pinecone/core-2020-05-10-deduplication huggingface dataset:
Identification of molecular and physiological responses to chronic environmental challenge in an invasive species: the Pacific oyster, Crassostrea gigas

Understanding the environmental responses of an invasive species is critical in predicting how ecosystem composition may be transformed in the future, especially under climate change. In this study, Crassostrea gigas, a species well adapted to the highly variable intertidal environment, was exposed to the chronic environmental challenges of temperature (19 and 24°C) and pH (ambient seawater and a reduction of 0.4 pH units) in an extended 3-month laboratory-based study. Physiological parameters were measured (condition index, shell growth, respiration, excretion rates, O:N ratios, and ability to repair shell damage) alongside molecular analyses. Temperature was by far the most important stressor, as demonstrated by reduced condition indexes and shell growth at 24°C, with relatively little effect detected for pH. Transcriptional profiling using candidate genes and SOLiD sequencing of mantle tissue revealed that classical “stress” genes, previously reported to be upregulated under acute temperature challenges, were not significantly expressed in any of the treatments, emphasizing the different response between acute and longer term chronic stress. The transcriptional profiling also elaborated on the cellular responses underpinning the physiological results, including the identification of the PI3K/AKT/mTOR pathway as a potentially novel marker for chronic environmental challenge. This study represents a first attempt to understand the energetic consequences of cumulative thermal stress on the intertidal C. gigas which could significantly impact on coastal ecosystem biodiversity and function in the future
Second-Order Eikonal Corrections for A(e,e'p)

The first-order eikonal approximation is frequently adopted in interpreting
the results of $A(e,e'p)$ measurements. Glauber calculations, for example,
typically adopt the first-order eikonal approximation. We present an extension
of the relativistic eikonal approach to $A(e,e'p)$ which accounts for
second-order eikonal corrections. The numerical calculations are performed
within the relativistic optical model eikonal approximation. The nuclear
transparency results indicate that the effect of the second-order eikonal
corrections is rather modest, even at $Q^{2} \approx 0.2$ (GeV/c)$^2$. The same
applies to polarization observables, left-right asymmetries, and differential
cross sections at low missing momenta. At high missing momenta, however, the
second-order eikonal corrections are significant and bring the calculations in
closer agreement with the data and/or the exact results from models adopting
partial-wave expansions.Comment: 16 pages, 4 figures, 1 table, submitted to Phys. Lett.
Particle acceleration by fluctuating electric fields at a magnetic field
  null point

Particle acceleration consequences from fluctuating electric fields
superposed on an X-type magnetic field in collisionless solar plasma are
studied. Such a system is chosen to mimic generic features of dynamic
reconnection, or the reconnective dissipation of a linear disturbance. We
explore numerically the consequences for charged particle distributions of
fluctuating electric fields superposed on an X-type magnetic field. Particle
distributions are obtained by numerically integrating individual charged
particle orbits when a time varying electric field is superimposed on a static
X-type neutral point. This configuration represents the effects of the passage
of a generic MHD disturbance through such a system. Different frequencies of
the electric field are used, representing different possible types of wave. The
electric field reduces with increasing distance from the X-type neutral point
as in linear dynamic magnetic reconnection. The resulting particle
distributions have properties that depend on the amplitude and frequency of the
electric field. In many cases a bimodal form is found. Depending on the
timescale for variation of the electric field, electrons and ions may be
accelerated to different degrees and often have energy distributions of
different forms. Protons are accelerated to $\gamma$-ray producing energies and
electrons to and above hard X-ray producing energies in timescales of 1 second.
The acceleration mechanism is possibly important for solar flares and solar
noise storms but is also applicable to all collisionless plasmas.Comment: 13 pages, 8 figure
Measurement of the centrality dependence of J/{\psi} yields and
  observation of Z production in lead-lead collisions with the ATLAS detector
  at the LHC

Using the ATLAS detector, a centrality-dependent suppression has been
observed in the yield of J/{\psi} mesons produced in the collisions of lead
ions at the Large Hadron Collider. In a sample of minimum-bias lead-lead
collisions at a nucleon-nucleon centre of mass energy \surd sNN = 2.76 TeV,
corresponding to an integrated luminosity of about 6.7 {\mu}b^{-1}, J/{\psi}
mesons are reconstructed via their decays to {\mu}+{\mu}- pairs. The measured
J/{\psi} yield, normalized to the number of binary nucleon-nucleon collisions,
is found to significantly decrease from peripheral to central collisions. The
centrality dependence is found to be qualitatively similar to the trends
observed at previous, lower energy experiments. The same sample is used to
reconstruct Z bosons in the {\mu}+{\mu}- final state, and a total of 38
candidates are selected in the mass window of 66 to 116 GeV. The relative Z
yields as a function of centrality are also presented, although no conclusion
can be inferred about their scaling with the number of binary collisions,
because of limited statistics. This analysis provides the first results on
J/{\psi} and Z production in lead-lead collisions at the LHC.Comment: Submitted to Physics Letters
Pipeline model of a Fermi-sea electron pump

The use of a band offset between the two leads of an electron pump driven by
a local oscillating voltage is shown to increase the pump current dramatically.
The structure of the electron transmission suggests the existence of dominant
inelastic channels which we call pipelines. This permits the formulation of a
simple model that gives a physical account of the numerical results for a
realistic device. A spectral analysis reveals the pump current to be carried by
scattering states with initial energy deep within the Fermi sea and not at its
surface, thereby rendering the effect insensitive to temperature. We show this
is compatible with the current flowing near the Fermi surface in the leads.Comment: 6 pages in RevTex4 (beta4), 4 figures; status: accepted for
  publication reason for replacement: A more detailed discussion of the
  differences to Ref. [5] has been provided & new reference adde
Spin-independent and double-spin cos(phi) asymmetries in semi-inclusive
  pion electroproduction

We consider the cos(phi) dependence of the longitudinal double-spin asymmetry
for charged pion electroproduction in semi-inclusive deep inelastic scattering,
emphasizing intrinsic transverse momentum effects. This azimuthal asymmetry
allows to measure the cos(phi) moments of the unpolarized and double-spin
cross-section, simultaneously. The size of the asymmetry, in the approximation
where all twist-3 interaction-dependent distribution and fragmentation
functions are set to zero, is estimated for HERMES kinematics; both the
spin-independent and the double-spin cos(phi) moments are predicted to be
sizeable and negative.Comment: LaTeX, 4 pages, 4 figures. Discussion on the acceptance effects
  added; recent parameterizations of distribution and fragmentation functions
  used, figures replaced. Final version to appear in Physics Letters
Hadron Multiplicity in Lepton-Nucleon Interactions

Multi-hadron production in inelastic neutrino-nucleon interactions is
investigated within the framework of the quark-gluon string model. The
contributions of the planar (one-Reggeon exchange) and cylindrical (one-Pomeron
exchange) graphs to different observables is computed using a Monte Carlo
program for the generation of hadrons produced from the decay of colorless
quark-antiquark strings. The suggested approach results in a satisfactory
description of the experimental data on $\nu(\bar\nu) N\to\mu^-(\mu^+) h X$
reactions obtained recently at CERN by the NOMAD Collaboration. The data
extends over a wide range of initial neutrino energies $E_\nu$ $<$ 200 GeV/c
and momentum transfers 1 $<$ Q $<$ 7 GeV/c, well into the region where
perturbative QCD calculations are not applicable.Comment: 10 pages, 5 figure
Probing the mechanism of EWSB with a rho parameter defined in terms of
  Higgs couplings

A definition of the rho parameter based on the Higgs couplings with the gauge
bosons, rho_h= g_{hWW}}/c^2_W g_{hZZ}, is proposed as a new probe into the
origin of the mechanism of electroweak symmetry breaking. While $\rho_h=1$
holds in the SM, deviations from one are predicted in models with extended
Higgs sector.
  We derive a general expresion of rho_h for a model with arbitrary Higgs
multiplets, and discuss its size within the context of specific models with
Higgs triplets, including the ``Little Higgs'' models recently proposed. We
find the even for Higgs models that incorporate the custodial symmetry to make
rho=1, one could have rho_h\neq 1, which could be tested at the level of a few
percent, with the precision Higgs meassurements expected at the NLC.Comment: 12 pages, 2 figure
Finite-size scaling investigation of the liquid-liquid critical point in
  ST2 water and its stability with respect to crystallization

The liquid-liquid critical point scenario of water hypothesizes the existence
of two metastable liquid phases---low-density liquid (LDL) and high-density
liquid (HDL)---deep within the supercooled region. The hypothesis originates
from computer simulations of the ST2 water model, but the stability of the LDL
phase with respect to the crystal is still being debated. We simulate
supercooled ST2 water at constant pressure, constant temperature and constant
number of molecules N for N<=729 and times up to 1000 ns. We observe clear
differences between the two liquids, both structural and dynamical. Using
several methods, including finite-size scaling, we confirm the presence of a
liquid-liquid phase transition ending in a critical point. We find that the LDL
is stable with respect to the crystal in 98% of our runs (we perform 372 runs
for LDL or LDL-like states), and in 100% of our runs for the two largest system
sizes (N=512 and 729, for which we perform 136 runs for LDL or LDL-like
states). In all these runs tiny crystallites grow and then melt within 1000 ns.
Only for N<=343 we observe six events (over 236 runs for LDL or LDL-like
states) of spontaneous crystallization after crystallites reach an estimated
critical size of about 70+/-10 molecules.Comment: 17 pages, 27 figure
On the Marginally Relevant Operator in z=2 Lifshitz Holography

We study holographic renormalization and RG flow in a strongly-coupled
Lifshitz-type theory in 2+1 dimensions with dynamical exponent z=2. The
bottom-up gravity dual we use is 3+1 dimensional Einstein gravity coupled to a
massive vector field. This model contains a marginally relevant operator around
the Lifshitz fixed point. We show how holographic renormalization works in the
presence of this marginally relevant operator without the need to introduce
explicitly cutoff-dependent counterterms. A simple closed-form expression is
found for the renormalized on-shell action. We also discuss how asymptotically
Lifshitz geometries flow to AdS in the interior due to the marginally relevant
operator. We study the behavior of the renormalized entanglement entropy and
confirm that it decreases monotonically along the Lifshitz-to-AdS RG flow.Comment: 28 pages, 5 figures, v2: updated sec. 4.4, references added, typos
  correcte
New Phases in O'Raifeartaigh-like Models and $R$-symmetry Breaking

We study $\mathcal{N}=1$ models in which supersymmetry and $R$-symmetry are
broken spontaneously. We find that even the simplest well-known
O'Raifeartaigh-like models exhibit previously unnoticed phases and dynamics.
D-terms play an important role in the dynamics, creating a runaway behavior at
tree-level which is stabilized radiatively at a large scale. This leads to a
dynamically-generated hierarchy of scales. Additionally, this mechanism
generically leads to a spontaneously broken $R$-symmetry without fine tuning
the couplings of the theory. These are arguably the simplest known models that
break the $R$-symmetry spontaneously.Comment: 15 page
Microscopic Calibration and Validation of Car-Following Models -- A
  Systematic Approach

Calibration and validation techniques are crucial in assessing the
descriptive and predictive power of car-following models and their suitability
for analyzing traffic flow. Using real and generated floating-car and
trajectory data, we systematically investigate following aspects: Data
requirements and preparation, conceptional approach including local
maximum-likelihood and global LSE calibration with several objective functions,
influence of the data sampling rate and measuring errors, the effect of data
smoothing on the calibration result, and model performance in terms of fitting
quality, robustness, parameter orthogonality, completeness and plausible
parameter values.Comment: Presentation at the 20th ISTTT in Noordwijk, the Netherlands, 201
Lagrangian Fuzzy Dynamics of Physical and Non-Physical Systems

In this paper, we show how to study the evolution of a system, given
imprecise knowledge about the state of the system and the dynamics laws. Our
approach is based on Fuzzy Set Theory, and it will be shown that the
\emph{Fuzzy Dynamics} of a $n$-dimensional system is equivalent to Lagrangian
(or Hamiltonian) mechanics in a $n+1$-dimensional space. In some cases,
however, the corresponding Lagrangian is more general than the usual one and
could depend on the action. In this case, Lagrange's equations gain a non-zero
right side proportional to the derivative of the Lagrangian with respect to the
action. Examples of such systems are unstable systems, systems with dissipation
and systems which can remember their history. Moreover, in certain situations,
the Lagrangian could be a set-valued function. The corresponding equations of
motion then become differential inclusions instead of differential equations.
We will also show that the principal of least action is a consequence of the
causality principle and the local topology of the state space and not an
independent axiom of classical mechanics.
  We emphasize that our adaptation of Lagrangian mechanics does not use or
depend on specific properties of the physical system being modeled. Therefore,
this Lagrangian approach may be equally applied to \emph{non-physical} systems.
An example of such an application is presented as well.Comment: 6 figure
The Nature of Extreme Emission Line Galaxies at z=1-2: Kinematics and
  Metallicities from Near-Infrared Spectroscopy

We present near-infrared spectroscopy of a sample of 22 Extreme Emission Line
Galaxies at redshifts 1.3 < z < 2.3, confirming that these are low-mass (M* =
10^8 - 10^9 M_sun) galaxies undergoing intense starburst episodes (M*/SFR ~
10-100 Myr). The sample is selected by [O III] or H{\alpha} emission line flux
and equivalent width using near-infrared grism spectroscopy from the 3D-HST
survey. High-resolution NIR spectroscopy is obtained with LBT/LUCI and
VLT/X-SHOOTER. The [O III]/H{\beta} line ratio is high (> 5) and [N
II]/H{\alpha} is always significantly below unity, which suggests a low
gas-phase metallicity. We are able to determine gas-phase metallicities for 7
of our objects using various strong-line methods, with values in the range
0.05-0.30 Z_sun and with a median of 0.15 Z_sun; for 3 of these objects we
detect [O III]{\lambda}4363 which allows for a direct constraint on the
metallicity. The velocity dispersion, as measured from the nebular emission
lines, is typically ~50 km/s. Combined with the observed star-forming activity,
the Jeans and Toomre stability criteria imply that the gas fraction must be
large (> 2/3), consistent with the difference between our dynamical and stellar
mass estimates. The implied gas depletion time scale (several hundred Myr) is
substantially longer than the inferred mass-weighted ages (~50 Myr), which
further supports the emerging picture that most stars in low-mass galaxies form
in short, intense bursts of star formation.Comment: Resubmitted to ApJ after first referee report, 18 pages, 14 figures,
  4 table
Residence times of receptors in dendritic spines analyzed by simulations
  in empirical domains

Analysis of high-density superresolution imaging of receptors reveal the
organization of dendrites at the nano-scale resolution. We present here
simulations in empirical live cell images, which allows converting local
information extracted from short range trajectories into simulations of long
range trajectories. Based on these empirical simulations, we compute the
residence time of an AMPA receptor (AMPAR) in dendritic spines that accounts
for receptors local interactions and geometrical organization. We report here
that depending on the type of the spine, the residence time varies from one to
five minutes. Moreover, we show that there exists transient organized
structures, previously described as potential wells that can regulate the
trafficking of AMPARs to dendritic spines.Comment: 19 page
High-resolution, 3D radiative transfer modeling : I. The grand-design
  spiral galaxy M51

Context: Dust reprocesses about half of the stellar radiation in galaxies.
The thermal re-emission by dust of absorbed energy is considered driven merely
by young stars and, consequently, often applied to trace the star formation
rate in galaxies. Recent studies have argued that the old stellar population
might anticipate a non-negligible fraction of the radiative dust heating.
  Aims: In this work, we aim to analyze the contribution of young (< 100 Myr)
and old (~ 10 Gyr) stellar populations to radiative dust heating processes in
the nearby grand-design spiral galaxy M51 using radiative transfer modeling.
High-resolution 3D radiative transfer (RT) models are required to describe the
complex morphologies of asymmetric spiral arms and clumpy star-forming regions
and model the propagation of light through a dusty medium.
  Methods: In this paper, we present a new technique developed to model the
radiative transfer effects in nearby face-on galaxies. We construct a
high-resolution 3D radiative transfer model with the Monte-Carlo code SKIRT
accounting for the absorption, scattering and non-local thermal equilibrium
(NLTE) emission of dust in M51. The 3D distribution of stars is derived from
the 2D morphology observed in the IRAC 3.6 {\mu}m, GALEX FUV, H{\alpha} and
MIPS 24 {\mu}m wavebands, assuming an exponential vertical distribution with an
appropriate scale height. The dust geometry is constrained through the
far-ultraviolet (FUV) attenuation, which is derived from the observed
total-infrared-to-far-ultraviolet luminosity ratio. The stellar luminosity,
star formation rate and dust mass have been scaled to reproduce the observed
stellar spectral energy distribution (SED), FUV attenuation and infrared SED.
(abridged)Comment: Accepted for publication in Astronomy & Astrophysics, 23 pages, 15
  figure
Wess-Zumino actions and Dirichlet Boundary Conditions for Super p-branes
  with Exotic Fractions of Supersymmetry

The general solutions in the models of closed and open superstring and super
p-branes with exotic fractions of the N=1 supersymmetry are considered and the
spontaneously broken character of the $OSp(1,2M)$ symmetry of the models is
established. It is shown that extending these models by Wess-Zumino terms
generates the Dirichlet boundary conditions for superstring and super p-branes.
Using the generalized Wess-Zumino terms new $OSp(1,2M)$ invariant super p-brane
and Dp-brane-like actions preserving $\frac{M-1}{M}$ fraction of supersymmetry
are proposed. For M=32 these models suggest new superbrane vacua of M-theory
preserving 31 from 32 global supersymmetries.Comment: Latex, 13 page
The Self-Gravitational Corrections as the Source for Stiff Matter on the
  Brane in $SAdS_5$ Bulk

A $D3-$ brane with non-zero energy density is considered as the boundary of a
five dimensional Schwarzschild anti de Sitter bulk background. Taking into
account the semi-classical corrections to the black hole entropy that arise as
a result of the self-gravitational effect, and employing the AdS/CFT
correspondence, we obtain the self-gravitational correction to the first
Friedmann-like equation. The additional term in the Hubble equation due to the
self-gravitational effect goes as $a^{-6}$. Thus, the self-gravitational
corrections act as a source of stiff matter contrary to standard FRW cosmology
where the charge of the black hole plays this role.Comment: 7 pages, no figur
The form factor of the pion in "point-form" of relativistic dynamics revisited

The electromagnetic form factor of the pion is calculated in the "point-form" of relativistic quantum mechanics using simple, phenomenological wave functions. It is found that the squared charge radius of the pion is predicted one order of magnitude larger than the experimental value and the asymptotic behavior expected from QCD cannot be reproduced. The origin of these discrepancies is analyzed. The present results confirm previous ones obtained from a theoretical model and call for major improvements in the implementation of the "point-form" approach
Exact solution for the spin-$s$ XXZ quantum chain with non-diagonal
  twists

We study integrable vertex models and quantum spin chains with toroidal
boundary conditions. An interesting class of such boundaries is associated with
non-diagonal twist matrices. For such models there are no trivial reference
states upon which a Bethe ansatz calculation can be constructed, in contrast to
the well-known case of periodic boundary conditions. In this paper we show how
the transfer matrix eigenvalue expression for the spin-$s$ XXZ chain twisted by
the charge-conjugation matrix can in fact be obtained. The technique used is
the generalization to spin-$s$ of the functional relation method based on
``pair-propagation through a vertex''. The Bethe ansatz-type equations obtained
reduce, in the case of lattice size $N=1$, to those recently found for the
Hofstadter problem of Bloch electrons on a square lattice in a magnetic field.Comment: 25 pages, LaTe
Supersymmetric Black Holes in $N=8$ Supergravity

We study the embedding of extreme (multi-) dilaton black hole solutions for
the values of the parameter $a=\sqrt{3},1,1/\sqrt{3},0$ in $N=4$ and $N=8$
four-dimensional supergravity. For each black hole solution we find different
embeddings in $N=4$ supergravity which have different numbers of unbroken
supersymmetries. When embedded in $N=8$ supergravity, all different embeddings
of the same solution have the same number of unbroken supersymmetries. Thus,
there is a relation between the value of the parameter $a$ and the number of
unbroken supersymmetries in $N=8$ supergravity, but not in $N=4$, and the
different embeddings must be related by dualities of the $N=8$ theory which are
not dualities of the $N=4$ theory. The only exception in this scheme is a {\it
dyonic} embedding of the $a=0$ black-hole solution which seems to break all
supersymmetries both in the $N=4$ and in the $N=8$ theories.Comment: A few references and comments have been adde