1. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)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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2. |
- Hyde, K. D., et al.
(author)
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Global consortium for the classification of fungi and fungus-like taxa
- 2023
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In: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
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Journal article (peer-reviewed)abstract
- The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and fungus-like taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, 'to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation', or 'are there too many genera in the Boletales?' and even more importantly, 'what should be done with the tremendously diverse 'dark fungal taxa?' There are undeniable differences in mycologists' perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others' work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.
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6. |
- Groenen, M. A., et al.
(author)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Journal article (peer-reviewed)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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7. |
- Crous, P. W., et al.
(author)
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Fusarium : more than a node or a foot-shaped basal cell
- 2021
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In: Studies in mycology. - : CENTRAALBUREAU SCHIMMELCULTURE. - 0166-0616 .- 1872-9797. ; :98
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Journal article (peer-reviewed)abstract
- Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
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9. |
- Barnes, DR, et al.
(author)
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Breast and Prostate Cancer Risks for Male BRCA1 and BRCA2 Pathogenic Variant Carriers Using Polygenic Risk Scores
- 2022
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In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 1460-2105 .- 0027-8874. ; 114:1, s. 109-122
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Journal article (peer-reviewed)abstract
- BackgroundRecent population-based female breast cancer and prostate cancer polygenic risk scores (PRS) have been developed. We assessed the associations of these PRS with breast and prostate cancer risks for male BRCA1 and BRCA2 pathogenic variant carriers.Methods483 BRCA1 and 1318 BRCA2 European ancestry male carriers were available from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). A 147-single nucleotide polymorphism (SNP) prostate cancer PRS (PRSPC) and a 313-SNP breast cancer PRS were evaluated. There were 3 versions of the breast cancer PRS, optimized to predict overall (PRSBC), estrogen receptor (ER)–negative (PRSER-), or ER-positive (PRSER+) breast cancer risk.ResultsPRSER+ yielded the strongest association with breast cancer risk. The odds ratios (ORs) per PRSER+ standard deviation estimates were 1.40 (95% confidence interval [CI] =1.07 to 1.83) for BRCA1 and 1.33 (95% CI = 1.16 to 1.52) for BRCA2 carriers. PRSPC was associated with prostate cancer risk for BRCA1 (OR = 1.73, 95% CI = 1.28 to 2.33) and BRCA2 (OR = 1.60, 95% CI = 1.34 to 1.91) carriers. The estimated breast cancer odds ratios were larger after adjusting for female relative breast cancer family history. By age 85 years, for BRCA2 carriers, the breast cancer risk varied from 7.7% to 18.4% and prostate cancer risk from 34.1% to 87.6% between the 5th and 95th percentiles of the PRS distributions.ConclusionsPopulation-based prostate and female breast cancer PRS are associated with a wide range of absolute breast and prostate cancer risks for male BRCA1 and BRCA2 carriers. These findings warrant further investigation aimed at providing personalized cancer risks for male carriers and informing clinical management.
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10. |
- Faatz, B., et al.
(author)
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Simultaneous operation of two soft x-ray free-electron lasers driven by one linear accelerator
- 2016
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In: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 18
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Journal article (peer-reviewed)abstract
- Extreme-ultraviolet to x-ray free-electron lasers (FELs) in operation for scientific applications are up to now single-user facilities. While most FELs generate around 100 photon pulses per second, FLASH at DESY can deliver almost two orders of magnitude more pulses in this time span due to its superconducting accelerator technology. This makes the facility a prime candidate to realize the next step in FELs-dividing the electron pulse trains into several FEL lines and delivering photon pulses to several users at the same time. Hence, FLASH has been extended with a second undulator line and self-amplified spontaneous emission (SASE) is demonstrated in both FELs simultaneously. FLASH can now deliver MHz pulse trains to two user experiments in parallel with individually selected photon beam characteristics. First results of the capabilities of this extension are shown with emphasis on independent variation of wavelength, repetition rate, and photon pulse length.
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12. |
- Chauvin, G., et al.
(author)
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Discovery of a warm, dusty giant planet around HIP 65426
- 2017
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 605
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Journal article (peer-reviewed)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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13. |
- Keppler, M., et al.
(author)
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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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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 617
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Journal article (peer-reviewed)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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14. |
- Schmit, Stephanie L, et al.
(author)
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Novel Common Genetic Susceptibility Loci for Colorectal Cancer.
- 2019
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In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 111:2, s. 146-157
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Journal article (peer-reviewed)abstract
- Background: Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk.Methods: We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided.Results: The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0.Conclusions: This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.
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15. |
- Huyghe, Jeroen R., et al.
(author)
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Discovery of common and rare genetic risk variants for colorectal cancer
- 2019
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In: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 51:1, s. 76-
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Journal article (peer-reviewed)abstract
- To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 x 10(-8), bringing the number of known independent signals for CRC to similar to 100. New signals implicate lower-frequency variants, Kruppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
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16. |
- Lacour, S., et al.
(author)
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The mass of β Pictoris c from β Pictoris b orbital motion
- 2021
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 654
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Journal article (peer-reviewed)abstract
- Aims. We aim to demonstrate that the presence and mass of an exoplanet can now be effectively derived from the astrometry of another exoplanet.Methods. We combined previous astrometry of β Pictoris b with a new set of observations from the GRAVITY interferometer. The orbital motion of β Pictoris b is fit using Markov chain Monte Carlo simulations in Jacobi coordinates. The inner planet, β Pictoris c, was also reobserved at a separation of 96 mas, confirming the previous orbital estimations.Results. From the astrometry of planet b only, we can (i) detect the presence of β Pictoris c and (ii) constrain its mass to 10.04(-3.10)(+4.53) M-Jup. If one adds the astrometry of β Pictoris c, the mass is narrowed down to 9.15(-1.06)(+1.08) M-Jup. The inclusion of radial velocity measurements does not affect the orbital parameters significantly, but it does slightly decrease the mass estimate to 8.89(-0.75)(+0.75) M-Jup. With a semimajor axis of 2.68 +/- 0.02 au, a period of 1221 +/- 15 days, and an eccentricity of 0.32 +/- 0.02, the orbital parameters of β Pictoris c are now constrained as precisely as those of β Pictoris b. The orbital configuration is compatible with a high-order mean-motion resonance (7:1). The impact of the resonance on the planets' dynamics would then be negligible with respect to the secular perturbations, which might have played an important role in the eccentricity excitation of the outer planet.
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17. |
- Desidera, S., et al.
(author)
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The SPHERE infrared survey for exoplanets (SHINE) I. Sample definition and target characterization
- 2021
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 651
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Journal article (peer-reviewed)abstract
- Context. Large surveys with new-generation high-contrast imaging instruments are needed to derive the frequency and properties of exoplanet populations with separations from ~5 to 300 au. A careful assessment of the stellar properties is crucial for a proper understanding of when, where, and how frequently planets form, and how they evolve. The sensitivity of detection limits to stellar age makes this a key parameter for direct imaging surveys.Aims. We describe the SpHere INfrared survey for Exoplanets (SHINE), the largest direct imaging planet-search campaign initiated at the VLT in 2015 in the context of the SPHERE Guaranteed Time Observations of the SPHERE consortium. In this first paper we present the selection and the properties of the complete sample of stars surveyed with SHINE, focusing on the targets observed during the first phase of the survey (from February 2015 to February 2017). This early sample composed of 150 stars is used to perform a preliminary statistical analysis of the SHINE data, deferred to two companion papers presenting the survey performance, main discoveries, and the preliminary statistical constraints set by SHINE.Methods. Based on a large database collecting the stellar properties of all young nearby stars in the solar vicinity (including kinematics, membership to moving groups, isochrones, lithium abundance, rotation, and activity), we selected the original sample of 800 stars that were ranked in order of priority according to their sensitivity for planet detection in direct imaging with SPHERE. The properties of the stars that are part of the early statistical sample wererevisited, including for instance measurements from the Gaia Data Release 2. Rotation periods were derived for the vast majority of the late-type objects exploiting TESS light curves and dedicated photometric observations.Results. The properties of individual targets and of the sample as a whole are presented.
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18. |
- Langlois, M., et al.
(author)
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The SPHERE infrared survey for exoplanets (SHINE) : II. Observations, data reduction and analysis, detection performances, and initial results
- 2021
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 651
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Journal article (peer-reviewed)abstract
- Context. In recent decades, direct imaging has confirmed the existence of substellar companions (exoplanets or brown dwarfs) on wide orbits (>10 au) around their host stars. In striving to understand their formation and evolution mechanisms, in 2015 we initiated the SPHERE infrared survey for exoplanets (SHINE), a systematic direct imaging survey of young, nearby stars that is targeted at exploring their demographics.Aims. We aim to detect and characterize the population of giant planets and brown dwarfs beyond the snow line around young, nearby stars. Combined with the survey completeness, our observations offer the opportunity to constrain the statistical properties (occurrence, mass and orbital distributions, dependency on the stellar mass) of these young giant planets.Methods. In this study, we present the observing and data analysis strategy, the ranking process of the detected candidates, and the survey performances for a subsample of 150 stars that are representative of the full SHINE sample. Observations were conducted in a homogeneous way between February 2015 and February 2017 with the dedicated ground-based VLT/SPHERE instrument equipped with the IFS integral field spectrograph and the IRDIS dual-band imager, covering a spectral range between 0.9 and 2.3 μm. We used coronographic, angular, and spectral differential imaging techniques to achieve the best detection performances for this study, down to the planetary mass regime.Results. We processed, in a uniform manner, more than 300 SHINE observations and datasets to assess the survey typical sensitivity as a function of the host star and of the observing conditions. The median detection performance reached 5σ-contrasts of 13 mag at 200 mas and 14.2 mag at 800 mas with the IFS (YJ and YJH bands), and of 11.8 mag at 200 mas, 13.1 mag at 800 mas, and 15.8 mag at 3 as with IRDIS in H band, delivering one of the deepest sensitivity surveys thus far for young, nearby stars. A total of sixteen substellar companions were imaged in this first part of SHINE: seven brown dwarf companions and ten planetary-mass companions.These include two new discoveries, HIP 65426 b and HIP 64892 B, but not the planets around PDS70 that had not been originally selected for the SHINE core sample. A total of 1483 candidates were detected, mainly in the large field of view that characterizes IRDIS. The color-magnitude diagrams, low-resolution spectrum (when available with IFS), and follow-up observations enabled us to identify the nature (background contaminant or comoving companion) of about 86% of our subsample. The remaining cases are often connected to crowded-field follow-up observations that were missing. Finally, even though SHINE was not initially designed for disk searches, we imaged twelve circumstellar disks, including three new detections around the HIP 73145, HIP 86598, and HD 106906 systems.Conclusions. Nowadays, direct imaging provides a unique opportunity to probe the outer part of exoplanetary systems beyond 10 au to explore planetary architectures, as highlighted by the discoveries of: one new exoplanet, one new brown dwarf companion, and three new debris disks during this early phase of SHINE. It also offers the opportunity to explore and revisit the physical and orbital properties of these young, giant planets and brown dwarf companions (relative position, photometry, and low-resolution spectrum in near-infrared, predicted masses, and contrast in order to search for additional companions). Finally, these results highlight the importance of finalizing the SHINE systematic observation of about 500 young, nearby stars for a full exploration of their outer part to explore the demographics of young giant planets beyond 10 au and to identify the most interesting systems for the next generation of high-contrast imagers on very large and extremely large telescopes.
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19. |
- Birney, Ewan, et al.
(author)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Journal article (peer-reviewed)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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20. |
- Boccaletti, A., et al.
(author)
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Observations of fast-moving features in the debris disk of AU Mic on a three-year timescale : Confirmation and new discoveries
- 2018
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 614
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Journal article (peer-reviewed)abstract
- Context. The nearby and young M star AU Mic is surrounded by a debris disk in which we previously identified a series of large-scale arch-like structures that have never been seen before in any other debris disk and that move outward at high velocities. Aims. We initiated a monitoring program with the following objectives: (1) track the location of the structures and better constrain their projected speeds, (2) search for new features emerging closer in, and ultimately (3) understand the mechanism responsible for the motion and production of the disk features. Methods. AU Mic was observed at 11 different epochs between August 2014 and October 2017 with the IR camera and spectrograph of SPHERE. These high-contrast imaging data were processed with a variety of angular, spectral, and polarimetric differential imaging techniques to reveal the faintest structures in the disk. We measured the projected separations of the features in a systematic way for all epochs. We also applied the very same measurements to older observations from the Hubble Space Telescope (HST) with the visible cameras STIS and ACS. Results. The main outcomes of this work are (1) the recovery of the five southeastern broad arch-like structures we identified in our first study, and confirmation of their fast motion (projected speed in the range 4-12 km s(-1) ); (2) the confirmation that the very first structures observed in 2004 with ACS are indeed connected to those observed later with STIS and now SPHERE; (3) the discovery of two new very compact structures at the northwest side of the disk (at 0.40 '' and 0.55 '' in May 2015) that move to the southeast at low speed; and (4) the identification of a new arch-like structure that might be emerging at the southeast side at about 0.4 from the star (as of May 2016). Conclusions. Although the exquisite sensitivity of SPHERE allows one to follow the evolution not only of the projected separation, but also of the specific morphology of each individual feature, it remains difficult to distinguish between possible dynamical scenarios that may explain the observations. Understanding the exact origin of these features, the way they are generated, and their evolution over time is certainly a significant challenge in the context of planetary system formation around M stars.
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21. |
- Vigan, A., et al.
(author)
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The SPHERE infrared survey for exoplanets (SHINE) : III. The demographics of young giant exoplanets below 300 au with SPHERE
- 2021
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 651
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Journal article (peer-reviewed)abstract
- The SpHere INfrared Exoplanet (SHINE) project is a 500-star survey performed with SPHERE on the Very Large Telescope for the purpose of directly detecting new substellar companions and understanding their formation and early evolution. Here we present an initial statistical analysis for a subsample of 150 stars spanning spectral types from B to M that are representative of the full SHINE sample. Our goal is to constrain the frequency of substellar companions with masses between 1 and 75 MJup and semimajor axes between 5 and 300 au. For this purpose, we adopt detection limits as a function of angular separation from the survey data for all stars converted into mass and projected orbital separation using the BEX-COND-hot evolutionary tracks and known distance to each system. Based on the results obtained for each star and on the 13 detections in the sample, we use a Markov chain Monte Carlo tool to compare our observations to two different types of models. The first is a parametric model based on observational constraints, and the second type are numerical models that combine advanced core accretion and gravitational instability planet population synthesis. Using the parametric model, we show that the frequencies of systems with at least one substellar companion are 23.0−9.7+13.5, 5.8−2.8+4.7, and 12.6−7.1+12.9% for BA, FGK, and M stars, respectively. We also demonstrate that a planet-like formation pathway probably dominates the mass range from 1–75 MJup for companions around BA stars, while for M dwarfs, brown dwarf binaries dominate detections. In contrast, a combination of binary star-like and planet-like formation is required to best fit the observations for FGK stars. Using our population model and restricting our sample to FGK stars, we derive a frequency of 5.7−2.8+3.8%, consistent with predictions from the parametric model. More generally, the frequency values that we derive are in excellent agreement with values obtained in previous studies.
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22. |
- Chen, Zhishan, et al.
(author)
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Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
- 2024
-
In: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
-
Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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23. |
- Rodet, L., et al.
(author)
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Dynamical masses of M-dwarf binaries in young moving groups I. The case of TWA22 and GJ2060
- 2018
-
In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 618
-
Journal article (peer-reviewed)abstract
- Context. Evolutionary models are widely used to infer the mass of stars, brown dwarfs, and giant planets. Their predictions are thought to be less reliable at young ages (<200 Myr) and in the low-mass regime (< 1 M-circle dot). GJ 2060AB and TWA22AB are two rare astrometric M-dwarf binaries, respectively members of the AB Doradus (AB Dor) and Beta Pictoris (beta Pic) moving groups. As their dynamical mass can be measured to within a few years, they can be used to calibrate the evolutionary tracks and set new constraints on the age of young moving groups.Aims. We provide the first dynamical mass measurement of GJ 2060 and a refined measurement of the total mass of TWA22. We also characterize the atmospheric properties of the individual components of GJ 2060 that can be used as inputs to the evolutionary models.Methods. We used NaCo and SPHERE observations at VLT and archival Keck/NIRC2 data to complement the astrometric monitoring of the binaries. We combined the astrometry with new HARPS radial velocities (RVs) and FEROS RVs of GJ 2060. We used a Markov chain MonteCarlo (MCMC) module to estimate posteriors on the orbital parameters and dynamical masses of GJ 2060AB and TWA22AB from the astrometry and RVs. Complementary data obtained with the integral field spectrograph VLT /SINFONI were gathered to extract the individual near-infrared (1.1-2.5 mu m) medium-resolution (R similar to 1500 2000) spectra of GJ 2060A and B. We compared the spectra to those of known objects and to grids of BT-SETTL model spectra to infer the spectral type, bolometric luminosities, and temperatures of those objects.Results. We find a total mass of 0 : 18 +/- 0 : 02 M-circle dot for TWA22, which is in good agreement with model predictions at the age of the fi Pic moving group. We obtain a total mass of 1 : 09 +/- 0 : 10 M-circle dot for GJ 2060. We estimate a spectral type of M1 +/- 0.5, L/L-circle dot = -1.20 +/- 0.05 dex, and T-eff = 3700 +/- 100 K for GJ 2060 A. The B component is a M3 +/- 0 : 5 dwarf with L/L-circle dot = 1.63 +/- 0.05 dex and T-eff = 3400 +/- 100 K. The dynamical mass of GJ 2060AB is inconsistent with the most recent models predictions (BCAH15, PARSEC) for an AB Dor age in the range 50-150 Myr. It is 10%-20% (1-2 sigma, depending on the assumed age) above the model's predictions, corresponding to an underestimation of 0.10-0.20 M fi. Coevality suggests a young age for the system (similar to 50 Myr) according to most evolutionary models.Conclusions. TWA22 validates the predictions of recent evolutionary tracks at similar to 20 Myr. On the other hand, we evidence a 1-2 sigma mismatch between the predicted and observed mass of GJ 2060 AB. This slight departure may indicate that one of the stars hosts a tight companion. Alternatively, this would confirm the model's tendency to underestimate the mass of young low-mass stars.
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24. |
- Bonnefoy, M., et al.
(author)
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First light of the VLT planet finder SPHERE IV. Physical and chemical properties of the planets around HR8799
- 2016
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 587
-
Journal article (peer-reviewed)abstract
- Context. The system of four planets discovered around the intermediate-mass star HR8799 offers a unique opportunity to test planet formation theories at large orbital radii and to probe the physics and chemistry at play in the atmospheres of self-luminous young (similar to 30 Myr) planets. We recently obtained new photometry of the four planets and low-resolution (R similar to 30) spectra of HR8799 d and e with the SPHERE instrument (Paper III).Aims. In this paper (Paper IV), we aim to use these spectra and available photometry to determine how they compare to known objects, what the planet physical properties are, and how their atmospheres work.Methods. We compare the available spectra, photometry, and spectral energy distribution (SED) of the planets to field dwarfs and young companions. In addition, we use the extinction from corundum, silicate (enstatite and forsterite), or iron grains likely to form in the atmosphere of the planets to try to better understand empirically the peculiarity of their spectrophotometric properties. To conclude, we use three sets of atmospheric models (BT-SETTL14, Cloud-AE60, Exo-REM) to determine which ingredients are critically needed in the models to represent the SED of the objects, and to constrain their atmospheric parameters (T-eff, log g, M/H).Results. We find that HR8799d and e properties are well reproduced by those of L6-L8 dusty dwarfs discovered in the field, among which some are candidate members of young nearby associations. No known object reproduces well the properties of planets b and c. Nevertheless, we find that the spectra and WISE photometry of peculiar and/or young early-T dwarfs reddened by submicron grains made of corundum, iron, enstatite, or forsterite successfully reproduce the SED of these planets. Our analysis confirms that only the Exo-REM models with thick clouds fit (within 2 sigma) the whole set of spectrophotometric datapoints available for HR8799 d and e for T-eff = 1200 K, log g in the range 3.0-4.5, and M/H = +0.5. The models still fail to reproduce the SED of HR8799c and b. The determination of the metallicity, log g, and cloud thickness are degenerate.Conclusions. Our empirical analysis and atmospheric modelling show that an enhanced content in dust and decreased CIA of H-2 is certainly responsible for the deviation of the properties of the planet with respect to field dwarfs. The analysis suggests in addition that HR8799c and b have later spectral types than the two other planets, and therefore could both have lower masses.
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25. |
- Cheetham, A., et al.
(author)
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Discovery of a brown dwarf companion to the star HIP 64892
- 2018
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 615
-
Journal article (peer-reviewed)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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26. |
- Garcia-Lopez, R., et al.
(author)
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A measure of the size of the magnetospheric accretion region in TW Hydrae
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 584:7822, s. 547-550
-
Journal article (peer-reviewed)abstract
- Stars form by accreting material from their surrounding disks. There is a consensus that matter flowing through the disk is channelled onto the stellar surface by the stellar magnetic field. This is thought to be strong enough to truncate the disk close to the corotation radius, at which the disk rotates at the same rate as the star. Spectro-interferometric studies in young stellar objects show that hydrogen emission (a well known tracer of accretion activity) mostly comes from a region a few milliarcseconds across, usually located within the dust sublimation radius1–3. The origin of the hydrogen emission could be the stellar magnetosphere, a rotating wind or a disk. In the case of intermediate-mass Herbig AeBe stars, the fact that Brackett γ (Brγ) emission is spatially resolved rules out the possibility that most of the emission comes from the magnetosphere4–6 because the weak magnetic fields (some tenths of a gauss) detected in these sources7,8 result in very compact magnetospheres. In the case of T Tauri sources, their larger magnetospheres should make them easier to resolve. The small angular size of the magnetosphere (a few tenths of a milliarcsecond), however, along with the presence of winds9,10 make the interpretation of the observations challenging. Here we report optical long-baseline interferometric observations that spatially resolve the inner disk of the T Tauri star TW Hydrae. We find that the near-infrared hydrogen emission comes from a region approximately 3.5 stellar radii across. This region is within the continuum dusty disk emitting region (7 stellar radii across) and also within the corotation radius, which is twice as big. This indicates that the hydrogen emission originates in the accretion columns (funnel flows of matter accreting onto the star), as expected in magnetospheric accretion models, rather than in a wind emitted at much larger distance (more than one astronomical unit).
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27. |
- Koutoulaki, M., et al.
(author)
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The GRAVITY young stellar object survey: IV. The CO overtone emission in 51 Oph at sub-au scales
- 2021
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 645
-
Journal article (peer-reviewed)abstract
- Context. 51 Oph is a Herbig Ae/Be star that exhibits strong near-infrared CO ro-vibrational emission at 2.3 μm, most likely originating in the innermost regions of a circumstellar disc. Aims. We aim to obtain the physical and geometrical properties of the system by spatially resolving the circumstellar environment of the inner gaseous disc. Methods. We used the second-generation Very Large Telescope Interferometer instrument GRAVITY to spatially resolve the continuum and the CO overtone emission. We obtained data over 12 baselines with the auxiliary telescopes and derive visibilities, and the differential and closure phases as a function of wavelength. We used a simple local thermal equilibrium ring model of the CO emission to reproduce the spectrum and CO line displacements. Results. Our interferometric data show that the star is marginally resolved at our spatial resolution, with a radius of ∼10.58 ± 2.65R·. The K-band continuum emission from the disc is inclined by 63° ± 1°, with a position angle of 116° ± 1°, and 4 ± 0.8 mas (0.5 ± 0.1 au) across. The visibilities increase within the CO line emission, indicating that the CO is emitted within the dust-sublimation radius. By modelling the CO bandhead spectrum, we derive that the CO is emitted from a hot (T = 1900-2800 K) and dense (NCO = (0.9-9) × 1021 cm-2) gas. The analysis of the CO line displacement with respect to the continuum allows us to infer that the CO is emitted from a region 0.10 ± 0.02 au across, well within the dust-sublimation radius. The inclination and position angle of the CO line emitting region is consistent with that of the dusty disc. Conclusions. Our spatially resolved interferometric observations confirm the CO ro-vibrational emission within the dust-free region of the inner disc. Conventional disc models exclude the presence of CO in the dust-depleted regions of Herbig AeBe stars. Ad hoc models of the innermost disc regions, that can compute the properties of the dust-free inner disc, are therefore required.
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28. |
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29. |
- Vigan, A., et al.
(author)
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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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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 587
-
Journal article (peer-reviewed)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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30. |
- Zurlo, A., et al.
(author)
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First light of the VLT planet finder SPHERE III. New spectrophotometry and astrometry of the HR 8799 exoplanetary system
- 2016
-
In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 587
-
Journal article (peer-reviewed)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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31. |
- Amemiya, Chris T., et al.
(author)
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The African coelacanth genome provides insights into tetrapod evolution
- 2013
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 496:7445, s. 311-316
-
Journal article (peer-reviewed)abstract
- The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.
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32. |
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33. |
- Garatti, A. Caratti o., et al.
(author)
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The GRAVITY young stellar object survey: II. First spatially resolved observations of the CO bandhead emission in a high-mass YSO
- 2020
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 635
-
Journal article (peer-reviewed)abstract
- Context. The inner regions of the discs of high-mass young stellar objects (HMYSOs) are still poorly known due to the small angular scales and the high visual extinction involved. Aims. We deploy near-infrared spectro-interferometry to probe the inner gaseous disc in HMYSOs and investigate the origin and physical characteristics of the CO bandhead emission (2.3-2.4 m). Methods. We present the first GRAVITY/VLTI observations at high spectral (R = 4000) and spatial (mas) resolution of the CO overtone transitions in NGC2024 IRS 2. Results. The continuum emission is resolved in all baselines and is slightly asymmetric, displaying small closure phases (8). Our best ellipsoid model provides a disc inclination of 34 1, a disc major axis position angle (PA) of 166 1, and a disc diameter of 3:99 0:09 mas (or 1.69 0.04 au, at a distance of 423 pc). The small closure phase signals in the continuum are modelled with a skewed rim, originating from a pure inclination effect. For the first time, our observations spatially and spectrally resolve the first four CO bandheads. Changes in visibility, as well as differential and closure phases across the bandheads are detected. Both the size and geometry of the CO-emitting region are determined by fitting a bidimensional Gaussian to the continuum-compensated CO bandhead visibilities. The CO-emitting region has a diameter of 2.740:08 0:07 mas (1.16 0.03 au), and is located in the inner gaseous disc, well within the dusty rim, with inclination and PA matching the dusty disc geometry, which indicates that both dusty and gaseous discs are coplanar. Physical and dynamical gas conditions are inferred by modelling the CO spectrum. Finally, we derive a direct measurement of the stellar mass of M 14:7 M by combining our interferometric and spectral modelling results.
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34. |
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35. |
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36. |
- Sissa, E., et al.
(author)
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New disk discovered with VLT/SPHERE around the M star GSC 07396-00759
- 2018
-
In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 613
-
Journal article (peer-reviewed)abstract
- Debris disks are usually detected through the infrared excess over the photospheric level of their host star. The most favorable stars for disk detection are those with spectral types between A and K, while the statistics for debris disks detected around low-mass M-type stars is very low, either because they are rare or because they are more difficult to detect. Terrestrial planets, on the other hand, may be common around M-type stars. Here, we report on the discovery of an extended (likely) debris disk around the M-dwarf GSC 07396-00759. The star is a wide companion of the close accreting binary V4046 Sgr. The system probably is a member of the beta Pictoris Moving Group. We resolve the disk in scattered light, exploiting high-contrast, high-resolution imagery with the two near-infrared subsystems of the VLT/SPHERE instrument, operating in the YJ bands and the H2H3 doublet. The disk is clearly detected up to 1.5 '' (similar to 110 au) from the star and appears as a ring, with an inclination i similar to 83 degrees, and a peak density position at similar to 70 au. The spatial extension of the disk suggests that the dust dynamics is affected by a strong stellar wind, showing similarities with the AU Mic system that has also been resolved with SPHERE. The images show faint asymmetric structures at the widest separation in the northwest side. We also set an upper limit for the presence of giant planets to 2 M-J. Finally, we note that the 2 resolved disks around M-type stars of 30 such stars observed with SPHERE are viewed close to edge-on, suggesting that a significant population of debris disks around M dwarfs could remain undetected because of an unfavorable orientation.
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37. |
- Bonnefoy, M., et al.
(author)
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The GJ 504 system revisited Combining interferometric, radial velocity, and high contrast imaging data
- 2018
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 618
-
Journal article (peer-reviewed)abstract
- Context. The G-type star GJ504A is known to host a 3-35 M-Jup companion whose temperature, mass, and projected separation all contribute to making it a test case for planet formation theories and atmospheric models of giant planets and light brown dwarfs. Aims. We aim at revisiting the system age, architecture, and companion physical and chemical properties using new complementary interferometric, radial-velocity, and high-contrast imaging data. Methods. We used the CHARA interferometer to measure GJ504A's angular diameter and obtained an estimation of its radius in combination with the HIPPARCOS parallax. The radius was compared to evolutionary tracks to infer a new independent age range for the system. We collected dual imaging data with IRDIS on VLT/SPHERE to sample the near-infrared (1.02-2.25 mu m) spectral energy distribution (SED) of the companion. The SED was compared to five independent grids of atmospheric models (petitCODE, Exo-REM, BT-SETTL, Morley et al., and ATMO) to infer the atmospheric parameters of GJ 504b and evaluate model-to-model systematic errors. In addition, we used a specific model grid exploring the effect of different C/O ratios. Contrast limits from 2011 to 2017 were combined with radial velocity data of the host star through the MESS2 tool to define upper limits on the mass of additional companions in the system from 0.01 to 100 au. We used an MCMC fitting tool to constrain the companion's orbital parameters based on the measured astrometry, and dedicated formation models to investigate its origin. Results. We report a radius of 1.35 +/- 0.04 R-circle dot for GJ504A. The radius yields isochronal ages of 21 +/- 2 Myr or 4.0 +/- 1.8 Gyr for the system and line-of-sight stellar rotation axis inclination of 162.4(-4.3)(+3.8) degrees or 18.6(-3.8)(+4.3) degrees. We re-detect the companion in the Y2, Y3, J3, H2, and K1 dual-band images. The complete 1-4 mu m SED shape of GJ504b is best reproduced by T8-T9.5 objects with intermediate ages (<= 1.5Gyr), and/or unusual dusty atmospheres and/or super-solar metallicities. All atmospheric models yield T-eff = 550 +/- 50 K for GJ504b and point toward a low surface gravity (3.5-4.0 dex). The accuracy on the metallicity value is limited by model-to-model systematics; it is not degenerate with the C/O ratio. We derive log L/L-circle dot = 6.15 +/- 0.15 dex for the companion from the empirical analysis and spectral synthesis. The luminosity and T-eff yield masses of M = 1.3(-0.3)(+0.6) M-Jup and M = 23(-9)(+10) M-Jup for the young and old age ranges, respectively. The semi-major axis (sma) is above 27.8 au and the eccentricity is lower than 0.55. The posterior on GJ 504b's orbital inclination suggests a misalignment with the rotation axis of GJ 504A. We exclude additional objects (90% prob.) more massive than 2.5 and 30 M-Jup with semi-major axes in the range 0.01-80 au for the young and old isochronal ages, respectively. Conclusions. The mass and semi-major axis of GJ 504b are marginally compatible with a formation by disk-instability if the system is 4 Gyr old. The companion is in the envelope of the population of planets synthesized with our core-accretion model. Additional deep imaging and spectroscopic data with SPHERE and JWST should help to confirm the possible spin-orbit misalignment and refine the estimates on the companion temperature, luminosity, and atmospheric composition.
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38. |
- Faulx, M. D., et al.
(author)
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Obstructive sleep apnea and its management in patients with atrial fibrillation: An International Collaboration of Sleep Apnea Cardiovascular Trialists (INCOSACT) global survey of practicing cardiologists
- 2022
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In: International journal of cardiology: Heart and Vasculature (IJCHA). - : Elsevier BV. - 2352-9067. ; 42
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Journal article (peer-reviewed)abstract
- Background: Among international cardiologists it is unclear whether equipoise exists regarding the benefit of diagnosing and managing obstructive sleep apnea (OSA) to improve atrial fibrillation (AF) outcomes and whether clinical practice and equipoise are linked. Methods: Between January 2019 and June 2020 we distributed a web-based 12-question survey regarding OSA and AF management to practicing cardiologists in 16 countries. Results: The United States, Japan, Sweden, and Turkey accounted for two-thirds of responses. 863 cardiologists responded; half were general cardiologists, a quarter electrophysiologists. Responses regarding treating OSA with CPAP to improve AF endpoints were mixed. 33% of respondents referred AF patients for OSA screening. OSA was diagnosed in 48% of referred patients and continuous positive airway pressure (CPAP) was prescribed for 59% of them. Nearly 70% of respondents believed randomized controlled trials (RCTs) of OSA treatment in AF patients were necessary and indicated willingness to contribute to such trials. Conclusions: There was no clinical equipoise among surveyed cardiologists; a majority expressed certainty that combined OSA and AF treatment is superior to AF treatment alone for improving AF outcomes. However, a minority of surveyed cardiologists referred AF patients for OSA testing, and while half of screened AF patients had OSA, CPAP was prescribed in little more than half of them, reflecting the view that better clinical trial evidence is needed to support this practice. Our results underscore the need for larger, multi-national prospective studies of OSA treatment and AF outcomes to inform more uniform society guideline recommendations.
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39. |
- Hamdi, Yosr, et al.
(author)
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Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression : identification of a modifier of breast cancer risk at locus 11q22.3
- 2017
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In: Breast Cancer Research and Treatment. - : Springer Science and Business Media LLC. - 0167-6806 .- 1573-7217. ; 161:1, s. 117-134
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Journal article (peer-reviewed)abstract
- Purpose: Cis-acting regulatory SNPs resulting in differential allelic expression (DAE) may, in part, explain the underlying phenotypic variation associated with many complex diseases. To investigate whether common variants associated with DAE were involved in breast cancer susceptibility among BRCA1 and BRCA2 mutation carriers, a list of 175 genes was developed based of their involvement in cancer-related pathways. Methods: Using data from a genome-wide map of SNPs associated with allelic expression, we assessed the association of ~320 SNPs located in the vicinity of these genes with breast and ovarian cancer risks in 15,252 BRCA1 and 8211 BRCA2 mutation carriers ascertained from 54 studies participating in the Consortium of Investigators of Modifiers of BRCA1/2. Results: We identified a region on 11q22.3 that is significantly associated with breast cancer risk in BRCA1 mutation carriers (most significant SNP rs228595 p = 7 × 10−6). This association was absent in BRCA2 carriers (p = 0.57). The 11q22.3 region notably encompasses genes such as ACAT1, NPAT, and ATM. Expression quantitative trait loci associations were observed in both normal breast and tumors across this region, namely for ACAT1, ATM, and other genes. In silico analysis revealed some overlap between top risk-associated SNPs and relevant biological features in mammary cell data, which suggests potential functional significance. Conclusion: We identified 11q22.3 as a new modifier locus in BRCA1 carriers. Replication in larger studies using estrogen receptor (ER)-negative or triple-negative (i.e., ER-, progesterone receptor-, and HER2-negative) cases could therefore be helpful to confirm the association of this locus with breast cancer risk.
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40. |
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41. |
- Thomas, Minta, et al.
(author)
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Combining Asian and European genome-wide association studies of colorectal cancer improves risk prediction across racial and ethnic populations
- 2023
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Journal article (peer-reviewed)abstract
- Polygenic risk scores (PRS) have great potential to guide precision colorectal cancer (CRC) prevention by identifying those at higher risk to undertake targeted screening. However, current PRS using European ancestry data have sub-optimal performance in non-European ancestry populations, limiting their utility among these populations. Towards addressing this deficiency, we expand PRS development for CRC by incorporating Asian ancestry data (21,731 cases; 47,444 controls) into European ancestry training datasets (78,473 cases; 107,143 controls). The AUC estimates (95% CI) of PRS are 0.63(0.62-0.64), 0.59(0.57-0.61), 0.62(0.60-0.63), and 0.65(0.63-0.66) in independent datasets including 1681-3651 cases and 8696-115,105 controls of Asian, Black/African American, Latinx/Hispanic, and non-Hispanic White, respectively. They are significantly better than the European-centric PRS in all four major US racial and ethnic groups (p-values < 0.05). Further inclusion of non-European ancestry populations, especially Black/African American and Latinx/Hispanic, is needed to improve the risk prediction and enhance equity in applying PRS in clinical practice.
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42. |
- Thomas, M, et al.
(author)
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Combining Asian-European Genome-Wide Association Studies of Colorectal Cancer Improves Risk Prediction Across Race and Ethnicity
- 2023
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In: medRxiv : the preprint server for health sciences. - : Cold Spring Harbor Laboratory.
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Journal article (other academic/artistic)abstract
- Polygenic risk scores (PRS) have great potential to guide precision colorectal cancer (CRC) prevention by identifying those at higher risk to undertake targeted screening. However, current PRS using European ancestry data have sub-optimal performance in non-European ancestry populations, limiting their utility among these populations. Towards addressing this deficiency, we expanded PRS development for CRC by incorporating Asian ancestry data (21,731 cases; 47,444 controls) into European ancestry training datasets (78,473 cases; 107,143 controls). The AUC estimates (95% CI) of PRS were 0.63(0.62-0.64), 0.59(0.57-0.61), 0.62(0.60-0.63), and 0.65(0.63-0.66) in independent datasets including 1,681-3,651 cases and 8,696-115,105 controls of Asian, Black/African American, Latinx/Hispanic, and non-Hispanic White, respectively. They were significantly better than the European-centric PRS in all four major US racial and ethnic groups (p-values<0.05). Further inclusion of non-European ancestry populations, especially Black/African American and Latinx/Hispanic, is needed to improve the risk prediction and enhance equity in applying PRS in clinical practice.
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43. |
- Armstrong, A J, et al.
(author)
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Long-term Survival and Biomarker Correlates of Tasquinimod Efficacy in a Multicenter Randomized Study of Men with Minimally Symptomatic Metastatic Castration-Resistant Prostate Cancer.
- 2013
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In: Clinical Cancer Research. - 1078-0432 .- 1557-3265. ; 19:24, s. 6891-6901
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Journal article (peer-reviewed)abstract
- PURPOSE: Tasquinimod (Active Biotech) is an oral immunomodulatory, anti-angiogenic, and anti-metastatic agent that delayed metastatic disease progression in a randomized placebo-controlled phase II trial in men with metastatic castration-resistant prostate cancer (mCRPC). Here, we report long-term survival with biomarker correlates from this trial.EXPERIMENTAL DESIGN: Two hundred and one (134 tasquinimod and 67 placebo) men with mCRPC were evaluated. Forty-one men randomized to placebo crossed over to tasquinimod. Survival data were collected with a median follow-up time of 37 months. Exploratory biomarker studies at baseline and over time were collected to evaluate potential mechanism-based correlates with tasquinimod efficacy including progression-free survival (PFS) and overall survival (OS).RESULTS: With 111 mortality events, median OS was 33.4 months for tasquinimod versus 30.4 months for placebo overall, and 34.2 versus 27.1 months in men with bone metastases (n = 136), respectively. Multivariable analysis demonstrated an adjusted HR of 0.52 [95% confidence interval (CI), 0.35-0.78; P = 0.001] for PFS and 0.64 (95% CI, 0.42-0.97; P = 0.034) for OS, favoring tasquinimod. Time-to-symptomatic progression was improved with tasquinimod (P = 0.039, HR = 0.42). Toxicities tended to be mild in nature and improved over time. Biomarker analyses suggested a favorable impact on bone alkaline phosphatase and lactate dehydrogenase (LDH) over time and a transient induction of inflammatory biomarkers, VEGF-A, and thrombospondin-1 levels with tasquinimod. Baseline levels of thrombospondin-1 less than the median were predictive of treatment benefit.CONCLUSIONS: The survival observed in this trial of men with minimally symptomatic mCRPC suggests that the prolongation in PFS with tasquinimod may lead to a survival advantage in this setting, particularly among men with skeletal metastases, and has a favorable risk:benefit ratio.
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44. |
- Braasch, Ingo, et al.
(author)
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The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
- 2016
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 48:4, s. 427-437
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Journal article (peer-reviewed)abstract
- To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
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45. |
- Gratton, R., et al.
(author)
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Searching for the near-infrared counterpart of Proxima c using multi-epoch high-contrast SPHERE data at VLT
- 2020
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 638
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Journal article (peer-reviewed)abstract
- Context. Proxima Centauri is the closest star to the Sun and it is known to host an Earth-like planet in its habitable zone; very recently a second candidate planet was proposed based on radial velocities. At quadrature, the expected projected separation of this new candidate is larger than 1 arcsec, making it a potentially interesting target for direct imaging.Aims. While identification of the optical counterpart of this planet is expected to be very difficult, successful identification would allow for a detailed characterization of the closest planetary system.Methods. We searched for a counterpart in SPHERE images acquired over four years through the SHINE survey. In order to account for the expected large orbital motion of the planet, we used a method that assumes the circular orbit obtained from radial velocities and exploits the sequence of observations acquired close to quadrature in the orbit. We checked this with a more general approach that considers Keplerian motion, called K-stacker.Results. We did not obtain a clear detection. The best candidate has signal-to-noise ratio (S/N) = 6.1 in the combined image. A statistical test suggests that the probability that this detection is due to random fluctuation of noise is <1%, but this result depends on the assumption that the distribution of noise is uniform over the image, a fact that is likely not true. The position of this candidate and the orientation of its orbital plane fit well with observations in the ALMA 12 m array image. However, the astrometric signal expected from the orbit of the candidate we detected is 3 away from the astrometric motion of Proxima as measured from early Gaia data. This, together with the unexpectedly high flux associated with our direct imaging detection, means we cannot confirm that our candidate is indeed Proxima c.Conclusions. On the other hand, if confirmed, this would be the first observation in imaging of a planet discovered from radial velocities and the second planet (after Fomalhaut b) of reflecting circumplanetary material. Further confirmation observations should be done as soon as possible.
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46. |
- Mueller, A., et al.
(author)
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Orbital and atmospheric characterization of the planet within the gap of the PDS70 transition disk
- 2018
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 617
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Journal article (peer-reviewed)abstract
- Context. The observation of planets in their formation stage is a crucial but very challenging step in understanding when, how, and where planets form. PDS 70 is a young pre-main sequence star surrounded by a transition disk, in the gap of which a planetary-mass companion has recently been discovered. This discovery represents the first robust direct detection of such a young planet, possibly still at the stage of formation.Aims. We aim to characterize the orbital and atmospheric properties of PDS 70 b, which was first identified on May 2015 in the course of the SHINE survey with SPHERE, the extreme adaptive-optics instrument at the VLT.Methods. We obtained new deep SPHERE/IRDIS imaging and SPHERE/IFS spectroscopic observations of PDS 70 b. The astrometric baseline now covers 6 yr, which allowed us to perform an orbital analysis. For the first time, we present spectrophotometry of the young planet which covers almost the entire near-infrared range (0.96-3.8 mu m). We use different atmospheric models covering a large parameter space in temperature, log g, chemical composition, and cloud properties to characterize the properties of the atmosphere of PDS 70 b.Results. PDS 70 b is most likely orbiting the star on a circular and disk coplanar orbit at similar to 22 au inside the gap of the disk. We find a range of models that can describe the spectrophotometric data reasonably well in the temperature range 1000-1600 K and log g no larger than 3.5 dex. The planet radius covers a relatively large range between 1.4 and 3.7 R-J with the larger radii being higher than expected from planet evolution models for the age of the planet of 5.4 Myr. Conclusions. This study provides a comprehensive data set on the orbital motion of PDS 70 b, indicating a circular orbit and a motion coplanar with the disk. The first detailed spectral energy distribution of PDS 70 b indicates a temperature typical of young giant planets. The detailed atmospheric analysis indicates that a circumplanetary disk may contribute to the total planetflux.
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47. |
- Nounu, Aayah, et al.
(author)
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A combined proteomics and mendelian randomization approach to investigate the effects of aspirin-targeted proteins on colorectal cancer
- 2021
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In: Cancer Epidemiology, Biomarkers and Prevention. - : Elsevier. - 1055-9965 .- 1538-7755. ; 30:3, s. 564-575
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Journal article (peer-reviewed)abstract
- Background: Evidence for aspirin’s chemopreventative properties on colorectal cancer (CRC) is substantial, but its mechanism of action is not well-understood. We combined a proteomic approach with Mendelian randomization (MR) to identify possible new aspirin targets that decrease CRC risk.Methods: Human colorectal adenoma cells (RG/C2) were treated with aspirin (24 hours) and a stable isotope labeling with amino acids in cell culture (SILAC) based proteomics approach identified altered protein expression. Protein quantitative trait loci (pQTLs) from INTERVAL (N ¼ 3,301) and expression QTLs (eQTLs) from the eQTLGen Consortium (N ¼ 31,684) were used as genetic proxies for protein and mRNA expression levels. Two-sample MR of mRNA/protein expression on CRC risk was performed using eQTL/pQTL data combined with CRC genetic summary data from the Colon Cancer Family Registry (CCFR), Colorectal Transdisciplinary (CORECT), Genetics and Epidemiology of Colorectal Cancer (GECCO) consortia and UK Biobank (55,168 cases and 65,160 controls).Results: Altered expression was detected for 125/5886 proteins. Of these, aspirin decreased MCM6, RRM2, and ARFIP2 expression, and MR analysis showed that a standard deviation increase in mRNA/protein expression was associated with increased CRC risk (OR: 1.08, 95% CI, 1.03–1.13; OR: 3.33, 95% CI, 2.46–4.50; and OR: 1.15, 95% CI, 1.02–1.29, respectively).Conclusions: MCM6 and RRM2 are involved in DNA repair whereby reduced expression may lead to increased DNA aberrations and ultimately cancer cell death, whereas ARFIP2 is involved in actin cytoskeletal regulation, indicating a possible role in aspirin’s reduction of metastasis.Impact: Our approach has shown how laboratory experiments and population-based approaches can combine to identify aspirin-targeted proteins possibly affecting CRC risk.
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48. |
- Nounu, Aayah, et al.
(author)
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Salicylic Acid and Risk of Colorectal Cancer : A Two-Sample Mendelian Randomization Study
- 2021
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In: Nutrients. - : MDPI. - 2072-6643. ; 13:11
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Journal article (peer-reviewed)abstract
- Salicylic acid (SA) has observationally been shown to decrease colorectal cancer (CRC) risk. Aspirin (acetylsalicylic acid, that rapidly deacetylates to SA) is an effective primary and secondary chemopreventive agent. Through a Mendelian randomization (MR) approach, we aimed to address whether levels of SA affected CRC risk, stratifying by aspirin use. A two-sample MR analysis was performed using GWAS summary statistics of SA (INTERVAL and EPIC-Norfolk, N = 14,149) and CRC (CCFR, CORECT, GECCO and UK Biobank, 55,168 cases and 65,160 controls). The DACHS study (4410 cases and 3441 controls) was used for replication and stratification of aspirin-use. SNPs proxying SA were selected via three methods: (1) functional SNPs that influence the activity of aspirin-metabolising enzymes; (2) pathway SNPs present in enzymes' coding regions; and (3) genome-wide significant SNPs. We found no association between functional SNPs and SA levels. The pathway and genome-wide SNPs showed no association between SA and CRC risk (OR: 1.03, 95% CI: 0.84-1.27 and OR: 1.08, 95% CI: 0.86-1.34, respectively). Results remained unchanged upon aspirin use stratification. We found little evidence to suggest that an SD increase in genetically predicted SA protects against CRC risk in the general population and upon stratification by aspirin use.
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49. |
- Peretti, S., et al.
(author)
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Orbital and spectral analysis of the benchmark brown dwarf HD 4747B
- 2019
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 631
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Journal article (peer-reviewed)abstract
- Context. The study of high-contrast imaged brown dwarfs and exoplanets depends strongly on evolutionary models. To estimate the mass of a directly imaged substellar object, its extracted photometry or spectrum is used and adjusted with model spectra together with the estimated age of the system. These models still need to be properly tested and constrained. HD 4747B is a brown dwarf close to the H burning mass limit, orbiting a nearby (d = 19.25 +/- 0.58 pc), solar-type star (G9V); it has been observed with the radial velocity method for over almost two decades. Its companion was also recently detected by direct imaging, allowing a complete study of this particular object.Aims. We aim to fully characterize HD 4747B by combining a well-constrained dynamical mass and a study of its observed spectral features in order to test evolutionary models for substellar objects and to characterize its atmosphere.Methods. We combined the radial velocity measurements of High Resolution Echelle Spectrometer (HIRES) and CORALIE taken over two decades and high-contrast imaging of several epochs from NACO, NIRC2, and SPHERE to obtain a dynamical mass. From the SPHERE data we obtained a low-resolution spectrum of the companion from Y to H band, and two narrow band-width photometric measurements in the K band. A study of the primary star also allowed us to constrain the age of the system and its distance.Results. Thanks to the new SPHERE epoch and NACO archival data combined with previous imaging data and high-precision radial velocity measurements, we were able to derive a well-constrained orbit. The high eccentricity (e = 0.7362 +/- 0.0025) of HD 4747B is confirmed, and the inclination and the semi-major axis are derived (i = 47.3 +/- 1.6 degrees, a = 10.01 +/- 0.21 au). We derive a dynamical mass of m(B) = 70.0 +/- 1.6 M-Jup, which is higher than a previous study but in better agreement with the models. By comparing the object with known brown dwarfs spectra, we derive a spectral type of L9 and an effective temperature of 1350 +/- 50 K. With a retrieval analysis we constrain the oxygen and carbon abundances and compare them with the values from the HR 8799 planets.
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50. |
- Bouckaert, R., et al.
(author)
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BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
- 2019
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In: Plos Computational Biology. - : Public Library of Science (PLoS). - 1553-7358. ; 15:4
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Journal article (peer-reviewed)abstract
- Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release. Author summary Bayesian phylogenetic inference methods have undergone considerable development in recent years, and joint modelling of rich evolutionary data, including genomes, phenotypes and fossil occurrences is increasingly common. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing scientific software is increasingly crucial to advancement in many fields of biology. The challenges range from practical software development and engineering, distributed team coordination, conceptual development and statistical modelling, to validation and testing. BEAST 2 is one such computational software platform for phylogenetics, population genetics and phylodynamics, and was first announced over 4 years ago. Here we describe the full range of new tools and models available on the BEAST 2.5 platform, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics.
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