cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.5tj7x6
title: Occurrence Download

description: A dataset containing 5240 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pulmonaria saccharata Mill.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5240 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076786-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.8186499
title: Cross-species Comparison Reveals Therapeutic Vulnerabilities Halting Glioblastoma Progression

description: The growth of a tumor is tightly linked to the distribution of its cells along a continuum of activation states. Here, we systematically decode the activation state architecture (ASA) in a glioblastoma (GBM) patient cohort through comparison to adult murine neural stem cells. Modelling of these data forecast how tumor cells organize to sustain growth and identifies rate of activation as the main predictor of growth. Accordingly, patients with a higher quiescence fraction exhibit improved outcomes. Further, DNA methylation arrays enable ASA-related patient stratification. Comparison of healthy and malignant gene expression dynamics reveals dysregulation of the Wnt-antagonist SFRP1 at the quiescence to activation transition. SFRP1 overexpression renders GBM quiescent and increases overall survival of tumor-bearing mice. Surprisingly, it does so through reprogramming the tumor’s stem-like methylome into an astrocyte-like one. Our findings offer a framework for patient stratification, biomarker identification, and development of therapeutic avenues to halt GBM progression.

Pre-print on bioRxiv

Data



confocal_raw.zip contains the max-projected stainings of the ROIs. The 3D confocal images that were used to segment the nuclei are not included due to their size, but can be made available on request. The voxel size is (1., 0.142, 0.142) um/pixel.

confocal_segmentation.zip contains the nuclei segmentation that was obtained using mesmer and a custom 3D stitching approach.

resolve_raw.zip contains the raw data as produced by Resolve Bioscience, i.e. raw 3D transcript counts and a 2D DAPI stain.

resolve_registered.zip contains the spatial transcript counts after 3D registration, so their coordinate system is aligned to the confocal images and segmentations.

segmentation_pipeline.zip contains the code that was used to process the data from raw images and transcript counts to the final segmented cells.

segmentation_result.zip contains the final result of the segmentation, as well as the code that does the celltype assignment and neighbourhood enrichment.


The code that was used to process and segment the spatial data can also be found on GitHub (anders-biostat/ResolveTools).

Parameters



The original transcripts are aligned with the Resolve DAPI images, and their voxels have size (0.3125, 0.138, 0.138) microns (zyx, respectively).

Our confocal images have a voxel size of (1., 0.142, 0.142) microns (zyx, respectively).
DOI: 10.5281/zenodo.8186500
title: Cross-species Comparison Reveals Therapeutic Vulnerabilities Halting Glioblastoma Progression

description: The growth of a tumor is tightly linked to the distribution of its cells along a continuum of activation states. Here, we systematically decode the activation state architecture (ASA) in a glioblastoma (GBM) patient cohort through comparison to adult murine neural stem cells. Modelling of these data forecast how tumor cells organize to sustain growth and identifies rate of activation as the main predictor of growth. Accordingly, patients with a higher quiescence fraction exhibit improved outcomes. Further, DNA methylation arrays enable ASA-related patient stratification. Comparison of healthy and malignant gene expression dynamics reveals dysregulation of the Wnt-antagonist SFRP1 at the quiescence to activation transition. SFRP1 overexpression renders GBM quiescent and increases overall survival of tumor-bearing mice. Surprisingly, it does so through reprogramming the tumor’s stem-like methylome into an astrocyte-like one. Our findings offer a framework for patient stratification, biomarker identification, and development of therapeutic avenues to halt GBM progression.

Pre-print on bioRxiv

Data



confocal_raw.zip contains the max-projected stainings of the ROIs. The 3D confocal images that were used to segment the nuclei are not included due to their size, but can be made available on request. The voxel size is (1., 0.142, 0.142) um/pixel.

confocal_segmentation.zip contains the nuclei segmentation that was obtained using mesmer and a custom 3D stitching approach.

resolve_raw.zip contains the raw data as produced by Resolve Bioscience, i.e. raw 3D transcript counts and a 2D DAPI stain.

resolve_registered.zip contains the spatial transcript counts after 3D registration, so their coordinate system is aligned to the confocal images and segmentations.

segmentation_pipeline.zip contains the code that was used to process the data from raw images and transcript counts to the final segmented cells.

segmentation_result.zip contains the final result of the segmentation, as well as the code that does the celltype assignment and neighbourhood enrichment.


The code that was used to process and segment the spatial data can also be found on GitHub (anders-biostat/ResolveTools).

Parameters



The original transcripts are aligned with the Resolve DAPI images, and their voxels have size (0.3125, 0.138, 0.138) microns (zyx, respectively).

Our confocal images have a voxel size of (1., 0.142, 0.142) microns (zyx, respectively).
DOI: 10.3886/e231344
title: Replication data for: Heterogeneity in Risky Choice Behavior in a Broad Population

description: We analyze risk preferences using an experiment with real incentives in a representative sample of 1,422 Dutch respondents. Our econometric model incorporates four structural parameters that vary with observed and unobserved characteristics: utility curvature, loss
aversion, preferences toward the timing of uncertainty resolution, and the propensity to choose randomly rather than on the basis of preferences. We find that all four parameters contribute to explaining choice behavior. The structural parameters are significantly associated with socioeconomic variables, but it is essential to incorporate unobserved heterogeneity in each of them to match the rich variety of choice patterns in the data. (JEL D12, D81)
DOI: 10.3886/e231344v1
title: Replication data for: Heterogeneity in Risky Choice Behavior in a Broad Population

description: We analyze risk preferences using an experiment with real incentives in a representative sample of 1,422 Dutch respondents. Our econometric model incorporates four structural parameters that vary with observed and unobserved characteristics: utility curvature, loss
aversion, preferences toward the timing of uncertainty resolution, and the propensity to choose randomly rather than on the basis of preferences. We find that all four parameters contribute to explaining choice behavior. The structural parameters are significantly associated with socioeconomic variables, but it is essential to incorporate unobserved heterogeneity in each of them to match the rich variety of choice patterns in the data. (JEL D12, D81)
DOI: 10.21233/vqck-g924
title: LDDsite3820 ostracode surface sample dataset

description: Raw data for the LDDsite3820 ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/spf0-q782
title: Lake CI12 water chemistry dataset

description: Raw data for the Lake CI12 water chemistry dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/n0pq-6311
title: KYLE17 pollen surface sample dataset

description: Raw data for the KYLE17 pollen surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/c985-2214
title: Appleman Lake pollen dataset

description: Raw data for the Appleman Lake pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.388g2d
title: Occurrence Download

description: A dataset containing 365 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ilex sugerokii var. brevipedunculata (Maxim.) S.Y.Hu",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2010",
 "HasCoordinate is true"
 ]
}

 The dataset includes 365 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023476-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/75me-k530
title: 520 pollen surface sample dataset

description: Raw data for the 520 pollen surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.3ce47s
title: Occurrence Download

description: A dataset containing 235 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Mexico, Nicaragua, Belize, Guatemala, Costa Rica, El Salvador, Honduras, Panama)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Platymiscium dimorphandrum Donn.Sm."
 ]
}

 The dataset includes 235 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023477-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/hbap-5t09
title: LDDsite3174 ostracode surface sample dataset

description: Raw data for the LDDsite3174 ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/ft3s-qc87
title: Lake CI29 water chemistry dataset

description: Raw data for the Lake CI29 water chemistry dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.5284/1129621
title: Images from a Buildings Investigation at The Former London Inn, 33 Fore Street, Redruth, Cornwall, Sep 2022- Feb 2023

description: This collection comprises of images from a Historic Building Recording and Investigation, at The Former London Inn, 33 Fore Street, Redruth, Cornwall. Work was carried out by South West Archaeology between September 2022 and February 2023. The building is Grade II listed and was redefined in the 18th century into a three-storey townhouse.
DOI: 10.21233/gt35-0d09
title: Gamble [11LW10] macroinvertebrate dataset

description: Raw data for the Gamble [11LW10] macroinvertebrate dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.5284/1129612
title: Report and Site Records from a Level 2 Historic Building Survey at Hunter House, Goodramgate, York, March 2015

description: This collection consists of a report and site records from a Level 2 historic building survey of an attic space in Hunter House, Goodramgate, York. Works were conducted by AOC Archaeology in March 2015, prior to conversion of the existing building into fourteen apartments. The attic of Hunter House provided evidence for various phases of remodelling expected of historic buildings in city centres.
DOI: 10.15468/dl.ptm7kv
title: Occurrence Download

description: A dataset containing 2047 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Baptisia tinctoria (L.) R.Br.",
 "Year 2019-2024"
 ]
}

 The dataset includes 2047 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023480-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/csea-yr75
title: Dorothy Lake diatom surface sample dataset

description: Raw data for the Dorothy Lake diatom surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.sv8ee9
title: Occurrence Download

description: A dataset containing 5452 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Patrones biogeográficos de vegas de la Puna Argentina"
 ]
}

 The dataset includes 5452 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023478-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vgfra7
title: Occurrence Download

description: A dataset containing 652567 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 Sitta pygmaea Vigors, 1839",
 "Year is greater than or equal to 1950",
 {
 "or" : [
 "GadmGid is USA",
 "GadmGid is CAN",
 "GadmGid is MEX"
 ]
 }
 ]
}

 The dataset includes 652567 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023459-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/06ve-1x64
title: Conklin Quarry macroinvertebrate dataset

description: Raw data for the Conklin Quarry macroinvertebrate dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.fbjmxx
title: Occurrence Download

description: A dataset containing 1068 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Osmundastrum cinnamomeum var. fokiense (Copel.) Tagawa",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2010",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1068 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023481-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/p2d1-2n91
title: Velsen Hoogovens pollen dataset

description: Raw data for the Velsen Hoogovens pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/v9xk-vh17
title: Mercer Cave [UCMPV67108] vertebrate fauna dataset

description: Raw data for the Mercer Cave [UCMPV67108] vertebrate fauna dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/2dt8-z209
title: LDDsite3420 ostracode surface sample dataset

description: Raw data for the LDDsite3420 ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/9eys-xc82
title: Hornet Peatland testate amoebae surface sample dataset

description: Raw data for the Hornet Peatland testate amoebae surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.qnfe55
title: Occurrence Download

description: A dataset containing 3237 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Mexico, Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica, Panama, Belize)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Leucaena leucocephala (Lam.) de Wit"
 ]
}

 The dataset includes 3237 records from 118 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023483-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/c48x-k313
title: Staples River water chemistry dataset

description: Raw data for the Staples River water chemistry dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.yask3n
title: Occurrence Download

description: A dataset containing 17826 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Lobelia siphilitica L.",
 "Year 2019-2024"
 ]
}

 The dataset includes 17826 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023482-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/00581
title: Chandra X-ray Observatory ObsId 00581

description: ULTRA DEEP AXAF OBSERVATION WITH ACIS
DOI: 10.21233/rrjy-pz22
title: LDDsite2379 ostracode surface sample dataset

description: Raw data for the LDDsite2379 ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.uauf26
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Rhododendron dauricum L."
 ]
}

 The dataset includes 62 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023484-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/ja2z-j077
title: Mossy Lake water chemistry dataset

description: Raw data for the Mossy Lake water chemistry dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dpvue3
title: Inventory of arthropods in Azorean Islands lava tubes and volcanic pits

description: This manuscript reports on the biological materials of arthropods sampled by the members and collaborators of the University of Azores since the 1990’s on subterranean environments of the Azores. We will highlight the occurrence of endemic species in new localities, therefore increasing their known distribution range. These new records will update the conservation priority of the distinct caves, and records of unidentified taxa can call the attention of prospective taxonomists that might be keen on studying these materials.A total of 75 species and subspecies are listed plus 16 taxa identified at family or genus level. The 75 identified taxa include 17 endemic species, from which eleven are cave adapted species.
DOI: 10.21233/qfht-5h21
title: LDDsite955 water chemistry dataset

description: Raw data for the LDDsite955 water chemistry dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.sbj2wc
title: Occurrence Download

description: A dataset containing 2186 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Pycnanthemum virginianum (L.) T.Durand & B.D.Jacks. ex B.L.Rob. & Fernald",
 "Year 2019-2024"
 ]
}

 The dataset includes 2186 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023486-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/8g15-hf44
title: Roberts Creek pollen surface sample dataset

description: Raw data for the Roberts Creek pollen surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.