| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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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| 2. |
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| 3. |
- Ade, P. A. R., et al.
(author)
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A Constraint on Primordial B-modes from the First Flight of the Spider Balloon-borne Telescope
- 2022
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In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 927:2
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Journal article (peer-reviewed)abstract
- We present the first linear polarization measurements from the 2015 long-duration balloon flight of SPIDER, which is an experiment that is designed to map the polarization of the cosmic microwave background (CMB) on degree angular scales. The results from these measurements include maps and angular power spectra from observations of 4.8% of the sky at 95 and 150 GHz, along with the results of internal consistency tests on these data. While the polarized CMB anisotropy from primordial density perturbations is the dominant signal in this region of sky, Galactic dust emission is also detected with high significance. Galactic synchrotron emission is found to be negligible in the SPIDER bands. We employ two independent foreground-removal techniques to explore the sensitivity of the cosmological result to the assumptions made by each. The primary method uses a dust template derived from Planck data to subtract the Galactic dust signal. A second approach, which constitutes a joint analysis of SPIDER and Planck data in the harmonic domain, assumes a modified-blackbody model for the spectral energy distribution of the dust with no constraint on its spatial morphology. Using a likelihood that jointly samples the template amplitude and r parameter space, we derive 95% upper limits on the primordial tensor-to-scalar ratio from Feldman-Cousins and Bayesian constructions, finding r < 0.11 and r < 0.19, respectively. Roughly half the uncertainty in r derives from noise associated with the template subtraction. New data at 280 GHz from SPIDER´s second flight will complement the Planck polarization maps, providing powerful measurements of the polarized Galactic dust emission.
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| 4. |
- Bergman, A. S., et al.
(author)
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280 GHz Focal Plane Unit Design and Characterization for the SPIDER-2 Suborbital Polarimeter
- 2018
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In: Journal of Low Temperature Physics. - : Springer Science and Business Media LLC. - 0022-2291 .- 1573-7357. ; 193:5-6, s. 1075-1084
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Journal article (peer-reviewed)abstract
- We describe the construction and characterization of the 280 GHz bolometric focal plane units (FPUs) to be deployed on the second flight of the balloon-borne SPIDER instrument. These FPUs are vital to SPIDER's primary science goal of detecting or placing an upper limit on the amplitude of the primordial gravitational wave signature in the cosmic microwave background (CMB) by constraining the B-mode contamination in the CMB from Galactic dust emission. Each 280 GHz focal plane contains a 16 x 16 grid of corrugated silicon feedhorns coupled to an array of aluminum-manganese transition-edge sensor (TES) bolometers fabricated on 150 mm diameter substrates. In total, the three 280 GHz FPUs contain 1530 polarization-sensitive bolometers (765 spatial pixels) optimized for the low loading environment in flight and read out by time-division SQUID multiplexing. In this paper, we describe the mechanical, thermal, and magnetic shielding architecture of the focal planes and present cryogenic measurements which characterize yield and the uniformity of several bolometer parameters. The assembled FPUs have high yields, with one array as high as 95% including defects from wiring and readout. We demonstrate high uniformity in device parameters, finding the median saturation power for each TES array to be similar to 3 pW at 300 mK with a less than 6% variation across each array at 1 sigma. These focal planes will be deployed alongside the 95 and 150 GHz telescopes in the SPIDER-2 instrument, slated to fly from McMurdo Station in Antarctica in December 2018.
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| 5. |
- de Leon, Jerome, et al.
(author)
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NEAR-IR HIGH-RESOLUTION IMAGING POLARIMETRY OF THE SU Aur DISK : CLUES FOR TIDAL TAILS?
- 2015
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In: Astrophysical Journal Letters. - 2041-8205 .- 2041-8213. ; 806:1
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Journal article (peer-reviewed)abstract
- We present new high-resolution (similar to 0.09) H-band imaging observations of the circumstellar disk around the T Tauri star SU Aur. Our observations with Subaru-HiCIAO have revealed the presence of scattered light as close as 0.15 (similar to 20 AU) to the star. Within our image, we identify bright emission associated with a disk with a minimum radius of similar to 90 AU, an inclination of similar to 35 degrees from the plane of the sky, and an approximate PA of 15 degrees for the major axis. We find a brightness asymmetry between the northern and southern sides of the disk due to a non-axisymmetric disk structure. We also identify a pair of asymmetric tail structures extending east and west from the disk. The western tail extends at least 2.5 (350 AU) from the star, and is probably associated with a reflection nebula previously observed at optical and near-IR wavelengths. The eastern tail extends at least 1. (140 AU) at the present signal-to-noise. These tails are likely due to an encounter with an unseen brown dwarf, but our results do not exclude the explanation that these tails are outflow cavities or jets.
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| 6. |
- Endres, Sonja, et al.
(author)
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A New Perspective at the Ship-Air-Sea-Interface : The Environmental Impacts of Exhaust Gas Scrubber Discharge
- 2018
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In: Frontiers in Marine Science. - : FRONTIERS MEDIA SA. - 2296-7745. ; 5
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Research review (peer-reviewed)abstract
- Shipping emissions are likely to increase significantly in the coming decades, alongside increasing emphasis on the sustainability and environmental impacts of the maritime transport sector. Exhaust gas cleaning systems ("scrubbers"), using seawater or fresh water as cleaning media for sulfur dioxide, are progressively used by shipping companies to comply with emissions regulations. Little is known about the chemical composition of the scrubber effluent and its ecological consequences for marine life and biogeochemical processes. If scrubbers become a central tool for atmospheric pollution reduction from shipping, modeling, and experimental studies will be necessary to determine the ecological and biogeochemical effects of scrubber wash water discharge on the marine environment. Furthermore, attention must be paid to the regulation and enforcement of environmental protection standards concerning scrubber use. Close collaboration between natural scientists and social scientists is crucial for progress toward sustainable shipping and protection of the marine environment.
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| 7. |
- Filippini, J. P., et al.
(author)
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In-Flight Gain Monitoring of SPIDER's Transition-Edge Sensor Arrays
- 2022
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In: Journal of Low Temperature Physics. - : Springer Science and Business Media LLC. - 0022-2291 .- 1573-7357. ; 209:3-4, s. 649-657
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Journal article (peer-reviewed)abstract
- Experiments deploying large arrays of transition-edge sensors (TESs) often require a robust method to monitor gain variations with minimal loss of observing time. We propose a sensitive and non-intrusive method for monitoring variations in TES responsivity using small square waves applied to the TES bias. We construct an estimator for a TES's small-signal power response from its electrical response that is exact in the limit of strong electrothermal feedback. We discuss the application and validation of this method using flight data from SPIDER, a balloon-borne telescope that observes the polarization of the cosmic microwave background with more than 2000 TESs. This method may prove useful for future balloon- and space-based instruments, where observing time and ground control bandwidth are limited.
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| 8. |
- Follette, Katherine B., et al.
(author)
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SEEDS ADAPTIVE OPTICS IMAGING OF THE ASYMMETRIC TRANSITION DISK OPH IRS 48 IN SCATTERED LIGHT
- 2015
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In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 798:2
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Journal article (peer-reviewed)abstract
- We present the first resolved near-infrared imagery of the transition disk Oph IRS 48 (WLY 2-48), which was recently observed with ALMA to have a strongly asymmetric submillimeter flux distribution. H-band polarized intensity images show a similar to 60 AU radius scattered light cavity with two pronounced arcs of emission, one from northeast to southeast and one smaller, fainter, and more distant arc in the northwest. K-band scattered light imagery reveals a similar morphology, but with a clear third arc along the southwestern rim of the disk cavity. This arc meets the northwestern arc at nearly a right angle, revealing the presence of a spiral arm or local surface brightness deficit in the disk, and explaining the east-west brightness asymmetry in the H-band data. We also present 0.8-5.4 mu m IRTF SpeX spectra of this object, which allow us to constrain the spectral class to A0 +/- 1 and measure a low mass accretion rate of 10(-8.5) M-circle dot yr(-1), both consistent with previous estimates. We investigate a variety of reddening laws in order to fit the multiwavelength spectral energy distribution of Oph IRS 48 and find a best fit consistent with a younger, higher luminosity star than previous estimates.
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| 9. |
- Gambrel, A. E., et al.
(author)
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The XFaster Power Spectrum and Likelihood Estimator for the Analysis of Cosmic Microwave Background Maps
- 2021
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In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 922:2
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Journal article (peer-reviewed)abstract
- We present the XFaster analysis package, a fast, iterative angular power spectrum estimator based on a diagonal approximation to the quadratic Fisher matrix estimator. It uses Monte Carlo simulations to compute noise biases and filter transfer functions and is thus a hybrid of both Monte Carlo and quadratic estimator methods. In contrast to conventional pseudo-Cℓ–based methods, the algorithm described here requires a minimal number of simulations and does not require them to be precisely representative of the data to estimate accurate covariance matrices for the bandpowers. The formalism works with polarization-sensitive observations and also data sets with identical, partially overlapping, or independent survey regions. The method was first implemented for the analysis of BOOMERanG data and also used as part of the Planck analysis. Here we describe the full, publicly available analysis package, written in Python, as developed for the analysis of data from the 2015 flight of the Spider instrument. The package includes extensions for self-consistently estimating null spectra and estimating fits for Galactic foreground contributions. We show results from the extensive validation of XFaster using simulations and its application to the Spider data set.
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| 10. |
- Genereux, Diane P., et al.
(author)
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A comparative genomics multitool for scientific discovery and conservation
- 2020
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In: Nature. - : NATURE RESEARCH. - 0028-0836 .- 1476-4687. ; 587:7833, s. 240-245
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Journal article (peer-reviewed)abstract
- A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal-including 131 previously uncharacterized species-from the Zoonomia Project provides data that support biological discovery, medical research and conservation. The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.
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