pinecone/core-2020-05-10-deduplication huggingface dataset:
Synthesis, microstructure and thermal expansion studies on Ca0·5+x/2Sr0·5+x/2Zr4P6−2xSi2xO24 system prepared by co-precipitation method

We report on the synthesis, microstructure and thermal expansion studies on Ca0·5 + x/2Sr0·5 + x/2Zr4P6 − 2xSi2xO24 (x = 0·00 to 1·00) system which belongs to NZP family of low thermal expansion ceramics. The ceramics synthesized by co-precipitation method at lower calcination and the sintering temperatures were in pure NZP phase up to x = 0·37. For x ≥ 0·5, in addition to NZP phase, ZrSiO4 and Ca2P2O7 form as secondary phases after sintering. The bulk thermal expansion behaviour of the members of this system was studied from 30 to 850 °C. The thermal expansion coefficient increases from a negative value to a positive value with the silicon substitution in place of phosphorous and a near zero thermal expansion was observed at x = 0·75. The amount of hysteresis between heating and cooling curves increases progressively from x = 0·00 to 0·37 and then decreases for x > 0·37. The results were analysed on the basis of formation of the silicon based glassy phase and increase in thermal expansion anisotropy with silicon substitution
Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field
  Development

Atomic partial charges appear in the Coulomb term of many force-field models
and can be derived from electronic structure calculations with a myriad of
atoms-in-molecules (AIM) methods. More advanced models have also been proposed,
using the distributed nature of the electron cloud and atomic multipoles. In
this work, an electrostatic force field is defined through a concise
approximation of the electron density, for which the Coulomb interaction is
trivially evaluated. This approximate "pro-density" is expanded in a minimal
basis of atom-centered s-type Slater density functions, whose parameters are
optimized by minimizing the Kullback-Leibler divergence of the pro-density from
a reference electron density, e.g. obtained from an electronic structure
calculation. The proposed method, Minimal Basis Iterative Stockholder (MBIS),
is a variant of the Hirshfeld AIM method but it can also be used as a
density-fitting technique. An iterative algorithm to refine the pro-density is
easily implemented with a linear-scaling computational cost, enabling
applications to supramolecular systems. The benefits of the MBIS method are
demonstrated with systematic applications to molecular databases and extended
models of condensed phases. A comparison to 14 other AIM methods shows its
effectiveness when modeling electrostatic interactions. MBIS is also suitable
for rescaling atomic polarizabilities in the Tkatchenko-Sheffler scheme for
dispersion interactions.Comment: 61 pages, 12 figures, 2 table
Neutral and non-neutral collisionless plasma equilibria for twisted flux
  tubes: The Gold-Hoyle model in a background field

We calculate exact one-dimensional collisionless plasma equilibria for a
continuum of flux tube models, for which the total magnetic field is made up of
the `force-free' Gold-Hoyle magnetic flux tube embedded in a uniform and
anti-parallel background magnetic field. For a sufficiently weak background
magnetic field, the axial component of the total magnetic field reverses at
some finite radius. The presence of the background magnetic field means that
the total system is not exactly force-free, but by reducing its magnitude the
departure from force-free can be made as small as desired. The distribution
function for each species is a function of the three constants of motion;
namely the Hamiltonian and the canonical momenta in the axial and azimuthal
directions. Poisson's Equation and Amp\`{e}re's Law are solved exactly, and the
solution allows either electrically neutral or non-neutral configurations,
depending on the values of the bulk ion and electron flows. These equilibria
have possible applications in various solar, space and astrophysical contexts,
as well as in the laboratory
Measuring the Higgs-bottom coupling in weak boson fusion.

We study Higgs production through weak boson fusion with subsequent decay to bottom quarks. By combining jet substructure techniques and matrix element methods in different limits we motivate this channel as a probe of the bottom-Yukawa interactions in the boosted regime. In particular we ameliorate the “no-go” results of cut-and-count analyses in this channel. After applying a data-driven reconstruction approach we find that the Higgs-bottom coupling can be limited to View the MathML source with 600 fb−1
Emergent stem cell homeostasis in the C. elegans germline is revealed by hybrid modeling.

One figure and two movies are available at http://www.biophysj.org/biophysj/supplemental/S0006-3495(15)00589-5.The establishment of homeostasis among cell growth, differentiation, and apoptosis is of key importance for organogenesis. Stem cells respond to temporally and spatially regulated signals by switching from mitotic proliferation to asymmetric cell division and differentiation. Executable computer models of signaling pathways can accurately reproduce a wide range of biological phenomena by reducing detailed chemical kinetics to a discrete, finite form. Moreover, coordinated cell movements and physical cell-cell interactions are required for the formation of three-dimensional structures that are the building blocks of organs. To capture all these aspects, we have developed a hybrid executable/physical model describing stem cell proliferation, differentiation, and homeostasis in the Caenorhabditis elegans germline. Using this hybrid model, we are able to track cell lineages and dynamic cell movements during germ cell differentiation. We further show how apoptosis regulates germ cell homeostasis in the gonad, and propose a role for intercellular pressure in developmental control. Finally, we use the model to demonstrate how an executable model can be developed from the hybrid system, identifying a mechanism that ensures invariance in fate patterns in the presence of instability.B.A.H. is presently supported by the Royal Society (University Research Fellowship).Peer-reviewedPublisher Versio
Enterohaemorrhagic E. coli modulates an ARF6:Rab35 signalling axis to prevent recycling endosome maturation during infection

Enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC/EHEC) manipulate a plethora of host cell processes to establish infection of the gut mucosa. This manipulation is achieved via the injection of bacterial effector proteins into host cells using a Type III secretion system. We have previously reported that the conserved EHEC and EPEC effector EspG disrupts recycling endosome function, reducing cell surface levels of host receptors through accumulation of recycling cargo within the host cell. Here we report that EspG interacts specifically with the small GTPases ARF6 and Rab35 during infection. These interactions target EspG to endosomes and prevent Rab35-mediated recycling of cargo to the host cell surface. Furthermore, we show that EspG has no effect on Rab35-mediated uncoating of newly formed endosomes, and instead leads to the formation of enlarged EspG/TfR/Rab11 positive, EEA1/Clathrin negative stalled recycling structures. Thus, this paper provides a molecular framework to explain how EspG disrupts recycling whilst also reporting the first known simultaneous targeting of ARF6 and Rab35 by a bacterial pathogen
Energy-efficient information transfer by visual pathway synapses.

The architecture of computational devices is shaped by their energy consumption. Energetic constraints are used to design silicon-based computers but are poorly understood for neural computation. In the brain, most energy is used to reverse ion influxes generating excitatory postsynaptic currents (EPSCs) and action potentials. Thus, EPSCs should be small to minimize energy use, but not so small as to impair information transmission. We quantified information flow through the retinothalamic synapse in the visual pathway in brain slices, with cortical and inhibitory input to the postsynaptic cell blocked. Altering EPSC size with dynamic clamp, we found that a larger-than-normal EPSC increased information flow through the synapse. Thus, the evolutionarily selected EPSC size does not maximize retinal information flow to the cortex. By assessing the energy used on postsynaptic ion pumping and action potentials, we show that, instead, the EPSC size optimizes the ratio of retinal information transmitted to energy consumed. These data suggest maximization of information transmission per energy used as a synaptic design principle
On the equatorial Ekman layer

This is the author accepted manuscript. The final version is available from Cambridge University Press via the DOI in this record.The steady incompressible viscous flow in the wide gap between spheres rotating rapidly about a common axis at slightly different rates (small Rossby number) has a long and celebrated history. The problem is relevant to the dynamics of geophysical and planetary core flows, for which, in the case of electrically conducting fluids, the possible operation of a dynamo is of considerable interest. A comprehensive asymptotic study, in the small Ekman number limit E≪1, was undertaken by Stewartson (J. Fluid Mech., vol. 26, 1966, pp. 131–144). The mainstream flow, exterior to the E1/2 Ekman layers on the inner/outer boundaries and the shear layer on the inner sphere tangent cylinder C, is geostrophic. Stewartson identified a complicated nested layer structure on C, which comprises relatively thick quasigeostrophic E2/7- (inside C) and E1/4E1/4- (outside C) layers. They embed a thinner ageostrophic E1/3 shear layer (on C), which merges with the inner sphere Ekman layer to form the E2/5-equatorial Ekman layer of axial length E1/5. Under appropriate scaling, this E2/5-layer problem may be formulated, correct to leading order, independent of E. Then the Ekman boundary layer and ageostrophic shear layer become features of the far-field (as identified by the large value of the scaled axial coordinate z) solution. We present a numerical solution of the previously unsolved equatorial Ekman layer problem using a non-local integral boundary condition at finite z to account for the far-field behaviour. Adopting z−1 as a small parameter we extend Stewartson’s similarity solution for the ageostrophic shear layer to higher orders. This far-field solution agrees well with that obtained from our numerical model.F.M. and E.D. have been partially funded by the ANR project Dyficolti ANR-13-BS01-0003-01. F.M. acknowledges a PhD mobility grant from Institut de Physique du Globe de Paris. A.M.S. visited ENS, Paris (19–25 October 2014), while F.M. and E.D. visited the School of Mathematics and Statistics, Newcastle University (respectively, 7–25 September 2015 and 25–30 November 2015); the authors wish to thank their respective host institutions for their hospitality and support
Multivariate and repeated measures (MRM): A new toolbox for 2 dependent and multimodal group-level neuroimaging data

Repeated measurements and multimodal data are common in neuroimaging research. Despite this, conventional approaches to group level analysis ignore these repeated measurements in favour of multiple between-subject models using contrasts of interest. This approach has a number of drawbacks as certain designs and comparisons of interest are either not possible or complex to implement. Unfortunately, even when attempting to analyse group level data within a repeated-measures framework, the methods implemented in popular software packages make potentially unrealistic assumptions about the covariance structure across the brain. In this paper, we describe how this issue can be addressed in a simple and efficient manner using the multivariate form of the familiar general linear model (GLM), as implemented in a new MATLAB toolbox. This multivariate framework is discussed, paying particular attention to methods of inference by permutation. Comparisons with existing approaches and software packages for dependent group-level neuroimaging data are made. We also demonstrate how this method is easily adapted for dependency at the group level when multiple modalities of imaging are collected from the same individuals. Follow-up of these multimodal models using linear discriminant functions (LDA) is also discussed, with applications to future studies wishing to integrate multiple scanning techniques into investigating populations of interest.This work was supported by a MRC Centenary Early Career Award (MR/J500410/1). The example datasets were collected using support from an MRC DTP studentship and an MRC grant (G0900593).This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.neuroimage.2016.02.05
Search for light top squark pair production in final states with leptons and b-jets with the ATLAS detector in √s = 7 TeV proton–proton collisions

The results of a search for pair production of light top squarks are presented, using 4.7 fb[superscript −1] √s = 7 TeV proton–proton collisions collected with the ATLAS detector at the Large Hadron Collider. This search targets top squarks with masses similar to, or lighter than, the top quark mass. Final states containing exclusively one or two leptons (e,μ), large missing transverse momentum, light-flavour jets and b-jets are used to reconstruct the top squark pair system. Event-based mass scale variables are used to separate the signal from a large t[bar over t] background. No excess over the Standard Model expectations is found. The results are interpreted in the framework of the Minimal Supersymmetric Standard Model, assuming the top squark decays exclusively to a chargino and a b-quark, while requiring different mass relationships between the Supersymmetric particles in the decay chain. Light top squarks with masses between 123–167 GeV are excluded for neutralino masses around 55 GeV.European Organization for Nuclear ResearchUnited States. Dept. of EnergyNational Science Foundation (U.S.)Brookhaven National Laborator
Subglacial processes on an Antarctic ice stream bed. 1: Sediment transport and bedform genesis inferred from marine geophysical data

The spatial pattern and morphometry of bedforms and their relationship to sediment thickness have been analysed in the Marguerite Bay Palaeo-ice stream Trough, western Antarctic Peninsula. Over 17 000 glacial landforms were measured from geophysical datasets, and sediment thickness maps were generated from acoustic sub-bottom profiler data. These analyses reveal a complex bedform pattern characterised by considerable spatial diversity, influenced heavily by the underlying substrate. The variability in length and density of mega-scale lineations indicates an evolving bedform signature, whereby landforms are preserved at different stages of maturity. Lineation generation and attenuation is associated with regions of thick, soft till where deformation was likely to be the greatest. The distribution of soft till and the localised extent of grounding-zone wedges (GZWs) indicate a dynamic sedimentary system characterised by considerable spatio-temporal variability in sediment erosion, transport and deposition. Formation of GZWs on the outer shelf of Marguerite Trough, within the error range of the radiocarbon dates, requires large sediment fluxes (upwards of 1000 m 3 a −1 (m grounding line width) −1 ), and a >1 m thick mobile till layer, or rapid basal sliding velocities (upwards of 6 km a −1 )
Balancing redox cofactor generation and ATP synthesis : key microaerobic responses in thermophilic fermentations

Geobacillus thermoglucosidasius is a Gram-positive, thermophilic bacterium capable of ethanologenic fermentation of both C5 and C6 sugars and may have possible use for commercial bioethanol production [Tang et al., 2009; Taylor et al. (2009) Trends Biotechnol 27(7): 398–405]. Little is known about the physiological changes that accompany a switch from aerobic (high redox) to microaerobic/fermentative (low redox) conditions in thermophilic organisms. The changes in the central metabolic pathways in response to a switch in redox potential were analyzed using quantitative real-time PCR and proteomics. During low redox (fermentative) states, results indicated that glycolysis was uniformly up-regulated, the Krebs (tricarboxylic acid or TCA) cycle non-uniformly down-regulated and that there was little to no change in the pentose phosphate pathway. Acetate accumulation was accounted for by strong down-regulation of the acetate CoA ligase gene (acs) in addition to up-regulation of the pta and ackA genes (involved in acetate production), thus conserving ATP while reducing flux through the TCA cycle. Substitution of an NADH dehydrogenase (down-regulated) by an up-regulated NADH:FAD oxidoreductase and up-regulation of an ATP synthase subunit, alongside the observed shifts in the TCA cycle, suggested that an oxygen-scavenging electron transport chain likely remained active during low redox conditions. Together with the observed up-regulation of a glyoxalase and down-regulation of superoxide dismutase, thought to provide protection against the accumulation of toxic phosphorylated glycolytic intermediates and reactive oxygen species, respectively, the changes observed in G. thermoglucosidasius NCIMB 11955 under conditions of aerobic-to-microaerobic switching were consistent with responses to low pO2 stress.The authors wish to acknowledge the University of the Western Cape and the National Research Foundation (South Africa) for funding.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0290/hb201
Automorphisms ofZd-subshifts of finite type

AbstractLet (Σ, σ) be a Zd-subshift of finite type. Under a strong irreducibility condition (strong specification), we show that Aut(Σ) contains any finite group. For Zd-subshift of finite type without strong specification, examples show that topological mixing is not sufficient to give any finite group in the automorphism group in general: in particular, End(Σ) may be an abelian semigroup. For an example of a topologically mixing Z2-subshift of finite type, the endomorphism semigroup and automorphism group are computed explicitly. This subshift has periodic-point permutations that do not extend to automorphisms
Sensitivity of OMI SO2 measurements to variable eruptive behaviour at Soufrière Hills Volcano, Montserrat

AbstractSince 2004, the satellite-borne Ozone Mapping Instrument (OMI) has observed sulphur dioxide (SO2) plumes during both quiescence and effusive eruptive activity at Soufrière Hills Volcano, Montserrat. On average, OMI detected a SO2 plume 4–6 times more frequently during effusive periods than during quiescence in the 2008–2010 period. The increased ability of OMI to detect SO2 during eruptive periods is mainly due to an increase in plume altitude rather than a higher SO2 emission rate. Three styles of eruptive activity cause thermal lofting of gases (Vulcanian explosions; pyroclastic flows; a hot lava dome) and the resultant plume altitudes are estimated from observations and models. Most lofting plumes from Soufrière Hills are derived from hot domes and pyroclastic flows. Although Vulcanian explosions produced the largest plumes, some produced only negligible SO2 signals detected by OMI. OMI is most valuable for monitoring purposes at this volcano during periods of lava dome growth and during explosive activity
Sal-like 4 (SALL4) suppresses CDH1 expression and maintains cell dispersion in basal-like breast cancer

AbstractIn cell cultures, the dispersed phenotype is indicative of the migratory ability. Here we characterized Sal-like 4 (SALL4) as a dispersion factor in basal-like breast cancer. Our shRNA-mediated SALL4 knockdown system and SALL4 overexpression system revealed that SALL4 suppresses the expression of adhesion gene CDH1, and positively regulates the CDH1 suppressor ZEB1. Cell behavior analyses showed that SALL4 suppresses intercellular adhesion and maintains cell motility after cell–cell interaction and cell division, which results in the dispersed phenotype. Our findings indicate that SALL4 functions to suppress CDH1 expression and to maintain cell dispersion in basal-like breast cancer
Women, Weather, and Woes: The Triangular Dynamics of Female-Headed Households, Economic Vulnerability, and Climate Variability in South Africa

SummaryExisting gender inequality is believed to be heightened as a result of weather events and climate-related disasters that are likely to become more common in the future. We show that an already marginalized group—female-headed households in South Africa—is differentially affected by relatively modest levels of variation in rainfall, which households experience on a year-to-year basis. Data from three waves of the National Income Dynamics Survey in South Africa allow us to follow incomes of 4,162 households from 2006 to 2012. By observing how household income is affected by variation in rainfall relative to what is normally experienced during the rainy season in each district, our study employs a series of naturally occurring experiments that allow us to identify causal effects. We find that households where a single head can be identified based on residency or work status are more vulnerable to climate variability than households headed by two adults. Single male-headed households are more vulnerable because of lower initial earnings and, to a lesser extent, other household characteristics that contribute to economic disadvantages. However, this can only explain some of the differential vulnerability of female-headed households. This suggests that there are traits specific to female-headed households, such as limited access to protective social networks or other coping strategies, which makes this an important dimension of marginalization to consider for further research and policy in South Africa and other national contexts. Households headed by widows, never-married women, and women with a non-resident spouse (e.g., “left-behind” migrant households) are particularly vulnerable. We find vulnerable households only in districts where rainfall has a large effect on agricultural yields, and female-headed households remain vulnerable when accounting for dynamic impacts of rainfall on income
Non-linear Q-clouds around Kerr black holes

AbstractQ-balls are regular extended ‘objects’ that exist for some non-gravitating, self-interacting, scalar field theories with a global, continuous, internal symmetry, on Minkowski spacetime. Here, analogous objects are also shown to exist around rotating (Kerr) black holes, as non-linear bound states of a test scalar field. We dub such configurations Q-clouds. We focus on a complex massive scalar field with quartic plus hexic self-interactions. Without the self-interactions, linear clouds have been shown to exist, in synchronous rotation with the black hole horizon, along 1-dimensional subspaces – existence lines – of the Kerr 2-dimensional parameter space. They are zero modes of the superradiant instability. Non-linear Q-clouds, on the other hand, are also in synchronous rotation with the black hole horizon; but they exist on a 2-dimensional subspace, delimited by a minimal horizon angular velocity and by an appropriate existence line, wherein the non-linear terms become irrelevant and the Q-cloud reduces to a linear cloud. Thus, Q-clouds provide an example of scalar bound states around Kerr black holes which, generically, are not zero modes of the superradiant instability. We describe some physical properties of Q-clouds, whose backreaction leads to a new family of hairy black holes, continuously connected to the Kerr family