cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.gfmt3c
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Daucus carota subsp. azoricus Franco",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000953-150512124619364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3f7p6p
title: Occurrence Download

description: A dataset containing 7207 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Agama agama (Linnaeus, 1758)"
 ]
}

 The dataset includes 7207 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0263368-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kc8d56
title: Occurrence Download

description: A dataset containing 12406 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "Geometry POLYGON ((-64.05508 46.5043, -63.69141 46.5043, -63.69141 46.80189, -64.05508 46.80189, -64.05508 46.5043))"
 ]
}

 The dataset includes 12406 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013179-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cuhgnf
title: Occurrence Download

description: A dataset containing 2342 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is Palicourea padifolia (Willd. ex Schult.) C.M.Taylor & Lorence"
 ]
}

 The dataset includes 2342 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004191-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y8md7o
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Turtur abyssinicus (Sharpe, 1902)",
 "InstitutionCode is AMNH"
 ]
}

 The dataset includes 17 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000953-150528172251762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.94z62k
title: Occurrence Download

description: A dataset containing 3858 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hemidactylus platyurus (Schneider, 1797)"
 ]
}

 The dataset includes 3858 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0263390-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.27mjan
title: Occurrence Download

description: A dataset containing 15760 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Commelina diffusa Burm.f."
 ]
}

 The dataset includes 15760 records from 602 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051351-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.527uom
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caulokaempferia saksuwaniae K.Larsen"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000953-150615163101818/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gteph9
title: Occurrence Download

description: A dataset containing 250 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Mauritia flexuosa L.f."
 ]
}

 The dataset includes 250 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0263394-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15470/jow7hd
title: Fungal members of the rhizosphere microbiota of Quercus ilex subsp. ballota

description: The general objective of thE WP7 is to advance our understanding of the impacts of global change drivers - mainly climate change and exotic pathogens - on the above- and below-ground biodiversity of Mediterranean forests and silvopastoral agrosystems, and to use the resulting information to propose management tools aim to improve the resistance and resilience of these forests in scenarios of increasing abiotic and biotic stress. We will focus our research on forests and dehesas of evergreen Quercus species (Quercus suber and Quercus ilex) in Andalusia, due to their strategic ecological and economic importance and their current vulnerability status as a result of increasing aridity and the invasion of the aggressive exotic pathogen Phytophthora cinammomi.
DOI: 10.15468/dl.2bwv6b
title: Occurrence Download

description: A dataset containing 5194 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Thalictrum minus subsp. thunbergii (DC.) Vorosch."
 ]
}

 The dataset includes 5194 records from 136 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051346-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xrdubk
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Buddleja skutchii C.V.Morton",
 "Country is Costa Rica",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 38 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000953-150922153815467/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.49pc28
title: Occurrence Download

description: A dataset containing 61668 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Harmonia axyridis (Pallas, 1773)"
 ]
}

 The dataset includes 61668 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0186083-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ydkb4v
title: Occurrence Download

description: A dataset containing 832 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Argentina",
 "TaxonKey is Cetacea"
 ]
}

 The dataset includes 832 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020689-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jtqs3t
title: Occurrence Download

description: A dataset containing 2967 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sphoeroides pachygaster (Müller & Troschel, 1848)"
 ]
}

 The dataset includes 2967 records from 114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051112-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.du1leb
title: Occurrence Download

description: A dataset containing 157003 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Liliaceae",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 157003 records from 414 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000953-160118175350007/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.476uc7
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pristimantis petersorum"
 ]
}

 The dataset includes 31 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018256-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/32013
title: Chandra X-ray Observatory ObsId 32013

description: A TREASURY SURVEY PROBING THE BARYON & ENERGY CYCLE AND X-RAY BINARY EVOLUTION IN GALAXIES AT HIGH ANGULAR RESOLUTION
DOI: 10.25574/32017
title: Chandra X-ray Observatory ObsId 32017

description: The sounds of feedback: deep and wide imaging of the cool core of the Perseus cluster
DOI: 10.25345/c5nv99q50
title: MassIVE MSV000100053 - APOE4 drives widespread changes to the hepatic proteome and alters metabolic function
title: Unbiased data independent acquisition (DIA) proteomic analysis on APOE3 and APOE4 targeted replacement mice whole livers, isolated liver mitochondria, and APOE3 and APOE4 human iPSC derived hepatocyte like cells (iHLCs). Protein samples were extracted using chloroform/methanol phase separation with a subsequent trypsin digestion to acquire peptides. Samples were analyzed using liquid chromatography mass spectrometry (LC/MS) on a Orbitrap Exploris 480 (Thermo Scientific).
DOI: 10.15468/dl.muwvrc
title: Occurrence Download

description: A dataset containing 97 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phytophthora chlamydospora",
 "HasCoordinate is true",
 "Year is greater than or equal to 1980"
 ]
}

 The dataset includes 97 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018257-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdb9at
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dicyema multimegalum",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018258-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17730882
title: Prioritizing neuroactive ligands using motif-guided docking and zebrafish profiling

description: Virtual screening of ultra-large chemical libraries is a highly effective strategy for early-stage drug discovery. However, these pipelines often yield thousands of molecules that pass computational filters, and in silico-derived interaction energies do not consistently predict experimental efficacy. Furthermore, high-affinity hits do not necessarily function effectively in an organism with tissues, barriers, and extensive off-target possibilities. Thus, a major hurdle in drug discovery is the prioritization of top candidates for rodent testing, which is effortful and costly. Here, we introduce Rosetta Engine for Anchoring Ligands with a Motif (“REAL-M”), a novel computational screening algorithm that uses structural interaction data from the Protein Data Bank (PDB) to guide ligand placement and selection. Using the hypocretin receptor as a test case for this computational pipeline, 28 of 30 predicted antagonists significantly blocked binding of the cognate peptide agonist in a PRESTO-Tango cell-based reporter assay, including six chemically diverse molecules with comparable efficacy to commercial antagonists. Three molecules significantly mitigated hypocretin-induced larval zebrafish hyperactivity. Secondary testing with a zebrafish hcrtr2 null mutant ensured that behavioral phenotypes were not due to off-target interactions, which we did observe with the FDA-approved drug suvorexant. This pipeline is readily adaptable to the thousands of zebrafish proteins with highly conserved binding pockets.
DOI: 10.5281/zenodo.17730881
title: Prioritizing neuroactive ligands using motif-guided docking and zebrafish profiling

description: Virtual screening of ultra-large chemical libraries is a highly effective strategy for early-stage drug discovery. However, these pipelines often yield thousands of molecules that pass computational filters, and in silico-derived interaction energies do not consistently predict experimental efficacy. Furthermore, high-affinity hits do not necessarily function effectively in an organism with tissues, barriers, and extensive off-target possibilities. Thus, a major hurdle in drug discovery is the prioritization of top candidates for rodent testing, which is effortful and costly. Here, we introduce Rosetta Engine for Anchoring Ligands with a Motif (“REAL-M”), a novel computational screening algorithm that uses structural interaction data from the Protein Data Bank (PDB) to guide ligand placement and selection. Using the hypocretin receptor as a test case for this computational pipeline, 28 of 30 predicted antagonists significantly blocked binding of the cognate peptide agonist in a PRESTO-Tango cell-based reporter assay, including six chemically diverse molecules with comparable efficacy to commercial antagonists. Three molecules significantly mitigated hypocretin-induced larval zebrafish hyperactivity. Secondary testing with a zebrafish hcrtr2 null mutant ensured that behavioral phenotypes were not due to off-target interactions, which we did observe with the FDA-approved drug suvorexant. This pipeline is readily adaptable to the thousands of zebrafish proteins with highly conserved binding pockets.
DOI: 10.15468/dl.v5kzv4
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pristimantis phalaroinguinis"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018259-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bdjmu9
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phytophthora chrysanthemi",
 "HasCoordinate is true",
 "Year is greater than or equal to 1980"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018260-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.he3akg
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dicyema vincentense",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018261-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s7uc5x
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pristimantis phalarus"
 ]
}

 The dataset includes 11 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018262-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17729139
title: Neural Surrogate HMC: On Using Neural Likelihoods for Hamiltonian Monte Carlo in Simulation-Based Inference
title: Dataset Part 1/4

description: Data and results used in the paper "Neural Surrogate HMC: On Using Neural Likelihoods for Hamiltonian Monte Carlo in Simulation-Based Inference" by Wolniewicz et al. The code used to work with this data can be found on GitHub: https://github.com/hawaii-ai/GalacticCosmicRays.



ams_pamela_observations.zip: .dat files with the observations from PAMELA and AMS-02 used for generating posterior samples.

nn_models.zip: all the NN .keras files used to produce results (these are used to create Figure 3 in the paper).

posterior_predictive_test.zip: .dat files with flux values used to perform the posterior predictive test in the paper.

train_test_data.zip: .h5 files that contain the train and test data used to train and test the NN models (and perform the posterior predictive test).

logprobs_d1_b0_init1_hmc1.zip: log probability .csv files from sampling for the two intervals shown in the paper in Figures 11 and 14 (AMS-02 interval #48, and PAMELA interval #107).

predictions_d1_b0_init1_hmc1.zip: prediction .csv files from sampling for the two intervals shown in the paper in Figures 11 and 14 (AMS-02 interval #48, and PAMELA interval #107).

posterior_predictive_samples.zip: all posterior samples for various NN models and bootstrapped training datasets across a subset of 100 held-out simulation runs (these are used to create Figures 8 and 9 in the paper).

all_sample_files.zip: all posterior samples for various NN models, HMC initializations, and bootstrapped training datasets.





d1_b0_sample_files.zip: all posterior samples for the non-bootstrapped data versions (these are used to create Figures 10, 11, and 14 in the paper).




Naming convention of sample and model files:



There are two kinds of dataset sampling: b1 for bootstrap-sampled training data, and b0 for non-bootstrapped. b0 is only used for training on the entire training set.

There are 5 random HMC re-initializations: hmc1, hmc2, hmc3, hmc4, and hmc5

There are 5 bootstrap sampled datasets: d1, d2, d3, d4, and d5

There are 5 NN model re-initializations: init1, init2, init3, init4, and init5

Training data is of size: 0.0001, 0.001, 0.01, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0


Dataset 1/4 contains all the train and test data, NN model files, posterior predictive test observation and posterior samples, AMS-02 and PAMELA observation and posterior samples (non-bootstrap sampled datasets), and the logprobs and predictions needed to recreate Figures 10, 11, and 14 from the paper.
DOI: 10.15468/dl.6bsatc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phytophthora cichorii",
 "HasCoordinate is true",
 "Year is greater than or equal to 1980"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018263-251120083545085/datasets/export for details.
DOI: 10.15468/dl.r79sut
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dicyemennea spencerense",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018264-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4zufsb
title: Occurrence Download

description: A dataset containing 8060833 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is Oceania",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 8060833 records from 502 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018230-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uhdt2u
title: Occurrence Download

description: A dataset containing 524 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pristimantis phoxocephalus"
 ]
}

 The dataset includes 524 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018268-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.88zhcr
title: Occurrence Download

description: A dataset containing 385114 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Origanum vulgare",
 "HasCoordinate is true"
 ]
}

 The dataset includes 385114 records from 2346 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018217-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2gnyx3
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vaccinium whitfordii Merr."
 ]
}

 The dataset includes 91 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0129658-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qew9ub
title: Occurrence Download

description: A dataset containing 2789 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Argentina",
 "Country is Bolivia (Plurinational State of)",
 "Country is Peru",
 "Country is United States of America",
 "Country is Brazil",
 "Country is Ecuador"
 ]
 },
 "TaxonKey is Solanum boliviense Dunal"
 ]
}

 The dataset includes 2789 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008127-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yj8459
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erica occulta E.G.H.Oliv."
 ]
}

 The dataset includes 55 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045560-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.999t33
title: Occurrence Download

description: A dataset containing 231 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Geophagus harreri Gosse, 1976"
 ]
}

 The dataset includes 231 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0117018-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.