cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
An Androgen Receptor NH 2 -terminal Conserved Motif Interacts with the COOH Terminus of the Hsp70-interacting Protein (CHIP)
Creators: name: Bai, Suxia
name: Patterson, Cam
name: Hnat, Andrew T.
name: He, Bin
name: Kalman, Rebecca I.
name: Wilson, Elizabeth M.
name: Minges, John T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: The NH2-terminal sequence of steroid receptors is highly variable between different receptors and in the same receptor from different species. In this study, a primary sequence homology comparison identified a 14-amino acid NH2-terminal motif of the human androgen receptor (AR) that is common to AR from all species reported, including the lower vertebrates. The evolutionarily conserved motif is unique to AR, with the exception of a partial sequence in the glucocorticoid receptor of higher species. The presence of the conserved motif in AR and the glucocorticoid receptor and its absence in other steroid receptors suggests convergent evolution. The function of the AR NH2-terminal conserved motif was suggested from a yeast two-hybrid screen that identified the COOH terminus of the Hsp70-interacting protein (CHIP) as a binding partner. We found that CHIP functions as a negative regulator of AR transcriptional activity by promoting AR degradation. In support of this, two mutations in the AR NH2-terminal conserved motif previously identified in the transgenic adenocarcinoma of mouse prostate model reduced the interaction between CHIP and AR. Our results suggest that the AR NH2-terminal domain contains an evolutionarily conserved motif that functions to limit AR transcriptional activity. Moreover, we demonstrate that the combination of comparative sequence alignment and yeast two-hybrid screening using short conserved peptides as bait provides an effective strategy to probe the structure-function relationships of steroid receptor NH2-terminal domains and other intrinsically unstructured transcriptional regulatory proteins.
Premartensite to martensite transition and its implications on the origin of modulation in Ni2MnGa ferromagnetic shape memory alloy
Creators: name: Singh, Sanjay
name: Bednarcik, J.
name: Barman, S. R.
name: Felser, C.
name: Pandey, Dhananjai
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We present here results of temperature dependent high resolution synchrotron x-ray powder diffraction study of sequence of phase transitions in Ni2MnGa. Our results show that the incommensurate martensite phase results from the incommensurate premartensite phase, and not from the austenite phase assumed in the adaptive phase model. The premartensite phase transforms to the martensite phase through a first order phase transition with coexistence of the two phases in a broad temperature interval (~40K), discontinuous change in the unit cell volume as also in the modulation wave vector across the transition temperature and considerable thermal hysteresis in the characteristic transition temperatures. The temperature variation of the modulation wave vector q shows smooth analytic behaviour with no evidence for any devilish plateau corresponding to an intermediate or ground state commensurate lock-in phases. The existence of the incommensurate 7M like modulated structure down to 5K suggests that the incommensurate 7M like modulation is the ground state of Ni2MnGa and not the Bain distorted tetragonal L10 phase or any other lock-in phase with a commensurate modulation. These findings can be explained within the framework of the soft phonon model.
(1703) Florence Baines
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.
Analysis of the Role of Ubiquitin-interacting Motifs in Ubiquitin Binding and Ubiquitylation
Creators: name: Miller, Stephanie L.H.
name: O'Bryan, John P.
name: Malotky, Erica
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: The ubiquitin-interacting motif (UIM) is a short peptide motif with the dual function of binding ubiquitin and promoting ubiquitylation. This motif is conserved throughout eukaryotes and is present in numerous proteins involved in a wide variety of cellular processes including endocytosis, protein trafficking, and signal transduction. We previously reported that the UIMs of epsin were both necessary and sufficient for its ubiquitylation. In this study, we found that many, but not all, UIM-containing proteins were ubiquitylated. When expressed as chimeric fusion proteins, most UIMs promoted ubiquitylation of the chimera. In contrast to previous studies, we found that UIMs do not exclusively promote monoubiquitylation but rather a mixture of mono-, multi-, and polyubiquitylation. However, UIM-dependent polyubiquitylation does not lead to degradation of the modified protein. UIMs also bind polyubiquitin chains of varying lengths and to different degrees, and this activity is required for UIM-dependent ubiquitylation. Mutational analysis of the UIM revealed specific amino acids that are important for both polyubiquitin binding and ubiquitin conjugation. Finally we provide evidence that UIM-dependent ubiquitylation inhibits the interaction of UIM-containing proteins with other ubiquitylated cellular proteins. Our results suggest a new model for the ubiquitylation of UIM-containing proteins.
Uniformisation et automatisation du monitoring des tensions dans les suspentes et haubans de ponts
Creators: name: Toussaint, Patrice
name: Denoël, Vincent
name: Rutten, Christophe
name: Verstraelen, Edouard
name: Auguste, Thierry
name: Geuzaine, Margaux
Publisher: name: Academic Journal of Civil Engineering
Year: 2021

description: La détermination des tensions des haubans et suspentes de ponts par mesures accélérométriques est maitrisée et utilisée depuis longtemps au SPW (Service Public de Wallonie), mais la procédure utilisée souffrait de certaines limitations. Le projet présenté, issu d’une collaboration avec l’Université de Liège et la société V2i spécialisée dans l’acquisition et le traitement vibratoire a permis de développer un système performant d’instrumentation basé sur cette technique : • Les algorithmes d’acquisition et de traitement des données issues des accéléromètres sans fil permettent un calcul précis des tensions pour toute géométrie complexe des suspentes (raideur flexionnelle, encastrements partiels, …) • Les données traitées sont transmises sur le cloud et permettent un suivi sécuritaire en continu via une gestion automatisée des alertes mises en place
description: Academic Journal of Civil Engineering, Vol 38 No 2 (2021): Special Issue - Diagnobéton 2021
New evolutionary models for pre-main sequence and main sequence low-mass stars down to the hydrogen-burning limit
Creators: name: Baraffe, I.
name: Homeier, D.
name: Allard, F.
name: Chabrier, G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present new models for low-mass stars down to the hydrogen-burning limit that consistently couple atmosphere and interior structures, thereby superseding the widely used BCAH98 models. The new models include updated molecular linelists and solar abundances, as well as atmospheric convection parameters calibrated on 2D/3D radiative hydrodynamics simulations. Comparison of these models with observations in various colour-magnitude diagrams for various ages shows significant improvement over previous generations of models. The new models can solve flaws that are present in the previous ones, such as the prediction of optical colours that are too blue compared to M dwarf observations. They can also reproduce the four components of the young quadruple system LkCa 3 in a colour-magnitude diagram with one single isochrone, in contrast to any presently existing model. In this paper we also highlight the need for consistency when comparing models and observations, with the necessity of using evolutionary models and colours based on the same atmospheric structures.
description: 7 pages, 8 figures, Astronomy & Astrophysics in press
(1704) John Wrigley Willans
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.
(1702) Jane Eleanor Baines
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.
Evaluation non destructive de l'endommagement mécaniques du béton par émission acoustique - Application au monitoring de la maquette VerCorS
Creators: name: SEIF EDDINE, HAMDI
name: Sbartaï, Zoubir Mehdi
name: Saliba, Jacqueline
name: Henault, Jean-Marie
name: Boniface, Antoine
Publisher: name: Academic Journal of Civil Engineering
Year: 2021

description: Cette étude présente les résultats d’Emission Acoustique (EA) obtenus lors de deux campagnes d’essais sur la maquette Vercors à l’échelle 1/3 d’une enceinte de confinement de centrale nucléaire sur le site R&D d’EDF. La première campagne a été effectuée en juillet 2017. La deuxième campagne d’essais a été effectuée en mars 2019. L’objectif de ces essais est de mettre en évidence la propagation ou non de fissures ou la réouverture de fissures déjà existantes sous sollicitations. Pour répondre à cet objectif, l’instrumentation par EA s’est focalisée, dans les deux cas, sur la même zone pré-fissurée de la surface du béton. L’ensemble des données de localisation présentées ici ont été obtenues avec l’utilisation de l’algorithme par maillage adaptatif en 2D (Boniface, 2017). Les résultats obtenus sur Vercors ne permettent pas de mettre en évidence un chemin de fissuration. En revanche l’activité acoustique faible et diffuse sur la zone couverte par les capteurs suggère une simple ouverture de fissure sans propagation.
description: Academic Journal of Civil Engineering, Vol 38 No 2 (2021): Special Issue - Diagnobéton 2021
Meade et al_Supplemental Appendix 1_R2.doc from Substantial reduction in thermo-suitable microhabitat for a rainforest marsupial under climate change
Creators: name: Meade, Jessica
name: VanDerWal, Jeremy
name: Storlie, Collin
name: Williams, Stephen
name: Gourret, Arnaud
name: Krockenberger, Andrew
name: Welbergen, Justin
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: Increases in mean temperatures caused by anthropogenic climate change increase the frequency and severity of temperature extremes. Although extreme temperature events are likely to become increasingly important drivers of species' response to climate change, the impacts are poorly understood due mainly to a lack of understanding of species’ physiological responses to extreme temperatures. The physiological response of Pseudochirops archeri (green ringtail possum) to temperature extremes has been well studied, demonstrating that heterothermy is used to reduce evaporative water loss at temperatures greater than 30°C. Dehydration is likely to limit survival when animals are exposed to a critical thermal regime of greater than or equal to 30°C, for greater than or equal to 5 h, for greater than or equal to four consecutive days. In this study, we use this physiological information to assess P. archeri's vulnerability to climate change. We identify areas of current thermo-suitable habitat (validated using sightings), then estimate future thermo-suitable habitat for P. archeri, under four emission scenarios. Our projections indicate that up to 86% of thermo-suitable habitat could be lost by 2085, a serious conservation concern for the species. We demonstrate the potential applicability of our approach for generating spatio-temporally explicit predictions of the vulnerability of species to extreme temperature events, providing a focus for efficient and targeted conservation and habitat restoration management.
Data Processing Pipeline for Pointing Observations of Lunar-based Ultraviolet Telescope
Creators: name: Meng, Xian-Min
name: Cao, Li
name: Qiu, Yu-Lei
name: Wu, Chao
name: Wang, Jing
name: Han, Xu-Hui
name: Deng, Jin-Song
name: Xin, Li-Ping
name: Cai, Hong-Bo
name: Wei, Jian-Yan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We describe the data processing pipeline developed to reduce the pointing observation data of Lunar-based Ultraviolet Telescope (LUT), which belongs to the Chang'e-3 mission of the Chinese Lunar Exploration Program. The pointing observation program of LUT is dedicated to monitor variable objects in a near-ultraviolet (245-345 nm) band. LUT works in lunar daytime for sufficient power supply, so some special data processing strategies have been developed for the pipeline. The procedures of the pipeline include stray light removing, astrometry, flat fielding employing superflat technique, source extraction and cosmic rays rejection, aperture and PSF photometry, aperture correction, and catalogues archiving, etc. It has been intensively tested and works smoothly with observation data. The photometric accuracy is typically ~0.02 mag for LUT 10 mag stars (30 s exposure), with errors come from background noises, residuals of stray light removing, and flat fielding related errors. The accuracy degrades to be ~0.2 mag for stars of 13.5 mag which is the 5σ detection limit of LUT.
description: 10 pages, 7 figures, 4 tables. Minor changes and some expounding words added. Version accepted for publication in Astrophysics and Space Science (Ap&SS)
Apurinic/Apyrimidinic Endonuclease (APE/REF-1) Haploinsufficient Mice Display Tissue-specific Differences in DNA Polymerase β-Dependent Base Excision Repair
Creators: name: Raffoul, Julian J.
name: Heydari, Ahmad R.
name: Nakamura, Jun
name: Friedberg, Errol C.
name: Cabelof, Diane C.
name: Meira, Lisiane B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Apurinic/apyrimidinic (AP) endonuclease (APE) is a multifunctional protein possessing both DNA repair and redox regulatory activities. In base excision repair (BER), APE is responsible for processing spontaneous, chemical, or monofunctional DNA glycosylase-initiated AP sites via its 5'-endonuclease activity and 3'-"end-trimming" activity when processing residues produced as a consequence of bifunctional DNA glycosylases. In this study, we have fully characterized a mammalian model of APE haploinsufficiency by using a mouse containing a heterozygous gene-targeted deletion of the APE gene (Apex(+/-)). Our data indicate that Apex(+/-) mice are indeed APE-haploinsufficient, as exhibited by a 40-50% reduction (p < 0.05) in APE mRNA, protein, and 5'-endonuclease activity in all tissues studied. Based on gene dosage, we expected to see a concomitant reduction in BER activity; however, by using an in vitro G:U mismatch BER assay, we observed tissue-specific alterations in monofunctional glycosylase-initiated BER activity, e.g. liver (35% decrease, p < 0.05), testes (55% increase, p < 0.05), and brain (no significant difference). The observed changes in BER activity correlated tightly with changes in DNA polymerase beta and AP site DNA binding levels. We propose a mechanism of BER that may be influenced by the redox regulatory activity of APE, and we suggest that reduced APE may render a cell/tissue more susceptible to dysregulation of the polymerase beta-dependent BER response to cellular stress.
Nonlocal resonances in weak turbulence of gravity-capillary waves
Creators: name: Aubourg, Quentin
name: Mordant, Nicolas
Publisher: name: arXiv
Year: 2015
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: We report a laboratory investigation of weak turbulence of water surface waves in the gravity-capillary crossover. By using time-space resolved profilometry and a bicoherence analysis, we observe that the nonlinear processes involve 3-wave resonant interactions. By studying the solutions of the resonance conditions we show that the nonlinear interaction is dominantly 1D and involves collinear wave vectors. Furthermore taking into account the spectral widening due to weak nonlinearity explains that nonlocal interactions are possible between a gravity wave and high frequency capillary ones. We observe also that nonlinear 3-wave coupling is possible among gravity waves and we raise the question of the relevance of this mechanism for oceanic waves.
description: accepted for publication in Physical Review Letters
Chiral degeneracies and Fermi-surface Chern numbers in bcc Fe
Creators: name: Gosalbez-Martinez, Daniel
name: Souza, Ivo
name: Vanderbilt, David
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The degeneracies in the spinor bandstructure of bcc Fe are studied from first principles. We find numerous isolated band touchings carrying chiral charges of magnitude one (Weyl points) or two (double-Weyl nodes), as well as nonchiral degeneracy loops (nodal rings). Some degeneracies are located on symmetry lines or planes in the Brillouin zone and others at generic low-symmetry points, realizing all possible scenarios consistent with the magnetic point group. We clarify the general theory relating the chiral band touchings to the Chern numbers of the Fermi sheets enclosing them, and use this approach to determine the Chern numbers on the Fermi surface of bcc Fe. Although most Fermi sheets enclose Weyl nodes, in almost all cases the net enclosed charge vanishes for symmetry reasons, resulting in a vanishing Chern number. The exceptions are two inversion-symmetric electron pockets along the symmetry line $Δ$ parallel to the magnetization. Each of them surrounds a single Weyl point, leading to Chern numbers of $\pm 1$. These small topological pockets contribute a sizable amount to the nonquantized part of the intrinsic anomalous Hall conductivity, proportional to their reciprocal-space separation. Variation of the Fermi level (or other system parameters) may lead to a touching event between Fermi sheets, accompanied by a transfer of Chern number between them.
description: The Supplemental Material prepared for the revised version of the manuscript can be found at http://cfm.ehu.es/ivo/suppl-gosalbez15.pdf
Asymptotic behavior of Palais-Smale sequences associated with fractional Yamabe type equations
Creators: name: Fang, Yi
name: Gonzalez, Maria del Mar
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: In this paper, we analyze the asymptotic behavior of Palais-Smale sequences associated with fractional Yamabe type equations on an asymptotically hyperbolic Riemannian manifold. We prove that Palais-Smale sequences can be decomposed into the solution of the limit equation plus a finite number of bubbles, which are the rescaling of the fundamental solutions to the fractional Yamabe equation on Euclidean space. We also verify the non-interfering fact for multi-bubbles.
description: 29 pages
Evaluation of the Economic Efficiency of Composting and Liquefying Processes of Swine Waste
Creators: name: Yoon, Youngman
name: Yoon, Youngman
Publisher: name: Unknown
Year: 2009
Subjects: subject: Livestock Production/Industries
subject: pig slurry
subject: biomass
subject: operating cost

description: To evaluate the economical efficiency of composting and liquefying processes of pig waste biomass, pig slurry recycling facilities were classified into with four types and the operating cost of each facility type was evaluated using technical data. The type I facility adopted both composting and liquefying processes after solid-liquid separation. The type II and III facilities adopted only the composting process and the liquefying process without the solid-liquid separation, respectively. And the type IV facility adopted the SCB(Slurry Composting Bio-filtration) process. Having taken into account slurry treatment income, organic fertilizer sale and the effect of chemical fertilizer substitution, the type I, III and IV facilities showed profits of 9,222, 11,739, 10192 won/m3, respectively. And the type II facility incurred a deficit of 1,776 won/m3.
Bacterial Penetration of Bladder Epithelium through Lipid Rafts
Creators: name: Duncan, Matthew J.
name: Carson, Johnny L.
name: Abraham, Soman N.
name: Shin, Jeoung Sook
name: Li, Guojie
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Type 1 fimbriated Escherichia coli represents the most common human uropathogen, owing much of its virulence to invasion of the uroepithelium, which is highly impermeable due to the preponderance of uroplakins and highly ordered lipid components. We sought to elucidate the molecular basis for E. coli invasion of the bladder epithelium by employing human 5637 bladder epithelial cells, and we found the following: (i) intracellular E. coli associated with caveolae and lipid raft components; (ii) RNA(i) reduction of caveolin-1 expression inhibited bacterial invasion; (iii) a signaling molecule required for E. coli invasion was located in lipid rafts and physically associated with caveolin-1; (iv) bacterial invasion was inhibited by lipid raft disrupting/usurping agents. In the mouse bladder, the E. coli type 1 fimbrial receptor, uroplakin Ia, was located in lipid rafts, and lipid raft disruptors inhibited E. coli invasion. Cumulatively, E. coli uroepithelial invasion occurs through lipid rafts, which, paradoxically, contribute to bladder impermeability.
Solitons for the inverse mean curvature flow
Creators: name: Drugan, Gregory
name: Lee, Hojoo
name: Wheeler, Glen
Publisher: name: arXiv
Year: 2015
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53C44

description: We investigate self-similar solutions to the inverse mean curvature flow in Euclidean space. In the case of one dimensional planar solitons, we explicitly classify all homothetic solitons and translators. Generalizing Andrews' theorem that circles are the only compact homothetic planar solitons, we apply the Hsiung-Minkowski integral formula to prove the rigidity of the hypersphere in the class of compact expanders of codimension one. We also establish that the moduli space of compact expanding surfaces of codimension two is big. Finally, we update the list of Huisken-Ilmanen's rotational expanders by constructing new examples of complete expanders with rotational symmetry, including topological hypercylinders, called infinite bottles, that interpolate between two concentric round hypercylinders.
description: typos corrected
NFFA-Europe Pilot - D14.1 - Definition of relevant safe-by-design protocols for access by users
Creators: name: Amenitsch, H.
name: Ciancio, R.
name: Capria, E.T.
name: Castillo Michel, H.
name: Colpo, P.
name: Dal Zilio, S.
name: Keller, T. F.
name: Isaxon, C.
name: Petrovykh, D.
name: Pinto, I.
name: Stratakis, E.
Publisher: name: Zenodo
Year: 2022

description: This deliverable describes a set of workflows aiming for studying the interactions between ENMs and biological systems with an advanced ‘safe by design’ experimental platform.
description: WP14 - A safe-by design platform for nanomaterials
Phantom behavior via cosmological creation of particles
Creators: name: Nunes, Rafael C.
name: Pavón, Diego
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Recent determinations of the equation of state of dark energy hint that this may well be of the phantom type, i.e., $w_{de} < -1$. If confirmed by future experiments, this would strongly point to the existence of fields that violate the dominant energy condition, which are known to present serious theoretical difficulties. This paper presents an alternative to this possibility, namely, that the measured equation of state, $w_{de}$, is in reality an effective one, the equation of state of the quantum vacuum, $w_Λ = -1$, plus the negative equation of state, $w_{c}$, associated to the production of particles by the gravitational field acting on the vacuum. To illustrate this, three phenomenological models are proposed and constrained with recent observational data.
description: 20 pages, 6 eps figures, to be published in the Physical Review D
Binding of the Factor IX γ-Carboxyglutamic Acid Domain to the Vitamin K-dependent γ-Glutamyl Carboxylase Active Site Induces an Allosteric Effect That May Ensure Processive Carboxylation and Regulate the Release of Carboxylated Product
Creators: name: Lin, Pen Jen
name: Straight, David L.
name: Stafford, Darrel W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Propeptides of the vitamin K-dependent proteins bind to an exosite on gamma-glutamyl carboxylase; while they are bound, multiple glutamic acids in the gamma-carboxyglutamic acid (Gla) domain are carboxylated. The role of the propeptides has been studied extensively; however, the role of the Gla domain in substrate binding is less well understood. We used kinetic and fluorescence techniques to investigate the interactions of the carboxylase with a substrate containing the propeptide and Gla domain of factor IX (FIXproGla41). In addition, we characterized the effect of the Gla domain and carboxylation on propeptide and substrate binding. For the propeptide of factor IX (proFIX18), FIXproGla41, and carboxylated FIXproGla41, the Kd values were 50, 2.5, and 19.7 nM and the koff values were 273 x 10(-5), 9 x 10(-5), and 37 x 10(-5) s(-1), respectively. The koff of proFIX18 is reduced 3-fold by FLEEL and 9-fold by the Gla domain (residues 1-46) of FIX. The pre-steady state rate constants for carboxylation of FIXproGla41 was 0.02 s(-1) in enzyme excess and 0.016 s(-1) in substrate excess. The steady state rate in substrate excess is 4.5 x 10(-4) s(-1). These results demonstrate the following. 1) The pre-steady state carboxylation rate constant of FIXproGla41 is significantly slower than that of FLEEL. 2) The Gla domain plays an allosteric role in substrate-enzyme interactions. 3) Carboxylation reduces the allosteric effect. 4) The similarity between the steady state carboxylation rate constant and product dissociation rate constant suggests that product release is rate-limiting. 5) The increased dissociation rate after carboxylation contributes to the release of product.
(1697) Charlotte Baines
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.
Crystal Structure and Mutational Analysis of Heparan Sulfate 3- O -Sulfotransferase Isoform 1
Creators: name: Linhardt, Robert J.
name: Negishi, Masahiko
name: Lee, Karen A.
name: Liu, Jian
name: Pedersen, Lars C.
name: Edavettal, Suzanne C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Heparan sulfate interacts with antithrombin, a protease inhibitor, to regulate blood coagulation. Heparan sulfate 3-O-sulfotransferase isoform 1 performs the crucial last step modification in the biosynthesis of anticoagulant heparan sulfate. This enzyme transfers the sulfuryl group (SO(3)) from 3'-phosphoadenosine 5'-phosphosulfate to the 3-OH position of a glucosamine residue to form the 3-O-sulfo glucosamine, a structural motif critical for binding of heparan sulfate to antithrombin. In this study, we report the crystal structure of 3-O-sulfotransferase isoform 1 at 2.5-A resolution in a binary complex with 3'-phosphoadenosine 5'-phosphate. This structure reveals residues critical for 3'-phosphoadenosine 5'-phosphosulfate binding and suggests residues required for the binding of heparan sulfate. In addition, site-directed mutagenesis analyses suggest that residues Arg-67, Lys-68, Arg-72, Glu-90, His-92, Asp-95, Lys-123, and Arg-276 are essential for enzymatic activity. Among these essential amino acid residues, we find that residues Arg-67, Arg-72, His-92, and Asp-95 are conserved in heparan sulfate 3-O-sulfotransferases but not in heparan N-deacetylase/N-sulfotransferase, suggesting a role for these residues in conferring substrate specificity. Results from this study provide information essential for understanding the biosynthesis of anticoagulant heparan sulfate and the general mechanism of action of heparan sulfate sulfotransferases.
Supplementary Table 2 from Determining consistent prognostic biomarkers of overall survival and vascular invasion in hepatocellular carcinoma.
Creators: name: Menyhárt, Otília
name: Nagy, Ádám
name: Győrffy, Balázs
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Health Care
subject: Diseases
subject: 111706 Epidemiology
subject: FOS: Health sciences

description: List of 226 biomarkers significant in the two ethnic groups including Cox proportional hazards regression p-values. Red: 82 significant biomarker candidates were shared among Asian and White/Caucasian cohorts. Biomarkers significant only in the Asian cohort are labeled with green, and in the White/Caucasian cohort in blue. p-values in black are not significant.
title: The Impact of Incarceration on Income Inequality in the United States, 1962 - 2014
Creators: name: Childree, Aaron
Publisher: name: Georgia State University
Year: 2020

description: Income inequality in the United States has been rising significantly in recent decades, and there is a growing body of research that examines the economic, political, and policy factors influencing this phenomenon. Criminal justice policy and mass incarceration are critical but understudied elements of the relationship between public policy decisions and economic inequality. Crime policy may have a significant impact on the income distribution because its effects reach far beyond those who have direct contact with the criminal justice system. This paper seeks a better understanding of this relationship by examining the impact of the incarceration rate on the share of income going to the bottom 50 percent of earners in the United States from 1962 – 2014. Through time series regression analysis, I find that increases in the incarceration rate lead to significant decreases in the share of income going to the bottom 50 percent, even after controlling for other critical factors, including the crime rate, unemployment rate, union membership, partisan composition of Congress, and percentage of Americans with a college degree. This finding demonstrates that criminal justice policy should play a more prominent role in the conversation surrounding income inequality and shows that policies seeking to reduce the incarceration rate can create a more equitable income distribution.
Supplementary Table 3 from Determining consistent prognostic biomarkers of overall survival and vascular invasion in hepatocellular carcinoma.
Creators: name: Menyhárt, Otília
name: Nagy, Ádám
name: Győrffy, Balázs
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Health Care
subject: Diseases
subject: 111706 Epidemiology
subject: FOS: Health sciences

description: Functional grouping of significant prognostic biomarker candidates in the Asian cohort by DAVID gene ontology analysis.
Exosome Secretion by Leishmania infantum: modulate innate and adaptive immune responses and create an environment permissive for early infection
Creators: name: Vitale, Fabrizio
name: Castelli, Germano
name: Bruno, Federica
name: Migliazzo, Antonella
name: Saieva, Laura
name: Alessandro, Riccardo
Publisher: name: INFN Open Access Repository
Year: 2017

description: In recent years, several studies demonstrated the role of exosomes in intercellular communications. Specialized secretion systems are used by numerous bacterial pathogens to export virulence factors into host target cells. Leishmania deliver effectors proteins into host cells; however, the mechanisms involved have remained elusive. The aim of this study was to isolate, characterize Leishmania infantum exosomes and to investigate the biological activity of exosomes in macrophage cultures.Human cell lines used were U937 cells and macrophages derived from U937 after treatment with 25 ng/ml PMA.Western blot assay used antibodies to HSP70, HSP83/90. Exosomes were collected by L. infantum -conditioned medium by ultracentrifugation.IL10, IFN?, IL1?IL1?, IL12, IL4 and IL18 secretion were evaluated by ELISA kit.We first purified extracellular vesicles shed by L. Infantum promastigotes and amastigotes on a sucrose gradient and
 later we characterized these extracellular vesicles for HSP70, HSP83/90 and acetylcholinesterase. Furthermore we
 performed a NanoSight nanoparticle tracking analysis revealed an average of the mode value of 76 ± 5 nm for
 promastigotes and 94± 5 nm for amastigotes exosomes. All these data demonstrated that L. Infantum released
 exosomes. The treatment of U937 cells with 10 μg/ml of promastigote and amastigote exosomes showed an increase
 in motility of these cells that can facilitate the progression of infection. We showed also an overproduction of IL10 by
 macrophages after treatment with exosomes that support parasite persistence and disease establishment, while
 exosomes limited the production of IFN-? and IL12 that block the parasite killing and host protection, as well as the
 production of IL1?, IL1? and IL4. Regarding IL18 production,that is involved in the Th1-type immune responses,L.
 exosomes determined a reduction in the production of IL18 in U937 monocyte culturescompared to control. Value that
 does not vary instead macrophages cultures.
Crystal Structures of Phosphodiesterases 4 and 5 in Complex with Inhibitor 3-Isobutyl-1-methylxanthine Suggest a Conformation Determinant of Inhibitor Selectivity
Creators: name: Liu, Yudong
name: Corbin, Jackie D.
name: Francis, Sharron H.
name: Ke, Hengming
name: Huai, Qing
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Cyclic nucleotide phosphodiesterases (PDEs) are a superfamily of enzymes controlling cellular concentrations of the second messengers cAMP and cGMP. Crystal structures of the catalytic domains of cGMP-specific PDE5A1 and cAMP-specific PDE4D2 in complex with the nonselective inhibitor 3-isobutyl-1-methylxanthine have been determined at medium resolution. The catalytic domain of PDE5A1 has the same topological folding as that of PDE4D2, but three regions show different tertiary structures, including residues 79-113, 208-224 (H-loop), and 341-364 (M-loop) in PDE4D2 or 535-566, 661-676, and 787-812 in PDE5A1, respectively. Because H- and M-loops are involved in binding of the selective inhibitors, the different conformations of the loops, thus the distinct shapes of the active sites, will be a determinant of inhibitor selectivity in PDEs. IBMX binds to a subpocket that comprises key residues Ile-336, Phe-340, Gln-369, and Phe-372 of PDE4D2 or Val-782, Phe-786, Gln-817, and Phe-820 of PDE5A1. This subpocket may be a common site for binding nonselective inhibitors of PDEs.
(1698) Edward Baines
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.
Extracting H$α$ flux from photometric data in the J-PLUS survey
Creators: name: Vilella-Rojo, G.
name: Viironen, K.
name: López-Sanjuan, C.
name: Cenarro, A. J.
name: Varela, J.
name: Díaz-García, L. A.
name: Cristóbal-Hornillos, D.
name: Ederoclite, A.
name: Marín-Franch, A.
name: Moles, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present the main steps that will be taken to extract H$α$ emission flux from Javalambre Photometric Local Universe Survey (J-PLUS) photometric data. For galaxies with $z\lesssim0.015$, the H$α$+[NII] emission is covered by the J-PLUS narrow-band filter $F660$. We explore three different methods to extract the H$α$ + [NII] flux from J-PLUS photometric data: a combination of a broad-band and a narrow-band filter ($r'$ and $F660$), two broad-band and a narrow-band one ($r'$, $i'$ and $F660$), and a SED-fitting based method using 8 photometric points. To test these methodologies, we simulated J-PLUS data from a sample of 7511 SDSS spectra with measured H$α$ flux. Based on the same sample, we derive two empirical relations to correct the derived H$α$+[NII] flux from dust extinction and [NII] contamination. We find that the only unbiased method is the SED fitting based one. The combination of two filters underestimates the measurements of the H$α$ + [NII] flux by a 28%, while the three filters method by a 9%. We study the error budget of the SED-fitting based method and find that, in addition to the photometric error, our measurements have a systematic uncertainty of a 4.3%. Several sources contribute to this uncertainty: differences between our measurement procedure and the one used to derive the spectroscopic values, the use of simple stellar populations as templates, and the intrinsic errors of the spectra, which were not taken into account. Apart from that, the empirical corrections for dust extinction and [NII] contamination add an extra uncertainty of 14%. Given the J-PLUS photometric system, the best methodology to extract H$α$ + [NII] flux is the SED-fitting based one. Using this method, we are able to recover reliable H$α$ fluxes for thousands of nearby galaxies in a robust and homogeneous way.
description: 11 pages, 14 figures. Minor changes to match the published version
title: Novel one-pot methods for the synthesis of heterocycles and functional aromatic compounds
Creators: name: Henry, Martyn Craig
Publisher: name: University of Glasgow
Year: 2020
Subjects: subject: Organic chemistry, transition metal-catalysis, heterocycles, one-pot reactions

description: This PhD focused on the development of transition metal-catalysed one-pot processes for the rapid and selective formation of aryl C–N and C–O bonds from unactivated aryl C–H bonds. The key feature, common to all the processes, was the activation of aryl rings via a regioselective, iron triflimide-catalysed halogenation. After a brief description of a new iodination process in the first R&D section of this thesis, the second section details the development of a one-pot intermolecular aryl C–N bond forming process by copper-catalysed cross-coupling of in situ generated aryl iodides with unactivated N-nucleophiles. The third section describes the extension of this methodology for the synthesis of indolines and 2,3-dihydrobenzofurans by intramolecular cross-coupling with pendant N- or O-nucleophiles. In addition to the synthesis of small libraries of heterocycles, this one-pot process was used as the key reaction in the 8-step total synthesis of neolignan natural product, (+)-obtusafuran. The fourth and fifth sections detail the development of several one-pot processes for the synthesis of benzo[b]furans, benzoxazoles and benzothiazoles directly from the corresponding α-arylketones, N-arylbenzamides and N-arylthiobenzamides. Mechanistic insights as well as the synthesis of a range of biologically active heterocycles are presented.
Different Regions in Skeletal and Cardiac Muscle Ryanodine Receptors Are Involved in Transducing the Functional Effects of Calmodulin
Creators: name: Yamaguchi, Naohiro
name: Meissner, Gerhard
name: Xu, Le
name: Evans, Kelly E.
name: Pasek, Daniel A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Calmodulin (CaM) inhibits the skeletal muscle ryanodine receptor-1 (RyR1) and cardiac muscle RyR2 at micromolar Ca(2+) but activates RyR1 and inhibits RyR2 at submicromolar Ca(2+) by binding to a single, highly conserved CaM-binding site. To identify regions responsible for the differential regulation of RyR1 and RyR2 by CaM, we generated chimeras encompassing and flanking the CaM-binding domain. We found that the exchange of the N- and C-terminal flanking regions differentially affected RyR1 and RyR2. A RyR1/RyR2 chimera with an N-terminal flanking RyR2 substitution (RyR2 amino acid (aa) 3537-3579) was activated by CaM in single channel measurements at both submicromolar and micromolar Ca(2+). A RyR2/RyR1 chimera with a C-terminal flanking the 86-amino acid RyR1 substitution (RyR1 aa 3640-3725) bound (35)S-CaM but was not inhibited by CaM at submicromolar Ca(2+). In this region, five non-conserved amino acid residues (RyR1 aa 3680 and 3682-3685 and RyR2 aa 3647 and 3649-3652) differentially affect RyR helical probability. Substitution of the five amino acid residues in RyR1 with those of RyR2 showed responses to CaM comparable with wild type RyR1. In contrast, substitution of the five amino acid residues in RyR2 with those of RyR1 showed loss of CaM inhibition, whereas substitution of the five RyR2 sequence residues in the RyR2 chimera containing the RyR1 calmodulin-binding domain and C-flanking sequence restored wild type RyR2 inhibition by CaM at submicromolar Ca(2+). The results suggest that different regions are involved in CaM modulation of RyR1 and RyR2. They further suggest that five non-conserved amino acids in the C-terminal region flanking the CaM-binding domain have a key role in CaM inhibition of RyR2.
(1699) Thomas Blackburn Baines
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.
Dominant-negative Inhibition of Pheromone Receptor Signaling by a Single Point Mutation in the G Protein α Subunit
Creators: name: Hooks, Shelley B.
name: Wu, Yuh Lin
name: Dohlman, Henrik G.
name: Harden, T. Kendall
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: In yeast, two different constitutive mutants of the G protein alpha subunit have been reported. Gpa1(Q323L) cannot hydrolyze GTP and permanently activates the pheromone response pathway. Gpa1(N388D) was also proposed to lack GTPase activity, yet it has an inhibitory effect on pheromone responsiveness. We have characterized this inhibitory mutant (designated Galpha(ND)) and found that it binds GTP, interacts with G protein betagamma subunits, and exhibits full GTPase activity in vitro. Although pheromone leads to dissociation of the receptor from wild-type G protein, the same treatment promotes stable association of the receptor with Galpha(ND). We conclude that agonist binding to the receptor promotes the formation of a nondissociable complex with Galpha(ND), and in this manner prevents activation of the endogenous wild-type G protein. Dominant-negative mutants may be useful in matching specific receptors and their cognate G proteins and in determining mechanisms of G protein signaling specificity.
Supplementary Table 1 from Determining consistent prognostic biomarkers of overall survival and vascular invasion in hepatocellular carcinoma.
Creators: name: Menyhárt, Otília
name: Nagy, Ádám
name: Győrffy, Balázs
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Health Care
subject: Diseases
subject: 111706 Epidemiology
subject: FOS: Health sciences

description: The list of 318 biomarkers containing 305 individual genes and 13 composite-biomarkers out of the 355 relevant publications. Expression levels conferring worse prognosis are based on the original articles, not inevitably congruent with the results of the current analysis.
(1700) John William Baines
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.