cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1: of Genomic insights into host adaptation between the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei)
Creators: name: Chongjing Xia
name: Meinan Wang
name: Chuntao Yin
name: Cornejo, Omar
name: Hulbert, Scot
name: Xianming Chen
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Figure S1. The 17-mer depth distributions of the Illumina reads used to estimate the genome sizes of Pst (93â 210) and Psh (93TX-2) isolates of Puccinia striiformis used in this study. Figure S2. Comparisons of functional annotations between wheat-hosted and barley-hosted stripe rust and powdery mildew fungi. Figure S3. Collinearity analysis of syntenic blocks among three Puccinia striiformis isolates. Figure S4. Examples of missing genomic regions by reciprocal mapping of Illumina sequence reads. Figure S5. An overview of a large syntenic region between isolates Ps (93â 210) and Psh (93TX-2) of Puccinia striiformis. 4. Figure S6. An overview of the mitochondrial (mt) genomes of isolates Pst (93â 210) and Psh (93Tx-2) representing Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh), respectively. Figure S7. IGV screenshot showing examples of exclusively expressed genes revealed by reciprocal mapping of Illumina RNA-Seq reads. Figure S8. Genome assembly pipeline used for genome assembly in this study. See details in Methods. (DOCX 4535 kb)
A simple note for HDF4/HDF-EOS2 to CF Mapping
Creators: name: Yang, Kent
Publisher: name: Zenodo
Year: 2013

description: Summary of the document: To support the OPeNDAP Hyrax 1.9 release, this document provides a simple note for mapping HDF4/HDF-EOS2 data to CF (Climate and Forecast) conventions. It starts with name conventions, advising to replace characters not allowed by CF with underscores. For HDF-EOS2, it suggests prefixing variable names with corresponding grid/swath/zonal-average names for multi-grid/multi-swath/multi-zonal-average files. For HDF4 SDS objects, names are mapped to CF by connecting ancestor Vgroup paths with underscores. Vdata fields are mapped similarly, with "vdata" prefixed to the path and "vdf" used to connect to the field name. To avoid name clashes, added SDS objects in HDF-EOS2 files have "NONEOS" appended. Dimensions in HDF-EOS2 map to CF dimensions, while fake dimensions may be added to SDS or Vdata fields in HDF4. Latitude and longitude are retrieved properly and given CF units. CF attributes like _FillValue, valid_range, scale_factor, and add_offset are adjusted to follow CF conventions for various NASA HDF-EOS2 and HDF4 products.
Making Damped Lyman Alpha Systems in Semi-Analytic Models
Creators: name: Maller, Ariyeh H.
name: Somerville, Rachel S.
name: Prochaska, Jason X.
name: Primack, Joel R.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The velocity profiles of weak metal absorption lines can be used to observationally probe the kinematic state of gas in damped Lyman-alpha systems. Prochaska and Wolfe have argued that the flat distribution of velocity widths combined with the asymmetric line profiles indicate that the DLAS are disks with large rotation velocities. An alternative explanation has been proposed by Haehnelt, Steinmetz, and Rauch, in which the observed large velocity widths and asymmetric profiles can be produced by lines of sight passing through two or more clumps each having relatively small internal velocity dispersions. We investigate the plausibility of this scenario in the context of semi-analytic models based on hierarchical merging trees and including simple treatments of gas dynamics, star formation, supernova feedback, and chemical evolution. We find that all the observed properties of the metal-line systems including the distribution of velocities and the asymmetric profiles, can be reproduced by lines of sight passing through sub-clumps that are bound within larger virialized dark matter halos. In order to produce enough multiple hits, we find that the cold gas must be considerably more extended than the optical radius of the proto-galaxies, perhaps even beyond the tidal radius of the sub-halo. This could occur due to tidal stripping or supernova-driven outflows.
description: 4 pages, 2 figures, uses aipproc.sty, to appear in After the Dark Ages: The 9th Annual October Astrophysics Conference
Complex Langevin calculations in finite density QCD at large $μ/T$ with the deformation technique
Creators: name: Nagata, Keitaro
name: Nishimura, Jun
name: Shimasaki, Shinji
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: It is well known that investigating QCD at finite density by standard Monte Carlo methods is extremely difficult due to the sign problem. Some years ago, the complex Langevin method with gauge cooling was shown to work at high temperature, i.e., in the deconfined phase. The same method was also applied to QCD in the so-called heavy dense limit in the whole temperature region. In this paper we attempt to apply this method to the large $μ/T$ regime with moderate quark mass using four-flavor staggered fermions on a $4^3\times 8$ lattice. While a straightforward application faces with the singular-drift problem, which spoils the validity of the method, we overcome this problem by the deformation technique proposed earlier. Explicit results for the quark number density and the chiral condensate obtained in this way for $3.2\leq μ/T\leq 5.6$ are compared with the results for the phase-quenched model obtained by the standard rational hybrid Monte Carlo calculation. This reveals a clear difference, which is qualitatively consistent with the Silver Blaze phenomenon.
description: 14 pages, 5 figures; (v2) a typo for the lattice size in the abstract was corrected; (v3) detailed discussions on the interpretation of the results added; version published in PRD
Additional file 2: of Civil servants' demand for social health insurance in Northwest Ethiopia
Creators: name: Sahilu Yeshiwas
name: Mengistu Kiflie
name: Atinkut Zeleke
name: Mihiretu Kebede
Publisher: name: figshare
Year: 2018
Subjects: subject: Molecular Biology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Science Policy
subject: 60506 Virology

description: Questionaire. (DOCX 23 kb)
Experiments with LISA Pathfinder: Cosmic Rays and Fundamental Physics
Creators: name: Baird, Jonathon
Publisher: name: Imperial College London
Year: 2018

description: The Laser Interferometer Space Antenna (LISA) Pathfinder experiment successfully demonstrated that a future gravitational wave detector in space is possible with current technology. Results from a selection of the many experiments performed by this state of the art gravity gradiometer are presented in this thesis. In the first half, groundwork for projection of test mass charging to the LISA mission will be provided by an analysis of the Pathfinder radiation monitor data. To do this, an existing GEANT4 model for the monitor is developed and a new component representing the on board processing of signal hits added. The second half of this thesis relates to fundamental physics with gravity gradiometers, with an emphasis on measuring the gravitational constant in space. The measurements will be presented with arguments for a number of improvements so that future gradiometers can improve on the results outlined in this work.
Constraining the IMF using TeV gamma ray absorption
Creators: name: Bullock, J. S.
name: Somerville, R. S.
name: MacMinn, D.
name: Primack, J. R.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Gamma rays of ~TeV energies from distant sources suffer attenuation due to pair production off of ~1 micron EBL photons. We may exploit this process in order to indirectly measure the EBL and constrain models of galaxy formation. Here, using semi-analytic models of galaxy formation, we examine how gamma ray absorption may be used as an indirect probe of the stellar initial mass function (IMF), although there is a degeneracy with dust modeling. We point out that with the new generation of gamma ray telescopes including STACEE, MAGIC, HESS, VERITAS, and Milagro, we should soon possess a wealth of new data and a new method for probing the nature of the IMF.
description: contribution to "TeV Astrophysics of Extragalactic Sources" VERITAS workshop, editors M. Catanese, J. Quinn, T. Weekes; 3 pages 1 figure
Additional file 2: of 3D imaging of PSD-95 in the mouse brain using the advanced CUBIC method
Creators: name: Huazheng Liang
name: Hongqin Wang
name: Shaoshi Wang
name: Francis, Richard
name: Paxinos, George
name: Xufeng Huang
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Materials and methods. (DOC 30 kb)
Optical Number Count Estimation of IRIS Far-Infrared Survey of Galaxies
Creators: name: Hirashita, H.
name: Takeuchi, T. T.
name: Ohta, K.
name: Shibai, H.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Infrared Imaging Surveyor (IRIS) is a satellite which will be launched at the beginning of 2003. One of the main purposes of the IRIS mission is an all-sky survey in the far-infrared region with a flux limit much deeper than that of IRAS. Detection of a large number of galaxies ($\sim several \times 10^6$ in the whole sky) is expected in this survey. We investigated the expected optical and near-infrared (NIR) number counts of galaxies detected by the far-infrared scanner (FIS) of IRIS (hereafter, IRIS galaxies) and possibility of optical and NIR follow-up of them. The spectral energy distribution and the luminosity function of the IRIS galaxies are modeled based on the properties of galaxies observed by IRAS. The IRIS galaxies are divided into two populations according to their infrared luminosities ($L_{IR}$); normal spirals ($L_{IR}<10^{10}\LO$) and starbursts ($L_{IR}>10^{10}\LO$). The expected number counts of IRIS galaxies for both of the populations are calculated in $B$ and $H$ bands. We show that about 60 normal galaxies and about 80 starburst galaxies are detected per square degree in both of the two bands, when galaxy evolution is not taken into account. All of the normal population of IRIS galaxies are located at the redshift $z\ltsim 0.1$. As for the starburst population, we also calculated number of galaxies with a simple model of evolution. The total number of starburst population predicted by the evolution model is larger by 20% than that expected from the non-evolution model. In the evolution model, the numbers of low-z ($z<1$), intermediate-z ($13$) galaxies are 100, 20, and 0.2 per square degree, respectively.
description: 18 pages LaTeX, 9 figures, to appear in PASJ
Cryogenic ion trap system for high-fidelity near-field microwave-driven quantum logic
Creators: name: Weber, M. A.
name: Löschnauer, C.
name: Wolf, J.
name: Gely, M. F.
name: Hanley, R. K.
name: Goodwin, J. F.
name: Ballance, C. J.
name: Harty, T. P.
name: Lucas, D. M.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We report the design, fabrication, and characterization of a cryogenic ion trap system for the implementation of quantum logic driven by near-field microwaves. The trap incorporates an on-chip microwave resonator with an electrode geometry designed to null the microwave field component that couples directly to the qubit, while giving a large field gradient for driving entangling logic gates. We map the microwave field using a single $^{43}$Ca$^+$ ion, and measure the ion trapping lifetime and motional mode heating rates for one and two ions.
description: 18 pages, 13 figures
Turdus canorus Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Aves
Passeriformes
Turdidae
Turdus
Turdus canorus

description: Turdus canorus [spec. nov.]
T. griseus, subtus ferrugineus, linea alba ad latera capitis, cauda rotundata. Chin. Lagerstr. 11.
Turdus chinensis. Osb. it. 309.
Turdus fuscus benghalensis non maculatus. Edw. av. 184. t. 184.
Baniah bove benghala. Alb. av. 3. p. 18. t. 19.
Habitat in Benghala, China.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 169, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
$p$-adic multiple $L$-functions and cyclotomic multiple harmonic values
Creators: name: Furusho, Hidekazu
name: Jarossay, David
Publisher: name: arXiv
Year: 2018
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics

description: We show that the special values at tuples of positive integers of the $p$-adic multiple $L$-function introduced by the first-named author et al. can be expressed in terms of the cyclotomic multiple harmonic values introduced by the second-named author.
description: 10 pages, to appear in Int. J. Number Theory
Density of the level sets of the metric mean dimension for homeomorphisms
Creators: name: Acevedo, Jeovanny de Jesus Muentes
name: Ibarra, Sergio Romaña
name: Cantillo, Raibel Arias
Publisher: name: arXiv
Year: 2022
Subjects: subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics

description: Let $N$ be an $n$-dimensional compact riemannian manifold, with $n\geq 2$. In this paper, we prove that for any $α\in [0,n]$, the set consisting of homeomorphisms on $N$ with lower and upper metric mean dimensions equal to $α$ is dense in $\text{Hom}(N)$. More generally, given $α,β\in [0,n]$, with $α\leq β$, we show the set consisting of homeomorphisms on $N$ with lower metric mean dimension equal to $α$ and upper metric mean dimension equal to $β$ is dense in $\text{Hom}(N)$. Furthermore, we also give a proof that the set of homeomorphisms with upper metric mean dimension equal to $n$ is residual in $\text{Hom}(N)$.
title: ADCO, Cartulaire de Cîteaux pour les domaines de Beaune (XVe siècle), Cart. 177 (11 H 289), 197 folios, f. 0323
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2015
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: cartulaire
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Cartulaire de Cîteaux pour les domaines de Beaune (XVe siècle), Archives départementales de la Côte-d'Or, Cart. 177 (11 H 289), 197 folios, f. 0323, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire de Cîteaux pour les possessions d’Izeure (XVe siècle), Archives départementales de la Côte-d'Or, Cart. 177 (11 H 289), 197 folios, f. 0323, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
Turdus orpheus Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Aves
Passeriformes
Turdidae
Turdus
Turdus orpheus

description: Turdus orpheus [spec. nov.]
T. dorso fusco, pectore rectricibusque lateralibus albidis, alis fascia alba. Brown. jam. 469.
Turdus cinereus minor. Edw. av. 78. t. 78.
Habitat in America.
Cauda longa rotundata. Rectrices extimae albae. E terra elevatus cantilena spectatorem rapit in sui admirationem.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 169, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Filtration of interstellar hydrogen in the two-shock heliospheric interface: Inferences on the local interstellar electron density
Creators: name: Izmodenov, V. V.
name: Geiss, J.
name: Lallement, R.
name: Gloeckler, G.
name: Baranov, V. B.
name: Malama, Y. G.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The solar system is moving through the partially ionized local interstellar cloud (LIC). The ionized matter of the LIC interacts with the expanding solar wind forming the heliospheric interface. The neutral component (interstellar atoms) penetrates through the heliospheric interface into the heliosphere, where it is measured directly "in situ" as pick-up ions and neutral atoms (and as anomalous cosmic rays) or indirectly through resonant scattering of solar Ly-alpha. When crossing the heliospheric interface, interstellar atoms interact with the plasma component through charge exchange. This interaction leads to changes of both neutral gas and plasma properties. The heliospheric interface is also the source of radio emissions which have been detected by the Voyager since 1983. In this paper, we have used a kinetic model of the flow of the interstellar atoms with updated values of velocity, temperature, and density of the circumsolar interstellar hydrogen and calculated how all quantities which are directly associated to the observations vary as a function of the interstellar proton number density. These quantities are the degree of filtration, the temperature and the velocity of the interstellar H atoms in the inner heliosphere, the distances to the bow shock (BS), heliopause, and termination shock, and the plasma frequencies in the LIC, at the BS and in the maximum compression region around the heliosphere which constitutes the "barrier" for radio waves formed in the interstellar medium. Comparing the model results with recent pickup ion data, Ly- alpha measurements, and low-frequencies radio emissions, we have searched for a number density of protons in the local interstellar cloud compatible with all observations.
description: 14 pages, 5 figures, JGR-Space Physics, accepted, AGU preprint style
Growth and differentiation factor 15 causes skeletal muscle wasting in pulmonary arterial hypertension through actions on transforming growth factor β activated kinase 1
Creators: name: Garfield, Ben
Publisher: name: Imperial College London
Year: 2017

description: Muscle wasting is an important complication of a wide range chronic diseases. Pulmonary arterial hypertension (PAH) is no different. Novel targets and treatments are required to help improve outcomes in patients with PAH complicated by muscle wasting. GDF-15 is prognostic marker in PAH and has been shown to cause muscle wasting in vitro and in vivo. The pathway through which GDF-15 acts in muscle cells is not established. I used a human study, animal models of PAH; the monocrotaline (MCT) rat; and Sugen/hypoxia mouse, as well as C2C12 muscle cells to determine whether GDF-15 and its downstream signals may be important in the development of muscle wasting and low physical activity in PAH. Muscle wasting and low physical activity were associated with poor outcomes in a population of patients with PAH. Circulating GDF-15 levels were associated with markers of muscle strength and size in 2 animal models and in patients with PAH. In the MCT rat the pulmonary vasculature was an important site of production of GDF-15. GDF-15 acted by increasing the expression of ubiquitin ligases, which are involved in muscle wasting. GDF-15 decreased the activity of SMAD 1, 5 whilst increasing transforming growth factor β activated kinase 1 (TAK1) phosphorylation in muscle cells. Antagonising TAK1 with 5(Z)-7-oxozeaenol partially prevented muscle loss and rises in ubiquitin ligase expression in muscle cells and prevented weight loss in some MCT rats treated for 9 days with the drug. Muscle wasting and low physical activity are potentially modifiable risk factors for poor prognosis in PAH. GDF-15 may be a useful biomarker of muscle loss in PAH. Antagonising GDF-15 through its downstream mediator TAK1 requires further evaluation in animal models and patients with PAH to establish its usefulness in clinical practice.
On Efficient and Scalable Computation of the Nonparametric Maximum Likelihood Estimator in Mixture Models
Creators: name: Zhang, Yangjing
name: Cui, Ying
name: Sen, Bodhisattva
name: Toh, Kim-Chuan
Publisher: name: arXiv
Year: 2022
Subjects: subject: Methodology (stat.ME)
subject: Optimization and Control (math.OC)
subject: Statistics Theory (math.ST)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: In this paper we study the computation of the nonparametric maximum likelihood estimator (NPMLE) in multivariate mixture models. Our first approach discretizes this infinite dimensional convex optimization problem by fixing the support points of the NPMLE and optimizing over the mixture proportions. In this context we propose, leveraging the sparsity of the solution, an efficient and scalable semismooth Newton based augmented Lagrangian method (ALM). Our algorithm beats the state-of-the-art methods~\cite{koenker2017rebayes, kim2020fast} and can handle $n \approx 10^6$ data points with $m \approx 10^4$ support points. Our second procedure, which combines the expectation-maximization (EM) algorithm with the ALM approach above, allows for joint optimization of both the support points and the probability weights. For both our algorithms we provide formal results on their (superlinear) convergence properties.
 The computed NPMLE can be immediately used for denoising the observations in the framework of empirical Bayes. We propose new denoising estimands in this context along with their consistent estimates. Extensive numerical experiments are conducted to illustrate the effectiveness of our methods. In particular, we employ our procedures to analyze two astronomy data sets: (i) Gaia-TGAS Catalog~\cite{anderson2018improving} containing $n \approx 1.4 \times 10^6$ data points in two dimensions, and (ii) the $d=19$ dimensional data set from the APOGEE survey~\cite{majewski2017apache} with $n \approx 2.7 \times 10^4$.
Some possible astrophysical aplications of diamond anvil cells
Creators: name: Celebonovic, V.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: This is a short review of the methodology of static high pressure exeperiments in diamond anvil cells,and some of their possible applications an astrophysics.As the paper was originally published in 1993.,an addendum hints at some of the recent developements in the field.
description: plain LaTeX,no figures
Estimating Ambient Air Pollution Using Structural Properties of Road Networks
Creators: name: Berrisford, Liam J
name: Ribeiro, Eraldo
name: Menezes, Ronaldo
Publisher: name: arXiv
Year: 2022
Subjects: subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences

description: In recent years, the world has become increasingly concerned with air pollution. Particularly in the global north, countries are implementing systems to monitor air pollution on a large scale to aid decision-making. Such efforts are essential but they have at least three shortcomings: (1) they are costly and are difficult to implement expediently; (2) they focus on urban areas, which is where most people live, but this choice is prone to inequalities; and (3) the process of estimating air pollution lacks transparency. In this paper, we demonstrate that we can estimate air pollution using open-source information about the structural properties of roads; we focus on England and Wales in the United Kingdom (UK) in this paper although the methods here described are not dependent on specific datasets. Our approach makes it possible to implement an inexpensive method of estimating air pollution concentrations to an accuracy level that can underpin policymakers' decisions while providing an estimate in all districts, not just urban areas, and in a process that is transparent and explainable. Impact Statement. We show that a linear regression model using a single structural property -- length of the track and unclassified road network within 0.36% of districts within England and Wales (in the UK) -- can accurately estimate which districts are the most polluted. The model presents a transparent and low-cost, yet effective, alternative to more expensive models such as the one currently used by DEFRA in the UK. The model has apparent practical uses for policymakers who want to pursue clean-air initiatives but lack the capital to invest in comprehensive monitoring networks. Its low implementation cost, accessible model design, and worldwide coverage of the dataset provide a basis for implementing systems to estimate air pollution concentrations in low-income countries.
description: Main File 18 pages, 9 Figures, 3 Tables. Supplementary File 19 pages, 10 figures, 14 tables. Edited to fix tex issues, and improve prose and methodology
Additional file 4: of Mucosal associated invariant T cells from human breast ducts mediate a Th17-skewed response to bacterially exposed breast carcinoma cells
Creators: name: Zumwalde, Nicholas
name: Haag, Jill
name: Gould, Michael
name: Gumperz, Jenny
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Figure S3. IFN-Îł vs. IL-17A production by in vitro-expanded MAIT lines after PMA/ionomycin stimulation. In vitro-expanded MAIT cells derived from breast duct (left column) or from PBMCs (right column) were stimulated with PMA and ionomycin, and expression of IFN-Îł and IL-17A was assessed by intracellular cytokine staining. (PDF 252 kb)
The detection of extragalactic $^{15}$N: Consequences for nitrogen nucleosynthesis and chemical evolution
Creators: name: Chin, Yi-nan
name: Henkel, Christian
name: Langer, Norbert
name: Mauersberger, Rainer
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Detections of extragalactic $^{15}$N are reported from observations of the rare hydrogen cyanide isotope HC$^{15}$N toward the Large Magellanic Cloud (LMC) and the core of the (post-) starburst galaxy NGC 4945. Accounting for optical depth effects, the LMC data from the massive star-forming region N113 infer a $^{14}N/^{15}$N ratio of 111 $\pm$ 17, about twice the $^{12}C/^{13}$C value. For the LMC star-forming region N159HW and for the central region of NGC 4945, $^{14}N/^{15}$N ratios are also $\approx$ 100. The $^{14}N/^{15}$N ratios are smaller than all interstellar nitrogen isotope ratios measured in the disk and center of the Milky Way, strongly supporting the idea that $^{15}$N is predominantly of `primary' nature, with massive stars being its dominant source. Although this appears to be in contradiction with standard stellar evolution and nucleosynthesis calculations, it supports recent findings of abundant $^{15}$N production due to rotationally induced mixing of protons into the helium-burning shells of massive stars.
description: 15 pages including one postscript figure, accepted for publication by ApJ Letter, further comments: please contact Yi-nan Chin
Relationship of macrophage function and phenotype in COPD
Creators: name: Tilman, Jessica Dorsie
Publisher: name: Imperial College London
Year: 2017

description: Chronic obstructive pulmonary disease (COPD) is associated with elevated inflammatory signals, protease activity and reduced clearance of pathogens. Macrophages are key in driving inflammatory signals that are subsequently followed by resolution of inflammation and return to steady state. In pathologies such as COPD, macrophages may drive development and progression of disease by loss of regulation of inflammatory signals, which, in turn, may be due to changes in phenotype and loss of cell plasticity. This thesis investigated the ability of macrophages to adapt to changes in microenvironment and establish whether cell plasticity is lost in COPD cells leading to a ‘fixed’ inflammatory state. Monocyte-derived macrophages (MDM) and human lung tissue macrophages were cultured in either GM-CSF (pro-inflammatory) or M-CSF (resolving) to evaluate the effect on cell phenotype, function and plasticity between non-smokers, smokers and COPD patients, with the hypothesis that COPD cells would remain inflammatory regardless of environment. COPD cells released higher levels of pro-inflammatory cytokines following LPS stimulation compared to control cells, and this could be further enhanced when cultured in GM-CSF compared to M-CSF. Non-smoker and smoker cells could be driven to become less inflammatory in the presence of M-CSF, while COPD cells could not. COPD cells also demonstrated elevated protease activity and defects in phagocytosis compared to controls, but these were not affected by growth factors. Analysis of macrophage subsets based on cell density highlighted morphological and functional differences in both MDM and tissue macrophages, suggesting that phenotype may be predetermined in monocytes, and not purely influenced by environment. Furthermore, macrophage phenotype in COPD may be influenced by epigenetic modifications, driving changes in gene expression and cell function. KLF4 and CSF1R, which have a role in dampening inflammatory response, were downregulated in COPD and may be one mechanism driving inflammation. COPD macrophages show several defects compared to smokers and non-smokers, in both MDM and tissue macrophages, and demonstrated unilateral plasticity to become more inflammatory. Targeting these processes may therefore allow development of novel anti-inflammatory therapies for this disease.
Relativistic Corrections to the Sunyaev-Zel'dovich Effect for Clusters of Galaxies. III. Polarization Effect
Creators: name: Itoh, Naoki
name: Nozawa, Satoshi
name: Kohyama, Yasuharu
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We extend the formalism of the relativistic thermal and kinematic Sunyaev-Zel'dovich effects and include the polarization of the cosmic microwave background photons. We consider the situation that a cluster of galaxies is moving with a velocity \vec{v} with respect to the cosmic microwave background radiation. In the present formalism, polarization of the scattered cosmic microwave background radiation caused by the proper motion of a cluster of galaxies is naturally derived as a special case of the kinematic Sunyaev-Zel'dovich effect. The relativistic corrections are included also in a natural way. Our results are in complete agreement with the recent results of the relativistic corrections obtained by Challinor, Ford and Lasenby with an entirely different method as well as the nonrelativistic limit obtained by Sunyaev and Zel'dovich. The relativistic correction becomes to be significant in the Wien region.
description: 13 pages + 2 figures, LaTeX with AASMS macro. accepted for publication in ApJ
Turdus polyglottos Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Aves
Passeriformes
Turdidae
Turdus
Turdus polyglottos

description: Turdus polyglottos [spec. nov.]
T. obscure cinereus, subtus pallide cinereus, macula alarum albida.
Turdus minor caeruleo-albus immaculatus. Sloan. jam. 2. p. 306. t. 256. f. 3. Catesb. car. 1. p. 27. t. 27. Raj. av. 185. n. 31.
Mocking-bird. Kalm. itin. 2. p. 335.
Habitat in Virginia.
Eximia voce cantillat & cantu instruitur.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 169, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Additional file 1: of Civil servants' demand for social health insurance in Northwest Ethiopia
Creators: name: Sahilu Yeshiwas
name: Mengistu Kiflie
name: Atinkut Zeleke
name: Mihiretu Kebede
Publisher: name: figshare
Year: 2018
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental 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: Developmental Biology
subject: Cancer
subject: Science Policy
subject: 60506 Virology

description: Government offices, total number of civil servants and civil servants proportionally allocated in the sample. (DOCX 17 kb)
Integrated Bayesian approach to incorporate prior biological knowledge in the investigation of genetic variants associated with lung function
Creators: name: Das Neves Sousa Pereira, Miguel Maria
Publisher: name: Imperial College London
Year: 2018

description: Genetic association studies aim to identify single-nucleotide polymorphisms (SNPs) that are associated with complex diseases and traits. These studies, especially those performed at the genome-wide level, have successfully identified many SNPs associated with several diseases but current findings explain only a small fraction of their estimated genetic component. This thesis contributes to the scientific literature by developing a novel statistical approach for the analysis of genetic association studies and by applying it to the discovery of new SNPs associated with lung function. Lung function has an estimated genetic component of ~40% and an important epidemiological impact since low lung function has been associated with all-cause mortality. First, I investigate a Bayesian hierarchical shrinkage model that performs a joint analysis of SNPs and includes biological information about the SNPs in the analysis. The approach involves creating a score of biological knowledge retrieved from online databases which is used to inform the shrinkage towards a null SNP effect. The performance of this approach was investigated in a simulation study and a real data example where the true associations were known. It consistently outperformed the standard analysis, where SNPs are analysed separately using linear regression models. Second, I apply the approach developed to data from the large UK Biobank study to investigate the effects on lung function of variants located in 403 genes related to lung development. The results from this analysis were then replicated using three independent cohorts. The combination of the standard analysis with the Bayesian approach allowed the identification of 65 new variants in 31 different genes, which nearly doubles the number of known variants associated with lung function. Finally, I present Bioshrink, a user-friendly R Shiny application that is freely accessible and allows third-party users to apply the Bayesian approach to their own genetic association studies.
EPA Transcriptomic Assessment Product (ETAP) for Perfluoro-3-Methoxypropanoic Acid
Creators: name: Brennan, Amanda
name: Chang, Daniel
name: Cowden, John
name: Davidson-Fritz, Sarah
name: Dean, Jeffry
name: Devito, Michael
name: Ford, Jermaine
name: Everett, Logan
name: Harrill, Alison
name: Hester, Susan
name: Hughes, Michael
name: Lambert, Jason
name: Lizarraga, Lucina
name: Mezencev, Roman
name: MacMillan, Denise
name: Patlewicz, Grace
name: Chialton, Kristina
name: Thomas, Russell
name: Vitense, Kelsey
name: Wehmas, Leah
name: Renyer, Aero
name: Auerbach, Scott
name: Casey, Warren
Publisher: name: The United States Environmental Protection Agency’s Center for Computational Toxicology and Exposure
Year: 2024
Subjects: classificationCode: 321407
subject: Toxicology (incl. clinical toxicology)

description: The EPA Transcriptomic Assessment Product (ETAP) is a human health assessment that utilizes a standardized short-term in vivo study design and data analysis procedures to develop transcriptomic-based reference values for data poor chemicals. The reference value represents the daily dose of the chemical that would likely be without appreciable risk to human health over a lifetime. This dataset corresponds to the transcriptomic studies on perfluoro-3-methoxypropanoic acid (DTXSID70191136). More information about ETAP is available at: https://www.epa.gov/etap.Science Inventory, CCTE products: https://cfpub.epa.gov/si/si_public_search_results.cfm?advSearch=true&showCriteria=2&keyword=CCTE&TIMSType=&TIMSSubTypeID=&epaNumber=&ombCat=Any&dateBeginPublishedPresented=07/01/2017&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&DEID=&personName=&personID=&role=Any&journalName=&journalID=&publisherName=&publisherID=&sortBy=pubDate&count=25
Loxia cristata Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Aves
Passeriformes
Fringillidae
Loxia
Loxia cristata

description: Loxia cristata [spec. nov.]
L. albicans, fronte cristata, uropygio pedibusque rubris, rectricibus intermediis longissimis.
Habitat in Aethiopia. J. Burmannus.
Avis inter maximas sui generis. Crista Maris rubra, Feminae alba. Pectus in mare rubrum. Rectrices cinereae: intermediae duae duplo longiores.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 172, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Effects of Ram-Pressure from Intracluster Medium on the Star Formation Rate of Disk Galaxies in Clusters of Galaxies
Creators: name: Fujita, Yutaka
name: Nagashima, Masahiro
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Using a simple model of molecular cloud evolution, we have quantitatively estimated the change of star formation rate (SFR) of a disk galaxy falling radially into the potential well of a cluster of galaxies. The SFR is affected by the ram-pressure from the intracluster medium (ICM). As the galaxy approaches the cluster center, the SFR increases to twice the initial value, at most, in a cluster with high gas density and deep potential well, or with a central pressure of $\sim 10^{-2} cm^{-3} keV$ because the ram-pressure compresses the molecular gas of the galaxy. However, this increase does not affect the color of the galaxy significantly. Further into the central region of the cluster ($\lesssim 1$ Mpc from the center), the SFR of the disk component drops rapidly due to the effect of ram-pressure stripping. This makes the color of the galaxy redder and makes the disk dark. These effects may explain the observed color, morphology distribution and evolution of galaxies in high-redshift clusters. By contrast, in a cluster with low gas density and shallow potential well, or the central pressure of $\sim 10^{-3} cm^{-3} keV$, the SFR of a radially infalling galaxy changes less significantly, because neither ram-pressure compression nor stripping is effective. Therefore, the color of galaxies in poor clusters is as blue as that of field galaxies, if other environmental effects such as galaxy-galaxy interaction are not effective. The predictions of the model are compared with observations.
description: 19 pages, 9 figures, to appear in ApJ
Possibilistic (and other) notions of contextuality
Creators: name: Simmons, Andrew William
Publisher: name: Imperial College London
Year: 2018

description: Since Bell, Kochen and Specker formulated the first notions of contextuality, a number of frameworks have been created to help make philosophical and mathematical sense of the concept. Two of the most common are the Equivalence-based approach due to Spekkens, and the Sheaf-theoretic framework of Abramsky and Brandenburger. Each of these can support a hierarchy of strengths of contextuality, which can include possibilistic concepts. This thesis will explore the differences between the two approaches, and explore what can be demonstrated by using weaker notions of noncontextuality. Notions of noncontextuality are important for proving no-go theorems which highlight that many properties that are true of classical mechanics fail to be compatible with quantum predictions. Often, the notions of noncontextuality used are very strong assumptions, and even weaker flavours of noncontextuality can be used to draw the same, or similar conclusions. An important class of such notions are, possibilistic assumptions that only care about whether or not events are possible or impossible, rather than the exact Born rule probabilities that are applied to events. Even these weaker notions are often impossible to resolve with the logical structure and predictions of quantum theory. Contextuality has been demonstrated to be a resource for many quantum computational operations, and the contextual fraction has been shown to be an important resource. We introduce a metric that can differentiate between different quantum mechanical scenarios with contextual fraction 1, and demonstrate analogues of CHSH and Tsirelson bounds for this quantity. We also investigate the computational complexity of calculating the values of some metrics for nonlocality and contextuality, completing the classification of possibilistic nonlocality scenarios, as well as other metrics of nonlocality analogous to our metric of maximal contextuality.
Bose enhancement, the Liouville effective action and the high multiplicity tail in p-A collisions
Creators: name: Kovner, Alex
name: Skokov, Vladimir V.
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: In the framework of dense-dilute CGC approach we study fluctuations in the multiplicity of produced particles in p-A collisions. We show that the leading effect that drives the fluctuations is the Bose enhancement of gluons in the proton wave function. We explicitly calculate the moment generating function that resums the effects of Bose enhancement. We show that it can be understood in terms of the Liouville effective action for the composite field which is identified with the fluctuating density, or saturation momentum of the proton. The resulting probability distribution turns out to be very close to the gamma-distribution. We also calculate the first correction to this distribution which is due to pairwise Hanbury Brown-Twiss correlations of produced gluons.
description: 15 pages, 3 figures; version accepted for publication
A pulsational approach to the luminosity of Horizontal Branch stellar structures
Creators: name: De Santis, R.
name: Cassisi, S.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We discuss an alternative approach to constrain the absolute bolometric luminosity of Zero Age Horizontal Branch structures by using the observational pulsational properties of ab type RR Lyrae stars and theoretical expectations concerning both the relation connecting the pulsational properties of these variables to their evolutionary ones, as luminosity, mass and effective temperature and, also the location in the H-R diagram for the fundamental pulsators instability strip boundaries. Since the main goal of this work is to obtain an evaluation of the ZAHB bolometric luminosity as much as possible independent on stellar evolution theory, we have minimized the use of evolutionary prescriptions, being the only adopted evolutionary input the allowed mass range for fundamental pulsators. Nevertheless, the effects on our final results related to the use of these evolutionary prescriptions have been carefully checked. The reliability of the suggested method to obtain the ZAHB luminosity is shown by applying it to a selected sample of globular clusters (GCs), whose heavy elements abundance covers almost all the complete GCs metallicity range. The results obtained for the ZAHB bolometric luminosities have been compared with evolutionary prescriptions on such quite important quantity as given by recent evolutionary computations has been also performed. The existence of evident mismatches between current results and some evolutionary models has been verified and discussed.
description: 15 pages, 1 table, 15 figures, postscript file, To be published in MNRAS
New Near-Infrared Spectroscopy of the High Redshift Quasar B 1422+231 at z=3.62
Creators: name: Murayama, T.
name: Taniguchi, Y.
name: Evans, A. S.
name: Sanders, D. B.
name: Hodapp, K. -W.
name: Kawara, K.
name: Arimoto, N.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present new near-infrared (rest-frame UV-to-optical) spectra of the high redshift, gravitationally lensed quasar B 1422+231 (z=3.62). Diagnostic emission lines of FeII, [OIII]5007, and Hb, commonly used to determine the excitation, ionization, and chemical abundances of radio-quiet and radio-loud quasars, were detected. Our new data show that the ratio FeII(UV)/Hb=18.1+-4.6 and FeII(optical)/Hb=2.3+-0.6 are higher than those reported by Kawara et al. (1996) by factors of 1.6 and 3.3, respectively, although the ration [OIII]5007/Hb=0.19+-0.02 is nearly the same between the two measurements. The discrepancy of the line flux ratios between the measurements is likely due to improved data and fitting procedures rather that to intrinsic variability. While approximately half of the high-z quasars observed to date have much more extreme FeII(optical)/Hb ratios, the line ratio measured for B 422+231 are consistent with the observed range of FeII(optical) ratios of low-z quasars.
description: 5 pages, 1 table, 4 figures. To appear in The Astronomical Journal