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| 2. |
- Bastard, Paul, et al.
(author)
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Preexisting autoantibodies to type I IFNs underlie critical COVID-19 pneumonia in patients with APS-1.
- 2021
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In: The Journal of experimental medicine. - 1540-9538. ; 218:7
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Journal article (peer-reviewed)abstract
- Patients with biallelic loss-of-function variants of AIRE suffer from autoimmune polyendocrine syndrome type-1 (APS-1) and produce a broad range of autoantibodies (auto-Abs), including circulating auto-Abs neutralizing most type I interferons (IFNs). These auto-Abs were recently reported to account for at least 10% of cases of life-threatening COVID-19 pneumonia in the general population. We report 22 APS-1 patients from 21 kindreds in seven countries, aged between 8 and 48 yr and infected with SARS-CoV-2 since February 2020. The 21 patients tested had auto-Abs neutralizing IFN-α subtypes and/or IFN-ω; one had anti-IFN-β and another anti-IFN-ε, but none had anti-IFN-κ. Strikingly, 19 patients (86%) were hospitalized for COVID-19 pneumonia, including 15 (68%) admitted to an intensive care unit, 11 (50%) who required mechanical ventilation, and four (18%) who died. Ambulatory disease in three patients (14%) was possibly accounted for by prior or early specific interventions. Preexisting auto-Abs neutralizing type I IFNs in APS-1 patients confer a very high risk of life-threatening COVID-19 pneumonia at any age.
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| 3. |
- Eberhardt, Andrew, et al.
(author)
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Classical field approximation of ultralight dark matter: Quantum break times, corrections, and decoherence
- 2024
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In: Physical Review D. - : American Physical Society (APS). - 2470-0010 .- 2470-0029. ; 109:8
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Journal article (peer-reviewed)abstract
- The classical field approximation is widely used to better understand the predictions of ultralight dark matter. Here, we use the truncated Wigner approximation method to test the classical field approximation of ultralight dark matter. This method approximates a quantum state as an ensemble of independently evolving realizations drawn from its Wigner function. The method is highly parallelizable and allows the direct simulation of quantum corrections and decoherence times in systems many times larger than have been previously studied in reference to ultralight dark matter. Our study involves simulation of systems in 1, 2, and 3 spatial dimensions. We simulate three systems, the condensation of a Gaussian random field in three spatial dimensions, a stable collapsed object in three spatial dimensions, and the merging of two stable objects in two spatial dimensions. We study the quantum corrections to the classical field theory in each case. We find that quantum corrections grow exponentially during nonlinear growth with the timescale being approximately equal to the system dynamical time. In stable systems the corrections grow quadratically. We also find that the primary effect of quantum corrections is to reduce the amplitude of fluctuations on the de Broglie scale in the spatial density. Finally, we find that the timescale associated with decoherence due to gravitational coupling to baryonic matter is at least as fast as the quantum corrections due to gravitational interactions. These results are consistent with the predictions of the classical field theory being accurate.
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| 4. |
- Eberhardt, Andrew, et al.
(author)
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Field moment expansion method for interacting bosonic systems
- 2021
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In: Physical Review D. - : American Physical Society (APS). - 2470-0010 .- 2470-0029. ; 104:8
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Journal article (peer-reviewed)abstract
- We introduce a numerical method and PYTHON package, CHiMES, that simulates quantum systems initially well approximated by mean field theory using a second order extension of the classical field approach. We call this the field moment expansion method. In this way, we can accurately approximate the evolution of first and second field moments beyond where the mean field theory breaks down. This allows us to estimate the quantum break time of a classical approximation without any calculations external to the theory. We investigate the accuracy of the field moment expansion using a number of well studied quantum test problems. Interacting bosonic systems similar to scalar field dark matter are chosen as test problems. We find that successful application of this method depends on two conditions: the quantum system must initially be well described by the classical theory, and the growth of the higher order moments must be hierarchical.
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| 5. |
- Eberhardt, Andrew, et al.
(author)
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Investigating the use of field solvers for simulating classical systems
- 2020
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In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 101:4
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Journal article (peer-reviewed)abstract
- We explore the use of field solvers as approximations of classical Vlasov-Poisson systems. This correspondence is investigated in both electrostatic and gravitational contexts. We demonstrate the ability of field solvers to be excellent approximations of problems with cold initial condition into the nonlinear regime. We also investigate extensions of the Schrodinger-Poisson system that employ multiple stacked cold streams, and the von Neumann-Poisson equation as methods that can successfully reproduce the classical evolution of warm initial conditions. We then discuss how appropriate simulation parameters need to be chosen to avoid interference terms, aliasing, and wave behavior in the field solver solutions. We present a series of criteria clarifying how parameters need to be chosen in order to effectively approximate classical solutions.
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| 6. |
- Eberhardt, Andrew, et al.
(author)
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Single classical field description of interacting scalar fields
- 2022
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In: Physical Review D. - : American Physical Society (APS). - 2470-0010 .- 2470-0029. ; 105:3
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Journal article (peer-reviewed)abstract
- We test the degree to which interacting Bosonic systems can be approximated by a classical field as total occupation number is increased. This is done with our publicly available code repository, QIBS, a new massively parallel solver for these systems. We use a number of toy models well studied in the literature and track when the classical field description admits quantum corrections, called the quantum breaktime. This allows us to test claims in the literature regarding the rate of convergence of these systems to the classical evolution. We test a number of initial conditions, including coherent states, number eigenstates, and field number states. We find that of these initial conditions, only number eigenstates do not converge to the classical evolution as occupation number is increased. We find that systems most similar to scalar field dark matter exhibit a logarithmic enhancement in the quantum breaktime with total occupation number. Systems with contact interactions or with field number state initial conditions, and linear dispersions, exhibit a power law enhancement. Finally, we find that the breaktime scaling depends on both model interactions and initial conditions.
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| 7. |
- Eberhardt, Andrew, et al.
(author)
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When quantum corrections alter the predictions of classical field theory for scalar field dark matter
- 2022
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In: Physical Review D. - 2470-0010 .- 2470-0029. ; 106:10
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Journal article (peer-reviewed)abstract
- We investigate the timescale on which quantum corrections alter the predictions of classical field theory for scalar field dark matter. This is accomplished by including second-order terms in the evolution proportional to the covariance of the field operators. When this covariance is no longer small compared to the mean field value, we say that the system has reached the “quantum breaktime,” and the predictions of classical field theory will begin to differ from those of the full quantum theory. While holding the classical field theory evolution fixed, we determine the change of the quantum breaktime as the total occupation number is increased. This provides a novel numerical estimation of the breaktime based at high occupations ntot and mode number N=256. We study the collapse of a sinusoidal overdensity in a single spatial dimension. We find that the breaktime scales as log(ntot) prior to shell crossing and then as a power law following the collapse. If we assume that the collapsing phase is representative of halos undergoing nonlinear growth, this implies that the quantum breaktime of typical systems may be as large as ∼30 of dynamical times even at occupations of ntot∼10100.
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| 8. |
- Jung, Minyong, et al.
(author)
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The AGORA High-resolution Galaxy Simulations Comparison Project. V. Satellite Galaxy Populations in a Cosmological Zoom-in Simulation of a Milky Way-Mass Halo
- 2024
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In: Astrophysical Journal. - 0004-637X. ; 964:2
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Journal article (peer-reviewed)abstract
- We analyze and compare the satellite halo populations at z ∼ 2 in the high-resolution cosmological zoom-in simulations of a 1012 M ⊙ target halo (z = 0 mass) carried out on eight widely used astrophysical simulation codes (Art-I, Enzo, Ramses, Changa, Gadget-3, Gear, Arepo-t, and Gizmo) for the AGORA High-resolution Galaxy Simulations Comparison Project. We use slightly different redshift epochs near z = 2 for each code (hereafter “z ∼ 2”) at which the eight simulations are in the same stage in the target halo’s merger history. After identifying the matched pairs of halos between the CosmoRun simulations and the DMO simulations, we discover that each CosmoRun halo tends to be less massive than its DMO counterpart. When we consider only the halos containing stellar particles at z ∼ 2, the number of satellite galaxies is significantly fewer than that of dark matter halos in all participating AGORA simulations and is comparable to the number of present-day satellites near the Milky Way or M31. The so-called “missing satellite problem” is fully resolved across all participating codes simply by implementing the common baryonic physics adopted in AGORA and the stellar feedback prescription commonly used in each code, with sufficient numerical resolution (≲100 proper pc at z = 2). We also compare other properties such as the stellar mass-halo mass relation and the mass-metallicity relation. Our work highlights the value of comparison studies such as AGORA, where outstanding problems in galaxy formation theory are studied simultaneously on multiple numerical platforms.
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| 9. |
- Kim, Ji Hoon, et al.
(author)
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THE AGORA HIGH-RESOLUTION GALAXY SIMULATIONS COMPARISON PROJECT. II. ISOLATED DISK TEST
- 2016
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In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 833:2
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Journal article (peer-reviewed)abstract
- Using an isolated Milky Way-mass galaxy simulation, we compare results from nine state-of-the-art gravito-hydrodynamics codes widely used in the numerical community. We utilize the infrastructure we have built for the AGORA High-resolution Galaxy Simulations Comparison Project. This includes the common disk initial conditions, common physics models (e.g., radiative cooling and UV background by the standardized package Grackle) and common analysis toolkit yt, all of which are publicly available. Subgrid physics models such as Jeans pressure floor, star formation, supernova feedback energy, and metal production are carefully constrained across code platforms. With numerical accuracy that resolves the disk scale height, we find that the codes overall agree well with one another in many dimensions including: gas and stellar surface densities, rotation curves, velocity dispersions, density and temperature distribution functions, disk vertical heights, stellar clumps, star formation rates, and Kennicutt-Schmidt relations. Quantities such as velocity dispersions are very robust (agreement within a few tens of percent at all radii) while measures like newly formed stellar clump mass functions show more significant variation (difference by up to a factor of ∼3). Systematic differences exist, for example, between mesh-based and particle-based codes in the low-density region, and between more diffusive and less diffusive schemes in the high-density tail of the density distribution. Yet intrinsic code differences are generally small compared to the variations in numerical implementations of the common subgrid physics such as supernova feedback. Our experiment reassures that, if adequately designed in accordance with our proposed common parameters, results of a modern high-resolution galaxy formation simulation are more sensitive to input physics than to intrinsic differences in numerical schemes.
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| 10. |
- Manry, Jérémy, et al.
(author)
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The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies.
- 2022
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 1091-6490. ; 119:21
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Journal article (peer-reviewed)abstract
- Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection fatality rate (IFR) doubles with every 5 y of age from childhood onward. Circulating autoantibodies neutralizing IFN-α, IFN-ω, and/or IFN-β are found in ∼20% of deceased patients across age groups, and in ∼1% of individuals aged <70 y and in >4% of those >70 y old in the general population. With a sample of 1,261 unvaccinated deceased patients and 34,159 individuals of the general population sampled before the pandemic, we estimated both IFR and relative risk of death (RRD) across age groups for individuals carrying autoantibodies neutralizing type I IFNs, relative to noncarriers. The RRD associated with any combination of autoantibodies was higher in subjects under 70 y old. For autoantibodies neutralizing IFN-α2 or IFN-ω, the RRDs were 17.0 (95% CI: 11.7 to 24.7) and 5.8 (4.5 to 7.4) for individuals <70 y and ≥70 y old, respectively, whereas, for autoantibodies neutralizing both molecules, the RRDs were 188.3 (44.8 to 774.4) and 7.2 (5.0 to 10.3), respectively. In contrast, IFRs increased with age, ranging from 0.17% (0.12 to 0.31) for individuals <40 y old to 26.7% (20.3 to 35.2) for those ≥80 y old for autoantibodies neutralizing IFN-α2 or IFN-ω, and from 0.84% (0.31 to 8.28) to 40.5% (27.82 to 61.20) for autoantibodies neutralizing both. Autoantibodies against type I IFNs increase IFRs, and are associated with high RRDs, especially when neutralizing both IFN-α2 and IFN-ω. Remarkably, IFRs increase with age, whereas RRDs decrease with age. Autoimmunity to type I IFNs is a strong and common predictor of COVID-19 death.
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