cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26870461
title: AutoMIND: model configurations, simulations, target observations (experimental data), and trained deep generative models

description: Data here include:Training (prior samples) and discovered (posterior samples) parameter configurations of the clustered-AdEx spiking neural network,summary features of the corresponding simulations,summary features of the target observations (on which posterior density estimators are conditioned),and trained deep generative models (Normalizing Flow-based neural density estimators).For details, see: Gao et al., 2024, Deep inverse modeling reveals dynamic-dependent invariances in neural circuit mechanisms.<br>Data directories are organized as follows:./training_prior_samples/training.zip: 1-million parameter configurations and summary features from model simulations used to train deep generative models.heldout.zip: additional network simulations not used for DGM training, a subset of which was used as synthetic observations../discovered_posterior_samples/organoids.zip: discovered model configurations consistent with human brain organoid network burst across development. See ./organoid_predictives.png.mouse-vis.zip: discovered model configurations consistent with population firing rate PSD of Neuropixels recordings from mouse visual areas. See ./allen_predicitves_all.png.mouse-hc.zip: discovered model configurations consistent with population firing rate PSD of Neuropixels recordings from mouse hippocampal areas. See ./allen_predicitves_all.png.synthetic.zip: discovered model configurations consistent with population firing rate PSD of synthetic observations, i.e., held-out network simulations. See ./synthetic.png.<b>NOTE</b>: all zip files also contain the prior distribution, posterior density estimator, and config files necessary for running the simulations and analyses../dgms/burst_posterior.pickle: trained conditional density estimator that approximates the posterior distribution conditioned on network burst summary features.psd_posterior.pickle: trained conditional density estimator that approximates the posterior distribution. conditioned on network firing rate power spectral densities../observations/allenvc_summary: population firing rate PSD of Neuropixels recordings.synthetic_summary: various summary features of synthetic observations (i.e., held-out network simulations).organoid_summary: population firing burst statistics of organoid multi-electrode array recordings.<br>It's recommended to keep the full path when downloading and unzipping for consistency with e.g., code demo.Note that the raw simulation (i.e., spike times from recorded neurons) data files are too large and exceed the figshare upload file size limit. They will be provided elsewhere and linked here.
DOI: 10.6084/m9.figshare.26870461.v2
title: AutoMIND: model configurations, simulations, target observations (experimental data), and trained deep generative models

description: Data here include:Training (prior samples) and discovered (posterior samples) parameter configurations of the clustered-AdEx spiking neural network,summary features of the corresponding simulations,summary features of the target observations (on which posterior density estimators are conditioned),and trained deep generative models (Normalizing Flow-based neural density estimators).For details, see: Gao et al., 2024, Deep inverse modeling reveals dynamic-dependent invariances in neural circuit mechanisms.<br>Data directories are organized as follows:./training_prior_samples/training.zip: 1-million parameter configurations and summary features from model simulations used to train deep generative models.heldout.zip: additional network simulations not used for DGM training, a subset of which was used as synthetic observations../discovered_posterior_samples/organoids.zip: discovered model configurations consistent with human brain organoid network burst across development. See ./organoid_predictives.png.mouse-vis.zip: discovered model configurations consistent with population firing rate PSD of Neuropixels recordings from mouse visual areas. See ./allen_predicitves_all.png.mouse-hc.zip: discovered model configurations consistent with population firing rate PSD of Neuropixels recordings from mouse hippocampal areas. See ./allen_predicitves_all.png.synthetic.zip: discovered model configurations consistent with population firing rate PSD of synthetic observations, i.e., held-out network simulations. See ./synthetic.png.<b>NOTE</b>: all zip files also contain the prior distribution, posterior density estimator, and config files necessary for running the simulations and analyses../dgms/burst_posterior.pickle: trained conditional density estimator that approximates the posterior distribution conditioned on network burst summary features.psd_posterior.pickle: trained conditional density estimator that approximates the posterior distribution. conditioned on network firing rate power spectral densities../observations/allenvc_summary: population firing rate PSD of Neuropixels recordings.synthetic_summary: various summary features of synthetic observations (i.e., held-out network simulations).organoid_summary: population firing burst statistics of organoid multi-electrode array recordings.<br>It's recommended to keep the full path when downloading and unzipping for consistency with e.g., code demo.Note that the raw simulation (i.e., spike times from recorded neurons) data files are too large and exceed the figshare upload file size limit. They will be provided elsewhere and linked here.
DOI: 10.15468/dl.wr75u2
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ludwigia brenanii H.Hara"
 ]
}

 The dataset includes 43 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028072-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.epp4qf
title: Occurrence Download

description: A dataset containing 6166 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gagea bohemica (Zauschn.) Schult. & Schult.f.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 6166 records from 188 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028071-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nxyfut
title: Occurrence Download

description: A dataset containing 104 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Galium austriacum Jacq.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 104 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028077-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ej32kz
title: Occurrence Download

description: A dataset containing 212 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ludwigia senegalensis (DC.) Troch."
 ]
}

 The dataset includes 212 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028075-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14186867
title: Electronic supplemental material (ESM) for: Are consumers willing to pay more for sustainable wine? A pre-registered systematic review and meta-analysis

description: Electronic supplemental material (ESM) for: Are consumers willing to pay more for sustainable wine? A pre-registered systematic review and meta-analysis
DOI: 10.15468/dl.x2zkwg
title: Occurrence Download

description: A dataset containing 3025 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-68.47413 -35.27437,105.47413 -35.27437,105.47413 34.27437,-68.47413 34.27437,-68.47413 -35.27437))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Badula Juss."
 ]
}

 The dataset includes 3025 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028076-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dgwd7y
title: Occurrence Download

description: A dataset containing 7209 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liometopum Mayr, 1861"
 ]
}

 The dataset includes 7209 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028073-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f5w84d
title: Occurrence Download

description: A dataset containing 20491 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Atta Fabricius, 1804"
 ]
}

 The dataset includes 20491 records from 149 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028074-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hn8va2
title: Occurrence Download

description: A dataset listing the 2322 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Italy",
 "GadmGid is ITA.6.7.14_1",
 "GbifRegion is Europe and Central Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 2322 records were derived from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028054-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6ukb56
title: Occurrence Download

description: A dataset containing 669 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ludwigia stenorraphe (Brenan) H.Hara"
 ]
}

 The dataset includes 669 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028079-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z3c7da
title: Occurrence Download

description: A dataset containing 265 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gelasia villosa (Scop.) Cass.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 265 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028080-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ujjjat
title: Occurrence Download

description: A dataset containing 3023 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((41.59552 -28.4366,68.32699 -29.51765,70.68564 -9.56733,55.35435 -7.99489,37.27131 -14.57948,41.59552 -28.4366))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Badula Juss."
 ]
}

 The dataset includes 3023 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028083-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q33pmx
title: Occurrence Download

description: A dataset containing 2869 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material citation, Specimen, Occurrence evidence)",
 "Country is one of (Mexico, Costa Rica, Guatemala, Honduras, Panama, El Salvador, Nicaragua)",
 "Geometry POLYGON((-122.53651 4.47918,-62.46349 4.47918,-62.46349 28.52082,-122.53651 28.52082,-122.53651 4.47918))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Abronia Gray, 1838"
 ]
}

 The dataset includes 2869 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028082-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.46bf7s
title: Occurrence Download

description: A dataset containing 1363 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ludwigia affinis (DC.) H.Hara"
 ]
}

 The dataset includes 1363 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028085-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bsx72a
title: Occurrence Download

description: A dataset containing 20736 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Loxodonta africana (Blumenbach, 1797)"
 ]
}

 The dataset includes 20736 records from 153 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028081-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5kydug
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Genista holopetala (Fleischm. ex W.D.J.Koch) Bald.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028086-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v8tpp5
title: Occurrence Download

description: A dataset containing 12386 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Spain",
 "OccurrenceStatus is Present",
 "TaxonKey is Sciurus vulgaris Linnaeus, 1758"
 ]
}

 The dataset includes 12386 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028084-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13750795
title: Differential impact of impaired steryl ester biosynthesis on the metabolome of tomato seeds and fruits

description: Steryl esters (SE) are a storage pool of sterols that accumulates in cytoplasmic lipid droplets and helps to maintaining plasma membrane sterol homeostasis throughout plant growth and development. Ester formation of plant SE is catalyzed by phospholipid:sterol acyltransferase (PSAT) and acyl-CoA:sterol acyltransferase (ASAT), which transfer long-chain fatty acid groups to free sterols from phospholipids and acyl-CoA, respectively. Comparative mass spectrometry-based metabolomic analysis between ripe fruits and seeds of a tomato (Solanum lycopersicum cv Micro-Tom) mutant lacking functional PSAT and ASAT enzymes (slasat1xslpsat1) shows that disruption of SE biosynthesis has a differential impact on the metabolome of these organs, including changes in the relative proportions of free and glycosylated sterols. Significant perturbations were observed in the fruit lipidome in contrast to the mild effect detected in the lipidome of seeds. A contrasting response was also observed in phenylpropanoid metabolism, which is down-regulated in fruits and appears to be stimulated in seeds. Comparison of global metabolic changes using volcano plot analysis suggests that disruption of SE biosynthesis favors a general state of metabolic activation that is more evident in seeds than fruits. Interestingly, there is an induction of autophagy in both tissues, which may contribute along with other metabolic changes to the phenotypes of early seed germination and enhanced fruit resistance to Botrytis cinerea displayed by the slasat1xslpsat1 mutant. The results of this study reveal unreported connections between SE metabolism and the metabolic status of plant cells, and lay the basis for further studies aimed at elucidating the mechanisms underlying the observed effects.

 

Data: 

W1-54; AxP LC polar.zip: raw files LC-polar

W1-1 (1)-(54); AxP LC lipid.zip: raw files lipid LC

GCtomato.zip: raw files GC polar

spreadsheet (.csv) with sample IDs
DOI: 10.5281/zenodo.13750796
title: Differential impact of impaired steryl ester biosynthesis on the metabolome of tomato seeds and fruits

description: Steryl esters (SE) are a storage pool of sterols that accumulates in cytoplasmic lipid droplets and helps to maintaining plasma membrane sterol homeostasis throughout plant growth and development. Ester formation of plant SE is catalyzed by phospholipid:sterol acyltransferase (PSAT) and acyl-CoA:sterol acyltransferase (ASAT), which transfer long-chain fatty acid groups to free sterols from phospholipids and acyl-CoA, respectively. Comparative mass spectrometry-based metabolomic analysis between ripe fruits and seeds of a tomato (Solanum lycopersicum cv Micro-Tom) mutant lacking functional PSAT and ASAT enzymes (slasat1xslpsat1) shows that disruption of SE biosynthesis has a differential impact on the metabolome of these organs, including changes in the relative proportions of free and glycosylated sterols. Significant perturbations were observed in the fruit lipidome in contrast to the mild effect detected in the lipidome of seeds. A contrasting response was also observed in phenylpropanoid metabolism, which is down-regulated in fruits and appears to be stimulated in seeds. Comparison of global metabolic changes using volcano plot analysis suggests that disruption of SE biosynthesis favors a general state of metabolic activation that is more evident in seeds than fruits. Interestingly, there is an induction of autophagy in both tissues, which may contribute along with other metabolic changes to the phenotypes of early seed germination and enhanced fruit resistance to Botrytis cinerea displayed by the slasat1xslpsat1 mutant. The results of this study reveal unreported connections between SE metabolism and the metabolic status of plant cells, and lay the basis for further studies aimed at elucidating the mechanisms underlying the observed effects.

 

Data: 

W1-54; AxP LC polar.zip: raw files LC-polar

W1-1 (1)-(54); AxP LC lipid.zip: raw files lipid LC

GCtomato.zip: raw files GC polar

spreadsheet (.csv) with sample IDs
DOI: 10.6084/m9.figshare.27875562
title: Source data for graphs and charts for 'Over 60% precipitation transformed into terrestrial water storage in global river basins from 2002 to 2021'

description: The crucial role of precipitation as a primary driver for terrestrial water cycle is well-established. However, quantifying the transformation of daily precipitation into terrestrial water storage remains a challenge. Here we address this by introducing a quantitative metric, average daily fraction of precipitation transformed into terrestrial water storage (DF<sub>P-TWS</sub>), providing a important advancement into the dynamics of water storage by utilizing the enhanced terrestrial water storage statistical reconstruction method and water storage data from the Gravity Recovery and Climate Experiment satellites and their follow-on mission. This dataset provides the source data for graphs and charts in this study, including DF<sub>P-TWS</sub>, DF<sub>P-SSM</sub>, and their driver data. We encourage all figures to be drawn in Generic Mapping Tools.
DOI: 10.6084/m9.figshare.27875562.v1
title: Source data for graphs and charts

description: The crucial role of precipitation as a primary driver for terrestrial water cycle is well-established. However, quantifying the transformation of daily precipitation into terrestrial water storage remains a challenge. Here we address this by introducing a quantitative metric, average daily fraction of precipitation transformed into terrestrial water storage (DF<sub>P-TWS</sub>), providing a important advancement into the dynamics of water storage by utilizing the enhanced terrestrial water storage statistical reconstruction method and water storage data from the Gravity Recovery and Climate Experiment satellites and their follow-on mission. This dataset provides the source data for graphs and charts in this study, including DF<sub>P-TWS</sub>, DF<sub>P-SSM</sub>, and their driver data. We encourage all figures to be drawn in Generic Mapping Tools.
DOI: 10.15468/dl.ewheuv
title: Occurrence Download

description: A dataset listing the 907 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Italy",
 "GadmGid is ITA.6.9.14_1",
 "GbifRegion is Europe and Central Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 907 records were derived from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028059-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cz95z3
title: Occurrence Download

description: A dataset containing 2727 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Spain, Portugal)",
 "DatasetKey is one of (Observation.org, Nature data from around the World, iNaturalist Research-grade Observations, Biodiversity4all Research-Grade Observations)",
 "TaxonKey is Ameles spallanzania Rossi, 1792"
 ]
}

 The dataset includes 2727 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019981-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mzqqcg
title: Occurrence Download

description: A dataset containing 243902 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Spain, Portugal)",
 "TaxonKey is Cervus elaphus Linnaeus, 1758"
 ]
}

 The dataset includes 243902 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069672-250525065834625/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.28777829
title: Replication package of "An empirical evaluation of white-box and black-box test case prioritization techniques in CPSs modeled in Simulink"

description: Replication package of the paper.
DOI: 10.34740/kaggle/dsv/11366615
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.25582/data.2024-02.3033734/2548594
title: Data for EMSL Project 60579 from February 2024
DOI: 10.25582/data.2024-02.3033736/2548595
title: Data for EMSL Project 60579 from February 2024
DOI: 10.25582/data.2024-02.3033737/2548596
title: Data for EMSL Project 60579 from February 2024
DOI: 10.25582/data.2024-02.3033738/2548597
title: Data for EMSL Project 60579 from February 2024