cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14248992
title: Spatially resolved transcriptomics of benign and malignant peripheral nerve sheath tumors

description: Background: 

Peripheral nerve sheath tumors (PNSTs) encompass entities with different cellular differentiation and degrees of malignancy. Spatial heterogeneity complicates diagnosis and grading of PNSTs in some cases. In malignant PNST (MPNST) for example, single cell sequencing data has shown dissimilar differentiation states of tumor cells. Here, we aimed at determining the spatial and biological heterogeneity of PNSTs.

Methods: 

We performed spatial transcriptomics on formalin-fixed paraffin-embedded diseased peripheral nerve tissue. We used spatial clustering and weighted correlation network analysis to construct niche-similarity networks and gene expression modules. We determined differential expression in primary pathologies, analysed pathways to investigate the biological significance of identified meta-signatures, integrated the transcriptional data with histological features and existing single cell data, and validated expression data by immunohistochemistry. 

Results: 

We identified distinct transcriptional signatures differentiating PNSTs. We observed spatial transcriptional heterogeneity within hybrid PNSTs (HPNSTs) and immune cells preferentially infiltrating the neurofibroma component. S100b and Vimentin were validated as markers for schwannomas and schwannoma components of HPNSTs, while APOD highlights neurofibroma components of HPNSTs. Furthermore, we mapped cells with different differentiation states, including Schwann cell precursors, neural crest-like cells and those with mesenchymal transition in MPNST in space. 

Conclusions:

This pilot study shows that spatial transcriptomics can be applied to PNSTs to gain insight into their biology. It helps establishing new markers, provides spatial information about cellular composition and distribution of cellular differentiation states. Hence, it is a powerful tool for integrating morphological and high-dimensional molecular data with the potential to facilitate PNSTs classification in the future.
DOI: 10.5281/zenodo.14248993
title: Spatially resolved transcriptomics of benign and malignant peripheral nerve sheath tumors

description: Background: 

Peripheral nerve sheath tumors (PNSTs) encompass entities with different cellular differentiation and degrees of malignancy. Spatial heterogeneity complicates diagnosis and grading of PNSTs in some cases. In malignant PNST (MPNST) for example, single cell sequencing data has shown dissimilar differentiation states of tumor cells. Here, we aimed at determining the spatial and biological heterogeneity of PNSTs.

Methods: 

We performed spatial transcriptomics on formalin-fixed paraffin-embedded diseased peripheral nerve tissue. We used spatial clustering and weighted correlation network analysis to construct niche-similarity networks and gene expression modules. We determined differential expression in primary pathologies, analysed pathways to investigate the biological significance of identified meta-signatures, integrated the transcriptional data with histological features and existing single cell data, and validated expression data by immunohistochemistry. 

Results: 

We identified distinct transcriptional signatures differentiating PNSTs. We observed spatial transcriptional heterogeneity within hybrid PNSTs (HPNSTs) and immune cells preferentially infiltrating the neurofibroma component. S100b and Vimentin were validated as markers for schwannomas and schwannoma components of HPNSTs, while APOD highlights neurofibroma components of HPNSTs. Furthermore, we mapped cells with different differentiation states, including Schwann cell precursors, neural crest-like cells and those with mesenchymal transition in MPNST in space. 

Conclusions:

This pilot study shows that spatial transcriptomics can be applied to PNSTs to gain insight into their biology. It helps establishing new markers, provides spatial information about cellular composition and distribution of cellular differentiation states. Hence, it is a powerful tool for integrating morphological and high-dimensional molecular data with the potential to facilitate PNSTs classification in the future.
DOI: 10.15468/dl.jnenh8
title: Occurrence Download

description: A dataset containing 0 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 (Phyllostachys compressus Uyeki)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007843-241126133413365/datasets/export for details.
DOI: 10.15468/dl.aw7tem
title: Occurrence Download

description: A dataset containing 41126 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 (Calendula arvensis L.)"
 ]
}

 The dataset includes 41126 records from 622 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007844-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t7yvun
title: Occurrence Download

description: A dataset containing 2060 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bartramia longicauda (Bechstein, 1812)",
 "HasCoordinate is True",
 "Country is United States of America",
 "Year is greater than or equal to 1999",
 "Year is less than or equal to 2001",
 "Month is greater than or equal to January",
 "Month is less than or equal to December",
 "HasGeospatialIssue is False",
 "DecimalLatitude is greater than or equal to 24.5",
 "DecimalLatitude is less than or equal to 49.5",
 "DecimalLongitude is greater than or equal to -125.0",
 "DecimalLongitude is less than or equal to -66.5"
 ]
}

 The dataset includes 2060 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0383673-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mkdr9k
title: Occurrence Download

description: A dataset containing 787 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Senecio auricula Bourgeau ex Coss."
 ]
}

 The dataset includes 787 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014527-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h6shtp
title: Occurrence Download

description: A dataset containing 3799763 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingCountry is Mexico",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 3799763 records from 408 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069294-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nn5htv
title: Occurrence Download

description: A dataset containing 10975 species occurrences available in GBIF matching the query:
{
 "GadmGid" : [
 "is one of (BRA.16.89_2, BRA.11.48_2)"
 ]
}

 The dataset includes 10975 records from 129 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009291-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ktwnke
title: Occurrence Download

description: A dataset containing 256509 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Biodiversity Research and Teaching Collections - TCWC Vertebrates"
 ]
}

 The dataset includes 256509 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018426-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eywx7c
title: Occurrence Download

description: A dataset containing 63285 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bromus commutatus Guss. ex Steud., 1854, Bromus inermis Leyss., Bromus tectorum L.)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 63285 records from 385 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0159945-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18739/a27659h36
title: Arctic Observing Network (AON) observations from the 2020-2022 Beaufort shelf-edge mooring array

description: This submission contains data collected as a part of the 2020-2022 Beaufort shelf-edge mooring array, which was designed to investigate the manner in which the continental shelves communicate with the interior Arctic basin. Funding was provided by the National Science Foundation (NSF). This submission contains data from the BS3 mooring site, which has collected a consistent and detailed timeseries of physical oceanographic observations beginning in 2002 until present. Funding for this long-term data collection has been supported by the NSF Arctic Observing Network. The Arctic Observing Network (AON) program encourages proposals to make long-term field observations to detect and understand Arctic system change occurring on time scales longer than the duration of a typical NSF research grant. These projects should address major drivers and/or impacts of system change and generate data intended for wider use by the scientific research community in understanding the changing Arctic system. Data included in this submission support the documentation of ocean properties advected from the Pacific into the Chukchi and Beaufort Sea region. More information on this component of the AON project can be found at http://aon.whoi.edu/.
DOI: 10.15468/dl.d5psg9
title: Occurrence Download

description: A dataset containing 3174 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Striga Lour."
 ]
}

 The dataset includes 3174 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002277-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3zb4g4
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Selatium brockii (De Man, 1887)"
 ]
}

 The dataset includes 70 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0132353-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w9hmkn
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "Geometry POLYGON((-7.19048 35.86793,-0.31695 35.86793,-0.31695 38.64138,-7.19048 38.64138,-7.19048 35.86793))",
 "HasGeospatialIssue is false",
 "TaxonKey is Maytenus senegalensis (Lam.) Exell"
 ]
}

 The dataset includes 73 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002269-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cj3fwg
title: Occurrence Download

description: A dataset containing 1417 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is China",
 {
 "or" : [
 "TaxonKey is Paguma Gray, 1831",
 "TaxonKey is Lophura nycthemera (Linnaeus, 1758)"
 ]
 }
 ]
}

 The dataset includes 1417 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0358783-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zr6jvc
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Fossil, Machine Observation)",
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Trichechus inunguis (Natterer, 1883)"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012131-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ef9mbu
title: Occurrence Download

description: A dataset containing 203204 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Rhinanthus antiquus (Sterneck) Schinz & Thell., Rhinanthus minor L., Rhinolophus hipposideros (Bechstein, 1800), Rhithrogena alpestris Eaton, 1885)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 203204 records from 552 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0326235-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h4p2m8
title: Occurrence Download

description: A dataset containing 508 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Oryza sativa L."
 ]
}

 The dataset includes 508 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000594-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15151/esrf-es-2003420925
title: BAG for the Structural Biology Groups in Madrid

description: This proposal is a collaborative effort of the Structural Biology Groups of Madrid with the objective to form a strong core of scientist devoted to this area of
research in Spain. It is composed of 21 groups distributed in 4 research Institutes.
DOI: 10.15151/esrf-es-1976132059
title: Austrian Crystallographic Diffraction Consortium

description: The Austrian Crystallographic Diffraction Consortium (ACDC) BAG aims at supporting several macromolecular structural biology groups across Austria (in total
20 research groups at 9 institutions in 4 cities). We employ mainly the technique of X-ray crystallography to characterize macromolecular biological complexes,
but also solution scattering approaches are frequently used to characterize dynamic assemblies. Approval of this BAG will be essential for researchers in all
our groups to carry out their structural studies on various health-related and basic research-oriented topics, which are targeted at characterizing large molecular
assemblies or proteins currently under-represented in the PDB, including membrane proteins. Corresponding high-resolution diffraction data are only obtainable
through the use of synchrotron radiation sources. Thus regular synchrotron access is highly desirable to maintain a competitive advantage in our individual
research fields.
DOI: 10.15151/esrf-es-2066394728
title: Beamline alignment and partial completion of previous experiment LS3397

description: After beamline alignment we will continue imaging a sample from experiment LS3397
DOI: 10.15151/esrf-es-1975503605
title: The Iberian cryoEM community BAG (II)

description: The Iberian cryoEM BAG is a large consortium (~40 groups) composed of Portuguese and Spanish laboratories working in biologically relevant problems including disease related metabolic enzymes, antibiotic resistance, DNA replication and DNA maintenance, protein synthesis, virus structure and its replication/transcription mechanisms, and macromolecular complexes involved in the control of key cellular processes like protein folding and degradation. For these research groups electron cryomicroscopy is a fundamental tool and access to ESRF facilities is essential to achieve their objectives.
DOI: 10.15151/esrf-es-1976053536
title: CryoEM-BAG France: Structural Biology using cryoEM in France

description: This proposal gathers Principal investigators from Institutions across France that use cryoEM to unravel the molecular mechanisms associated with different fundamental biological processes. Scientists belong to 10 centres that currently use CM01 for cryoEM. All the PIs in this application were part of the previous BAG MX2441, with one new member who has previously submitted samples to CM01 via rolling access. For this reason, and due to more regular use of microscope time from current users we have asked for a moderate increase in the number of shifts ( from 42 to 50).
According to our listing, over 18 projects are ready for data collection at ESRF CM01. Projects include the study of bacterial secretion systems (Bordeaux, Lyon, Paris), viruses and their infection mechanisms (Marseille), translation and its control (Bordeaux, Toulouse, Paris, Strasbourg), transcription (Strasbourg, Paris), cancer (Paris, Bordeaux, Toulouse) and macromolecular transport (Bordeaux, Lyon, Strasbourg).
DOI: 10.15468/dl.2evxfg
title: Occurrence Download

description: A dataset containing 238 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is one of (Madagascar, South Africa, Liberia, Senegal, Sierra Leone, Cameroon, Chad, Congo, Democratic Republic of the, Congo, Gabon, Ethiopia, Tanzania, United Republic of, Mozambique, Malawi, Zambia, Zimbabwe, Kenya, Uganda, South Sudan, Sudan)",
 "DatasetKey is one of (Ecological inventory of Borassus aethiopum (Mart.) populations in the Pendjari Biosphere Reserve, Benin. Data mobilized in the framework of JRS Benin project, Data on agroforestry plant species of Benin, Census of the threatened species of Benin., Données d’occurrence des espèces animales et végétales identifiées sur certains sites de reboisement dans le région de l’Extrême-Nord du Cameroun, Diversité des espèces menacées des zones classées et terroirs villageois du Bénin (Afrique de l'Ouest)., Census of agroforestry plant species of Benin (West Africa) by SOS Biodiversity, Diversité floristique des espèces menacées prioritaires du Bénin (Afrique de l'Ouest)., FLOTROP, a massive contribution to plant diversity data for open ecosystems in Tropical Africa., iNaturalist Research-grade Observations, Palmiers sauvages du Bénin)",
 "OccurrenceStatus is Present",
 "TaxonKey is Borassus aethiopum Mart."
 ]
}

 The dataset includes 238 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000798-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9e748w
title: Occurrence Download

description: A dataset containing 719 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is January",
 "OccurrenceStatus is Present",
 "TaxonKey is Ornithorhynchus anatinus (Shaw, 1799)",
 "Year 2006-2025"
 ]
}

 The dataset includes 719 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000800-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2s85wq
title: Occurrence Download

description: A dataset containing 1932517 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "Geometry POLYGON((1.3 48,3.7 48,3.7 49.5,1.3 49.5,1.3 48))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Insecta"
 ]
}

 The dataset includes 1932517 records from 2569 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000772-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qz4vur
title: Occurrence Download

description: A dataset containing 4028 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((4.63127 44.84424,7.5505 44.84424,7.5505 46.81983,4.63127 46.81983,4.63127 44.84424))",
 "Country is France",
 "Year is 2025",
 "KingdomKey is Animalia"
 ]
}

 The dataset includes 4028 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011054-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.