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Deconvolution of pro- and antiviral genomic responses in Zika virus-infected and bystander macrophages.
Genome-wide investigations of host-pathogen interactions are often limited by analyses of mixed populations of infected and uninfected cells, which lower sensitivity and accuracy. To overcome these obstacles and identify key mechanisms by which Zika virus (ZIKV) manipulates host responses, we developed a system that enables simultaneous characterization of genome-wide transcriptional and epigenetic changes in ZIKV-infected and neighboring uninfected primary human macrophages. We demonstrate that transcriptional responses in ZIKV-infected macrophages differed radically from those in uninfected neighbors and that studying the cell population as a whole produces misleading results. Notably, the uninfected population of macrophages exhibits the most rapid and extensive changes in gene expression, related to type I IFN signaling. In contrast, infected macrophages exhibit a delayed and attenuated transcriptional response distinguished by preferential expression of IFNB1 at late time points. Biochemical and genomic studies of infected macrophages indicate that ZIKV infection causes both a targeted defect in the type I IFN response due to degradation of STAT2 and reduces RNA polymerase II protein levels and DNA occupancy, particularly at genes required for macrophage identity. Simultaneous evaluation of transcriptomic and epigenetic features of infected and uninfected macrophages thereby reveals the coincident evolution of dominant proviral or antiviral mechanisms, respectively, that determine the outcome of ZIKV exposure
Quantum recoil effects in finite-time disentanglement of two distinguishable atoms
Starting from the requirement of distinguishability of two atoms by their
positions, it is shown that photon recoil has a strong influence on finite-time
disentanglement and in some cases prevents its appearance. At near-field inter
atomic distances well localized atoms, with maximally one atom being initially
excited, may suffer disentanglement at a single finite time or even at a series
of equidistant finite times, depending on their mean inter atomic distance and
their initial electronic preparation.Comment: 13 pages, 1 figure, submitted to Physical Review on august 2
Suppression of decoherence by bath ordering
The dynamics of two coupled spins-1/2 coupled to a spin-bath is studied as an
extended model of the Tessieri-Wilkie Hamiltonian \cite{TWmodel}. The pair of
spins served as an open subsystem were prepared in one of the Bell states and
the bath consisted of some spins-1/2 is in a thermal equilibrium state from the
very beginning. It is found that with the increasing the coupling strength of
the bath spins, the bath forms a resonant antiferromagnetic order. The
polarization correlation between the two spins of the subsystem and the
concurrence are recovered in some extent to the isolated subsystem. This
suppression of the subsystem decoherence may be used to control the quantum
devices in practical applications.Comment: 32 pages, Chinese Physics (accepted
Moving Atom-Field Interaction: Correction to Casimir-Polder Effect from Coherent Back-action
The Casimir-Polder force is an attractive force between a polarizable atom
and a conducting or dielectric boundary. Its original computation was in terms
of the Lamb shift of the atomic ground state in an electromagnetic field (EMF)
modified by boundary conditions along the wall and assuming a stationary atom.
We calculate the corrections to this force due to a moving atom, demanding
maximal preservation of entanglement generated by the moving atom-conducting
wall system. We do this by using non-perturbative path integral techniques
which allow for coherent back-action and thus can treat non-Markovian
processes. We recompute the atom-wall force for a conducting boundary by
allowing the bare atom-EMF ground state to evolve (or self-dress) into the
interacting ground state. We find a clear distinction between the cases of
stationary and adiabatic motions. Our result for the retardation correction for
adiabatic motion is up to twice as much as that computed for stationary atoms.
We give physical interpretations of both the stationary and adiabatic atom-wall
forces in terms of alteration of the virtual photon cloud surrounding the atom
by the wall and the Doppler effect.Comment: 16 pages, 2 figures, clarified discussions; to appear in Phys. Rev.
Blocking Zika virus vertical transmission.
The outbreak of the Zika virus (ZIKV) has been associated with increased incidence of congenital malformations. Although recent efforts have focused on vaccine development, treatments for infected individuals are needed urgently. Sofosbuvir (SOF), an FDA-approved nucleotide analog inhibitor of the Hepatitis C (HCV) RNA-dependent RNA polymerase (RdRp) was recently shown to be protective against ZIKV both in vitro and in vivo. Here, we show that SOF protected human neural progenitor cells (NPC) and 3D neurospheres from ZIKV infection-mediated cell death and importantly restored the antiviral immune response in NPCs. In vivo, SOF treatment post-infection (p.i.) decreased viral burden in an immunodeficient mouse model. Finally, we show for the first time that acute SOF treatment of pregnant dams p.i. was well-tolerated and prevented vertical transmission of the virus to the fetus. Taken together, our data confirmed SOF-mediated sparing of human neural cell types from ZIKV-mediated cell death in vitro and reduced viral burden in vivo in animal models of chronic infection and vertical transmission, strengthening the growing body of evidence for SOF anti-ZIKV activity
The Rotating-Wave Approximation: Consistency and Applicability from an Open Quantum System Analysis
We provide an in-depth and thorough treatment of the validity of the
rotating-wave approximation (RWA) in an open quantum system. We find that when
it is introduced after tracing out the environment, all timescales of the open
system are correctly reproduced, but the details of the quantum state may not
be. The RWA made before the trace is more problematic: it results in incorrect
values for environmentally-induced shifts to system frequencies, and the
resulting theory has no Markovian limit. We point out that great care must be
taken when coupling two open systems together under the RWA. Though the RWA can
yield a master equation of Lindblad form similar to what one might get in the
Markovian limit with white noise, the master equation for the two coupled
systems is not a simple combination of the master equation for each system, as
is possible in the Markovian limit. Such a naive combination yields inaccurate
dynamics. To obtain the correct master equation for the composite system a
proper consideration of the non-Markovian dynamics is required.Comment: 17 pages, 0 figures
Moving Atom-Field Interactions: Quantum Motional Decoherence and Relaxation
The reduced dynamics of an atomic qubit coupled both to its own quantized
center of mass motion through the spatial mode functions of the electromagnetic
field, as well as the vacuum modes, is calculated in the influence functional
formalism. The formalism chosen can describe the entangled non-Markovian
evolution of the system with a full account of the coherent back-action of the
environment on the qubit. We find a slight increase in the decoherence due to
the quantized center of mass motion and give a condition on the mass and qubit
resonant frequency for which the effect is important. In optically resonant
alkali-metal atom systems, we find the effect to be negligibly small. The
framework presented here can nevertheless be used for general considerations of
the coherent evolution of qubits in moving atoms in an electromagnetic field.Comment: 9 pages, 1 figure, minor change
Entanglement, recoherence and information flow in an accelerated detector - quantum field system: Implications for black hole information issue
We study an exactly solvable model where an uniformly accelerated detector is
linearly coupled to a massless scalar field initially in the Minkowski vacuum.
Using the exact correlation functions we show that as soon as the coupling is
switched on one can see information flowing from the detector to the field and
propagating with the radiation into null infinity. By expressing the reduced
density matrix of the detector in terms of the two-point functions, we
calculate the purity function in the detector and study the evolution of
quantum entanglement between the detector and the field. Only in the ultraweak
coupling regime could some degree of recoherence in the detector appear at late
times, but never in full restoration. We explicitly show that under the most
general conditions the detector never recovers its quantum coherence and the
entanglement between the detector and the field remains large at late times. To
the extent this model can be used as an analog to the system of a black hole
interacting with a quantum field, our result seems to suggest in the prevalent
non-Markovian regime, assuming unitarity for the combined system, that black
hole information is not lost but transferred to the quantum field degrees of
freedom. Our combined system will evolve into a highly entangled state between
a remnant of large area (in Bekenstein's black hole atom analog) without any
information of its initial state, and the quantum field, now imbued with
complex information content not-so-easily retrievable by a local observer.Comment: 16 pages, 12 figures; minor change
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