pinecone/core-2020-05-10-deduplication huggingface dataset:
Consistent dust and gas models for protoplanetary disks. I. Disk shape,
  dust settling, opacities, and PAHs

We propose a set of standard assumptions for the modelling of Class II and
III protoplanetary disks, which includes detailed continuum radiative transfer,
thermo-chemical modelling of gas and ice, and line radiative transfer from
optical to cm wavelengths. We propose new standard dust opacities for disk
models, we present a simplified treatment of PAHs sufficient to reproduce the
PAH emission features, and we suggest using a simple treatment of dust
settling. We roughly adjust parameters to obtain a model that predicts typical
Class II T Tauri star continuum and line observations. We systematically study
the impact of each model parameter (disk mass, disk extension and shape, dust
settling, dust size and opacity, gas/dust ratio, etc.) on all continuum and
line observables, in particular on the SED, mm-slope, continuum visibilities,
and emission lines including [OI] 63um, high-J CO lines, (sub-)mm CO
isotopologue lines, and CO fundamental ro-vibrational lines. We find that
evolved dust properties (large grains) often needed to fit the SED, have
important consequences for disk chemistry and heating/cooling balance, leading
to stronger emission lines in general. Strong dust settling and missing disk
flaring have similar effects on continuum observations, but opposite effects on
far-IR gas emission lines. PAH molecules can shield the gas from stellar UV
radiation because of their strong absorption and negligible scattering
opacities. The observable millimetre-slope of the SED can become significantly
more gentle in the case of cold disk midplanes, which we find regularly in our
T Tauri models. We propose to use line observations of robust chemical tracers
of the gas, such as O, CO, and H2, as additional constraints to determine some
key properties of the disks, such as disk shape and mass, opacities, and the
dust/gas ratio, by simultaneously fitting continuum and line observations.Comment: accepted by A&A, 36 pages, 30 figures, 5 table
Generalized $\mu-\tau$ reflection symmetry and leptonic CP violation

We propose a generalized $\mu-\tau$ reflection symmetry to constrain the
lepton flavor mixing parameters. We obtain a new correlation between the
atmospheric mixing angle $\theta_{23}$ and the "Dirac" CP violation phase
$\delta_{\rm CP}$. Only in a specific limit our proposed CP transformation
reduces to standard $\mu-\tau$ reflection, for which $\theta_{23}$ and
$\delta_{CP}$ are both maximal. The "Majorana" phases are predicted to lie at
their CP-conserving values with important implications for the neutrinoless
double beta decay rates. We also study the phenomenological implications of our
scheme for present and future neutrino oscillation experiments including T2K,
NO$\nu$A and DUNE.Comment: 14 pages, 9 figures, latex, Final version to appear in Physics
  Letters
Extension of the $CPT$ Theorem to non-Hermitian Hamiltonians and
  Unstable States

We extend the $CPT$ theorem to quantum field theories with non-Hermitian
Hamiltonians and unstable states. Our derivation is a quite minimal one as it
requires only the time independent evolution of scalar products, invariance
under complex Lorentz transformations, and a non-standard but nonetheless
perfectly legitimate interpretation of charge conjugation as an anti-linear
operator. The first of these requirements does not force the Hamiltonian to be
Hermitian. Rather, it forces its eigenvalues to either be real or to appear in
complex conjugate pairs, forces the eigenvectors of such conjugate pairs to be
conjugates of each other, and forces the Hamiltonian to admit of an anti-linear
symmetry. The latter two requirements then force this anti-linear symmetry to
be $CPT$, while forcing the Hamiltonian to be real rather than Hermitian. Our
work justifies the use of the $CPT$ theorem in establishing the equality of the
lifetimes of unstable particles that are charge conjugates of each other. We
show that the Euclidean time path integrals of a $CPT$ symmetric theory must
always be real. In the quantum-mechanical limit the key results of the $PT$
symmetry program of Bender and collaborators are recovered, with the
$C$-operator of the $PT$ symmetry program being identified with the linear
component of the charge conjugation operator.Comment: 6 pages. Final version, to appear in Physics Letters
CALIFA, the Calar Alto Legacy Integral Field Area survey: IV. Third
  Public data release

This paper describes the Third Public Data Release (DR3) of the Calar Alto
Legacy Integral Field Area (CALIFA) survey. Science-grade quality data for 667
galaxies are made public, including the 200 galaxies of the Second Public Data
Release (DR2). Data were obtained with the integral-field spectrograph
PMAS/PPak mounted on the 3.5m telescope at the Calar Alto Observatory. Three
different spectral setups are available, i) a low-resolution V500 setup
covering the wavelength range 3749-7500 AA (4240-7140 AA unvignetted) with a
spectral resolution of 6.0 AA (FWHM), for 646 galaxies, ii) a medium-resolution
V1200 setup covering the wavelength range 3650-4840 AA (3650-4620 AA
unvignetted) with a spectral resolution of 2.3 AA (FWHM), for 484 galaxies, and
iii) the combination of the cubes from both setups (called COMBO), with a
spectral resolution of 6.0 AA and a wavelength range between 3700-7500 AA
(3700-7140 AA unvignetted), for 446 galaxies. The Main Sample, selected and
observed according to the CALIFA survey strategy covers a redshift range
between 0.005 and 0.03, spans the color-magnitude diagram and probes a wide
range of stellar mass, ionization conditions, and morphological types. The
Extension Sample covers several types of galaxies that are rare in the overall
galaxy population and therefore not numerous or absent in the CALIFA Main
Sample. All the cubes in the data release were processed using the latest
pipeline, which includes improved versions of the calibration frames and an
even further improved im- age reconstruction quality. In total, the third data
release contains 1576 datacubes, including ~1.5 million independent spectra. It
is available at http://califa.caha.es/DR3.Comment: 23 pages, 15 figures, accepted to be published in A&
Reconnaissance of the HR 8799 exosolar system. II. Astrometry and orbital motion

This is the final version of the article. Available from the American Astronomical Society / IOP Publishing via the DOI in this record.We present an analysis of the orbital motion of the four substellar objects orbiting HR 8799. Our study relies on the published astrometric history of this system augmented with an epoch obtained with the Project 1640 coronagraph with an integral field spectrograph (IFS) installed at the Palomar Hale telescope. We first focus on the intricacies associated with astrometric estimation using the combination of an extreme adaptive optics system (PALM-3000), a coronagraph, and an IFS. We introduce two new algorithms. The first one retrieves the stellar focal plane position when the star is occulted by a coronagraphic stop. The second one yields precise astrometric and spectrophotometric estimates of faint point sources even when they are initially buried in the speckle noise. The second part of our paper is devoted to studying orbital motion in this system. In order to complement the orbital architectures discussed in the literature, we determine an ensemble of likely Keplerian orbits for HR 8799bcde, using a Bayesian analysis with maximally vague priors regarding the overall configuration of the system. Although the astrometric history is currently too scarce to formally rule out coplanarity, HR 8799d appears to be misaligned with respect to the most likely planes of HR 8799bce orbits. This misalignment is sufficient to question the strictly coplanar assumption made by various authors when identifying a Laplace resonance as a potential architecture. Finally, we establish a high likelihood that HR 8799de have dynamical masses below 13 MJup, using a loose dynamical survival argument based on geometric close encounters. We illustrate how future dynamical analyses will further constrain dynamical masses in the entire system
A generalized empirical interpolation method : application of reduced basis techniques to data assimilation

In an effort to extend the classical lagrangian interpolation tools, new interpolating methods that use general interpolating functions are explored. The method analyzed in this paper, called Generalized Empirical Interpolation Method (GEIM), belongs to this class of new techniques. It generalizes the plain Empirical Interpolation Method by replacing the evaluation at interpolating points by application of a class of interpolating linear functions. The paper is divided into two parts: first, the most basic properties of GEIM (such as the well-posedness of the generalized interpolation problem that is derived) will be analyzed. On a second part, a numerical example will illustrate how GEIM, if considered from a reduced basis point of view, can be used for the real-time reconstruction of experiments by coupling data assimilation with numerical simulations in a domain decomposition framework
Theoretical and Experimental SHG Angular Intensity Patterns from Healthy and Proteolysed Muscles.

International audienceSHG angular intensity pattern (SHG-AIP) of healthy and proteolysed muscle tissues are simulated and imaged here for the first time to our knowledge. The role of the spatial distribution of second-order nonlinear emitters on SHG-AIP is highlighted. SHG-AIP with two symmetrical spots is found to be a signature of healthy muscle whereas SHG-AIP with one centered spot in pathological mdx muscle is found to be a signature of myofibrillar disorder. We also show that SHG-AIP provides information on the three-dimensional structural organization of myofibrils in physiological and proteolysed muscle. Our results open an avenue for future studies aimed at unraveling more complex physiological and pathological fibrillar tissues organization
Abnormal blood-brain barrier permeability in normal appearing white matter in multiple sclerosis investigated by MRI

Objectives: To investigate whether blood–brain barrier (BBB) permeability is disrupted in normal appearing
white matter in MS patients, when compared to healthy controls and whether it is correlated with MS clinical
characteristics.
Methods: Dynamic contrast-enhanced MRI was used to measure BBB permeability in 27 patients with MS and
compared to 24 matched healthy controls.
Results: Permeability measured as Ktrans was significantly higher in periventricular normal appearingwhite matter
(NAWM) and thalamic gray matter in MS patients when compared to healthy controls, with periventricular
NAWMshowing the most pronounced difference. Recent relapse coincided with significantly higher permeability
in periventricular NAWM, thalamic gray matter, and MS lesions. Immunomodulatory treatment and recent
relapsewere significant predictors of permeability inMS lesions and periventricular NAWM. Our results suggest
that after an MS relapse permeability gradually decreases, possibly an effect of immunomodulatory treatment.
Conclusions: Our results emphasize the importance of BBB pathology in MS, which we find to be most prominent
in the periventricular NAWM, an area prone to development of MS lesions. Both the facts that recent relapse
appears to cause widespread BBB disruption and that immunomodulatory treatment seems to attenuate this
effect indicate that BBB permeability is intricately linked to the presence of MS relapse activity. This may reveal
further insights into the pathophysiology of MS.© 2013 The Authors. Published by Elsevier Inc. All rights reserved. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike License, which permits non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited
Search for diphoton resonances in the mass range from 150 to 850 GeV in pp collisions at sqrt(s) = 8 TeV

Results are presented of a search for heavy particles decaying into two photons. The analysis is based on a View the MathML source19.7fb−1 sample of proton–proton collisions at View the MathML sources=8TeV collected with the CMS detector at the CERN LHC. The diphoton mass spectrum from 150 to 850View the MathML sourceGeV is used to search for an excess of events over the background. The search is extended to new resonances with natural widths of up to 10% of the mass value. No evidence for new particle production is observed and limits at 95% confidence level on the production cross section times branching fraction to diphotons are determined. These limits are interpreted in terms of two-Higgs-doublet model parameters
In situ study of the initial stages of diamond deposition on 3C–SiC (100) surfaces: Towards the mechanisms of diamond nucleation

The mechanisms involved in the diamond nucleation on 3C–SiC surfaces have been investigated using a sequential in situ approach using electron spectroscopies (XPS, XAES and ELS). Moreover, diamond crystals have been studied by HRSEM. The in situ nucleation treatment allows a high diamond nucleation density close to 4 × 1010 cm− 2. During the in situ enhanced nucleation treatment under plasma, a negative bias was applied to the sample. The formation of an amorphous carbon phase and the roughening of the 3C–SiC surface have been observed. The part of these competing mechanisms in diamond nucleation is discussed
A Higher Frobenius–Schur Indicator Formula for Group-Theoretical Fusion Categories

International audienceGroup-theoretical fusion categories are defined by data concerning finite groups and their cohomology: A finite group G endowed with a three-cocycle ω, and a subgroup H ⊂ G endowed with a two-cochain whose coboundary is the restriction of ω. The objects of the category are G-graded vector spaces with suitably twisted H-actions; the associativity of tensor products is controlled by ω. Simple objects are parametrized in terms of projective representations of finite groups, namely of the stabilizers in H of right H-cosets in G, with respect to two-cocycles defined by the initial data. We derive and study general formulas that express the higher Frobenius-Schur indicators of simple objects in a group-theoretical fusion category in terms of the group-theoretical and cohomological data defining the category and describing its simples
Local administration of WIN 55,212-2 reduces chronic granuloma-associated angiogenesis in rat by inhibiting NF-kappaB activation

Chronic inflammation is often associated with granuloma formation that is a hallmark of many human diseases. The transcription factor nuclear factor-kappa B (NF-κB) plays a central role in this process by regulating the expression of several pro-inflammatory genes. Cannabinoids (CBs) from Cannabis sativa L. exert a large number of biological effects including anti-inflammatory and anti-angiogenic effects. In this study, we investigated the role of CBs on granuloma formation induced by λ-carrageenin-soaked sponge implant in rat. Our results show that local administration of WIN 55,212-2, a CB1/CB2 agonist, given daily or at time of implantation significantly decreased weight and neo-angiogenesis in granuloma tissue and inhibited nuclear factor-kappa B (NF-κB)/DNA binding that was associated with a reduced inducible nitric oxide synthase (iNOS), cyclooxygenase 2 (COX-2), tumor necrosis factor alpha (TNF-α), and vascular endothelial growth factor (VEGF) messenger RNA (mRNA) and protein expression. Also, arachidonyl-2-chloroethylamide (ACEA), a CB1 selective agonist, and JWH-015, a CB2 selective agonist, exhibited the same effects that were reversed by SR141716-A and SR144528, respectively, CB1 and CB2 selective antagonists. These results indicate that CBs given locally may represent a potential therapeutic tool in controlling chronic inflammation avoiding psychotropic effects
Elliptic flow of electrons from heavy-flavour hadron decays at mid-rapidity in Pb-Pb collisions at √ s N N = 2.76 TeV

The elliptic flow of electrons from heavy-flavour hadron decays at mid-rapidity (|y| < 0.7) is measured in Pb-Pb collisions at √sNN−−−=2.76 TeV with ALICE at the LHC. The particle azimuthal distribution with respect to the reaction plane can be parametrized with a Fourier expansion, where the second coefficient (v2) represents the elliptic flow. The v2 coefficient of inclusive electrons is measured in three centrality classes (0–10%, 10–20% and 20–40%) with the event plane and the scalar product methods in the transverse momentum (pT) intervals 0.5–13 GeV/c and 0.5–8 GeV/c, respectively. After subtracting the background, mainly from photon conversions and Dalitz decays of neutral mesons, a positive v2 of electrons from heavy-flavour hadron decays is observed in all centrality classes, with a maximum significance of 5.9σ in the interval 2 < pT < 2.5 GeV/c in semi-central collisions (20–40%). The value of v2 decreases towards more central collisions at low and intermediate pT (0.5 < pT < 3 GeV/c). The v2 of electrons from heavy-flavour hadron decays at mid-rapidity is found to be similar to the one of muons from heavy-flavour hadron decays at forward rapidity (2.5 < y < 4). The results are described within uncertainties by model calculations including substantial elastic interactions of heavy quarks with an expanding strongly-interacting medium
In the pursuit of a semantic similarity metric based on UMLS annotations for articles in PubMed Central

Motivation
Although full-text articles are provided by the publishers in electronic formats, it remains a challenge to find related work beyond the title and abstract context. Identifying related articles based on their abstract is indeed a good starting point; this process is straightforward and does not consume as many resources as full-text based similarity would require. However, further analyses may require in-depth understanding of the full content. Two articles with highly related abstracts can be substantially different regarding the full content. How similarity differs when considering title-and-abstract versus full-text and which semantic similarity metric provides better results when dealing with full-text articles are the main issues addressed in this manuscript.

Methods
We have benchmarked three similarity metrics – BM25, PMRA, and Cosine, in order to determine which one performs best when using concept-based annotations on full-text documents. We also evaluated variations in similarity values based on title-and-abstract against those relying on full-text. Our test dataset comprises the Genomics track article collection from the 2005 Text Retrieval Conference. Initially, we used an entity recognition software to semantically annotate titles and abstracts as well as full-text with concepts defined in the Unified Medical Language System (UMLS®). For each article, we created a document profile, i.e., a set of identified concepts, term frequency, and inverse document frequency; we then applied various similarity metrics to those document profiles. We considered correlation, precision, recall, and F1 in order to determine which similarity metric performs best with concept-based annotations. For those full-text articles available in PubMed Central Open Access (PMC-OA), we also performed dispersion analyses in order to understand how similarity varies when considering full-text articles.

Results
We have found that the PubMed Related Articles similarity metric is the most suitable for full-text articles annotated with UMLS concepts. For similarity values above 0.8, all metrics exhibited an F1 around 0.2 and a recall around 0.1; BM25 showed the highest precision close to 1; in all cases the concept-based metrics performed better than the word-stem-based one. Our experiments show that similarity values vary when considering only title-and-abstract versus full-text similarity. Therefore, analyses based on full-text become useful when a given research requires going beyond title and abstract, particularly regarding connectivity across articles.

Availability
Visualization available at ljgarcia.github.io/semsim.benchmark/, data available at http://dx.doi.org/10.5281/zenodo.13323.The authors acknowledge the support from the members of Temporal Knowledge Bases Group at Universitat Jaume I. Funding: LJGC and AGC are both self-funded, RB is funded by the “Ministerio de Economía y Competitividad” with contract number TIN2011-24147
'James Fitzpiers Fitzgerald, Captain Thomas Lee, and the problem of 'secret traitors': conflicted loyalties during the Nine Years' War, 1594-1603'

Existing evidence pertaining to Ireland’s Nine Years’ War (1594–1603) strongly lends itself to the impression that the majority of Old English Palesmen, at least those of higher social status, chose to support the English crown during this conflict rather than their co-religionist Gaelic Irish countrymen. Loyalties, however, were anything but straightforward and could depend on any number of cultural values, social concerns, and economic incentives. Nevertheless, James Fitzpiers Fitzgerald, a ‘Bastard Geraldine’ who served as sheriff of Kildare, seemed to have been driven by a genuine sense of duty to the English crown and establishment. With the outbreak of hostilities in the 1590s, Fitzpiers proved to be a devout crown servitor, risking life and limb to confront the English queen’s Irish enemies. But, in late 1598 he suddenly, and somewhat inexplicably, threw his lot in with the Irish confederacy, defying the government he had once championed. During the ensuing investigation, the Dublin administration accumulated much damning evidence against Fitzpiers, including a patriotic plea from rebel leader Hugh O’Neill which urged Fitzpiers to defend his Irish homeland from the oppressions of English Protestant rule. Yet, at the very same time, a counter case was made by Fitzpiers’s controversial English friend, Captain Thomas Lee, which argued that Fitzpiers’s actions were more loyal than anyone could have imagined. Through an examination of Fitzpiers’s perplexing case, this paper will explore the complicated nature of allegiances in 1590s Ireland and how loyalties were not always what they seemed
Practice and assessment of oral skills in developing online preparatory materials through the InGenio authoring shell.

The practice of oral skills is a basic requirement of learning or teaching a new language, as one of the main goals in the field of language learning is developing oral communicative competence, especially needed in contexts where the students¿ L2 is the vehicular language and therefore the main means of interaction. The InGenio online authoring tool allows designers of new materials, as well as language teachers and students, to rethink and imagine new ways of dealing with practice and assessment of listening and speaking skills thanks to the flexibility of its templates, resources and tools. This article explores the ways in which the InGenio utilities, solutions and learning materials are being expanded and updated in order to address oral practice and assessment in a more efficient and effective manner making the most of these improvements to provide new learning opportunities. Keywords: practice; assessment; listening; speaking; online learning materia