cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6209565
title: Land use fractions and human impact index in 101 Canadian lake watersheds

description: Land use fractions (urban, mines, agriculture, pasture, forestry, managed grassland, water and natural landscape) and associated human impact index in 101 lake watersheds sampled as part the NSERC Canadian Lake Pulse Network project. Land use and human impact index were calculated as described in Huot et al. (2019).

Lakes IDs with respective locations (longitude and latitude coordinates) and Continental Basin allocations can be found here: https://doi.org/10.5281/zenodo.4701262

 

If you use these data, please cite:

Paquette et al., 2022 C. Paquette, K. Griffiths, I. Gregory-Eaves, B.E. Beisner Zooplankton assemblage structure and diversity since pre-industrial times in relation to land use Glob. Ecol. Biogeogr., 31 (2022), pp. 2337-2352,  https://doi.org/10.1111/geb.13575

 

Reference

Huot, Y., C. A. Brown, G. Potvin, and others. 2019. The NSERC Canadian Lake Pulse Network: A national assessment of lake health providing science for water management in a changing climate. Sci. Total Environ. 695: 133668. doi:10.1016/j.scitotenv.2019.133668
DOI: 10.5281/zenodo.6209564
title: Land use fractions and human impact index in 101 Canadian lake watersheds

description: Land use fractions (urban, mines, agriculture, pasture, forestry, managed grassland, water and natural landscape) and associated human impact index in 101 lake watersheds sampled as part the NSERC Canadian Lake Pulse Network project. Land use and human impact index were calculated as described in Huot et al. (2019).

Lakes IDs with respective locations (longitude and latitude coordinates) and Continental Basin allocations can be found here: https://doi.org/10.5281/zenodo.4701262

 

If you use these data, please cite:

Paquette et al., 2022 C. Paquette, K. Griffiths, I. Gregory-Eaves, B.E. Beisner Zooplankton assemblage structure and diversity since pre-industrial times in relation to land use Glob. Ecol. Biogeogr., 31 (2022), pp. 2337-2352,  https://doi.org/10.1111/geb.13575

 

Reference

Huot, Y., C. A. Brown, G. Potvin, and others. 2019. The NSERC Canadian Lake Pulse Network: A national assessment of lake health providing science for water management in a changing climate. Sci. Total Environ. 695: 133668. doi:10.1016/j.scitotenv.2019.133668
DOI: 10.15468/dl.9vnvpv
title: Occurrence Download

description: A dataset listing the 4137962 species recorded in GBIF matching the query:
{
 "OccurrenceStatus" : [
 "is Present"
 ]
}

 The dataset's 4137962 records were derived from 88274 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004871-260120142942310/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.31125631
title: Supplementary data for: <b>Stabilising evolution of carbapenem resistance through core–accessory genome co-adaptation in </b><b><i>Acinetobacter baumannii</i></b>

description: Carbapenem-resistant <i>Acinetobacter baumannii</i> (CRAB) is a critical global health threat, yet the evolutionary mechanisms that stabilise resistance within high-risk lineages remain poorly defined. Using genomic, phenotypic, and phylogenetic analysis of 1,872 <i>A. baumannii</i> genomes, including a 16-year clinical collection from Eastern Europe, we show that carbapenem resistance evolves through two convergent pathways driven by core–accessory genome co-adaptation. Genome-wide association analysis reveals that acquisition of plasmid-borne bla<sub>OXA-72</sub> is repeatedly accompanied by a lineage-specific core SNP that enhances resistance expression, while a second pathway involves chromosomal integration of bla<sub>OXA-23</sub> and transcriptional activation via ISAba1 insertion. Machine learning models demonstrate that carbapenem MICs cannot be predicted from gene presence alone, highlighting the contribution of epistatic and regulatory variation. Time-resolved phylogenies show that both resistance mechanisms have independently emerged and expanded in multiple international clones, including a recently diverged lineage originating in Belarus. Together, these findings reveal how the interplay between chromosomal background and mobile genetic elements enables the long-term persistence and repeated emergence of carbapenem resistance. By resolving the genomic basis of resistance stabilisation, this work provides a mechanistic framework for anticipating AMR evolution and identifying emerging high-risk clones.
DOI: 10.6084/m9.figshare.31125631.v1
title: Supplementary data for: <b>Stabilising evolution of carbapenem resistance through core–accessory genome co-adaptation in </b><b><i>Acinetobacter baumannii</i></b>

description: Carbapenem-resistant <i>Acinetobacter baumannii</i> (CRAB) is a critical global health threat, yet the evolutionary mechanisms that stabilise resistance within high-risk lineages remain poorly defined. Using genomic, phenotypic, and phylogenetic analysis of 1,872 <i>A. baumannii</i> genomes, including a 16-year clinical collection from Eastern Europe, we show that carbapenem resistance evolves through two convergent pathways driven by core–accessory genome co-adaptation. Genome-wide association analysis reveals that acquisition of plasmid-borne bla<sub>OXA-72</sub> is repeatedly accompanied by a lineage-specific core SNP that enhances resistance expression, while a second pathway involves chromosomal integration of bla<sub>OXA-23</sub> and transcriptional activation via ISAba1 insertion. Machine learning models demonstrate that carbapenem MICs cannot be predicted from gene presence alone, highlighting the contribution of epistatic and regulatory variation. Time-resolved phylogenies show that both resistance mechanisms have independently emerged and expanded in multiple international clones, including a recently diverged lineage originating in Belarus. Together, these findings reveal how the interplay between chromosomal background and mobile genetic elements enables the long-term persistence and repeated emergence of carbapenem resistance. By resolving the genomic basis of resistance stabilisation, this work provides a mechanistic framework for anticipating AMR evolution and identifying emerging high-risk clones.
DOI: 10.5281/zenodo.6209389
title: Sub-fossil crustacean zooplankton relative abundances from 101 lakes across Canada

description: This data set contains cladoceran sub-fossil relative abundances for 101 lakes across Canada sampled as part of the NSERC Canadian Lake Pulse Network project. Lakes were sampled once, over three summers (2017-2018-2019). Cores were collected using a gravity corer in the deepest point of each lake and were sectioned on site with a vertical extruder. Each lake was sampled for a “top” sediment sample, represented by the first centimeter of the surface of the sediment core, and a “bottom” sediment sample, corresponding to the 1 cm of sediment located between 3 and 4 cm from the base of the core. Cladoceran extraction and preparation followed the protocol from Korhola and Rautio (2001). Cladocerans were identified using DM 2500 Leica compound inverted microscope under 200X-400X magnification with a minimal count size of 100 individuals. Identification at the species, genus, or species complex level followed Szeroczynska and Sarmaja-Korjonen (2007) and Korosi and Smol (2012a; b).

Sites are identified with Lake ID number, followed by “T” for top samples and “B” for bottom samples. Lakes IDs with respective locations (longitude and latitude coordinates) and Continental Basin allocations can be found here: https://doi.org/10.5281/zenodo.4701262

 

If you use these data, please cite:

Paquette et al., 2022 C. Paquette, K. Griffiths, I. Gregory-Eaves, B.E. Beisner Zooplankton assemblage structure and diversity since pre-industrial times in relation to land use Glob. Ecol. Biogeogr., 31 (2022), pp. 2337-2352,  https://doi.org/10.1111/geb.13575

 

 

References

Korhola, A., and M. Rautio. 2001. Cladocera and other branchiopod crustaceans, p. 225–234. In J.P. Smol, H.J.B. Birks, and W.M. Last [eds.], Tracking Environmental Change Using Lake Sediments. Springer.

Korosi, J. B., and J. P. Smol. 2012a. An illustrated guide to the identification of cladoceran subfossils from lake sediments in northeastern North America: Part 1-the Daphniidae, Leptodoridae, Bosminidae, Polyphemidae, Holopedidae, Sididae, and Macrothricidae. J. Paleolimnol. 48: 571–586. doi:10.1007/S10933-012-9632-3

Korosi, J. B., and J. P. Smol. 2012b. An illustrated guide to the identification of cladoceran subfossils from lake sediments in northeastern North America: Part 2-the Chydoridae. J. Paleolimnol. 48: 587–622.

Szeroczyfiska, K., and K. Sarmaja-Korjonen. 2007. Atlas of Subfossil Cladocera from Central and Northern Europe, Friends of the Lower Vistula Society, Warsaw, Pol.
DOI: 10.5281/zenodo.6209390
title: Sub-fossil crustacean zooplankton relative abundances from 101 lakes across Canada

description: This data set contains cladoceran sub-fossil relative abundances for 101 lakes across Canada sampled as part of the NSERC Canadian Lake Pulse Network project. Lakes were sampled once, over three summers (2017-2018-2019). Cores were collected using a gravity corer in the deepest point of each lake and were sectioned on site with a vertical extruder. Each lake was sampled for a “top” sediment sample, represented by the first centimeter of the surface of the sediment core, and a “bottom” sediment sample, corresponding to the 1 cm of sediment located between 3 and 4 cm from the base of the core. Cladoceran extraction and preparation followed the protocol from Korhola and Rautio (2001). Cladocerans were identified using DM 2500 Leica compound inverted microscope under 200X-400X magnification with a minimal count size of 100 individuals. Identification at the species, genus, or species complex level followed Szeroczynska and Sarmaja-Korjonen (2007) and Korosi and Smol (2012a; b).

Sites are identified with Lake ID number, followed by “T” for top samples and “B” for bottom samples. Lakes IDs with respective locations (longitude and latitude coordinates) and Continental Basin allocations can be found here: https://doi.org/10.5281/zenodo.4701262

 

If you use these data, please cite:

Paquette et al., 2022 C. Paquette, K. Griffiths, I. Gregory-Eaves, B.E. Beisner Zooplankton assemblage structure and diversity since pre-industrial times in relation to land use Glob. Ecol. Biogeogr., 31 (2022), pp. 2337-2352,  https://doi.org/10.1111/geb.13575

 

 

References

Korhola, A., and M. Rautio. 2001. Cladocera and other branchiopod crustaceans, p. 225–234. In J.P. Smol, H.J.B. Birks, and W.M. Last [eds.], Tracking Environmental Change Using Lake Sediments. Springer.

Korosi, J. B., and J. P. Smol. 2012a. An illustrated guide to the identification of cladoceran subfossils from lake sediments in northeastern North America: Part 1-the Daphniidae, Leptodoridae, Bosminidae, Polyphemidae, Holopedidae, Sididae, and Macrothricidae. J. Paleolimnol. 48: 571–586. doi:10.1007/S10933-012-9632-3

Korosi, J. B., and J. P. Smol. 2012b. An illustrated guide to the identification of cladoceran subfossils from lake sediments in northeastern North America: Part 2-the Chydoridae. J. Paleolimnol. 48: 587–622.

Szeroczyfiska, K., and K. Sarmaja-Korjonen. 2007. Atlas of Subfossil Cladocera from Central and Northern Europe, Friends of the Lower Vistula Society, Warsaw, Pol.
DOI: 10.7488/ds/3817
title: The effects of caloric restriction on adipose tissue and metabolic health are sex- and age-dependent

description: These are the source data and code underlying the figures presented in our published manuscript (eLife, https://doi.org/10.7554/eLife.88080) and its related preprint (https://doi.org/10.1101/2022.02.20.481222). For further details please see the file named readme_Sex_Differences_Adipose_Tissue_Metabolism_dataset_v2023_03_02.txt.
description: The dataset consists of three Excel files, two code files (in R) and one readme (.txt) file, as follows: 1. Sex_Differences_Paper_Source_Data_all_figures_v2023_03_02.xlsx - This Excel file contains the source data for the figures presented in the manuscript. 2. MASTER_ Pubmed_result Mice NOT reviews_v2022_04_17.xlsx - This Excel files contains data that are the basis for review of publication of caloric restriction in mice; the data are summarised in Figure 1 and Supplemental Figure 1 of the manuscript. 3. MASTER_ Pubmed_result Humans NOT reviews_v2022_04_25.xlsx - This Excel files contains data that are the basis for review of publication of caloric restriction in humans; the data are summarised in Figure 1 and Supplemental Figure 1 of the manuscript. 4. PCA_for Ben_v3_ceramides.R - This file is R code used for doing the Principal Component Analyses (PCA) of ceramide data that is presented in Figure 6D of the manuscript. 5. 230302_DESeq2_WT.R - This file is R code used for RNAseq data analysis, including generating the volcano plots in Figure 7B and Supplemental Figure 11A of the manuscript. 6. readme_Sex_Differences_Adipose_Tissue_Metabolism_dataset_v2023_03_02.txt - This is the metadata file that you are currently reading. Relationship between files, if important: File 1 contains sheets of summary data. The first sheet, entitled 'Figures 1A-D, S1B', was generated based on the data provided in files 2 and 3. The sheet entitled 'Figure 6D' was generated using the code in file 4 ('PCA_for Ben_v3_ceramides.R'). The sheets entitled 'Figure 7A' was generated using the code in file 4 (230302_DESeq2_WT.R). The sixth file is this readme file.
DOI: 10.5281/zenodo.18271391
title: A physiologically relevant in vitro 3-D melanoma skin model for targeted therapy assessment

description: Authors:

Rahul Rimal1*, Max Urbanczyk1*, Yvonne Elbs Glatz1, Markus Rottmar1

*Contributed equally

1 Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland

 

Link to the publication (DOI): TBD

 

 

Journal: TBD

 

 

Contents:

This repository contains all data that were used to compile the figures of the paper.
DOI: 10.5281/zenodo.18271390
title: A physiologically relevant in vitro 3-D melanoma skin model for targeted therapy assessment

description: Authors:

Rahul Rimal1*, Max Urbanczyk1*, Yvonne Elbs Glatz1, Markus Rottmar1

*Contributed equally

1 Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, Lerchenfeldstrasse 5, St. Gallen, 9014, Switzerland

 

Link to the publication (DOI): TBD

 

 

Journal: TBD

 

 

Contents:

This repository contains all data that were used to compile the figures of the paper.
DOI: 10.15468/dl.6gq86s
title: Occurrence Download

description: A dataset containing 5808 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ursus maritimus"
 ]
}

 The dataset includes 5808 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004907-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17617/3.h5t0w4
title: Raw dataset and analysis scripts for Google Click Identifier in YouTube Ads measurement

description: This collection contains the raw dataset and analysis scripts used to reproduce our study on Google Click Identifier in YouTube Ads measurement. The findings are detailed in the paper "Clicking into Exposure: Uncovering Privacy Risks of Google Click Identifier in YouTube Ads," published in the 26th Privacy Enhancing Technologies Symposium (PETS 2026.2).
DOI: 10.34740/kaggle/dsv/14582955
title: BOS Kemdikbud
DOI: 10.6084/m9.figshare.31126237
title: Leaching of silver from used crystalline silicon PV modules using I<sub>2</sub>-KI full factorial experimental design

description: The scale of solar photovoltaic (PV) power generation is growing exponentially. However, the service life of crystalline silicon photovoltaic modules is typically around 25 years, primarily due to light-induced degradation (LID) and related degradation mechanisms. Waste solar crystalline silicon (c-Si) PV modules are a kind of hazardous waste, and green recycling of precious metals in waste solar c-Si PV modules needs to be solved urgently. To address the recycling problem, green dismantling of panels and green leaching of cells are used. Freeze cracking method is selected to separate the cell wafers from used crystalline silicon PV panels. Recovery of silver from used crystalline silicon cell wafers was carried out using I<sub>2</sub>-KI as a green leaching reagent. Full factorial experimental design for leaching rate is carried out using MINITAB software. A regression equation on the leaching rate of silver as a response value is established. Iodine concentration, potassium iodide concentration, solid–liquid ratio, and pH are the influencing factors in the regression equation. The parameters for the optimal solution of silver leaching rate were iodine concentration of 0.3 mol/L, solid–liquid ratio of 1:10, pH of 9.6, and potassium iodide concentration of 0.8 mol/L. The results of the response optimization are verified by three sets of parallel experiments, and the silver leaching rate is obtained as 96.62%.
DOI: 10.6084/m9.figshare.31126237.v1
title: Leaching of silver from used crystalline silicon PV modules using I<sub>2</sub>-KI full factorial experimental design

description: The scale of solar photovoltaic (PV) power generation is growing exponentially. However, the service life of crystalline silicon photovoltaic modules is typically around 25 years, primarily due to light-induced degradation (LID) and related degradation mechanisms. Waste solar crystalline silicon (c-Si) PV modules are a kind of hazardous waste, and green recycling of precious metals in waste solar c-Si PV modules needs to be solved urgently. To address the recycling problem, green dismantling of panels and green leaching of cells are used. Freeze cracking method is selected to separate the cell wafers from used crystalline silicon PV panels. Recovery of silver from used crystalline silicon cell wafers was carried out using I<sub>2</sub>-KI as a green leaching reagent. Full factorial experimental design for leaching rate is carried out using MINITAB software. A regression equation on the leaching rate of silver as a response value is established. Iodine concentration, potassium iodide concentration, solid–liquid ratio, and pH are the influencing factors in the regression equation. The parameters for the optimal solution of silver leaching rate were iodine concentration of 0.3 mol/L, solid–liquid ratio of 1:10, pH of 9.6, and potassium iodide concentration of 0.8 mol/L. The results of the response optimization are verified by three sets of parallel experiments, and the silver leaching rate is obtained as 96.62%.
DOI: 10.5281/zenodo.18339883
title: SwiftMHC suppelementary data

description: Supplementary data for publication: https://doi.org/10.1101/2025.01.20.633893.Contains data collected on 7726 IEDB 9-mer HLA-A*02:01 peptide MHC complexes.

Contains data collected on 202 X-ray structures of 9-mer HLA-A*02:01 peptide MHC complexes.
DOI: 10.5281/zenodo.14968655
title: SwiftMHC suppelementary data

description: Supplementary data for publication: https://doi.org/10.1101/2025.01.20.633893.Contains data collected on 7726 IEDB 9-mer HLA-A*02:01 peptide MHC complexes.

Contains data collected on 202 X-ray structures of 9-mer HLA-A*02:01 peptide MHC complexes.
DOI: 10.15468/dl.4b44h2
title: Occurrence Download

description: A dataset containing 181416 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Actinostemon, Adenopeltis, Algernonia, Anomostachys, Balakata, Bonania, Colliguaja, Conosapium, Dalembertia, Dendrocousinsia, Dendrothrix, Excoecaria, Falconeria, Gradyana, Grimmeodendron, Gymnanthes, Hippomane, Homalanthus, Hura, Incadendron, Mabea, Maprounea, Microstachys, Neoshirakia, Ophthalmoblapton, Pachystroma, Pleradenophora, Pseudosenefeldera, Rhodothyrsus, Sapium, Sclerocroton, Sebastiania, Senefeldera, Senefelderopsis, Shirakiopsis, Spegazziniophytum, Spirostachys, Stillingia, Triadica)"
 ]
}

 The dataset includes 181416 records from 851 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004864-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ktuy76
title: Occurrence Download

description: A dataset containing 431 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Allium textile A.Nelson & J.F.Macbr.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 431 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007184-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/ds/7100753
title: Cold_Supply_Chain_Data
DOI: 10.15468/dl.vu35bw
title: Occurrence Download

description: A dataset containing 1741588 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "DatasetKey is EOD – eBird Observation Dataset",
 "Year 2023-2024"
 ]
}

 The dataset includes 1741588 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006909-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ykqqar
title: Occurrence Download

description: A dataset containing 22100 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (iNaturalist Research-grade Observations, Great Backyard Bird Count, Point Reyes Bird Observatory - Point Counts, Observation.org, Nature data from around the World, NABU|naturgucker, NEON breeding landbird point counts, Ontario Breeding Bird Atlas 2001-2005, Temporal and spatial variation of waterbirds at Sayula Lagoon, Jalisco, Mexico: a five-year winter season study, Avifauna de la laguna Madre de Tamaulipas)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pelecanus erythrorhynchos",
 "Year 1970-2020"
 ]
}

 The dataset includes 22100 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006929-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.arv5qd
title: Occurrence Download

description: A dataset containing 7265580 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phaeophyceae"
 ]
}

 The dataset includes 7265580 records from 1502 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006915-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17706019
title: Dataset: Modelling Suffusion in Porous Media Using a Particle Scale Linear Decay Function
DOI: 10.5281/zenodo.15322249
title: Dataset: Modelling Suffusion in Porous Media Using a Particle Scale Linear Decay Function