cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.we5yrq
title: Occurrence Download

description: A dataset containing 171 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rasbora trilineata Steindachner, 1870",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 171 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030047-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pnfe4q
title: Occurrence Download

description: A dataset containing 3069 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-94.57993 18.17717,-94.63486 18.10931,-94.5607 17.95783,-94.29703 17.97873,-94.12125 18.02836,-94.06906 18.11192,-94.11301 18.21631,-94.57993 18.17717))",
 "TaxonKey is Tracheophyta",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3069 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011790-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mg8zbd
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trifolium pseudomedium Hausskn."
 ]
}

 The dataset includes 55 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0134252-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mrq2qk
title: Occurrence Download

description: A dataset containing 1746 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantago virginica L.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1746 records from 99 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0142611-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y5jevs
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Horsfieldia coriacea W.J.de Wilde"
 ]
}

 The dataset includes 22 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030052-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qpzfcl
title: Occurrence Download

description: A dataset containing 146 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus bernardinus M.E.Jones"
 ]
}

 The dataset includes 146 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011791-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jzq27y
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adesmia bijuga Phil."
 ]
}

 The dataset includes 5 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0090936-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t9bpn6
title: Occurrence Download

description: A dataset containing 428 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rasbora borapetensis Smith, 1934",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 428 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030064-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vw7t4m
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vaccinium albidens H.Lév. & Vaniot"
 ]
}

 The dataset includes 14 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0134253-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mv6c9s
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anredera cordifolia (Ten.) Steenis",
 "Country is Mexico",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 12 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011791-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gyjmbr
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium tortifrons Dahlst. ex Johanss. & Sam."
 ]
}

 The dataset includes 39 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030068-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zjrswx
title: Occurrence Download

description: A dataset containing 233 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation"
 ]
 },
 "Country is India",
 "Geometry POLYGON((72.53613 19.83691,71.5166 19.55566,77.28223 6.86426,78.89942 9.21973,74.29395 19.7666,72.53613 19.83691))",
 "OccurrenceStatus is Present",
 "TaxonKey is Ratufa indica (Erxleben, 1777)"
 ]
}

 The dataset includes 233 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0100130-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qxy9si
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "TaxonKey is Alvimia C.E.Calderón ex Soderstr. & Londoño",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 78 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011791-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w4u2mk
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Devario acrostomus (Fang & Kottelat, 1999)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029953-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cfpq8z
title: Occurrence Download

description: A dataset containing 2199 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Araucaria araucana (Molina) K.Koch"
 ]
}

 The dataset includes 2199 records from 138 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0090949-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lyonqk
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((13.35938 37.71859,-7.73438 39.36828,-22.5 21.28937,-14.76562 -4.91583,4.21875 -11.1784,9.84375 -34.30714,32.34375 -43.58039,54.14063 -25.79989,54.14063 0,54.14063 15.96133,40.07812 17.97873,35.15625 30.14513,13.35938 37.71859))",
 "TaxonKey is Felis catus Linnaeus, 1758"
 ]
}

 The dataset includes 95 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011791-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vewjvu
title: Occurrence Download

description: A dataset containing 195 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Asplenium trilobum Cav."
 ]
}

 The dataset includes 195 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0090950-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xkxrwv
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Horsfieldia fulva (King) Warb."
 ]
}

 The dataset includes 51 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030165-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zuvpzv
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-118.38867 32.69487,-112.76367 15.45368,-93.42773 11.3508,-86.2207 17.30869,-85.69336 22.26876,-94.83398 26.11599,-104.50195 32.84267,-118.38867 32.69487))",
 "TaxonKey is Echeveria derenbergii J.A.Purpus",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011791-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6v357s
title: Occurrence Download

description: A dataset containing 760 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-75.53616 6.41015,-75.51006 6.36785,-75.42835 6.40879,-75.45582 6.45109,-75.53616 6.41015))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata"
 ]
}

 The dataset includes 760 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139323-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h6dyk8
title: Occurrence Download

description: A dataset containing 948 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Argentina, Uruguay)",
 "TaxonKey is Rhinella arenarum (Hensel, 1867)",
 "Year 1000-2020"
 ]
}

 The dataset includes 948 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030012-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4121/8e1c6604-53c7-4905-8ef9-4a6b2acc4e7a
title: Supplementary data for the paper 'eHMI on the vehicle or on the infrastructure? A driving simulator study'

description: Automated vehicles (AVs) may require the implementation of an external human-machine interface (eHMI) to communicate their intentions to human-driven vehicles. The optimal placement of the eHMI, either on the AV itself or as part of the road infrastructure, remains undetermined. The current driving simulator study investigated the effect of eHMI positioning on human driving behavior, during the approach and execution of right turns at T-intersections. Forty-three participants drove under three conditions: absence of eHMI, eHMI on the AV (eHMIv), and eHMI integrated into the infrastructure (eHMIi). Participants encountered AVs that either yielded or did not yield to their vehicles. The results regarding the placement of the eHMI showed that both concepts are advantageous, but for different reasons. eHMIv was appreciated because implicit and explicit communication are congruent, although the AV must first be visually identified to respond to it. eHMIi was appreciated because a familiar cue is always at a known location in the environment; as a result, participants braked earlier for the intersection and came less close to the AV (which can be interpreted as a safety advantage or efficiency disadvantage). Although there are limitations to the current driving simulator study, this research provides important insights into the fundamental question of how information placement affects drivers’ visual attention demands and driving behavior, topics that are important in view of the development of future cities.
DOI: 10.4121/8e1c6604-53c7-4905-8ef9-4a6b2acc4e7a.v1
title: Supplementary data for the paper 'eHMI on the vehicle or on the infrastructure? A driving simulator study'

description: Automated vehicles (AVs) may require the implementation of an external human-machine interface (eHMI) to communicate their intentions to human-driven vehicles. The optimal placement of the eHMI, either on the AV itself or as part of the road infrastructure, remains undetermined. The current driving simulator study investigated the effect of eHMI positioning on human driving behavior, during the approach and execution of right turns at T-intersections. Forty-three participants drove under three conditions: absence of eHMI, eHMI on the AV (eHMIv), and eHMI integrated into the infrastructure (eHMIi). Participants encountered AVs that either yielded or did not yield to their vehicles. The results regarding the placement of the eHMI showed that both concepts are advantageous, but for different reasons. eHMIv was appreciated because implicit and explicit communication are congruent, although the AV must first be visually identified to respond to it. eHMIi was appreciated because a familiar cue is always at a known location in the environment; as a result, participants braked earlier for the intersection and came less close to the AV (which can be interpreted as a safety advantage or efficiency disadvantage). Although there are limitations to the current driving simulator study, this research provides important insights into the fundamental question of how information placement affects drivers’ visual attention demands and driving behavior, topics that are important in view of the development of future cities.
DOI: 10.15468/dl.nx8qvy
title: Occurrence Download

description: A dataset containing 154 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Uvaria microcarpa Champ. ex Benth.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 154 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0142606-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2kt2ww
title: Occurrence Download

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

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030079-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zy5fxm
title: Occurrence Download

description: A dataset containing 38212 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Geranoaetus melanoleucus (Vieillot, 1819)",
 "HasCoordinate is True",
 "Year is greater than or equal to 1900",
 "Year is less than or equal to 2021",
 "Month is greater than or equal to January",
 "Month is less than or equal to December",
 "HasGeospatialIssue is False"
 ]
}

 The dataset includes 38212 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0345270-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.agqm89
title: Occurrence Download

description: A dataset containing 8278 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium tomentosum (L.) L."
 ]
}

 The dataset includes 8278 records from 144 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030001-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.df59ey
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Liomera margaritata"
 ]
}

 The dataset includes 61 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043337-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.25sfcg
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tamiasciurus mearnsi"
 ]
}

 The dataset includes 39 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043343-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16981364
title: Protein Models: Autoimmunity-associated DIORA1 binds the MRCK family of serine/threonine kinases and controls cell motility

description: Models generated for the interaction between DIORA1 and MRCKB with massive sampling using AFsample (Wallner, 2022)

File descriptions

The data is compressed with zstandard to extract an archive use the following command:



tar --use-compress-program=unzstd -xvf all_models_scores.tar.zst


all_models_scores.tar.zst - Contains scores for all generated models, extracts to the folder all_models/selected_models.tar.zst - Contains top-ranked selected models that are also highlighted in the paper, extracts to selected_models/

Models for different interaction partners

All models and corresponding results *.pkl (distogram removed to save space) are archived in different files for each interaction partner.

Stoichiometry 1:1 (main text)

KIM_diora_1_1.tar.zst (2.2GB) - All 3000 models generated for the KIM region of MRCKB to interact with DIORA1.MRCKB_1020_1582-diora1_1_214.tar.zst (3.9GB) - All 3,000 models generated for the MRCKB range 1020-1582 corresponding to the C1-PH-CNH domains.

Different models with different stoichiometries  (Supplementary Information)

KIM_diora1_1_2.tar.zst (1.9GB) - 3,000 models for KIM:DIORA1 1:2KIM_diora1_2_1.tar.zst (1.4GB) - 3,000 models for KIM:DIORA1 2:1KIM_diora1_2_2.tar.zst (2.6GB) - 3,000 models for KIM:DIORA1 2:2

MRCKB_1020_1582-diora1_1_214_1_2.tar.zst  (5.3GB) - 3,000 models for C1-PH-CNH:DIORA1 1:2MRCKB_1020_1582-diora1_1_214_2_1.tar.zst (8.8GB) - 3,000 models for C1-PH-CNH:DIORA1 2:1MRCKB_1020_1582-diora1_1_214_2_2.tar.zst (10.8GB) - 3,000 models for C1-PH-CNH:DIORA1 2:2

 

Modelling protocol

Models generated for the interaction between DIORA1 and MRCKB with massive sampling using AFsample (Wallner, 2022)

Code: http://wallnerlab.org/AFsample

Alphafold was run with dropout activated at inference using all 15 (3x5) neural network models available for multimeric prediction:



model_[1-5]_multimer

model_[1-5]_multimer_v2

model_[1-5]_multimer_v3


The following command was used to generate 200 models per neural network model, 3000 (15x200) models in total for each modeling input



python alphafoldv2.3.1/run_alphafold.py--dropout--nstruct 200--use_precomputed_msas
--data_dir=/proj/beyondfold/apps/alphafold_data
--template_mmcif_dir=/proj/beyondfold/apps/alphafold_data/pdb_mmcif/mmcif_files
--obsolete_pdbs_path=/proj/beyondfold/apps/alphafold_data/pdb_mmcif/obsolete.dat
--mgnify_database_path=/proj/beyondfold/users/x_bjowa/databases/mgnify/mgy_all.fa
--uniref90_database_path=/proj/beyondfold/apps/alphafold_data/uniref90/uniref90.fasta
--max_template_date=3000-01-01
--use_gpu_relax=True
--model_preset=multimer
--db_preset=full_dbs
--uniref30_database_path=/proj/beyondfold/apps/alphafold_data/uniclust30/UniRef30_2021_03/UniRef30_2021_03
--bfd_database_path=/proj/beyondfold/apps/alphafold_data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
--pdb_seqres_database_path=/proj/beyondfold/apps/alphafold_data/pdb_seqres/pdb_seqres.txt
--uniprot_database_path=/proj/beyondfold/apps/alphafold_data/uniprot/uniprot.fasta