pinecone/core-2020-05-10-deduplication huggingface dataset:
The Transcription Elongation Factor NusA Is Required for Stress-Induced Mutagenesis in Escherichia coli

SummaryStress-induced mutagenesis describes the accumulation of mutations that occur in nongrowing cells, in contrast to mutagenesis that occurs in actively dividing populations, and has been referred to as stationary-phase or adaptive mutagenesis. The most widely studied system for stress-induced mutagenesis involves monitoring the appearance of Lac+ revertants of the strain FC40 under starvation conditions in Escherichia coli [1]. The SOS-inducible translesion DNA polymerase DinB [2–4] plays an important role in this phenomenon. Loss of DinB (DNA pol IV) function results in a severe reduction of Lac+ revertants [5, 6]. We previously reported that NusA, an essential component of elongating RNA polymerases, interacts with DinB [7]. Here we report our unexpected observation that wild-type NusA function is required for stress-induced mutagenesis. We present evidence that this effect is unlikely to be due to defects in transcription of lac genes but rather is due to an inability to adapt and mutate in response to environmental stress. Furthermore, we extended our analysis to the formation of stress-induced mutants in response to antibiotic treatment, observing the same striking abolition of mutagenesis under entirely different conditions. Our results are the first to implicate NusA as a crucial participant in the phenomenon of stress-induced mutagenesis
Defect scaling Lee–Yang model from the perturbed DCFT point of view

AbstractWe analyze the defect scaling Lee–Yang model from the perturbed defect conformal field theory (DCFT) point of view. First the defect Lee–Yang model is solved by calculating its structure constants from the sewing relations. Integrable defect perturbations are identified in conformal defect perturbation theory. Then pure defect flows connecting integrable conformal defects are described. We develop a defect truncated conformal space approach (DTCSA) to analyze the one parameter family of integrable massive perturbations in finite volume numerically. Fusing the integrable defect to an integrable boundary the relation between the IR and UV parameters can be derived from the boundary relations. We checked these results by comparing the spectrum for large volumes to the scattering theory
Pro-oxidant activity of indicaxanthin from Opuntia ficus indica modulates arachidonate metabolism and prostaglandin synthesis through lipid peroxide production in LPS-stimulated RAW 264.7 macrophages

AbstractMacrophages come across active prostaglandin (PG) metabolism during inflammation, shunting early production of pro-inflammatory towards anti-inflammatory mediators terminating the process. This work for the first time provides evidence that a phytochemical may modulate the arachidonate (AA) metabolism in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages, promoting the ultimate formation of anti-inflammatory cyclopentenone 15deoxy-PGJ2. Added 1h before LPS, indicaxanthin from Opuntia Ficus Indica prevented activation of nuclear factor-κB (NF-κB) and over-expression of PGE2 synthase-1 (mPGES-1), but up-regulated cyclo-oxygenase-2 (COX-2) and PGD2 synthase (H-PGDS), with final production of the anti-inflammatory cyclopentenone. The effects were positively related with concentration between 50 and 100µM. Indicaxanthin did not have any effect in the absence of LPS.A kinetic study investigating the redox status of LPS-stimulated macrophages between 0.5 and 12h, either in the absence or in the presence of 50–100µM indicaxanthin, revealed a differential control of ROS production, with early (0.5–3h) modest inhibition, followed by a progressive (3–12h) concentration-dependent enhancement over the level induced by LPS alone. In addition, indicaxanthin caused early (0.5–3h) concentration-dependent elevation of conjugated diene lipid hydroperoxides, and production of hydroxynonenal-protein adducts, over the amount induced by LPS. In LPS-stimulated macrophages indicaxanthin did not affect PG metabolism when co-incubated with either an inhibitor of NADPH oxidase or vitamin E. It is concluded that LPS-induced pro-oxidant activity of indicaxanthin at the membrane level allows formation of signaling intermediates whose accumulation modulates PG biosynthetic pathway in inflamed macrophages
Deformation structures associated with the Trachyte Mesa intrusion, Henry Mountains, Utah: Implications for sill and laccolith emplacement mechanisms

AbstractDeformation structures in the wall rocks of igneous intrusions emplaced at shallow crustal depths preserve an important record of how space was created for magma in the host rocks. Trachyte Mesa, a small Oligocene age intrusion in the Henry Mountains, Utah, is composed of a series of stacked tabular, sheet-like intrusions emplaced at 3–3.5 km depth into sandstone-dominated sedimentary sequences of late Palaeozoic–Mesozoic age. New structural analysis of the spatial distribution, geometry, kinematics and relative timings of deformation structures in the host rocks of the intrusion has enabled the recognition of distinct pre-, syn-, and late-stage-emplacement deformation phases. Our observations suggest a two-stage growth mechanism for individual sheets where radial growth of a thin sheet was followed by vertical inflation. Dip-slip faults formed during vertical inflation; they are restricted to the tips of individual sheets due to strain localisation, with magma preferentially exploiting these faults, initiating sill (sheet) climbing. The order in which sheets are stacked impacts on the intrusion geometry and associated deformation of wall rocks. Our results offer new insights into the incremental intrusion geometries of shallow-level magmatic bodies and the potential impact of their emplacement on surrounding host rocks
Extensive MIS 3 glaciation in southernmost Patagonia revealed by cosmogenic nuclide dating of outwash sediments

AbstractThe timing and extent of former glacial advances can demonstrate leads and lags during periods of climatic change and their forcing, but this requires robust glacial chronologies. In parts of southernmost Patagonia, dating pre-global Last Glacial Maximum (gLGM) ice limits has proven difficult due to post-deposition processes affecting the build-up of cosmogenic nuclides in moraine boulders. Here we provide ages for the Río Cullen and San Sebastián glacial limits of the former Bahía Inútil–San Sebastián (BI-SSb) ice lobe on Tierra del Fuego (53–54°S), previously hypothesised to represent advances during Marine Isotope Stages (MIS) 12 and 10, respectively. Our approach uses cosmogenic 10Be and 26Al exposure dating, but targets glacial outwash associated with these limits and uses depth-profiles and surface cobble samples, thereby accounting for surface deflation and inheritance. The data reveal that the limits formed more recently than previously thought, giving ages of 45.6 ka (+139.9−14.3) for the Río Cullen, and 30.1 ka (+45.6−23.1) for the San Sebastián limits. These dates indicate extensive glaciation in southern Patagonia during MIS 3, prior to the well-constrained, but much less extensive MIS 2 (gLGM) limit. This suggests the pattern of ice advances in the region was different to northern Patagonia, with the terrestrial limits relating to the last glacial cycle, rather than progressively less extensive glaciations over hundreds of thousands of years. However, the dates are consistent with MIS 3 glaciation elsewhere in the southern mid-latitudes, and the combination of cooler summers and warmer winters with increased precipitation, may have caused extensive glaciation prior to the gLGM
3D interacting CFTs and generalized Higgs phenomenon in higher spin theories on AdS

AbstractWe study a duality, recently conjectured by Klebanov and Polyakov, between higher-spin theories on AdS4 and O(N) vector models in 3D. These theories are free in the UV and interacting in the IR. At the UV fixed point, the O(N) model has an infinite number of higher-spin conserved currents. In the IR, these currents are no longer conserved for spin s>2. In this Letter, we show that the dual interpretation of this fact is that all fields of spin s>2 in AdS4 become massive by a Higgs mechanism, that leaves the spin-2 field massless. We identify the Higgs field and show how it relates to the RG flow connecting the two CFTs, which is induced by a double trace deformation
Kinase-Dead BRAF and Oncogenic RAS Cooperate to Drive Tumor Progression through CRAF

SummaryWe describe a mechanism of tumorigenesis mediated by kinase-dead BRAF in the presence of oncogenic RAS. We show that drugs that selectively inhibit BRAF drive RAS-dependent BRAF binding to CRAF, CRAF activation, and MEK–ERK signaling. This does not occur when oncogenic BRAF is inhibited, demonstrating that BRAF inhibition per se does not drive pathway activation; it only occurs when BRAF is inhibited in the presence of oncogenic RAS. Kinase-dead BRAF mimics the effects of the BRAF-selective drugs and kinase-dead Braf and oncogenic Ras cooperate to induce melanoma in mice. Our data reveal another paradigm of BRAF-mediated signaling that promotes tumor progression. They highlight the importance of understanding pathway signaling in clinical practice and of genotyping tumors prior to administering BRAF-selective drugs, to identify patients who are likely to respond and also to identify patients who may experience adverse effects.PaperCli
Numerical Study of the Entropy Loss of Dimerization and the Folding Thermodynamics of the GCN4 Leucine Zipper

AbstractA lattice-based model of a protein and the Monte Carlo simulation method are used to calculate the entropy loss of dimerization of the GCN4 leucine zipper. In the representation used, a protein is a sequence of interaction centers arranged on a cubic lattice, with effective interaction potentials that are both of physical and statistical nature. The Monte Carlo simulation method is then used to sample the partition functions of both the monomer and dimer forms as a function of temperature. A method is described to estimate the entropy loss upon dimerization, a quantity that enters the free energy difference between monomer and dimer, and the corresponding dimerization reaction constant. As expected, but contrary to previous numerical studies, we find that the entropy loss of dimerization is a strong function of energy (or temperature), except in the limit of large energies in which the motion of the two dimer chains becomes largely uncorrelated. At the monomer-dimer transition temperature we find that the entropy loss of dimerization is approximately five times smaller than the value that would result from ideal gas statistics, a result that is qualitatively consistent with a recent experimental determination of the entropy loss of dimerization of a synthetic peptide that also forms a two-stranded α-helical coiled coil
Mackey functors, induction from restriction functors and coinduction from transfer functors

AbstractBoltje's plus constructions extend two well-known constructions on Mackey functors, the fixed-point functor and the fixed-quotient functor. In this paper, we show that the plus constructions are induction and coinduction functors of general module theory. As an application, we construct simple Mackey functors from simple restriction functors and simple transfer functors. We also give new proofs for the classification theorem for simple Mackey functors and semisimplicity theorem of Mackey functors
Axial dark matter: The case for an invisible Z′

AbstractWe consider the possibility that fermionic dark matter (DM) interacts with the Standard Model fermions through an axial Z′ boson. As long as Z′ decays predominantly into dark matter, the relevant LHC bounds are rather loose. Direct dark matter detection does not significantly constrain this scenario either, since dark matter scattering on nuclei is spin-dependent. As a result, for a range of the Z′ mass and couplings, the DM annihilation cross section is large enough to be consistent with thermal history of the Universe. In this framework, the thermal WIMP paradigm, which currently finds itself under pressure, is perfectly viable
A first principle hybrid functional calculation of TmGe3+-VGe defect complexes in germanium

AbstractBy means of density functional theory (DFT), using the screened Heyd, Scuseria, and Ernzerhof (HSE06) hybrid functional we present results of the TmGe3+-VGe defect complexes in germanium (Ge). The formation energies of the first (fnn), second (snn), third (tnn) and fourth (ftnn) nearest neighbour configurations of VGe-VGe were examined. The charge state transition levels for all these configurations were examined as well. The TmGe3+-VGe complexes were found to have a positive binding energies for the neutral charge state in the fnn and ftnn configurations. The thermodynamic transition levels revealed that the TmGe3+-VGe induced shallow levels in the band gap for the fnn, tnn and ftnn configurations and deep level for the tnn configuration. The snn configuration showed no charge state transition level, the − 2 charge state was stable for all Fermi energies in the band gap. The TmGe3+-VGe displayed evidence of a single donor level (+1/0) and an acceptor level (−1/−2) within the band gap. Charge state controlled metastability was exhibited by the TmGe3+-VGe
Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling

SummaryDietary lipids may influence the abundance of circulating inflammatory microbial factors. Hence, inflammation in white adipose tissue (WAT) induced by dietary lipids may be partly dependent on their interaction with the gut microbiota. Here, we show that mice fed lard for 11 weeks have increased Toll-like receptor (TLR) activation and WAT inflammation and reduced insulin sensitivity compared with mice fed fish oil and that phenotypic differences between the dietary groups can be partly attributed to differences in microbiota composition. Trif−/− and Myd88−/− mice are protected against lard-induced WAT inflammation and impaired insulin sensitivity. Experiments in germ-free mice show that an interaction between gut microbiota and saturated lipids promotes WAT inflammation independent of adiposity. Finally, we demonstrate that the chemokine CCL2 contributes to microbiota-induced WAT inflammation in lard-fed mice. These results indicate that gut microbiota exacerbates metabolic inflammation through TLR signaling upon challenge with a diet rich in saturated lipids
Individual Differences in Psychology Undergraduates’ Development of Research Methods Knowledge and Skills

AbstractNot all psychology undergraduates appear to benefit from participating in research methodology classes. This longitudinal study tracked how students’ knowledge of research methods developed throughout their three-year undergraduate psychology degree. Card sorting procedures measuring knowledge of research methods terminology were repeated at four time-points across three years then analyzed using multidimensional scaling. There was no significant improvement in students’ research methods structural knowledge after a year, but there was by the end of students’ second year. Knowledge did not improve after students’ final year of study. Various metacognitive and motivational variables were significant correlates of research methods knowledge and research skills. Structural knowledge of research methods terminology appears to be developed from formal methodology training and is not improved upon after completion of a final year research project dissertation. Improving metacognitive skills and increasing motivation for methodology classes may be linked to better development of research methods knowledge and research skills
Search for anomalous single top quark production in association with a photon in pp collisions at √s = 8 TeV

The result of a search for flavor changing neutral currents (FCNC) through single top quark production in association with a photon is presented. The study is based on proton-proton collisions at a center-of-mass energy of 8 TeV using data collected with the CMS detector at the LHC, corresponding to an integrated luminosity of 19.8 fb[superscript −1]. The search for tγ events where t → Wb and W → μν is conducted in final states with a muon, a photon, at least one hadronic jet with at most one being consistent with originating from a bottom quark, and missing transverse momentum. No evidence of single top quark production in association with a photon through a FCNC is observed. Upper limits at the 95% confidence level are set on the tuγ and tcγ anomalous couplings and translated into upper limits on the branching fraction of the FCNC top quark decays: ℬ(t → uγ) < 1.3 × 10− 4 and ℬ(t → cγ) < 1.7 × 10[superscript − 3]. Upper limits are also set on the cross section of associated tγ production in a restricted phase-space region. These are the most stringent limits currently available.United States. Dept. of EnergyNational Science Foundation (U.S.
Supersymmetric AdS(5) solutions of massive IIA supergravity

Motivated by a recently found class of AdS(7) solutions, we classify AdS(5) solutions in massive IIA, finding infinitely many new analytical examples. We reduce the general problem to a set of PDEs, determining the local internal metric, which is a fibration over a surface. Under a certain simplifying assumption, we are then able to analytically solve the PDEs and give a complete list of all solutions. Among these, one class is new and regular. These spaces can be related to the AdS(7) solutions via a simple universal map for the metric, dilaton and fluxes. The natural interpretation of this map is that the dual CFT6 and CFT4 are related by twisted compactification on a Riemann surface Sigma(g). The ratio of their free energy coefficients is proportional to the Euler characteristic of Sigma(g). As a byproduct, we also find the analytic expression for the AdS(7) solutions, which were previously known only numerically. We determine the free energy for simple examples: it is a simple cubic function of the flux integers.DFG/GRK/1463ERC Advanced Grant “SyDuGraM”IISN-BelgiumCommunauté Francaise de BelgiqueBelgian FNRS-FRSINFNERC/FP7/2007-2013MIUR-FIRB/RBFR10QS5
First measurement of the polarization observable E and helicity-dependent cross sections in single π 0 photoproduction from quasi-free nucleons

The double-polarization observable E and the helicity-dependent cross sections sigma(1/2) and sigma(3/2) have been measured for the first time for single pi(0) photoproduction from protons and neutrons bound in the deuteron at the electron accelerator facility MAMI in Mainz, Germany. The experiment used a circularly polarized photon beam and a longitudinally polarized deuterated butanol target. The reaction products, recoil nucleons and decay photons from the pi(0) meson were detected with the Crystal Ball and TAPS electromagnetic calorimeters. Effects from nuclear Fermi motion were removed by a kinematic reconstruction of the pi N-0 final state. A comparison to data measured with a free proton target showed that the absolute scale of the cross sections is significantly modified by nuclear final-state interaction (FSI) effects. However, there is no significant effect on the asymmetry E since the sigma(1/2) and sigma(3/2) components appear to be influenced in a similar way. Thus, the best approximation of the two helicity-dependent cross sections for the free neutron is obtained by combining the asymmetry E measured with quasi-free neutrons and the unpolarized cross section corrected for FSI effects under the assumption that the FSI effects are similar for neutrons and protons
Expanding the Bethe/Gauge Dictionary

We expand the Bethe/Gauge dictionary between the XXX Heisenberg spin chain
and 2d N = (2,2) supersymmetric gauge theories to include aspects of the
algebraic Bethe ansatz. We construct the wave functions of off-shell Bethe
states as orbifold defects in the A-twisted supersymmetric gauge theory and
study their correlation functions. We also present an alternative description
of off-shell Bethe states as boundary conditions in an effective N = 4
supersymmetric quantum mechanics. Finally, we interpret spin chain R-matrices
as correlation functions of Janus interfaces for mass parameters in the
supersymmetric quantum mechanics.Comment: 50 pages, 16 figure
A complete two-loop, five-gluon helicity amplitude in Yang-Mills theory.

We compute the integrand of the full-colour, two-loop, five-gluon scattering amplitude in pure Yang-Mills theory with all helicities positive, using generalized unitarity cuts. Tree-level BCJ relations, satisfied by amplitudes appearing in the cuts, allow us to deduce all the necessary non-planar information for the full-colour amplitude from known planar data. We present our result in terms of irreducible numerators, with colour factors derived from the multi-peripheral colour decomposition. Finally, the leading soft divergences are checked to reproduce the expected infrared behaviour
Holography with a Landau pole.

Holography for UV-incomplete gauge theories is important but poorly understood. A paradigmatic example is d = 4,   N=4N=4  super Yang-Mills coupled to Nf quark flavors, which possesses a Landau pole at a UV scale ΛLP. The dual gravity solution exhibits a UV singularity at a finite proper distance along the holographic direction. Despite this, holographic renormalization can be fully implemented via analytic continuation to an AdS solution. The presence of a UV cut-off manifests itself in several interesting ways. At energies E ≪ ΛLP no pathologies appear, as expected from effective field theory. In contrast, at scales E ≲ ΛLP the gravitational potential becomes repulsive, and at temperatures T ≲ ΛLP the specific heat becomes negative. Although we focus on   N=4N=4  super Yang-Mills with flavor, our qualitative results apply to a much more general class of theories, since they only depend on the fact that the metric near the UV singularity is a hyper-scaling violating metric with exponent θ > d − 1
Proton-sensitive transitions of renal type II Na(+)-coupled phosphate cotransporter kinetics.

In the kidney proximal tubule, acidification of the glomerular filtrate leads to an inhibition of inorganic phosphate (P(i)) reabsorption by type II Na(+)-coupled cotransporters (NaPi-II). As external pH also alters the divalent/monovalent P(i) ratio, it has been difficult to separate putative proton interactions with the cotransporter from direct titration of divalent P(i), the preferred species transported. To distinguish between these possibilities and identify pH-sensitive transitions in the cotransport cycle, the pH-dependent kinetics of two NaPi-II isoforms, expressed in Xenopus laevis oocytes, were investigated electrophysiologically. At -50 mV, both isoforms showed >70% suppression of electrogenic response for an external pH change from 8.0 to 6.2, not attributable to titration of divalent P(i). This was accompanied by a progressive removal of steady-state voltage dependence. The NaPi-II-related uncoupled slippage current was unaffected by a pH change from 7.4 to 6.2, with no shift in the reversal potential, which suggested that protons do not function as substrate. The voltage-dependence of pre-steady-state relaxations was shifted to depolarizing potentials in 100 mM and 0 mM Na(ext)(+) and two kinetic components were resolved, the slower of which was pH-dependent. The changes in kinetics are predicted by a model in which protons interact with the empty carrier and final Na(+) binding step