pinecone/core-2020-05-10-deduplication huggingface dataset:
Making sense of low oxygen sensing

Plant-specific group VII Ethylene Response Factor (ERF) transcription factors have emerged as pivotal regulators of flooding and low oxygen responses. In rice (Oryza sativa), these proteins regulate contrasting strategies of flooding survival. Recent studies on Arabidopsis thaliana group VII ERFs show they are stabilized under hypoxia but destabilized under oxygen-replete conditions via the N-end rule pathway of targeted proteolysis. Oxygen-dependent sequestration at the plasma membrane maintains at least one of these proteins, RAP2.12, under normoxia. Remarkably, SUB1A, the rice group VII ERF that enables prolonged submergence tolerance, appears to evade oxygen-regulated N-end rule degradation. We propose that the turnover of group VII ERFs is of ecological relevance in wetland species and might be manipulated to improve flood tolerance of crops
Search for Higgs boson decays to a photon and a Z boson in pp collisions at s√=7 and 8 TeV with the ATLAS detector

A search is reported for a neutral Higgs boson in the decay channel H→ZγH→Zγ, Z→ℓ+ℓ−Z→ℓ+ℓ− (ℓ=e,μℓ=e,μ), using 4.5 fb−1 of pp   collisions at View the MathML sources=7 TeV and 20.3 fb−1 of pp   collisions at View the MathML sources=8 TeV, recorded by the ATLAS detector at the CERN Large Hadron Collider. The observed distribution of the invariant mass of the three final-state particles, mℓℓγmℓℓγ, is consistent with the Standard Model hypothesis in the investigated mass range of 120–150 GeV. For a Higgs boson with a mass of 125.5 GeV, the observed upper limit at the 95% confidence level is 11 times the Standard Model expectation. Upper limits are set on the cross section times branching ratio of a neutral Higgs boson with mass in the range 120–150 GeV between 0.13 and 0.5 pb for View the MathML sources=8 TeV at 95% confidence level.We acknowledge the support of ANPCyT, Argentina; YerPhI, Armenia; ARC, Australia; BMWF and FWF, Austria; ANAS, Azerbaijan; SSTC, Belarus; CNPq and FAPESP, Brazil; NSERC, NRC and CFI, Canada; CERN; CONICYT, Chile; CAS, MOST and NSFC, China; COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Republic; DNRF, DNSRC and Lundbeck Foundation, Denmark; EPLANET, ERC and NSRF, European Union; IN2P3-CNRS, CEA-DSM/IRFU, France; GNSF, Georgia; BMBF, DFG, HGF, MPG and AvH Foundation, Germany; GSRT and NSRF, Greece; ISF, MINERVA, GIF, I-CORE and Benoziyo Center, Israel; INFN, Italy; MEXT and JSPS, Japan; CNRST, Morocco; FOM and NWO, Netherlands; BRF and RCN, Norway; MNiSW and NCN, Poland; GRICES and FCT, Portugal; MNE/IFA, Romania; MES of Russia and ROSATOM, Russian Federation; JINR; MSTD, Serbia; MSSR, Slovakia; ARRS and MIZS, Slovenia; DST/NRF, South Africa; MINECO, Spain; SRC and Wallenberg Foundation, Sweden; SER, SNSF and Cantons of Bern and Geneva, Switzerland; NSC, Taiwan; TAEK, Turkey; STFC, the Royal Society and Leverhulme Trust, United Kingdom; DOE and NSF, United States of America
Vertical slice modelling of nonlinear Eady waves using a compatible
  finite element method

A vertical slice model is developed for the Euler-Boussinesq equations with a
constant temperature gradient in the direction normal to the slice (the
Eady-Boussinesq model). The model is a solution of the full three-dimensional
equations with no variation normal to the slice, which is an idealized problem
used to study the formation and subsequent evolution of weather fronts. A
compatible finite element method is used to discretise the governing equations.
To extend the Charney-Phillips grid staggering in the compatible finite element
framework, we use the same node locations for buoyancy as the vertical part of
velocity and apply a transport scheme for a partially continuous finite element
space. For the time discretisation, we solve the semi-implicit equations
together with an explicit strong-stability-preserving Runge-Kutta scheme to all
of the advection terms. The model reproduces several quasi-periodic lifecycles
of fronts despite the presence of strong discontinuities. An asymptotic limit
analysis based on the semi-geostrophic theory shows that the model solutions
are converging to a solution in cross-front geostrophic balance. The results
are consistent with the previous results using finite difference methods,
indicating that the compatible finite element method is performing as well as
finite difference methods for this test problem. We observe dissipation of
kinetic energy of the cross-front velocity in the model due to the lack of
resolution at the fronts, even though the energy loss is not likely to account
for the large gap on the strength of the fronts between the model result and
the semi-geostrophic limit solution.Comment: 27 pages, 13 figures. Revised version, accepted for publication in
  JC
Differential forms and Clifford analysis

In this paper we use a calculus of differential forms which is defined using an axiomatic approach. We then define integration of differential forms over chains in a new way and we present a short proof of Stokes' formula using distributional techniques. We also consider differential forms in Clifford analysis, vector differentials and their powers.
This framework enables an easy proof for a Cauchy's formula on a k-surface. Finally, we discuss how to compute winding numbers in terms of the monogenic Cauchy kernel and the vector differentials with a new approach which does not involve cohomology of differential forms
Stoichiometric control of co-crystal formation by solvent free continuous co-crystallization (SFCC).

yesReproducible control of stoichiometry and difficulties in large scale production have been identified as two of the major challenges to commercial uptake of pharmaceutical co-crystals. The aim of this research was to extend the application of SFCC to control stoichiometry in caffeine: maleic acid co-crystals. Both 1:1 and 2:1 caffeine: maleic acid co-crystals were produced by control of the feedstock composition and process conditions. It was also observed that formation of 2:1 stoichiometry co-crystals involved formation of a 1:1 co-crystal which was subsequently transformed to 2:1 co-crystals. The investigation of stoichiometric transformation revealed that although 1:1 co-crystals could be converted into 2:1 form with addition of excess caffeine, the reverse was not possible in the presence of excess maleic acid. However, conversion from 2:1 into 1:1 was only achieved by melt seeding with the phase pure 1:1 co-crystals. This investigation demonstrates that stoichiometric control can be achieved by SFCC by control of parameters such as extrusion temperature.Checked with HR, Clive Wood is a student - sm 20/06/201
FOXA1 repression is associated with loss of BRCA1 and increased promoter methylation and chromatin silencing in breast cancer.

© 2015 Macmillan Publishers Limited All rights reserved.FOXA1 expression correlates with the breast cancer luminal subtype and patient survival. RNA and protein analysis of a panel of breast cancer cell lines revealed that BRCA1 deficiency is associated with the downregulation of FOXA1 expression. Knockdown of BRCA1 resulted in the downregulation of FOXA1 expression and enhancement of FOXA1 promoter methylation in MCF-7 breast cancer cells, whereas the reconstitution of BRCA1 in Brca1-deficent mouse mammary epithelial cells (MMECs) promoted Foxa1 expression and methylation. These data suggest that BRCA1 suppresses FOXA1 hypermethylation and silencing. Consistently, the treatment of MMECs with the DNA methylation inhibitor 5-aza-2′-deoxycitydine induced Foxa1 mRNA expression. Furthermore, treatment with GSK126, an inhibitor of EZH2 methyltransferase activity, induced FOXA1 expression in BRCA1-deficient but not in BRCA1-reconstituted MMECs. Likewise, the depletion of EZH2 by small interfering RNA enhanced FOXA1 mRNA expression. Chromatin immunoprecipitation (ChIP) analysis demonstrated that BRCA1, EZH2, DNA methyltransferases (DNMT)1/3a/3b and H3K27me3 are recruited to the endogenous FOXA1 promoter, further supporting the hypothesis that these proteins interact to modulate FOXA1 methylation and repression. Further co-immunoprecipitation and ChIP analysis showed that both BRCA1 and DNMT3b form complexes with EZH2 but not with each other, consistent with the notion that BRCA1 binds to EZH2 and negatively regulates its methyltransferase activity. We also found that EZH2 promotes and BRCA1 impairs the deposit of the gene silencing histone mark H3K27me3 on the FOXA1 promoter. These associations were validated in a familial breast cancer patient cohort. Integrated analysis of the global gene methylation and expression profiles of a set of 33 familial breast tumours revealed that FOXA1 promoter methylation is inversely correlated with the transcriptional expression of FOXA1 and that BRCA1 mutation breast cancer is significantly associated with FOXA1 methylation and downregulation of FOXA1 expression, providing physiological evidence to our findings that FOXA1 expression is regulated by methylation and chromatin silencing and that BRCA1 maintains FOXA1 expression through suppressing FOXA1 gene methylation in breast cancer
Micro-tweezers : design, fabrication, simulation and testing of a pneumatically actuated micro-gripper for micromanipulation and microtactile sensing

This paper presents a novel micro-gripper design with the dual functions of manipulation and force sensing. The device consists of two parallel plates, each mounted on torsion bars, which can be made to rotate towards or away from each other by use of a pneumatically- or hydraulically-actuated elastic membrane. The plates can be conveniently fabricated using photo-etching and the design allows for a range of ratios between actuation pressure and tip opening displacement and force. The elastic gripping tips can be designed to provide sufficient compliance that their strain can be used to monitor and control the gripping force. An exemplar device has been fabricated and its behaviour characterised by a series of mechanical measurements of force and displacement. These measurements have been rationalised using a simple analytical model, backed up with finite element analysis to emphasise the design variables and scalability. This exemplar device, with a maximum tip opening amplitude of 1 mm and maximum force output of 50 mN, has also been demonstrated to perform pick-and-place operations with 200 μm micro-beads
Search for top quark decays t → qH with H → γγ using the ATLAS detector

A search is performed for flavour-changing neutral currents in the decay of a top quark to an up-type (c, u) quark and a Higgs boson, where the Higgs boson decays to two photons. The proton-proton collision data set used corresponds to 4.7 fb[superscript −1] at √s = 7 TeV and 20.3 fb[superscript −1] at √s = 8 TeV collected by the ATLAS experiment at the LHC. Top quark pair events are searched for in which one top quark decays to qH and the other decays to bW. Both the hadronic and the leptonic decay modes of the W boson are used. No significant signal is observed and an upper limit is set on the t → qH branching ratio of 0.79 at the 95% confidence level. The corresponding limit on the tqH coupling combination √λ[2 over tcH] + λ[2 over tuH] is 0.17.United States. Dept. of EnergyNational Science Foundation (U.S.)Brookhaven National Laborator
First measurement of the cross section for top-quark pair production in proton–proton collisions at √s = 7 TeV

The first measurement of the cross section for top-quark pair production in pp collisions at the Large Hadron Collider at center-of-mass energy √s = 7 TeV has been performed using a data sample corresponding to an integrated luminosity of 3.1±0.3 pb[superscript −1] recorded by the CMS detector. This result utilizes the final state with two isolated, highly energetic charged leptons, large missing transverse energy, and two or more jets. Backgrounds from Drell–Yan and non-W/Z boson production are estimated from data. Eleven events are observed in the data with 2.1±1.0 events expected from background. The measured cross section is 194±72(stat.)±24(syst.)±21(lumi.) pb, consistent with next-to-leading order predictions.European Organization for Nuclear ResearchUnited States. Dept. of EnergyNational Science Foundation (U.S.
On elliptic Calogero–Moser systems for complex crystallographic reflection groups

To every irreducible finite crystallographic reflection group (i.e., an irreducible finite reflection group G acting faithfully on an abelian variety X), we attach a family of classical and quantum integrable systems on X (with meromorphic coefficients). These families are parametrized by G  -invariant functions of pairs (T,s), where T is a hypertorus in X (of codimension 1), and s∈G is a reflection acting trivially on T. If G is a real reflection group, these families reduce to the known generalizations of elliptic Calogero–Moser systems, but in the non-real case they appear to be new. We give two constructions of the integrals of these systems – an explicit construction as limits of classical Calogero–Moser Hamiltonians of elliptic Dunkl operators as the dynamical parameter goes to 0 (implementing an idea of V. Buchstaber, G. Felder and A. Veselov (1994) [BFV]), and a geometric construction as global sections of sheaves of elliptic Cherednik algebras for the critical value of the twisting parameter. We also prove algebraic integrability of these systems for values of parameters satisfying certain integrality conditions.National Science Foundation (U.S.) (Grant DMS-0504847)National Science Foundation (U.S.) (Grant DMS-0854764
Deverbal semantics and the Montagovian generative lexicon ΛTyn

We propose a lexical account of action nominals, in particular of deverbalnominalisations, whose meaning is related to the event expressed by their baseverb. The literature about nominalisations often assumes that the semantics ofthe base verb completely defines the structure of action nominals. We arguethat the information in the base verb is not sufficient to completely determinethe semantics of action nominals. We exhibit some data from differentlanguages, especially from Romance language, which show that nominalisationsfocus on some aspects of the verb semantics. The selected aspects, however,seem to be idiosyncratic and do not automatically result from the internalstructure of the verb nor from its interaction with the morphological suffix. We therefore propose a partially lexicalist approach view of deverbal nouns. Itis made precise and computable by using the Montagovian Generative Lexicon, atype theoretical framework introduced by Bassac, Mery and Retor'e in thisjournal in 2010. This extension of Montague semantics with a richer type systemeasily incorporates lexical phenomena like the semantics of action nominals inparticular deverbals, including their polysemy and (in)felicitouscopredications
Revealing the cold dust in low-metallicity environments: I. Photometry analysis of the Dwarf Galaxy Survey with Herschel

Context. We present new photometric data from our Herschel Guaranteed Time Key Programme, the Dwarf 
Galaxy Survey (DGS),
dedicated to the observation of the gas and dust in low-metallicity environments. A total of 48 
dwarf galaxies were observed with the PACS and SPIRE instruments onboard the Herschel Space 
Observatory at 70, 100, 160, 250, 350, and 500 µm.
Aims. The goal of this paper is to provide reliable far infrared (FIR) photometry for the DGS 
sample and to analyse the FIR/submillimetre (submm) behaviour of the DGS galaxies. We focus on a 
systematic comparison of the derived FIR properties (FIR luminosity, LFIR, dust mass, Mdust , dust 
temperature, T, emissivity index, β) with more metal-rich galaxies and investigate the detection of 
a potential submm excess.
Methods. The data reduction method is adapted for each galaxy in order to derive the most reliable 
photometry from the final maps. The derived PACS flux densities are compared with the Spitzer MIPS 
70 and 160 µm bands. We use colour-colour diagrams to analyse the FIR/submm behaviour of the DGS 
galaxies and modified blackbody fitting procedures to determine their dust properties. To study the 
variation in these dust properties with metallicity, we also include galaxies from the Herschel 
KINGFISH sample, which contains more metal-rich environments, totalling 109 galaxies.
Results. The location of the DGS galaxies on Herschel colour-colour diagrams highlights the 
differences in dust grain properties and/or global environments of low-metallicity dwarf galaxies. 
The dust in DGS galaxies is generally warmer than in KINGFISH galaxies (TDGS  ∼ 32 K and TKINGFIS H 
 ∼ 23 K). The emissivity index, β, is ∼ 1.7 in the DGS, however metallicity does not make
a strong effect on β. The proportion of dust mass relative to stellar mass is lower in 
low-metallicity galaxies: Mdust /Mstar  ∼ 0.02%
for the DGS versus 0.1% for KINGFISH. However, per unit dust mass, dwarf galaxies emit about six 
times more in the FIR/submm
than higher metallicity galaxies. Out of the 22 DGS galaxies detected at 500 µm, about 41% present 
an excess in the submm beyond the explanation of our dust SED model, and this excess can go up to 
150% above the prediction from the model. The excess mainly appears in lower metallicity galaxies 
(12+log(O/H) ;S 8.3), and the strongest excesses are detected in the most metal-poor galaxies. 
However, we so stress the need for observations longwards of the Herschel wavelengths to detect any 
submm excess appearing beyond 500      .Norwegian Lis
The Chevalley group G2(2) of order 12096 and the octonionic root system of E7

AbstractThe octonionic root system of the exceptional Lie algebra E8 has been constructed from the quaternionic roots of F4 using the Cayley-Dickson doubling procedure where the roots of E7 correspond to the imaginary octonions. It is proven that the automorphism group of the octonionic root system of E7 is the adjoint Chevalley group G2(2) of order 12096. One of the four maximal subgroups of G2(2) of order 192 preserves the quaternion subalgebra of the E7 root system. The other three maximal subgroups of orders 432; 192 and 336 are the automorphism groups of the root systems of the maximal Lie algebras E6×U(1), SU(2)×SO(12) and SU(8) respectively. The 7-dimensional manifolds built with the use of these discrete groups could be of potential interest for the compactification of the M-theory in 11-dimension
On the structure and probabilistic interpretation of Askey–Wilson densities and polynomials with complex parameters

AbstractWe give equivalent forms of the Askey–Wilson polynomials expressing them with the help of the Al-Salam–Chihara polynomials. After restricting parameters of the Askey–Wilson polynomials to complex conjugate pairs we expand the Askey–Wilson weight function in the series similar to the Poisson–Mehler expansion formula and give its probabilistic interpretation. In particular this result can be used to calculate explicit forms of ‘q-Hermite’ moments of the Askey–Wilson density, hence enabling calculation of all moments of the Askey–Wilson density. On the way (by setting certain parameter q to 0) we get some formulae useful in the rapidly developing so-called ‘free probability’
Study of the deformation-driving νd5/2 orbital in 6728Ni39 using one-neutron transfer reactions

AbstractThe νg9/2,d5/2,s1/2 orbitals are assumed to be responsible for the swift onset of collectivity observed in the region below 68Ni. Especially the single-particle energies and strengths of these orbitals are of importance. We studied such properties in the nearby 67Ni nucleus, by performing a (d,p)-experiment in inverse kinematics employing a post-accelerated radioactive ion beam (RIB) at the REX-ISOLDE facility. The experiment was performed at an energy of 2.95 MeV/u using a combination of the T-REX particle detectors, the Miniball γ-detection array and a newly-developed delayed-correlation technique as to investigate μs-isomers. Angular distributions of the ground state and multiple excited states in 67Ni were obtained and compared with DWBA cross-section calculations, leading to the identification of positive-parity states with substantial νg9/2 (1007 keV) and νd5/2 (2207 keV and 3277 keV) single-particle strengths up to an excitation energy of 5.8 MeV. 50% of the νd5/2 single-particle strength relative to the νg9/2-orbital is concentrated in and shared between the first two observed 5/2+ levels. A comparison with extended Shell Model calculations and equivalent (3He, d) studies in the region around 9040Zr50 highlights similarities for the strength of the negative-parity pf and positive-parity g9/2 state, but differences are observed for the d5/2 single-particle strength
Matter–antimatter asymmetry generated by loop quantum gravity

AbstractWe show that loop quantum gravity provides new mechanisms through which observed matter–antimatter asymmetry in the Universe can naturally arise at temperatures less than GUT scale. This is enabled through the introduction of a new length scale L, much greater than Planck length (lP), to obtain semiclassical weave states in the theory. This scale which depends on the momentum of the particle modifies the dispersion relation for different helicities of fermions and leads to lepton asymmetry
Developing priority variables (“ecosystem Essential Ocean Variables” — eEOVs) for observing dynamics and change in Southern Ocean ecosystems

AbstractReliable statements about variability and change in marine ecosystems and their underlying causes are needed to report on their status and to guide management. Here we use the Framework on Ocean Observing (FOO) to begin developing ecosystem Essential Ocean Variables (eEOVs) for the Southern Ocean Observing System (SOOS). An eEOV is a defined biological or ecological quantity, which is derived from field observations, and which contributes significantly to assessments of Southern Ocean ecosystems. Here, assessments are concerned with estimating status and trends in ecosystem properties, attribution of trends to causes, and predicting future trajectories. eEOVs should be feasible to collect at appropriate spatial and temporal scales and are useful to the extent that they contribute to direct estimation of trends and/or attribution, and/or development of ecological (statistical or simulation) models to support assessments. In this paper we outline the rationale, including establishing a set of criteria, for selecting eEOVs for the SOOS and develop a list of candidate eEOVs for further evaluation. Other than habitat variables, nine types of eEOVs for Southern Ocean taxa are identified within three classes: state (magnitude, genetic/species, size spectrum), predator–prey (diet, foraging range), and autecology (phenology, reproductive rate, individual growth rate, detritus). Most candidates for the suite of Southern Ocean taxa relate to state or diet. Candidate autecological eEOVs have not been developed other than for marine mammals and birds. We consider some of the spatial and temporal issues that will influence the adoption and use of eEOVs in an observing system in the Southern Ocean, noting that existing operations and platforms potentially provide coverage of the four main sectors of the region — the East and West Pacific, Atlantic and Indian. Lastly, we discuss the importance of simulation modelling in helping with the design of the observing system in the long term.Regional boundary: south of 30°S