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| 3. |
- 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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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
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Tidskriftsartikel (refereegranskat)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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- Chen, Jo-Hsin, et al.
(författare)
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HERSCHEL HIFI OBSERVATIONS OF O-2 TOWARD ORION: SPECIAL CONDITIONS FOR SHOCK ENHANCED EMISSION
- 2014
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Ingår i: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 793:2, s. Article nr. 111 -
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Tidskriftsartikel (refereegranskat)abstract
- We report observations of molecular oxygen (O-2) rotational transitions at 487 GHz, 774 GHz, and 1121 GHz toward Orion Peak A. The O-2 lines at 487 GHz and 774 GHz are detected at velocities of 10-12 km s(-1) with line widths similar to 3 km s(-1); however, the transition at 1121 GHz is not detected. The observed line characteristics, combined with the results of earlier observations, suggest that the region responsible for the O-2 emission is similar or equal to 9" (6 x 10(16) cm) in size, and is located close to the H-2 Peak 1 position (where vibrationally excited H-2 emission peaks), and not at Peak A, 23" away. The peak O-2 column density is similar to 1.1 x 10(18) cm(-2). The line velocity is close to that of the 621 GHz water maser emission found in this portion of the Orion Molecular Cloud, and having a shock with velocity vector lying nearly in the plane of the sky is consistent with producing maximum maser gain along the line of sight. The enhanced O-2 abundance compared to that generally found in dense interstellar clouds can be explained by passage of a low-velocity C shock through a clump with preshock density 2 x 10(4) cm(-3), if a reasonable flux of UV radiation is present. The postshock O-2 can explain the emission from the source if its line-of-sight dimension is similar or equal to 10 times larger than its size on the plane of the sky. The special geometry and conditions required may explain why O-2 emission has not been detected in the cores of other massive star-forming molecular clouds.
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- Goldsmith, Paul F., et al.
(författare)
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Herschel Measurements of Molecular Oxygen in Orion
- 2011
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Ingår i: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 737:2, s. 96 (1-17)
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Tidskriftsartikel (refereegranskat)abstract
- We report observations of three rotational transitions of molecular oxygen (O2) in emission from the H2 Peak 1 position of vibrationally excited molecular hydrogen in Orion. We observed the 487 GHz, 774 GHz, and 1121 GHz lines using the Heterodyne Instrument for the Far Infrared on the Herschel Space Observatory, having velocities of 11 km s–1 to 12 km s–1 and widths of 3 km s–1. The beam-averaged column density is N(O2) = 6.5 × 1016 cm–2, and assuming that the source has an equal beam-filling factor for all transitions (beam widths 44, 28, and 19''), the relative line intensities imply a kinetic temperature between 65 K and 120 K. The fractional abundance of O2 relative to H2 is (0.3-7.3) × 10–6. The unusual velocity suggests an association with a ~5'' diameter source, denoted Peak A, the Western Clump, or MF4. The mass of this source is ~10 Msun and the dust temperature is ≥150 K. Our preferred explanation of the enhanced O2 abundance is that dust grains in this region are sufficiently warm (T ≥ 100 K) to desorb water ice and thus keep a significant fraction of elemental oxygen in the gas phase, with a significant fraction as O2. For this small source, the line ratios require a temperature ≥180 K. The inferred O2 column density sime5 × 1018 cm–2 can be produced in Peak A, having N(H2) sime 4 × 1024 cm–2. An alternative mechanism is a low-velocity (10-15 km s–1) C-shock, which can produce N(O2) up to 1017 cm–2.
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- Liseau, René, 1949, et al.
(författare)
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Multi-line detection of O2 toward rho Ophiuchi A
- 2012
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 541
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Tidskriftsartikel (refereegranskat)abstract
- Context. Models of pure gas-phase chemistry in well-shielded regions of molecular clouds predict relatively high levels of molecular oxygen, O-2, and water, H2O. These high abundances imply high cooling rates, leading to relatively short timescales for the evolution of gravitationally unstable dense cores, forming stars and planets. Contrary to expectations, the dedicated space missions SWAS and Odin typically found only very small amounts of water vapour and essentially no O-2 in the dense star-forming interstellar medium. Aims. Only toward rho OphA did Odin detect a very weak line of O-2 at 119 GHz in a beam of size 10 arcmin. The line emission of related molecules changes on angular scales of the order of some tens of arcseconds, requiring a larger telescope aperture such as that of the Herschel Space Observatory to resolve the O-2 emission and pinpoint its origin. Methods. We use the Heterodyne Instrument for the Far Infrared (HIFI) aboard Herschel to obtain high resolution O-2 spectra toward selected positions in the rho Oph A core. These data are analysed using standard techniques for O2 excitation and compared to recent PDR-like chemical cloud models. Results. The N-J = 3(3)-1(2) line at 487.2 GHz is clearly detected toward all three observed positions in the rho Oph A core. In addition, an oversampled map of the 5(4)-3(4) transition at 773.8 GHz reveals the detection of the line in only half of the observed area. On the basis of their ratios, the temperature of the O-2 emitting gas appears to vary quite substantially, with warm gas (greater than or similar to 50 K) being adjacent to a much colder region, of temperatures lower than 30 K. Conclusions. The exploited models predict that the O-2 column densities are sensitive to the prevailing dust temperatures, but rather insensitive to the temperatures of the gas. In agreement with these models, the observationally determined O-2 column densities do not seem to depend strongly on the derived gas temperatures, but fall into the range N(O-2) = 3 to greater than or similar to 6 x 10(15) cm(-2). Beam-averaged O-2 abundances are about 5 x 10(-8) relative to H-2. Combining the HIFI data with earlier Odin observations yields a source size at 119 GHz in the range of 4 to 5 arcmin, encompassing the entire rho Oph A core. We speculate that one of the reasons for the generally very low detection rate of O-2 is the short period of time during which O-2 molecules are reasonably abundant in molecular clouds.
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- Yildiz, U. A., et al.
(författare)
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Deep observations of O-2 toward a low-mass protostar with Herschel-HIFI
- 2013
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 558
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Tidskriftsartikel (refereegranskat)abstract
- Context. According to traditional gas-phase chemical models, O-2 should be abundant in molecular clouds, but until recently, attempts to detect interstellar O-2 line emission with ground-and space-based observatories have failed. Aims. Following the multi-line detections of O-2 with low abundances in the Orion and. Oph A molecular clouds with Herschel, it is important to investigate other environments, and we here quantify the O-2 abundance near a solar-mass protostar. Methods. Observations of molecular oxygen, O-2, at 487 GHz toward a deeply embedded low-mass Class 0 protostar, NGC 1333IRAS 4A, are presented, using the Heterodyne Instrument for the Far Infrared (HIFI) on the Herschel Space Observatory. Complementary data of the chemically related NO and CO molecules are obtained as well. The high spectral resolution data are analysed using radiative transfer models to infer column densities and abundances, and are tested directly against full gas-grain chemical models.Results. The deep HIFI spectrum fails to show O-2 at the velocity of the dense protostellar envelope, implying one of the lowest abundance upper limits of O-2/H-2 at = 6x 10-9 (3s). The O-2/CO abundance ratio is less than 0.005. However, a tentative (4.5s) detection of O-2 is seen at the velocity of the surrounding NGC 1333 molecular cloud, shifted by 1 km s-1 relative to the protostar. For the protostellar envelope, pure gas-phase models and gas-grain chemical models require a long pre-collapse phase (similar to 0.7-1 x 106 years), during which atomic and molecular oxygen are frozen out onto dust grains and fully converted to H2O, to avoid overproduction of O2 in the dense envelope. The same model also reproduces the limits on the chemically related NO molecule if hydrogenation of NO on the grains to more complex molecules such as NH2OH, found in recent laboratory experiments, is included. The tentative detection of O-2 in the surrounding cloud is consistent with a low-density PDR model with small changes in reaction rates.
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