cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16753747
title: UW-TransStereo: Underwater Stereo Vision Dataset for Transparent Object Detection & Ranging

description: Robust detection and ranging of transparent debris in water is challenging due to refraction, low contrast, backscatter, and turbidity. We present a paired, multi-environment stereo dataset acquired with a stereo camera, comprising 25 paired stereo vision recordings totalling over 9,000 stereo frame pairs across air and four underwater conditions (freshwater, freshwater with enhancement, saltwater, and saltwater with suspended pellets), covering three bottle targets (two transparent plastic bottles with filled and unfilled variants, and a brown glass medicine bottle), with per-frame detections, depth and dimension (H x W x D) estimates, over 5,000 labelled measurements across environment–bottle combinations (frames, detections, ROI samples), and analysis-ready detector spreadsheets and scripts. To promote reproducible use, we provide a standard evaluation protocol with well-defined accuracy measures—mean absolute error (MAE), root mean square error (RMSE), coefficient of determination (R2), and mean signed error (bias)—and report the proportion of frames with valid estimates (``valid%''), including vertical region-of-interest (ROI) sampling (upper/centre/lower). We include a lightweight ``basicEnhance'' variant to illustrate how pre-processing can be benchmarked against the same protocol without retraining models. Users can load the paired .svo2/.xlsx files to benchmark alternative detectors or compare ranging strategies across the five environmental conditions. The release is intended as a neutral testbed for benchmarking underwater transparent-object perception and for stress-testing stereo ranging under refractive media. File naming, storage structure, and missing-value conventions (including explicit use of not-a-number, NaN) are documented to ease integration. All raw stereo streams, detector outputs, qualitative screenshots, and analysis scripts are published here with a persistent digital object identifier (DOI) to enable citation and long-term reuse.

The repository contains multiple versions of an object detection system, progressing from simple confidence-based detection to advanced 3D analysis with the following key features:



Real-time object detection using YOLO models (YOLOv5/YOLOv8)

3D depth integration with ZED stereo cameras

Object dimension measurement (width, height, depth)

Multi-point distance sampling for accurate measurements

Real-time data export to Excel with timestamps

Screenshot capture with visual distance markers

Pause/resume functionality for detailed analysis

SVO recording support for offline processing

3D visualization with OpenGL rendering
DOI: 10.15468/dl.f7qu68
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"USA.44.169_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010848-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18252592
title: Cerastium rivulare Cambess. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.5281/zenodo.18252593
title: Cerastium rivulare Cambess. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.5281/zenodo.18252599
title: Cerastium rivulariastrum Möschl & Pedersen. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.5281/zenodo.18252598
title: Cerastium rivulariastrum Möschl & Pedersen. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.5281/zenodo.18252604
title: Cerastium selloi Schltdl. ex Rohrb. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.5281/zenodo.18252605
title: Cerastium selloi Schltdl. ex Rohrb. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.15468/dl.qpkj9j
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"USA.44.171_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010849-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18252609
title: Cerastium tomentosum L. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.5281/zenodo.18252610
title: Cerastium tomentosum L. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.5281/zenodo.18252612
title: Cerastium viscosum L. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.5281/zenodo.18252611
title: Cerastium viscosum L. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.15468/dl.rpbtpc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"USA.44.173_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010850-260108223611665/datasets/export for details.
DOI: 10.15468/dl.s4g4be
title: Occurrence Download

description: A dataset containing 98351 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Setaria pumila"
 ]
}

 The dataset includes 98351 records from 1281 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036880-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pgstv2
title: Occurrence Download

description: A dataset containing 1206 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astilbe japonica"
 ]
}

 The dataset includes 1206 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036982-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wsh9gp
title: Occurrence Download

description: A dataset containing 1377 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astilbe grandis"
 ]
}

 The dataset includes 1377 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036981-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f5a8r7
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Marenzelleria viridis",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036983-250811113504898/datasets/export for details.
DOI: 10.15468/dl.zd9kpk
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Marenzelleria viridis",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036984-250811113504898/datasets/export for details.
DOI: 10.15468/dl.bu26kw
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Marenzelleria viridis",
 "Country is France",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036986-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.seqd7v
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hedychium coronarium",
 "Country is Palau",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036985-250811113504898/datasets/export for details.
DOI: 10.15468/dl.phss48
title: Occurrence Download

description: A dataset containing 1115 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Moraea ochroleuca"
 ]
}

 The dataset includes 1115 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036990-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7au6fe
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hedychium coronarium",
 "Country is Saint Lucia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036987-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4tttxn
title: Occurrence Download

description: A dataset containing 750 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hedychium coronarium",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 750 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036989-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qa3akn
title: Occurrence Download

description: A dataset containing 300 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphrasia oakesii"
 ]
}

 The dataset includes 300 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036988-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f4v8yn
title: Occurrence Download

description: A dataset containing 11806 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eurybia divaricata"
 ]
}

 The dataset includes 11806 records from 166 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036991-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e929aq
title: Occurrence Download

description: A dataset containing 3887 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Plantas y hongos asociados a la construcción de la Intersección Aguazul, corredor Villavicencio - Yopal"
 ]
}

 The dataset includes 3887 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000531-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18738/t8/rtpycw
title: Fecundity Compensation Data

description: Raw Data with Preliminary Analyses
DOI: 10.18738/t8/sszwvr
title: TESS Sector 82 Transients

description: TESS light curves for Transients Discovered in Sector 82.
DOI: 10.18738/t8/r0wrix
title: Analysis programs

description: These are four analysis programs used to process the data
DOI: 10.18738/t8/umvgjp
title: Ground-Water and Surface-Water Hydrology of Camp Bowie, Brown County, Texas GIS Data

description: GIS Data for Camp Bowie from the Ground-Water and Surface-Water Hydrology of Camp Bowie, Brown County, Texas report
DOI: 10.18738/t8/xd8ggi
title: Replication Data for: "Impact of ENSO-like tropical Pacific decadal variability on the relative frequency of El Niño and La Niña events"

description: Contains model output for TPDV-ENSO study
DOI: 10.18738/t8/scdxzq
title: Bolivar Sabine beach profile 2002. Sand sample. Data files

description: Data files from sand samples accompanying Bolivar Sabine beach profile 2002.
DOI: 10.18738/t8/x1z95u
title: Bermuda beach profile 2007-2008

description: Historic beach profile data of Galveston Island
DOI: 10.15468/dl.7anzut
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Andrena angelesia Timberlake, 1951"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012144-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5285/38083202924c4785bc61b6e511ad3389
title: NCAS Long Term Observations: SNR winds from the NCAS Mobile Radar Wind Profiler unit 1 deployed at the Met Office Meteorological Research Unit, Cardington, v8.0 (20080924-20090130)

description: Vertical profiles of signal to noise ratio (SNR) and winds measurements from the NCAS Mobile Radar Wind Profiler unit 1 deployed at the Met Office Meteorological Research Unit, Cardington. These observations were taken as part of the National Centre for Atmospheric Science (NCAS) long term observations between 20080924 and 20090130.

Data products from this deployment include: snr-winds

For further details of this deployment and the associated dataset please see the internal file metadata.

These data conform to the NCAS data standards and are available under the UK Government Open Licence agreement. Acknowledgement of NCAS as the data provider is required whenever and wherever these data are used.
DOI: 10.57967/hf/5269
title: sa-data
DOI: 10.15468/dl.fzcaxg
title: Occurrence Download

description: A dataset containing 2240099 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aves",
 "Year is 2008",
 "Month is February"
 ]
}

 The dataset includes 2240099 records from 492 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002626-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17521040
title: Pangenome graphs for pks+/- E. coli in the NORM hybrid assembly collection

description: Contains files for three pangenome graphs used in the study "Co-evolution between colibactin production and resistance is linked to clonal expansions in Escherichia coli": one for hybrid assemblies containing the colibactin production genes (pks+), one for assemblies without them (pks-), and a final graph with both datasets.

For pks+ assemblies, an interactive annotated graph is available as a set of .html files in the zip archive `NORM_pks_neighborhood_graph_html.zip`.

References

Data

Isolation, sequencing, and assembly are described in the following two studies:

[1] Gladstone et al. "Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study". The Lancet Microbe (2021). doi: 10.1016/S2666-5247(21)00031-8.

[2] Arredondo-Alonso et al. "Plasmid-driven strategies for clone success in Escherichia coli". Nature communications (2025). doi: 10.1038/s41467-025-57940-1.

Sequencing data is available from the European Nucleotide Archive under accession numbers PRJEB45354 and PRJEB57633.

Genome annotation

Genome annotation was performed using bakta v1.10.4 (GitHub: oschwengers/bakta) against full database v5.1 dated 2024-01-19 (doi: 10.5281/zenodo.10522951):

[3] Schwengers et al. "Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification." Microbial genomics (2021). doi: 10.1099/mgen.0.000685.

Annotation files are available in a separate Zenodo upload: doi: 10.5281/zenodo.17453317.

Pangenome inference

Pangenome inference from the annotations was performed using panaroo v1.5.2 (GitHub: gtonkinhill/panaroo) with the “--clean-mode strict” and “--remove-invalid-genes” options:

[4] Tonkin-Hill et al. "Producing polished prokaryotic pangenomes with the Panaroo pipeline." Genome Biology (2020). doi: 10.1186/s13059-020-02090-4.
DOI: 10.5281/zenodo.17521041
title: Pangenome graphs for pks+/- E. coli in the NORM hybrid assembly collection

description: Contains files for three pangenome graphs used in the study "Co-evolution between colibactin production and resistance is linked to clonal expansions in Escherichia coli": one for hybrid assemblies containing the colibactin production genes (pks+), one for assemblies without them (pks-), and a final graph with both datasets.

For pks+ assemblies, an interactive annotated graph is available as a set of .html files in the zip archive `NORM_pks_neighborhood_graph_html.zip`.

References

Data

Isolation, sequencing, and assembly are described in the following two studies:

[1] Gladstone et al. "Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study". The Lancet Microbe (2021). doi: 10.1016/S2666-5247(21)00031-8.

[2] Arredondo-Alonso et al. "Plasmid-driven strategies for clone success in Escherichia coli". Nature communications (2025). doi: 10.1038/s41467-025-57940-1.

Sequencing data is available from the European Nucleotide Archive under accession numbers PRJEB45354 and PRJEB57633.

Genome annotation

Genome annotation was performed using bakta v1.10.4 (GitHub: oschwengers/bakta) against full database v5.1 dated 2024-01-19 (doi: 10.5281/zenodo.10522951):

[3] Schwengers et al. "Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification." Microbial genomics (2021). doi: 10.1099/mgen.0.000685.

Annotation files are available in a separate Zenodo upload: doi: 10.5281/zenodo.17453317.

Pangenome inference

Pangenome inference from the annotations was performed using panaroo v1.5.2 (GitHub: gtonkinhill/panaroo) with the “--clean-mode strict” and “--remove-invalid-genes” options:

[4] Tonkin-Hill et al. "Producing polished prokaryotic pangenomes with the Panaroo pipeline." Genome Biology (2020). doi: 10.1186/s13059-020-02090-4.
DOI: 10.11588/duerer.online.691aed5315460
title: Das Dürerhaus in Nürnberg, 185887
DOI: 10.6084/m9.figshare.29050040
title: Data for "Magnesium and silicon isotopic evidence revealing a non-chondritic inner solar system origin for the ureilite parent body"

description: Table S1: Bulk major element compositions (wt. %) of ureilites analyzed using ICP-OES in this study.Table S2: Si isotope compositions of standards and ureilites analyzed in this study.Table S3: Mg isotope compositions of standards and ureilites analyzed in this study (Double spike).Table S4: Summary of Si and Mg isotope compositions of different types of meteorites reported in the literature since 2008.Table S5: Bulk composition of the chondrite samples used in this study (in wt%, expanded CMAS system).
DOI: 10.6084/m9.figshare.29050040.v2
title: Data for "Magnesium and silicon isotopic evidence revealing a non-chondritic inner solar system origin for the ureilite parent body"

description: Table S1: Bulk major element compositions (wt. %) of ureilites analyzed using ICP-OES in this study.Table S2: Si isotope compositions of standards and ureilites analyzed in this study.Table S3: Ma isotope compositions of standards and ureilites analyzed in this study (Double spike).Table S4: Summary of Si and Mg isotope compositions of different types of meteorites reported in the literature since2008.
DOI: 10.6084/m9.figshare.29050040.v3
title: Data for "Magnesium and silicon isotopic evidence revealing a non-chondritic inner solar system origin for the ureilite parent body"

description: Table S1: Bulk major element compositions (wt. %) of ureilites analyzed using ICP-OES in this study.Table S2: Si isotope compositions of standards and ureilites analyzed in this study.Table S3: Mg isotope compositions of standards and ureilites analyzed in this study (Double spike).Table S4: Summary of Si and Mg isotope compositions of different types of meteorites reported in the literature since 2008.Table S5: Bulk composition of the chondrite samples used in this study (in wt%, expanded CMAS system).