cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11345024.v3
title: MEQ-30 for "John"

description: Excel spreadsheet<br><b><br></b>
DOI: 10.6084/m9.figshare.11344919
title: SPM-2nd-FilesORC

description: second_level result
DOI: 10.6084/m9.figshare.11344916
title: SPM-2nd-FilesSRC

description: second_level result
DOI: 10.6084/m9.figshare.11344967.v1
title: B-bar data.xlsx

description: Isogeometric analysis of thin Reissner-Mindlin shells: locking phenomena and B-bar method
DOI: 10.6084/m9.figshare.11344970.v1
title: B-bar Data

description: Research Data
DOI: 10.6084/m9.figshare.11344913
title: SPM-2nd-FilesSRC_v.s_ORC

description: second_level result
DOI: 10.6084/m9.figshare.11344913.v1
title: SRC_v.s_ORC

description: second_level result
DOI: 10.6084/m9.figshare.11344916.v1
title: SRC

description: second_level result
DOI: 10.6084/m9.figshare.11344265
title: Fogarty Pilot Study Transcripts-ALL.doc

description: Data set from project on "mental health" in rural Nigeria.
DOI: 10.6084/m9.figshare.11344271
title: Dataset for the article « Portuguese Pinus nigra populations : genetic diversity, structure and relationships inferred by SSR markers » published in Annals of Forest Science, 2020, by Alexandra DIAS, Guia GIOVANELLI, Bruno FADY, Ilaria SPANU, Giovanni G VENDRAMIN, Francesca BAGNOLI, Ana CARVALHO, Maria Emília SILVA, José LIMA-BRITO, José Luís LOUSADA, Maria João GASPAR.

description: SSR database obtained by thirteen SSR markers for six populations of Pinus nigra in Portugal. The populations are representative of the species distribution in Portugal: Manteigas and Vale do Zêzere (center), Campeã and Vila Pouca de Aguiar (north) and Paredes de Coura and Caminha (northwest).
DOI: 10.6084/m9.figshare.11344265.v1
title: Fogarty Pilot Study Transcripts-ALL.doc

description: Data set from project on "mental health" in rural Nigeria.
DOI: 10.6084/m9.figshare.11344262
title: Source data for Figure 1: Cdiff abundance and community composition of two subjects over one year

description: These data pertain to Figure 1 of VanInsberghe et al and summarize all of the information necessary to reproduce that figure, including:<br>- "Cdiff_abundance.csv" which summarizes the abundance of C. difficile in both subjects in each sample<br>- "Phyla_Family_abundance.csv" which summarizes the abundance of all major families in all the major phyla present in the human gut over time. These data summarize the changes to the coarse-grained taxonomic composition of the microbiota over time.
DOI: 10.6084/m9.figshare.11344232
title: Genetic differentiation coefficient (Gst) and differentiation index of allele frequencies Jost’s D estimated per SSR locus, and total mean value (± s.d.) determined in the 13 SSR markers.

description: Genetic differentiation coefficient (Gst) and differentiation index of allele frequencies Jost’s D estimated per SSR locus, and total mean value (± s.d.) determined in the 13 SSR markers.
DOI: 10.6084/m9.figshare.11344262.v1
title: Source data for Figure 1: Cdiff abundance and community composition of two subjects over one year

description: These data pertain to Figure 1 of VanInsberghe et al and summarize all of the information necessary to reproduce that figure, including:<br>- "Cdiff_abundance.csv" which summarizes the abundance of C. difficile in both subjects in each sample<br>- "Phyla_Family_abundance.csv" which summarizes the abundance of all major families in all the major phyla present in the human gut over time. These data summarize the changes to the coarse-grained taxonomic composition of the microbiota over time.
DOI: 10.6084/m9.figshare.11344145
title: Source data for Figure 2: C. difficile, V. cholera, and major phylogenetic group abundance

description: These data pertain to Figure 2 from VanInsberghe et al. and contain all necessary data to reproduce that figure, including:<br>- "Cdiff_Vchol_read_counts.csv" which summarizes the abundance of both C. difficile and V. cholerae in the subjects from Hsaio et al. hospitalized for V. cholera infections over time. <br>- "Phyla_Family_abundance.csv" which summarizes the abundance of all major families in all the major phyla present in the human gut over time. These data summarize the changes to the coarse-grained taxonomic composition of the microbiota over time.
DOI: 10.6084/m9.figshare.11344232.v1
title: Genetic differentiation coefficient (Gst) and differentiation index of allele frequencies Jost’s D estimated per SSR locus, and total mean value (± s.d.) determined in the 13 SSR markers.

description: Genetic differentiation coefficient (Gst) and differentiation index of allele frequencies Jost’s D estimated per SSR locus, and total mean value (± s.d.) determined in the 13 SSR markers.
DOI: 10.6084/m9.figshare.11344271.v1
title: SSR database

description: SSR database obtained by thirteen SSR markers for six populations of Pinus nigra in Portugal.
DOI: 10.6084/m9.figshare.11344097
title: Genetic diversity statistics assayed per Portuguese P. nigra population and SSR locus.

description: Genetic diversity statistics assayed per Portuguese <i>P. nigra </i>population and SSR <i>locus</i>. Notes: na - observed number of alleles; ne - effective number of alleles (Kimura and Crow 1964); <i>I</i> - Shannon’s Information Index (Lewontin 1972); <i>h</i> – Nei’s gene diversity index (Nei 1973); Ho – observed heterozygosity; He – expected heterozygosity (Levene 1949); the F – fixation index; and s.d. – standard deviation.
DOI: 10.6084/m9.figshare.11344145.v1
title: Source data for Figure 2: C. difficile, V. cholera, and major phylogenetic group abundance

description: These data pertain to Figure 2 from VanInsberghe et al. and contain all necessary data to reproduce that figure, including:<br>- "Cdiff_Vchol_read_counts.csv" which summarizes the abundance of both C. difficile and V. cholerae in the subjects from Hsaio et al. hospitalized for V. cholera infections over time. <br>- "Phyla_Family_abundance.csv" which summarizes the abundance of all major families in all the major phyla present in the human gut over time. These data summarize the changes to the coarse-grained taxonomic composition of the microbiota over time.
DOI: 10.6084/m9.figshare.11344073
title: Raw Data- EFDs

description: All information related to obtaining the Fourier elliptical descriptors. Each folder contains the analysis output files in the Shape program, for 5, 10, 15, 20, 25 and 30 harmonics. From these files, the rest of the multivariate and statistical analyzes were derived.
DOI: 10.6084/m9.figshare.11344094
title: Source Data for Figure 4B: bray-curtis dissimilarity and C. difficile abundance

description: These data pertain to Figure 4B from VanInsberghe et al. They include the bray-curtis dissimilarity of the day after treatment to the three days prior to treatment from each mouse. As well, the peak abundance of C. difficile in these mice is shown.
DOI: 10.6084/m9.figshare.11344109
title: Source data for Figure 3: infant azithromycin clinical trial 16S amplicon sequencing summary and patient metadata

description: These data pertain to Figure 3 of VanInsberghe et al. They include a table that summarizes all patient metadata (including whether that individual was a placebo or treatment group), and the C. difficile read counts and relative abundance in each sample. These data can be used to reproduce all statistical analyses and graphs in Figure 3.
DOI: 10.6084/m9.figshare.11344271.v2
title: Online resources: Portuguese Pinus nigra populations: genetic diversity, structure and relationships inferred by SSR markers

description: <b>Online resources 1</b>: Genetic diversity statistics assayed per Portuguese <i>P. nigra </i>population and SSR <i>locus</i>. Notes: na - observed number of alleles; ne - effective number of alleles (Kimura and Crow 1964); <i>I</i> - Shannon’s Information Index (Lewontin 1972); <i>h</i> – Nei’s gene diversity index (Nei 1973); Ho – observed heterozygosity; He – expected heterozygosity (Levene 1949); the F – fixation index; and s.d. – standard deviation. <b>Online resources 2</b>: Genetic differentiation coefficient (Gst) and differentiation index of allele frequencies Jost’s D estimated per SSR locus, and total mean value (± s.d.) determined in the 13 SSR markers. <b>Online resources 3</b>: PCoA based on the pooled SSR data using the Nei’s genetic distance coefficient (Nei 1978), showing the projection of the six Portuguese<i> P. nigra </i>populations Manteigas, Vale do Zêzere, Campeã, Vila Pouca de Aguiar, Caminha and Paredes de Coura and seven foreign samples representative of the subspecies <i>dalmatica</i>, <i>pallasiana</i>,<i> laricio</i>,<i> nigra</i>, <i>salzmannii.</i>The cumulative percentage of total variation explained by the first three coordinates was 74.50%. <b>Online resources 4</b>: SSR database obtained by thirteen SSR markers for six populations of Pinus nigra in Portugal. The populations are representative of the species distribution in Portugal: Manteigas and Vale do Zêzere (center), Campeã and Vila Pouca de Aguiar (north) and Paredes de Coura and Caminha (northwest).
DOI: 10.6084/m9.figshare.11344094.v1
title: Source Data for Figure 4B: bray-curtis dissimilarity and C. difficile abundance

description: These data pertain to Figure 4B from VanInsberghe et al. They include the bray-curtis dissimilarity of the day after treatment to the three days prior to treatment from each mouse. As well, the peak abundance of C. difficile in these mice is shown.
DOI: 10.6084/m9.figshare.11344097.v1
title: Genetic diversity statistics assayed per Portuguese P. nigra population and SSR locus.

description: Genetic diversity statistics assayed per Portuguese <i>P. nigra </i>population and SSR <i>locus</i>. Notes: na - observed number of alleles; ne - effective number of alleles (Kimura and Crow 1964); <i>I</i> - Shannon’s Information Index (Lewontin 1972); <i>h</i> – Nei’s gene diversity index (Nei 1973); Ho – observed heterozygosity; He – expected heterozygosity (Levene 1949); the F – fixation index; and s.d. – standard deviation.
DOI: 10.6084/m9.figshare.11344073.v1
title: Raw Data- EFDs

description: All information related to obtaining the Fourier elliptical descriptors. Each folder contains the analysis output files in the Shape program, for 5, 10, 15, 20, 25 and 30 harmonics. From these files, the rest of the multivariate and statistical analyzes were derived.
DOI: 10.6084/m9.figshare.11344109.v1
title: Source data for Figure 3: infant azithromycin clinical trial 16S amplicon sequencing summary and patient metadata

description: These data pertain to Figure 3 of VanInsberghe et al. They include a table that summarizes all patient metadata (including whether that individual was a placebo or treatment group), and the C. difficile read counts and relative abundance in each sample. These data can be used to reproduce all statistical analyses and graphs in Figure 3.
DOI: 10.6084/m9.figshare.11344067
title: Source data for Extended Data 2: C. difficile abundance and mouse fecal microbiome coarse grained phylogenetic content over time

description: These data pertain to Extended Data 2 of VanInsberghe et al, and contain all of the raw data necessary to reproduce that figure. These data include:<br>- "Cdiff_relative_abundance.csv" which contains all of the relative abundances of C. difficile in all of the samples collected from the four groups of mice over the full 14 days of sampling.<br>- "Phyla_Family_graphs.csv" contains the abundances of each major taxonomic Family in each of the Phyla present in the fecal microbiome of these mice. Taxonomic predictions were performed using Silva, and only intend to give a coarse-grain view of the community stability and contents over time.
DOI: 10.6084/m9.figshare.11344271.v3
title: Online resources: Portuguese Pinus nigra populations: genetic diversity, structure and relationships inferred by SSR markers

description: <b>Online resources 1</b>: SSR database obtained by thirteen SSR markers for six populations of Pinus nigra in Portugal. The populations are representative of the species distribution in Portugal: Manteigas and Vale do Zêzere (center), Campeã and Vila Pouca de Aguiar (north) and Paredes de Coura and Caminha (northwest).<b>Online resources 2</b>: Genetic diversity statistics assayed per Portuguese P. nigra population and SSR locus. Notes: na - observed number of alleles; ne - effective number of alleles (Kimura and Crow 1964); I - Shannon’s Information Index (Lewontin 1972); h – Nei’s gene diversity index (Nei 1973); Ho – observed heterozygosity; He – expected heterozygosity (Levene 1949); the F – fixation index; and s.d. – standard deviation.<b>Online resources 3</b>: Genetic differentiation coefficient (Gst) and differentiation index of allele frequencies (Jost’s D) estimated per SSR locus, and total mean value (± standard deviation, s.d.) determined with the 13 SSR markers.<b>Online resources 4</b>: PCoA based on the pooled SSR data using the Nei’s genetic distance coefficient (Nei 1978), showing the projection of the six Portuguese P. nigra populations apart from the seven foreign samples representative of the subspecies dalmatica, pallasiana, laricio, nigra and salzmannii. The cumulative percentage of total variation explained by the first three coordinates was 74.50%.
DOI: 10.6084/m9.figshare.11344271.v5
title: Dataset for the article « Portuguese Pinus nigra populations : genetic diversity, structure and relationships inferred by SSR markers » published in Annals of Forest Science, 2020, by Alexandra DIAS, Guia GIOVANELLI, Bruno FADY, Ilaria SPANU, Giovanni G VENDRAMIN, Francesca BAGNOLI, Ana CARVALHO, Maria Emília SILVA, José LIMA-BRITO, José Luís LOUSADA, Maria João GASPAR.

description: SSR database obtained by thirteen SSR markers for six populations of Pinus nigra in Portugal. The populations are representative of the species distribution in Portugal: Manteigas and Vale do Zêzere (center), Campeã and Vila Pouca de Aguiar (north) and Paredes de Coura and Caminha (northwest).
DOI: 10.6084/m9.figshare.11344010
title: Source data for Extended Data 4B: C. difficile colony forming unit counts from fecal samples of mice during blooms

description: These data pertain to Extended Data 4, specifically to the colony counts in panel B of that figure. Stool pellets were anaerobically homogenized and gently centrifuged to remove macroscopic fiber and undigested food particles. The supernatant was resuspended in 250 uL total, then 100uL of the undiluted and 10^-1 dilution was plated on CCFA plates and incubated overnight anaerobically. All data necessary to replicate panel B of Extended Data 4 are presented.
DOI: 10.6084/m9.figshare.11344067.v1
title: Source data for Extended Data 2: C. difficile abundance and mouse fecal microbiome coarse grained phylogenetic content over time

description: These data pertain to Extended Data 2 of VanInsberghe et al, and contain all of the raw data necessary to reproduce that figure. These data include:<br>- "Cdiff_relative_abundance.csv" which contains all of the relative abundances of C. difficile in all of the samples collected from the four groups of mice over the full 14 days of sampling.<br>- "Phyla_Family_graphs.csv" contains the abundances of each major taxonomic Family in each of the Phyla present in the fecal microbiome of these mice. Taxonomic predictions were performed using Silva, and only intend to give a coarse-grain view of the community stability and contents over time.
DOI: 10.6084/m9.figshare.11343971
title: Rhesus Morphometrics.xlsx

description: Morphometric data were collected from free-ranging rhesus macaques during the annual capture-release season on Cayo Santiago. Reproductive success data were extracted from the Cayo Santiago pedigree, and demographic data were extracted from the long-term demographic database. All animal IDs are dummy-coded, including those in the pedigree, which has been pruned for use in heritability analyses.
DOI: 10.6084/m9.figshare.11344010.v1
title: Source data for Extended Data 4B: C. difficile colony forming unit counts from fecal samples of mice during blooms

description: These data pertain to Extended Data 4, specifically to the colony counts in panel B of that figure. Stool pellets were anaerobically homogenized and gently centrifuged to remove macroscopic fiber and undigested food particles. The supernatant was resuspended in 250 uL total, then 100uL of the undiluted and 10^-1 dilution was plated on CCFA plates and incubated overnight anaerobically. All data necessary to replicate panel B of Extended Data 4 are presented.
DOI: 10.6084/m9.figshare.11344271.v4
title: Dataset for the article « Portuguese Pinus nigra populations : genetic diversity, structure and relationships inferred by SSR markers » published in Annals of Forest Science, 2020, by Alexandra DIAS, Guia GIOVANELLI, Bruno FADY, Ilaria SPANU, Giovanni G VENDRAMIN, Francesca BAGNOLI, Ana CARVALHO, Maria Emília SILVA, José LIMA-BRITO, José Luís LOUSADA, Maria João GASPAR.

description: SSR database obtained by thirteen SSR markers for six populations of Pinus nigra in Portugal. The populations are representative of the species distribution in Portugal: Manteigas and Vale do Zêzere (center), Campeã and Vila Pouca de Aguiar (north) and Paredes de Coura and Caminha (northwest).
DOI: 10.6084/m9.figshare.11344007
title: The raw data of habitat selection research

description: The original data is obtained by measuring the habitat variables of the used plots and paired random plots, including the data of three seasons.
DOI: 10.6084/m9.figshare.11343971.v1
title: Rhesus Morphometrics.xlsx

description: Morphometric data were collected from free-ranging rhesus macaques during the annual capture-release season on Cayo Santiago. Reproductive success data were extracted from the Cayo Santiago pedigree, and demographic data were extracted from the long-term demographic database. All animal IDs are dummy-coded, including those in the pedigree, which has been pruned for use in heritability analyses.
DOI: 10.6084/m9.figshare.11344007.v1
title: The raw data of habitat selection research

description: The original data is obtained by measuring the habitat variables of the used plots and paired random plots, including the data of three seasons.
DOI: 10.6084/m9.figshare.11343953
title: Source data for Extended Data 4C: C. difficile colony PCR raw gel images

description: These data correspond to Extended Data 4 of VanInsberghe et al. To verify that the isolates obtained from mouse fecal samples were the both (1) C. difficile, and (2) the same genotype as the inoculating strain, we performed two different colony PCR assays and visualized the results on 1% agarose gels. The PCR assay rplP amplifies a C. difficile marker and verifies (1), and the assay rSAM amplifies a genotype specific marker that verifies (2). The raw gel images are named according to the assay they represent, and the layout of these gels in the figure Extended Data 4 is shown in the PDF named "gel_image_layout_key.pdf".
DOI: 10.6084/m9.figshare.11343965
title: Gill net catch counts for Cod and Dolly Varden

description: Catch information for cod <i>Gadus morhua</i>, which were collected in Kandalaksha Bay, White Sea, Russia, in 2014, and Dolly Varden <i>Salvelinus malma</i>, which were collected in Kronotskoe Lake in Eastern Kamchatka, Russia, in 2013. In both places fish were caught with identical monofilament gill nets of different mesh sizes with a 0.5 hanging ratio. The length of the nets was 30 m for cod and 15 m for Dolly Varden and the height of the nets was 1.5 m in both cases. The duration of the fishing operation was 12 h (from sunset to dawn) for both species and number of fishing operations was 11 for cod and 9 for Dolly Varden. Dolly Varden were caught with gill nets of 22, 25, 30 and 35 mm mesh size (knot to knot) and cod were caught with gill nets of 20, 25 and 30 mm mesh size. The different mesh size nets were set together and were fished concurrently. In both cases nets were set in the afternoon and retrieved the following morning. In total, 694 cod and 783 Dolly Varden were caught.
DOI: 10.6084/m9.figshare.11343920
title: Source data for spore and vegetative cell density analysis - raw images and raw counts

description: To compare the efficiency of bead-beading based DNA extraction kits on C. difficile spore versus vegetatively growing cells, we grew one anaerobic culture overnight and one spore preparation using chlorspore media. Before extracting DNA, the cell density was normalized by counting cells in both cultures and diluting to a consistent density. The power of magnification is 10x higher in the spore images. These data correspond to analyses described only in-text in VanInsberghe at al.
DOI: 10.6084/m9.figshare.11343953.v1
title: Source data for Extended Data 4C: C. difficile colony PCR raw gel images

description: These data correspond to Extended Data 4 of VanInsberghe et al. To verify that the isolates obtained from mouse fecal samples were the both (1) C. difficile, and (2) the same genotype as the inoculating strain, we performed two different colony PCR assays and visualized the results on 1% agarose gels. The PCR assay rplP amplifies a C. difficile marker and verifies (1), and the assay rSAM amplifies a genotype specific marker that verifies (2). The raw gel images are named according to the assay they represent, and the layout of these gels in the figure Extended Data 4 is shown in the PDF named "gel_image_layout_key.pdf".
DOI: 10.6084/m9.figshare.11343902
title: Source data for Extended Data 3: stool bacterial cell density, C. difficile abundance - including raw images and raw counts

description: These data correspond to Extended Data 3 of VanInsberghe et al. To directly count the cell density in mouse fecal samples, we homogenized stool pellets of known mass, mounted on microscope slides, and stained using FITC.<br>These data include:<br>- All of the raw fluorescence images used for counting cells<br>- "cell_counts.csv" contains all of the raw cell counts from our cell counting scripts (also available on github - https://github.com/polzlab/VanInsberghe_2019_Cdiff_colonization)<br>- "extended_data_3_source.xlsx" contains the C. difficile abundance measurements also included in Extended Data 3, including both the 16S rRNA amplicon sequencing measurements, and the rplP qPCR measurements.
DOI: 10.6084/m9.figshare.11343965.v2
title: Gill net catch counts for Cod and Dolly Varden

description: Catch information for cod <i>Gadus morhua</i>, which were collected in Kandalaksha Bay, White Sea, Russia, in 2014, and Dolly Varden <i>Salvelinus malma</i>, which were collected in Kronotskoe Lake in Eastern Kamchatka, Russia, in 2013. In both places fish were caught with identical monofilament gill nets of different mesh sizes with a 0.5 hanging ratio. The length of the nets was 30 m for cod and 15 m for Dolly Varden and the height of the nets was 1.5 m in both cases. The duration of the fishing operation was 12 h (from sunset to dawn) for both species and number of fishing operations was 11 for cod and 9 for Dolly Varden. Dolly Varden were caught with gill nets of 22, 25, 30 and 35 mm mesh size (knot to knot) and cod were caught with gill nets of 20, 25 and 30 mm mesh size. The different mesh size nets were set together and were fished concurrently. In both cases nets were set in the afternoon and retrieved the following morning. In total, 694 cod and 783 Dolly Varden were caught.
DOI: 10.6084/m9.figshare.11343902.v1
title: Source data for Extended Data 3: stool bacterial cell density, C. difficile abundance - including raw images and raw counts

description: These data correspond to Extended Data 3 of VanInsberghe et al. To directly count the cell density in mouse fecal samples, we homogenized stool pellets of known mass, mounted on microscope slides, and stained using FITC.<br>These data include:<br>- All of the raw fluorescence images used for counting cells<br>- "cell_counts.csv" contains all of the raw cell counts from our cell counting scripts (also available on github - https://github.com/polzlab/VanInsberghe_2019_Cdiff_colonization)<br>- "extended_data_3_source.xlsx" contains the C. difficile abundance measurements also included in Extended Data 3, including both the 16S rRNA amplicon sequencing measurements, and the rplP qPCR measurements.