pinecone/core-2020-05-10-deduplication huggingface dataset:
Analysis of clinical and environmental Candida parapsilosis isolates by microsatellite genotyping—a tool for hospital infection surveillance

Candida parapsilosis emerged as an important opportunistic pathogen, causing candidaemia worldwide. Nosocomial outbreaks triggered by this species have been frequently described, particularly in cancer patients. For a better understanding of its epidemiology, several typing methods are used and microsatellite analysis has been reported as highly discriminant. The main objective of this work was to study C. parapsilosis isolates by application of microsatellite genotyping to distinguish epidemiologically related strains, compare clinical and environmental isolates and determine possible routes of dispersion of the isolates in the hospital setting. A total of 129 C. parapsilosis isolates from different origins, including hospital environment and hands of healthcare workers, were genotyped using four microsatellite markers. The isolates were recovered from different health institutions. Analysis of C. parapsilosis isolates from hospital environment showed great genotypic diversity; however, the same or very similar genotypes were also found. The same multilocus genotype was shared by isolates recovered from the hand of a healthcare worker, from the hospital environment and from patients of the same healthcare institution, suggesting that these could be possible routes of transmission and that infections due to C. parapsilosis may be mainly related with exogenous transmission to the patient. Examination of sequential isolates from the same patients showed that colonizing and bloodstream isolates had the same multilocus genotype in the majority of cases. We demonstrate that this typing method is able to distinguish clonal clusters from genetically unrelated genotypes and can be a valuable tool to support epidemiologic investigations in the hospital setting
On the Super Higgs Effect in Extended Supergravity

We consider the reduction of supersymmetry in N-extended four dimensional supergravity via the super Higgs mechanism in theories without cosmological constant. We provide an analysis largely based on the properties of long and short multiplets of Poincaré supersymmetry. Examples of the super Higgs phenomenon are realized in spontaneously broken N=8 supergravity through the Scherk-Schwarz mechanism and in superstring compactification in presence of brane fluxes. In many models the massive vectors count the difference in number of the translation isometries of the scalar sigma-model geometries in the broken and unbroken phase
On the surface of superfluids

Developing on a recent work on localized bubbles of ordinary relativistic
fluids, we study the comparatively richer leading order surface physics of
relativistic superfluids, coupled to an arbitrary stationary background metric
and gauge field in $3+1$ and $2+1$ dimensions. The analysis is performed with
the help of a Euclidean effective action in one lower dimension, written in
terms of the superfluid Goldstone mode, the shape-field (characterizing the
surface of the superfluid bubble) and the background fields. We find new terms
in the ideal order constitutive relations of the superfluid surface, in both
the parity-even and parity-odd sectors, with the corresponding transport
coefficients entirely fixed in terms of the first order bulk transport
coefficients. Some bulk transport coefficients even enter and modify the
surface thermodynamics. In the process, we also evaluate the stationary first
order parity-odd bulk currents in $2+1$ dimensions, which follows from four
independent terms in the superfluid effective action in that sector. In the
second part of the paper, we extend our analysis to stationary surfaces in
$3+1$ dimensional Galilean superfluids via the null reduction of null
superfluids in $4+1$ dimensions. The ideal order constitutive relations in the
Galilean case also exhibit some new terms similar to their relativistic
counterparts. Finally, in the relativistic context, we turn on slow but
arbitrary time dependence and answer some of the key questions regarding the
time-dependent dynamics of the shape-field using the second law of
thermodynamics. A linearized fluctuation analysis in $2+1$ dimensions about a
toy equilibrium configuration reveals some new surface modes, including
parity-odd ones. Our framework can be easily applied to model more general
interfaces between distinct fluid-phases.Comment: 52+1 pages, 4 table
Insights into the influence of solvent polarity on the crystallization of poly(ethylene oxide) spin-coated thin films via in situ grazing incidence wide angle x-ray scattering

yesControlling polymer thin-film morphology and crystallinity is crucial for a wide range
of applications, particularly in thin-film organic electronic devices. In this work, the
crystallization behavior of a model polymer, poly(ethylene oxide) (PEO), during spincoating
is studied. PEO films were spun-cast from solvents possessing different
polarities (chloroform, THF and methanol) and probed via in situ grazing incidence
wide angle x-ray scattering. The crystallization behavior was found to follow the
solvent polarity order (where chloroform < THF < methanol) rather than the solubility
order (where THF > chloroform > methanol). When spun-cast from non-polar
chloroform, crystallization largely followed Avrami kinetics, resulting in the formation
of morphologies comprising large spherulites. PEO solutions cast from more polar
solvents (THF and methanol) do not form well-defined highly crystalline
morphologies and are largely amorphous with the presence of small crystalline
regions. The difference in morphological development of PEO spun-cast from polar
solvents is attributed to clustering phenomena that inhibit polymer crystallization.
This work highlights the importance of considering individual components of polymer
solubility, rather than simple total solubility, when designing processing routes for the
generation of morphologies with optimum crystallinities or morphologies
All three-loop four-point correlators of half-BPS operators in planar NN = 4 SYM.

We obtain the planar correlation function of four half-BPS operators of arbitrary weights, up to three loops. Our method exploits only elementary properties of the integrand of the planar correlator, such as its symmetries and singularity structure. This allows us to write down a general ansatz for the integrand. The coefficients in the ansatz are fixed by means of a powerful light-cone OPE relation between correlators with different weights. Our result is formulated in terms of a limited number of functions built from known one-, two- and three-loop conformal integrals. These results are useful for checking recent integrability predictions for the OPE structure constants
STAT3 and STAT6 Signaling Pathways Synergize to Promote Cathepsin Secretion from Macrophages via IRE1α Activation.

Tumor-associated macrophages play critical roles during tumor progression by promoting angiogenesis, cancer cell proliferation, invasion, and metastasis. Cysteine cathepsin proteases, produced by macrophages and cancer cells, modulate these processes, but it remains unclear how these typically lysosomal enzymes are regulated and secreted within the tumor microenvironment. Here, we identify a STAT3 and STAT6 synergy that potently upregulates cathepsin secretion by macrophages via engagement of an unfolded protein response (UPR) pathway. Whole-genome expression analyses revealed that the TH2 cytokine interleukin (IL)-4 synergizes with IL-6 or IL-10 to activate UPR via STAT6 and STAT3. Pharmacological inhibition of the UPR sensor IRE1α blocks cathepsin secretion and blunts macrophage-mediated cancer cell invasion. Similarly, genetic deletion of STAT3 and STAT6 signaling components impairs tumor development and invasion in vivo. Together, these findings demonstrate that cytokine-activated STAT3 and STAT6 cooperate in macrophages to promote a secretory phenotype that enhances tumor progression in a cathepsin-dependent manner
Optimizing the Entrainment Geometry of a Dry Powder Inhaler: Methodology and Preliminary Results

This is the final version of the article. It first appeared from Springer via http://dx.doi.org/10.1007/s11095-016-1992-3$\textit{Purpose}$ For passive dry powder inhalers (DPIs) entrainment and emission of the aerosolized drug dose depends strongly on device geometry and the patient’s inhalation manoeuvre. We propose a computational method for optimizing the entrainment part of a DPI. The approach assumes that the pulmonary delivery location of aerosol can be determined by the timing of dose emission into the tidal airstream.

$\textit{Methods}$ An optimization algorithm was used to iteratively perform computational fluid dynamic (CFD) simulations of the drug emission of a DPI. The algorithm seeks to improve performance by changing the device geometry. Objectives were to achieve drug emission that was: A) independent of inhalation manoeuvre; B) similar to a target profile. The simulations used complete inhalation flow-rate profiles generated dependent on the device resistance. The CFD solver was OpenFOAM with drug/air flow simulated by the Eulerian-Eulerian method.

$\textit{Results}$ To demonstrate the method, a 2D geometry was optimized for inhalation independence (comparing two breath profiles) and an early-bolus delivery. Entrainment was both shear-driven and gas-assisted. Optimization for a delay in the bolus delivery was not possible with the chosen geometry.

$\textit{Conclusions}$ Computational optimization of a DPI geometry for most similar drug delivery has been accomplished for an example entrainment geometry.Engineering and Physical Sciences Research Council PhD studentship (Grant ID: EP/ M506485/1
The orbital-specific-virtual local coupled cluster singles and doubles method

We extend the orbital-specific-virtual tensor factorization, introduced for local Møller-Plesset perturbation theory in Ref. [J. Yang, Y. Kurashige, F. R. Manby and G. K. L. Chan, J. Chem. Phys. 134, 044123 (2011)10.1063/1.3528935], to local coupled cluster singles and doubles theory (OSV-LCCSD). The method is implemented by modifying an efficient projected-atomic-orbital local coupled cluster program (PAO-LCCSD) described recently, [H.-J. Werner and M. Schütz, J. Chem. Phys. 135, 144116 (2011)10.1063/1.3641642]. By comparison of both methods we find that the compact representation of the amplitudes in the OSV approach affords various advantages, including smaller computational time requirements (for comparable accuracy), as well as a more systematic control of the error through a single energy threshold. Overall, the OSV-LCCSD approach together with an MP2 correction yields small domain errors in practical calculations. The applicability of the OSV-LCCSD is demonstrated for molecules with up to 73 atoms and realistic basis sets (up to 2334 basis functions)
On the relationship between standard intersection cuts,\ud
lift-and-project cuts, and generalized intersection cuts

We examine the connections between the classes of cuts in the title. We show\ud
that lift-and-project (L&P) cuts from a given disjunction are equivalent to generalized\ud
intersection cuts (GICs) from the family of polyhedra obtained by taking positive com-\ud
binations of the complements of the inequalities of each term of the disjunction. While\ud
L&P cuts from split disjunctions are known to be equivalent to standard intersection\ud
cuts (SICs) from the strip obtained by complementing the terms of the split, we show\ud
that L&P cuts from more general disjunctions may not be equivalent to any SIC. In\ud
particular, we give easily verifiable necessary and sufficient conditions for a L&P cut\ud
from a given disjunction D to be equivalent to a SIC from the polyhedral counterpart\ud
of D. Irregular L&P cuts, i.e. those that violate these conditions, have interesting\ud
properties. For instance, unlike the regular ones, they may cut off part of the corner\ud
polyhedron associated with the LP solution from which they are derived. Furthermore,\ud
they are not exceptional: their frequency exceeds that of regular cuts. A numerical\ud
example illustrates some of the above properties
Quarkonium production at the LHC: a phenomenological analysis of
  surprisingly simple data patterns

The LHC quarkonium production measurements reveal a startling observation:
the J/$\psi$, $\psi$(2S), $\chi_{c1,2}$ and $\Upsilon$(nS) $p_{\rm
T}$-differential cross sections are compatible with one universal momentum
scaling pattern. Considering also the absence of strong polarizations of
directly and indirectly produced S-wave mesons, we are led to the conclusion
that there is currently no evidence of a dependence of the partonic production
mechanisms on the quantum numbers and mass of the final state. The experimental
observations supporting this universal production scenario are remarkably
significant, as shown by a new analysis approach, unbiased by specific
theoretical calculations of partonic cross sections, which are only considered
a posteriori, in comparisons with the data-driven results.Comment: Submitted to Phys. Lett.
Search for neutral Higgs bosons of the minimal supersymmetric standard model in pp collisions at root s= 8TeV with the ATLAS detector

A search for the neutral Higgs bosons predicted by the Minimal Supersymmetric Standard Model (MSSM) is reported. The analysis is performed on data from proton-proton collisions at a centre-of-mass energy of 8 TeV collected with the ATLAS detector at the Large Hadron Collider. The samples used for this search were collected in 2012 and correspond to integrated luminosities in the range 19.5-20.3 fb -1. The MSSM Higgs bosons are searched for in the tau tau final state. No significant excess over the expected background is observed, and exclusion limits are derived for the production cross section times branching fraction of a scalar particle as a function of its mass. The results are also interpreted in the MSSM parameter space for various benchmark scenarios.G. Aad … P. Jackson … L. Lee … A. Petridis … N. Soni ... M. White ... et al. (The ATLAS Collaboration
Differential top-antitop cross-section measurements as a function of observables constructed from final-state particles using pp collisions at √s =7  TeV in the ATLAS detector

Various differential cross-sections are measured in top-quark pair (tt ¯) events produced in proton-proton collisions at a centre-of-mass energy of √s =7  TeV at the LHC with the ATLAS detector. These differential cross-sections are presented in a data set corresponding to an integrated luminosity of 4.6  fb¯¹. The differential cross-sections are presented in terms of kinematic variables, such as momentum, rapidity and invariant mass, of a top-quark proxyreferred to as the pseudo-top-quark as well as the pseudo-top-quark pair system. The dependence of the measurement on theoretical models is minimal. The measurements are performed on tt ¯ events in the lepton+jets channel, requiring exactly one charged lepton and at least four jets with at least two of them tagged as originating from a b -quark. The hadronic and leptonic pseudo-top-quarks are defined via the leptonic or hadronic decay mode of the W  boson produced by the top-quark decay in events with a single charged lepton. Differential cross-section measurements of the pseudo-top-quark variables are compared with several Monte Carlo models that implement next-to-leading order or leading-order multi-leg matrix-element calculations
Search for squarks and gluinos in events with isolated leptons, jets and missing transverse momentum at √s =8  TeV with the ATLAS detector

The results of a search for supersymmetry in final states containing at least one isolated lepton (electron or muon), jets and large missing transverse momentum with the ATLAS detector at the Large Hadron Collider are reported. The search is based on proton-proton collision data at a centre-of-mass energy s√=8 TeV collected in 2012, corresponding to an integrated luminosity of 20 fb−1. No significant excess above the Standard Model expectation is observed. Limits are set on supersymmetric particle masses for various supersymmetric models. Depending on the model, the search excludes gluino masses up to 1.32 TeV and squark masses up to 840 GeV. Limits are also set on the parameters of a minimal universal extra dimension model, excluding a compactification radius of 1/Rc = 950 GeV for a cut-off scale times radius (ΛRc) of approximately 30
Intermediate and Long-Term Outcomes of Survivors of Acute Kidney Injury Episodes : A Large Population-Based Cohort Study

Acknowledgements Support: We acknowledge the data management support of Grampian Data Safe Haven and the associated financial support of NHS Research Scotland, through NHS Grampian investment in the Grampian Data Safe Haven. Dr Sawhney is supported by a Clinical Research Training Fellowship from the Wellcome Trust (reference no. 102729/Z/13/Z). We also acknowledge support from The Farr Institute of Health Informatics Research, which is supported by a 10-funder consortium: Arthritis Research UK, the British Heart Foundation, Cancer Research UK, the Economic and Social Research Council, the Engineering and Physical Sciences Research Council, the Medical Research Council, the National Institute of Health Research, the National Institute for Social Care and Health Research (Welsh Assembly Government), the Chief Scientist Office (Scottish Government Health Directorates), and the Wellcome Trust (Medical Research Council grant no: Scotland MR/K007017/1). The funders of this study had no role in study design; collection, analysis, and interpretation of data; writing the report; and the decision to submit the report for publication.Peer reviewedPublisher PD
Cripto-independent Nodal signaling promotes positioning of the A–P axis in the early mouse embryo

AbstractDuring early mouse development, the TGFβ-related protein Nodal specifies the organizing centers that control the formation of the anterior–posterior (A–P) axis. EGF-CFC proteins are important components of the Nodal signaling pathway, most likely by acting as Nodal coreceptors. However, the extent to which Nodal activity depends on EGF-CFC proteins is still debated. Cripto is the earliest EGF-CFC gene expressed during mouse embryogenesis and is involved in both A–P axis orientation and mesoderm formation. To investigate the relation between Cripto and Nodal in the early mouse embryo, we removed the Nodal antagonist Cerberus 1 (Cer1) and simultaneously Cripto, by generating Cer1;Cripto double mouse mutants. We observed that two thirds of the Cer1;Cripto double mutants are rescued in processes that are severely compromised in Cripto−/− embryos, namely A–P axis orientation, anterior mesendoderm and posterior neuroectoderm formation. The observed rescue is strongly reduced in Cer1;Cripto;Nodal triple mutants, suggesting that Nodal can signal extensively in the absence of Cripto, if Cer1 is also inhibited. This signaling activity drives A–P axis positioning. Our results provide evidence for the existence of Cripto-independent signaling mechanisms, by which Nodal controls axis specification in the early mouse embryo
On the continuity of the commutative limit of the 4d N=4 non-commutative super Yang–Mills theory

AbstractWe study the commutative limit of the non-commutative maximally supersymmetric Yang–Mills theory in four dimensions (N=4 SYM), where non-commutativity is introduced in the two spacelike directions. The commutative limits of non-commutative spaces are important in particular in the applications of non-commutative spaces for regularisation of supersymmetric theories (such as the use of non-commutative spaces as alternatives to lattices for supersymmetric gauge theories and interpretations of some matrix models as regularised supermembrane or superstring theories), which in turn can play a prominent role in the study of quantum gravity via the gauge/gravity duality. In general, the commutative limits are known to be singular and non-smooth due to UV/IR mixing effects. We give a direct proof that UV effects do not break the continuity of the commutative limit of the non-commutative N=4 SYM to all order in perturbation theory, including non-planar contributions. This is achieved by establishing the uniform convergence (with respect to the non-commutative parameter) of momentum integrals associated with all Feynman diagrams appearing in the theory, using the same tools involved in the proof of finiteness of the commutative N=4 SYM
Ideals generated by 2-minors, collections of cells and stack polyominoes

AbstractIn this paper we study ideals generated by quite general sets of 2-minors of an m×n-matrix of indeterminates. The sets of 2-minors are defined by collections of cells and include 2-sided ladders. For convex collections of cells it is shown that the attached ideal of 2-minors is a Cohen–Macaulay prime ideal. Primality is also shown for collections of cells whose connected components are row or column convex. Finally the class group of the ring attached to a stack polyomino and its canonical class is computed, and a classification of the Gorenstein stack polyominoes is given
Spectral optimization for the Stekloff–Laplacian: The stability issue

AbstractWe consider the problem of minimizing the first non-trivial Stekloff eigenvalue of the Laplacian, among sets with given measure. We prove that the Brock–Weinstock inequality, asserting that optimal shapes for this spectral optimization problem are balls, can be improved by means of a (sharp) quantitative stability estimate. This result is based on the analysis of a certain class of weighted isoperimetric inequalities already proved in Betta et al. (1999) [2]: we provide some new (sharp) quantitative versions of these, achieved by means of a suitable calibration technique
Memory-dependent effects on palatability in mice

AbstractWhile palatability depends on the properties of particular foods, it is also determined by prior experience, suggesting that memory affects the hedonic value of a substance. Here, we report two procedures that affect palatability in mice: negative contrast and flavour habituation. A microstructure analysis of licking behaviour was employed, with the lick cluster size (the number of licks made in quick succession before a pause) used as a measure of palatability. It was first confirmed that lick cluster size increased monotonically as a function of sucrose concentration, whereas consumption followed an inverted U-shaped function. In a successive negative contrast procedure it was found that when shifted from a high sucrose concentration (32%) to a low sucrose concentration (4%), mice made smaller lick clusters than a group that only received the low concentration. Mice exposed to flavours (cherry or grape Kool Aid) mixed with sucrose (16%) made larger lick clusters for familiar flavours compared to novel flavours. This habituation effect was evident after short (5min) and long (24h) test intervals. Both successive negative contrast and flavour habituation failed to affect levels of consumption. Collectively, the results show that prior experience can have effects on lick cluster size that are equivalent to increasing or decreasing the sweetness of a solution. Thus, palatability is not a fixed property of a substance but is dependent on expectation or familiarity that occurs as a result of memory