cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25592/uhhfdm.18255
title: Supporting Information Data for the Publication "Predicting Ligand Binding Modes by Scaffold-Guided Structure Refinement"

description: This dataset is part of the supporting information for the publication "Predicting Ligand Binding Modes by Scaffold-Guided Structure Refinement" by Pletzer-Zelgert et.al.

It contains a directory for each of the three protein targets discussed in the publication FABP4, ADCY10 and PDE10. These directories will contain the following files:<br>
• Initial models used as input (One for FABP4 and ADCY10, Five for PDE10).<br>
• One file containing all series ligands in the SDF format.<br>
• One txt file containing ligand names, ligand SMILES and measured activities.<br>
• One csv file containing all information from the evaluation.<br>
• One subdirectory containing the successfully identified model as a pdb file containing<br>
the protein, an SD file containing the docked ligand poses, as well as one Mol2 file<br>
containing the representative scaffold for the cluster.
DOI: 10.25592/uhhfdm.18236
title: Supporting Information Data for the Publication "Predicting Ligand Binding Modes by Scaffold-Guided Structure Refinement"

description: This dataset is part of the supporting information for the publication "Predicting Ligand Binding Modes by Scaffold-Guided Structure Refinement" by Pletzer-Zelgert et.al.

It contains a directory for each of the three protein targets discussed in the publication FABP4, ADCY10 and PDE10. These directories will contain the following files:<br>
• Initial models used as input (One for FABP4 and ADCY10, Five for PDE10).<br>
• One file containing all series ligands in the SDF format.<br>
• One txt file containing ligand names, ligand SMILES and measured activities.<br>
• One csv file containing all information from the evaluation.<br>
• One subdirectory containing the successfully identified model as a pdb file containing<br>
the protein, an SD file containing the docked ligand poses, as well as one Mol2 file<br>
containing the representative scaffold for the cluster.
DOI: 10.71819/sgblnr
title: TotalEnergies | Projeto de Caracterização Ambiental (PCA)/ Environmental Baseline Study (EBS) dos Blocos S-M-1711 e S-M-1815, Bacia de Santos: Fitoplâncton

description: Dados de amostras de fitoplâncton coletadas no ano de 2023, durante campanha oceanográfica nos Blocos S-M-1711 e S-M-1815, Bacia de Santos, em esforço de caracterização ambiental da área dos referidos blocos.
DOI: 10.15468/dl.njm45d
title: Occurrence Download

description: A dataset containing 396799 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Helminthostachys zeylanica, Ophioglossum reticulatum, Lindsaea ensifolia, Histiopteris incisa, Nephrolepis hirsutula, Xanthocyparis nootkatensis, Cupressus cashmeriana, Cupressus duclouxiana, Cupressus funebris, Cupressus chengiana, Cupressus dupreziana, Widdringtonia whytei, Callitris baileyi, Callitris neocaledonica, Callitris sulcata, Athrotaxis selaginoides, Athrotaxis laxifolia, Athrotaxis cupressoides, Larix kaempferi, Larix decidua, Larix laricina, Larix mastersiana, Larix potaninii, Larix griffithii, Larix occidentalis, Larix sibirica, Lagarostrobos franklinii, Microcachrys tetragona, Pherosphaera hookeriana, Psilotum nudum, Microlaena stipoides, Chordifex sphacelatus, Lepidobolus chaetocephalus, Calorophus erostris, Desmocladus myriocladus, Desmocladus parthenicus, Desmocladus fasciculatus, Schoenus subflavus, Schoenus racemosus, Schoenus subfascicularis, Schoenus pleiostemoneus, Schoenus brevisetis, Schoenus curvifolius, Gahnia ancistrophylla, Gahnia australis, Carpha curvata, Carpha rodwayi, Caustis dioica, Rhynchospora corymbosa, Lepidosperma leptostachyum)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 396799 records from 1504 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004779-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pbzy6p
title: Occurrence Download

description: A dataset containing 10606695 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erithacus rubecula"
 ]
}

 The dataset includes 10606695 records from 6609 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004818-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zts27a
title: Occurrence Download

description: A dataset containing 2837 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Portunus sanguinolentus (Herbst, 1783)"
 ]
}

 The dataset includes 2837 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007183-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5jqvyd
title: Occurrence Download

description: A dataset containing 2986876 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aglaonema nitidum (Jack) Kunth, Ambystoma mavortium Baird, 1850, Anser caerulescens (Linnaeus, 1758), Dendrosenecio johnstonii (Oliv.) B.Nord., Enicostema axillare (Lam.) A.Raynal, Diploderma polygonatum Hallowell, 1861, Juncus arcticus Willd., Lepidomeda mollispinis Miller & Hubbs, 1960, Matricaria chamomilla L., Pulsatilla montana (Hoppe) Rchb., Salicornia europaea (Moss) Lambinon & Vanderp., Abroma augustum (L.) L.fil., Callianthe darwinii (Hook.fil.) Donnell, Callianthe megapotamica (A.Spreng.) Dorr, Abutilon striatum Dicks., Acmella grandiflora (Turcz.) R.K.Jansen, Adenophyllum porophyllum (Cav.) Hemsl., Aeschynanthus hookeri C.B.Clarke, Aesculus flava Sol., Alectryon oleifolius (Desf.) S.T.Reynolds, Allium senescens L., Naucoria scolecina (Fr.) Quél., Amalaraeus penicilliger (Grube, 1851), Amanita excelsa (Fr.) Bertill., Ampelopsis glandulosa (Wall.) Momiy., Anatoecus dentatus (Scopoli, 1763), Anatoecus icterodes (Nitzsch, 1818), Lycopsis arvensis L., Anthurium pentaphyllum (Aubl.) G.Don, Anthurus muellerianus Kalchbr., Anthus petrosus (Montagu, 1798), Apodanthera undulata A.Gray, Archaeopsylla erinacei (Bouché, 1835), Prunus mandshurica (Maxim.) Koehne, Arpophyllum giganteum Hartw. ex Lindl., Arundinaria gigantea (Walter) Muhl., Asplenium trichomanes L., Astragalus creticus Lam., Biserrula pelecinus L., Astragalus vogelii (Webb) Bornm., Austropotamobius fulcisianus (Ninni, 1886), Balanus crenatus Bruguière, 1789, Bauhinia glauca (Clark, Mackinder & Banks, 2017) Clark, Mackinder & Banks, 2017, Betula pendula Roth, Boehmeria clidemioides Miq., Bouvardia ×hybrida Hogarth ex Bosse, Brachyglottis compacta (Kirk) B.Nord., Kalanchoe daigremontiana Raym.-Hamet & H.Perrier, Kalanchoe prolifera (Bowie ex Hook.) Raym.-Hamet, Bufonia macropetala Willk.)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1970"
 ]
}

 The dataset includes 2986876 records from 4525 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009696-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17563961
title: Dutch word2vec embeddings trained on OpenSubtitles Part 1

description: This dataset contains the subs2vec embeddings for Dutch, as presented in https://zenodo.org/records/17243814. The embeddings were trained on large-scale subtitle corpora and represent semantic vector spaces derived from naturalistic language use in films and television from the OpenSubtitles 2018 datasets: https://opus.nlpl.eu/OpenSubtitles/corpus/version/OpenSubtitles. 

For this language, we provide all embedding variants explored in the study. Specifically, the dataset includes vectors generated under different combinations of:



Dimensionality: multiple vector sizes (e.g., 100, 200, 300, …)

Window size: varying context windows (e.g., 2, 5, 10, …)

Each file corresponds to a unique configuration (dimension × window size). 


Each file contains the vocabulary for that language (column 1) and then the embedding values (columns 2 through dimension size + 1). 

If you use this dataset, please cite:



Manuscript: https://doi.org/10.5281/zenodo.17243812 

Data: This Zenodo dataset (using the DOI provided here)
DOI: 10.5281/zenodo.17563962
title: Dutch word2vec embeddings trained on OpenSubtitles Part 1

description: This dataset contains the subs2vec embeddings for Dutch, as presented in https://zenodo.org/records/17243814. The embeddings were trained on large-scale subtitle corpora and represent semantic vector spaces derived from naturalistic language use in films and television from the OpenSubtitles 2018 datasets: https://opus.nlpl.eu/OpenSubtitles/corpus/version/OpenSubtitles. 

For this language, we provide all embedding variants explored in the study. Specifically, the dataset includes vectors generated under different combinations of:



Dimensionality: multiple vector sizes (e.g., 100, 200, 300, …)

Window size: varying context windows (e.g., 2, 5, 10, …)

Each file corresponds to a unique configuration (dimension × window size). 


Each file contains the vocabulary for that language (column 1) and then the embedding values (columns 2 through dimension size + 1). 

If you use this dataset, please cite:



Manuscript: https://doi.org/10.5281/zenodo.17243812 

Data: This Zenodo dataset (using the DOI provided here)
DOI: 10.5281/zenodo.17566504
title: Dutch word2vec embeddings trained on OpenSubtitles Part 2

description: This dataset contains the subs2vec embeddings for Dutch, as presented in https://zenodo.org/records/17243814. The embeddings were trained on large-scale subtitle corpora and represent semantic vector spaces derived from naturalistic language use in films and television from the OpenSubtitles 2018 datasets: https://opus.nlpl.eu/OpenSubtitles/corpus/version/OpenSubtitles. 

For this language, we provide all embedding variants explored in the study. Specifically, the dataset includes vectors generated under different combinations of:



Dimensionality: multiple vector sizes (e.g., 100, 200, 300, …)

Window size: varying context windows (e.g., 2, 5, 10, …)

Each file corresponds to a unique configuration (dimension × window size). 


Each file contains the vocabulary for that language (column 1) and then the embedding values (columns 2 through dimension size + 1). 

If you use this dataset, please cite:



Manuscript: https://doi.org/10.5281/zenodo.17243812 

Data: This Zenodo dataset (using the DOI provided here)
DOI: 10.5281/zenodo.17566503
title: Dutch word2vec embeddings trained on OpenSubtitles Part 2

description: This dataset contains the subs2vec embeddings for Dutch, as presented in https://zenodo.org/records/17243814. The embeddings were trained on large-scale subtitle corpora and represent semantic vector spaces derived from naturalistic language use in films and television from the OpenSubtitles 2018 datasets: https://opus.nlpl.eu/OpenSubtitles/corpus/version/OpenSubtitles. 

For this language, we provide all embedding variants explored in the study. Specifically, the dataset includes vectors generated under different combinations of:



Dimensionality: multiple vector sizes (e.g., 100, 200, 300, …)

Window size: varying context windows (e.g., 2, 5, 10, …)

Each file corresponds to a unique configuration (dimension × window size). 


Each file contains the vocabulary for that language (column 1) and then the embedding values (columns 2 through dimension size + 1). 

If you use this dataset, please cite:



Manuscript: https://doi.org/10.5281/zenodo.17243812 

Data: This Zenodo dataset (using the DOI provided here)
DOI: 10.5281/zenodo.17566092
title: Norwegian word2vec embeddings trained on OpenSubtitles

description: This dataset contains the subs2vec embeddings for Norwegian, as presented in https://zenodo.org/records/17243814. The embeddings were trained on large-scale subtitle corpora and represent semantic vector spaces derived from naturalistic language use in films and television from the OpenSubtitles 2018 datasets: https://opus.nlpl.eu/OpenSubtitles/corpus/version/OpenSubtitles. 

For this language, we provide all embedding variants explored in the study. Specifically, the dataset includes vectors generated under different combinations of:



Dimensionality: multiple vector sizes (e.g., 100, 200, 300, …)

Window size: varying context windows (e.g., 2, 5, 10, …)

Each file corresponds to a unique configuration (dimension × window size). 


Each file contains the vocabulary for that language (column 1) and then the embedding values (columns 2 through dimension size + 1). 

If you use this dataset, please cite:



Manuscript: https://doi.org/10.5281/zenodo.17243812 

Data: This Zenodo dataset (using the DOI provided here)
DOI: 10.5281/zenodo.17566091
title: Norwegian word2vec embeddings trained on OpenSubtitles

description: This dataset contains the subs2vec embeddings for Norwegian, as presented in https://zenodo.org/records/17243814. The embeddings were trained on large-scale subtitle corpora and represent semantic vector spaces derived from naturalistic language use in films and television from the OpenSubtitles 2018 datasets: https://opus.nlpl.eu/OpenSubtitles/corpus/version/OpenSubtitles. 

For this language, we provide all embedding variants explored in the study. Specifically, the dataset includes vectors generated under different combinations of:



Dimensionality: multiple vector sizes (e.g., 100, 200, 300, …)

Window size: varying context windows (e.g., 2, 5, 10, …)

Each file corresponds to a unique configuration (dimension × window size). 


Each file contains the vocabulary for that language (column 1) and then the embedding values (columns 2 through dimension size + 1). 

If you use this dataset, please cite:



Manuscript: https://doi.org/10.5281/zenodo.17243812 

Data: This Zenodo dataset (using the DOI provided here)
DOI: 10.15468/dl.48cx8w
title: Occurrence Download

description: A dataset containing 485 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "DatasetKey is one of (iNaturalist Research-grade Observations, Observation.org, Nature data from around the World)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Erythrocebus patas",
 "Year 2022-2025"
 ]
}

 The dataset includes 485 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031148-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.etet2w
title: Occurrence Download

description: A dataset containing 244 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hylodes nasus"
 ]
}

 The dataset includes 244 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031151-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4xvej2
title: Occurrence Download

description: A dataset containing 2771 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((113.56854 17.69831,123.69709 29.49511,153.12951 31.75914,143.23926 47.24988,135.9182 73.21469,80.15151 61.06041,94.68897 45.68884,93.61655 23.88263,113.56854 17.69831))",
 "TaxonKey is Sambucus williamsii"
 ]
}

 The dataset includes 2771 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031150-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.akaaqu
title: Occurrence Download

description: A dataset containing 227 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bursera roseana",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 227 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031154-251025141854904/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.29414348
title: Adaptive osmoregulation in successive flushes of <i>Agaricus bisporus </i>enhances nutritional value of second flush mushrooms via elevated protein and free amino acid production

description: <i>Agaricus bisporus</i>, a widely cultivated edible button mushroom, is grown on composted substrates in successive flushes. While the first flush exhibits highest yields, later flushes exhibit reduced productivity. These differences are due to physico-chemical changes of the substrate: e.g. nutrient and water availability. Mushroom growth relies on maintaining an osmotic gradient between the substrate and fruiting body to allow resource translocation to the mushrooms. Classically, mannitol is known as the most important osmolyte in <i>A. bisporus</i> mushrooms. In this study, we investigated osmotic regulation during mushroom development over two flushes. We found that under standard cultivation conditions, the profile of organic osmolytes varies significantly between flushes in response to a changing substrate composition. During the first flush, when carbon is still abundant, mannitol is the dominant organic osmolyte supporting fruiting body expansion. In contrast, the second flush occurs under carbon-limited conditions, prompting a shift in osmotic strategy: fruiting bodies accumulate more nitrogen, with free amino acids contributing substantially to osmotic potential, reaching up to 11% of the dry weight, thereby enhancing nutritional value. This is one of the highest levels found in unprocessed food. These findings reveal a dynamic osmotic adaptation mechanism in <i>A. bisporus</i>, where different osmolytes are utilized depending on substrate nutrient availability. This metabolic flexibility likely helps sustaining growth under suboptimal conditions and results in mushrooms with improved nutritional quality in later flushes. Understanding the interplay between substrate composition, osmolyte profiles, and fruiting body physiology offers new avenues for optimizing mushroom yield and quality in commercial systems.
DOI: 10.6084/m9.figshare.29414348.v1
title: Adaptive osmoregulation in successive flushes of <i>Agaricus bisporus </i>enhances nutritional value of second flush mushrooms via elevated protein and free amino acid production

description: <i>Agaricus bisporus</i>, a widely cultivated edible button mushroom, is grown on composted substrates in successive flushes. While the first flush exhibits highest yields, later flushes exhibit reduced productivity. These differences are due to physico-chemical changes of the substrate: e.g. nutrient and water availability. Mushroom growth relies on maintaining an osmotic gradient between the substrate and fruiting body to allow resource translocation to the mushrooms. Classically, mannitol is known as the most important osmolyte in <i>A. bisporus</i> mushrooms. In this study, we investigated osmotic regulation during mushroom development over two flushes. We found that under standard cultivation conditions, the profile of organic osmolytes varies significantly between flushes in response to a changing substrate composition. During the first flush, when carbon is still abundant, mannitol is the dominant organic osmolyte supporting fruiting body expansion. In contrast, the second flush occurs under carbon-limited conditions, prompting a shift in osmotic strategy: fruiting bodies accumulate more nitrogen, with free amino acids contributing substantially to osmotic potential, reaching up to 11% of the dry weight, thereby enhancing nutritional value. This is one of the highest levels found in unprocessed food. These findings reveal a dynamic osmotic adaptation mechanism in <i>A. bisporus</i>, where different osmolytes are utilized depending on substrate nutrient availability. This metabolic flexibility likely helps sustaining growth under suboptimal conditions and results in mushrooms with improved nutritional quality in later flushes. Understanding the interplay between substrate composition, osmolyte profiles, and fruiting body physiology offers new avenues for optimizing mushroom yield and quality in commercial systems.
DOI: 10.15468/dl.fph6ps
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bursera rupicola",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 55 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031155-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.feb9m9
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bursera rzedowskii",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 11 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031156-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w8rwnn
title: Occurrence Download

description: A dataset containing 1004 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "Geometry POLYGON((-75.77435 4.61322,-75.74973 4.61322,-75.74973 4.62871,-75.77435 4.62871,-75.77435 4.61322))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata"
 ]
}

 The dataset includes 1004 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031158-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yb9wcj
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hylodes ornatus"
 ]
}

 The dataset includes 28 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031159-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7914/ctax-ca85
title: NEONOR2 temporary seismic deployment

description: Temporary deployment of 27 seismic stations installed in Northern Norway as part of the Petromaks2 funded project NEONOR2.
DOI: 10.15468/dl.erv9kb
title: Occurrence Download

description: A dataset containing 489718 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pteroglossus"
 ]
}

 The dataset includes 489718 records from 485 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031100-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fd6wuh
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "DatasetKey is Naturalis Biodiversity Center (NL) - Botany",
 "TaxonKey is Desmopsis"
 ]
}

 The dataset includes 78 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031160-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.