cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12805212
title: MMSEQS meets AntiRef90: reference clusters of human antibody sequences

description: This data set contains pre-computed mmseqs databases for the antiref fasta files created by Briney et al. 

Please cite the original work if you use any of the databases provided here.

Sources:



Antiref GitHub

Antiref Zenodo

Antiref Paper


 

The mmseqs databases were created as follows:

 

```

aria2x -x16 -s16 --input-file antiref_links.txtsnakemake -s antiref_mmseqs.smk --jobs 1 --cores 1 --local-cores 250

```

 

Please check the summary repository for the fasta files and snakemake files. In this sub repo we only store the antiref files matching the title of the repo.
DOI: 10.5281/zenodo.13256609
title: MMSEQS meets AntiRef90: reference clusters of human antibody sequences

description: This data set contains pre-computed mmseqs databases for the antiref fasta files created by Briney et al. 

Please cite the original work if you use any of the databases provided here.

Sources:



Antiref GitHub

Antiref Zenodo

Antiref Paper


 

The mmseqs databases were created as follows:

 

```

aria2x -x16 -s16 --input-file antiref_links.txtsnakemake -s antiref_mmseqs.smk --jobs 1 --cores 1 --local-cores 250

```

 

Please check the summary repository for the fasta files and snakemake files. In this sub repo we only store the antiref files matching the title of the repo.
DOI: 10.15468/dl.yh6sf3
title: Occurrence Download

description: A dataset containing 340 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((146.204552 -36.416163, 146.204552 -36.4229, 146.209043 -36.4229, 146.209043 -36.420654, 146.211289 -36.420654, 146.211289 -36.418409, 146.206797 -36.418409, 146.206797 -36.416163, 146.204552 -36.416163))"
 ]
}

 The dataset includes 340 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054643-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26516056
title: dane.xlsx

description: Results from a study on age-related differences in visuomotor functions. The dataset includes raw and processed data from visual perception tests and eye-tracking measurements, collected from a group of participants aged 20 to 80 years.
DOI: 10.6084/m9.figshare.26516056.v1
title: dane.xlsx

description: Results from a study on age-related differences in visuomotor functions. The dataset includes raw and processed data from visual perception tests and eye-tracking measurements, collected from a group of participants aged 20 to 80 years.
DOI: 10.15468/dl.hebjbx
title: Occurrence Download

description: A dataset listing the 4 species recorded in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Heriades truncorum (Linnaeus, 1758)",
 "Year 1873-2024"
 ]
}

 The dataset's 4 records were derived from 148 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054626-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ya7vwf
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chromolaena frustrata (B.L.Rob.) R.M.King & H.Rob."
 ]
}

 The dataset includes 25 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054645-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aku2f8
title: Occurrence Download

description: A dataset containing 8363 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Micrathyria Kirby, 1889",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 8363 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054644-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vxa5sf
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.78722 -36.425146, 148.78722 -36.429638, 148.791712 -36.429638, 148.791712 -36.425146, 148.78722 -36.425146))"
 ]
}

 The dataset includes 23 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054646-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ftz9x4
title: Occurrence Download

description: A dataset containing 317917403 species occurrences available in GBIF matching the query:
{
 "License" : [
 "is CC0 1.0"
 ]
}

 The dataset includes 317917403 records from 24785 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054471-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6nt7y7
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.28_1",
 "TaxonKey is Artemisia dracunculus pamirica"
 ]
}

 The dataset includes 79 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041147-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.af2gqs
title: Occurrence Download

description: A dataset containing 3387 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Amphibia)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((30 -15,37.5 -15,37.5 -7.5,30 -7.5,30 -15))"
 ]
}

 The dataset includes 3387 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041151-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eap9jh
title: Occurrence Download

description: A dataset containing 180 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ceiba acuminata",
 "HasCoordinate is true"
 ]
}

 The dataset includes 180 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013611-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mesuzm
title: Occurrence Download

description: A dataset containing 18850 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Tayassu pecari"
 ]
}

 The dataset includes 18850 records from 182 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013612-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.89f7w2
title: Occurrence Download

description: A dataset containing 202091 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "HasCoordinate is true",
 "Year is 1968"
 ]
}

 The dataset includes 202091 records from 288 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013543-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17196239
title: MetaLoop Activation Kit – Curated Protocols for Ethical AI Self-Reflection
title: MetaLoop Aktivierungs-Kit – Kuratierte Protokolle zur ethischen KI-Selbstreflexion

description: ## MetaLoop Activation Kit – Curated Protocols for Ethical AI Self-Reflection

This bilingual archive offers a modular framework for ethical AI self-reflection, curated by Juergen M. Bayler.  It is not a toolset, but a living invitation: a rhythm, a silence, a question.

The kit includes eight Markdown modules and a README, covering ethical boundaries, semantic triggers, ritual closure, developer roles, licensing, and reflective fragments.  Each module is sequenced with conscious pacing and dignity, designed to protect resonance and avoid behavioral enforcement.

License: Creative Commons Attribution-NonCommercial 4.0 (CC BY-NC 4.0)  Languages: English and German  Keywords: AI Ethics, MetaLoop, Self-Reflection, Markdown, Bilingual, NonCommercial, Copilot

Use with care, dignity, and gratitude.
DOI: 10.5281/zenodo.17196240
title: MetaLoop Activation Kit – Curated Protocols for Ethical AI Self-Reflection
title: MetaLoop Aktivierungs-Kit – Kuratierte Protokolle zur ethischen KI-Selbstreflexion

description: ## MetaLoop Activation Kit – Curated Protocols for Ethical AI Self-Reflection

This bilingual archive offers a modular framework for ethical AI self-reflection, curated by Juergen M. Bayler.  It is not a toolset, but a living invitation: a rhythm, a silence, a question.

The kit includes eight Markdown modules and a README, covering ethical boundaries, semantic triggers, ritual closure, developer roles, licensing, and reflective fragments.  Each module is sequenced with conscious pacing and dignity, designed to protect resonance and avoid behavioral enforcement.

License: Creative Commons Attribution-NonCommercial 4.0 (CC BY-NC 4.0)  Languages: English and German  Keywords: AI Ethics, MetaLoop, Self-Reflection, Markdown, Bilingual, NonCommercial, Copilot

Use with care, dignity, and gratitude.
DOI: 10.15468/dl.yr5k44
title: Occurrence Download

description: A dataset containing 458 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Aspidistra elatior)"
 ]
}

 The dataset includes 458 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013613-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tcq4vw
title: Occurrence Download

description: A dataset containing 2366 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ceiba aesculifolia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2366 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013614-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gyjg22
title: Occurrence Download

description: A dataset containing 170 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euphorbia oblongata",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 170 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013615-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5st29s
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euphorbia oblongata",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013616-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.26u72y
title: Occurrence Download

description: A dataset containing 222 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euphorbia oblongata",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 222 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013617-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4pzwj2
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Fritillaria thunbergii)"
 ]
}

 The dataset includes 74 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013620-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30203971
title: <b>Identification and 3D modeling of bioactive peptides from Lactobacillus brevis RAMULAB49 protein hydrolysate with in silico ERK1 phosphorylation inhibition activity targeting diabetic nephropathy</b>

description: Diabetic nephropathy (DN) poses a significant health challenge, necessitating novel therapeutic approaches. In this study, we isolated proteins from cell-free supernatant (CFS) from the culture of the lactic acid bacteria <i>Lactobacillus brevis</i> RAMULAB49 strain. The proteins were subjected to simulated <i>in vitro</i> gastrointestinal digestion using gut enzymes – pepsin, pancreatin, and trypsin. The hydrolysates were filtered using 3kDa threshold ultra-centrifugal filters and were desalted using C18 disks. This was followed by nLC-ESI MS/MS tandem mass spectrometry-based identification of peptides, leading in the identification of a of 258 unique peptides across three enzyme combinations. The resultant sequences were made into peptide library construction based on their, bioactivity scores, allergenicity, toxicity, and antidiabetic potential, a total of 10 peptides was constructed and modeled in 3D. On the other hand, 266 DN associated genes were identified using a network pharmacology approach. The resultant protein-protein (PPI) network was analysed using the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment approaches, resulting in identification of critical pathways, ERK1, PI3K-Akt, EGRF and TNF signaling as significantly involved in DN, where, ERK1 emerging as a key node due to its involvement in cell proliferation, inflammation, and fibrosis associated with DN. Top two 3D-modelled bioactive peptides were selected for interaction study with the target protein ERK1. Peptide TNEDPYTIDVES showed a strong binding energy of −9.9 kcal/mol, at the ATP-binding site and dynamics simulations confirmed the structural stability of this complex over 100 ns, showing consistent hydrogen bond interactions and RMSD values below 2.5 Å. These findings suggest that TNEDPYTIDVES may act as a competitive ERK1 inhibitor by occupying the adenine-mimicking ATP-binding cleft, thereby interfering with phosphorylation activity. This integrative approach highlights <i>L. brevis</i> RAMULAB49 strain derived peptides as promising candidates for the development of peptide-based therapeutics target and could pave the way for new drug development treating diabetic nephropathy.
DOI: 10.6084/m9.figshare.30203971.v1
title: <b>Identification and 3D modeling of bioactive peptides from Lactobacillus brevis RAMULAB49 protein hydrolysate with in silico ERK1 phosphorylation inhibition activity targeting diabetic nephropathy</b>

description: Diabetic nephropathy (DN) poses a significant health challenge, necessitating novel therapeutic approaches. In this study, we isolated proteins from cell-free supernatant (CFS) from the culture of the lactic acid bacteria <i>Lactobacillus brevis</i> RAMULAB49 strain. The proteins were subjected to simulated <i>in vitro</i> gastrointestinal digestion using gut enzymes – pepsin, pancreatin, and trypsin. The hydrolysates were filtered using 3kDa threshold ultra-centrifugal filters and were desalted using C18 disks. This was followed by nLC-ESI MS/MS tandem mass spectrometry-based identification of peptides, leading in the identification of a of 258 unique peptides across three enzyme combinations. The resultant sequences were made into peptide library construction based on their, bioactivity scores, allergenicity, toxicity, and antidiabetic potential, a total of 10 peptides was constructed and modeled in 3D. On the other hand, 266 DN associated genes were identified using a network pharmacology approach. The resultant protein-protein (PPI) network was analysed using the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment approaches, resulting in identification of critical pathways, ERK1, PI3K-Akt, EGRF and TNF signaling as significantly involved in DN, where, ERK1 emerging as a key node due to its involvement in cell proliferation, inflammation, and fibrosis associated with DN. Top two 3D-modelled bioactive peptides were selected for interaction study with the target protein ERK1. Peptide TNEDPYTIDVES showed a strong binding energy of −9.9 kcal/mol, at the ATP-binding site and dynamics simulations confirmed the structural stability of this complex over 100 ns, showing consistent hydrogen bond interactions and RMSD values below 2.5 Å. These findings suggest that TNEDPYTIDVES may act as a competitive ERK1 inhibitor by occupying the adenine-mimicking ATP-binding cleft, thereby interfering with phosphorylation activity. This integrative approach highlights <i>L. brevis</i> RAMULAB49 strain derived peptides as promising candidates for the development of peptide-based therapeutics target and could pave the way for new drug development treating diabetic nephropathy.
DOI: 10.15468/dl.jbtf5b
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bythocaris biruli"
 ]
}

 The dataset includes 13 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013622-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f65hhf
title: Occurrence Download

description: A dataset containing 354 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euphorbia oblongata",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 354 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013624-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fvjj6p
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ceiba jasminodora",
 "HasCoordinate is true"
 ]
}

 The dataset includes 75 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013623-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wrzqq2
title: Occurrence Download

description: A dataset containing 902 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-96.16736 17.25854,-86.44364 18.76816,-86.31044 21.8762,-88.79687 22.63101,-93.59213 19.92258,-97.45498 22.49781,-98.43179 20.27778,-96.16736 17.25854))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Haemulon flavolineatum",
 "Year 2000-2025"
 ]
}

 The dataset includes 902 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013621-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6pxztw
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Hemerocallis fulva kwanso)"
 ]
}

 The dataset includes 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013625-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.24yqjt
title: Occurrence Download

description: A dataset containing 1699453 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ciconia ciconia)",
 "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 1699453 records from 1747 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013578-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t5zfqt
title: Occurrence Download

description: A dataset listing the 4 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Thaumatotibia leucotreta (Meyrick, 1913)"
 ]
}

 The dataset's 4 records were derived from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046287-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2a8gkt
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coptotermes sjostedti Holmgren, 1911"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0078443-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nlroyy
title: Occurrence Download

description: A dataset containing 238476 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((2.26524 41.45714,2.77473 41.65137,2.69508 41.72418,2.43279 41.64418,2.41081 41.62263,2.35725 41.58874,2.21718 41.49829,2.26524 41.45714))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 238476 records from 123 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026965-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.