pinecone/core-2020-05-10-deduplication huggingface dataset:
The Evolution of Virulence in RNA Viruses under a Competition–Colonization Trade-Off

RNA viruses exist in large intra-host populations which display great genotypic and phenotypic diversity. We analyze a model of viral competition between two viruses infecting a constantly replenished cell pool. We assume a trade-off between the ability of the virus to colonize new cells (cell killing rate or virulence) and its local competitiveness (replicative success within coinfected cells). We characterize the conditions that allow for viral spread by means of the basic reproductive number and show that a local coexistence equilibrium exists, which is asymptotically stable. At this equilibrium, the less virulent competitor has a reproductive advantage over the more virulent colonizer reflected by a larger equilibrium population size of the competitor. The equilibria at which one virus outcompetes the other one are unstable, i.e., a second virus is always able to permanently invade. We generalize the two-virus model to multiple viral strains, each displaying a different virulence. To account for the large phenotypic diversity in viral populations, we consider a continuous spectrum of virulences and present a continuum limit of this multiple viral strains model that describes the time evolution of an initial continuous distribution of virulence without mutations. We provide a proof of the existence of solutions of the model equations, analytically assess the properties of stationary solutions, and present numerical approximations of solutions for different initial distributions. Our simulations suggest that initial continuous distributions of virulence evolve toward a distribution that is extremely skewed in favor of competitors. At equilibrium, only the least virulent part of the population survives. The discrepancy of this finding in the continuum limit with the two-virus model is attributed to the skewed equilibrium subpopulation sizes and to the transition to a continuum. Consequently, in viral quasispecies with high virulence diversity, the model predicts collective virulence attenuation. This result may contribute to understanding virulence attenuation, which has been reported in several experimental studies
Tuning the Plasmonic Response up : Hollow Cuboid Metal Nanostructures

Article publicat sota la llicència AuthorChoice de l'American Chemical Society: https://pubs.acs.org/userimages/ContentEditor/1404932937291/authorchoice_form.pdfWe report the fine-tuning of the localized surface plasmon resonances (LSPRs) from ultraviolet to near-infrared by nanoengineering the metal nanoparticle morphologies from solid Ag nanocubes to hollow AuAg nanoboxes and AuAg nanoframes. Spatially resolved mapping of plasmon resonances by electron energy loss spectroscopy (EELS) revealed a homogeneous distribution of highly intense plasmon resonances around the hollow nanostructures and the interaction, that is, hybridization, of inner and outer plasmon fields for the nanoframe. Experimental findings are accurately correlated with the boundary element method (BEM) simulations demonstrating that the homogeneous distribution of the plasmon resonances is the key factor for their improved plasmonic properties. As a proof of concept for these enhanced plasmonic properties, we show the effective label free sensing of bovine serum albumin (BSA) of single-walled AuAg nanoboxes in comparison with solid Au nanoparticles, demonstrating their excellent performance for future biomedical applications
Stability of the superconducting state in YBa_2Cu_3O_7

The nonadiabatic Heisenberg model (NHM) proposed as an extension of the
Heisenberg model makes a contribution to the eigenstate problem of
superconductivity. The Hamiltonian H^n derived within this group-theoretical
model has superconducting eigenstates if and only if the considered material
possesses a narrow, roughly half-filled "superconducting" energy band of
special symmetry in its band structure. This paper shows that the
high-temperature superconductor YBa_2Cu_3O_7 possesses such a superconducting
band. This new result together with previous observations about other
superconductors and non-superconductors corroborates the theoretical evidence
within the NHM that stable superconducting states are connected with
superconducting bands. It is proposed that the type of superconductivity, i.e.,
whether the material is a conventional low-T_c or a high-T_c superconductor, is
determined by the energetically lowest boson excitations that carry the crystal
spin 1*hbar and are sufficiently stable to transport this crystal spin-angular
momentum through the crystal. This mechanism provides the electron-phonon
mechanism that enters the BCS theory in conventional superconductors
Study of exclusive two-photon production of W+W− in pp collisions at s√=7 TeV and constraints on anomalous quartic gauge couplings

A search for exclusive or quasi-exclusive W+W− production by photon-photon interactions, pp → p(*)W+W−p(*), at s√=7 TeV is reported using data collected by the CMS detector with an integrated luminosity of 5.05 fb−1. Events are selected by requiring a μ ±e∓ vertex with no additional associated charged tracks and dilepton transverse momentum p T(μ ±e∓) > 30 GeV. Two events passing all selection requirements are observed in the data, compared to a standard model expectation of 2.2 ± 0.4 signal events with 0.84 ± 0.15 background. The tail of the dilepton p T distribution is studied for deviations from the standard model. No events are observed with p T  > 100 GeV. Model-independent upper limits are computed and compared to predictions involving anomalous quartic gauge couplings. The limits on the parameters aW0,C/Λ2 with a dipole form factor and an energy cutoff Λcutoff = 500 GeV are of the order of 10−4
A strongly-coupled zig-zag transition.

The zig-zag symmetry transition is a phase transition in 1D quantum wires, in which a Wigner lattice of electrons transitions to two staggered lattices. Previous studies model this transition as a Luttinger liquid coupled to a Majorana fermion. The model exhibits interesting RG flows, involving quenching of velocities in subsectors of the theory. We suggest an extension of the model which replaces the Majorana fermion by a more general CFT; this includes an experimentally realizable case with two Majorana fermions. We analyse the RG flow both in field theory and using AdS/CFT techniques in the large central charge limit of the CFT. The model has a rich phase structure with new qualitative features, already in the two Majorana fermion case. The AdS/CFT calculation involves considering back reaction in space-time to capture subleading effects
Precise Higgs-background predictions: merging NLO QCD and squared quark-loop corrections to four-lepton + 0,1 jet production

We present precise predictions for four-lepton plus jets production at the LHC obtained within the fully automated Sherpa+OpenLoops framework. Off-shell intermediate vector bosons and related interferences are consistently included using the complex-mass scheme. Four-lepton plus 0- and 1-jet final states are described at NLO accuracy, and the precision of the simulation is further increased by squared quark-loop NNLO contributions in the gg -> 4l, gg -> 4l+g, gq -> 4l+q, and qq -> 4l+g channels. These NLO and NNLO contributions are matched to the Sherpa parton shower, and the 0- and 1-jet final states are consistently merged using the MEPS@NLO technique. Thanks to Sudakov resummation, the parton shower provides improved predictions and uncertainty estimates for exclusive observables. This is important when jet vetoes or jet bins are used to separate four-lepton final states arising from Higgs decays, diboson production, and top-pair production. Detailed predictions are presented for the ATLAS and CMS H->WW analyses at 8 TeV in the 0- and 1-jet bins. Assessing renormalisation-, factorisation- and resummation-scale uncertainties, which reflect also unknown subleading Sudakov logarithms in jet bins, we find that residual perturbative uncertainties are as small as a few percent
A substellar component orbiting the F-star 30 Ari B

CONTEXT: Most current radial velocity planet search programs have
concentrated on stars of one solar mass. Our knowledge on the frequency of
giant planets and brown dwarf companions to more massive stars is thus rather
limited. In the case of solar-like stars, the frequency of short-period brown
dwarf companions and very massive planets seems to be low. AIMS: Here we
present evidence for a substellar companion to 30 Ari B, an F-star of 1.16
$\pm$ 0.04 $\rm M_\odot$ that is a member of a hierarchical triple system.
METHODS: The companion was detected by means of precise radial velocity
measurements using the 2-m Alfred-Jensch telescope and its 'echelle
spectrograph. An iodine absorption cell provided the wavelength reference for
precise stellar radial velocity measurements. RESULTS: We analyzed our radial
velocity measurements and derived an orbit to the companion with period, P=
335.1+/-2.5 days, eccentricity e = 0.289+/-0.092, and mass function f(m) =
(6.1+/-1.7)*10E-7 Modot. CONCLUSIONS: We conclude that the radial velocity
variations of 30 Ari B are due to a companion with $m$ sin $i$ of $9.88\pm0.94$
$\rm M_{Jup}$ that is either a massive planet or a brown dwarf. {The object
thus belongs to the rare class of massive planets and brown dwarfs orbiting
main- sequence stars.Comment: 8 pages, 15 figures, paper accepted by Astronomy and Astrophysic
Low Voltage I-V Characteristics in Magnetic Tunnel Junctions

We show that elastic currents that take into account variations of the tunnel
transmitivity with voltage and a large ratio of majority to minority spin
densities of states of the $s$ band, can account for the low voltage current
anomalies observed in magnet-oxide-magnet junctions. The anomalies can be
positive, negative or have a mixed form, depending of the position of the Fermi
level in the $s$ band, in agreement with observations. Magnon contribution is
negligible small to account for the sharp drop of the magnetoresistance with
the voltage bias.Comment: 8 pages, 3 postscript figure
Quantum Coulomb Glass: Anderson localization in an interacting system

The quantum Coulomb glass model describes disordered interacting electrons on
the insulating side of a metal-insulator transition. By taking quantum
fluctuations into account it can describe not only the localized limit but also
the weakly localized regime. We discuss several possibilities to generalize the
concept of Anderson localization to interacting electron systems such as the
quantum Coulomb glass and define criteria for localization. The corresponding
physical quantities are calculated by numerically exact diagonalization. The
results indicate that single-particle excitations close to the Fermi energy
become more strongly localized under the influence of interaction.Comment: 5 pages RevTeX, 4 figures, to appear in Proc. VII Int. Conf. on
  Hopping and Related Phenomen
Exact Extended Supersymmetry on a Lattice: Twisted N=2 Super Yang-Mills
  in Two Dimensions

We propose a lattice action for two dimensional super Yang-Mills theory with
a twisted N=2 supersymmetry. The extended supersymmetry is fully and exactly
realized on the lattice. The method employed is quite general and its extension
to the N=4 supersymmetry in four dimensions is briefly presented. The lattice
has a new type of ``fermionic'' links, where odd Grassmann variables,
supercharges and fermionic connections sit. The Leibniz rule is preserved on
the lattice, although in a modified ``shifted'' form that takes into account
the link nature of both derivatives and supercharges. Superfields are
semi-local objects and superfield expansion is naturally embedded in the
lattice structure. The Dirac-K\"ahler twist generates the extended twisted
supersymmetry, turning the multiplicity of species doublers into the
multiplicity due to the extended supersymmetry. In this way the balance between
bosonic and fermionic degrees of freedom is preserved.Comment: 15 pages, 11 figure
HALOGAS: HI Observations and Modeling of the Nearby Edge-on Spiral
  Galaxy NGC 4565

We present 21-cm observations and models of the neutral hydrogen in NGC 4565,
a nearby, edge-on spiral galaxy, as part of the Westerbork Hydrogen Accretion
in LOcal GAlaxieS (HALOGAS) survey. These models provide insight concerning
both the morphology and kinematics of HI above, as well as within, the disk.
NGC 4565 exhibits a distinctly warped and asymmetric disk with a flaring layer.
Our modeling provides no evidence for a massive, extended HI halo. We see
evidence for a bar and associated radial motions. Additionally, there are
indications of radial motions within the disk, possibly associated with a ring
of higher density. We see a substantial decrease in rotational velocity with
height above the plane of the disk (a lag) of -40 +5/-20 km/s/kpc and -30
+5/-30 km s/kpc in the approaching and receding halves, respectively. This lag
is only seen within the inner ~4.75' (14.9 kpc) on the approaching half and
~4.25' (13.4 kpc) on the receding, making this a radially shallowing lag, which
is now seen in the HI layers of several galaxies. When comparing results for
NGC 4565 and those for other galaxies, there are tentative indications of high
star formation rate per unit area being associated with the presence of a halo.
Finally, HI is found in two companion galaxies, one of which is clearly
interacting with NGC 4565.Comment: 17 pages, 16 figures, accepted for publication in the Astrophysical
  Journal, modified affiliatio
Inflation and Dark Matter in the Higgs Portal of Classically Scale
  Invariant Standard Model

We consider a minimal classically scale-invariant extension of the Standard
Model. In this theory, the Higgs mechanism is triggered and the electroweak
symmetry breaking is generated radiatively by the Coleman-Weinberg sector which
is coupled to the SM Higgs. We extend the Higgs portal interactions of the
theory to include an additional singlet which is also non-minimally coupled to
gravity. This generates a single-field slow-roll inflation mechanism in the
effective field theory formulation which is robust up to Planck scales. Our
approach does not require integrating in any additional new physics degrees of
freedom to unitarise the theory in the sub-Planckian regime where inflation
happens. As a result, no large threshold corrections appear in our approach to
inflation so that the electroweak scale and the SM Higgs mass are not affected.
The singlet field responsible for inflation also gives a viable dark matter
candidate in our model. We also discuss the relation between classical
scale-invariance of the effective theory and the possible local scale
invariance of the full theory and comment on the naturalness of the electroweak
scale.Comment: v2: References added, minor corrections, matches JHEP version, 23
  page
Verification of first-principles codes: comparison of total energies,
  phonon frequencies, electron-phonon coupling and zero-point motion correction
  to the gap between ABINIT and QE/Yambo

With the ever-increasing sophistication of codes, the verification of the
implementation of advanced theoretical formalisms becomes critical. In
particular, cross comparison between different codes provides a strong hint in
favor of the correctness of the implementations, and a measure of the
(hopefully small) possible numerical differences. We lead a rigorous and
careful study of the quantities that enter in the calculation of the zero-point
motion renormalization of the direct band gap of diamond due to electron-phonon
coupling, starting from the total energy, and going through the computation of
phonon frequencies and electron-phonon matrix elements. We rely on two
independent implementations : Quantum Espresso + Yambo and ABINIT. We provide
the order of magnitude of the numerical discrepancies between the codes, that
are present for the different quantities: less than $10^{-5}$ Hartree per atom
on the total energy (-5.722 Ha/at), less than 0.07 cm$^{-1}$ on the
$\Gamma,L,X$ phonon frequencies (555 to 1330 cm$^{-1}$), less than 0.5% on the
square of the electron-phonon matrix elements and less than 4 meV on the
zero-point motion renormalization of each eigenenergies (44 to 264 meV). Within
our approximations, the DFT converged direct band gap renormalization in
diamond due to the electron-phonon coupling is -0.409 eV (reduction of the band
gap).Comment: 11 pages, 5 figure
Single-Valued Hamiltonian via Legendre-Fenchel Transformation and Time
  Translation Symmetry

Under conventional Legendre transformation, systems with a non-convex
Lagrangian will result in a multi-valued Hamiltonian as a function of conjugate
momentum. This causes problems such as non-unitary time evolution of quantum
state and non-determined motion of classical particles, and is physically
unacceptable. In this work, we propose a new construction of single-valued
Hamiltonian by applying Legendre-Fenchel transformation, which is a
mathematically rigorous generalization of conventional Legendre transformation,
valid for non-convex Lagrangian systems, but not yet widely known to the
physics community. With the new single-valued Hamiltonian, we study spontaneous
breaking of time translation symmetry and derive its vacuum state. Applications
to theories of cosmology and gravitation are discussed.Comment: Journal Version, 16pp. All results + conclusions un-changed, only
  minor refinements to clarify the importance of our new LFT method and its
  physics applications; references adde
Semiclassical pair production rate for time-dependent electrical fields
  with more than one component: -WKB-approach and world-line instantons

We present an analytic calculation of the semiclassical electron-positron
pair creation rate by time-dependent electrical fields. We use two methods,
first the imaginary time method in the WKB-approximation and second the
world-line instanton approach. The analytic tools for both methods are
generalized to time-dependent electric fields with more than one component. For
the WKB method an expansion of the momentum spectrum of produced pairs around
the canonical momentum $\vec{P}=0$ is presented which simplifies the
computation of the pair creation rate. We argue that the world-line instanton
method of [Dunne et al., Phys. Rev. D73, 065028 (2006)] implicitly performs
this expansion of the momentum spectrum around $\vec{P}=0$. Accordingly the
generalization to more than one component is shown to agree with the WKB result
obtained via this expansion. However the expansion is only a good approximation
for the cases where the momentum spectrum is peaked around $\vec{P}=0$. Thus
the expanded WKB result and the world-line instanton method of [Dunne et al.,
Phys. Rev. D73, 065028 (2006)] as well as the generalized method presented here
are only applicable in these cases. We study the two component case of a
rotating electric field and find a new analytic closed form for the momentum
spectrum using the generalized WKB method. The momentum spectrum for this field
is not peaked around $\vec{P}=0$.Comment: 19 pages, 2 figures, V2: some passages shortened, importance of the
  location of the peak of the momentum spectrum clarified, final version to
  appear in Nucl. Phys.
Generalized Poincare algebras and Lovelock-Cartan gravity theory

We show that the Lagrangian for Lovelock-Cartan gravity theory can be
re-formulated as an action which leads to General Relativity in a certain
limit. In odd dimensions the Lagrangian leads to a Chern-Simons theory
invariant under the generalized Poincar\'{e} algebra $\mathfrak{B}_{2n+1},$
while in even dimensions the Lagrangian leads to a Born-Infeld theory invariant
under a subalgebra of the $\mathfrak{B}_{2n+1}$ algebra. It is also shown that
torsion may occur explicitly in the Lagrangian leading to new torsional
Lagrangians, which are related to the Chern-Pontryagin character for the
$B_{2n+1}$ group.Comment: v2: 18 pages, minor modification in the title, some clarifications in
  the abstract, introduction and section 2, section 4 has been rewritten, typos
  corrected, references added. Accepted for publication in Physic letters
Stellar Population gradients in galaxy discs from the CALIFA survey

While studies of gas-phase metallicity gradients in disc galaxies are common,
very little has been done in the acquisition of stellar abundance gradients in
the same regions. We present here a comparative study of the stellar
metallicity and age distributions in a sample of 62 nearly face-on, spiral
galaxies with and without bars, using data from the CALIFA survey. We measure
the slopes of the gradients and study their relation with other properties of
the galaxies. We find that the mean stellar age and metallicity gradients in
the disc are shallow and negative. Furthermore, when normalized to the
effective radius of the disc, the slope of the stellar population gradients
does not correlate with the mass or with the morphological type of the
galaxies. Contrary to this, the values of both age and metallicity at $\sim$2.5
scale-lengths correlate with the central velocity dispersion in a similar
manner to the central values of the bulges, although bulges show, on average,
older ages and higher metallicities than the discs. One of the goals of the
present paper is to test the theoretical prediction that non-linear coupling
between the bar and the spiral arms is an efficient mechanism for producing
radial migrations across significant distances within discs. The process of
radial migration should flatten the stellar metallicity gradient with time and,
therefore, we would expect flatter stellar metallicity gradients in barred
galaxies. However, we do not find any difference in the metallicity or age
gradients in galaxies with without bars. We discuss possible scenarios that can
lead to this absence of difference.Comment: 24 pages, 17 figures, accepted for publication in A&
Charged Renyi entropies and holographic superconductors

Charged Renyi entropies were recently introduced as a measure of entanglement
between different charge sectors of a theory. We investigate the phase
structure of charged Renyi entropies for CFTs with a light, charged scalar
operator. The charged Renyi entropies are calculated holographically via areas
of charged hyperbolic black holes. These black holes can become unstable to the
formation of scalar hair at sufficiently low temperature; this is the
holographic superconducting instability in hyperbolic space. This implies that
the Renyi entropies can be non-analytic in the Renyi parameter n. We find the
onset of this instability as a function of the charge and dimension of the
scalar operator. We also comment on the relation between the phase structure of
these entropies and the phase structure of a holographic superconductor in flat
space.Comment: 21 pages, 6 figure