jet flowing within the cavity using intensity and velocity maps, finding that its wiggling is consistent with the orbital period of the central binary. The cavity and the jet do not share the same position angle, suggesting that the jet is itself experiencing a precession motion possibly due to the wide M-dwarf companion.Conclusions. We propose a scenario that closely agrees with the general expectation of a magneto-centrifugal-launched jet. These results build upon the extensive studies already conducted on R CrA.
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| 9. |
- Vigan, A., et al.
(författare)
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First light of the VLT planet finder SPHERE I. Detection and characterization of the substellar companion GJ 758 B
- 2016
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 587
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Tidskriftsartikel (refereegranskat)abstract
- GJ 758 B is a brown dwarf companion to a nearby (15.76%) solar-type, metal-rich (M/H = +0.2 dex) main-sequence star (G9V) that was discovered with Subaru/HiCIAO in 2009. From previous studies, it has drawn attention as being the coldest (similar to 600 K) companion ever directly imaged around a neighboring star. We present new high-contrast data obtained during the commissioning of the SPHERE instrument at the Very Large Telescope (VLT). The data was obtained in Y-, J-, H-, and K-s-bands with the dual-band imaging (DBI) mode of IRDIS, thus providing a broad coverage of the full near-infrared (near-IR) range at higher contrast and better spectral sampling than previously reported. In this new set of high-quality data, we report the re-detection of the companion, as well as the first detection of a new candidate closer-in to the star. We use the new eight photometric points for an extended comparison of GJ 758 B with empirical objects and four families of atmospheric models. From comparison to empirical object, we estimate a T8 spectral type, but none of the comparison objects can accurately represent the observed near-IR fluxes of GJ 758 B. From comparison to atmospheric models, we attribute a T-eff = 600 +/- 100 K, but we find that no atmospheric model can adequately fit all the fluxes of GJ 758 B. The lack of exploration of metal enrichment in model grids appears as a major limitation that prevents an accurate estimation of the companion physical parameters. The photometry of the new candidate companion is broadly consistent with L-type objects, but a second epoch with improved photometry is necessary to clarify its status. The new astrometry of GJ 758 B shows a significant proper motion since the last epoch. We use this result to improve the determination of the orbital characteristics using two fitting approaches: Least-Squares Monte Carlo and Markov chain Monte Carlo. We confirm the high-eccentricity of the orbit (peak at 0.5), and find a most likely semi-major axis of 46.05 AU. We also use our imaging data, as well as archival radial velocity data, to reject the possibility that this is a false positive effect created by an unseen, closer-in, companion. Finally, we analyze the sensitivity of our data to additional closer-in companions and reject the possibility of other massive brown dwarf companions down to 4-5 AU.
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| 10. |
- Zurlo, A., et al.
(författare)
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First light of the VLT planet finder SPHERE III. New spectrophotometry and astrometry of the HR 8799 exoplanetary system
- 2016
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 587
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Tidskriftsartikel (refereegranskat)abstract
- Context. The planetary system discovered around the young A-type HR8799 provides a unique laboratory to: a) test planet formation theories; b) probe the diversity of system architectures at these separations, and c) perform comparative (exo)planetology.Aims. We present and exploit new near-infrared images and integral-field spectra of the four gas giants surrounding HR8799 obtained with SPHERE, the new planet finder instrument at the Very Large Telescope, during the commissioning and science verification phase of the instrument (July-December 2014). With these new data, we contribute to completing the spectral energy distribution (SED) of these bodies in the 1.0-2.5 mu m range. We also provide new astrometric data, in particular for planet e, to further constrain the orbits.Methods. We used the infrared dual-band imager and spectrograph (IRDIS) subsystem to obtain pupil-stabilized, dual-band H2H3 (1.593 mu m, 1.667 mu m), K1K2 (2.110 mu m, 2.251 mu m), and broadband J (1.245 mu m) images of the four planets. IRDIS was operated in parallel with the integral field spectrograph (IFS) of SPHERE to collect low-resolution (R similar to 30), near-infrared (0.94-1.64 mu m) spectra of the two innermost planets HR8799 d and e. The data were reduced with dedicated algorithms, such as the Karhunen-Loeve image projection (KLIP), to reveal the planets. We used the so-called negative planets injection technique to extract their photometry, spectra, and measure their positions. We illustrate the astrometric performance of SPHERE through sample orbital fits compatible with SPHERE and literature data.Results. We demonstrated the ability of SPHERE to detect and characterize planets in this kind of systems, providing spectra and photometry of its components. The spectra improve upon the signal-to-noise ratio of previously obtained data and increase the spectral coverage down to the Y band. In addition, we provide the first detection of planet e in the J band. Astrometric positions for planets HR8799 bcde are reported for the epochs of July, August, and December 2014. We measured the photometric values in J, H2H3, K1K2 bands for the four planets with a mean accuracy of 0.13 mag. We found upper limit constraints on the mass of a possible planet f of 3-7 M-Jup. Our new measurements are more consistent with the two inner planets d and e being in a 2d:1e or 3d:2e resonance. The spectra of HR8799 d and e are well matched by those of L6-8 field dwarfs. However, the SEDs of these objects are redder than field L dwarfs longward of 1.6 mu m.
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