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1.
  • Abolfathi, Bela, et al. (creator_code:aut_t)
  • The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
  • 2018
  • record:In_t: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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2.
  • Blanton, Michael R., et al. (creator_code:aut_t)
  • Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
  • 2017
  • record:In_t: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
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3.
  • Hess, Timo, et al. (creator_code:aut_t)
  • Dissecting the genetic heterogeneity of gastric cancer
  • 2023
  • record:In_t: EBioMedicine. - : Elsevier. - 2352-3964. ; 92
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Background: Gastric cancer (GC) is clinically heterogenous according to location (cardia/non-cardia) and histopathology (diffuse/intestinal). We aimed to characterize the genetic risk architecture of GC according to its subtypes. Another aim was to examine whether cardia GC and oesophageal adenocarcinoma (OAC) and its precursor lesion Barrett's oesophagus (BO), which are all located at the gastro-oesophageal junction (GOJ), share polygenic risk architecture.Methods: We did a meta-analysis of ten European genome-wide association studies (GWAS) of GC and its subtypes. All patients had a histopathologically confirmed diagnosis of gastric adenocarcinoma. For the identification of risk genes among GWAS loci we did a transcriptome-wide association study (TWAS) and expression quantitative trait locus (eQTL) study from gastric corpus and antrum mucosa. To test whether cardia GC and OAC/BO share genetic aetiology we also used a European GWAS sample with OAC/BO.Findings: Our GWAS consisting of 5816 patients and 10,999 controls highlights the genetic heterogeneity of GC according to its subtypes. We newly identified two and replicated five GC risk loci, all of them with subtype-specific association. The gastric transcriptome data consisting of 361 corpus and 342 antrum mucosa samples revealed that an upregulated expression of MUC1, ANKRD50, PTGER4, and PSCA are plausible GC-pathomechanisms at four GWAS loci. At another risk locus, we found that the blood-group 0 exerts protective effects for non-cardia and diffuse GC, while blood-group A increases risk for both GC subtypes. Furthermore, our GWAS on cardia GC and OAC/BO (10,279 patients, 16,527 controls) showed that both cancer entities share genetic aetiology at the polygenic level and identified two new risk loci on the single-marker level.Interpretation: Our findings show that the pathophysiology of GC is genetically heterogenous according to location and histopathology. Moreover, our findings point to common molecular mechanisms underlying cardia GC and OAC/BO. 
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4.
  • Akiyama, Eiji, et al. (creator_code:aut_t)
  • SPIRAL STRUCTURE AND DIFFERENTIAL DUST SIZE DISTRIBUTION IN THE LkH alpha 330 DISK
  • 2016
  • record:In_t: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 152:6
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Dust trapping accelerates the coagulation of dust particles, and, thus, it represents an initial step toward the formation of planetesimals. We report H-band (1.6 mu m) linear polarimetric observations and 0.87 mm interferometric continuum observations toward a transitional disk around LkH alpha 330. As a. result, a pair of spiral arms were detected in the H-band emission, and an asymmetric (potentially arm-like) structure was detected in the 0.87 mm continuum emission. We discuss the origin of the spiral arm and the asymmetric structure. and suggest that a massive unseen planet is the most plausible explanation. The possibility of dust trapping and grain growth causing the asymmetric structure was also investigated through the opacity index (beta) by plotting the observed spectral energy distribution slope between 0.87 mm from our Submillimeter Array observation and 1.3 mm from literature. The results imply that grains are indistinguishable from interstellar medium-like dust in the east side (beta = 2.0 +/- 0.5) but are much smaller in the west side beta = 0.7(-0.4)(+0.5), indicating differential dust size distribution between the two sides of the disk. Combining the results of near-infrared and submillimeter observations, we conjecture that the spiral arms exist at the upper surface and an asymmetric structure resides in the disk interior. Future observations at centimeter wavelengths and differential polarization imaging in other bands (Y-K) with extreme AO imagers are required to understand how large dust grains form and to further explore the dust distribution in the disk.
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5.
  • Mayama, Satoshi, et al. (creator_code:aut_t)
  • Subaru Near-infrared Imaging Polarimetry of Misaligned Disks around the SR 24 Hierarchical Triple System
  • 2020
  • record:In_t: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 159:1
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The SR 24 multistar system hosts both circumprimary and circumsecondary disks, which are strongly misaligned with each other. The circumsecondary disk is circumbinary in nature. Interestingly, both disks are interacting, and they possibly rotate in opposite directions. To investigate the nature of this unique twin disk system, we present 01 resolution near-infrared polarized intensity images of the circumstellar structures around SR 24, obtained with HiCIAO mounted on the Subaru 8.2 m telescope. Both the circumprimary disk and the circumsecondary disk are resolved and have elongated features. While the position angle of the major axis and radius of the near-IR (NIR) polarization disk around SR 24S are 55° and 137 au, respectively, those around SR 24N are 110° and 34 au, respectively. With regard to overall morphology, the circumprimary disk around SR 24S shows strong asymmetry, whereas the circumsecondary disk around SR 24N shows relatively strong symmetry. Our NIR observations confirm the previous claim that the circumprimary and circumsecondary disks are misaligned from each other. Both the circumprimary and circumsecondary disks show similar structures in 12CO observations in terms of its size and elongation direction. This consistency is because both NIR and 12CO are tracing surface layers of the flared disks. As the radius of the polarization disk around SR 24N is roughly consistent with the size of the outer Roche lobe, it is natural to interpret the polarization disk around SR 24N as a circumbinary disk surrounding the SR 24Nb–Nc system.
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6.
  • Zhang, Rong, et al. (creator_code:aut_t)
  • ISL1 is a major susceptibility gene for classic bladder exstrophy and a regulator of urinary tract development
  • 2017
  • record:In_t: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Previously genome-wide association methods in patients with classic bladder exstrophy (CBE) found association with ISL1, a master control gene expressed in pericloacal mesenchyme. This study sought to further explore the genetics in a larger set of patients following-up on the most promising genomic regions previously reported. Genotypes of 12 markers obtained from 268 CBE patients of Australian, British, German Italian, Spanish and Swedish origin and 1,354 ethnically matched controls and from 92 CBE case-parent trios from North America were analysed. Only marker rs6874700 at the ISL1 locus showed association (p = 2.22 x 10(-08)). A meta-analysis of rs6874700 of our previous and present study showed a p value of 9.2 x 10(-19). Developmental biology models were used to clarify the location of ISL1 activity in the forming urinary tract. Genetic lineage analysis of Isl1-expressing cells by the lineage tracer mouse model showed Isl1-expressing cells in the urinary tract of mouse embryos at E10.5 and distributed in the bladder at E15.5. Expression of isl1 in zebrafish larvae staged 48 hpf was detected in a small region of the developing pronephros. Our study supports ISL1 as a major susceptibility gene for CBE and as a regulator of urinary tract development.
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7.
  • Chang, Dan, et al. (creator_code:aut_t)
  • The evolutionary and phylogeographic history of woolly mammoths : a comprehensive mitogenomic analysis
  • 2017
  • record:In_t: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.
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8.
  • Currie, Thayne, et al. (creator_code:aut_t)
  • SCExAO/CHARIS Direct Imaging Discovery of a 20 au Separation, Low-mass Ratio Brown Dwarf Companion to an Accelerating Sun-like Star
  • 2020
  • record:In_t: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8205 .- 2041-8213. ; 904:2
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • We present the direct imaging discovery of a substellar companion to the nearby Sun-like star, HD 33632 Aa, at a projected separation of similar to 20 au, obtained with SCExAO/CHARIS integral field spectroscopy complemented by Keck/NIRC2 thermal infrared imaging. The companion, HD 33632 Ab, induces a 10.5 sigma astrometric acceleration on the star as detected with the Gaia and Hipparcos satellites. SCExAO/CHARIS JHK (1.1-2.4 mu m) spectra and Keck/NIRC2 L-p (3.78 mu m) photometry are best matched by a field L/T transition object: an older, higher-gravity, and less dusty counterpart to HR 8799 cde. Combining our astrometry with Gaia/Hipparcos data and archival Lick Observatory radial velocities, we measure a dynamical mass of 46.4 8 M-J and an eccentricity of e < 0.46 at 95% confidence. HD 33632 Ab's mass and mass ratio (4.0% 0.7%) are comparable to the low-mass brown dwarf GJ 758 B and intermediate between the more massive brown dwarf HD 19467 B and the (near-)planet-mass companions to HR 2562 and GJ 504. Using Gaia to select for direct imaging observations with the newest extreme adaptive optics systems can reveal substellar or even planet-mass companions on solar system-like scales at an increased frequency compared to blind surveys.
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9.
  • Currie, Thayne, et al. (creator_code:aut_t)
  • SCExAO/CHARIS Near-infrared Direct Imaging, Spectroscopy, and Forward-Modeling of kappa And b : A Likely Young, Low-gravity Superjovian Companion
  • 2018
  • record:In_t: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 156:6
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • We present SCExAO/CHARIS high-contrast imaging/JHK integral field spectroscopy of kappa And b, a directly imaged low-mass companion orbiting a nearby B9V star. We detect kappa And b at a high signal-to-noise ratio and extract high-precision spectrophotometry using a new forward-modeling algorithm for (A-)LOCI complementary to KLIP-FM developed by Pueyo et al. kappa And b's spectrum best resembles that of a low-gravity LO-L1 dwarf (L0-L1 gamma). Its spectrum and luminosity are very well matched by 2MASS J0141-4633 and several other 12.5-15 M-J free-floating members of the 40 Myr old Tuc-Hor Association, consistent with a system age derived from recent interferometric results for the primary, a companion mass at/near the deuterium-burning limit (13(-2)(+12) M-J), and a companion-to-primary mass ratio characteristic of other directly imaged planets (q similar to 0.0051(-0.001)(+0.005)). We did not unambiguously identify additional, more closely orbiting companions brighter and more massive than kappa And b down to p similar to 0.'' 3 (15 au). SCExAO/CHARIS and complementary Keck/NIRC2 astrometric points reveal clockwise orbital motion. Modeling points toward a likely eccentric orbit: a subset of acceptable orbits include those that are aligned with the star's rotation axis. However, kappa And b's semimajor axis is plausibly larger than 55 au and in a region where disk instability could form massive companions. Deeper high-contrast imaging of kappa And and low-resolution spectroscopy from extreme adaptive optics systems such as SCExAO/CHARIS and higher-resolution spectroscopy from Keck/OSIRIS or, later, IRIS on the Thirty Meter Telescope could help to clarify kappa And b's chemistry and whether its spectrum provides an insight into its formation environment.
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10.
  • Currie, Thayne, et al. (creator_code:aut_t)
  • Subaru/SCExAO First-light Direct Imaging of a Young Debris Disk around HD 36546
  • 2017
  • record:In_t: Astrophysical Journal Letters. - 2041-8205 .- 2041-8213. ; 836:1
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • We present H-band scattered light imaging of a bright debris disk around the A0 star HD 36546 obtained from the Subaru Coronagraphic Extreme Adaptive Optics (SCExAO) system with data recorded by the HiCIAO camera using the vector vortex coronagraph. SCExAO traces the disk from r similar to 0.3 to r similar to 1 (34-114 au). The disk is oriented in a near east-west direction (PA similar to 75 degrees), is inclined by i similar to 70 degrees-75 degrees, and is strongly forward-scattering (g > 0.5). It is an extended disk rather than a sharp ring; a second, diffuse dust population extends from the disk's eastern side. While HD 36546 intrinsic properties are consistent with a wide age range (t similar to 1-250 Myr), its kinematics and analysis of coeval stars suggest a young age (3-10 Myr) and a possible connection to Taurus-Auriga's star formation history. SCExAO's planet-to-star contrast ratios are comparable to the first-light Gemini Planet Imager contrasts; for an age of 10 Myr, we rule out planets with masses comparable to HR 8799 b beyond a projected separation of 23 au. A massive icy planetesimal disk or an unseen super-Jovian planet at r > 20 au may explain the disk's visibility. The HD 36546 debris disk may be the youngest debris disk yet imaged, is the first newly identified object from the now-operational SCExAO extreme AO system, is ideally suited for spectroscopic follow-up with SCExAO/CHARIS in 2017, and may be a key probe of icy planet formation and planet-disk interactions.
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