cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4290758
title: Development of an RT-qPCR assay for the specific detection of a distinct genetic lineage of the infectious bursal disease virus

description: The infectious bursal disease virus (IBDV) is a major health threat to the world’s poultry industry despite intensive controls including proper biosafety practices and vaccination. IBDV (<i>Avibirnavirus, Birnaviridae</i>) is a non-enveloped virus with a bisegmented double-stranded RNA genome. The virus is traditionally classified into classic, variant and very virulent strains, each with different epidemiological relevance and clinical implications. Recently, a novel worldwide spread genetic lineage was described and denoted as distinct (d) IBDV. Here, we report the development and validation of a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay for the specific detection of dIBDVs in the global poultry industry. The assay employs a TaqMan-MGB probe that hybridizes with a unique molecular signature of dIBDV. The assay successfully detected all the assessed strains belonging to the dIBDV genetic lineage, showing high specificity and absence of cross-reactivity with non-dIBDVs, IBDV-negative samples and other common avian viruses. Using serial dilutions of <i>in vitro</i>-transcribed RNA we obtained acceptable PCR efficiencies and determination coefficients, and relatively small intra- and inter-assay variability. The assay demonstrated a wide dynamic range between 10<sup>3</sup> and 10<sup>8</sup> RNA copies/reaction. This rapid, specific and quantitative assay is expected to improve IBDV surveillance and control worldwide and to increase our understanding of the molecular epidemiology of this economically detrimental poultry pathogen.
DOI: 10.6084/m9.figshare.4290758.v1
title: Development of an RT-qPCR assay for the specific detection of a distinct genetic lineage of the infectious bursal disease virus

description: The infectious bursal disease virus (IBDV) is a major health threat to the world’s poultry industry despite intensive controls including proper biosafety practices and vaccination. IBDV (<i>Avibirnavirus, Birnaviridae</i>) is a non-enveloped virus with a bisegmented double-stranded RNA genome. The virus is traditionally classified into classic, variant and very virulent strains, each with different epidemiological relevance and clinical implications. Recently, a novel worldwide spread genetic lineage was described and denoted as distinct (d) IBDV. Here, we report the development and validation of a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay for the specific detection of dIBDVs in the global poultry industry. The assay employs a TaqMan-MGB probe that hybridizes with a unique molecular signature of dIBDV. The assay successfully detected all the assessed strains belonging to the dIBDV genetic lineage, showing high specificity and absence of cross-reactivity with non-dIBDVs, IBDV-negative samples and other common avian viruses. Using serial dilutions of <i>in vitro</i>-transcribed RNA we obtained acceptable PCR efficiencies and determination coefficients, and relatively small intra- and inter-assay variability. The assay demonstrated a wide dynamic range between 10<sup>3</sup> and 10<sup>8</sup> RNA copies/reaction. This rapid, specific and quantitative assay is expected to improve IBDV surveillance and control worldwide and to increase our understanding of the molecular epidemiology of this economically detrimental poultry pathogen.
DOI: 10.6084/m9.figshare.4290752
title: Intertwined superfluid and density wave order in two dimensional 4He

description: Superfluidity is a manifestation of the operation of the laws of quantum mechanics on a macroscopic scale. The conditions under which superfluidity becomes manifest have been extensively explored experimentally in both quantum liquids (liquid <sup>4</sup>He being the canonical example) and ultra-cold atomic gases ( 1, 2), including as a function of dimensionality ( 3,4). Of particular interest is the hitherto unresolved question whether a solid can be superfluid ( 5, 6). Here we report the identification of a new state of quantum matter with intertwined superfluid and density wave order in a system of two-dimensional bosons subject to a triangular lattice potential. Using a torsional oscillator we have measured the superfluid response of the second atomic layer of <sup>4</sup>He adsorbed on the surface of graphite, over a wide temperature range down to 2 mK. Superfluidity is observed over a narrow range of film densities, emerging suddenly and subsequently collapsing towards a quantum critical point. The unusual temperature dependence of the superfluid density in the limit of zero temperature and the absence of a clear superfluid onset temperature are explained, self-consistently, by an ansatz for the excitation spectrum, reflecting density wave order, and a quasi-condensate wave function breaking both gauge and translational symmetry. <br> 1. Leggett, A. J., <i>Quantum Liquids</i> (Oxford University Press, London, 2006). 2. Nozieres P & Pines , D., <i>The Theory of Quantum Liquids Vol. II</i> (Addison-Wesley, 1990). 3. Bishop, D. J. & Reppy, J. D., Study of the superfluid transition in two-dimensional 4He films. <i>Phys. Rev. Lett.</i> <b>40</b>, 1727-1730 (1978). 4. Hadzibabic, Z., Kruger, P., Cheneau, M., Battelier, B. & Dalibard, J., Berezinskii-Kosterlitz-Thouless crossover in a trapped atomic gas. <i>Nature</i> <b>441</b>, 1118-1121 (2006). 5. Leggett, A. J., Can a solid be superfluid? <i>Phys. Rev. Lett. </i><b>25</b>, 1543-1546 (1970). 6. Balibar, S., The enigma of supersolidity. <i>Nature</i> <b>464</b>, 176-182 (2010). <br><br><br><br> <br>
DOI: 10.6084/m9.figshare.4290752.v1
title: Intertwined superfluid and density wave order in two dimensional 4He

description: Superfluidity is a manifestation of the operation of the laws of quantum mechanics on a macroscopic scale. The conditions under which superfluidity becomes manifest have been extensively explored experimentally in both quantum liquids (liquid <sup>4</sup>He being the canonical example) and ultra-cold atomic gases ( 1, 2), including as a function of dimensionality ( 3,4). Of particular interest is the hitherto unresolved question whether a solid can be superfluid ( 5, 6). Here we report the identification of a new state of quantum matter with intertwined superfluid and density wave order in a system of two-dimensional bosons subject to a triangular lattice potential. Using a torsional oscillator we have measured the superfluid response of the second atomic layer of <sup>4</sup>He adsorbed on the surface of graphite, over a wide temperature range down to 2 mK. Superfluidity is observed over a narrow range of film densities, emerging suddenly and subsequently collapsing towards a quantum critical point. The unusual temperature dependence of the superfluid density in the limit of zero temperature and the absence of a clear superfluid onset temperature are explained, self-consistently, by an ansatz for the excitation spectrum, reflecting density wave order, and a quasi-condensate wave function breaking both gauge and translational symmetry. <br> 1. Leggett, A. J., <i>Quantum Liquids</i> (Oxford University Press, London, 2006). 2. Nozieres P & Pines , D., <i>The Theory of Quantum Liquids Vol. II</i> (Addison-Wesley, 1990). 3. Bishop, D. J. & Reppy, J. D., Study of the superfluid transition in two-dimensional 4He films. <i>Phys. Rev. Lett.</i> <b>40</b>, 1727-1730 (1978). 4. Hadzibabic, Z., Kruger, P., Cheneau, M., Battelier, B. & Dalibard, J., Berezinskii-Kosterlitz-Thouless crossover in a trapped atomic gas. <i>Nature</i> <b>441</b>, 1118-1121 (2006). 5. Leggett, A. J., Can a solid be superfluid? <i>Phys. Rev. Lett. </i><b>25</b>, 1543-1546 (1970). 6. Balibar, S., The enigma of supersolidity. <i>Nature</i> <b>464</b>, 176-182 (2010). <br><br><br><br> <br>
DOI: 10.6084/m9.figshare.4290734
title: Reis_et_al Tree stems data.xlsx

description: This data represents stem diameters of tree stems from 30 plots of Seasonally Dry Tropical Forest in an enclave forest patch in Minas Gerais, Brazil. Plots 1-10 are plots on the edge, 11-20 are plots 100m into the forest, and plots 21-30 are plots in the interior of the forest (200m from the edge).
DOI: 10.6084/m9.figshare.4290734.v1
title: Reis_et_al Tree stems data.xlsx

description: This data represents stem diameters of tree stems from 30 plots of Seasonally Dry Tropical Forest in an enclave forest patch in Minas Gerais, Brazil. Plots 1-10 are plots on the edge, 11-20 are plots 100m into the forest, and plots 21-30 are plots in the interior of the forest (200m from the edge).
DOI: 10.6084/m9.figshare.4290425
title: Diversity partitioning in Permian and Early Triassic benthic ecosystems of the Western USA: a comparison

description: This paper compares the relative contributions of within-habitat diversity [alpha-diversity] and between-habitat-diversity [beta-diversity] to regional diversity [gamma-diversity] in marine benthic communities of the western US before and after the end-Permian mass extinction. We found that presumably cool-water faunas from the Permian Gerster Limestone and the Park City Formation had low alpha- and beta-diversities, comparable to those of low diverse faunas of the Early Triassic. In contrast, tropical Permian faunas had much higher alpha-diversities and a variable pattern of beta-diversity: Whereas faunas of space-limited bioherms show a positive correlation between beta-diversity and gamma-diversity, beta-diversity in level-bottom faunas is elevated only when gamma-diversity is very high (&gt;250 species). This contrasting pattern probably reflects differential effects of interspecific competition on habitat partitioning. In low-competitive level-bottom faunas, species are able to coexist until competition forces species into their ecological optima, thereby increasing beta-diversity. This effect occurs at much lower gamma-diversities in more competitive reef-bound faunas, causing the observed positive correlation between beta- and gamma-diversity. We suggest that differences in the level of interspecific competition and hence diversity partitioning between Permian and Triassic benthic communities result from the higher average metabolic rates in the Mesozoic mollusc-dominated benthos in contrast to their Permian counterparts.
DOI: 10.6084/m9.figshare.4290425.v1
title: Diversity partitioning in Permian and Early Triassic benthic ecosystems of the Western USA: a comparison

description: This paper compares the relative contributions of within-habitat diversity [alpha-diversity] and between-habitat-diversity [beta-diversity] to regional diversity [gamma-diversity] in marine benthic communities of the western US before and after the end-Permian mass extinction. We found that presumably cool-water faunas from the Permian Gerster Limestone and the Park City Formation had low alpha- and beta-diversities, comparable to those of low diverse faunas of the Early Triassic. In contrast, tropical Permian faunas had much higher alpha-diversities and a variable pattern of beta-diversity: Whereas faunas of space-limited bioherms show a positive correlation between beta-diversity and gamma-diversity, beta-diversity in level-bottom faunas is elevated only when gamma-diversity is very high (&gt;250 species). This contrasting pattern probably reflects differential effects of interspecific competition on habitat partitioning. In low-competitive level-bottom faunas, species are able to coexist until competition forces species into their ecological optima, thereby increasing beta-diversity. This effect occurs at much lower gamma-diversities in more competitive reef-bound faunas, causing the observed positive correlation between beta- and gamma-diversity. We suggest that differences in the level of interspecific competition and hence diversity partitioning between Permian and Triassic benthic communities result from the higher average metabolic rates in the Mesozoic mollusc-dominated benthos in contrast to their Permian counterparts.
DOI: 10.6084/m9.figshare.4290377
title: Effects of local and landscape factors on distributional dynamics

description: Occupancy data for pygmy owls across 13 years (2001-2013) in Sonora, Mexico and estimates of local and landscape factors <br>
DOI: 10.6084/m9.figshare.4290377.v1
title: Effects of local and landscape factors on distributional dynamics

description: Occupancy data for pygmy owls across 13 years (2001-2013) in Sonora, Mexico and estimates of local and landscape factors <br>
DOI: 10.6084/m9.figshare.4290266
title: Supplemental material for Knight et al. 2016 Front. Microbiol

description: <i>Clostridium difficile</i> PCR Ribotype 014 assembled and annotated genomes.<br><br>Supplementary data for article<br><br><b>Knight DR, Squire MM, Collins DA and Riley TV </b> (2016). Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission. <i>Front. Microbiol.</i> <b>7</b>:2138. doi: 10.3389/fmicb.2016.02138<br><br>See spreadsheet for details<br>
DOI: 10.6084/m9.figshare.4290266.v1
title: 224808 Knight et al. Clostridium difficile PCR Ribotype 014 annotated genomes

description: Clostridium difficile PCR Ribotype 014 genomes (n=44)<br>See spreadsheet for details<br><br>Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission<br>Daniel R. Knight, Michele M. Squire, Deirdre A. Collins, Thomas V. Riley<br><br>Frontiers in Microbiology, In Review Dec 2016<br>
DOI: 10.6084/m9.figshare.4290266.v2
title: 224808 Knight et al. Clostridium difficile PCR Ribotype 014 annotated genomes

description: Clostridium difficile PCR Ribotype 014 assembled and annotated genomes from:<br><br>Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission<br>Daniel R. Knight, Michele M. Squire, Deirdre A. Collins, Thomas V. Riley<br><br>Frontiers in Microbiology, In Review Dec 2016<br>See spreadsheet for details<br>
DOI: 10.6084/m9.figshare.4290266.v3
title: 224808 Knight et al. Clostridium difficile PCR Ribotype 014 annotated genomes

description: Clostridium difficile PCR Ribotype 014 assembled and annotated genomes from:<br><br>Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission<br>Daniel R. Knight, Michele M. Squire, Deirdre A. Collins, Thomas V. Riley<br><br>Frontiers in Microbiology, In Review Dec 2016<br>See spreadsheet for details<br>
DOI: 10.6084/m9.figshare.4290266.v4
title: 224808 Knight et al. Clostridium difficile PCR Ribotype 014 annotated genomes

description: Clostridium difficile PCR Ribotype 014 assembled and annotated genomes from:<br><br>Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission<br>Daniel R. Knight, Michele M. Squire, Deirdre A. Collins, Thomas V. Riley<br><br>Frontiers in Microbiology, In Review Dec 2016<br>See spreadsheet for details<br>
DOI: 10.6084/m9.figshare.4290266.v5
title: 224808 Knight et al. Clostridium difficile PCR Ribotype 014 annotated genomes

description: Clostridium difficile PCR Ribotype 014 assembled and annotated genomes from:<br><br>Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission<br>Daniel R. Knight, Michele M. Squire, Deirdre A. Collins, Thomas V. Riley<br><br>Frontiers in Microbiology, In Review Dec 2016<br>See spreadsheet for details<br>
DOI: 10.6084/m9.figshare.4290266.v6
title: 224808 Knight et al. Clostridium difficile PCR Ribotype 014 annotated genomes

description: Clostridium difficile PCR Ribotype 014 assembled and annotated genomes from:<br><br>Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission<br>Daniel R. Knight, Michele M. Squire, Deirdre A. Collins, Thomas V. Riley<br><br>Frontiers in Microbiology, In Review Dec 2016<br>See spreadsheet for details<br>
DOI: 10.6084/m9.figshare.4290266.v8
title: Knight DR et al. (2016). Front. Microbiol. 7:2138. Supplementary data

description: <i>Clostridium difficile</i> PCR Ribotype 014 assembled and annotated genomes.<br><br>Supplementary data for article<br><br><b>Knight DR, Squire MM, Collins DA and Riley TV </b> (2016). Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission. <i>Front. Microbiol.</i> <b>7</b>:2138. doi: 10.3389/fmicb.2016.02138<br><br>See spreadsheet for details<br>
DOI: 10.6084/m9.figshare.4290266.v7
title: 224808 Knight et al. Clostridium difficile PCR Ribotype 014 annotated genomes

description: <i>Clostridium difficile</i> PCR Ribotype 014 assembled and annotated genomes.<br><br>Supplementary data<br><br><b>Daniel R. Knight, Michele M. Squire, Deirdre A. Collins, Thomas V. Riley. </b>Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission.<br><br>Frontiers in Microbiology, In Review Dec 2016<br>See spreadsheet for details<br>
DOI: 10.6084/m9.figshare.4290239
title: PSTH_examples_figureS1

description: Data files for sample zebra finch PSTH plots shown in figure S1.
DOI: 10.6084/m9.figshare.4290239.v1
title: PSTH_examples_figureS1

description: Data files for sample zebra finch PSTH plots shown in figure S1.
DOI: 10.6084/m9.figshare.4290131
title: LM_dir_and_vel_pigeon_BG_edit

description: Pigeon LM direction and velocity data
DOI: 10.6084/m9.figshare.4290131.v1
title: LM_dir_and_vel_pigeon_BG_edit

description: Pigeon LM direction and velocity data
DOI: 10.6084/m9.figshare.4290128
title: PIGEON-PSTH-direction

description: Pigeon direction data. Each file is an individual LM cell.<br>Data and R script of analyses in support of the study: "Neurons responsive to global visual motion have unique tuning properties in hummingbirds"
DOI: 10.6084/m9.figshare.4290125
title: example bootstrap output

description: R workspaces showing sample bootstrap analyses for direction and speed data.
DOI: 10.6084/m9.figshare.4290128.v1
title: PIGEON-PSTH-direction

description: Pigeon direction data. Each file is an individual LM cell.<br>Data and R script of analyses in support of the study: "Neurons responsive to global visual motion have unique tuning properties in hummingbirds"
DOI: 10.6084/m9.figshare.4290122
title: 2015-ZF-PSTH-speed

description: Zebra finch speed data. Each file is an individual LM cell.<br>Data and R script of analyses in support of the study: "Neurons responsive to global visual motion have unique tuning properties in hummingbirds"
DOI: 10.6084/m9.figshare.4290122.v1
title: 2015-ZF-PSTH-speed

description: Zebra finch speed data. Each file is an individual LM cell.<br>Data and R script of analyses in support of the study: "Neurons responsive to global visual motion have unique tuning properties in hummingbirds"
DOI: 10.6084/m9.figshare.4290125.v1
title: example bootstrap output

description: R workspaces showing sample bootstrap analyses for direction and speed data.
DOI: 10.6084/m9.figshare.4290113
title: 2015-CALAN-PSTH-speed

description: Hummingbird speed data. Each file is an individual LM cell. <br>Data and R script of analyses in support of the study: "Neurons responsive to global visual motion have unique tuning properties in hummingbirds"<br><br>
DOI: 10.6084/m9.figshare.4290119
title: 2015-ZF-PSTH-direction

description: Zebra finch direction data. Each file is an individual LM cell.<br>Data and R script of analyses in support of the study: "Neurons responsive to global visual motion have unique tuning properties in hummingbirds"<br><br>
DOI: 10.6084/m9.figshare.4290119.v1
title: 2015-ZF-PSTH-direction

description: Zebra finch direction data. Each file is an individual LM cell.<br>Data and R script of analyses in support of the study: "Neurons responsive to global visual motion have unique tuning properties in hummingbirds"<br><br>
DOI: 10.6084/m9.figshare.4290113.v1
title: 2015-CALAN-PSTH-speed

description: Hummingbird speed data. Each file is an individual LM cell. <br>Data and R script of analyses in support of the study: "Neurons responsive to global visual motion have unique tuning properties in hummingbirds"<br><br>
DOI: 10.6084/m9.figshare.4290110
title: Data from - Field-evolved Resistance in Corn Earworm to Cry Proteins Expressed by Transgenic Sweet Corn. PLoS ONE 11 (12), e0169115

description: This file contains the data used for characterizing the field-evolved resistance in corn earworm to Cry proteins expressed by transgenic sweet corn. Field efficacy data were collected for hybrids through yearly field experiments, laboratory bioassays with a comparator susceptible population, and data on abundance of corn earworm through black light traps. These data are provided in 7 different tabs in the file. Please see the methods section and the supplementary data in the publication for the descriptions of these experiments and data. <br>
DOI: 10.6084/m9.figshare.4290110.v2
title: Data from - Field-evolved Resistance in Corn Earworm to Cry Proteins Expressed by Transgenic Sweet Corn. PLoS ONE 11 (12), e0169115

description: This file contains the data used for characterizing the field-evolved resistance in corn earworm to Cry proteins expressed by transgenic sweet corn. Field efficacy data were collected for hybrids through yearly field experiments, laboratory bioassays with a comparator susceptible population, and data on abundance of corn earworm through black light traps. These data are provided in 7 different tabs in the file. Please see the methods section and the supplementary data in the publication for the descriptions of these experiments and data. <br>
DOI: 10.6084/m9.figshare.4290110.v1
title: Data from - Field-evolved Resistance in Corn Earworm to Cry Proteins Expressed by Transgenic Sweet Corn

description: This file contains the data used for characterizing the field-evolved resistance in corn earworm to Cry proteins expressed by transgenic sweet corn. Field efficacy data were collected for hybrids through yearly field experiments, laboratory bioassays with a comparator susceptible population, and data on abundance of corn earworm through black light traps. These data are provided in 7 different tabs in the file. Please see the methods section and the supplementary data in the publication for the descriptions of these experiments and data. <br>
DOI: 10.6084/m9.figshare.4290044
title: Abrolhos viromes - reads

description: These fasta files contain reads after QC as described in Silveira et al., 2017 "Bacteriophage genomic signatures and transfer of bacterial virulence genes in coral reefs".
DOI: 10.6084/m9.figshare.4290056
title: Pacific coral reef viromes

description: Pacific coral reef viromes analyzed in Silveira et al., 2017 "Bacteriophage genomic signatures and transfer of bacterial virulence genes in coral reefs" and first published in Knowles et al., 2016 "Lytic to temperate switching of viral communities".
DOI: 10.6084/m9.figshare.4289993
title: 3YRKPOPSURVEY_Q14_1FAVE-DRAFT

description: 334 Responses collected 4/16/2012 - 4/01/2015 in response to the question, "Name your favorite group OR artist and explain why that artist is your favorite.."
DOI: 10.6084/m9.figshare.4289993.v2
title: 3YRKPOPSURVEY_Q14_1FAVE-DRAFT

description: 334 Responses collected 4/16/2012 - 4/01/2015 in response to the question, "Name your favorite group OR artist and explain why that artist is your favorite.."