cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Figure S6o from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
Mechanism of Redox-mediated Guanine Nucleotide Exchange on Redox-active Rho GTPases
Creators: name: Heo, Jongyun
name: Campbell, Sharon L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Rho GTPases regulate multiple cellular processes including actin cytoskeletal rearrangements, transcriptional regulation, and oxidant production. The studies described herein demonstrate that small molecule redox agents, in addition to protein regulatory factors, can regulate the activity of redox-active Rho GTPases. A novel (GXXXXGK(S/T)C) motif, conserved in a number of Rho GTPases, appears critical for redox-mediated guanine nucleotide dissociation in vitro. A detailed molecular mechanism for redox regulation of GXXXXGK(S/T)C motif-containing Rho GTPases is proposed.
Appendix B from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Sensitivity analyses
(1626) Jane Honora Wicksteed
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Figure S1 from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
Multi-wavelength features of Fermi Bubbles as signatures of a Galactic wind
Creators: name: Sarkar, Kartick Chandra
name: Nath, Biman B.
name: Sharma, Prateek
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Using hydrodynamical simulations, we show for the first time that an episode of star formation in the center of the Milky Way, with a star-formation-rate (SFR) $\sim 0.5$ M$_\odot$ yr$^{-1}$ for $\sim 30$ Myr, can produce bubbles that resemble the Fermi Bubbles (FBs), when viewed from the solar position. The morphology, extent and multi-wavelength observations of FBs, especially X-rays, constrain various physical parameters such as SFR, age, and the circum-galactic medium (CGM) density. We show that the interaction of the CGM with the Galactic wind driven by a star formation in the central region can explain the observed surface brightness and morphological features of X-rays associated with the Fermi Bubbles. Furthermore, assuming that cosmic ray electrons are accelerated {\it in situ} by shocks and/or turbulence, the brightness and morphology of gamma-ray emission and the microwave haze can be explained. The kinematics of the cold and warm clumps in our model also matches with recent observations of absorption lines through the bubbles.
description: 14 pages, 12 figures, Accepted for publication in MNRAS
MEKK4 Is an Effector of the Embryonic TRAF4 for JNK Activation
Creators: name: Johnson, Gary L.
name: Abell, Amy N.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: TRAF4 has previously been shown to activate JNK through an unknown mechanism. Here, we show that endogenous TRAF4 and MEKK4 associate in both human K562 cells and mouse E10.5 embryos. TRAF4 interacts with the kinase domain of MEKK4. However, this association does not require MEKK4 kinase activity. The interaction of MEKK4 and TRAF4 are further demonstrated by the colocalization of TRAF4 and MEKK4 in cells. Importantly, although TRAF4 has little or no ability to activate JNK independently, coexpression of TRAF4 and MEKK4 results in synergistic activation of JNK that is inhibited by a kinase-inactive mutant of MEKK4, MEKK4K1361R. MEKK4 binds the TRAF domain of TRAF4 and MEKK4/TRAF4 activation of JNK is inhibited by expression of the TRAF domain. Furthermore, TRAF4 stimulates MEKK4 kinase activity by promoting MEKK4 oligomerization and JNK activation can be stimulated by chemical induction of MEKK4 dimerization. The findings identify MEKK4 as the MAPK kinase kinase for TRAF4 regulation of the JNK pathway.
Recursive Solutions of Lagrangian Perturbation Theory
Creators: name: Matsubara, Takahiko
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: In the standard perturbation theory (SPT) of self-gravitating Newtonian fluid in an expanding universe, recurrence relations for higher-order solutions are well known and play an important role both in practical applications and in theoretical investigations. The recurrence relations in Lagrangian perturbation theory (LPT), however, had not been known for a long time. Recently, two different kinds of recurrence relations in LPT have been proposed in limited cases. In this paper, we generalize those methods, and most generally derive the recurrence relations, which are capable to include any initial condition in general models of cosmology. The fastest-growing modes in the general relations are identified, and simplified recurrence relations with accurate approximation for the time-dependence are obtained.
description: 15 pages, no figure, typos corrected, matches published version
Membrane Topology Mapping of Vitamin K Epoxide Reductase by in Vitro Translation/Cotranslocation
Creators: name: Von Heijne, Gunnar
name: Nicchitta, Christopher
name: Tie, Jian Ke
name: Stafford, Darrel W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Membrane topology mapping of vitamin K epoxide reductase by in vitro translation/cotranslocation.
Figure S4 from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation.
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
Collisionless Shocks and TeV Neutrinos before Supernova Shock Breakout from an Optically Thick Wind
Creators: name: Giacinti, G.
name: Bell, A. R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: During a supernova explosion, a radiation-dominated shock (RDS) travels through its progenitor. A collisionless shock (CS) is usually assumed to replace it during shock breakout (SB). We demonstrate here that for some realistic progenitors enshrouded in optically thick winds, such as possibly SN 2008D, a CS forms deep inside the wind, soon after the RDS leaves the core, and therefore significantly before SB. The RDS does not survive the transition from the core to the thick wind when the wind close to the core is not sufficiently dense to compensate for the $r^{-2}$ dilution of photons due to shock curvature. This typically happens when the shock velocity is $\lesssim 0.1 {\rm c} \, (\frac{u_{\rm w}}{10\,{\rm km/s}}) (\frac{\dot{M}}{5 \cdot 10^{-4} \, {\rm M}_\odot {\rm /yr}})^{-1} (\frac{r_\ast}{10^{13}\,{\rm cm}})$, where $u_{\rm w}$, $\dot{M}$ and $r_\ast$ are respectively the wind velocity, mass-loss rate and radius of the progenitor star. The radiative CS results in a hard spectrum of the photon flash at breakout, which would produce an X-ray flash. Cosmic ray acceleration would start before SB, for such progenitors. A fraction of secondary TeV neutrinos can reach the observer up to more than ten hours before the first photons from breakout, providing information on the invisible layers of the progenitor.
description: 8 pages (2 columns), 2 figures. Accepted for publication in the Monthly Notices of the Royal Astronomical Society
The resonant nature of tidal stirring of disky dwarf galaxies orbiting the Milky Way
Creators: name: Lokas, Ewa L.
name: Semczuk, Marcin
name: Gajda, Grzegorz
name: D'Onghia, Elena
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Using N-body simulations we study the tidal evolution of initially disky dwarf galaxies orbiting a Milky Way-like host, a process known to lead to the formation of dwarf spheroidal galaxies. We focus on the effect of the orientation of the dwarf galaxy disk's angular momentum with respect to the orbital one and find very strong dependence of the evolution on this parameter. We consider four different orientations: the exactly prograde, the exactly retrograde and two intermediate ones. Tidal evolution is strongest for the exactly prograde and weakest for the exactly retrograde orbit. In the prograde case the stellar component forms a strong bar and remains prolate until the end of the simulation, while its rotation is very quickly replaced by random motions of the stars. In the retrograde case the dwarf remains oblate, does not form a bar and loses rotation very slowly. In the two cases of intermediate orientation of the disk, the evolution is between the two extremes, suggesting a monotonic dependence on the inclination. We interpret the results in terms of the resonance between the angular velocity of the stars in the dwarf and its orbital motion by comparing the measurements from simulations to semi-analytic predictions. We conclude that resonant effects are the most important mechanism underlying the tidal evolution of disky dwarf galaxies.
description: 10 pages, 10 figures, minor revision, accepted for publication in ApJ
General Relativistic and Newtonian White Dwarfs
Creators: name: Boshkayev, Kuantay
name: Rueda, Jorge A.
name: Ruffini, Remo
name: Siutsou, Ivan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The properties of uniformly rotating white dwarfs (RWDs) are analyzed within the framework of Newton's gravity and general relativity. In both cases Hartle's formalism is applied to construct the internal and external solutions to the field equations. The white dwarf (WD) matter is described by the Chandrasekhar equation of state. The region of stability of RWDs is constructed taking into account the mass-shedding limit, inverse $β$-decay instability, and the boundary established by the turning points of constant angular momentum $J$ sequences which separates stable from secularly unstable configurations. We found the minimum rotation period $\sim0.28$ s in both cases and maximum rotating masses $\sim1.534 M_{\odot}$ and $\sim1.516 M_{\odot}$ for the Newtonian and general relativistic WDs, respectively. By using the turning point method we show that general relativistic WDs can indeed be axisymmetrically unstable whereas the Newtonian WDs are stable.
description: 7 pages, 3 figures, 1 table. The Thirteenth Marcel Grossmann Meeting: On Recent Developments in Theoretical and Experimental General Relativity, Astrophysics and Relativistic Field Theories - Proceedings of the MG13 Meeting on General Relativity (in 3 Volumes). Edited by ROSQUIST KJELL ET AL
Mitochondrial Glycerol-3-phosphate Acyltransferase-1 Is Essential in Liver for the Metabolism of Excess Acyl-CoAs
Creators: name: Ilkayeva, Olga R.
name: Neschen, Susanne
name: Coleman, Rosalind A.
name: Cline, Gary W.
name: Muoio, Deborah M.
name: Romanelli, Anthony J.
name: Shulman, Gerald I.
name: Hammond, Linda E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: In vitro studies suggest that the mitochondrial glycerol-3-phosphate acyltransferase-1 (mtGPAT1) isoform catalyzes the initial and rate-controlling step in glycerolipid synthesis and aids in partitioning acyl-CoAs toward triacylglycerol synthesis and away from degradative pathways. To determine whether the absence of mtGPAT1 would increase oxidation of acyl-CoAs and restrict the development of hepatic steatosis, we fed wild type and mtGPAT1-/- mice a diet high in fat and sucrose (HH) for 4 months to induce the development of obesity and a fatty liver. Control mice were fed a diet low in fat and sucrose (LL). With the HH diet, absence of mtGPAT1 resulted in increased partitioning of acyl-CoAs toward oxidative pathways, demonstrated by 60% lower hepatic triacylglycerol content and 2-fold increases in plasma beta-hydroxybutyrate, acylcarnitines, and hepatic mRNA expression of mitochondrial HMG-CoA synthase. Despite the increase in fatty acid oxidation, liver acyl-CoA levels were 3-fold higher in the mtGPAT1-/- mice fed both diets. A lack of difference in CPT1 and FAS mRNA expression between genotypes suggested that the increased acyl-CoA content was not because of increased de novo synthesis, but instead, to an impaired ability to use long-chain acyl-CoAs derived from the diet, even when the dietary fat content was low. Hyperinsulinemia and reduced glucose tolerance on the HH diet was greater in the mtGPAT1-/- mice, which did not suppress the expression of the gluconeogenic genes glucose-6-phosphatase and phosphoenolpyruvate carboxykinase. This study demonstrates that mtGPAT1 is essential for normal acyl-CoA metabolism, and that the absence of hepatic mtGPAT1 results in the partitioning of fatty acids away from triacylglycerol synthesis and toward oxidation and ketogenesis.
Figure S5 from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation.
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
Novel Role for Amphiregulin in Protection from Liver Injury
Creators: name: Berasain, Carmen
name: Castillo, Josefa
name: Prieto, Jesus
name: Santamaría, Monica
name: Lee, David C.
name: Erroba, Elena
name: Avila, Matías A.
name: García-Trevijano, Elena E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Clinically, the Fas and Fas ligand system plays a central role in the development of hepatocyte apoptosis, a process contributing to a broad spectrum of liver diseases. Therefore, the development of therapies aimed at the inhibition of hepatocyte apoptosis is a major issue. Activation of the epidermal growth factor receptor has been shown to convey survival signals to the hepatocyte. To learn about the endogenous response of epidermal growth factor receptor ligands during Fas-mediated liver injury we investigated the expression of epidermal growth factor, transforming growth factor alpha, heparin-binding epidermal growth factor-like growth factor, betacellulin, epiregulin, and amphiregulin in the liver of mice challenged with Fas-agonist antibody. Amphiregulin expression, barely detectable in healthy liver, was significantly up-regulated. Amphiregulin administration abrogated Fas-mediated liver injury in mice and showed direct anti-apoptotic effects in primary hepatocytes. Amphiregulin activated the Akt and signal transducer and activator of transcription-3 survival pathways, and up-regulated Bcl-xL expression. Amphiregulin knock-out mice showed signs of chronic liver damage in the absence of any noxious treatment, and died faster than wild type mice in response to lethal doses of Fas-agonist antibody. In contrast, these mice were more resistant against sublethal liver damage, supporting the hypothesis that chronic liver injury can precondition hepatocytes inducing resistance to subsequent cell death. These results show that amphiregulin is a protective factor induced in response to liver damage and that it may be therapeutic in liver diseases.
(1623) Stephen Kay Jones
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Appendix A from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Details of morphological measurements
Cosmology and stability in scalar tensor bigravity with non-minimal kinetic coupling gravity
Creators: name: Darabi, F.
name: Mousavi, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We generalize the scalar tensor bigravity models to the non-minimal kinetic coupling scalar tensor bigravity models with two scalar fields whose kinetic terms are non-minimally coupled to two Einstein tensors constructed by two metrics. We show that a broad class of expanding universes can be explained by some solutions of this model. Then, we study the stability issue of the solutions by means of imposing homogeneous perturbation on the equations of motion and extract the stable solutions.
description: 18 pages
(1624) William Roscoe
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Generating, dragging and releasing dark solitons in elongated Bose-Einstein condensates
Creators: name: Hans, I.
name: Stockhofe, J.
name: Schmelcher, P.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: We theoretically analyze quasi-one-dimensional Bose-Einstein condensates under the influence of a harmonic trap and a narrow potential defect that moves through the atomic cloud. Performing simulations on the mean field level, we explore a robust mechanism in which a single dark soliton is nucleated and immediately pinned by the moving defect, making it possible to drag it to a desired position and release it there. We argue on a perturbative level that a defect potential which is attractive to the atoms is suitable for holding and moving dark solitons. The soliton generation protocol is investigated over a wide range of model parameters and its success is systematically quantified by a suitable fidelity measure, demonstrating its robustness against parameter variations, but also the need for tight focusing of the defect potential. Holding the soliton at a stationary defect for long times may give rise to dynamical instabilities, whose origin we explore within a Bogoliubov-de Gennes linearization analysis. We show that iterating the generation process with multiple defects offers a perspective for initializing multiple soliton dynamics with freely chosen initial conditions.
description: 10 pages, 8 figures
The resolved star-formation relation in nearby active galactic nuclei
Creators: name: Casasola, Viviana
name: Hunt, Leslie
name: Combes, Francoise
name: Garcia-Burillo, Santiago
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present an analysis of the relation between star formation rate (SFR) surface density (sigmasfr) and mass surface density of molecular gas (sigmahtwo), commonly referred to as the Kennicutt-Schmidt (K-S) relation, at its intrinsic spatial scale, i.e. the size of giant molecular clouds (10-150 pc), in the central, high-density regions of four nearby low-luminosity active galactic nuclei (AGN). We used interferometric IRAM CO(1-0) and CO(2-1), and SMA CO(3-2) emission line maps to derive sigmahtwo and HST-Halpha images to estimate sigmasfr. Each galaxy is characterized by a distinct molecular SF relation at spatial scales between 20 to 200 pc. The K-S relations can be sub-linear, but also super-linear, with slopes ranging from 0.5 to 1.3. Depletion times range from 1 and 2Gyr, compatible with results for nearby normal galaxies. These findings are valid independently of which transition, CO(1-0), CO(2-1), or CO(3-2), is used to derive sigmahtwo. Because of star-formation feedback, life-time of clouds, turbulent cascade, or magnetic fields, the K-S relation might be expected to degrade on small spatial scales (<100 pc). However, we find no clear evidence for this, even on scales as small as 20 pc, and this might be because of the higher density of GMCs in galaxy centers which have to resist higher shear forces. The proportionality between sigmahtwo and sigmasfr found between 10 and 100 Msun/pc2 is valid even at high densities, 10^3 Msun/pc2. However, by adopting a common CO-to-H2 conversion factor (alpha_CO), the central regions of the galaxies have higher sigmasfr for a given gas column than those expected from the models, with a behavior that lies between the mergers/high-redshift starburst systems and the more quiescent star-forming galaxies, assuming that the first ones require a lower value of alpha_CO.
description: 22 pages, 8 figures, Accepted for publication in Astronomy and Astrophysics
Thermodynamic consistency of the charge response in dynamical mean-field based approaches
Creators: name: van Loon, Erik G. C. P.
name: Hafermann, Hartmut
name: Lichtenstein, Alexander I.
name: Katsnelson, Mikhail I.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We consider the thermodynamic consistency of the charge response function in the (extended) Hubbard model. In DMFT, thermodynamic consistency is preserved. We prove that the static, homogeneous DMFT susceptibility is consistent as long as vertex corrections obtained from the two-particle impurity correlation function are included. In presence of a nonlocal interaction, the problem may be treated within extended DMFT (EDMFT), or its diagrammatic extension, the dual boson approach. We show that here, maintaining thermodynamic consistency requires knowledge of three- and four-particle impurity correlation functions, which are typically neglected. Nevertheless, the dual boson approximation to the response is remarkably close to consistency. This holds even when two-particle vertex corrections are neglected. EDMFT is consistent only in the strongly correlated regime and near half-filling, where the physics is predominantly local.
description: 11 pages (incl. appendix), 4 figures
An Unbiased Hessian Representation for Monte Carlo PDFs
Creators: name: Carrazza, Stefano
name: Forte, Stefano
name: Kassabov, Zahari
name: Latorre, Jose Ignacio
name: Rojo, Juan
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We develop a methodology for the construction of a Hessian representation of Monte Carlo sets of parton distributions, based on the use of a subset of the Monte Carlo PDF replicas as an unbiased linear basis, and of a genetic algorithm for the determination of the optimal basis. We validate the methodology by first showing that it faithfully reproduces a native Monte Carlo PDF set (NNPDF3.0), and then, that if applied to Hessian PDF set (MMHT14) which was transformed into a Monte Carlo set, it gives back the starting PDFs with minimal information loss. We then show that, when applied to a large Monte Carlo PDF set obtained as combination of several underlying sets, the methodology leads to a Hessian representation in terms of a rather smaller set of parameters (CMC-H PDFs), thereby providing an alternative implementation of the recently suggested Meta-PDF idea and a Hessian version of the recently suggested PDF compression algorithm (CMC-PDFs). The mc2hessian conversion code is made publicly available together with (through LHAPDF6) a Hessian representations of the NNPDF3.0 set, and the CMC-H PDF set.
description: 27 pages, 17 figures; v2: replaced plots in Fig.1 which had a conflict with google chrome inline viewer; v3: final version, to be published in EPJC; figs 5,10,11,13 updated with new (more accurate) choice of parameters
p53 Monitors Replication Fork Regression by Binding to “Chickenfoot” Intermediates
Creators: name: Griffith, Jack D.
name: Subramanian, Deepa
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The tumor suppressor protein, p53, utilizes multiple mechanisms to ensure faithful transmission of the genome including regulation of DNA replication, repair, and recombination. Monitoring these pathways may involve direct binding of p53 to the DNA intermediates of these processes. In this study, we generated templates resembling stalled replication forks and utilized electron microscopy to examine p53 interactions with these substrates. Our results show that p53 bound with high affinity to the junction of stalled forks, whereas two cancer-derived p53 mutants showed weak binding. Additionally, some of the templates were rearranged to form "chickenfoot" structures in the presence of p53. These were mostly formed due to p53 trapping intermediates of spontaneous fork regression; however, in a small population, the protein appeared to be promoting their formation. Collectively, these results demonstrate the importance of sequence-independent binding in p53-mediated maintenance of genomic integrity.
Orbitals from local RDMFT: Are they Kohn-Sham or Natural Orbitals?
Creators: name: Theophilou, Iris
name: Lathiotakis, Nektarios N.
name: Gidopoulos, Nikitas I.
name: Rubio, Angel
name: Helbig, Nicole
Publisher: name: arXiv
Year: 2015
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: Recently, an approximate theoretical framework was introduced, called local reduced density matrix functional theory (local-RDMFT), where functionals of the one-body reduced density matrix (1-RDM) are minimized under the additional condition that the optimal orbitals satisfy a single electron Schrödinger equation with a local potential. In the present work, we focus on the character of these optimal orbitals. In particular, we compare orbitals obtained by local-RDMFT with those obtained with the full minimization (without the extra condition) by contrasting them against the exact NOs and orbitals from a density functional calculation using the local density approximation (LDA). We find that the orbitals from local-RMDFT are very close to LDA orbitals, contrary to those of the full minimization that resemble the exact NOs. Since local RDMFT preserves the good quality of the description of strong static correlation, this finding opens the way to a mixed density/density matrix scheme, where Kohn-Sham orbitals obtain fractional occupations from a minimization of the occupation numbers using 1-RDM functionals. This will allow for a description of strong correlation at a cost only minimally higher than a density functional calculation.
(1625) Mary Hilda Wicksteed
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Peroxisome Proliferator-activated Receptor γ Suppresses Proximal α1(I) Collagen Promoter via Inhibition of p300-facilitated NF-I Binding to DNA in Hepatic Stellate Cells
Creators: name: Tsukamoto, Hidekazu
name: Rippe, Richard A.
name: Yavrom, Sharon
name: Xiong, Shigang
name: Chen, Li
name: Wang, Jiaohong
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Depletion of peroxisome proliferator-activated receptor gamma (PPARgamma) represents one of the key molecular changes that underlie transdifferentiation (activation) of hepatic stellate cells in the genesis of liver fibrosis (Miyahara, T., Schrum, L., Rippe, R., Xiong, S., Yee, H. F., Jr., Motomura, K., Anania, F. A., Willson, T. M., and Tsukamoto, H. (2000) J. Biol. Chem. 275, 35715-35722; Hazra, S., Xiong, S., Wang, J., Rippe, R. A., Krishna, V., Chatterjee, K., and Tsukamoto, H. (2004) J. Biol. Chem. 279, 11392-11401). In support of this notion, ectopic expression of PPARgamma suppresses hepatic stellate cells activation markers, most notably expression of alpha1(I) procollagen. However, the mechanisms underlying this antifibrotic effect are largely unknown. The present study utilized deletion-reporter gene constructs of proximal 2.2-kb alpha1(I) procollagen promoter to demonstrate that a region proximal to -133 bp is where PPARgamma exerts its inhibitory effect. Within this region, two DNase footprints with Sp1 and reverse CCAAT box sites exist. NF-I, but not CCAAT DNA-binding factor/NF-Y, binds to the proximal CCAAT box in hepatic stellate cells. A mutation of this site almost completely abrogates the promoter activity. NF-I mildly but independently stimulates the promoter activity and synergistically promotes Sp1-induced activity. PPARgamma inhibits NF-I binding to the most proximal footprint (-97/-85 bp) and inhibits its transactivity. The former effect is mediated by the ability of PPARgamma to inhibit p300-facilitated NF-I binding to DNA as demonstrated by chromatin immunoprecipitation assay.
Peroxisome Proliferator-activated Receptor γ-independent Activation of p38 MAPK by Thiazolidinediones Involves Calcium/Calmodulin-dependent Protein Kinase II and Protein Kinase R: CORRELATION WITH ENDOPLASMIC RETICULUM STRESS
Creators: name: Chen, Ching Shih
name: Graves, Lee M.
name: Shiau, Chung Wai
name: Gardner, Olivia S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The thiazolidinediones (TZDs) are synthetic peroxisome proliferator-activated receptor gamma (PPARgamma) ligands that promote increased insulin sensitivity in type II diabetic patients. In addition to their ability to improve glucose homeostasis, TZDs also exert anti-proliferative effects by a mechanism that is unclear. Our laboratory has shown that two TZDs, ciglitazone and troglitazone, rapidly induce calcium-dependent p38 mitogen-activated protein kinase (MAPK) phosphorylation in liver epithelial cells. Here, we further characterize the mechanism responsible for p38 MAPK activation by PPARgamma ligands and correlate this with the induction of endoplasmic reticulum (ER) stress. Specifically, we show that TZDs rapidly activate the ER stress-responsive pancreatic eukaryotic initiation factor 2alpha (eIF2alpha) kinase or PKR (double-stranded RNA-activated protein kinase)-like endoplasmic reticulum kinase/pancreatic eIF2alpha kinase, and that activation of these kinases is correlated with subsequent eIF2alpha phosphorylation. Interestingly, PPARgamma ligands not only activated calcium/calmodulin-dependent kinase II (CaMKII) 2-fold over control, but the selective CaMKII inhibitor, KN-93, attenuated MKK3/6 and p38 as well as PKR and eIF2alpha phosphorylation. Although CaMKII was not affected by inhibition of PKR with 2-aminopurine, phosphorylation of MKK3/6 and p38 as well as eIF2alpha were significantly reduced. Collectively, these data provide evidence that CaMKII is a regulator of PKR-dependent p38 and eIF2alpha phosphorylation in response to ER calcium depletion by TZDs. Furthermore, using structural derivatives of TZDs that lack PPARgamma ligand-binding activity as well as a PPARgamma antagonist, we show that activation of these kinase signaling pathways is PPARgamma-independent.
Figure S5 from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
(1621) Mary Harrison
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
SGRs and AXPs as massive fast rotating highly magnetized white dwarfs: the case of SGR 0418+5729
Creators: name: Boshkayev, Kuantay
name: Rueda, Jorge A.
name: Ruffini, Remo
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We describe one of the so-called low magnetic field magnetars SGR 0418+5729, as a massive fast rotating highly magnetized white dwarf following Malheiro et. al. 2012. We give bounds for the mass, radius, moment of inertia, and magnetic field for these sources, by requesting the stability of realistic general relativistic uniformly rotating configurations. Based on these parameters, we improve the theoretical prediction of the lower limit of the spin-down rate of SGR 0418+5729. In addition, we compute the electron cyclotron frequencies corresponding to the predicted surface magnetic fields.
description: 6 pages, 1 figure, 1 table. The Thirteenth Marcel Grossmann Meeting: On Recent Developments in Theoretical and Experimental General Relativity, Astrophysics and Relativistic Field Theories - Proceedings of the MG13 Meeting on General Relativity (in 3 Volumes). Edited by Rosquist Kjell et. al
pH-dependent Intraluminal Organization of Mucin Granules in Live Human Mucous/Goblet Cells
Creators: name: Olsen, John C.
name: Chua, Michael
name: Boucher, Richard C.
name: Perez-Vilar, Juan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: To study the mechanism of gel-forming mucin packaging within mucin granules, we generated human mucous/goblet cells stably expressing a recombinant MUC5AC domain fused to green fluorescent protein (GFP). The fusion protein, named SHGFP-MUC5AC/CK, accumulated in the granules together with native MUC5AC. Inhibition of protein synthesis or disorganization of the Golgi complex did not result in diminished intragranular SHGFP-MUC5AC/CK signals, consistent with long-term storage of the fusion protein. However, SHGFP-MUC5AC/CK was rapidly discharged from the granules upon incubation of the cells with ATP, an established mucin secretagogue. Several criteria indicated that SHGFP-MUC5AC/CK was not covalently linked to endogenous MUC5AC. Analysis of fluorescence recovery after photobleaching suggested that the intragranular SHGFP-MUC5AC/CK mobile fraction and mobility were significantly lower than in the endoplasmic reticulum lumen. Incubation of the cells with bafilomycin A1, a specific inhibitor of the vacuolar H+-ATPase, did not alter the fusion protein mobility, although it significantly increased (approximately 20%) the intragranular SHGFP-MUC5AC/CK mobile fraction. In addition, the granules in bafilomycin-incubated cells typically exhibited a heterogeneous intraluminal distribution of the fluorescent fusion protein. These results are consistent with a model of mucin granule intraluminal organization with two phases: a mobile phase in which secretory proteins diffuse as in the endoplasmic reticulum lumen but at a lower rate and an immobile phase or matrix in which proteins are immobilized by noncovalent pH-dependent interactions. An intraluminal acidic pH, maintained by the vacuolar H+-ATPase, is one of the critical factors for secretory protein binding to the immobile phase and also for its organization.