cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3785569
title: Data from: Microbe-dependent heterosis in maize

description: Data and statistical code associated with the manuscript "Microbe-dependent heterosis in maize" Wagner, Maggie R.; Tang, Clara; Salvato, Fernanda; Clouse, Kayla M.; Bartlett, Alexandria; Vintila, Simina; Phillips, Laura; Sermons, Shannon; Hoffmann, Mark; Balint-Kurti, Peter J.; Kleiner, Manuel (2021) PNAS July 27, 2021 118 (30) e2021965118; https://doi.org/10.1073/pnas.2021965118

19 October 2020: new version posted to add fum_16S_ITS.zip



Archive containing processed 16S and ITS amplicon data (i.e., ASV tables) from the soil fumigation experiment. In addition, it contains all code and accessory files used to process and analyze the sequence data. The archive contains its own readme.txt with details on the files and their usage.


27 July 2021: new version 3 posted to add Expt4_data.xlsx and SynCom_colonization_data.xlsx . New version 4 posted to include the updated README and analytical code (mdh_analysis_revised.R)



Expt4_data.xlsx = Raw data from Experiment 4 (Kansas field experiment, summer 2020)

SynCom_colonization_data.xlsx = Raw measurements of colonization rates of SynCom bacterial strains in 4 maize genotypes


Funding: National Science Foundation, IOS-2033621
DOI: 10.5281/zenodo.5140243
title: Data from: Microbe-dependent heterosis in maize

description: Data and statistical code associated with the manuscript "Microbe-dependent heterosis in maize" Wagner, Maggie R.; Tang, Clara; Salvato, Fernanda; Clouse, Kayla M.; Bartlett, Alexandria; Vintila, Simina; Phillips, Laura; Sermons, Shannon; Hoffmann, Mark; Balint-Kurti, Peter J.; Kleiner, Manuel (2021) PNAS July 27, 2021 118 (30) e2021965118; https://doi.org/10.1073/pnas.2021965118

19 October 2020: new version posted to add fum_16S_ITS.zip



Archive containing processed 16S and ITS amplicon data (i.e., ASV tables) from the soil fumigation experiment. In addition, it contains all code and accessory files used to process and analyze the sequence data. The archive contains its own readme.txt with details on the files and their usage.


27 July 2021: new version 3 posted to add Expt4_data.xlsx and SynCom_colonization_data.xlsx . New version 4 posted to include the updated README and analytical code (mdh_analysis_revised.R)



Expt4_data.xlsx = Raw data from Experiment 4 (Kansas field experiment, summer 2020)

SynCom_colonization_data.xlsx = Raw measurements of colonization rates of SynCom bacterial strains in 4 maize genotypes


Funding: National Science Foundation, IOS-2033621
DOI: 10.15468/dl.h4hy4d
title: Occurrence Download

description: A dataset containing 1486 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Digitaria sanguinalis",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1486 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026339-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2drs43
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Triumfetta rhomboidea",
 "Country is Vanuatu",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026340-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9vawx2
title: Occurrence Download

description: A dataset containing 529 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is South America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (June, July)",
 "OccurrenceStatus is Present",
 "TaxonKey is Chloephaga rubidiceps",
 "Year 1970-2025"
 ]
}

 The dataset includes 529 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026341-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a5sx6h
title: Occurrence Download

description: A dataset containing 419 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Digitaria setigera",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 419 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026342-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13821005
title: Data from: Persistent legacy effects on soil metagenomes facilitate plant adaptive responses to drought

description: Source data and code associated with the paper "Precipitation legacy effects on soil microbiotafacilitate adaptive drought responses in plants" by Ginnan et al, currently in press at Nature Microbiology. Pre-print is available on biorxiv. Funding: National Science Foundation, IOS-2016351
DOI: 10.5281/zenodo.13821006
title: Data from: Persistent legacy effects on soil metagenomes facilitate plant adaptive responses to drought

description: Source data and code associated with the paper "Precipitation legacy effects on soil microbiotafacilitate adaptive drought responses in plants" by Ginnan et al, currently in press at Nature Microbiology. Pre-print is available on biorxiv. Funding: National Science Foundation, IOS-2016351
DOI: 10.15468/dl.pm9eac
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Terminalia superba",
 "Country is Burundi",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026343-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g9g63p
title: Occurrence Download

description: A dataset containing 182892862 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 182892862 records from 13825 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026194-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26601301
title: Additional file 4 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 4. Contains the output from DESeq2 for the differential gene expression of the 14-day samples.
DOI: 10.6084/m9.figshare.26601292
title: Additional file 1 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 1. Contains the metadata for the RNA-seq libraries used here.
DOI: 10.6084/m9.figshare.26601295.v1
title: Additional file 2 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 2. Contains the updated GO term annotations for Oncopeltus fasciatus.
DOI: 10.6084/m9.figshare.26601298
title: Additional file 3 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 3. Contains the output from DESeq2 for the differential gene expression of the 7-day samples.
DOI: 10.6084/m9.figshare.26601307
title: Additional file 6 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 6. Contains the output from topGO for the GO term overrepresentation analysis of the 14-day samples.
DOI: 10.6084/m9.figshare.26601313.v1
title: Additional file 8 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 8. Contains the raw data for figure one, nuclei count of dividing gametes.
DOI: 10.6084/m9.figshare.26601292.v1
title: Additional file 1 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 1. Contains the metadata for the RNA-seq libraries used here.
DOI: 10.6084/m9.figshare.26601295
title: Additional file 2 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 2. Contains the updated GO term annotations for Oncopeltus fasciatus.
DOI: 10.6084/m9.figshare.26601307.v1
title: Additional file 6 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 6. Contains the output from topGO for the GO term overrepresentation analysis of the 14-day samples.
DOI: 10.6084/m9.figshare.26601313
title: Additional file 8 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 8. Contains the raw data for figure one, nuclei count of dividing gametes.
DOI: 10.6084/m9.figshare.26601304.v1
title: Additional file 5 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 5. Contains the output from topGO for the GO term overrepresentation analysis of the 7-day samples.
DOI: 10.6084/m9.figshare.26601310.v1
title: Additional file 7 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 7. Contains the output from topGO for the GO term overrepresentation analysis of the Bewick et al. [9] and 14-day samples overlap
DOI: 10.6084/m9.figshare.26601301.v1
title: Additional file 4 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 4. Contains the output from DESeq2 for the differential gene expression of the 14-day samples.
DOI: 10.6084/m9.figshare.26601304
title: Additional file 5 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 5. Contains the output from topGO for the GO term overrepresentation analysis of the 7-day samples.
DOI: 10.6084/m9.figshare.26601310
title: Additional file 7 of The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus

description: Additional file 7. Contains the output from topGO for the GO term overrepresentation analysis of the Bewick et al. [9] and 14-day samples overlap
DOI: 10.15468/dl.uwyadc
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((144.432616 -36.876552, 144.432616 -36.890026, 144.434862 -36.890026, 144.434862 -36.896764, 144.439354 -36.896764, 144.439354 -36.885535, 144.441599 -36.885535, 144.441599 -36.883289, 144.455074 -36.883289, 144.455074 -36.885535, 144.459566 -36.885535, 144.459566 -36.883289, 144.45732 -36.883289, 144.45732 -36.876552, 144.455074 -36.876552, 144.455074 -36.878797, 144.450583 -36.878797, 144.450583 -36.876552, 144.443845 -36.876552, 144.443845 -36.878797, 144.439354 -36.878797, 144.439354 -36.876552, 144.432616 -36.876552)), ((144.434862 -36.896764, 144.432616 -36.896764, 144.432616 -36.901255, 144.428125 -36.901255, 144.428125 -36.907993, 144.434862 -36.907993, 144.434862 -36.896764)), ((144.439354 -36.896764, 144.439354 -36.89901, 144.443845 -36.89901, 144.443845 -36.91473, 144.441599 -36.91473, 144.441599 -36.916976, 144.448337 -36.916976, 144.448337 -36.921467, 144.443845 -36.921467, 144.443845 -36.923713, 144.455074 -36.923713, 144.455074 -36.905747, 144.459566 -36.905747, 144.459566 -36.907993, 144.464057 -36.907993, 144.464057 -36.912484, 144.466303 -36.912484, 144.466303 -36.905747, 144.464057 -36.905747, 144.464057 -36.89901, 144.459566 -36.89901, 144.459566 -36.896764, 144.455074 -36.896764, 144.455074 -36.890026, 144.443845 -36.890026, 144.443845 -36.892272, 144.441599 -36.892272, 144.441599 -36.896764, 144.439354 -36.896764), (144.450583 -36.89901, 144.455074 -36.89901, 144.455074 -36.901255, 144.450583 -36.901255, 144.450583 -36.89901)), ((144.441599 -36.916976, 144.434862 -36.916976, 144.434862 -36.921467, 144.441599 -36.921467, 144.441599 -36.916976)), ((144.466303 -36.912484, 144.466303 -36.91473, 144.470795 -36.91473, 144.470795 -36.912484, 144.466303 -36.912484)))"
 ]
}

 The dataset includes 88 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066707-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18126/acd8-rj94
title: Candidate perovskite compositions from "Machine Learning Materials Properties with Accurate Predictions, Uncertainty Estimates, Domain Guidance, and Persistent Online Accessibility" by Jacobs et al
DOI: 10.17632/w8zndbs4dj.1
title: Rizk et al., 2024_DIB_article

description: Plant leaf samples were collected from non-treated and with ZnO nanoparticles foliar-treated wheat stands under drought stress circumstances, and raw RNA-seq data were obtained from these samples using the Illumina-NGS method.
DOI: 10.5281/zenodo.10689974
title: Southern California Bight ROMS solution

description: Mutli-year ROMS solution of  the Southern California Bight at dx=300m resolution. Daily averaged current (u,v,w), tracers (temperature, salinity, oxygen), and stratification interpolated at 450m and 700m. The data is in matlab format.  

Illustrative animations of the cross-sill transport and horizontal distributions of T and O2 in the SMB+SPB and SBB

This dataset is analysed in a manuscript entitled "Circulation and dispersal in California's Borderland Basins" by McWilliams James, Damien Pierre, and Kessouri Faycal.
DOI: 10.5281/zenodo.10689975
title: Southern California Bight ROMS solution

description: Mutli-year ROMS solution of  the Southern California Bight at dx=300m resolution. Daily averaged current (u,v,w), tracers (temperature, salinity, oxygen), and stratification interpolated at 450m and 700m. The data is in matlab format.  

This dataset is analysed in a manuscript entitled "Circulation and dispersal in California's Borderland Basins" by McWilliams James, Damien Pierre, and Kessouri Faycal.
DOI: 10.5281/zenodo.13314437
title: Southern California Bight ROMS solution

description: Mutli-year ROMS solution of  the Southern California Bight at dx=300m resolution. Daily averaged current (u,v,w), tracers (temperature, salinity, oxygen), and stratification interpolated at 450m and 700m. The data is in matlab format.  

Illustrative animations of the cross-sill transport and horizontal distributions of T and O2 in the SMB+SPB and SBB

This dataset is analysed in a manuscript entitled "Circulation and dispersal in California's Borderland Basins" by McWilliams James, Damien Pierre, and Kessouri Faycal.
DOI: 10.15468/dl.kp9xh8
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((149.512613 -32.490506, 149.512613 -32.492752, 149.519351 -32.492752, 149.519351 -32.490506, 149.512613 -32.490506))"
 ]
}

 The dataset includes 45 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066708-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h5se6m
title: Occurrence Download

description: A dataset containing 16121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample, Material citation, Specimen, Living Specimen)",
 "Geometry POLYGON((54.19458 -46.48044,166.74854 -46.48044,166.74854 -1.48044,54.19458 -1.48044,54.19458 -46.48044))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Olea europaea L."
 ]
}

 The dataset includes 16121 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066710-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/2n4vgpvzgs.1
title: Rivea ornata Pollination Data (Chitchak et al.)

description: Trades-offs between pollinator attraction and florivore defense maximize reproductive success in the self-incompatible Rivea ornata (Convolvulaceae)

Natthaphong Chitchak, Alyssa B. Stewart, and Paweena Traiperm

Rivea ornata, a rare species from the morning glory family, exhibits uncommon characteristics compared to other typical morning glories, including nocturnal flowers that fit the classic moth pollination syndrome. However, the accuracy of its predicted pollination syndrome and its mating system have never been assessed. Additionally, R. ornata flowers attract not only pollinators but also florivores, potentially reducing plant reproductive success. Therefore, this study examined two populations of R. ornata in Thailand and assessed traits related to pollinator attraction and reward, determined its mating system, identified floral visitors and effective pollinators, and investigated the effect of florivory on reproductive success. Rivea ornata is highly fertile but self-incompatible and an obligate outcrosser, rendering it highly dependent on pollinators. Lepidopterans, particularly nocturnal hawk moths, were found to account for a significant proportion of all visits and were the sole effective pollinators of this plant species, in correspondence with its predicted pollination syndrome. Surprisingly, florivory did not significantly reduce reproductive success. This phenomenon may be explained by the strategies employed by R. ornata, which align with the optimal defense hypothesis and functional trade-offs. Specifically, R. ornata appears to invest resources in defending key floral structures while, simultaneously, guard ants are conspicuously absent from flowers, resulting in some florivore damage to non-vital floral organs but ensuring that pollinators are not deterred by ants and thus maintaining high pollinator visitation rates. Our findings indicate that reproduction-related traits in R. ornata, including those involved in pollinator attraction and reward and florivore defense, are highly effective and work in concert to maximize plant reproductive success. Therefore, a main risk that R. ornata faces is the decline or disappearance of hawk moths and other lepidopterans given its extreme specialization and high dependence on pollinators, and conservation efforts should include habitat protection for both R. ornata and its pollinators.
DOI: 10.15468/dl.8z4vcm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((144.540414 -36.921467, 144.540414 -36.923713, 144.54266 -36.923713, 144.54266 -36.921467, 144.540414 -36.921467))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066711-240626123714530/datasets/export for details.
DOI: 10.15468/dl.g7wxrj
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((149.539563 -32.490506, 149.541809 -32.490506, 149.541809 -32.48826, 149.539563 -32.48826, 149.539563 -32.490506)), ((149.539563 -32.490506, 149.535071 -32.490506, 149.535071 -32.492752, 149.532826 -32.492752, 149.532826 -32.497243, 149.53058 -32.497243, 149.53058 -32.499489, 149.532826 -32.499489, 149.532826 -32.501735, 149.535071 -32.501735, 149.535071 -32.497243, 149.539563 -32.497243, 149.539563 -32.490506)))"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066712-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26601379
title: Additional file 1 of Ssc-mir-221-3p regulates melanin production in Xiang pigs melanocytes by targeting the TYRP1 gene

description: Additional file 1: Table S1. Significantly differentially expressed miRNAs between black and white coated skin tissues of Jianbai Xiang pigs. Table S2. KEGG pathway related list of miRNA target genes and genes with significant differential expression enriched in melanogenes. Table S3. Physicochemical properties of TYR gene family members. Table S4. Fragment details for siRNA. Table S5. miRNA-221-3P and mRNAs primer sequences. Table S6. Different qRT-PCR reaction systems and reaction conditions for miRNA and mRNA. Table S7. Primer sequences for qRT-PCR. Table S8. Details of the xiang pig mRNA and miRAN sequencing data. Table S9. Alignment information to the reference genome.
DOI: 10.6084/m9.figshare.26601379.v1
title: Additional file 1 of Ssc-mir-221-3p regulates melanin production in Xiang pigs melanocytes by targeting the TYRP1 gene

description: Additional file 1: Table S1. Significantly differentially expressed miRNAs between black and white coated skin tissues of Jianbai Xiang pigs. Table S2. KEGG pathway related list of miRNA target genes and genes with significant differential expression enriched in melanogenes. Table S3. Physicochemical properties of TYR gene family members. Table S4. Fragment details for siRNA. Table S5. miRNA-221-3P and mRNAs primer sequences. Table S6. Different qRT-PCR reaction systems and reaction conditions for miRNA and mRNA. Table S7. Primer sequences for qRT-PCR. Table S8. Details of the xiang pig mRNA and miRAN sequencing data. Table S9. Alignment information to the reference genome.
DOI: 10.17632/n6293b4ggc.1
title: Heart attack risk prediction: a more productive, reduced, and cleansed ARFF dataset for machine learning

description: The authors utilized the Cleveland Heart Disease Dataset from the University of California, Irvine (UCI) Machine Learning Repository (https://doi.org/10.24432/C52P4X). This dataset, dating back to 1988, combines four separate datasets. It consists of 13 attributes and one additional target variable, including 303 instances, and it contains no missing values.
We used relevance to select and rank attributes, which allowed us to pick a subset with seven attributes and a target variable, resulting in a smaller dataset (254 instances at seven attributes). 
Primary datasets often require updates in clinical practice, which involve thorough data reduction and denoising. This data engineering process typically enhances the predictive power of the datasets, especially when using the classification algorithm known as IBk (Aha, D.W., Kibler, D. & Albert, M.K. Instance-based learning algorithms. Mach Learn 6, 37–66 (1991). https://doi.org/10.1007/BF00153759) which we applied to the reduced dataset. For instance, Accuracy has risen to 97.2% from 88.4%, and other performance indicators have shown statistically significant improvement.
DOI: 10.15468/dl.3csnbp
title: Occurrence Download

description: A dataset containing 93 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abies lasiocarpa var. arizonica (Merriam) Lemmon",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "Year is greater than or equal to 1960",
 {
 "or" : [
 "Country is Canada",
 "Country is United States of America",
 "Country is Mexico"
 ]
 },
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 93 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066713-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.