cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Transverse electron-scale instability in relativistic shear flows
Creators: name: Alves, E. P.
name: Grismayer, T.
name: Fonseca, R. A.
name: Silva, L. O.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Electron-scale surface waves are shown to be unstable in the transverse plane of a shear flow in an initially unmagnetized plasma, unlike in the (magneto)hydrodynamics case. It is found that these unstable modes have a higher growth rate than the closely related electron-scale Kelvin-Helmholtz instability in relativistic shears. Multidimensional particle-in-cell simulations verify the analytic results and further reveal the emergence of mushroom-like electron density structures in the nonlinear phase of the instability, similar to those observed in the Rayleigh Taylor instability despite the great disparity in scales and different underlying physics. Macroscopic ($\gg c/ω_{pe}$) fields are shown to be generated by these microscopic shear instabilities, which are relevant for particle acceleration, radiation emission and to seed MHD processes at long time-scales.
Enhanced Amino Acid Selection in Fully Evolved Tryptophanyl-tRNA Synthetase, Relative to Its Urzyme, Requires Domain Motion Sensed by the D1 Switch, a Remote Dynamic Packing Motif
Creators: name: Delarue, Marc
name: Carter Jr., Charles W.
name: Koehl, Patrice
name: Weinreb, Violetta
name: Li, Li
name: Chandrasekaran, Srinivas Niranj
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: We previously showed (Li, L., and Carter, C. W., Jr. (2013) J. Biol. Chem. 288, 34736–34745) that increased specificity for tryptophan versus tyrosine by contemporary Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) over that of TrpRS Urzyme results entirely from coupling between the anticodon-binding domain and an insertion into the Rossmann-fold known as Connecting Peptide 1. We show that this effect is closely related to a long range catalytic effect, in which side chain repacking in a region called the D1 Switch, accounts fully for the entire catalytic contribution of the catalytic Mg2+ ion. We report intrinsic and higher order interaction effects on the specificity ratio, (kcat/Km)Trp/(kcat/Km)Tyr, of 15 combinatorial mutants from a previous study (Weinreb, V., Li, L., and Carter, C. W., Jr. (2012) Structure 20, 128–138) of the catalytic role of the D1 Switch. Unexpectedly, the same four-way interaction both activates catalytic assist by Mg2+ ion and contributes −4.4 kcal/mol to the free energy of the specificity ratio. A minimum action path computed for the induced-fit and catalytic conformation changes shows that repacking of the four residues precedes a decrease in the volume of the tryptophan-binding pocket. We suggest that previous efforts to alter amino acid specificities of TrpRS and glutaminyl-tRNA synthetase (GlnRS) by mutagenesis without extensive, modular substitution failed because mutations were incompatible with interdomain motions required for catalysis.
RESIK Solar X-ray flare element abundances on a non-isothermal assumption
Creators: name: Sylwester, B.
name: Phillips, K. J. H.
name: Sylwester, J.
name: Kepa, A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Solar X-ray spectra from the RESIK crystal spectrometer on the {\em CORONAS-F} spacecraft (spectral range $3.3-6.1$~Å) are analyzed for thirty-three flares using a method to derive abundances of Si, S, Ar, and K, emission lines of which feature prominently in the spectra. For each spectrum, the method first optimizes element abundances then derives the differential emission measure as a function of temperature based on a procedure given by Sylwester et al. and Withbroe. This contrasts with our previous analyses of RESIK spectra in which an isothermal assumption was used. The revised abundances (on a logarithmic scale with $A({\rm H}) = 12$) averaged for all the flares in the analysis are $A({\rm Si}) = 7.53 \pm 0.08$ (previously $7.89 \pm 0.13$), $A({\rm S}) = 6.91 \pm 0.07$ ($7.16 \pm 0.17$), $A({\rm Ar}) = 6.47 \pm 0.08$ ($6.45 \pm 0.07$), and $A({\rm K}) = 5.73 \pm 0.19$ ($5.86 \pm 0.20$), with little evidence for time variations of abundances within the evolution of each flare. Our previous estimates of the Ar and K flare abundances are thus confirmed by this analysis but those for Si and S are reduced. This suggests the flare abundances of Si and Ar are very close to the photospheric abundance or solar proxies, while S is significantly less than photospheric and the K abundance is much higher than photospheric. These estimates differ to some extent from those in which a single enhancement factor applies to elements with first ionization potential less than 10~eV.
description: 4 figures
Myeloid cell MHC I expression drives CD8+ T cell activation in nonalcoholic steatohepatitis
Creators: name: Atkins H.M.
name: Hess P.
name: Adams V.R.
name: Collins L.B.
name: Scheidemantle G.
name: Kennedy A.
name: Holmes J.
name: Lodge M.
name: Johnson A.J.
name: Williams T.I.
name: Liu X.
Publisher: name: Frontiers Media SA
Year: 2023

description: Background & aims: Activated CD8+ T cells are elevated in Nonalcoholic steatohepatitis (NASH) and are important for driving fibrosis and inflammation. Despite this, mechanisms of CD8+ T cell activation in NASH are largely limited. Specific CD8+ T cell subsets may become activated through metabolic signals or cytokines. However, studies in NASH have not evaluated the impact of antigen presentation or the involvement of specific antigens. Therefore, we determined if activated CD8+ T cells are dependent on MHC class I expression in NASH to regulate fibrosis and inflammation. Methods: We used H2Kb and H2Db deficient (MHC I KO), Kb transgenic mice, and myeloid cell Kb deficient mice (LysM Kb KO) to investigate how MHC class I impacts CD8+ T cell function and NASH. Flow cytometry, gene expression, and histology were used to examine hepatic inflammation and fibrosis. The hepatic class I immunopeptidome was evaluated by mass spectrometry. Results: In NASH, MHC class I isoform H2Kb was upregulated in myeloid cells. MHC I KO demonstrated protective effects against NASH-induced inflammation and fibrosis. Kb mice exhibited increased fibrosis in the absence of H2Db while LysM Kb KO mice showed protection against fibrosis but not inflammation. H2Kb restricted peptides identified a unique NASH peptide Ncf2 capable of CD8+ T cell activation in vitro. The Ncf2 peptide was not detected during fibrosis resolution. Conclusion: These results suggest that activated hepatic CD8+ T cells are dependent on myeloid cell MHC class I expression in diet induced NASH to promote inflammation and fibrosis. Additionally, our studies suggest a role of NADPH oxidase in the production of Ncf2 peptide generation.
(3899) John Barclay McBride
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.
Optimization of the Combined Proton Acceleration Regime with a Target Composition Scheme
Creators: name: Yao, W. P.
name: Li, B. W.
name: Zheng, C. Y.
name: Liu, Z. J.
name: Yan, X. Q.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: A target composition scheme to optimize the combined proton acceleration regime is presented and verified by two-dimensional particle-in-cell (2D PIC) simulations by using an ultra-intense circularly-polarized (CP) laser pulse irradiating an overdense hydrocarbon (CH) target, instead of a pure hydrogen (H) one. The combined acceleration regime is a two-stage proton acceleration scheme combining the radiation pressure dominated acceleration (RPDA) stage and the laser wakefield acceleration (LWFA) stage sequentially together. With an ultra-intense CP laser pulse irradiating an overdense CH target, followed by an underdense tritium plasma gas, protons with higher energies (from about $20$ GeV up to about $30$ GeV) and lower energy spreads (from about $18\%$ down to about $5\%$ in full-width at half-maximum, or FWHM) are generated, as compared to the use of a pure H target. It is because protons can be more stably pre-accelerated in the first RPDA stage when using CH targets. With the increase of the carbon-to-hydrogen density ratio, the energy spread is lower and the maximum proton energy is higher. It also shows that for the same laser intensity around $10^{22}$ $Wcm^{-2}$, using the CH target will lead to a higher proton energy, as compared to the use of a pure H target. Additionally, proton energy can be further increased by employing a longitudinally negative gradient of a background plasma density.
description: 16 pages, 8 figures
Mid-IR femtosecond frequency conversion by soliton-probe collision in phase-mismatched quadratic nonlinear crystals
Creators: name: Liu, Xing
name: Zhou, Binbin
name: Guo, Hairun
name: Bache, Morten
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We show numerically that ultrashort self-defocusing temporal solitons colliding with a weak pulsed probe in the near-IR can convert the probe to the mid-IR. A near-perfect conversion efficiency is possible for a high effective soliton order. The near-IR self-defocusing soliton can form in a quadratic nonlinear crystal (beta-barium borate) in the normal dispersion regime due to cascaded (phase-mismatched) second-harmonic generation, and the mid-IR converted wave is formed in the anomalous dispersion regime between $λ=2.2-2.4~μ\rm m$ as a resonant dispersive wave. This process relies on non-degenerate four-wave mixing mediated by an effective negative cross-phase modulation term caused by cascaded soliton-probe sum-frequency generation.
description: Longer version with appendix
Fibroblast Growth Factor-based Signaling through Synthetic Heparan Sulfate Blocks Copolymers Studied Using High Cell Density Three-dimensional Cell Printing
Creators: name: Dordick, Jonathan S.
name: Liu, Jian
name: Otto, Nigel J.
name: Green, Dixy E.
name: Xu, Yongmei
name: Linhard, Robert J.
name: Sterner, Eric
name: DeAngelis, Paul L.
name: Li, Guoyun
name: Li, Lingyun
name: Masuko, Sayaka
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Four well-defined heparan sulfate (HS) block copolymers containing S-domains (high sulfo group content) placed adjacent to N-domains (low sulfo group content) were chemoenzymatically synthesized and characterized. The domain lengths in these HS block co-polymers were ∼40 saccharide units. Microtiter 96-well and three-dimensional cell-based microarray assays utilizing murine immortalized bone marrow (BaF3) cells were developed to evaluate the activity of these HS block co-polymers. Each recombinant BaF3 cell line expresses only a single type of fibroblast growth factor receptor (FGFR) but produces neither HS nor fibroblast growth factors (FGFs). In the presence of different FGFs, BaF3 cell proliferation showed clear differences for the four HS block co-polymers examined. These data were used to examine the two proposed signaling models, the symmetric FGF2-HS2-FGFR2 ternary complex model and the asymmetric FGF2-HS1-FGFR2 ternary complex model. In the symmetric FGF2-HS2-FGFR2 model, two acidic HS chains bind in a basic canyon located on the top face of the FGF2-FGFR2 protein complex. In this model the S-domains at the non-reducing ends of the two HS proteoglycan chains are proposed to interact with the FGF2-FGFR2 protein complex. In contrast, in the asymmetric FGF2-HS1-FGFR2 model, a single HS chain interacts with the FGF2-FGFR2 protein complex through a single S-domain that can be located at any position within an HS chain. Our data comparing a series of synthetically prepared HS block copolymers support a preference for the symmetric FGF2-HS2-FGFR2 ternary complex model.
Age, growth, reproduction and diet of the whiting, Merlangius merlangus euxinus (Nordmann, 1840), in the southeastern Black Sea
Creators: name: MAZLUM, Rahşan Evren
name: BİLGİN, Sabri
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2014

description: Age structure, growth, reproduction and diet of the whiting, Merlangius merlangus euxinus, were studied on a total of 598 whiting between December 2004 and November 2005 in the southeastern Black Sea. The total length of females was statistically higher than the one of males (t test, p < 0.001). The age range estimated was up to 6 years for females and 5 years for males. To obtain reliable estimates of growth parameters, three growth models (von Bertalanffy, Gompertz and Richards) were applied for both sexes. Gompertz (AIC = 1901.46) and von Bertalanffy (AIC = 1853.71) were the most suitable models to fit age-length data for females and von Bertalanffy considered as the most suitable growth model due to goodness of fit for males. Spawning occurred throughout the year with three peaks: firstly end of winter, secondly middle of spring and thirdly end of autumn. Whiting mostly feed on three fish species: anchovy (IRI% = 35.01), whiting (IRI% = 34.07) and sprat (IRI% = 22.81). ANOSIM showed that significant differences in the prey species composition existed between the seasons (R = 0.1149, p < 0.001) and SIMPER analysis also revealed that the most contributing species to the differences between seasons was anchovy.
Fede religiosa e identità nazionale in Italia e in Russia nel XIX Secolo: una riflessione storico-filosofica sugli ideali dell’istruzione e della cultura
Creators: name: Capilupi, Stefano Maria
Publisher: name: Gli Argonauti. Rivista di Studi Storico-Educativi e Pedagogici
Year: 2025
Subjects: Istruzione; storia; nazione; identità religiosa; universalità; Russia; Italia; riforme; progresso; stagnazione; Education; history; nation; religious identity; universality; Russia; Italy; reforms; progress; stagnation

description: Il contributo offre un quadro delle riforme russe verificatisi nel mondo dell’istruzione nel XIX secolo, con particolare attenzione alle metodiche inerenti all’insegnamento della storia, tema assai delicato e anche oggi di nuovo attuale dal punto di vista della dialettica sempre viva in Russia fra le esigenze del potere e quelle del libero insegnamento e della libera ricerca. Inoltre, il lavoro introduce un parallelo con i più generali fermenti ideologici italiani dell’epoca nell’ottica del rapporto fra fede religiosa e identità nazionale, offrendo una nuova riflessione sulla tensione esistente nella cultura russa fra l’idea di nazione e quella di universalità.

First of all, in the text, a brief summary of the Russian reforms that took place in the world of education in the nineteenth century is made, with particular attention to the methods inherent in the teaching of history – a very delicate subject and even today again relevant from the point of view of the ever-alive dialectic in Russia between the demands of power and those of free teaching and free research. Then, in this Russian historical framework of complex and difficult relationships between education, religion, national principle and philosophy, a parallel is introduced with the more general Italian ideological ferments of the time from the point of view of the relationship between religious faith and national identity. It ends with a new reflection on the tension existing in Russian culture between the idea ofnation and that ofuniversality.
description: Gli Argonauti. Rivista di Studi Storico-Educativi e Pedagogici, V. 4, N. 2 (2024)
G Protein Signaling Modulator-3 Inhibits the Inflammasome Activity of NLRP3
Creators: name: Gall, Bryan J.
name: Buckley, Brian K.
name: Laroche, Geneviève
name: Giguère, Patrick M.
name: Wilson, Justin E.
name: Ezekwe, Ejiofor A.D.
name: Kebaier, Chahnaz
name: Duncan, Joseph A.
name: Ting, Jenny P.
name: Siderovski, David P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Inflammasomes are multi-protein complexes that regulate maturation of the interleukin 1β-related cytokines IL-1β and IL-18 through activation of the cysteine proteinase caspase-1. NOD-like receptor family, pyrin domain containing 3 (NLRP3) protein is a key component of inflammasomes that assemble in response to a wide variety of endogenous and pathogen-derived danger signals. Activation of the NLRP3-inflammasome and subsequent secretion of IL-1β is highly regulated by at least three processes: transcriptional activation of both NLRP3 and pro-IL-1β genes, non-transcriptional priming of NLRP3, and final activation of NLRP3. NLRP3 is predominantly expressed in cells of the hematopoietic lineage. Using a yeast two-hybrid screen, we identified the hematopoietic-restricted protein, G protein signaling modulator-3 (GPSM3), as a NLRP3-interacting protein and a negative regulator of IL-1β production triggered by NLRP3-dependent inflammasome activators. In monocytes, GPSM3 associates with the C-terminal leucine-rich repeat domain of NLRP3. Bone marrow-derived macrophages lacking GPSM3 expression exhibit an increase in NLRP3-dependent IL-1β, but not TNF-α, secretion. Furthermore, GPSM3-null mice have enhanced serum and peritoneal IL-1β production following Alum-induced peritonitis. Our findings suggest that GPSM3 acts as a direct negative regulator of NLRP3 function.
High Finesse Fiber Fabry-Perot Cavities: Stabilization and Mode Matching Analysis
Creators: name: Gallego, Jose
name: Ghosh, Sutapa
name: Alavi, Seyed Khalil
name: Alt, Wolfgang
name: Martinez-Dorantes, Miguel
name: Meschede, Dieter
name: Ratschbacher, Lothar
Publisher: name: arXiv
Year: 2015
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Fiber Fabry-Perot cavities, formed by micro-machined mirrors on the end-facets of optical fibers, are used in an increasing number of technical and scientific applications, where they typically require precise stabilization of their optical resonances. Here, we study two different approaches to construct fiber Fabry-Perot resonators and stabilize their length for experiments in cavity quantum electrodynamics with neutral atoms. A piezo-mechanically actuated cavity with feedback based on the Pound-Drever-Hall locking technique is compared to a novel rigid cavity design that makes use of the high passive stability of a monolithic cavity spacer and employs thermal self-locking and external temperature tuning. Furthermore, we present a general analysis of the mode matching problem in fiber Fabry-Perot cavities, which explains the asymmetry in their reflective line shapes and has important implications for the optimal alignment of the fiber resonators. Finally, we discuss the issue of fiber-generated background photons. We expect that our results contribute towards the integration of high-finesse fiber Fabry-Perot cavities into compact and robust quantum-enabled devices in the future.
description: The Supplemental Material is included in the source code of the article that can be downloaded from this arXiv page (see "Other formats"). Peer-reviewed version with changes to text and figures
POLARITÉ ET SYMÉTRIE DANS LE PROCESSUS D'EMBRYOGENÈSE SOMATIQUE CHEZ METRIDIUM SENILE FIMBRIATUM (VERRILL)
Creators: name: POLTEVA, D.G.
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 1969

description: The morpho-functional reconstruction following the disturbance of a living system, can be realized by a process of regeneration or by a somatic embryogenesis, according to the level of organization of the animal, its degree of integration and the nature of the disintegrating factor. The fragments of regenerationofMetridium senile fimbriatumreconstituethestructuralplanof the original polyp by a transversal regulation of the symmetry. After certain operations which are increasing the disintegration of the fragment, the regulation is realized by a somatic embryogenesis of one or several polyps, representing the apparition of new axis of symmetry, sometimes followed by an inversion of the polarity. This somatic embryogenesis has been observed on long stripes or on rings cut on the circumference of the pedial disc of the sea-anemone. It appearsinthreedifferentforms.
1. Morphogenetical regeneration on the basis of the structural anatomicalelements of the original animal; the original polarity is conserved and the regulation of the symmetry tends to reconstruct the primitive polyp. But the ontogenesis of the new animal begins by the formation of 4-6 pairs of proto- mesenteriums, as in a normal embryogenesis.
2. Regulation on a higher level, including the apparition of a new principalaxis of symmetry and the inversion of the polarity; the ancient mesenteriums are not implied in the new formation and the process of destruction in the ancienttissuesisparticularlyextensive.
3. Local process of somatica! embryogenesis, not unlike the budding ; the“bud” is built as an évagination of the wall of one of the cavities of the polyp constructedwitha stripeoraringoftissueoftheoriginalsea-anemone;the creation of the anatomical elements of the new individual is not at all linked to thepreexistingelements.
Two varieties of Metridium senile fimbriatum are coexisting in the gulf of Peter the Great (Japanese Sea); one living in the depth the other being coastal, living in the zone of surf. Our experiments have been made with the seco
Gene Model 129 ( Gm129 ) Encodes a Novel Transcriptional Repressor That Modulates Circadian Gene Expression
Creators: name: Annayev, Yunus
name: Lieb, Jason D.
name: Adar, Sheera
name: Ye, Rui
name: Sancar, Aziz
name: Chiou, Yi Ying
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The mammalian circadian clock is a molecular oscillator composed of a feedback loop that involves transcriptional activators CLOCK and BMAL1, and repressors Cryptochrome (CRY) and Period (PER). Here we show that a direct CLOCK·BMAL1 target gene, Gm129, is a novel regulator of the feedback loop. ChIP analysis revealed that the CLOCK·BMAL1·CRY1 complex strongly occupies the promoter region of Gm129. Both mRNA and protein levels of GM129 exhibit high amplitude circadian oscillations in mouse liver, and Gm129 gene encodes a nuclear-localized protein that directly interacts with BMAL1 and represses CLOCK·BMAL1 activity. In vitro and in vivo protein-DNA interaction results demonstrate that, like CRY1, GM129 functions as a repressor by binding to the CLOCK·BMAL1 complex on DNA. Although Gm129−/− or Cry1−/−Gm129−/− mice retain a robust circadian rhythm, the peaks of Nr1d1 and Dbp mRNAs in liver exhibit a significant phase delay compared with control. Our results suggest that, in addition to CRYs and PERs, the GM129 protein contributes to the transcriptional feedback loop by modulating CLOCK·BMAL1 activity as a transcriptional repressor.
Fluid/gravity correspondence: A nonconformal realization in compactified D4 branes
Creators: name: Wu, Chao
name: Chen, Yidian
name: Huang, Mei
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We develop the framework of boundary derivative expansion (BDE) formalism of fluid/gravity correspondence in compactified D4-brane system, which is a nonconformal background used in top-down holographic QCD models. Such models contain the D4-D6 model and the Sakai-Sugimoto (SS) model, with the background of the compactified black D4 branes under the near horizon limit. By using the dimensional reduction technique, we derive a 5D Einstein gravity minimally coupled with 3 scalar fields from the 10D D4-brane background. Following the BDE formalism of fluid/gravity correspondence in the conformal background, we directly derive all the first order transport coefficients for nonconformal gluonic matter. The results of the ratio of the bulk to shear viscosity and the sound speed agree with those obtained from the Green-Kubo method. This agreement guarantees the validity of the BDE formalism of fluid/gravity duality in the nonconformal D-brane background, which can be used to calculate the second order transport coefficients in nonconformal background.
description: 25 pages
Parameter estimation on gravitational waves from neutron-star binaries with spinning components
Creators: name: Farr, Ben
name: Berry, Christopher P. L.
name: Farr, Will M.
name: Haster, Carl-Johan
name: Middleton, Hannah
name: Cannon, Kipp
name: Graff, Philip B.
name: Hanna, Chad
name: Mandel, Ilya
name: Pankow, Chris
name: Price, Larry R.
name: Sidery, Trevor
name: Singer, Leo P.
name: Urban, Alex L.
name: Vecchio, Alberto
name: Veitch, John
name: Vitale, Salvatore
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Inspiraling binary neutron stars are expected to be one of the most significant sources of gravitational-wave signals for the new generation of advanced ground-based detectors. We investigate how well we could hope to measure properties of these binaries using the Advanced LIGO detectors, which began operation in September 2015. We study an astrophysically motivated population of sources (binary components with masses $1.2~\mathrm{M}_\odot$--$1.6~\mathrm{M}_\odot$ and spins of less than $0.05$) using the full LIGO analysis pipeline. While this simulated population covers the observed range of potential binary neutron-star sources, we do not exclude the possibility of sources with parameters outside these ranges; given the existing uncertainty in distributions of mass and spin, it is critical that analyses account for the full range of possible mass and spin configurations. We find that conservative prior assumptions on neutron-star mass and spin lead to average fractional uncertainties in component masses of $\sim 16\%$, with little constraint on spins (the median $90\%$ upper limit on the spin of the more massive component is $\sim 0.7$). Stronger prior constraints on neutron-star spins can further constrain mass estimates, but only marginally. However, we find that the sky position and luminosity distance for these sources are not influenced by the inclusion of spin; therefore, if LIGO detects a low-spin population of BNS sources, less computationally expensive results calculated neglecting spin will be sufficient for guiding electromagnetic follow-up.
description: 10 pages, 9 figures
Glucose Starvation Inhibits Autophagy via Vacuolar Hydrolysis and Induces Plasma Membrane Internalization by Down-regulating Recycling
Creators: name: Buelto, Destiney
name: Prosser, Derek C.
name: Duncan, Mara C.
name: Ganser, Laura R.
name: Martinez-Marquez, Jorge Y.
name: Wendland, Beverly
name: Lang, Michael J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Cellular energy influences all aspects of cellular function. Although cells can adapt to a gradual reduction in energy, acute energy depletion poses a unique challenge. Because acute depletion hampers the transport of new energy sources into the cell, the cell must use endogenous substrates to replenish energy after acute depletion. In the yeast Saccharomyces cerevisiae, glucose starvation causes an acute depletion of intracellular energy that recovers during continued glucose starvation. However, how the cell replenishes energy during the early phase of glucose starvation is unknown. In this study, we investigated the role of pathways that deliver proteins and lipids to the vacuole during glucose starvation. We report that in response to glucose starvation, plasma membrane proteins are directed to the vacuole through reduced recycling at the endosomes. Furthermore, we found that vacuolar hydrolysis inhibits macroautophagy in a target of rapamycin complex 1-dependent manner. Accordingly, we found that endocytosis and hydrolysis are required for survival in glucose starvation, whereas macroautophagy is dispensable. Together, these results suggest that hydrolysis of components delivered to the vacuole independent of autophagy is the cell survival mechanism used by S. cerevisiae in response to glucose starvation.
Compactified Twistor Fibration and Topology of Ward Unitons
Creators: name: Plansangkate, Prim
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Differential Geometry (math.DG)
subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We use the compactified twistor correspondence for the (2+1)-dimensional integrable chiral model to prove a conjecture of Ward. In particular, we construct the correspondence space of a compactified twistor fibration and use it to prove that the second Chern numbers of the holomorphic vector bundles, corresponding to the uniton solutions of the integrable chiral model, equal the third homotopy classes of the restricted extended solutions of the unitons. Therefore we deduce that the total energy of a time-dependent uniton is proportional to the second Chern number.
Representing higher-order dependencies in networks
Creators: name: Xu, Jian
name: Wickramarathne, Thanuka L.
name: Chawla, Nitesh V.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Social and Information Networks (cs.SI)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences
subject: H.2.8

description: To ensure the correctness of network analysis methods, the network (as the input) has to be a sufficiently accurate representation of the underlying data. However, when representing sequential data from complex systems such as global shipping traffic or web clickstream traffic as networks, conventional network representations that implicitly assume the Markov property (first-order dependency) can quickly become limiting. This assumption holds that when movements are simulated on the network, the next movement depends only on the current node, discounting the fact that the movement may depend on several previous steps. However, we show that data derived from many complex systems can show up to fifth-order dependencies. In these cases, the oversimplifying assumption of the first-order network representation can lead to inaccurate network analysis results. To address this problem, we propose the Higher-Order Network (HON) representation that can discover and embed variable orders of dependencies in a network representation. Through a comprehensive empirical evaluation and analysis, we establish several desirable characteristics of HON, including accuracy, scalability, and direct compatibility with the existing suite of network analysis methods. We illustrate how HON can be applied to a broad variety of tasks, such as random walking, clustering, and ranking, and we demonstrate that by using it as input, HON yields more accurate results without any modification to these tasks.
description: 38 pages, 9 figures, 3 tables, 2 algorithms
Glyceraldehyde-3-phosphate Dehydrogenase Is Activated by Lysine 254 Acetylation in Response to Glucose Signal
Creators: name: Liu, Mengxi
name: Feng, Xu
name: Li, Tingting
name: Zhou, Xin
name: Sun, Yiping
name: Wang, Zhen
name: Xu, Yanping
name: Guan, Kun Liang
name: Das, Indrani
name: Xiong, Yue
name: Lei, Qun Ying
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The altered metabolism in most tumor cells consists of elevated glucose uptake and increased glycolysis even in the presence of high oxygen tension. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an obligatory enzyme in glycolysis. Here, we report that acetylation at lysine 254 (K254) increases GAPDH activity in response to glucose. Furthermore, acetylation of GAPDH (K254) is reversibly regulated by the acetyltransferase PCAF and the deacetylase HDAC5. Substitution of K254 to glutamine compromises the ability of GAPDH to support cell proliferation and tumor growth. Our study reveals a mechanism of GAPDH enzyme activity regulation by acetylation and its critical role in cellular regulation.
Ab Initio Theory of Superconductivity in a Magnetic Field I. : Spin Density Functional Theory For Superconductors and Eliashberg Equations
Creators: name: Linscheid, A.
name: Sanna, A.
name: Essenberger, F.
name: Gross, E. K. U.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We present a first-principles approach to describe magnetic and superconducting systems and the phenomena of competition between these electronic effects. We develop a density functional theory: SpinSCDFT, by extending the Hohenberg-Kohn theorem and constructing the non-interacting Kohn- Sham system. An exchange-correlation functional for SpinSCDFT is derived from the Sham Schlüter connection between the SpinSCDFT Kohn-Sham and a self-energy in Eliashberg approximation. The reference Eliashberg equations for superconductors in the presence of magnetism are also derived and discussed.
New insights and research prospects from the ocean microbiome
Creators: name: Teske, Andreas
Publisher: name: Frontiers Media SA
Year: 2024

description: Researchers with a certain amount of experience cannot help noticing the fast turnover of software tools and databases in the bioinformatics landscape. In order to thrive, metagenomic analysis and annotation tools have to remain up to date in terms of content, organization, and taxonomy; they have to be maintained by a devoted team of curators; and they should offer access and handles for a diverse and active user community that prevents them from falling into disuse. Finally, long-term institutional support is essential for staying power and longevity in this ever-changing field. The KAUST Metagenomic Analysis Platform (KMAP) appears among the latest entries within the field of large-scale metagenomic analysis and annotation. In their Frontiers in Science article, Laiolo and colleagues deliver an impressive rollout for the KMAP by assembling and analyzing an extensive global marine metagenome dataset, the Global Ocean Gene Catalog 1.0, which represents over 2,000 metagenomic samples predominantly from the open ocean and, to a smaller extent, from coastal waters and benthos. Numerous marine metagenomic samples from the European Nucleotide Archive (ENA; www.ebi.ac.uk/ena) were extracted as of May 2018 for processing in the KMAP, which includes quality control of readings and assembly of metagenomes. The large volume of this marine gene survey imposes some limits on the level of phylogenetic and functional detail that can be accommodated in a paper of reasonable length; therefore, this study emphasizes broad occurrence patterns of microbial classes and phyla, and major metabolic pathways.
Glycosylation and Cross-linking in Bone Type I Collagen
Creators: name: Pleshko, Nancy
name: Deguchi, Yoshizumi
name: Perdivara, Irina
name: Sricholpech, Marnisa
name: Terajima, Masahiko
name: Yamauchi, Mitsuo
name: Tomer, Kenneth B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Fibrillar type I collagen is the major organic component in bone, providing a stable template for mineralization. During collagen biosynthesis, specific hydroxylysine residues become glycosylated in the form of galactosyl- and glucosylgalactosyl-hydroxylysine. Furthermore, key glycosylated hydroxylysine residues, α1/2-87, are involved in covalent intermolecular cross-linking. Although cross-linking is crucial for the stability and mineralization of collagen, the biological function of glycosylation in cross-linking is not well understood. In this study, we quantitatively characterized glycosylation of non-cross-linked and cross-linked peptides by biochemical and nanoscale liquid chromatography-high resolution tandem mass spectrometric analyses. The results showed that glycosylation of non-cross-linked hydroxylysine is different from that involved in cross-linking. Among the cross-linked species involving α1/2-87, divalent cross-links were glycosylated with both mono- and disaccharides, whereas the mature, trivalent cross-links were primarily monoglycosylated. Markedly diminished diglycosylation in trivalent cross-links at this locus was also confirmed in type II collagen. The data, together with our recent report (Sricholpech, M., Perdivara, I., Yokoyama, M., Nagaoka, H., Terajima, M., Tomer, K. B., and Yamauchi, M. (2012) Lysyl hydroxylase 3-mediated glucosylation in type I collagen: molecular loci and biological significance. J. Biol. Chem. 287, 22998–23009), indicate that the extent and pattern of glycosylation may regulate cross-link maturation in fibrillar collagen.
Magnetization damping in noncollinear spin valves with antiferromagnetic interlayer couplings
Creators: name: Chiba, Takahiro
name: Bauer, Gerrit E. W.
name: Takahashi, Saburo
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We study the magnetic damping in the simplest of synthetic antiferromagnets, i.e. antiferromagnetically exchange-coupled spin valves in which applied magnetic fields tune the magnetic configuration to become noncollinear. We formulate the dynamic exchange of spin currents in a noncollinear texture based on the spindiffusion theory with quantum mechanical boundary conditions at the ferrromagnet|normal-metal interfaces and derive the Landau-Lifshitz-Gilbert equations coupled by the static interlayer non-local and the dynamic exchange interactions. We predict non-collinearity-induced additional damping that can be sensitively modulated by an applied magnetic field. The theoretical results compare favorably with published experiments.
description: 9 pages, 5 figures
(3901) Agnes Barclay
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.
Guanine Nucleotide-binding Protein (Gα) Endocytosis by a Cascade of Ubiquitin Binding Domain Proteins Is Required for Sustained Morphogenesis and Proper Mating in Yeast
Creators: name: Sacks, Carly M.
name: Dixit, Gauri
name: Dohlman, Henrik G.
name: Baker, Rachael
name: Torres, Matthew P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Heterotrimeric G proteins are well known to transmit signals from cell surface receptors to intracellular effector proteins. There is growing appreciation that G proteins are also present at endomembrane compartments, where they can potentially interact with a distinct set of signaling proteins. Here, we examine the cellular trafficking function of the G protein α subunit in yeast, Gpa1. Gpa1 contains a unique 109-amino acid insert within the α-helical domain that undergoes a variety of posttranslational modifications. Among these is monoubiquitination, catalyzed by the NEDD4 family ubiquitin ligase Rsp5. Using a newly optimized method for G protein purification together with biophysical measures of structure and function, we show that the ubiquitination domain does not influence enzyme activity. By screening a panel of 39 gene deletion mutants, each lacking a different ubiquitin binding domain protein, we identify seven that are necessary to deliver Gpa1 to the vacuole compartment including four proteins (Ede1, Bul1, Ddi1, and Rup1) previously not known to be involved in this process. Finally, we show that proper endocytosis of the G protein is needed for sustained cellular morphogenesis and mating in response to pheromone stimulation. We conclude that a cascade of ubiquitin-binding proteins serves to deliver the G protein to its final destination within the cell. In this instance and in contrast to the previously characterized visual system, endocytosis from the plasma membrane is needed for proper signal transduction rather than for signal desensitization.
(3902) Peter Edwin Pettersen
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.
Massive Thermal Acceleration of the Emergence of Primordial Chemistry, the Incidence of Spontaneous Mutation, and the Evolution of Enzymes
Creators: name: Richard, Wolfenden
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Kelvin considered it unlikely that sufficient time had elapsed on the earth for life to have reached its present level of complexity. In the warm surroundings in which life first appeared, however, elevated temperatures would have reduced the kinetic barriers to reaction. Recent experiments disclose the profound extent to which very slow reactions are accelerated by elevated temperatures, collapsing the time that would have been required for early events in primordial chemistry before the advent of enzymes. If a primitive enzyme, like model catalysts and most modern enzymes, accelerated a reaction by lowering its enthalpy of activation, then the rate enhancement that it produced would have increased automatically as the environment cooled, quite apart from any improvements in catalytic activity that arose from mutation and natural selection. The chemical events responsible for spontaneous mutation are also highly sensitive to temperature, furnishing an independent mechanism for accelerating evolution.
Vertebral column morphology of the Bengal snapper, Lutjanus bengalensis (Bloch, 1790), from the Oman Sea
Creators: name: JAWAD, Laith A.
name: AL-HASSANI, Luqman
name: AL-KINDI, Abdullah
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2014

description: Based on a morphometrical study of the length, height, width and vertebral central width of the successive vertebrae constituting the vertebral column, the vertebral column of Lutjanus bengalensis was divided into four morphologically distinct regions: anterior, middle and posterior regions, and urostyle region. This allows characteristic- looking vertebral profiles to be drawn. Differences in vertebral length present in different regions of the vertebral column show regionalization in this structure. These morphological parameters express morphotypes that seem to have a functional link with the subcarangiform mode of swimming of L. bengalensis.
Mechanism of Photosignaling by Drosophila Cryptochrome: ROLE OF THE REDOX STATUS OF THE FLAVIN CHROMOPHORE
Creators: name: Ozturk, Nuri
name: Sancar, Aziz
name: Selby, Christopher P.
name: Zhong, Dongping
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Cryptochrome (CRY) is the primary circadian photoreceptor in Drosophila. Upon light absorption, dCRY undergoes a conformational change that enables it to bind to Timeless (dTIM), as well as to two different E3 ligases that ubiquitylate dTIM and dCRY, respectively, resulting in their proteolysis and resetting the phase of the circadian rhythm. Purified dCRY contains oxidized flavin (FADox), which is readily photoreduced to the anionic semiquinone through a set of 3 highly conserved Trp residues (Trp triad). The crystal structure of dCRY has revealed a fourth Trp (Trp-536) as a potential electron donor. Previously, we reported that the Trp triad played no role in photoinduced proteolysis of dCRY in Drosophila cells. Here we investigated the role of the Trp triad and Trp-536, and the redox status of the flavin on light-induced proteolysis of both dCRY and dTIM and resetting of the clock. We found that both oxidized (FADox) and reduced (FAD⨪) forms of dCRY undergo light-induced conformational change in vitro that enable dCRY to bind JET and that Trp triad and Trp-536 mutations that block known or presumed intraprotein electron transfer reactions do not affect dCRY phototransduction under bright or dim light in vivo as measured by light-induced proteolysis of dCRY and dTIM in Drosophila S2R+ cells. We conclude that both oxidized and reduced forms of dCRY are capable of photosignaling.
Counting function of magnetic resonances for exterior problems
Creators: name: Bruneau, Vincent
name: Sambou, Diomba
Publisher: name: arXiv
Year: 2015
Subjects: subject: Spectral Theory (math.SP)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We study the asymptotic distribution of the resonances near the Landau levels $Λ\_q =(2q+1)b$, $q \in \mathbb{N}$, of the Dirichlet (resp. Neumann, resp. Robin) realization in the exterior of a compact domain of $\mathbb{R}^3$ of the 3D Schr{ö}dinger operator with constant magnetic field of scalar intensity $b\textgreater{}0$. We investigate the corresponding resonance counting function and obtain the main asymptotic term. In particular, we prove the accumulation of resonances at the Landau levels and the existence of resonance free sectors. In some cases, it provides the discreteness of the set of embedded eigenvalues near the Landau levels.
(3903) Ida Christopha Christophessen
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.