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- Imanishi, T., et al.
(författare)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
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Tidskriftsartikel (refereegranskat)abstract
- The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
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- Mizuki, T., et al.
(författare)
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Orbital Characterization of GJ1108A System, and Comparison of Dynamical Mass with Model-derived Mass for Resolved Binaries
- 2018
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 865:2
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Tidskriftsartikel (refereegranskat)abstract
- We report an orbital characterization of GJ1108Aab that is a low-mass binary system in the pre-main-sequence phase. Via the combination of astrometry using adaptive optics and radial velocity measurements, an eccentric orbital solution of e = 0.63 is obtained, which might be induced by the Kozai-Lidov mechanism with a widely separated GJ1108B system. Combined with several observed properties, we confirm that the system is indeed young. Columba is the most probable moving group, to which the GJ1108A system belongs, although its membership to the group has not been established. If the age of Columba is assumed for GJ1108A, the dynamical masses of both GJ1108Aa and GJ1108Ab (M-dynamical,M-GJ1108Aa= 0.72 +/- 0.04 M-circle dot and M-dynamical,M-GJ1108Ab = 0.30 +/- 0.03 M-circle dot) are more massive than what an evolutionary model predicts based on the age and luminosities. We consider that the discrepancy in mass comparison can be attributed to an age uncertainty; the system is likely older than stars in Columba, and effects that are not implemented in classical models such as accretion history and magnetic activity are not preferred to explain the mass discrepancy. We also discuss the performance of the evolutionary model by compiling similar low-mass objects in the evolutionary state based on the literature. Consequently, it is suggested that the current model on average reproduces the mass of resolved low-mass binaries without any significant offsets.
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- Akiyama, E., et al.
(författare)
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DISCOVERY OF A DISK GAP CANDIDATE AT 20 AU IN TW HYDRAE
- 2015
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Ingår i: Astrophysical Journal Letters. - 2041-8205 .- 2041-8213. ; 802:2
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Tidskriftsartikel (refereegranskat)abstract
- We present a new Subaru/HiCIAO high-contrast H-band polarized intensity (PI) image of a nearby transitional disk associated with TW Hydrae. The scattered light from the disk was detected from 0 ''.2 to 1 ''.5 (11-81 AU) and the PI image shows a clear axisymmetric depression in PI at similar to 0 ''.4 (similar to 20 AU) from the central star, similar to the similar to 80 AU gap previously reported from Hubble Space Telescope images. The azimuthal PI profile also shows that the disk beyond 0 ''.2 is almost axisymmetric. We discuss two possible scenarios explaining the origin of the PI depression: (1) a gap structure may exist at similar to 20 AU from the central star because of a shallow slope seen in the PI profile, and (2) grain growth may be occurring in the inner region of the disk. Multi-band observations at near-infrared and millimeter/submillimeter wavelengths play a complementary role in investigating dust opacity and may help reveal the origin of the gap more precisely.
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- Grady, C., et al.
(författare)
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The outer disks of Herbig stars from the UV to NIR
- 2015
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Ingår i: Astrophysics and Space Science. - : Springer Science and Business Media LLC. - 0004-640X .- 1572-946X. ; 355:2, s. 253-266
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Forskningsöversikt (refereegranskat)abstract
- Spatially-resolved imaging of Herbig stars and related objects began with HST, but intensified with commissioning of high-contrast imagers on 8-m class telescopes. The bulk of the data taken from the ground have been polarized intensity imagery at H-band, with the majority of the sources observed as part of the Strategic Exploration of Exoplanets and Disks with Subaru (SEEDS) survey. Sufficiently many systems have been imaged that we discuss disk properties in scattered, polarized light in terms of groups defined by the IR spectral energy distribution. We find novel phenomena in many of the disks, including spiral density waves, and discuss the disks in terms of clearing mechanisms. Some of the disks have sufficient data to map the dust and gas components, including water ice dissociation products.
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- Helminiak, K. G., et al.
(författare)
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SEEDS DIRECT IMAGING OF THE RV-DETECTED COMPANION TO V450 ANDROMEDAE, AND CHARACTERIZATION OF THE SYSTEM
- 2016
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 832:1
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Tidskriftsartikel (refereegranskat)abstract
- We report the direct imaging detection of a low-mass companion to a young, moderately active star V450. And, that was previously identified with the radial velocity (RV) method. The companion was found in high-contrast images obtained with the Subaru Telescope equipped with the HiCIAO camera and AO188 adaptive optics system. From the public ELODIE and SOPHIE archives we extracted available high-resolution spectra and RV measurements, along with RVs from the Lick planet search program. We combined our multi-epoch astrometry with these archival, partially unpublished RVs, and found that the companion is a low-mass star, not a brown dwarf, as previously suggested. We found the best-fitting dynamical masses to be m(1) = 1.141(-0.091)(+0.037)and m(2) = 0.279(-0.020)(+0.023) M-circle dot. We also performed spectral analysis of the SOPHIE spectra with the iSpec code. Hipparcos time-series photometry shows a periodicity of P = 5.743 day, which is also seen in the SOPHIE spectra as an RV modulation of the star A. We interpret it as being caused by spots on the stellar surface, and the star to be rotating with the given period. From the rotation and level of activity, we found that the system is 380(-100)(+220) Myr old, consistent with an isochrone analysis (220(-90)(+2120) Myr). This work may serve as a test case for future studies of low-mass stars, brown dwarfs, and exoplanets by combination of RV and direct imaging data.
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| 10. |
- Asensio-Torres, Ruben, et al.
(författare)
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Polarimetry and flux distribution in the debris disk around HD 32297
- 2016
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 593
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Tidskriftsartikel (refereegranskat)abstract
- We present high-contrast angular differential imaging (ADI) observations of the debris disk around HD32297 in H-band, as well as the first polarimetric images for this system in polarized differential imaging (PDI) mode with Subaru/HICIAO. In ADI, we detect the nearly edge-on disk at > 5 sigma levels from similar to 0.45 '' to similar to 1.7 '' (50-192AU) from the star and recover the spine deviation from the midplane already found in previous works. We also find for the first time imaging and surface brightness (SB) indications for the presence of a gapped structure on both sides of the disk at distances of similar to 0.75 '' (NE side) and similar to 0.65 '' (SW side). Global forward-modelling work delivers a best-fit model disk and well-fitting parameter intervals that essentially match previous results, with high-forward scattering grains and a ring located at 110AU. However, this single ring model cannot account for the gapped structure seen in our SB profiles. We create simple double ring models and achieve a satisfactory fit with two rings located at 60 and 95AU, respectively, low-forward scattering grains and very sharp inner slopes. In polarized light we retrieve the disk extending from similar to 0.25-1.6 '', although the central region is quite noisy and high S/N are only found in the range similar to 0.75-1.2 ''. The disk is polarized in the azimuthal direction, as expected, and the departure from the midplane is also clearly observed. Evidence for a gapped scenario is not found in the PDI data. We obtain a linear polarization degree of the grains that increases from similar to 10% at 0.55 '' to similar to 25% at 1.6 ''. The maximum is found at scattering angles of similar to 90 degrees, either from the main components of the disk or from dust grains blown out to larger radii.
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