cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14826462
title: Prevalence and correlates of the head turning sign in mild cognitive impairment and dementia due to neurodegenerative, chronic cerebrovascular, and mixed etiologies

description: Dataset associated with the paper "Prevalence and correlates of the head turning sign in mild cognitive impairment and dementia due to neurodegenerative, chronic cerebrovascular, and mixed etiologies". These datasets cannot be made publicly available on legal and ethical grounds but can be made available upon reasonable request of interested researchers to the Corresponding Author(s), who will forward a request for a data transfer agreement to the relevant Ethical Committee(s). Please, write to Dr. Federico Verde (f.verde@auxologico.it).
DOI: 10.15468/dl.5hxau7
title: Occurrence Download

description: A dataset listing the 11892 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "TaxonKey is Mammalia"
 ]
}

 The dataset's 11892 records were derived from 928 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018326-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pcvjhk
title: Occurrence Download

description: A dataset containing 418 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Abronia taeniata (Wiegmann, 1828)"
 ]
}

 The dataset includes 418 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018355-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14811975
title: Supporting data: Structure-based simulations for large protein assemblies

description: Dataset description:

gprotein: - inputs: contains the inputs as they should be copied into MEGO_ROOT to make multi-ego work  - multi-ego: contains the simulations that are done with multi-ego    - equilibrium simulations: contains the native state simulations with multi-ego    - folding_simulations: contains scripts necessary to run and analyse folding simulations - training: plain MD used for training

ab_titration: - mego_inputs: contains the abeta_ligand input directory as it should be copied into MEGO_ROOT/inputs/ to make multi-ego work for the Ab42:10074-G5 complex  - calculate_Kd.ipynb: jupyter notebook to run the analysis of the in silico titration  - scripts: all the scripts to prepare the titration simulation directories and to perform the post-simulation analysis 

aav7: the directory as it should be put in MEGO_ROOT/inputs to run the simulation
DOI: 10.5281/zenodo.14811976
title: Supporting data: Structure-based simulations for large protein assemblies

description: Dataset description:

gprotein: - inputs: contains the inputs as they should be copied into MEGO_ROOT to make multi-ego work  - multi-ego: contains the simulations that are done with multi-ego    - equilibrium simulations: contains the native state simulations with multi-ego    - folding_simulations: contains scripts necessary to run and analyse folding simulations - training: plain MD used for training

ab_titration: - mego_inputs: contains the abeta_ligand input directory as it should be copied into MEGO_ROOT/inputs/ to make multi-ego work for the Ab42:10074-G5 complex  - calculate_Kd.ipynb: jupyter notebook to run the analysis of the in silico titration  - scripts: all the scripts to prepare the titration simulation directories and to perform the post-simulation analysis 

aav7: the directory as it should be put in MEGO_ROOT/inputs to run the simulation
DOI: 10.5281/zenodo.10958545
title: brpop package datasets
DOI: 10.5281/zenodo.10958546
title: brpop package datasets
DOI: 10.5281/zenodo.10960347
title: brpop package datasets
DOI: 10.5281/zenodo.13946759
title: brpop package datasets
DOI: 10.5281/zenodo.13946877
title: brpop package datasets
DOI: 10.5281/zenodo.14825360
title: brpop package datasets
DOI: 10.5281/zenodo.14825514
title: brpop package datasets
DOI: 10.5281/zenodo.14826487
title: brpop package datasets
DOI: 10.15468/dl.kvcyrj
title: Occurrence Download

description: A dataset containing 418 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Abronia taeniata (Wiegmann, 1828)"
 ]
}

 The dataset includes 418 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018356-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14826481
title: Quantification tables of SNr molecular organization

description: Quantification tables associated with the manuscript Segregated basal ganglia output pathways correspond to genetically divergent neuronal subclasses.
DOI: 10.5281/zenodo.14826482
title: Quantification tables of SNr molecular organization

description: Quantification tables associated with the manuscript Segregated basal ganglia output pathways correspond to genetically divergent neuronal subclasses.
DOI: 10.34740/kaggle/dsv/10680778
title: Lung Cancer Risk & Trends Across 25 Countries
DOI: 10.5285/2cc3a34f-30fc-cd5e-e063-7086abc0dc3d
title: Coccolithophore community composition and abundance by light microscopy from CTD bottles and surface underway samples during the Atlantic Meridional Transect AMT19 (JC039) cruise in October-December 2009

description: This dataset contains coccolithophore abundance data from CTD bottles and surface underway samples collected during the JC039 cruise in the Atlantic between Falmouth, UK and Punta Arenas, Chile in October-December 2009. Niskin samples were collected during the pre-dawn CTD (second cast of the day) from six light depths (1%, 7%, 14%, 33%, 55%, 97%) and from two deeper (down to 200 m) depths for coccolith enumeration. Samples were collected from the non-toxic water supply 3 times per day, approximately every 3 to 4 hours spaced between CTD stations. Coccolith and cell counts were collected on Millipore HA (nitrocellulose) filters which were rinsed with a potassium tetraborate buffer and frozen at 20 °C. Samples were then dried and mounted onto slides using Norland Optical Adhesive. These were then enumerated by birefringence microscopy (Balch et al. 2011). These data were collected by scientists from the Bigelow Laboratory for Ocean Sciences and contribute to the Atlantic Meridional Transect (AMT) project.
DOI: 10.5281/zenodo.14825517
title: Data for "Temperature dependent energy gap for Yu-Shiba-Rusinov states at the quantum phase transition"

description: Data used for the generation of the Figures in the work "Temperature dependent energy gap for Yu-Shiba-Rusinov states at the quantum phase transition". The data columns are labeled the same as in the publication.
DOI: 10.5281/zenodo.14825518
title: Data for "Temperature dependent energy gap for Yu-Shiba-Rusinov states at the quantum phase transition"

description: Data used for the generation of the Figures in the work "Temperature dependent energy gap for Yu-Shiba-Rusinov states at the quantum phase transition". The data columns are labeled the same as in the publication.
DOI: 10.15468/dl.ew68c9
title: Occurrence Download

description: A dataset listing the 2586 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "TaxonKey is Squamata"
 ]
}

 The dataset's 2586 records were derived from 223 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018321-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6q3gj4
title: Occurrence Download

description: A dataset containing 1662 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nassella tenuissima (Trin.) Barkworth"
 ]
}

 The dataset includes 1662 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018357-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ncztgj
title: Occurrence Download

description: A dataset containing 219 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Canada",
 "Country is Canada"
 ]
 },
 "TaxonKey is one of (Polypodium appalachianum Haufler & Windham)"
 ]
}

 The dataset includes 219 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018358-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12582373
title: CRABS CLAW-independent floral nectary development in Penstemon barbatus

description: Data and Scripts for the "CRABS CLAW-independent floral nectary development in Penstemon barbatus" manuscript.

 

Scripts:



fastp.sh - filter and quality trim reads using fastp on all samples

1ribo_detect.sh - detect and filter rRNA. Example script for 1 sample.

gffread.sh - convert P. barbatus genome annotation GFF to a GTF for use in STAR

star_initalize.sh - initalize STAR for the P. barbatus genome

1star_ribo.sh - Example script for aligning reads from 1 sample to the genome.

htseq_ribo.sh - counting reads for each sample using HTseq

deseq2_code.R - R script for running the transcriptome tissue comparisons in DEseq2 with the output from HTseq.

deseq_PCA.R - R script for the generation of the PCA plots for the samples. To be used in conjuction with the deseq2_code.R script.

20230321_topGO_script.R - R script for Gene Ontology analyses in topGO.

area_perimeter_cor.R - R script for vasculature ANOVAs.


 

Data:



Genome files



4_LG_2022_maker.all.maker.proteins.fasta - protein sequences for all genes in the P. barbatus genome in Wessinger et al. 2023

4_LG_2022_maker.all.maker.noseq.gff - GFF file for all genes in the P. barbatus genome in Wessinger et al. 2023



HTseq output trimmed to only the counts (excludes other log information) - trimmed_htseq_35404342.txt

DEseq2 output 



Early stage



barb_early_nect_nonect_FDR0.01_LFC0.csv

barb_early_nect_nonect_FDR0.01_LFC0.annotated.csv



Late stage



barb_late_nect_nonect_FDR0.01_LFC0.csv

barb_late_nect_nonect_FDR0.01_LFC0.annotated.csv



Nectar removal



barb_stage5_6_FDR0.01_LFC0.csv

barb_stage5_6_FDR0.01_LFC0.annotated.csv





Orthofinder output - N0.tsv

Vasculature raw data - 20231025_bud_measurements_pbarb.csv

Archive_Images directory - contains raw section images stained with either Alcian Blue & Safranin O or
DOI: 10.5281/zenodo.12582374
title: CRABS CLAW-independent floral nectary development in Penstemon barbatus

description: Data and Scripts for the "CRABS CLAW-independent floral nectary development in Penstemon barbatus" manuscript.

 

Scripts:



fastp.sh - filter and quality trim reads using fastp on all samples

1ribo_detect.sh - detect and filter rRNA. Example script for 1 sample.

gffread.sh - convert P. barbatus genome annotation GFF to a GTF for use in STAR

star_initalize.sh - initalize STAR for the P. barbatus genome

1star_ribo.sh - Example script for aligning reads from 1 sample to the genome.

htseq_ribo.sh - counting reads for each sample using HTseq

deseq2_code.R - R script for running the transcriptome tissue comparisons in DEseq2 with the output from HTseq.

deseq_PCA.R - R script for the generation of the PCA plots for the samples. To be used in conjuction with the deseq2_code.R script.

20230321_topGO_script.R - R script for Gene Ontology analyses in topGO.

area_perimeter_cor.R - R script for vasculature ANOVAs.


 

Data:



Genome files



4_LG_2022_maker.all.maker.proteins.fasta - protein sequences for all genes in the P. barbatus genome in Wessinger et al. 2023

4_LG_2022_maker.all.maker.noseq.gff - GFF file for all genes in the P. barbatus genome in Wessinger et al. 2023



HTseq output trimmed to only the counts (excludes other log information) - trimmed_htseq_35404342.txt

DEseq2 output 



Early stage



barb_early_nect_nonect_FDR0.01_LFC0.csv

barb_early_nect_nonect_FDR0.01_LFC0.annotated.csv



Late stage



barb_late_nect_nonect_FDR0.01_LFC0.csv

barb_late_nect_nonect_FDR0.01_LFC0.annotated.csv



Nectar removal



barb_stage5_6_FDR0.01_LFC0.csv

barb_stage5_6_FDR0.01_LFC0.annotated.csv





Orthofinder output - N0.tsv

Vasculature raw data - 20231025_bud_measurements_pbarb.csv
DOI: 10.5281/zenodo.14825894
title: CRABS CLAW-independent floral nectary development in Penstemon barbatus

description: Data and Scripts for the "CRABS CLAW-independent floral nectary development in Penstemon barbatus" manuscript.

 

Scripts:



fastp.sh - filter and quality trim reads using fastp on all samples

1ribo_detect.sh - detect and filter rRNA. Example script for 1 sample.

gffread.sh - convert P. barbatus genome annotation GFF to a GTF for use in STAR

star_initalize.sh - initalize STAR for the P. barbatus genome

1star_ribo.sh - Example script for aligning reads from 1 sample to the genome.

htseq_ribo.sh - counting reads for each sample using HTseq

deseq2_code.R - R script for running the transcriptome tissue comparisons in DEseq2 with the output from HTseq.

deseq_PCA.R - R script for the generation of the PCA plots for the samples. To be used in conjuction with the deseq2_code.R script.

20230321_topGO_script.R - R script for Gene Ontology analyses in topGO.

area_perimeter_cor.R - R script for vasculature ANOVAs.


 

Data:



Genome files



4_LG_2022_maker.all.maker.proteins.fasta - protein sequences for all genes in the P. barbatus genome in Wessinger et al. 2023

4_LG_2022_maker.all.maker.noseq.gff - GFF file for all genes in the P. barbatus genome in Wessinger et al. 2023



HTseq output trimmed to only the counts (excludes other log information) - trimmed_htseq_35404342.txt

DEseq2 output 



Early stage



barb_early_nect_nonect_FDR0.01_LFC0.csv

barb_early_nect_nonect_FDR0.01_LFC0.annotated.csv



Late stage



barb_late_nect_nonect_FDR0.01_LFC0.csv

barb_late_nect_nonect_FDR0.01_LFC0.annotated.csv



Nectar removal



barb_stage5_6_FDR0.01_LFC0.csv

barb_stage5_6_FDR0.01_LFC0.annotated.csv





Orthofinder output - N0.tsv

Vasculature raw data - 20231025_bud_measurements_pbarb.csv

Archive_Images directory - contains raw section images stained with either Alcian Blue & Safranin O or
DOI: 10.15468/dl.9phrje
title: Occurrence Download

description: A dataset containing 418 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Abronia taeniata (Wiegmann, 1828)"
 ]
}

 The dataset includes 418 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018359-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7cd9gc
title: Occurrence Download

description: A dataset containing 22667697 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Corvus splendens Vieillot, 1817, Corvus frugilegus Linnaeus, 1758, Corvus corone Linnaeus, 1758, Corvus cornix Linnaeus, 1758, Corvus macrorhynchos Wagler, 1827, Corvus levaillantii Lesson, 1831, Corvus culminatus Sykes, 1832, Corvus ruficollis Lesson, 1831, Corvus corax Linnaeus, 1758)"
 ]
}

 The dataset includes 22667697 records from 7165 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018320-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.16508.05768
title: Opinion on postdoctoral dissertation of Cygnar by professor Mikielewicz
DOI: 10.15468/dl.6g54pt
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Comastoma tenellum"
 ]
}

 The dataset includes 21 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041749-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.23245.15842
title: Galeotti's Russia Analysis
DOI: 10.13140/rg.2.2.15800.26888
title: CDF Perfect 3D-curve example h1&g1
DOI: 10.13140/rg.2.2.16219.69921
title: IMG 6997 - ResearchGate Achievement - July 4, 2021
DOI: 10.15468/dl.y387fe
title: Occurrence Download

description: A dataset containing 219 records in GBIF matching the query:
 
SELECT
 level0gid,
 GBIF_ISEA3HCode(
 9, 
 decimalLatitude,
 decimalLongitude,
 COALESCE(coordinateUncertaintyInMeters, 1000)
 ) AS geogrid_id,
 COUNT(DISTINCT speciesKey) AS unique_species_count
FROM occurrence
WHERE level0gid='BWA'
AND kingdomKey IN (1, 6) -- Animals and Plants only
AND coordinateUncertaintyInMeters &lt;= 2000
AND hasGeospatialIssues = FALSE
AND hasCoordinate = TRUE
AND occurrenceStatus = 'PRESENT'
GROUP BY level0gid, geogrid_id;


 The dataset's 219 records were derived from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041734-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2md44t
title: Occurrence Download

description: A dataset listing the 21 species recorded in GBIF matching the query:
{
 "and" : [
 "GadmGid is CAN.1.2.30_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Bombus Latreille, 1802"
 ]
}

 The dataset's 21 records were derived from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0258390-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rtwpx5
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Leopardus tigrinus (Schreber, 1775)"
 ]
}

 The dataset includes 18 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0213812-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2g2tw4
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Guatemala",
 "DatasetKey is Senckenberg - CeDAMar Resource"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0233056-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bnndcn
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Living Specimen, Specimen)",
 "Country is Japan",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Prunus padus L., Prunus padus Brandis, Prunus padus Ledeb., Prunus padus Nakai)"
 ]
}

 The dataset includes 48 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0213824-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k9dxxh
title: Occurrence Download

description: A dataset containing 144 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Grangea lyrata (DC.) Fayed"
 ]
}

 The dataset includes 144 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0233077-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e5j2np
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pomponia yayeyamana Kato, 1933",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0221084-220831081235567/datasets/export for details.
DOI: 10.15468/dl.e2b4rc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Crossocerus takeuchii Tsuneki & Tanaka, 1955",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0221088-220831081235567/datasets/export for details.
DOI: 10.15468/dl.qrvjjz
title: Occurrence Download

description: A dataset listing the 8 species recorded in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "GadmGid is one of (COL.30.22_2)",
 "Locality is one of (vereda china alta, caserío, río la china, antes de la unión con el río totare, río la china, río la china, estación 2, río la china, antes unión con el río totare, río la china, estación 1)"
 ]
 }
 ]
}

 The dataset's 8 records were derived from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0258410-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x38zq6
title: Occurrence Download

description: A dataset containing 271689 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is FrogID"
 ]
}

 The dataset includes 271689 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0232243-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q5k33f
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acanthosaura capra Günther, 1861",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0213872-220831081235567/datasets/export for details.
DOI: 10.15468/dl.whhuf8
title: Occurrence Download

description: A dataset containing 666 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Netherlands, Germany, United Kingdom of Great Britain and Northern Ireland, Sweden, France, Austria, Luxembourg, Belgium)",
 "TaxonKey is Cacoxenus indagator Loew, 1858"
 ]
}

 The dataset includes 666 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0233063-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hepwks
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cathartes aura (Linnaeus, 1758)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0213823-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.