cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Structure and Dynamics of Zymogen Human Blood Coagulation Factor X
Creators: name: Darden, Tom
name: Venkateswarlu, Divi
name: Pedersen, Lee G.
name: Perera, Lalith
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: The solution structure and dynamics of the human coagulation factor X (FX) have been investigated to understand the key structural elements in the zymogenic form that participates in the activation process. The model was constructed based on the 2.3-A-resolution x-ray crystallographic structure of active-site inhibited human FXa (PDB:1XKA). The missing gamma-carboxyglutamic acid (GLA) and part of epidermal growth factor 1 (EGF1) domains of the light chain were modeled based on the template of GLA-EGF1 domains of the tissue factor (TF)-bound FVIIa structure (PDB:1DAN). The activation peptide and other missing segments of FX were introduced using homology modeling. The full calcium-bound model of FX was subjected to 6.2 ns of molecular dynamics simulation in aqueous medium using the AMBER6.0 package. We observed significant reorientation of the serine-protease (SP) domain upon activation leading to a compact multi-domain structure. The solution structure of zymogen appears to be in a well-extended conformation with the distance between the calcium ions in the GLA domain and the catalytic residues estimated to be approximately 95 A in contrast to approximately 83 A in the activated form. The latter is in close agreement with fluorescence studies on FXa. The S1-specificity residues near the catalytic triad show significant differences between the zymogen and activated structures.
Replication: Measuring the influence of typologically diverse target language properties on input processing at the initial stages of acquisition
Creators: name: Watorek, Marzena
name: Rast, Rebekah
name: Xinyue Cécilia Yu
name: Trévisiol, Pascale
name: Majdoub, Hedi
name: Qianwen Guan
name: Xiaoliang Huang
Publisher: name: Zenodo
Year: 2020

description: This study applies a “first exposure” approach to second language acquisition, based
 on data collected from learners’ very first contact with the target language. The
 VILLA project (Varieties of Initial Learners in Language Acquisition: Controlled
 classroom input and elementary forms of linguistic organisation) (Dimroth et al. 2013)
 has made a significant contribution to the development of methodological tools
 used to observe initial input processing in the first 14 hours of exposure to a target
 language (Polish) by native speakers of five different languages (Italian, French,
 English, German and Dutch). The VILLA project dataset allows for a new type
 of analysis, which compares, under the same controlled input conditions, the
 performance of learners with different native languages exposed to the same target
 language. With a view to expanding and strengthening the cross-linguistic
 dimension of second language acquisition research, replications of the VILLA
 methodology with new source-target language combinations are in the planning stages. This chapter presents the design of three replications in which three separate groups of
 French native speakers will be exposed, in an instructional setting, to Modern
 Standard Arabic, Mandarin Chinese or Japanese, all typologically different from Polish.
 The design of these pilot projects draws on the same organizational principles of
 the VILLA Polish language course, in that learners will be exposed to an unfamiliar
 language and their performance in the new target language will be tested at
 various intervals by means of tasks adapted from the VILLA database.
 Two specific challenges have arisen while designing replications of the VILLA
 project that involve different target languages. The first concerns the target
 language input learners will receive in that the choice of linguistic paradigms to be
 presented in the input must allow for comparability across VILLA and its replication studies. The other concerns tasks in Arabic, Chinese and Japanese that must be
 designed based on the Polish model, while also allowing for comparability across
 studies. This chapter reflects on these challenges and decisions made about a
 variety of methodological issues regarding replications when source-target language
 combinations differ from the initial study.
(101476) Thomas King Okey
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.
Thermodynamically Irreversible Gating of Ryanodine Receptors in Situ Revealed by Stereotyped Duration of Release in Ca2+ Sparks
Creators: name: Stern, Michael D.
name: Lakatta, Edward G.
name: Ríos, Eduardo
name: Song, Long Sheng
name: Meissner, Gerhard
name: Xu, Le
name: Wang, Shi Qiang
name: Cheng, Heping
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: For a single or a group of Markov channels gating reversibly, distributions of open and closed times should be the sum of positively weighted decaying exponentials. Violation of this microscopic reversibility has been demonstrated previously on a number of occasions at the single channel level, and has been attributed to possible channel coupling to external sources of free energy. Here we show that distribution of durations of Ca(2+) release underlying Ca(2+) sparks in intact cardiac myocytes exhibits a prominent mode at approximately 8 ms. Analysis of the cycle time for repetitive sparks at hyperactive sites revealed no intervals briefer than approximately 35 ms and a mode at approximately 90 ms. These results indicate that, regardless of whether Ca(2+) sparks are single-channel or multi-channel in origin, they are generated by thermodynamically irreversible stochastic processes. In contrast, data from planar lipid bilayer experiments were consistent with reversible gating of RyR under asymmetric cis (4 microM) and trans Ca(2+) (10 mM), suggesting that the irreversibility for Ca(2+) spark genesis may reside at a supramolecular level. Modeling suggests that Ca(2+)-induced Ca(2+) release among adjacent RyRs may couple the external energy derived from Ca(2+) gradients across the SR to RyR gating in situ, and drive the irreversible generation of Ca(2+) sparks.
Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis.
Creators: name: Osei-Amponsah, R
name: Skinner, Benjamin
name: Adjei, DO
name: Bauer, J
name: Larson, G
name: Affara, Nabeel
name: Sargent, Carole
Publisher: name: Apollo - University of Cambridge Repository
Year: 2017
Subjects: D-Loop
gene sequencing
local pigs
SNP genotyping

description: BACKGROUND: The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA, MC1R, Y-chromosome sequence polymorphisms, and genome-wide SNP genotyping. RESULTS: The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed both European and Asian genetic signatures, with differences between the geographical zones. Black coat colour is the most predominant within the breed, with black MC1R alleles of both Asian and European origin. European alleles for spotting are present at a low frequency in the sample set, and may account for the occurrence of spotted piglets in some APD litters. PCA analysis of SNP data revealed a strong location and breed effect on clustering of local Ghanaian pigs. On a global level, Ghanaian local pigs cluster closely with European pigs of commercial origin, but we identified intervals via FST analyses that may elucidate loci for ADP specific traits. CONCLUSIONS: The presence of both European and Asian contributions, with differences between geographical zones probably reflects trading and colonial influences. Understanding the effects of admixture on important adaptive and economic traits of the ADP and other local breeds in Africa is critical for developing sustainable conservation programmes to prevent the decline of these genetic resources.
description: The authors are grateful to Cambridge in Africa Research Excellence (CAPREx) for the award of Post-doctoral Fellowship to ROA, and the Alborada Trust for supporting the Research. G.L is supported by the European Research Council (337574-UNDEAD), and BMS is supported by BBSRC grant number BB/N000129/1. CAS is funded by the Department of Pathology and Hughes Hall, Cambridge.
Effects of Water Soluble Phosphotidylserine on Bovine Factor Xa: Functional and Structural Changes Plus Dimerization
Creators: name: Wang, Jianfang
name: Majumder, Rinku
name: Lentz, Barry R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Previous work has shown that two molecules of a soluble form of phosphatidylserine, C6PS, bind to human and bovine factor Xa. Activity measurements along with the fluorescence of active-site-labeled human factor Xa showed that two linked sites specifically regulate the active site conformation and proteolytic activity of the human enzyme. These results imply, but cannot demonstrate, a C6PS-induced factor Xa conformational change. The purpose of this paper is to extend these observations to bovine factor Xa and to demonstrate that they do reflect conformational changes. We report that the fluorescence of active-site-labeled bovine factor Xa also varied with C6PS concentration in a sigmoidal manner, whereas amidolytic activity of unlabeled enzyme varied in a simple hyperbolic fashion, also as seen for human factor Xa. C6PS induced a 70-fold increase in bovine factor Xa's autolytic activity, consistent with the 60-fold increase in proteolytic activity reported for human factor Xa. In addition, circular dichroism spectroscopy clearly demonstrated that C6PS binding to bovine factor Xa induces secondary structural changes. In addition, C6PS binding to the tighter of the two sites triggered structural changes that lead to Ca2+-dependent dimer formation, as demonstrated by changes in intrinsic fluorescence and quantitative native gel electrophoresis. Dimerization produced further change in secondary structure, either inter- or intramolecularly. These results, along with results presented previously, support a model in which C6PS binds in a roughly sequential fashion to two linked sites whose occupancy in both human and bovine factor Xa elicits different structural and functional responses.
Sifting attacks in finite-size quantum key distribution
Creators: name: Pfister, Corsin
name: Lütkenhaus, Norbert
name: Wehner, Stephanie
name: Coles, Patrick J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A central assumption in quantum key distribution (QKD) is that Eve has no knowledge about which rounds will be used for parameter estimation or key distillation. Here we show that this assumption is violated for iterative sifting, a sifting procedure that has been employed in some (but not all) of the recently suggested QKD protocols in order to increase their efficiency. We show that iterative sifting leads to two security issues: (1) some rounds are more likely to be key rounds than others, (2) the public communication of past measurement choices changes this bias round by round. We analyze these two previously unnoticed problems, present eavesdropping strategies that exploit them, and find that the two problems are independent. We discuss some sifting protocols in the literature that are immune to these problems. While some of these would be inefficient replacements for iterative sifting, we find that the sifting subroutine of an asymptotically secure protocol suggested by Lo et al (2005 J. Cryptol. 18 133-65), which we call LCA sifting, has an efficiency on par with that of iterative sifting. One of our main results is to show that LCA sifting can be adapted to achieve secure sifting in the finite-key regime. More precisely, we combine LCA sifting with a certain parameter estimation protocol, and we prove the finite-key security of this combination. Hence we propose that LCA sifting should replace iterative sifting in future QKD implementations. More generally, we present two formal criteria for a sifting protocol that guarantee its finite-key security. Our criteria may guide the design of future protocols and inspire a more rigorous QKD analysis, which has neglected sifting-related attacks so far.
description: Published version. 14+22 pages
(101475) Caroline Newman
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.
On the relationship between epistemology and methodology: A reanalysis of grammatical gender in additional-language Spanish
Creators: name: Aarnes Gudmestad
Publisher: name: Zenodo
Year: 2020
Subjects: epistemology
methodology
grammatical gender
Spanish
SLA

description: In the current study I explore the relationship between epistemology and
 methodology through a reanalysis of production data on grammatical gender in additional-language Spanish that were analysed in Gudmestad et al. (2019). This reanalysis consists of a shift in the epistemology from the one adopted by Gudmestad et al.,
 where gender marking, which occurs between nouns and both determiners and
 adjectives, is a unified linguistic phenomenon. In contrast, the assumption in the
 present investigation is that the acquisition of gender marking entails learning gender
 assignment and gender agreement, two different learning processes that are
 observable in language behaviour with determiners and adjectives, respectively. In
 order to reflect critically on the relationship between epistemology and methodology and specifically on its influence on the interpretation of learner data, I conduct
 a multi-step analysis that is guided by the differentiation between gender
 assignment, which can be observed on determiners, and gender agreement, which can
 be observed on adjectives. I also discuss how the interpretation of the findings can
 be impacted by the epistemology that guides the current study.
A joint explanation of W-mass and muon g-2 in 2HDM
Creators: name: Han, Xiao-Fang
name: Wang, Fei
name: Wang, Lei
name: Yang, Jin Min
name: Zhang, Yang
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Since both $W$-mass and muon $g-2$ can be affected by the mass splittings among extra Higgs bosons $(H,~A,~H^\pm)$ in a 2HDM, we take a model with $μ$-$τ$ LFV interactions to examine the two anomalies reported respectively by CDF II and FNAL. We obtain the following observations: (i) Combined with theoretical constraints, the CDF $W$-mass measurement disfavors $H$ or $A$ to degenerate in mass with $H^\pm$, but allows $H$ and $A$ to degenerate. The mass splitting between $H^\pm$ and $H/A$ is required to be larger than 10 GeV. The $m_{H^\pm}$ and $m_{A}$ are favored to be smaller than 650 GeV for $m_H<120$ GeV, and allowed to have more large values with increasing of $m_H$. (ii) After imposing other relevant experimental constraints, there are parameter spaces that simultaneously satisfy (at $2σ$ level) the CDF $W$-mass, the FNAL muon $g-2$ and the data of lepton universality in $τ$ decays, but the mass splittings among extra Higgs bosons are strictly constrained.
description: References added, some discussions improved. Published in Chinese Physics C
(101474) Edwin Newman
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.
Explicit Water Near the Catalytic I Helix Thr in the Predicted Solution Structure of CYP2A4
Creators: name: Pedersen, Lars C.
name: Darden, Tom A.
name: Perera, Lalith
name: Pedersen, Lee G.
name: Gorokhov, Anna
name: Johnson, Eric F.
name: Negishi, Masahiko
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: The solution structure of mouse cytochrome P450 2A4 (CYP2A4), a monooxygenase of deoxysteroids, was obtained using homology modeling and molecular dynamics. The solvent-equilibrated CYP2A4 preserves the essential features of CYP450s. A comparison of the models CYP2A4 and CYP2A4 with testosterone bound CYP2A4/T illustrates the changes induced by the binding of the substrate. Experimental evidence links four amino acid residues to the catalytic activity, substrate specificity, and regioselectivity of this enzyme. Three of the four amino acids are found within contact distance of the testosterone substrate, and therefore may control the binding of the substrate through direct interaction. Remarkably, a water complex previously observed in x-ray crystal structure forms near the bulge in the central I helix that contains a conserved Thr. The properties of the I helix are computed in the context of the presence or absence of ligand.
Near-Infrared Variability in the Orion Nebula Cluster
Creators: name: Rice, Thomas S.
name: Reipurth, Bo
name: Wolk, Scott J.
name: Vaz, Luiz Paulo
name: Cross, N. J. G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Using the United Kingdom Infrared Telescope on Mauna Kea, we have carried out a new near-infrared J, H, K monitoring survey of almost a square degree of the star-forming Orion Nebula Cluster with observations on 120 nights over three observing seasons, spanning a total of 894 days. We monitored ~15,000 stars down to J=20 using the WFCAM instrument, and have extracted 1203 significantly variable stars from our data. By studying variability in young stellar objects (YSOs) in the H-K, K color-magnitude diagram, we are able to distinguish between physical mechanisms of variability. Many variables show color behavior indicating either dust-extinction or disk/accretion activity, but we find that when monitored for longer periods of time, a number of stars shift between these two variability mechanisms. Further, we show that the intrinsic timescale of disk/accretion variability in young stars is longer than that of dust-extinction variability. We confirm that variability amplitude is statistically correlated with evolutionary class in all bands and colors. Our investigations of these 1203 variables have revealed 73 periodic AA Tau type variables, many large-amplitude and long-period (P > 15 day) YSOs, including three stars showing widely-spaced periodic brightening events consistent with circumbinary disk activity, and four new eclipsing binaries. These phenomena and others indicate the activity of long-term disk/accretion variability processes taking place in young stars. We have made the light curves and associated data for these 1203 variables available online.
description: Corrected typo in author name
Mechanical analysis of a dynamical phase transition for particles in a channel
Creators: name: Dolezal, Jakub
name: Jack, Robert L.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We analyse biased ensembles of trajectories for a two-dimensional system of particles, evolving by Langevin dynamics in a channel geometry. This bias controls the degree of particle clustering. On biasing to large clustering, we observe a dynamical phase transition where the particles break symmetry and accumulate at one of the walls. We analyse the mechanical properties of this symmetry-broken state using the Irving-Kirkwood stress tensor. The biased ensemble is characterised by body forces which originate in random thermal noises, but have finite averages in the presence of the bias. We discuss the connection of these forces to Doob's transform and optimal control theory.
description: 10 pages, authors' accepted version
(101473) Mary Newman
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.
Student perceptions of a guided inquiry approach to a service-taught ordinary differential equations course
Creators: name: Hyland, Diarmaid
name: van Kampen, Paul
name: Nolan, Brien
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: This paper reports on data obtained during semi-structured interviews with students who had recently experienced a guided inquiry approach to learning ordinary differential equations (ODEs) in a service-taught module. Previous research identified the strengths and weaknesses of similar cohorts of students. The results from that research informed the design of an intervention (15 guided inquiry tutorials) which sought to improve the outcomes for students taking a subsequent version of the module. This paper reports on the data gathered during interviews with these students that describe their perceptions of the guided inquiry approach used. The students noticed the change in emphasis toward conceptual understanding that the intervention was trying to instil. They cited the change in questioning style most frequently as being where they saw this change, but also noted the prevalence of group work and change in interaction pattern as keys to its success. Thus, by probing students’ opinions in this way, we find validation for a guided inquiry approach to teaching ordinary differential equations in third level that emphasizes active learning and lateral interactions among students. The students’ personal goal orientation and the goal structure of the learning environment are also discussed.
Higher rank 1+1 integrable Landau-Lifshitz field theories from associative Yang-Baxter equation
Creators: name: Atalikov, K.
name: Zotov, A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mathematical Physics (math-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences

description: We propose a construction of 1+1 integrable Heisenberg-Landau-Lifshitz type equations in the ${\rm gl}_N$ case. The dynamical variables are matrix elements of $N\times N$ matrix $S$ with the property $S^2={\rm const}\cdot S$. The Lax pair with spectral parameter is constructed by means of a quantum $R$-matrix satisfying the associative Yang-Baxter equation. Equations of motion for ${\rm gl}_N$ Landau-Lifshitz model are derived from the Zakharov-Shabat equations. The model is simplified when ${\rm rank}(S)=1$. In this case the Hamiltonian description is suggested. The described family of models includes the elliptic model coming from ${\rm GL}_N$ Baxter-Belavin elliptic $R$-matrix. In $N=2$ case the widely known Sklyanin's elliptic Lax pair for XYZ Landau-Lifshitz equation is reproduced. Our construction is also valid for trigonometric and rational degenerations of the elliptic $R$-matrix.
description: 8 pages, minor corrections
Asymmetric diffusion of cosmic rays
Creators: name: Medvedev, Mikhail V.
name: Medvedev, Viktor V.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Cosmic ray propagation is diffusive because of pitch angle scattering by waves. We demonstrate that if the high-amplitude magnetohydrodynamic turbulence with $\tilde B/\langle B\rangle \sim 1$ is present on top of the mean field gradient, the diffusion becomes asymmetric. As an example, we consider the vertical transport of cosmic rays in our Galaxy propagating away from a point-like source. We solve this diffusion problem analytically using a one-dimensional Markov chain analysis. We obtained that the cosmic ray density markedly differs from the standard diffusion prediction and has a sizable effect on their distribution throughout the galaxy. The equation for the continuous limit is also derived, which shows limitations of the convection-diffusion equation.
description: 6 pages, 7 figures. Submitted to Physics of Plasmas
Internet-Based Image Analysis Quantifies Contractile Behavior of Individual Fibroblasts inside Model Tissue
Creators: name: Taylor, Lansing L.
name: Christoffer Lagerholm, B.
name: Vanni, Steven
name: Lanni, Frederick
name: Otey, Carol
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: In a cell-populated collagen gel, intrinsic fiber structure visible in differential interference contrast images can provide markers for an in situ strain gauge to quantify cell-gel mechanics, while optical sections of fluorescent protein distribution capture cytoskeletal kinematics. Mechanics quantification can be derived automatically from timelapse differential interference contrast images using a Deformation Quantification and Analysis software package accessible online at http://dqa.web.cmu.edu. In our studies, fibroblast contractile machinery was observed to function entirely within pseudopods, while GFP-alpha-actinin concentrated in pseudopod tips and cortex. Complex strain patterns around individual cells showed instances of both elastic and inelastic strain transmission, suggesting a role in observed long-range alignment of cells.
Persistent homology analysis of a generalized Aubry-André-Harper model
Creators: name: He, Yu
name: Xia, Shiqi
name: Angelakis, Dimitris G.
name: Song, Daohong
name: Chen, Zhigang
name: Leykam, Daniel
Publisher: name: arXiv
Year: 2022
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Observing critical phases in lattice models is challenging due to the need to analyze the finite time or size scaling of observables. We study how the computational topology technique of persistent homology can be used to characterize phases of a generalized Aubry-André-Harper model. The persistent entropy and mean squared lifetime of features obtained using persistent homology behave similarly to conventional measures (Shannon entropy and inverse participation ratio) and can distinguish localized, extended, and crticial phases. However, we find that the persistent entropy also clearly distinguishes ordered from disordered regimes of the model. The persistent homology approach can be applied to both the energy eigenstates and the wavepacket propagation dynamics.
description: Published version. 8 pages, 9 figures
Analysing interaction in primary school language classes: Multilevel annotation and analysis with EXMARaLDA
Creators: name: Hilton, Heather E.
name: Osborne, John
Publisher: name: Zenodo
Year: 2020
Subjects: early language learning
classroom interaction
transcription methodology
teaching methodology

description: Language classrooms provide a rich terrain for language acquisition research, and
 classroom observation has a long history (Passy 1885; Brebner 1898) This interest
 has resulted in a considerable set of transcribing conventions and observation grids,
 but the analytical techniques have varied little since the initial conversation
 analyses of the 1970s and 1980s: transcription is often done without the aid of dedicated software and analyses are carried out by hand.
 As part of an exploratory study of elementary school foreign language learning, a
 French research team observed two classesduring their first year of beginning-level
 English lessons.
 This chapter presents the methodology adopted for transcribing and annotating
 the lessons using EXMARaLDA (Schmidt & Wörner 2014)and analyzes the ways
 in which well-designed transcription software can contribute to an
 understanding of methodological and interactional classroom variables, and how they may affect emergent language knowledge and skill in the classroom. Video-linked
 transcription and multi-tiered annotation in EXMARaLDA can enable automatic and
 semi-automatic analyses of various aspects of the classroom experienceOur analyses compare the two classrooms and explore features of these young learners’
 initial contact with new words and their semantic-grammatical properties.
Ligand-Receptor Kinetics Measured by Total Internal Reflection with Fluorescence Correlation Spectroscopy
Creators: name: Thompson, Nancy L.
name: Lieto, Alena M.
name: Cush, Randall C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Total internal reflection excitation used in combination with fluorescence correlation spectroscopy (TIR-FCS) is a method for characterizing the dynamic behavior and absolute concentrations of fluorescent molecules near or at the interface of a planar substrate and a solution. In this work, we demonstrate for the first time the use of TIR-FCS for examining the interaction kinetics of fluorescent ligands in solution which specifically and reversibly associate with receptors in substrate-supported planar membranes. Fluorescence fluctuation autocorrelation functions were obtained for a fluorescently labeled IgG reversibly associating with the mouse receptor FcγRII, which was purified and reconstituted into substrate-supported planar membranes. Data were obtained as a function of the IgG solution concentration, the Fc receptor surface density, the observation area size, and the incident intensity. Best fits of the autocorrelation functions to appropriate theoretical forms gave measures of the average surface density of bound IgG, the local solution concentration of IgG, the kinetic rate constant for surface dissociation, and the rate of diffusion through the depth of the evanescent field. The average number of observed fluorescent molecules, both in solution and bound to the surface, scaled with the solution concentration of IgG, observation area size, and Fc receptor surface density as expected. The dissociation rate constant and rate of diffusion through the evanescent field agree with previous results, and all measured parameters were independent of the incident intensity.
(101472) James Newman
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.
Behavior and electrophysiological effects on striatum-nigra circuit after high frequency stimulation. Relevance to Parkinson and Epilepsy
Creators: name: Tchaikovsky, Igor
name: Lucena, Marilia Marinho
name: da Silveira Andrade da Costa, Belmira-Lara
name: Garcia-Cairasco, Norberto
name: Carelli, Pedro Valadão
name: Cairrao, Marcelo
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Neuroscience
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Science Policy

description: The phenomenon of plasticity in the striatum, and its relation with the striatum-nigra neuronal circuit has clinical and neurophysiological relevance to Parkinson and epilepsy. High frequency stimulation (HFS) can induce neural plasticity. Furthermore, it is possible to induce plasticity in the dorsal striatum and this can be modulated by substantia nigra activity. But it has not been shown yet what would be the effects in the striatum-nigra circuit after plasticity induction in striatum with HSF. Literature also misses a detailed description of the way back loop of the circuit: the striatal firing rate after substantia nigrás inhibition. We here conducted: First Experiment, application of HFS in dorsomedial striatum and measure of spontaneous and longlasting behavior expression in the open field three days later; Second, application of single pulses on dorsomedial striatum and measure of the evoked potentials in substantia nigra before and after HFS; Third Experiment: inhibition of substantia nigra and recording of the firing rate of dorsomedial striatum. HFS in dorsomedial striatum caused increased locomotion behaviors, but not classical stereotypy. However, rats had either an increase or decrease in substantia nigrás evoked potentials. Also, substantia nigrás inhibition caused an increase in dorsomedial striatum firing rate. Present data are suggestive of a potential application of HFS in striatum, as an attempt to modulate behavior rigidity and hypokinesia of diseases involving the basal ganglia, especially Parkinson´s Disease.
Location of Ryanodine and Dihydropyridine Receptors in Frog Myocardium
Creators: name: Tijskens, Pierre
name: Meissner, Gerhard
name: Franzini-Armstrong, Clara
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Frog myocardium depends almost entirely on calcium entry from extracellular spaces for its beat-to-beat activation. Atrial myocardium additionally shows internal calcium release under certain conditions, but internal release in the ventricle is absent or very low. We have examined the content and distribution of the sarcoplasmic reticulum (SR) calcium release channels (ryanodine receptors, RyRs) and the surface membrane calcium channels (dihydropyridine receptors, DHPRs) in myocardium from the two atria and the ventricle of the frog heart using binding of radioactive ryanodine, immunolabeling of RyR and DHPR, and thin section and freeze-fracture electron microscopy. In cells from both types of chambers, the SR forms peripheral couplings and in both chambers peripheral couplings colocalize with clusters of DHPRs. However, although a low level of high affinity binding of ryanodine is detectable and RyRs are present in peripheral couplings of the atrium, the ventricle shows essentially no ryanodine binding and RyRs are not detectable either by electron microscopy or immunolabeling. The results are consistent with the lack of internal calcium release in the ventricle, and raise questions regarding the significance of DHPR at peripheral couplings in the absence of RyR. Interestingly, the free SR membrane in both heart chambers shows a low but equal density of intramembrane particles representing the Ca2+ ATPase.
(101471) Elizabeth Newman
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.
Investigating non-minimal flavour-violating CMSSM in the light of Higgs-Boson mass using information theory
Creators: name: Gupta, Surabhi
name: Gupta, Sudhir Kumar
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Flavour-violating interactions of the stop-quarks are expected to provide an additional few GeV contributions to the Higgs-Boson mass, particularly when mix with scharm-quarks, thereby allowing reduced supersymmetry (SUSY) breaking scale compared to flavour-conserving constrained minimal supersymmetric Standard Model (CMSSM). Inspired by this, we analyse the interactions mentioned above in the context of CMSSM using the information entropy of the Higgs-Boson for a wider region of flavour-violating CMSSM parameter space $(m_0,m_{1/2},A_0,$ $\tanβ,sgn(μ),δ_{ct}^{ij})$, where $δ_{ct}^{ij}$ represents the flavour-violating coupling of the top-quark with the charm-quark and $i, j$ defining left and right chiralities of squarks. Our information-theoretic analysis of the model mentioned above reveals the most favourable values of $(m_0, m_{1/2},A_0, \tanβ,δ_{ct}^{ij})$ as $(4.30 {\rm~TeV}, 2.32 {\rm~TeV}, -4.96{\rm~ TeV},$ $ 22.8,0.037)$ and $(4.16 {\rm ~TeV},$ $3.89~{\rm TeV},-4.10~{\rm TeV}, 19.4, 0.039)$ for $(i, j) = (L, R)$ and $(R, L)$, respectively, corresponding to the maximum entropy which suggest the SUSY breaking scale to be about $5$ TeV, thereby allowing considerable low values of sparticles masses than the flavour-conserving CMSSM.
description: 17 pages, 8 figures
Proposal of a risk model for vehicular traffic: A Boltzmann-type kinetic approach
Creators: name: Freguglia, Paolo
name: Tosin, Andrea
Publisher: name: arXiv
Year: 2015
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 35Q20, 35Q70, 90B20

description: This paper deals with a Boltzmann-type kinetic model describing the interplay between vehicle dynamics and safety aspects in vehicular traffic. Sticking to the idea that the macroscopic characteristics of traffic flow, including the distribution of the driving risk along a road, are ultimately generated by one-to-one interactions among drivers, the model links the personal (i.e., individual) risk to the changes of speeds of single vehicles and implements a probabilistic description of such microscopic interactions in a Boltzmann-type collisional operator. By means of suitable statistical moments of the kinetic distribution function, it is finally possible to recover macroscopic relationships between the average risk and the road congestion, which show an interesting and reasonable correlation with the well-known free and congested phases of the flow of vehicles.
description: 23 pages, 3 figures, Commun. Math. Sci., 2016
Transcribing interlanguage: The case of verb-final [e] in L2 French
Creators: name: Leclercq, Pascale
Publisher: name: Zenodo
Year: 2020
Subjects: transcription
data interpretation
L2 French
verbal morphology
interlanguage

description: This chapter aims at shedding some light on the place of transcription in the data
 interpretation process. More specifically, it focuses on the example of verb-final [e]
 in oral second-language French, which causes interpretation problems when con-
 text does not provide disambiguation cues. Through an analysis of three studies on
 this phenomenon (Herschensohn 2001; Prévost 2007b,a; Granget 2015), displaying
 a variety of theoretical frameworks (generative versus functional) and transcrip-
 tion options (written- and spoken-centric approaches), I show that transcription
 choices, whether made intuitively or in a theory-constrained manner, are often
 problematic as they entail an early categorization of data, even before data coding
 and analysis, thereby introducing an interpretive bias (Mondada 2007). Finally, I
 draw conclusions and offer suggestions regarding best transcription practices.
Degradation of Phosphorene in Air: Understanding at Atomic Level
Creators: name: Wang, Gaoxue
name: Slough, William J.
name: Pandey, Ravindra
name: Karna, Shashi P.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Phosphorene is a promising two dimensional (2D) material with a direct band gap, high carrier mobility, and anisotropic electronic properties. Phosphorene-based electronic devices, however, are found to degrade upon exposure to air. In this paper, we provide an atomic level understanding of stability of phosphorene in terms of its interaction with O2 and H2O. The results based on density functional theory together with first principles molecular dynamics calculations show that O2 could spontaneously dissociate on phosphorene at room temperature. H2O will not strongly interact with pristine phosphorene, however, an exothermic reaction could occur if phosphorene is first oxidized. The pathway of oxidation first followed by exothermic reaction with water is the most likely route for the chemical degradation of the phosphorene-based devices in air.
Combined Fast Reversible Liquid-like Elastic Deformation with Topological Phase Transition in Na$_3$Bi
Creators: name: Cheng, Xiyue
name: Li, Ronghan
name: Li, Dianzhong
name: Li, Yiyi
name: Chen, Xing-Qiu
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: By means of first-principles calculations, we identified the structural phase transition of Na$_3$Bi from hexagonal ground state to cubic $cF$16 phase above 0.8 GPa, in agreement with the experimental findings. Upon the releasing of pressure, \emph{cF}16 phase of Na$_3$Bi is mechanically stable at ambient condition. The calculations revealed that the $cF$16 phase is topological semimetal, in similarity to well-known HgTe and it even exhibits an unusually low $C^\prime$ modulus (only about 1.9 GPa) and a huge anisotropy, $A^u$ of as high as 11, the third highest value among all known cubic crystals in their elastic behaviors. These facts render \emph{cF}16-type Na$_3$Bi very soft with a liquid-like elastic deformation in the (110)$$ slip system. Importantly, as accompanied with this deformation, Na$_3$Bi shows a topological phase transition from a topological semimetal state at its strain-free cubic phase to a topological insulating state at its distorted phase. Because the $C^\prime$ elastic deformation almost costs no energy in a reversible and liquid-like soft manner, \emph{cF}16-type Na$_3$Bi would potentially provide a fast on/off switching way between topological insulator and topological semimetal, which would be beneficial to the quantum electronic devices for practical applications.
description: 5 pages, 4 figures
Potential pitfalls of interpreting data from English-French tandem conversations
Creators: name: Scheuer, Sylwia
name: Horgues, Céline
Publisher: name: Zenodo
Year: 2020
Subjects: tandem learning
corrective feedback
communication breakdowns
data coding
NS-NNS interactions
English L1 and L2 speakers
French L1 and L2 speakers

description: The chapter focuses on methodological issues involved in analysing, coding and
 interpreting data from the Spécificités des Interactions verbales dans le cadre de
 Tandems linguistiques Anglais-Français (Characteristics of English/French spoken
 tandem interactions) corpus of English-French tandem exchanges. Each of the 21
 tandem pairs recorded consisted of a native speaker of English and a native speaker
 of French. The participants were video and audio recorded while performing tasks
 (conversation and reading) in both languages. So far, two major threads of research
 on the corpus data have emerged: corrective feedback and communication break-
 downs. We have attempted to gain insights as to when or why corrective feedback
 is given to the non-native tandem partner and when or why communication be-
 tween the partners gets compromised. Findings from those previous thematic areas
 serve as the basis for the present study. The major challenge we have encountered
 in conducting the analyses is the ambiguity and complexity of our conversational
 data. Both corrective feedback and communication breakdowns may have multi-
 ple – and not always obvious – causes and may or may not be clearly signalled
 by the participants. In the chapter, we discuss the various problems we faced and
 addressed while coding the data, as well as how the methodological choices we
 made affect our results and conclusions. The discussion is amply illustrated with
 examples from the corpus.