1. |
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2. |
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3. |
- Gould, A., et al.
(författare)
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MOA-2010-BLG-523:" Failed Planet"= RS CVn Star
- 2013
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Ingår i: Astrophysical Journal. - 0004-637X. ; 763:2
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Tidskriftsartikel (refereegranskat)abstract
- The Galactic bulge source MOA-2010-BLG-523S exhibited short-term deviations from a standard microlensing light curve near the peak of an A(max) similar to 265 high-magnification microlensing event. The deviations originally seemed consistent with expectations for a planetary companion to the principal lens. We combine long-term photometric monitoring with a previously published high-resolution spectrum taken near peak to demonstrate that this is an RS CVn variable, so that planetary microlensing is not required to explain the light-curve deviations. This is the first spectroscopically confirmed RS CVn star discovered in the Galactic bulge.
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4. |
- Ryu, Y. -H., et al.
(författare)
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OGLE-2016-BLG-1190Lb : The First Spitzer Bulge Planet Lies Near the Planet/Brown-dwarf Boundary
- 2018
-
Ingår i: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 155:1
-
Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of OGLE-2016-BLG-1190Lb, which is likely to be the first Spitzer microlensing planet in the Galactic bulge/ bar, an assignation that can be confirmed by two epochs of high-resolution imaging of the combined source-lens baseline object. The planet's mass, M-p = 13.4 +/- 0.9 M-J, places it right at the deuteriumburning limit, i. e., the conventional boundary between planets and brown dwarfs. Its existence raises the question of whether such objects are really planets (formed within the disks of their hosts) or failed stars (lowmass objects formed by gas fragmentation). This question may ultimately be addressed by comparing disk and bulge/bar planets, which is a goal of the Spitzer microlens program. The host is a G dwarf, M-host = 0.89. +/- 0.07 M-circle dot, and the planet has a semimajor axis a similar to 2.0 au. We use Kepler K2 Campaign 9 microlensing data to break the lens-mass degeneracy that generically impacts parallax solutions from Earth-Spitzer observations alone, which is the first successful application of this approach. The microlensing data, derived primarily from near-continuous, ultradense survey observations from OGLE, MOA, and three KMTNet telescopes, contain more orbital information than for any previous microlensing planet, but not quite enough to accurately specify the full orbit. However, these data do permit the first rigorous test of microlensing orbital-motion measurements, which are typically derived from data taken over < 1% of an orbital period.
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5. |
- Callaway, EM, et al.
(författare)
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A multimodal cell census and atlas of the mammalian primary motor cortex
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 598:7879, s. 86-102
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Tidskriftsartikel (refereegranskat)abstract
- Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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6. |
- Simpson, E. K., et al.
(författare)
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WASP-37b : A 1.8 MJ exoplanet transiting a metal-poor star
- 2011
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Ingår i: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 141:1, s. 8-
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Tidskriftsartikel (refereegranskat)abstract
- We report on the discovery of WASP-37b, a transiting hot Jupiter orbiting an m(v) = 12.7 G2-type dwarf, with a period of 3.577469 +/- 0.000011 d, transit epoch T-0 = 2455338.6188 +/- 0.0006 (HJD; dates throughout the paper are given in Coordinated Universal Time (UTC)), and a transit duration 0.1304(-0.0017)(+0.0018) d. The planetary companion has a mass M-p = 1.80 +/- 0.17 M-J and radius R-p = 1.16(-0.06)(+0.07) R-J, yielding a mean density of 1.15(-0.15)(+0.12) rho(J). From a spectral analysis, we find that the host star has M-star = 0.925 +/- 0.120 M-circle dot, R-star = 1.003 +/- 0.053 R-circle dot, T-eff = 5800 +/- 150 K, and [Fe/H] = -0.40 +/- 0.12. WASP-37 is therefore one of the lowest metallicity stars to host a transiting planet.
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7. |
- Simpson, E. K., et al.
(författare)
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Independent Discovery of the Transiting Exoplanet HAT-P-14b
- 2011
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Ingår i: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 141:5, s. 161-
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Tidskriftsartikel (refereegranskat)abstract
- We present SuperWASP observations of HAT-P-14b, a hot Jupiter discovered by Torres et al. The planet was found independently by the SuperWASP team and named WASP-27b after follow-up observations had secured the discovery, but prior to the publication by Torres et al. Our analysis of HAT-P-14/WASP-27 is in good agreement with the values found by Torres et al. and we provide additional evidence against astronomical false positives. Due to the brightness of the host star, V-mag = 10, HAT-P-14b is an attractive candidate for further characterization observations. The planet has a high impact parameter and the primary transit is close to grazing. This could readily reveal small deviations in the orbital parameters indicating the presence of a third body in the system, which may be causing the small but significant orbital eccentricity. Our results suggest that the planet may undergo a grazing secondary eclipse. However, even a non-detection would tightly constrain the system parameters.
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8. |
- Björkman, Anne, 1981, et al.
(författare)
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Plant functional trait change across a warming tundra biome
- 2018
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 562:7725, s. 57-62
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Tidskriftsartikel (refereegranskat)abstract
- The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature–trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.
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9. |
- Bouchy, F., et al.
(författare)
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WASP-21b : a hot-Saturn exoplanet transiting a thick disc star
- 2010
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 519, s. A98-
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Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of WASP-21b, a new transiting exoplanet discovered by the Wide Angle Search for Planets ( WASP) Consortium and established and characterized with the FIES, SOPHIE, CORALIE and HARPS fiber-fed echelle spectrographs. A 4.3-d period, 1.1% transit depth and 3.4-h duration are derived for WASP-21b using SuperWASP-North and high precision photometric observations at the Liverpool Telescope. Simultaneous fitting to the photometric and radial velocity data with a Markov Chain Monte Carlo procedure leads to a planet in the mass regime of Saturn. With a radius of 1.07 R-Jup and mass of 0.30 M-Jup, WASP-21b has a density close to 0.24 rho(Jup) corresponding to the distribution peak at low density of transiting gaseous giant planets. With a host star metallicity [Fe/H] of -0.46, WASP-21b strengthens the correlation between planetary density and host star metallicity for the five known Saturn-like transiting planets. Furthermore there are clear indications that WASP-21b is the first transiting planet belonging to the thick disc.
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10. |
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11. |
- Street, R. A., et al.
(författare)
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WASP-24 B : A new transiting close-in hot jupiter orbiting a late F-star
- 2010
-
Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 720:1, s. 337-343
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Tidskriftsartikel (refereegranskat)abstract
- We report the discovery of a new transiting close-in giant planet, WASP-24 b, in a 2.341 day orbit, 0.037 AU from its F8-9 type host star. By matching the star's spectrum with theoretical models, we infer an effective temperature T-eff = 6075 +/- 100 K and a surface gravity of log g = 4.15 +/- 0.10. A comparison of these parameters with theoretical isochrones and evolutionary mass tracks places only weak constraints on the age of the host star, which we estimate to be 3.8(-1.2)(+1.3) Gyr. The planetary nature of the companion was confirmed by radial velocity measurements and additional photometric observations. These data were fit simultaneously in order to determine the most probable parameter set for the system, from which we infer a planetary mass of 1.071(-0.038)(+0.036) M-Jup and radius 1.3(-0.037)(+0.039) R-Jup.
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12. |
- Jaimes, R. Figuera, et al.
(författare)
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Many new variable stars discovered in the core of the globular cluster NGC 6715 (M54) with EMCCD observations
- 2016
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 592
-
Tidskriftsartikel (refereegranskat)abstract
- Context. We show the benefits of using electron-multiplying CCDs and the shift-and-add technique as a tool to minimise the effects of atmospheric turbulence, such as blending between stars in crowded fields, and to avoid saturated stars in the fields observed. We intend to complete, or improve on, the census of the variable star population in globular cluster NGC 6715. Aims. Our aim is to obtain high-precision time-series photometry of the very crowded central region of this stellar system via the collection of better angular resolution images than has been previously achieved with conventional CCDs on ground-based telescopes. Methods. Observations were carried out using the Danish 1.54-m telescope at the ESO La Silla observatory in Chile. The telescope is equipped with an electron-multiplying CCD that enables short-exposure-time images to be obtained (ten images per second) that were stacked using the shift-and-add technique to produce the normal-exposure-time images (minutes). The high precision photometry was performed via difference image analysis employing the DanDIA pipeline. We attempted automatic detection of variable stars in the field. Results. We statistically analysed the light curves of 1405 stars in the crowded central region of NGC 6715 to automatically identify the variable stars present in this cluster. We found light curves for 17 previously known variable stars near the edges of our reference image (16 RR Lyrae and 1 semi-regular) and we discovered 67 new variables (30 RR Lyrae, 21 irregular (long-period type), 3 semi-regular, 1 W Virginis, 1 eclipsing binary, and 11 unclassified). Photometric measurements for these stars are available in electronic form through the Strasbourg Astronomical Data Centre.
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13. |
- Bianco, Federica B., et al.
(författare)
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Optimization of the Observing Cadence for the Rubin Observatory Legacy Survey of Space and Time : A Pioneering Process of Community-focused Experimental Design
- 2022
-
Ingår i: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 258:1
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Tidskriftsartikel (refereegranskat)abstract
- Vera C. Rubin Observatory is a ground-based astronomical facility under construction, a joint project of the National Science Foundation and the U.S. Department of Energy, designed to conduct a multipurpose 10 yr optical survey of the Southern Hemisphere sky: the Legacy Survey of Space and Time. Significant flexibility in survey strategy remains within the constraints imposed by the core science goals of probing dark energy and dark matter, cataloging the solar system, exploring the transient optical sky, and mapping the Milky Way. The survey's massive data throughput will be transformational for many other astrophysics domains and Rubin's data access policy sets the stage for a huge community of potential users. To ensure that the survey science potential is maximized while serving as broad a community as possible, Rubin Observatory has involved the scientific community at large in the process of setting and refining the details of the observing strategy. The motivation, history, and decision-making process of this strategy optimization are detailed in this paper, giving context to the science-driven proposals and recommendations for the survey strategy included in this Focus Issue.
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14. |
- Usher, Christopher, et al.
(författare)
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Rubin Observatory LSST Stars Milky Way and Local Volume Star Clusters Roadmap
- 2023
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Ingår i: Publications of the Astronomical Society of the Pacific. - 0004-6280 .- 1538-3873. ; 135:1049
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Tidskriftsartikel (refereegranskat)abstract
- The Vera C. Rubin Observatory will undertake the Legacy Survey of Space and Time, providing an unprecedented, volume-limited catalog of star clusters in the Southern Sky, including Galactic and extragalactic star clusters. The Star Clusters subgroup of the Stars, Milky Way and Local Volume Working Group has identified key areas where Rubin Observatory will enable significant progress in star cluster research. This roadmap represents our science cases and preparation for studies of all kinds of star clusters from the Milky Way out to distances of tens of megaparsecs.
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15. |
- Björkman, Anne, 1981, et al.
(författare)
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Tundra Trait Team: A database of plant traits spanning the tundra biome
- 2018
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Ingår i: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 27:12, s. 1402-1411
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Tidskriftsartikel (refereegranskat)abstract
- © 2018 The Authors Global Ecology and Biogeography Published by John Wiley & Sons Ltd Motivation: The Tundra Trait Team (TTT) database includes field-based measurements of key traits related to plant form and function at multiple sites across the tundra biome. This dataset can be used to address theoretical questions about plant strategy and trade-offs, trait–environment relationships and environmental filtering, and trait variation across spatial scales, to validate satellite data, and to inform Earth system model parameters. Main types of variable contained: The database contains 91,970 measurements of 18 plant traits. The most frequently measured traits (>1,000 observations each) include plant height, leaf area, specific leaf area, leaf fresh and dry mass, leaf dry matter content, leaf nitrogen, carbon and phosphorus content, leaf C:N and N:P, seed mass, and stem specific density. Spatial location and grain: Measurements were collected in tundra habitats in both the Northern and Southern Hemispheres, including Arctic sites in Alaska, Canada, Greenland, Fennoscandia and Siberia, alpine sites in the European Alps, Colorado Rockies, Caucasus, Ural Mountains, Pyrenees, Australian Alps, and Central Otago Mountains (New Zealand), and sub-Antarctic Marion Island. More than 99% of observations are georeferenced. Time period and grain: All data were collected between 1964 and 2018. A small number of sites have repeated trait measurements at two or more time periods. Major taxa and level of measurement: Trait measurements were made on 978 terrestrial vascular plant species growing in tundra habitats. Most observations are on individuals (86%), while the remainder represent plot or site means or maximums per species. Software format: csv file and GitHub repository with data cleaning scripts in R; contribution to TRY plant trait database (www.try-db.org) to be included in the next version release.
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16. |
- Fossati, L., et al.
(författare)
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Metals in the exosphere of the highly irradiated planet WASP-12b
- 2010
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Ingår i: Astrophysical Journal Letters. - 2041-8205. ; 714:2, s. L222-L227
-
Tidskriftsartikel (refereegranskat)abstract
- We present near-UV transmission spectroscopy of the highly irradiated transiting exoplanet WASP-12b, obtained with the Cosmic Origins Spectrograph on the Hubble Space Telescope. The spectra cover three distinct wavelength ranges: NUVA (2539-2580 angstrom), NUVB (2655-2696 angstrom), and NUVC (2770-2811 angstrom). Three independent methods all reveal enhanced transit depths attributable to absorption by resonance lines of metals in the exosphere of WASP-12b. Light curves of total counts in the NUVA and NUVC wavelength ranges show a detection at a 2.5 sigma level. We detect extra absorption in the Mg II lambda lambda 2800 resonance line cores at the 2.8 sigma level. The NUVA, NUVB, and NUVC light curves imply effective radii of 2.69 +/- 0.24 R-J, 2.18 +/- 0.18 R-J, and 2.66 +/- 0.22 R-J respectively, suggesting the planet is surrounded by an absorbing cloud which overfills the Roche lobe. We detect enhanced transit depths at the wavelengths of resonance lines of neutral sodium, tin, and manganese, and at singly ionized ytterbium, scandium, manganese, aluminum, vanadium, and magnesium. We also find the statistically expected number of anomalous transit depths at wavelengths not associated with any known resonance line. Our data are limited by photon noise, but taken as a whole the results are strong evidence for an extended absorbing exosphere surrounding the planet. The NUVA data exhibit an early ingress, contrary to model expectations; we speculate this could be due to the presence of a disk of previously stripped material.
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17. |
- Hirao, Yuki, et al.
(författare)
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OGLE-2017-BLG-0406 : Spitzer Microlens Parallax Reveals Saturn-mass Planet Orbiting M-dwarf Host in the Inner Galactic Disk
- 2020
-
Ingår i: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 160:2
-
Tidskriftsartikel (refereegranskat)abstract
- We report the discovery and analysis of the planetary microlensing event OGLE-2017-BLG-0406, which was observed both from the ground and by the Spitzer satellite in a solar orbit. At high magnification, the anomaly in the light curve was densely observed by ground-based-survey and follow-up groups, and it was found to be explained by a planetary lens with a planet/host mass ratio of q = 7.0 x 10(-4) from the light-curve modeling. The ground-only and Spitzer-only data each provide very strong one-dimensional (1D) constraints on the 2D microlens parallax vector pi(E). When combined, these yield a precise measurement of pi(E) and of the masses of the host M-host = 0.56 +/- 0.07 M-circle dot and planet M-planet = 0.41 +/- 0.05 M-Jup. The system lies at a distance D-L = 5.2 +/- 0.5 kpc from the Sun toward the Galactic bulge, and the host is more likely to be a disk population star according to the kinematics of the lens. The projected separation of the planet from the host is a(perpendicular to) = 3.5 +/- 0.3 au (i.e., just over twice the snow line). The Galactic-disk kinematics are established in part from a precise measurement of the source proper motion based on OGLE-IV data. By contrast, the Gaia proper-motion measurement of the source suffers from a catastrophic 10 sigma error.
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18. |
- Maqueo Chew, Y. Gomez, et al.
(författare)
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Fundamental properties of the pre-main sequence eclipsing stars of MML 53 and the mass of the tertiary
- 2019
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 623
-
Tidskriftsartikel (refereegranskat)abstract
- We present the most comprehensive analysis to date of the Upper Centaurus Lupus eclipsing binary MML 53 (with P-EB = 2.097892 d), and for the first time, confirm the bound-nature of the third star (in a P-3 similar to 9 yr orbit) by constraining its mass dynamically. Our analysis is based on new and archival spectra and time-series photometry, spanning 80% of one orbit of the outer component. From the spectroscopic analysis, we determined the temperature of the primary star to be 4880 +/- 100 K. The study of the close binary incorporated treatment of spots and dilution by the tertiary in the light curves, allowing for the robust measurement of the masses of the eclipsing components within 1% (M-1 = 1.0400 +/- 0.0067 M-circle dot and M-2 = 0.8907 +/- 0.0058 M-circle dot), their radii within 4.5% (R-1 = 1.283 +/- 0.043 R-circle dot and R-2 = 1.107 +/- 0.049 R-circle dot), and the temperature of the secondary star (T-eff,T-2 = 4379 +/- 100 K). From the analysis of the eclipse timings, and the change in systemic velocity of the eclipsing binary and the radial velocities of the third star, we measured the mass of the outer companion to be 0.7 M-circle dot (with a 20% uncertainty). The age we derived from the evolution of the temperature ratio between the eclipsing components is fully consistent with previous, independent estimates of the age of Upper Centaurus Lupus (16 +/- 2 Myr). At this age, the tightening of the MML 53 eclipsing binary has already occurred, thus supporting close-binary formation mechanisms that act early in the stars' evolution. The eclipsing components of MML 53 roughly follow the same theoretical isochrone, but appear to be inflated in radius (by 20% for the primary and 10% for the secondary) with respect to recent evolutionary models. However, our radius measurement of the 1.04 M-circle dot primary star of MML 53 is in full agreement with the independent measurement of the secondary of NP Per which has the same mass and a similar age. The eclipsing stars of MML 53 are found to be larger but not cooler than predicted by non-magnetic models, it is not clear what is the mechanism that is causing the radius inflation given that activity, spots and/or magnetic fields slowing their contraction, require the inflated stars to be cooler to remain in thermal equilibrium.
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19. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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20. |
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21. |
- Hebb, L., et al.
(författare)
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MML 53 : a new low-mass, pre-main sequence eclipsing binary in the Upper Centaurus-Lupus region discovered by SuperWASP
- 2010
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 522:2, s. A37-
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Tidskriftsartikel (refereegranskat)abstract
- We announce the discovery of a new low-mass, pre-main sequence eclipsing binary, MML 53. Previous observations of MML 53 found it to be a pre-main sequence spectroscopic multiple associated with the 15-22 Myr Upper Centaurus-Lupus cluster. We identify the object as an eclipsing binary for the first time through the analysis of multiple seasons of time series photometry from the SuperWASP transiting planet survey. Re-analysis of a single archive spectrum shows MML 53 to be a spatially unresolved triple system of young stars which all exhibit significant lithium absorption. Two of the components comprise an eclipsing binary with period, P = 2.097891(6) +/- 0.000005 and mass ratio, q similar to 0.8. Here, we present the analysis of the discovery data.
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22. |
- Heindel, Jerrold J., et al.
(författare)
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Parma consensus statement on metabolic disruptors
- 2015
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Ingår i: Environmental Health. - : BioMed Central (BMC). - 1476-069X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- A multidisciplinary group of experts gathered in Parma Italy for a workshop hosted by the University of Parma, May 16-18, 2014 to address concerns about the potential relationship between environmental metabolic disrupting chemicals, obesity and related metabolic disorders. The objectives of the workshop were to: 1. Review findings related to the role of environmental chemicals, referred to as "metabolic disruptors", in obesity and metabolic syndrome with special attention to recent discoveries from animal model and epidemiology studies; 2. Identify conclusions that could be drawn with confidence from existing animal and human data; 3. Develop predictions based on current data; and 4. Identify critical knowledge gaps and areas of uncertainty. The consensus statements are intended to aid in expanding understanding of the role of metabolic disruptors in the obesity and metabolic disease epidemics, to move the field forward by assessing the current state of the science and to identify research needs on the role of environmental chemical exposures in these diseases. We propose broadening the definition of obesogens to that of metabolic disruptors, to encompass chemicals that play a role in altered susceptibility to obesity, diabetes and related metabolic disorders including metabolic syndrome.
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23. |
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24. |
- Myburg, Alexander A., et al.
(författare)
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Systems and Synthetic Biology of Forest Trees : A Bioengineering Paradigm for Woody Biomass Feedstocks
- 2019
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 10
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Forskningsöversikt (refereegranskat)abstract
- Fast-growing forest plantations are sustainable feedstocks of plant biomass that can serve as alternatives to fossil carbon resources for materials, chemicals, and energy. Their ability to efficiently harvest light energy and carbon from the atmosphere and sequester this into metabolic precursors for lignocellulosic biopolymers and a wide range of plant specialized metabolites make them excellent biochemical production platforms and living biorefineries. Their large sizes have facilitated multi-omics analyses and systems modeling of key biological processes such as lignin biosynthesis in trees. High-throughput 'omics' approaches have also been applied in segregating tree populations where genetic variation creates abundant genetic perturbations of system components allowing construction of systems genetics models linking genes and pathways to complex trait variation. With this information in hand, it is now possible to start using synthetic biology and genome editing techniques in a bioengineering approach based on a deeper understanding and rational design of biological parts, devices, and integrated systems. However, the complexity of the biology and interacting components will require investment in big data informatics, machine learning, and intuitive visualization to fully explore multi-dimensional patterns and identify emergent properties of biological systems. Predictive systems models could be tested rapidly through high-throughput synthetic biology approaches and multigene editing. Such a bioengineering paradigm, together with accelerated genomic breeding, will be crucial for the development of a new generation of woody biorefinery crops.
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25. |
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26. |
- Street, K A, et al.
(författare)
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Rat synapsin 1 promoter mediated transgene expression in testicular cell types
- 2005
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Ingår i: DNA and Cell Biology. - : Mary Ann Liebert Inc. - 1044-5498 .- 1557-7430. ; 24:2, s. 133-140
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Tidskriftsartikel (refereegranskat)abstract
- Previous reports described the rat synapsin 1 promoter as primarily neuron selective. However, ectopic expression of a transgene under the rat synapsin 1 promoter was also detected in testis from some transgenic mouse lines. Here we investigate which cells within the testis express a transgene consisting of the rat synapsin 1 promoter fused with luciferase. Synapsin 1-luciferase expression vectors were introduced into HeLa cells, into TM3 cells derived from mouse testicular Leydig cells, and into one-cell embryos to make transgenic mice. Indirect immunofluorescence suggests that nontransfected TM3 cells do not express endogenous synapsin 1. TM3 stable transfectants, however, expressed luciferase under the direction of the synapsin 1 promoter, in both promoter orientations. HeLa cells displayed only low levels of activity. Transgenic mice carrying the synapsin 1-luciferase construct displayed high levels of luciferase activity in the brain, spinal cord, and testis. Enriched populations of prepuberal types A and B spermatogonia and adult Leydig cells, pachytene spermatocytes, and round spermatids prepared from transgenic mice all displayed substantial luciferase activity. Thus, the rat synapsin 1 promoter can mediate reporter gene expression in neurons and testicular cell types.
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27. |
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28. |
- Liu, Hui, et al.
(författare)
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Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
- 2021
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
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29. |
- Müller, Niels A., et al.
(författare)
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A single gene underlies the dynamic evolution of poplar sex determination.
- 2020
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Ingår i: Nature Plants. - : Springer Nature. - 2055-0278 .- 2055-026X. ; 6:6, s. 630-637
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Tidskriftsartikel (refereegranskat)abstract
- Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR–Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes.
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30. |
- Nystedt, Björn, et al.
(författare)
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The Norway spruce genome sequence and conifer genome evolution
- 2013
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 497:7451, s. 579-584
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Tidskriftsartikel (refereegranskat)abstract
- Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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31. |
- Wegrzyn, Jill L., et al.
(författare)
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Cyberinfrastructure to Improve Forest Health and Productivity : The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment
- 2019
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 10
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Forskningsöversikt (refereegranskat)abstract
- Despite tremendous advancements in high throughput sequencing, the vast majority of tree genomes, and in particular, forest trees, remain elusive. Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing pipelines. The tree databases reviewed here serve as secondary repositories for community data. They vary in their focal species, the data they curate, and the analytics provided, but they are united in moving toward a goal of centralizing both data access and analysis. They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype and phenotype data. The organism databases of today are no longer simply catalogs or containers of genetic information. These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments. These resources are striving to integrate across diverse experimental designs, sequence types, and related measures through ontologies, community standards, and web services. Efficient, simple, and robust platforms that enhance the data generated by the research community, contribute to improving forest health and productivity.
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