cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.2bj47t
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Epinephelus grammicus"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015482-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16746716
title: Role of oxygen for surface pretreatment in atomic layer deposition on graphene

description: This is the data used to plot all the figures in the manuscript "Role of oxygen for surface pretreatment in atomic layer deposition on graphene" by Nam Ta, Hao Bui, Linh Nguyen, Hung Dang and Hoa Nghiem.

Below are the descriptions of all the uploaded files:



figures.tar.gz: the data and the Python scripts (in the form of a Jupyter notebook) to plot each figure in the manuscript

charge_density_difference.tar.gz: raw data (Gaussian cube files) for all charge density and charge density difference data in use

neb.tar.gz: output files for the Nudged Elastic Band (NEB) for oxygen migrating from a b site to another b site via the h site (bhb) or via the t site (btb)

phonon.tar.gz: output files for phonon calculations using Phonopy
DOI: 10.5281/zenodo.16746715
title: Role of oxygen for surface pretreatment in atomic layer deposition on graphene

description: This is the data used to plot all the figures in the manuscript "Role of oxygen for surface pretreatment in atomic layer deposition on graphene" by Nam Ta, Hao Bui, Linh Nguyen, Hung Dang and Hoa Nghiem.

Below are the descriptions of all the uploaded files:



figures.tar.gz: the data and the Python scripts (in the form of a Jupyter notebook) to plot each figure in the manuscript

charge_density_difference.tar.gz: raw data (Gaussian cube files) for all charge density and charge density difference data in use

neb.tar.gz: output files for the Nudged Elastic Band (NEB) for oxygen migrating from a b site to another b site via the h site (bhb) or via the t site (btb)

phonon.tar.gz: output files for phonon calculations using Phonopy
DOI: 10.15468/dl.etx5ye
title: Occurrence Download

description: A dataset containing 709 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Espadarana prosoblepon"
 ]
}

 The dataset includes 709 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015483-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yb2hyw
title: Occurrence Download

description: A dataset containing 110 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemidactylus mabouia",
 "Country is Jamaica",
 "HasCoordinate is true"
 ]
}

 The dataset includes 110 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015484-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gczz6r
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemidactylus mabouia",
 "Country is Paraguay",
 "HasCoordinate is true"
 ]
}

 The dataset includes 32 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015485-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q2vbye
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Serranus latifasciatus"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015486-250802193616735/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.29829155
title: <b>Poyang Lake inundation dynamics dataset (1980-2020): onset, cessation, and duration of inundation at three hydrological stations (Duchang, Wucheng, and Tangyin)</b>

description: Poyang Lake inundation dynamics dataset (1980-2020): onset, cessation, and duration of inundation at three hydrological stations (Duchang, Wucheng, and Tangyin)
DOI: 10.6084/m9.figshare.29829155.v2
title: <b>Poyang Lake inundation dynamics dataset (1980-2020): onset, cessation, and duration of inundation at three hydrological stations (Duchang, Wucheng, and Tangyin)</b>

description: Poyang Lake inundation dynamics dataset (1980-2020): onset, cessation, and duration of inundation at three hydrological stations (Duchang, Wucheng, and Tangyin)
DOI: 10.6084/m9.figshare.29829155.v1
title: <b>Poyang Lake inundation dynamics dataset (1980-2020): onset, cessation, and duration of inundation at three hydrological stations (Duchang, Wucheng, and Tangyin)</b>

description: Poyang Lake inundation dynamics dataset (1980-2020): onset, cessation, and duration of inundation at three hydrological stations (Duchang, Wucheng, and Tangyin)
DOI: 10.15468/dl.7svfxz
title: Occurrence Download

description: A dataset containing 258 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is South Africa",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Polistes marginalis"
 ]
}

 The dataset includes 258 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015487-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16747142
title: Pro-Environmental Behaviors, Dark Triad Traits, and Green Culture
DOI: 10.5281/zenodo.16747143
title: Pro-Environmental Behaviors, Dark Triad Traits, and Green Culture
DOI: 10.5519/qd.t5ikmupi
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.15468/dl.yt3jfp
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bathyclarias filicibarbis)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015488-250802193616735/datasets/export for details.
DOI: 10.25934/pr00009962
title: Exploring risk factors and prognosis in cancer patients receiving immune checkpoint inhibitor therapy with immune-related adverse events 

description: Background: In recent years, immune checkpoint inhibitors (ICIs) have become the standard treatment for many types of cancer. ICIs work by enhancing the ability of the immune system to recognise and attack cancer cells, but they are also known to cause side effects due to the overactivation of the immune system. These immune-related side effects or adverse events (irAEs) can sometimes be serious, leading to treatment interruption and affecting the quality of life of patients. However, the risk factors for the onset of irAEs and their relationship to patient background factors, such as race, age, gender, type of cancer, other medical conditions (comorbidities), and organs to which the cancer has spread (metastases) have not yet been fully elucidated.

The purpose of this study is to use the Vivli platform to comprehensively analyze the relationship between irAEs associated with ICIs and patient background factors.

Aim: This aims to identify patient background factors that indicate a high risk of irAEs and to lead to improvements in prevention and management methods.  We will also analyze the incidence, onset timing, and severity of irAEs and their correlation with patient background factors, clinical pathological factors of cancer, and the relationship between the onset of irAEs, treatment efficacy, and patient prognosis (the likely outcome or course of a disease).

Research method: This study is a retrospective study based on clinical trials where ICI treatment was administered, obtained in Vivli platform.

Significance: By clarifying the risk factors for irAEs associated with ICIs, including differences based on patient background factors and prognosis, this study aims to contribute to the improvement of clinical management methods and the development of personalized ICI treatment strategies.
DOI: 10.15468/dl.xc2g78
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemidactylus mabouia",
 "Country is Portugal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 48 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015491-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gkqnux
title: Occurrence Download

description: A dataset containing 152 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemidactylus mabouia",
 "Country is Peru",
 "HasCoordinate is true"
 ]
}

 The dataset includes 152 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015490-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.77785w
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Priacanthichthys maderaspatensis"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015489-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hyetfs
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cordia macrophylla"
 ]
}

 The dataset includes 88 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015493-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fvujwb
title: Occurrence Download

description: A dataset containing 386 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Notropis ammophilus)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 386 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015492-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uskpt4
title: Occurrence Download

description: A dataset containing 730 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Epinephelus macrospilos"
 ]
}

 The dataset includes 730 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015494-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15341025
title: Supporting data for Exploring Molecular Equilibrium Geometries in Static and Quantized Fields
DOI: 10.5281/zenodo.16746704
title: Supporting data for Exploring Molecular Equilibrium Geometries in Static and Quantized Fields
DOI: 10.15468/dl.cruxph
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemidactylus mabouia",
 "Country is Saint Lucia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 20 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015495-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ba6j6v
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemidactylus mabouia",
 "Country is Saint Vincent and the Grenadines",
 "HasCoordinate is true"
 ]
}

 The dataset includes 28 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015496-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16746478
title: A national peatland database for the Republic of Ireland (AUGER project)

description: As part of the AUGER project, funded by the Irish Environmental Project Agency, a peatland sampling campaign was conducted between May 2017 and July 2019 across the Republic of Ireland to ascertain a wide range of peatland properties. A multi-stage (hierarchical) stratified sampling with three stages was devised. 50 ombrotrophic raised and blanket bogs (270 sampling points, 4024 soil samples) were surveyed across prevalent land use categories: natural, grassland, forestry, peat extraction (both industrial and domestic) as well as various management options (deep drained, shallow drained, rewetted). Physical landscape features were determined using a list of criteria. Vegetation data was collected using vegetation relevées. Peat sampling was conducted with a ‘Russian’ peat sampler. Laboratory analysis of disturbed and non-disturbed samples yielded values for 15 peat properties and peat depth.  In addition, aater table monitoring was conducted at 8 peatland sites (natural lowland blanket bog as well as under forestry, grassland, domestic peat extraction and natural raised bog as well as under forestry, both drained and rewetted, and under domestic peat extraction), using a OTT Orpheus Mini logger over a period of 2 years.
DOI: 10.5281/zenodo.16746479
title: A national peatland database for the Republic of Ireland (AUGER project)

description: As part of the AUGER project, funded by the Irish Environmental Project Agency, a peatland sampling campaign was conducted between May 2017 and July 2019 across the Republic of Ireland to ascertain a wide range of peatland properties. A multi-stage (hierarchical) stratified sampling with three stages was devised. 50 ombrotrophic raised and blanket bogs (270 sampling points, 4024 soil samples) were surveyed across prevalent land use categories: natural, grassland, forestry, peat extraction (both industrial and domestic) as well as various management options (deep drained, shallow drained, rewetted). Physical landscape features were determined using a list of criteria. Vegetation data was collected using vegetation relevées. Peat sampling was conducted with a ‘Russian’ peat sampler. Laboratory analysis of disturbed and non-disturbed samples yielded values for 15 peat properties and peat depth.  In addition, aater table monitoring was conducted at 8 peatland sites (natural lowland blanket bog as well as under forestry, grassland, domestic peat extraction and natural raised bog as well as under forestry, both drained and rewetted, and under domestic peat extraction), using a OTT Orpheus Mini logger over a period of 2 years.
DOI: 10.15468/dl.fvhyg6
title: Occurrence Download

description: A dataset containing 2197 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Museo Laboratorio de Entomología (MENT-UT)"
 ]
}

 The dataset includes 2197 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015497-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16741649
title: Phold Database 3.16M Remaining Protein Structure Predictions

description: Repository containing 1,802,498 protein structures consituting all proteins in Phold DB 3.16M that are not in Phold Search DB 1.36M. All Phold Search DB 1.36M structures can be found at https://doi.org/10.5281/zenodo.16739199. These are all efam and enVhog proteins that were not able to be assigned PHROGs and have no annotated functional label.

Specifically, the large `final_combined_phold_db_3M16_efam_envhog_no_phrog.tar.xz` tarball consists of:

* 158,898 extremely conservative efam proteins <3000AA  without an assigned PHROG group are in `efam`. These have been chunked into batches of 5000 `.pdb` files for file-system sanity

* 1,638,667 enVhog proteins <3000AA without an assigned PHROG group are in `envhog`. These have also been chunked into batches of 5000 files.

There is an additional smaller tarball `envhogs_renamed_3000_plus.tar.gz` containing

* 4933 `.pdb` files of enVhog proteins 3000+ AA have been fragmented as described in the Phold manuscript (i.e. proteins were chunked into equal fragments under 3000AA so a 5000AA protein has two 2500AA chunks, a 8100AA protein has three 2700AA chunks). These fragments are indicated as `_1` `_2` etc. These are in a separate top level tarball (`envhogs_renamed_3000_plus.tar.gz`)

All structures are named as they appear in the Phold DB 3.16M

# Recombining the large tarball

Due to the large size of uploading the tarball `final_combined_phold_db_3M16_efam_envhog_no_phrog.tar.xz1`, I had significant difficulties in uploading it to Zenodo. Accordingly, I split it into ten smaller chunks as follows (using Linux split command):

`split --bytes=5G --suffix-length=3 --numeric-suffixes final_combined_phold_db_3M16_efam_envhog_no_phrog.tar.xz final_combined_phold_db_3M16_efam_envhog_no_phrog.tar.xz_part_`

To recombine into the original larger tarball, download all the chunks in this record and combine

`cat final_combined_phold_db_3M16_efam_envhog_no_phrog.tar.xz_part_??? > final_combined_phold_db_3M16_efam_envhog_no_phrog.tar.xz`
DOI: 10.5281/zenodo.16741650
title: Phold Database 3.16M Remaining Protein Structure Predictions

description: Repository containing 1,802,498 protein structures consituting all proteins in Phold DB 3.16M that are not in Phold Search DB 1.36M. All Phold Search DB 1.36M structures can be found at https://doi.org/10.5281/zenodo.16739199. These are all efam and enVhog proteins that were not able to be assigned PHROGs and have no annotated functional label.

Specifically, the large `final_combined_phold_db_3M16_efam_envhog_no_phrog.tar.xz` tarball consists of:

* 158,898 extremely conservative efam proteins <3000AA  without an assigned PHROG group are in `efam`. These have been chunked into batches of 5000 `.pdb` files for file-system sanity

* 1,638,667 enVhog proteins <3000AA without an assigned PHROG group are in `envhog`. These have also been chunked into batches of 5000 files.

There is an additional smaller tarball `envhogs_renamed_3000_plus.tar.gz` containing

* 4933 `.pdb` files of enVhog proteins 3000+ AA have been fragmented as described in the Phold manuscript (i.e. proteins were chunked into equal fragments under 3000AA so a 5000AA protein has two 2500AA chunks, a 8100AA protein has three 2700AA chunks). These fragments are indicated as `_1` `_2` etc. These are in a separate top level tarball (`envhogs_renamed_3000_plus.tar.gz`)

All structures are named as they appear in the Phold DB 3.16M

# Recombining the large tarball

Due to the large size of uploading the tarball `final_combined_phold_db_3M16_efam_envhog_no_phrog.tar.xz1`, I had significant difficulties in uploading it to Zenodo. Accordingly, I split it into ten smaller chunks as follows (using Linux split command):

`split --bytes=5G --suffix-length=3 --numeric-suffixes final_combined_phold_db_3M16_efam_envhog_no_phrog.tar.xz final_combined_phold_db_3M16_efam_envhog_no_phrog.tar.xz_part_`

To recombine into the original larger tarball, download all the chunks in this record and combine

`cat final_combined_phold_db_3M16_efam_envhog_no_phrog.tar.xz_part_??? > final_combined_phold_db_3M16_efam_envhog_no_phrog.tar.xz`
DOI: 10.15468/dl.jpx4t8
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ADF3601"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015499-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2kbfg7
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cobitis stephanidisi)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015498-250802193616735/datasets/export for details.
DOI: 10.15468/dl.9c7p3p
title: Occurrence Download

description: A dataset containing 25970488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Phacelia distans, Phacelia hastata, Phacelia heterophylla, Pholistoma auritum, Physaria vitulifera, Plagiobothrys lithocaryus, Platanus occidentalis, Potentilla simplex, Prunus americana, Prunus amygdalus, Prunus armeniaca, Prunus avium, Prunus cerasus, Prunus demissa, Prunus fasciculata, Prunus ilicifolia, Prunus persica, Prunus serotina, Prunus subcordata, Prunus virginiana, Prunus virginiana, Ranunculaceae, Pyrus calleryana, Pyrus communis, Quercus alba, Quercus falcata, Quercus nigra, Quercus velutina, Ranunculus hispidus, Ranunculus ophioglossifolius, Raphanus raphanistrum, Rhamnus betulifolia, Rhamnus crocea, Rhododendron japonicum, Rhus ovata, Rhus trilobata, Ribes aureum, Ribes cereum, Ribes leptanthum, Ribes malvaceum, Ribes menziesii, Ribes nevadense, Ribes roezlii, Ribes viscosissimum, Rosa multiflora, Rubus allegheniensis, Rubus allegheniensis, Rubus argutus, Rubus deliciosus, Rubus, Rubus flagellaris, Rubus idaeus, Rubus moluccanus, Rubus parviflorus, Rubus ursinus, Salix bebbiana, Salix brachycarpa, Salix exigua, Salix fragilis, Salix gracilistyla, Salix humilis, Salix lasiandra, Salix lasiolepis, Salix nigra, Salix pentandra, Salix petiolaris, Salix sericea, Salvia carduacea, Salvia sonomensis, Sanguinaria canadensis, Senecio salignus, Senecio vulgaris, Silene, Sisyrinchium montanum, Smilax glauca, Solanum dulcamara, Stellaria media, Stenotopsis linearifolia, Taraxacum campylodes, Taraxacum officinale, Taraxacum vulgare, Thlaspi arvense, Toxicodendron radicans, Toxicodendron rydbergii, Trifolium barnebyi, Trifolium hirtum, Trifolium pratense, Trifolium repens, Vaccinium atrococcum, Vaccinium corymbosum, Viburnum recognitum, Viburnum tinus, Vicia cracca, Vicia villosa, Viola kitaibeliana, Viola lanceolata, Viola sororia, Wyethia mollis)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 25970488 records from 7895 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015481-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.