cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.7du6h7
title: Occurrence Download

description: A dataset containing 548 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is AUS.6_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Varanus giganteus"
 ]
}

 The dataset includes 548 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045007-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4jfhxu
title: Occurrence Download

description: A dataset containing 2646 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Country is Germany",
 "DecimalLongitude is greater than or equal to 6.63733740246749",
 "DecimalLongitude is less than 6.64039695565188",
 "DecimalLatitude is greater than or equal to 47.27011",
 "DecimalLatitude is less than or equal to 55.05864"
 ]
}

 The dataset includes 2646 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045011-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qasq7m
title: Occurrence Download

description: A dataset containing 10233 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-5.29976 46.95124,-1.34134 46.95124,-1.34134 49.11899,-5.29976 49.11899,-5.29976 46.95124))",
 "HasGeospatialIssue is false",
 "TaxonKey is Bombus"
 ]
}

 The dataset includes 10233 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045009-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5284/1136827
title: Digital Archive from an Archaeological Excavation at Evenlode Road, Moreton-in-Marsh, Gloucestershire, November 2020 to February 2021

description: This collection consists of site images and record, a spreadsheet and database, a report, and GIS data from an archaeological excavation at land east of Evenlode Road, Moreton-in-Marsh, Gloucestershire. Works were conducted by Cotswold Archaeology between November 2020 and February 2021. The earliest cut features and deposits were dated by pottery to the later Iron Age and belonged to an open settlement. These included several roundhouses clustered around a central area containing small enclosures.
DOI: 10.15468/dl.jgt7n5
title: Occurrence Download

description: A dataset containing 174 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is AUS.6_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Aspidites ramsayi"
 ]
}

 The dataset includes 174 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045012-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5518/180
title: Data associated with 'Spin-orbit interaction in InAs/GaSb heterostructures quantified by weak antilocalization'

description: We study the spin-orbit interaction (SOI) in InAs/GaSb and InAs quantum wells. We show through temperature- and gate-dependent magnetotransport measurements of weak antilocalization that the dominant spin-orbit relaxation mechanism in our low-mobility heterostructures is Elliott-Yafet and not Dyakonov-Perel in the form of the Rashba or Dresselhaus SOI as previously suggested. We compare our findings with recent work on this material system and show that the SOI length lies within the same range. The SOI length may be controlled using an electrostatic gate, opening up prospects for developing spintronic applications.
DOI: 10.15468/dl.sctsct
title: Occurrence Download

description: A dataset containing 152 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Distribution of Pheronema species from the N.E. Atlantic and the Mediterranean"
 ]
}

 The dataset includes 152 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045013-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3334/cdiac/otg.ndp076
title: Global distribution of total inorganic carbon and total alkalinity below the deepest winter mixed layer depths (NCEI Accession 0117350)

description: Modeling the global ocean-atmosphere carbon dioxide system is becoming increasingly important to greenhouse gas policy. These models require initialization with realistic three-dimensional (3-D) oceanic carbon fields. This report presents an approach to establishing these initial conditions from an extensive global database of ocean carbon dioxide (CO2) system measurements and well-developed interpolation methods. These methods are limited to waters below the deepest mixed layer. The data used for these interpolations include the recent high-quality data sets from the World Ocean Circulation Experiment (WOCE), Joint Global Ocean Flux Study (JGOFS), and Ocean-Atmosphere Carbon Exchange Study (OACES) programs. The interpolation methodology employs correlation between CO2 system properties and other more widely measured properties: potential temperature, salinity, and apparent oxygen utilization. The correlations are computed for each profile, and the coefficients are interpolated to the 1А з 1А з 32 vertical-layer grid at a monthly temporal resolution. Finally, the gridded coefficients are applied to a global monthly climatology of ocean temperature, salinity, and oxygen to compute total CO2 (TCO2) and total alkalinity (TALK) for the 3-D grid. This approach offers advantages over spin up of a single profile in defining spatial variation in CO2 system properties because it reduces initialization time and provides a more accurate carbon field. The results provide an unprecedented "view" of the global distribution of TALK and TCO2 in the ocean. These results as well as those from the monthly mixed layer depths can be used in diagnostic and prognostic global ocean models.
DOI: 10.15468/dl.nbge2b
title: Occurrence Download

description: A dataset containing 667 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melitaea didyma",
 "HasCoordinate is true",
 "Geometry POLYGON ((6.224439 46.56151, 6.224439 48.43216, 8.984551 48.43216, 8.984551 46.56151, 6.224439 46.56151))",
 "Year is greater than or equal to 2020",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 667 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045014-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wd8gcv
title: Occurrence Download

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

 The dataset includes 32 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045016-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17626890
title: Landscape-scale patterns of beta-diversity in Amazonian canopy trees reveals environmental filtering beyond neutral expectations

description: This deposit contains the data and scripts associated with the manuscript, "Landscape-scale patterns of beta-diversity in Amazonian canopy trees reveals environmental filtering beyond neutral expectations." This work addresses a fundamental challenge in ecology: disentangling the roles of deterministic (niche) and stochastic (neutral) processes in structuring hyperdiverse tropical forests.

 

This study quantifies community turnover (beta-diversity) of large canopy trees (≥40 cm DBH) across a vast 5,100 ha contiguous landscape of terra firme forest in the Brazilian Amazon.



Critical Scale: The analysis reveals community turnover patterns operating at an intermediate spatial scale (4.8 km to 15 km) that is typically overlooked by traditional small forest plots (∼700 m) or large-scale, sparse plot networks.

 


Data Resolution: The study uses a spatially explicit, species-level inventory of 377 canopy tree species and over 283,000 stems.

 





Methodology
The analysis employs a three-pronged approach to robustly test community assembly mechanisms:



Scale Quantification: Mantel Correlograms were used to quantify the spatial scale of autocorrelation in canopy tree composition, revealing patterns persist up to 4.8 km and dissimilarity continues to 8.4 km.

Variance Partitioning: Generalized Dissimilarity Models (GDM) were implemented to partition compositional variance into components explained by Geographic Distance (D) and Environmental factors (E), using high-resolution topographical proxies (Topographic Wetness Index, Elevation)

Neutral Null Testing: Spatially-explicit neutral coalescent simulations (pycoalescence/rcoalescence) were used to test whether stochastic processes alone could reproduce the observed spatial turnover patterns and diversity levels.


Data and Code Reproducibility

This repository provides all necessary files to fully reproduce the results

Analysis Scripts (Sequential Order):





01_Calculate_topographical_variables.R: Derives topographical rasters from the DEM.




02_Extract_block_topographical_variables.R: Extracts mean topographical metrics to 3 ha blocks.




03_Spatial_analyses.R: Calculates distance matrices, runs the Mantel correlogram, and performs the GDM analysis (Outputting R2 and GDM splines).




04_Prepare_rasters_for_neutral_sims.R: Creates the background, fine, and sample rasters for the coalescence model using the pre-processed density data.




05_Run_neutral_simulations.R: Defines the parameter space and sequentially runs the spatially explicit neutral simulations (rcoalescence) across all parameter sets and speciation rates.




06_Analyse_neutral_simulations.R: Calculates the observed baseline uncertainty (ϵ) and loops through all simulation results to perform the final comparisons against the observed splines and richness bounds, concluding the main analysis.
DOI: 10.5281/zenodo.17626891
title: Landscape-scale patterns of beta-diversity in Amazonian canopy trees reveals environmental filtering beyond neutral expectations

description: This deposit contains the data and scripts associated with the manuscript, "Landscape-scale patterns of beta-diversity in Amazonian canopy trees reveals environmental filtering beyond neutral expectations." This work addresses a fundamental challenge in ecology: disentangling the roles of deterministic (niche) and stochastic (neutral) processes in structuring hyperdiverse tropical forests.

 

This study quantifies community turnover (beta-diversity) of large canopy trees (≥40 cm DBH) across a vast 5,100 ha contiguous landscape of terra firme forest in the Brazilian Amazon.



Critical Scale: The analysis reveals community turnover patterns operating at an intermediate spatial scale (4.8 km to 15 km) that is typically overlooked by traditional small forest plots (∼700 m) or large-scale, sparse plot networks.

 


Data Resolution: The study uses a spatially explicit, species-level inventory of 377 canopy tree species and over 283,000 stems.

 





Methodology
The analysis employs a three-pronged approach to robustly test community assembly mechanisms:



Scale Quantification: Mantel Correlograms were used to quantify the spatial scale of autocorrelation in canopy tree composition, revealing patterns persist up to 4.8 km and dissimilarity continues to 8.4 km.

Variance Partitioning: Generalized Dissimilarity Models (GDM) were implemented to partition compositional variance into components explained by Geographic Distance (D) and Environmental factors (E), using high-resolution topographical proxies (Topographic Wetness Index, Elevation)

Neutral Null Testing: Spatially-explicit neutral coalescent simulations (pycoalescence/rcoalescence) were used to test whether stochastic processes alone could reproduce the observed spatial turnover patterns and diversity levels.


Data and Code Reproducibility

This repository provides all necessary files to fully reproduce the results

Analysis Scripts (Sequential Order):





01_Calculate_topographical_variables.R: Derives topographical rasters from the DEM.




02_Extract_block_topographical_variables.R: Extracts mean topographical metrics to 3 ha blocks.




03_Spatial_analyses.R: Calculates distance matrices, runs the Mantel correlogram, and performs the GDM analysis (Outputting R2 and GDM splines).




04_Prepare_rasters_for_neutral_sims.R: Creates the background, fine, and sample rasters for the coalescence model using the pre-processed density data.




05_Run_neutral_simulations.R: Defines the parameter space and sequentially runs the spatially explicit neutral simulations (rcoalescence) across all parameter sets and speciation rates.




06_Analyse_neutral_simulations.R: Calculates the observed baseline uncertainty (ϵ) and loops through all simulation results to perform the final comparisons against the observed splines and richness bounds, concluding the main analysis.
DOI: 10.23729/fd-4324791a-9a90-369e-9e23-cb457d0a3f48
title: Chikungunya virus macrodomain  in complex with an inhibitor

description: Raw diffraction images
DOI: 10.15468/dl.nvx3gh
title: Occurrence Download

description: A dataset listing the 186892 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "PublishingOrg is 1928bdf0-f5d2-11dc-8c12-b8a03c50a862"
 ]
}

 The dataset's 186892 records were derived from 25128 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044993-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25582/data.2024-04.3095949/2561600
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3095953/2561601
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3095960/2561602
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3095962/2561603
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3095964/2561604
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3095965/2561605
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3095966/2561606
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3095967/2561607
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3095968/2561608
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3095969/2561609
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3095970/2561610
title: Data for EMSL Project 51287 from April 2024
DOI: 10.25582/data.2024-04.3095972/2561611
title: Data for EMSL Project 51287 from April 2024
DOI: 10.3535/34g-321-1zz
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7zs-zm9-bsn
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7wx-4ev-tbz
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1e9-mkm-svm
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nc8-b64-svb
title: Bovidae Gray, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.gwvdkw
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tridax procumbens",
 "Country is Timor-Leste",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024207-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/2ld-1m6-4v8
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a56-nfq-v73
title: Hystrix Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qyk-2b4-kzs
title: Maianthemum F.H.Wigg.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3he-j2j-k79
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cxe-v0r-9e3
title: Rodentia Bowdich, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pma-tsr-t4z
title: Lepidophyllum Cass.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tke-9cj-7dh
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/22l-tva-ebq
title: Phyllolepidum Trinajstic

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/eph-axz-a20
title: Trichospermum Blume

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rd9-gaa-9cn
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ywg-21z-5bw
title: Capricornis sumatraensis (Bechstein, 1799)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tqy-65b-n1m
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rsf-bs7-5s2
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tnk-drk-069
title: Orthiopteris Copel.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9sz-awz-5nm
title: Elephas maximus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/k06-2an-055
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/baf-kjz-zlr
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l0s-fw4-10r
title: Muntiacus muntjak (Zimmermann, 1780)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ms9-v29-gm6
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/267-42a-179
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q7c-3am-4be
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hck-j5y-xep
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lm8-gk8-zmv
title: Maianthemum F.H.Wigg.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mtn-x4j-jw7
title: Orthiopteris Copel.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qsz-v3n-5pf
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8an-wzv-sn0
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l7x-wyl-0yj
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qll-6gc-c3j
title: †Ginkgo adiantoides (Unger) Heer

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vna-c9x-2fv
title: Varanus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/52c-2n6-qey
title: Lepidophyllum Cass.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9j1-bbf-k22
title: Hystrix Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h7y-hry-1yn
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1la-dme-5da
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2l5-8d1-ckl
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4d3-dgj-nfl
title: Orthiopteris Copel.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a51-x9y-s49
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0w2-3qn-44c
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qbr-atr-vah
title: Orthiopteris Copel.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25549/inscriptifact-ouc110821687
title: Persepolis Fortification Elamite Tablet 2273.103, Fort 2273.103

description: [Text Description:] Administrative text ❧ [Text or Publication Number Note:] Fort 2273.103 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Clay tablet with cuneiform text. ❧ [Physical Object Note:] All edges broken, except for small part of bottom edge.
DOI: 10.25549/inscriptifact-ouc110821588
title: Persepolis Fortification Elamite Tablet 2273.103, Fort 2273.103

description: [Text Description:] Administrative text ❧ [Text or Publication Number Note:] Fort 2273.103 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Clay tablet with cuneiform text. ❧ [Physical Object Note:] All edges broken, except for small part of bottom edge.
DOI: 10.25549/inscriptifact-ouc110821592
title: Persepolis Fortification Elamite Tablet 2273.103, Fort 2273.103

description: [Text Description:] Administrative text ❧ [Text or Publication Number Note:] Fort 2273.103 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Clay tablet with cuneiform text. ❧ [Physical Object Note:] All edges broken, except for small part of bottom edge.
DOI: 10.5281/zenodo.17593009
title: CAT-Q-PL validation data
DOI: 10.5281/zenodo.17593010
title: CAT-Q-PL validation data