cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17813359
title: Experimental Validation of Pemivibart (VYD2311) Escape in Four Clinically Flagged SARS-CoV-2 Genomes: Evidence of Functional Resistance Despite Pipeline Classification Artifacts

description: This dataset documents a targeted re-evaluation of four SARS-CoV-2 sequences (SRR36291578, SRR29992357, SRR28971845, ERR15656806) previously flagged in our surveillance systems as exhibiting pemivibart (VYD2311) resistance.

Using a custom, codon-resolution bioinformatic pipeline, we confirm:

F486P in 2/4 samples (SRR29992357, SRR28971845)F456L in 1/4 samples (ERR15656806)S371F (non-escape) in all 4 samplesNo canonical escape mutation in SRR36291578Critically, our initial pipeline underclassified resistance due to two key design limitations:

Inclusion of S371F as an escape mutation (biologically irrelevant for VYD2311)Overly stringent resistance threshold (requiring ≥3 mutations, whereas ≥1 of F456L/K444T/F486P is sufficient per FDA EUA and neutralization data)

Upon manual BAM inspection and biological reinterpretation, 3 of 4 samples harbor validated pemivibart escape mutations, consistent with prior global trends reported in our larger dataset (DOI: 10.5281/zenodo.17201049).

This work demonstrates:

The high specificity of F456L/F486P as resistance markersThe risk of false-negative classification when bioinformatic rules do not reflect therapeutic thresholdsThe ongoing relevance of pemivibart escape monitoring, even as variant prevalence shifts.

Files included:

pemivibart_results/ (full pipeline output)manual_validation_notes.txt (IGV screenshots and codon-level summaries)corrected_classification_summary.csvMethods: BWA-MEM alignment → iVar/bcftools variant calling → codon-based escape analysis (NC_045512.2 coordinates)Reference: Wuhan-Hu-1 (NC_045512.2)Therapeutic context: Pemivibart (VYD2311) FDA EUA, 2024

Study by: Tahir HB
DOI: 10.5281/zenodo.17813360
title: Experimental Validation of Pemivibart (VYD2311) Escape in Four Clinically Flagged SARS-CoV-2 Genomes: Evidence of Functional Resistance Despite Pipeline Classification Artifacts

description: This dataset documents a targeted re-evaluation of four SARS-CoV-2 sequences (SRR36291578, SRR29992357, SRR28971845, ERR15656806) previously flagged in our surveillance systems as exhibiting pemivibart (VYD2311) resistance.

Using a custom, codon-resolution bioinformatic pipeline, we confirm:

F486P in 2/4 samples (SRR29992357, SRR28971845)F456L in 1/4 samples (ERR15656806)S371F (non-escape) in all 4 samplesNo canonical escape mutation in SRR36291578Critically, our initial pipeline underclassified resistance due to two key design limitations:

Inclusion of S371F as an escape mutation (biologically irrelevant for VYD2311)Overly stringent resistance threshold (requiring ≥3 mutations, whereas ≥1 of F456L/K444T/F486P is sufficient per FDA EUA and neutralization data)

Upon manual BAM inspection and biological reinterpretation, 3 of 4 samples harbor validated pemivibart escape mutations, consistent with prior global trends reported in our larger dataset (DOI: 10.5281/zenodo.17201049).

This work demonstrates:

The high specificity of F456L/F486P as resistance markersThe risk of false-negative classification when bioinformatic rules do not reflect therapeutic thresholdsThe ongoing relevance of pemivibart escape monitoring, even as variant prevalence shifts.

Files included:

pemivibart_results/ (full pipeline output)manual_validation_notes.txt (IGV screenshots and codon-level summaries)corrected_classification_summary.csvMethods: BWA-MEM alignment → iVar/bcftools variant calling → codon-based escape analysis (NC_045512.2 coordinates)Reference: Wuhan-Hu-1 (NC_045512.2)Therapeutic context: Pemivibart (VYD2311) FDA EUA, 2024

Study by: Tahir HB
DOI: 10.15468/dl.txxk7p
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dinaromys bogdanovi",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 88 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027804-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17802550
title: Characterization of Pre-Established Phytoremediation Field Trials Thirteen Years After Establishment

description: The uploaded GeoPackage contains geospatial data physico-chemical properties of soil of pre-established monitoring plots at the former Nitrastur industrial site. The dataset is provided within the framework of the Horizon Europe pHYBi project (PHYtomanagement as a sustainable feedstock source of lignocellulosic based high value bio based products for textile applications) and documents the spatial configuration soil characterisation of the experimental plantations. The trees at these plots were originally planted under the previous I+DARTS LIFE11 ENV/ES/000547 proyect and pHYBi now performs a follow up 13 years later to monitor site conditions and assess the performance of the phytoremediation actions implemented there.
DOI: 10.5281/zenodo.17802551
title: Characterization of Pre-Established Phytoremediation Field Trials Thirteen Years After Establishment

description: The uploaded GeoPackage contains geospatial data physico-chemical properties of soil of pre-established monitoring plots at the former Nitrastur industrial site. The dataset is provided within the framework of the Horizon Europe pHYBi project (PHYtomanagement as a sustainable feedstock source of lignocellulosic based high value bio based products for textile applications) and documents the spatial configuration soil characterisation of the experimental plantations. The trees at these plots were originally planted under the previous I+DARTS LIFE11 ENV/ES/000547 proyect and pHYBi now performs a follow up 13 years later to monitor site conditions and assess the performance of the phytoremediation actions implemented there.
DOI: 10.17026/ar/jiwfjf
title: PAN-00103851 - disc-shaped spindle whorl (handmade pottery)

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00103851&lt;/p&gt;
description: Modified: 2025-08-29T09:40:36+02:00
DOI: 10.5517/ccdc.csd.cc2p14qm
title: CCDC 2473760: Experimental Crystal Structure Determination

description: Related Article: keliang chen|2025|CSD Communication|||
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: 10.15468/dl.gapzpt
title: Occurrence Download

description: A dataset containing 3793 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dikerogammarus haemobaphes)",
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Specimen, Machine Observation, Occurrence evidence)",
 "Year is greater than or equal to 1971",
 "Year is less than or equal to 2025",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 3793 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027806-251120083545085/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.cc2p989l
title: CCDC 2481559: Experimental Crystal Structure Determination

description: Related Article: hongxiang zhou|2025|CSD Communication|||
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: 10.15468/dl.knqny7
title: Occurrence Download

description: A dataset containing 3793 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dikerogammarus haemobaphes)",
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Specimen, Machine Observation, Occurrence evidence)",
 "Year is greater than or equal to 1971",
 "Year is less than or equal to 2025",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 3793 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027809-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4sd3z6
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diplogale hosei",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 18 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027808-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qkgvx8
title: Occurrence Download

description: A dataset containing 36730 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Material sample)"
 ]
 }
 },
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (INTRODUCED)"
 ]
 }
 },
 "TaxonKey is Geoglossomycetes"
 ]
}

 The dataset includes 36730 records from 379 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027807-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m55jq5
title: Occurrence Download

description: A dataset containing 158 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dalbergia parviflora Roxb."
 ]
}

 The dataset includes 158 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020467-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cvffwn
title: Occurrence Download

description: A dataset containing 25874 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Museu Paraense Emílio Goeldi - Ichthyology Collection"
 ]
}

 The dataset includes 25874 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005302-171002173027117/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qup48r
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stelis rufobrunnea (Lindl.) L.O.Williams"
 ]
}

 The dataset includes 33 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0196512-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8a4bn3
title: Occurrence Download

description: A dataset containing 3528 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Browallia americana L."
 ]
}

 The dataset includes 3528 records from 188 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0362021-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mae7u5
title: Occurrence Download

description: A dataset containing 108 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Corydoras arcuatus Elwin, 1938"
 ]
}

 The dataset includes 108 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027671-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.az5kcz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bena prasinana (Linnaeus, 1758)",
 {
 "not" : {
 "DatasetKey" : [
 "is Global database of alien macrofungi"
 ]
 }
 },
 {
 "or" : [
 "Country is Poland",
 "Country is Poland"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0394188-210914110416597/datasets/export for details.
DOI: 10.15468/dl.wmaci5
title: Occurrence Download

description: A dataset containing 27599750 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Mexico"
 ]
}

 The dataset includes 27599750 records from 2091 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005302-171113114016250/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dhaumz
title: Occurrence Download

description: A dataset listing the 587251 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 587251 records were derived from 6547 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050298-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.btc3mq
title: Occurrence Download

description: A dataset containing 1090 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ips pini (Say & T., 1826)",
 {
 "or" : [
 "Country is United States of America",
 "Country is Canada",
 "Continent is North America"
 ]
 }
 ]
}

 The dataset includes 1090 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127763-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vh38me
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stanhopea deltoidea Lem."
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140686-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-26938
title: Correspondence book No. 1 of Pentecostal Missionary Union [PMU], 1914-1920

description: [description english/roman)] Pentecostal Missionary Union [PMU] Correspondence book No. 2 including 61 pages of subject index; 2011 pages of PMU outgoing correspondence;
DOI: 10.15468/dl.twrk8z
title: Occurrence Download

description: A dataset containing 284 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Masonhalea richardsonii (Hook.) Kärnefelt",
 "Year 1982-2021"
 ]
}

 The dataset includes 284 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0430677-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9uxfhw
title: Occurrence Download

description: A dataset containing 488 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Records of fauna and flora of Sumskyj district of Sumy region in 2022"
 ]
}

 The dataset includes 488 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0147310-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2mu4zq
title: Occurrence Download

description: A dataset containing 91330 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Alle alle (Linnaeus, 1758)"
 ]
}

 The dataset includes 91330 records from 177 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0184412-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e524jh
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-13599.0",
 "Country is one of (Spain, Portugal)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Narcissus hedraeanthus (Webb & Heldr.) Colmeiro",
 "Year 2000-2022"
 ]
}

 The dataset includes 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0433177-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-27200
title: Correspondence book No. 1 of Pentecostal Missionary Union [PMU], 1914-1920

description: [description english/roman)] Pentecostal Missionary Union [PMU] Correspondence book No. 2 including 61 pages of subject index; 2011 pages of PMU outgoing correspondence;
DOI: 10.15468/dl.683nfg
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Taraxacum appositum M.P.Christ."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005278-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pweqzu
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ips typographus (C.Linnaeus, 1758)",
 {
 "or" : [
 "Country is United States of America",
 "Country is Canada",
 "Continent is North America"
 ]
 }
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127765-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-27213
title: Correspondence book No. 1 of Pentecostal Missionary Union [PMU], 1914-1920

description: [description english/roman)] Pentecostal Missionary Union [PMU] Correspondence book No. 2 including 61 pages of subject index; 2011 pages of PMU outgoing correspondence;
DOI: 10.15468/dl.6gbzpd
title: Occurrence Download

description: A dataset containing 203402 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Matricaria discoidea DC.)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 203402 records from 526 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0245205-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5bq28z
title: Occurrence Download

description: A dataset containing 34381 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Verbascum sinuatum L."
 ]
}

 The dataset includes 34381 records from 362 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005266-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5ytxqj
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-80.1840897999999953 25.8514143999999995, -80.1840897999999953 25.8527966099999986, -80.1840897999999953 25.8546724599999997, -80.1840897999999953 25.8559559300000004, -80.1840897999999953 25.8574368700000008, -80.1840897999999953 25.8595101800000009, -80.1840897999999953 25.8612873000000008, -80.1824108699999982 25.8612873000000008, -80.1811269600000003 25.8612873000000008, -80.1788554200000050 25.8612873000000008, -80.1758925500000004 25.8612873000000008, -80.1745098800000022 25.8612873000000008, -80.1722383400000069 25.8612873000000008, -80.1708557000000042 25.8612873000000008, -80.1708557000000042 25.8599050900000016, -80.1708557000000042 25.8575355999999985, -80.1708557000000042 25.8554622899999984, -80.1708557000000042 25.8535864400000008, -80.1708557000000042 25.8514143999999995, -80.1736210100000051 25.8514143999999995, -80.1755962600000061 25.8514143999999995, -80.1780653200000017 25.8514143999999995, -80.1795467599999938 25.8514143999999995, -80.1818183000000033 25.8514143999999995, -80.1840897999999953 25.8514143999999995))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 60 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0093229-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-27115
title: Correspondence book No. 1 of Pentecostal Missionary Union [PMU], 1914-1920

description: [description english/roman)] Pentecostal Missionary Union [PMU] Correspondence book No. 2 including 61 pages of subject index; 2011 pages of PMU outgoing correspondence;