cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17725635
title: Supplementary data for: "Rewriting protein alphabets with language models"

description: This repository contains the benchmarking data associated with the manuscript: "Rewriting protein alphabets with language models". The data is organized into three main archive files and one standalone result file, which together contain all necessary sequences, search results, and metadata required for reproducing the experiments and analyses presented in the paper.

SCOPe40 Benchmarking Data (scope40.tar.gz)

This file includes SCOPe40 (v2.08) sequences, sequence alignments, and the files necessary for reproducing all the benchmarked methods in the paper:



Sequences:  standard amino acid, TEA, 3Di and DSSP.

Family/Superfamily/Fold sensitivities: MMseqs2-TEA/CV, MMseqs2-amino-acid sequences, MMseqs2-3Di, Foldseek, EBA, plus the ablations and the "exhaustive" searches combining different sequence representations.


Multidomain Benchmarking Data (multidomain.tar.gz)

This file includes the multidomain benchmark sequences and search results:



Sequences: standard amino acid and TEA sequences for both the target and query sets.

Search results:  MMseqs2-TEA, MMseqs2-amino-acid sequences, Foldseek.


40k-pLDDT set (40kplddtset.tar.gz)

Set described in the paper for entropy analysis and pLDDT mapping, includes:



Sequences:  standard amino acid, TEA, DSSP, and 3Di.

Entropies: both average and per-residue TEA Shannon entropy values.

pLDDT: from both AlphaFold2 and ESMFold predictions.

Predicted Structures: ESMFold predicted structures.


Singletons search results (singletons_vs_all_search_18_3.m8.gz)

The search results from the singleton analysis discussed in Section 2.4 ("Improving functional annotation...") of the manuscript.
DOI: 10.5281/zenodo.17725634
title: Supplementary data for: "Rewriting protein alphabets with language models"

description: This repository contains the benchmarking data associated with the manuscript: "Rewriting protein alphabets with language models". The data is organized into three main archive files and one standalone result file, which together contain all necessary sequences, search results, and metadata required for reproducing the experiments and analyses presented in the paper.

SCOPe40 Benchmarking Data (scope40.tar.gz)

This file includes SCOPe40 (v2.08) sequences, sequence alignments, and the files necessary for reproducing all the benchmarked methods in the paper:



Sequences:  standard amino acid, TEA, 3Di and DSSP.

Family/Superfamily/Fold sensitivities: MMseqs2-TEA/CV, MMseqs2-amino-acid sequences, MMseqs2-3Di, Foldseek, EBA, plus the ablations and the "exhaustive" searches combining different sequence representations.


Multidomain Benchmarking Data (multidomain.tar.gz)

This file includes the multidomain benchmark sequences and search results:



Sequences: standard amino acid and TEA sequences for both the target and query sets.

Search results:  MMseqs2-TEA, MMseqs2-amino-acid sequences, Foldseek.


40k-pLDDT set (40kplddtset.tar.gz)

Set described in the paper for entropy analysis and pLDDT mapping, includes:



Sequences:  standard amino acid, TEA, DSSP, and 3Di.

Entropies: both average and per-residue TEA Shannon entropy values.

pLDDT: from both AlphaFold2 and ESMFold predictions.

Predicted Structures: ESMFold predicted structures.


Singletons search results (singletons_vs_all_search_18_3.m8.gz)

The search results from the singleton analysis discussed in Section 2.4 ("Improving functional annotation...") of the manuscript.
DOI: 10.6084/m9.figshare.30859916
title: Supplementary data: Racial and ethnic differences in diagnosis, healthcare utilization and 1-year outcomes for patients with significant tricuspid regurgitation

description: <b>These are peer-reviewed supplementary materials for the article</b><b> </b><b>'</b><b>Racial and ethnic differences in diagnosis, healthcare utilization and 1-year outcomes for patients with significant tricuspid regurgitation</b><b>'</b><b> </b><b>published in the</b><b> </b><b><i>Journal of Comparative Effectiveness Research</i></b><b>.</b><b>Supplemental Table 1: </b>Patient identification criteria for significant tricuspid regurgitation, by race/ethnicity<b>Supplemental Table 2:</b> Comorbidity burden over time.<b>Supplemental Table 3:</b> Unadjusted hazard ratios for one-year post-significant tricuspid regurgitation events, by race and ethnicity.<b>Supplemental Table 4: </b>Hazard ratios for all explanatory variables for all-cause mortality.<b>Supplemental Table 5: </b>Hazard ratios for all explanatory variables for heart failure hospitalization.<b>Background:</b> The impact of race and ethnicity on prognosis and clinical outcomes in patients with significant tricuspid regurgitation (sTR) is not well understood. <b>Aim: </b>Describe healthcare utilization trends preceding the development of sTR and assess clinical outcomes 1-year post-sTR status by race and ethnicity. <b>Materials & methods:</b> We conducted a retrospective, longitudinal descriptive study using data from a large database containing electronic health record and insurance claims information.We employed multivariate modeling to assess the relationship between 1-year clinical outcomes and mutually exclusive race/ethnicity groups and other baseline factors. <b>Results: </b>Black patients were more likely to be identified as having sTR as inpatients when compared with White patients (p &lt; 0.001) and had fewer outpatient visits to cardiac specialists before and after developing sTR (p &lt; 0.01). Black and Hispanic patients with sTR were at increased risk of heart failure hospitalization compared with White patients at 1 year (adjusted HR: 1.21, 95% CI: 1.16–1.26, p &lt; 0.001 and adjusted HR: 1.10, 95% CI: 1.02–1.19, p &lt; 0.05 respectively). However, both Black and Hispanic patients had lower 1-year mortality thanWhite patients in the adjusted model. <b>Conclusion:</b> Black and Hispanic patients are less likely to have received outpatient care by a cardiac specialist prior to the development of sTR, and have higher rates of heart failure hospitalization after diagnosis. In contrast, their mortality rates following sTR identification are lower than White patients. Further investigation into the underlying mechanisms of these observations is needed to improve TR related outcomes.
DOI: 10.6084/m9.figshare.30859916.v1
title: Supplementary data: Racial and ethnic differences in diagnosis, healthcare utilization and 1-year outcomes for patients with significant tricuspid regurgitation

description: <b>These are peer-reviewed supplementary materials for the article</b><b> </b><b>'</b><b>Racial and ethnic differences in diagnosis, healthcare utilization and 1-year outcomes for patients with significant tricuspid regurgitation</b><b>'</b><b> </b><b>published in the</b><b> </b><b><i>Journal of Comparative Effectiveness Research</i></b><b>.</b><b>Supplemental Table 1: </b>Patient identification criteria for significant tricuspid regurgitation, by race/ethnicity<b>Supplemental Table 2:</b> Comorbidity burden over time.<b>Supplemental Table 3:</b> Unadjusted hazard ratios for one-year post-significant tricuspid regurgitation events, by race and ethnicity.<b>Supplemental Table 4: </b>Hazard ratios for all explanatory variables for all-cause mortality.<b>Supplemental Table 5: </b>Hazard ratios for all explanatory variables for heart failure hospitalization.<b>Background:</b> The impact of race and ethnicity on prognosis and clinical outcomes in patients with significant tricuspid regurgitation (sTR) is not well understood. <b>Aim: </b>Describe healthcare utilization trends preceding the development of sTR and assess clinical outcomes 1-year post-sTR status by race and ethnicity. <b>Materials & methods:</b> We conducted a retrospective, longitudinal descriptive study using data from a large database containing electronic health record and insurance claims information.We employed multivariate modeling to assess the relationship between 1-year clinical outcomes and mutually exclusive race/ethnicity groups and other baseline factors. <b>Results: </b>Black patients were more likely to be identified as having sTR as inpatients when compared with White patients (p &lt; 0.001) and had fewer outpatient visits to cardiac specialists before and after developing sTR (p &lt; 0.01). Black and Hispanic patients with sTR were at increased risk of heart failure hospitalization compared with White patients at 1 year (adjusted HR: 1.21, 95% CI: 1.16–1.26, p &lt; 0.001 and adjusted HR: 1.10, 95% CI: 1.02–1.19, p &lt; 0.05 respectively). However, both Black and Hispanic patients had lower 1-year mortality thanWhite patients in the adjusted model. <b>Conclusion:</b> Black and Hispanic patients are less likely to have received outpatient care by a cardiac specialist prior to the development of sTR, and have higher rates of heart failure hospitalization after diagnosis. In contrast, their mortality rates following sTR identification are lower than White patients. Further investigation into the underlying mechanisms of these observations is needed to improve TR related outcomes.
DOI: 10.17026/ar/vptszi
title: PAN-00169222 - seal with long connecting strip

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00169222&lt;/p&gt;
description: Modified: 2025-11-11T13:35:08+01:00
DOI: 10.5281/zenodo.15335450
title: Global River Water Quality Archive (GRQA)

description: A major problem related to large-scale water quality modeling has been the lack of available observation data with a good spatiotemporal coverage. This has affected the reproducibility of previous studies and the potential improvement of existing models. In addition to the observation data itself, insufficient or poor quality metadata has also discouraged researchers to integrate the already available datasets. Therefore, improving both the availability and quality of open water quality data woould increase the potential to implement predictive modeling on a global scale. We aim to address the aforementioned issues by presenting the new Global River Water Quality Archive (GRQA) by integrating data from five existing global and regional sources: Canadian Environmental Sustainability Indicators program (CESI), Global Freshwater Quality Database (GEMStat), GLObal RIver Chemistry database (GLORICH), European Environment Agency (Waterbase) and USGS Water Quality Portal (WQP). The resulting dataset covering the timeframe 1898 - 2023 contains a total of over 17 million observations for 43 different forms of some of the most important water quality parameters, focusing on nutrients, carbon, oxygen and sediments. Supplementary metadata and statistics are provided with the observation time series to improve the usability of the dataset.

GRQA data processing scripts are available at https://doi.org/10.5281/zenodo.5082147.

Last update: 2025-05-04

Changes since GRQA_v1.3

The updated dataset now includes the observations from the latest versions of GEMStat and Waterbase. These additions extend the time series to 2023 in many sites, particularly in Europe.

An overview of all the files in the dataset can be found in README_v1.4.md.

Statistical overview of all 43 parameters is given in the data catalog file GRQA_data_catalog_v1.4.pdf.

For more information about the development of this dataset look for Virro, H., Amatulli, G., Kmoch, A., Shen, L., and Uuemaa, E.: GRQA: Global River Water Quality Archive, Earth Syst. Sci. Data, 13, 5483–5507, https://doi.org/10.5194/essd-13-5483-2021, 2021.
DOI: 10.5281/zenodo.5097436
title: Global River Water Quality Archive (GRQA)

description: A major problem related to large-scale water quality modeling has been the lack of available observation data with a good spatiotemporal coverage. This has affected the reproducibility of previous studies and the potential improvement of existing models. In addition to the observation data itself, insufficient or poor quality metadata has also discouraged researchers to integrate the already available datasets. Therefore, improving both the availability and quality of open water quality data woould increase the potential to implement predictive modeling on a global scale. We aim to address the aforementioned issues by presenting the new Global River Water Quality Archive (GRQA) by integrating data from five existing global and regional sources: Canadian Environmental Sustainability Indicators program (CESI), Global Freshwater Quality Database (GEMStat), GLObal RIver Chemistry database (GLORICH), European Environment Agency (Waterbase) and USGS Water Quality Portal (WQP). The resulting dataset covering the timeframe 1898 - 2023 contains a total of over 17 million observations for 43 different forms of some of the most important water quality parameters, focusing on nutrients, carbon, oxygen and sediments. Supplementary metadata and statistics are provided with the observation time series to improve the usability of the dataset.

GRQA data processing scripts are available at https://doi.org/10.5281/zenodo.5082147.

Last update: 2025-05-04

Changes since GRQA_v1.3

The updated dataset now includes the observations from the latest versions of GEMStat and Waterbase. These additions extend the time series to 2023 in many sites, particularly in Europe.

An overview of all the files in the dataset can be found in README_v1.4.md.

Statistical overview of all 43 parameters is given in the data catalog file GRQA_data_catalog_v1.4.pdf.

For more information about the development of this dataset look for Virro, H., Amatulli, G., Kmoch, A., Shen, L., and Uuemaa, E.: GRQA: Global River Water Quality Archive, Earth Syst. Sci. Data, 13, 5483–5507, https://doi.org/10.5194/essd-13-5483-2021, 2021.
DOI: 10.15468/dl.vrg7k7
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((112.672 -1.57782, 112.60171 -1.583385, 112.53315 -1.599946, 112.468007 -1.627092, 112.407883 -1.664158, 112.354259 -1.710231, 112.308454 -1.764176, 112.271597 -1.824667, 112.244595 -1.890213, 112.228115 -1.959203, 112.222562 -2.029937, 112.228076 -2.100674, 112.244522 -2.169673, 112.271496 -2.235233, 112.308335 -2.295741, 112.354134 -2.349705, 112.407764 -2.395797, 112.467906 -2.43288, 112.533077 -2.46004, 112.601672 -2.476609, 112.672 -2.482178, 112.742328 -2.476609, 112.810923 -2.46004, 112.876094 -2.43288, 112.936236 -2.395797, 112.989866 -2.349705, 113.035665 -2.295741, 113.072504 -2.235233, 113.099478 -2.169673, 113.115924 -2.100674, 113.121438 -2.029937, 113.115885 -1.959203, 113.099405 -1.890213, 113.072403 -1.824667, 113.035546 -1.764176, 112.989741 -1.710231, 112.936117 -1.664158, 112.875993 -1.627092, 112.81085 -1.599946, 112.74229 -1.583385, 112.672 -1.57782))"},{"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/0046986-251120083545085/datasets/export for details.
DOI: 10.15468/dl.eqm9j8
title: Occurrence Download

description: A dataset containing 12721 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "OccurrenceStatus is Present",
 "TaxonKey is Ecballium elaterium",
 "Year 2015-2025"
 ]
}

 The dataset includes 12721 records from 105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046987-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/sn4hh6
title: A New Species of Parascorpaena Bleeker, 1876 (Teleostei: Scorpaenidae) from Taiwan

description: This dataset contains the digitized treatments in Plazi based on the original journal article Chou, Tak-Kei, Liao, Te-Yu (2022): A New Species of Parascorpaena Bleeker, 1876 (Teleostei: Scorpaenidae) from Taiwan. Zoological Studies 61 (9): 1-12, DOI: 10.6620/ZS.2022.61-09, URL: http://dx.doi.org/10.15468/sn4hh6
DOI: 10.15468/dl.tdnky3
title: Occurrence Download

description: A dataset containing 1288 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "DecimalLatitude is greater than or equal to 69.085278",
 "DecimalLatitude is less than or equal to 74.085278",
 "DecimalLongitude is greater than or equal to 135.0",
 "DecimalLongitude is less than or equal to 140.0",
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 1288 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046988-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2p87jr
title: CCDC 2480574: Experimental Crystal Structure Determination

description: Related Article: Qiu Sun, Julian Hauda, David Tymann, Patrick W. Antoni, Richard Goddard, Max M. Hansmann|2025|Angew.Chem.,Int.Ed.|64|e202518689|doi:10.1002/anie.202518689
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p87ks
title: CCDC 2480575: Experimental Crystal Structure Determination

description: Related Article: Qiu Sun, Julian Hauda, David Tymann, Patrick W. Antoni, Richard Goddard, Max M. Hansmann|2025|Angew.Chem.,Int.Ed.|64|e202518689|doi:10.1002/anie.202518689
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p87lt
title: CCDC 2480576: Experimental Crystal Structure Determination

description: Related Article: Qiu Sun, Julian Hauda, David Tymann, Patrick W. Antoni, Richard Goddard, Max M. Hansmann|2025|Angew.Chem.,Int.Ed.|64|e202518689|doi:10.1002/anie.202518689
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p87mv
title: CCDC 2480577: Experimental Crystal Structure Determination

description: Related Article: Qiu Sun, Julian Hauda, David Tymann, Patrick W. Antoni, Richard Goddard, Max M. Hansmann|2025|Angew.Chem.,Int.Ed.|64|e202518689|doi:10.1002/anie.202518689
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p87nw
title: CCDC 2480578: Experimental Crystal Structure Determination

description: Related Article: Qiu Sun, Julian Hauda, David Tymann, Patrick W. Antoni, Richard Goddard, Max M. Hansmann|2025|Angew.Chem.,Int.Ed.|64|e202518689|doi:10.1002/anie.202518689
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p87px
title: CCDC 2480579: Experimental Crystal Structure Determination

description: Related Article: Qiu Sun, Julian Hauda, David Tymann, Patrick W. Antoni, Richard Goddard, Max M. Hansmann|2025|Angew.Chem.,Int.Ed.|64|e202518689|doi:10.1002/anie.202518689
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p91nq
title: CCDC 2481353: Experimental Crystal Structure Determination

description: Related Article: Shina Quek, Ren Ishizeki, Zheng-Feng Zhang, Ming-Der Su, Rahul Kumar Siwatch, Cheuk-Wai So|2025|Inorg.Chem.|||doi:10.1021/acs.inorgchem.5c04031
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.17026/ar/kukxn1
title: PAN-00180202 - double looped buckle with separate bar

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00180202&lt;/p&gt;
description: Modified: 2025-11-11T10:27:17+01:00
DOI: 10.5517/ccdc.csd.cc2p91pr
title: CCDC 2481354: Experimental Crystal Structure Determination

description: Related Article: Shina Quek, Ren Ishizeki, Zheng-Feng Zhang, Ming-Der Su, Rahul Kumar Siwatch, Cheuk-Wai So|2025|Inorg.Chem.|||doi:10.1021/acs.inorgchem.5c04031
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p91qs
title: CCDC 2481355: Experimental Crystal Structure Determination

description: Related Article: Shina Quek, Ren Ishizeki, Zheng-Feng Zhang, Ming-Der Su, Rahul Kumar Siwatch, Cheuk-Wai So|2025|Inorg.Chem.|||doi:10.1021/acs.inorgchem.5c04031
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p958g
title: CCDC 2481465: Experimental Crystal Structure Determination

description: Related Article: Lisa Körtgen, David van Gerven, Sean S. Sebastian, Tim Kleinöder, Uwe Ruschewitz|2025|Z.Anorg.Allg.Chem.||e202500199|doi:10.1002/zaac.202500199
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.