cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.sy62vf
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dichilus gracilis Eckl. & Zeyh."
 ]
}

 The dataset includes 74 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021045-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0sb23a
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cryphalus fulmineus Wood, 1989"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008924-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jrahqm
title: Occurrence Download

description: A dataset containing 47 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)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Rhinoplax vigil (Pennant, 1781)"
 ]
}

 The dataset includes 47 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050292-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kajwzd
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Damrongia lacunosa (Hook.fil.) D.J.Middleton & A.Weber"
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021048-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rv3ehv
title: Occurrence Download

description: A dataset containing 101 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriocaulon bongense Engl. & Ruhland"
 ]
}

 The dataset includes 101 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050316-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j6m97d
title: Occurrence Download

description: A dataset containing 423 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tropaeolum pentaphyllum Lam."
 ]
}

 The dataset includes 423 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008924-160526112335914/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zhwecb
title: Occurrence Download

description: A dataset containing 146 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dendrobium bracteosum Rchb.f."
 ]
}

 The dataset includes 146 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021030-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hcr256
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Exbucklandia longipetala H.T.Chang"
 ]
}

 The dataset includes 37 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050335-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fbfhil
title: Occurrence Download

description: A dataset containing 154731 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pitangus sulphuratus (Linnaeus, 1766)"
 ]
}

 The dataset includes 154731 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008924-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6dduh8
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ichthyostoma thulinii Hedrén & Vollesen"
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027809-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mwqczs
title: Occurrence Download

description: A dataset containing 154 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)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Odontophrynus occidentalis (Berg, 1896)"
 ]
}

 The dataset includes 154 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040124-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k1w5qv
title: Occurrence Download

description: A dataset containing 34874 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Parabuteo unicinctus (Temminck, 1824)"
 ]
}

 The dataset includes 34874 records from 120 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008925-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hxgy4h
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dinochloa prunifera S.Dransf."
 ]
}

 The dataset includes 15 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021036-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g9528t
title: Occurrence Download

description: A dataset containing 559435 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)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Rumex acetosella L.)"
 ]
}

 The dataset includes 559435 records from 2653 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027786-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13167021
title: Binary black-hole simulation SXS:BBH:0005

description: Simulation of a black-hole binary system evolved by the SpEC code.
DOI: 10.5281/zenodo.13167022
title: Binary black-hole simulation SXS:BBH:0005

description: Simulation of a black-hole binary system evolved by the SpEC code.
DOI: 10.5281/zenodo.13118107
title: China Bird Observation Dataset 001 (285 bird species)
title: Species observation data
DOI: 10.5281/zenodo.13118108
title: China Bird Observation Dataset 001 (285 bird species)
title: Species observation data
DOI: 10.5281/zenodo.13167018
title: China Bird Observation Dataset 001 (285 bird species)
title: Species observation data
DOI: 10.5281/zenodo.13167041
title: Binary black-hole simulation SXS:BBH:0004

description: Simulation of a black-hole binary system evolved by the SpEC code.
DOI: 10.5281/zenodo.13167042
title: Binary black-hole simulation SXS:BBH:0004

description: Simulation of a black-hole binary system evolved by the SpEC code.
DOI: 10.5281/zenodo.12684512
title: Two-time correlation function based on speckle patterns from x-ray photon correlation spectroscopy associated with "Intermittent cluster dynamics and temporal fractional diffusion in a bulk metallic glass" (scientific article published in Nature Communications, 2024)

description: This dataset consists of contrast data, i.e., the two-time correlation function, based on speckle patterns measured at the at the 8ID-E beamline of the Advanced Photon Source at Argonne National Laboratory.

Experimental details are stated in the paper specified under "related work" and in the accompanying supplementary information.

You are welcome to use this dataset in compliance with the CC BY 4.0 licence assigned to this dataset.

Any questions regarding the data can be addressed to birte.riechers@bam.de who would also appreciate a note if you find the data useful.

____________________________________________________________________

The data consists of 32 text files in total, which correspond to the main and lower panel Figure 2 of the main publication. 

30 of these text files are contrast data, which are named "contrast_DT250s_nn.text" wiith "nn" as the identifier of consecutive data sets going from 1 to 30. Each data set consists of p rows and q columns, DT250s denotes the time resolution of data points, which is 250 s along both row and column values.

The data set called "Time_Contrast_1to30s.txt" states the start time in seconds of the first data point of each of the thirty contrast data set.

The data set called "ScatteredIntensity.txt" states the scattered intensity at full time resolution, i.e. 2.5 s.

The files are plain text files with the data points separated by "space" along rows and "new line" along columns.
DOI: 10.5281/zenodo.12684513
title: Two-time correlation function based on speckle patterns from x-ray photon correlation spectroscopy associated with "Intermittent cluster dynamics and temporal fractional diffusion in a bulk metallic glass" (scientific article published in Nature Communications, 2024)

description: This dataset consists of contrast data, i.e., the two-time correlation function, based on speckle patterns measured at the at the 8ID-E beamline of the Advanced Photon Source at Argonne National Laboratory.

Experimental details are stated in the paper specified under "related work" and in the accompanying supplementary information.

You are welcome to use this dataset in compliance with the CC BY 4.0 licence assigned to this dataset.

Any questions regarding the data can be addressed to birte.riechers@bam.de who would also appreciate a note if you find the data useful.

____________________________________________________________________

The data consists of 32 text files in total, which correspond to the main and lower panel Figure 2 of the main publication. 

30 of these text files are contrast data, which are named "contrast_DT250s_nn.text" wiith "nn" as the identifier of consecutive data sets going from 1 to 30. Each data set consists of p rows and q columns, DT250s denotes the time resolution of data points, which is 250 s along both row and column values.

The data set called "Time_Contrast_1to30s.txt" states the start time in seconds of the first data point of each of the thirty contrast data set.

The data set called "ScatteredIntensity.txt" states the scattered intensity at full time resolution, i.e. 2.5 s.

The files are plain text files with the data points separated by "space" along rows and "new line" along columns.
DOI: 10.5281/zenodo.13167049
title: Binary black-hole simulation SXS:BBH:0034

description: Simulation of a black-hole binary system evolved by the SpEC code.
DOI: 10.5281/zenodo.13167050
title: Binary black-hole simulation SXS:BBH:0034

description: Simulation of a black-hole binary system evolved by the SpEC code.
DOI: 10.5281/zenodo.13167056
title: Binary black-hole simulation SXS:BBH:0039

description: Simulation of a black-hole binary system evolved by the SpEC code.
DOI: 10.5281/zenodo.13167057
title: Binary black-hole simulation SXS:BBH:0039

description: Simulation of a black-hole binary system evolved by the SpEC code.
DOI: 10.15468/dl.4zkj8b
title: Occurrence Download

description: A dataset containing 7073245 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is NOR",
 "HasCoordinate is true",
 "TaxonKey is one of (Tracheophyta)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 7073245 records from 315 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045556-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12571947
title: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.

description: Bulk ATAC-seq data of tumour samples result in an averaged signal across different cell-types (cancer, stromal, vascular and immune cells). We propose a deconvolution framework called EPIC-ATAC, which relies on newly identified cell-type specific ATAC-Seq marker peaks and reference profiles for all major cancer-relevant cell-types to predict the proportions of each cell-type.

To evaluate EPIC-ATAC, we generated a bulk ATAC-Seq dataset from peripheral blood mononuclear cells (PBMCs) samples, from which the number of cells in each cell-type has been estimated using flow cytometry, as ground truth for cell proportions. The data provided in this Zenodo deposit correspond to:

- The raw counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts.txt

- The normalized (TPM-like) counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts_norm.txt

- The cell fractions of each cell type in each sample: PBMC_cell_fractions.txt

- The peaks called in each sample using MACS2 (*narrow.peaks): *_normalized.narrowPeak

- Bed files listing ATAC-Seq fragments for each sample: *.bed

We also evaluated EPIC-ATAC on multiple pseudobulks generated from single-cell ATAC-Seq data. We provide rds files containing the pseudobulks data used in our work for the evaluation of EPIC-ATAC. The rds files are located in the zip file "pseudobulks.zip".

The file "additional_data.tar.gz" contains additional files used to generate the reference profiles in EPIC-ATAC and required to run some of the code available on the following GitHub repository: GfellerLab/EPIC-ATAC_manuscript.
DOI: 10.5281/zenodo.8358718
title: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.

description: Bulk ATAC-seq data of tumour samples result in an averaged signal across different cell-types (cancer, stromal, vascular and immune cells). We propose a deconvolution framework called EPIC-ATAC (https://doi.org/10.7554/eLife.94833.1), which relies on newly identified cell-type specific ATAC-Seq marker peaks and reference profiles for all major cancer-relevant cell-types to predict the proportions of each cell-type.

To evaluate EPIC-ATAC, we generated a bulk ATAC-Seq dataset from peripheral blood mononuclear cells (PBMCs) samples, from which the number of cells in each cell-type has been estimated using flow cytometry, as ground truth for cell proportions. The data provided in this Zenodo deposit correspond to:

- The raw counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts.txt

- The normalized (TPM-like) counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts_norm.txt

- The cell fractions of each cell type in each sample: PBMC_cell_fractions.txt

- The peaks called in each sample using MACS2 (*narrow.peaks): *_normalized.narrowPeak

- Bed files listing ATAC-Seq fragments for each sample: *.bed

We also evaluated EPIC-ATAC on multiple pseudobulks generated from single-cell ATAC-Seq data. We provide rds files containing the pseudobulks data used in our work for the evaluation of EPIC-ATAC. The rds files are located in the zip file "pseudobulks.zip".

The file "additional_data.zip" contains additional files used to generate the reference profiles in EPIC-ATAC and to reproduce the main analyses performed in the manuscript: https://doi.org/10.7554/eLife.94833.1. These files are required to run the code available on the following GitHub repository: GfellerLab/EPIC-ATAC_manuscript.
DOI: 10.5281/zenodo.8358719
title: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.

description: Bulk ATAC-seq data of tumour samples result in an averaged signal across different cell-types (cancer, stromal, vascular and immune cells). We propose a deconvolution framework called EPIC-ATAC, which relies on newly identified cell-type specific ATAC-Seq marker peaks and reference profiles for all major cancer-relevant cell-types to predict the proportions of each cell-type. To evaluate EPIC-ATAC, we generated a newly generated bulk ATAC-Seq dataset from peripheral blood mononuclear cells (PBMCs) samples, from which the number of cells in each cell-type has been estimated using flow cytometry, as ground truth for cell proportions. The data provided in this Zenodo deposit correspond to: - The raw counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts.txt - The normalized (TPM-like) counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts_norm.txt - The cell fractions of each cell type in each sample: PBMC_cell_fractions.txt - The peaks called in each sample using MACS2 (*narrow.peaks): *_normalized.narrowPeak - Bed files listing ATAC-Seq fragments for each sample: *.bed We also evaluated EPIC-ATAC on multiple pseudobulks generated from single-cell ATAC-Seq data. We provide here rds files containing the pseudobulk data used in our work for the evaluation of EPIC-ATAC.
DOI: 10.5281/zenodo.8431792
title: Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.

description: Bulk ATAC-seq data of tumour samples result in an averaged signal across different cell-types (cancer, stromal, vascular and immune cells). We propose a deconvolution framework called EPIC-ATAC, which relies on newly identified cell-type specific ATAC-Seq marker peaks and reference profiles for all major cancer-relevant cell-types to predict the proportions of each cell-type. To evaluate EPIC-ATAC, we generated a newly generated bulk ATAC-Seq dataset from peripheral blood mononuclear cells (PBMCs) samples, from which the number of cells in each cell-type has been estimated using flow cytometry, as ground truth for cell proportions. The data provided in this Zenodo deposit correspond to: - The raw counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts.txt - The normalized (TPM-like) counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts_norm.txt - The cell fractions of each cell type in each sample: PBMC_cell_fractions.txt - The peaks called in each sample using MACS2 (*narrow.peaks): *_normalized.narrowPeak - Bed files listing ATAC-Seq fragments for each sample: *.bed We also evaluated EPIC-ATAC on multiple pseudobulks generated from single-cell ATAC-Seq data. We provide here rds files containing the pseudobulk data used in our work for the evaluation of EPIC-ATAC.
DOI: 10.5517/ccdc.csd.cc2jcntd
title: CCDC 2334914: Experimental Crystal Structure Determination

description: Related Article: Salah S. Massoud, Franz A. Mautner, Febee R. Louka, Nahed M. H. Salem, Roland C. Fischer, Ana Torvisco, Ján Vančo, Jan Belza, Zdeněk Dvořák, Zdeněk Trávníček|2024|Dalton Trans.|53|12261|doi:10.1039/D4DT00942H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2jcnvf
title: CCDC 2334915: Experimental Crystal Structure Determination

description: Related Article: Salah S. Massoud, Franz A. Mautner, Febee R. Louka, Nahed M. H. Salem, Roland C. Fischer, Ana Torvisco, Ján Vančo, Jan Belza, Zdeněk Dvořák, Zdeněk Trávníček|2024|Dalton Trans.|53|12261|doi:10.1039/D4DT00942H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2jcnwg
title: CCDC 2334916: Experimental Crystal Structure Determination

description: Related Article: Salah S. Massoud, Franz A. Mautner, Febee R. Louka, Nahed M. H. Salem, Roland C. Fischer, Ana Torvisco, Ján Vančo, Jan Belza, Zdeněk Dvořák, Zdeněk Trávníček|2024|Dalton Trans.|53|12261|doi:10.1039/D4DT00942H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2jcnxh
title: CCDC 2334917: Experimental Crystal Structure Determination

description: Related Article: Salah S. Massoud, Franz A. Mautner, Febee R. Louka, Nahed M. H. Salem, Roland C. Fischer, Ana Torvisco, Ján Vančo, Jan Belza, Zdeněk Dvořák, Zdeněk Trávníček|2024|Dalton Trans.|53|12261|doi:10.1039/D4DT00942H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2jcnyj
title: CCDC 2334918: Experimental Crystal Structure Determination

description: Related Article: Salah S. Massoud, Franz A. Mautner, Febee R. Louka, Nahed M. H. Salem, Roland C. Fischer, Ana Torvisco, Ján Vančo, Jan Belza, Zdeněk Dvořák, Zdeněk Trávníček|2024|Dalton Trans.|53|12261|doi:10.1039/D4DT00942H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2jcnzk
title: CCDC 2334919: Experimental Crystal Structure Determination

description: Related Article: Salah S. Massoud, Franz A. Mautner, Febee R. Louka, Nahed M. H. Salem, Roland C. Fischer, Ana Torvisco, Ján Vančo, Jan Belza, Zdeněk Dvořák, Zdeněk Trávníček|2024|Dalton Trans.|53|12261|doi:10.1039/D4DT00942H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.