cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25342924
title: Fine-tuning Pre-trained Antibody Language Models for Antigen Specificity Prediction

description: AbstractAntibodies play a crucial role in the adaptive immune response, with their specificity to antigens being a fundamental determinant of immune function. Accurate prediction of antibody antigen specificity is vital for understanding immune responses, guiding vaccine design, and developing antibody-based therapeutics. In this study, we explore the effect of fine-tuning pre-trained antibody language models in improving binding specificity prediction to SARS-CoV-2 spike protein and influenza hemagglutinin. We fine-tuned four pre-trained antibody language models on labeled data specific to these antigens and demonstrated that fine-tuned language model classifiers exhibit enhanced predictive accuracy compared to classifiers trained on pre-trained model embeddings. Additionally, we investigated the change of model attention activations after fine-tuning to gain insights into the molecular basis of antigen recognition by antibodies. Furthermore, we applied the fine-tuned models to BCR repertoire data related to influenza and SARS-CoV-2 vaccination, demonstrating their ability to capture changes in repertoire following vaccination. Overall, our study highlights the effect of fine-tuning on pre-trained antibody language models as valuable tools to improve antigen specificity prediction.CodeAll code used for model training and testing is available on bitbucket https://bitbucket.org/kleinstein/projects/src/master/Wang2024/ . <br>An archived version of the Bitbucket repository is included in <i>code.zip</i>.DataThe following files are included in <i>data.zip</i><br><i>S_FULL.parquet</i>: Sequence and labels for S binding prediction (full-length).<br><i>S_CDR3.parquet</i>: Sequence and labels for S binding prediction (CDR3 only).<br><i>HA</i><i>_FULL</i><i>.parquet</i>: Sequence and labels for HA binding prediction (full-length).<br><i>HA</i><i>_FULL</i><i>.parquet</i>: Sequence and labels for HA binding prediction (CDR3 only).<br><i>S_repertoires.parquet</i>: Repertoires used for S binding prediction<br><i>HA_repertoires.parquet</i>: Repertoires used for HA binding prediction<br>
DOI: 10.5281/zenodo.10986548
title: ELITE SLWR: global 1km 5-min SLUR at SIN Grid-Aqua (2007_228-243)

description: The Essential thermal Infrared remoTe sEnsing (ELITE) product suite currently has four types of products, including land surface temperature (LST: clear-sky and all-sky), emissivity (NBE: narrowband emissivity; BBE: broadband emissivity; and spectral emissivity), the component of surface radiation and energy budget (SLUR: surface longwave upwelling radiation; SLDR: surface longwave downward radiation SLDR; SLNR: surface longwave net radiation), and the component of Earth’s radiation budget (OLR; outgoing longwave radiation; RSR: reflected solar radiation). The spatial-temporal resolutions of the ELITE products are mainly determined by the employed satellite data sources. For more information about ELITE products, please refer to the website (https://elite.bnu.edu.cn).

This dataset is ELITE surface longwave upward radiation (SLUR) product at 1km spatial resolution and 5-min temporal resolution. It is provided on a Sinusoidal grid and ranges from 2000 to 2022 (continuously updated). This dataset was generated from the Moderate Resolution Imaging Spectrometer (MODIS) data using the algorithms developed by Cheng et al. (2016).

This is the ELITE SLUR product in 2007 (DOY: 228-243). Please click here to download the ELITE SLUR product in 2007 (DOY: 244-258).

Dataset Characteristics:



Spatial Coverage: Global

Temporal Coverage: 2007-8-16 ~ 2007-8-31

Spatial Resolution: 1 km

Temporal Resolution: 5-min

Data Format: h5

Projection: Sinusoidal

Scale: 0.05

Offset: -1000


Citation(Please cite these papers when using the data):



Cheng, J., & Liang, S. (2016). Global estimates for high spatial resolution clear-sky land surface upwelling longwave radiation from MODIS data. IEEE Transactions on Geoscience and Remote Sensing, 54, 4115-4129.


If you have any questions, please contact Prof. Jie Cheng (eliteqrs@126.com).
DOI: 10.15468/dl.fb4efe
title: Occurrence Download

description: A dataset containing 303 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Urocystis occulta (Wallr.) Rabenh.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 303 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035184-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10988142
title: ELITE SLWR: global 1km 5-min SLUR at SIN Grid-Aqua (2007_244-258)

description: The Essential thermal Infrared remoTe sEnsing (ELITE) product suite currently has four types of products, including land surface temperature (LST: clear-sky and all-sky), emissivity (NBE: narrowband emissivity; BBE: broadband emissivity; and spectral emissivity), the component of surface radiation and energy budget (SLUR: surface longwave upwelling radiation; SLDR: surface longwave downward radiation SLDR; SLNR: surface longwave net radiation), and the component of Earth’s radiation budget (OLR; outgoing longwave radiation; RSR: reflected solar radiation). The spatial-temporal resolutions of the ELITE products are mainly determined by the employed satellite data sources. For more information about ELITE products, please refer to the website (https://elite.bnu.edu.cn).

This dataset is ELITE surface longwave upward radiation (SLUR) product at 1km spatial resolution and 5-min temporal resolution. It is provided on a Sinusoidal grid and ranges from 2000 to 2022 (continuously updated). This dataset was generated from the Moderate Resolution Imaging Spectrometer (MODIS) data using the algorithms developed by Cheng et al. (2016).

This is the ELITE SLUR product in 2007 (DOY: 244-258). Please click here to download the ELITE SLUR product in 2007 (DOY: 259-273).

Dataset Characteristics:



Spatial Coverage: Global

Temporal Coverage: 2007-9-1 ~ 2007-9-15

Spatial Resolution: 1 km

Temporal Resolution: 5-min

Data Format: h5

Projection: Sinusoidal

Scale: 0.05

Offset: -1000


Citation(Please cite these papers when using the data):



Cheng, J., & Liang, S. (2016). Global estimates for high spatial resolution clear-sky land surface upwelling longwave radiation from MODIS data. IEEE Transactions on Geoscience and Remote Sensing, 54, 4115-4129.


If you have any questions, please contact Prof. Jie Cheng (eliteqrs@126.com).
DOI: 10.15468/dl.7kj8dx
title: Occurrence Download

description: A dataset containing 41541 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pyrrharctia isabella J.E.Smith, 1797)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 41541 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035183-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8h6fe3
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Claviceps africana Freder., Mantle & De Milliano)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 17 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035186-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y8pz9u
title: Occurrence Download

description: A dataset containing 2689 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Syntomeida epilais Walker, 1854)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2689 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035187-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fm4qd8
title: Occurrence Download

description: A dataset containing 2330 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Material citation, Material sample, Human Observation, Machine Observation)",
 "TaxonKey is Prionailurus bengalensis (Kerr, 1792)"
 ]
}

 The dataset includes 2330 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035188-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.byha6f
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Otocryptis beddomei Boulenger, 1885"
 ]
}

 The dataset includes 33 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008014-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vezqp8
title: Occurrence Download

description: A dataset containing 267 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anolis petersii Bocourt, 1873"
 ]
}

 The dataset includes 267 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013490-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.265ykh
title: Occurrence Download

description: A dataset containing 6315 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chenopodium ambrosioides L."
 ]
}

 The dataset includes 6315 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066097-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zvhmzn
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nanoastegotherium prostatum Carlini et al., 1997"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022116-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0zjgyo
title: Occurrence Download

description: A dataset containing 719 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhynchostele Rchb.f.",
 "Country is Mexico"
 ]
}

 The dataset includes 719 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008682-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yyt08f
title: Occurrence Download

description: A dataset containing 1962 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Diplopoda"
 ]
}

 The dataset includes 1962 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006452-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yzlgfk
title: Occurrence Download

description: A dataset containing 1520 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Lepisorus mucronatus (Fée) Li Wang"
 ]
}

 The dataset includes 1520 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005634-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pdryvg
title: Occurrence Download

description: A dataset containing 100 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllomedusa camba De la Riva, 1999"
 ]
}

 The dataset includes 100 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008682-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n5c392
title: Occurrence Download

description: A dataset containing 396 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Benin",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "or" : [
 "TaxonKey is Lippia multiflora Moldenke",
 "TaxonKey is Lantana camara L."
 ]
 }
 ]
}

 The dataset includes 396 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016507-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fx3v8e
title: Occurrence Download

description: A dataset containing 2044 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Martynia annua L.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2044 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023999-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w4jep4
title: Occurrence Download

description: A dataset containing 125 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alouatta palliata (Gray, 1849)",
 "Country is Costa Rica",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 125 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008685-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3wdkvb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphorbia damasoi Oudejans"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0205027-230224095556074/datasets/export for details.
DOI: 10.15468/dl.dwd42n
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schizaeaceae",
 "HasCoordinate is TRUE",
 "Country is Ecuador"
 ]
}

 The dataset includes 0 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014689-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ehw3pk
title: Occurrence Download

description: A dataset containing 6047 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-124.54102 14.77488,-77.95898 14.77488,-77.95898 39.50404,-124.54102 39.50404,-124.54102 14.77488))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ursus americanus Pallas, 1780"
 ]
}

 The dataset includes 6047 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008177-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qtbma9
title: Occurrence Download

description: A dataset containing 2787427 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Bryophyte data for Great Britain from the British Bryological Society held by BRC: Atlas 2014"
 ]
}

 The dataset includes 2787427 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008685-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9xb673
title: Occurrence Download

description: A dataset containing 14124 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is United States of America",
 "Country is Canada",
 "Country is Mexico"
 ]
 },
 "TaxonKey is Lactuca serriola L."
 ]
}

 The dataset includes 14124 records from 139 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016506-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kxfsbs
title: Occurrence Download

description: A dataset containing 139 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Megachile pruina Smith, 1853"
 ]
}

 The dataset includes 139 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017806-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eaqm2f
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Machaonia portoricensis Baill."
 ]
}

 The dataset includes 88 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008690-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gx3jg7
title: Occurrence Download

description: A dataset containing 3007 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Sclerurus guatemalensis (Hartlaub, 1844)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3007 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033597-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3qypxd
title: Occurrence Download

description: A dataset containing 3788 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Callosciurus erythraeus (Pallas, 1779)"
 ]
}

 The dataset includes 3788 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007510-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.plgzcd
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Brachygobius Bleeker, 1874",
 "Country is India"
 ]
}

 The dataset includes 14 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008691-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jc5sg5
title: Occurrence Download

description: A dataset containing 102246 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-10.74 34.26,44.24 34.26,44.24 71.24,-10.74 71.24,-10.74 34.26))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Geum rivale L.",
 "Year 2000-2020"
 ]
}

 The dataset includes 102246 records from 257 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021000-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r9j74d
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fukomys mechowii (Peters, 1881)"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066119-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tqfw8n
title: Occurrence Download

description: A dataset containing 532 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anableps anableps (Linnaeus, 1758)"
 ]
}

 The dataset includes 532 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008691-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bp6jpt
title: Occurrence Download

description: A dataset containing 439 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "TaxonKey is Myriopteris gracillima (D.C.Eaton) J.Sm.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 439 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031494-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jfubbr
title: Occurrence Download

description: A dataset containing 3381 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lama G.Cuvier, 1800"
 ]
}

 The dataset includes 3381 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007523-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ar69lt
title: Occurrence Download

description: A dataset containing 76482 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Afghanistan"
 ]
}

 The dataset includes 76482 records from 276 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008692-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.98nll4
title: Occurrence Download

description: A dataset containing 56738 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Geometry POLYGON((-85.94604 35.0246,-85.37476 33.24236,-85.28687 30.21541,-81.15601 30.10142,-80.32104 31.75993,-82.03491 35.24024,-85.94604 35.0246))",
 "HasCoordinate is true",
 {
 "or" : [
 "TaxonKey is Peucaea aestivalis (M.H.K.Lichtenstein, 1823)",
 "TaxonKey is Colinus virginianus (Linnaeus, 1758)",
 "TaxonKey is Passerina ciris (Linnaeus, 1758)",
 "TaxonKey is Picoides borealis (Vieillot, 1809)",
 "TaxonKey is Lanius ludovicianus Linnaeus, 1766"
 ]
 },
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 56738 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027283-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.