cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.85fytc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pithecellobium dulce",
 "Country is Marshall Islands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019632-250802193616735/datasets/export for details.
DOI: 10.15468/dl.fwd66x
title: Occurrence Download

description: A dataset containing 79274 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is UKR.6_1",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 79274 records from 198 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019573-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fjwx8p
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pithecellobium dulce",
 "Country is Mauritius",
 "HasCoordinate is true"
 ]
}

 The dataset includes 38 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019633-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16752776
title: Daten der Notaufnahmesurveillance

description: Der Datensatz 'Notaufnahmesurveillance' enthält aggregierte Daten der Routinedokumentation aus einer Auswahl deutscher Notaufnahmen aus dem AKTIN-Notaufnahmeregister und bildet die Grundlage für die Notaufnahmesurveillance am RKI.
DOI: 10.15468/dl.uybwdk
title: Occurrence Download

description: A dataset containing 240491 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Phalacrocorax varius)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 240491 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019603-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b36mgj
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pithecellobium dulce",
 "Country is Mozambique",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019634-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k6gt2a
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Schistura bucculenta)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019635-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mggdqb
title: Occurrence Download

description: A dataset containing 635925 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is Mozambique",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 635925 records from 445 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019557-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w8kr96
title: Occurrence Download

description: A dataset containing 494 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Phalcoboenus carunculatus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 494 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019636-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dfmzzv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Hypotaenidia owstoni)",
 "Country is one of (Afghanistan, Armenia, Azerbaijan, Bahrain, Bangladesh, Bhutan, Brunei Darussalam, Cambodia, China, Cyprus, Georgia, Hong Kong, India, Indonesia, Iran (Islamic Republic of), Iraq, Israel, Japan, Jordan, Kazakhstan, Korea (Democratic People’s Republic of), Korea, Republic of, Kuwait, Kyrgyzstan, Lao People’s Democratic Republic, Lebanon, Macao, Malaysia, Maldives, Mongolia, Myanmar, Nepal, Oman, Pakistan, Palestine, State of, Philippines, Qatar, Saudi Arabia, Singapore, Sri Lanka, Syrian Arab Republic, Tajikistan, Thailand, Timor-Leste, Türkiye, Turkmenistan, United Arab Emirates, Uzbekistan, Viet Nam, Yemen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019638-250802193616735/datasets/export for details.
DOI: 10.15468/dl.5tywvt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Hypotaenidia owstoni)",
 "Country is one of (Bermuda, Canada, Greenland, Saint Pierre and Miquelon, United States of America)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019637-250802193616735/datasets/export for details.
DOI: 10.5284/1122714
title: Data from Building Survey Work at The Old Barn, Birmingham Road, Coleshill, Warwickshire, 2020-2022 (HS2 Phase One)

description: This collection comprises image, text, photogrammetry, laser scanning, GIS and CAD data from building survey work at The Old Barn, Birmingham Road, Coleshill, Warwickshire.The work was undertaken by COPA: Cotswold Oxford Pre-Construct Archaeology in two phases, prior to and during the demolition of the structures as part of the main works for HS2 between October 2020 and October to December 2022. The site comprises two adjacent groups of buildings identified as non-designated heritage assets and known as the Capitol Joinery Timber Yard and the Old Barn Guesthouse.
DOI: 10.5281/zenodo.15058112
title: The evolution of cheaper workers facilitated larger societies and accelerated diversification in ants

description: Supplementary material related to the manuscript: "The evolution of cheaper workers facilitated larger societies and accelerated diversification in ants". 

Python scripts. Automated segmentation and data extraction scripts for processing 3D µ-CT scans.R scripts. Statistical and phylogenetic comparative analysis scripts used in this study.

Dataset S1. Extracted cuticle and body volume measurements for all scanned specimens.Dataset S2. Manually segmented cuticle and body volume measurements for validation of the automated segmentation method.Dataset S3. Colony size data.Dataset S4. Presence of cuticular spines on the mesosoma at the genus level.Dataset S5. Climatic data, including mean annual temperature and precipitation from species distribution records.Dataset S6. Dietary classification of species and genus into four ecological categories: predator, omnivore, herbivore, and fungivore.Dataset S7. Foraging strata classification including hypogeic, arboreal and epigeic strategies at the genus level.

Segmentation results. Segmented images generated by our program for automatic segmentation.
description: Trade-offs between quantity and quality are common in the organization and evolution of biological, technological, and economic systems. In social insects, shifts from solitary organisms to complex societies bring this dilemma to the colony scale: producing fewer robust units or many cheaper ones. We investigate how cuticle investment—a major nutritional cost—shaped the evolution of ant societies and diversification. Using a computer vision approach on 3D X-ray microtomography scans of 880 specimens from 507 species, we show that larger colonies were facilitated by reducing exoskeleton investment rather than miniaturizing workers. Reduced cuticle investment was associated with accelerated diversification rates in ants, whereas other candidates—colony size and worker size—didn’t correlate with diversification. Diet and climate had measurable but secondary effects on cuticle investment. Our results support a hypothesis whereby evolving cheaper but more numerous units through reduced investment in structural tissues was a strategic trend in the evolution and diversification of complex insect societies.
DOI: 10.5281/zenodo.15546461
title: The evolution of cheaper workers facilitated larger societies and accelerated diversification in ants

description: Supplementary material related to the manuscript: "The evolution of cheaper workers facilitated larger societies and accelerated diversification in ants". 

Python scripts. Automated segmentation and data extraction scripts for processing 3D µ-CT scans.R scripts. Statistical and phylogenetic comparative analysis scripts used in this study.

Dataset S1. Extracted cuticle and body volume measurements for all scanned specimens.Dataset S2. Manually segmented cuticle and body volume measurements for validation of the automated segmentation method.Dataset S3. Colony size data.Dataset S4. Presence of cuticular spines on the mesosoma at the genus level.Dataset S5. Climatic data, including mean annual temperature and precipitation from species distribution records.Dataset S6. Dietary classification of species and genus into four ecological categories: predator, omnivore, herbivore, and fungivore.Dataset S7. Foraging strata classification including hypogeic, arboreal and epigeic strategies at the genus level.

Segmentation results. Segmented images generated by our program for automatic segmentation.
description: Trade-offs between quantity and quality are common in the organization and evolution of biological, technological, and economic systems. In social insects, shifts from solitary organisms to complex societies bring this dilemma to the colony scale: producing fewer robust units or many cheaper ones. We investigate how cuticle investment—a major nutritional cost—shaped the evolution of ant societies and diversification. Using a computer vision approach on 3D X-ray microtomography scans of 880 specimens from 507 species, we show that larger colonies were facilitated by reducing exoskeleton investment rather than miniaturizing workers. Reduced cuticle investment was associated with accelerated diversification rates in ants, whereas other candidates—colony size and worker size—didn’t correlate with diversification. Diet and climate had measurable but secondary effects on cuticle investment. Our results support a hypothesis whereby evolving cheaper but more numerous units through reduced investment in structural tissues was a strategic trend in the evolution and diversification of complex insect societies.
DOI: 10.15468/dl.enybjk
title: Occurrence Download

description: A dataset containing 191 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Phalcoboenus megalopterus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 191 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019640-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mj5zf9
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gymnapogon vanderbilti"
 ]
}

 The dataset includes 24 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019641-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w3z5sa
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Hypotaenidia owstoni)",
 "Country is one of (Anguilla, Antigua and Barbuda, Argentina, Aruba, Bahamas, Barbados, Belize, Bolivia (Plurinational State of), Bonaire, Sint Eustatius and Saba, Bouvet Island, Brazil, Cayman Islands, Chile, Colombia, Costa Rica, Cuba, Curaçao, Dominica, Dominican Republic, Ecuador, El Salvador, Falkland Islands (Malvinas), French Guiana, Grenada, Guadeloupe, Guatemala, Guyana, Haiti, Honduras, Jamaica, Martinique, Mexico, Montserrat, Nicaragua, Panama, Paraguay, Peru, Puerto Rico, Saint Barthélemy, Saint Kitts and Nevis, Saint Lucia, Saint Martin (French part), Saint Vincent and the Grenadines, Sint Maarten (Dutch part), South Georgia and the South Sandwich Islands, Suriname, Trinidad and Tobago, Turks and Caicos Islands, Uruguay, Venezuela (Bolivarian Republic of), Virgin Islands (British), Virgin Islands (U.S.))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019639-250802193616735/datasets/export for details.
DOI: 10.5281/zenodo.16752004
title: Data, Results, and Scripts for "Decoding RNA Triple Helices: Identification from Sequence and Secondary Structure"

description: This repository contains datasets, results, and scripts associated with the following manuscript:

Matarrese, M. A. G., Quadrini, M., Luchetti, N., Di Petta, F., Durante, D., Ballarino, M., Chiodo, L., & Tesei, L. (2025). Decoding RNA Triple Helices: Identification from Sequence and Secondary Structure.

The software tool TripleMatcher, used to process the data and generate the results presented in the manuscript, is available at:

https://github.com/bdslab/triplematcher

Please refer to the documentation of the TripleMatcher tool at:

https://github.com/bdslab/triplematcher/blob/master/README.md

dataset/ Folder

This folder contains the three main datasets used in the paper:



ValidationDataset/: Includes full information about the 8 RNA secondary structures used to define and validate the triple helix pattern described in the paper.

PredictedValidationDataset/: Contains predicted RNA secondary structures for the same 8 molecules from ValidationDataset, obtained using 8 different folding tools.

SearchDataset/: A large dataset of RNA secondary structures with associated 3D PDB entries. It is used to identify novel triple helices via the TripleMatcher tool.


This folder includes a README.md file with further details.

results/ Folder

This folder contains the results obtained from processing the datasetsusing the TripleMatcher tool:



ValidationDatasetResults/: Contains the outputs of the Matcher and 3DFilter components applied to the ValidationDataset, along with validation and zone aggregation data.

PredictedValidationDatasetResults/: Contains the outputs of the Matcher and 3DFilter components applied to the PredictedValidationDataset, as well as evaluation metrics and zone aggregation data.

SearchDatasetResults/: Contains the outputs of the Matcher and 3DFilter components applied to the SearchDataset, with additional data on zone aggregation.


This folder includes a README.md file with detailed descriptions of the contents.

scripts/ Folder

This folder contains all the Python scripts used to post-process the output of the TripleMatcher tool and generate the final results reported in the paper.

This folder includes a README.md file with detailed descriptions of the contents.

Funding

This work was supported by the European Union - NextGenerationEU - National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.1, under the PRIN 2022 PNRR call (Min. Decree No. 1409, dated September 14, 2022), project: P2022FFEWN RNA secondary structures and their relationship with function: application to non-coding RNAs (RNA2Fun), CUP: J53D23014960001.
DOI: 10.15468/dl.3sqaqa
title: Occurrence Download

description: A dataset containing 6802 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bufo gargarizans",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6802 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019642-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7gynfx
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pithecellobium dulce",
 "Country is Nepal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019644-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7f8bk7
title: Occurrence Download

description: A dataset containing 1297 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Geometry POLYGON((-56.14179 -40.51112,-56.14679 -40.40006,-55.73559 -40.37933,-55.75273 -40.12483,-55.5852 -40.11422,-55.60481 -39.62675,-55.17157 -39.61173,-55.93016 -39.24427,-56.72998 -40.23233,-56.14179 -40.51112))",
 "Geometry POLYGON((-56.72998 -40.23233,-57.37247 -41.00387,-56.5705 -41.38585,-56.0702 -40.80985,-56.12802 -40.81246,-56.14179 -40.51112,-56.72998 -40.23233))"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 1297 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019643-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/dbt-xbl-cw1
title: Pongo pygmaeus (Linnaeus, 1760)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pgv-3b2-8fz
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a1w-0c3-xcx
title: Pongo pygmaeus (Linnaeus, 1760)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t46-20h-5cw
title: Bovidae Gray, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7lb-fvy-k4r
title: Elephas Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x77-k2a-2hw
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/llb-br0-mtv
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/am2-f5e-wz0
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cln-rzn-smn
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c6h-65x-cqs
title: Cervus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qqf-hqj-dw3
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.yz5hkp
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cetengraulis mysticetus",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021992-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/xdj-5xg-5yc
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z1g-5pr-5al
title: Muntiacus muntjak (Zimmermann, 1780)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lck-2c4-6xb
title: Pongo pygmaeus (Linnaeus, 1760)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sl2-701-gh8
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/j4l-pdn-yg5
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lvz-2cw-bjm
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tfc-n2g-a21
title: Hexaprotodon Falconer & Cautley, 1836

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7q5-qsf-tjg
title: Symphalangus syndactylus (Raffles, 1821)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pd7-cc5-dk6
title: Bovidae Gray, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6py-fp9-btp
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tfe-pkr-64g
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3h2-w0l-1gk
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ayg-41z-zda
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g93-2yd-nwz
title: Cervus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dwx-dew-sep
title: Varanus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qsj-6xs-2d9
title: Homo sapiens Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kep-tqa-h97
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ydg-sa1-vj4
title: Crocodylus

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.