pinecone/core-2020-05-10-deduplication huggingface dataset:
Augmenting B with control annotations

CSP||B is an integration of the process algebra Communicating Sequential Processes (CSP), and the B-Method, which enables consistent controllers to be written for B machines in a verifiable way. Controllers are consistent if they call operations only when they are enabled. Previous work has established a way of verifying consistency between controllers and machines by translating control flow to AMN and showing that a control loop invariant is preserved. This paper offers an alternative approach, which allows fragments of control flow expressed as annotations to be associated with machine operations. This enables designers’ understanding about local relationships between successive operations to be captured at the point the operations are written, and used later when the controller is developed. Annotations provide a bridge between controllers and machines, expressing the relevant aspects of control flow so that controllers can be verified simply by reference to the annotations without the need to consider the details of the machine operations. This paper presents the approach through two instances of annotations with their associated control languages, covering recursion, prefixing, choice, and interrupt
Geological evidence for paleotsunamis along eastern Sicily (Italy): an overview

We present geological evidence for paleotsunamis
along the  230 km-long coast of eastern Sicily (Italy); combining
this information with historical data, we reconstruct
a unique history of tsunami inundations. We integrate data
on 38 paleotsunami deposits (from fine sand layers to boulders)
collected at 11 sites (one offshore). The geological data
record traces of large tsunamis which have occurred during
the past 4 millennia. Chronological constrains include 14C,
210Pb and 137Cs, OSL and tephrochronology. When compatible,
the age of the paleotsunami deposits is associated
to historical events, but it is also used to highlight unknown
tsunamis. Average tsunami recurrence interval (between 320
and 840 yr) and minimum inland tsunami ingressions (often
greater than the historical ones) were estimated at several
sites. On the basis of this work, the tsunami catalogue
is implemented by two unknown tsunamis which occurred
during the first millennium BC and by one unknown regional
tsunami, which occurred in 650–770 AD. By including this
latter event in the eastern Sicily catalogue, we estimate an
average recurrence interval for strong tsunamis of ca. 385 yr.
Comparison and merging of historical and geological data
can definitely contribute to a better understanding of regional
and local tsunami potential and provides robust parameters to
be used in tsunami hazard estimates
DNAI2 mutations can cause primary ciliary dyskinesia with outer dynein arm defects.

Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disorder characterized by recurrent infections of the airways and randomization of left/right\ud
body asymmetry. The phenotype results from dysfunction of motile cilia of the\ud
respiratory epithelium and the embryonic node. Dysmotile sperm tails often cause\ud
infertility in male PCD patients. Underlying ultrastructural defects frequently involve\ud
outer dynein arms (ODA), which are responsible for generation of cilia movement.\ud
We recently showed that recessive mutations of DNAH5 encoding a heavy dynein chain are frequently found in PCD with ODA defects. Genes (DNAI1, TXNDC3, DNAH11) encoding for other ODA components can also account for PCD. Here, we analyzed the protein expression of the ODA intermediate chain DNAI2 and found sub-localization throughout respiratory cilia and sperm tails. Mutational screening of 105 PCD families revealed in one affected a homozygous mutation within the facultative splice acceptor site of exon 4. RNA studies confirmed absence of exon 4 in all transcripts predicting a premature stop codon. Consistently mutant respiratory\ud
cells lacked DNAI2 expression and exhibited ODA defects by electron microscopy.\ud
High-resolution immunofluorescence imaging demonstrated mis-localization of DNAH5 indicating that DNAI2 is essential for assembly of these ODA components. In addition we report homozygous loss-of-function DNAI2 mutations located within the\ud
obligatory splice donor site of exon 11 in four affected individuals with ODA defects\ud
originating from a consanguineous PCD family that showed significant linkage to the DNAI2 locus in a total genome scan. In summary, we provide the first evidence that DNAI2 can account for PCD with ODA defects
Ligand-Occupied Integrin Internalization Links Nutrient Signaling to Invasive Migration.

Integrin trafficking is key to cell migration, but little is known about the spatiotemporal organization of integrin endocytosis. Here, we show that α5β1 integrin undergoes tensin-dependent centripetal movement from the cell periphery to populate adhesions located under the nucleus. From here, ligand-engaged α5β1 integrins are internalized under control of the Arf subfamily GTPase, Arf4, and are trafficked to nearby late endosomes/lysosomes. Suppression of centripetal movement or Arf4-dependent endocytosis disrupts flow of ligand-bound integrins to late endosomes/lysosomes and their degradation within this compartment. Arf4-dependent integrin internalization is required for proper lysosome positioning and for recruitment and activation of mTOR at this cellular subcompartment. Furthermore, nutrient depletion promotes subnuclear accumulation and endocytosis of ligand-engaged α5β1 integrins via inhibition of mTORC1. This two-way regulatory interaction between mTORC1 and integrin trafficking in combination with data describing a role for tensin in invasive cell migration indicate interesting links between nutrient signaling and metastasis.Peer-reviewedPublisher Versio
Novel BPS Wilson loops in three-dimensional quiver Chern-Simons-matter
  theories

We show that generic three-dimensional $\mathcal N=2$ quiver super
Chern-Simons-matter theories admit Bogomol'nyi-Prasad-Sommerfield (BPS)
Drukker-Trancanelli (DT) type Wilson loops. We investigate both Wilson loops
along timelike infinite straight lines in Minkowski spacetime and circular
Wilson loops in Euclidean space. In Aharnoy-Bergman-Jafferis-Maldacena theory,
we find that generic BPS DT type Wilson loops preserve the same number of
supersymmetries as Gaiotto-Yin type Wilson loops. There are several free
parameters for generic BPS DT type Wilson loops in the construction, and
supersymmetry enhancement for Wilson loops happens for special values of the
parameters.Comment: V1, 5 pages; V2, 13 pages, circular Wilson loops added, published
  versio
Form factors in $B\to \pi\pi\ell\bar\nu_\ell$ from QCD light-cone sum
  rules

The form factors of the semileptonic $B\to \pi\pi\ell\bar\nu$ decay are
calculated from QCD light-cone sum rules with the distribution amplitudes of
dipion states. This method is valid in the kinematical region, where the
hadronic dipion state has a small invariant mass and simultaneously a large
recoil. The derivation of the sum rules is complicated by the presence of an
additional variable related to the angle between the two pions. In particular,
we realize that not all invariant amplitudes in the underlying correlation
function can be used, some of them generating kinematical singularities in the
dispersion relation. The two sum rules that are free from these ambiguities are
obtained in the leading twist-2 approximation, predicting the $\bar{B}^0\to
\pi^+\pi^0$ form factors $F_{\perp}$ and $F_{\parallel}$ of the vector and
axial $b\to u$ current, respectively. We calculate these form factors at the
momentum transfers $0<q^2\lesssim 12 $ GeV$^2$ and at the dipion mass close to
the threshold $4m_\pi^2$. The sum rule results indicate that the contributions
of the higher partial waves to the form factors are suppressed with respect to
the lowest $P$-wave contribution and that the latter is not completely
saturated by the $\rho$-meson term.Comment: 17 pages, 4 figures, a few comments and references added, version to
  be published in Nucl.Phys.
dHybrid: a massively parallel code for hybrid simulations of space plasmas

A massively parallel simulation code, called \textit{dHybrid}, has been developed to perform global scale studies of space plasma interactions. This code is based on an explicit hybrid model; the numerical stability and parallel scalability of the code are studied. A stabilization method for the explicit algorithm, for regions of near zero density, is proposed. Three-dimensional hybrid simulations of the interaction of the solar wind with unmagnetized artificial objects are presented, with a focus on the expansion of a plasma cloud into the solar wind, which creates a diamagnetic cavity and drives the Interplanetary Magnetic Field out of the expansion region. The dynamics of this system can provide insights into other similar scenarios, such as the interaction of the solar wind with unmagnetized planets
THE BROWN DWARF KINEMATICS PROJECT. II. DETAILS ON NINE WIDE COMMON PROPER MOTION VERY LOW MASS COMPANIONS TO NEARBY STARS

We report on nine wide common proper motion systems containing late-type M, L, or T companions. We confirm six previously reported companions, and identify three new systems. The ages of these systems are determined using diagnostics for both stellar primaries and low-mass secondaries and masses for the secondaries are inferred using evolutionary models. Of our three new discoveries, the M3+T6.5 pair G 204-39 and SDSS J1758+4633 has an age constrained to 0.5-1.5 Gyr making the secondary a potentially useful brown dwarf benchmark. The G5+L4 pair G 200-28 and SDSS J1416+5006 has a projected separation of ~25,000 AU making it one of the widest and lowest binding energy systems known to date. The system containing NLTT 2274 and SDSS J0041+1341 is an older M4+L0 (>4.5 Gyr) pair which shows Hα activity in the secondary but not the primary making it a useful tracer of age/mass/activity trends. Two of the nine systems have discrepant component ages that emerge from stellar or ultracool diagnostics indicating possible shortcomings in our understanding of the age diagnostics of stars and brown dwarfs. We find a resolved binary frequency for widely separated (>100 AU) low-mass companions (i.e., at least a triple system) which is at least twice the frequency found for the field ultracool dwarf population. The ratio of triples to binaries and quadruples to binaries is also high for this sample: 3:5 and 1:4, respectively, compared to 8 pc sample values of 1:4 and 1:26. The additional components in these wide companion systems indicates a formation mechanism that requires a third or fourth component to maintain gravitational stability or facilitate the exchange of angular momentum. The binding energies for the nine multiples discussed in this text are among the lowest known for wide low-mass systems, suggesting that weakly bound, low-to-intermediate mass (0.2 M sun < M [subscript tot]< 1.0 M sun) multiples can form and survive to exist in the field (1-8 Gyr)
Measurement of the t(t)over-barW and t(t)over-barZ production cross sections in pp collisions at root s=8 TeV with the ATLAS detector

Çetin, Serkant Ali (Dogus Author)The production cross sections of top-quark pairs in association with massive vector bosons have been measured using data from pp collisions at √s = 8 TeV. The dataset corresponds to an integrated luminosity of 20.3 fb−1 collected by the ATLAS detector in 2012 at the LHC. Final states with two, three or four leptons are considered. A fit to the data considering the tt¯W and tt¯Z processes simultaneously yields a significance of 5.0σ (4.2σ) over the background-only hypothesis for tt¯W (tt¯Z) production. The measured cross sections are (Formula presented.) fb and (Formula presented.) fb. The background-only hypothesis with neither tt¯W nor tt¯Z production is excluded at 7.1σ. All measurements are consistent with next-to-leading-order calculations for the tt¯W and tt¯Z processes
Summary of the searches for squarks and gluinos using root s = 8 TeV pp collisions with the ATLAS experiment at the LHC

Çetin, Serkant Ali (Dogus Author)A summary is presented of ATLAS searches for gluinos and first- and second-generation squarks in final states containing jets and missing transverse momentum, with or without leptons or b-jets, in the s=8$$ \sqrt{s}=8 $$ TeV data set collected at the Large Hadron Collider in 2012. This paper reports the results of new interpretations and statistical combinations of previously published analyses, as well as a new analysis. Since no significant excess of events over the Standard Model expectation is observed, the data are used to set limits in a variety of models. In all the considered simplified models that assume R-parity conservation, the limit on the gluino mass exceeds 1150 GeV at 95% confidence level, for an LSP mass smaller than 100 GeV. Furthermore, exclusion limits are set for left-handed squarks in a phenomenological MSSM model, a minimal Supergravity/Constrained MSSM model, R-parity-violation scenarios, a minimal gauge-mediated supersymmetry breaking model, a natural gauge mediation model, a non-universal Higgs mass model with gaugino mediation and a minimal model of universal extra dimensions
Compositionality in dataflow synchronous languages: specification & distributed code generation

International audienceModularity is advocated as a solution for the design of large systems; the mathematical translation of this concept is often that of compositionality. This paper is devoted to the issues of compositionality for modular code generation, in dataflow synchronous languages. As careless reuse of object code in new or evolving system designs fails to work, we first concentrate on what are the additional features needed to abstract programs for the purpose of code generation: we show that a central notion is that of scheduling specification as resulting from a causality analysis of the given program. Using this notion, we study separate compilation for synchronous programs. An entire section is devoted to the formal study of causality and scheduling specifications. Then we discuss the issue of distributed implementation using an asynchronous medium of communication. Our main results are that it is possible to characterize those synchronous programs which can be distributed on an asynchronous architecture without loosening semantic properties. Two new notions of endochrony and isochrony are introduced for this purpose. As a result, we derive a theory for synthesizing additional schedulers and protocols needed to guarantee the correctness of distributed code generation. Corresponding algorithms are implemented in the framework of the DC + common format for synchronous languages, and the V4 release of the SIGNAL language
Prednisolone with vs without pentoxifylline and survival of patients with severe alcoholic hepatitis: A randomized clinical trial

Importance Prednisolone or pentoxifylline is recommended for severe alcoholic hepatitis, a life-threatening disease. The benefit of their combination is unknown.Objective To determine whether the addition of pentoxifylline to prednisolone is more effective than prednisolone alone.Design, Setting, and Participants Multicenter, randomized, double-blind clinical trial conducted between December 2007 and March 2010 in 1 Belgian and 23 French hospitals of 270 patients aged 18 to 70 years who were heavy drinkers with severe biopsy-proven alcoholic hepatitis, as indicated by recent onset of jaundice in the prior 3 months and a Maddrey score of at least 32. Duration of follow-up was 6 months. The last included patient completed the study in October 2010. None of the patients were lost to follow-up for the main outcome.Intervention Patients were randomly assigned to receive either a combination of 40 mg of prednisolone once a day and 400 mg of pentoxifylline 3 times a day (n=133) for 28 days, or 40 mg of prednisolone and matching placebo (n=137) for 28 days.Main Outcomes and Measures Six-month survival, with secondary end points of development of hepatorenal syndrome and response to therapy based on the Lille model, which defines treatment nonresponders after 7 days of initiation of treatment.Results In intention-to-treat analysis, 6-month survival was not different in the pentoxifylline-prednisolone and placebo-prednisolone groups (69.9% [95% CI, 62.1%-77.7%] vs 69.2% [95% CI; 61.4%-76.9%], P = .91), corresponding to 40 vs 42 deaths, respectively. In multivariable analysis, only the Lille model and the Model for End-Stage Liver Disease score were independently associated with 6-month survival. At 7 days, response to therapy assessed by the Lille model was not significantly different between the 2 groups (Lille model score, 0.41 [95% CI, 0.36-0.46] vs 0.40 [95% CI, 0.35-0.45], P = .80). The probability of being a responder was not different in both groups (62.6% [95% CI, 53.9%-71.3%] vs 61.9% [95% CI, 53.7%-70.3%], P = .91). The cumulative incidence of hepatorenal syndrome at 6 months was not significantly different in the pentoxifylline-prednisolone and the placebo-prednisolone groups (8.4% [95% CI, 4.8%-14.8%] vs 15.3% [95% CI, 10.3%-22.7%], P = .07).Conclusion and Relevance In patients with alcoholic hepatitis, 4-week treatment with pentoxifylline and prednisolone, compared with prednisolone alone, did not result in improved 6-month survival. The study may have been underpowered to detect a significant difference in incidence of hepatorenal syndrome, which was less frequent in the group receiving pentoxifylline
On the Bargmann-Michel-Telegdi equations, and spin-orbit coupling: a tribute to Raymond Stora

LaTeX, 14 pages.International audienceThe Bargmann-Michel-Telegdi equations describing the motions of a spinning, charged, relativistic particle endowed with an anomalous magnetic moment in an  electromagnetic field, are reconsidered. They are shown to duly stem from the linearization of the characteristic distribution of a pre-symplectic structure refining the original one of Souriau. In this model, once specialized to the case of a static electric-like field, the angular momentum and energy given by the associated moment map now correctly restore the spin-orbit coupling term. This is the state-of-the-art of unfinished joint work with Raymond Stora
Galactic cosmic rays on extrasolar Earth-like planets
 : 
II. Atmospheric implications

International audienceContext. Theoretical arguments indicate that close-in terrestial exoplanets may have weak magnetic fields, especially in the case of planets more massive than Earth (super-Earths). Planetary magnetic fields, however, constitute one of the shielding layers that protect the planet against cosmic-ray particles. In particular, a weak magnetic field results in a high flux of Galactic cosmic rays that extends to the top of the planetary atmosphere.Aims. We wish to quantify the flux of Galactic cosmic rays to an exoplanetary atmosphere as a function of the particle energy and of the planetary magnetic moment.Methods. We numerically analyzed the propagation of Galactic cosmic-ray particles through planetary magnetospheres. We evaluated the efficiency of magnetospheric shielding as a function of the particle energy (in the range 16 MeV ≤ E ≤ 524 GeV) and as a function of the planetary magnetic field strength (in the range 0 M⊕ ≤ M ≤ 10 M⊕). Combined with the flux outside the planetary magnetosphere, this gives the cosmic-ray energy spectrum at the top of the planetary atmosphere as a function of the planetary magnetic moment.Results. We find that the particle flux to the planetary atmosphere can be increased by more than three orders of magnitude in the absence of a protecting magnetic field. For a weakly magnetized planet (ℳ = 0.05 ℳ⊕), only particles with energies below 512 MeV are at least partially shielded. For a planet with a magnetic moment similar to that of Earth, this limit increases to to 32 GeV, whereas for a strongly magnetized planet (ℳ = 10.0 ℳ⊕), partial shielding extends up to 200 GeV. Over the parameter range we studied, strong shielding does not occur for weakly magnetized planets. For a planet with a magnetic moment similar to that of Earth, particles with energies below 512 MeV are strongly shielded, and for strongly magnetized planets, this limit increases to 10 GeV.Conclusions. We find that magnetic shielding strongly controls the number of cosmic-ray particles reaching the planetary atmosphere. The implications of this increased particle flux are discussed in a companion article
Evolution of the mass, size, and star formation rate in high redshift merging galaxies

International audienceContext. In Λ-CDM models, galaxies are thought to grow both through continuous cold gas accretion coming from the cosmic web and episodic merger events. The relative importance of these different mechanisms at different cosmic epochs is nevertheless not yet understood well.Aims. We aim to address questions related to galaxy mass assembly through major and minor wet merging processes in the redshift range 1 < z < 2, an epoch that corresponds to the peak of cosmic star formation history. A significant fraction of Milky Way-like galaxies are thought to have undergone an unstable clumpy phase at this early stage. We focus on the behavior of the young clumpy disks when galaxies are undergoing gas-rich galaxy mergers.Methods. Using the adaptive mesh-refinement code RAMSES, we build the Merging and Isolated high redshift Adaptive mesh refinement Galaxies (MIRAGE) sample. It is composed of 20 mergers and 3 isolated idealized disks simulations, which sample disk orientations and merger masses. Our simulations can reach a physical resolution of 7 parsecs, and include star formation, metal line cooling, metallicity advection, and a recent physically-motivated implementation of stellar feedback that encompasses OB-type stars radiative pressure, photo-ionization heating, and supernovae.Results. The star formation history of isolated disks shows a stochastic star formation rate, which proceeds from the complex behavior of the giant clumps. Our minor and major gas-rich merger simulations do not trigger starbursts, suggesting a saturation of the star formation due to the detailed accounting of stellar feedback processes in a turbulent and clumpy interstellar medium fed by substantial accretion from the circumgalactic medium. Our simulations are close to the normal regime of the disk-like star formation on a Schmidt-Kennicutt diagram. The mass–size relation and its rate of evolution in the redshift range 1 < z < 2 matches observations, suggesting that the inside-out growth mechanisms of the stellar disk do not necessarily require cold accretion