cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Computer Modeling of Halogen Bonds and Other $σ$-Hole Interactions
Creators: name: Kolář, Michal H.
name: Hobza, Pavel
Publisher: name: arXiv
Year: 2017
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: In the field of noncovalent interactions a new paradigm has recently become popular. It stems from the analysis of molecular electrostatic potentials and introduces a label, which has recently attracted enormous attention. The label is σ-hole, and it was first used in connection with halogens. It initiated a renaissance of interest in halogenated compounds, and later on, when found also on other groups of atoms (chalcogens, pnicogens, tetrels and aerogens), it resulted in a new direction of research of intermolecular interactions. In this review, we summarize advances from about the last 10 years in understanding those interactions related to σ-hole. We pay particular attention to theoretical and computational techniques, which play a crucial role in the field.
description: 111 pages, 22 figures, published
title: Elders: Elders and ancestors (version 3), or how the Latami family settled in the plain of Yongning
Creators: name: Michaud, Alexis
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Yongning Na
subject: nru

description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
title: Renaming: how one used to change a child's name to give it a happier start in life
Creators: name: Michaud, Alexis
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Yongning Na
subject: nru

description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Dihadron fragmentation functions in the quark-jet model: Longitudinally polarized quarks
Creators: name: Matevosyan, Hrayr H.
name: Kotzinian, Aram
name: Thomas, Anthony W.
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We study the dihadron fragmentation functions (DiFF) of longitudinally polarized quarks into pion pairs. The quark-jet framework is used to model the sequential hadronization of a polarized quark into hadrons, where the polarization transfer to the remnant quark in each hadron emission step is calculated using the spin density matrix formalism. Using Monte Carlo (MC) simulations of the hadronization process, we find a nonvanishing helicity dependent DiFF, $G_1^\perp$ , which is also related to the longitudinal jet handedness. A method is developed for extracting the angular moments of this DiFF, which enter the expressions for the azimuthal asymmetries for an electron-positron annihilation process into two pairs of hadrons from back-to-back jets and the dihadron production in semi-inclusive deep inelastic scattering. Finally, we derive explicit integral expressions for DiFFs where only two hadrons are emitted by a quark and use them to validate our MC results for both unpolarized and helicity dependent DiFFs.
description: 10 pages, 8 figures. Updated to version published in PRD: added discussions, clarifications and references
Additional file 3 of Alignment-free clustering of large data sets of unannotated protein conserved regions using minhashing
Creators: name: Abnousi, Armen
name: Broschat, Shira
name: Ananth Kalyanaraman
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: 60506 Virology

description: Cluster Evaluation for data set #9 (PDF 74 kb)
Additional file 1 of 25-Hydroxycholesterol amplifies microglial IL-1β production in an apoE isoform-dependent manner
Creators: name: Wong, Man Ying
name: Lewis, Michael
name: Doherty, James J.
name: Shi, Yang
name: Cashikar, Anil G.
name: Amelianchik, Anna
name: Tymchuk, Svitlana
name: Sullivan, Patrick M.
name: Qian, Mingxing
name: Covey, Douglas F.
name: Petsko, Gregory A.
name: Holtzman, David M.
name: Paul, Steven M.
name: Luo, Wenjie
Publisher: name: figshare
Year: 2020
Subjects: subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Marine Biology
subject: Mental Health
subject: Virology

description: Additional file 1: Figure S1. a). Expression of CH25H, Cyp27a1 and Cyp7b1 in different cell types in brain based on the Stanford transcriptome database generated by Barres and colleagues (http://www.brainrnaseq.org). b). GC-MS analysis of 25-HC levels in the conditioned medium (left) and total protein levels of cell lysate of primary mouse microglia from wild-type and CH25H-/- mice treated with LPS (0, 0.1, 1, 10, 100, 1000ng/ml). Figure S2a. Differential expression of CH25H or its ortholog in a comparison within one of the datasets. Fold-Changes are relative to non-transgenic, untreated, normal, adult, cortical or parenchymal microglia as appropriate, or, for the last two comparisons, relative to non-myeloid CNS cells (Friedman, et al Cell Report, 2018) http://researchpub.gene.com/BrainMyeloidLandscape. 2b. Relative CH25H gene expression in nonphagocytic (NP) and phagocytic (P) wild-type (WT) or apoe-/- (KO) microglia by RNA seq analysis data generated by Krasemann et al, (Immunity, 47:566, 2017). Figure S3. A schematic diagram for the mechanism associated with 25-HC in amplifying IL-1b production via inflammasome activation.
Deep LOFAR observations of the merging galaxy cluster CIZA J2242.8+5301
Creators: name: Hoang, D. N.
name: Shimwell, T. W.
name: Stroe, A.
name: Akamatsu, H.
name: Brunetti, G.
name: Donnert, J. M. F.
name: Intema, H. T.
name: Mulcahy, D. D.
name: Röttgering, H. J. A.
name: van Weeren, R. J.
name: Bonafede, A.
name: Brüggen, M.
name: Cassano, R.
name: Chyży, K. T.
name: Enßlin, T.
name: Ferrari, C.
name: de Gasperin, F.
name: Gu, L.
name: Hoeft, M.
name: Miley, G. K.
name: Orrú, E.
name: Pizzo, R.
name: White, G. J.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Previous studies have shown that CIZA J2242.8+5301 (the 'Sausage' cluster, $z=0.192$) is a massive merging galaxy cluster that hosts a radio halo and multiple relics. In this paper we present deep, high fidelity, low-frequency images made with the LOw-Frequency Array (LOFAR) between 115.5 and 179 MHz. These images, with a noise of 140 mJy/beam and a resolution of $θ_{\text{beam}}=7.3"\times5.3"$, are an order of magnitude more sensitive and five times higher resolution than previous low-frequency images of this cluster. We combined the LOFAR data with the existing GMRT (153, 323, 608 MHz) and WSRT (1.2, 1.4, 1.7, 2.3 GHz) data to study the spectral properties of the radio emission from the cluster. Assuming diffusive shock acceleration (DSA), we found Mach numbers of $\mathcal{M}_{n}=2.7{}_{-0.3}^{+0.6}$ and $\mathcal{M}_{s}=1.9_{-0.2}^{+0.3}$ for the northern and southern shocks. The derived Mach number for the northern shock requires an acceleration efficiency of several percent to accelerate electrons from the thermal pool, which is challenging for DSA. Using the radio data, we characterised the eastern relic as a shock wave propagating outwards with a Mach number of $\mathcal{M}_{e}=2.4_{-0.3}^{+0.5}$, which is in agreement with $\mathcal{M}_{e}^{X}=2.5{}_{-0.2}^{+0.6}$ that we derived from Suzaku data. The eastern shock is likely to be associated with the major cluster merger. The radio halo was measured with a flux of $346\pm64\,\text{mJy}$ at $145\,\text{MHz}$. Across the halo, we observed a spectral index that remains approximately constant ($α^{\text{145 MHz-2.3 GHz}}_{\text{across \(\sim\)1 Mpc}^2}=-1.01\pm0.10$) after the steepening in the post-shock region of the northern relic. This suggests a generation of post-shock turbulence that re-energies aged electrons.
title: Buried alive (version 2)
Creators: name: Michaud, Alexis
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Yongning Na
subject: nru

description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Additional file 6: of Hospital readmissions with acute infectious diseases in New Zealand children
Creators: name: Seibt, Silvia
name: Gilchrist, Catherine
name: Reed, Peter
name: Best, Emma
name: Harnden, Anthony
name: Camargo, Carlos
name: Grant, Cameron
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy
subject: 60506 Virology
subject: FOS: Biological sciences
subject: Computational Biology

description: Associations of demographic and illness characteristics with risk of hospital readmission with a second UTI within 12Â months of a first hospital admission with a UTI. (DOCX 75 kb)
Schur complement preconditioners for multiple saddle point problems of block tridiagonal form with application to optimization problems
Creators: name: Sogn, Jarle
name: Zulehner, Walter
Publisher: name: arXiv
Year: 2017
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: The importance of Schur complement based preconditioners are well-established for classical saddle point problems in $\mathbb{R}^N \times \mathbb{R}^M$. In this paper we extend these results to multiple saddle point problems in Hilbert spaces $X_1\times X_2 \times \cdots \times X_n$. For such problems with a block tridiagonal Hessian and a well-defined sequence of associated Schur complements, sharp bounds for the condition number of the problem are derived which do not depend on the involved operators. These bounds can be expressed in terms of the roots of the difference of two Chebyshev polynomials of the second kind. If applied to specific classes of optimal control problems the abstract analysis leads to new existence results as well as to the construction of efficient preconditioners for the associated discretized optimality systems.
title: Buried alive (version 3)
Creators: name: Michaud, Alexis
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Yongning Na
subject: nru

description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Multiplicity of solutions for a class of elliptic problem of $p$-Laplacian type with a $p$-Gradient term
Creators: name: Chaouai, Zakariya
name: Maatouk, Soufiane
Publisher: name: arXiv
Year: 2017
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: We consider the following problem $$(P) \begin{cases} -Δ_{p}u= c(x)|u|^{q-1}u+μ|\nabla u|^{p}+h(x) & \ \ \mbox{ in }Ω, u=0 & \ \ \mbox{ on } \partialΩ, \end{cases}$$ where $Ω$ is a bounded set in $\mathbb{R}^{N}$ ($N\geq 3$) with a smooth boundary, $10$, $μ\in \mathbb{R}^{*}$, and $c$ and $ h$ belong to $L^{k}(Ω)$ for some $k>\frac{N}{p}$. In this paper, we assume that $c\gneqq 0$ a.e. in $Ω$ and $h$ without sign condition, then we prove the existence of at least two bounded solutions under the condition that $\|c\|_{k}$ and $\|h\|_{k}$ are suitably small. For this purpose, we use the Mountain Pass theorem, on an equivalent problem to $(P)$ with variational structure. Here, the main difficulty is that the nonlinearity term considered does not satisfy Ambrosetti and Rabinowitz condition. The key idea is to replace the former condition by the \textbf{nonquadraticity condition at infinity}.
title: Healing: How diseases used to be treated through rituals
Creators: name: Michaud, Alexis
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Yongning Na
subject: nru

description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
MOESM3 of TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees
Creators: name: Sauvage, Thomas
name: Plouviez, Sophie
name: Schmidt, William
name: Fredericq, Suzanne
Publisher: name: figshare
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Additional file 3. Example command line for multiple alignment in MUSCLE and maximum likelihood estimation RAXML to rapidly produce exploratory tree.
How do spiral arm contrasts relate to bars, disk breaks and other fundamental galaxy properties?
Creators: name: Bittner, Adrian
name: Gadotti, Dimitri A.
name: Elmegreen, Bruce G.
name: Athanassoula, E.
name: Elmegreen, Debra M.
name: Bosma, Albert
name: Muñoz-Mateos, Juan-Carlos
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We investigate how the properties of spiral arms relate to other fundamental galaxy properties, including bars and disc breaks. We use previously published measurements of those properties, and our own measurements of arm and bar contrasts for a large sample of galaxies, using $3.6 \mathrm{μm}$ images from the Spitzer Survey of Stellar Structure in Galaxies (S4G). Flocculent galaxies are clearly distinguished from other spiral arm classes, especially by their lower stellar mass and surface density. Multi-armed and grand-design galaxies are similar in most of their fundamental parameters, excluding some bar properties and the bulge-to-total ratio. Based on these results, we revisit the sequence of spiral arm classes, and discuss classical bulges as a necessary condition for standing spiral wave modes in grand-design galaxies. We find a strong correlation between bulge-to-total ratio and bar contrast, and a weaker correlation between arm and bar contrasts. Barred and unbarred galaxies exhibit similar arm contrasts, but the highest arm contrasts are found exclusively in barred galaxies. Interestingly, the bar contrast, and its increase from flocculent to grand-design galaxies, is systematically more significant than that of the arm contrast. We corroborate previous findings concerning a connection between bars and disc breaks. In particular, in grand-design galaxies the bar contrast correlates with the normalised disc break radius. This does not hold for other spiral arm classes or the arm contrast. Our measurements of arm and bar contrast and radial contrast profiles are publicly available.
description: Accepted for publication in MNRAS; 20 pages, 17 figures, 4 tables
HEK VI: On the Dearth of Galilean Analogs in Kepler and the Exomoon Candidate Kepler-1625b I
Creators: name: Teachey, Alex
name: Kipping, David M.
name: Schmitt, Allan R.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Exomoons represent an outstanding challenge in modern astronomy, with the potential to provide rich insights into planet formation theory and habitability. In this work, we stack the phase-folded transits of 284 viable moon hosting Kepler planetary candidates, in order to search for satellites. These planets range from Earth-to-Jupiter sized and from ${\sim}$0.1-to-1.0 AU in separation - so-called "warm" planets. Our data processing includes two-pass harmonic detrending, transit timing variations, model selection and careful data quality vetting to produce a grand light curve with an r.m.s. of 5.1 ppm. We find that the occurrence rate of Galilean-analog moon systems for planets orbiting between ${\sim}$0.1 and 1.0 AU can be constrained to be $η<0.38$ to 95% confidence for the 284 KOIs considered, with a 68.3% confidence interval of $η=0.16_{-0.10}^{+0.13}$. A single-moon model of variable size and separation locates a slight preference for a population of short-period moons with radii ${\sim}0.5$ $R_{\oplus}$ orbiting at 5-10 planetary radii. However, we stress that the low Bayes factor of just 2 in this region means it should be treated as no more than a hint at this time. Splitting our data into various physically-motivated subsets reveals no strong signal. The dearth of Galilean-analogs around warm planets places the first strong constraint on exomoon formation models to date. Finally, we report evidence for an exomoon candidate Kepler-1625b I, which we briefly describe ahead of scheduled observations of the target with the Hubble Space Telescope.
description: Accepted to The Astronomical Journal October 14, 2017. TTV posteriors are available at https://github.com/alexteachey/TTV_posteriors
Additional file 4: of Analysis of MAPK and MAPKK gene families in wheat and related Triticeae species
Creators: name: Goyal, Ravinder
name: Tulpan, Dan
name: Chomistek, Nora
name: Dianevys González-Peña Fundora
name: West, Connor
name: Ellis, Brian
name: Frick, Michele
name: Laroche, André
name: Foroud, Nora
Publisher: name: figshare
Year: 2018
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
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: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: Genomic sequence of Triticeae MPKs. Genomic DNA sequences were obtained from Ensembl. Font colour of predicted genes differentiate UTRs (orange), exons (blue), introns (grey), sequences upstream/downstream of the predicted gene (green). Where Ensembl predictions for exon-intron structure did not match available transcript data, alternative exons are proposed and highlighted in yellow; corresponding accessions have an ‘X’ suffix. Black nucleotides are used for genomic sequence for which Ensembl did not predict a gene sequence or for predicted ncRNA sequences, where proposed exon sequences are highlighted in yellow. The underlined nucleotides highlighted in various colours indicate nucleotide variants as defined by Ensembl. (DOCX 452 kb)
Influence of Ethylene Oxide and Gamma Irradiation Sterilization Processes on the Properties of Poly-L-Lactic-Acid (PLLA) Materials
Creators: name: Krug, Natalie
name: Zarges, Jan-Christoph
name: Heim, Hans-Peter
Publisher: name: Universität Kassel
Year: 2023
Subjects: subject: bioplastics
subject: poly-L-lactic-acid (PLLA)
subject: sterilization
subject: gamma irradiation
subject: ethylene oxide
subject: single-use products
subject: medical devices
subject: 530
subject: 540
subject: Medizinisches Gerät
subject: Biopolymere
subject: Ethylenoxid
subject: Gammabestrahlung

description: Gefördert durch den Publikationsfonds der Universität Kassel
title: Seeds: How mankind obtained seeds and learnt to grow crops (version 2)
title: Semences : comment l'humanité a obtenu les semences et appris à mettre les terres en culture (version 2)
titleType: AlternativeTitle
title: 种子：人类如何得到了农作物的种子（第二次讲述版本）
titleType: AlternativeTitle
Creators: name: Michaud, Alexis
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Yongning Na
subject: nru

description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Additional file 2: of The acquisition of question intonation by Vietnamese learners of English
Creators: name: Anh-Thư Nguyễn
name: Đích Đào
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Space Science
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: Science Policy
subject: Computational Biology

description: F0 contours and prosodic labelling of the final tunes Statements. (DOCX 60 kb)
Perceptions of Inequality and Fiscal Policy Preferences
Creators: name: Van Der Weele, Joel
name: Sund, Oda Kristine Storstad
name: Douenne, Thomas
Publisher: name: OSF Registries
Year: 2023
Subjects: subject: Social and Behavioral Sciences

description: The aim of this study is to improve our understanding of citizens’ perception of inequalities in two specific ways: i) by documenting whether citizens hold accurate beliefs about wealth and income inequality (including their own relative position), and ii) by causally identifying the impact of these variables on citizens’ inequality acceptance and preferences for redistribution. For identification, the study relies on a 4 × 3 between-subject survey experiment ran by online Longitudinal Internet studies for the Social Sciences panel (LISS) on a representative sample of the Dutch population (N = 4500). The experimental data is linked to registry data provided by the Centraal Bureau voor de Statistiek (CBS), providing high-quality background information on the actual wealth and income of participants. Focusing on the potential differences between wealth and income inequality, the duality of the Dutch economy makes for ideal conditions to address our research questions. According to the OECD, the Netherlands is a country with a high degree of income equality but also of great wealth inequality. For instance, the top 10% of households in the Netherlands own 62% of the wealth, which is the highest share in the OECD after the U.S. (OECD 2018). Our survey experiment is divided into two parts. The first part of the survey documents any discrepancies between people’s perception of inequalities and the actual degree of inequality in the Netherlands, both in income and wealth. It also serves to document whether people correctly perceive their own situation in the income and wealth distributions. The second part of the survey is designed to understand how these (mis)perceptions causally affect people’s attitude towards inequalities, meritocratic beliefs, and their preferences for redistributive policies. In order to causally identify these effects, we exploit experimental variations in people’s beliefs obtained from randomized information provision in the LISS panel about people’s actual position in the income and wealth distribution, and actual wealth and/or income inequality.
Beyond linear galaxy alignments
Creators: name: Blazek, Jonathan
name: MacCrann, Niall
name: Troxel, M. A.
name: Fang, Xiao
Publisher: name: arXiv
Year: 2017
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Galaxy intrinsic alignments (IA) are a critical uncertainty for current and future weak lensing measurements. We describe a perturbative expansion of IA, analogous to the treatment of galaxy biasing. From an astrophysical perspective, this model includes the expected large-scale alignment mechanisms for galaxies that are pressure-supported (tidal alignment) and rotation-supported (tidal torquing) as well as the cross-correlation between the two. Alternatively, this expansion can be viewed as an effective model capturing all relevant effects up to the given order. We include terms up to second order in the density and tidal fields and calculate the resulting IA contributions to two-point statistics at one-loop order. For fiducial amplitudes of the IA parameters, we find the quadratic alignment and linear-quadratic cross terms can contribute order-unity corrections to the total intrinsic alignment signal at $k\sim0.1\,h^{-1}{\rm Mpc}$, depending on the source redshift distribution. These contributions can lead to significant biases on inferred cosmological parameters in Stage IV photometric weak lensing surveys. We perform forecasts for an LSST-like survey, finding that use of the standard "NLA" model for intrinsic alignments cannot remove these large parameter biases, even when allowing for a more general redshift dependence. The model presented here will allow for more accurate and flexible IA treatment in weak lensing and combined probes analyses, and an implementation is made available as part of the public FAST-PT code. The model also provides a more advanced framework for understanding the underlying IA processes and their relationship to fundamental physics.
description: 21 pages, including 3 figures and appendix. Related code available at https://github.com/JoeMcEwen/FAST-PT
Closed extended $r$-spin theory and the Gelfand-Dickey wave function
Creators: name: Buryak, Alexandr
name: Clader, Emily
name: Tessler, Ran J.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Algebraic Geometry (math.AG)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We study a generalization of genus-zero $r$-spin theory in which exactly one insertion has a negative-one twist, which we refer to as the "closed extended" theory, and which is closely related to the open $r$-spin theory of Riemann surfaces with boundary. We prove that the generating function of genus-zero closed extended intersection numbers coincides with the genus-zero part of a special solution to the system of differential equations for the wave function of the $r$-th Gelfand-Dickey hierarchy. This parallels an analogous result for the open $r$-spin generating function in the companion paper to this work.
description: v3: 25 pages, minor corrections according to referee's remarks
title: Tiger: How the tiger attacked a woman and her daughter (version 2)
title: La mère et sa fille face au tigre (version 2)
titleType: AlternativeTitle
title: 母女与老虎（第二次讲述版本）
titleType: AlternativeTitle
Creators: name: Michaud, Alexis
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Yongning Na
subject: nru

description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
title: Seeds: How mankind obtained seeds and learnt to grow crops (version1)
Creators: name: Michaud, Alexis
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2014
Subjects: subject: Yongning Na
subject: nru

description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Generation of inclined protoplanetary discs and misaligned planets through mass accretion I: Coplanar secondary discs
Creators: name: Xiang-Gruess, M.
name: Kroupa, P.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We study the three-dimensional evolution of a viscous protoplanetary disc which accretes gas material from a second protoplanetary disc during a close encounter in an embedded star cluster. The aim is to investigate the capability of the mass accretion scenario to generate strongly inclined gaseous discs which could later form misaligned planets. We use smoothed particle hydrodynamics to study mass transfer and disc inclination for passing stars and circumstellar discs with different masses. We explore different orbital configurations to find the parameter space which allows significant disc inclination generation. \citet{Thi2011} suggested that significant disc inclination and disc or planetary system shrinkage can generally be produced by the accretion of external gas material with a different angular momentum. We found that this condition can be fullfilled for a large range of gas mass and angular momentum. For all encounters, mass accretion from the secondary disc increases with decreasing mass of the secondary proto-star. Thus, higher disc inclinations can be attained for lower secondary stellar masses. Variations of the secondary disc's orientation relative to the orbital plane can alter the disc evolution significantly. The results taken together show that mass accretion can change the three-dimensional disc orientation significantly resulting in strongly inclined discs. In combination with the gravitational interaction between the two star-disc systems, this scenario is relevant for explaining the formation of highly inclined discs which could later form misaligned planets.
description: 13 pages, accepted for publication in MNRAS
Additional file 5: of Hospital readmissions with acute infectious diseases in New Zealand children
Creators: name: Seibt, Silvia
name: Gilchrist, Catherine
name: Reed, Peter
name: Best, Emma
name: Harnden, Anthony
name: Camargo, Carlos
name: Grant, Cameron
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Biotechnology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: FOS: Biological sciences
subject: Computational Biology

description: Associations of demographic and illness characteristics with risk of hospital readmission with a second skin and soft tissue infection within 12Â months of a first hospital admission with a skin and soft tissue infection. (DOCX 91 kb)
title: Housebuilding: the process of building a house (version 2)
title: La construction d'une maison (version 2)
titleType: AlternativeTitle
title: 建房子的过程 (第二次讲述版本)
titleType: AlternativeTitle
Creators: name: Michaud, Alexis
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2017
Subjects: subject: Yongning Na
subject: nru

description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Additional file 1 of Efficacy and safety of esketamine for sedation among patients undergoing gastrointestinal endoscopy: a systematic review and meta-analysis
Creators: name: Lian, Xianghong
name: Lin, Yunzhu
name: Luo, Ting
name: Jing, Yang
name: Yuan, Hongbo
name: Guo, Yixin
Publisher: name: figshare
Year: 2023
Subjects: Space Science
Medicine
Biological Sciences not elsewhere classified
Cancer
Science Policy

description: Additional file 1: Figure S1. Forest plots of the recovery time with different dosage of esketaime (mg/kg).
Phase transitions and adiabatic preparation of a fractional Chern insulator in a boson cold atom model
Creators: name: Motruk, Johannes
name: Pollmann, Frank
Publisher: name: arXiv
Year: 2017
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We investigate the fate of hardcore bosons in a Harper-Hofstadter model which was experimentally realized by Aidelsburger et al. [Nature Physics 11 , 162 (2015)] at half filling of the lowest band. We discuss the stability of an emergent fractional Chern insulator (FCI) state in a finite region of the phase diagram that is separated from a superfluid state by a first-order transition when tuning the band topology following the protocol used in the experiment. Since crossing a first-order transition is unfavorable for adiabatically preparing the FCI state, we extend the model to stabilize a featureless insulating state. The transition between this phase and the topological state proves to be continuous, providing a path in parameter space along which an FCI state could be adiabatically prepared. To further corroborate this statement, we perform time-dependent DMRG calculations which demonstrate that the FCI state may indeed be reached by adiabatically tuning a simple product state.
description: 7 pages, 7 figures, published version
Additional file 2 of Alignment-free clustering of large data sets of unannotated protein conserved regions using minhashing
Creators: name: Abnousi, Armen
name: Broschat, Shira
name: Ananth Kalyanaraman
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: 60506 Virology

description: Data Set Compositions (PDF 29 kb)
Additional file 2 of Efficacy and safety of esketamine for sedation among patients undergoing gastrointestinal endoscopy: a systematic review and meta-analysis
Creators: name: Lian, Xianghong
name: Lin, Yunzhu
name: Luo, Ting
name: Jing, Yang
name: Yuan, Hongbo
name: Guo, Yixin
Publisher: name: figshare
Year: 2023
Subjects: Space Science
Medicine
Biological Sciences not elsewhere classified
Cancer
Science Policy

description: Additional file 2: Figure S2. Forest plots of the propofol dose with different dosage of esketaime (mg/kg).
Oort spike comets with large perihelion distances
Creators: name: Królikowska, Małgorzata
name: Dybczyński, Piotr A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: The complete sample of large-perihelion nearly-parabolic comets discovered during the period 1901-2010 is studied starting from their orbit determination. Next, an orbital evolution that includes three perihelion passages (previous-observed-next) is investigated where a full model of Galactic perturbations and perturbations from passing stars have been incorporated. We show that the distribution of planetary perturbations suffered by actual large-perihelion comets during their passage through the Solar system has a deep, unexpected minimum around zero which indicates a lack of "almost unperturbed" comets. By a series of simulations we show that this deep well is moderately resistant to some diffusion of orbital elements of analysed comets. It seems reasonable to state that the observed stream of these large-perihelion comets experienced a series of specific planetary configurations when passing through the planetary zone. An analysis of the past dynamics of these comets clearly shows that dynamically new comets may appear only when their original semimajor axes are greater than 20 000 au. However, only for semimajor axes longer than 40 000 au dynamically old comets are completely not present. We demonstrated that the observed $1/a_{\rm ori}$ distribution exhibits a local minimum separating dynamically new from dynamically old comets. Long-term dynamical studies reveal a large variety of orbital behaviour. Several interesting examples of action of passing stars are also described, in particular the impact of Gliese 710 which will pass close to the Sun in the future. However, none of the obtained stellar perturbations is sufficient to change the dynamical status of analysed comets.
description: 41 pages, 20 figures, accepted for publication in MNRAS (Accepted 2017 August 16. Received 2017 August 16; in original form 2017 March 28)
MOESM2 of TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees
Creators: name: Sauvage, Thomas
name: Plouviez, Sophie
name: Schmidt, William
name: Fredericq, Suzanne
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
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: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Science Policy

description: Additional file 2. Details of color and annotation information saved within the TAXA block of FigTreeâ s NEXUS file.
title: Food shortage: how parents set out to sell children, and then changed their mind
title: Disette
titleType: AlternativeTitle
title: 忍饥挨饿
titleType: AlternativeTitle
Creators: name: Michaud, Alexis
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Yongning Na
subject: nru

description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
title: A cell–ECM screening method to predict breast cancer metastasis
Creators: name: Barney, Lauren E.
name: Dandley, E. C.
name: Jansen, Lauren
name: Reich, Nicholas G.
name: Mercurio, A. M.
name: Peyton, Shelly
Publisher: name: University of Massachusetts Amherst
Year: 2015
Subjects: subject: Chemical Engineering
subject: FOS: Chemical engineering

description: Breast cancer preferentially spreads to the bone, brain, liver, and lung. The clinical patterns of this tissue-specific spread (tropism) cannot be explained by blood flow alone, yet our understanding of what mediates tropism to these physically and chemically diverse tissues is limited. While the micro- environment has been recognized as a critical factor in governing metastatic colonization, the role of the extracellular matrix (ECM) in mediating tropism has not been thoroughly explored. We created a simple biomaterial platform with systematic control over the ECM protein density and composition to determine if integrin binding governs how metastatic cells diﬀerentiate between secondary tissue sites. Instead of examining individual behaviors, we compiled large patterns of phenotypes associated with adhesion to and migration on these controlled ECMs. In combining this novel analysis with a simple biomaterial platform, we created an in vitro fingerprint that is predictive of in vivo metastasis. This rapid biomaterial screen also provided information on how b1, a2, and a6 integrins might mediate metastasis in patients, providing insights beyond a purely genetic analysis. We propose that this approach of screening many cell–ECM interactions, across many different heterogeneous cell lines, is predictive of in vivo behavior, and is much simpler, faster, and more economical than complex 3D environments or mouse models. We also propose that when specifically applied toward the question of tissue tropism in breast cancer, it can be used to provide insight into certain integrin subunits as therapeutic targets.
Additional file 4: of Hospital readmissions with acute infectious diseases in New Zealand children
Creators: name: Seibt, Silvia
name: Gilchrist, Catherine
name: Reed, Peter
name: Best, Emma
name: Harnden, Anthony
name: Camargo, Carlos
name: Grant, Cameron
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Biotechnology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: 60506 Virology
subject: FOS: Biological sciences
subject: Computational Biology

description: Associations of demographic and illness characteristics with risk of hospital readmission with a second enteric infection within 12Â months of a first hospital admission with an enteric infection. (DOCX 86 kb)
Perception, attitude, awareness and perspective towards sustainability practices in relation to climate change among nurses globally: a systematic review protocol
Creators: name: Akore Yeboah, Ebenezer
name: Adegboye, Amanda
name: Kneafsey, Rosie
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Nursing
subject: FOS: Health sciences
subject: Medicine and Health Sciences
subject: climate change
subject: environmental sustainability
subject: mixed methods
subject: nursing

description: This mixed methods systematic review protocol seeks to identify studies on the perception, attitude, awareness and perspective towards sustainability practices in relation to climate change among nurses globally.
A comprehensive comparison of relativistic particle integrators
Creators: name: Ripperda, Bart
name: Bacchini, Fabio
name: Teunissen, Jannis
name: Xia, Chun
name: Porth, Oliver
name: Sironi, Lorenzo
name: Lapenta, Giovanni
name: Keppens, Rony
Publisher: name: arXiv
Year: 2017
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We compare relativistic particle integrators commonly used in plasma physics showing several test cases relevant for astrophysics. Three explicit particle pushers are considered, namely the Boris, Vay, and Higuera-Cary schemes. We also present a new relativistic fully implicit particle integrator that is energy conserving. Furthermore, a method based on the relativistic guiding center approximation is included. The algorithms are described such that they can be readily implemented in magnetohydrodynamics codes or Particle-in-Cell codes. Our comparison focuses on the strengths and key features of the particle integrators. We test the conservation of invariants of motion, and the accuracy of particle drift dynamics in highly relativistic, mildly relativistic, and non-relativistic settings. The methods are compared in idealized test cases, i.e., without considering feedback on the electrodynamic fields, collisions, pair creation, or radiation. The test cases include uniform electric and magnetic fields, $\mathbf{E}\times\mathbf{B}$-fields, force-free fields, and setups relevant for high-energy astrophysics, e.g., a magnetic mirror, a magnetic dipole, and a magnetic null. These tests have direct relevance for particle acceleration in shocks and in magnetic reconnection.
description: Matching published version in ApJS
Additional file 1: of The acquisition of question intonation by Vietnamese learners of English
Creators: name: Anh-Thư Nguyễn
name: Đích Đào
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: Science Policy

description: English statements and questions. (DOCX 14 kb)
title: Zürcher statistische Nachrichten 1924
title: Zür. stat. Nachr.
titleType: AlternativeTitle
title: Zürcher statistische Nachrichten
titleType: AlternativeTitle
title: Zürcher statistische Nachrichten
titleType: AlternativeTitle
title: Zürcher statistische Nachrichten
titleType: AlternativeTitle
Creators: name: (:Unkn) Unknown
Publisher: name: Buchdruckerei Berichthaus
Year: 1925
Subjects: subject: 314 Allgemeine Statistiken zu Europa
subject: 330 Wirtschaft
subject: Zürich
subject: Amtliche Statistik
subject: Immobilienmarkt
subject: Bevölkerungsstatistik
subject: Wirtschaftsstatistik

description: Enthält vier Vierteljahreshefte, eine Jahresübersicht und einen Stadtplan auf S. 168.
The brightness of the Red Giant Branch tip: Theoretical framework, a set of reference models, and predicted observables
Creators: name: Serenelli, Aldo
name: Weiss, Achim
name: Cassisi, Santi
name: Salaris, Maurizio
name: Pietrinferni, Adriano
Publisher: name: arXiv
Year: 2017
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The brightness of the tip of the Red Giant Branch is a useful reference quantity for several fields of astrophysics. An accurate theoretical prediction is needed for such purposes. Aims. We intend to provide a solid theoretical prediction for it, valid for a reference set of standard physical assumptions, and mostly independent of numerical details. We examine the dependence on physical assumptions and numerical details, for a wide range of metallicities and masses, and based on two different stellar evolution codes. We adjust differences between the codes to treat the physics as identical as possible. After we have succeeded in reproducing the tip brightness between the codes, we present a reference set of models based on the most up to date physical inputs, but neglecting microscopic diffusion, and convert theoretical luminosities to observed infrared colours suitable for observations of resolved populations of stars and include analytic fits to facilitate their use. We find that consistent use of updated nuclear reactions, including an appropriate treatment of the electron screening effects, and careful time-stepping on the upper red giant branch are the most important aspects to bring initially discrepant theoretical values into agreement. Small, but visible differences remain unexplained for very low metallicities and mass values at and above 1.2 Msun, corresponding to ages younger than 4 Gyr. The colour transformations introduce larger uncertainties than the differences between the two stellar evolution codes. We demonstrate that careful stellar modeling allows an accurate prediction for the luminosity of the Red Giant Branch tip. Differences to empirically determined brightnesses may result either from insufficient colour transformations or from deficits in the constitutional physics. We present the best-tested theoretical reference values to date.
description: 14 pages, 12 figures, 2 tables. Accepted for publication in A&A
title: Spatial orientation: combinations between verbs and prefixes/adverbials indicating spatial orientation. Speaker F4.
Creators: name: Michaud, Alexis
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Yongning Na
subject: nru

description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Microwave photonics with superconducting quantum circuits
Creators: name: Gu, Xiu
name: Kockum, Anton Frisk
name: Miranowicz, Adam
name: Liu, Yu-xi
name: Nori, Franco
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: In the past 20 years, impressive progress has been made both experimentally and theoretically in superconducting quantum circuits, which provide a platform for manipulating microwave photons. This emerging field of superconducting quantum microwave circuits has been driven by many new interesting phenomena in microwave photonics and quantum information processing. For instance, the interaction between superconducting quantum circuits and single microwave photons can reach the regimes of strong, ultra-strong, and even deep-strong coupling. Many higher-order effects, unusual and less familiar in traditional cavity quantum electrodynamics with natural atoms, have been experimentally observed, e.g., giant Kerr effects, multi-photon processes, and single-atom induced bistability of microwave photons. These developments may lead to improved understanding of the counterintuitive properties of quantum mechanics, and speed up applications ranging from microwave photonics to superconducting quantum information processing. In this article, we review experimental and theoretical progress in microwave photonics with superconducting quantum circuits. We hope that this global review can provide a useful roadmap for this rapidly developing field.
description: Review article, 170 pages (main text 101 pages), 35 figures, 5 tables, 1362 references; v2: a few more references added, typos corrected; Physics Reports (in press)
Additional file 3 of Efficacy and safety of esketamine for sedation among patients undergoing gastrointestinal endoscopy: a systematic review and meta-analysis
Creators: name: Lian, Xianghong
name: Lin, Yunzhu
name: Luo, Ting
name: Jing, Yang
name: Yuan, Hongbo
name: Guo, Yixin
Publisher: name: figshare
Year: 2023
Subjects: Space Science
Medicine
Biological Sciences not elsewhere classified
Cancer
Science Policy

description: Additional file 3: Figure S3. Forest plots of the complications with different dosage of esketaime (mg/kg).