pinecone/core-2020-05-10-deduplication huggingface dataset:
‘Particle genetics’: treating every cell as unique

Genotype–phenotype relations are usually inferred from a deterministic point of view. For example, quantitative trait loci (QTL), which describe regions of the genome associated with a particular phenotype, are based on a mean trait difference between genotype categories. However, living systems comprise huge numbers of cells (the ‘particles’ of biology). Each cell can exhibit substantial phenotypic individuality, which can have dramatic consequences at the organismal level. Now, with technology capable of interrogating individual cells, it is time to consider how genotypes shape the probability laws of single cell traits. The possibility of mapping single cell probabilistic trait loci (PTL), which link genomic regions to probabilities of cellular traits, is a promising step in this direction. This approach requires thinking about phenotypes in probabilistic terms, a concept that statistical physicists have been applying to particles for a century. Here, I describe PTL and discuss their potential to enlarge our understanding of genotype–phenotype relations
Cogenesis in a universe with vanishing B–L within a gauged U(1)x extension

AbstractWe consider a gauged U(1)x extension of the standard model and of the minimal supersymmetric standard model where the dark matter fields are charged under U(1)x and carry lepton number while the standard model fields and fields of the minimal supersymmetric standard model are neutral under U(1)x. We consider leptogenesis in this class of models with all fundamental interactions having no violation of lepton number, and the total B–L in the universe vanishes. Such leptogenesis leads to equal and opposite lepton numbers in the visible sector and in the dark sector, and thus also produces asymmetric dark matter. Part of the lepton number generated in the leptonic sector subsequently transfer to the baryonic sector via sphaleron interactions. The stability of the dark particles is protected by the U(1)x gauge symmetry. A kinetic mixing between the U(1)x and the U(1)Y gauge bosons allows for dissipation of the symmetric component of dark matter. The case when U(1)x is U(1)B–L is also discussed for the supersymmetric case. This case is particularly interesting in that we have a gauged U(1)B–L which ensures the conservation of B–L with an initial condition of a vanishing B–L in the universe. Phenomenological implications of the proposed extensions are discussed, which includes implications for electroweak physics, neutrino masses and mixings, and lepton flavor changing processes such as ℓi→ℓjγ. We also briefly discuss the direct detection of the dark matter in the model
A central closure construction for certain algebra extensions. Applications to Hopf actions

AbstractAlgebra extensions A⊆B where A is a left B-module such that the B-action extends the multiplication in A are ubiquitous. We encounter examples of such extensions in the study of group actions, group gradings or more general Hopf actions as well as in the study of the bimodule structure of an algebra. In this paper we are extending R.Wisbauer's method of constructing the central closure of a semiprime algebra using its multiplication algebra to those kinds of algebra extensions. More precisely if A is a k-algebra and B some subalgebra of End(A) that contains the multiplication algebra of A, then the self-injective hull A^ of A as B-module becomes a k-algebra provided A does not contain any nilpotent B-stable ideals. We show that under certain assumptions A^ can be identified with a subalgebra of the Martindale quotient ring of A. This construction is then applied to Hopf module algebras
Structural dynamics and physicochemical properties of pDNA/DODAB:MO lipoplexes: Effect of pH and anionic lipids in inverted non-lamellar phases versus lamellar phases

AbstractDioctadecyldimethylammonium bromide (DODAB):Monoolein (MO) lipoplexes have mainly been studied within the range of high molar ratios of DODAB, with noticeable transfection efficiencies in the Human Embryonic Kidney (HEK, a.k.a. 293T) cell line. In this work, we intend to study the effect of high MO content on the structure and physicochemical properties of pDNA/DODAB:MO lipoplexes to achieve some correlation with their transfection efficiency. Static/Dynamic Light Scattering and Cryo-TEM imaging were used to characterize the size/morphology of DNA/DODAB:MO lipoplexes at different DODAB:MO contents (2:1, 1:1, 1:2) and charge ratios (CRs) (+/−). Nile Red fluorescence emission was performed to detect changes in microviscosity, hydration and polarity of DNA/DODAB:MO systems. Lipoplexes stability at physiological pH values and in the presence of anionic lipids was evaluated by Förster Resonance Energy Transfer (FRET). Physicochemical/structural data were complemented with transfection studies in HEK cells using the β-galactosidase reporter gene activity assay. This work reports the coexistence of multilamellar and non-lamellar inverted phases in MO-richer lipoplexes (DODAB:MO 1:2 and 1:4), leading to transfection efficiencies comparable to those of multilamellar (DODAB-richer) lipoplexes, but at higher charge ratios [CR (+/−)=6.0] and without dose-effect response. These results may be related to the structural changes of lipoplexes promoted by high MO content
Measurement of $b$-hadron pair production with the ATLAS detector in
  proton-proton collisions at $\sqrt{s}=8$ TeV

A measurement of $b$-hadron pair production is presented, based on a data set
corresponding to an integrated luminosity of 11.4 fb$^{-1}$ of proton--proton
collisions recorded at $\sqrt{s}=8$ TeV with the ATLAS detector at the LHC.
Events are selected in which a $b$-hadron is reconstructed in a decay channel
containing $J/\psi \rightarrow \mu\mu$, and a second $b$-hadron is
reconstructed in a decay channel containing a muon. Results are presented in a
fiducial volume defined by kinematic requirements on three muons based on those
used in the analysis. The fiducial cross section is measured to be $17.7 \pm
0.1 ($stat.$) \pm 2.0 ($syst.$)$ nb. A number of normalised differential cross
sections are also measured, and compared to predictions from the Pythia8,
Herwig++, MadGraph5\_aMC@NLO+Pythia8 and Sherpa event generators, providing new
constraints on heavy flavour production.Comment: 49 pages in total, author list starting page 28, 10 figures, 1 table,
  submitted to JHEP. All figures including auxiliary figures are available at
  https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/BPHY-2015-04
$q$-Poincar\'e supersymmetry in $AdS_5/CFT_4$

We consider the exact S-matrix governing the planar spectral problem for
strings on $AdS_5\times S^5$ and $\mathcal N=4$ super Yang-Mills, and we show
that it is invariant under a novel "boost" symmetry, which acts as a
differentiation with respect to the particle momentum. This generator leads us
also to reinterpret the usual centrally extended $\mathfrak{psu}(2|2)$
symmetry, and to conclude that the S-matrix is invariant under a $q$-Poincar\'e
supersymmetry algebra, where the deformation parameter is related to the 't
Hooft coupling. We determine the two-particle action (coproduct) that turns out
to be non-local, and study the property of the new symmetry under crossing
transformations. We look at both the strong-coupling (large tension in the
string theory) and weak-coupling (spin-chain description of the gauge theory)
limits; in the former regime we calculate the cobracket utilising the universal
classical r-matrix of Beisert and Spill. In the eventuality that the boost has
higher partners, we also construct a quantum affine version of 2D Poincar\'e
symmetry, by contraction of the quantum affine algebra
$U_q(\widehat{\mathfrak{sl}_2})$ in Drinfeld's second realisation.Comment: 35 pages. Added discussion on antipode in the presence of the phase.
  Published versio
Search for massive resonances decaying into WW, WZ or ZZ bosons in proton-proton collisions at sqrt(s) = 13 TeV

A search is presented for new massive resonances decaying to WW, WZ or ZZ bosons in ℓνqq¯¯ and qq¯¯qq¯¯ final states. Results are based on data corresponding to an integrated luminosity of 2.3-2.7 fb−1 recorded in proton-proton collisions at s√=13 TeV with the CMS detector at the LHC. Decays of spin-1 and spin-2 resonances into two vector bosons are sought in the mass range 0.6-4.0 TeV. No significant excess over the standard model background is observed. Combining the results of the ℓνqq¯¯ and qq¯¯qq¯¯ final states, cross section and mass exclusion limits are set for models that predict heavy spin-1 and spin-2 resonances. This is the first search for a narrow-width spin-2 resonance at s√=13 TeV
Measurements of top-quark pair to Z-boson cross-section ratios at s√=13 , 8, 7 TeV with the ATLAS detector

Ratios of top-quark pair to Z-boson cross sections measured from proton-proton collisions at the LHC centre-of-mass energies of s√=13 TeV, 8 TeV, and 7 TeV are presented by the ATLAS Collaboration. Single ratios, at a given s√ for the two processes and at different s√ for each process, as well as double ratios of the two processes at different s√, are evaluated. The ratios are constructed using previously published ATLAS measurements of the tt¯ and Z-boson production cross sections, corrected to a common phase space where required, and a new analysis of Z → ℓ+ℓ− where ℓ = e, μ at s√=13 TeV performed with data collected in 2015 with an integrated luminosity of 3.2 fb−1. Correlations of systematic uncertainties are taken into account when evaluating the uncertainties in the ratios. The correlation model is also used to evaluate the combined cross section of the Z → e+e− and the Z → μ+μ− channels for each s√ value. The results are compared to calculations performed at next-to-next-to-leading-order accuracy using recent sets of parton distribution functions. The data demonstrate significant power to constrain the gluon distribution function for the Bjorken-x values near 0.1 and the light-quark sea for x < 0.02
RASOR : an advanced instrument for soft x-ray reflectivity and diffraction. \ud

We report the design and construction of a novel soft x-ray diffractometer installed at Diamond Light Source. The beamline endstation RASOR is constructed for general users and designed primarily for the study of single crystal diffraction and thin film reflectivity. The instrument is comprised of a limited three circle (θ, 2θ, and χ) diffractometer with an additional removable rotation (ϕ) stage. It is equipped with a liquid helium cryostat, and post-scatter polarization analysis. Motorized motions are provided for the precise positioning of the sample onto the diffractometer center of rotation, and for positioning the center of rotation onto the x-ray beam. The functions of the instrument have been tested at Diamond Light Source, and initial test measurements are provided, demonstrating the potential of the instrument.\u
Neutral modes of a two-dimensional vortex and their link to persistent cat's eyes

This paper considers the relaxation of a smooth two-dimensional vortex to axisymmetry after the application of an instantaneous, weak external strain field. In this limit the disturbance decays exponentially in time at a rate that is linked to a pole of the associated linear inviscid problem (known as a Landau pole). As a model of a typical vortex distribution that can give rise to cat’s eyes, here distributions are examined that have a basic Gaussian shape but whose profiles have been artificially flattened about some radius rc. A numerical study of the Landau poles for this family of vortices shows that as rc is varied so the decay rate of the disturbance moves smoothly between poles as the decay rates of two Landau poles cross. Cat’s eyes that occur in the nonlinear evolution of a vortex lead to an axisymmetric azimuthally averaged profile with an annulus of approximately uniform vorticity, rather like the artificially flattened profiles investigated. Based on the stability of such profiles it is found that finite thickness cat’s eyes can persist (i.e., the mean profile has a neutral mode) at two distinct radii, and in the limit of a thin flattened region the result that vanishingly thin cat’s eyes only persist at a single radius is recovered. The decay of nonaxisymmetric perturbations to these flattened profiles for larger times is investigated and a comparison made with the result for a Gaussian profile
Could a Resource be Simultaneously a Schedule according to the REA Ontology

This paper describes using of the Resource-Event-Agent (REA) framework to model
enterprise planning at operational level. The aim is to further utilize the possibilities and
potential of the framework in the areas with prevailing conversion rather than exchange
processes. During the modeling we came across the situation when an entity may be viewed
as two different REA concepts, which breaks the REA ontology. In the next of the paper we
suggest some rational possibility how to solve the problem. The paper also partly mentions
the mechanism of inner or nested classes that can be used for implementation of the two
different views on the entity in the given context.
Long run performance of IPOs and the role of financial analysts: some French evidence

This paper examines the long-run performance of French initial public offerings (IPOs) carried out between
1991 and 2005. Using various methodologies, we found that IPOs in our sample performed poorly relative
to the comparison portfolios over the 1991–2005 horizon in contrast to that reported by prior studies of
the French market. This abnormal long-run performance is more severe for orphan IPOs (those without
financial analysts’ recommendations) than for non-orphan IPOs the first year following the offerings (a
statistically significant difference). In contrast to the widely held belief, this evidence suggests that analyst
coverage is indeed not important to the issuing firm. Investors pay more attention to non-orphan IPOs when
they are not book built, venture capital backed, underwritten by a large syndicate and less underpriced.
Over the 1991–2005 period, an analyst’s affiliation does not appear to matter. This result is inconsistent
with the conflict of interest hypothesis. During the first year of issuance, analysts’ recommendations are
associated with the success of a newly public firm. However, once we extend the horizon to 3 or 5 years
after the issuance, we can find that analysts’ recommendations are not significantly related to the long-run performance of IPOs.
Output, renewable energy consumption and trade in Africa

We use panel cointegration techniques to examine the relationship between renewable energy consumption, trade and output in a sample of 11 African countries covering the period 1980-2008. The results from panel error correction model reveal that there is evidence of bidirectional causality between output and exports and between output and imports in both the short-run and the long-run. However, in the short-run, there is no evidence of causality between output and renewable energy consumption and between trade (exports or imports) and renewable energy consumption. In the long-run, the FMOLS panel approach estimation shows that renewable energy consumption and trade (exports or imports) have a statistically significant and positive impact on output. Policies recommendations are that, in the long-run, international trade enables African countries to benefit from technology transfer and to build the human and physical capacities needed to produce more renewable energies, which in turn increases their output.
Nonparametric Estimation of the Link Function Including Variable Selection

Nonparametric methods for the estimation of the link function in generalized linear models are able to avoid bias in the regression parameters. But for the estimation of the link typically the full model, which includes all predictors, has been used. When the number of predictors is large these methods fail since the full model can not be estimated. In the present article a boosting type method is proposed that simultaneously selects predictors and estimates the link function. The method performs quite well in simulations and real data examples.
Measurement of Z$^0$-boson production at large rapidities in Pb-Pb
  collisions at $\sqrt{s_{\rm NN}}=5.02$ TeV

The production of Z$^0$ bosons at large rapidities in Pb-Pb collisions at
$\sqrt{s_{\rm NN}}=5.02$ TeV is reported. Z$^0$ candidates are reconstructed in
the dimuon decay channel (${\rm Z}^0 \rightarrow \mu^+\mu^-$), based on muons
selected with pseudo-rapidity $-4.0<\eta<-2.5$ and $p_{\rm T}>20$ GeV/$c$. The
invariant yield and the nuclear modification factor, $R_{\rm AA}$, are
presented as a function of rapidity and collision centrality. The value of
$R_{\rm AA}$ for the 0-20% central Pb-Pb collisions is $0.67 \pm 0.11 \,
\mbox{(stat.)} \, \pm 0.03 \, \mbox{(syst.)} \, \pm 0.06 \, \mbox{(corr.
syst.)}$, exhibiting a deviation of $2.6 \sigma$ from unity. The results are
well-described by calculations that include nuclear modifications of the parton
distribution functions, while the predictions using vacuum PDFs deviate from
data by $2.3\sigma$ in the 0-90% centrality class and by $3\sigma$ in the 0-20%
central collisions.Comment: 19 pages, 4 captioned figures, 2 tables, authors from page 14,
  published version, figures at
  http://aliceinfo.cern.ch/ArtSubmission/node/410
KAM for autonomous quasi-linear perturbations of KdV

We prove the existence and the stability of Cantor families of quasi-periodic, small amplitude solutions of quasi-linear (i.e. strongly nonlinear) autonomous Hamiltonian differentiable perturbations of KdV. This is the first result that extends KAM theory to quasi-linear autonomous and parameter independent PDEs. The core of the proof is to find an approximate inverse of the linearized operators at each approximate solution and to prove that it satisfies tame estimates in Sobolev spaces. A symplectic decoupling procedure reduces the problem to the one of inverting the linearized operator restricted to the normal directions. For this aim we use pseudo-differential operator techniques to transform such linear PDE into an equation with constant coefficients up to smoothing remainders. Then a linear KAM reducibility technique completely diagonalizes such operator. We introduce the “initial conditions” as parameters by performing a “weak” Birkhoff normal form analysis, which is well adapted for quasi-linear perturbations. © 2015 Elsevier Masson SA
Reconstruction and identification of hadronic tau-decays in ATLAS

The identification of tau -jets from the hadronic tau -decay is crucial for the study of many physics channels like the production of Higgs bosons decaying to tau or SUSY. The tau-jet reconstruction in ATLAS is performed starting from the energy deposited in the calorimeters or also combining measurements from calorimeter and tracking with an energy-flow technique. Quantities built both from the calorimeters and from the inner detector are used to identify tau -jets against other jets. In the talk we will review the performance of tau-jet reconstruction and identification, showing that the excellent tau-efficiency versus the jet-rejection obtained in ATLAS will allow the study of channels where the background from jets is potentially very large
Rationalized Computer-Aided Design of Matrix-Metalloprotease-Selective Prodrugs

YesMatrix metalloproteinases (MMPs) are central to cancer development and metastasis. They are highly active in the tumor environment and absent or inactive in normal tissues; therefore they represent viable targets for cancer drug discovery. In this study we evaluated in silico docking to develop MMP-subtype-selective tumor-activated prodrugs. Proof of principle for this therapeutic approach was demonstrated in vitro against an aggressive human glioma model, with involvement of MMPs confirmed using pharmacological inhibition
Study of the $D$ $^0$ $p$ amplitude in $\Lambda $$ _b$$ ^0 \to $$D$ $^0$ $p\pi ^−$ decays

An amplitude analysis of the decay $\Lambda $$ _b$$ ^0 \to $$D$ $^0$ $p\pi ^−$ is performed in the part of the phase space containing resonances in the $D$ $^0$ $p$ channel. The study is based on a data sample corresponding to an integrated luminosity of 3.0 $fb^{−1}$ of pp collisions recorded by the LHCb experiment. The spectrum of excited $\Lambda$$_c$$^+$ states that decay into $D$ $^0$ $p$ is studied. The masses, widths and quantum numbers of the $\Lambda_c(2880)^+$ and $\Lambda_c(2940)^+$ resonances are measured. The constraints on the spin and parity for the $\Lambda_c(2940)^+$ state are obtained for the first time. A near-threshold enhancement in the $D$ $^0$ $p$ amplitude is investigated and found to be consistent with a new resonance, denoted the $\Lambda_c(2860)^+$, of spin 3/2 and positive parity
Localisation in a growth model with interaction.

This paper concerns the long term behaviour of a growth model describing a random sequential allocation of particles on a finite cycle graph. The model can be regarded as a reinforced urn model with graph-based interaction. It is motivated by cooperative sequential adsorption, where adsorption rates at a site depend on the configuration of existing particles in the neighbourhood of that site. Our main result is that, with probability one, the growth process will eventually localise either at a single site, or at a pair of neighbouring sites
Global non-potential magnetic models of the solar corona during the March 2015 eclipse

Funding: UK Science and Technology Facilities Council (STFC) (ARY, DHM).Seven different models are applied to the same problem of simulating the Sun’s coronal magnetic field during the solar eclipse on 2015 March 20. All of the models are non-potential, allowing for free magnetic energy, but the associated electric currents are developed in significantly different ways. This is not a direct comparison of the coronal modelling techniques, in that the different models also use different photospheric boundary conditions, reflecting the range of approaches currently used in the community. Despite the significant differences, the results show broad agreement in the overall magnetic topology. Among those models with significant volume currents in much of the corona, there is general agreement that the ratio of total to potential magnetic energy should be approximately 1.4. However, there are significant differences in the electric current distributions; while static extrapolations are best able to reproduce active regions, they are unable to recover sheared magnetic fields in filament channels using currently available vector magnetogram data. By contrast, time-evolving simulations can recover the filament channel fields at the expense of not matching the observed vector magnetic fields within active regions. We suggest that, at present, the best approach may be a hybrid model using static extrapolations but with additional energization informed by simplified evolution models. This is demonstrated by one of the models.Publisher PDFPeer reviewe