cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17789448
title: Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies

description: This Zenodo record provides all processed datasets, MAGPIE inputs, and analysis scripts associated with the MAGPIE manuscript (Williams et al).

 

AbstractRecent developments in spatially resolved -omics have enabled the joint study of gene expression, metabolite levels and tissue morphology, offering greater insights into biological pathways. Integrating these modalities from matched tissue sections to probe spatially-coordinated processes, however, remains challenging.Here we introduce MAGPIE, a framework for co-registering spatially resolved transcriptomics, metabolomics, and tissue morphology from the same or consecutive sections.We show MAGPIE’s generalisability and scalability on spatial multi-omics data from multiple tissues, combining Visium with MALDI and DESI mass spectrometry imaging. MAGPIE was also applied to new multimodal datasets generated with a specialised sampling strategy to characterise the metabolic and transcriptomic landscape in an in vivo model of drug-induced pulmonary fibrosis and to link small-molecule co-detection with endogenous lung responses.MAGPIE demonstrates the refined resolution and enhanced interpretability that spatial multimodal analyses provide for studying tissue injury especially in pharmacological contexts, and delivers a modular, accessible workflow for data integration

The repository is designed to enable reproducibility of integrative multi-omics analyses performed in the manuscript and facilitate extended analysis of the new and previously published datasets.

 



 

1. MAGPIE Inputs


The file magpie_inputs.zip contains separate folders for each dataset used in the manuscript. Each folder includes:





MSI data in a peak-by-pixel table (MSI_intensities) along with (x,y)-coordinates and other metadata (MSI_metadata) and (if available) an MSI H&E image (MSI_HE)

Visium Space Ranger outputs (from outs/ folder)




These inputs are ready to be used directly with the MAGPIE pipeline (see the MAGPIE GitHub repository).

 





 

2. Analysis scripts and processed data


The figure_notebooks.zip file contains qmd files and rendered htmls showing how the manuscript figures were generated and data/ which contains processed semla objects and other saved outputs used by these scripts. 

 

For more details on the contents of this record, see README.md
DOI: 10.17026/ar/f2gh7b
title: PAN-00178038 - composite hooked-clasp with one hook/eye group B

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00178038&lt;/p&gt;
description: Modified: 2025-08-07T14:26:33+02:00
DOI: 10.5281/zenodo.17768166
title: TU-GUT-SUSY-Technical Paper

description: TU-GUT-SUSY: Tensoriale Unificato

Teoria della Grande Unificazione con

Supersimmetria

Simone Soliman

Ricercatore indipendente, Roma, Italia

Mechudzu@outlook.it

30 novembre 2025
DOI: 10.15468/dl.vqgpe8
title: Occurrence Download

description: A dataset containing 133610 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "TaxonKey is Canis lupus"
 ]
}

 The dataset includes 133610 records from 414 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022980-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17767128
title: TU-GUT-SUSY Unified Field Theory

description: ═══════════════════════════════════════════════════════════════════════════════

          TU-GUT-SUSY PAPER COMPLETO - SIMON SOLIMAN

 

📄 FORMATO: PDF professionale 22 pagine

✅ MATEMATICA: 0.00% errore ρ_DM

✅ TEST: Protocollo 4.2σ pronto

✅ PUBBLICAZIONE: Zenodo/arXiv ready

✅ PRIORITÀ: 29 Nov 2024 15:45 UTC

 

CREATORE: SIMON SOLIMAN

DATA: 29 NOVEMBRE 2024

═══════════════════════════════════════════════════════════════════════════════
DOI: 10.34740/kaggle/dsv/13963085
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.vmj4cc
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phyllopodopsyllus aegypticus",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023010-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kke8tn
title: Occurrence Download

description: A dataset containing 27306 species occurrences available in GBIF matching the query:
{
 "and" : [
 "SpeciesKey is Vespa velutina",
 "Year is one of (2024, 2025)",
 "HasCoordinate is true",
 "Geometry POLYGON((4.0 44.0, 12.0 44.0, 12.0 50.0, 4.0 50.0, 4.0 44.0))"
 ]
}

 The dataset includes 27306 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023011-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3bvag9
title: Occurrence Download

description: A dataset containing 27306 species occurrences available in GBIF matching the query:
{
 "and" : [
 "SpeciesKey is Vespa velutina",
 "Year is one of (2024, 2025)",
 "HasCoordinate is true",
 "Geometry POLYGON((4.0 44.0, 12.0 44.0, 12.0 50.0, 4.0 50.0, 4.0 44.0))"
 ]
}

 The dataset includes 27306 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023012-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6fc8hs
title: Occurrence Download

description: A dataset containing 8707 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dicaeum cruentatum (Linnaeus, 1758)"
 ]
}

 The dataset includes 8707 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017760-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k9kyue
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helichrysum arwae J.R.I.Wood"
 ]
}

 The dataset includes 12 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019607-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ykkdzx
title: Occurrence Download

description: A dataset containing 130 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Laguncularia racemosa (L.) C.F.Gaertn."
 ]
}

 The dataset includes 130 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0185957-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bawgmd
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Guatemala",
 "DatasetKey is Base de datos para la xiloteca del Instituto de Biología de la UNAM"
 ]
}

 The dataset includes 27 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017761-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.78y2jc
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Haplophyllum armenum Spach"
 ]
}

 The dataset includes 44 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019618-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ccjkzj
title: Occurrence Download

description: A dataset containing 774 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amsonia Walter",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is North America"
 ]
}

 The dataset includes 774 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0159132-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r2aycm
title: Occurrence Download

description: A dataset containing 1575 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lysiloma latisiliquum (L.) Benth."
 ]
}

 The dataset includes 1575 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017762-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c488vt
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Haplophyllum blanchei Boiss."
 ]
}

 The dataset includes 31 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019641-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.97b2gq
title: Occurrence Download

description: A dataset containing 1633 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "TaxonKey is Coccoloba barbadensis Jacq."
 ]
}

 The dataset includes 1633 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0159068-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.umittd
title: Occurrence Download

description: A dataset containing 305 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Camera trap database of Tiger from Rajaji National Park, Uttarakhand"
 ]
}

 The dataset includes 305 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017765-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5mstg9
title: Occurrence Download

description: A dataset containing 135 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aldama flava (Hemsl.) E.E.Schill. & Panero"
 ]
}

 The dataset includes 135 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139491-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eftcnj
title: Occurrence Download

description: A dataset containing 102 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Xylosma pancheri Guillaumin"
 ]
}

 The dataset includes 102 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139490-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gnwtyn
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium anatonum Dahlst."
 ]
}

 The dataset includes 21 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022532-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cbiwh4
title: Occurrence Download

description: A dataset containing 2025 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dahlia ×pinnata Cav."
 ]
}

 The dataset includes 2025 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001925-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fuuenr
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Guatemala",
 "DatasetKey is CNAC/Coleccion Nacional de Acaros"
 ]
}

 The dataset includes 27 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017765-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/yxwrp9
title: 2012_Ville de Digne les Bains_1

description: 2012_Digne-les-Bains:Ville de Digne les Bains:Festival Inventerre
DOI: 10.15468/cbwgjz
title: Plan de gestion 2016 - 2020 du site du domaine de Rodié (47) mené par le CEN Nouvelle-Aquitaine-Observations faunistiques (inventaire) réalisées par le CEN Aquitaine

description: Observations faunistiques (inventaire) réalisées par le CEN Aquitaine. Il n'y a pas de protocole associé à ce jeu de donnée (observations réalisées in situ)
DOI: 10.15468/dl.p8hn5a
title: Occurrence Download

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

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022524-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9bb6tx
title: Occurrence Download

description: A dataset containing 148 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Adoxa L.",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is North America"
 ]
}

 The dataset includes 148 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0159075-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a7dwap
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Saurodactylus fasciatus Werner, 1931"
 ]
}

 The dataset includes 48 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017765-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s9zxds
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hoya davidcummingii Kloppenb."
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022549-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.euw78j
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Bothrops bilineatus (Wied-Neuwied, 1821)"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0181374-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rqhrzv
title: Occurrence Download

description: A dataset containing 1265 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mimosa bahamensis Benth."
 ]
}

 The dataset includes 1265 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017766-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z4v656
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hoya densifolia Turcz."
 ]
}

 The dataset includes 15 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022560-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mrdcuh
title: Occurrence Download

description: A dataset containing 485 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Vincetoxicum biglandulosum (Endl.) Kuntze"
 ]
}

 The dataset includes 485 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004542-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pyygu2
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Guatemala",
 "DatasetKey is CNAC/Coleccion Nacional de Acaros"
 ]
}

 The dataset includes 27 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017766-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3bkmxh
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium andrasovszkyi Zahn"
 ]
}

 The dataset includes 20 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022562-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2y4unc
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year is greater than or equal to 1970",
 "TaxonKey is Xanthomonas axonopodis Starr & Garces, 1950",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 41 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0204857-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fqevy5
title: Occurrence Download

description: A dataset containing 294 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adeia whitneyi (A.Gray) G.L.Nesom"
 ]
}

 The dataset includes 294 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139492-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3pwikc
title: Occurrence Download

description: A dataset containing 104 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Casearia nigricans Sleumer"
 ]
}

 The dataset includes 104 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027519-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9g28d8
title: Occurrence Download

description: A dataset containing 280 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ceratolimon feei (Girard) M.B.Crespo & Lledó"
 ]
}

 The dataset includes 280 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087672-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q7cywe
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dactylopsis digitata (Aiton) N.E.Br."
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0201385-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8jfjjq
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Viola stoloniflora Yokota & Higa"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139493-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15472/vpx8qd
title: Caracterización de endoparásitos y ectoparásitos de murciélagos (Mammalia, Chiroptera) de Leticia, Amazonas, Colombia

description: A pesar de la relevancia biológica y ecológica que representan los parásitos de murciélagos, y siendo Colombia el segundo país con mayor diversidad de especies de murciélagos en el mundo, son pocos los estudios realizados enfocados en la riqueza parasitaria de estos mamíferos voladores. En el conocimiento de los autores, ningún estudio en el Amazonas colombiano.
description: En el presente trabajo se caracterizaron endoparásitos y ectoparásitos de murciélagos capturados entre julio y agosto del 2021 en 5 puntos de captura asociados a la ciudad de Leticia, Amazonas.
description: Un total de 44 murciélagos, distribuidos en 26 especies y 6 familias (Phyllostomidae, Vespertillionidae, Molossidae, Noctilionidae, Thyropteridae, Emballonuridae) se inspeccionaron en búsqueda de parásitos, de los cuales 21 individuos estuvieron parasitados por un total de 181 endo- y ectoparásitos distribuidos en 10 familias, como son: Nematoda: Capillaridae, Molineidae, Onchocercidae, Rictulariidae; Acanthocephala: Oligocanthorhynchidae; Plathyelminthes: Dicrocoeliidae, Lecithodendriidae, Hymenolepididae; Diptera: Hippoboscidae, Acari: Spinturnicidae.
description: Todos los registros del presente trabajo son nuevos reportes de localidad para Colombia. Se reporta, el cistacanto Neoncicola, cestodos del género Vampirolepis y cestodos sin identificar, el nemátodo Pterygodermatites (Paucipectines), la mosca Strebla machadoi y los ácaros Spinturnix surinamensis y Periglischrus tonatii parasitando, por primera vez, murciélagos en Colombia. Se reportan también nuevas asociaciones huésped-parásito.