cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48577/jpl.bj1th9
title: Maritime Continent water cycle as a key forcing for decadal variation of upper-ocean salinity in the southeast Indian Ocean

description: Argo measurements illustrate pronounced decadal variation of salinity in the southeast Indian Ocean (SEIO) that is coherent in the upper 70 m, with freshening during 2004-2010 followed by salinification during 2011-2019. The SEIO decadal salinity variation contributed to over half the magnitude of decadal sea level variation in this region. Previous studies suggested several possible factors contributing to SEIO decadal salinity signal: SEIO local winds, remote winds in the tropical Pacific forcing the Indonesian Throughflow (ITF) that advects salinity signal into the SEIO, SEIO local freshwater flux, remote freshwater flux over the Maritime Continent (MC). These studies did not agree on a key forcing mechanism. Here, we attribute decadal variation of SEIO salinity by isolating the contributions of freshwater and wind stress forcings through sensitivity experiments using the ocean modeling and state estimation system of the Estimating the Circulation and Climate of the Ocean (ECCO) project. Our causality analysis reveals that Maritime Continent surface freshwater flux is the key for decadal variation of SEIO salinity. Decadal variation in local or remote winds and SEIO local freshwater flux, implicated to be important by some previous studies, play little role. Salt budget analysis suggests that the advection of the salinity gradient, induced by the decadal variation of freshwater content over the MC, into the SEIO is the main oceanic process transmitting the MC water cycle effect to the SEIO.
DOI: 10.17028/rd.lboro.30639911
title: Supplementary information files for "Parent reports of eating behaviour and feeding practices: effects of parent and child sex"

description: Supplementary files for article "Parent reports of eating behaviour and feeding practices: effects of parent and child sex"<br><br>Research on parental feeding practices has focused on mothers, often overlooking fathers' perspectives and the influence of child sex. This study examined (1) differences between fathers' and mothers' own eating behaviours, their use of feeding practices, and perceptions of their children's eating behaviours, and (2) the role of child sex in these perceptions and practices. Parents (N = 784; 145 fathers and 639 mothers) of preschoolers (3–5 years, 51.3 % female) from the UK completed an online survey assessing their eating behaviours and feeding practices, and their child's eating behaviours. There were significant sex differences in parents' eating behaviours, with mothers reporting more emotional overeating, hunger, satiety responsiveness, and slowness in eating. Mothers and fathers did not differ in their reports of children's eating behaviours. Girls were reported to have higher levels of satiety responsiveness than boys. When exploring the interaction of parent and child sex in reports of eating behaviour, fathers reported that girls had more desire to drink. Mothers and fathers differed in their reported use of some feeding practices. Both mothers and fathers reported greater use of food for emotion regulation with girls than boys. Fathers used more encouragement of balance and variety with boys. These findings highlight distinct patterns in feeding practices and eating behaviours, influenced by both parent and child sex, suggesting that girls may be at greater risk of receiving feeding practices that contribute to the development of emotional eating. These results emphasize the need to consider the role of sex in future research and the development of tailored feeding guidance.<br><br>© The Author(s), CC BY 4.0
DOI: 10.17028/rd.lboro.30639911.v1
title: Supplementary information files for "Parent reports of eating behaviour and feeding practices: effects of parent and child sex"

description: Supplementary files for article "Parent reports of eating behaviour and feeding practices: effects of parent and child sex"<br><br>Research on parental feeding practices has focused on mothers, often overlooking fathers' perspectives and the influence of child sex. This study examined (1) differences between fathers' and mothers' own eating behaviours, their use of feeding practices, and perceptions of their children's eating behaviours, and (2) the role of child sex in these perceptions and practices. Parents (N = 784; 145 fathers and 639 mothers) of preschoolers (3–5 years, 51.3 % female) from the UK completed an online survey assessing their eating behaviours and feeding practices, and their child's eating behaviours. There were significant sex differences in parents' eating behaviours, with mothers reporting more emotional overeating, hunger, satiety responsiveness, and slowness in eating. Mothers and fathers did not differ in their reports of children's eating behaviours. Girls were reported to have higher levels of satiety responsiveness than boys. When exploring the interaction of parent and child sex in reports of eating behaviour, fathers reported that girls had more desire to drink. Mothers and fathers differed in their reported use of some feeding practices. Both mothers and fathers reported greater use of food for emotion regulation with girls than boys. Fathers used more encouragement of balance and variety with boys. These findings highlight distinct patterns in feeding practices and eating behaviours, influenced by both parent and child sex, suggesting that girls may be at greater risk of receiving feeding practices that contribute to the development of emotional eating. These results emphasize the need to consider the role of sex in future research and the development of tailored feeding guidance.<br><br>© The Author(s), CC BY 4.0
DOI: 10.15468/dl.ceatcj
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phacellula",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039408-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7929/issda/atiifd
title: Quarterly National Household Survey (QNHS) Module on Disability, Q2 2002

description: The Quarterly National Household Survey (QNHS) began in September 1997 and ran until Q2 2017 when it was replaced by the Labour Force Survey (LFS). While the main purpose of the QNHS was the production of quarterly labour force estimates, the QHNS also conducted special modules on different social topics each quarter. This special module was on disability in the workforce. Please note that due to CSO restrictions, these files cannot be matched to their associated microdata files
DOI: 10.15468/dl.b7cgr6
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "Geometry POLYGON ((-73.173752 45.53377, -73.124313 45.53377, -73.124313 45.569832, -73.173752 45.569832, -73.173752 45.53377))",
 "TaxonKey is Tracheophyta",
 "Year is greater than 2010",
 "GadmGid is CAN.11_1",
 "DatasetKey is one of (Herbier Louis-Marie (QFA) - Collection de plantes vasculaires, Herbier du Québec (QUE) - Collection de plantes vasculaires, Jardin botanique de Montréal (JBM), Marie-Victorin Herbarium (MT) - Plantes vasculaires, National Collection of Vascular Plants (DAO), UQTR-herbarium (Herbier Estelle-Lacoursière))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 41 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039409-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15491061
title: Mucosal viral infection elicits long-lived IgA responses via Type 1 follicular helper T cells

description: Original Data for the manuscript:

Mucosal viral infection elicits long-lived IgA responses via Type 1 follicular helper T cells

Kei Haniuda, Natalie M. Edner, Yuko Makita, Sandhya Appiah, Tania H. Watts, Gregory F. Wu, Thamotharampillai Dileepan and Jennifer L. Gommerman

Cell 2025 https://doi.org/10.1016/j.cell.2025.07.022

bioRxiv 2025.01.27.635134; https://doi.org/10.1101/2025.01.27.635134

Please cite the journal publication when using any of this data.

The raw data can be available from GSE287277 where barcodes, features and matrix gz files are stored.

Original scRNA-seq data:







Experiment 1




D7_1_barcodes.tsv.gz

D7_1_features.tsv.gz

D7_1_matrix.mtx.gz









Experiment 2




D7_2_barcodes.tsv.gz

D7_2_features.tsv.gz

D7_2_matrix.mtx.gz

 

Processed scRNA-seq data:

CD4.cca2.rds --> Fully processed Seurat objects for CD4 T cell all

CD4RV.cca2.rds --> Fully processed Seurat objects for RV T cell only (VP4 and VP6)

 

Script:

1stRun.R --> R script for experiment 1 (use original data from Experiment 1)

2ndRun.R --> R script for experiment 2 (use original data from Experiment 2)

Integration.all.R --> R script for integration of experiment 1 and 2 (for CD4 T cell all)

Integration.RVonly.R --> R script for integration of experiment 1 and 2 (for RV T cell only)

 

Package versions:

Seurat: 5.0.1, patchwork 1.2.0, dplyr 1.1.4, ggplot2 3.4.4, sctransform 0.4.1, glmGamPoi 1.14.0, viridis 0.6.5, scCustomize 2.0.1, gprofiler2 0.2.2
DOI: 10.5281/zenodo.15491060
title: Mucosal viral infection elicits long-lived IgA responses via Type 1 follicular helper T cells

description: Original Data for the manuscript:

Mucosal viral infection elicits long-lived IgA responses via Type 1 follicular helper T cells

Kei Haniuda, Natalie M. Edner, Yuko Makita, Sandhya Appiah, Tania H. Watts, Gregory F. Wu, Thamotharampillai Dileepan and Jennifer L. Gommerman

Cell 2025 https://doi.org/10.1016/j.cell.2025.07.022

bioRxiv 2025.01.27.635134; https://doi.org/10.1101/2025.01.27.635134

Please cite the journal publication when using any of this data.

The raw data can be available from GSE287277 where barcodes, features and matrix gz files are stored.

Original scRNA-seq data:







Experiment 1




D7_1_barcodes.tsv.gz

D7_1_features.tsv.gz

D7_1_matrix.mtx.gz









Experiment 2




D7_2_barcodes.tsv.gz

D7_2_features.tsv.gz

D7_2_matrix.mtx.gz

 

Processed scRNA-seq data:

CD4.cca2.rds --> Fully processed Seurat objects for CD4 T cell all

CD4RV.cca2.rds --> Fully processed Seurat objects for RV T cell only (VP4 and VP6)

 

Script:

1stRun.R --> R script for experiment 1 (use original data from Experiment 1)

2ndRun.R --> R script for experiment 2 (use original data from Experiment 2)

Integration.all.R --> R script for integration of experiment 1 and 2 (for CD4 T cell all)

Integration.RVonly.R --> R script for integration of experiment 1 and 2 (for RV T cell only)

 

Package versions:

Seurat: 5.0.1, patchwork 1.2.0, dplyr 1.1.4, ggplot2 3.4.4, sctransform 0.4.1, glmGamPoi 1.14.0, viridis 0.6.5, scCustomize 2.0.1, gprofiler2 0.2.2
DOI: 10.25829/x1sh-3k57
title: Aboveground plant biomass collected in 2017 from the Drought Experiment at the Jena Experiment site

description: The Jena drought experiment was established to investigate how plant biodiversity influences ecosystem responses to prolonged summer drought, and how drought and diversity interact to affect aboveground productivity. This dataset contains aboveground plant biomass data collected in 2017 from this drought experiment. The experiment includes two drought treatments: (1) a roofed subplot excluding rainfall to simulate drought, and (2) a roofed and watered subplot serving as a control. Biomass of all target plant species was harvested separately to allow species-specific productivity assessments. Sampling was conducted twice per year (spring and summer) within the core area of each plot, which was not fertilized
DOI: 10.15468/dl.97mk8b
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "Geometry POLYGON ((-73.173752 45.53377, -73.124313 45.53377, -73.124313 45.569832, -73.173752 45.569832, -73.173752 45.53377))",
 "TaxonKey is Tracheophyta",
 "Year is greater than 2010",
 "GadmGid is CAN.11_1",
 "DatasetKey is one of (Herbier Louis-Marie (QFA) - Collection de plantes vasculaires, Herbier du Québec (QUE) - Collection de plantes vasculaires, Jardin botanique de Montréal (JBM), Marie-Victorin Herbarium (MT) - Plantes vasculaires, National Collection of Vascular Plants (DAO), UQTR-herbarium (Herbier Estelle-Lacoursière))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 41 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039410-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/fmwvksr66f
title: PRJNA1088471 SARS-CoV-2 Wastewater Sequences Processed

description: The data come from NCBI BioProject PRJNA1088471, as originally analyzed in Overton et. al (2024). These data are short read sequences from wastewater in Toronto, Ontario. See Overton et. al (2024) for a detailed description of the genomic sequencing process.

Data processing involved alignment of the short reads to the Wuhan-1 reference sequence (NC_045512) with `minimap2` v2.28, identifying the mutations relative to the reference, and recording the number of times a mutation was observed (counts) and the depth of coverage. The frequency is calculated as the counts divided by the coverage. The mutation pre-processing pipeline is available at \url{https://github.com/DASL-Lab/data-treatment-plant}, and heavily relies on the GromStole pipeline (\url{https://github.com/PoonLab/gromstole}).

After being processed into counts and coverage, the data were filtered to only include mutations that are relevant to analysis. There were many mutations with either consistently low counts (possibly due to sequencing errors) or low coverage. 

We found all mutations that had both a frequency of at least 0.1 and a frequency below 0.9 (with a coverage at least 40) at at least two time points during the study in any location. This ensures that we have all of the mutations that were potentially part of a circulating lineage without relying on lineage definitions.

Overton, Alyssa K., Jennifer J. Knapp, Opeyemi U. Lawal, et al. “Genomic Surveillance of a Canadian Airport Wastewater Samples Allows Early Detection of Emerging SARS-CoV-2 Lineages.” Preprint, April 9, 2024. https://doi.org/10.21203/rs.3.rs-4183960/v1.
DOI: 10.17632/fmwvksr66f.2
title: PRJNA1088471 SARS-CoV-2 Wastewater Sequences Processed

description: The data come from NCBI BioProject PRJNA1088471, as originally analyzed in Overton et. al (2024). These data are short read sequences from wastewater in Toronto, Ontario. See Overton et. al (2024) for a detailed description of the genomic sequencing process.

Data processing involved alignment of the short reads to the Wuhan-1 reference sequence (NC_045512) with `minimap2` v2.28, identifying the mutations relative to the reference, and recording the number of times a mutation was observed (counts) and the depth of coverage. The frequency is calculated as the counts divided by the coverage. The mutation pre-processing pipeline is available at \url{https://github.com/DASL-Lab/data-treatment-plant}, and heavily relies on the GromStole pipeline (\url{https://github.com/PoonLab/gromstole}).

After being processed into counts and coverage, the data were filtered to only include mutations that are relevant to analysis. There were many mutations with either consistently low counts (possibly due to sequencing errors) or low coverage. 

We found all mutations that had both a frequency of at least 0.1 and a frequency below 0.9 (with a coverage at least 40) at at least two time points during the study in any location. This ensures that we have all of the mutations that were potentially part of a circulating lineage without relying on lineage definitions.

Overton, Alyssa K., Jennifer J. Knapp, Opeyemi U. Lawal, et al. “Genomic Surveillance of a Canadian Airport Wastewater Samples Allows Early Detection of Emerging SARS-CoV-2 Lineages.” Preprint, April 9, 2024. https://doi.org/10.21203/rs.3.rs-4183960/v1.
DOI: 10.15468/dl.vpdukx
title: Occurrence Download

description: A dataset containing 347519 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anthyllis vulneraria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 347519 records from 1533 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039379-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.npw72b
title: Occurrence Download

description: A dataset containing 16076 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "TaxonKey is one of (Porifera)"
 ]
}

 The dataset includes 16076 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014778-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rqck5s
title: Occurrence Download

description: A dataset containing 63472 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tragopogon dubius Scop."
 ]
}

 The dataset includes 63472 records from 986 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008421-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11106327
title: Kappa matrices presented in "An EFT approach to baryon number violation: lower limits on the new physics scale and correlations between nucleon decay modes" arXiv:2312.13361

description: In this archive we provide the kappa matrices introduced in Sec 2.4 of our paper An EFT approach to baryon number violation: lower limits on the new physics scale and correlations between nucleon decay modes 2312.13361, also published in JHEP. These are the numerical values that are presented as matrix plots in Appendix C. Here they are packaged into CSV files, whose first row is the row/column label.

Please consult the README for further information on how to use these data.

Version 3: Fixed error common to d=7 matrices.
DOI: 10.5281/zenodo.11106328
title: Kappa matrices presented in "An EFT approach to baryon number violation: lower limits on the new physics scale and correlations between nucleon decay modes" arXiv:2312.13361

description: In this archive we provide the kappa matrices introduced in Sec 2.4 of our paper An EFT approach to baryon number violation: lower limits on the new physics scale and correlations between nucleon decay modes 2312.13361. These are the numerical values that are presented as matrix plots in Appendix C. Here they are packaged into CSV files, whose first row is the row/column label.

Please consult the README for further information on how to use these data.
DOI: 10.5281/zenodo.12664770
title: Kappa matrices presented in "An EFT approach to baryon number violation: lower limits on the new physics scale and correlations between nucleon decay modes" arXiv:2312.13361

description: In this archive we provide the kappa matrices introduced in Sec 2.4 of our paper An EFT approach to baryon number violation: lower limits on the new physics scale and correlations between nucleon decay modes 2312.13361, also published in JHEP. These are the numerical values that are presented as matrix plots in Appendix C. Here they are packaged into CSV files, whose first row is the row/column label.

Please consult the README for further information on how to use these data.

Version 2: Updated n->K+e- file following identification of minor typo in the paper.
DOI: 10.5281/zenodo.15552436
title: Kappa matrices presented in "An EFT approach to baryon number violation: lower limits on the new physics scale and correlations between nucleon decay modes" arXiv:2312.13361

description: In this archive we provide the kappa matrices introduced in Sec 2.4 of our paper An EFT approach to baryon number violation: lower limits on the new physics scale and correlations between nucleon decay modes 2312.13361, also published in JHEP. These are the numerical values that are presented as matrix plots in Appendix C. Here they are packaged into CSV files, whose first row is the row/column label.

Please consult the README for further information on how to use these data.

Version 3: Fixed error common to d=7 matrices.
DOI: 10.15468/dl.qnf8wj
title: Occurrence Download

description: A dataset containing 1856 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Ennomos erosaria (Denis & Schiffermüller), 1775"
 ]
}

 The dataset includes 1856 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002688-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/pef-ps8-jdr
title: Cervus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tnt-7wd-4n3
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/852-fnt-az7
title: Emydidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/emk-l57-9ww
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7me-rty-wx8
title: Bovidae Gray, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5yv-qyj-bsk
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8b4-w2t-9z1
title: Pongo pygmaeus (Linnaeus, 1760)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cyr-5ag-lmp
title: Varanus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mjb-js8-7ns
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lr7-erd-yw0
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rvg-8a7-sjp
title: Cervus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8n6-7j3-jre
title: Bovidae Gray, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/82k-5eh-6jm
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r9y-1e0-xj6
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/64m-58z-rbk
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d0v-xws-kz0
title: Pongo pygmaeus (Linnaeus, 1760)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dvp-m20-xfg
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.