cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12916136.v1
title: Additional file 1 of Determinants of survival of the bovine blastocyst to cryopreservation stress: treatment with colony stimulating factor 2 during the morula-to-blastocyst transition and embryo sex

description: Additional file 1. Data collected for the experiments.
DOI: 10.6084/m9.figshare.3513740
title: Appendix A. A table presenting the detection ability of shifts in ecosystem variance and a figure showing the spatial variance and mean abundance of cod and prey in the Scotian Shelf and Pavlof Bay time series.

description: A table presenting the detection ability of shifts in ecosystem variance and a figure showing the spatial variance and mean abundance of cod and prey in the Scotian Shelf and Pavlof Bay time series.
DOI: 10.6084/m9.figshare.3513740.v1
title: Appendix A. A table presenting the detection ability of shifts in ecosystem variance and a figure showing the spatial variance and mean abundance of cod and prey in the Scotian Shelf and Pavlof Bay time series.

description: A table presenting the detection ability of shifts in ecosystem variance and a figure showing the spatial variance and mean abundance of cod and prey in the Scotian Shelf and Pavlof Bay time series.
DOI: 10.6084/m9.figshare.3513737
title: Appendix A. Maps and climate diagrams for study sites.

description: Maps and climate diagrams for study sites.
DOI: 10.6084/m9.figshare.3513737.v1
title: Appendix A. Maps and climate diagrams for study sites.

description: Maps and climate diagrams for study sites.
DOI: 10.6084/m9.figshare.12916156.v1
title: Additional file 11 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 11: Table S8. Overall significantly differentially abundant KOs. Significantly differentially abundant KOs associated with metabolically important pathways in the rumen when comparing 40% (40vs80) and 60% (60vs80) MER diet treatments versus the 80% treatment. Differential abundance was calculated using the likelihood ratio test (LRT) in DESeq2 and was considered statistically significant at FDR (adjusted p-value)
DOI: 10.6084/m9.figshare.12916159
title: Additional file 12 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 12: Table S9. Contribution of differentially abundant MAGs to metabolic pathways. Absolute counts of KOs associated with significantly differentially abundant MAGs comparing 40% and 60% MER diet treatments versus the 80% treatment. Counts for each taxonomic group in each diet treatment are aggregated into metabolically important pathways within the rumen (KO counts). Using the absolute counts, the log 2 fold change (LFC) of the counts in the 40% and 60% diet treatments has been calculated to give proportional change in contribution of each taxonomic group to each metabolic pathway when compared to the 80% diet treatment (LFC vs 80%).
DOI: 10.6084/m9.figshare.12916165
title: Additional file 14 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 14: Table S11. Taxonomy Table of MAGs. Complete taxonomy table adapted from Table S1 to be used as input for phyloseq and DESeq2 analyses.
DOI: 10.6084/m9.figshare.12916168
title: Additional file 15 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 15: R Script for DESeq2 and phyloseq analyses. R script to perform MAG and KO level using the likelihood ratio test (LRT) in DESeq2. Analyses identify significantly differentially abundant MAGs and KOs when the more restrictive 40% and 60% MER diet treatments are contrasted against the 80% MER diet treatment. Statistical analysis of the ruminal community structure is performed using the Adonis2 PERMANOVA analysis. Principal coordinate analysis (PCoA) and canonical analysis of principal coordinates (CAP) ordination plots are generated using phyloseq and ggplot2.
DOI: 10.6084/m9.figshare.12916168.v1
title: Additional file 15 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 15: R Script for DESeq2 and phyloseq analyses. R script to perform MAG and KO level using the likelihood ratio test (LRT) in DESeq2. Analyses identify significantly differentially abundant MAGs and KOs when the more restrictive 40% and 60% MER diet treatments are contrasted against the 80% MER diet treatment. Statistical analysis of the ruminal community structure is performed using the Adonis2 PERMANOVA analysis. Principal coordinate analysis (PCoA) and canonical analysis of principal coordinates (CAP) ordination plots are generated using phyloseq and ggplot2.
DOI: 10.6084/m9.figshare.12916159.v1
title: Additional file 12 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 12: Table S9. Contribution of differentially abundant MAGs to metabolic pathways. Absolute counts of KOs associated with significantly differentially abundant MAGs comparing 40% and 60% MER diet treatments versus the 80% treatment. Counts for each taxonomic group in each diet treatment are aggregated into metabolically important pathways within the rumen (KO counts). Using the absolute counts, the log 2 fold change (LFC) of the counts in the 40% and 60% diet treatments has been calculated to give proportional change in contribution of each taxonomic group to each metabolic pathway when compared to the 80% diet treatment (LFC vs 80%).
DOI: 10.6084/m9.figshare.3513734
title: Appendix B. Schematic diagrams of the salt marsh intertidal gradient at study sites illustrating differences in physical conditions and plant species occurrence and dominance among major vegetation zones.

description: Schematic diagrams of the salt marsh intertidal gradient at study sites illustrating differences in physical conditions and plant species occurrence and dominance among major vegetation zones.
DOI: 10.6084/m9.figshare.12916153.v1
title: Additional file 10 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 10: Table S7. Matrix of KO counts per Sample. KO counts per MAG (Table S3) were multiplied by the abundance of each MAG per sample (Table S5) to generate a KO per sample matrix representing the functional potential of the microbiome associated with each sample to be used as input for phyloseq and DESeq2 analyses.
DOI: 10.6084/m9.figshare.12916162.v1
title: Additional file 13 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 13: Table S10. Metadata Table for Metagenome Samples. Metadata table containing Sample ID, Period, Animal and Diet treatment information for each sample adapted from Table 7 to be used as input for phyloseq and DESeq2 analyses.
DOI: 10.6084/m9.figshare.12916165.v1
title: Additional file 14 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 14: Table S11. Taxonomy Table of MAGs. Complete taxonomy table adapted from Table S1 to be used as input for phyloseq and DESeq2 analyses.
DOI: 10.6084/m9.figshare.12916186.v1
title: Additional file 5 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 5: Table S2. Minimum Jaccard distances. Minimum Jaccard distance between all genomes within a single dataset from either African MAGs (MAG), Scottish RUGs (RUG1), RUG 2.0 (RUG2) or Hungate collection (HUN); between two datasets (MAGvRUG1, MAGvRUG2, MAGvHUN, RUG1vRUG2, RUG1vHUN, RUG1vMAG, HUNvRUG1, HUNvRUG2, HUNvMAG, RUG2vRUG1, RUG2vHUN, RUG2vMAG); between a given dataset and all other datasets combined (MAGvAll, RUGvAll, RUG2vAll, HUNvAll).
DOI: 10.6084/m9.figshare.12916189
title: Additional file 6 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 6: Table S3. KEGG Functional Annotations of MAGs. Counts of proteins in each MAG with a hit in the KEGG database for a KEGG ortholog (KO_Counts).
DOI: 10.6084/m9.figshare.3513734.v1
title: Appendix B. Schematic diagrams of the salt marsh intertidal gradient at study sites illustrating differences in physical conditions and plant species occurrence and dominance among major vegetation zones.

description: Schematic diagrams of the salt marsh intertidal gradient at study sites illustrating differences in physical conditions and plant species occurrence and dominance among major vegetation zones.
DOI: 10.6084/m9.figshare.12916156
title: Additional file 11 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 11: Table S8. Overall significantly differentially abundant KOs. Significantly differentially abundant KOs associated with metabolically important pathways in the rumen when comparing 40% (40vs80) and 60% (60vs80) MER diet treatments versus the 80% treatment. Differential abundance was calculated using the likelihood ratio test (LRT) in DESeq2 and was considered statistically significant at FDR (adjusted p-value)
DOI: 10.6084/m9.figshare.12916162
title: Additional file 13 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 13: Table S10. Metadata Table for Metagenome Samples. Metadata table containing Sample ID, Period, Animal and Diet treatment information for each sample adapted from Table 7 to be used as input for phyloseq and DESeq2 analyses.
DOI: 10.6084/m9.figshare.12916186
title: Additional file 5 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 5: Table S2. Minimum Jaccard distances. Minimum Jaccard distance between all genomes within a single dataset from either African MAGs (MAG), Scottish RUGs (RUG1), RUG 2.0 (RUG2) or Hungate collection (HUN); between two datasets (MAGvRUG1, MAGvRUG2, MAGvHUN, RUG1vRUG2, RUG1vHUN, RUG1vMAG, HUNvRUG1, HUNvRUG2, HUNvMAG, RUG2vRUG1, RUG2vHUN, RUG2vMAG); between a given dataset and all other datasets combined (MAGvAll, RUGvAll, RUG2vAll, HUNvAll).
DOI: 10.6084/m9.figshare.12916195
title: Additional file 8 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 8: Table S5. Matrix of read counts per MAG. Read counts per MAG were calculated based on reads mapped to all contigs of a MAG, corrected for contig length and GC content bias. Used as input for phyloseq and DESeq2 analyses.
DOI: 10.6084/m9.figshare.12916192
title: Additional file 7 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 7: Table S4. CAZyme Functional Annotations of MAGs. Counts of proteins in each MAG with a hit in the dbCAN CAZyme database (CAZy_Counts).
DOI: 10.6084/m9.figshare.12916195.v1
title: Additional file 8 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 8: Table S5. Matrix of read counts per MAG. Read counts per MAG were calculated based on reads mapped to all contigs of a MAG, corrected for contig length and GC content bias. Used as input for phyloseq and DESeq2 analyses.
DOI: 10.6084/m9.figshare.12916189.v1
title: Additional file 6 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 6: Table S3. KEGG Functional Annotations of MAGs. Counts of proteins in each MAG with a hit in the KEGG database for a KEGG ortholog (KO_Counts).
DOI: 10.6084/m9.figshare.12916192.v1
title: Additional file 7 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 7: Table S4. CAZyme Functional Annotations of MAGs. Counts of proteins in each MAG with a hit in the dbCAN CAZyme database (CAZy_Counts).
DOI: 10.6084/m9.figshare.12916153
title: Additional file 10 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 10: Table S7. Matrix of KO counts per Sample. KO counts per MAG (Table S3) were multiplied by the abundance of each MAG per sample (Table S5) to generate a KO per sample matrix representing the functional potential of the microbiome associated with each sample to be used as input for phyloseq and DESeq2 analyses.
DOI: 10.6084/m9.figshare.3513731
title: Appendix C. ANOVA tables for the effects of parasitic plant removal on arcsine-transformed relative abundance of host-plant community associates.

description: ANOVA tables for the effects of parasitic plant removal on arcsine-transformed relative abundance of host-plant community associates.
DOI: 10.6084/m9.figshare.12916183
title: Additional file 4 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 4: Table S1. Taxonomic classifications of 850 winning African MAGs. Taxonomic classifications reported for each of the three following methods: CheckM, DIAMOND and PhyloPhlAn.
DOI: 10.6084/m9.figshare.12916198.v1
title: Additional file 9 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 9: Table S6. Significantly differentially abundant MAGs. Significantly differentially abundant MAGs comparing 40% (40vs80) and 60% (60vs80) MER diet treatments versus the 80% treatment. Differential abundance was calculated using the likelihood ratio test (LRT) in DESeq2 and was considered statistically significant at FDR (adjusted p-value)
DOI: 10.6084/m9.figshare.12916183.v1
title: Additional file 4 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 4: Table S1. Taxonomic classifications of 850 winning African MAGs. Taxonomic classifications reported for each of the three following methods: CheckM, DIAMOND and PhyloPhlAn.
DOI: 10.6084/m9.figshare.3513731.v1
title: Appendix C. ANOVA tables for the effects of parasitic plant removal on arcsine-transformed relative abundance of host-plant community associates.

description: ANOVA tables for the effects of parasitic plant removal on arcsine-transformed relative abundance of host-plant community associates.
DOI: 10.6084/m9.figshare.3513728
title: Appendix A. Tables showing data used in the PWS herring hypothesis testing with the herring population model, estimates and the standard errors of recruitment and adult survival from mortality sources other than fishing for the best single-factor model, and estimated parameter coefficients, their standard errors, and corresponding coefficient of variation for each of the 19 hypotheses for the model with the additional 1993 mortality parameter.

description: Tables showing data used in the PWS herring hypothesis testing with the herring population model, estimates and the standard errors of recruitment and adult survival from mortality sources other than fishing for the best single-factor model, and estimated parameter coefficients, their standard errors, and corresponding coefficient of variation for each of the 19 hypotheses for the model with the additional 1993 mortality parameter.
DOI: 10.6084/m9.figshare.3513728.v1
title: Appendix A. Tables showing data used in the PWS herring hypothesis testing with the herring population model, estimates and the standard errors of recruitment and adult survival from mortality sources other than fishing for the best single-factor model, and estimated parameter coefficients, their standard errors, and corresponding coefficient of variation for each of the 19 hypotheses for the model with the additional 1993 mortality parameter.

description: Tables showing data used in the PWS herring hypothesis testing with the herring population model, estimates and the standard errors of recruitment and adult survival from mortality sources other than fishing for the best single-factor model, and estimated parameter coefficients, their standard errors, and corresponding coefficient of variation for each of the 19 hypotheses for the model with the additional 1993 mortality parameter.
DOI: 10.6084/m9.figshare.12916198
title: Additional file 9 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

description: Additional file 9: Table S6. Significantly differentially abundant MAGs. Significantly differentially abundant MAGs comparing 40% (40vs80) and 60% (60vs80) MER diet treatments versus the 80% treatment. Differential abundance was calculated using the likelihood ratio test (LRT) in DESeq2 and was considered statistically significant at FDR (adjusted p-value)
DOI: 10.6084/m9.figshare.3513725
title: Appendix A. Separate the contribution of vegetation type to fire occurrence from other factors in calculating fire initiation probability and fire ignition rate.

description: Separate the contribution of vegetation type to fire occurrence from other factors in calculating fire initiation probability and fire ignition rate.
DOI: 10.6084/m9.figshare.3513725.v1
title: Appendix A. Separate the contribution of vegetation type to fire occurrence from other factors in calculating fire initiation probability and fire ignition rate.

description: Separate the contribution of vegetation type to fire occurrence from other factors in calculating fire initiation probability and fire ignition rate.
DOI: 10.6084/m9.figshare.3513722
title: Appendix A. Modeling the second definition of nonoverlapping chains.

description: Modeling the second definition of nonoverlapping chains.
DOI: 10.6084/m9.figshare.3513722.v1
title: Appendix A. Modeling the second definition of nonoverlapping chains.

description: Modeling the second definition of nonoverlapping chains.
DOI: 10.6084/m9.figshare.3513719
title: Appendix A. Attribute summary for 45 stands of Pinus pinaster or Pinus radiata that were studied in Galicia, Spain.

description: Attribute summary for 45 stands of Pinus pinaster or Pinus radiata that were studied in Galicia, Spain.
DOI: 10.6084/m9.figshare.3513719.v1
title: Appendix A. Attribute summary for 45 stands of Pinus pinaster or Pinus radiata that were studied in Galicia, Spain.

description: Attribute summary for 45 stands of Pinus pinaster or Pinus radiata that were studied in Galicia, Spain.
DOI: 10.6084/m9.figshare.3513716
title: Appendix A. Predictor code definitions.

description: Predictor code definitions.
DOI: 10.6084/m9.figshare.3513716.v1
title: Appendix A. Predictor code definitions.

description: Predictor code definitions.
DOI: 10.6084/m9.figshare.3513713
title: Appendix A. Akaike weights of the models explaining nestbox occupancy by Tree Swallows at seven spatial scales along a gradient of agricultural intensification in southern Québec, 2005–2006.

description: Akaike weights of the models explaining nestbox occupancy by Tree Swallows at seven spatial scales along a gradient of agricultural intensification in southern Québec, 2005–2006.
DOI: 10.6084/m9.figshare.3513713.v1
title: Appendix A. Akaike weights of the models explaining nestbox occupancy by Tree Swallows at seven spatial scales along a gradient of agricultural intensification in southern Québec, 2005–2006.

description: Akaike weights of the models explaining nestbox occupancy by Tree Swallows at seven spatial scales along a gradient of agricultural intensification in southern Québec, 2005–2006.
DOI: 10.6084/m9.figshare.3513710
title: Appendix B. ΔmAICc of the models explaining nestbox occupancy by Tree Swallows at seven spatial scales along a gradient of agricultural intensification in southern Québec, 2005–2006.

description: ΔmAICc of the models explaining nestbox occupancy by Tree Swallows at seven spatial scales along a gradient of agricultural intensification in southern Québec, 2005–2006.
DOI: 10.6084/m9.figshare.3513710.v1
title: Appendix B. ΔmAICc of the models explaining nestbox occupancy by Tree Swallows at seven spatial scales along a gradient of agricultural intensification in southern Québec, 2005–2006.

description: ΔmAICc of the models explaining nestbox occupancy by Tree Swallows at seven spatial scales along a gradient of agricultural intensification in southern Québec, 2005–2006.
DOI: 10.5281/zenodo.3872379
title: Merged output log files from collect_environment.sh

description: Output from scripts that gathers execution environment information on Summit, Fugaku, and Oakforest-PACS.
DOI: 10.6073/pasta/0b0495bf10ecfe9e09a04959f3402ba9
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 2 meteorological station: 5-minute summary wind and air temperature data: 2013 - ongoing

description: This data package contains 5-minute air temperature and wind summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-2 met station. Average air temperature, wind speed, and wind direction are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. This is a subset of baseline weather data collected at the 15 Jornada Basin LTER CSIS study blocks, New Mexico. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. The met station variables measured include air temperature, precipitation, relative humidity, wind direction, wind speed. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively . This is an ONGOING dataset.
DOI: 10.6073/pasta/4556e61061a75025fa0a37096a282470
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 3 meteorological station: 30-minute summary data: 2017 - ongoing

description: This data package contains 30-minute air temperature, relative humidity, and wind summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-1 met station. Average air temperature, relative humidity, wind speed, wind direction, and precipitation are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. The met station variables measured include air temperature, precipitation, relative humidity, wind direction, wind speed. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively. This is an ONGOING dataset.