cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of Variations in association of nasal microbiota with virulent and non-virulent strains of Glaesserella (Haemophilus) parasuis in weaning piglets
Creators: name: Mahmmod, Yasser
name: Correa-Fiz, Florencia
name: Aragon, Virginia
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 1. The results of univariable model analyses of virulent strains (A), non-virulent strains (B), and relative abundance of G. parasuis (C), expressed as natural logarithm at family level taxa. A Univariable logistic regression for potential risk factors and nasal microbiota at family level associated with the presence of virulent strains of G. parasuis (virGp) infection (P-value ≤ 0.25) in 51 piglets in 7 Spanish farms. B Univariable logistic regression for potential risk factors and nasal microbiota at family level associated with the presence of non-virulent strains of G. parasuis (non-virGp) infection (P-value ≤ 0.25) in 51 piglets in 7 Spanish farms. C Univariable linear regression for potential risk factors and nasal microbiota at family level associated with relative abundance of G. parasuis, expressed as natural logarithm, (P ≤ 0.25) in 51 piglets in 7 Spanish farms.
Geometric distinguishability measures limit quantum channel estimation and discrimination
Creators: name: Katariya, Vishal
name: Wilde, Mark M.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Physics (quant-ph)
subject: Information Theory (cs.IT)
subject: Mathematical Physics (math-ph)
subject: Statistics Theory (math.ST)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Quantum channel estimation and discrimination are fundamentally related information processing tasks of interest in quantum information science. In this paper, we analyze these tasks by employing the right logarithmic derivative Fisher information and the geometric Rényi relative entropy, respectively, and we also identify connections between these distinguishability measures. A key result of our paper is that a chain-rule property holds for the right logarithmic derivative Fisher information and the geometric Rényi relative entropy for the interval $α\in(0,1) $ of the Rényi parameter $α$. In channel estimation, these results imply a condition for the unattainability of Heisenberg scaling, while in channel discrimination, they lead to improved bounds on error rates in the Chernoff and Hoeffding error exponent settings. More generally, we introduce the amortized quantum Fisher information as a conceptual framework for analyzing general sequential protocols that estimate a parameter encoded in a quantum channel, and we use this framework, beyond the aforementioned application, to show that Heisenberg scaling is not possible when a parameter is encoded in a classical-quantum channel. We then identify a number of other conceptual and technical connections between the tasks of estimation and discrimination and the distinguishability measures involved in analyzing each. As part of this work, we present a detailed overview of the geometric Rényi relative entropy of quantum states and channels, as well as its properties, which may be of independent interest.
description: 170 pages, 7 figures, accepted for publication in Quantum Information Processing
Residence Time Distribution of Sand Grains in the 1-Dimensional Abelian Sandpile Model
Creators: name: Pradhan, Punyabrata
name: Nagar, Apoorva
Publisher: name: arXiv
Year: 2004
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study the probability distribution of residence time, $T$, of the sand grains in the one dimensional abelian sandpile model on a lattice of $L$ sites, for $T<>L^2$. The distribution function decays as $\exp(-\frac{K_LT}{L^2})$. We numerically calculate the coefficient $K_L$ for the value of $L$ upto 150 . Interestingly the distribution function has a scaling form $\frac{1}{L^a}f(\frac{T}{L^b})$ with $a \neq b$ for large $L$.
description: 4 pages, 3 figures
Additional file 8 of Iron in airway macrophages and infective exacerbations of chronic obstructive pulmonary disease
Creators: name: Ho, Terence
name: Nichols, Matthew
name: Nair, Gayatri
name: Radford, Katherine
name: Kjarsgaard, Melanie
name: Huang, Chynna
name: Bhalla, Anurag
name: Lavigne, Nicola
name: Mukherjee, Manali
name: Surette, Michael
name: Macri, Joseph
name: Nair, Parameswaran
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 8: Table S3: Negative binomial regression model.
Additional file 2 of Variations in association of nasal microbiota with virulent and non-virulent strains of Glaesserella (Haemophilus) parasuis in weaning piglets
Creators: name: Mahmmod, Yasser
name: Correa-Fiz, Florencia
name: Aragon, Virginia
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Ecology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 2. Illustration of the associations between the relative abundance of Glaesserella parasuis, expressed as natural logarithm in 51 piglets and significantly variables presented in the final model including farm management factors (production system and health status) and nasal microbiota members at family (A) and genus (B) taxa. A Plotting the association between the relative abundance of Glaesserella parasuis, expressed as natural logarithm in 51 piglets and significantly variables (P ≤ 0.05) presented in the final model including farm management factors (production system and health status) and nasal microbiota members at family level (Bacteroidaceae, Chitinophagaceae, Streptococcaceae, and Mycoplasmataceae). B Plotting the association between the relative abundance of Glaesserella parasuis, expressed as natural logarithm in 51 piglets and significantly variables (P ≤ 0.05) presented in the final model including farm management factors (production system and health status) and nasal microbiota members at genus level (Alloprevotella, Streptococcus, Clostridium XI, Oscillibacter, Kingella and Actinobacillus).
Plagusiidae Dana 1851
Creators: name: Guinot, Daniėle
Publisher: name: Zenodo
Year: 2007
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Malacostraca
Decapoda
Plagusiidae

description: Family Plagusiidae Dana, 1851  Plagusinae Dana, 1851: 288; 1852: 333, 368 (incorrect spelling).
Plagusiinae Miers, 1878: 147; Alcock, 1900: 289, 436; Guinot, 1978: 285; 1979: 106, 144, 151, 155, 206, 209; Manning & Holthuis, 1981: 238; Williams, 1984: 462; Hartnoll, 1992: 51; Ng, 1998: 1139; Guinot & Bouchard, 1998: 664.
Plagusiidae v. Sternberg & Cumberlidge, 1998: 120, 133; Schubart et al., 2000: 183, 184; 2002: 29; Martin & Davis, 2001: 75; Ng et al., 2001: 47; Davie, 2002: 436; Poore, 2004: 512; Števčić, 2005: 126; Schubart et al. 2006: 193, 198.
 Type genus: Plagusia Latreille, 1804 (type species Cancer depressus Fabricius, 1775, by monotypy and designation by Latreille, 1810: 422; gender feminine).
description: Published as part of Guinot, Daniėle, 2007, A new genus of the family Plagusiidae Dana, 1851, close to Plagusia Latreille, 1804 (Crustacea, Decapoda, Brachyura), pp. 27-33 in Zootaxa 1498 (1) on page 28, DOI: 10.11646/zootaxa.1498.1.2, http://zenodo.org/record/5086866
Screening properties of quark-gluon plasma obtained from distribution and correlation functions of the constituent quasiparticle model
Creators: name: Filinov, V.
name: Larkin, A.
name: Fortov, V.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences
subject: G.m

description: Based on the constituent quasiparticle model of quark-gluon plasma (QGP), the matrix elements of the density operator and the Wigner function in the color phase space are presented in form of color path integrals over Wiener and SU(3) group Haar measures. Monte Carlo calculations of quark and gluon momentum distributions and spatial pair distribution functions have been carried out for the strongly coupled QGP plasma in thermal equilibrium at zero baryon chemical potential. The Debye screening mass and the running coupling constant have been obtained from the spatial pair distribution function and are in agreement with the available lattice QCD data. At densities related to the average interparticle distance more than 0.4 fm the gluon bound states in the form of glueballs have been found. Comparison with the Maxwell Boltzmann distribution shows significant influence of interparticle interaction on high energy asymptotics of the momentum distribution functions, resulting in appearance of quantum tails. The new color pair correlation function has been introduced, and related new color screening mass has been discussed.
description: 14 pages, 14 figures,
A Barren Landscape?
Creators: name: Robbins, Daniel
name: Sethi, Savdeep
Publisher: name: arXiv
Year: 2004
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Astrophysics (astro-ph)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We consider the generation of a non-perturbative superpotential in F-theory compactifications with flux. We derive a necessary condition for the generation of such a superpotential in F-theory. For models with a single volume modulus, we show that the volume modulus is never stabilized by either abelian instantons or gaugino condensation. We then comment on how our analysis extends to a larger class of compactifications. From our results, it appears that among large volume string compactifications, metastable de Sitter vacua (should any exist) are non-generic.
description: 14 pages, comments added
Additional file 1 of Evaluation of peptide-rich root extracts of Calliandria portoriscensis (Jacq.) Benth (Mimosaceae) for in vitro antimicrobial activity and brine shrimp lethality
Creators: name: Omonike Ogbole
name: Nkiruka Ndabai
name: Toluwanimi Akinleye
name: Attah, Alfred
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Physiology
subject: FOS: Biological sciences
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: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Additional file 1. MALDI TOF MS data showing monoisotopic mass/charge ratios for the peptide-rich pre-purified aqueous extracts of Calliandra porturescensis collected from South-west Nigeria. Identified peptide masses ranges from 2.0 KDa to 2.6 KDa.
MOESM3 of Comprehensive profiling of alternative splicing landscape during cold acclimation in tea plant
Creators: name: Li, Yeyun
name: Mi, Xiaozeng
name: Zhao, Shiqi
name: Zhu, Junyan
name: Guo, Rui
name: Xia, Xiaobo
name: Liu, Lu
name: Liu, Shengrui
name: Wei, Chaoling
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Additional file 3: Table S3. The genome and sequencing sequence of the AS transcript.
Fano effect on the neutron elastic scattering by open-shell nuclei
Creators: name: Mizuyama, K.
name: Le, N. Nhu
name: Hao, T. V. Nhan
Publisher: name: arXiv
Year: 2019
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: By focusing on the asymmetric shape of cross section, we analyze the pairing effect on the partial wave components of cross section for neutron elastic scattering off stable and unstable nuclei within the Hartree-Fock-Bogoliubov (HFB) framework. Explicit expressions for Fano parameters $q_{lj}$ and $ε_{lj}$ have been derived and the pairing effects have been analyzed in term of these parameters, and the Fano effect was found on the neutron elastic scattering off the stable nucleus in terms of the pairing correlation. Fano effect was appeared as the asymmetric line-shape of the cross section caused by the small absolute value of $q_{lj}$ due to the small pairing effect on the deep-lying hole state of the stable nucleus. In the case of the unstable nuclei, the large $q_{lj}$ value is expected because of the small absolute value of the Fermi energy. The quasiparticle resonance with the large $q_{lj}$ forms the Breit-Wigner type shape in the elastic scattering cross section.
description: Submitted to Physical Review C
Freyella elegans
Creators: name: Jangoux, Michel
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Echinodermata
Asteroidea
Brisingida
Freyellidae
Freyella
Freyella elegans

description: spinosa Perrier, 1885, Freyella
Freyella spinosa Perrier, 1885: 5 ‒ Perrier, 1894: 85, pl. 7, figs 1-7.
Freyella elegans ‒ Clark & Downey 1992: 484.
CURRENT STATUS. — Freyella elegans (Verrill, 1884).
TYPE MATERIAL. — Mauritania • 1 syntype; station 96; off Mauritanian coast; Talisman expedition; 1883; 19°16’N, 20°20’W; depth 2330 m; MNHN-IE-2014-356 • 1 syntype; station 97; same as for preceding; 19°12’N, 20°17’W; depth 2324 m; MNHN-IE-2014-22 • 3 syntypes; same as for preceding; MNHN-IE-2014-431 • 1 syntype, same as for preceding; MNHN-IE-2014-277.
description: Published as part of Jangoux, Michel, 2022, The type specimens of extant asteroids (Echinodermata) in the Muséum national d'Histoire naturelle of Paris, pp. 259-334 in Zoosystema 44 (11) on page 318, DOI: 10.5252/zoosystema2022v44a11, http://zenodo.org/record/6616817
Three-mode entanglement by interlinked nonlinear interactions in optical $χ^{(2)}$ media
Creators: name: Ferraro, A.
name: Paris, M. G. A.
name: Allevi, A.
name: Andreoni, A.
name: Bondani, M.
name: Puddu, E.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We address the generation of fully inseparable three-mode entangled states of radiation by interlinked nonlinear interactions in $χ^{(2)}$ media. We show how three-mode entanglement can be used to realize symmetric and asymmetric telecloning machines, which achieve optimal fidelity for coherent states. An experimental implementation involving a single nonlinear crystal where the two interactions take place simultaneously is suggested. Preliminary experimental results showing the feasibility and the effectiveness of the interaction scheme with seeded crystal are also presented.
description: Revised Version. To appear in JOSA B
Topological modes in relativistic hydrodynamics
Creators: name: Liu, Yan
name: Sun, Ya-Wen
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: We show that gapless modes in relativistic hydrodynamics could become topologically nontrivial by weakly breaking the conservation of energy momentum tensor in a specific way. This system has topological semimetal-like crossing nodes in the spectrum of hydrodynamic modes that require the protection of a special combination of translational and boost symmetries in two spatial directions. We confirm the nontrivial topology from the existence of an undetermined Berry phase. These energy momentum non-conservation terms could naturally be produced by an external gravitational field that comes from a reference frame change from the original inertial frame, i.e. by fictitious forces in a non-inertial reference frame. This non-inertial frame is the rest frame of an accelerating observer moving along a trajectory of a helix. This suggests that topologically trivial modes could become nontrivial by being observed in a special non-inertial reference frame, and this fact could be verified in laboratories, in principle. Finally, we propose a holographic realization of this system.
description: 8 pages, 2 figures; v2: published version
Davusia Guinot 2007, n.gen.
Creators: name: Guinot, Daniėle
Publisher: name: Zenodo
Year: 2007
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Malacostraca
Decapoda
Plagusiidae
Davusia

description: Genus Davusia n.gen.
 Plagusia — Dana, 1852 pro parte: 368; Healy & Yaldwyn, 1970 pro parte: 98; Guinot, 1979 pro parte: 144, 151, 209; Dawson, 1987: 41, 43; Guinot & Bouchard 1998 pro parte: 664; Schubart & Ng, 2000 pro parte: 334; Davie, 2002 pro parte: 439; Poore, 2004 pro parte: 513, 514. (Non Plagusia Latreille, 1804).
 Type species: Plagusia glabra Dana, 1852, by present designation. Gender feminine.
Other species included: Monotypic.
Etymology: It is a pleasure to dedicate this genus to my colleague P.J.F. Davie in recognition for his important contribution to carcinology and who had also recognized the unique generic status of this Australian species (Davie, pers. com.). Gender: feminine.
description: Published as part of Guinot, Daniėle, 2007, A new genus of the family Plagusiidae Dana, 1851, close to Plagusia Latreille, 1804 (Crustacea, Decapoda, Brachyura), pp. 27-33 in Zootaxa 1498 (1) on page 28, DOI: 10.11646/zootaxa.1498.1.2, http://zenodo.org/record/5086866
ACBAR: The Arcminute Cosmology Bolometer Array Receiver
Creators: name: Runyan, M. C.
name: Ade, P. A. R.
name: Bhatia, R. S.
name: Bock, J. J.
name: Daub, M. D.
name: Goldstein, J. H.
name: Haynes, C. V.
name: Holzapfel, W. L.
name: Kuo, C. L.
name: Lange, A. E.
name: Leong, J.
name: Lueker, M.
name: Newcomb, M.
name: Peterson, J. B.
name: Ruhl, J.
name: Sirbi, G.
name: Torbet, E.
name: Tucker, C.
name: Turner, A. D.
name: Woolsey, D.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We describe the Arcminute Cosmology Bolometer Array Receiver (ACBAR); a multifrequency millimeter-wave receiver designed for observations of the Cosmic Microwave Background (CMB) and the Sunyaev-Zel'dovich effect in clusters of galaxies. The ACBAR focal plane consists of a 16-pixel, background-limited, 240 mK bolometer array that can be configured to observe simultaneously at 150, 220, 280, and 350 GHz. With 4-5' FWHM Gaussian beam sizes and a 3 degree azimuth chop, ACBAR is sensitive to a wide range of angular scales. ACBAR was installed on the 2 m Viper telescope at the South Pole in January 2001. We describe the design of the instrument and its performance during the 2001 and 2002 observing seasons.
description: 59 pages, 16 figures -- updated to reflect version published in ApJS
Additional file 1 of Ultra-processed food and incident type 2 diabetes: studying the underlying consumption patterns to unravel the health effects of this heterogeneous food category in the prospective Lifelines cohort
Creators: name: Duan, Ming-Jie
name: Vinke, Petra C.
name: Navis, Gerjan
name: Corpeleijn, Eva
name: Dekker, Louise H.
Publisher: name: figshare
Year: 2022
Subjects: subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1: Figures S1-S3 and Tables S1-S10. Fig. S1. Timeline of data collection of the Lifelines cohort study. Fig. S2. Study flow chart for exclusions and diagnosis of type 2 diabetes cases. Fig. S3. Overall contribution of ultra-processed food to total diet. Table S1. Categorization of food-items in ultra-processed food categories. Table S2. Calculation of PROCAM diabetes risk score algorithm. Table S3. Contribution of ultra-processed food sub-groups to overall intake of ultra-processed food. Table S4. Sensitivity analysis on missing data - ultra-processed food intake and incident type 2 diabetes. Table S5. Sensitivity analysis on excluding participants with only 24 months of follow-up. Table S6. Sensitivity analysis using energy-adjusted intake of ultra-processed food. Table S7. Factor loadings of ultra-processed food products within their corresponding consumption patterns. Table S8. Baseline characteristics across different ultra-processed food consumption patterns. Table S9. Sensitivity analysis of ultra-processed food consumption patterns using random half sample. Table S10. Sensitivity analysis on missing data - ultra-processed food intake/consumption patterns and diabetes risk at baseline.
Anharmonicity and Ultra-Low Thermal Conductivity in Lead-Free Halide Double Perovskites
Creators: name: Klarbring, Johan
name: Hellman, Olle
name: Abrikosov, Igor A.
name: Simak, Sergei I.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The lead-free halide double perovskite class of materials offers a promising venue for resolving issues related to toxicity of Pb and long-term stability of the lead-containing halide perovskites. We present a first-principles study of the lattice vibrations in Cs$_2$AgBiBr$_6$ , the prototypical compound in this class, and show that the lattice dynamics of Cs$_2$AgBiBr$_6$ is highly anharmonic, largely in regards to tilting of AgBr$_6$ and BiBr$_6$ octahedra. Using an energy and temperature dependent phonon spectral function, we then show how the experimentally observed cubic-to-tetragonal phase transformation is caused by the collapse of a soft phonon branch. We finally reveal that the softness and anharmonicity of Cs$_2$AgBiBr$_6$ yield an ultra-low thermal conductivity, unexpected of high symmetry cubic structures.
Coulomb scattering of quantum dipoles in QED
Creators: name: Blok, B.
Publisher: name: arXiv
Year: 2004
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We calculate the total scattering cross-section of a dynamical quantum electrically neutral dipole in QED of the infinitely heavy charge and of the infinitely heavy dipole in the leading order in electromagnetic coupling constant.
description: 7 pages, no figures
Calibrating the Galaxy Halo - Black Hole Relation Based on the Clustering of Quasars
Creators: name: Wyithe, Stuart
name: Loeb, Abraham
Publisher: name: arXiv
Year: 2004
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The observed number counts of quasars may be explained either by long-lived activity within rare massive hosts, or by short-lived activity within smaller, more common hosts. It has been argued that quasar lifetimes may therefore be inferred from their clustering length, which determines the typical mass of the quasar host. Here we point out that the relationship between the mass of the black-hole and the circular velocity of its host dark-matter halo is more fundamental to the determination of the clustering length. In particular, the clustering length observed in the 2dF quasar redshift survey is consistent with the galactic halo - black-hole relation observed in local galaxies, provided that quasars shine at ~10-100% of their Eddington luminosity. The slow evolution of the clustering length with redshift inferred in the 2dF quasar survey favors a black-hole mass whose redshift-independent scaling is with halo circular velocity, rather than halo mass. These results are independent from observations of the number counts of bright quasars which may be used to determine the quasar lifetime and its dependence on redshift. We show that if quasar activity results from galaxy mergers, then the number counts of quasars imply an episodic quasar lifetime that is set by the dynamical time of the host galaxy rather than by the Salpeter time. Our results imply that as the redshift increases, the central black-holes comprise a larger fraction of their host galaxy mass and the quasar lifetime gets shorter.
description: 10 pages, 5 figures. Submitted to ApJ
Soil Biogeochemical Cycle Couplings Inferred from a Function-Taxon Network
Creators: name: Ma, Bin
name: Erinne Stirling
name: Yuanhui Liu
name: Kankan Zhao
name: Jizhong Zhou
name: Brajesh K Singh
name: Caixian Tang
name: Dahlgren, Randy A
name: Jianming Xu
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: Soil biogeochemical cycles and their interconnections play a critical role in regulating functions and services of environmental systems. However, the coupling of soil biogeochemical processes with their mediating microbes remains poorly understood. Here, we identified key microbial taxa regulating soil biogeochemical processes by exploring biomarker genes and taxa of contigs assembled from metagenomes of forest soils collected along a latitudinal transect (18° N to 48° N) in eastern China. Among environmental and soil factors, soil pH was a sensitive indicator for functional gene composition and diversity. A function-taxon bipartite network inferred from metagenomic contigs identified the microbial taxa regulating coupled biogeochemical cycles between carbon and phosphorus, nitrogen and sulfur, and nitrogen and iron. Our results provide novel evidence for the coupling of soil biogeochemical cycles, identify key regulating microbes, and demonstrate the efficacy of a new approach to investigate the processes and microbial taxa regulating soil ecosystem functions.
Astraeus I: The interplay between galaxy formation and reionization
Creators: name: Hutter, Anne
name: Dayal, Pratika
name: Yepes, Gustavo
name: Gottlöber, Stefan
name: Legrand, Laurent
name: Ucci, Graziano
Publisher: name: arXiv
Year: 2020
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We introduce a new self-consistent model of galaxy evolution and reionization, ASTRAEUS (semi-numerical rAdiative tranSfer coupling of galaxy formaTion and Reionization in N-body dArk mattEr simUlationS), which couples a state-of-the-art N-body simulation with the semi-analytical galaxy evolution DELPHI and the semi-numerical reionization scheme CIFOG. ASTRAEUS includes all the key processes of galaxy formation and evolution (including accretion, mergers, supernova and radiative feedback) and follows the time and spatial evolution of the ionized regions in the intergalactic medium (IGM). Importantly, it explores different radiative feedback models that cover the physically plausible parameter space, ranging from a weak and delayed to a strong and immediate reduction of gas mass available for star formation. From our simulation suite that covers the different radiative feedback prescriptions and ionization topologies, we find that radiative feedback continuously reduces star formation in galaxies with $M_h<10^{9.5}M_{\odot}$ upon local reionization; larger mass halos are unaffected even for the strongest and immediate radiative feedback cases during reionization. For this reason, the ionization topologies of different radiative feedback scenarios differ only on scales smaller than $1-2$Mpc, and significant deviations are only found when physical parameters (e.g. the escape fraction of ionizing photons) are altered based on galactic properties. Finally, we find observables (the ultra-violet luminosity function, stellar mass function, reionization histories and ionization topologies) are hardly affected by the choice of the used stellar population synthesis models that either model single stars or binaries.
description: 26 pages, 16 figures, accepted for publication in MNRAS
Experimental demonstration of a high quality factor photonic crystal microcavity
Creators: name: Srinivasan, Kartik
name: Barclay, Paul E.
name: Painter, Oskar
name: Chen, Jianxin
name: Cho, Alfred Y.
name: Gmachl, Claire
Publisher: name: arXiv
Year: 2003
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Sub-threshold measurements of a photonic crystal (PC) microcavity laser operating at 1.3 microns show a linewidth of 0.10 nm, corresponding to a quality factor Q ~ 1.3x10^4. The PC microcavity mode is a donor-type mode in a graded square lattice of air holes, with a theoretical Q ~ 10^5 and mode volume Veff ~ 0.25 cubic half-wavelengths in air. Devices are fabricated in an InAsP/InGaAsP multi-quantum well membrane and are optically pumped at 830 nm. External peak pump power laser thresholds as low as 100 microWatts are also observed.
MOESM10 of Crowdsourcing in health and medical research: a systematic review
Creators: name: Wang, Cheng
name: Han, Larry
name: Stein, Gabriella
name: Day, Suzanne
name: Bien-Gund, Cedric
name: Mathews, Allison
name: Ong, Jason
name: Zhao, Pei-Zhen
name: Wei, Shu-Fang
name: Walker, Jennifer
name: Chou, Roger
name: Lee, Amy
name: Chen, Angela
name: Bayus, Barry
name: Tucker, Joseph
Publisher: name: figshare
Year: 2020
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 10: Table S16. GRADE evidence profile for studies exploring out-of-hospital CPR.
Additional file 2 of High-throughput sequencing of virus-infected Cucurbita pepo samples revealed the presence of Zucchini shoestring virus in Zimbabwe
Creators: name: Karavina, Charles
name: Ibaba, Jacques
name: Gubba, Augustine
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
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: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 2. Amino acid sequence identities of the Zucchini shoestring virus (ZSSV) isolates. Table displaying the amino acid sequence identities in percentage between all ZSSV isolates available on GenBank.
3D dynamical evolution of the interstellar gas in the Gould Belt
Creators: name: Perrot, Christophe A.
name: Grenier, Isabelle A.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The dynamical evolution of the Gould Belt has been modelled in 3D and confronted to the spatial and velocity distributions of all HI and H2 clouds found within a few hundred parsecs from the Sun and to the Hipparcos distances of the nearby OB associations. The model describes the expansion of a shock wave that sweeps momentum from the ambient medium and it includes the effects of the Galactic differential rotation and its gravitational torque, as well as interstellar density gradients within and away from the Galactic plane, possible fragmentation and drag forces in the late stages, and an initial rotation of the system. The best fit to the data yields values for the current Belt semi-axes of 373 +- 5 pc and 233 +- 5 pc, and an inclination of 17.2 +- 0.5 degrees, in agreement with earlier results. A different Belt orientation, however, results from new H2 data and distance information. The present Belt rim is found to coincide with most of the nearby OB associations and H2 clouds, but its expansion bears little relation to the average association velocities. An initial kinetic energy of (1.0 +- 0.1) 10^(45) J and an expansion age of 26.4 +- 0.4 Myr are required, in agreement with earlier 2D estimates. The factor of 2 discrepancy between the Belt dynamical age and its stellar nuclear age could not be solved by adding a vertical dimension in the expansion, drag forces, fragmentation, or an initial rotation. Allowing the Belt to cross the Galactic disc in the early stages requires a longer age of 52 Myr, but yields a very poor fit to the data.
description: 15 pages, 9 figures, accepted for publication in Astronomy & Astrophysics
Additional file 2 of Lipocalin-2 promotes NSCLC progression by activating the JAK2/STAT3 signaling pathway
Creators: name: Zhang, Jinjin
name: Xu, Qin
name: Sun, Gengyun
Publisher: name: figshare
Year: 2025
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Supplementary Material 2
New plots and parameter degeneracies in neutrino oscillations
Creators: name: Yasuda, Osamu
Publisher: name: arXiv
Year: 2004
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: It is shown that eightfold degeneracy in neutrino oscillations is easily seen by plotting constant probabilities in the $(\sin^22θ_{13}, 1/s^2_{23})$ plane. Using this plot, we discuss how an additional long baseline measurement resolves degeneracies after the JPARC experiment measures the oscillation probabilities $P(ν_μ\toν_e)$ and $P(\barν_μ\to\barν_e)$ at $|Δm^2_{31}|L/4E=π/2$. By measuring $P(ν_μ\toν_e)$ or $P(\barν_μ\to\barν_e)$, the sgn($Δm_{31}^2$) ambiguity is resolved better at longer baselines and the $δ\leftrightarrowπ-δ$ ambiguity is resolved better when $||Δm^2_{31}|L/4E-π/2|$ is larger. The $θ_{23}$ ambiguity may be resolved as a byproduct if $||Δm^2_{31}|L/4E-π|$ is small and the CP phase $δ$ turns out to satisfy $|\cos(δ+|Δm^2_{31}|L/4E)|\sim1$. It is pointed out that the low energy option ($E\sim$1GeV) at the off-axis NuMI experiment may be useful in resolving these ambiguities. The $ν_e\toν_τ$ channel offers a promising possibility which may potentially resolve all the ambiguities.
description: 29 pages, 12 sets of figures. For "Focus on Neutrino Physics" issue of New Journal of Physics
Additional file 1 of High-throughput sequencing of virus-infected Cucurbita pepo samples revealed the presence of Zucchini shoestring virus in Zimbabwe
Creators: name: Karavina, Charles
name: Ibaba, Jacques
name: Gubba, Augustine
Publisher: name: figshare
Year: 2020
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 1. Nucleotide sequence identities of the Zucchini shoestring virus (ZSSV) isolates. Table displaying the nucleotide sequence identities in percentage between all ZSSV isolates available on GenBank.
Tracing the Dynamical Mass in Galaxy Disks Using HI Velocity Dispersion and its Implications for the Dark Matter Distribution in Galaxies
Creators: name: Das, Mousumi
name: McGaugh, Stacy
name: Ianjamasimanana, Roger
name: Schombert, James
name: Dwarakanath, K. S.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present a method to derive the dynamical mass of face-on galaxy disks using their neutral hydrogen (HI) velocity dispersion. We have applied the method to nearby, gas rich galaxies that have extended HI gas disks and have low inclinations. The galaxy sample includes 4 large disk galaxies; NGC628, NGC6496, NGC3184, NGC4214 and 3 dwarf galaxies DDO46, DDO63 and DDO187. We have used archival data from the THINGS and LITTLE THINGS surveys to derive the HI gas distributions and SPITZER mid-infrared images to determine the stellar disk mass distributions. We examine the disk dynamical and baryonic mass ratios in the extreme outer disks where there is HI gas but no visible stellar disk. We find that for the large galaxies the disk dynamical and Hi gas mass surface densities are comparable in the outer disks. But in the smaller dwarf galaxies, for which the total HI gas mass dominates the baryonic mass i.e. M(HI)>M(stars), the disk dynamical mass is much larger than the baryonic mass. For these galaxies there must either be a very low luminosity stellar disk which provides the vertical support for the HI gas disk or there is halo dark matter associated with their disks, which is possible if the halo has an oblate shape so that the inner part of the dark matter halo is concentrated around the disk. Our results are important for explaining the equilibrium of HI disks in the absence of stellar disks, and is especially important for gas rich, dwarf galaxies that appear to have significant dark matter masses associated with their disks.
description: 13 pages, 4 figures and 2 tables. To appear in ApJ
Folsomides semiparvulus Fjellberg 1993
Creators: name: Abrantes, Eduardo Assis
name: Mendonça, Maria Cleide De
Publisher: name: Zenodo
Year: 2007
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Entognatha
Collembola
Isotomidae
Folsomides
Folsomides semiparvulus

description: Folsomides semiparvulus Fjellberg, 1993
 Material examined. Brazil, Restinga de Maricá, Maricá City, Rio de Janeiro State, 5 specimens in slides Nº 1278 CM / MNRJ, 28.i.2003, 18 specimens in slides Nº 1279 CM / MNRJ, 28.i.2003, L.H. Fernandes & E.A. Abrantes. coll. Collected in sand dunes, first record to Brazil.
 Remarks. This species, originally described for “Punta del Hidalgo ” (Teneriff), later recorded to México (Kováč & Palacios-Vargas 1996), was found together with F. parvulus Stach, 1922 The examination of the material, agree with the original description.
description: Published as part of Abrantes, Eduardo Assis & Mendonça, Maria Cleide De, 2007, New species and a new record of Isotomidae (Collembola) from the coast of Brazil, pp. 55-60 in Zootaxa 1500 (1) on page 58, DOI: 10.11646/zootaxa.1500.1.2, http://zenodo.org/record/5088000
Trapping and manipulating neutral atoms with electrostatic fields
Creators: name: Krüger, P.
name: Luo, X.
name: Klein, M. W.
name: Brugger, K.
name: Haase, A.
name: Wildermuth, S.
name: Groth, S.
name: Bar-Joseph, I.
name: Folman, R.
name: Schmiedmayer, J.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We report on experiments with cold thermal $^7$Li atoms confined in combined magnetic and electric potentials. A novel type of three-dimensional trap was formed by modulating a magnetic guide using electrostatic fields. We observed atoms trapped in a string of up to six individual such traps, a controlled transport of an atomic cloud over a distance of 400$μ$m, and a dynamic splitting of a single trap into a double well potential. Applications for quantum information processing are discussed.
description: 4 pages, 4 figures
Gamma-Ray Bursts: The Underlying Model
Creators: name: Waxman, E.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: A pedagogical derivation is presented of the ``fireball'' model of gamma-ray bursts, according to which the observable effects are due to the dissipation of the kinetic energy of a relativistically expanding wind, a ``fireball.'' The main open questions are emphasized, and key afterglow observations, that provide support for this model, are briefly discussed. The relativistic outflow is, most likely, driven by the accretion of a fraction of a solar mass onto a newly born (few) solar mass black hole. The observed radiation is produced once the plasma has expanded to a scale much larger than that of the underlying ``engine,'' and is therefore largely independent of the details of the progenitor, whose gravitational collapse leads to fireball formation. Several progenitor scenarios, and the prospects for discrimination among them using future observations, are discussed. The production in gamma- ray burst fireballs of high energy protons and neutrinos, and the implications of burst neutrino detection by kilometer-scale telescopes under construction, are briefly discussed.
description: In "Supernovae and Gamma Ray Bursters", ed. K. W. Weiler, Lecture Notes in Physics, Springer-Verlag (in press); 26 pages, 2 figures
Additional file 6 of Stimulants associated with reduced risk of hospitalization for motor vehicle accident injury in patients with obstructive sleep apnea-a nationwide cohort study
Creators: name: Yi-Chang Lin
name: Tien-Yu Chen
name: Wu-Chien Chien
name: Chi-Hsiang Chung
name: Hsin-An Chang
name: Kao, Yu-Chen
name: Chien-Sung Tsai
name: Chih-Sheng Lin
name: Nian-Shen Tzeng
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Additional file 6: Table S5. Distribution of Treatment surgery.
Dataset for reproducing results from "Unsupervised learning of pixel clustering in Mueller matrix images for mapping microstructural features in pathological tissues"
Creators: name: Wan, Jiachen
name: Dong, Yang
name: Yao, Yue
name: Xiao, Weijin
name: Huang, Ruqi
name: Xue, Jin-Hao
name: Peng, Ran
name: Pei, Haojie
name: Tian, Xuewu
name: Liao, Ran
name: He, Honghui
name: Zeng, Nan
name: Li, Chao
name: Ma, Hui
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 400304
subject: Biomedical imaging

description: This dataset suppots the manuscript named "Mapping microstructural features of pathological tissues by pixel clustering of Mueller matrix images". It contains the minimum data requied to reproduce the results in the paper. 
The dataset consists 222 ROIs from hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) samples, numbered from 1 to 222 respectively. Each .npz file includes several attributes: (1) the Mueller matrix image of the respective region (named m11, m12, etc.), (2) the pathological descriptive label of the region (tissue_type_label and cancer_type_label), as well as (3) availible H&E-stained images of the corresponding region (HE_img).
Identifying non-affine softening modes in glassy polymer networks: A pathway to chemical design
Creators: name: Elder, Robert M.
name: Zaccone, Alessio
name: Sirk, Timothy W.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Using molecular simulations and theory, we develop an explicit mapping of the contribution of molecular relaxation modes in glassy thermosets to the shear modulus, where the relaxations were tuned by altering the polarity of side groups. Specifically, motions at the domain, segmental, monomer, and atomic levels are taken from molecular dynamics snapshots and directly linked with the viscoelasticity through a framework based in the lattice dynamics of amorphous solids. This unique approach provides direct insight into the roles of chemical groups in the stress response, including the timescale and spatial extent of relaxations during mechanics. Two thermoset networks with differing concentrations of polar side groups were examined, dicyclopentadiene (DCPD) and 5-norbornene-2-methanol (NBOH). A machine learning method is found to be effective for quantifying large-scale correlated motions while more local chemical relaxations are readily identified by direct inspection. The approach is broadly applicable and enables rapid predictions of the frequency-dependent modulus for any glass.
Additional file 1 of Sublethal enteroviral infection exacerbates disease progression in an ALS mouse model
Creators: name: Xue, Yuan Chao
name: Liu, Huitao
name: Mohamud, Yasir
name: Bahreyni, Amirhossein
name: Zhang, Jingchun
name: Cashman, Neil R.
name: Luo, Honglin
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Neuroscience
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: 60506 Virology
subject: Computational Biology

description: Additional file 1: Fig. S1. Sublethal CVB3 infection leads to ALS-related pathologies in vivo. Representative images of SQSTM1/p62 and ubiquitin immunohistochemical staining in the hippocampus regions of the brain from mock- and CVB3-injected C57BL/6J or SOD1G85R mice at day 10 PI or week 60 PI (or humane endpoint) as indicated. The red arrows indicate SQSTM1/p62 or ubiquitin positive inclusions. Black boxes on the top right illustrate the enlarged images. Scale bar = 100 μm.
Additional file 7 of Stimulants associated with reduced risk of hospitalization for motor vehicle accident injury in patients with obstructive sleep apnea-a nationwide cohort study
Creators: name: Yi-Chang Lin
name: Tien-Yu Chen
name: Wu-Chien Chien
name: Chi-Hsiang Chung
name: Hsin-An Chang
name: Kao, Yu-Chen
name: Chien-Sung Tsai
name: Chih-Sheng Lin
name: Nian-Shen Tzeng
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Additional file 7: Table S6. Factors of traffic injury by using Cox regression among OSA patients in different treatments.
Lanthanide-radical magnetic coupling in [LnPc$_2$]$^0$: Competing exchange mechanisms captured via ab initio multi-reference calculations
Creators: name: Huang, Haibei
name: Heuvel, Willem Van den
name: Soncini, Alessandro
Publisher: name: arXiv
Year: 2020
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Atomic and Molecular Clusters (physics.atm-clus)
subject: Chemical Physics (physics.chem-ph)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We present a computational investigation of the intramolecular exchange coupling in [LnPc$_2$]$^0$ (Ln = Tb, Dy, Ho, and Er) between the Ln$^{3+}$ 4f electrons and the spin-1/2 radical on the phthalocyanine ligands. A series of ab initio multi-configurational/multi-reference Complete/Restricted Active Space Self-Consistent-Field calculations (CASSCF/RASSCF), including non-perturbative spin--orbit coupling, were performed on [LnPc$_2$]$^0$ and on the smaller model compound [LnPz$_2$]$^0$. We find that the exchange coupling mechanisms are restricted by symmetry, but also dependent on the spin polarization effect triggered by the Pc$_2$ ligands $π$--$π^*$ excitations. The calculated exchange splittings are small, amounting to at most a few cm$^{-1}$, in disagreement with previous literature reports of strong antiferromagnetic coupling, but in good agreement with recent EPR experiments on [TbPc$_2$]$^0$. Furthermore, the coupling strength is found to decrease from [TbPc$_2$]$^0$ to [ErPc$_2$]$^0$, with decreasing number of unpaired electron spins in the lanthanide ground (Hund's rule) Russell--Saunders term.
description: 20 pages, 2 figures