cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Climbing Halo Merger Trees with TreeFrog
Creators: name: Elahi, Pascal J.
name: Poulton, Rhys J. J.
name: Tobar, Rodrigo J.
name: Canas, Rodrigo
name: Lagos, Claudia del P.
name: Power, Chris
name: Robotham, Aaron S. G.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present TreeFrog, a massively parallel halo merger tree builder that is capable comparing different halo catalogues and producing halo merger trees. The code is written in c++11, use the MPI and OpenMP API's for parallelisation, and includes python tools to read/manipulate the data products produced. The code correlates binding energy sorted particle ID lists between halo catalogues, determining optimal descendant/progenitor matches using multiple snapshots, a merit function that maximises the number of shared particles using pseudo-radial moments, and a scheme for correcting halo merger tree pathologies. Focusing on VELOCIraptor catalogues for this work, we demonstrate how searching multiple snapshots spanning a dynamical time significantly reduces the number of stranded halos, those lacking a descendant or a progenitor, critically correcting poorly resolved halos. We present a new merit function that improves the distinction between primary and secondary progenitors, reducing tree pathologies. We find FOF accretion rates and merger rates show similar mass ratio dependence. The model merger rates from Poole et al, (2017) agree with the measured net growth of halos through mergers.
description: 18 pages in main text, 23 pages total, 15 figures, 3 tables. Accepted for publication in PASA. Code is available from https://www.github.com/pelahi/TreeFrog
Stationary state in a two-temperature model with competing dynamics
Creators: name: Szolnoki, Attila
Publisher: name: arXiv
Year: 1999
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: A two-dimensional half-filled lattice gas model with nearest-neighbor attractive interaction is studied where particles are coupled to two thermal baths at different temperatures $T_1$ and $T_2$. The hopping of particles is governed by the heat bath at temperature $T_1$ with probability $p$ and the other heat bath $(T_2)$ with probability $1-p$ independently of the hopping direction. On a square lattice the vertical and horizontal interfaces become unstable while interfaces are stable in the diagonal directions. As a consequence, particles condense into a tilted square in the novel ordered state. The $p$-dependence of the resulting nonequilibrium stationary state is studied by Monte Carlo simulation and dynamical mean-field approximation as well.
description: 4 pages, to be published in PRE
Natural Strain Variation and Antibody Neutralization of Dengue Serotype 3 Viruses
Creators: name: Accavitti-Loper, Mary Ann
name: de Alwis, Ruklanthi
name: Wahala, Wahala M. P. B.
name: de Silva, Aravinda M.
name: Donaldson, Eric F.
name: Baric, Ralph S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Dengue viruses (DENVs) are emerging, mosquito-borne flaviviruses which cause dengue fever and dengue hemorrhagic fever. The DENV complex consists of 4 serotypes designated DENV1-DENV4. Following natural infection with DENV, individuals develop serotype specific, neutralizing antibody responses. Monoclonal antibodies (MAbs) have been used to map neutralizing epitopes on dengue and other flaviviruses. Most serotype-specific, neutralizing MAbs bind to the lateral ridge of domain III of E protein (EDIII). It has been widely assumed that the EDIII lateral ridge epitope is conserved within each DENV serotype and a good target for vaccines. Using phylogenetic methods, we compared the amino acid sequence of 175 E proteins representing the different genotypes of DENV3 and identified a panel of surface exposed amino acids, including residues in EDIII, that are highly variant across the four DENV3 genotypes. The variable amino acids include six residues at the lateral ridge of EDIII. We used a panel of DENV3 mouse MAbs to assess the functional significance of naturally occurring amino acid variation. From the panel of antibodies, we identified three neutralizing MAbs that bound to EDIII of DENV3. Recombinant proteins and naturally occurring variant viruses were used to map the binding sites of the three MAbs. The three MAbs bound to overlapping but distinct epitopes on EDIII. Our empirical studies clearly demonstrate that the antibody binding and neutralization capacity of two MAbs was strongly influenced by naturally occurring mutations in DENV3. Our data demonstrate that the lateral ridge “type specific” epitope is not conserved between strains of DENV3. This variability should be considered when designing and evaluating DENV vaccines, especially those targeting EDIII.
On the Universality Class of Monopole Percolation in Scalar QED
Creators: name: Fernandez, L. A.
name: Martin-Mayor, V.
Publisher: name: arXiv
Year: 1998
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study the critical properties of the monopole-percolation transition in U(1) lattice gauge theory coupled to scalars at infinite ($β=0$) gauge coupling. We find strong scaling corrections in the critical exponents that must be considered by means of an infinite-volume extrapolation. After the extrapolation, our results are as precise as the obtained for the four dimensional site-percolation and, contrary to previously stated, fully compatible with them.
description: 11 pages, 3 figures
Coexistence of native and denatured phases in a single protein-like molecule
Creators: name: Du, Rose
name: Grosberg, Alexander Yu.
name: Tanaka, Toyoichi
Publisher: name: arXiv
Year: 1999
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Quantitative Biology (q-bio)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: In order to understand the nuclei which develop during the course of protein folding and unfolding, we examine phase segregation of a single heteropolymer chain which occurs in equilibrium. These segregated conformations are characterized by a nucleus of monomers which are superimposable upon the native conformation. We computationally generate the phase segregation by applying a ``folding pressure,'' or adding an energetic bonus for native monomer-monomer contacts. The computer models reveal a fundamental difference in the nucleation process between heteropolymeric and the more familiar vapor-liquid systems: in a polymer system, some nuclei hinder folding via topological constraints and must be partially destroyed in order for folding to proceed. To illustrate this finding, we examine the kinetics of protein unfolding in the long chain limit through scaling arguments. We find that because of the topological constraints, the critical nucleus size is of the order of the entire chain size so that unfolding time scales as $\exp [c N^{2/3} ]$, where $N$ and $c$ are the chain length and a constant.
description: 4 pages, 4 figures
Time of day of vaccination does not influence antibody responses to pneumococcal and annual influenza vaccination in a cohort of healthy older adults.
Creators: name: Faustini, Siân E
name: Backhouse, Claire
name: Duggal, Niharika A
name: Toellner, Kai-Michael
name: Harvey, Ruth
name: Drayson, Mark T
name: Lord, Janet M
name: Richter, Alex G
Publisher: name: The Francis Crick Institute
Year: 2025
Subjects: classificationCode: Infectious Disease
subject: Infectious Disease

description: Vaccines are less immunogenic in older adults, partly due to immunosenescence. Having previously shown that morning influenza vaccination may be more immunogenic in older adults (mean age 71), we assessed if this could be replicated in a younger cohort (mean age 57) and with a T-cell independent vaccine. This study examined whether diurnal timing of a single dose of Pneumovax® (PPV-23) and seasonal influenza vaccine influenced antibody responses in 140 healthy adults over the age of 50. Pneumococcal serotype-specific (PnPS) antibodies and Haemagglutination Inhibition Assays (HAI) were used to characterize antibody responses at Baseline, 1, 4, and 52 weeks post-vaccination. Protective thresholds were set at 0.35 μg/mL for two-thirds of PnPS tested (WHO≥8/12PnPS) and a titre of ≥40 HAI for H1N1, H3N2, and B/Victoria strains. Both AM and PM cohorts showed increased Pn-specific antibodies to one PPV-23 dose at weeks 1, 4, and 52; however, time of day did not significantly influence antibody responses. Baseline immunity for pneumococcus was high (57.1 % AM, 50.0 % PM had WHO≥8/12PnPS), and immunity was maintained with at least 7/12 serotypes elevated at 52 weeks. Time of day did not alter short- or long-term influenza antibody responses. H1N1 had the highest baseline immunity (67.6 % AM, 48.6 % PM had ≥40 HAI) and the most increased responses at week 4 post-vaccination (92.8 % AM, 94.1 % PM) that were maintained at 52 weeks post-vaccination (91.7 % AM, 89.3 % PM). The poorest serotype immunity was for the B/Victoria strain at all time points. Although time of day did not influence vaccine immunogenicity in AM and PM cohorts, sustained cohort-wide antibody responses were demonstrated in an older population. Identifying 18 % of the total cohort exhibited suboptimal responses to pneumococcal or influenza vaccines underscores the imperative for enhancing vaccine efficacy within this age group to reduce morbidity and mortality.
Towards an Open Access publication workflow for monographs for University Presses
Creators: name: Schrader, Antonia
Publisher: name: Zenodo
Year: 2019
Subjects: university press
institutional publishing
open access
academic publishing
scholarly communications

description: This is a presentation by Antonia Schrader from OA-HVerlag from the AEUP 2nd Conference in Brno, Czech Republic, 13–14 June 2019 “(Re-)Shaping University Presses and Institutional Publishing”.
NMR-based metabolic study of leaves of three species of Actinidia with different degrees of susceptibility to Pseudomonas syringae pv. actinidiae
Creators: name: Sciubba, Fabio
name: Cocco, Maria Enrica Di
name: Angori, Giulia
name: Spagnoli, Mariangela
name: Salvador, Flavio Roberto De
name: Engel, Petra
name: Delfini, Maurizio
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology

description: Bacterial canker of Actinidia, caused by the bacterium Pseudomonas syringae pv. actinidiae (Psa), is the most serious disease of these plants worldwide. Leaves of three species of Actinidia, namely A. chinensis var. chinensis, A. chinensis var. deliciosa and A. arguta, having different degrees of tolerance to Psa, were analyzed by Nuclear Magnetic Resonance spectroscopy. Aqueous extracts of leaves were studied and several metabolites, classified as organic acids, amino acids, carbohydrates, phenols and other metabolites, were identified by 1D and 2D NMR experiments and quantified. The metabolic profiles of these species were compared through univariate statistical analysis ANOVA and multivariate PCA. Levels of metabolites with known antibacterial activity, such as caffeic and chlorogenic acids, were observed to be higher in the A. arguta samples. Moreover, these metabolites have different Pearson correlation patterns among the three Actinidia species, suggesting a difference at the phenylpropanoid biosynthetic pathway.
Gauged O(n) spin models in one dimension
Creators: name: Hasenbusch, M.
name: Horgan, R. R.
Publisher: name: arXiv
Year: 1998
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We consider a gauged O(n) spin model, n >= 2, in one dimension which contains both the pure O(n) and RP(n-1) models and which interpolates between them. We show that this model is equivalent to the non-interacting sum of the O(n) and Ising models. We derive the mass spectrum that scales in the continuum limit, and demonstrate that there are two universality classes, one of which contains the O(n) and RP(n-1) models and the other which has a tuneable parameter but which is degenerate in the sense that it arises from the direct sum of the O(n) and Ising models.
description: 9 pages, no figures, LaTeX source
A new iridoid diglycoside from Sambucus ebulus L
Creators: name: Tomassini, Lamberto
name: Ventrone, Antonio
name: Frezza, Claudio
name: Cometa, Maria Francesca
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine

description: The phytochemical examination of the polar constituents of Sambucus ebulus L. leaves led to the identification of patrinoside (1) and of a new diglycoside iridoid, patrinoside-aglycone-11-O-[β-D-glucopyranosyl-(1→6)-2′-deoxy-β-D-glucopyranoside] (trivially named as sambuloside) (2). Both of these structures have been assigned by spectroscopic means (NMR and MS).
Quantum dynamics and spectroscopy of dihalogens in solid matrices. II. Theoretical aspects and G-MCTDH simulations of time-resolved coherent Raman spectra of Schrödinger cat states of the embedded $\mathrm{I_2 Kr_{18}}$ cluster
Creators: name: Picconi, David
name: Cina, Jeffrey A.
name: Burghardt, Irene
Publisher: name: arXiv
Year: 2018
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: This companion paper to [D. Picconi et al., J. Chem. Phys. 150 (2019)] presents quantum dynamical simulations, using the Gaussian-based multiconfigurational time-dependent Hartree (G-MCTDH) method, of time-resolved coherent Raman four-wave-mixing spectroscopic experiments for the iodine molecule embedded in a cryogenic crystal krypton matrix. These experiments monitor the time-evolving vibrational coherence between two wave packets created in a quantum superposition (i. e. a 'Schrödinger cat state') by a pair of pump pulses which induce electronic $B\ ^3Π_u\left(0^+\right) \longleftarrow X\ ^1Σ_g^+$ transitions. A theoretical description of the spectroscopic measurement is developed, which elucidates the connection between the nonlinear signals and the wave packet coherence. The analysis provides an effective means to simulate the spectra for several different optical conditions with a minimum number of quantum dynamical propagations. The G-MCTDH method is used to calculate and interpret the time-resolved coherent Raman spectra of two selected initial superpositions for a $\mathrm{I_2 Kr_{18}}$ cluster embedded in a frozen Kr cage. The time- and frequency-dependent signals carry information about the molecular mechanisms of dissipation and decoherence, which involve vibrational energy transfer to the stretching mode of the four 'belt' Kr atoms. The details of these processes and the number of active solvent modes depend in a non-trivial way on the specific initial superposition.
Polymer confinement in undulated membrane boxes and tubes
Creators: name: Dotera, Tomonari
name: Suzuki, Yasuo Y.
Publisher: name: arXiv
Year: 2000
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We consider quantum particle or Gaussian polymer confinement between two surfaces and in cylinders with sinusoidal undulations. In terms of the variational method, we show that the quantum mechanical wave equations have lower ground state energy in these geometries under long wavelength undulations, where bulges are formed and waves are localized in the bulges. It turns out correspondingly that Gaussian polymer chains in undulated boxes or tubes acquire higher entropy than in exactly flat or straight ones. These phenomena are explained by the uncertainty principle for quantum particles, and by a "polymer confinement rule" for Gaussian polymers. If membrane boxes or tubes are flexible, polymer-induced undulation instability is suggested. We find that the wavelength of undulations at the threshold of instability for a membrane box is almost twice the distance between two walls of the box. Surprisingly we find that the instability for tubes begins with a shorter wavelength compared to the "Rayleigh" area-minimizing instability.
description: 6 pages, 2 figures, submitted to Phys. Rev. E
A new method for analyzing ground-state landscapes: ballistic search
Creators: name: Hartmann, Alexander K.
Publisher: name: arXiv
Year: 1999
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: A ``ballistic-search'' algorithm is presented which allows the identification of clusters (or funnels) of ground states in Ising spin glasses even for moderate system sizes. The clusters are defined to be sets of states, which are connected in state-space by chains of zero-energy flips of spins. The technique can also be used to estimate the sizes of such clusters. The performance of the method is tested with respect to different system sizes and choices of parameters. As an application the ground-state funnel structure of two-dimensional +or- J spin glasses of systems up to size L=20 is analyzed by calculating a huge number of ground states per realization. A T=0 entropy per spin of s_0=0.086(4)k_B is obtained.
description: 10 pages, 11 figures, 35 references, revtex
Impurity corrections to the thermodynamics in spin chains using a transfer-matrix DMRG method
Creators: name: Rommer, Stefan
name: Eggert, Sebastian
Publisher: name: arXiv
Year: 1998
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We use the density matrix renormalization group (DMRG) for transfer matrices to numerically calculate impurity corrections to thermodynamic properties. The method is applied to two impurity models in the spin-1/2 chain, namely a weak link in the chain and an external impurity spin. The numerical analysis confirms the field theory calculations and gives new results for the crossover behavior.
description: 9 pages in revtex format including 5 embedded figures (using epsf). To appear in PRB. The latest version in PDF format can be found at http://fy.chalmers.se/~eggert/papers/DMRGimp.pdf
NMR-based metabolic study of leaves of three species of Actinidia with different degrees of susceptibility to Pseudomonas syringae pv. actinidiae
Creators: name: Sciubba, Fabio
name: Cocco, Maria Enrica Di
name: Angori, Giulia
name: Spagnoli, Mariangela
name: Salvador, Flavio Roberto De
name: Engel, Petra
name: Delfini, Maurizio
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology

description: Bacterial canker of Actinidia, caused by the bacterium Pseudomonas syringae pv. actinidiae (Psa), is the most serious disease of these plants worldwide. Leaves of three species of Actinidia, namely A. chinensis var. chinensis, A. chinensis var. deliciosa and A. arguta, having different degrees of tolerance to Psa, were analyzed by Nuclear Magnetic Resonance spectroscopy. Aqueous extracts of leaves were studied and several metabolites, classified as organic acids, amino acids, carbohydrates, phenols and other metabolites, were identified by 1D and 2D NMR experiments and quantified. The metabolic profiles of these species were compared through univariate statistical analysis ANOVA and multivariate PCA. Levels of metabolites with known antibacterial activity, such as caffeic and chlorogenic acids, were observed to be higher in the A. arguta samples. Moreover, these metabolites have different Pearson correlation patterns among the three Actinidia species, suggesting a difference at the phenylpropanoid biosynthetic pathway.
Gravitational perturbations of non-singular black holes in conformal gravity
Creators: name: Chen, Che-Yu
name: Chen, Pisin
Publisher: name: arXiv
Year: 2019
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: It is believed that in the near future, gravitational wave detections will become a promising tool not only to test gravity theories, but also to probe extremely curved spacetime regions in our universe, such as the surroundings of black holes. In this paper, we investigate the quasinormal modes (QNMs) of the axial gravitational perturbations of a class of non-singular black holes conformally related to the Schwarzschild black hole. These non-singular black holes can be regarded as the vacuum solution of a family of conformal gravity theories which are invariant under conformal transformations. After conformal symmetry is broken, these black holes produce observational signatures different from those of the Schwarzschild black hole, such as their QNM frequencies. We assume that the spacetime is described by the Einstein equation with the effective energy momentum tensor of an anisotropic fluid. The master equation describing the QNMs is derived, and the QNM frequencies are evaluated with the Wentzel-Kramers-Brillouin (WKB) method up to the 6th order. As expected, the QNM spectra of these non-singular black holes deviate from those of the Schwarzschild black hole, indicating the possibility of testing these black hole solutions with the help of future gravitational wave detections.
description: 11 pages, 5 figures
Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates
Creators: name: Roach, Jeff
name: Cherkis, Karen
name: Jones, Corbin D.
name: Mukhtar, M. Shahid
name: Romanchuk, Artur
name: Baltrus, David A.
name: Chang, Jeff H.
name: Nishimura, Marc T.
name: Dangl, Jeffery L.
name: Grant, Sarah R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Closely related pathogens may differ dramatically in host range, but the molecular, genetic, and evolutionary basis for these differences remains unclear. In many Gram- negative bacteria, including the phytopathogen Pseudomonas syringae, type III effectors (TTEs) are essential for pathogenicity, instrumental in structuring host range, and exhibit wide diversity between strains. To capture the dynamic nature of virulence gene repertoires across P. syringae, we screened 11 diverse strains for novel TTE families and coupled this nearly saturating screen with the sequencing and assembly of 14 phylogenetically diverse isolates from a broad collection of diseased host plants. TTE repertoires vary dramatically in size and content across all P. syringae clades; surprisingly few TTEs are conserved and present in all strains. Those that are likely provide basal requirements for pathogenicity. We demonstrate that functional divergence within one conserved locus, hopM1, leads to dramatic differences in pathogenicity, and we demonstrate that phylogenetics-informed mutagenesis can be used to identify functionally critical residues of TTEs. The dynamism of the TTE repertoire is mirrored by diversity in pathways affecting the synthesis of secreted phytotoxins, highlighting the likely role of both types of virulence factors in determination of host range. We used these 14 draft genome sequences, plus five additional genome sequences previously reported, to identify the core genome for P. syringae and we compared this core to that of two closely related non-pathogenic pseudomonad species. These data revealed the recent acquisition of a 1 Mb megaplasmid by a sub-clade of cucumber pathogens. This megaplasmid encodes a type IV secretion system and a diverse set of unknown proteins, which dramatically increases both the genomic content of these strains and the pan-genome of the species.
Additional file 1 of New benzimidazole derivative compounds with in vitro fasciolicidal properties
Creators: name: Valderas-García, Elora
name: Castilla-Gómez de Agüero, Verónica
name: González del Palacio, Laura
name: Galli, Giulio
name: Escala, Nerea
name: Ruiz-Somacarrera, Marta
name: González-Warleta, Marta
name: del Olmo, Esther
name: Balaña-Fouce, Rafael
name: Martínez-Valladares, María
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified

description: Additional file 1: Table S1. Virtual absorption, distribution, metabolism, excretion (ADME) predictions of BZD31 by SwissADME website. Table S2. Virtual absorption, distribution, metabolism, excretion and toxicity (ADMET) predictions of BZD31 obtained in preADMET website.
Additional file 1 of Environmental factors and spatiotemporal distribution of Japanese encephalitis after vaccination campaign in Guizhou Province, China (2004–2016)
Creators: name: Zhao, Suye
name: Li, Yidan
name: Fu, Shihong
name: Liu, Ming
name: Li, Fan
name: Liu, Chunting
name: Yu, Jing
name: Rui, Liping
name: Wang, Dingming
name: Wang, Huanyu
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1: Figure S1. GDP per capita of counties in Guizhou Province. Figure S2. The climate variability including cumulative precipitation, average temperature. Figure S3. The land use of urban area, cropland, water body and vegetation coverage of counties in Guizhou Province.
Influence of a knot on the strength of a polymer strand
Creators: name: Saitta, A. Marco
name: Soper, Paul D.
name: Wasserman, E.
name: Klein, Michael L.
Publisher: name: arXiv
Year: 1999
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Many experiments have been done to determine the relative strength of different knots, and these show that the break in a knotted rope almost invariably occurs at a point just outside the `entrance' to the knot. The influence of knots on the properties of polymers has become of great interest, in part because of their effect on mechanical properties. Knot theory applied to the topology of macromolecules indicates that the simple trefoil or `overhand' knot is likely to be present with high probability in any long polymer strand. Fragments of DNA have been observed to contain such knots in experiments and computer simulations. Here we use {\it ab initio} computational methods to investigate the effect of a trefoil knot on the breaking strength of a polymer strand. We find that the knot weakens the strand significantly, and that, like a knotted rope, it breaks under tension at the entrance to the knot.
description: 3 pages, 4 figures
Lifetime Effects in Color Superconductivity at Weak Coupling
Creators: name: Manuel, Cristina
Publisher: name: arXiv
Year: 2000
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Superconductivity (cond-mat.supr-con)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Present computations of the gap of color superconductivity in weak coupling assume that the quarks which participate in the condensation process are infinitely long-lived. However, the quasiparticles in a plasma are characterized by having a finite lifetime. In this article we take into account this fact to evaluate its effect in the computation of the color gap. By first considering the Schwinger-Dyson equations in weak coupling, when one-loop self-energy corrections are included, a general gap equation is written in terms of the spectral densities of the quasiparticles. To evaluate lifetime effects, we then model the spectral density by a Lorentzian function. We argue that the decay of the quasiparticles limits their efficiency to condense. The value of the gap at the Fermi surface is then reduced. To leading order, these lifetime effects can be taken into account by replacing the coupling constant of the gap equation by a reduced effective one.
description: 16 pages, 2 figures; explanations on the role of the Meissner effect added; 2 references added; accepted for publication in PRD
Anisotropic inflation with coupled $\boldsymbol{p}$-forms
Creators: name: Almeida, Juan P. Beltrán
name: Guarnizo, Alejandro
name: Kase, Ryotaro
name: Tsujikawa, Shinji
name: Valenzuela-Toledo, César A.
Publisher: name: arXiv
Year: 2019
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study the cosmology in the presence of arbitrary couplings between $p$-forms in 4-dimensional space-time for a general action respecting gauge symmetry and parity invariance. The interaction between 0-form (scalar field $ϕ$) and 3-form fields gives rise to an effective potential $V_{\rm eff}(ϕ)$ for the former after integrating out the contribution of the latter. We explore the dynamics of inflation on an anisotropic cosmological background for a coupled system of 0-, 1-, and 2-forms. In the absence of interactions between 1- and 2-forms, we derive conditions under which the anisotropic shear endowed with nearly constant energy densities of 1- and 2-forms survives during slow-roll inflation for an arbitrary scalar potential $V_{\rm eff}(ϕ)$. If 1- and 2-forms are coupled to each other, we show the existence of a new class of anisotropic inflationary solutions in which the energy density of 2-form is sustained by that of 1-form through their interactions. Our general analytic formulas for the anisotropic shear are also confirmed by the numerical analysis for a concrete inflaton potential.
description: 23 pages, 4 figures, version to be published in JCAP
JKLMR conjecture and Batyrev construction
Creators: name: Aleshkin, Konstantin
name: Belavin, Alexander
name: Litvinov, Alexey
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We study a mirror interpretation of the relation between the exact partition functions of N=(2,2) gauged linear sigma-models (GLSM) on the 2d sphere and Kahler potentials on the moduli spaces of the CY manifolds proposed by Jockers et al. We use the Batyrev mirror construction for establishing the explicit relation between GLSM and the corresponding mirror family of the Calabi-Yau manifolds, defined as hypersurfaces in weighted projective spaces. We demonstrate how to do this by the explicit calculation in the case of the quintic threefold and its mirror.
description: Misprints corrected
Carbon films with a novel sp2 network structure
Creators: name: Alexandrou, I.
name: Scheibe, H. -J.
name: Kiely, C. J.
name: Papworth, A. J.
name: Amaratunga, G. A. J.
name: Schultrich, B.
Publisher: name: arXiv
Year: 1999
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Laser-Arc evaporation of a graphite target has been used to deposit carbon films that exhibit high hardness (45 GPa) and elastic recovery (85%). High Resolution Electron Microscopy (HREM) and Electron Energy Loss Spectroscopy (EELS) were subsequently used to study the microstructure and bonding of the resultant layers. The structure of the films from HREM is seen to consist of a dense array of parallel curved graphene sheet segments packed in various orientations. EELS reveals that the films are comprised of mainly sp2 bonded carbon. The results suggest that a new form of carbon thin film with fullerene-like structure can be realised. In order to explain how a predominantly sp2 bonded material can exhibit such a high hardness, a simple model is proposed to correlate the excellent mechanical properties with the observed structure.
description: Paper submitted to Physical Review B
The Source-Goal asymmetry in spatial language: language-general vs. language-specific aspects
Creators: name: Johanson, Megan
name: Selimis, Stathis
name: Papafragou, Anna
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Prior research has demonstrated a linguistic asymmetry between the sources and goals of motion events, with goals being mentioned more frequently compared to sources in motion descriptions by both children and adults. Here we explore the potency and features of this asymmetry comparing linguistic production data from children and adults who speak typologically different languages (English vs. Greek). We show that the asymmetry is robust cross-linguistically and can therefore plausibly be considered a shared, potentially universal feature of spatial language. However, the Source-Goal asymmetry does not surface uniformly across different morphosyntactic devices (verbs vs. adpositions) used to encode motion across languages. Thus a shared bias in spatial language interacts with language-specific aspects of spatial encoding.
Motion in a rocked ratchet with spatially periodic friction
Creators: name: Dan, Debasis
name: Mahato, Mangal C.
name: Jayannavar, A. M.
Publisher: name: arXiv
Year: 2000
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We present a detailed study of the transport and energetics of a Brownian particle moving in a periodic potential in the presence of an adiabatic external periodic drive. The particle is considered to move in a medium with periodic space dependent friction with the same periodicity as that of the potential but with a phase lag. We obtain several results, most of them arising due to the medium being inhomogeneous and are sensitive to the phase lag. When the potential is symmetric we show that efficiency of energy transduction can be maximised as a function of noise strength or temperature. However, in the case of asymmtertic potential the temperature may or may not facilitate the energy conversion but current reversals can be obtained as a function of temperature and the amplitude of the periodic drive. The reentrant behaviour of current can also be seen as a function of phase lag.
Flux-line entanglement as the mechanism of melting transition in high-temperature superconductors in a magnetic field
Creators: name: Nonomura, Yoshihiko
name: Hu, Xiao
name: Tachiki, Masashi
Publisher: name: arXiv
Year: 1998
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: The mechanism of the flux-line-lattice (FLL) melting in anisotropic high-T_c superconductors in ${\bf B}\parallel {\bf \hat{c}}$ is clarified by Monte Carlo simulations of the 3D frustrated XY model. The percentage of entangled flux lines abruptly changes at the melting temperature T_m, while no sharp change can be found in the number and size distribution of vortex loops around T_m. Therefore, the origin of this melting transition is the entanglement of flux lines. Scaling behaviors of physical quantities are consistent with the above mechanism of the FLL melting. The Lindemann number is also evaluated without any phenomenological arguments.
description: 10 pages, 5 Postscript figures, RevTeX; changed content and figures, Phys. Rev. B Rapid Commun. in press
Telling the Whole Tale via Reproducible Data Reuse
Creators: name: Jones, Matthew B.
Publisher: name: Zenodo
Year: 2019
Subjects: research object
computational reproducibility
provenance

description: Whole Tale provides a platform for reproducible research in which researchers can access data from archival repositories, mix that with locally uploaded data, and build and run reproducible analyses and models in common computing platforms like RStudio and Jupyter, among others. Data can be accessed by reference from DataONE and Dataverse, and then the results can be published to DataONE repositories with a DOI in a re-executable research object format that preserves data, code, and results for later inspection and re-execution. These archived 'tales' can be run on the Whole Tale platform by other researchers, or can be downloaded and run locally through Docker-based execution environments saved in the tale. Whole Tale provides a mature platform for reproducible research that preserves code, data, and compute environments in a manner that allows other researchers to interpret and re-use all products of research.
In vitro and in silico investigation of caprylic acid effect on multi drug resistant (MDR) Klebsiella pneumoniae biofilm
Creators: name: Abhishek Gupta
name: Cheepurupalli, Lalitha
name: S. Vigneswaran
name: Rathore, Sudarshan Singh
name: S. Suma Mohan
name: Jayapradha Ramakrishnan
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Communicated by Ramaswamy H. Sarma
Additional file 1 of Optimization of a mouse model of pancreatic cancer to simulate the human phenotypes of metastasis and cachexia
Creators: name: Spadafora, Victoria
name: Pryce, Benjamin R.
name: Oles, Alexander
name: Talbert, Erin E.
name: Romeo, Martin
name: Vaena, Silvia
name: Berto, Stefano
name: Ostrowski, Michael C.
name: Wang, David J.
name: Guttridge, Denis C.
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Supplementary Material 1.
Transport Mean Free Path for Magneto-Transverse Light Diffusion
Creators: name: Lacoste, D.
name: van Tiggelen, B. A.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: We derive an expression for the transport mean free path $\ell^*_\perp$ associated with magneto-transverse light diffusion for a random collection of Faraday-active Mie scatterers. This expression relates the magneto-transverse diffusion in multiple scattering directly to the magneto-transverse scattering of a single scatterer.
description: 5 pages, 1 figure, Latex, accepted for publication in Europhysics Letters
On the Calculation of the Quality Factor in Contemporary Photonic Resonant Structures
Creators: name: Christopoulos, Thomas
name: Tsilipakos, Odysseas
name: Sinatkas, Georgios
name: Kriezis, Emmanouil E.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Applied Physics (physics.app-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The correct numerical calculation of the resonance characteristics and, principally, the quality factor $Q$ of contemporary photonic and plasmonic resonant systems is of utmost importance, since $Q$ defines the bandwidth and affects nonlinear and spontaneous emission processes. Here, we comparatively assess the commonly used methods for calculating $Q$ using spectral simulations with commercially available, general-purpose software. We study the applicability range of these methods through judiciously selected examples covering different material systems and frequency regimes from the far-infrared to the visible. We care in highlighting the underlying physical and numerical reasons limiting the applicability of each one. Our findings demonstrate that in contemporary systems (plasmonics, 2D materials) $Q$ calculation is not trivial, mainly due to the physical complication of strong material dispersion and light leakage. Our work can act as a reference for the mindful and accurate calculation of the quality factor and can serve as a handbook for its evaluation in guided-wave and free-space photonic and plasmonic resonant systems.
Optical Detection and Storage of Entanglement in Plasmonically Coupled Quantum Dot Qubits
Creators: name: Otten, M.
name: Gray, S. K.
name: Kolmakov, G. V.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Quantum Physics (quant-ph)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Recent proposals and advances in quantum simulations, quantum cryptography and quantum communications substantially rely on quantum entanglement formation. Contrary to the conventional wisdom that dissipation destroys quantum coherence, coupling with a dissipative environment can also generate entanglement. We consider a system composed of two quantum dot qubits coupled with a common, damped surface plasmon mode; each quantum dot is also coupled to a separate photonic cavity mode. Cavity quantum electrodynamics calculations show that upon optical excitation by a femtosecond laser pulse, entanglement of the quantum dot excitons occurs, and the time evolution of the $g^{(2)}$ pair correlation function of the cavity photons is an indicator of the entanglement. We also show that the degree of entanglement is conserved during the time evolution of the system. Furthermore, if coupling of the photonic cavity and quantum dot modes is large enough, the quantum dot entanglement can be transferred to the cavity modes to increase the overall entanglement lifetime. This latter phenomenon can be viewed as a signature of entangled, long-lived quantum dot exciton-polariton formation. The preservation of total entanglement in the strong coupling limit of the cavity/quantum dot interactions suggests a novel means of entanglement storage and manipulation in high-quality optical cavities.
description: 26 pages, 7 figures
Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections
Creators: name: Wang, Shuyi
name: Salazar-Gonzalez, Jesus F.
name: Shen, Tongye
name: Magaret, Craig A.
name: Schief, William R.
name: Gaschen, Brian
name: Gilbert, Peter B.
name: Li, Hui
name: Keele, Brandon F.
name: Letvin, Norman L.
name: Anderson, Jeffrey A.
name: Hicks, Charles B.
name: Saag, Michael S.
name: Decker, Julie M.
name: Goepfert, Paul A.
name: Lapedes, Alan S.
name: Cohen, Myron S.
name: DeCamp, Allan C.
name: Asmal, Mohammed
name: Bhattacharya, Tanmoy
name: Ping, Li-Hua
name: Gao, Feng
name: Jiang, Chunlai
name: Gnanakaran, S.
name: Tomaras, Georgia D.
name: Daniels, Marcus
name: Swanstrom, Ronald
name: Krishnamoorthy, Mohan
name: Blattner, William A.
name: Markowitz, Martin
name: Eron, Joseph J.
name: Hraber, Peter T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Here we have identified HIV-1 B clade Envelope (Env) amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. To accomplish this, we compared thousands of sequences derived by single genome amplification from several hundred individuals that were sampled either early in infection or were chronically infected. Samples were divided at the outset into hypothesis-forming and validation sets, and we used phylogenetically corrected statistical strategies to identify signatures, systematically scanning all of Env. Signatures included single amino acids, glycosylation motifs, and multi-site patterns based on functional or structural groupings of amino acids. We identified signatures near the CCR5 co-receptor-binding region, near the CD4 binding site, and in the signal peptide and cytoplasmic domain, which may influence Env expression and processing. Two signatures patterns associated with transmission were particularly interesting. The first was the most statistically robust signature, located in position 12 in the signal peptide. The second was the loss of an N-linked glycosylation site at positions 413–415; the presence of this site has been recently found to be associated with escape from potent and broad neutralizing antibodies, consistent with enabling a common pathway for immune escape during chronic infection. Its recurrent loss in early infection suggests it may impact fitness at the time of transmission or during early viral expansion. The signature patterns we identified implicate Env expression levels in selection at viral transmission or in early expansion, and suggest that immune evasion patterns that recur in many individuals during chronic infection when antibodies are present can be selected against when the infection is being established prior to the adaptive immune response.