1403 Publications

SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures

Rhonda A. Lizewski, R. Sealfon, O. Troyanskaya, et al.

Marine recruits training at Parris Island experienced an unexpectedly high rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, despite preventive measures including a supervised, 2-week, pre-entry quarantine. We characterize SARS-CoV-2 transmission in this cohort.

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Incompressible active phases at an interface. Part 1. Formulation and axisymmetric odd flows

L. Jia, William T. M. Irvine, M. Shelley

Inspired by the recent realization of a two-dimensional (2-D) chiral fluid as an active monolayer droplet moving atop a 3-D Stokesian fluid, we formulate mathematically its free-boundary dynamics. The surface droplet is described as a general 2-D linear, incompressible and isotropic fluid, having a viscous shear stress, an active chiral driving stress and a Hall stress allowed by the lack of time-reversal symmetry. The droplet interacts with itself through its driven internal mechanics and by driving flows in the underlying 3-D Stokes phase. We pose the dynamics as the solution to a singular integral–differential equation, over the droplet surface, using the mapping from surface stress to surface velocity for the 3-D Stokes equations. Specializing to the case of axisymmetric droplets, exact representations for the chiral surface flow are given in terms of solutions to a singular integral equation, solved using both analytical and numerical techniques. For a disc-shaped monolayer, we additionally employ a semi-analytical solution that hinges on an orthogonal basis of Bessel functions and allows for efficient computation of the monolayer velocity field, which ranges from a nearly solid-body rotation to a unidirectional edge current, depending on the subphase depth and the Saffman–Delbrück length. Except in the near-wall limit, these solutions have divergent surface shear stresses at droplet boundaries, a signature of systems with codimension-one domains embedded in a 3-D medium. We further investigate the effect of a Hall viscosity, which couples radial and transverse surface velocity components, on the dynamics of a closing cavity. Hall stresses are seen to drive inward radial motion, even in the absence of edge tension.

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Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection

Male sex is a major risk factor for SARS-CoV-2 infection severity. To understand the basis for this sex difference, we studied SARS-CoV-2 infection in a young adult cohort of United States Marine recruits. Among 2,641 male and 244 female unvaccinated and seronegative recruits studied longitudinally, SARS-CoV-2 infections occurred in 1,033 males and 137 females. We identified sex differences in symptoms, viral load, blood transcriptome, RNA splicing, and proteomic signatures. Females had higher pre-infection expression of antiviral interferon-stimulated gene (ISG) programs. Causal mediation analysis implicated ISG differences in number of symptoms, levels of ISGs, and differential splicing of CD45 lymphocyte phosphatase during infection. Our results indicate that the antiviral innate immunity set point causally contributes to sex differences in response to SARS-CoV-2 infection. A record of this paper’s transparent peer review process is included in the supplemental information.

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November 1, 2022

Accurate de novo design of membrane-traversing macrocycles

G. Bhardwaj, G. Bhardwaj, J. O’Connor, V. Mulligan, et al.

We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability and oral bioavailability. We designed 184 6–12 residue macrocycles with a wide range of predicted structures containing noncanonical backbone modifications and experimentally determined structures of 35; 29 are very close to the computational models. With such control, we show that membrane permeability can be systematically achieved by ensuring all amide (NH) groups are engaged in internal hydrogen bonding interactions. 84 designs over the 6–12 residue size range cross membranes with an apparent permeability greater than 1 × 10−6 cm/s. Designs with exposed NH groups can be made membrane permeable through the design of an alternative isoenergetic fully hydrogen-bonded state favored in the lipid membrane. The ability to robustly design membrane-permeable and orally bioavailable peptides with high structural accuracy should contribute to the next generation of designed macrocycle therapeutic

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September 15, 2022

Chemodynamical Signatures of Bar Resonances in the Galactic Disk: Current Data and Future Prospects

A. Wheeler , I. Abril-Cabezas, W. H. Trick, F. Fragkoudi, M. Ness

The Galactic disk exhibits complex chemical and dynamical substructure thought to be induced by the bar, spiral arms, and satellites. Here, we explore the chemical signatures of bar resonances in action and velocity space, and characterize the differences between the signatures of corotation (CR) and higher-order resonances using test particle simulations. Thanks to recent surveys, we now have large data sets containing metallicities and kinematics of stars outside the solar neighborhood. We compare the simulations to the observational data from Gaia EDR3 and LAMOST DR5 and find weak evidence for a slow bar with the "hat" moving group (250 km s−1 ≲ vϕ ≲ 270 km s−1) associated with its outer Lindblad resonance and "Hercules" (170 km s−1 ≲ vϕ ≲ 195 km s−1) with CR. While constraints from current data are limited by their spatial footprint, stars closer in azimuth than the Sun to the bar's minor axis show much stronger signatures of the bar's outer Lindblad and CR resonances in test particle simulations. Future data sets with greater azimuthal coverage, including the final Gaia data release, will allow reliable chemodynamical identification of bar resonances.

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The Open Cluster Chemical Abundances and Mapping Survey. VI. Galactic Chemical Gradient Analysis from APOGEE DR17

N. Meyers, J. Donor, T. Spoo, P. M. Frinchaboy, K. Cunha, A. Price-Whelan, S. R. Majewski, R. L. Beaton, G. Zasowski, J. O'Connell, A. E. Ray, D. Bizyaev, C. Chiappini, D. A. García-Hernández, D. Geisler, H. Jönsson, R. R. Lane, P. Longa-Peña, I. Minchev, D. Minniti, C. Nitschelm, A. Roman-Lopes

The goal of the Open Cluster Chemical Abundances and Mapping (OCCAM) survey is to constrain key Galactic dynamic and chemical evolution parameters by the construction and analysis of a large, comprehensive, uniform data set of infrared spectra for stars in hundreds of open clusters. This sixth contribution from the OCCAM survey presents analysis of SDSS/APOGEE Data Release 17 (DR17) results for a sample of stars in 150 open clusters, 94 of which we designate to be "high-quality" based on the appearance of their color–magnitude diagram. We find the APOGEE DR17-derived [Fe/H] values to be in good agreement with those from previous high-resolution spectroscopic open cluster abundance studies. Using a subset of the high-quality sample, the Galactic abundance gradients were measured for 16 chemical elements, including [Fe/H], for both Galactocentric radius (RGC) and guiding center radius (Rguide). We find an overall Galactic [Fe/H] versus RGC gradient of −0.073 ± 0.002 dex kpc−1 over the range of 6 > RGC < 11.5 kpc, and a similar gradient is found for [Fe/H] versus Rguide. Significant Galactic abundance gradients are also noted for O, Mg, S, Ca, Mn, Na, Al, K, and Ce. Our large sample additionally allows us to explore the evolution of the gradients in four age bins for the remaining 15 elements.

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Modules for Experiments in Stellar Astrophysics (MESA): Time-Dependent Convection, Energy Conservation, Automatic Differentiation, and Infrastructure

A. Jermyn, E. B. Bauer, J. Schwab, R. Farmer, W. H. Ball, E. P. Bellinger, A. Dotter, M. Joyce, P. Marchant, J. S. G. Mombarg, W. M. Wolf, T. L. S. Wong, G. C. Cinquegrana, E. Farrell, R. Smolec, A. Thoul, M. Cantiello, F. Herwig, O. Toloza, L. Bildsten, R. H. D. Townsend, F. X. Timmes

We update the capabilities of the open-knowledge software instrument Modules for Experiments in Stellar Astrophysics (MESA). The new auto_diff module implements automatic differentiation in MESA, an enabling capability that alleviates the need for hard-coded analytic expressions or finite difference approximations. We significantly enhance the treatment of the growth and decay of convection in MESA with a new model for time-dependent convection, which is particularly important during late-stage nuclear burning in massive stars and electron degenerate ignition events. We strengthen MESA's implementation of the equation of state, and we quantify continued improvements to energy accounting and solver accuracy through a discussion of different energy equation features and enhancements. To improve the modeling of stars in MESA we describe key updates to the treatment of stellar atmospheres, molecular opacities, Compton opacities, conductive opacities, element diffusion coefficients, and nuclear reaction rates. We introduce treatments of starspots, an important consideration for low-mass stars, and modifications for superadiabatic convection in radiation-dominated regions. We describe new approaches for increasing the efficiency of calculating monochromatic opacities and radiative levitation, and for increasing the efficiency of evolving the late stages of massive stars with a new operator split nuclear burning mode. We close by discussing major updates to MESA's software infrastructure that enhance source code development and community engagement.

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August 7, 2022

Quantitative models for building and growing fated small cell networks

Small cell clusters exhibit numerous phenomena typically associated with complex systems, such as division of labour and programmed cell death. A conserved class of such clusters occurs during oogenesis in the form of germline cysts that give rise to oocytes. Germline cysts form through cell divisions with incomplete cytokinesis, leaving cells intimately connected through intercellular bridges that facilitate cyst generation, cell fate determination and collective growth dynamics. Using the well-characterized Drosophila melanogaster female germline cyst as a foundation, we present mathematical models rooted in the dynamics of cell cycle proteins and their interactions to explain the generation of germline cell lineage trees (CLTs) and highlight the diversity of observed CLT sizes and topologies across species. We analyse competing models of symmetry breaking in CLTs to rationalize the observed dynamics and robustness of oocyte fate specification, and highlight remaining gaps in knowledge. We also explore how CLT topology affects cell cycle dynamics and synchronization and highlight mechanisms of intercellular coupling that underlie the observed collective growth patterns during oogenesis. Throughout, we point to similarities across organisms that warrant further investigation and comment on the extent to which experimental and theoretical findings made in model systems extend to other species.

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Streams on FIRE: Populations of Detectable Stellar Streams in the Milky Way and FIRE

N. Shipp, N. Panithanpaisal, L. Necib, R. Sanderson, D. Erkal, T. S. Li, I. B. Santistevan, A. Wetzel, L. R. Cullinane, A. P. Ji, S.E. Koposov, K. Kuehn, G. F. Lewis, A. B. Pace, D. B. Zucker, J. Bland-Hawthorn, E. Cunningham, S. Y. Kim, S. Lilleengen, J. Moreno, S. Sharma

We present the first detailed study comparing the populations of stellar streams in cosmological simulations to observed Milky Way dwarf galaxy streams. In particular, we compare streams identified around Milky Way analogs in the FIRE-2 simulations to stellar streams observed by the Southern Stellar Stream Spectroscopic Survey (S5). For an accurate comparison between the stream populations, we produce mock Dark Energy Survey (DES) observations of the FIRE streams and estimate the detectability of their tidal tails and progenitors. The number and stellar mass distributions of detectable stellar streams is consistent between observations and simulations. However, there are discrepancies in the distributions of pericenters and apocenters, with the detectable FIRE streams, on average, forming at larger pericenters (out to > 110 kpc) and surviving only at larger apocenters (> 40 kpc) than those observed in the Milky Way. We find that the population of high-stellar mass dwarf galaxy streams in the Milky Way is incomplete. Interestingly, a large fraction of the FIRE streams would only be detected as satellites in DES-like observations, since their tidal tails are too low-surface brightness to be detectable. We thus predict a population of yet-undetected tidal tails around Milky Way satellites, as well as a population of fully undetected low surface brightness stellar streams, and estimate their detectability with the Rubin Observatory. Finally, we discuss the causes and implications of the discrepancies between the stream populations in FIRE and the Milky Way, and explore future avenues for tests of satellite disruption in cosmological simulations.

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August 3, 2022

Reading the CARDs: The Imprint of Accretion History in the Chemical Abundances of the Milky Way’s Stellar Halo

E. Cunningham, R. Sanderson, K. Johnston, N. Panithanpaisal, M. Ness, A. Wetzel, S. R. Loebman, I. Escala, D. Horta, C-A. Faucher-Giguère

In the era of large-scale spectroscopic surveys in the Local Group, we can explore using chemical abundances of halo stars to study the star formation and chemical enrichment histories of the dwarf galaxy progenitors of the Milky Way (MW) and M31 stellar halos. In this paper, we investigate using the chemical abundance ratio distributions (CARDs) of seven stellar halos from the Latte suite of FIRE-2 simulations. We attempt to infer galaxies' assembly histories by modeling the CARDs of the stellar halos of the Latte galaxies as a linear combination of template CARDs from disrupted dwarfs, with different stellar masses M⋆ and quenching times t100. We present a method for constructing these templates using present-day dwarf galaxies. For four of the seven Latte halos studied in this work, we recover the mass spectrum of accreted dwarfs to a precision of <10 percent. For the fraction of mass accreted as a function of t100, we find the residuals of 20–30 percent for five of the seven simulations. We discuss the failure modes of this method, which arise from the diversity of star formation and chemical enrichment histories that dwarf galaxies can take. These failure cases can be robustly identified by the high model residuals. Although the CARDs modeling method does not successfully infer the assembly histories in these cases, the CARDs of these disrupted dwarfs contain signatures of their unusual formation histories. Our results are promising for using CARDs to learn more about the histories of the progenitors of the MW and M31 stellar halos.

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